@article {pmid41792508,
year = {2026},
author = {Li, M and Li, Y and Li, C and Liu, A and Liu, Y and Li, Y and Xiao, J and Zhang, D and Jin, Y and Wang, G and Pang, X and Jiang, K and Yin, Y},
title = {Dynamic reorganisation of intratumoural bacterial florae during colorectal cancer progression.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41792508},
issn = {1532-1827},
support = {81874235/82030081//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) exhibits distinct bacterial community compositions compared to healthy mucosae, which intimately correlate with CRC clinical outcomes. There is a lack of explanation for the inducements of microbiota remodelling.

METHODS: FISH experiments and 16S rRNA sequencing were conducted to determine the inducements of various bacterial colonisation within tissues. Community cultivation was conducted to estimate the capacity of tumours to remodel bacterial communities. Metagenomic analyses were utilised to determine the remodelled communities of CRC with distant metastasis. Scratch tests and three-dimensional (3D) cultivation were employed to investigate the influence of specific taxa on tumour cell behaviours.

RESULTS: Colorectal tumours exhibit heterogeneous and individualised preferences in constantly remodelling intratumoural bacterial florae. Various degrees of colorectal gland differentiation within tumours cause heterogeneous intratumoural bacterial colonisation. CRC progression further alters bacterial community composition. Particularly, Prevotella is significantly enriched in the newly established communities colonising the primary foci of metastatic CRC. Furthermore, Prevotella intermedia (P. intermedia) promotes the invasion, migration, and ectopic tumorigenesis of CRC cells.

CONCLUSIONS: Individual evaluation of the preference of tumours in microbiota may pave the way to the development of CRC therapeutic strategies, and Prevotella is an emerging genus worthy of clinical attention.},
}

@article {pmid41792155,
year = {2026},
author = {Benoit, G and James, R and Raguideau, S and Alabone, G and Goodall, T and Chikhi, R and Quince, C},
title = {High-quality metagenome assembly from nanopore reads with nanoMDBG.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69760-y},
pmid = {41792155},
issn = {2041-1723},
support = {BBX011089/1,BBS/E/ER/230002C,BB/CSP1720/1,BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 872539, 956229, 101047160 and 101088572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Third-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies (ONT) platform has increased to a per-base error rate of 1-2%. However, current metagenome assemblers are optimized for HiFi and do not scale to the large data sets that ONT enables. We present nanoMDBG, an evolution of metaMDBG, which supports the latest ONT reads through an error correction pre-processing step in minimizer-space. Across a range of ONT datasets, including a large 400 Gbp soil sample, nanoMDBG reconstructs up to twice as many high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. Critically, the latest ONT technology can now produce comparable MAG construction results as those obtained using PacBio HiFi at the same sequencing depth.},
}

@article {pmid41791848,
year = {2026},
author = {Louca, P and Manning, S and Hackney, E and Sharp, L and Hull, MA and Koo, S and Young, GR and Taylor, GS and Dunneram, Y and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and El-Omar, EM and , and Stewart, CJ and Rees, CJ},
title = {Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337478},
pmid = {41791848},
issn = {1468-3288},
abstract = {BACKGROUND: While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions.

OBJECTIVE: To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia.

DESIGN: Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates.

RESULTS: Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R[2]=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone).

CONCLUSION: This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.},
}

@article {pmid41791723,
year = {2026},
author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M},
title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70264},
doi = {10.1111/1462-2920.70264},
pmid = {41791723},
issn = {1462-2920},
support = {IITG/R&D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; },
abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.},
}

@article {pmid41791469,
year = {2026},
author = {Ma, J and Liu, J and Guo, Z and Zhu, M and Chai, Z and Jiang, F and Li, Z and Liang, Z and Jiang, Z},
title = {Characteristics of the microbial carbon pump in kelp farming areas and the impact of artificial reefs: A metagenomic and ecological perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124166},
doi = {10.1016/j.envres.2026.124166},
pmid = {41791469},
issn = {1096-0953},
abstract = {The microbial carbon pump (MCP) can transform labile dissolved organic carbon (LDOC) into recalcitrant dissolved organic carbon (RDOC), yet how sedimentary MCP efficiency is regulated by natural gradients of organic carbon input remains unclear. In this study, we investigated sediments in a kelp farming environment, leveraging the contrast between artificial reef (AR) areas and adjacent non-reef (NR) areas. We combined full-length 16S rRNA sequencing, metagenomics, and fluorescent dissolved organic matter (FDOM) characterization to compare microbial processing under these contrasting depositional regimes. Elevated LDOC inputs in the AR zones were associated with reshaped community metabolic profiles and with enhanced turnover and potential formation of RDOC. High substrate availability was linked to coordinated metabolic functional potential, in which increased genetic potential for upstream catabolism covaried with genomic features indicative of expanded acetyl-CoA supply potential. This putative metabolic overflow was more strongly associated with the mevalonate (MVA) pathway than with the alternative methylerythritol phosphate pathway, consistent with a potential routing toward isoprenoid and terpenoid backbone biosynthesis and the formation of carboxyl-rich alicyclic molecule (CRAM) precursors. Genome-resolved reconstructions further suggested metabolic complementarity among taxa, with predicted cross-feeding interactions that could help sustain carbon processing in MVA-enriched copiotrophs. Overall, humic-like FDOM signals co-vary with organic loading driven by artificial reefs, indicating that these engineering interventions serve as controllable levers, providing a scientific basis for optimizing the carbon sink function of marine ranching through strategic artificial reef deployment.},
}

@article {pmid41791253,
year = {2026},
author = {Fu, CX and Cai, JJ and Liu, JL and Qiu, GY and Chen, XD and Zhang, JB and Qiao, M and Tong, WB and Guo, B},
title = {Mechanistic investigation of the associations between bacterial community composition and cadmium distribution in Zizania latifolia.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119972},
doi = {10.1016/j.ecoenv.2026.119972},
pmid = {41791253},
issn = {1090-2414},
abstract = {The role of bacteria in external niches regulating cadmium (Cd(II)) in plant tissues remains unclear. We explored Cd(II) profiles and identified bacterial contributors among phyllosphere, rhizoplane, and rhizosphere of four Zizania latifolia varieties through integrated metagenomic and chemical analyses. Zizania latifolia accumulated Cd(II) in leaves (0.06-0.77 mg/kg), roots (0.73-1.57 mg/kg), and rhizosphere (0.43-3.15 mg/kg), respectively. The highest enrichment coefficient (leaf-Cd(II)/soil-Cd(II)) was observed in Genotype 3 (0.6). Among top 10 genus-level bacteria, Enterococcus in phyllosphere, Streptomyces and Dechloromonas in rhizoplane, and Bradyrhizobium, Pseudolabrys, Mycobacterium, and Dechloromonas in rhizosphere were significantly related to Cd(II). Enterococcus adsorbed Cd(II) by extracellular polysaccharides and precipitated Cd(II) sulfide. Rhizoplane and rhizosphere bacteria absorbed Cd(II) by cell-surface functional groups, and fixed Cd(II) through synthesizing polyphosphate and driving Fe (II) oxidation. Additionally, 64.4%-80% of bacteria were shared between rhizoplane and rhizosphere, 5.5%-6.9% between rhizoplane and phyllosphere, and 4.4%-6.1% between rhizosphere and phyllosphere. Metagenomic analysis indicated that Cd(II) disturbed bacterial secretion system and amino acid metabolic pathways. These findings provided comprehensive insights into interrelationships between Cd(II) and bacteria in leaves, roots, and rhizosphere of Zizania latifolia, offering valuable foundations for developing targeted strategies to mitigate Cd(II) accumulation in aquatic vegetables.},
}

@article {pmid41790921,
year = {2026},
author = {Wang, J and Jiang, B},
title = {Utilizing metagenomic next-generation sequencing to diagnose central nervous system infections after craniotomy.},
journal = {Journal of infection in developing countries},
volume = {20},
number = {2},
pages = {263-270},
doi = {10.3855/jidc.21771},
pmid = {41790921},
issn = {1972-2680},
mesh = {Humans ; *Craniotomy/adverse effects ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Prospective Studies ; Middle Aged ; *Central Nervous System Infections/diagnosis/microbiology ; Adult ; *Metagenomics/methods ; Aged ; Sensitivity and Specificity ; Bacteria/genetics/isolation & purification/classification ; Young Adult ; *Postoperative Complications/diagnosis/microbiology ; Adolescent ; },
abstract = {INTRODUCTION: Postoperative central nervous system (CNS) infections in craniotomy patients diagnosed through clinical signs and cerebrospinal fluid (CSF) bacterial culture, pose a challenge due to the morbidity and mortality of bacterial meningitis. The objective of this study was to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosing CNS infections post craniotomy.

METHODOLOGY: A prospective study compared mNGS with traditional diagnostics from January 2021 to October 2023. Patients with suspected post-craniotomy intracranial infections were enrolled, following guidelines and regulations.

RESULTS: mNGS and traditional culture diagnosed 111 patients with suspected intracranial infections. mNGS showed higher sensitivity (62.5% vs. 25%). Traditional culture excelled in specificity and positive predictive value. Of the 18 mNGS-positive samples, 12 were culture-negative. mNGS detected pathogens such as Candida albicans (2 cases), Enterobacter cloacae (1 case), Enterococcus faecalis (1 case), Klebsiella pneumoniae (2 cases), Pseudomonas aeruginosa (1 case), Staphylococcus aureus (2 cases), Staphylococcus epidermidis (2 cases), and Streptococcus haemolyticus (1 case). Some pathogens were likely missed due to prior antibiotic use and fastidious growth requirements. Physicians adjusted treatments based on mNGS pathogen detection for culture-negative patients. Empirical therapy continued for patients with negative results until more diagnostic information was available.

