@article {pmid41887505,
year = {2026},
author = {Wang, Q and Zhang, J and Xia, Y and Zha, M and Li, J and Jambal, T and Dorjgotov, D and Tseveen, S and Chen, Y},
title = {Traditional fermented goat milk products in Mongolia: Analysis from the perspective of metagenomics to metabolomics.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27796},
pmid = {41887505},
issn = {1525-3198},
abstract = {Mongolia is known for its rich dairy traditions, with goat milk representing a distinctive and valuable dairy resource. Fermentation improves the quality and nutritional value of goat milk, which is closely associated with microbial activity. As traditional Mongolian fermented dairy products primarily depend on natural fermentation, investigating the microbial and metabolic changes during this process is essential for understanding product quality. In this observational study, raw goat milk (RGM) and fermented goat milk (FGM) samples were collected from Mongolia, and a total of 102 microbial species were identified using shotgun metagenomic sequencing. The RGM contained a higher proportion of viruses and nonlactic acid bacteria (non-LAB), including Macrococcus caseolyticus. Following fermentation, the microbial community composition shifted, becoming dominated by LAB species such as Lactobacillus helveticus and Lactobacillus delbrueckii, with beneficial microorganisms attaining predominant abundance. A total of 22 differential metabolites were identified between RGM and FGM. Approximately half of these metabolites were related to AA metabolism, while the remainder were involved in energy metabolism, antioxidant processes, and lipid metabolism. Spearman correlation analysis suggested that LAB, primarily Lactobacillus species, were positively associated with the abundance of metabolites such as organic acids and AA in the fermented products. In contrast, the presence of pathogenic microorganisms such as viruses showed a negative correlation with fermentation efficiency markers. It was hypothesized as a potential factor affecting product quality, possibly through disrupting host microbial metabolism. Overall, this observational study identifies understanding of the factors governing FGM quality and provides a scientific foundation for improving the goat milk industry and harnessing microbial resources in traditional fermented dairy products.},
}

@article {pmid41887507,
year = {2026},
author = {Scott, J and Brouard, JS and Drouin, G and Ouellet, DR and Ster, C and Petri, RM},
title = {Microbiota Changes in Rumen and Milk Corresponding to Dietary Protein Intake in Transition Dairy Cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27576},
pmid = {41887507},
issn = {1525-3198},
abstract = {During the transition period in dairy cows, the incidence of disease increases due to a negative energy balance affecting both the metabolic and immune health status. Limiting milk production at the beginning of lactation improves the metabolic status of cows. However, past strategies tested to achieve this reduction either negatively impacted milk yield for the rest of the lactation or were difficult to implement on large-scale dairy farms. This study evaluated the impact of a temporary reduction in metabolizable protein (MP) supply during the transition period on the rumen and milk microbiota and their metabolic composition. Treatment cows (n = 5) were fed 80% of their MP needs (80MP) from 14 d before calving to 14 d after calving, before being switched to a 100% MP diet (100MP) for an additional 14 d. Control cows (n = 6) were fed 100MP for the entire experiment. Samples of rumen content and milk were taken in the immediate Postpartum phase (PP) on d 2 and 7, as well as after dietary change in the experimental Recovery phase (RP) on d 21 and 28 postpartum. All samples were extracted for DNA and analyzed using shotgun metagenomic sequencing (Illumina NovaSeq). Milk samples were additionally analyzed for composition, and rumen fluid was analyzed for short-chain fatty acids and ammonia-N. Significant changes to the microbial composition were almost exclusively associated to effect of day of sampling, with the exception being the family Micrococcaceae, which was found to be differentially abundant in the 100MP compared with the 80% group in PP milk samples. This study used a metagenomics approach to understanding the impact of altered protein supply on rumen and milk microbiota, to better understand impacts on these separate ecosystems.},
}

@article {pmid41887601,
year = {2026},
author = {Wei, Y and Liu, Q and Gong, Z and Han, GZ},
title = {Unveiling the cryptic diversity and distribution of elements related to virophage mavirus through deep mining of pPolB proteins.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.03.009},
pmid = {41887601},
issn = {1995-820X},
abstract = {Virophages are unique double-stranded DNA (dsDNA) viruses that parasitize viruses of Nucleocytoviricota (NCVs). While conventionally viewed as a viral group, growing evidence suggests that "virophage" is better understood as a parasitic lifestyle, rather than a natural group. Despite this conceptual shift, their diversity and evolution remain largely obscure and contentious. Through deep mining of protein-primed type B DNA polymerase (pPolB) in 7,041 eukaryotic genomes and 12,053 metagenomes sampled globally, we expand the diversity of pPolB-carrying mavirus virophage-related elements (pMVREs), which include virophages, transpovirons, and Polinton-like viruses (PLVs). Our phylogenomic and metagenomic mining reveals the widespread distribution of pMVREs in eukaryotic genomes (97/7,041, 1.38%) and global environments (2,450/12,053, 20.33%). pMVREs possess genome architectures of high plasticity and promiscuity. The presence of pMVREs and NCVs is statistically correlated in both eukaryotic genomes and global metagenomes, supporting a specific co-occurrence association between pMVREs and NCVs. Moreover, pMVRE diversity and composition exhibit strong heterogeneity across global ecosystems. Together, this study unveils a vast diversity of virophage-related elements and provides insights into the intricate relationship among virophages, transpovirons, PLVs, pMVREs, and NCVs.},
}

@article {pmid41887858,
year = {2026},
author = {Zheng, D and Li, D and Wang, J},
title = {Beyond ammonia-oxidizing bacteria-centric paradigms: Geobacter-assisted anodic anaerobic ammonia oxidation.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {399-408},
doi = {10.1016/j.jes.2025.07.035},
pmid = {41887858},
issn = {1001-0742},
mesh = {*Geobacter/metabolism/physiology ; *Ammonia/metabolism ; Oxidation-Reduction ; Electrodes ; Anaerobiosis ; Biofilms ; Bacteria/metabolism ; *Anaerobic Ammonia Oxidation ; },
abstract = {Anodic anaerobic ammonium oxidation (anodic anammox) presents a sustainable approach for nitrogen removal, yet its bioelectrochemical mechanisms remain unclear due to biofilm complexity and undefined roles of electroactive microorganisms (EAMs). This study reveals that nitrite (NO2[-]) is the direct product of ammonia-oxidizing bacteria (AOB)-driven anodic anammox, with extracellular electron transfer (EET) mediated by indirect mechanisms via redox shuttles. Metagenomic analysis identified two ammonia oxidation pathways: (1) a novel short-range nitrification pathway (NH4[+] → NO2[-]) governed by ncd2 genes, and (2) a traditional ammonia oxidation pathway (NH4[+] → NH2OH) facilitated by amoABC. Intriguingly, Geobacter exhibited potential NH2OH oxidation capability, bridging AOB activity and electrode respiration. Functional inhibition experiments demonstrated that EAMs-derived electron shuttles and reactive oxygen species (ROS) are critical for enhancing EET efficiency, with ROS serving as a key electron acceptor for AOB under anaerobic conditions. Spatial and metabolic synergy between EAMs and AOB-via substrate cross-feeding, cofactor provision, and electron transfer-was essential for maintaining biofilm stability. These findings challenge the conventional view of AOB-driven anodic anaerobic anammox mechanisms and provide new insights into sustainable nitrogen removal in engineered bioelectrochemical systems.},
}

*Geobacter/metabolism/physiology
*Ammonia/metabolism
Oxidation-Reduction
Electrodes
Anaerobiosis
Biofilms
Bacteria/metabolism
*Anaerobic Ammonia Oxidation

@article {pmid41887859,
year = {2026},
author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z},
title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {409-419},
doi = {10.1016/j.jes.2025.05.033},
pmid = {41887859},
issn = {1001-0742},
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Soil/chemistry ; *Antinematodal Agents/toxicity ; Ecosystem ; *Microbiota/drug effects ; RNA, Ribosomal, 16S ; Bacteria ; Organophosphorus Compounds ; Thiazolidines ; },
abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.},
}

*Soil Microbiology
*Soil Pollutants/toxicity
Soil/chemistry
*Antinematodal Agents/toxicity
Ecosystem
*Microbiota/drug effects
RNA, Ribosomal, 16S
Bacteria
Organophosphorus Compounds
Thiazolidines

@article {pmid41887904,
year = {2026},
author = {Jin, R and Chen, C and Zhang, J and Li, Y and Wu, Y and Wang, F and Chen, Z and Huang, T and Cheng, Q and Yu, X and Jia, P},
title = {Solid waste dumping differentially impacts soil prokaryotic, fungal, and viral communities: Insights from metagenomics.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {867-879},
doi = {10.1016/j.jes.2025.10.021},
pmid = {41887904},
issn = {1001-0742},
mesh = {*Soil Microbiology ; Metagenomics ; *Microbiota ; Fungi ; *Solid Waste ; Soil/chemistry ; Soil Pollutants/analysis ; *Refuse Disposal ; Environmental Monitoring ; },
abstract = {Rapid urbanization and industrialization have dramatically increased global solid waste generation, placing immense pressure on waste management systems. In many developing countries, illegal and uncontrolled dumping remains widespread, yet its ecological impacts, particularly on soil microbial communities, are still poorly understood. To address this knowledge gap, we applied high-throughput amplicon sequencing and metagenomic profiling to analyze soil microbiomes across three categories of solid waste dumping. Our results show that solid waste dumping significantly altered both biotic and abiotic components of soil ecosystems. Soil properties shifted abruptly, with elevated pH and increased concentrations of pollutants such as petroleum hydrocarbons and fluorides. Microbial communities were extensively restructured, exhibiting both taxonomic turnover and functional adaptations. Viral communities displayed greater sensitivity to dumping-induced disturbances than prokaryotic or fungal communities. These findings provide new insights into soil microbiome responses to anthropogenic pollution and highlight taxon-specific adaptation strategies. To our knowledge, this is among the first comparative studies integrating prokaryotic, fungal, and viral responses to solid waste dumping using high-throughput molecular approaches. Our findings present a novel perspective that may guide future monitoring efforts and enhance approaches to environmental damage identification and assessment.},
}

*Soil Microbiology
Metagenomics
*Microbiota
Fungi
*Solid Waste
Soil/chemistry
Soil Pollutants/analysis
*Refuse Disposal
Environmental Monitoring

@article {pmid41888119,
year = {2026},
author = {Rodríguez-Varela, R and Pochon, Z and Mas-Sandoval, A and Yaka, R and Fortes-Lima, CA and García Rubio, A and Márquez-Grant, N and Marí, J and Graziani, G and Ferrer Abárzuza, A and Vicente, M and Lorca-Francisco, L and Linderholm, A and Lagerholm, VK and Arauna, LR and Pérez-Ramallo, P and Krzewińska, M and Schlebusch, CM and Götherström, A},
title = {Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41888119},
issn = {2041-1723},
support = {2019-00849_VR//Vetenskapsrådet (Swedish Research Council)/ ; },
mesh = {Humans ; History, Medieval ; *Islam/history ; Spain ; *Burial/history ; *Genetic Variation ; Metagenomics ; Gene Flow ; *Leprosy/microbiology/history/genetics ; DNA, Ancient/analysis ; Male ; Cemeteries ; },
abstract = {Ibiza, an island in present-day Spain, was conquered in 902 CE by the Umayyad Emirate of Córdoba. The island remained under Islamic rule until 1235. Here, we analyse the genetic and metagenomic profiles of 13 individuals from an Islamic cemetery in Ibiza, dated to 950-1150 CE. Genome-wide analyses reveal heterogeneity, with ancestry components from Europe, North Africa, and Sub-Saharan Africa. Our analyses estimate that North African gene flow occurred two to seven generations before these individuals lived, suggesting admixture following the Islamic conquest of Iberia and potentially on Ibiza itself. Notably, two individuals trace their Sub-Saharan origins to distinct regions, Senegambia and present-day southern Chad, providing direct evidence of trans-Saharan connections via military and slave networks documented in contemporary Arabic sources. Metagenomic analyses detect several pathogens in this community, with one individual carrying Mycobacterium leprae, offering insight into the presence of leprosy in Ibiza. Our findings align with the historically documented two-pulse demographic model, indicating an initial settlement following the early tenth-century conquest and a second influx associated with Almoravid movements in the twelfth century. These securely dated genomes offer insights into medieval population dynamics and health in the Balearics.},
}

Humans
History, Medieval
*Islam/history
Spain
*Burial/history
*Genetic Variation
Metagenomics
Gene Flow
*Leprosy/microbiology/history/genetics
DNA, Ancient/analysis
Male
Cemeteries

@article {pmid41888125,
year = {2026},
author = {Fu, J and Zhang, J and He, R and Dong, Q and Mao, H and Shen, W and Wu, W and Chen, X and Ma, W and Zhai, Q and Chen, L and Zhou, H and Hu, S and He, Y and Qi, C},
title = {A global metagenomic atlas of aging identifies a microbiota phase transition associated with disease risk.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00970-4},
pmid = {41888125},
issn = {2055-5008},
support = {2023A1515012538//Basic and Applied Basic Research Foundation of Guangdong Province/ ; NSFC82300623//National Natural Science Foundation of China/ ; NSFC82272391//National Natural Science Foundation of China/ ; NSFC82302610//National Natural Science Foundation of China/ ; 2019YFA0802300//National Key Research and Development Program of China/ ; },
abstract = {Biological aging has been associated with altered risk of aging-related diseases, but the contribution of the gut microbiota to this process remains poorly understood. Here, we constructed an interpretable gut microbiota age clock using metagenomic data from 8115 fecal samples across five continents. We discovered a key microbial perturbation occurring at 56-60 years of chronological age, which was validated in an independent cohort of 2263 metagenomes. This perturbation was associated with a decline in ecological stability and substantial changes in the abundance of core species. Notably, the association between gut microbiota age and diseases was identified to be significantly altered before and after this inflection time. Moreover, within-species analyses uncovered phylogenetic divergence for seven age-related species, such as Escherichia coli, alongside functional alterations in older individuals, including enhanced cell motility, carbohydrate metabolism and horizontal gene transfer. Overall, our global gut microbiome atlas uncovers a critical age transition phase, highlighting opportunities for microbiota-based therapies and offering novel insights into evolutionary dynamics during aging.},
}

@article {pmid41888178,
year = {2026},
author = {Ariaeenejad, S and Abedanzadeh, S},
title = {Enhanced stability and reusability of metagenomic laccase via immobilization on functionalized mesoporous silica for antibiotic contaminant removal.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41888178},
issn = {2045-2322},
mesh = {*Laccase/chemistry/metabolism/genetics ; *Silicon Dioxide/chemistry ; *Enzymes, Immobilized/chemistry/metabolism ; *Anti-Bacterial Agents/chemistry/isolation & purification/metabolism ; Enzyme Stability ; Porosity ; *Metagenome ; Water Pollutants, Chemical/chemistry ; Biodegradation, Environmental ; Metagenomics ; Doxycycline/chemistry ; Imidazoles/chemistry ; },
abstract = {The extensive application of tetracycline antibiotics in agriculture and medicine has led to persistent contamination of aquatic and terrestrial ecosystems, disrupting microbial communities and contributing to the spread of antibiotic resistance. Conventional treatment methods often suffer from poor efficiency, limited stability, and high environmental costs, underscoring the need for robust and sustainable alternatives. Here, we present a biocatalytic platform in which a metagenome-derived laccase (PersiLac1) is covalently immobilized onto imidazole-functionalized SBA-15 mesoporous silica to overcome the limitations of free laccase, including low stability and high leaching. Immobilization markedly enhanced thermal stability, reusability, and catalytic efficiency toward the degradation of doxycycline (DC) and tetracycline (TC). The optimized system exhibited minimal enzyme leaching (9.6% at 25 °C; 22.0% at 80 °C) and achieved removal efficiencies of 76.7 ± 2.8% for DC and 53.7 ± 2.1% for TC within 24 h. High removal performance was maintained even at elevated antibiotic concentrations (200 mg L[-1]), with 43.9% and 42.8% removal for DC and TC, respectively. The immobilized laccase retained over 83% (DC) and 73% (TC) of its initial activity after 10 consecutive reuse cycles. To the best of our knowledge, this is the first report of integrating a metagenomic laccase with an imidazole-functionalized SBA-15 support for antibiotic degradation, offering a unique combination of enhanced stability, high reusability, and environmentally relevant performance. These findings highlight the potential of this immobilization strategy as a sustainable and high-performance solution for the remediation of antibiotic contaminants in water systems.},
}

*Laccase/chemistry/metabolism/genetics
*Silicon Dioxide/chemistry
*Enzymes, Immobilized/chemistry/metabolism
*Anti-Bacterial Agents/chemistry/isolation & purification/metabolism
Enzyme Stability
Porosity
*Metagenome
Water Pollutants, Chemical/chemistry
Biodegradation, Environmental
Metagenomics
Doxycycline/chemistry
Imidazoles/chemistry

@article {pmid41888223,
year = {2026},
author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K},
title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44250-9},
pmid = {41888223},
issn = {2045-2322},
support = {4020052//Center for International Scientific Studies & Collaborations (CISSC)/ ; },
abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.},
}

@article {pmid41888360,
year = {2026},
author = {Belay, G and Suarez, C and Simachew, A and Paul, CJ},
title = {Microorganisms and functional genes in an aerobic-anoxic integrated gold mine wastewater treatment system.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41888360},
issn = {1573-0972},
}

@article {pmid41888867,
year = {2026},
author = {Tao, M and Fan, Y and Qian, L and Liu, H and Ming, Y and Yu, X and Wu, K and Niu, M and Yan, Q and Huang, X and He, Z},
title = {Microbially driven methane and sulfur cycling processes and coupling mechanisms in mangrove sediments.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00877-9},
pmid = {41888867},
issn = {2524-6372},
support = {2021M703751//China Postdoctoral Science Foundation/ ; SML2023SP205, SML2024SP002, SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42430707, 52070196, 32370113 and 92251306//National Natural Science Foundation of China/ ; 2024A1515010931//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {BACKGROUND: Methane (CH4) as a powerful greenhouse gas is the second largest contributor to global climate warming. Mangrove sediments are an important natural source of biogenic CH4 with rich organic carbon (C) and diverse sulfur (S) compounds, ideally for studying CH4 and S cycling processes and coupling mechanisms. Here we sampled mangrove sediment cores and analyzed their key microbial groups, key environmental factors and possible coupling mechanisms for CH4 and S cycling by metagenome sequencing approaches.

RESULTS: Our results showed that Methanomicrobiales and Methanophagales were predominant methanogens, Methanospirareceae was a representative of anaerobic methanotrophic archaea (ANME), and Desulfobacteraceae and Desulfobulbaceae were abundant sulfate-reducing bacteria (SRB), while Ectothiorhodospiraceae, Chromatiaceae and Comamonadaceae were dominant S-oxidizers. Correlation network analysis revealed positive interactions among methanogens, ANME and SRB. Also, metagenome-assembled genome (MAG) analysis indicated interspecies hydrogen transfer and extracellular electron exchange via conductive pili, flagella, and cytochromes were potential coupling mechanisms between methanogens and SRB. ANME could form consortia with SRB by intermediate metabolites (e.g., acetate) and/or direct interspecies electron transfer (e.g., flagella, pili, cytochromes). Furthermore, methanogen MAGs encoded thiosulfate oxidation and partial sulfate reduction pathways, while the ANME MAGs possessed potentials for S disproportionation and incomplete sulfate reduction. Additionally, SO4[2-], total sulfur, moisture content and salinity were important environmental factors affecting the microbial community structure and gene families involved in CH4 and S cycling.

CONCLUSION: This study provides novel insights into coupling mechanisms of CH4 and S cycling processes in mangrove sediments, having important implications for mitigating global warming.},
}

@article {pmid41888912,
year = {2026},
author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH},
title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02379-9},
pmid = {41888912},
issn = {2049-2618},
support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; },
abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.

RESULTS: We discovered that diatoms exude a C6-sulfated α-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.

CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome.},
}

@article {pmid41889037,
year = {2026},
author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS},
title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109518},
doi = {10.1016/j.identj.2026.109518},
pmid = {41889037},
issn = {1875-595X},
abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.

METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.

RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.

CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.},
}

@article {pmid41889316,
year = {2026},
author = {Niyazi, HA and Niyazi, HA and AbdulMajed, H and Juma, N and Helmi, N and Alqarni, M and Saleh, BH and Zubair, M and Alfadil, A and Alhazmi, W and Alharbi, OS and Halabi, WS and Altalhi, R and Moglad, E and Alharbi, MT and Gazzaz, M and Alharthi, TM and Altayb, HN and Ibrahem, K},
title = {Pan-genome analysis and phylogenetic characterization of Klebsiella pneumoniae from global isolates.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/17460913.2026.2617118},
pmid = {41889316},
issn = {1746-0921},
abstract = {AIMS: This study aimed to investigate the global genetic diversity, evolutionary relationships, and antimicrobial resistance (AMR) profiles of Klebsiella pneumoniae by performing a comprehensive pan-genome and phylogenetic analysis across worldwide isolates.

MATERIALS AND METHODS: A total of 72,057 K. pneumoniae genomes were retrieved from the NCBI database, from which 91 high-quality representative genomes each from a unique country were selected based on completeness, metadata availability, and sequence quality. Genomic assemblies were assessed using QUAST, annotated with PROKKA, and analyzed for pan-genomic composition and phylogenetic relatedness using standard bioinformatics pipelines.

RESULTS: The pan-genome revealed a large accessory component, reflecting extensive genomic plasticity and adaptability. QUAST analysis indicated significant variability in genome size and contig number, while PROKKA annotation identified diverse coding sequences, tRNA, rRNA, and AMR genes. Phylogenetic clustering demonstrated both geographically localized and globally disseminated lineages, suggesting regional adaptation and intercontinental transmission.

CONCLUSIONS: This study provides a global perspective on the genomic diversity and evolutionary patterns of K. pneumoniae. The widespread presence of AMR determinants underscores the urgent need for continuous genomic surveillance and integration of metagenomic approaches to improve monitoring, infection control, and therapeutic strategies against multidrug-resistant strains.},
}

@article {pmid41889516,
year = {2026},
author = {Mao, J and Jin, Q and Ye, D and Yang, Y},
title = {Case Report: A rare presentation of pulmonary tuberculosis with extensive ground-glass opacities in an immunocompetent patient: lessons from metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1696371},
pmid = {41889516},
issn = {2296-858X},
abstract = {Pulmonary tuberculosis (PTB) is typically diagnosed through sputum smear microscopy and culture. However, diagnosis is challenging in patients with atypical radiological features and negative conventional tests. Ground-glass opacities (GGOs) are common but non-specific computed tomography (CT) findings and are rarely observed in immunocompetent PTB patients. We report the first case of an immunocompetent 53-year-old female presenting with extensive bilateral GGOs without classic clinical symptoms. Conventional microbiological cultures, acid-fast staining, and serological assays were all negative. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Mycobacterium tuberculosis, further supported by a positive T-spot TB assay. Standard anti-tuberculosis therapy led to complete resolution of GGOs over nine months, confirmed by follow-up CT imaging. This case underscores the diagnostic challenge of atypical PTB presenting with non-classical CT manifestations in an immunocompetent host. It highlights the decisive role of mNGS as a complementary tool in cases where conventional methods fail, enabling timely diagnosis, precise treatment, and improved patient outcomes.},
}

@article {pmid41889550,
year = {2026},
author = {Xiu, Q and He, H and Liu, Z and Ou, X and Meng, Y and Zhao, K and Yang, Q and Zhang, X and Hou, Y and Yao, S and Gao, P and Xia, W},
title = {Biosurfactant-driven desorption and remediation of heavy oil contaminated soils underpinned by molecular simulations and microbial dynamics.},
journal = {RSC advances},
volume = {16},
number = {18},
pages = {16316-16328},
pmid = {41889550},
issn = {2046-2069},
abstract = {This study integrates molecular dynamics simulations and bench-scale experiments to investigate the adsorption and desorption behaviors of heavy oil on five mineral substrates: SiO2, kaolinite, muscovite, and Ca[2+]-/Na[+]-montmorillonite. Adsorption followed Langmuir isotherms, with montmorillonite exhibiting the highest capacities (0.061-0.062 molecules per Å[2] for aromatics in simulations; 0.086-0.091 g g[-1] in bench-scale tests) and SiO2 the lowest (0.027 pcs per Å[2]; 0.013 g g[-1]). Among four biosurfactants evaluated-rhamnolipid, sophorolipid, trehalose lipid, and mannosylerythritol lipid-sophorolipid consistently achieved the greatest desorption efficiency, removing up to 99.63% of adsorbed oil from Na[+]-montmorillonite and 96.04% from field-contaminated soil. 16S rRNA and metagenomic sequencing revealed an increased abundance of hydrocarbon-degrading bacteria within the soil microbial community, highlighting a synergistic effect between biosurfactant-induced desorption and biodegradation. These findings underscore the critical roles of mineralogical properties, oil fraction characteristics, and biosurfactant selection in soil washing treatment. This work presents a viable and eco-friendly strategy for remediating crude oil-contaminated soils, with important implications for optimizing large-scale environmental restoration efforts.},
}

@article {pmid41889698,
year = {2026},
author = {Almatrafi, R and Alasiri, A and Almuneef, G and Al-Hazzani, AA and Alghoribi, MF and Hakami, M and Arafah, AM and Alotibi, RS and Alrabiah, S and Alqurainy, N and Ajina, R and Aldriwesh, MG},
title = {First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study.},
journal = {Frontiers in aging},
volume = {7},
number = {},
pages = {1733638},
pmid = {41889698},
issn = {2673-6217},
abstract = {INTRODUCTION: The gut microbiome undergoes dynamic changes with aging across diverse healthy populations. However, data from Saudi Arabia remain limited. This pilot study investigated age-related variations in the gut microbiome among healthy Saudi adults to characterize region-specific microbial signatures and identify taxa potentially associated with aging in a healthy population.

METHODS: We established the Saudi Aging and Microbiome Study (SAMS) to investigate age-related changes in fecal microbiome of Saudi adults. In this pilot phase, 145 healthy participants aged 19-69 years were enrolled. Shotgun metagenomic sequencing was performed to profile fecal microbiome at the species level. Microbial diversity and taxonomic composition were compared across five age groups. Spearman and confounder-adjusted partial Spearman correlation were applied to identify taxa significantly associated with chronological age.

RESULTS: We analyzed fecal microbiome of 145 healthy adults distributed among five age groups: G1 (19-29 years, n = 33; 22.7%), G2 (30-39 years, n = 30; 20.7%), G3 (40-49 years, n = 27; 18.6%), G4 (50-59 years, n = 31; 21.4%), and G5 (60-69 years, n = 24; 16.6%). Of these, 75 (51.7%) were male, and 70 (48.3%) were female. Alpha diversity increased from young to older adulthood for observed richness and Shannon indexes (all q < 0.05). Beta diversity also varied significantly with age (PERMANOVA R [2] = 0.13, q = 0.023), indicating distinct microbial community structures in healthy older adults. At the phylum level, Firmicutes significantly increased with age (FC = 1.35; q = 0.026), whereas Bacteroidota decreased (FC = 0.59; q = 0.01). Consistent with these trends, Blautia obeum showed positive correlations, while Bacteroides thetaiotaomicron and Phocaeicola vulgatus showed negative correlations with chronological age.

CONCLUSION: In healthy Saudi adults, increasing age was associated with higher microbial diversity and compositional shifts at phylum and species levels. These age-associated microbial taxa might represent biomarkers of healthy aging and suggest an enhanced community capacity for short-chain fatty acids (SCFAs) production, a hypothesis warranting validation through future functional analyses.},
}

@article {pmid41889866,
year = {2026},
author = {Van Camp, AG and Park, J and Ozcelik, E and Eskiocak, O and Ozler, KA and Papciak, K and Subhash, S and Alwaseem, H and Ergin, I and Chung, C and Shah, V and Yueh, B and Fein, MR and Durmaz, C and Mozsary, C and Kilic, E and Garipcan, A and Damle, N and Najjar, D and Nelson, TM and Ryon, KA and Butler, DJ and Patel, CJ and Thaiss, CA and Birsoy, K and Mason, CE and Meydan, C and Tierney, BT and Beyaz, S},
title = {Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.17.708620},
pmid = {41889866},
issn = {2692-8205},
abstract = {Dietary fat composition modulates host physiology and the gut microbiome, but the long-term effects of specific fat sources and the extent to which these changes resolve after dietary reversal remain incompletely defined. Here, we present a longitudinal multi-omic resource of mice maintained for one year on a purified control diet, seven high-fat diets differing in predominant fat source, or reversal regimens in which animals were switched from high-fat to control diet after 4 or 9 months. We further incorporated two cohorts with distinct pre-existing microbiome configurations to determine how baseline community structure shapes diet-induced remodeling of the gut microbiome ecosystem. By integrating longitudinal phenotyping, fecal metagenomics, fecal metabolomics, plasma metabolomics and lipidomics, and intestinal single-cell RNA sequencing, we defined the shared and dietary fat-specific responses across host and microbiome compartments. Baseline microbiome composition strongly influenced microbial responses to diet, indicating that pre-existing community structure is a major determinant of dietary ecosystem remodeling. Although many altered features shifted toward baseline after dietary reversal, only approximately half of diet-associated microbial changes recovered within the study window. A subset of taxa exhibited persistent alterations, including sustained depletion of Lactobacillus johnsonii and Bifidobacterium pseudolongum and sustained enrichment of Alistipes finegoldii , consistent with a "microbiome memory" of prior high-fat diet exposure. This memory effect is mirrored in the host, by sustained suppression of major histocompatibility complex class II (MHC-II) gene expression in intestinal epithelial cells after dietary reversal. These findings indicate that dietary fats leave a lasting imprint on the host-microbiome interactome that survives dietary intervention. Together, these data establish a resource for defining how dietary fat source, baseline microbiome composition, and dietary history shape host-microbiome states. The entire resource is available online as an RShiny app.},
}

@article {pmid41890171,
year = {2026},
author = {Zhao, S and Sai, Y and Jia, M and Qiao, Y and Guo, W and Ding, W and Shao, X and Zheng, Y},
title = {Comprehensive insights into the mechanism of flavor formation in Cheonggukjang: Integration of metagenomics, volatomics, and metabolomics.},
journal = {Food chemistry: X},
volume = {35},
number = {},
pages = {103756},
pmid = {41890171},
issn = {2590-1575},
abstract = {Microbial metabolism shapes the unique flavor profile of Cheonggukjang; however, the formation pathways of characteristic flavor compounds mediated by microbiota remain unclear, hindering precise quality control. To fill this gap, this study innovatively integrated metagenoics, volatilomics, and metabolomics to systematically decode the flavor formation mechanism during Cheonggukjang fermentation. Volatile compound analysis defined three fermentation stages for Cheonggukjang (0-18, 18-60, and 60-72 h), identifying the 60-72 h period as the most critical for flavor formation. A total of 15 key flavor compounds were identified, with 10 designated stage-specific flavor markers. LefSe analysis revealed that Bacillus subtilis, Bacillus velezensis, Caldibacillus thermoamylovorans, and Bacillus licheniformis were the key biomarkers across different fermentation stages, while redundancy analysis (RDA) indicated that total sugar as the key driver of microbial succession. Additionally, this study reconstructed the metabolic network responsible for characteristic flavor formation and identified C. thermoamylovorans, B. licheniformis, B. velezensis, B. subtilis, Bacillus paralicheniformis, and Caldibacillus hisashii as core functional microbiota modulating amino acid metabolic to drive flavor development. This study lays a theoretical framework for standardizing Cheonggukjang production and targeted regulating its flavor quality.},
}

@article {pmid41890980,
year = {2026},
author = {Shi, Y and Sanderson, H and Chuan, J and Khan, IUH and Sunohara, M and Craiovan, E and Lapen, DR and Diarra, M and Chen, W},
title = {Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101384},
pmid = {41890980},
issn = {2352-7714},
abstract = {Freshwater systems embedded in agricultural landscapes serve as dynamic reservoirs and conduits for fecal-associated microbes, zoonotic pathogens, and antimicrobial resistance (ARG) and virulence factor (VF) genes. Yet factors that govern their densities and diversity remain a research challenge. From 2016 to 2021, we conducted a longitudinal water surveillance in an agriculturally dominated river basin in eastern Ontario, Canada; characterizing fecal-associated bacterial communities using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Agricultural drainage ditches consistently harbored higher fecal-associated bacterial diversity with pronounced seasonal shifts; i.e., higher levels during larger flow periods in spring and fall. Elevated discharge was associated with enrichment of genera containing zoonotic or opportunistic pathogens, such as those in Pseudomonas, Sphingomonas, and Massilia. Conditionally rare taxa (CRTs), although typically low in abundance, accounted for ∼12.6% of all pathogen-associated genera and disproportionately contributed to community turnover, highlighting their role as transient reservoirs of microbial risk. Shotgun metagenomics detected 27 ARGs, primarily at mixed-use sites, and 14 VFs, mainly in agricultural ditches. Clinically relevant β-lactamase genes (e.g., oxa, imp, sme) co-occurred with metal-resistance operons, a pattern suggestive of possible co-selection, although selective agents were not directly measured. Although the prevalence of ARG and VF was low (<5% of samples), their ecological context indicates potential transmission pathways. Limited overlap in ARGs between short-read and metagenome-assembled genome (MAG)-based profiling reflects their complementary strength: gene-level sensitivity versus host-resolved analysis. Together, these findings demonstrate the utility of integrated amplicon and shotgun metagenomic surveillance for proactive One Health risk assessment in agricultural watersheds.},
}

@article {pmid41891006,
year = {2026},
author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D},
title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.11.26348025},
pmid = {41891006},
abstract = {UNLABELLED: Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity, and can miss transmission involving low-abundance and co-colonizing strains. Here we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures collected between 2020 and 2025 at a single hospital. GI populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters, including six clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.

IMPACT STATEMENT: VREfm bloodstream infection is often seeded from bacteria colonizing the gut. The genetic diversity within gut and blood VREfm populations, and the role of this diversity in bacterial transmission, has been difficult to resolve as genomic surveillance typically relies on sequencing a clonal clinical isolate from each patient. Using culture-enriched metagenomic sequencing of matched GI tract and bloodstream VREfm populations from 35 patients at a single hospital, we found that the GI tract reservoir contained VREfm populations with greater strain and variant diversity than populations collected from the bloodstream. By integrating population sequencing with a large collection of VREfm clinical isolate genomes, we further demonstrate that different strains co-colonizing the GI tract of the same patient can reside in multiple putative transmission clusters, revealing potential transmission links that clone-based approaches are likely to miss. These findings demonstrate the potential utility of culture-enriched metagenomic sequencing for higher-resolution hospital surveillance of bacterial transmission. Applying this approach to other bacterial pathogens could improve our ability to detect and interpret transmission involving heterogeneous microbial populations that colonize and infect hospitalized patients.

DATA SUMMARY: Patient demographic data and clinical characteristics can be found in Table S1 (online Supplementary Material). All sequencing data generated in this study has been deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969, with sample accession numbers listed in Table S2 . Sequences used to construct the local reference strain database are available at NCBI BioProject PRJNA475751, with accession numbers listed in Table S3 . Variants identified in single-strain blood and GI populations are listed in Table S4 . Accession numbers for clinical isolate genomes included in transmission analyses are listed in Table S5 .

REPOSITORIES: Sequencing data generated in this study is deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969.},
}

@article {pmid41891018,
year = {2026},
author = {Basso, M and Hildebrand, F and Winder, C and Baker, DJ and Manders, R and Barberis, M and Gibbons, SM and Cohen Kadosh, K},
title = {Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.18.26348688},
pmid = {41891018},
abstract = {Background Emerging evidence highlights the gut-brain axis as a key pathway linking diet and anxiety, yet the key determinants remain unclear. Most studies have focused on single components of diet and rarely integrate long- and short-term intake. Furthermore, prior gut-brain work has focused on microbiome composition, while functional features remain underexplored. In this study, we investigated associations between long- and short-term dietary intake, gut microbiome composition and functions, and anxiety in a subclinical cohort of 46 females (18-24 years) from the United Kingdom. Results Long-term diet quality was assessed using the Healthy Eating Index (HEI-2020) derived from a food frequency questionnaire, stratifying participants into lower and higher diet quality clusters. Short-term dietary intake was assessed via 24-hour recalls. Shotgun metagenomics of stool samples was used to assess differences in alpha and beta diversity indices, species abundances, and bacterial pathways putatively metabolizing gut-brain-axis-relevant molecules. Anxiety was measured using the State-Trait Anxiety Inventory (state subscale STAI-s). Regression models identified diet quality (HEI cluster) as the primary dietary feature of anxiety variation. The presence of Ruminococcus gnavus and Flavonifractor plautii and the abundances of Bilophila wadsworthia and Bacteroides thetaiotaomicron were positively associated with anxiety. The presence of Feacalibacterium prausnitzii and greater abundances of butyrate, propionate, and GABA synthesis pathways were inversely associated with anxiety. Non-linear models revealed a U-shaped relationship between inositol synthesis and STAI-s. Finally, we found that habitual diet quality may modulate anxiety-related responses to short-term dietary variation. Conclusions These findings reveal widespread links between long-term diet quality, microbiota composition and function, and anxiety symptoms. These results point towards several promising targets for prebiotic, probiotic, postbiotic, and dietary interventions aimed at reducing anxiety.},
}

@article {pmid41891399,
year = {2026},
author = {Elsheikh, M and Ibrahim, MA and Fares, S and Bhongade, M and Adhem, K and Ramirez-Morales, XI and Kaseb, AO and Petrosino, J and Hassan, MM and Jalal, PK},
title = {Influence of Gut Microbiota on Response to Immune Check Point Inhibitors in MASLD Patients With HCC: Unraveling the Connection.},
journal = {Cancer medicine},
volume = {15},
number = {4},
pages = {e71738},
doi = {10.1002/cam4.71738},
pmid = {41891399},
issn = {2045-7634},
support = {R21CA293626/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Liver Neoplasms/drug therapy/immunology/microbiology/complications ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications ; Dysbiosis/microbiology ; Drug Resistance, Neoplasm ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment for various cancers, including advanced hepatocellular carcinoma (HCC). However, a significant proportion of patients with HCC, particularly those with metabolic dysfunction-associated liver disease (MASLD), exhibit resistance to ICI therapy. Studies have revealed that the presence of specific gut bacteria, such as Akkermansia, Bifidobacterium, and Lachnoclostridium, is associated with improved outcomes with ICI-treated HCC patients. Conversely, the overgrowth of bacteria like Enterobacteriaceae is linked to resistance to therapy. This review investigates the role of gut microbiota in shaping immune checkpoint inhibitor responses in MASLD-related hepatocellular carcinoma, focusing on how dysbiosis may contribute to ICI resistance and exploring microbiome modulation strategies, such as fecal microbiota transplantation and probiotics, aiming to optimize therapeutic outcomes.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Liver Neoplasms/drug therapy/immunology/microbiology/complications
*Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications
Dysbiosis/microbiology
Drug Resistance, Neoplasm
Fecal Microbiota Transplantation
Probiotics/therapeutic use

@article {pmid41891696,
year = {2026},
author = {Toth, CRA and Molenda, O and Nesbø, CL and Luo, F and Devine, CE and Chen, X and Wu, K and Xiao, JZ and Puri, R and Guo, S and Bawa, N and Wang, P-H and Wei, Y and Flick, R and Edwards, EA},
title = {Identification of a highly expressed gene cluster likely coding for benzene activation enzymes in a methanogenic enrichment culture.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0208325},
doi = {10.1128/aem.02083-25},
pmid = {41891696},
issn = {1098-5336},
abstract = {UNLABELLED: The oil refinery (OR) consortium is a model methanogenic enrichment culture used to study anaerobic benzene degradation. Over half of the culture's bacterial community consists of two closely related Desulfobacterota strains, designated ORM2a and ORM2b, whose mechanisms of benzene activation are unknown. Three proteomics data sets were integrated and analyzed using high-quality OR metagenomes and metagenome-assembled genomes (MAGs), including a complete circularized ORM2a MAG, to identify active metabolic pathways and proteins expressed during methanogenic benzene degradation. Among the proteins identified were Bam-like subunits of an ATP-independent benzoyl-CoA degradation pathway, as well as downstream β-oxidation proteins yielding acetate. The most abundant proteins identified mapped to two ORM2a gene clusters of unknown function. Homologous and syntenic gene clusters were identified in the MAGs of ORM2b and a sulfate-reducing Pelotomaculum that also degrades benzene, as well as in nine contigs assembled from hydrothermal vent metagenomes. Extensive homology and structural predictions suggest that the first cluster-termed the "Magic" gene cluster-encodes for enzymes catalyzing the chemically challenging activation of benzene and subsequent transformation steps yielding benzoyl-CoA. The second ("Nanopod") gene cluster encodes a transmembrane complex that may facilitate benzene transport across the cell membrane. Phylogenomic analyses place ORM2a and ORM2b within a novel genus of strict anaerobes specialized for benzene degradation, which we propose naming "Candidatus Anaerobenzenivorax."

