@article {pmid41765668,
year = {2026},
author = {Nian, YP and Ning, SS and Li, SS and Yu, PB and Meng, Y and Zhao, X and Ren, RQ and Yan, J and Han, XY and Zheng, ZX and Zhang, QF and Wang, X and Zhang, Y},
title = {[Investigation and management of the first case of human infection with avian influenza A(H10N3) virus in northern China].},
journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi},
volume = {47},
number = {2},
pages = {275-280},
doi = {10.3760/cma.j.cn112338-20250616-00397},
pmid = {41765668},
issn = {0254-6450},
abstract = {Objective: To summarize and analyze the epidemiological characteristics and field investigation of the first case of human infection with avian influenza A(H10N3) virus in northern China and to provide reference for the investigation and management of human infection with animal-derived influenza in the future. Methods: Case epidemiological investigation, identification and medical observation of co-exposed people and close contacts, and tracing investigation and analysis of infection source were carried out. Samples were collected from the case, co-exposed persons, close contacts, poultry, and the external environment. Real-time fluorescent quantitative RT-PCR was used to detect influenza A virus. The positive samples were subjected to metagenomic sequencing and compared. Results: This is the first case of human infection with the avian influenza A(H10N3) virus in northern China, and a third-party laboratory performed the detection. The patient became ill on April 13, 2025, with no history of contact with similar cases prior to symptom onset but with a history of exposure to poultry. The macrogene test of bronchoalveolar lavage fluid was positive for avian influenza A(H10N3) virus on April 28, 2025. A total of 168 samples were collected from co-exposed individuals, close contacts, poultry, and the external environment, and all were negative for avian influenza A(H10N3) virus. Metagenomic sequencing analysis showed that the sequence had high homology with the human infection case of avian influenza A(H10N3) virus reported in Guangxi Zhuang Autonomous Region in December 2024. After taking emergency measures such as medical observation of close contacts, harmless treatment of poultry in the sick home, and disinfection of suspected exposure places, no secondary cases occurred. The case was cured and discharged on May 14. Conclusions: The source of the first human case of avian influenza A(H10N3) infection in northern China remains unclear, but no human-to-human transmission has been found. It is important to improve the sensitivity of surveillance for new subtypes of animal-derived influenza viruses, such as avian influenza A(H10N3), and to strengthen joint prevention and control between health and animal husbandry departments to support scientific approaches to preventing and controlling human infection with these viruses.},
}

@article {pmid41765557,
year = {2026},
author = {Wang, M and Zhao, J and Gao, J and Cai, S and Gu, Y and Liu, Y and Gao, L and Xu, Y and Wu, Y and Zhou, Z and Zhang, J and Tian, W},
title = {Deciphering the potential of Bacillus cereus HS-9 in cadmium bioremediation and ensuring rice safety.},
journal = {Journal of environmental sciences (China)},
volume = {162},
number = {},
pages = {573-583},
doi = {10.1016/j.jes.2025.05.044},
pmid = {41765557},
issn = {1001-0742},
abstract = {Cadmium (Cd) contamination in agricultural soils poses significant environmental and health risks due to its non-degradable and bio-magnifying nature. With the global imperative for eco-friendly Cd remediation strategies, microbial bioremediation emerges as a promising approach. Here, Bacillus cereus HS-9 was isolated from Cd-contaminated paddy soil using LB medium supplemented with 5 mg/L of Cd. HS-9 exhibited an impressive Cd removal efficiency of 95.44 % at a concentration of 5 mg/L. A rice pot experiment was conducted using Cd-contaminated soil, with HS-9 inoculation as the treatment group and non-inoculated soil as the control. The treatment group resulted in a 38.99 % reduction in soil Cd availability and a 34.33 % decrease in rice Cd content without affecting rice yield. The microbial community of the rice rhizosphere was analyzed using metagenome sequencing. The results revealed an increased abundance of czcA, frnE, and irlS genes in the soil microbiome, indicating enhanced Cd resistance and efflux capabilities. Microbial community showed significant shifts towards a beneficial microbial consortium, particularly marked by increases in Lysobacter and Sphingomonas genera which are known for their roles in heavy metal resistance and bioremediation. B. cereus HS-9 demonstrated significant potential for the bioremediation of Cd-contaminated soil. This study provides foundation for the development of microbial-based strategies for the eco-friendly remediation of heavy metal-polluted agricultural lands.},
}

@article {pmid41765316,
year = {2026},
author = {Lyu, Y and Ye, Y and Zhang, C and Zhong, W and Zhu, L},
title = {Bisphenol A bis (diphenyl phosphate) Disrupted Tryptophan Metabolism Through Microbiota Dysbiosis to Promote Intestinal Toxicity.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124140},
doi = {10.1016/j.envres.2026.124140},
pmid = {41765316},
issn = {1096-0953},
abstract = {Organophosphorus flame retardants (OPFRs) are associated with intestinal injury. Bisphenol A bis(diphenyl phosphate) (BDP), an emerging OPFR that is widely present in organisms and humans, may induce intestinal toxicity, yet the effect and underlying mechanism remains unclear. In this study, zebrafish were exposed to BDP at 2, 20 and 200 μg/L for 21 days. Distinct histopathological changes in the intestine of zebrafish were observed, and the relative expressions of mucus secretion and tight junction related genes (MUC-2, Occuludin a and ZO-1) were all downregulated. Through the integrated analysis combining metabolomics and metagenomics, the results demonstrated that BDP exposure downregulated the abundances of microbiota Peptostreptococcus, Clostridium, Bombilactobacillus and Sporolactobacillus in zebrafish intestines, to depress tryptophan metabolism and eventually reduce the abundances of tryptophan metabolites. As a result, the expression of AhR, an important receptor activated by tryptophan metabolites, was inhibited to downregulate IL-22 expression, promoting intestinal toxicity. In vivo experiment with indole-3-propionic acid supplement alleviated the pathological changes, which further confirmed that BDP destroyed microbiota-tryptophan metabolism homeostasis to interfere with the AhR-IL-22 axis, eventually promoted pathological toxicity in the intestines. This study highlights vulnerability of intestines to BDP, and provides first insight into the mechanism through which BDP threats intestinal health.},
}

@article {pmid41765175,
year = {2026},
author = {Clarke, BC and Ordinola-Zapata, R and Noblett, WC and Gould, M and Staley, C},
title = {Taxonomy and Virulence Factors in the Root Canal Microbiome: Metagenomic Insights by Lesion Size and Clinical Factors in Primary Endodontic Infections.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.02.016},
pmid = {41765175},
issn = {1878-3554},
abstract = {INTRODUCTION: This study aimed to investigate the taxonomic and functional profiles of the root canal microbiome in teeth with large versus small periapical lesions, examining the influence of clinical variables on microbial composition and functional pathways.

METHODS: Samples from 25 teeth with large (>8mm) and 20 with small periapical lesions (<2mm) were analyzed. Quantitative PCR, 16S next-generation and whole genome sequencing (WGS) were used to assess microbial load, diversity, and composition. Functional predictions were performed using the KEGG and MetaCyc databases. Alpha diversity was calculated using Shannon and Chao1 indices. Beta diversity was assessed using ANOSIM and PERMANOVA. Significant variables were explored using MaAsLin3. Kruskal-Wallis tests were used for univariate comparisons.

RESULTS: Teeth with large lesions exhibited significantly higher bacterial load (p = 0.011), but comparable alpha diversity and number of species per group in 16S and Whole genome analysis (P > 0.05). Lesion size showed significance by ANOSIM (p = 0.04) but not in PERMANOVA (p = 0.36). Age was significant in both beta diversity tests, but the effect size only explained 3.6% of the variance. All clinical variables were not significant in 16S analysis for beta diversity. MetaCyc pathway analysis identified percussion sensitivity as the most influential clinical variable in both tests (ANOSIM R = 0.182, p = 0.012; PERMANOVA R[2] = 0.063, p = 0.046). MaAsLin3 modeling revealed enrichment of enzymatic pathways involved in methionine and cysteine-related metabolism.

CONCLUSIONS: Large periapical lesions contain significantly higher bacterial load, but similar diversity compared to small lesions. Functional predictions suggest bacterial metabolic activity may contribute to mechanical allodynia in endodontic infections.},
}

@article {pmid41764980,
year = {2026},
author = {Xie, J and Hu, T and He, J and Cai, Y and Wu, Q and Li, L and Liu, H},
title = {Genome characterization and evolutionary analysis of a novel Anativirus from a wild Muscovy duck in Guangdong, China.},
journal = {Virology},
volume = {618},
number = {},
pages = {110849},
doi = {10.1016/j.virol.2026.110849},
pmid = {41764980},
issn = {1096-0341},
abstract = {A novel member of the genus Anativirus was identified and characterized from a naturally deceased wild Muscovy duck (Cairina moschata) collected in Maoming, Guangdong Province, China. This strain, provisionally designated Anativirus GD2411, was detected through metagenomic next-generation sequencing (mNGS), which yielded a complete genome of 8,085 nucleotides. The genome comprises a single open reading frame (nt 413-7,873) encoding the canonical picornaviral polyprotein, flanked by a 5' untranslated region (UTR; 412 nt) and a 3' UTR (209 nt) with a poly(A) tail. Whole-genome nucleotide identity analysis revealed that GD2411 clustered with duck-origin strains, sharing 88.0% identity with CH01 and 81.2% with TW90, but only 50.6% with the chicken-derived strain CHK1. High amino acid conservation was observed across functional regions, particularly in 2C (≥91.9%), 3C (≥92.4%), and 3D (≥97.0%), reflecting the preservation of RNA-dependent RNA polymerase function. Phylogenetic analyses based on complete genomes and 3D protein sequences using maximum likelihood methods consistently placed GD2411 within the duck Anativirus clade, indicating a close evolutionary relationship with TW90 and CH01. Although an experimental infection model was not established, PCR screening revealed broad gastrointestinal distribution of the virus, with the highest viral load detected in the cecum, suggesting fecal-oral transmission as a primary route. These findings provide preliminary evidence of Anativirus infection in wild Muscovy ducks in southern China, though the limited sample size precludes definitive conclusions regarding host range expansion. The highly conserved 3D region is highlighted as a potential target for antiviral therapy or vaccine development.},
}

@article {pmid41764931,
year = {2026},
author = {Wang, G and Wei, J and Qiu, G and Guo, Z and Wang, W and Liu, X and Song, Y},
title = {Mechanism of activated carbon enhanced activated sludge (ACEAS) in treating recalcitrant chemical wastewater.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129058},
doi = {10.1016/j.jenvman.2026.129058},
pmid = {41764931},
issn = {1095-8630},
abstract = {Recalcitrant chemical accident wastewater, especially nitrobenzene-containing wastewater, has posed a significant treatment challenge due to complex hazardous compounds as well as elevated toxicity. Activated carbon combined activated sludge processes can effectively remove hazardous organic pollutants from chemical wastewater. However, the interaction mechanism between activated carbon and activated sludge remains unclear. This study proposed the activated carbon enhanced activated sludge (ACEAS) process for treating nitrobenzene-containing wastewater. Combined with material characterization and metagenomic analysis, the removal efficiency of nitrobenzene was evaluated, and the interaction mechanisms between activated carbon and activated sludge was further investigated. The key findings include: The effluent nitrobenzene concentration in conventional activated sludge (AS) process was 6.5 and 9.2 times higher than in the original ACEAS (OS) and regenerated ACEAS (RS) processes, respectively. Without activated carbon replenishment, chemical oxygen demand (COD) removal efficiency in OS and RS processes increased by 10.19%-15.86% and 11.41%-14.60%, respectively, compared to AS process during long-term operation (6-24 h). Due to the formation of biofilms on the surface of activated carbon, and the content of C-O/C=O and C-N/C=N on OS increased by 13.2% and 17.3%, respectively, compared to original activated carbon (OC). Eventually, four enhanced mechanisms of activated carbon were proposed, each contributing to distinct degradation stages in the ACEAS system. In prophase, activated carbon might reduce toxicity and improve microbial degradation capacity by adsorption. During metaphase, biofilms on activated carbon surface further diminished adsorption/desorption effect. In the telophase, microbial carrier's fixation affected strengthens, reshaping microbial community structure, functional gene expression, and metabolic pathway selection, thereby enhancing activated sludge degradation efficiency.},
}

@article {pmid41764882,
year = {2026},
author = {Huang, L and Feng, L and Sun, Y and Li, Z and Deng, L and Zhang, P and Li, X and Gao, D and Wang, Y and Deng, S and Shen, F and Fang, D},
title = {Oxygen stress drives overcompensation of carbon sources for enhanced polymer denitrification.},
journal = {Water research},
volume = {296},
number = {},
pages = {125631},
doi = {10.1016/j.watres.2026.125631},
pmid = {41764882},
issn = {1879-2448},
abstract = {Dissolved oxygen (DO) is traditionally considered as a strong inhibitor of denitrification. However, its impact on polymer-based denitrification, where carbon bioavailability is rate-limiting, remains poorly understood. Here, we investigated the response of a polycaprolactone (PCL)-supported biofilm system to long-term DO stress (2-8 mg/L). Contrary to conventional expectations, elevating DO from 2 to 8 mg/L significantly accelerated nitrate removal (from 8.06 to 10.50 mg N/L) rather than suppressing it. Stoichiometric modeling and metabolomic analysis revealed an oxygen-induced carbon release mechanism, where high DO stimulated the secretion of extracellular esterases and intensified the β-oxidation pathway, increasing polymer carbon release by 17.71 mg/L. This excess carbon overcompensated for aerobic consumption, effectively alleviating electron donor limitations. Metagenomics further confirmed a structural shift towards an oxygen-tolerant consortium, with significant enrichment of dual-function genera (e.g., Pseudoxanthomonas) and enhanced coupling of respiratory chain complexes (I-III). The biofilm achieved spatial decoupling, utilizing the outer aerobic layer for rapid hydrolysis and oxygen consumption to protect the inner anoxic denitrification zone. These findings overturn the strict anoxic requirement for denitrification, providing a robust strategy for advanced nitrate removal in oxygen-fluctuating tailwaters.},
}

@article {pmid41764843,
year = {2026},
author = {Das, N and Pandey, P},
title = {Striking a microbial balance: Rhizoremediation of crude oil-contaminated soils suppresses resistomes and reconstructs hydrocarbon-degrading microbial networks.},
journal = {The Science of the total environment},
volume = {1022},
number = {},
pages = {181586},
doi = {10.1016/j.scitotenv.2026.181586},
pmid = {41764843},
issn = {1879-1026},
abstract = {Integrated plant-microbe systems are crucial for restoring hydrocarbon- and heavy metal-contaminated soils. Here, Azadirachta indica inoculated with a hydrocarbon-degrading bacterial consortium (SynCom) was used in microcosm and field trials to remediate chronically oil-contaminated soils. SynCom treatment enhanced degradation of total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs) up to 99%, reduced heavy metal concentrations, and neutralized soil pH, while improving organic matter, soil aggregation, and nutrient mobilization (N, P, K). Metagenomic analyses revealed a shift from Proteobacteria to Actinobacteria, with a 10-fold reduction in antibiotic resistance genes, particularly multidrug resistance and efflux pump genes. Key functional taxa (Nocardioides, Bradyrhizobium japonicum, Rhodopseudomonas) were enriched, correlating with enhanced nutrient cycling, soil enzyme activity, and hydrocarbon degradation. Functional gene profiling indicated reduced oxidative stress and ecological recovery. This study demonstrates that targeted rhizoremediation effectively detoxifies soils while mitigating ARGs dissemination, offering a sustainable One Health-aligned strategy for environmental and public health protection.},
}

@article {pmid41764831,
year = {2026},
author = {Peng, X and Zhang, L},
title = {Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {2},
pages = {117321},
doi = {10.1016/j.diagmicrobio.2026.117321},
pmid = {41764831},
issn = {1879-0070},
abstract = {Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagnostic methods such as culture, PCR, and immunological assays are widely used, they are limited by long processing times, narrow detection scopes, and poor capability for identifying unknown pathogens. untargeted shotgun metagenomic sequencing (mNGS), as a non-targeted, high-throughput detection technology, enables broad-spectrum identification of diverse microorganisms and functional gene annotation, making it an increasingly important complement in infectious disease diagnostics. This review summarizes the clinical value of mNGS in key scenarios such as neurological, respiratory, and bloodstream infections. It also discusses its utility in antimicrobial resistance (AMR) monitoring and personalized therapy, highlights current challenges in sensitivity, bioinformatics analysis, and result interpretation, and briefly explores future directions involving artificial intelligence (AI), multi-omics integration, and healthcare information system integration. The goal is to provide a reference for the standardized application of mNGS in infectious disease diagnosis and treatment.},
}

@article {pmid41764643,
year = {2026},
author = {Zeller, LM and Schorn, S and Nicolas-Asselineau, L and Zopfi, J and Ahmerkamp, S and Schubert, CJ and Lepori, F and Kuypers, MMM and Graf, JS and Milucka, J},
title = {Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag043},
pmid = {41764643},
issn = {1751-7370},
abstract = {Bacterial endosymbionts of the family Ca. Azoamicaceae obligately associate with anaerobic ciliates belonging to the class Plagiopylea. The symbionts' unique role for their host involves anaerobic respiration of nitrate and generation of ATP, analogous to the role of mitochondria in aerobic eukaryotes. As this symbiosis remains so far uncultured, insights into its functioning have been mainly inferred from environmental metagenomes. Here we investigated the distribution and environmental role of this symbiosis in the anoxic basins of two freshwater lakes Zug and Lugano (Switzerland) over a course of several years. We found that the environmental niche of the ciliate host is defined by the combined effects of sulfide, oxygen and nitrate, the latter of which is essential for the symbiont's respiratory function. Moreover, the distribution and abundances of ciliates with denitrifying endosymbionts in the water column suggests that they may substantially contribute to nitrate consumption in Lake Zug. Our microscopic analyses further demonstrated a coordinated division of the Candidatus Azoamicus ciliaticola symbionts and their ciliate hosts, implying a vertical inheritance of denitrifying symbionts. These observations offer new insights into the evolution of ciliates with denitrifying endosymbionts and their ecological role in oxygen-depleted lakewaters.},
}

@article {pmid41764576,
year = {2026},
author = {Li, J and Ren, J and Xu, J and He, J and Xu, J and Yin, Q and Yao, J and Wu, S},
title = {Ability of the Chinese herbal residue to alleviate short-distance transportation stress in sheep through the remodeling of the rumen microbiome-metabolism axis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41764576},
issn = {1674-9782},
support = {2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 32573272//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
abstract = {BACKGROUND: Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota‒metabolism axis.

RESULTS: Twenty first-lambing East Friesian × Hu sheep hybrids weighing 54.49 ± 7.94 kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet + 50 g/d CMR) feeding at 4 h after approximately 300 km of short-distance transport. Results indicated that 4 h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, α-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.

CONCLUSION: This study confirmed that 4 h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.},
}

@article {pmid41764388,
year = {2026},
author = {Zhu, K and Amirali, A and Auch, B and Babler, KM and Biswas, P and Bowie, K and Choudhary, S and Currall, BB and Grills, GS and Healy, HG and Liachko, I and Lucaci, AG and Mason, CE and Sharkey, M and Shigeno Risse-Adams, O and Shukla, BS and Sisson, Z and Stevenson, M and Williams, SL and Zulli, A and Peccia, J and Solo-Gabriele, HM},
title = {Proof-of-concept of host attribution of antimicrobial resistance genes using wastewater Hi-C metagenome sequencing.},
journal = {Journal of water and health},
volume = {24},
number = {2},
pages = {148-159},
pmid = {41764388},
issn = {1477-8920},
support = {//4Catalyzer/ ; U01DA053941/DA/NIDA NIH HHS/United States ; P30AI073961/NH/NIH HHS/United States ; },
abstract = {The proliferation of antimicrobial resistance genes (ARGs) poses public health risks globally, with wastewater treatment plants (WWTPs) serving as dissemination hubs for horizontal gene transfer. In this study, we evaluated the potential of applying Hi-C sequencing coupled with metagenomic bioinformatics for surveillance of ARGs and other microbial fitness traits using samples from WWTPs. Hi-C sequencing has the advantage over other molecular approaches by directly associating genes conveying fitness to their host microbe, plus to their element type (in plasmids, phages, or within the core genome of its host microbe). Results from Hi-C analyses confirm results from more laborious approaches by showing that aminoglycoside resistance is disseminated by plasmids. Mercury resistance was found in Zoogloea bacteria. Resistance genes to quaternary ammonium compounds were found within bacteriophages. Results from this study provide proof-of-concept for the potential value of Hi-C metagenome sequencing in wastewater attribution studies by illustrating the breadth of information that can be obtained about the microbial community, the exchange of genes, and their interconnections. We believe that with further development, Hi-C sequencing can be integrated into routine monitoring of wastewater for the purpose of providing near-real-time information about the dissemination of fitness traits, including ARGs.},
}

@article {pmid41764386,
year = {2026},
author = {Mtetwa, HN and Amoah, ID and Mthethwa-Hlongwa, NP and Pieerneef, R and Kumari, S and Bux, F and Reddy, P},
title = {Decoding mycobacterial ecology in Sub-Saharan African wastewater: metagenomic and metatranscriptomic insights for tuberculosis surveillance.},
journal = {Journal of water and health},
volume = {24},
number = {2},
pages = {109-127},
pmid = {41764386},
issn = {1477-8920},
support = {96086//South African Medical Research Council/ ; },
abstract = {Tuberculosis (TB) remains a major public health challenge in sub-Saharan Africa, driven by high transmission, delayed diagnosis, and limited surveillance. This study presents one of the first integrated applications of shotgun metagenomic and metatranscriptomic sequencing to investigate Mycobacterium communities in wastewater across six TB-endemic countries: Cameroon, Ghana, Kenya, Nigeria, South Africa, and Uganda. Twelve untreated and treated wastewater samples were analysed to characterise taxonomic composition, strain-level diversity, and transcriptional activity. Metagenomic analyses revealed diverse Mycobacterium communities, including M. tuberculosis, M. canettii, M. bovis, and members of the M. avium complex. Metatranscriptomic data detected MTBC-associated transcripts, indicating transcriptional activity and/or persistence of MTBC RNA signals in wastewater, with higher signal predominance in influent samples, consistent with community-level shedding. Metagenome-assembled genomes (MAGs) recovered from South Africa, Cameroon, and Uganda showed >82% completeness and included zoonotic species. MTBC strains clustered into Lineages 1, 2, 4, and 6, with animal-adapted strains linked to livestock and rodents, highlighting One Health relevance. Overall, this dual-omics approach supports wastewater-based epidemiology as a scalable tool for TB surveillance in high-burden settings.},
}

@article {pmid41763967,
year = {2026},
author = {Boix-Amorós, A and Bu, K and Blank, RB and Cantor, A and Gutiérrez-Casbas, A and Rodríguez-Lago, I and Marin-Jimenez, I and Sanz, J and Masmitja, JG and Trujillo, E and Muñoz, MC and Vivar, MLG and Carrillo, M and Hernández, MVH and Calvet, X and Salaet, MA and Romero, MI and García, AB and Pérez, S and Llorente, JFG and Gonzalez-Lama, Y and Argumánez, CM and Plaza, Z and Domínguez, M and Cañete, JD and Diaz-Gonzalez, JF and Scher, JU and Clemente, JC},
title = {Microbial signatures in psoriatic arthritis distinguish disease phenotypes and newly diagnosed inflammatory bowel disease independent of faecal calprotectin.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ard.2026.01.018},
pmid = {41763967},
issn = {1468-2060},
abstract = {OBJECTIVES: There is growing evidence of microbial involvement in immune-mediated inflammatory diseases, including psoriatic arthritis (PsA) and inflammatory bowel disease (IBD). However, it remains unclear whether different PsA phenotypes exhibit distinct microbial profiles. Furthermore, up to 4% of patients with PsA have comorbid IBD, which often remains undiagnosed. We hypothesised that the gut microbiome distinguishes PsA subphenotypes and serves as a biomarker of IBD in patients with PsA independent of faecal calprotectin (fCAL).