CONCLUSIONS: mNGS detects post-neurosurgery CNS infections, especially hard-to-cultivate microorganisms. While mNGS has advantages, traditional culture's higher positive predictive value confirms infections and remains indispensable. Combining mNGS with traditional methods provides a comprehensive diagnostic strategy, aiding physicians in accurately identifying infections, reducing misdiagnosis, and offering personalized treatment plans to improve outcomes and quality of life.},
}

Humans
*Craniotomy/adverse effects
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Prospective Studies
Middle Aged
*Central Nervous System Infections/diagnosis/microbiology
Adult
*Metagenomics/methods
Aged
Sensitivity and Specificity
Bacteria/genetics/isolation & purification/classification
Young Adult
*Postoperative Complications/diagnosis/microbiology
Adolescent

@article {pmid41790828,
year = {2026},
author = {Carrillo, A and Hageman, E and Chittick, L and Mackey, AI and Ndlovu, KS and Tian, F and Gilbert, NE and Muratore, D and Vik, D and LeCleir, GR and Sun, C and Jang, HB and Pavan, RR and Weitz, JS and Wilhelm, SW and Sullivan, MB},
title = {Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts.},
journal = {PLoS biology},
volume = {24},
number = {3},
pages = {e3003474},
doi = {10.1371/journal.pbio.3003474},
pmid = {41790828},
issn = {1545-7885},
abstract = {Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning to be incorporated into predictive modeling, high-frequency ocean virus dynamics remain understudied due to methodological challenges. Here we sampled stratified Bermuda Atlantic Time Series (BATS) waters for 112 hours at sub-daily 4- (surface) or 12- (deep chlorophyll maximum) hour intervals, purified viral particles from these samples, sequenced their metagenomes, and used the resulting data to characterize high-frequency virus community dynamics. Aggregated community diversity metrics changed with depth, but were not statistically significant temporally at a fixed location. However, finer-scale population-level analyses revealed both depth and temporal change, including physicochemical depth-driven differences and, in surface waters, thousands of viral populations that exhibited statistically significant diel rhythms. Statistical analyses revealed three main archetypes of temporal dynamics that themselves differed in abundance patterns, host predictions, viral taxonomy, and gene functions. Among these, highlights include viruses resembling an archetype with a night peaking pattern in activity that include an over-representation of viruses that putatively infect Prochlorococcus, a phototrophic cyanobacteria. Together, these efforts provide baseline community- and population-scale short-time-frame observations relevant to future climate state modeling.},
}

@article {pmid41790792,
year = {2026},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Shotgun metagenomic profiling reveals Bacillus-dominated bacterial communities in urban rooftop and surface garden soils of Bangladesh.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344114},
doi = {10.1371/journal.pone.0344114},
pmid = {41790792},
issn = {1932-6203},
mesh = {*Soil Microbiology ; Bangladesh ; *Bacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; Gardens ; Soil/chemistry ; Biodiversity ; },
abstract = {Urban rooftop and surface garden systems play a critical role in food security in densely populated regions, yet their soil microbiomes remain understudied. To date, no baseline data exists on rooftop and surface garden soil microbiomes in Bangladesh. Understanding these communities is vital for enhancing soil health, nutrient cycling, and resilience for sustainable, climate-adapted urban agriculture. This study therefore investigated the bacterial diversity and community structure of rooftop and surface garden soils across Dhaka and Gazipur, Bangladesh. The goal was to uncover location- and garden-type-specific patterns that influence soil functionality. Using shotgun metagenomics of 27 garden soil samples (seven Dhaka rooftop [DRG], six Dhaka surface [DSG], eight Gazipur rooftop [GRG], and six Gazipur surface [GSG]), we identified 755 bacterial species dominated by Firmicutes (65-83%) and Proteobacteria (3-25%). While alpha diversity was consistent across sites (p > 0.05), beta diversity revealed distinct community structuring (p = 0.017), with surface gardens harboring greater bacterial richness (DSG:717, GSG:750 species) and elevated Bacteroidota (DSG:11.5%, GSG:2.7%) compared to rooftop soils. Strikingly, Bacillus species dominated all soils (>53% relative abundance) but exhibited location-specific distributions. DRG soils were notably enriched with B. paralicheniformis (28.3%) and B. licheniformis (25.2%). In contrast, DSG was characterized by B. cereus sensu lato (16.0%), Brevibacillus agri (12.1%), and Flavobacterium thermophilum (11.4%). GRG soils were dominated by B. cereus sensu lato (42.4%) and B. agri (11.5%). GSG soils showed diverse Bacillus species, including B. stratosphericus (14.6%), B. licheniformis (12.7%), B. safensis (9.7%), and B. altitudinis (8.8%). Of 41 detected Bacillus species, more than 58.0% were shared across gardens, yet their abundances varied with microhabitat. Moreover, KEGG profiling revealed marked functional divergence among urban garden soils. Carbohydrate metabolism dominated all sites (9.30-11.07%). DRG was uniquely enriched in photosynthesis (8.40%) and methane metabolism (8.62%), whereas DSG, GRG, and GSG showed higher oxidative phosphorylation (3.75-4.08%), two-component systems (3.24-3.73%), and biosynthetic pathways. This study unveils the ecological dominance of Bacillus species in urban agricultural soils, with location-driven compositional and functional shift. These findings are pivotal for optimizing sustainable urban agriculture in rapidly developing regions, where soil bacteriomes can be harnessed to improve crop resilience and food security.},
}

*Soil Microbiology
Bangladesh
*Bacillus/genetics/classification/isolation & purification
*Metagenomics/methods
*Microbiota/genetics
Gardens
Soil/chemistry
Biodiversity

@article {pmid41790499,
year = {2026},
author = {Liu, G and Bai, P and Ren, M and Li, Q and Li, T},
title = {Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis.},
journal = {Microbial genomics},
volume = {12},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001665},
pmid = {41790499},
issn = {2057-5858},
abstract = {The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.},
}

@article {pmid41790111,
year = {2026},
author = {Kumar, K},
title = {Cultivation of Yet-to-be Cultured Microorganisms: Advances, Strategies, and Prospects.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag066},
pmid = {41790111},
issn = {1365-2672},
abstract = {More than 99% of microorganisms in the natural environment are not readily culturable using standard laboratory techniques. These microbes can be reservoirs of novel metabolites and biomolecules having pharmaceutical applications against bacterial infections, chronic diseases, and antibiotic resistance. Given this, our work is a comprehensive synthesis of recent advances in understanding, detection, and cultivation of "yet-to-be cultured" (YTBC) microbes. We highlight physiological traits that restrict their domestication under standard laboratory conditions. Some of the factors that may influence are their metabolic dormancy, specialized nutrient demands, siderophore-mediated iron acquisition, microbial signaling, and interspecies interactions. The review discusses various strategies, such as simulated natural environments, co-culture, and advanced bioreactor systems, which can be implemented to cultivate them. We reviewed recent metagenomic approaches and single-cell isolation methods, including label-based techniques (e.g., fluorescence in situ hybridization), label-free approaches such as Raman-activated cell sorting, and high-throughput tools like flow cytometry. We also examined culture-dependent approaches, including co-cultivation with helper strains with a special emphasis on bioreactor-based systems, diffusion chamber, hollow-fiber membrane chamber, high-throughput isolation chip (ichip), and encapsulation. Overall, this review provides a roadmap to unlock the biotechnological potential of YTBC microbes by outlining new technologies, methodological trends, and important knowledge gaps.},
}

@article {pmid41790075,
year = {2026},
author = {Kong, C and Jin, Y and Guo, F and Yang, Y and Liu, G and Chen, Z and Li, J and Wang, Q and Ma, Y},
title = {Revealing the Antagonistic Interactions of Faecalibacterium prausnitzii and Bacteroides fragilis in Colorectal Cancer.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.12.030},
pmid = {41790075},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Maladaptation of host-microbe metabolic interactions plays a crucial role in development of colorectal cancer (CRC). However, remains a lack of comprehensive studies using multi-omics analysis to illustrate host-microbe metabolic interactions in CRC.

METHODS: We collected and analyzed 440 stool samples from a discovery cohort in Shanghai China (255 patients with CRC and 185 healthy controls). Each sample was subjected to metagenomic sequencing and nontargeted liquid chromatography mass spectrometry. Fresh-frozen specimens of tumors and matched adjacent normal mucosae were extracted from 62 patients with CRC, and whole exome sequencing and RNA sequencing were performed to explore host genomic patterns and host-microbe metabolic interactions. Finally, relationships detected in the discovery cohort were validated against independent cohorts, organoid models, and mice experiments.

RESULTS: The relationship between disrupted microbial homeostasis and CRC progression is characterized by Bacteroides fragilis enrichment and reduction of Faecalibacterium prausnitzii. F prausnitzii metabolizes tryptophan into picolinic acid (PIA) via the enzyme 2-amino-3-carboxymuconate semialdehyde decarboxylase, with PIA exerting an antagonistic effect on enterotoxigenic B fragilis-mediated tumor progression. Mechanistically, enterotoxigenic B fragilis up-regulates the expression of genes associated with poor differentiation and recurrence, namely TCERG1 and CKAP2, and PIA induces tumor cell apoptosis by down-regulating these 2 genes. Independent validation cohorts and murine models corroborated that a tryptophan-rich diet effectively elevates circulating PIA levels, suggesting its potential as an anticancer dietary intervention.

CONCLUSIONS: Our research characterized a representative microbe-metabolite-host regulatory pathway occurring in CRC, namely the F prausnitzii-PIA-TCERG1/CKAP2 axis antagonizing enterotoxigenic B fragilis-induced CRC progression. As a treatment option, we highlight the therapeutic potential inherent in a tryptophan-rich diet and in manipulating microbial composition targeting the F prausnitzii-PIA axis to prevent CRC.},
}

@article {pmid41789948,
year = {2026},
author = {Yadav, S and Yang, T and MacLean, MA and El-Naggar, MY},
title = {Metagenome-assembled genome sequence of Candidatus Electrothrix sp. NPCB-01 from Southern California marine sediments.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0002526},
doi = {10.1128/mra.00025-26},
pmid = {41789948},
issn = {2576-098X},
abstract = {Cable bacteria conduct long-distance electron transport in sediments but are not yet isolated in pure culture. We report the metagenome-assembled genome of Candidatus Electrothrix sp. NPCB-01 from Newport Bay, California. This 3.46-Mb genome encodes sulfur oxidation, nitrogen and carbon metabolism, and nickel homeostasis genes, expanding resources for these electroactive microbes.},
}

@article {pmid41789923,
year = {2026},
author = {Yao, J and Yang, C and Wang, H and Zhang, C and Meng, J},
title = {Metagenomic analysis of gut bacteria in different developmental instars of Spodoptera litura.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0208125},
doi = {10.1128/spectrum.02081-25},
pmid = {41789923},
issn = {2165-0497},
abstract = {Spodoptera litura is a globally distributed agricultural pest across Asia and Australia (EPPO database, https://gd.eppo.int/taxon/PRODLI/distribution), whose gut microbiota significantly influences host feeding, digestion, immunity, and development. We used whole metagenomic sequencing to analyze the diversity and functional roles of gut bacteria at different developmental stages (eggs, first to sixth instar larvae, pupae, and adults). Findings revealed that Pseudomonadota predominated at the phylum level, with notable differences across instars: Bacillota was dominant in young larvae, whereas Verrucomicrobiota was added in older larvae, eggs, pupae, and adults. At the genus level, Pseudomonas dominated, Enterococcus was prevalent in larvae, and Piscirickettsia was prevalent in eggs, pupae, and adults. Metagenomic analysis identified numerous carbohydrate-active enzymes (CAZy database) aiding in plant cell wall polysaccharide digestion. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated differential gene expression in metabolism and xenobiotic degradation across instars, with metabolic gene annotation levels declining as development progressed. Detoxification-related enzyme genes were predominantly expressed in early instar larvae and adults, uncovering microbial origins of these enzymes.IMPORTANCEOur study provides evidence that the gut microbiota significantly modulates the physiology of Spodoptera litura, with profound effects on its dietary habits, metabolic processes, and host fitness. Using whole metagenomic sequencing, we analyzed gut bacteria across different life stages. At the phylum level, Pseudomonadota and Bacillota were dominant, while at the genus level, Pseudomonas was the most abundant taxon. Metagenomic analysis identified enzymes aiding in plant cell wall digestion. Kyoto Encyclopedia of Genes and Genomes analysis showed varying gene expression in metabolism and detoxification, with higher expression in early instar larvae and adults. This research enhances understanding of S. litura gut microbiota-host interactions and supports novel pest control strategies targeting gut microbiota.},
}