IMPORTANCE: Benzene is a widespread, persistent, and toxic pollutant that can accumulate in anoxic environments such as groundwater and sediments. Benzene can be metabolized in the absence of oxygen; however, despite decades of research, the biochemical mechanisms for benzene activation under anaerobic conditions remain unproven. This study provides strong genetic and proteomic evidence for a new suite of enzymes that initiate anaerobic benzene activation. These findings lay a foundation for future biochemical studies and expand our understanding of how microbes carry out difficult chemical reactions in the absence of oxygen.},
}

@article {pmid41891698,
year = {2026},
author = {Li, Y and Ji, M and Tu, Q},
title = {Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143425},
doi = {10.1128/msystems.01434-25},
pmid = {41891698},
issn = {2379-5077},
abstract = {Archaea are widespread in Earth's ecosystems, contributing to ecosystem multifunctioning and stability. Compared to bacteria, our understanding of the biodiversity and underlying drivers of archaeal communities in representative ecosystems remains much less tapped. In this study, the macro- and micro-diversity of mudflat intertidal archaeomes were comprehensively analyzed at a large geographic scale, aiming to resolve the ecological drivers determining the variations in archaeal biodiversity. The compositions of mudflat intertidal archaeal taxa highly varied, especially the dominant Thaumarcheota and Euryarchaeota, but maintained relatively stable functional potential across space, demonstrating that functional traits were selected by the ecosystem in priority. While archaeal communities carried important functional traits mediating various biogeochemical cycling processes, horizontal gene transfer played critical roles in endowing functional genes for many archaeal lineages, such as the citric acid cycle in Methanosarcinia and various amino acid metabolism genes in Thermoplasmata. Spatial scaling, including latitudinal diversity gradient and distance-decay patterns (DDR), was clearly observed for archaeal taxonomic groups, but only DDR was weakly observed for functional traits. Intra-population genetic variations were significantly and positively associated with community macro-diversity, demonstrating covariations between nucleotide-level micro- and community-level macro-diversity. The compositions of intertidal archaeomes were mainly structured by homogeneous selection, with different phylogenetic bins being shaped by distinct ecological processes and remarkable variations across different sites. The study contributes to a comprehensive insight into the mechanisms shaping archaeal diversity and ecological characteristics within a fluctuating ecosystem.IMPORTANCEThe dynamic intertidal mudflat ecosystems host intense biogeochemical activities mediated by microbial communities, among which archaea contribute as an essential component but remain much less understood compared to bacteria. To gain better insights into the diversity, functional potential, and ecological drivers of archaeal communities in intertidal mudflats, archaeal phylogenetic signatures and genomic sequences were recovered via amplicon sequencing of 16S rRNA genes and shotgun metagenomes, targeting both macro- and micro-diversity. The results showed that archaeal taxonomic composition highly varied across space, whereas the functional potential remained relatively stable. Horizontal gene transfer served as an important source of archaeal metabolic diversity, obtaining additional genes linked to key biochemical pathways. The dominance of environmental selection further demonstrated the ecological forces governing archaeal communities in highly variable coastal habitats. This study established a large-scale framework for understanding the microbial ecology of intertidal archaeomes in dynamic coastal ecosystems.},
}

@article {pmid41892210,
year = {2026},
author = {Liang, X and Li, X and Mi, N and Wu, Y and Wu, J and Chen, H and Liu, D},
title = {Early-Life Diarrhea Disrupts Antioxidant-Immune Homeostasis and Gut Microbiota in Suckling Calves.},
journal = {Biology},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biology15060450},
pmid = {41892210},
issn = {2079-7737},
support = {YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Au-tonomous Region/ ; 2024LHMS03054//nner Mongolia Natural Science Foundation Project/ ; },
abstract = {Calf diarrhea is a common early-life disorder that adversely affects growth, oxidative balance, immune function, and intestinal microbiota, thereby compromising health and production performance. This study systematically investigates the effects of naturally occurring diarrhea in 7-day-old suckling calves on oxidative stress, immune responses, intestinal barrier integrity, and gut microbiota structure and function. Fecal scores, serum antioxidant and immune indices, and intestinal permeability markers were measured, and fecal samples were subjected to metagenomic sequencing. Diarrhea-affected calves exhibited higher fecal scores, increased oxidative stress indicated by reduced total antioxidant capacity, elevated lipid peroxidation, and altered antioxidant enzyme activities. Humoral immunity was impaired, inflammatory responses were dysregulated, and intestinal barrier function was disrupted. Gut microbial diversity declined, showing a depletion in health-associated taxa and the enrichment of opportunistic pathogens. Correlation analyses revealed that pathogenic bacteria abundance positively associated with diarrhea severity, oxidative stress, inflammation, and barrier disruption, while beneficial genera correlated with antioxidant and immune function. Functional profiling indicated a microbial shift from amino acid metabolism and antioxidant homeostasis toward carbohydrate and energy metabolism under diarrheic conditions. These findings highlight the pivotal role of gut microbiota dysbiosis in diarrhea pathogenesis and provide a foundation for developing microbiome-targeted interventions to improve calf health.},
}

@article {pmid41892424,
year = {2026},
author = {Gomes, E and Mesquita, TG and Serra, P and Araújo, D and Almeida, C and Machado, A and Oliveira, R and Castro, J},
title = {Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030262},
pmid = {41892424},
issn = {2079-6382},
support = {https://doi.org/10.54499/2024.13640.PEX//Fundação para a Ciência e Tecnologia/ ; https://doi.org/10.54499/2022.07654.PTDC//Fundação para a Ciência e Tecnologia/ ; APTA4shiga (number 14840)//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical global public health threat, with the food chain serving as a significant transmission route connecting animals, environment, and humans. This review adopts a One Health perspective to analyze the key drivers of AMR dissemination across animal agriculture, aquaculture and food processing. We evaluate detection methodologies, contrasting the regulatory gold standard of culture-based phenotypic testing with rapid molecular advancements, including Whole Genome Sequencing (WGS), metagenomics, and emerging CRISPR-Cas diagnostics. While molecular tools offer unprecedented speed and resolution, challenges such as matrix interference, the viable but non-culturable (VBNC) state, and the genotype-phenotype disconnect remain. Finally, integrated mitigation strategies are also described, ranging from on-farm antimicrobial stewardship and innovative biofilm control to consumer hygiene practices. It is essential to bridge the technical and regulatory gaps in AMR surveillance in order to develop effective interventions and ensure a safer food system.},
}

@article {pmid41892439,
year = {2026},
author = {Gomes-Gonçalves, S and Bento, JT and Moreira, G and Mourão, J and Cruz, R and Esteves, F and Baptista, AL and Pereira, MA and Caseiro, P and Carreira, P and Figueira, L and Mesquita, JR},
title = {Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030277},
pmid = {41892439},
issn = {2079-6382},
support = {PRR-C05-i03-I-000190//RumiRes project-"Vigilância epidemiológica de resistências antimicrobianas e resíduos medicamentosos em Pequenos ruminantes da Região Centro"/ ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored.

METHODS: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal.

RESULTS: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin.

CONCLUSIONS: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies.},
}

@article {pmid41892455,
year = {2026},
author = {Dashti, AA and Vali, L and Walsh, F},
title = {Metagenomic Profiling of Soil Microbiomes and Resistomes in Arid Ecosystems of Kuwait.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030294},
pmid = {41892455},
issn = {2079-6382},
support = {(RN01/15))//Kuwait University/ ; (code EASREF).//University of Gloucestershire/ ; },
abstract = {Background/Objective: This study addresses a significant knowledge gap in the literature concerning antibiotic resistance genes (ARGs) in arid soils by employing metagenomic approaches to characterise their diversity, using Kuwait as a model environment. Methods: Soil samples were collected from two agriculturally managed sites (K1 and K3) and one coastal unmanaged site (K2), representing distinct ecological conditions. Results: Taxonomic profiling revealed notable variation in microbial communities at both the phylum and genus levels. Alpha diversity analyses based on the Chao1 and Shannon indices indicated that agricultural soils exhibited greater microbial richness and diversity than the coastal soil. Beta diversity analysis further demonstrated substantial differences in microbial community composition among the sites. Consistent with previous soil microbiome studies, ARGs such as tetA, aac(3)-Ib, sul1, qep, muxB, mexW, mexB, and macB were detected across the sites. However, the identification of distinct clinically relevant resistance genes, including ugd, blaOXA-18, blaCMY-19, blaMOX-7, blaFOX-7, blaLRA-12, and novA, suggests the influence of site-specific or extreme selective pressures. Conclusions: Several of the detected ARGs appear to be rare or previously unreported in soil environments. Although the sample size is too small to support broad generalisations, the detection of ugd in soil is particularly noteworthy, suggesting that soils may serve as reservoirs of polymyxin resistance, potentially undermining the effectiveness of polymyxin antibiotics.},
}

@article {pmid41892478,
year = {2026},
author = {Scarlata, GGM and Belančić, A and Štimac, D and Fajkić, A and Meštrović, T and Abenavoli, L},
title = {Bacteriophage Therapy Against Shigella spp.: A Precision Antimicrobial Strategy.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030317},
pmid = {41892478},
issn = {2079-6382},
abstract = {Shigellosis remains a significant global cause of infectious colitis, increasingly complicated by multidrug-resistant strains and the microbiota-disrupting effects of broad-spectrum antibiotics. Although conventional antimicrobial therapy can reduce symptom duration and bacterial shedding, it also contributes to gut dysbiosis, loss of colonization resistance, and further selection for antimicrobial resistance. These challenges have renewed interest in precision antimicrobial strategies, particularly bacteriophage therapy, which provides strain-level specificity and preserves the gut microbiota. This narrative review evaluates the biological rationale, preclinical and early clinical evidence, safety considerations, and translational challenges associated with bacteriophage therapy targeting Shigella spp. The historical development and mechanistic basis of phage therapy are summarized, with emphasis on the advantages of obligately lytic phages, receptor-specific targeting, self-amplification at infection sites, and activity against both planktonic and biofilm-associated bacteria. Recent microbiota research indicates that shigellosis is closely associated with early and persistent disruption of gut ecology, including depletion of short-chain fatty acids-producing taxa and reduced microbial resilience. Phage-based approaches may reduce pathogen burden while preserving beneficial microbial communities. Evidence from in vitro systems, animal models, human intestinal organoids, and a Phase 1 clinical trial demonstrates targeted efficacy and favorable safety profiles for Shigella-specific phages and phage cocktails. Major barriers to clinical adoption include immune interactions, phage resistance dynamics, genomic safety screening, regulatory classification, and the need for standardized susceptibility testing. Future directions emphasize the development of personalized phage therapy platforms that integrate rapid diagnostics, phage libraries, metagenomics, and artificial intelligence-assisted matching to enable scalable, precision treatment.},
}

@article {pmid41892488,
year = {2026},
author = {Mise, K and Wasai-Hara, S and Itoh, H},
title = {Global terrestrial distribution of N2O-reducing Acidobacteriota members.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag073},
pmid = {41892488},
issn = {1751-7370},
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, and soil is its largest terrestrial source. Microbial N2O reductase (NosZ) is the only known enzyme capable of reducing N2O to N2, making nosZ-harboring prokaryotes important sinks in terrestrial ecosystems. Despite being among the most abundant and ubiquitous bacterial phyla in soil, the potential role of Acidobacteriota in N2O reduction remains largely unexplored. In this study, we addressed this gap using genomic, metagenomic, and physiological analyses. We first analyzed 199,602 prokaryotic genomes, including genomes from both isolated strains and metagenome-assembled genomes. We found that 491 Acidobacteriota genomes harbored nosZ, predominantly the Sec-dependent NosZ gene (nosZII). Global metagenomic analysis of 321 soil samples revealed that Acidobacteriota nosZII is one of the most abundant groups of nosZ and distributed across different continents. Among Acidobacteriota, nosZII from the class Vicinamibacteria was the most prevalent in the soils. Finally, we provide the physiological evidence of N2O-reducing activity in Acidobacteriota by demonstrating that the Vicinamibacteria type strain, Luteitalea pratensis KCTC52215T, can reduce N2O. Taken together, these findings highlight the previously overlooked potential role of Acidobacteriota as a global N2O sink and underscore the need to include them in future studies on soil N2O dynamics.},
}

@article {pmid41892593,
year = {2026},
author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A},
title = {Sulfoquinovose degradation by cow rumen microbiota.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag069},
pmid = {41892593},
issn = {1751-7370},
abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.},
}

@article {pmid41892682,
year = {2026},
author = {Murgina, O and Stafeeva, K and Karaulova, S and Vostrikova, A and Kononova, S and Chursina, D and Pozdeeva, S and Makogonova, A and Burakova, I and Pogorelova, S and Morozova, P and Smirnova, Y and Syromyatnikov, M and Shutikov, V and Mikhailov, E and Gureev, A},
title = {Probiotic Bacillus subtilis, but Not a Lactobacillus spp., Ameliorates Cognitive Impairment in a Mouse Model of LPS and Zidovudine-Induced Neuroinflammation.},
journal = {Brain sciences},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/brainsci16030340},
pmid = {41892682},
issn = {2076-3425},
support = {FZGW-2024-0003//Mikhail Syromyatnikov/ ; },
abstract = {Background/Objectives: The gut-brain axis is increasingly recognized as a critical modulator of cognitive function. This study investigated the neurotoxic effects of combined exposure to bacterial lipopolysaccharide (LPS) and the antiretroviral drug zidovudine (ZDV) in a mouse model, and evaluated the protective potential of two probiotic interventions: Bacillus subtilis and a mixture of lactobacilli. Methods: Cognitive function was assessed using the Morris water maze (MWM). Gut microbiota composition was analyzed by 16S rRNA sequencing, and intestinal morphology was examined histologically. Gene expression of neuroinflammatory markers and mitophagy-related genes in brain tissue was quantified by RT-PCR. Plasma levels of cell-free mitochondrial DNA (cf-mtDNA) were measured as a marker of mitochondrial damage. Results: Combined LPS + ZDV exposure induced systemic inflammation, impaired spatial memory, damaged the intestinal mucosa, and caused dysbiosis characterized by an increase in pro-inflammatory Muribaculaceae. In the brain, LPS + ZDV significantly upregulated Tnfa expression, confirming neuroinflammation. Bacillus subtilis administration prevented cognitive deficits, maintained Tnfa at control levels, and significantly reduced Il1b and Il6 expression compared to the LPS + ZDV group. This was accompanied by activation of the PINK1/PTEN-dependent mitophagy pathway, prevention of cf-mtDNA release, and restoration of gut microbial diversity. In contrast, the Lactobacilli mixture not only failed to improve outcomes but was associated with exacerbated intestinal damage, more pronounced cognitive dysfunction, and no reduction in neuroinflammatory markers. Conclusions: Combined exposure to LPS and ZDV induces gut-brain axis dysfunction characterized by neuroinflammation, cognitive impairment, intestinal damage, and dysbiosis. Bacillus subtilis effectively preserves cognitive function through activation of PINK1/PTEN-dependent mitophagy and suppression of neuroinflammation, highlighting its potential as a therapeutic candidate for cognitive impairments associated with gut-brain axis dysfunction. The contrasting effects of the lactobacilli mixture underscore the critical importance of strain-specificity in probiotic interventions.},
}

@article {pmid41893096,
year = {2026},
author = {Fan, J and Liu, S and Zhang, H and Jin, C and Wu, N},
title = {Dysbiosis of the Gut-Lung Axis and Its Immune Correlates During Pulmonary Cryptococcus neoformans Infection.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/jof12030163},
pmid = {41893096},
issn = {2309-608X},
support = {Grant No. 2023YFC2506004//National Key Research and Development Program of China/ ; },
abstract = {Cryptococcus neoformans is a major fungal pathogen responsible for life-threatening meningitis, especially in immunocompromised individuals. Although the gut-lung axis is known to regulate immune responses in respiratory infections, its role in cryptococcosis remains unclear. This study aimed to define the dynamic changes in the gut and lung microbiota and their relationship with host immunity during C. neoformans infection. Using a mouse model, we found that pulmonary infection induced significant dysbiosis in both the lung and gut microbiota, marked by decreased beneficial commensals and increased opportunistic pathogens. Integrated analysis showed these microbial shifts were closely associated with distinct immune responses: lung dysbiosis correlated with a strong IL-17-mediated pulmonary inflammatory response, while gut dysbiosis was linked to systemic immune activation in the spleen. Functional metagenomic prediction further revealed widespread disruption in microbial metabolic pathways, including energy metabolism and biosynthesis, in both sites. Importantly, a positive correlation was observed between lung and gut dysbiosis, indicating an interconnected gut-lung axis during cryptococcosis. These findings demonstrate that C. neoformans infection causes coordinated disruptions in microbiota and immunity across the gut-lung axis, underscoring the microbiome as a critical modulator of host response and suggesting potential avenues for microbiome-targeted therapies.},
}

@article {pmid41893137,
year = {2026},
author = {Francis, DV and Kishorkumar, M and Ahmed, ZFR and Neumann, EG and Kurup, SS},
title = {Molecular Advances and Sustainable Strategies in Mushroom Production for Food Security: A Review.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/jof12030205},
pmid = {41893137},
issn = {2309-608X},
support = {21R097//ARIFSID/ ; },
abstract = {Mushrooms offer a promising solution for sustainable food production due to their nutritional value, low resource requirements, and ability to grow in diverse environments. As interest in mushrooms grows, it is important to understand where current research is focused and where key gaps remain. A bibliometric analysis of 776 research articles indexed in Web of Science revealed a strong emphasis on yield, substrate reuse, and enzymatic degradation, but limited attention to molecular approaches, climate adaptation, and studies from arid regions such as the Middle East. Building on these findings, this review explores the ecological diversity of mushrooms and their adaptations across tropical, temperate, boreal, and arid ecosystems. It discusses the role of mycorrhizal and microbial interactions in nutrient cycling and environmental resilience, including desert truffle symbioses. Key pathways and genetic regulation involved in lignin degradation are outlined, along with recent advancements in transcriptomics, proteomics, genomics, metabolomics, and metagenomics that support improved cultivation and bioactive compound production. The review also addresses sustainable practices, such as microbiome integration and resource recycling, to enhance mushroom farming. The aim is to bring together ecological insights and molecular strategies to support sustainable mushroom production, particularly in regions facing resource and climate challenges.},
}

@article {pmid41893308,
year = {2026},
author = {Yeerjiang, B and Manaer, T and Liu, X and Bieerdimulati, R and Nabi, X},
title = {Mechanistic Insights into Lactobacillus harbinensis and Other Probiotics Regulating Lipid Metabolism in T2DM Mice via the PPARγ-LXRα-NPC1L1 Signaling Pathway Based on Multi-Omics Analysis.},
journal = {Metabolites},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/metabo16030157},
pmid = {41893308},
issn = {2218-1989},
support = {No. 82260640//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: Intestinal dysbiosis is a pivotal trigger of type 2 diabetes mellitus (T2DM). Our previous studies confirmed that composite probiotics derived from fermented camel milk (CPCM), containing Lactobacillus harbinensis and 13 other strains, can ameliorate glucose and lipid metabolism in T2DM mice by reshaping bile acid profiles, and its effect may be associated with the PPARγ-LXRα-NPC1L1 signaling pathway. Methods: Metagenomic analysis characterized alterations in intestinal microbiota structure and functional genes post-CPCM intervention, proteomic analysis detected changes in protein expression profiles related to glucose and lipid metabolism in mice, and Caco-2 cells were used for in vitro validation to clarify the regulatory effect of exopolysaccharides (EPS) (the active component of CPCM) on the PPARγ-LXRα-NPC1L1 signaling pathway. Results: The results showed that CPCM significantly improved glucose and lipid metabolism and remodeled the intestinal flora structure in mice, markedly enriching beneficial bacteria such as Lactobacillus and Akkermansia and enhancing the expression of functional genes related to the peroxisome proliferator-activated receptor (PPAR) signaling pathway and short-chain fatty acid synthesis in the microbiota. Proteomic analysis revealed that CPCM reversed the expression of key proteins involved in fatty acid oxidation and transport, thereby restoring the function of the PPAR signaling pathway. In vitro experiments validated that extracellular polysaccharides, the active component of CPCM, significantly upregulated the expression of PPARγ and liver X receptor α (LXRα) and inhibited the expression of Niemann-Pick C1-Like 1 (NPC1L1), a cholesterol absorption transporter, in Caco-2 cells. Conclusions: In conclusion, CPCM ameliorates glucose and lipid metabolic disorders in T2DM through multiple mechanisms: reshaping the intestinal probiotic community, enhancing its beneficial metabolic functions, restoring the activity of the PPARγ-LXRα signaling pathway, and subsequently downregulating NPC1L1.},
}