METHODS: We obtained samples from 192 patients with axial or peripheral PsA and no prior diagnosis of IBD enrolled in the EISER study. Patients with elevated fCAL and subclinical IBD symptoms underwent colonoscopy with intestinal biopsy. Stool samples were used to measure fCAL, and gut microbiome was characterised using shotgun metagenomics. Serum samples were used for cytokine profiling.

RESULTS: Axial PsA had lower alpha diversity and loss of several commensals compared with peripheral PsA, as well as a depletion of microbial biotin and arginine metabolism and higher levels of IL-23, IL-17F, and IL-8. Five subjects had newly diagnosed IBD which was characterised by a depletion of tryptophan and vitamin B6 metabolism. They also showed significant enrichment of several taxa compared to non-IBD and with a larger effect size than fCAL.

CONCLUSIONS: Our results identify a distinct microbiome and immune profile in axial PsA, with lower microbiome diversity, a depletion of commensals and protective microbial mechanisms, and higher levels of some proinflammatory cytokines. In patients with newly diagnosed IBD, we identified microbial taxa associated with the condition yet independent of fCAL, the current clinical standard.},
}

@article {pmid41763050,
year = {2026},
author = {Cai, F and Wang, C and Liu, H and Shen, J and Wang, J and Yang, Y and Wang, X},
title = {Partitioning dynamics and microbial responses drive the fate of polycyclic aromatic hydrocarbons in a plateau lake.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129097},
doi = {10.1016/j.jenvman.2026.129097},
pmid = {41763050},
issn = {1095-8630},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are persistent organic contaminants of concern in freshwater drinking-water sources, yet their environmental fate in hydrologically dynamic plateau lakes remains poorly constrained. Here, we investigated the multi-compartment distribution, apparent particle-water partitioning, microbial functional potential, and associated ecological and human-health risks of PAHs in Erhai Lake, a large subtropical plateau lake in southwestern China. PAHs were quantified simultaneously in the dissolved, suspended particulate, and surface-sediment phases across three seasons. Dissolved low-molecular-weight PAHs dominated the water column, exhibiting pronounced seasonal variability with summer peaks (12.9-49.8 ng L[-1]) driven by intensified tourism and hydrological inputs. In contrast, high-molecular-weight PAHs preferentially accumulated in sediments, forming depositional hotspots in the southern basin. Apparent organic-carbon-normalized partition coefficients (KOC,app) revealed that suspended particulates act as dynamic regulators of PAH transport and microbial accessibility. Metagenomic analysis revealed that the distribution of PAH-degradation-related functional genes co-varied with chemical partitioning patterns, suggesting potential microbial mediation of PAH fate. Ecological and human health risk assessments, including probabilistic Monte Carlo simulations, indicated that PAH-related risks remained within a low-risk regime across all seasons. Collectively, these findings provide a mechanistic framework for understanding how partitioning and microbial metabolism jointly regulate the fate of PAHs in plateau lakes, offering critical insights for the management of sensitive freshwater resources.},
}

@article {pmid41762837,
year = {2026},
author = {Wang, Y and Zhang, X and Wu, Y and Sun, X and Zhang, X and Lv, J},
title = {Biodegradation pathway of organophosphate esters in sludge composting implications for environmental safety.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141622},
doi = {10.1016/j.jhazmat.2026.141622},
pmid = {41762837},
issn = {1873-3336},
abstract = {Organophosphate esters (OPEs) are emerging contaminants of growing concern, and there is limited information about the bacterial transformation during sludge composting. In this study, under the stress of 100 mg/kg ∑7OPEs, three bacterial strains with degradation capabilities-Bacillus subtilis, Bacillus licheniformis, and Ralstonia pickettii-were screened and isolated, and a synthetic bacterial community (SynCom) was constructed. During 55 days sludge composting, the concentration of ∑7OPEs decreased significantly. In CK, TnBP degraded the fastest (> 90%). For the exogenous OPE-added groups strengthened with SynCom (T1B and T2B), the removal rates of TCPP and TPhP were nearly complete (> 93%). However, high concentrations of ∑7OPEs inhibited the degradation of compounds such as TCrP and EHDPP. Hydrolysis was identified as the preferentially initiated pathway for ∑7OPEs degradation during sludge composting. Functional enzyme such as phosphatase, as well as bacterial strains from the Rhodococcus and Paracoccus, synergistically participated in the degradation process. Multiple linear regression analysis confirmed that SynCom promoted ∑7OPEs removal by boosting phosphomonoesterase activity and enriching phosphatase-producing microorganisms. pH and total phosphorus (TP) emerged as critical environmental factors influencing this degradation. Composting significantly lowered OPE-associated ecological risks, ensuring the safe resource recovery of sludge. This study focused on the biological removal of OPEs during sludge composting. It first systematically evaluated the biodegradation efficiency of ∑7OPEs and clarified core metabolic pathways. Furthermore, key microbial communities and functional genes associated with ∑7OPEs degradation were identified, revealing their regulatory roles. It provides scientific support for controlling OPEs pollution and promoting sludge resource utilization.},
}

@article {pmid41762508,
year = {2026},
author = {Zhang, L and Jiang, L and Zhang, Z and Wang, Y and Yao, C and Yu, K and Tao, H and Sun, W and He, X and Gu, J and Qian, X},
title = {Unraveling metal-organic frameworks impact on resistome and virome dynamics in swine manure anaerobic digestion via metagenomic.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129121},
doi = {10.1016/j.jenvman.2026.129121},
pmid = {41762508},
issn = {1095-8630},
abstract = {Livestock manure is a major hotspot of antibiotic resistance genes (ARGs). However, the efficacy and mechanisms of anaerobic digestion (AD) in reducing ARGs, along with the ecological roles and risks of viral communities, remain poorly understood. This study demonstrates that AD significantly reduces total ARG abundance and diversity, with addition of metal-organic frameworks (MOFs) further enhancing the reduction of high-risk and clinically critical ARGs. ARG abundance decline was primarily driven by core ARGs, whereas diversity reduction was mainly attributed to the depletion of rare ARGs. ARGs exhibit a broad host distribution, alongside pervasive pathogenic host species. Viral communities display high diversity and novelty, with the Drexlerviridae family as the dominant virome. Viruses exhibit strong host specificity, with Actinobacteria (47.4%) and Atribacterota (12.7%) as primary hosts. Only eight viral contigs carried ANT(6)-Ia and lsa(B), indicating limited viral contribution to ARG horizontal transfer. Viruses enhance host metabolic capabilities by introducing diverse and unique auxiliary metabolic genes (AMGs). The AD process predominantly influences viral diversity, lifestyle, and AMG carriage. Mechanistically, AD reduces ARGs via decreasing co-occurrence frequencies of ARGs and plasmids, coupled with reduced abundances of ARG-hosting. These findings provide new insights for optimizing AD processes to control the diffusion of ARGs.},
}

@article {pmid41762498,
year = {2026},
author = {Jiang, PY and Tang, H and Tong, WK and Liu, J and Liu, K and Tang, W and Liu, JB and Gao, MT and Liu, N and Hu, J and Li, J},
title = {Interface modification of membrane substrates: Mitigating microbial interfacial adhesion and augmenting adsorptive capacity for seawater uranium recovery.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129080},
doi = {10.1016/j.jenvman.2026.129080},
pmid = {41762498},
issn = {1095-8630},
abstract = {Seawater is endowed with vast reserves of high-value trace metals (gold, lithium, uranium) for resource recovery. However, their extremely low concentrations entail extensive, long-duration seawater processing in membrane-based systems, leading to pronounced microbial fouling and a substantial deterioration in adsorption efficiency. Given that practical membrane modules possess a multi-component architecture, this study mitigated microbial fouling via indigo modification of membrane supporting substrates, while maintaining the structural and functional integrity of the adsorptive membrane. This approach avoids the impairment of adsorption sites and porous structures induced by direct antimicrobial modification of the membrane. Column breakthrough experiments were employed to assess the fouling characteristics and severity of membrane modules in terms of macroscopic retention and structural evolution. Before modification, the membrane module exhibited interception rates of 79.8% and 77.3% for single strains and in-situ marine microbial communities (multiple strains), respectively, which were reduced to 45.6% and 57.1% after modification. Analysis using the dual-kinetic-site attachment-detachment model demonstrated that indigo-modified substrates reduced Langmuirian attachment and ripening, while the functional complementarity within microbial communities mitigated these effects. Metagenomic analysis confirmed that the modification selectively suppressed the attachment of microorganisms with strong adhesion and biofilm-forming ability. In a 28-day adsorption validation in real seawater, the modification increased the uranium adsorption capacity from 1.05 to 2.38 mg/g, effectively attenuating the performance decline induced by microbial contamination. The spatially decoupled integration of substrate anti-adhesion and membrane adsorption offers a new paradigm for membrane module design and optimization, extending its application potential in marine uranium recovery.},
}

@article {pmid41762491,
year = {2026},
author = {Yan, S and Li, R and Shen, X and Li, Y and Zhang, L and Xu, M and Xie, S},
title = {Redox potential drives divergent microbial carbon fixation in mangrove wetland sediments, with ammonium exerting context-dependent effects.},
journal = {Marine pollution bulletin},
volume = {227},
number = {},
pages = {119457},
doi = {10.1016/j.marpolbul.2026.119457},
pmid = {41762491},
issn = {1879-3363},
abstract = {Mangrove wetlands represent dynamic coastal interfaces where redox conditions and nutrient cycling shape microbial communities and their biogeochemical functions. However, tidal-driven siltation continuously transports sediment from low- to high-tide zones, altering sediment redox potential and nutrient content. The microbial responses to these changes, particularly the response mechanisms of carbon-fixing microorganisms, remain unclear. We integrated metagenomic and metatranscriptomic sequencing with [13]C and [15]N isotope labeling to examine how oxidation-reduction potential (ORP) and ammonium (NH4[+]) availability regulate microbial assembly and metabolism in mangrove sediments. ORP emerged as the primary determinant of microbial composition and diversity, while NH4[+] exerted variable effects on microbial traits. Under high ORP, CBBL-microorganisms predominantly utilized the cmmG CO2-concentrating mechanism, and carbon fixation rates decreased with increasing NH4[+] concentration. Under low ORP, CBBM-harboring genera dominated, primarily utilizing another mechanism cmmE, while NH4[+] had little effect and total organic carbon (TOC) exerted stronger control. ORP thus acts as the dominant environmental filter, with NH4[+] selectively affecting nitrifiers and carbon-fixing taxa. This was the first study to simultaneously measure ammonia oxidation and carbon fixation rate in mangrove sediments, revealing their mechanistic coupling. This work provides new mechanistic insights into the regulation of microbial metabolic potential in mangrove ecosystems and contributes to a broader understanding of their resilience and function in coastal biogeochemical cycles under fluctuating climate and environmental conditions.},
}

@article {pmid41762466,
year = {2026},
author = {Ma, Q and López, MJ and Zhang, S and Jin, L and Wei, D and Yang, J and Liu, J and Ruan, Z},
title = {Carbon source-dependent activation of herbicide-mixture degradation in a synthetic microbial community enriched from black soil.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141615},
doi = {10.1016/j.jhazmat.2026.141615},
pmid = {41762466},
issn = {1873-3336},
abstract = {The extensive use of herbicides in agriculture has resulted in persistent soil contamination. Although microbial degradation of single herbicides has been extensively investigated, the responses and co-metabolism of microbial consortia to complex herbicide mixtures remain unclear. This study aimed to investigate the influence of a simple carbon source (glucose) on herbicide degradation by a natural microbial consortium (NMC) and identify key degraders for constructing an efficient synthetic microbial community (SynCom). An NMC enriched from herbicide-stressed agricultural black soil in Northeast China was inoculated into mineral salt media containing a mixture of herbicides (atrazine, nicosulfuron and mesotrione) as the sole carbon/nitrogen source, without (MSM) or with glucose supplementation (GSM). Significant herbicide degradation occurred only in the GSM system, with degradation rates of 97.27% for nicosulfuron, 68.00% for mesotrione, and 22.91% for atrazine after 8 days. Integrated 16S rRNA gene sequencing and metagenomic analysis linked the glucose amendment to a specific shift in the microbial community structure and activation of central carbon metabolism (tricarboxylic acid [TCA] and glycolytic), which enhanced cellular energy supply and environmental acidification for co-metabolic degradation of herbicides. In contrast, metabolism in the MSM system was biased toward biosynthesis. Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa. Metagenomic screening showed that these taxa were enriched for functional genes associated with herbicide degradation, including atzF (allophanate hydrolase) and gst (glutathione S-transferase). A simplified four-isolate SynCom, constructed based on these functional associations, degraded the herbicide mixtures more efficiently than either the individual isolates or the NMC in the GSM system. These findings elucidate the role of labile carbon in driving the co-metabolism of complex herbicides and provide direct candidate strains and a construction strategy, facilitating practical bioremediation applications.},
}

@article {pmid41762461,
year = {2026},
author = {Shen, S and Wang, L and An, X and Liu, H and Shi, M and Tu, Y and Ji, W and He, Z and Li, A},
title = {Basin governance coincides with lower MGE loads yet rewired ARG mobility: a hazard‑oriented, platform‑centric assessment.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141608},
doi = {10.1016/j.jhazmat.2026.141608},
pmid = {41762461},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) serve as critical indicators for evaluating the ecological success of river restoration policies. We investigated the restructuring of the riverine resistome in the Yangtze River following the implementation of the "Ten-Year Fishing Ban" and the Yangtze River Protection Law. Using basin-wide surveys in the Jiangsu reach (2021 vs. 2023), we integrated shotgun metagenomics and RT-qPCR functional validation with a noise-filtering sampling design to assess how the removal of anthropogenic pressures reshaped resistance dissemination. Results show that policy-driven ecological recovery significantly altered microbial assembly mechanisms. While total ARG abundance declined, microbial communities shifted toward a more dispersal-dominated regime, with neutral model fits increasing from 0.817 to 0.913. Crucially, RT-qPCR analysis confirmed that the transcriptional activity of key resistance elements remained significantly elevated relative to a pristine baseline, suggesting persistent functional risks despite lower overall abundance. As localized selective pressures relaxed, the resistome transitioned toward integrated genetic platforms, evidenced by a significant rise in the mosaic index (MGI) from 12.81% to 22.50% (p < 0.05). Structural equation modeling (R2 = 0.766) identified a dominant sequential pathway from environmental co-selectors to mobile genetic elements and subsequently to ARGs, with intensified roles for integrons and insertion sequences (intI1, IS26). These findings demonstrate that policy success requires evaluation through both abundance-based and structural indicators. We propose a platform-centric surveillance framework incorporating the mosaic index as an early-warning tool for environmental agencies.},
}

@article {pmid41762333,
year = {2026},
author = {Pavan, JS and Deeksha, PM and Rajarushi, CN and Paschapur, AU and Rishika, KS and Ramakrishnan, B and Subramanian, S},
title = {Gut microbiota-mediated nitrogen recycling in the white Grub Holotrichia longipennis: A model for microbiome-targeted pest control.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41762333},
issn = {1573-0972},
}

@article {pmid41762314,
year = {2026},
author = {Dabravolski, SA and Vatlin, AA and Pavshintsev, VV and Mitkin, NA and Maltseva, ON and Orekhov, AN},
title = {A metagenomic perspective on microbial hydrocarbon degradation: uncovering novel pathways and community dynamics.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {5},
pages = {},
pmid = {41762314},
issn = {1573-2983},
support = {202760-2-000//RUDN University/ ; },
abstract = {The microbial degradation of petroleum hydrocarbons is a fundamental biogeochemical process and a cornerstone of environmental bioremediation. While traditional culture-based studies have outlined the basic principles, the advent of metagenomics has revolutionised our understanding by revealing the full genetic and functional diversity of hydrocarbon-degrading communities in situ. This review synthesises the current state of knowledge on both aerobic and anaerobic hydrocarbon biodegradation, providing a critical comparative analysis of traditional versus multi-omics methodologies. We provide an in-depth examination of aerobic mechanisms, initiated by oxygenases (e.g., alkB, PAH-RHDα), and contrast them with the diverse array of anaerobic activation pathways, including fumarate addition (bssA) and the recently elucidated direct carboxylation pathway for polycyclic aromatic hydrocarbons (PAHs). Furthermore, we highlight groundbreaking metagenomic insights into anaerobic benzene degradation and the critical role of syntrophic networks driven by interspecies electron transfer. Finally, we present specific case studies demonstrating the translation of genomic data into practical bioremediation strategies, such as the rational design of synthetic consortia. This review charts these recent advances, highlights remaining knowledge gaps, and outlines future directions for harnessing multi-omics to translate genomic potential into effective, field-scale environmental solutions.},
}

@article {pmid41762228,
year = {2026},
author = {Liu, T and Ding, H and Lv, Z and Yan, C and Feng, S and Lu, D and Hang, F and Meng, X},
title = {Lactobacillus Taiwanensis Inhibits Gallstone Formation by Regulating Ileal Metabolism.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41762228},
issn = {1432-0991},
support = {82270598//National Natural Science Foundation of China/ ; },
abstract = {In recent years, gut microbiota has been recognized to participate in gallstone formation via the gut-liver axis, yet the specific changes and roles of ileal microbiota remain unclear. This study aims to investigate the effects of microbial communities in different digestive tract segments on the formation of gallstones and the underlying mechanisms. Six-week-old C57BL/6J mice were randomly divided into a lithogenic diet group and a normal diet group. Ileal and colonic contents were collected separately for metagenomic sequencing.The Lactobacillus taiwanensis gavage model was constructed to compare its effects on gallstone formation and ileal metabolism. An intraperitoneal injection model of Lipoxin A4 (LXA4) was established to investigate the mechanisms by which Lactobacillus taiwanensis and LXA4 inhibit gallstone through Western blot analysis and ELISA methods. We found that there were significant differences in the intestinal microbiota between the group with gallstone formation and the control group in the small intestine and colon. Species-level analysis indicated that the lithogenic diet reduced the abundance of Lactobacillus taiwanensis in the small intestine. When Lactobacillus taiwanensis was administered intragastrically to mice, the incidence of gallstones decreased. Through metabolomics analysis and experimental verification, we demonstrated that Lactobacillus taiwanensis could down-regulate the expression of NETs in the liver and bile by increasing the level of LXA4, thereby reducing gallstone. The ileal and colonic microbiota exert site-specific effects in gallstone formation. Lactobacillus taiwanensis may inhibit gallstone formation by regulating ileal metabolism, may contribute to prevention and treatment of gallstones.},
}

@article {pmid41761979,
year = {2026},
author = {Guo, Z and Gao, Z and Zhao, Y and Ni, X and Zhang, W and Li, L and Ren, S and Li, Q and Guo, D and Yue, L and Liu, Y and Lin, L and Fan, S and Hai, X},
title = {Administering Bifidobacterium pseudolongum With Arsenic Trioxide Attenuates Acute Promyelocytic Leukemia in Mice by Restoring Immune Microenvironment and Intestinal Homeostasis.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {2},
pages = {48584},
doi = {10.31083/FBL48584},
pmid = {41761979},
issn = {2768-6698},
support = {82274028//National Natural Science Foundation of China/ ; 2022ZX02C09//Heilongjiang Key R&D Program/ ; //Fundamental Research Funds for the Provincial Universities in Heilongjiang Province (2025)/ ; JJ2025PL0189//Natural Science Foundation of Heilongjiang Province/ ; 2024M10//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2024M25//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 230000253533210000086//2025 Central Government Fiscal Subsidy Fund for Medical Care Compliance and Capacity Enhancement (Traditional Chinese Medicine Undertakings and Inheritance and Development Component)/ ; },
abstract = {OBJECTIVE: Arsenic trioxide (ATO) is a cornerstone of acute promyelocytic leukemia (APL) therapy but induces severe gut microbiota dysbiosis, limiting its efficacy and safety. This study investigated whether adjunctive Bifidobacterium pseudolongum (BP) could mitigate these adverse effects and enhance therapeutic outcomes.