@article {pmid41789917,
year = {2026},
author = {Chen, D and Zhang, Z and Wang, S and Li, W and He, Y and Zhang, W and Sun, W and Chen, M and Zou, S and Qian, X},
title = {Differential assembly and functional roles of bacterial communities in coniferous and mixed conifer-broadleaf forest soils.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0062725},
doi = {10.1128/msphere.00627-25},
pmid = {41789917},
issn = {2379-5042},
abstract = {Forest soils harbor a diverse array of bacteria that play a crucial role in nutrient cycling. However, the differential effects of coniferous versus mixed conifer-broadleaf forests on the distribution of both abundant and rare bacterial taxa remain poorly understood. In this study, we integrated 16S rRNA gene amplicon sequencing with metagenomic shotgun sequencing to conduct a comparative analysis of soil bacterial communities in a conifer plantation and an adjacent mixed conifer-broadleaf forest, specifically examining their community structure, assembly mechanisms, co-occurrence networks, and functional potential. Both abundant and rare taxa showed significant differences in community composition between the two forest types. Soil pH and organic matter content significantly influenced the total and abundant bacterial communities, while available phosphorus and potassium were key determinants of rare community composition. Co-occurrence network analysis revealed that abundant communities formed highly clustered, simplified networks, contrasting with more fragmented and keystone-rich networks in rare communities. Null model analyses indicated that community assembly was largely driven by stochastic processes, with ecological drift accounting for about 80% of the variation in total and rare communities, and dispersal limitation explaining nearly 72% of the variation in abundant communities. Functional predictions indicated that bacterial communities in mixed forests were enriched in pathways linked to glycosylation, carbohydrate degradation, and nitrogen fixation, while coniferous forests favored pathways related to autophagy, signaling, and stress responses. This study highlights the complementary roles of abundant and rare bacterial taxa in forest soil ecosystems and underscores the importance of preserving mixed forests to sustain microbial functional diversity.IMPORTANCEForest soils host a complex web of common and rare bacteria that quietly regulate nutrient cycles. By comparing pure conifer stands with mixed conifer-broadleaf forests, we found that abundant species underpin essential functions while rarer microbes fill specialized niches. Acidity and nutrients strongly influence which bacteria thrive; mixed stands favored microbes that break down carbohydrates and fix nitrogen, whereas conifer soils supported organisms adapted to stress and nutrient-poor conditions. These findings emphasize the importance of preserving diverse forest ecosystems for soil health, carbon storage, and effective forest management strategies in climate change adaptation.},
}

@article {pmid41789915,
year = {2026},
author = {Chen, S and Li, Y and Xue, J and Hao, Y and Shaalan, MGA and Ghallab, EHS and Guo, Z and Jin, S and Fang, Y and I M Khater, E and Li, S},
title = {Metagenomic sequencing reveals viral diversity of mosquitoes from Egypt: co-circulation of multiple insect-specific viruses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0213525},
doi = {10.1128/spectrum.02135-25},
pmid = {41789915},
issn = {2165-0497},
abstract = {UNLABELLED: Mosquito-borne virus surveillance is pivotal for investigating mosquito viromes, facilitating understanding of viral evolutionary histories and genetic diversity. Natural viral communities in mosquitoes include not only insect-specific viruses (ISVs) but also viruses infecting symbiotic microorganisms. In this study, a total of 654 mosquito samples-encompassing species from the Aedes and Culex genera-were collected from Egypt and subjected to metagenomic sequencing analysis. Over 130 virus species were identified, grouped into 35 families or equivalent taxonomic ranks. Detected ISVs included Culex flavivirus (CxFV), Kustavi Toti-like virus, Hanko Toti virus 5, Culex phasma-like virus (CPLV), Culex Iflavi-like virus 1, Culex Iflavi-like virus 4, Guadeloupe Culex rhabdovirus (GCRV), and Sarawak virus, confirming concurrent ISV circulation in Egyptian mosquitoes. Phylogenetic analyses of these ISVs revealed their closest evolutionary affinities to viral genome sequences originating from the Middle East, Europe, Oceania, and Asia. Specifically, Egyptian CxFV strains exhibited a closer genetic relationship with the tropical lineage within the Latin American/Caribbean/Africa genotype. Furthermore, our study uncovered 10 putative novel viruses, which are distributed across seven viral families: Amagaviridae, Chrysoviridae, Mitoviridae, Totiviridae, Virgaviridae, Narnaviridae, and Orthomyxoviridae. Collectively, our findings emphasize the necessity for more in-depth investigations into arthropod viromes-encompassing both mosquitoes and ticks-in Egypt, as well as in neighboring African and Middle Eastern countries. Such research is critical for enhancing our understanding of viral diversity and evolutionary biology, elucidating their roles in mosquito-pathogen-host interactions, and exploring their potential as biocontrol agents against vector-borne diseases of public health importance.

IMPORTANCE: Mosquito-borne viruses are estimated to cause over 100 million human infections annually, making surveillance of these pathogens increasingly crucial amid growing international travel and trade. Egypt, situated in northeastern Africa, serves as a geopolitical and geographical hub connecting Asia, Europe, and Africa-a unique location that complicates the surveillance of mosquito-borne viruses. Arboviruses persist in nature through cyclical transmission between arthropod vectors (e.g., mosquitoes, ticks, and midges) and susceptible vertebrate hosts. Despite this, systematic investigations into mosquito viromes remain relatively scarce in Egypt. The present study aimed to explore the genetic diversity and evolutionary relationships of mosquito-associated viruses in Egypt using metaviromic sequencing. Our findings significantly expand the current knowledge of both known and previously uncharacterized mosquito-associated viruses in the region, while also providing complete genome sequences of several viruses that may infect arthropods or vertebrates, and potentially interfere with the replication of pathogenic arboviruses.},
}

@article {pmid41789894,
year = {2026},
author = {Liu, M and Wang, L and Liu, J and Yuan, Q and Zhang, Y and Wu, S and Zhang, Y and Guo, R and Zhang, Y and Lu, T and Yan, Q and Li, S and Xing, G and Dong, B and Zheng, N},
title = {Gut virome and metabolic associations in patients with acute pancreatitis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0140025},
doi = {10.1128/msystems.01400-25},
pmid = {41789894},
issn = {2379-5077},
abstract = {Acute pancreatitis (AP) is a frequent inflammatory disorder with outcomes ranging from mild disease to severe forms marked by infection and organ failure. Gut microenvironment disruption and barrier dysfunction are increasingly recognized as key drivers of AP progression, yet most microbiome studies have focused on bacteria. The gut virome modulates bacterial ecology and host immune responses and remains poorly characterized in AP. We aimed to comprehensively profile virome alterations in AP and evaluate their associations with disease severity, etiology, and clinical parameters. Metagenomic sequencing data from AP patients and healthy controls (HCs) were analyzed using the viromic tools. Viral diversity, taxonomy, functional composition, and predicted viral-host linkages were profiled. Microbial-viral-metabolite networks were constructed, and classification performance was evaluated using random forest models. AP viromes exhibited significantly reduced Shannon and Simpson diversity and distinct β-diversity separation from HCs. AP-enriched phages predominantly targeted Parabacteroides, Escherichia, and Bacteroides, while HC-enriched phages were linked to SCFA-producing commensals. Functional analysis revealed enrichment of replication- and lysis-related auxiliary metabolic genes (AMGs) in AP-enriched viral operational taxonomic units (vOTUs), whereas HC-associated vOTUs carried stability-related functions. Severity- and etiology-stratified analyses indicated consistent enrichment of Peduoviridae infecting Enterobacteriaceae and higher prevalence of eukaryotic viruses in advanced stages. Network analyses revealed denser microbial-viral-metabolite interactions in AP, correlated with hepatobiliary and lipid metabolic markers. A minimal seven-virus panel achieved an AUC of 97.5% for AP classification. AP is characterized by profound gut virome remodeling reflecting disease severity and etiology, with diagnostic and mechanistic relevance for future therapeutic strategies.IMPORTANCEThis study highlights the gut virome as a previously underappreciated component of acute pancreatitis (AP)-associated dysbiosis and suggests that viral communities may influence disease severity and metabolic disturbances beyond bacterial effects alone. By demonstrating the diagnostic potential of virome-based signatures, our findings support expanding microbiome research in AP to include viral components, with implications for improved disease stratification and future therapeutic development.},
}

@article {pmid41789433,
year = {2026},
author = {Eldholm, V and Straume, D and Brynildsrud, OB},
title = {Assessing sequencing-based pathogen surveillance of a recreational swimming area in Oslo, Norway.},
journal = {Access microbiology},
volume = {8},
number = {2},
pages = {},
pmid = {41789433},
issn = {2516-8290},
abstract = {Sequencing-based surveillance can enable rapid and sensitive detection of environmental pathogens. The Oslofjord inlet is relatively narrow and is exposed to substantial human activity, including occasional wastewater contamination. Restricted water exchange also allows for occasional summer heat spells with elevated water temperatures. Thus, infections stemming from wastewater contamination and seasonal opportunistic pathogens are potential health threats to recreational users of the fjord. In this pilot study, we assess the suitability of sequencing-based surveillance for the detection of pathogens at a popular urban location for recreational water activities, employing both long- and short-read sequencing platforms, paired with selective culturing. We find both metagenomic and full-length 16S sequencing to be promising tools for surveillance of seasonal opportunistic Vibrio pathogens. Furthermore, we identified Rhodoferax abundance to be a potentially attractive indicator of sewage contamination using low to medium-depth full-length 16S sequencing. Selective plating revealed minimal abundance of culturable extended-spectrum β-lactam-resistant bacteria, of which none were detected by metagenomic sequencing. Metagenomic analyses did, however, pick up several other β-lactamases in various bacterial taxa, including some that were closely related to those identified by selective plating and sequencing.},
}

@article {pmid41789009,
year = {2026},
author = {Cao, HT and Sun, RJ and Qian, QY and Yang, D and Sun, YY and Zhao, LY and Zhang, GY and Zhang, MD and Gu, H and Cao, HW and Wang, B and Huang, YW and Yang, YL},
title = {Molecular characterization and evolutionary dynamics of a recombinant PDCoV strain in a swine diarrhea epidemic with SADS-CoV co-infection.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1749819},
pmid = {41789009},
issn = {2297-1769},
abstract = {Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus that poses a significant threat to the swine industry. In this study, a novel PDCoV strain, designated PDCoV-ZJHZ2024, was identified from fecal samples of diarrheic pigs in China. Metagenomic analysis revealed co-detection of PDCoV and swine acute diarrhea syndrome coronavirus (SADS-CoV), with the microbial community predominantly composed of bacteria and characterized by abnormal enrichment of Bacillus cereus and pronounced gut microbiota dysbiosis. Genomic analyses demonstrated that PDCoV-ZJHZ2024 has undergone independent recombination events involving the ORF1b region and the spike (S) gene, accompanied by cross-regional genetic exchange, highlighting the critical role of recombination in PDCoV evolution and diversification. Codon usage analysis further indicated that codon preferences in this strain are primarily shaped by natural selection, potentially conferring enhanced translational efficiency in the host. Collectively, these findings underscore the evolutionary adaptability and transmission potential of PDCoV-ZJHZ2024 and provide new insights into PDCoV evolutionary dynamics, thereby informing future surveillance efforts and prevention strategies in swine populations.},
}

@article {pmid41788684,
year = {2026},
author = {Cao, W and Li, R and Zhang, H and Zhang, T and Pan, H and Sun, W and Wang, L and Ke, J and Petersen, JD and Zhang, P},
title = {Exploratory multi-omics analysis of gut microbiota and fecal metabolites in relation to serum S-equol levels in older adults with osteoporosis from a tropical community: a pilot study.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1784894},
pmid = {41788684},
issn = {2296-861X},
abstract = {BACKGROUND: Osteoporosis (OP) is a multifactorial skeletal disorder influenced by host metabolism, inflammation, and gut microbiota-derived metabolites such as S-equol. However, the interplay between intestinal microbiota, S-equol production, and host metabolic profiles in OP remains incompletely understood.