@article {pmid41893658,
year = {2026},
author = {Lisjak, A and Correa Lopes, B and Pilla, R and Nemec, A and Lampreht Tratar, U and Suchodolski, JS and Tozon, N},
title = {Assessment of Fecal Microbiota in Healthy Dogs and Dogs with Cutaneous Mast Cell Tumors Treated with Electrochemotherapy Combined with Gene Electrotransfer of IL-12.},
journal = {Veterinary sciences},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/vetsci13030241},
pmid = {41893658},
issn = {2306-7381},
support = {P3-0428, P4-0053, P3-0003, and J4-2546//The Slovenian Research and Innovation Agency/ ; The microbiome research at the Gastrointestinal Laboratory at Texas A&M University is in part funded through Purina PetCare Research Excellence Fund//Purina PetCare Research Excellence Fund/ ; },
abstract = {Cancer is a major health concern, with its incidence rate continuing to increase. There is growing interest in the microbiota and its role in carcinogenesis, as it significantly influences physiological and pathological processes. Various aspects of the microbiome have been shown to have both anti-tumor and pro-tumor effects. Advances in techniques such as high-throughput DNA sequencing have greatly improved our understanding of microbial populations in the human and canine gut. We aimed to (1) characterize the intestinal microbiota of healthy dogs and dogs with cutaneous mast cell tumors (MCTs), (2) assess changes in the intestinal microbiota of dogs undergoing electrochemotherapy (ECT) combined with gene electrotransfer (GET) of the IL-12 plasmid (IL-12), and (3) explore possible associations with the expression of immune markers Programmed cell death protein 1 (PD-1), Programmed death-ligand 1 (PD-L1), and Granzyme B (GZMB) in MCT tissue. Stool samples were collected from healthy dogs (n = 24) and dogs with MCTs (n = 24) before and after ECT and IL-12 GET. DNA was extracted from the samples, and shallow shotgun sequencing was performed. Immunohistochemistry was performed on the tumors to assess the expression of PD-1, PD-L1, and GZMB. The dysbiosis index, alpha diversity, and beta diversity did not differ between groups. Regarding microbial composition, Bifidobacterium animalis, Corynebacterium variabile, Lactobacillus johnsonii, Pediococcus pentosaceus, Streptococcus anginosus, Streptococcus equinus, Streptococcus intermedius, Clostridium thermobutyricum, Megasphaera elsdenii, and Anaerobiospirillum sp. were found in lower relative abundance in feces of dogs with MCTs, while Bacteroides togonis, Lactobacillus amylolyticus, Prevotella sp. CAG:279, and Megamonas hypermegale were more abundant compared to healthy dogs. Our study provides further insight into the composition of the gut microbiota in dogs with MCTs, where ECT and IL-12 GET did not lead to major shifts. We were unable to establish any association between the expression of immune markers and the microbiota.},
}

@article {pmid41893667,
year = {2026},
author = {Karakaya, E and Satıcıoğlu, İB and Yarım, D and Güran, Ö and Güran, C and Alpman, U and Atalan, G and Abay, S and Aydın, F},
title = {Culture and Metagenomic Insights into the Ear Microbiota in Dogs with Healthy Ears and Otitis Externa.},
journal = {Veterinary sciences},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/vetsci13030250},
pmid = {41893667},
issn = {2306-7381},
support = {TSA-2022-12342 and THD-2024-13751//Erciyes University/ ; },
abstract = {The canine ear microbiota plays an important role in ear health, and dysbiosis is associated with otitis externa (OE) and antimicrobial resistance (AMR). This study aims to investigate the ear microbiota of dogs with healthy ears and OE using bacterial culture-based methods and shotgun metagenomic sequencing, and to screen for AMR and virulence-associated genetic signatures. Ear swab specimens from 100 healthy and 100 OE-affected dogs were analyzed. The isolates obtained via bacterial culture were identified by MALDI-TOF MS and 16S rRNA sequencing. Metagenomic analysis was performed via Illumina shotgun sequencing. The most commonly defined species in healthy dogs in culture were Staphylococcus pseudintermedius (24.5%) and Staphylococcus epidermidis (5.7%); in dogs with OE, the most commonly defined species were S. pseudintermedius (30.5%), and Clostridium perfringens (4.5%). In healthy samples, metagenomic analysis revealed higher relative abundances of Bacteroides fragilis (15.8%) and Ezakiella coagulans (8.2%), while S. pseudintermedius (38.7%) dominated in OE. AMR profiling demonstrated diverse resistance determinants, including efflux pump systems and methicillin resistance-associated genes. In conclusion, the present study shows that S. pseudintermedius is a predominant member of canine ear microbiota, with higher presence in OE highlighting microbial shifts, and demonstrates that combining culture and metagenomic analyses provides a concise view of microbial communities and clinical relevance.},
}

@article {pmid41893692,
year = {2026},
author = {Shehla, S and Obaid, MK and Niaz, S and Khan, MA and Ahmad, AA and Abdel-Maksoud, MA and Alamri, A and Alrokayan, S and Shoaib, M and Shams, S and Ren, Q},
title = {Shotgun Metagenomics Reveals Microbial Diversity, Resistome, and Plasmidome in Dairy Cattle Feces.},
journal = {Veterinary sciences},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/vetsci13030275},
pmid = {41893692},
issn = {2306-7381},
support = {ORF-RC-2026-2600//King Saud University/ ; },
abstract = {Fecal microbiota are shaped by upstream digestive processes and reflect the outcome of host-microbe interactions, including the resistant microbial fraction that survives to be excreted. This is particularly crucial for assessing zoonotic risks and environmental contamination, as feces are the primary source of dissemination, which is considered an emerging One Health threat. Therefore, we conducted a pilot study to obtain the exploratory findings regarding the cattle GIT microbial composition, potential resistome, and their transmission drivers, such as plasmids, using metagenomic analysis from different districts in Khyber Pakhtunkhwa (KP) province, Pakistan. For this purpose, a total of 150 fecal samples (50 from each district) of healthy cattle were collected from various farms in Mardan (FC1), Peshawar (FC2), and Dera Ismail Khan (FC3) districts. Total DNA from each sample was extracted, pooled (FC1, FC2, and FC3), and sequenced via the Illumina platform. Bacteria were the highly abundant kingdom, while Pseudomonadota and Bacillota were dominant phyla in all samples. Caryophanon latum and Escherichia coli were highly abundant at the species level. A large resistome (40-49 genes), including critical genes, such as tet(X), blaOXA-427, and plasmidomes (16-22), such as IncF, was detected in the samples. The prominence of certain commensal or opportunistic pathogens in the fecal microbiota may indicate the presence of sub-clinical gastrointestinal disruptions or disease that may affect cattle herds. The fecal resistome is extensive, identifying dairy cattle in these regions as important reservoirs for AMR genes capable of spreading via HGT. This pilot study establishes that the fecal microbiota of dairy cattle in this region are not merely a waste product but a complex ecosystem, rich in microbiota of One Health significance.},
}

@article {pmid41893724,
year = {2026},
author = {Qiu, Q and Gong, T and Du, L and Li, W and Hu, Y and Li, D and Zhou, C and Liu, W},
title = {Comparative Analysis of Microbial Community Structure and Function in the Gut of South China Tigers Under Different Dietary Treatments.},
journal = {Veterinary sciences},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/vetsci13030307},
pmid = {41893724},
issn = {2306-7381},
support = {2110499//Diagnosis and Treatment of Genetic Diseases and Training for Stereotypic Behaviors in South China Tigers at Changsha Ecological Zoo/ ; 2110499//Artificial breeding of Reeves's pheasant (Syrmaticus reevesii) at Changsha Ecological Zoo/ ; },
abstract = {The gut microbiota is a crucial component of a tiger's health and plays a significant role in adapting to changes in food and the environment. Although extensive studies have been carried out on the gut microbiota of tigers, investigating the responses of gut microbial composition and function to preadaptation to wild predation patterns under captive conditions is particularly significant for South China tigers, given that it is the only tiger subspecies existing solely in captive settings at present. Here, we performed shotgun metagenomic sequencing for a comprehensive analysis of the gut microbiota of South China tigers assigned to two dietary groups (live prey group, LP group; frozen meat group, FM group), thereby generating abundant valuable data for this endangered subspecies. The results indicated that the core intestinal microbial composition was similar between the two dietary groups. Differential analysis revealed associations between dietary treatments and microbial abundance in the intestines of South China tigers. Functional gene analysis revealed that the LP group exhibited upregulation of genes and pathways related to antimicrobial resistance, bacterial infection-related disease, cell motility and proliferation, while the FM group displayed efficient energy metabolism. A total of 1251 antibiotic resistance genes (ARGs) were identified in the gut microbiome of South China tigers. The core resistome mainly included resistance to peptides, glycopeptides, tetracyclines, fluoroquinolones, and macrolides. In addition, the differences in ARGs between the LP group and FM group may be related to a broader range of animal tissues of live prey and the processing conditions of frozen meat. In summary, although feeding live prey did not change the core framework of the gut microbiota in South China tigers, it was associated with differences in microbial abundance, metabolic pathways, and antibiotic resistance gene profiles.},
}

@article {pmid41894043,
year = {2026},
author = {Tian, X and Feng, Y and Wang, C and Zhao, W and Xue, L and Zhu, L and Ji, X and Wang, H and Gu, Y and Jiang, Q and Zhang, J},
title = {Analysis of the characteristics of rumen microorganisms and their metabolites and plasma metabolites in crossbred beef cattle at different stages.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41894043},
issn = {1573-7446},
support = {2021BEF01002//Major Project of Science and Technology ofNingxia Autonomous Region/ ; 2023AAC03050//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; },
}

@article {pmid41894133,
year = {2026},
author = {Zhang, X and Chen, L and Wang, F and Xu, X and Wu, Y and Xu, J and Xu, Y and He, X},
title = {Torque teno virus in the lower respiratory tract: association with immunosuppression but not mortality in severe pneumonia-a multicenter retrospective cohort study.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41894133},
issn = {1435-4373},
support = {2024C3186//Key Research and Development Program of Zhejiang Province/ ; GZY-ZJ-KJ-24030//Major Project of National-Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; },
}

@article {pmid41894264,
year = {2026},
author = {Yu, Y and Hong, S and Wang, Z and Li, S and Zhang, S},
title = {Leptospirosis-induced diffuse alveolar hemorrhage: A rare case report from a non-epidemic area and literature review.},
journal = {Medicine},
volume = {105},
number = {13},
pages = {e48131},
doi = {10.1097/MD.0000000000048131},
pmid = {41894264},
issn = {1536-5964},
support = {No. LY21H100002//Zhejiang Natural Science Foundation Project/ ; No.2024C31025//Science and Technology Plan Project of zhoushan/ ; },
mesh = {Humans ; Female ; *Leptospirosis/complications/diagnosis/drug therapy ; Aged ; *Hemorrhage/etiology/diagnosis/microbiology ; *Pulmonary Alveoli/pathology ; *Lung Diseases/etiology/diagnosis/microbiology ; Shock, Septic/etiology ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {RATIONALE: Leptospirosis is an uncommon cause of severe pneumonia and diffuse alveolar hemorrhage (DAH), particularly in non-endemic areas, posing a significant diagnostic challenge. This case highlights the critical role of advanced molecular diagnostics in identifying this rare and life-threatening presentation.

PATIENT CONCERNS: A 65-year-old woman presented with an acute onset of high fever, chest tightness, and rapidly progressive shortness of breath.

DIAGNOSES: The patient was initially misdiagnosed with severe community-acquired pneumonia. She subsequently developed septic shock and multiple organ dysfunction syndrome. A definitive diagnosis of leptospirosis-induced DAH was confirmed through metagenomic next-generation sequencing, reverse transcription quantitative PCR, and subsequent seroconversion shown by immunoglobulin M enzyme-linked immunosorbent assay.

INTERVENTIONS: Upon diagnosis, targeted antimicrobial therapy with intravenous penicillin was initiated. Supportive care included management of septic shock and lung-protective ventilation for concomitant acute respiratory distress syndrome.

OUTCOMES: Following the confirmation of leptospirosis and initiation of targeted treatment, the patient's condition gradually stabilized. After a course of intensive care, she made a full recovery and was successfully discharged.

LESSONS: This case underscores that leptospirosis can present as fulminant DAH even in non-endemic regions. A high index of suspicion, aided by epidemiological clues and the rapid application of metagenomic next-generation sequencing/reverse transcription quantitative PCR, is crucial for timely diagnosis. Prompt targeted antimicrobial therapy combined with intensive organ support is essential for a favorable outcome in severe cases.},
}

Humans
Female
*Leptospirosis/complications/diagnosis/drug therapy
Aged
*Hemorrhage/etiology/diagnosis/microbiology
*Pulmonary Alveoli/pathology
*Lung Diseases/etiology/diagnosis/microbiology
Shock, Septic/etiology
Anti-Bacterial Agents/therapeutic use

@article {pmid41894564,
year = {2026},
author = {McCartin, LJ and Vohsen, SA and Wood, AL and Horowitz, J and Orozco-Juarbe, JJ and Pittoors, N and Morrissey, D and Vaga, CF and Hansel, CM and Collins, AG and Quattrini, AM and Herrera, S},
title = {Accounting for Intra- and Intergenomic Sequence Variation in Reference Barcodes Improves eDNA Metabarcoding Biodiversity Assessment.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70130},
doi = {10.1111/1755-0998.70130},
pmid = {41894564},
issn = {1755-0998},
support = {NA18OAR0110289//NOAA Ocean Exploration/ ; NA21OAR0110202//NOAA Ocean Exploration/ ; NA18NOS4780166//National Centers for Coastal Ocean Science/ ; //Smithsonian Institution/ ; //Smithsonian Women's Committee/ ; //Bureau of Ocean Energy Management/ ; 2000013668//National Academies of Sciences, Engineering, and Medicine/ ; //NOAA Fisheries Office of Science and Technology/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; Puerto Rico ; *Anthozoa/genetics/classification ; *Genetic Variation ; *Metagenomics/methods ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Environmental DNA (eDNA) metabarcoding can rapidly characterise biodiversity, yet its accuracy and effectiveness are limited by incomplete DNA barcode reference databases. We evaluated how comprehensive reference databases that include sequence variation within genomes (intragenomic) and across individuals and species (intergenomic) improve eDNA-based biodiversity assessments. We collected coral tissue and water samples at deep sites offshore Puerto Rico for reference barcoding and eDNA metabarcoding. Genome skimming coral specimens yielded 28S barcodes for 314 of 346 samples (90.8%) and revealed divergent intragenomic 28S lineages in multiple octocoral families. Incorporating local reference barcodes substantially changed ASV taxonomic classifications: 22 ASVs (8.9%) gained genus-level resolution, 19 ASVs (7.7%) were reassigned to different genera, and 14 ASVs (5.7%) lost incorrect genus-level classifications. Thus, incomplete reference databases produce not only unclassified ASVs but also false positive detections and ecologically meaningful misclassifications. When intragenomic 28S lineages were excluded from the reference database, 18 ASVs (7.4%) could not be classified to family or genus, demonstrating that unrecognised intragenomic variation can be mistaken for unsampled taxa. Integrating reference genome skimming and eDNA metabarcoding expanded known coral family richness by 36% at depths shallower than 1000 m and by 181% at depths greater than 1000 m. eDNA also detected two coral families previously unknown off Puerto Rico and nearby islands, underscoring its potential for biodiversity discovery.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
Animals
*DNA, Environmental/genetics
Puerto Rico
*Anthozoa/genetics/classification
*Genetic Variation
*Metagenomics/methods
RNA, Ribosomal, 28S/genetics

@article {pmid41894872,
year = {2026},
author = {Chen, H and Chai, Z and Chen, J and Song, C and Zheng, M},
title = {Anthraquinone-2-sulfonate enhances endogenous denitrification and phosphorus removal: Electron shuttle-mediated syntrophic partnerships.},
journal = {Water research},
volume = {298},
number = {},
pages = {125783},
doi = {10.1016/j.watres.2026.125783},
pmid = {41894872},
issn = {1879-2448},
abstract = {Endogenous denitrification (EnD) and denitrifying phosphorus removal (DPR) offer distinct advantages for low-carbon wastewater treatment, yet the nutrient removal performance is often constrained by inefficient electron transfer and nitrite/free nitrous acid (FNA) inhibition. Here, we demonstrate that anthraquinone-2-sulfonate (AQS) acts as an effective redox mediator to overcome these bottlenecks. With nitrate (NO3[-]-N) as the electron acceptor, the addition of 0.05 mmol/L AQS significantly amplified the electron transfer system activity (ETSA) by 3.66-fold. Consequently, this enhancement promoted the NO3[-]-N removal rate to 25.90 mg/(g VSS·h) (12.65-fold increase) and increased the phosphorus uptake rate to 3.69 mg/(g VSS·h) (1.95-fold improvement), achieving removal efficiencies of 96.22±1.00 % and 96.03±2.98 % for phosphorus and nitrogen, respectively. Moreover, when nitrite (NO2[-]-N) served as the electron acceptor, AQS enhanced the phosphorus uptake rate and nitrogen removal rate by 1.69-fold and 1.54-fold, respectively. Microbial analysis revealed a robust syntrophic partnership wherein Thauera, Candidatus Competibacter and Defluviicoccus (functioning as denitrifying glycogen-accumulating organisms) efficiently reduced NO3[-]-N to NO2[-]-N, which was subsequently scavenged by Dechloromonas and Candidatus Accumulibacter clade Ⅱ (functioning as denitrifying polyphosphate-accumulating organisms) for coupled phosphorus uptake. Metagenomic analysis further indicated that AQS facilitated electron transfer from Complexes I/Ⅱ to nitrate reductase and Complex Ⅲ, accelerating NO2[-]-N generation while alleviating FNA toxicity via coupled electron transfer from Cyt c to nitrite reductase. Crucially, this accelerated electron flux potentially intensified the proton motive force, suggesting an enhanced capacity for ATP generation to fuel the upregulation of phosphate transport (pit/pst) and polyphosphate synthesis (ppk) genes. These findings highlight AQS as a promising strategy to regulate electron transfer kinetics and metabolic coupling for advanced nutrient removal.},
}

@article {pmid41894881,
year = {2026},
author = {Zhao, Y and Li, Y and Zheng, Y and Yan, P and Lai, Y and Wang, X and Zhuang, LL and Zhang, J},
title = {Enhanced co-removal of nutrients and glyphosate from rural sewage in siphon-driven constructed wetlands: Optimization and mechanisms.},
journal = {Water research},
volume = {298},
number = {},
pages = {125812},
doi = {10.1016/j.watres.2026.125812},
pmid = {41894881},
issn = {1879-2448},
abstract = {Constructed wetlands (CWs) often suffer from limited carbon/oxygen availability and poorly controlled redox conditions, constraining pollutant removal from rural sewage. Hence, siphon-driven CWs (S-CWs) were optimized for the co-removal of the typical rural pollutant glyphosate (N-(phosphonomethyl)glycine, PMG) and typical wastewater pollutants (carbon (C), nitrogen (N), phosphorus (P)). S-CWs exhibited strong PMG resilience, tolerating up to 8 mg/L, and achieved 50.91-92.14%, 50.93-56.82% and 96.19-97.18% for PMG, N and P removal, respectively. These results indicated superior performance compared with unaerated and aerated CWs. Mechanistic analysis showed that PMG removal was dominated by biodegradation in the aerobic, carbon-enriched inlet area of S-CWs. This process was driven by genera such as Alcaligenes and Geobacillus, and enzymes like PhnI, PhnJ via aminomethylphosphonic acid (AMPA) and C-P lyase pathways, as confirmed by metagenomics and AlphaFold 3 predictions. PMG transiently inhibited N removal by suppressing denitrification but not nitrification. However, microbial adaptation over 135 days restored N removal along the first 50% pathway, even under high PMG stress (10 mg/L). In contrast, P removal was more persistently inhibited throughout the system, as the additional PMG-derived P increased total P load and accelerated substrate adsorption saturation. Long-term operation confirmed the robustness of S-CWs, including reduced effluent toxicity, healthier plant growth, lower oxidative stress, and minimal clogging (only 1.40-13.53% porosity decline). These observations highlight the hydraulic stability and long-term suitability of S-CWs for treating PMG-laden rural wastewater.},
}

@article {pmid41881444,
year = {2026},
author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML},
title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.},
journal = {BMJ open respiratory research},
volume = {13},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003864},
pmid = {41881444},
issn = {2052-4439},
mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Bronchoscopy ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Lung Diseases/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Chronic Disease ; },
abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.

METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.

RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95% CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics ≤3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).

CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.},
}

Humans
Male
Female
Cross-Sectional Studies
Bronchoscopy
Middle Aged
Aged
*Anti-Bacterial Agents/therapeutic use
*Microbiota/genetics
Bronchoalveolar Lavage Fluid/microbiology
Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy
Case-Control Studies
*Lung Diseases/microbiology/drug therapy
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Chronic Disease

@article {pmid41881804,
year = {2026},
author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C},
title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70315},
doi = {10.1111/mec.70315},
pmid = {41881804},
issn = {1365-294X},
support = {FONDECYT N°1191769//Agencia Nacional de Investigación y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigación y Desarrollo/ ; Doctoral scholarship N°21201700//Agencia Nacional de Investigación y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. & The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Charadriiformes/virology/physiology ; *Animal Migration ; *Virome/genetics ; Feces/virology ; Metagenomics ; Metagenome ; },
abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Charadriiformes/virology/physiology
*Animal Migration
*Virome/genetics
Feces/virology
Metagenomics
Metagenome

@article {pmid41881873,
year = {2026},
author = {Zhao, C and Yao, R and Xiong, M and Liu, X and Yu, J and Jumpponen, A and Romantschuk, M and Ur Rahman, S and Hui, N},
title = {Microbial exposure and antibiotic resistance gene dynamics shift between indoor and outdoor school activities.},
journal = {Ecotoxicology and environmental safety},
volume = {314},
number = {},
pages = {120044},
doi = {10.1016/j.ecoenv.2026.120044},
pmid = {41881873},
issn = {1090-2414},
abstract = {School curricular and extracurricular activities, including indoor study and sports like basketball, significantly impact adolescent physical and mental health. However, their effects on hand and nasal microbiomes, particularly regarding antibiotic resistance genes (ARGs), are underexplored. Here, we recruited 42 junior middle school students in Shanghai to investigate microbial composition and ARGs, collecting 336 hand and nasal samples after handwashing, indoor study, indoor basketball, and outdoor basketball. Our results showed that playing basketball either indoors or outdoors increased microbial diversity in nasal cavities and on hands, compared to post-handwashing. Notably, nasal microbiomes were predominantly derived from hand microbiomes, regardless of the activity performed. Among ARGs, macB genes were more abundant after outdoor basketball than indoor basketball, with this difference more pronounced in nasal cavities than on hands. Metagenomic sequencing identified Aureimonas phyllosphaerae as the primary macB gene host. Although this bacterium harbors ARGs, it is non-pathogenic and lacks mobile genetic elements, indicating a low potential for horizontal gene transfer or interspecies ARG transmission. Collectively, even though students may be exposed to more ARGs during outdoor activities, the health risks are likely minimal because the observed ARG bacteria are non-pathogenic and the likelihood of interspecies ARG transmission is low.},
}

@article {pmid41881888,
year = {2026},
author = {Tuveng, TR and Hagen, LH and Rese, M and Eijsink, VGH and Arntzen, MØ},
title = {Meta-omics profiling of denitrifying bacterial communities with lignin as carbon source.},
journal = {Microbiological research},
volume = {308},
number = {},
pages = {128503},
doi = {10.1016/j.micres.2026.128503},
pmid = {41881888},
issn = {1618-0623},
abstract = {Lignin is the most abundant renewable source of aromatic carbon and its microbial depolymerization and metabolism under aerobic conditions is well studied. However, lignin breakdown in the absence of oxygen remains poorly understood. In this study, we established long-term bacterial enrichment cultures supplied with diverse lignin preparations as the sole carbon source under denitrifying conditions. Denitrification dynamics were followed by monitoring nitrogenous gases. Metagenomics analysis of eight enrichments involving five lignins recovered 62 metagenome-assembled genomes (MAGs), several of which encoded enzymes for both denitrification and anaerobic metabolism of aromatic compounds. Quantitative metaproteomics confirmed expression of such enzymes and additionally showed that several MAGs expressed multiple oxidoreductases and uncharacterised proteins that are potential candidates for involvement in lignin modification. The detection of several oxygen-dependent oxidoreductases despite anaerobic conditions prompts intriguing discussion of potential mechanistic explanations. This systems-level study expands our understanding of bacterial processing of lignin-associated carbon in anaerobic environments and suggests enzymatic targets for further exploration of lignin depolymerization under oxygen-limited conditions.},
}

@article {pmid41882035,
year = {2026},
author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK},
title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36646-4},
pmid = {41882035},
issn = {2045-2322},
support = {2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; },
abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.},
}

@article {pmid41882344,
year = {2026},
author = {Muammar, A and Retnaningrum, E and Daryono, BS and Prijambada, ID and Yashima, Y and Peterbauer, C},
title = {A fast workflow to explore active enzymes from environmental samples through functional metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {41882344},
issn = {1432-0614},
mesh = {*Metagenomics/methods ; Feces/microbiology ; Workflow ; Animals ; *Cellulases/genetics/metabolism ; Indonesia ; Multiplex Polymerase Chain Reaction ; Gene Library ; Metagenome ; },
abstract = {Functional metagenomics has emerged as an effective tool for discovering novel enzymes directly from environmental samples, overcoming the limitations of traditional culture-based methods. In this study, we used a functional metagenomic approach on stool samples from Axis kuhlii, an endemic deer species from Indonesia, to identify active cellulases. We created an efficient workflow for expression of metagenomic sequences directly in Komagatella phaffii by combining metagenomic sequencing to investigate enzyme diversity, multiplex PCR to build a genes library, and rolling circle amplification (RCA) to streamline the cloning process, eliminating the need for intermediate Escherichia coli transformation and propagation steps. Furthermore, a semi-high-throughput screening method was used to evaluate multiple samples at once, allowing for the rapid identification of active enzymes. Using this approach, we discovered five endoglucanases and three β-glucosidases with confirmed enzyme activity. This study shows that functional metagenomics can bridge the gap between computational predictions and experimental validation, providing a reliable platform for enzyme discovery and characterization from complex environmental microbiomes. KEY POINTS: • We established K. phaffii expression of metagenomic sequences via multiplex PCR and RCA. • This approach links metagenomic and activity screening to enable enzyme discovery. • Eight active cellulases were obtained from environmental samples through this approach.},
}

*Metagenomics/methods
Feces/microbiology
Workflow
Animals
*Cellulases/genetics/metabolism
Indonesia
Multiplex Polymerase Chain Reaction
Gene Library
Metagenome

@article {pmid41882399,
year = {2026},
author = {Çilkiz, M},
title = {Microbial Biotechnology in Agriculture.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {251-306},
pmid = {41882399},
issn = {0079-6484},
mesh = {*Agriculture/methods ; *Biotechnology/methods ; Soil Microbiology ; Metagenomics/methods ; Crops, Agricultural/growth & development/microbiology ; Metabolomics/methods ; Fertilizers ; },
abstract = {Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.},
}

*Agriculture/methods
*Biotechnology/methods
Soil Microbiology
Metagenomics/methods
Crops, Agricultural/growth & development/microbiology
Metabolomics/methods
Fertilizers

@article {pmid41882401,
year = {2026},
author = {Erözden, AA and Tavşanlı, N and Çalışkan, M and Arıkan, M},
title = {Microbial Omics.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {333-366},
pmid = {41882401},
issn = {0079-6484},
mesh = {*Metabolomics/methods ; *Proteomics/methods ; *Genomics/methods ; Metagenomics/methods ; *Computational Biology/methods ; Transcriptome ; Microbiota ; *Bacteria/genetics/metabolism ; },
abstract = {Omics technologies have revolutionized research across diverse fields, and their increasing use in microbiology has provided new opportunities for understanding microbial life. These methods enable detailed investigation of the molecular biology of individual organisms as well as the complex interactions within microbial communities. In this chapter, we describe key single-organism omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, as well as meta-omics techniques such as metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics. We also discuss integrative multi-omics strategies for studying microbial ecosystems. For each omics method, we outline its main features, experimental and bioinformatic workflows, major applications, and commonly used computational tools, thereby providing a practical guide for researchers aiming to explore microbial structure, function and interactions at multiple molecular levels.},
}

*Metabolomics/methods
*Proteomics/methods
*Genomics/methods
Metagenomics/methods
*Computational Biology/methods
Transcriptome
Microbiota
*Bacteria/genetics/metabolism

@article {pmid41882608,
year = {2026},
author = {Chen, M and Wu, Z and Du, Y and Jiang, J and Feng, J},
title = {Construction of caries risk assessment scale and oral microecology analysis of adolescents with fixed orthodontic treatment.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08114-y},
pmid = {41882608},
issn = {1472-6831},
}

@article {pmid41882673,
year = {2026},
author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C},
title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08013-4},
pmid = {41882673},
issn = {1479-5876},
abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.

METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.

RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.

CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.

TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.},
}

@article {pmid41882801,
year = {2026},
author = {Langlois, A and Duplessis, M and Ronholm, J and Vincent, AT and Poulin-Laprade, D and Petri, RM},
title = {Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00554-9},
pmid = {41882801},
issn = {2524-4671},
}

@article {pmid41883029,
year = {2026},
author = {Dip, SA and Mallick, D and Acharjee Shuvo, U and Barua Soumma, S and Rafsani, F and Kumar Paul, B and Ahmed Moumi, N and Ahmed, S and Zhang, L},
title = {Large language model agents for biological intelligence across genomics, proteomics, spatial biology, and biomedicine.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
doi = {10.1093/bib/bbag110},
pmid = {41883029},
issn = {1477-4054},
support = {2125798//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2344169//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2319522//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; },
mesh = {*Genomics/methods ; *Proteomics/methods ; Humans ; *Computational Biology/methods ; *Artificial Intelligence ; Large Language Models ; },
abstract = {Large language models (LLMs) are evolving from passive predictors into agentic systems capable of planning, tool-use, and multimodal reasoning. This shift is especially consequential for biology, where complex, noisy, and multi-scale data require adaptive and integrative computational strategies. In this review, we provide the first systematic synthesis of LLM-based agents across genomics, molecular biology, imaging, biomedical analysis, and automated bioinformatics workflows. We analyze >60 emerging systems and organize them within a unifying framework that characterizes agentic traits, such as autonomous decision-making, external tool invocation, memory, and self-correction. Across domains, agentic LLMs show early promise in enabling multi-step analysis, linking heterogeneous evidence, and supporting exploratory scientific tasks. At the same time, our comparative assessment highlights consistent challenges, including unstable reasoning, limited biological grounding, retrieval misalignment, and barriers to reproducibility and biosafety. We conclude by outlining opportunities for trustworthy and collaborative biological agents, including multimodal integration, closed-loop experimental design, and robust evaluation practices. This survey aims to clarify the emerging landscape and chart a path toward reliable agentic systems for biological discovery.},
}

*Genomics/methods
*Proteomics/methods
Humans
*Computational Biology/methods
*Artificial Intelligence
Large Language Models

@article {pmid41883089,
year = {2026},
author = {Duchêne, C and Jaubert, M and Falciatore, A},
title = {Beyond red/far-red sensing: phytochrome perception of the marine light field by microalgae.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71128},
pmid = {41883089},
issn = {1469-8137},
support = {ANR-25-CE20-4776//Agence Nationale de la Recherche/ ; ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; ANR-25-CE20-1717//Agence Nationale de la Recherche/ ; ANR-11-LABX-0011-01//Agence Nationale de la Recherche/ ; 101082304//Fourth Framework Programme/ ; },
abstract = {Phytochromes (PHYs) are a major group of photoreceptors, described as red and far-red light sensors in land plants. Recent genomic and metagenomic explorations have revealed the presence of PHYs also in various eukaryotic microalgae originating from distinct endosymbiotic events. Growing evidence indicates that these PHYs are spectrally and functionally tuned to shorter wavelengths, which are prevalent in the aquatic environments as depth increases. Investigations using emerging phytoplankton model species, along with environmental surveys, are uncovering new PHY-mediated responses that likely influence their growth and distribution in marine environments. This Tansley Insight explores the implications of these discoveries for understanding the evolution and functional significance of this major photoreceptor class in the upper ocean, where light drives both energy and information flow.},
}

@article {pmid41883376,
year = {2026},
author = {Mao, C and Wang, Y and Li, X and Kong, Q and Al-Farraj, SA and Xu, EG and Grossart, HP and Huang, J and Song, W},
title = {Resistance Gene Dynamics, Biogeochemical Coupling, and Ecological Risks in Sediments of Anthropogenically Impacted Lake Wetlands in China.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {3},
pages = {420-433},
pmid = {41883376},
issn = {2833-8278},
abstract = {Antibiotic resistance is a growing global threat to both public health and ecosystem stability. While the "One Health" framework emphasizes the need to monitor antibiotic resistance genes (ARGs) across diverse environments worldwide, the risks posed by ARGs in lakes affected by human activities, particularly in lake sediments that serve as natural reservoirs of ARGs, remain poorly understood. Metagenomics enables culture-independent analysis of microbial communities and resistance genes, providing essential insights into ARG dynamics. This study investigates microbial communities, ARGs, metal resistance genes (MRGs), and mobile genetic elements (MGEs) in sediments from Lake Donghu and Lake Weishan in China, two contrasting lake ecosystems subject to urbanization and agricultural activities for over four decades, using high-throughput metagenomic sequencing and assembly. ARGs and MRGs were more strongly influenced by deterministic environmental factors, particularly heavy metals (Cd, Pb, Cu), whereas microbial community structures were predominantly shaped by stochastic processes. Metagenomic binning yielded 293 metagenome-assembled genomes (MAGs), 125 of which were identified as potential ARG hosts, with Proteobacteria and Desulfobacterota being the most common. These hosts frequently cocarried MGEs, virulence factor genes (VFGs), and MRGs and exhibited metabolic pathways linked to carbon, nitrogen, and greenhouse gas (CO2 and N2O) cycling. Dissolved organic carbon (DOC) was determined as a key factor influencing microbial metabolism and promoting resistance gene dissemination. Our findings highlight a tight coupling between ARG dissemination, microbial ecological functions, and biogeochemical processes, underscoring ecosystem-level risks associated with resistance proliferation in human-impacted wetlands of China and elsewhere.},
}

@article {pmid41883694,
year = {2026},
author = {Feigl, V and Röhberg, MZ and Masa, K and Hegedűs, H and Janek, Z and Deák, V and Fehér, C and Buda, K and Medgyes-Horváth, A},
title = {Extremophilic microbial isolates and metagenomic analysis of Greek and Hungarian bauxite residues.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {50},
number = {},
pages = {e00956},
pmid = {41883694},
issn = {2215-017X},
abstract = {Bauxite residue (BR) is an extreme environment for microorganisms. The aim of the work was to isolate extremophilic microorganisms for further biotechnological applications, such as bioleaching or waste rehabilitation. At the same time, metagenomic analysis was performed to monitor short-term changes in deposited BR. We isolated and identified alkaliphilic and extreme halotolerant strains of Nesterenkonia massiliensis, N. natronophila, Micrococcus luteus, Aspergillus iizukae, Gibellulopsis serrae, and G. nigrescens from Greek and Hungarian BRs. Most strains were siderophore producers, cellulose degraders and produced oxalic and acetic acids. Metagenomic analysis revealed a shift in the most abundant bacterial classes from the freshly produced BR during 1 month and 3 months of storage: from Gammaproteobacteria (29% relative abundance), to Actinomycetes (31%) and Gammaproteobacteria (39%), respectively. Metagenomic analysis showed the presence of Nesterenkonia species. These results highlight the diverse microbiome of BR and underscore its potential as a valuable reservoir of extremophilic microorganisms.},
}

@article {pmid41883790,
year = {2026},
author = {Way, J and Sherman, T and Leleika, S and Crippen, K and Wilson, R and Fida, TT},
title = {Enrichment and comparative metagenomics of microbes involved in biocorrosion of gas transport or storage steel infrastructure.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771929},
pmid = {41883790},
issn = {1664-302X},
abstract = {Biocorrosion, also known as microbiologically influenced corrosion (MIC), is the deterioration of metals caused by microbial activities that compromise the structural integrity, reliability, and safety of steel infrastructure. To identify the genetic determinants that MIC-causing microorganisms may use to attack steel infrastructure, field samples from natural gas infrastructure with a potential history of MIC were collected, enriched for different MIC categories, and subjected to whole-genome shotgun sequencing for metagenomic analysis. Biofilms were grown on carbon steel coupons or glass slides as attachment substrates to assess differences in microbial community composition and metabolic activities. The highest corrosion activities were observed in enrichments dominated by acid-producing bacteria (APB) and hydrogen-utilizing bacteria. APB enrichments resulted in the highest accumulation of organic acids and a severe decrease in culture fluid pH. A total of 57 metagenome-assembled genomes were recovered from the biofilms, some of which differed between carbon steel coupons and glass slide substrates. The metagenomes contained most of the known genes implicated in MIC and sulfide production, with substantial variation in estimated gene copy numbers among metagenomes and attachment substrates. Overall, comparative analysis of these biofilm metagenomes enriched from natural gas production and processing infrastructure highlights similarities to microbial communities commonly observed in oil production and processing systems and provides an overview of candidate genes that may be used as molecular probes for MIC.},
}

@article {pmid41883806,
year = {2026},
author = {Peng, L and Zhang, Y and Li, X and Hu, Z},
title = {Integrated multi-omics analysis reveals gut microbiota and metabolic characteristics in coronary heart disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1743914},
pmid = {41883806},
issn = {1664-302X},
abstract = {BACKGROUND: Coronary heart disease (CHD) is a leading cause of morbidity and mortality worldwide. Increasing evidence indicates that gut microbiota dysbiosis contributes to CHD pathogenesis through metabolic, inflammatory, and coagulation-related mechanisms. However, comprehensive multi-omics investigations of individuals with CHD remain limited. In this study, we aimed to characterize the multi-omics features of CHD and to identify potential diagnostic biomarkers.

METHODS: The study included 10 patients with clinically diagnosed CHD and 10 healthy controls. Blood and fecal samples were collected for further analysis. The gut microbiota composition was assessed using 16S ribosomal RNA high-throughput sequencing, and shotgun metagenomic sequencing was further performed to evaluate microbial functional potential through the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and differential pathway analysis. Non-targeted metabolomic profiling was performed using ultra-high-performance liquid chromatography coupled with Orbitrap mass spectrometry, and quantitative proteomic analysis was conducted using liquid chromatography-tandem mass spectrometry. Functional interaction networks between differentially expressed metabolites and proteins were constructed using Spearman correlation analysis, and the diagnostic potential of candidate biomarkers was evaluated using receiver operating characteristic (ROC) curve analysis.

RESULTS: At the phylum level, the CHD group exhibited an increased abundance of Pseudomonadota and a decreased abundance of Bacillota and Actinomycetota. At the genus level, Escherichia-Shigella, Bacteroides, and Klebsiella were significantly enriched, whereas Bifidobacterium and Faecalibacterium were decreased in abundance. Shotgun metagenomic analysis revealed functional remodeling of gut microbiota in CHD, with upregulation of KEGG pathways related to energy metabolism, inflammatory signaling, and host-microbe interactions. Serum metabolomics and proteomic analyses identified 32 differentially expressed metabolites and 38 differentially expressed proteins, respectively. Correlation analysis revealed significant associations between phospholipid metabolites and apolipoproteins, inflammatory mediators and the complement system, asymmetric dimethylarginine and endothelial function-related proteins, and oxidative stress metabolites and antioxidant proteins. ROC analysis identified several potential biomarkers with high diagnostic value.

CONCLUSION: We demonstrate that individuals with CHD exhibit significant gut microbiota dysbiosis, distinct metabolic pathway alterations, and aberrant expression of coagulation- and inflammatory-related proteins. These findings provide novel insights into potential targets for CHD prevention and treatment strategies.},
}

@article {pmid41884347,
year = {2026},
author = {Liu, H and Li, J and Yang, K and Li, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T},
title = {Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2647511},
pmid = {41884347},
issn = {2000-2297},
abstract = {BACKGROUND: Long-term heavy metal exposure poses health risks, and non-invasive biomarkers for early detection are needed.

OBJECTIVE: This study investigated whether oral microbiome alterations can serve as a non-invasive indicator of long-term HMs exposure and associated early biological effects.

DESIGN: Soil, buccal mucosa, blood, and urine samples were collected from contaminated (CA) and uncontaminated (UA) areas. Soil contamination was assessed, and internal biomarkers were measured. Oral bacterial diversity was analyzed using metagenomic sequencing.