METHODS: 16S rRNA gene sequencing data of gut microbiota were obtained from a cohort of 22 APL patients treated with ATO-based regimens (20 of 22 data were obtained and analysis further), accessible under BioProject ID PRJNA935705. To evaluate the within-sample microbial community richness and evenness, alpha and beta diversity indices were calculated. Using a murine APL model, we compared ATO monotherapy with ATO+BP co-treatment. Analyses included fecal metagenomic sequencing, single-cell RNA sequencing (sc-RNA-seq), flow cytometric immune profiling, and assessment of intestinal tight junction proteins (claudin-1, occludin, and ZO-1) via immunofluorescence.

RESULTS: ATO treatment significantly reduced gut microbial diversity and depleted beneficial taxa. Sc-RNA-seq data showed that ATO could orchestrate the APL immune microenvironment mainly through functional activation of CD8+ T cells and monocytes. BP supplementation restored microbial homeostasis and synergistically enhanced ATO's antileukemic effect, reducing the leukemic burden in peripheral blood by 72% and in bone marrow by 64% compared to ATO alone. Mechanistically, BP preserved intestinal barrier integrity by upregulating tight junction protein expression and modulated anti-tumor immunity, notably increasing bone marrow CD8+ T cells by 2.21-fold.

CONCLUSIONS: BP is an effective adjunct to ATO therapy, counteracting gut dysbiosis, intestinal damage, and the immune microenvironment while synergistically improving antileukemic efficacy. Targeting the gut-leukemia axis with BP represents a promising strategy for improving the precision and safety of APL treatment.},
}

@article {pmid41761378,
year = {2026},
author = {Biggel, M and Oberhänsli, T and Kümmerlen, D and Walkenhorst, M and Stephan, R and Holinger, M},
title = {Diversity and abundance of antimicrobial resistance genes in manure from pig farms with varying antibiotic use: a long-read metagenomic sequencing approach.},
journal = {Porcine health management},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40813-026-00496-3},
pmid = {41761378},
issn = {2055-5660},
support = {04.1240.PZ//Swiss Expert Committee for Biosafety (SECB)/ ; },
}

@article {pmid41760690,
year = {2026},
author = {Sammons, SL and Kuntz, TM and DiLullo, M and Morgan, XC and Martin, A and Hughes, ME and Rahman, T and Barroso-Sousa, R and Ogayo, ER and Giordano, J and Ryan, S and Waks, AG and Schlam, I and Ligibel, J and Lin, NU and Garrido-Castro, AC and Mittendorf, EA and Tolaney, SM},
title = {The landscape of the intestinal microbiome among patients with newly diagnosed invasive breast cancer and ductal carcinoma in situ (DCIS).},
journal = {NPJ breast cancer},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41523-026-00922-3},
pmid = {41760690},
issn = {2374-4677},
support = {P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; Dana-Farber Cancer Institute project number 6395601//Massachusetts Life Sciences Center/ ; },
abstract = {The intestinal microbiome shapes immune responses and is associated with patient outcomes in cancer following immunotherapy. We evaluated differences between the intestinal microbiome profiles of patients with early-stage invasive breast cancer (BC) and ductal carcinoma in situ (DCIS) by subtype using whole genome metagenomic sequencing. There were no significant differences in microbiome composition between DCIS and invasive BC as measured by alpha diversity (p = 0.20, ANOVA) or beta diversity (p = 0.52, PERMANOVA). Within invasive BC, patients with hormone receptor-positive (HR +)/HER2 + BC differed significantly in beta diversity relative to other subtypes (p < 0.05), with differences in six species (q < 0.25). Bacteroides ovatus was significantly more abundant in patients with stage III BC vs. stage I (p = 0.0003). Functional pathway analysis using HUMAnN3 revealed stage-specific enrichment of amino acid biosynthesis and nucleotide-related pathways. Altogether, these findings highlight potential microbial signatures associated with BC subtype and stage.},
}

@article {pmid41760689,
year = {2026},
author = {Yarlina, VP and Tandra, JL and Indiarto, R and Andoyo, R and Harlina, PW and Ubaidillah, NHN and Lani, MN},
title = {Unraveling Tempeh through omics: a scoping review of fermentation pathways and functional health benefits.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00754-2},
pmid = {41760689},
issn = {2396-8370},
support = {No. 2245/UN6/N/PT.01.03/2025//Universitas Padjadjaran/ ; },
abstract = {Tempeh, a traditional Indonesian fermented soybean product, is widely recognized for its functional properties and for containing bioactive compounds produced by microbial fermentation. This study integrates recent advances in multi-omics technologies to elucidate the microbial community dynamics, enzymatic pathways, and metabolite transformation underlying Tempeh's health-promoting characteristics. A bibliometric analysis of studies published between January 2000 and August 2025, indexed in Scopus, PubMed,Web of Science, and ScienceDirect identified 36 relevant articles that met predefined inclusion criteria. Metagenomic and transcriptomic evidence highlights the important roles of Rhizopus species and associated Lactic acid bacteria in fermentation, supported by the presence of genes encoding key enzymes such as phytases, amylases, and proteases. Proteomic and peptidomic analyses have further identified bioactive short peptides exhibiting antioxidant and angiotensin-converting enzyme (ACE) inhibitory activities. Metabolomic profiling revealed elevated levels of amino acids, γ-aminobutyric acid (GABA), and isoflavone aglycones, compounds linked to various health benefits. Collectively, these multi-omics insights provide a mechanistic understanding of Tempeh's functional potential and highlight opportunities for innovation in fermentation optimization and clinical translation. Future integration of standardized fermentation protocols with targeted human studies will be essential to advance Tempeh from a traditional food to a globally recognized functional food product.},
}

@article {pmid41759636,
year = {2026},
author = {Liang, L and Su, S and Peng, L and Zhuang, H and Chen, Y and Cao, Y},
title = {Development of Mycobacterium tuberculosis post in vitro fertilization and embryo transfer: A case series derived from a multi-omics analysis and literature review.},
journal = {Microbial pathogenesis},
volume = {214},
number = {},
pages = {108408},
doi = {10.1016/j.micpath.2026.108408},
pmid = {41759636},
issn = {1096-1208},
abstract = {The extensive progress in assisted reproductive technology has facilitated successful pregnancies through in vitro fertilization and embryo transfer (IVF-ET) for patients facing infertility. Pregnancy induces substantial endocrine and immune alterations that may diminish immune function, consequently heightening vulnerability to Mycobacterium tuberculosis (M.tb) infection or reactivation. Hematogenous disseminated pulmonary tuberculosis (TB), tuberculous meningitis, and potential congenital TB are serious complications that may arise after IVF-ET, posing significant risks to both maternal and fetal health. The clinical manifestations of TB during pregnancy frequently coincide with non-typical pregnancy symptoms, and the nonspecific characteristics of early-stage presentations render prompt diagnosis especially difficult. The existing literature on this subject is sparse, primarily consisting of isolated case studies involving individual participants, thereby yielding insufficient data and inadequate representations to comprehensively clarify this clinical emergency. This paper presents a case series of patients with normal immune function who developed hematogenous disseminated TB, including placental and central nervous system involvement, subsequent to IVF-ET. We showcased the multi-omic findings, including metagenomic sequencing and histopathological analyses, from patients with twin and singleton pregnancies and presented an extensive literature review. Additionally, we used metagenomic next-generation sequencing (mNGS) to detect pathogenic microorganisms in blood, bronchoalveolar lavage fluid (BALF), and cerebrospinal fluid (CSF) samples. Rare histopathological findings of placental TB were also documented, providing direct pathological evidence relevant to congenital TB. These findings expand the limited clinical evidence on TB following IVF-ET and underscore the importance of heightened clinical vigilance and multimodal diagnostic strategies in this high-risk population.},
}

@article {pmid41759557,
year = {2026},
author = {Yang, W and Shi, L and Li, X and Rao, F and Luo, R and Huang, C},
title = {Alterations in the gut virome of children with allergic rhinitis: enrichment of pro-inflammatory bacteriophages and depletion of fungal viruses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0327625},
doi = {10.1128/spectrum.03276-25},
pmid = {41759557},
issn = {2165-0497},
abstract = {This study aimed to characterize the gut virome in children with allergic rhinitis (AR) and explore its interactions with immune markers and allergens. Metagenomic sequencing was performed on fecal samples from 16 AR and 17 healthy control (HC) children. Viral genes (VGs) were identified and taxonomically annotated using BLASTP against the NCBI NR database. Virome diversity, differential abundance, and correlations with IgE were analyzed using LEfSe, random forest, and Spearman correlation. While alpha diversity did not differ, beta diversity revealed subtle compositional trends. Taranisvirus was enriched in AR and positively correlated with total IgE (ρ = 0.4647, P = 0.045). Mitovirus and Duamitovirus were depleted in AR and negatively correlated with allergens. Virus-bacteria co-occurrence network analysis revealed a reconfigured ecological interactome in AR, characterized by pro-phage-centric associations that may disrupt mucosal immune homeostasis. Random forest identified total IgE, milk, and dust mite as top discriminators. This first study of the gut virome in pediatric AR reveals a pro-inflammatory phage enrichment and protective fungal virus depletion, implicating the virome in modulating Th2 immunity. These findings suggest a potential correlation between virome alterations and allergic diseases, which may inform future research on virome-targeted interventions.IMPORTANCEAllergic rhinitis is a prevalent childhood condition with a significant impact on quality of life, yet its pathogenesis is not fully understood. While the bacterial microbiome has been studied, the role of the gut virome remains largely unexplored. Our study provides the first evidence of gut virome dysbiosis in children with allergic rhinitis. We identified specific pro-inflammatory bacteriophages that are enriched and correlated with IgE levels, as well as protective fungal viruses that are depleted. These findings offer new perspectives on allergic disease pathogenesis by suggesting a potential role of the virome in modulating host immunity. This work not only opens a new avenue for understanding the environmental and microbial drivers of allergic diseases but also suggests the potential for novel virome-based diagnostics and therapeutic strategies, such as phage therapy, which could have a broad impact on clinical practice.This study is registered with ClinicalTrials.gov as ChiCTR2400085982.},
}

@article {pmid41759554,
year = {2026},
author = {Dai, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Xu, H and Sun, J},
title = {Insights into antibiotic resistomes from gut metagenome-assembled genomes of the free-range pigs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0240725},
doi = {10.1128/spectrum.02407-25},
pmid = {41759554},
issn = {2165-0497},
abstract = {The pig gut microbiome serves as a reservoir for antibiotic resistance genes (ARGs), which pose a threat to public health and environmental safety. To investigate the presence of ARGs carried by free-range pigs, which have frequent contact with humans and their environment, we characterized the resistome of the pig gut microbiome through metagenomic sequencing of fecal samples from 120 pigs across four provinces in China (Yunnan, Guizhou, Sichuan, and Jiangsu). By constructing metagenome-assembled genomes (MAGs) and gene catalogs, we explored the microbial community structure and ARG distribution. Our analysis revealed a highly diverse array of ARGs, particularly those conferring resistance to multidrug, glycopeptide, peptide, and tetracycline antibiotics. Bacillota A and Actinomycetota were the dominant phyla across samples. However, notable regional differences in microbiota composition and resistance profiles were observed. These differences were likely influenced by local farming practices and environmental conditions. Guizhou harbored 11 unique ARG types, followed by Sichuan (seven), which showed region-specific resistome signatures. Escherichia coli and other microbial taxa were closely linked with ARG abundance, suggesting potential vectors for horizontal gene transfer. Analysis of mobile genetic elements (MGEs) further supported this, revealing a strong linear correlation between MGE and ARG abundance, with transposase elements particularly associated with multidrug ARGs. These findings highlight the central role of MGEs in ARG dissemination and underscore the need for targeted strategies to curb antibiotic resistance in livestock systems. Regional variation in resistome profiles further emphasizes the influence of local agricultural practices on resistance dynamics.IMPORTANCEThe growing prevalence of antibiotic resistance poses a significant global health threat, making it imperative to trace the origins and transmission routes of ARGs. This study delivers a comprehensive genomic reference for the porcine gut microbiota and clarifies how regional farming practices shape distinct resistome profiles. Integrating these data with analyses of mobile genetic elements and microbial hosts reveals the complex interplay among host, microbiota, and environment, thereby extending current knowledge of the pig gut ecosystem. These findings provide an evidence-based foundation for targeted surveillance and intervention strategies to curb antibiotic resistance in livestock and safeguard public health.},
}

@article {pmid41759320,
year = {2026},
author = {Yin, Y and Wu, H and French, CE and Lu, Z},
title = {Triclosan induced restructuring of microbial communities and antibiotic resistance gene dynamics in activated sludge: insights and mitigation strategies.},
journal = {Water research},
volume = {296},
number = {},
pages = {125614},
doi = {10.1016/j.watres.2026.125614},
pmid = {41759320},
issn = {1879-2448},
abstract = {The widespread presence of emerging contaminants, such as triclosan (TCS), in environmental systems raises significant concerns regarding their ecological risks, particularly the propagation of antibiotic resistance genes (ARGs). In this study, sequencing batch reactors (SBRs) were exposed to a TCS concentration gradient to simulate the accumulation of TCS in activated sludge and to elucidate its effects on microbial community structure, ARG dissemination, and horizontal gene transfer (HGT). Using a multi-omics approach that integrated 16S rRNA amplicon sequencing, short- and long-read metagenomics, and genome-scale metabolic modeling, we demonstrated that increasing TCS concentrations progressively reduced microbial diversity and stability. At lower TCS concentrations (0-1.0 mg/L), ARG-carrying bacteria were enriched, whereas at higher concentrations (10 mg/L), TCS eliminated ARG-carrying bacteria and selected for strains rich in mobile genetic element (MGE). Notably, HGT led to genome expansion of Acidomonas methanolica (from 3.75 Mb to 7.13 Mb), disrupting the microbial interaction networks within the community. Additionally, the introduction of a triclosan-degrading hydrogel-magnetic biochar-engineered strain composite mitigated the destabilizing effects of TCS stress on the microbial community, enhanced its resilience, and facilitated TCS degradation, thus reducing associated environmental risks. Our findings highlight how gradient TCS exposure reshapes microbial communities, promotes the dominance of MGE-enriched taxa, and has profound implications for the ecological and evolutionary dynamics of microbial communities in aquatic ecosystems. This study provides novel insights into the role of emerging contaminants in the propagation of resistance and microbial adaptation.},
}

@article {pmid41759316,
year = {2026},
author = {Zhang, J and Zhang, Z and Shen, Z and Yu, Z and Chen, J and Zeng, L and Li, D and Yan, X and Li, B and Wong, JWC},
title = {PDG_DB: A comprehensive database unveils environmental distribution patterns of plastic-degrading genes via large-scale multi-omic data analysis.},
journal = {Water research},
volume = {296},
number = {},
pages = {125619},
doi = {10.1016/j.watres.2026.125619},
pmid = {41759316},
issn = {1879-2448},
abstract = {Plastic pollution has become a global environmental crisis, driving urgent research into plastic-degrading enzymes for achieving efficient green transformation and recycling of plastic waste. However, current plastic-degrading gene (PDG) databases remain fragmented and incomplete. Simultaneously, research has predominantly focused on laboratory-isolated strains with the limited exploration of the vast reservoir of PDGs in environmental metagenomes. To address these limitations, we employed large-scale environmental multi-omics analysis to systematically mine and characterize PDGs across diverse ecosystems. We constructed PDG_DB (https://github.com/Z-bioinfo/PDG_DB), a comprehensive PDG database containing 341 experimentally validated sequences categorized by substrate specificity. Large-scale multi-omics analysis across environmental samples identified 7,111 PDGs (3,612 non-redundant), with polyhydroxyalkanoate (PHAs) degrading genes predominating. Molecular docking revealed that novel putative PDGs for PHA degradation exhibited stronger binding affinity compared to known PDGs, demonstrating the necessity of mining novel enzymes from environmental sources. Most PDGs were bacterial, primarily from Pseudomonadota, with the genus Pseudomonas showing the broadest degradation range. Our global analysis of 5,466 datasets revealed high PDG abundance in East Asia, North Europe, America, and the oceans. Unexpectedly, drinking water systems harbored the highest PDG abundance, challenging assumptions about plastic contamination in potable water. PDG distribution varied by environment: soil favored genes for non-biodegradable plastics, while wastewater systems preferred those for biodegradable plastics. Metatranscriptomic analysis showed the highest PDG activity in marine environments. This work provides a comprehensive resource for PDGs, revealing distinctive global distribution patterns with drinking water systems as an unexpected reservoir. PDG_DB serves as a foundational database for identifying PDGs, facilitating future environmental monitoring and biotechnology applications.},
}

@article {pmid41759241,
year = {2026},
author = {Myers, PN and van Beijsterveldt, IALP and Snowden, SG and Eriksen, C and Nielsen, HB and Hughes, IA and Ong, KK and Hokken-Koelega, ACS and Koulman, A and Brix, S},
title = {Breastfed infants receiving formula supplementation show altered lipid and gut microbiota profiles at 3 months of age.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {59},
number = {},
pages = {106602},
doi = {10.1016/j.clnu.2026.106602},
pmid = {41759241},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Exclusive breastfeeding offers numerous health benefits. Despite advancements in formula, significant differences compared with breast milk remain. We aimed to assess how milk feeding type and volume at 3 months affect the infant plasma lipidome and gut microbiota.

METHODS: Infants were classified into exclusive breastfeeding (EBF), mixed feeding (MF), or exclusive formula feeding (EFF) groups based on feeding data collected prospectively across two European cohorts (n = 519). Lipidomics and shotgun metagenomics were applied to plasma and stool samples, respectively.

RESULTS: Feeding type explained major variation in both lipidomic and microbial profiles. Plasma lipids showed distinct signatures across groups, particularly in sphingomyelins and diacylglycerols. Microbiota diversity and species richness increased with formula exposure. Formula rich in intact whey protein was linked to higher S. thermophilus abundance in the infant gut. Random forest classification of feeding type using either lipidomic or gut microbiota features achieved high discriminatory accuracy (AUROC >0.90) in training and validation datasets.