OBJECTIVE: To conduct a preliminary multi-omics investigation integrating metagenomic and metabolomic analyses to identify gut microbiota and metabolite biomarkers associated with serum S-equol levels in older adults with OP.

METHODS: A cross-sectional study was conducted in 39 community-dwelling adults aged ≥50 years in Haikou, China. Participants were grouped into OP and control groups based on lumbar spine T-scores, using a cut-off value of ≤ - 2.5 to define osteoporosis. Serum biomarkers (S-equol, inflammatory cytokines, oxidative stress indicators) were assessed by ELISA. Fecal samples underwent metagenomic sequencing and untargeted metabolomics. LEfSe, Spearman correlation, machine learning, and KEGG enrichment were used to explore microbiota-metabolite-bone health axes.

RESULTS: Serum S-equol levels were significantly lower in the OP group compared to controls (3,561 ± 304 vs. 3,855 ± 469 pg/mL, p = 0.026), whereas most inflammatory markers were comparable between groups, apart from a modest increase in IL-1β in OP. Metagenomic analysis revealed a lower relative abundances of key SCFA-producing taxa in OP (e.g., Faecalibacterium prausnitzii, Roseburia hominis, Bacteroides uniformis). Metabolomic profiling identified distinct alterations in amino acid and tryptophan pathways, with KEGG analysis highlighting disruptions in glycerophospholipid, glycine-serine-threonine, and choline metabolism. Discriminative metabolites (e.g., Gln-Val-Ile-Asp., 5-oxooctanoic acid) showed diagnostic potential (AUC > 0.75). S-equol levels positively correlated with these beneficial microbes and with amino acid-related metabolites (e.g., D-tryptophan, 3-indoleacrylic acid, N-methylglutamate). Network and heatmap analyses illustrated differences in microbial-metabolite association patterns between groups.

CONCLUSION: In conclusion, low levels of serum S-equol in older adults with osteoporosis were associated with distinct changes in gut microbiota composition and fecal metabolic profiles in this pilot study.},
}

@article {pmid41788574,
year = {2026},
author = {Liang, ZW and Guan, YH and Lv, Z and Yang, SC and Zhao, M and Chen, JW},
title = {Metagenomics reveals an interaction among rhizosphere microbial community, soil properties and active ingredients in a medicinal crop Panax notoginseng.},
journal = {Journal of ginseng research},
volume = {50},
number = {2},
pages = {100918},
pmid = {41788574},
issn = {1226-8453},
abstract = {BACKGROUND: This study aimed to examine the effects of intensive cultivation practices on the rhizosphere microecology of Panax notoginseng. Additionally, we sought to compare these practices with an understory cultivation model that was intended to mimic native growth conditions, with the objective of improving the quality of Radix Notoginseng.

METHODS: The total saponin and active ingredient content in both cultivation methods were quantified using high-performance liquid chromatography (HPLC). The nutrients of the rhizosphere soils associated with both cultivation methods (understory cultivated P. notoginseng rhizosphere soil [UCPS] and intensive cultivated P. notoginseng rhizosphere soil [ICPS]) were analyzed. The microbial communities present in UCPS and ICPS were characterized using metagenomic sequencing.

RESULTS: The underground biomass accounted for 71.21 % and 74.00 % of the total biomass in understory cultivated P. notoginseng (UCPn) and intensively cultivated P. notoginseng (ICPn), respectively. The total saponin content in the main root of UCPn was found to be 109.24 ± 3.40 mg/g, compared to 91.31 ± 5.82 mg/g in ICPn. The concentration of medicinal ingredients (ginsenoside Rb1 + ginsenoside Rg1 + notoginsenoside R1) in UCPn was 10.83 %, while ICPn exhibited a higher concentration of 13.39 %. Microbial biomarkers identified in UCPS include Bradyrhizobium, Pseudomonas, and Paraburkholderia, which are associated with nitrogen cycling processes. In contrast, Variovorax and Sphingobium were predominant in ICPS, contributing to phosphorus metabolism.

CONCLUSION: Rhizosphere soil microbial biomarkers influence soil carbon nutrition, which directly impacts the quality of UCPn. The quality of ICPn is primarily determined by phosphorus-related biomarkers, with indirect influences from carbon and nitrogen nutrition.},
}

@article {pmid41788258,
year = {2026},
author = {Keles, E and Celik, O},
title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.},
journal = {Microbial cell (Graz, Austria)},
volume = {13},
number = {},
pages = {117-130},
pmid = {41788258},
issn = {2311-2638},
abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.},
}

@article {pmid41787302,
year = {2026},
author = {Li, Y and Liu, L and Long, M and Guan, D and Deng, W},
title = {Habitat-driven variation in gut microbiome composition and function of the pygmy grasshopper (Tetrix japonica) across diverse ecosystems in China.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12725-8},
pmid = {41787302},
issn = {1471-2164},
support = {2023GXNSFDA026037//Natural Science Foundation of Guangxi Province,China/ ; 32360124//National Natural Science Foundation of China/ ; },
}

@article {pmid41787208,
year = {2026},
author = {Fiola, TE and Rathore, RS and Akinbi, GO and Mwashote, B and Badisa, VLD and Chen, G and Ibeanusi, V},
title = {Investigation of water quality and microbial diversity in Mississippi's major land resource area.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41787208},
issn = {1614-7499},
support = {NR204423XXXXC125-F1-SA1-21//U.S. Department of Agriculture/ ; TOA/PO-NO: 0000663592//U.S. Department of Energy/ ; DE-EM0005308//U.S. Department of Energy/ ; 0000005948//U.S. Department of Energy/ ; },
abstract = {The purpose of this research is to assess the quality of water in the Nesbit farm, which is located in the Major Land Resource Area (MLRA) in Mississippi, United States of America. This is a land resource area that faces a high risk of nutrient runoff. This research did an in-depth analysis of the quality of water in the Nesbit farm in the MLRA in Mississippi in the United States of America. This research will help to address the problems associated with the quality of water in this region by using physicochemical analysis, microbial community analysis, water quality index analysis, and geospatial analysis. The quality of water in this region, the problems associated with the quality of water in this region, and the microbial communities for grazing land management are taken into consideration in this research. The results for water temperature were obtained as (32.23 ± 0.39 °C), slightly acidic pH values ranging from (6.23-6.52), heavy metals were below the permissible limits for water as per the World Health Organization. Total dissolved solids were in the range of (1.4-1.6 mg/L), and the levels of dissolved oxygen were low (2.49-3.45 mg/L), indicating organic enrichment. Nitrate (0.11-6.36 mg/L), phosphate (0.03-0.15 mg/L) were high in concentration. The WQI of Nesbit farm water quality was 7.35, which shows that water quality is excellent in spite of localized stressors. The principal component analysis showed that the first two components explained 85.7% of the variance, and the major contributing parameters were chloride and pH. The Pearson correlation analysis indicated that there is a positive correlation between lead, total dissolved solids, chloride, and nitrate, which could be related to runoff. The metagenomics analysis indicated that Proteobacteria (30-35%) and Bacteroidetes (13-17%) are dominant species, which could be related to low organic matter. The study has provided valuable insight into water quality for Mississippi grazing land, which could be useful for effective management and conservation of natural resources.},
}

@article {pmid41787125,
year = {2026},
author = {Schleper, C and Rodrigues-Oliveira, T},
title = {Asgard archaea: have we found our microbial ancestors?.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {41787125},
issn = {1460-2075},
support = {W1257//Austrian Science Fund (FWF)/ ; EFP 25//Austrian Science Fund (FWF)/ ; },
abstract = {The discovery of Asgard archaea about a decade ago has greatly reshaped our understanding of archaeal evolution and the origin of eukaryotes. Asgards are currently thought to be the closest prokaryotic relatives of eukaryotes and to represent the archaeal host lineage that participated in the endosymbiotic event leading to the first eukaryotic cell. The presence of numerous eukaryotic signature proteins in Asgard genomes supports this view and provides important insights into the deep evolutionary roots of eukaryotic cellular complexity. However, the close relationship between archaea and eukaryotes had been observed for decades, based on features that are shared in different molecular processes. This review discusses the discovery of Asgard archaea in the broader context of archaeal molecular and cellular biology and highlights how earlier findings foreshadowed their emergence. Primarily targeted at newcomers to the field, the review provides an overview of evolutionary innovations across the Archaea domain and discusses molecular and cellular features of cultivated Asgard strains in light of previous archaeal research.},
}

@article {pmid41787122,
year = {2026},
author = {Panagiotou, K and Geesink, P and Köstlbacher, S and de Zwaan, GH and Ettema, TJG},
title = {Diversity, ecology, cell biology and evolution of the Asgard archaea.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41787122},
issn = {1740-1534},
abstract = {The Asgard archaea are a clade of archaea that was first discovered through metagenomic surveys of marine sediments. The past decade has witnessed a substantial expansion of their genomic diversity, revealing diverse metabolic repertoires and providing insights into their ecological interactions and function. Notably, comprehensive phylogenomic analyses, together with the identification of numerous eukaryotic signature proteins in Asgard archaeal genomes, have provided compelling evidence that Asgard archaea had a central role in the emergence of eukaryotes. Studies have reported the characterization of cultured Asgard archaeal representatives, uncovering unique cell biological characteristics hinting at thus far undescribed lifestyles. Here, we review the current state of the research field focusing on these intriguing microorganisms and outline future research directions aiming to resolve their ecology, cell biology and evolution.},
}

@article {pmid41786830,
year = {2026},
author = {Nowak, RG and Gough, E and Holm, JH and Hu, F and Akinyombo, K and Okudo, C and Ozumba, PJ and Jonathan, EC and Tiamiyu, AB and Kokogho, A and Adebajo, SB and Shoyemi, E and Baral, SD and Lombardi, K and Peel, S and Lim, JN and Gaydos, CA and Manabe, YC and Sears, CL and Shardell, M and Ravel, J and Crowell, TA and Tuddenham, S},
title = {Metagenomic analysis reveals rectal microbiota features associated with HIV and behavioral factors in Nigerian men who have sex with men.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42119-5},
pmid = {41786830},
issn = {2045-2322},
support = {R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R01MH099001/MH/NIMH NIH HHS/United States ; },
}