RESULTS: Severe Cd and Pb contamination was found in CA soil. Participants in CA had elevated internal Cd levels, renal impairment, and immune alterations. Oral microbiome analysis revealed decreased alpha diversity, reduced network complexity, and a shift from beneficial to pathogenic keystone taxa in CA. Functional analysis showed enrichment of stress-response pathways, suppression of metabolic pathways, and increased pathways linked to human diseases. Specific bacterial taxa correlated with internal biomarker levels.

CONCLUSIONS: There is a close association between long-term HMs exposure and reproducible, multi-faceted shifts in the oral microbiome. The oral microbiome may represent a promising, non-invasive biomarker for assessing environmental exposure and its early biological impacts.},
}

@article {pmid41885442,
year = {2026},
author = {Rysava, M and Stredanska, K and Schwarzerova, J and Jakubickova, M and Cejkova, D and Aytan-Aktug, D and Otani, S and Dolejska, M and Palkovicova, J},
title = {Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0407425},
doi = {10.1128/spectrum.04074-25},
pmid = {41885442},
issn = {2165-0497},
abstract = {The expansion of intensive poultry farming has led to a substantial increase in antibiotic use, which, in turn, has promoted the accumulation of antibiotic resistance genes (ARGs). The chicken gut serves as a reservoir for these genes and provides favorable conditions for their horizontal transfer via mobile genetic elements, such as plasmids. Through this process, commensal bacteria can transfer ARGs to pathogens, facilitating their spread and increasing the risk of transmission to humans. In this study, long-read sequencing was used to characterize the plasmidome and resistome in 12 fecal samples from 3 houses of a commercial broiler chicken farm. All chickens received enrofloxacin in the first days of life, with one house additionally treated with sulfamethoxazole/trimethoprim combination. For comparison, metagenomic analysis using short-read sequencing was performed on the same samples. This study revealed the presence of various ARGs associated with resistance to 25 antibiotic classes. A strong genetic association between MOBP-type plasmids and fluoroquinolone resistance was observed within broiler chicken farms. Temporal trends indicated progressive mobilization of these ARGs, suggesting an increasing potential for horizontal gene transfer. While fluoroquinolone resistance expanded over time, diaminopyrimidine resistance remained stable despite the antibiotic treatment. Most ARGs were carried on small plasmids, and complete plasmid reconstructions ranged from 2.6 to 47.6 kb. Our findings demonstrate that plasmidome sequencing enables high-resolution detection of resistance-associated plasmids that may be overlooked by conventional metagenomic approaches. The observed patterns are consistent with an association between fluoroquinolone use in poultry farms and the presence of plasmid-mediated resistance genes with potential for horizontal dissemination.IMPORTANCEDespite the crucial role of plasmids in antimicrobial resistance (AMR) dissemination, studies focusing on plasmidomes, defined as the complete set of plasmids, remain limited. This study is the evidence that chicken farms, where fluoroquinolone treatment is a standard practice, act as an important reservoir of plasmid-mediated antibiotic resistance which may not be revealed by commonly used approaches. Combining a metagenomic approach with a focus on plasmids enhances our ability to understand the genetic context and mechanisms underlying AMR transmission. The findings emphasize the importance of targeted plasmid analysis to improve surveillance and risk assessment of AMR transmission in microbial ecosystems.},
}

@article {pmid41885716,
year = {2026},
author = {Xu, H and Yang, H and Shi, Y and Hu, X and Zhang, L and Li, P and Ma, Y and Yang, T and Xu, Y and Dong, C and Shen, Q},
title = {Genotype-Dependent Rhizosphere Microbiome Assembly Improves Potassium Use Efficiency in Pear Rootstocks Under Low Potassium Stress.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70499},
pmid = {41885716},
issn = {1365-3040},
support = {32272802//National Science Foundation of China/ ; CARS-28-10//China Agriculture Research System/ ; },
abstract = {Potassium (K) is a vital nutrient for fruit quality in pears (Pyrus spp.), and rhizosphere microbes play a critical role in enhancing plant K uptake and utilization. To investigate the genotype-dependent influences of the rhizosphere microbiome on potassium use efficiency (KUE) in pears, we compared two rootstocks with contrasting KUE (Pyrus betulaefolia and Pyrus ussuriensis) using integrated pot and long-term field experiments, 16S rRNA amplicon sequencing, and metagenomic analyses. Synthetic community (SynCom) inoculation and transcriptome profiling were employed to elucidate the mechanisms underlying enhanced K acquisition. Under low-K conditions, P. betulaefolia recruited distinct microbial communities, which significantly improved K accumulation by upregulating genes (e.g., ATP1A, kdPB, and COG3158) associated with K transport and homoeostasis. Field trials further confirmed that P. betulaefolia-grafted trees sustained higher Bacillaceae abundance, superior fruit quality, and elevated K content than P. ussuriensis under K-deficient conditions. SynComs constructed from five Bacillaceae strains enhanced low-K tolerance by promoting root metabolic activity, stimulating root hair development, modulating K[+] transporter (e.g., NRT2.4) expression, and activating calcium-dependent signalling pathways. Inoculation with SynComs led to substantial improvements under K limitation, including a 105.86% increase in plant biomass, a 164.99% increase in K accumulation, and a 125.91% enhancement in the aboveground K utilisation index. These findings reveal that genotype-driven enrichment of Bacillaceae-dominated microbiomes significantly enhances pear KUE, offering mechanistic insights to guide the development of microbiome-based bioinoculants and breeding of "microbiome-responsive" rootstocks for sustainable fruit production under K-limiting conditions.},
}

@article {pmid41885787,
year = {2026},
author = {Ayed, M and Cadavez, V and Gonzales-Barron, U},
title = {Current research trends towards the control of protozoans in foods.},
journal = {Italian journal of food safety},
volume = {},
number = {},
pages = {},
doi = {10.4081/ijfs.2026.15114},
pmid = {41885787},
issn = {2239-7132},
abstract = {Protozoan parasites such as Cryptosporidium spp., Giardia duodenalis, Toxoplasma gondii and Cyclospora cayetanensis remain difficult-to-control hazards in food due to environmental persistence, low infectious doses, and the interpretability gap between nucleic acid detection and infectivity. This review synthesizes 4-year research trends shaping protozoan control in food systems, focusing on three critical pillars: matrix-adapted front-end processing (concentration, lysis, inhibitor management); inhibitor-resilient quantification; and sequencing-based attribution for outbreak investigation and source tracking. Recent benchmarking across wastewater, the water-soil-produce nexus, and food-relevant matrices repeatedly indicates - depending on matrix and study design - that upstream workflow steps often dominate analytical sensitivity and reproducibility. Accordingly, tiered analytical strategies are emerging in which the quantitative polymerase chain reaction (PCR) technique supports scalable screening, droplet digital PCR is used for decision-grade confirmation/quantification under inhibition and low-template conditions, and targeted sequencing or metagenomics is deployed selectively for traceback and contextual investigation. We integrate these developments into an actionable control framework that links prevention at the water-soil-plant interface with tiered analytics and viability-aware interpretation of post-intervention results. Research priorities ahead include harmonized performance reporting (recovery, inhibition controls, limit of detection/quantification), transparent endpoint hierarchy for intervention claims (detectability versus viability/infectivity), and interoperable sequence databases to enable cross-laboratory attribution and program-level learning. The field is moving from "can we detect?" towards "can we decide? - requiring reproducible front-end processing, inhibitor-resilient quantification, interoperable attribution resources, and endpoint discipline for intervention efficacy claims.},
}

@article {pmid41886617,
year = {2026},
author = {Qiao, Z and Chen, Z and Gong, H and Guo, X and Yu, H and Chen, L},
title = {Exogenous Elemental Sulfur Promoting Methane Production and Simultaneous Ammonia Nitrogen Removal in Anaerobic Digestion of Food Waste: Experimental Verification and Mechanism Analysis.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c18148},
pmid = {41886617},
issn = {1520-5851},
abstract = {The treatment of food waste (FW) via anaerobic digestion (AD) is frequently plagued by a low methane yield and ammonia (NH4[+]) inhibition. This study demonstrates that the addition of elemental sulfur (S[0]) effectively mitigates both of these issues. Through batch and continuous experiments, it was found that the specific methane yield was enhanced by up to 48.1% and the NH4[+] concentration decreased by 26.9% at the optimal S[0] dosages of 20 mg/L. Metagenomic analysis revealed a dual mechanism underlying this enhancement: at low dosages, S[0] provides a sulfur-containing functional group for the biosynthesis of methyl-coenzyme M, thereby accelerating the rate-limiting "methyl-transfer" step in methanogenesis; at high dosages, it promotes the biosynthesis of coenzyme A, which markedly enhances acidogenesis. Furthermore, S[0] alleviates NH4[+] inhibition by fostering a synergistic interaction between sulfate-reducing bacteria and anammox bacteria, which convert NH4[+] to N2. Continuous operation over 140 days confirmed the long-term stability and effectiveness of this S[0] addition strategy. This study provides mechanistic insights into S[0]-driven methanogenesis in complex organic waste (FW) and offers a cost-effective, sustainable approach to enhancing AD efficiency and stability.},
}

@article {pmid41886785,
year = {2026},
author = {Tian, M and Li, J and Dai, S and Ma, L},
title = {Clinical Characteristics and Management of Four Cases of Visceral Leishmaniasis-Associated Hemophagocytic Lymphohistiocytosis.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.25-0530},
pmid = {41886785},
issn = {1476-1645},
abstract = {The aim for the present study was to analyze clinical features, diagnostic approaches, and therapeutic strategies for visceral leishmaniasis (VL)-associated hemophagocytic lymphohistiocytosis (HLH) in pediatric patients. The clinical characteristics and test results of the children were summarized. Among the four patients, three resided in VL-endemic regions, and one had traveled to a VL-endemic region. All patients presented with recurrent fever (>38.5°C), hepatosplenomegaly, and decreased hemoglobin (HGB) levels ([78.75 ± 8.50] g/L) and platelet (PLT) counts ([59.50 ± 17.48] × 109/L). Before a definitive diagnosis could be made, patients exhibited progressive declines in white blood cell counts, HGB levels, and PLT counts, along with elevated triglyceride, serum cytokine (interleukin [IL]-6, IL-10, IL-2R, and tumor necrosis factor α) levels. Bone marrow aspirate smears revealed hemophagocytosis and Leishmania donovani (LD) bodies in all cases: two were diagnosed via direct identification of LD bodies, one was diagnosed through re-examination of bone marrow smears after confirming a travel history, and one was diagnosed via re-examination prompted by metagenomic next-generation sequencing, which revealed leishmaniasis. All the patients were initially diagnosed with HLH and received HLH-directed immunochemotherapy before VL diagnosis, with suboptimal response. After confirmation of VL, sodium stibogluconate therapy was initiated, resulting in a partial response in all cases. Etiological investigation is critical for HLH diagnosis. For VL-associated HLH, sodium stibogluconate as targeted therapy rapidly controls HLH, facilitates immunosuppression withdrawal, and significantly improves patient outcomes. White blood cell count, HGB level, PLT count, and lactate dehydrogenase level may serve as critical prognostic biomarkers for VL-associated HLH.},
}

@article {pmid41886955,
year = {2026},
author = {Ling, GC and Chen, SJ and Li, ZL and Yang, S and Xiao, YY and Xiao, M and Zhang, YY and Zhong, HJ and Zhang, JY and Li, Y and Xie, JJ},
title = {A microbiota-tryptophol-AhR axis mediates the gut-kidney protective effects of Hushen Tongfengtai Granules in hyperuricemic nephropathy.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158089},
doi = {10.1016/j.phymed.2026.158089},
pmid = {41886955},
issn = {1618-095X},
abstract = {BACKGROUND: Hyperuricemia (HUA) may result in hyperuricemic nephropathy (HN), and gut dysbiosis with barrier dysfunction can worsen disease progression. Hushen Tongfengtai granules (HSTFT), a traditional Chinese herbal prescription, have been used clinically to mitigate HUA and related renal injury. However, the mechanisms behind their effects remain to be explored.

OBJECTIVE: To find HSTFT to mitigate HN through mechanisms dependent on gut microbiota.

METHODS: Fecal metagenomics and UPLC-ESI-MS/MS metabolomics were employed to identify key microbial taxa and metabolites modulated by HSTFT. Antibiotic-treated mice were used to investigate the gut microbiota-dependent mechanisms of HSTFT. In vivo and in vitro experiments were further conducted to validate the ameliorative effects of HSTFT on gut dysbiosis and barrier dysfunction in HUA mice.

RESULTS: HSTFT could improve renal injury and intestinal barrier dysfunction in HUA. Fecal metagenomic analysis revealed enrichment of Bifidobacterium breve. Antibiotic depletion could abolish the therapeutic efficacy of HSTFT, while Bifidobacterium breve (B.breve) recolonization could restore intestinal and renal protection. Metabolomic analysis identified tryptophol as a key HSTFT-associated metabolite. Exogenous tryptophol (TOL) recapitulated the protective effects and may activate the aryl hydrocarbon receptor (AhR) pathway. The AhR antagonist CH223191 could inhibit the TOL/HSTFT-mediated protective effects on intestinal barrier integrity and renal function.

CONCLUSION: HSTFT could ameliorate HN by enhancing intestinal barrier integrity and renal protection, with the underlying mechanism involving upregulation of intestinal B.breve and its metabolite TOL via AhR pathway activation.},
}

@article {pmid41887041,
year = {2026},
author = {Huang, J and Fu, Z and Zhou, S and Hu, J and Yu, G and Qin, C and Ma, Z},
title = {Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101810},
doi = {10.1016/j.cbd.2026.101810},
pmid = {41887041},
issn = {1878-0407},
abstract = {The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.},
}

@article {pmid41887065,
year = {2026},
author = {Song, J and Hou, YN and Li, R and Feng, Z and Wang, AJ and Ren, N and Wei, W and Ni, BJ and Huang, C},
title = {Ectoine modulates mixotrophic denitrification pathway partitioning to sustain stable nitrogen and phenol removal under hypersaline stress.},
journal = {Water research},
volume = {298},
number = {},
pages = {125764},
doi = {10.1016/j.watres.2026.125764},
pmid = {41887065},
issn = {1879-2448},
abstract = {Hypersaline wastewater containing phenolic compounds imposes coupled osmotic and cytotoxic stresses that severely disrupts biological treatment processes. While compatible solutes are known to enhance cellular osmoprotection, their capacity to regulate microbial metabolic, particularly the balance between autotrophic and heterotrophic denitrification pathways under combined salinity stress remain poorly understood. This study reveals that the compatible solute ectoine modulates pathway partitioning in mixotrophic denitrification systems, enabling efficient nitrogen and phenol removal under 4% salinity. The ectoine amended reactor maintained nitrogen removal above 95% and phenol degradation above 80%, whereas the unprotected control collapsed to 34% and 33% respectively. Multi-scale mechanistic investigations revealed a coordinated protection cascade. First, ectoine enhanced cellular resilience by suppressing reactive oxygen species (ROS) by 88.2%, maintaining ATP level and electron transport activity, thereby preserving bioenergetic integrity. Second, structural fortification was achieved through intensified extracellular polymeric substance (EPS) production. The protein-to-polysaccharide ratio increased from 0.70 to 1.51 creating a protective matrix that stabilized membrane permeability and preserved catalytic enzymes, with nitrate reductase and nitrite reductase activities increasing 2.16- and 2.93-fold. Third, metagenomic profiling revealed community reconfiguration, with selective enrichment of halotolerant heterotrophs (Halomonas, Marinobacter) to 49% relative abundance. Aromatic‑degradation genes (catA, benB) rose by 7‑ and 48‑fold, while nitrogen‑metabolism genes (nasA, norC) remained high representation. This restructuring reversed pathway contributions from 81% sulfur-autotrophic dominance to 82% heterotrophic dominance. Ectoine thus functions as a metabolic modulator that links cellular stress alleviation and community-level functional potential to pathway repartitioning, offering a feasible strategy for the biotreatment of saline phenolic wastewater.},
}

@article {pmid41887066,
year = {2026},
author = {Wang, H and Wu, Y and Weng, H and Zhang, L and Peng, Y},
title = {Denitrification mode management selects resource-conserving consortia for low-carbon municipal wastewater treatment.},
journal = {Water research},
volume = {298},
number = {},
pages = {125775},
doi = {10.1016/j.watres.2026.125775},
pmid = {41887066},
issn = {1879-2448},
abstract = {Low-carbon municipal wastewater treatment increasingly relies on carbon-limited denitrification, yet how carbon limitation reorganizes denitrifying communities and their greenhouse-gas footprint remains poorly resolved. We implemented denitrification mode management in a municipal wastewater sequencing batch reactor by switching from anaerobic-aerobic (AO) to anaerobic-aerobic-anoxic (AOA) operation. This shift moved denitrification from an pre-anaerobic stage with higher carbon availability to a post-anoxic stage where readily available carbon was limited. We combined metagenomics and metatranscriptomics to link process performance with microbial traits and gene expression. The mode switch improved nitrogen removal from 67.1 ± 1.8% to 88.5 ± 3.9% and reduced carbon requirement from 4.9 ± 0.5 to 3.3 ± 0.4 mg COD per mg N removed, while decreasing the N2O emission factor from 0.024 to 0.005 mg N2O-N per mg NO3[-]-N and lowering CO2 and CH4 emissions by 20-30%. Carbon-limited post-denitrification selected taxa with smaller genomes, reduced metabolic redundancy and a pronounced shift from broad extracellular carbon catabolism and complete denitrification towards intracellular carbon storage and truncated denitrification. Intracellular carbon pools insulated organics at the single-cell level and buffered electron delivery across denitrification steps, enabling a division-of-labour network that prevents electron imbalance and suppresses N2O build-up. Together, these findings link denitrification mode management to trait-based community restructuring and offer a process-level framework for understanding low-carbon, low-emission nitrogen removal under carbon-limited conditions.},
}

@article {pmid41887069,
year = {2026},
author = {Qiang, H and Xu, X and Liu, Z and Heo, S and Yue, X and Zhou, A and Makinia, J},
title = {New insights into the interplay between chain elongation and homoacetogenesis in microbial electrosynthesis: Chloroform-enhanced medium-chain carboxylate production.},
journal = {Water research},
volume = {298},
number = {},
pages = {125790},
doi = {10.1016/j.watres.2026.125790},
pmid = {41887069},
issn = {1879-2448},
abstract = {Microbial electrosynthesis (MES)-assisted chain elongation (CE) is a promising strategy for sustainable medium-chain carboxylic acid (MCCA) production from waste streams. However, MES induces inevitable H2 evolution, and the understudied interaction between H2-driven homoacetogenesis and CE creates a critical knowledge gap. To resolve this metabolic conflict, chloroform (CHCl3) at 0.0075%-0.045% was used to inhibit homoacetogenesis, with systematic investigations on carbon flux distribution, functional microbial communities, and key metabolic pathways. Results showed 0.03% CHCl3 optimized MCCA production to 2902.8 ± 116.1 mg COD/L (103.0% increase), with electron efficiency (40.8%) and acetate utilization efficiency (94.3%) significantly higher than the Control (21.8% and 43.5%, respectively). Homoacetogenesis inhibition conserved reducing power (moderated H2, lowered NAD[+]/NADH) and redirected acetyl-CoA to drive CE. Microbial community analysis revealed enriched chain-elongating bacteria with more modular, cooperative interaction networks. Metagenomic analysis confirmed elevated abundances of reverse β-oxidation genes (e.g., ACAT, crt) and reduced homoacetogenesis genes (e.g., cooF, cooS) after treatment. Taxon-function contribution analysis identified Clostridium_kluyveri as the dominant functional agent for CE-related key genes. Economic and life-cycle assessments demonstrated a net economic gain of $1.61-4.22/m[3] and mitigated key environmental impacts due to improved product yield. This study elucidates how regulating the competition between homo-acetogens and chain-elongating bacteria directionally enhances CE, providing a novel ecological perspective and strategy for optimizing electricity-driven biomanufacturing processes.},
}

@article {pmid41887245,
year = {2026},
author = {Reddy, K and Sinha, P and Antcliffe, DB and McDowell, C and Bradley, PA and Black, L and Murphy, L and Barbaras, J and Conlon, J and Camporota, L and Ostermann, M and Hopkins, P and Szakmany, T and Cherian, S and Welters, I and Brealey, D and Parekh, D and Rostron, AJ and Bos, LDJ and Nichol, A and Shankar-Hari, M and Gordon, AC and Delucchi, K and O'Kane, CM and Matthay, MA and Calfee, CS and McAuley, DF and , },
title = {Bedside identification of subphenotypes in acute respiratory failure (PHIND): a multicentre, observational cohort study.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(26)00040-8},
pmid = {41887245},
issn = {2213-2619},
abstract = {BACKGROUND: Acute respiratory distress syndrome (ARDS) is a clinically defined, biologically heterogeneous condition with no proven disease-modifying therapies. Retrospective analyses have identified two biologically distinct subphenotypes (hyperinflammatory and hypoinflammatory) of ARDS, with differing outcomes and responses to therapy. Rapid identification of these subphenotypes in an actionable timeframe has previously not been possible. The PHIND study aimed to prospectively identify these subphenotypes and to demonstrate differing 60-day mortality.