CONCLUSION: Early nutrition is a critical determinant of the lipidome and gut microbiome during the breastfeeding phase.},
}

@article {pmid41759061,
year = {2026},
author = {Hong, S and Winkler, MH and Wang, ZW and Dhanasekar, A and Goel, R},
title = {Unveiling Metabolic Insights and Niche Differentiation of Microbial Communities in EBPR-Anammox Reactor through Integration of Long-Read Metagenomics and Metatranscriptomics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c17958},
pmid = {41759061},
issn = {1520-5851},
abstract = {In this manuscript, we report niche differentiation among important groups of organisms involved in phosphorus and nitrogen cycling, and the interplay between relevant metabolic pathways carried out by these key organisms. We employed nanopore-based long-read and Illumina-based short-read sequencing techniques for metagenomics and metatranscriptomics, respectively, on samples collected from an integrated fixed film activated sludge (IFAS) bioreactor run in the conventional A[2]O mode under low dissolved oxygen (DO) conditions. Among the recovered metagenome-assembled genomes (MAGs), >90 MAGs from each community were high-quality, including 39 and 30 MAGs that were close-circularized, from the floc and biofilm communities, respectively, with no or minimal contamination. Some Candidatus Accumulibacter strains encoded for either full or partial denitrification. Ca. Accumulibacter were very efficient in aerobic and anoxic inorganic phosphorus (Pi) uptake, while the second highly enriched Ca. Accumulibacter was as competitive for denitrification metabolism. The potential of nitrous oxide (N2O) emissions in both the floc and biofilm communities was nearly 20 times higher in the aerobic zone than in the anoxic zone. As opposed to our initial hypothesis that slow growers will mostly reside in biofilms, the expression of ammonium monooxygenase (amoABC) was higher in flocs than in biofilm communities.},
}

@article {pmid41758250,
year = {2026},
author = {Kumar, A and Bandyopadhyay, TK and Das, D},
title = {Bacterial laccases for green remediation of contaminants of emerging concern: from molecular cloning to metagenomic and computational insights.},
journal = {Biodegradation},
volume = {37},
number = {2},
pages = {},
pmid = {41758250},
issn = {1572-9729},
abstract = {Contaminants of emerging concern (CECs) are increasingly recognized for their persistence, widespread occurrence, and potential risks to environmental and human health. Their frequent detection in wastewater, surface water, drinking water, and food chains underscores the urgent need for sustainable remediation strategies. Laccases, versatile multicopper oxidases, have demonstrated strong potential for degrading organic pollutants through oxidative mechanisms that transform complex contaminants into less toxic products. While fungal laccases have been extensively studied, bacterial laccases are gaining attention due to their structural simplicity, stability under alkaline conditions (pH 7.5-9.0), and limited requirement for post translational modifications. Recent studies indicate that bacterial laccases can transform approximately 60-80% of industrial dyes, a major class of CECs, even in complex wastewater matrices. Despite notable progress, broader application of bacterial laccases remains constrained by limited enzyme stability under industrial operating conditions, reduced catalytic performance under high salinity, extreme pH, and mixed pollutant environments, and frequent dependence on costly redox mediators, highlighting the need for more robust enzymes and sustainable mediator alternatives. This review summarizes recent advances in bacterial laccase research, with emphasis on structural and substrate specific insights, molecular cloning, heterologous expression, and optimized purification strategies. It also highlights emerging approaches such as metagenomics and machine learning for identifying robust, thermostable, and alkali resistant bacterial laccases suitable for large scale applications. Collectively, these advances support green chemistry principles and contribute to multiple United Nations Sustainable Development Goals by enhancing wastewater treatment efficiency, reducing energy and chemical inputs, and promoting sustainable waste valorization.},
}

@article {pmid41758194,
year = {2026},
author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L},
title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638009},
doi = {10.1080/19490976.2026.2638009},
pmid = {41758194},
issn = {1949-0984},
abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.},
}

@article {pmid41758007,
year = {2026},
author = {Nieves-Morales, R and Quiles-Pérez, CJ and Rivera-Lopez, EO and Torres-Zapata, I and Rodriguez-Ramos, J and Rios-Velazquez, C},
title = {Metagenomic libraries data sets from the hypersaline benthic microbial mats of the Fraternidad Lagoon, Puerto Rico, using an indirect DNA extraction method.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0150425},
doi = {10.1128/mra.01504-25},
pmid = {41758007},
issn = {2576-098X},
abstract = {Microbial mats are biofilm formations that reflect early Earth ecosystems. To investigate their microbial diversity, an indirect DNA extraction method was applied to benthic ephemeral microbial mats from Fraternidad Saltern Lagoon during rainy and dry seasons. This approach yields high molecular DNA, suitable for metabolic and diversity analysis.},
}

@article {pmid41757938,
year = {2026},
author = {Hashimoto, K and Fukushima, K and Matsumoto, Y and Saito, H and Funauchi, A and Hamada, N and Yamauchi, J and Nitta, T and Motooka, D and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Komukai, S and Kumanogoh, A and Nakamura, S and Kida, H},
title = {Comparison of culture and culture-free methods for comprehensive identification of mycobacteria: a single-center prospective study.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0112825},
doi = {10.1128/jcm.01128-25},
pmid = {41757938},
issn = {1098-660X},
abstract = {The genus Mycobacterium, including Mycobacterium tuberculosis and over 200 nontuberculous mycobacteria (NTM), shows wide variability in clinical outcomes and drug susceptibility. Although culture-based identification remains the gold standard, slow mycobacterial growth delays diagnosis and treatment. In this study, we evaluated a novel culture-free method for subspecies-level identification directly from sputum. In this single-center prospective cohort study at Osaka Toneyama Medical Center, we analyzed 125 sputum samples from 115 patients with NTM pulmonary disease and 10 with non-NTM respiratory conditions. Samples were decontaminated using N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) or succinic acid. We compared the reference culture method (mycobacterial culture plus whole-genome sequencing) and a culture-free direct target capture sequencing method. Core genome multi-locus sequence typing identified subspecies in both workflows, covering 186 mycobacterial species, including M. tuberculosis. The 115 NTM cohort specimens yielded 57 smear-positive and 93 culture-positive results. The identified subspecies included 48 Mycobacterium avium subsp. hominissuis, 22 Mycobacterium intracellulare subsp. intracellulare, 5 subsp. chimaera, 7 Mycobacterium abscessus subsp. abscessus, 5 subsp. massiliense, 1 M. tuberculosis, and 5 other NTM species. The culture-free method showed a high identification rate for smear-positive specimens (75.4%) but a low identification rate for smear-negative specimens (13.9%). NALC-NaOH pretreatment resulted in higher accuracy (90.5%) than did succinic acid pretreatment (66.7%). Thus, our culture-free subspecies-level identification method achieved high accuracy, especially in alkaline-treated smear-positive sputum samples, achieving rates above 90%. This method is recommended in clinical practice for patients who require rapid diagnosis and timely initiation of appropriate treatment, bypassing time-consuming culture steps.IMPORTANCEAccurate identification of Mycobacterium species and subspecies is crucial for effective treatment, as drug susceptibility and clinical outcomes vary significantly among them. However, conventional diagnosis relies on culture-based methods that can take several weeks, critically delaying appropriate therapy. This study validates a novel culture-free method using target capture sequencing for the comprehensive, subspecies-level identification of over 186 mycobacterial species directly from sputum specimens. Our findings revealed the high accuracy of this approach for smear-positive specimens, especially with alkaline pretreatment. This rapid method is applicable in clinical settings and enables timely and precise treatment decisions, greatly benefiting patients who require urgent intervention.},
}

@article {pmid41757890,
year = {2026},
author = {Tarasov, K and Zarubin, M and Yakhnenko, A and Gangapshev, A and Kravchenko, E},
title = {Metagenomic analysis of the biofilm community at the oxic-anoxic interface of a deep-underground saline spring at the Baksan Neutrino Observatory.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0210325},
doi = {10.1128/spectrum.02103-25},
pmid = {41757890},
issn = {2165-0497},
abstract = {In this work, the first-ever metagenomic study of the microbial community from the deep-underground saline spring located at the Baksan Neutrino Observatory (BNO) (Kabardino-Balkaria, Russia) is presented. Using the metagenomic approach, we obtained 19 metagenome-assembled genomes (MAGs) attributed to the phyla Pseudomonadota (the dominant phyla), Planctomycetota, Myxococcota, Nitrospirota, Gemmatimonadota, Armatimonadota, and Cyanobacteriota. Archaea are generally absent in the metagenome. The microbial community of the Baksan Neutrino Observatory demonstrates a high metabolic diversity, including carbon dioxide-fixing, methane-oxidizing, dinitrogen-fixing, nitrate- and iron-reducing, anammox, nitrifying, and predatory bacteria. Hydrogen, methane, ammonia, and reduced iron compounds, present in the ecosystem, provide energy for primary organic production. The abundance and diversity of bacteria capable of carrying out various stages of the nitrogen cycle suggest that nitrogen compounds are of great significance for microbial community metabolism. On the basis of the Genome Taxonomy Database Toolkit classification of MAGs and comparison to the closest RefSeq genomes, we have identified six new genera, with the proposed names-"Candidatus Jinrbaksania," "Candidatus Neutrinellum," "Candidatus Jinrextremum," "Candidatus Inrsubterrania," "Candidatus Inralta," and "Candidatus Neutrinobacter." Comparative analysis with metagenomes of microbial communities from the deep underground granitic sites and karst caves reveals that the BNO microbial community represents a unique transitional ecosystem on the boundary between the deep anoxic and surface aerobic biosphere.IMPORTANCEThe deep biosphere makes up 12-20% of the Earth's biomass and is poorly studied due to its inaccessibility. To date, only a few metagenomic studies of local deep biospheres have been performed in Russia. The Baksan Neutrino Observatory (BNO) is a deep-underground laboratory, with some abandoned tunnels. One of them hosts a mineral spring saturated with volcanic gases from the peripheral magma chamber of Mount Elbrus. The metagenomic analysis of the biofilm from this mineral spring has revealed the presence of unique microbial community whose composition occupies a transitional position between deep-underground microbial communities and communities of karst caves. We believe that this study of the microbial metagenome of the saline spring of the BNO will make a valuable contribution to understanding the composition and functioning of microbial communities formed at the oxic-anoxic interface.},
}

@article {pmid41757865,
year = {2026},
author = {Hu, X and Shi, Z and Gao, Y and Zheng, H and Lin, L and Chen, JP and Chen, Y and Zhang, CX and Li, Y},
title = {Characterization of the dynamic microbiome evolution across thrips species.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70265},
pmid = {41757865},
issn = {1744-7917},
support = {2023J06040//Natural Science Foundation of Fujian Province/ ; //Ningbo Yongjiang grant/ ; 32472657//National Natural Science Foundation of China/ ; 32570491//National Natural Science Foundation of China/ ; },
abstract = {The insect microbiome profoundly influences host physiology and ecology, yet its composition and evolutionary dynamics in thrips remain poorly understood. Here, we present a systematic characterization of thrips-associated microbiomes through integrated metagenomic and culture-based approaches. Our analysis reveals that thrips microbiomes are dominated by both intracellular symbionts (e.g., Wolbachia and Spiroplasma) and extracellular taxa (e.g., Serratia, Pantoea, and Acinetobacter), with species-specific compositions exhibiting frequent gains and losses of bacterial lineages. We demonstrate that thrips microbiomes exhibit low interspecific microbial sharing, forming host-specific bacterial communities with minimal overlap between species. To address methodological challenges in microbiome research, we developed a dual-sequencing framework combining short-read sequencing (for comprehensive taxonomic detection) and long-read sequencing (for genomic verification), enabling the reconstruction of high-quality metagenome-assembled genomes that validated short-read findings. Furthermore, we isolated and sequenced the complete genomes of two dominant extracellular symbionts-Pantoea dispersa and Serratia marcescens-and performed pan-genome analyses. These revealed small core gene sets and expansive accessory genomes, including host-specific functional genes (e.g., hydrolases and neurotoxic N-acetyltransferases) likely involved in host adaptation. Our study provides a foundational genomic resource and a robust analytical pipeline for dissecting thrips microbiome evolution, with implications for understanding insect-microbe interactions and symbiont-mediated adaptations.},
}

@article {pmid41757490,
year = {2026},
author = {Wang, Y and Schleheck, D and Marinova, E and Wessels, M and Schaller, S and Anselmetti, FS and Schwalb, A and Pedersen, MW and Epp, LS},
title = {Prokaryotic assemblages recovered by sedimentary DNA record natural and human-driven disturbances over the past 13 500 years in a cultural landscape.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag031},
pmid = {41757490},
issn = {1751-7370},
abstract = {Bacteria and archaea are under-characterized in palaeoecological studies, despite their ubiquity, high diversity, and tight integration with the abiotic, biotic, and human-influenced environments. The complexity of their assemblages and difficulties in separating living- from paleo-prokaryotes render research challenging. Here we present an ancient metagenomic time-series of prokaryotes from a sediment core of Lake Constance, spanning the last 13 500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and characterised the DNA damage of taxa as collectively increasing with time. By constructing co-abundance networks, we recognize major assemblage groups, containing both dead and living microbes, that show specific dynamics: Short-term and often low-abundance assemblages are linked to the Pleistocene-Holocene transition, floods, and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa associated with various freshwater and soil environments persisted through millennia. By extricating different sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing nature- and human-caused long-term eco-evolutionary consequences.},
}

@article {pmid41757394,
year = {2026},
author = {Wang, Z and Kojima, R and Kiji, R and Fujita, K and Tachibana, R and Tsuchiya, R and Uchiyama, T and Minagawa, Y and Mizuno, T and Igarashi, K and Noji, H and Kamiya, M and Urano, Y},
title = {Low-Background Cancer Imaging with a Bioorthogonal Fluorescence Probe and Engineered Reporter Enzyme Bearing a Targeting Moiety.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c14173},
pmid = {41757394},
issn = {1520-5126},
abstract = {Combinatorial use of an antibody-reporter enzyme conjugate and a fluorescence probe activated by the enzyme is a powerful strategy for fluorescence-guided cancer surgery. However, conventional probes for typical reporter enzymes lack sufficient bioorthogonality, leading to high background signals in nontarget tissues. We screened a library of HMRef (rhodol derivative)-based fluorescence probes with various sugar moieties and found that HMRef-β-d-Fucose is bioorthogonal in mammalian systems but is activated by a metagenomic glycosidase, Td2F2. Directed evolution generated a mutant with a kcat/Km of 3.3 × 10[5]/M/sec, 7.3 times higher than wild-type Td2F2 and comparable to β-galactosidase (LacZ) with its corresponding probe. Theoretical calculation suggested the E296G mutation facilitates probe access to the enzyme's active site. In a proof-of-concept study, SKOV-3 cells, which endogenously express HER2, were visualized with minimal background in the mesentery of a mouse model using HMRef-β-d-Fucose and engineered Td2F2 conjugated or fused to a HER2-binding antibody or nanobody.},
}

@article {pmid41757357,
year = {2025},
author = {Secker, B and Nayak, A and Husain, AA and Arora, S and Nag, A and Shrivastava, SK and Singer, AC and Gomes, RL and Acheampong, E and Chidambaram, SB and Bhatnagar, T and Vetrivel, U and Kashyap, RS and Atterbury, RJ and Blanchard, AM and Monaghan, TM},
title = {Metagenomic insights into the urban-rural variation of antimicrobial resistance and pathogen reservoirs in untreated wastewater from central India.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722229},
pmid = {41757357},
issn = {1664-302X},
abstract = {INTRODUCTION: Rapid and scalable surveillance of antimicrobial resistance (AMR) is urgently needed in resource-constrained countries where routine monitoring is limited. Wastewater-based metagenomics offers a potential solution for early detection and geographic mapping of AMR.

METHODS: We conducted a retrospective DNA shotgun metagenomic analysis of untreated wastewater collected across Nagpur, India (February-April 2021). A total of 422 grab samples were pooled into 138 composite samples from 10 urban zones and rural catchments. The bacterial microbiota and resistome were profiled, and urban-rural patterns were compared using diversity metrics and correlation analyses.

RESULTS: Across all samples, 871 bacterial genera were detected, dominated by Proteobacteria, with frequent presence of Pseudomonas, Acinetobacter, Aeromonas, Acidovorax and Bacteroides. Beta diversity revealed statistically significant but subtle urban-rural compositional shifts. Of 33 globally important pathogens examined, 13 were detected at generally low relative abundance (<1%). Vibrio cholerae appeared in one sample, while Aeromonas spp. were most prevalent. Seven pathogens occurred in ≥10% of samples, with Aeromonas, Citrobacter, and Enterobacter differing significantly between locations (p < 0.05). The resistome comprised 606 unique antimicrobial resistance genes (ARGs), dominated by drug/biocide efflux determinants, followed by macrolide-lincosamide-streptogramin B genes driven largely by 23S rRNA mutations. Carbapenemases (blaNDM, blaKPC) and colistin resistance (mcr) were detected at lower abundance. Correlation analyses linked Pseudomonas with mexEF/emhABC efflux and copBCDRS copper resistance operon, Acinetobacter with oxa and dfrA, and Aeromonas with ctx, tetA, sul1, dfrB/F, and gyrA/parC.

DISCUSSION: These findings show that wastewater metagenomics sensitively resolved clinically relevant pathogens and ARGs in an Indian urban-rural setting, capturing nuanced geographic structure. Integrating routine DNA metagenomics into One Health environmental surveillance could strengthen AMR early warning and guide interventions in resource-constrained contexts.},
}

@article {pmid41757355,
year = {2025},
author = {Lai, CM and Xiao, XS and Liu, LW and Li, XL and Luo, YW and Liang, YQ and Cheng, Y and Qin, Y},
title = {The impact of nanodrugs on the metagenome of tobacco rhizosphere soil.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1715400},
pmid = {41757355},
issn = {1664-302X},
abstract = {The occurrence of tobacco diseases seriously restricts the healthy development of the tobacco industry. Soil microorganisms play an important role in regulating ecosystem functions. However, the impact of nanodrugs on the rhizosphere microbial community of tobacco and its related functions is still unclear. Therefore, this study combined field experiments to evaluate the effect of nanodrugs in reducing diseases and combined metagenomic sequencing to further explore the micro-ecological mechanism of nanodrugs in stably reducing soil biological barriers. The results show that nanodrugs can significantly improve the health level of tobacco. Metagenomic sequencing found that nanodrugs treatment increased the diversity and abundance of bacterial communities and could regulate the structure of soil microbial communities. It could selectively recruit beneficial microorganisms such as Sphingomonas, Bradyrhizobium, Pseudomonas, and Nocardioides to assist tobacco in disease control. GO function analysis showed that nanodrug treatment groups had significant enrichment of energy metabolism-related functions such as electron transfer activity, ATPase activity, and redox processes. KEGG pathway analysis showed that the relative abundance of key metabolic pathways such as fatty acid metabolism, aminoacyl-tRNA biosynthesis, ribosome, and purine metabolism was significantly increased. This study found that nanodrugs may indirectly promote plant health and alleviate tobacco diseases by shaping microbial community structure, enriching beneficial bacterial communities, and activating key metabolic pathways. These findings provide a theoretical basis for the application of NMs in the regulation of agricultural micro-ecosystems.},
}

@article {pmid41757098,
year = {2026},
author = {Duan, L and Baumgartner, WA and Wanyama, JW and Okyere, L and Alvarado, DA and Minhas, BF and Gaulke, CA},
title = {Sex-stratified Gut Microbiome Disruption is Associated with Altered Hepatic Gene Expression during Acute Azoxystrobin Exposure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.18.706612},
pmid = {41757098},
issn = {2692-8205},
abstract = {UNLABELLED: Azoxystrobin is a widely used fungicide that has been associated with to reproductive, neurological, and developmental defects. This chemical also disrupts gut microbial communities; however, if these perturbations contribute to the harms associated with exposure to azoxystrobin, this remains unclear. In this study, we investigated the effects of acute exposure to a series of concentrations (5-500 mg/kg) of azoxystrobin on the host and gut microbiota in zebrafish. Fecal amplicon and shotgun metagenomic sequencing was integrated with liver gene expression to quantify associations between microbiome disruption azoxystrobin toxicity in the host. Azoxystrobin exposure resulted in significant alteration in microbiome composition and functional potential in a dose- and sex-dependent manner. Microbial communities in exposed animals exhibited an increased abundance of xenobiotic metabolism pathways and decreased bacterial motility and lipopolysaccharide biosynthesis pathway metabolism. At the host level, histopathology identified increased biliary proliferation, most evident in medium- and high-dose fish. We also observed hepatic transcriptional changes consistent with a stress response, including altered redox-associated genes and reduced expression of lipid and small-molecule metabolic genes, with sex-stratified differences. Importantly, alterations in host transcriptional programming correlated with the compositional changes in exposed microbiota. Together, these results suggest concurrent impacts of azoxystrobin on gut microbiota and the liver implicate the microbiome as a potential contributor to changes in liver gene expression during exposure.

IMPORTANCE: Widespread fungicide use contaminates ecosystems worldwide, but the biological pathways underlying their effects on humans and other animals are not well understood. Using zebrafish (Danio rerio), we found that short-term exposure to the fungicide azoxystrobin was associated with changes in the gut microbiome, liver gene activity, and liver changes. Exposure produced dose- and sex-dependent shifts in microbial communities, including changes in predicted microbial functions involved in chemical metabolism, bacterial motility and defense. Compositional changes in the microbiome correlated with gene-expression changes consistent with stress and altered metabolism in exposed fish, suggesting that exposure induced disruption may contribute to exposure impact to the host. These results highlight a potential role for the microbiome in mediation of the impacts of azoxystrobin on host physiology. As such microbial based interventions could be a viable strategy to mitigate exposure impacts on health.},
}

@article {pmid41757095,
year = {2026},
author = {Wang, F and Holmes, AJ and Browne, GV and He, X and Bockmann, MR and Davis, KM and Hughes, TE and Adler, CJ},
title = {Ecological and evolutionary dynamics of the oral microbiome across childhood.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.13.705642},
pmid = {41757095},
issn = {2692-8205},
abstract = {Childhood represents a critical period for oral microbiome development, yet evolutionary trajectories and the relative roles of host and environment remain unclear. Using a large longitudinal metagenomic dataset of 920 samples from a twin cohort spanning the first decade of life, we characterised microbial shifts and population dynamics of key bacterial groups. Microbiome diversity was initially reduced and highly heterogeneous and became increasingly complex and convergent with age. Microbial community state was associated with developmental age, environment and in late childhood was surprisingly strongly associated with host genotype. Strain-level analyses revealed species-specific temporal patterns of genetic variation particularly within Streptococcus , reflecting adaptive responses to host and environmental pressures. Fusobacterium exhibited consistently high replication rates, indicating sustained growth dynamics. Phylogenetic reconstruction further revealed host and niche specific genomic diversification of Saccharibacteria lineages. These findings establish childhood as a decisive period of oral microbial evolution and highlight the role of host-microbiome and epithelial interactions in shaping community structure, providing guidance for oral management strategies that promote lifelong oral health.},
}

@article {pmid41757006,
year = {2026},
author = {Tran, HN and Kirven, KJ and Davenport, ER},
title = {SCiMS: Sex Calling in Metagenomic Sequences.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.17.705110},
pmid = {41757006},
issn = {2692-8205},
abstract = {BACKGROUND: Host sex is a critical determinant of microbial community structure, influenced by hormonal profiles, physiology, and sex-stratified behaviors. Despite its importance, sex metadata is frequently missing or mislabeled in microbiome studies. Existing genomic sex-calling tools often fail in low-host-biomass samples (e.g., stool) because they require high read depths to achieve reliability.

RESULTS: Here, we present SCiMS (Sex Calling in Metagenomic Sequences), a bioinformatic tool that leverages host-derived DNA within metagenomic datasets to accurately predict host sex, even at low host coverage. SCiMS uses sex-chromosome read density ratios within a Bayesian classifier to provide high-accuracy sex calls. In simulations, SCiMS achieves >85% accuracy with as few as 450 host reads. When applied to 1,339 samples from the Human Microbiome Project, SCiMS outperforms existing tools, showing higher accuracy and more balanced precision-recall tradeoffs across body sites. SCiMS also generalizes effectively to non-human hosts, achieving 100% accuracy in a murine dataset and outperforming alternatives in a chicken dataset with a ZW sex determination system.