@article {pmid41786809,
year = {2026},
author = {Nagy, NA and Laczkó, L and Freytag, C and Tóth, RB and Nagy, SV and Sramkó, G and Barta, Z},
title = {Draft genomes of two Lethrus species.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06978-x},
pmid = {41786809},
issn = {2052-4463},
abstract = {The superfamily Scarabaeoidae is a species-rich and diverse group within the order Coleoptera. The members of this taxon are of interest due to the diversity of their feeding and mating behaviour, and their ecological importance. Despite the size of the superfamily, only a few genomes have been published, leaving a large gap in our understanding of the evolution of these beetles. To reduce this gap, we generated third-generation sequencing data to describe the first genome assembly of Lethrus scoparius and to improve the assembly of Lethrus apterus. The genome of L. scoparius consists of 2,873 contigs with an N50 value of 301,243 bp. BUSCO analysis revealed 98.1% complete ortholog hits in the Endopterygota ortholog database. For the L. apterus genome, we were able to assemble 886 scaffolds with an N50 value of 1,378,308 bp and a complete BUSCO hit of 96.8%. We assigned functions to 15,252 genes in L. scoparius and 15,520 in L. apterus. These genomes may contribute to understanding the evolution of the superfamily.},
}

@article {pmid41786764,
year = {2026},
author = {Franciosa, I and Castelnuovo, G and Cantele, C and Cardenia, V and Bo, S and Ponzo, V and Goitre, I and Pontonio, E and Tortarolo, D and Verni, M and Bugianesi, E and Cordero, F and Beccuti, M and Cocolin, L and Ferrocino, I},
title = {Gut microbiome modulation by cricket, pea, and whey protein using the SHIME in vitro simulator.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00785-9},
pmid = {41786764},
issn = {2396-8370},
support = {D17G22000150001//NODES funding from the MUR - M4C2 1.5 of PNRR, funded by the European Union - NextGenerationEU, Mission 4 Component 1.5 - ECS00000036/ ; },
abstract = {Entomophagy is increasingly popular, and Acheta domesticus offers an ecologically sustainable protein alternative, but the effects on the human gut microbiome need further investigation. In this study, we investigated the impact of the intake of three isolated proteins: pea (plant), whey (animal), and cricket (insect) on gut microbiome of a single-donor using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Cricket protein intake was associated with potential beneficial taxa such as Bifidobacterium and Lactobacillus, genes related to vitamin biosynthesis and bacteriocin transport, and short and medium-chain fatty acids. Pea protein intake was associated with Faecalibacterium and Slackia, while whey protein with Butyricimonas and Lactobacillus. Metagenomic analysis revealed that pea intake led to increased lysine degradation genes, promoting SCFAs production. Each protein has its own unique characteristics that may contribute positively to gut health. Specifically, cricket protein intake appears to have beneficial effects, promoting the growth of potentially beneficial taxa and enhancing short-chain fatty acid production. The results of this study indicate that cricket protein does not exhibit any detrimental effects compared to pea and whey proteins.},
}

@article {pmid41786735,
year = {2026},
author = {Wen, Y and Gao, M and Wang, Z and Liu, X and Zhang, Y and Lin, G and He, P and Yang, H and Xiao, Y and Lyu, W},
title = {Dietary copper-driven colonic dysbiosis mediates oxidative stress and butyrate deficiency to facilitate the spread of resistome in pigs.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00949-1},
pmid = {41786735},
issn = {2055-5008},
support = {10417000025CE0615G//State Key Laboratory for Managing Biotic and Chemical Threats to the Safety of Agro-products/ ; 32372907//National Natural Science Foundation of China/ ; LR25C170001//Natural Science Foundation of Zhejiang Province/ ; },
abstract = {Copper-induced transmission of antimicrobial resistance has been well documented in livestock farming environments, but the in vivo mechanisms driving fecal resistome development remain unclear. Here, 120 mg/kg CuSO4 and copper-peptide were supplemented to piglets, and the fecal resistome development was first analyzed by metagenomic sequencing. In this study, dietary CuSO4 drove abundant and diverse ARGs and MRGs. Following CuSO4 deprivation, ARGs and copper resistance exhibited a persistent promotion, whereas most MRGs rapidly declined. The resistance development was characterized by abundant MGEs. This phenomenon expanded the multiple-antibiotic resistance reservoir in fecal community, which was preferentially harbored by pathogens. Furthermore, dietary CuSO4 disturbed colonic homeostasis, characterized by impaired epithelial integrity and reduced butyrate-producing bacteria abundance, which coincided with an oxidative stress environment and increased prevalence of multiple-resistant pathogens, such as Escherichia coli and Enterococcus spp. In vitro validation further supported these associations, showing that butyrate supplementation and hypoxic conditions alleviated Cu[2+]-induced ROS generation and reduced the frequency of ARGs conjugative transfer. Overall, this study suggests that dietary inorganic copper may contribute to microbial disturbances linked to oxidative stress and potentially facilitate antimicrobial resistance transmission among pathogens, highlighting organic copper as a sustainable alternative for mitigating resistance risks in farmed animals.},
}

@article {pmid41786734,
year = {2026},
author = {Gao, M and Delgado-Baquerizo, M and Xiong, C and Sáez-Sandino, T and Wang, J and Liang, J and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK},
title = {Dominance and natural suppression of bacterial plant pathogens across global soils.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70233-5},
pmid = {41786734},
issn = {2041-1723},
support = {DP230101448//Department of Education and Training | Australian Research Council (ARC)/ ; },
abstract = {Soils are the primary environmental reservoir of plant pathogens impacting food production and ecosystem productivity worldwide. Yet, some soils can also suppress pathogens through environmental and microbial regulation. Here we integrate 1602 soil metagenomes from 59 countries with a greenhouse experiment to identify 32 dominant pathogens, including Ralstonia solanacearum, Clavibacter michiganensis, and Streptomyces europaeiscabiei. Pathogen hotspots occur primarily in warm ecosystems and agricultural soils, whereas higher soil microbial diversity, increased soil organic carbon and colder climatic conditions are associated with lower pathogen prevalence. Non-pathogenic Streptomyces spp., arbuscular mycorrhizal fungi, and biosynthetic gene clusters encoding terpenes and polyketides are associated with reduced pathogen prevalence. Predictive modelling suggests that several dominant bacterial pathogens are likely to increase in prevalence under future climate scenarios, particularly in tropical and subtropical regions. By identifying global drivers of dominant pathogens and their suppression, this study provides a foundation for improved surveillance and management of plant disease risks under climate change.},
}

@article {pmid41786226,
year = {2026},
author = {Li, Y and Wang, WJ and Zhang, S and Luo, Q and Qian, NF and Chen, DZ and Jin, RC and Feng, LJ and Yang, GF},
title = {Chaotic effects in completely autotrophic nitrogen removal over nitrite process: how minor dissolved oxygen variations reshape microbial community and functional genes to drive divergent nitrogen removal.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134333},
doi = {10.1016/j.biortech.2026.134333},
pmid = {41786226},
issn = {1873-2976},
abstract = {To elucidate how dissolved oxygen (DO) regulates nitrogen removal in the completely autotrophic nitrogen removal over nitrite (CANON) process, three continuous-flow reactors were operated under micro-aerobic conditions. Results revealed that minor DO variations (0.36-0.51 mg/L) triggered dramatic bifurcation in performance and microbial ecology, demonstrating chaotic effects characterized by nonlinear dynamics and sensitive dependence on initial conditions. A superior total nitrogen removal rate of 0.38 kg/m[3]/d and a NH4[+]-N removal efficiency of 86.7% were achieved at 0.36 mg/L DO. However, a slight increase to 0.51 mg/L DO significantly enhanced nitrite-oxidizing bacteria (NOB) activity and nitrate accumulation. Lower DO favored anammox bacteria and their essential genes (hzs/hdh), while elevated DO promoted NOB competition and oxidative stress responses, evidenced by Fe-Mn SOD gene upregulation and altered extracellular polymers composition. Our findings establish a direct link between minor DO fluctuations and macro-scale functional outcomes, providing a mechanistic framework for predicting and controlling CANON process.},
}

@article {pmid41785649,
year = {2026},
author = {Dong, W and Ye, T and Zhang, Z and An, L and Peng, Y and Chen, Y and Zhang, Y and Ke, L and Chen, S and Zhao, S and Hu, Y},
title = {Quorum sensing-associated acid adaptation in bacterial communities during pit fermentation of sauce-flavor Baijiu.},
journal = {International journal of food microbiology},
volume = {453},
number = {},
pages = {111715},
doi = {10.1016/j.ijfoodmicro.2026.111715},
pmid = {41785649},
issn = {1879-3460},
abstract = {Sauce-flavor Baijiu is produced by multi-round solid-state fermentation under progressively increasing acidity, yet how bacterial communities adapt to this extreme acid stress and whether quorum sensing (QS)-associated features are involved remain unclear. Here, fermented grains from eight pit-fermentation rounds under both traditional and mechanized processes were analyzed by metagenomic sequencing and physicochemical profiling. The traditional process showed higher moisture, stronger and faster acidification, greater lactic acid accumulation, and more rapid depletion of reducing sugars and starch than the mechanized process. These conditions coincided with a sharper decline in bacterial α-diversity and convergence toward a community overwhelmingly dominated by Acetilactobacillus jinshanensis (>90%) in the traditional process, whereas the mechanized process maintained higher diversity and a multi-species core dominated by A. jinshanensis, Lactobacillus acetotolerans, Bacillus, and actinomycetes. Canonical correspondence analysis identified acidity (lactic acid) as a major environmental factor associated with these divergent trajectories. QS gene profiling revealed process-specific signatures, with the LuxS/AI-2-associated module being the most abundant QS-related feature and significantly enriched in the traditional process. Functional annotation uncovered coordinated enrichment of acid-adaptation genes (ATPF1A, clpP, ATPF1B, dnaK, and groEL) during mid-to-late stages under high acidity. Network analysis further highlighted tighter co-associations among A. jinshanensis, QS modules, and acid-adaptation genes, supporting a community-level QS-associated functional framework for ecological convergence. Collectively, this study links LuxS/AI-2-associated features to acid-adaptation capacity and A. jinshanensis dominance in high-acidity environment. These findings provide ecological insight into microbial resilience in high-acidity solid-state fermentations and offer QS-informed perspectives for future targeted validation in Baijiu production.},
}

@article {pmid41785576,
year = {2026},
author = {Poirier, S and Rondeau-Leclaire, J and Faticov, M and Roy, A and Lajeunesse, G and Lucier, JF and Tardif, S and Kembel, SW and Ziter, C and Laprise, C and Paquette, A and Girard, C and Laforest-Lapointe, I},
title = {Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients.},
journal = {The Science of the total environment},
volume = {1023},
number = {},
pages = {181623},
doi = {10.1016/j.scitotenv.2026.181623},
pmid = {41785576},
issn = {1879-1026},
abstract = {Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosol dynamics. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and plant particles composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and plant particles. Based on beta diversity, sampling period alone explained up to 40% of plant particle, 29% of fungal, and 11% of bacterial bioaerosol composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.},
}