METHODS: The PHIND study was a prospective, multicentre, observational cohort study conducted in intensive care units (ICUs) within the National Health Service in the UK and the Health Service Executive in Ireland. Adult patients aged 18 years and older with ARDS or acute hypoxaemic respiratory failure (AHRF) were enrolled within 72 h of onset of the syndrome. Eligible patients were required to be receiving invasive mechanical ventilation, non-invasive ventilation, or high-flow nasal oxygen. Plasma interleukin (IL-6) and soluble TNF receptor-1 (TNFR1) were quantified at enrolment using a near-patient benchtop immunoanalyser (Randox multiSTAT) with a run time of approximately 1 h. Together with plasma bicarbonate measured from an arterial blood sample, these values were used to prospectively determine subphenotypes on an individual patient basis using a validated parsimonious logistic regression model. The primary outcome was 60-day mortality. The study was registered on ClinicalTrials.gov, NCT04009330.

FINDINGS: Between Nov 22, 2019, and Sept 28, 2023, 1853 patients from 30 centres were screened for eligibility. Of these, 1328 were excluded and 525 were recruited into the study, with 512 individuals included. 308 (60%) patients were male, 204 (40%) were female, and mean age was 57·0 years (SD 15·1). 443 (87%) patients were white, 18 (4%) were Black, and 16 (3%) were Asian. 490 were subphenotyped using the near-patient assay: 89 (18%) were classified as hyperinflammatory and 401 (82%) as hypoinflammatory. The primary outcome of 60-day mortality was measured in 486 patients after four patients withdrew consent for confirmation of vital status. 60-day mortality was significantly higher in the hyperinflammatory group (45 [51%] of 88) than in the hypoinflammatory group (111 [28%] of 398; risk ratio 1·8 [95% CI 1·4-2·4], p<0·0001). After adjustment, hyperinflammatory patients had increased odds of 60-day mortality (adjusted odds ratio 2·7 [95% CI 1·6-4·4], p=0·0002).

INTERPRETATION: Rapid identification of ARDS inflammatory subphenotypes using a near-patient assay was feasible and associated with many clinical characteristics and outcomes consistent with those described in earlier retrospective studies, including mortality, prevalence of sepsis, and incidence of metabolic acidosis. These findings support the implementation of precision medicine approaches in ARDS and the urgent need for prospective, subphenotype-stratified interventional trials.

FUNDING: Innovate UK, Randox Laboratories, and Belfast Health & Social Care Trust.},
}

@article {pmid41887297,
year = {2026},
author = {Lin, X and Yang, J and Kong, H and Pu, L and Ma, P and Mu, W and Sheng, H and He, J and Zou, Y and Wang, Y and Guo, X and Zhang, S and Wang, S},
title = {Metagenomic analysis of the gut microbiota in Cryptosporidium-infected Tibetan sheep.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108461},
doi = {10.1016/j.micpath.2026.108461},
pmid = {41887297},
issn = {1096-1208},
abstract = {Cryptosporidium are important causative parasitic protozoa that cause gastrointestinal discomfort and diarrhea in humans and animals, posing a huge threat to public health. Ruminants serve as the main source of Cryptosporidium infection. However, the relationship between this intestinal parasite and host gut microbiota in Tibetan sheep remains almost unknown. In the present study, using nested PCR targeting the SSU rRNA gene, we detected Cryptosporidium in 9% (38/420) of fecal samples. The positive rate was significantly higher in 4-7 month-old lambs than in adult sheep. Infection of Cryptosporidium spp. was associated with limited overall structural and functional alterations of the host gut microbiota, characterized by increased the relative abundance of Escherichia and reduced functional pathways related to amino acid biosynthesis and nucleotide/nucleoside biosynthesis. Additionally, the data indicates that age served as a primary determinant of the gut microbiota, whereas Cryptosporidium load showed no significant association with microbial variation. Machine learning model analysis revealed that these differential microbial features could effectively discriminate between infected and uninfected animals. These findings elucidate that Cryptosporidium infection is associated with specific and limited gut microbiota alterations in sheep.},
}

@article {pmid41887416,
year = {2026},
author = {Zhang, L and Xie, J and Lu, Y and Kong, L and Zhou, L and Wu, S and Wang, W and Huang, J and Li, J and Cheng, S},
title = {Enhanced nitrogen removal and mitigated greenhouse gas emissions in bioelectrochemical system-modular moving bed wetland at low temperature: Functional zonation and multi-pathway electron transfer.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134493},
doi = {10.1016/j.biortech.2026.134493},
pmid = {41887416},
issn = {1873-2976},
abstract = {This study integrated bioelectrochemical systems (BESs) into modular moving bed constructed wetlands (MMBCWs) to mitigate low temperature constraints on nitrogen removal and greenhouse gas emissions. Conventional MMBCW, microbial fuel cell-MMBCW (MFC-MMBCW), and microbial electrolysis cell-MMBCW (MEC-MMBCW) were constructed to assess feasibility. Results showed that MEC-MMBCW achieved superior nitrogen removal and the lowest global warming potential under cold conditions. Biofilm characteristics and metagenomic analyses revealed that MEC-MMBCW established spatially stratified functional zones. Specifically, the anode promoted organic matter and ammonia oxidation, while enhanced denitrification outcompeted compensatory anammox in the cathode. Furthermore, a multi-pathway extracellular electron transfer (EET) network mediated by extracellular polymeric substances (EPS), cytochrome c, and conductive pili accelerated electron transfer rates. These mechanisms synergistically boosted metabolic potential and activated latent degradation pathways, enhancing treatment resilience. Consequently, MEC-MMBCW represents a viable strategy for sustainable wastewater treatment in cold regions.},
}

@article {pmid41887490,
year = {2026},
author = {Li, Z and Fu, J and Hu, J and Li, T and Xu, Y},
title = {Sediment-water interface reoxygenation by NO3-LDH promotes tetracycline degradation in sediments and modulates antibiotic resistance gene dynamics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124357},
doi = {10.1016/j.envres.2026.124357},
pmid = {41887490},
issn = {1096-0953},
abstract = {The widespread presence of antibiotics in aquatic sediments, together with hypoxic conditions, constrains oxygen-driven natural degradation, thereby prolonging their environmental persistence. In this work, nitrate-intercalated layered double hydroxide (NO3-LDH) was employed as a controlled-release nitrate amendment to alleviate interfacial oxygen limitation while minimizing the secondary environmental risks associated with the high release peaks of conventional nitrate reagents. As a result, NO3-LDH increased dissolved oxygen (DO) from 1.05 to 3.39 mg/L, enhanced TC removal from 64.5% to 89.8% within 15 d, and reduced the combined abundance of tetracycline resistance genes (tetA, tetQ, and tetS) by 53.0%. Mechanistically, DO enrichment increased •OH generation 1.94-fold and upregulated cytochrome P450-related genes, supporting coupled enhancement of abiotic oxidation and oxygen-dependent microbial transformation. The improved oxidative microenvironment also favored the enrichment of aerobic aromatic-degrading taxa, further promoting TC attenuation. Although overall antibiotic resistance genes (ARGs) levels declined, fluoroquinolone- and macrolide-associated ARGs exhibited a transient early increase, likely triggered by an abrupt redox perturbation upon oxygen recovery that imposed oxidative stress on anaerobic microorganisms, intensified ATP-demanding stress responses, and increased membrane permeability. As interfacial redox conditions stabilized and TC concentrations decreased, these stress responses subsided and ARGs abundances declined at later stages. Overall, restoring interfacial DO strengthens oxygen-driven natural antibiotic degradation and inhibits the long-term accumulation of ARGs, providing a mechanistically grounded strategy for in situ remediation of antibiotic-contaminated sediments.},
}

@article {pmid41876075,
year = {2026},
author = {Wu, H and Wang, H and Man, S and Yan, Q},
title = {Biogenic FeS Reshapes microbial interactions to regulate acetogenesis in CO2-Fed microbial electrosynthesis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134480},
doi = {10.1016/j.biortech.2026.134480},
pmid = {41876075},
issn = {1873-2976},
abstract = {Inefficient electron transfer and poorly coordinated microbial communities often limit stable CO2-to-acetate conversion in microbial electrosynthesis (MES). Herein, Shewanella oneidensis MR-1 was introduced to induce in situ biogenic FeS formation at the cathode to regulate microbial interactions and enhance acetogenesis. Under the acetogenesis dominant condition (RAT: sludge to MR-1 ratio of 2:1, Fe/S = 5/10 mM, initial MR-1 inoculation), acetate production reached 1330.6 mg L[-1] with the carbon recovery efficiency of 62.9%. Community and metagenomic analyses showed that FeS selectively enriched acetogens and Fe/S transforming microorganisms while restructuring functional pathways related to redox metabolism and energy conservation. Co-occurrence network analysis further revealed that FeS promoted coordinated, function oriented microbial interactions rather than competitive associations. This study highlights the role of biogenic FeS in linking electron transfer with microbial cooperation, providing a mechanistic basis for improving MES performance through community level regulation.},
}

@article {pmid41876513,
year = {2026},
author = {Jovicic, D and Anestis, K and Fiutowski, J and Jørgensen, BB and Kjeldsen, KU and Rotaru, AE},
title = {Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41876513},
issn = {2041-1723},
support = {1026-00159B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; Acetates/metabolism ; Oxidation-Reduction ; Electron Transport ; Phylogeny ; *Microbial Consortia/genetics ; Methane/metabolism ; Methanosarcina/metabolism/genetics ; Charcoal ; Cytochromes/metabolism/genetics ; Genome, Bacterial ; },
abstract = {Conductive particles are common in coastal sediments, yet their role in shaping methane-producing communities and pathways remains unclear. We applied genome-resolved metagenomics to a sediment-derived consortium serially transferred for a decade and obligately dependent on granular activated carbon (GAC). We discovered a particle-obligate food web composed of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The primary SAO electrogen, Candidatus Geosyntrophus acetoxidans, represents a new genus and possesses a complete acetate oxidation pathway and extracellular electron-transfer (EET) machinery, including two porin-cytochrome conduits, 43 additional multiheme cytochromes and conductive pili. A secondary SAO, a Lentimicrobium sp. with a giant PCC-cluster, supplies an alternative EET-linked acetate-oxidation route. Electrons from electrogens transfer via GAC to a Methanosarcina equipped with the heptaheme cytochrome MmcA and flagellin for electron uptake. These results provide a genomic blueprint of this particle-obligate environmental consortium and suggest an overlooked acetate-to-methane electron-transfer route in geoconductor-rich anoxic sediments.},
}

*Geologic Sediments/microbiology
*Metagenomics/methods
Acetates/metabolism
Oxidation-Reduction
Electron Transport
Phylogeny
*Microbial Consortia/genetics
Methane/metabolism
Methanosarcina/metabolism/genetics
Charcoal
Cytochromes/metabolism/genetics
Genome, Bacterial

@article {pmid41876637,
year = {2026},
author = {Wang, R and Ma, R and Cai, Y and Zhang, L and Lu, W and Zheng, W and Kong, J and Miao, Q and Li, X and Guan, L and Gao, Y and Chen, K and Kwan, ATH and McIntyre, RS and Xu, G and Yu, CK and Lam, BY and So, KF and Lin, K},
title = {Exploratory characterization of gut microbiota and cognitive profiles in adolescents with subthreshold depression: a shotgun metagenomics sequencing study.},
journal = {Npj mental health research},
volume = {5},
number = {1},
pages = {},
pmid = {41876637},
issn = {2731-4251},
support = {No. 2021A1515011361//Natural Science Foundation of Guangdong Province/ ; No. 202102020735//Science and Technology Program of Guangzhou/ ; No. 2024SRP208//Guangzhou Medical University Research Capacity Enhancement Program/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 82171531//National Natural Science Foundation of China/ ; No. PX-66221557//Guangzhou Medical University student innovation ability enhancement Program/ ; STG STG1/M-501/23-N//the Hong Kong RGC theme-based Strategic Target Grant Scheme/ ; },
abstract = {Subthreshold depression (SD) in adolescents is a prevalent condition associated with significant functional impairment and an increased risk of developing major depressive disorder. Currently, the lack of reliable objective markers complicates its accurate identification. Investigating the gut microbiome may offer novel insights into its underlying mechanisms. This study aimed to investigate the association between gut microbiome and cognitive function in adolescents with subthreshold Depression (SD). Thirty-eight adolescents with SD and 139 clinically-well (CW) adolescents were recruited. Gut microbiome and cognitive function were assessed by metagenomic sequencing and the MATRICS Consensus Cognitive Battery (MCCB), respectively. Compared with the CW adolescents, the SD group showed higher relative abundance of Spirochaetes, Synergistetes, Spirochaetia, Synergistia, Spirochaetales, Rhizobiales, Synergistales, Thermoanaerobacterales, Rhodospirillales, Synergistaceae, and Oxalobacteraceae at four levels. The Spatial Span scores were higher in the SD group compared to the CW group. Moreover, EggNOG analyses showed a significant negative correlation of the intracellular trafficking secretion, and vesicular transport with the Spatial Span scores. The KEGG pathway of the neurodegenerative diseases and translation was depleted in the microbiome of adolescents with SD. The higher abundance of Spirochaetes, Spirochaetia, and Spirochaetales was the best predictor of SD in adolescents. Our findings suggest that gut microbiome abnormalities, depressive symptoms, and cognitive influences co-occur in adolescents with SD, which may play a crucial role in the pathogenesis of SD and cognitive function in adolescent. Gut microbiome may serve as a potential biomarker for the identification and treatment of adolescents with SD.},
}

@article {pmid41876857,
year = {2026},
author = {Peñuelas, J and Zheng, B and Tariq, A and Sardans, J},
title = {Microbial phosphorus cycling in terrestrial ecosystems.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41876857},
issn = {1740-1534},
abstract = {Phosphorus is an essential yet often limiting macronutrient that shapes primary productivity and microbial activity in terrestrial ecosystems. Unlike carbon and nitrogen cycles, which have gaseous phases, the terrestrial phosphorus cycle is primarily governed by soil biogeochemistry, wherein microorganisms orchestrate key transformations. This Review synthesizes current knowledge of the microbial phosphorus cycle, emphasizing the diverse mechanisms used by bacteria, fungi and archaea to mobilize phosphorus (for example, via phosphatases such as PhoA and PhoD and organic acids such as citrate) and to directly enhance plant phosphorus uptake. We explore the ecological significance of these processes in maintaining soil health, supporting ecosystem productivity and influencing carbon sequestration. We propose the Microbial Phosphorus Adaptive Evolution Theory (MPAET): chronic phosphorus scarcity drives evolutionary and ecological shifts in microbial communities towards higher scavenging investment, polyphosphate handling and lipid remodelling. Furthermore, we examine how environmental factors, land use and climate modulate these shifts (for example, phoD expression increases under phosphorus stress), with cascading effects on ecosystem function and global phosphorus availability. New technologies such as metagenomics, [18]O-phosphate tracing and nanoscale secondary ion mass spectrometry are now revolutionizing our understanding of these dynamics. This Review underscores the critical need to integrate microbial phosphorus cycling into ecosystem models and to develop sustainable strategies for phosphorus smart management. Such approaches are essential for addressing global challenges related to soil degradation, food security and environmental change.},
}

@article {pmid41877267,
year = {2026},
author = {Peirson, LE and McKenney, EA and Patterson, JR and Beasley, JC and Périquet-Pearce, S and Cloete, C and Melton, MH and PetersonWood, B and Portas, R and Aschenborn, O and Lafferty, DJR},
title = {African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00553-w},
pmid = {41877267},
issn = {2524-4671},
support = {Financial Assistance Award no. DE-EM0005228//U.S. Department of Energy/ ; Peter White Scholar Award//Northern Michigan University/ ; },
abstract = {Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.},
}

@article {pmid41877288,
year = {2026},
author = {Wei, G and Liu, M and Huang, L and Chen, C},
title = {Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00551-y},
pmid = {41877288},
issn = {2524-4671},
support = {32272831//National Natural Science Foundation of China/ ; },
}

@article {pmid41877461,
year = {2026},
author = {Tagliabue, A and Furfaro, G and Pallavicini, A and Martino, F and Zane, L and Sattin, E and Valle, G and Piraino, S and Turon, X},
title = {Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70126},
doi = {10.1111/1755-0998.70126},
pmid = {41877461},
issn = {1755-0998},
support = {MCIU/AEI/10.13039/501100011033//BlueDNA PID2023-146307OB/ ; CCI 2014IT16M2OP005//Programma Operativo Nazionale Ricerca e Innovazione 2014-2020/ ; ECS00000043//Interconnected Nord-Est Innovation Ecosystem/ ; //European Regional Development Fund/ ; 2020J3W3WC//Italian Ministry of Education, Universities and Research/ ; D33C22000960007//National Recovery and Resilience Plan/ ; C93C22002810006//National Recovery and Resilience Plan/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Animals ; *Geologic Sediments ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; *Seawater ; },
abstract = {This study investigates the metazoan biodiversity in the Southern Adriatic Sea using environmental DNA (eDNA) metabarcoding. Sediment and adjacent water samples were collected from three sites (one pristine, two impacted by human activities) at three distances from the coast across two seasons. The complex four-factor experimental design (576 samples) addresses key sources of eDNA variability and provides a valuable comparison of markers (COI and 18S) and sample types, which remain rare in the literature. Results showed differences in the number and type of taxa identified, taxonomic resolution, and number of amplicon sequence variants (ASV) per operational taxonomic unit (OTU) across markers. The obtained overall community structure (beta-diversity) was similar for both markers. Sediment samples had higher OTU richness, but lower diversity than water samples. The two sample types provided distinct and only partially overlapping views of biodiversity. Sediment samples were rich in benthic species, whereas water samples featured mostly planktonic and nektonic species. Biodiversity varied by site and season, with sediment samples showing less seasonal variability. The pristine site did not host higher biodiversity than impacted sites, likely because of the latter's habitat heterogeneity. This study confirms the effectiveness of eDNA metabarcoding for biodiversity assessment in coastal ecosystems and provides a foundational dataset for future monitoring. By highlighting the complementary nature of COI and 18S markers and the role of sample type, this research supports integrating eDNA metabarcoding into routine environmental monitoring programs while emphasising the need for further standardisation and improved reference databases.},
}

*DNA Barcoding, Taxonomic/methods
*DNA, Environmental/genetics
Animals
*Geologic Sediments
*Biodiversity
*Aquatic Organisms/classification/genetics
RNA, Ribosomal, 18S/genetics
Electron Transport Complex IV/genetics
*Metagenomics/methods
*Seawater

@article {pmid41877907,
year = {2026},
author = {Xie, S and Zhang, H and Xie, Y and Liu, F and Ye, S and Liu, X and Lai, Z},
title = {Analysis of the Clinical Features of HSV-2 Encephalitis Confirmed by the mNGS Technique: Insights Derived from Seven Patient Studies.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {567731},
pmid = {41877907},
issn = {1178-6973},
abstract = {BACKGROUND: Herpes simplex virus type 2 (HSV-2) encephalitis is rare in immunocompetent adults. Diagnosis typically depends on cerebrospinal fluid (CSF) polymerase chain reaction (PCR), which has limited sensitivity and potential for false negatives. Metagenomic next-generation sequencing (mNGS) provides unbiased pathogen detection, facilitating rapid HSV-2 identification in CSF and minimizing misdiagnosis risks, especially in atypical cases or immunocompetent individuals. This study examines the diagnostic value of mNGS in a cohort of patients with HSV-2 encephalitis presenting atypically.

METHODS: A retrospective analysis was performed on patients diagnosed with HSV-2 encephalitis using mNGS at our institution between January 2022 and January 2025. Clinical characteristics, ancillary test results, and patient outcomes were analyzed to evaluate the diagnostic value of mNGS.