CONCLUSIONS: SCiMS provides an accurate, scalable, and cross-species generalizable solution for host sex classification in metagenomic datasets, even when host DNA is minimal. By enabling the recovery of missing sex metadata, it serves as a quality-control tool for ensuring the integrity of analyses in microbiome research. SCiMS is freely available at http://github.com/davenport-lab/SCiMS .},
}

@article {pmid41756881,
year = {2026},
author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Yardimci, GG and Merritt, JL},
title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.20.706901},
pmid = {41756881},
issn = {2692-8205},
abstract = {BACKGROUND: Inflammatory oral diseases are associated with reproducible shifts from commensal-dominated microbiota toward pathobiont-enriched communities, yet the ecological mechanisms underlying the emergence of inflammophiles remain poorly understood. This study aims to investigate if host-derived inflammatory environments act as selective pressures that restructure microbial metabolism and community organization during disease progression.

METHODS: We performed 16S rRNA gene sequencing of patient-matched pediatric dental plaque and odontogenic abscess specimens to capture microbial community transitions across an inflammatory ecological gradient. Community ecology modeling and inferred metagenomic analyses were used to identify taxa and functional programs associated with commensal and inflammophilic states.

RESULTS: Patient-matched comparisons revealed a reproducible ecological selection gradient linking inflammatory environments to expansion of metabolically specialized inflammophiles and depletion of carbohydrate-utilizing commensals. Commensal-dominated plaque communities exhibited anabolic, carbohydrate-centered metabolic capacity, whereas abscess microbiota were enriched for catabolic metabolism, amino acid fermentation, and antimicrobial resistance, consistent with adaptation to inflammation-driven nutrient landscapes and immune pressure.

CONCLUSIONS: These findings support a model in which host inflammation drives ecological restructuring of the oral microbiome toward metabolically adapted inflammophilic communities. Defining the metabolic requirements and selective pressures governing these transitions provides a framework for microbiome-directed therapeutic strategies aimed at restoring ecological stability during inflammatory dysbiosis.},
}

@article {pmid41756466,
year = {2026},
author = {Brunner, A and Mahout, M and Amoros, J and Rahmoun, M and Jarry, M and Bordenstein, SR and Bordenstein, SR and Trouche, B and Reveillaud, J},
title = {Extensive mobilome dynamics in a widespread endosymbiont: long read metagenomics reveal dimeric plasmids and highly fragmented prophages in Wolbachia from Culex pipiens.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8855126/v1},
pmid = {41756466},
issn = {2693-5015},
abstract = {Background The obligate, intracellular bacteria Wolbachia have gained increasing interest due to their selfish modifications of host arthropod reproduction, impacts on host evolution, and utility in vector control efforts to reduce arbovirus transmission. Despite their highly reduced genomes, Wolbachia harbor a rich global mobilome that includes phages and plasmids in mosquito vectors. However, these mobile genetic elements are structurally complex, and standard genome assemblies often fail to resolve their organization and their functional relationships, leaving gaps in our understanding of how they evolve, mobilize, and influence host genomes. Results Here, we present the first near-complete genome of Wolbachia and its mobile elements from the vector Culex pipiens molestus in Montpellier (France), reconstructed from Oxford Nanopore long read sequencing of single female ovaries without prior DNA amplification. Additional short reads from individuals of the same strain were used to assess and validate candidate mutations, particularly in repetitive regions. We report the assembly of a new dimeric form of the pWCP plasmid, providing evidence that the element is a replicating molecule and functionally active. We also observed extensive fragmentation of prophage WO regions despite long read sequencing, underscoring their structural complexity. Raw long read analyses recovered multiple alternative gene syntenies within WO regions, pointing to heterogeneous prophage architectures missed by the assembly and marked diversity of WO elements in Wolbachia of Culex pipiens (w Pip) group strains. Conclusions Taken together, our results show the high dynamism of the endosymbiont genome that is shaped by integrated and episomal active mobile elements.},
}

@article {pmid41756416,
year = {2026},
author = {Terns, M and Catchpole, R and McLean, J and John, ES and Reysenbach, AL and Krupovic, M},
title = {CRISPR spacers reveal diverse and abundant Thermococcales viruses in hydrothermal vents.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8799458/v1},
pmid = {41756416},
issn = {2693-5015},
abstract = {Viruses are the most pervasive biological entities on Earth and they profoundly shape host ecology and evolution. However, for many microbial lineages, knowledge of their viromes remains limited, especially for those inhabiting remote environments, including deep-sea ecosystems. Here, we leverage one of the most extensively cultivated and genomically characterized archaeal lineages, the Thermococcales, to identify novel viral genomes. By utilizing CRISPR spacers from isolates and spacer arrays reconstructed from metagenomes, we mined mobile genetic elements (MGEs) in 1,172 publicly available and newly sequenced hydrothermal vent metagenomic datasets. Comparative genomics and identification of viral hallmark proteins revealed 620 viral genomes across 19 taxonomic families, most of which were previously undescribed. Structural modeling of major capsid proteins (MCPs) revealed diverse virion morphotypes, including viruses with spindle-shaped, head-tailed, icosahedral, filamentous, ovoid and bacilliform virions, greatly expanding the previously limited Thermococcales virome. Family-level comparisons uncovered extensive flux of virus-encoded replication proteins that are evolutionarily and structurally distinct from host homologs, as well as dramatic variation in glycan-binding lectins suggestive of diverse infection strategies. Together, our results substantially broaden the Thermococcales virosphere and demonstrate the power of combining cultivated isolates with culture-independent, CRISPR-guided metagenomics to interrogate archaeal virus diversity and evolution.},
}

@article {pmid41756353,
year = {2026},
author = {Martins, GL and Monteiro, GGTN and Lange, M and de Freitas, AS and do Nascimento Silva Barbosa, L and van Leeuwen, J and de Carvalho Soares, JE and Hanada, RE and Gleixner, G and Tsai, SM},
title = {Land-use intensification reshapes microbial phosphorus cycling, organic matter composition, and phosphorus fractions in Amazonian soils.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag027},
pmid = {41756353},
issn = {2730-6151},
abstract = {Soil phosphorus (P) is a limiting factor for vegetation growth in the Amazon rainforest, where plants depend on microorganisms for organic matter cycling and nutrient uptake. While forest-to-agriculture conversion fundamentally reshapes plant-microbe-soil interactions and P cycling, these dynamics are further modulated by the intensity of land management. This study examined the 30-year effects of converting a primary forest into two contrasting systems: a low-intensity agroforest and a high-intensity citrus monoculture. We investigated how microbial and low molecular weight organic compounds (LMWCs) composition interacted with soil physicochemical attributes, acid phosphatase activity, and P fractions (labile, moderately labile, non-labile, and residual). Agroforest soils retained physicochemical and enzymatic attributes similar to the primary forest, while soils of the citrus plantation showed increased P in all fractions due to mineral fertilization and reduced soil organic matter content, mainly in deeper layers. Microbial and LMWC composition patterns reflected land-use, with agroforest representing an intermediate state between primary forest and citrus monoculture. Pseudomonadota and nutrient-rich LMWC were more abundant in the agroforest, whereas Ascomycota and nutrient-poor LMWC predominated the citrus plantation. Genes related to "P acquisition" were more abundant in forest and agroforest soils, while genes related to "P-compound synthesis" were more abundant in the citrus plantation. Labile P was negatively correlated with genes related to microbial metabolism, suggesting that reduced P availability may induce a boost in microbial activity for internal P-cycling. These findings demonstrate that forest-to-agriculture conversion strongly affects microbial functions, with responses aligning with land-use intensity and LMWC resource availability. Nonetheless, microbes adapt by shifting strategies: prioritizing mineralization and solubilization or favoring biosynthesis depending on P availability.},
}

@article {pmid41755800,
year = {2026},
author = {Ding, J and Wang, M and Xu, X and Wang, D and Chen, X and Li, S and Zheng, X and Che, Y and Deng, Y and Lam, TTY and Li, L and Zhang, T},
title = {Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e08389},
doi = {10.1002/advs.202508389},
pmid = {41755800},
issn = {2198-3844},
support = {T21-705/20-N//Theme-based Research Scheme/ ; 17202522//General Research Funds/ ; COVID1903015//Health and Medical Research Fund/ ; },
abstract = {The increasing global burden of antimicrobial resistance (AMR) has been identified as a critical public health crisis, necessitating the development of robust, real-time surveillance frameworks to evaluate AMR dynamics. Sewage surveillance is emerging as a promising tool that utilizes sewage fingerprinting to provide comprehensive and unbiased information on antibiotic resistance genes (ARGs) within human populations. Here, we conducted a large-scale, year-long field surveillance of resistome in the community sewage using both short- and long-read metagenomic sequencing. We examined samples collected from 95 geographically distributed sites across Hong Kong, covering a population of 4.8 million residents, during summer and winter seasons. Our findings revealed distinct seasonal patterns through high-resolution resistome profiling. We found that the resistome structures shifted from the community sewage collected at sewer manholes to the influent of wastewater treatment plants (WWTPs), driven by taxonomic variation. Notably, community sewage exhibited a significantly higher similarity to the resistome of human feces than WWTP influent, which provides insights for selecting suitable sampling sites for epidemiological ARG surveillance. The application of long-read sequencing markedly enhanced our understanding of the phylogenetic diversity of ARG hosts and uncovered a broad spectrum of potentially mobile ARGs with varied genetic backgrounds. Furthermore, we observed multiple local ARG transmission patterns and subsequently evaluated their potential threats to public health based on the gene trees to inform future epidemiological control strategies. Overall, this work expands our current understanding of community sewage for population-level AMR monitoring and establishes a baseline for advancing sewage surveillance efforts to better combat AMR.},
}

@article {pmid41754611,
year = {2026},
author = {Anderson, M and Orf, GS and Holzmayer, V and Olivo, A and Harris, BJ and Berg, MG and Yu, G and Achari, A and Federman, S and Chiu, CY and James, L and Mampunza, S and Cloherty, GA and Rodgers, MA},
title = {Next-Generation Sequencing Reveals Continued Circulation of Rare HIV-1 Subtypes in the Democratic Republic of the Congo and Refines the Estimate of the Emergence Dates of Three Subtypes.},
journal = {Viruses},
volume = {18},
number = {2},
pages = {},
pmid = {41754611},
issn = {1999-4915},
support = {NA//Abbott/ ; },
abstract = {HIV-1 diversified for decades within the Democratic Republic of the Congo (DRC) before spreading globally in the early 1980s. Thus, the DRC is home to some of the most ancestral and diverse HIV-1 strains. Recent serosurveys conducted from 2017 to 2019 in Kinshasa, DRC, indicated high prevalence of HIV-1, yet sequence data is lacking from this period. Given the history of circulating rare HIV-1 subtypes in the DRC, a viral whole-genome sequencing study was conducted to determine current diversity in the greater Kinshasa area. Next-generation sequencing (NGS) through metagenomic and target enrichment methods was conducted on 197 specimens collected from 2017 to 2019. A large array of HIV subtypes (A, B, C, D, F1, G, H, J, and K), circulating recombinant forms (CRF01_AE, CRF02_AG, CRF05_DF, CRF11_cpx, CRF13_cpx, CRF25_cpx, CRF 45_cpx, and CRF92_C2U), unique recombinant forms, and unclassifiable sequences were observed, with many branching in basal positions within, or outside of, many subtypes on phylogenetic trees. Incorporating these new sequences into Bayesian inference of phylogeny pushes back the dates of the most recent common ancestors of HIV-1 group M and the rare subtypes G, H, and J by between 3 and 7 years each. The DRC continues to harbor diverse and rare HIV-1 subtypes that could challenge diagnostic tests, treatments, and vaccines. In addition to shifting subtype emergence dates, the sequences from our study are evidence that rare strains continue to circulate and should be regularly monitored.},
}

@article {pmid41754608,
year = {2026},
author = {Zheng, H and Shankar, A and Osis, G and Burgin, A and Sheth, M and Kiani, KG and Duong, YT and Cowan, D and Switzer, WM},
title = {Identification of Significant Genomic Changes and Compartmentalization of Simian Foamy Virus in a Human Zoonotically Infected by a Chimpanzee (Pan troglodytes troglodytes).},
journal = {Viruses},
volume = {18},
number = {2},
pages = {},
pmid = {41754608},
issn = {1999-4915},
abstract = {Despite increasing reports of zoonotic simian foamy virus (SFV) infections globally, knowledge of its genetic adaptation in humans and impact on viral transmission and pathogenicity remains limited. We obtained complete SFV genomes using metagenomics analysis of viral isolates from peripheral blood lymphocytes (PBLs) and throat specimens from a worker (Case 6) and source chimpanzee (B1) that bit him. We analyzed viral diversity in three genomic regions (LTR, tas, and bet) involved in replication and latency using longitudinal specimens (PBLs, throat, saliva, urine, and semen) from Case 6 over five years, and PBLs from B1 and five additional chimpanzees over three years. Proviral loads were measured using a validated qPCR assay. Phylogenetic analysis revealed nearly identical SFV genomes in Case 6 and B1. Overall, bet sequences exhibited high genetic stability across body compartments and over time, with evidence of compartmentalization in Case 6 urine and semen specimens. G→A substitutions in GG and GA motifs in bet indicated heterogeneous APOBEC-associated editing across hosts and anatomical compartments following zoonotic transmission. Case 6 had significant deletions in the LTR region that were absent in B1 and other chimpanzees. Length variation in tas, including truncated forms, was observed across longitudinal specimens from Case 6, B1, and other chimpanzees. Proviral loads were consistently low and undetectable in most Case 6 urine specimens. Together, analysis of this SFV transmission pair identifies genomic changes likely to affect viral replication and persistence, highlighting mechanisms that may limit secondary transmission and pathogenicity of SFV in humans.},
}

@article {pmid41754522,
year = {2026},
author = {Atkins, H and Stegman, N and Putonti, C},
title = {Diverse Temperate Coliphages of the Urinary Tract.},
journal = {Viruses},
volume = {18},
number = {2},
pages = {},
pmid = {41754522},
issn = {1999-4915},
support = {1R15AI171873-05/NH/NIH HHS/United States ; },
abstract = {While Escherichia coli can be found in the bladders of females without lower urinary tract symptoms, its presence is often associated with urinary tract infections (UTIs). The genomic plasticity of E. coli, including urogenital strains, is largely shaped by the integration of prophages. Although genomic and metagenomic analyses of urinary E. coli and the urinary microbiome suggest that prophages are abundant, many represent uncharacterized species. Sequence analysis suggests that these prophages represent temperate phages. This study aimed to fill this gap, isolating and characterizing temperate phages from urinary E. coli strains. We assessed phage host range across a panel of urinary isolates, providing a critical first step for future work investigating their putative role in shaping E. coli populations within the urinary community. In total, 20 temperate urinary phages were evaluated. Phage morphology and genic content of these phages were determined via transmission electron microscopy (TEM) and whole-genome sequencing, respectively. Together, these analyses provide insight into the diversity, infectivity, and genomic composition of temperate coliphages from the female urinary tract.},
}

@article {pmid41754515,
year = {2026},
author = {Zaluzhnyi, V and Verhoeven, JTP and Stenson, GB and Lang, AS and Dufour, SC and Canuti, M},
title = {Characterization of a Novel, Highly Divergent Paramyxovirus Discovered in a Bearded Seal of Subarctic Canada.},
journal = {Viruses},
volume = {18},
number = {2},
pages = {},
pmid = {41754515},
issn = {1999-4915},
support = {RGPIN 2020-04131 (S.C.D.)//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Seals are keystone animals in the Arctic and a valuable resource for Indigenous communities, but their virome is poorly understood. Through a preliminary investigation of the virome of seven North Atlantic bearded seals (Erignathus barbatus) from northwest Newfoundland, Canada, we discovered a new member of the Paramyxoviridae, a family including important animal pathogens. The complete coding genome sequence (15,898 nt) of the novel paramyxovirus, which we named bearded seal-associated paramyxovirus 1 (BSAPV-1), encoded five core paramyxoviral proteins-nucleoprotein, matrix, fusion, hemagglutinin-neuraminidase, and polymerase-and three proteins with no identifiable homologues that may represent the phosphoprotein, a small hydrophobic protein, and a transmembrane protein. Phylogenetic analysis, including BSAPV-1 and all 153 currently known paramyxoviral species, positioned the novel virus in a long-branched clade with Wenzhou Pacific spadenose shark paramyxovirus (Skoliovirinae, Scoliodonvirus scoliodontis), its closest relative (pairwise identity of the L protein: 30.1%). According to ICTV criteria, BSAPV-1 is likely the first member of a novel paramyxoviral subfamily. As the virus was found in combined tracheal/fecal swabs of a single animal, we could not conclude whether this is a seal virus or a virus associated with seal food. This study expands our knowledge about marine paramyxoviruses, and future studies should investigate BSAPV-1 ecology, spread, and host spectrum.},
}

@article {pmid41754473,
year = {2026},
author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A},
title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754473},
issn = {2076-0817},
abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.},
}

@article {pmid41754413,
year = {2026},
author = {Kibenge, F and Kibenge, M and Vargas, D and Godoy, M},
title = {Amarilloviruses of Aquatic Animals.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754413},
issn = {2076-0817},
support = {I-11251070//FONDECYT/ ; },
abstract = {The family Flaviviridae has been expanded to include the highly divergent flavi-like viruses into three new families, Flaviviridae, Pestiviridae, and Hepaciviridae, in the order Amarillovirales. Classical flavivirids are small, enveloped viruses with positive-sense ssRNA genomes lacking a 3' poly(A) tail and ~9.0-13.0 kb in length, with a single open reading frame (ORF) encoding structural proteins at the N-terminus and nonstructural proteins at the C-terminus. Members infect a wide range of mammals, birds, and insects, and many are host-specific and pathogenic. Although the RNA-directed RNA polymerase (RdRP) gene sequences of the flavi-like viruses group phylogenetically with those of classical flavivirids, flavi-like viruses often encode larger polyproteins and possess substantially longer genomes of up to ~40 kb, and some have a 3' poly(A) tail. Their host range extends across the whole animal kingdom and angiosperm plants. This review describes the reported flavi-like viruses of aquatic animals, providing a meaningful update on all three new families in Amarillovirales that have been discovered using metagenomics in fish, crustaceans, mollusks, and echinoderms. These amarilloviruses include pathogenic viruses of aquatic animals, such as Cyclopterus lumpus virus (CLuV) detected in moribund lumpfish, and infectious precocity virus (IPV) found in iron prawn syndrome (IPS)-affected farmed giant freshwater prawns.},
}

@article {pmid41754400,
year = {2026},
author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M},
title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754400},
issn = {2076-0817},
abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.},
}

@article {pmid41754394,
year = {2026},
author = {Rabello, E and de-Paris, F},
title = {Tuberculosis Diagnostic Methods: Clinical Applicability, Implementation Challenges, and Integrated Testing Strategies.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754394},
issn = {2076-0817},
support = {https://ror.org/010we4y38.//This research was funded by the Fundo de Incentivo à Pesquisa e Eventos (FIPE) from the Hospital de Clínicas de Porto Alegre (HCPA) - https://ror.org/010we4y38./ ; },
abstract = {Tuberculosis (TB) remains one of the leading causes of death from a single infectious agent worldwide, a burden further exacerbated by HIV co-infection and the increasing prevalence of drug-resistant strains. Although a wide range of laboratory diagnostic methods are currently available, their applicability, implementation, and clinical impact vary substantially across healthcare settings with different levels of complexity and resources. This review provides a comprehensive overview of the main laboratory diagnostic methods for active and latent TB, emphasizing their clinical applicability, implementation challenges, and role within integrated diagnostic strategies. Conventional approaches, such as smear microscopy and culture, are discussed alongside modern diagnostic technologies, including automated nucleic acid amplification tests (NAATs), loop-mediated isothermal amplification (LAMP), line probe assays (LPAs), next-generation sequencing (NGS), and lateral flow assays, highlighting their strengths and limitations in distinct epidemiological and operational contexts. Unlike existing WHO guidelines and prior reviews that predominantly focus on test performance and recommendation status, this review adopts an implementation-oriented perspective, critically examining diagnostic methods in light of real-world constraints, regional disparities, and evidence gaps. Particular attention is given to limitations related to laboratory infrastructure, biosafety, workforce capacity, and sustainability, as well as to under-addressed areas such as latent TB, metagenomic approaches, and the investigation of co-pathogens. By integrating WHO guidance with contextual and operational considerations, this review aims to support rational test selection and the development of flexible, integrated diagnostic workflows tailored to local health system capacity, patient populations, and clinical scenarios, thereby strengthening the effectiveness and equity of TB diagnostic strategies.},
}

@article {pmid41754175,
year = {2026},
author = {Wang, Z and Wei, J and Huang, Z and Liu, X and Li, S and Fang, Z and Hu, L and Li, R and Tao, L and Li, C and Chen, H},
title = {Metagenomics and Machine Learning Identify TMA-Producing Serratia Induced by High-Fat/Choline Diet: A Novel Obesity Target for TMA.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754175},
issn = {2072-6643},
support = {2023ZYD0129//Sichuan Province Central Leading Local Science and Technology Development Special Project/ ; 2024YFD2101003//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: High-fat diet-induced metabolic disorders are associated with trimethylamine (TMA)/trimethylamine N-oxide (TMAO), whose production is linked to gut microbial choline metabolism. However, changes in specific gut microbiota under a high-fat diet and the relationship between these changes and choline in TMA/TMAO production remain unclear.