@article {pmid41785480,
year = {2026},
author = {Shekarriz, S and Vigod, SN and Bianco, T and Bala, A and Hao, C and Allard, JP and Hota, S and Poutanen, S and Surette, MG and Taylor, VH},
title = {The Safety, Efficacy, and Feasibility of Fecal Microbiota Transplantation in a Population With Bipolar Disorder During Depressive Episodes: A Pilot Parallel Arm Randomized Controlled Trial: Sécurité, efficacité et faisabilité de la transplantation de microbiote fécal chez une population atteinte de troubles bipolaires, au cours d'épisodes dépressifs : essai pilote contrôlé à répartition aléatoire et à groupes parallèles.},
journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
volume = {},
number = {},
pages = {7067437261420877},
doi = {10.1177/07067437261420877},
pmid = {41785480},
issn = {1497-0015},
abstract = {BackgroundThe gut microbiome has been proposed as a potential modifiable target to treat mental illness. This double-blind randomized control trial investigated fecal microbiota transplant (FMT) in bipolar disorder (BD) to assess efficacy, safety, and feasibility. The primary outcome evaluated the effectiveness of standard approved therapy for BD depression + FMT in individuals not responding to standard treatment, measured by change in the Montgomery-Åsberg Depression Rating Scale (MADRS) score from baseline to week 24. Secondary outcomes included FMT's impact on anxiety, global function, side-effects, and safety. The feasibility of this novel intervention was also assessed. Microbial analysis utilized whole-genome shotgun metagenomic sequencing, comparing outcomes between allogenic (donor) and autologous (participants own) FMT.MethodsA total of 35 participants (28 women and 7 men) with at least moderate depressive-phase BD (MADRS) were randomized to receive either allogenic FMT (n = 17) or autologous FMT (n = 18) via colonoscopy and were followed for 24 weeks.ResultsMADRS scores significantly improved from baseline to the last visit in both treatment arms. There was no significant difference between allogenic FMT (16.74-point improvement) and autologous FMT (15.4-point improvement) regarding clinical efficacy (t = -0.47, p-value = .64, 95% confidence interval [CI] = -7.3-4.6). Microbiota analysis showed that allogenic FMT let to a bacterial profile similar to the healthy donor and increased bacterial diversity at the 6-month mark, whereas those receiving autologous FMT did not. The intervention was well tolerated with no significant adverse events. Recruitment, randomization, and retention metrics support feasibility of a larger trial.ConclusionFeasibility and tolerability data indicate further investigation into microbial manipulation in BD is warranted. The absence of efficacy differences between the two types of FMT, despite microbial change, highlights the importance of a true placebo in future studies, as well as the importance of understanding exactly what bacteria are linked to improvements. ClinicalTrials.gov, NCT0327922.},
}

@article {pmid41785249,
year = {2026},
author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR},
title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1013185},
doi = {10.1371/journal.pcbi.1013185},
pmid = {41785249},
issn = {1553-7358},
abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.},
}

@article {pmid41785052,
year = {2026},
author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S},
title = {MDPD reveals specific microbial signatures in human pulmonary diseases.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
doi = {10.1093/bib/bbag017},
pmid = {41785052},
issn = {1477-4054},
abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.},
}

@article {pmid41715099,
year = {2026},
author = {Fan, W and Tan, T and Yang, C and Cao, Y and Jin, C and Liu, X and Shang, K and Wang, J and Xu, J and Li, Y},
title = {Indole-acetaldehyde from Rothia mucilaginosa activates the PXR/NRF2 axis to enhance alveolar macrophage phagocytosis and protect against ARDS.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {},
pmid = {41715099},
issn = {1465-993X},
support = {82102252//National Natural Science Foundation of China/ ; 82272245//National Natural Science Foundation of China/ ; 202440093, 2024ZZ1022//Shanghai Municipal Health Commission/ ; },
abstract = {BACKGROUND: Despite advances in therapeutic strategies, acute respiratory distress syndrome (ARDS) mortality remains high. Growing evidence links respiratory microbiome composition to ARDS outcomes. This investigation sought to elucidate how colonizing bacteria and their metabolites influence ARDS pathogenesis.

METHODS: Bronchoalveolar lavage fluid (BALF) from patients with pulmonary infections was analyzed by metagenomic next-generation sequencing (mNGS) to identify characteristic bacteria. Bacterial culture supernatants were analyzed by untargeted metabolomics (LC-MS) to identify metabolites. A murine ARDS model was established through intratracheal LPS instillation. Single-cell sequencing datasets from the GEO database were analyzed to reveal differential cell populations and functional alterations in murine ARDS. Potential molecular mechanisms were explored through molecular docking, RNA-seq analysis, Western boltting, and targeted gene knockdown in murine and cellular model.

RESULTS: R. mucilaginosa demonstrated enrichment in patients without ARDS (nARDS). The bacterial culture supernatant conferred substantial protection in murine models, whereas viable bacteria showed minimal efficacy. LC-MS analysis identified indole-3-acetaldehyde (IAAld) as the predominant metabolite in the supernatant. Single-cell sequencing suggested that resident alveolar macrophages (RAMs) were pivotal cells in murine ARDS model. IAAld enhanced RAMs phagocytosis, facilitating neutrophil and LPS clearance. Mechanistic studies revealed that IAAld likely activated PXR signaling, promoted NRF2 nuclear translocation, and upregulated the phagocytosis-related gene CD36. Targeted PXR knockdown eliminated these protective effects.

CONCLUSION: The respiratory commensal R. mucilaginosa synthesizes IAAld, which—independent of bacterial colonization per se—ameliorates ARDS through PXR/NRF2/CD36 axis activation, thereby enhancing macrophage phagocytic function. These findings suggest that therapeutic targeting of microbial metabolites represents a novel ARDS treatment paradigm.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-026-03551-3.},
}

@article {pmid41784373,
year = {2026},
author = {Aizpurua, O and Martin-Bideguren, G and Gaun, N and Alberdi, A},
title = {Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0369125},
doi = {10.1128/spectrum.03691-25},
pmid = {41784373},
issn = {2165-0497},
abstract = {Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyze the taxonomic and functional differences in the gut microbiota of 45 wild and captive European hares (Lepus europaeus), as well as to assess the impact of fresh grass supplementation to a pellet-based diet aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While grass supplementation induced some minor changes in the gut microbiota, it did not lead to statistically significant shifts toward a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggests that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions.IMPORTANCEThis study sheds light on the role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the collection of 860 near-complete genomes of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Grass supplementation to a pellet-based diet yielded limited success in restoring a microbiota similar to that of wild counterparts, highlighting the need for more tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasize that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.},
}

@article {pmid41784027,
year = {2026},
author = {Mekonnen, YT and Indio, V and Lucchi, A and Manfreda, G and Serraino, A and De Cesare, A},
title = {Detection of Chlamydia ibidis in the neck skin microbiome of broiler carcasses at the end of slaughter.},
journal = {Italian journal of food safety},
volume = {},
number = {},
pages = {},
doi = {10.4081/ijfs.2026.14726},
pmid = {41784027},
issn = {2239-7132},
abstract = {Chlamydia is the etiological agent of chlamydiosis in wild and domestic birds, mammals, and humans. In this study, Chlamydia reads were detected in the microbiome of the neck skin of 76 broiler carcasses collected in the same slaughterhouse at the end of the chilling tunnel. The carcasses originated from four different flocks of female Ross 308, reared in two broiler houses located in Northern Italy. One flock from each poultry house was sampled in 2019 and one flock in 2023. The carcass neck skin microbiome was investigated by shotgun metagenomic sequencing. Chlamydia reads displayed a mean relative abundance of 7.38%, with significant differences between carcasses obtained from the two poultry houses, sampled at both sampling times. Chlamydia ibidis was the prevalent species among time points and poultry houses. The zoonotic potential of C. ibidis and foodborne transmission have never been demonstrated. However, it is known that the genus Chlamydia has "spore"-like extracellular forms able to survive for months outside the host. Therefore, the presence of C. ibidis reads on broiler carcasses at the end of the chilling tunnel deserves further investigation. The results of this study highlight the feasibility of microbiome investigations to detect unexpected biological hazards in foods.},
}

@article {pmid41783570,
year = {2026},
author = {Lin, H and Zhu, XY and Xue, CX and Yao, P and Fu, L and Yang, Z and Zhang, XH and Moreau, JW},
title = {Metagenomics reveals diverse community of putative mercury methylators across different biogeochemical niches in Sansha Yongle blue hole.},
journal = {Marine life science & technology},
volume = {8},
number = {1},
pages = {206-220},
doi = {10.1007/s42995-025-00332-7},
pmid = {41783570},
issn = {2662-1746},
abstract = {UNLABELLED: Methylmercury (MeHg) is a potent neurotoxin and bioaccumulates in food webs. Microbial transformation of inorganic mercury (Hg) produces most of the MeHg in the marine environment. The gene pair hgcAB encodes for Hg methylation, a process predominantly attributed to anaerobic bacteria. However, recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns, although the mechanisms remain poorly understood. "Blue holes" are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles. Here, we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem. Yongle Blue Hole (YBH), currently the world's deepest known blue hole, was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment. Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation, driven by abundant and diverse Deltaproteobacteria. In the suboxic intermediate layer, Nitrospina and Myxococcota dominated the Hg-methylating community. Furthermore, Hg methylators were found to have different lifestyles (free-living or particle-associated) and to occupy distinct ecological niches within the YBH. In addition, the contribution of sinking particles to Hg methylation, especially in the deep anoxic water column, was highlighted. Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments. The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00332-7.},
}

@article {pmid41783404,
year = {2026},
author = {Liu, D and Ma, Y and Ma, Q and Huang, H and Li, T and Wang, J and Zhang, J and Cheng, X and Ge, X and Chen, Y and Zhang, Y},
title = {Clinical pathogen profiles and lung microbiome features in lung infection patients and concurrent cancer: insights from metagenomics next-generation sequencing.},
journal = {Open life sciences},
volume = {21},
number = {1},
pages = {20251220},
doi = {10.1515/biol-2025-1220},
pmid = {41783404},
issn = {2391-5412},
abstract = {Pulmonary infections in immunocompromised cancer patients present significant diagnostic and therapeutic challenges. From Dec 2021 to Aug 2023, 85 patients with pulmonary infection were enrolled and categorized into a cancer group (CP, n = 20) and a non-cancer control group (NCP, n = 18). Pathogen detection was performed using both mNGS and culture and lung microbiome analysis was conducted. mNGS demonstrated a significantly higher pathogen detection rate than culture (P < 0.0001). The CP group exhibited older age (P < 0.001), elevated neutrophil counts (NE) and higher procalcitonin (PCT) levels compared to the NCP group. Furthermore, fungal pathogens were significantly more prevalent in the CP group (P = 0.046). Both cancer status and advanced age were independent influencing factors for the detection of pulmonary fungi. Pulmonary microbiome analysis revealed no significant differences in α-diversity or β-diversity between groups. These findings indicate that mNGS offers superior sensitivity over culture. Cancer-related pulmonary infections present a distinct pathogen profile characterized by a higher prevalence of fungal pathogens. This underscores the need for enhanced clinical vigilance, especially among elderly cancer patients.},
}

@article {pmid41783251,
year = {2026},
author = {Nibbering, B and Nooij, S and Harmanus, C and Sanders, IMJG and Miedema, IM and Ducarmon, QR and Vossen, RHAM and Kloet, SL and Ardis, CK and Britton, RA and Yousefi, F and Bayne, J and Charavaryamath, C and Law, A and Murphy, ML and Sponseller, B and Burrough, ER and Ramirez, A and Mooyottu, S and Opriessnig, T and Kuijper, EJ and Roestenberg, M and Smits, WK},
title = {Characterization of the clade 4 non-toxigenic C. difficile isolate L-NTCD03 carrying the cfr(B) gene.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag010},
doi = {10.1093/femsmc/xtag010},
pmid = {41783251},
issn = {2633-6685},
abstract = {Clostridioides difficile infection (CDI) is a toxin-mediated gastro-intestinal disease. Yet, C. difficile is a phylogenetically diverse species that includes many non-toxigenic strains. In general, these are understudied, despite having significant potential impact for our understanding of the colonization process and as therapeutic modalities. Here, we present an in-depth characterization-including the complete genome sequence-of the non-toxigenic C. difficile strain L-NTCD03. This strain belongs to PCR ribotype 416, clade 4 and multilocus sequence type 39. It is resistant to multiple antimicrobials, but not those used for treatment of CDI. We validated the relevance of the cfr(B) gene from this strain in antimicrobial resistance to clindamycin, linezolid, retapamulin, and streptogramin A. We found the L-NTCD03 strain to be non-toxic in various assays. Altogether, L-NTCD03 is a promising candidate for developing into a live biotherapeutic product.},
}

@article {pmid41782849,
year = {2026},
author = {Fang, T and Hu, P and Zhang, Y and Hu, B and Miao, Q},
title = {Chronic Mycobacterium kansasii Pleural Infection Mimicking Metastatic Breast Cancer: A Seven-Year Diagnostic Odyssey and the Critical Role of Metagenomic Sequencing.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {580064},
doi = {10.2147/IDR.S580064},
pmid = {41782849},
issn = {1178-6973},
abstract = {INTRODUCTION: Nontuberculous mycobacteria such as Mycobacterium kansasii can mimic malignancy on imaging and pathology, leading to prolonged diagnostic uncertainty and inappropriate anticancer therapy.