RESULTS: Seven patients (2 males, 28.57%; 5 females, 71.43%) with a mean age of 33.57 years were included; one had pre-existing immunodeficiency (14.28%). Most presented atypical symptoms; six treated within three days fully recovered, while one with delayed treatment died. Mean follow-up was 14.71 ± 5.82 months. Higher viral sequence counts correlated with worse outcomes. Initial CSF analysis showed normal cell counts in one patient; all exhibited lymphocytic pleocytosis and elevated protein levels.

CONCLUSION: This study contributes to the limited clinical data on adult HSV-2 encephalitis by summarizing clinical manifestations and treatment outcomes, thereby informing improved diagnostic and management strategies. It also highlights the prognostic importance of early diagnosis and immune status assessment through the application of mNGS.},
}

@article {pmid41877920,
year = {2026},
author = {Zeng, F and Zhu, T and Chen, X and Huang, K and Liu, L and Wang, G and Mai, J and Zhang, S},
title = {Gut microbiota and metabolic status during pregnancy in captive Asian elephants.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1749490},
pmid = {41877920},
issn = {2297-1769},
abstract = {BACKGROUND: The gut microbiota is regarded as one of the key factors regulating host health. The gut microbiota and its connection to fecal metabolites are crucial for supporting fetal development and ensuring maternal health during reproductive stages. Although studies have examined Asian elephants, the composition and function of the gut microbiota in pregnant and non-pregnant captive Asian elephants have not been reported.

METHODS: We compared the fecal microbiota and fecal metabolites of pregnant (G1), non-pregnant (never gotten pregnant after reaching sexual maturity, G2), and subadult (G3) captive Asian elephants using metagenomic sequencing and untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics.

RESULTS: We found significant differences in the gut microbiota among the G1, G2, and G3 groups. The phylum Bacteroidetes showed notable differences between G1 and G2. The analysis of fecal metabolomics revealed significant differences in 49 metabolites between G1 and G2, of which 25 were upregulated and 24 were downregulated. These results suggested significant differences in the composition of gut microbiota and fecal metabolites during reproductive stages, while gut microbial diversity remained stable. These findings inform our ongoing research on the potential health conditions of captive Asian elephants, with the aim of better understanding the role of the gut microbiota in reproductive regulation.},
}

@article {pmid41877937,
year = {2025},
author = {Zhang, M and Pak, H and King, SD and Zuniga, AA and Hassan, YA and King, MD},
title = {Mitigating airborne pathogen risks in a full-scale meat processing facility.},
journal = {Total environment microbiology},
volume = {1},
number = {3},
pages = {},
pmid = {41877937},
issn = {3050-6417},
abstract = {Foodborne illnesses caused by Shiga toxin-producing Escherichia coli (STEC) and Salmonella represent a major public health concern, particularly in meat processing facilities where bioaerosols generated during processes like carcass spraying and dehiding can lead to contamination. In this study, we assessed airborne concentrations of STEC and Salmonella at multiple locations within a full-scale meat processing facility using quantitative polymerase chain reaction (qPCR) and Illumina MiSeq sequencing. Additionally, we utilized computational fluid dynamics (CFD) simulations to model airflow within the facility and evaluated the effectiveness of air curtains in mitigating the transfer of bioaerosols between high-risk (dehiding and tripe) and low-risk (chiller and fabrication) areas. qPCR results showed that pathogen concentrations in the dehiding rooms were 126 GCN/m[3] for STEC and 105 GCN/m[3] for Salmonella during spring, with levels rising significantly in summer (2198 GCN/m[3] for STEC and 1799 GCN/m[3] for Salmonella). Simulated airflow patterns revealed that entrained bioaerosols could be transported from unclean to clean areas, increasing the risk of cross-contamination. The use of air curtains effectively reduced this spread by creating barriers between high- and low-risk areas. Our findings suggest that bacterial survivability and aerosolization was enhanced in summer, highlighting the critical role of environmental factors and airflow management in controlling contamination risks. This study demonstrates the value of integrating experimental data with CFD simulations to assess pathogen spread and identify effective mitigation strategies in meat processing facilities.},
}

@article {pmid41878086,
year = {2026},
author = {Luo, D and Jia, S and He, W and Fan, Z and Yin, W},
title = {Periplaneta americana Powder Alleviates Neuropathic Pain and is Associated with Gut Microbiota Changes in Rats.},
journal = {Journal of pain research},
volume = {19},
number = {},
pages = {564911},
pmid = {41878086},
issn = {1178-7090},
abstract = {BACKGROUND: This study aims to evaluate the therapeutic potential of Periplaneta americana powder (PAP) in alleviating neuropathic pain in a rat model of sciatic nerve injury induced by chronic constriction injury (CCI), and to systematically analyze its effects on the composition and structure of the gut microbiota during the intervention process, with the goal of elucidating the mechanisms underlying the analgesic effects of PAP.

METHODS: A rat model of CCI was established (n = 12 per group), and PAP was administered for intervention. The analgesic effects were evaluated using mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL). Pathological changes in the spinal cord and colon tissues were examined via hematoxylin-eosin (HE) staining, and the expression of the astrocyte marker glial fibrillary acidic protein (GFAP) in the spinal cord was detected by immunohistochemistry. The expression levels of pro-inflammatory cytokines TNF-α and IL-1β in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were collected at the endpoint of treatment for metagenomic sequencing and analysis.

RESULTS: After PAP treatment, behavioral tests in CCI rats showed a significant increase in MWT and TWL (P < 0.05). Histological analysis revealed marked alleviation of spinal cord and colon tissue damage as well as reduced inflammatory cell infiltration (P < 0.05). Immunohistochemistry further demonstrated a significant decrease in GFAP expression in the spinal cord (P < 0.05). ELISA results showed that the expression levels of TNF-α and IL-1β in spinal cord tissues were significantly decreased (P < 0.05).Metagenomic analysis indicated that PAP reshaped the gut microbiota structure, increased the abundance of SCFA-producing bacteria, and was associated with the butyrate metabolism pathway.

CONCLUSION: This study indicates that PAP can significantly alleviate neuropathic pain in a rat model of sciatic nerve chronic constriction injury (CCI) and suppress the central inflammatory response.Notably, this effect is accompanied by changes in the gut microbiota, particularly characterized by a significant alteration in the abundance of short-chain fatty acid-producing bacteria. These results suggest that PAP not only possesses substantial analgesic effects but may also mediate the intervention of CCI-induced neuropathic pain by regulating the structure of the gut microbiota.},
}

@article {pmid41878266,
year = {2026},
author = {Huang, J and Yan, X and Su, Q and Tu, H and Yu, Z and Liu, D and Wu, B},
title = {Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1598786},
pmid = {41878266},
issn = {2235-2988},
mesh = {Humans ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; *Metagenomics ; *Virome ; *Bacteriophages/genetics/isolation & purification/classification ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Female ; Male ; Feces/microbiology/virology ; Enterococcus faecalis ; Gastrointestinal Tract/microbiology ; },
abstract = {INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.

METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.

RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).

DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.},
}

Humans
*Infant, Premature
*Gastrointestinal Microbiome/genetics
Infant, Newborn
*Metagenomics
*Virome
*Bacteriophages/genetics/isolation & purification/classification
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification
Female
Male
Feces/microbiology/virology
Enterococcus faecalis
Gastrointestinal Tract/microbiology

@article {pmid41878461,
year = {2026},
author = {Li, Z and Zhang, Y and Xu, D and Huang, B},
title = {Diagnostic and therapeutic journey of infantile endobronchial tuberculosis: a case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1778717},
pmid = {41878461},
issn = {2296-2360},
abstract = {BACKGROUND: Endobronchial tuberculosis (EBTB) in infants is rare and is often overlooked because of nonspecific clinical manifestations. Coexisting primary immunodeficiency and opportunistic infections further increased diagnostic and therapeutic complexity.

CASE PRESENTATION: We reported a male infant aged 40 days who presented with fever and mild cough. Chest imaging showed progressive bilateral nodular and granulomatous lesions despite broad-spectrum antibacterial therapy. Microbiological evaluation revealed positive T-SPOT.TB and GeneXpert MTB/RIF results from bronchoalveolar lavage fluid (BALF), while metagenomic next-generation sequencing identified Pneumocystis jirovecii. Genetic testing demonstrated a heterozygous IKZF1 mutation, consistent with underlying immunodeficiency. Serial bronchoscopies confirmed necrotizing endobronchial tuberculosis with airway stenosis. The patient received standard anti-tuberculosis therapy, systemic corticosteroids, trimethoprim-sulfamethoxazole, intravenous immunoglobulin, and repeated bronchoscopic intraluminal drug delivery. Clinical and radiological remission was achieved, with no airway sequelae during 18-month follow-up.

CONCLUSIONS: This case highlighted the unique coexistence of infantile EBTB, IKZF1-related immunodeficiency, and P. jirovecii coinfection. Early bronchoscopy played a pivotal diagnostic and therapeutic role. Repeated intraluminal bronchoscopic therapy combined with systemic treatment might prevent irreversible airway damage in severe pediatric EBTB.},
}

@article {pmid41878469,
year = {2026},
author = {de Azevedo, PS and Vedovatto, MM and de Freitas, PCG and Luz, RBS and Streit, RSA and Persinoti, GF},
title = {parsomics: a data-driven framework for metagenomics data integration powered by a local relational database.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag049},
pmid = {41878469},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenomics enables the analysis of complex microbial communities directly from environmental samples, resulting in massive datasets that are processed using multiple tools and workflows. Data integration is key for metagenomics research, however, challenges in data organization and management locally remain open in existing workflows.

RESULTS: We present parsomics, a lightweight and extensible data management tool designed for efficient local storage, organization, and integration of metagenomic analysis results. Built upon PostgreSQL and implemented in Python, parsomics leverages a user-defined configuration file to automatically construct a relational database tailored to metagenomics-based data. It is user-friendly, easy to deploy, and implements modular plugin-based extensions to support diverse data types and outputs. parsomics can be installed in every major GNU/Linux environment and currently focuses on prokaryotic metagenomics analysis.

parsomics is an open-source project and its source code is available at https://gitlab.com/parsomics under the GPLv3 license. Comprehensive documentation can be found at https://parsomics.org and https://api.parsomics.org.},
}

@article {pmid41878742,
year = {2026},
author = {Armijo-Godoy, G and Cottet, L and Rupayan, A and Carrasco, M and Levicoy, D and Salvo-Garrido, H},
title = {Functional and ecological characterization of Labrys methylaminiphilus subsp. lupini subsp. nov., associated with Lupinus luteus nodules in acidic soils of southern Chile.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1759558},
pmid = {41878742},
issn = {1664-302X},
abstract = {BACKGROUND: Members of the genus Labrys are widely distributed in soil and plant-associated environments, yet their ecological roles and functional contributions within plant-associated microbiomes remain poorly understood. Labrys methylaminiphilus strain La1 was isolated from nodules of Lupinus luteus growing in acidic soils of southern Chile, providing an opportunity to investigate strain-level traits relevant to plant-microbe interactions under environmental stress.

METHODS: Strain La1 was characterized using physiological and biochemical, chemotaxonomic, and genomic approaches, including whole-genome sequencing and comparative genomics. Functional traits related to plant interaction were assessed through in vitro assays for indole-3-acetic acid (IAA) production, antifungal activity against lupine pathogens, and in planta experiments evaluating plant growth under salinity and osmotic stress. The ecological distribution of closely related taxa was inferred from screening of publicly available environmental microbiomes using protologger pipeline.

RESULTS: Although strain La1 showed high genomic similarity to L. methylaminiphilus JLW10[T], it exhibited distinct phenotypic, metabolic, and ecological features. These included tolerance to acidic and moderately saline conditions, utilization of rhizosphere-associated carbon sources, and a fatty acid profile consistent with adaptation to terrestrial environments. Genomic analyses revealed genes related to stress tolerance, exopolysaccharide biosynthesis, carbohydrate-active enzymes, siderophore production, IAA synthesis, and non-ribosomal peptide synthetases. Consistent with these traits, La1 inhibited the growth of Colletotrichum lupini and Pleiochaeta setosa and significantly enhanced L. luteus biomass under osmotic and salinity stress. Metagenomic screening indicated that sequences closely related to La1 are predominantly associated with soil, rhizosphere, and plant-associated habitats.

CONCLUSION: This study demonstrates that strain La1 represents a functionally versatile and ecologically specialized lineage within L. methylaminiphilus, contributing traits relevant to plant-associated microbiomes in acidic soils. This integrated functional and ecological evidence supports the designation of Labrys methylaminiphilus subsp. lupini subsp. nov. and highlights the relevance of strain-level analyses for understanding plant-microbe interactions.},
}

@article {pmid41878750,
year = {2026},
author = {Du, Z and Li, L and Liu, J and Wang, H and Li, J and Xu, Y and Cui, L and Yin, J},
title = {Wheat-Dependent Exercise-Induced Anaphylaxis Patients on a Wheat-Free Diet Exhibit a Gut Microbiota Composition More Similar to Healthy Individuals.},
journal = {Journal of asthma and allergy},
volume = {19},
number = {},
pages = {464532},
pmid = {41878750},
issn = {1178-6965},
abstract = {PURPOSE: There are limited studies on the intestinal microbiome in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA), and changes in the gut microbiome in WDEIA patients after wheat-free diet have not been studied.

METHODS: This is a cross-sectional analysis. Fecal samples and clinical data were collected from 26 non-wheat-free patients with WDEIA, 11 wheat-free patients with WDEIA, and 24 healthy controls (HCs). The gut microbiota was evaluated through metagenomic sequencing.

RESULTS: The sequencing revealed differences in the gut microbiome between patients with WDEIA on a non-wheat-free diet and HCs; more specifically, the non-wheat-free group exhibited a downregulation of two families (Rikenellaceae and Odoribacteraceae), three genera (Alistipes, Odoribacter, and Catenibacterium), and four species (Bacteroides_stercoris, Alistipes_putredinis, Bacteroides_intestinalis, and Bacteroides_cellulosilyticus). A wheat-free diet is associated with intestinal flora more similar to the structure of healthy individuals. The species Bacteroides_stercoris was negatively correlated with T-IgE, and the genus Catenibacterium was negatively correlated with T-IgE, as well as wheat, gluten, or gliadin-specific IgE. The genus Catenibacterium was positively correlated with the healthy control-enriched "Apoptosis (ko04210)" pathway and negatively correlated with the non-wheat-free WDEIA group-enriched "Thyroid hormone signaling pathway (ko04919)" pathway.

CONCLUSION: Patients with WDEIA exhibit a specific gut microbiota signature and function, which demonstrated the potential association between the gut microbiome and WDEIA development. WDEIA patients on a wheat-free diet exhibit a gut microbiome composition more similar to healthy individuals.},
}

@article {pmid41878990,
year = {2026},
author = {Sun, Y and Li, Y and Temur, B and Lin, Y and Liu, Y and Yi, L and Sun, Z and Zhang, G and Li, J and Guo, Y and Li, L and Cai, J and Tian, W and Meng, G and Jiang, L and Fang, M and Ding, F and Zhou, X and Tu, C and He, B},
title = {Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17444},
doi = {10.1002/advs.202517444},
pmid = {41878990},
issn = {2198-3844},
support = {32130104//National Natural Science Foundation of China/ ; 2025-NK-112//Qinghai Science and Technology Achievement Transformation Special Project/ ; },
abstract = {Domestic herbivores have complex interactions with humans and wildlife, playing important roles in zoonotic and epizootic disease emergence and transmission. Yet their viral diversity and cross-species transmission dynamics remain understudied. Through pan-viromic profiling of 10,225 swabs and 4,304 serum samples from 5,710 adult individuals across China's five major herbivore-rearing provinces, we prepare the domestic herbivore viromic catalog of China (DhCN-Virome) comprising 1,085,360 viral metagenomes, nearly capturing their family-level viral diversity while expanding by 2.3-fold global subgenus-level viral diversity. Distinct viromic signatures emerge across herbivore species and sample types. Viral communities generally follow a "higher openness, greater stability" pattern, with animals raised in confined settings being more susceptible to external influences. Viral circulations, particularly involving viruses of health concern, occur primarily within herbivore species but also extensively between herbivores and other species, including potential human-herbivore and avian-horse viral transmission. Bacteriophages constitute the most abundant viral entities, characterized by lytic replication strategies with some targeting pathogenic bacterial hosts. These findings expand our knowledge of herbivore viral diversity patterns and ecological transmission dynamics, underscoring the need for unified disease management strategies across all herbivore species. Particularly, the risk viruses represent potential triggers for future outbreaks, necessitating urgent epidemiological surveillance and vaccination programs.},
}

@article {pmid41879294,
year = {2026},
author = {Liu, Y and Zhao, X and Gao, J and Xu, K},
title = {Therapeutic Evolution and Outcomes in EGPA Complicated by Diffuse Alveolar Hemorrhage: case-based review.},
journal = {Modern rheumatology case reports},
volume = {},
number = {},
pages = {},
doi = {10.1093/mrcr/rxag028},
pmid = {41879294},
issn = {2472-5625},
abstract = {BACKGROUND: Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare systemic vasculitis characterized by asthma, eosinophilia, and multi-organ involvement. Diffuse alveolar hemorrhage (DAH) is an uncommon but life-threatening pulmonary complication in EGPA.

CASE PRESENTATION: We report a 49-year-old previously healthy woman who presented initially with asthma-like symptoms and later developed fever, hemoptysis, cutaneous purpura, and periorbital edema. Laboratory evaluation revealed marked eosinophilia, anemia, elevated inflammatory markers, and strongly positive MPO-ANCA. Bronchoalveolar lavage fluid (BALF) was hemorrhagic and contained hemosiderin-laden macrophages, indicating DAH. Broad-spectrum antibiotics were empirically initiated but discontinued after metagenomic next-generation sequencing (mNGS) of BALF excluded infection. Bone marrow biopsy showed eosinophilic hyperplasia without clonal mutations. A diagnosis of MPO-ANCA positive EGPA with DAH was established. The patient received pulse methylprednisolone, prednisone, intravenous immunoglobulin, mepolizumab, and rituximab. Clinical symptoms improved rapidly, and radiological signs of alveolar hemorrhage nearly resolved within days.

CONCLUSION: Our case illustrates that integration of rituximab and mepolizumab with corticosteroids can achieve rapid remission and steroid sparing in EGPA-DAH. While evidence remains limited to case reports and small series, targeted biologics may fundamentally improve outcomes in this high-risk subset. Prospective studies are warranted to define optimal treatment strategies.},
}

@article {pmid41879323,
year = {2026},
author = {Mortensen, GA and Schmidt, H and Radivojac, P and Ye, Y and Haas, DM},
title = {Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0315525},
doi = {10.1128/spectrum.03155-25},
pmid = {41879323},
issn = {2165-0497},
abstract = {The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and gestational diabetes mellitus (GDM) remains poorly understood. This study explores how the gut microbiome differs between pregnant women with these conditions and healthy controls, using metagenomic sequencing to analyze microbial composition and function. Our findings reveal that women with GH and GDM exhibit greater microbiome variability and distinct shifts in bacterial communities compared to healthy pregnancies. Key beneficial bacteria, such as Bacteroides fragilis and Roseburia intestinalis, were reduced in cases, suggesting potential disruptions in gut-related metabolic and immune functions. In addition to multiple differentially abundant species of Sphingobacterium in cases versus controls, functional analysis indicated changes in carbohydrate and lipid metabolism, reinforcing the microbiome's connection to metabolic health. Furthermore, machine learning models demonstrated promising results in predicting disease status based on microbiome data, underscoring the potential for gut bacteria as potential predictive biomarkers for pregnancy-related conditions. These insights highlight the gut microbiome's role in pregnancy health and suggest it may be a promising target for future interventions aimed at reducing complications and improving maternal-fetal outcomes.IMPORTANCEGut microbial dysbiosis has been implicated in pregnancy complications, yet most studies rely on 16S rRNA sequencing, which limits resolution and functional insight. Here, using shotgun metagenomic sequencing and machine learning, we identified robust microbial taxonomic and functional signatures that distinguish gestational hypertension and gestational diabetes from healthy pregnancies. A combined feature set enabled accurate classification of disease status, with overlapping features between statistical and predictive frameworks underscoring biological relevance. Altogether, our study defines high-resolution microbiome signatures with translational potential as predictive biomarkers for maternal health, while also providing an open, reproducible analysis pipeline to support future investigations.},
}

@article {pmid41879886,
year = {2026},
author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F},
title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41879886},
issn = {1869-1889},
abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.},
}

@article {pmid41880538,
year = {2026},
author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, Á},
title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myag026},
pmid = {41880538},
issn = {1460-2709},
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, Gardnerella swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed greater abundance of Lactobacillus crispatus and Lactobacillus gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system (PTS), fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.},
}