METHODS: A total of 48 7-week-old male C57BL/6J mice were subjected to one-week acclimatization feeding, and then randomly divided into four groups (12 mice per group) to establish a 2 × 2 factorial design animal experiment: the control group (CON, basal diet), the choline-supplemented control group (CON + C, basal diet supplemented with 1% choline), the high-fat diet group (HF, high-fat diet), and the high-fat plus choline group (HF + C, high-fat diet supplemented with 1% choline). The experiment lasted for 9 weeks, during which dynamic monitoring of TMAO levels in mice was performed in the first 4 weeks. At the ninth week, the mice were sacrificed and samples were collected for subsequent assays, including the concentrations of TMA and TMAO in serum, colonic contents and feces; the pathological morphology of liver tissue, adipocyte staining characteristics and serum biochemical parameters; and the expression levels of key genes and proteins in liver, small intestine and colon tissues. Meanwhile, metagenomic analysis was conducted on colonic contents, combined with machine learning to predict the correlation between gut microbiota and TMA. In addition, gene cloning, multiple sequence alignment, molecular simulation and in vitro culture experiments were carried out to verify the TMA-producing function of the target strain.

RESULTS: This study elucidated that high-fat diet and high choline exert a significant interaction in TMA/TMAO production through a 2 × 2 animal experiment; meanwhile, the significantly increased TMA/TMAO levels co-induced by the two factors further exacerbate metabolic disorders. Notably, through combined metagenomics and machine learning, we identified Serratia marcescens as the primary TMA-producing microorganism under high-fat/choline diet induction. In vitro cultures simulating the intestinal environment revealed that the TMA conversion ability of Serratia marcescens is time-dependent, reaching 60 ± 2.49% after 24 h of anaerobic culture with choline chloride. Multiple sequence alignment and molecular simulation further demonstrated that the CutC enzyme of Serratia marcescens has a conserved amino acid sequence and high affinity for choline.

CONCLUSIONS: We uncovered a two-factor synergistic effect of a high-fat/choline diet on TMA/TMAO, and for the first time identified the genus Serratia as a TMA-producing bacterium. These findings provide a new potential target for intervening in metabolic disorders mediated by high-fat diet-induced TMAO elevation.},
}

@article {pmid41754080,
year = {2026},
author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F},
title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754080},
issn = {2072-6643},
support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; },
abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.},
}

@article {pmid41753780,
year = {2026},
author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Dass, SC},
title = {Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753780},
issn = {2076-2607},
support = {2020-67017-30776//USDA-NIFA/ ; },
abstract = {Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage-bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction-modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria-phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms.},
}

@article {pmid41753775,
year = {2026},
author = {Galisteo, C and Puente-Sánchez, F and de la Haba, RR and Bertilsson, S and Ventosa, A and Sánchez-Porro, C},
title = {Uncovering the Prokaryotic Diversity of Hypersaline Soils of Odiel Saltmarshes Natural Area Through Metagenome-Assembled Genomes.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753775},
issn = {2076-2607},
support = {PID2020-118136GB-I00//MCIN/AEI/10.13039/501100011033/ ; PID2023-148654NB-I00//MCIN/AEI/10.13039/501100011033/ ; 2022-04801//Swedish Research Council (Vetenskapsrådet)/ ; PRE2018-083242//Spanish Ministry of Science and Innovation/ ; },
abstract = {The hypersaline soils of the Odiel Saltmarshes Natural Area in Southwest Spain harbor highly diverse microbial communities adapted to extreme conditions. However, their genomic diversity remains largely unexplored. In addition to high salinity, these soils are contaminated with heavy metals, creating a hostile environment of great interest for studying extremophilic microorganisms and their metabolic adaptations. This study aims to characterize the uncovered prokaryotic taxa as Candidatus species inhabiting the hypersaline soils of the Odiel Saltmarshes, based on their metagenomic assembled genomic sequences. The reconstructed genomes were assessed for quality based on completeness and contamination thresholds and subsequently taxonomically classified. Comparative genomic analysis of six high-quality MAGs revealed key metabolic traits related to survival under extreme salinity and heavy metal conditions. The findings provide new insights about microbial diversity of hypersaline environments and expand the catalog of known prokaryotic genomes. Detailed characterization of six novel Candidatus taxa highlights the unique adaptations of these microorganisms, enhancing our understanding of life in extreme habitats.},
}

@article {pmid41753762,
year = {2026},
author = {Labrín-Sotomayor, NY and Becerra-Lucio, PA and Ruiz-González, H and Peña-Ramírez, YJ},
title = {Taxonomic and Functional Diversity of Leaves and Stem Endophytes of Eight Agave Species.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753762},
issn = {2076-2607},
support = {YJPR 5103711808 2024-2025 and NYLS 5103711911 research grants//El Colegio de la Frontera Sur/ ; },
abstract = {More than 63% of Mexico's territory is classified as arid or semiarid, where plants belonging to the genus Agave have evolved. Adaptation to drylands resulted from biochemical, physiological, and anatomical properties shared with other crassulacean plants; however, microbial symbionts also play critical roles in plants' growth, health, and drought tolerance. To explore endophytic communities in Agave plants, we used a shotgun metagenomic approach. The taxonomic and functional diversity of endophytes were studied in the leaves and stem organs of Agave americana, A.angustifolia, A. fourcroydes, A. karwinskii, A. potatorum, A. tequilana, A. cupreata, and A. rodacantha. The microbial community structure did not differ significantly among species, regardless of geographic origin or local environmental conditions, whereas significant differences were observed between organs. We found 4058 genera shared among organs, of which 957 genera are exclusive to the stem and 492 to the leaves. The community analysis of stems and leaves identified bacterial genera, including Acinetobacter, Klebsiella, Escherichia, Corynebacterium, and Streptomyces. Significant differences were also observed between organs in the functional annotations. The dominant functional categories were associated with cell signaling and protein metabolism in both organs.},
}

@article {pmid41753740,
year = {2026},
author = {Machineski, GDS and Menoncin, AS and Leonardo, HCL and Colozzi Filho, A},
title = {Riparian Forest Restoration Drives the Recovery of Soil Chemistry, Microbial Community Structure, and Enzymatic Activity in the Itaipu Reservoir Protection Zone.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753740},
issn = {2076-2607},
support = {Vitorias 4500074504 Itaipu/IDR-Paraná-Fapeagro//ITAIPU Binacional Convênio/ ; },
abstract = {Riparian forests play a critical role in protecting soil and water resources and maintaining ecosystem stability. In this study, we evaluated the response of soil chemical and microbial attributes to different stages of riparian forest restoration in the protection zone of the Itaipu Reservoir (Brazil). Soil samples were collected during summer and winter from sites representing four restoration stages (initial, 3, 19, and 30 years), as well as from an adjacent agricultural field and a native forest used as reference systems. We assessed soil chemical properties, microbial biomass carbon, basal respiration, enzymatic activities, and the soil microbial community structure using 16S rRNA gene sequencing. Principal component analysis (PCA) revealed a clear restoration gradient, with older restored sites progressively converging toward the native forest condition. Soil chemical properties showed gradual recovery along the restoration trajectory, with increases in soil organic carbon, cation exchange capacity, and base saturation. In contrast, the availability of P, K, Ca, and Mg declined at early restoration stages and increased with restoration age. Microbial biomass carbon increased by approximately 60% from early restoration to native forest conditions, while metabolic quotients (qCO2) decreased, indicating greater microbial efficiency and reduced metabolic stress. Enzyme activities related to C, P, and S cycling increased by 1.5- to 3-fold with restoration age. Sequencing analyses indicated a progressive convergence of microbial community composition toward that of the native forest, driven by shifts in relative abundance and the enrichment of forest-associated taxa, such as Verrucomicrobia and Acidobacteria, at advanced restoration stages. Overall, long-term riparian forest restoration promoted substantial recovery of soil chemical fertility and microbial community structure and functioning, reinforcing the role of soil microbiota as a sensitive indicator of ecosystem resilience and restoration success.},
}

@article {pmid41753722,
year = {2026},
author = {Ayilaran, E and Kilonzo-Nthenge, A},
title = {Metagenomic Insights into Antimicrobial Resistance in Small-Scale Poultry and Cattle Farms.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753722},
issn = {2076-2607},
support = {2018-68006-28103//National Institute of Food and Agriculture/ ; Grant No. 2018-68006-28103//United States Department of Agriculture/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical challenge to global health, with food animal production systems recognized as significant reservoirs of antimicrobial-resistant bacteria. This study evaluated the prevalence and distribution of antimicrobial resistance genes (ARGs) and virulence factors (VFs) across small-scale poultry and cattle farms. A total of 468 samples (soil, feces, water, and natural land soil) were collected from four farms and analyzed using shotgun metagenomics. Proteobacteria (34.91%) were the dominant phylum across environments, followed by Cyanobacteria (15.67%), Actinobacteria (14.95%), Firmicutes (10.57%), and Bacteroidetes (8.69%). Tetracycline (33.41%) and beta-lactam (30.30%) resistance genes were the most abundant, with macrolide (9.32%) and aminoglycoside (8.39%) resistance also detected. Both tetracycline and beta-lactam resistance genes were significantly enriched across sample types (p < 0.05). The detection of diverse VFs alongside ARGs highlights the pathogenic potential of bacterial communities in these production systems. Collectively, the findings reveal that small-scale animal farms are reservoirs of AMR with implications for public health through foodborne transmission. Targeted surveillance and control measures are necessary to prevent the dissemination of ARGs into the broader food chain and to safeguard both human and animal health.},
}

@article {pmid41753703,
year = {2026},
author = {Zhang, L and Xu, L and Zhang, Z and Liu, Z and Chen, Y},
title = {The Remediation Mechanism of Soil Atrazine Contamination by Vermicompost: A Metagenomic Perspective.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753703},
issn = {2076-2607},
support = {XDA28110201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {Atrazine persistence poses serious environmental threats. This study used metagenomics and qPCR to elucidate the remediation mechanism of vermicompost in atrazine degradation pathways. Seven treatments were established: unsterilized soil (CKn); sterilized soil amended with 45 (SsV1), 60 (SsV2), and 75 (SsV3) days of vermicompost; and unsterilized soil with the same vermicompost (SnV1, SnV2 and SnV3). Vermicompost significantly restructured soil microbial communities. SsV1 exhibited the highest Proteobacteria abundance (51.38%), while SsV3 markedly increased Bacteroidetes abundance (10.34%). Functional annotation revealed that vermicompost enriched carbohydrate metabolism-related COG units and upregulated CAZymes (e.g., CE1 and CE10 families), providing energy support for degrading microbial communities. Regarding metabolic pathways, SnV2 exhibited the highest atrazine degradation abundance (2.94%), significantly enriching Bauldia (4.84 RPKM) for dechlorination. During cyanuric acid ring-opening, SnV3 significantly enriched Pseudorhodoplanes (12.14 RPKM). During terminal mineralization, SsV2 increased Caenimonas abundance (15.25 RPKM) and introduced the exogenous genus Pseudorhodoplanes (7.78 RPKM). qPCR confirmed SnV2's trzN (day 20) and atzB (day 40) reached 9.03 × 10[4] and 6.95 × 10[7] copies/g, respectively. These findings indicate vermicompost accelerated atrazine mineralization by enriching degradative microbial communities and promoting key functional gene expression, with 60-day vermicompost demonstrating superior performance. This study provides a robust theoretical framework for remediating atrazine-contaminated soil by vermicompost.},
}

@article {pmid41753674,
year = {2026},
author = {Ece, G and Aktaş, A and Koyuncu Özyurt, Ö and Demirbakan, H and Alışkan, HE and Sağlık, İ and Zorbozan, O and Çetin Duran, A and Uğur, AR and Öcal, D and Uzunoğlu, E and Kaya, E and Mutlu Sarıgüzel, F and Bayındır, F and Yetkin, G and Altındiş, M and Yenice Aktaş, S and Kula Atik, T},
title = {Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753674},
issn = {2076-2607},
abstract = {The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice.},
}

@article {pmid41753649,
year = {2026},
author = {Feng, Y and Liu, S and Ke, H and Li, H and Zhao, H and Dang, X and Mou, C and Zhou, J and Huang, Z and Deng, Y and Li, Q},
title = {A Pseudotumorous Syndrome Associated with an As-Yet-Unidentified Eukaryotic Parasite Causing Functional Gonadal Arrest in Largefin Longbarbel Catfish (Hemibagrus macropterus).},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753649},
issn = {2076-2607},
support = {2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
abstract = {This study presents the first documented case of a disease syndrome in cultured largefin longbarbel catfish (Hemibagrus macropterus). The condition is characterized by massive abdominal pseudotumor formation, severe cachexia, and functional gonadal arrest. Comprehensive pathological investigation revealed that the pseudotumor was encapsulated by fibroblasts and primarily composed of host-derived, poorly differentiated hyperplastic cells, interspersed with invasive, basophilic Type III cells. These cells and associated inflammatory-fibrotic lesions were also disseminated in the gill, kidney and spleen. Systematic diagnostic approaches, including microbiology and transmission electron microscopy, found no evidence of conventional bacterial or viral pathogens. Metagenomic analysis further supported these findings and suggested a link to infection by an as-yet-unidentified eukaryotic parasite, with Microsporidia or Ichthyosporea being the primary candidates. Functional (KEGG) profiling of the pseudotumor tissue further revealed a molecular signature consistent with active cellular proliferation and metabolism. We propose that the pseudotumor acts as a metabolically active "nutrient sink," driving the systemic catabolism that underlies the severe cachexia and reproductive arrest. This work provides the first case of a eukaryotic parasite-induced pseudotumorous syndrome in fish, which represents an emerging threat to conservation aquaculture and offering novel insights into parasite-mediated host metabolic hijacking and tumor-mimicry.},
}

@article {pmid41753646,
year = {2026},
author = {Bosco, G and Vaccalluzzo, A and Russo, N and Pino, A and Caggia, C and Randazzo, CL},
title = {Effect of By-Products from Pistachio Skin on Gastrointestinal Microbiota of Healthy Lambs as Sustainable Feeding Ingredient.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753646},
issn = {2076-2607},
support = {Piano Nazionale Di Ripresa E Resilienza (PNRR) - Missione 4 Componente 2, Investimento 1.4 - D.D. 1032 17/06/2022, CN00000022//European Union Next-GenerationEU/ ; },
abstract = {Pistachio skin is a by-product that is considered a promising novel feed ingredient for ruminants; however, its role in shaping the lamb gastrointestinal tract microbiota is poorly studied. The present study aimed to investigate, through a metagenomics approach, the effects of integrating pistachio skin into the diet on the faecal and ruminal microbiota of healthy lambs. Faecal samples, collected at the beginning (d0) and 58 days after the start of the dietary treatment (d58), and ruminal samples, collected after slaughter, were subjected to Illumina MiSeq analysis of the 16S rRNA gene. The results revealed that, although temporal variations were observed, the supplementation of pistachio skin did not markedly affect the overall faecal microbiota structure. Conversely, specific rumen taxa were selectively modulated by the experimental diet. In conclusion, the use of pistachio skin as a feed ingredient can be considered a suitable and sustainable dietary strategy that modulates specific rumen microbial groups, thereby preserving the stability of the gut microbiota in lambs.},
}

@article {pmid41753645,
year = {2026},
author = {Liu, M and Zhao, L and Li, T and Li, X and Jiang, H and Yang, P},
title = {Deciphering the Arterial and Venous Blood Bacterial DNA Profile: Pioneering Insights into Coronary Heart Disease Etiology and Progression.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753645},
issn = {2076-2607},
support = {2023YFC3503702//National Key Research and Development Program of China/ ; No. ZRJY2023-QM11//Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; },
abstract = {BACKGROUND: Coronary heart disease (CHD) is the leading cause of death and disability worldwide. The human microbiota, particularly gut bacteria, plays a role in the development of CHD. However, determining the contribution of gut bacteria translocation to systemic circulation in the progression of atherosclerosis remains challenging.

METHODS AND RESULTS: In this exploratory study, we conducted 16S rRNA-based metagenomic analysis to characterize systemic bacterial profiles in a cohort of 27 patients with CHD (9 with severe coronary artery stenosis and 18 with mild to moderate stenosis). We compared microbial diversity between arterial and venous blood and across different blood fractions. For the first time, we observed higher microbial diversity in plasma than in serum. We also identified differences in microbial richness among arterial whole blood, venous whole blood, arterial plasma, venous plasma, arterial serum, and venous serum, with 15, 22, 43, 10, 4, and 3 genera showing significant differences, respectively. Many of the detected blood taxa belonged to genera typically found in intestinal, oral, or skin microbiota, although their precise source cannot be determined from this study.

CONCLUSIONS: Our study provides preliminary evidence of distinct bacterial profiles between arterial and venous blood fractions in patients with CHD, as determined by 16S rRNA sequencing. These findings should be interpreted with caution given the small sample size and the absence of a healthy control group, and they warrant confirmation in larger, controlled studies.},
}

@article {pmid41753632,
year = {2026},
author = {Wang, M and Tian, W and Liu, Z and Yan, D and Li, Y and Cao, A and Wang, Q and Fang, W},
title = {Differential Selection Effects of Continuous AITC Fumigation on Soil Microbial Communities and Functions and Identification of Tolerant Strains.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753632},
issn = {2076-2607},
support = {2024YFD1701900//The National Key R&D Program of China/ ; 32572893//The National Natural Science Foundation of China/ ; CAAS-CSAL-202401//The Innovation Project of the Chinese Academy of Agricultural Sciences/ ; },
abstract = {Allyl isothiocyanate (AITC) is effective as a bio-based fumigant in controlling soil-borne diseases; however, the selective pressure it exerts on soil microecology and evolutionary dynamics remains inadequately characterized. This study systematically investigated the remodeling effects of continuous AITC fumigation on soil microbial communities, functional genes, and functional strains by integrating metagenomic analysis and pure culture techniques. Results demonstrate that AITC drives directional selection from "sensitive" to "tolerant" microorganisms. Fungal communities exhibit greater cumulative damage than bacterial communities, with the proportion of significantly suppressed fungi increasing linearly from 9.3% at baseline to 35.7%. At the genus level, sensitive groups were predominantly enriched in pathogen-associated genera, e.g., Pseudomonas and Xanthomonas, whereas tolerant groups, represented by Bacillus and Streptomyces, maintained ecological dominance under continuous stress. Functionally, AITC induced differential evolution of functional gene repertoires. Nitrogen cycle genes (e.g., amoC) exhibited high negative sensitivity, with significant downregulation by 20%, whereas the TCA core module in the carbon cycle exhibited strong robustness. Virulence assays confirmed EC50 values for tolerant beneficial bacteria (Bacillus spp.) (>40 mg·L[-1]) were significantly higher than those for pathogens (1.3-7.9 mg/L). This study established a microbial "sensitive-tolerant" response framework under AITC stress, revealing the core potential of endogenous tolerant strains for the precise ecological restoration of fumigated soils.},
}

@article {pmid41753628,
year = {2026},
author = {Meinen-Jochum, J and Satheesh, V and Masonbrink, RE and Rodriguez-Gallegos, J and Wright, DA and Severin, AJ and Mellata, M},
title = {Sequencing and Analysis of Chicken Segmented Filamentous Bacteria Genome Revealed Unique Avian-Specific Features.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753628},
issn = {2076-2607},
support = {20236701539078//U.S. Department of Agriculture's National Institute of Food and Agriculture/ ; },
abstract = {Segmented filamentous bacteria (SFB) are host-specific, immune-modulating microorganisms that colonize the small intestine of various vertebrate species, playing a crucial role in stimulating immune maturation during early life. Previous research on the genomes of SFB from humans, rats, and mice has revealed significant differences among SFB strains associated with various hosts, suggesting that their evolution is closely linked to their relationships with specific hosts. However, the genome of SFB from chickens has not been extensively investigated. In this study, we present the metagenomic reconstruction of an SFB genome derived from the ileum of layer Lohmann Select Leghorn (LSL) chickens. We utilized Hi-C sequencing techniques to assemble the LSL-SFB and annotate the avian SFB from both turkeys and chickens. Our reference-guided consensus assembly, followed by Hi-C scaffolding, produced a high-quality genome for LSL-SFB. Our pangenomic analysis revealed substantial conservation of core gene clusters among mammalian SFB strains, but we also identified a distinct repertoire of genes in chicken and turkey SFB. Furthermore, metabolic network analysis indicated a reduced capacity for biosynthesis, signifying an increased reliance on the host, as shown by the absence of key biosynthetic and utilization pathways. We also discovered a unique flagellin subunit (fliC-2) in chicken SFB from different genetic lines and confirmed its interaction with the chicken flagellin receptor, Toll-like receptor five. This study provides the first high-quality genome and annotation of LSL-SFB, alongside that of turkeys, offering valuable insights into the mechanisms of host specificity and adaptation. Understanding the interactions between host-specific SFB and their hosts, as well as their role in promoting immune maturation, is essential for improving intestinal health.},
}