CASE REPORT: A 76-year-old woman with remote right breast carcinoma (mastectomy and adjuvant therapy in 1996) had a persistent right chest-wall lesion with rib changes and encapsulated pleural effusion repeatedly interpreted as metastatic disease from 2017 to 2023, despite multiple biopsies showing only fibrous hyperplasia. In August 2024, fever and cough prompted re-evaluation. PET-CT demonstrated a hypermetabolic pleura-adjacent lesion (SUVmax 10.8) without distant metastases. Plasma metagenomic next-generation sequencing (mNGS) yielded a low-level M. kansasii signal; pleural fluid mNGS identified 146 reads (94% relative abundance), later confirmed by culture. Targeted anti-NTM therapy stabilized the infection; however, the patient developed severe varicella-zoster virus infection and cardiac complications and subsequently died. The death was attributed to these complications rather than the progression of the M. kansasii infection.

CONCLUSION: Chronic M. kansasii pleural infection can masquerade as metastatic breast cancer for years. PET-CT alone is insufficient to distinguish infection from malignancy; careful imaging review combined with unbiased mNGS can establish the diagnosis and avert unnecessary anticancer therapy. Multidisciplinary collaboration is essential for timely recognition and management.},
}

@article {pmid41782011,
year = {2026},
author = {Wang, X and Tian, S and Zhang, Y and Yang, L and Hu, D and Wang, Z and Yang, X and Li, S and Wei, J and Zhou, W and Wang, S and Deng, L and Li, F and Hou, S and Li, P and Ru, J},
title = {Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02368-y},
pmid = {41782011},
issn = {2049-2618},
support = {CARS-42-2//China Agriculture Research System of MOF and MARA/ ; 32341055//National Natural Science Foundation of China/ ; 273124240//Deutsche Forschungsgemeinschaft/ ; 226-2025-00030//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE.

RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE.

CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.},
}

@article {pmid41781966,
year = {2026},
author = {Srivastava, AK and Mishra, P and Kumari, S and Uddin, N and Chen, S and Zhao, Y and Xie, X},
title = {Post translational modifications as biomarkers of soil microbe responses to nano-pesticides.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04231-6},
pmid = {41781966},
issn = {1477-3155},
support = {32272514//National Natural Science Foundation of China/ ; },
abstract = {Nano-pesticides represent a significant technology advancement in modern agricultural, offering improved target specificity and reduced chemical load. However, their potential to induce subtle, sub-lethal disturbance in soil microbial function remains poorly resolved and is not adequately capture by conventional indicators such as microbial diversity, abundance, or bulk enzymatic activity. The central novelty of this review lies in proposing post-translational modifications (PTMs) as functional, early-warning biomarkers for nano-pesticide induced microbial stress, providing a molecular resolution that bridges exposure and ecological outcome. This review critically examines the current evidence on nano-pesticides-microbiome interaction and PTM-centric framework to interpret microbial responses at the protein regulation level. We highlight phosphorylation, acetylation, and ubiquitination regulate microbial stress responses, modulating detoxification enzymes, efflux pumps, and cellular signalling pathways under nanoparticle-induced stress. Unlike prior reviews that emphasize toxicity endpoints or gene-level responses, this work integrates metaproteomic evidence demonstrating PTM enrichment within stress-responsive functional protein groups across real environmental datasets, underscoring their relevance as conserved biomarkers of adaptive and maladaptive responses. By integrating metagenomics with metaproteomic and metabolomics, this review illustrates how PTM profiling enables mechanistic insight into microbial adaptation, functional impairment, and resilience under nano-pesticide pressure. Furthermore, we introduce a systems-level perspective that combines PTM data with computational modelling and AI-assisted bioinformatics to predict microbiome shifts and ecological risk, an approach not previously synthesized within the context of nano-pesticide assessment. Collectively, this review bridges nanomaterial design, microbial molecular regulation, and environmental risk evaluation, and proposes PTM-based assessment as a new paradigm for developing microbiome-safe, eco-compatible nano-pesticides and advancing molecular environmental monitoring strategies.},
}

@article {pmid41781897,
year = {2026},
author = {Liu, D and Yu, S and Tian, X and Wang, Z and Lu, Y and Dai, Y and Hu, C and Ma, X and Mao, M and Xue, L and Yi, Z and Zhang, G and Li, S and Wang, Q and Zhang, Z and Tian, Z},
title = {Epidemiological investigation of an acute gastroenteritis outbreak associated with norovirus GΙΙ.17[P17] in a cross-border travel group - Shanghai Port, China, 2024.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12978-4},
pmid = {41781897},
issn = {1471-2334},
support = {2024HK149//General Administration of Customs Project/ ; 2022YFC2302800//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Norovirus is a leading cause of acute gastroenteritis and spreads efficiently in closed, mobile cohorts such as organized travel groups. This case is notable for the real-time detection and genomic confirmation of a cross-border outbreak at a port of entry, including near-identical Norovirus GΙΙ.17[P17] genomes and documented asymptomatic carriage, illustrating the practical value of integrated metagenomic surveillance in border health operations.

CASE PRESENTATION: On July 21, 2024, 26 travelers arrived at Shanghai Port after a 12-day group tour in Europe. Clinical interviews identified 15 individuals (57.7%) with diarrhea, nausea, dizziness, and abdominal pain; no hospitalizations occurred. On-site anal swab testing was negative for SARS-CoV-2, influenza A and B, Vibrio cholerae, and Escherichia coli. RT-qPCR detected Norovirus GII in 10 samples (38.5%), including two asymptomatic individuals. Metagenomic sequencing generated near-complete genomes for all RT-qPCR-positive samples, which were 99.9-100% identical and classified as Norovirus GΙΙ.17[P17], confirming a cross-border outbreak within the travel cohort. Prompt public health response measures were initiated by Shanghai Customs and CDC authorities.

CONCLUSIONS: This case demonstrates the feasibility and impact of rapid, genomically informed surveillance at the border for detecting and characterizing travel-associated enteric virus outbreaks. The findings underscore the need for robust port-of-entry monitoring, rapid diagnostics, and integrated genomic analysis to mitigate transmission in group travel settings.},
}

@article {pmid41781872,
year = {2026},
author = {Tian, N and Liu, M and Zhao, Y and Lian, Y and Jin, M and Yang, F},
title = {Gut microbiota dysbiosis and metabolic reprogramming in pediatric migraine: a multi-omics analysis revealing diagnostic biomarkers.},
journal = {The journal of headache and pain},
volume = {},
number = {},
pages = {},
doi = {10.1186/s10194-026-02315-0},
pmid = {41781872},
issn = {1129-2377},
support = {2022 Budget Approval No. 180 of Hebei Provincial Department of Finance//Provincial Medical Outstanding Talents Project funded by the Provincial Government in 2022/ ; Grant No. 20260868//Hebei Provincial Medical Science Research Project funded by the Health Commission of Hebei Province/ ; 2026 Hebei Provincial Introduction of Foreign Intelligence Project//Hebei Provincial Department of Science and Technology/ ; },
}

@article {pmid41780551,
year = {2027},
author = {Wolf, J and Goggin, KP and Inaba, Y and Allison, KJ and Ahmed, AA and Maron, G and Ferrolino, J and Lazure, L and Kohler, C and Brenner, A and Sun, Y and Tang, L and Gonzalez-Pena, V and Rubnitz, JE and Gawad, C and Margolis, EB and Thomas, P},
title = {Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101312},
doi = {10.1016/j.lanmic.2025.101312},
pmid = {41780551},
issn = {2666-5247},
abstract = {BACKGROUND: Patients receiving myelosuppressive chemotherapy or haematopoietic cell transplantation are at high risk for life-threatening bloodstream infections. A novel pre-emptive treatment paradigm guided by pathogen detection before symptoms appear might reduce this risk, but no validated screening test is available. This study evaluated the sensitivity and specificity of plasma microbial cell-free DNA metagenomic sequencing (mcfDNA-Seq) for predicting bloodstream infections in children and adolescents receiving therapy for high-risk leukaemia.

METHODS: In this prospective cohort study, between Aug 9, 2017, and Feb 28, 2022, leftover clinical plasma samples were prospectively collected up to once per day from patients who were younger than 25 years, receiving care for leukaemia at St Jude Children's Research Hospital (Memphis, TN, USA), and at high risk for life-threatening bloodstream infections. mcfDNA-Seq was used to identify pathogen DNA in blood samples obtained during the 7 days before to 1 day after bloodstream infection onset, and in control samples from the same population in the absence of fever or infection. The testing laboratory was masked to sample status. Primary outcomes were predictive sensitivity of mcfDNA-Seq for detecting the expected bloodstream infection pathogen during the 3 days preceding the day of bloodstream infection onset, with a prespecified favourable sensitivity of 50%, and predictive specificity of mcfDNA-Seq in control samples. Exploratory analyses comprised assessing sensitivity and specificity restricted to bacteria or common bloodstream infection pathogens, and after applying a data-derived DNA fragment concentration cutoff; estimating the predictive sensitivity on each of the 7 days before bloodstream infection onset; identifying clinical characteristics that affected predictive sensitivity or specificity; and examining the clinical relevance of additional organisms identified by mcfDNA-Seq during bloodstream infection episodes. Diagnostic sensitivity was also assessed on samples collected on the day of, or day after, diagnosis of bloodstream infection. This study is registered with ClinicalTrials.gov, NCT03226158.