@article {pmid41753592,
year = {2026},
author = {Özdemir, K},
title = {Characterization of a Boron-Tolerant Nocardia niigatensis Isolated from Boron-Rich Soils: Physiological, Enzymatic, and Genomic Insights.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753592},
issn = {2076-2607},
support = {BAP-19-1003-003//Bandırma Onyedi Eylül University Scientific Research Projects Coordination Unit (BAP)/ ; },
abstract = {In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective isolation techniques were employed to obtain Nocardia isolates, and species-level identification was achieved using both 16S rRNA gene sequencing and MALDI-TOF MS analysis, which consistently confirmed the isolate as N. niigatensis. In addition to molecular identification, the morphological, physiological, and biochemical characteristics of the strain were extensively investigated. The strain demonstrated notable boron tolerance, exhibiting robust growth at concentrations up to 50 mM, highlighting its potential applicability in the bioremediation of boron-contaminated environments. Physiological assays further revealed moderate halotolerance and a mesophilic growth profile, with optimal growth observed at 27-37 °C. Enzymatic screening indicated positive L-glutaminase activity, an enzyme of considerable industrial relevance. Moreover, API ZYM profiling revealed a broad enzymatic spectrum, including esterases, arylamidases, phosphatases, and glucosidases, suggesting substantial metabolic versatility. Antibiotic susceptibility testing showed sensitivity to doxycycline, tobramycin, and erythromycin, whereas resistance was observed against imipenem and several β-lactam antibiotics. Metagenomic analysis of boron-rich soils from two distinct mining sites revealed marked differences in microbial community composition, with variations in Actinobacteria abundance associated with mineral type. Overall, these findings emphasize the adaptive capacity and biotechnological potential of environmental Nocardia strains inhabiting chemically stressful ecosystems, warranting further genomic and metabolomic investigations.},
}

@article {pmid41753552,
year = {2026},
author = {Shulga, EY and Islamov, BR and Sukhanov, AY and Frolov, M and Laikov, AV and Trachtmann, NV and Validov, SZ},
title = {Biotechnological Potential and Metabolic Diversity of Lignin-Degrading Bacteria from Decaying Tilia cordata Wood.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753552},
issn = {2076-2607},
support = {FMEG-2025-0028//The government assignment for the FRC Kazan Scientific Center of RAS/ ; },
abstract = {Lignin is a complex aromatic polymer that constitutes a major fraction of plant biomass and represents a valuable renewable carbon resource. Naturally decaying wood serves as an environmental reservoir of microorganisms capable of degrading lignin. In this study, we isolated and characterized sixteen bacterial strains from decaying Tilia cordata wood using an enrichment culture technique with lignin as the sole carbon source. Taxonomic identification via 16S rRNA gene sequencing revealed microbial diversity spanning the genera Bacillus, Pseudomonas, Stenotrophomonas, and several members of the Enterobacteriaceae family, including Raoultella terrigena isolates. Metagenomic sequencing of the wood substrate revealed an exceptionally rich and balanced bacterial community (Shannon index H' = 5.07), dominated by Streptomyces, Bradyrhizobium, Bacillus, and Pseudomonas, likely reflecting a specialized consortium adapted to lignin rich late-stage decay. Functional phenotyping demonstrated that all isolates possess ligninolytic potential, evidenced by peroxidase/laccase-type activity through methylene blue decolorization. Dynamic Light Scattering (DLS) and HPLC analyses showed that some isolates, such as Raoultella terrigena MGMM806, effectively depolymerized lignosulfonate into low molecular weight fragments (1.23 nm), while others accumulated intermediate metabolites or completely mineralized the substrate. Growth profiling on monolignol substrates revealed a broad spectrum of catabolic specialization in lignin monomer degradation. The results demonstrate a complex system of metabolic partitioning within a natural bacterial consortium. This collection represents a foundational genetic resource for developing engineered biocatalysts and synthetic microbial communities aimed at the efficient conversion of lignin into valuable aromatic compounds.},
}

@article {pmid41752933,
year = {2026},
author = {Mahbub, MH and Hase, R and Yamaguchi, N and Asai, Y and Harada, M and Ichimura, N and Hayakawa, Y and Inohana, Y and Umakoshi, Y and Yamaguchi, R and Kimura, R and Tsujimura, H and Matsumoto, M and Higashijima, F and Yoshimoto, T and Kimura, K and Hirano, T and Ohishi, K and Doi, K and Matsunaga, K and Tanabe, T},
title = {Gut Microbial Diversity and Community Structure Are Largely Similar Between Apparently Healthy Elderly Japanese Males and Females: A Shotgun Metagenomic Study.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {2},
pages = {},
pmid = {41752933},
issn = {2075-1729},
support = {21K10397//This research was supported by a joint project funded by Yamaguchi Prefecture, Yamaguchi City, Shimadzu Corporation, Kao Corporation, and Kyodo Milk Industry Co., Ltd. It was also supported by a Grant-in-Aid for Scientific Research from the Japan Society/ ; },
abstract = {Sex differences in gut microbiota may affect health and aging, but evidence in elderly populations is limited and inconsistent. This study examined sex-specific similarities and differences in gut microbiota diversity and composition among apparently healthy elderly Japanese individuals using shotgun metagenomic sequencing. A cross-sectional study was conducted in 100 community-dwelling adults aged 75-83 years (54 males, 46 females). Fecal samples underwent metagenomic sequencing. Alpha and beta diversity were assessed across six taxonomic levels, and taxonomic differences were evaluated using non-parametric tests. No significant sex differences were observed in alpha diversity indices (Shannon, Simpson, evenness, Chao1) at any taxonomic level. Beta diversity based on Bray-Curtis dissimilarity and PCoA also showed no sex-specific clustering. However, certain taxa differed in relative abundance. Males showed higher abundances of Bacteroidota (phylum), Bacteroidia and Betaproteobacteria (class), and Bacteroidales and Burkholderiales (order) (p < 0.05). No significant differences were detected at the family, genus, or species levels. Overall, gut microbial diversity and community structure were largely similar between elderly males and females, with only modest sex-associated differences at higher taxonomic levels. These findings suggest that biological sex may have a limited influence on gut microbiota composition in advanced age and provide population-level reference data for future longitudinal and interventional studies in elderly cohorts.},
}

@article {pmid41752220,
year = {2026},
author = {Kareem, HA and Khan, MF},
title = {Current Research Advances and Future Prospects on Microbial Consortia for Sustainable PFAS Remediation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752220},
issn = {1422-0067},
support = {82930-NP//University College Dublin Internal Fund/ ; },
abstract = {Soil contamination by per- and polyfluoroalkyl substances (PFAS) represents a pressing environmental and public health concern due to the exceptional persistence of carbon-fluorine bonds, which prevent natural attenuation and limit the effectiveness of conventional remediation. Agricultural and industrial soils serve as long-term sinks for PFAS, continuously releasing these pollutants into groundwater and facilitating their transfer through the food chain. Conventional chemical and physical remediation methods are often costly, energy-intensive, and yield incomplete removal, underscoring the need for sustainable and biologically driven alternatives. Microbial consortia have emerged as a promising solution due to their metabolic complementarities, cross-feeding interactions, and ecological resilience, which together enable PFAS transformation and partial defluorination under complex soil and subsurface conditions. Key enzymes such as oxygenases, reductive dehalogenases, and hydrolases are often operating within co-metabolic networks, which play central roles in these processes. Advances in metagenomics, CRISPR-based functional screening, and metabolic modelling are rapidly uncovering novel PFAS-degrading microbes and pathways. Integration of machine learning with multi-omics and environmental datasets further enables the prediction of degradation mechanisms, identification of keystone degraders, and rational design of synthetic consortia. Emerging sustainable strategies, including biochar- and nutrient-amended soil microcosms, plant-microbe partnerships for coupled soil-groundwater phytoremediation, and bioelectrochemical systems that offer new avenues for enhancing PFAS biodegradation in situ. This review synthesises recent research progress and provides critical perspectives on the mechanistic, ecological, and engineering dimensions of PFAS bioremediation, proposing an integrated conceptual framework linking microbial consortia dynamics, enzymatic pathways, and environmental engineering interventions to guide scalable field applications and sustainable management of PFAS-contaminated soil-groundwater ecosystems.},
}

@article {pmid41752202,
year = {2026},
author = {Jung, S},
title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752202},
issn = {1422-0067},
support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; },
abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.},
}

@article {pmid41751141,
year = {2026},
author = {Xue, F and Zhang, F and Zhuang, Q and Jiang, L and Sun, M and Shang, J and Xiong, B},
title = {Metagenomic Insights into the Modulatory Effects of Thiamine Supplementation for Treating Subclinical Ketosis Dairy Cows.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {4},
pages = {},
pmid = {41751141},
issn = {2076-2615},
support = {20242BAB20311//Natural Science Foundation Project of Jiangxi Province/ ; 2024YFD1300600//Integrated Demonstration of Intelligent Feeding and Environmental Control Technologies for Cattle and Sheep/ ; },
abstract = {(1) Background: The objective of this study was to investigate the modulatory effects of thiamine on BHBA metabolism, milk yield, and the rumen microbial ecosystem. (2) Methods: A total of 24 SCK dairy cows with similar body conditions were selected and randomly allocated to SCK (SCK) or SCK with thiamine supplement (SCKT) treatment. Twelve healthy dairy cows served as the control (CON) treatment. Milk yield, milk quality, ruminal fermentability parameters, rumen and fecal microbial communities were further measured. (3) Results: Thiamine significantly decreased BHBA content, milk CFUs, and somatic cells, while significantly increasing milk yield, milk fat, acetate, and the A/P ratio (p < 0.05). Thiamine-treated cows exhibited significantly increased ruminal and fecal Proteobacteria but significantly decreased ruminal Firmicutes (p < 0.05) as well as fecal Spirochaetes and Cyanobacteria (p < 0.05), compared with SCK cows. Functional analysis showed that differential rumen bacteria exhibited high energy metabolism, nucleotide metabolism, and glycan biosynthesis and metabolism, while the metabolism of terpenoids and polyketides were the primary functional pathways of differential fecal microbiota. (4) Conclusions: Thiamine supplementation in SCK cows effectively alleviated subclinical ketosis by reducing BHBA content, enhancing ruminal fermentability, and proliferating rumen microbial communities, leading to improved milk yield in the early-lactation period.},
}

@article {pmid41751138,
year = {2026},
author = {Xu, Z and Liang, M and Li, J and Song, B and Zhang, M and Jiang, H and Chai, J and Zhao, J and Deng, F and Li, Y},
title = {16S rRNA Gene and Metagenomic Analysis Revealed an Association Between Cecal Microbiota and Pork Umami.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {4},
pages = {},
pmid = {41751138},
issn = {2076-2615},
support = {2023YFE0124400//National Key Research and Development Program of China/ ; 2023B10564001//Specific University Discipline Construction Project/ ; No. 32202715//National Natural Science Foundation of China/ ; },
abstract = {Umami is a key determinant of pork flavor, but the association between the intestinal microbial community and umami differences remains unclear. Here, we used the taste-sensing electronic tongue system to divide the Duroc × Landrace × Yorkshire pigs into high, medium and low groups. We combined 16S rRNA gene and shotgun metagenomic sequencing to study the differences in the microbial community composition and functional genes. The results showed that the microorganisms in the cecum of different groups had a similar core microbial community. The Shannon diversity analysis showed that there were no significant differences among the different groups. The Bray-Curtis distance indicated that there were differences in the bacterial communities between the high umami group and the other two groups. The LEfSe analysis and Spearman correlation analysis revealed that the uncultured species CAG-632 sp900539185 maintained a high abundance in the high umami group and was significantly correlated with umami. Metagenomic functional analysis revealed distinct functional signatures among umami groups, with enrichment of genes related to carbohydrate transport and metabolism, butanoate and other short-chain fatty acid pathways, nitrogen utilisation, cell-surface structures, adhesion and RNA metabolism in high umami groups. These research findings indicate that the differences in the delicious flavor of pork are more likely to be associated with specific microbial species and the functional characteristics of the cecal microbial community, rather than the overall situation of the entire microbial community.},
}

@article {pmid41751100,
year = {2026},
author = {Yang, L and Xu, Z and Liu, D},
title = {The Effects of Dual-Yeast Compound Preparation on the Intestinal Health and Metabolism of Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {4},
pages = {},
pmid = {41751100},
issn = {2076-2615},
support = {NDYB2022-5//Inner Mongolia Agricultural University High-level/excellent Doctoral Talent Introduction Research Project/ ; BR230118//University Basic Scientific Research Business Expenses Project-Young Teachers Research Ability Enhancement Fund Project, 2023 Financial Funds/ ; 2025MS03114//Natural Science Foundation of Inner Mongolia Autonomous Region Project/ ; SYKJZD202302//Discipline Project of College of Veterinary Medicine, Inner Mongolia Agricultural University/ ; },
abstract = {Microecological preparations exert beneficial effects on the health of young ruminant animals; however, the mechanism is unclear. As a result, the present study analyzed the effects of yeast cultures on the growth properties, microbiome, and metabolism of weaned lambs. In this study, a total of 20 weaned lambs were randomly, stochastically divided into four teams: the control group (Group A) were fed a basic diet; Group B were fed with Saccharomyces cerevisiae BC strain culture (30 g/head/d); Group C were fed with Kluyveromyces marquez XR4 strain culture (30 g/head/d); Group D were fed with a composite culture of the two yeast strains (30 g/head/d). The study lasted for 40 days, with daily records of lamb feed intake and weight. Lamb feces were collected regularly for metagenomic sequencing and metabolomics analysis. The average daily weight gain and average daily yield of Group D lambs were significantly higher than those of Group A lambs (p < 0.01). The feed utilization rate in the yeast-fed groups was considerably higher than in the control group (p < 0.05), indicating that the addition of yeast crops to lamb feed might improve lamb feed performance. Bacteroides and the mTOR signaling pathway were dramatically enriched in the intestines of weaned lambs in the yeast-culture-fed groups, and their expression levels of ketones and benzoic acid compounds were significantly upregulated. These results indicated that yeast culture had excellent effects on weaned lambs in regulating immunological functioning and the intestinal environment, protecting the enteric mucosal barrier, improving digestion and nutritional absorption, and enhancing antioxidant function. In summary, adding yeast culture to weaned lamb feed can generate a positive effect on its productivity performance and gut health. These findings provide novel insights into promoting the health of young ruminants.},
}

@article {pmid41751034,
year = {2026},
author = {Wang, J and Cheng, M and Huang, F and Chen, L and Xu, W and Cai, J and Chen, Z and Zhao, Y and Zhang, X},
title = {Metagenomic-Metabolomic Integration Reveals Gut Microbiota Dynamics and Metabolic Changes in Super-Geriatric Captive Giant Pandas.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {4},
pages = {},
pmid = {41751034},
issn = {2076-2615},
support = {2025ZNSFSC0252//the Science and Technology Project of Sichuan Province/ ; },
abstract = {Age-related changes throughout the lifespan are known to influence gut microbiota composition, microbial functional potential, and host-associated metabolic processes. Understanding these age-related variations is important for elucidating their potential physiological implications at different life stages. However, information regarding the gut microbiome and metabolomic characteristics of super-geriatric captive giant pandas (Ailuropoda melanoleuca) remains limited. In this study, fecal samples were collected from adult and super-geriatric captive giant pandas and analyzed using metagenomic sequencing combined with untargeted metabolomics. The gut microbiota of super-geriatric individuals exhibited a marked decrease in Bacillota and an enrichment of Pseudomonadota compared with adult individuals. Functional profiling revealed age-associated shifts in microbial metabolic potential, with a transition from biosynthesis-dominated pathways toward pathways related to substrate degradation and energy utilization. Metabolomic analyses further revealed pronounced metabolic alterations in super-geriatric giant pandas, including elevated levels of unsaturated fatty acids and changes in bile acid-related metabolites. Alterations in gut microbiota composition, particularly the relative enrichment of Pseudomonadota-associated taxa, were associated with inflammation-related metabolic features. Collectively, these findings indicate coordinated changes in gut microbial composition and metabolic profiles during aging. Overall, this study characterizes age-associated alterations in gut microbiota structure and fecal metabolic signatures in super-geriatric captive giant pandas, providing a scientific basis for future studies on microbiota-metabolism interactions and for improving nutritional management and health monitoring strategies in aged individuals of this endangered species.},
}

@article {pmid41750879,
year = {2026},
author = {Samantaray, P and Saha, S},
title = {Decoding the Microbial Diversity of Indian Fermented Foods: Integrating Ethnobiology, Multi-Omics and Functional Insights.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {41750879},
issn = {2304-8158},
support = {SRMAP/URG/SEED/2023-24/049//SRM University Andhra Pradesh/ ; },
abstract = {India's diverse culinary heritage includes a wide spectrum of traditional fermented foods that harbour complex microbial communities essential for flavour development, preservation, and nutritional enhancement. These microorganisms-primarily lactic acid bacteria, yeasts, and molds-contribute functional properties that extend beyond food transformation to confer health benefits, including probiotic potential and metabolic regulation. This review integrates classical microbiological studies with modern molecular approaches such as metagenomics, metatranscriptomics, and metabolomics to elucidate the microbial diversity of Indian fermented foods. It highlights how geography, substrates, and ethnic traditions shape region-specific microbial consortia sustained through long-standing ethno-microbiological practices. Special focus is given to the glycemic modulation achieved through microbial fermentation, wherein organic acid production and resistant starch formation lower glycemic index and improve glucose metabolism. These processes, along with enhanced nutrient bioavailability, vitamin synthesis, and immunomodulation, illustrate the broader functional potential of fermentation. The review also examines interactions between food-borne microbes and the human gut microbiota, underscoring implications for personalized nutrition. Finally, it discusses modernization and commercialization strategies and outlines future directions involving multi-omics integration, indigenous starter cultures, and microbiome-based innovations to harness India's microbial heritage for improved health and sustainable food development.},
}

@article {pmid41750451,
year = {2026},
author = {Agga, GE and Loughrin, J},
title = {Evaluation of Anaerobic Digestion Amended with Micro-Aeration and/or Sound Treatment on the Resistome and Virulence Factor Gene Profiles in Poultry Litter.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41750451},
issn = {2079-6382},
support = {5040-12630-007-000-D//U.S. Department of Agriculture, Agricultural Research Service/ ; },
abstract = {Background: Commercial broiler farms produce a large amount of litter that must be removed. Anaerobic digestion (AD) is animal manure management technology with the added benefit of producing reusable energy. Our team previously showed that the micro-aeration and sound treatment of animal manure during AD increase biogas production. However, their influence on antimicrobial resistance genes (ARGs) and bacterial virulence factor genes (VFGs) is unknown. Therefore, the objective of this study was to evaluate the effect of AD on the resistome and VFGs in poultry litter (PL) and see if the effect is modified by micro-aeration and/or sound treatments. Methods: A field experiment was conducted in four anaerobic digesters that consisted of a control (a standard AD system with no air or sound), micro-aeration, sound, and combined micro-aeration and sound treatments. Overall, 21 samples were collected and analyzed with shotgun metagenomic sequencing. The samples included digestate samples (n = 12) from the four digesters obtained at 6 (baseline, i.e., before beginning of micro-aeration and sound treatments), 23 and 42 weeks, raw PL samples (n = 4), two disks comprised of the same wood as the bedding material, an initial digestate seed sample, and two initial week 0 mix samples. Results: Across all sequence reads (n = 3190) obtained from 21 samples, over 80% of the resistome was composed of four antimicrobial classes: macrolides-lincosamides-streptogramins, tetracyclines, aminoglycosides, and glycopeptides. While the total number of ARGs declined in the control digestor, it increased over time in micro-aerated or sound-treated digesters, and their combination greatly increased the number of ARGs detected. This is a new finding, and it clearly shows that micro-aeration, sound, and their combination treatment during the anaerobic digestion of PL enriches ARGs. In contrast, sound-treated AD by itself significantly (p = 0.035) reduced the mean total ARG abundance compared to the control. The number and abundance of ARGs detected in the initial digestate and PL were lower than those in the AD samples, indicating their enrichment during the AD process. On the other hand, although the AD samples had a lower frequency and abundance of VFGs than the PL, AD did not completely remove the VFGs, and their detection frequency increased over time. While micro-aeration increased the abundance of VFGs compared to the control, this effect was countered by its combination with sound treatment, offering a good animal manure treatment strategy to reduce bacterial VFGs. Conclusions: Although additional research may be required, it was shown that while sound treatment may enrich the occurrence of ARGs, it seems promising to reduce the abundance of ARGs and VFGs during the AD of PL. On the other hand, micro-aeration, alone or when combined with sound treatment, increases the abundance of both ARGs and VFGs. Moreover, the study showed that AD, with or without micro-aeration and sound treatment, is not effective for the complete removal of ARGs and VFGs from poultry litter. Rather, AD systems may act as a hotspot for ARGs, and post-AD treatments such as composting need to be evaluated.},
}

@article {pmid41750446,
year = {2026},
author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Ferrante, M and Agodi, A},
title = {The Wastewater Resistome: A Shotgun Metagenomics Analysis of Urban Treatment Plants in Sicily.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41750446},
issn = {2079-6382},
support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) in wastewater represents a valuable reservoir of information for wastewater-based epidemiology (WBE) and a major environmental and public health concern, as wastewater treatment plants (WWTPs) are recognized hotspots for the accumulation and dissemination of antimicrobial resistance genes (ARGs). Within the One Health framework, and to better understand the contribution to AMR spread and the potential of metagenomic surveillance, this study aimed to characterize the taxonomic, functional, and resistome profiles of three WWTPs in Sicily, specifically those located in Catania, Giarre, and Syracuse. Methods: Sixty-nine composite influent samples were collected between February 2022 and December 2023. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq platform. Bioinformatic analyses were conducted to assess microbial community composition, functional pathways, and ARG prevalence across sites. Results: Dominant genera included Aliarcobacter, Bacteroides, and Acinetobacter. Site-specific taxonomic variations reflected differences in local microbial ecology. Functional profiling revealed enrichment in membrane-associated, ribosomal, and energy metabolism pathways, consistent with the expected functional redundancy of wastewater microbiomes. Resistome analysis detected a diverse and ubiquitous array of ARGs, dominated by β-lactam and macrolide resistance genes, followed by aminoglycoside, sulphonamide, and tetracycline classes. Conclusions: These findings highlight urban wastewater as a relevant reservoir and dissemination route for AMR and support the integration of metagenomic approaches into wastewater surveillance programs. By providing region-specific, integrated taxonomic, functional, and resistome data from Sicilian WWTPs, this study contributes to the growing body of evidence supporting WBE as a valuable tool for AMR monitoring and One Health-oriented risk assessment.},
}

@article {pmid41750438,
year = {2026},
author = {Suzhaeva, L and Egorova, S and Polev, D and Saitova, A and Starkova, D},
title = {Fluoroquinolone Resistance Patterns in Multidrug-Resistant Escherichia coli from the Gut Microbiota of Young Children.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41750438},
issn = {2079-6382},
abstract = {Background/Objectives: The high prevalence of fluoroquinolone-resistant E. coli in healthy children represents a significant public-health risk, facilitating the spread of antimicrobial resistance and increasing the potential for difficult-to-treat extraintestinal infections with severe clinical outcomes. This study aimed to investigate the prevalence of fluoroquinolone resistance in multidrug-resistant E. coli isolated from presumptively healthy children in St. Petersburg, Russia, with a particular focus on fluoroquinolone resistance determinants. Methods: Phenotypic AST was performed on 307 E. coli isolates from fecal pediatric samples, comprising 230 isolates from 2012 to 2013 and 77 isolates from 2021 to 2022. A subset (n = 47) of MDR isolates underwent whole-genome sequencing. Results: The frequency of MDR E. coli strains rose significantly from 15.7% to 32.5% over the study period. The most significant increases in resistance among E. coli strains were to third-generation cephalosporins (CTX, CTZ) and fluoroquinolones (CIP), rising fourfold over a decade. Based on phenotypic resistance profiles of MDR E. coli to quinolones, the highest resistance rates were observed for MFX (80.9%) followed by NAL (74.5%), LVX (44.7%) and CIP (40.4%). Genotypic analysis revealed distinct pathways: low-level NAL resistance required only an S83 mutation in gyrA, whereas low-level MFX resistance was predominantly conferred by a plasmid-borne qnr gene. In contrast, resistance to CIP and LVX involved at least three QRDR mutations: S83L and D87N/Y in gyrA, and S80I in parC. Notably, our study showed the predominance of the ST131 and ST38 clones in E. coli isolated from pediatric samples. Conclusions: Our findings suggest that the efficacy of moxifloxacin for empirical treatment of infections caused by MDR E. coli might be severely compromised. Overall, the current study highlights that the pediatric gut microbiota serves as a reservoir for resistant E. coli with the expansion of multidrug-resistant clones independently of direct antibiotic selection pressure.},
}

@article {pmid41749685,
year = {2026},
author = {Zhu, Y and Tang, Y and Qi, X and Zhu, X},
title = {Transformer Models, Graph Networks, and Generative AI in Gut Microbiome Research: A Narrative Review.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
pmid = {41749685},
issn = {2306-5354},
support = {Grant No. LCMYZHYX-KFKT202303//Open Project of the Sichuan Provincial Key Laboratory for Clinical Immunology and Translational Medicine/ ; Grant No. 2022JC03//Scientific Research Foundation of Chengdu Women's and Children's Central Hospital/ ; },
abstract = {BACKGROUND: The rapid advancement in artificial intelligence (AI) has fundamentally reshaped gut microbiome research by enabling high-resolution analysis of complex, high-dimensional microbial communities and their functional interactions with the human host.

OBJECTIVE: This narrative review aims to synthesize recent methodological advances in AI-driven gut microbiome research and to evaluate their translational relevance for therapeutic optimization, personalized nutrition, and precision medicine.

METHODS: A narrative literature review was conducted using PubMed, Google Scholar, Web of Science, and IEEE Xplore, focusing on peer-reviewed studies published between approximately 2015 and early 2025. Representative articles were selected based on relevance to AI methodologies applied to gut microbiome analysis, including machine learning, deep learning, transformer-based models, graph neural networks, generative AI, and multi-omics integration frameworks. Additional seminal studies were identified through manual screening of reference lists.

RESULTS: The reviewed literature demonstrates that AI enables robust identification of diagnostic microbial signatures, prediction of individual responses to microbiome-targeted therapies, and design of personalized nutritional and pharmacological interventions using in silico simulations and digital twin models. AI-driven multi-omics integration-encompassing metagenomics, metatranscriptomics, metabolomics, proteomics, and clinical data-has improved functional interpretation of host-microbiome interactions and enhanced predictive performance across diverse disease contexts. For example, AI-guided personalized nutrition models have achieved AUC exceeding 0.8 for predicting postprandial glycemic responses, while community-scale metabolic modeling frameworks have accurately forecast individualized short-chain fatty acid production.

CONCLUSIONS: Despite substantial progress, key challenges remain, including data heterogeneity, limited model interpretability, population bias, and barriers to clinical deployment. Future research should prioritize standardized data pipelines, explainable and privacy-preserving AI frameworks, and broader population representation. Collectively, these advances position AI as a cornerstone technology for translating gut microbiome data into actionable insights for diagnostics, therapeutics, and precision nutrition.},
}

@article {pmid41749291,
year = {2026},
author = {Haro-Moreno, JM and Díaz-Arinero, E and Aldeguer-Riquelme, B and Rubio-Portillo, E},
title = {Effects of marine heatwaves on the dynamics of marine coastal microbial communities.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00861-3},
pmid = {41749291},
issn = {2524-6372},
support = {CIGE/2022/21//Generalitat Valenciana/ ; },
abstract = {BACKGROUND: Climate change is projected to intensify and prolong marine heatwaves, characterized by abnormally high sea surface temperatures. These events can profoundly alter ecosystem composition and functioning, sometimes triggering mass mortality events. The Mediterranean Sea, due to its semi-enclosed nature, is particularly susceptible to warming, with future climate scenarios predicting a temperature increase of up to 3.8 °C and at least one persistent heatwave annually by 2100. Despite this vulnerability, the effects of marine heatwaves on seawater microbial and viral communities remain poorly understood.

RESULTS: Using microcosm experiments, we examined microbial and viral dynamics under control conditions (20 °C) and two simulated marine heatwaves (MHWs) (23 °C and 25 °C). By the end of the experiment, microbial assemblages in all three conditions were dominated by metagenome-assembled genomes (MAGs) that were not detected in the initial natural sample, indicating the competitive success of rare biosphere taxa over initially abundant species. Virulence factors and antibiotic resistance genes increased in relative abundance throughout the incubation, but such increase was amplified under warming conditions. Temperature also shaped viral strategies, with heatwaves showing a higher percentage of integrated lysogenic viruses compared to control samples. This trend was consistent with observations from natural samples, where lysogenic viruses peaked during warmer months.

CONCLUSIONS: The shift toward lysogeny observed under elevated temperatures may enhance horizontal gene transfer, accelerating the spread of virulence and antibiotic resistance genes. In fact, we observed an increased abundance of these genes in samples under heat stress. These processes could weaken ecosystem resilience, disrupt microbial-driven biogeochemical cycles, and amplify risks to marine and human health. Our study underscores the need to integrate microbial and viral responses into predictions of ocean functioning in a rapidly warming world.},
}

@article {pmid41749104,
year = {2026},
author = {Baz, L},
title = {Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12700-3},
pmid = {41749104},
issn = {1471-2164},
}

@article {pmid41748627,
year = {2026},
author = {Huang, Z and Petersen, JM},
title = {Recovery of metagenome-assembled genomes from Spartina alterniflora root microbiome in Fujian Province, China.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06914-z},
pmid = {41748627},
issn = {2052-4463},
support = {2025J01967//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; },
abstract = {The saltmarsh cordgrass Spartina alterniflora proliferates along the coast of China. Like all plants, S. alterniflora hosts a specific microbiome that plays crucial roles in sustaining plant growth and health. Till now, very few studies have investigated the root microbiome of S. alterniflora in China, where it is considered an invasive pest. Here, ~350 Gbp metagenomes of S. alterniflora were generated from 8 sampling sites in South Fujian Province, China. 798 bacterial metagenome-assembled genomes (MAGs) and 7 archaeal MAGs were obtained, which were de-replicated into 205 and 3 representative genomes at a 95% ANI cutoff. The recovered bacterial MAGs mainly belonged to Gammaproteobacteria, Alphaproteobacteria, Bacteroidia and Campylobacterota. Sedimenticolaceae were prevalent at all sampling sites, accounting for 4-30% of the corresponding MAGs. These genomic datasets provide a new resource for investigating S. alterniflora root microbiomes, particularly valuable considering current efforts to eradicate this species in China.},
}

@article {pmid41748159,
year = {2026},
author = {Liu, W and Lu, Y and Ng, SC and Chan, FK and Sung, JJ and Yu, J},
title = {Bacterial genomic structural variations in children with autism serve as diagnostic biomarkers.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337280},
pmid = {41748159},
issn = {1468-3288},
abstract = {BACKGROUND: Gut microbiota dysbiosis is linked to autism spectrum disorder (ASD) in children. However, the role of bacterial genomic structural variations (SVs) in ASD remains largely unexplored.

OBJECTIVE: We aimed to identify bacterial SVs associated with ASD and explore their mechanistic role and clinical application.

DESIGN: We collected faecal metagenomes from 452 children (261 ASD, 191 neurotypical) across an in-house and seven public datasets. Using linear mixed-effects modelling, we identified ASD-associated SVs and compositional shifts and validated candidate SVs in humanised gut microbiome mice.

RESULTS: We identified 100 bacterial SVs significantly associated with ASD (p<0.05). These SVs were enriched in genes involved in critical biological processes, including ion and amino acid metabolism and bacterial growth regulation in ASD. In particular, we found important SVs in Bacteroides uniformis related to thiamine and iron metabolism. Moreover, SVs in Ruminococcus torques were associated with the MazF (endoribonuclease toxin) and MazE (antitoxin) system, a key regulator of pathobiont proliferation. Validation in humanised mouse models confirmed significant correlations between these SV signatures and ASD-like behaviours, such as reduced social interaction and increased repetitive behaviours. Both phylogeographically conserved and regionally restricted SVs showed strong associations with ASD. A diagnostic model combining nine SVs and three bacterial species achieved an area under the receiver operating characteristic curve of 81.1%, outperforming models based solely on variable SVs (79.1%), deletion SVs (75.2%) or bacterial species abundance alone (72.3%).

CONCLUSION: Our findings suggest the significant role of bacterial genomic SVs in ASD and highlight their potential as diagnostic biomarkers.},
}

@article {pmid41748043,
year = {2026},
author = {Alvaro-Fuss, M and DeClercq, V and Blodgett, JM and Theou, O and Langille, MGI and Beiko, RG},
title = {Effect of bedrest on the human gut and oral microbiome: implications for frailty.},
journal = {Experimental gerontology},
volume = {216},
number = {},
pages = {113079},
doi = {10.1016/j.exger.2026.113079},
pmid = {41748043},
issn = {1873-6815},
abstract = {The physiological effects of spaceflight resemble those of ageing and prolonged inactivity, and ground-based microgravity analogs have emerged as promising models for studying frailty. The human microbiome is increasingly recognised for its role in age-associated decline, although precise mechanisms remain unclear. Here, we evaluate the gut and oral microbiomes of twenty-two participants, aged 55-65, who were enrolled in a head-down tilt bedrest (HDBR) study, the first Canadian HDBR study conducted in an older cohort. Participants were randomly assigned to an inactivity or multi-modality exercise intervention group for fourteen days of HDBR, followed by seven days of rehabilitation and additional follow-up appointments. Gut (n = 343) and oral (n = 344) taxonomic profiles were generated using V4-V5 16S rRNA gene sequencing from fecal and salivary samples collected throughout the study. Gut functional profiles were generated using metagenomic (n = 86) data, used for pathway inference, and metabolomic (n = 83) data. Frailty was measured using a 36-item frailty index. Inactivity-associated changes to the gut microbiome during HDBR included decreasing α-diversity, decreasing Akkermansia and Lactobacillus, and increasing Bacteroides. Exercise-associated changes included increasing gut Roseburia. Both gut and oral β-diversity were associated with frailty scores and individual frailty components. We conclude that inactivity-associated changes to the human microbiome are associated with the early stages of frailty development, and that exercise may serve as an effective countermeasure against these effects. These results may inform strategies to preserve the health of both older adults facing prolonged periods of inactivity, as well as astronauts during longer space exploration missions.},
}

@article {pmid41748019,
year = {2026},
author = {Piccinno, G and Asnicar, F},
title = {Advanced computational analysis in metagenomic studies to support precision medicine.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.02.018},
pmid = {41748019},
issn = {1469-0691},
abstract = {BACKGROUND: The human microbiome has been linked to host health and is suggested to play a direct role in the onset of certain human diseases, as well as in impacting treatment efficacy. Characterizing the microbiome composition and its interaction with the host is now supported by an established, continuously improving set of bioinformatic and statistical resources that enable reproducible answers to fundamental questions about microbiome sample composition and its association with sample and host information. Extensive evidence highlighted that, in a non-diseased state, the microbiome composition is determined by multiple factors, including the acquisition of microbes at birth, lifestyle, dietary patterns, social interactions, antibiotic use, or probiotic intake, among others. In disease states, the microbiome may alter its composition and, in some cases, present specific biomarkers, as in colorectal cancer. Some microbiome components have also been associated with improved immunotherapy response in clinical oncology, suggesting a potential beneficial role for certain species and supporting the use of the microbiome as an additional therapeutic tool in these scenarios.

OBJECTIVES: This review summarizes computational approaches for microbiome characterization, highlights key findings on microbiome-disease associations, and provides a perspective on directions and open questions relevant to address in the future.

SOURCES: We selected scientific studies and reviews, published in peer-reviewed journals, based on their impact in the field and relevance to the topic of this manuscript. Literature selection was conducted by reviewing scientific publications retrieved from major scientific databases, such as PubMed, and by combining with the authors' knowledge of the literature.

CONTENT: Here we review computational approaches to characterize and model the microbiome's structure in health and disease and discuss multi-cohort data analysis, integration, and validation methods.

IMPLICATIONS: Improved microbiome characterization supports precision medicine by informing prevention or treatment, leveraging refined microbiome signature and modulation strategies.},
}

@article {pmid41747907,
year = {2026},
author = {Wang, Z and Hong, Y},
title = {Atmospheric and room-temperature plasma mutagenesis of microalgae for efficient swine wastewater treatment and bioresource recovery.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134287},
doi = {10.1016/j.biortech.2026.134287},
pmid = {41747907},
issn = {1873-2976},
abstract = {In response to the serious harm of swine wastewater (SW) and the drawbacks of existing treatment technologies, this study innovatively applies atmospheric and room-temperature plasma (ARTP) mutagenesis, followed by a four-round screening process strategy (solid actual SW (ASW) medium, growth in liquid ASW, comprehensive performance in the sterilized ASW (S-ASW), final evaluation in the unsterilized ASW (US-ASW)) to cultivate high-performance mutant microalgae for the efficient treatment of ASW without complex and expensive pretreatment or other strengthening methods. Chlorella sorokiniana HWY30-4 was eventually selected for its good adaptability and ASW treatment performance. The removal efficiencies of Chlorella sorokiniana HWY30-4 to total nitrogen (TN), NH4[+]-N, and total phosphorus (TP) for US-ASW were 60.31%, 80.07%, and 94.12%, respectively. In addition, HWY30-4 accumulated abundant high-value substances (0.06 g/L polysaccharides, 0.13 g/L proteins, and 0.23 g/L lipids) while treating US-ASW. Metagenomics revealed that the performance enhancement mechanisms mainly involve the enhanced critical metabolic pathways, alongside beneficial microbial synergies. This study offers an efficient and viable route for simultaneous ASW treatment and bioresource recovery, underscoring the potential of ARTP-based strain improvement in strengthening the microalgal performance for environmental governance.},
}

@article {pmid41747903,
year = {2026},
author = {Li, LX and Yang, TT and Yuan, Y and Han, YL and Zhao, Q and Wang, WH and Sun, Y and Cao, XX and Jiang, XL and Li, T and Wang, X},
title = {Rapid enrichment of ternary carbon-fixing microbial consortia from anaerobic sludge via pressurized pre-autotrophic strategy for scalable microbial electrosynthesis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134276},
doi = {10.1016/j.biortech.2026.134276},
pmid = {41747903},
issn = {1873-2976},
abstract = {As a promising platform for microbially catalyzed carbon capture, microbial electrosynthesis (MES) is constrained by inoculation strategies that limit carbon fixation efficiency and scalability. Mixed-culture inocula outperform pure cultures in functional redundancy and ecological resilience in large systems, but slow acclimation and erratic community composition yield inconsistent performance. Here, this study present a pressurized pre-autotrophic (PA) strategy that rapidly enriches carbon-fixing microorganisms (CFMs) from anaerobic sludge, in comparison with direct autotrophic (DA) and electrode reversal (ER) strategies. PA increased CFM abundance to 51%, 3.5-fold higher than in DA-MES and ER-MES (both 15%). Acetate production in PA-MES reached 14.47 g·m[-2]·d[-1]. In addition to enhanced acetate productivity, PA-MES exhibited superior electrochemical performance, achieving the highest Faradaic efficiency for acetate and energy efficiency among the tested systems, together with the lowest energy consumption per unit acetate. Metagenomic analysis revealed a PA-defined core community with coordinated activation of the Wood-Ljungdahl, rTCA, and methanogenic pathways, providing redundant routes for stable CO2 fixation. By transforming mixed-culture inocula into a functionally cohesive carbon-fixing community, the PA strategy enables rapid startup and sustained carbon fixation, offering a practical framework for scalable MES.},
}

@article {pmid41747902,
year = {2026},
author = {Corso, D and Melita, M and Massaccesi, N and Quero, GM and Basili, M and Di Cesare, A and Sabatino, R and Sbaffi, T and Fazi, S and Rakaj, A and Luna, GM and Amalfitano, S},
title = {Constructed wetlands for aquaculture wastewater treatment: Insights on the structural and functional shifts of the aquatic microbial community.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134278},
doi = {10.1016/j.biortech.2026.134278},
pmid = {41747902},
issn = {1873-2976},
abstract = {Aquaculture practices generate nutrient-rich effluents with associated microbiological hazards, such as pathogens and antimicrobial resistance genes (ARGs). Despite their growing popularity as nature-based solutions, little is known about how constructed wetlands (CWs) affect the dynamics of microbial communities at the field scale. By combining flow cytometry, 16S rRNA gene sequencing, shotgun metagenomics, and metabolic potential assays, we investigated the structural and functional responses of the aquatic microbial community following the recurrent exposure to CW-treated effluents from an intensive marine fish farm (Orbetello lagoon, Italy). While the CW promoted abundant, metabolically active, and functionally redundant microbial communities, the phylogenetic composition diverged primarily between water and sediments. Microbial profiles in CW outlet waters converged towards those of the lagoon baselines, suggesting gradual ecological recovery. The CW attenuated the occurrence of potential pathogens, such as members of the genera Francisella and Campylobacter, and acted as a buffer system in ARG dissemination, with sediments serving as reservoirs of microbial and genetic signatures. Functional profiles, dominated by chemoheterotrophy, denitrification, and sulfur respiration, remained stable across environments, reflecting microbial resilience. Our results highlight CWs as effective, field-proven solutions to mitigate aquaculture wastewater impacts while preserving core ecosystem services.},
}

@article {pmid41747730,
year = {2026},
author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C},
title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.01.021},
pmid = {41747730},
issn = {1097-4172},
abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.},
}

@article {pmid41747725,
year = {2026},
author = {Chen, K and Liu, Y and Rong, J and Dai, N and Xu, C and Li, H and Zhong, L and Wang, B and Ji, Z and Xie, S and Xu, Y and Yang, F and Wang, J and Li, D and Gu, Y and Zhou, X and Li, Y and Chen, M and Chen, Y and Li, W and Tang, Z and Cai, J and Xu, J and Xia, S and Zhan, Q and Zhou, Z},
title = {Strain-level genetic heterogeneity and colonization dynamics drive microbiome therapeutic efficacy.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.02.002},
pmid = {41747725},
issn = {1934-6069},
abstract = {Fecal microbiota transplantation (FMT) has shown immunotherapeutic promise, yet its efficacy in non-small-cell lung cancer (NSCLC) remains unclear. We demonstrate that FMT improves anti-PD-1 efficacy and progression-free survival in a single-arm trial of advanced PD-L1-negative NSCLC. Analyzing over 2,000 metagenomes from diverse disease cohorts and healthy controls via a high-resolution strain-tracking framework, we reveal that phylogenetically distinct strains within identical species exert opposing therapeutic effects, resolving prior inconsistencies. We identify conserved ecological principles where engraftment relies on species-intrinsic metabolic and immune evasion traits. Crucially, successful colonization by specific beneficial strain variants correlates with positive clinical outcomes. Finally, we identify 38 priority species with robust engraftment potential and significant heterogeneity as candidates for precision therapeutics. These findings establish a strain-function-efficacy paradigm, elucidating the mechanistic basis of variable outcomes and guiding next-generation microbiome drug development.},
}