FINDINGS: 94 evaluable bloodstream infections occurred in 60 (38%) of 158 enrolled participants; 19 episodes were previously described in the pilot phase of this study. The predictive sensitivity of mcfDNA-Seq was 51·9% (95% CI 40·5-63·1) for all bloodstream infection episodes, 53·8% (42·2-65·2) for bacterial infection only, and 51·9% (40·5-63·1) when applying a DNA fragment concentration cutoff of 140 molecules per μL. Sensitivity was lowest at day -7 and increased daily until the day of diagnosis. Diagnostic sensitivity was 81·3% (95% CI 71·0-89·1) for all bloodstream infection episodes and 83·1% (72·9-90·7) for bacterial infections only. Predictive specificity was 82·7% (95% CI 76·0-88·2), but improved to 88·9% (83·0-93·3) for common bloodstream infection pathogens, and to 93·8% (88·9-97·0) when also applying the DNA fragment concentration cutoff. Predictive sensitivity was higher in participants with acute lymphoblastic leukaemia (adjusted odds ratio [aOR] 11·1 [1·7-74·2] vs those with acute myeloid leukaemia), and it was lower in polymicrobial infections (aOR 0·0 [0·0-0·2] vs monomicrobial Gram-positive infections). Clinical false-positive results were positively associated with gastrointestinal disturbance alone (p=0·037) or combined with recent administration of high-dose cytarabine (p=0·012). Additional organisms identified by mcfDNA-Seq that were not identified by blood culture were less likely than expected organisms to have an increasing DNA concentration during the days preceding bloodstream infection diagnosis.

INTERPRETATION: mcfDNA-Seq can detect causative pathogens before the onset of some bloodstream infection episodes in profoundly immunocompromised patients. Predictive specificity might be improved by restricting results to a subgroup of relevant organisms, excluding patients with high risk of false-positive results, or applying a higher concentration cutoff. Clinical trials are needed to evaluate mcfDNA-Seq-guided pre-emptive therapy for preventing life-threatening bloodstream infections in patients with high risk.

FUNDING: The National Cancer Institute, American Lebanese Syrian Associated Charities, St Jude Children's Research Hospital, and Karius.},
}

@article {pmid41780408,
year = {2026},
author = {Wu, H and Qi, F and Huo, Y and Li, R and Ye, M and Topp, E and Qiao, M and Zhu, Y},
title = {Feed additives increase soil risk from antibiotic resistance genes via distinct horizontal gene transfer pathways.},
journal = {Environment international},
volume = {209},
number = {},
pages = {110174},
doi = {10.1016/j.envint.2026.110174},
pmid = {41780408},
issn = {1873-6750},
abstract = {Non-antibiotic components of feed additives can enter farmland soils via livestock manure and accumulate persistently in agroecosystems, presenting potential environmental risks. We established soil microcosms, integrated metagenomes with viromes, and applied a contig-based horizontal gene transfer (HGT)-resolution pipeline to partition vector-level contributions, to assess how saccharin, copper, and their co-contamination affect soil gene flow and health risk. Results indicate divergent vector responses under additive stress: phage-host associations increased under saccharin (82 pairs vs. control 29 pairs), whereas copper strengthened plasmid-host associations. With saccharin, phage nucleotide diversity rose while synonymous nucleotide diversity declined, consistent with stronger purifying selection atop enhanced mutation supply, whereas copper increased lysogeny. Saccharin significantly elevated HGT frequency (∼50% increase), expanded donor-recipient phylogenetic span (class-level P < 0.05), and raised the phage-mediated share (∼100% increase). Copper primarily modestly increased the plasmid-mediated contribution (Cu 2.7%, HS 1.9%). Two-factor analyses revealed a significant antagonistic interaction between saccharin and copper, reducing overall HGT across taxonomic ranks under co-exposure. Although total ARG abundance did not change significantly, the health-risk index increased under saccharin, driven by enhanced ARG-MGE co-occurrence. Under co-contamination, auxiliary metabolic genes were enriched, suggesting phage-conferred metabolic empowerment that mitigates stress, partly explaining the antagonism. Altogether, our findings reveal that feed additives reshape vector-specific gene mobility and ARG risk, and they underpin a three-tiered risk-assessment framework that progresses from mere abundance to network-structured mobility and finally to mobility drivers incorporating phylogenetic transfer distance, offering a more mechanistic basis for soil-health management.},
}

@article {pmid41780396,
year = {2026},
author = {Xia, R and Shi, T and Liu, W and Li, G and Zhi, S and Luo, W and Xu, Z},
title = {Genome-resolved metagenomic insights into cornstalks-mediated reduction of pathogens and antibiotic resistomes during passively aerated static composting of swine manure.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129185},
doi = {10.1016/j.jenvman.2026.129185},
pmid = {41780396},
issn = {1095-8630},
abstract = {Passively aerated static composting is widely adopted for livestock manure treatment; however, its efficacy in eliminating antibiotic resistance genes (ARGs) and pathogens is often inadequate due to ineffective oxygen diffusion to restrict organic biodegradation and thus the formation of thermophilic condition. Despite extensive research on aerobic composting, the optimal amendment strategy and mechanistic role of crop stalks in shaping ARG dynamics during passively aerated static composting of swine manure remain unclear. Here, cornstalks and swine manure were representatively selected to elucidate how their passively aerated static composting was successfully initiated to improve ARG elimination using genome-resolved metagenomics and multivariate statistical analysis. Results show that adding 10% cornstalks significantly enhanced antibiotic resistome removal by improving composting properties (e.g. moisture content and oxygen permeability) and increasing temperature (above 65 °C). This improvement effectively inactivated bacterial hosts of ARGs and restrict horizontal gene transfer (HGT). Under these conditions, cornstalk addition promoted thermal inactivation of ARG hosts (e.g. Actinomycetota), particularly pathogenic antibiotic-resistant bacteria (e.g. Corynebacterium), thereby suppressing HGT. More importantly, chromosomally encoded mobile genetic elements (rather than plasmids and viruses) dominated HGT during composting. The transfer of multidrug, bacitracin, and macrolide-lincosamide-streptogramin resistance genes was primarily facilitated by intra-phylum HGT events, particularly within Bacillota. Cornstalk addition significantly accelerated inactivation of pathogens and ARG hosts (e.g. macrolide-lincosamide-streptogramin resistant bacteria), resulting in an increased removal of over 49.0% for both. These findings provide mechanistic insights into the optimization of passively aerated static composting for safe agricultural reuse of livestock manure.},
}

@article {pmid41780389,
year = {2026},
author = {Du, Y and Zhao, S and Gao, Y and Yan, Y and Kong, Y and Meng, W and Lu, X and Zheng, S and Mu, H and Chen, X and Kong, Q},
title = {The synergistic effect of algal-bacterial granular sludge in a sequencing batch reactor with tetracycline-containing synthetic livestock and poultry breeding wastewater.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129178},
doi = {10.1016/j.jenvman.2026.129178},
pmid = {41780389},
issn = {1095-8630},
abstract = {The concentration of environmental antibiotics, along with their ecological risk, has increased due to the continuous accumulation of livestock and poultry breeding wastewater (LPBW). In this study, two sequencing batch reactors (SBRs) were established-one equipped with algal-bacterial granular sludge (ABGS) and the other with aerobic granular sludge (AGS)-to investigate the treatment performance of tetracycline containing synthetic LPBW. Pollutant removal efficiency and underlying mechanisms were determined by analyzing the physiological and biochemical properties, dynamic changes in the microbial community, and the fate of antibiotic resistance genes (ARGs). Compared to AGS, ABGS resulted in faster granulation and greater lipid production. Exposure to tetracycline significantly altered the contents of extracellular polymeric substances (EPS) and chlorophyll. During the cultivation stage, the removal efficiencies of TN and TP by ABGS were 7.01% and 1.52% higher, respectively, than those by AGS. However, after tetracycline was added, the TN and TP removal efficiencies of ABGS decreased by 0.77% and 6.91%, respectively, compared to those of AGS. The tetracycline removal efficiency of ABGS reached 86.32%, which was 4.49% greater than that of AGS. Metagenomic analysis revealed that the relative abundances of Pseudomonas and Stenotrophomonas (key tetracycline-degrading bacteria) in ABGS were 36.61% and 66.82% greater, respectively, than those in AGS. After tetracycline was added, the relative abundances of tetracycline-related ARGs (tetX and MuxB) increased by 36.01% and 61.68%, respectively, in AGS but decreased by 53.98% and 5.71%, respectively, in ABGS. In this study, ABGS exhibited outstanding performance in enhancing the removal of pollutants from tetracycline-containing synthetic LPBW in SBR systems.},
}

@article {pmid41780383,
year = {2026},
author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X},
title = {Enhancing methane production in anaerobic digestion of food waste by Fe-MOF and Fe-MOF-derived carbon composites: Insights into properties, multi-omics analyses, and mechanisms.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129181},
doi = {10.1016/j.jenvman.2026.129181},
pmid = {41780383},
issn = {1095-8630},
abstract = {In this work, Fe-MOF and Fe-MOF-derived carbon composites (Fe-MDCs) derived at 300, 500, and 700 °C were first applied in anaerobic digestion to achieve efficient renewable energy production from food waste. The enhancement mechanism of methane yield was further explored using metagenomic and metaproteomic analysis. The results showed that compared with the control group, methane yield was enhanced by 9.66%-13.99%, 16.21%-23.56%, and 7.99%-19.84% in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups, respectively. Among them, Fe-MDC-500 possessed superior electronic conductivity and a higher specific surface area, which was beneficial for improving methane production by facilitating interspecies electron transfer and providing abundant surface sites for microbial attachment. Metagenomic analysis demonstrated that the functional microorganisms, key genes related to methane metabolism, and the activity of corresponding coenzymes were increased in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups. The poor syntrophic interaction resulted in the lowest methane yield under Fe-MOF-300 addition. Metaproteomic analysis indicated that the expressions of proteins related to quorum sensing system, transcription, and translation were also up-regulated, indicating that Fe-MDC-500 potentially promoted microbial communication among methanogenic and symbiotic microorganisms, ultimately boosting the metabolic activity of anaerobic digestion system. Meanwhile, the expressions of vital proteins involved in enzyme synthesis and catalytic bioconversion, including RNA polymerase, Ribosome, and Aminoacyl-tRNA biosynthesis, were significantly upregulated. This research clarified the mechanism of exogenous materials enhanced methane production by elucidating the key metabolic pathways and functional genes, which provided valuable insights for optimizing energy recovery system.},
}

@article {pmid41780243,
year = {2026},
author = {Sun, Y and Chen, R and van den Broek, S and Wen, J and Li, Y and Zeng, X and Su, S and Garland, G},
title = {Transmission and migration of antibiotic resistance genes following agricultural fertilization in sloping croplands.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141666},
doi = {10.1016/j.jhazmat.2026.141666},
pmid = {41780243},
issn = {1873-3336},
abstract = {Livestock manure, a major anthropogenic source of antibiotic resistance genes (ARGs) in agricultural soils due to residual veterinary antibiotics, is commonly used as a nutrient-rich fertilizer on sloping cropland. However, the role of landscape features, particularly topographic heterogeneity in shaping ARG transmission and migration remains poorly understood. In this study, we analyzed 76 metagenomes from five environmental habitats collected along three sloping cropland routes in the Dongting Lake region of China. Soil shared 276 ARG subtypes with other habitats, indicating manure fertilization on slopes facilitates ARGs diffusion across ecosystem. ARG abundance exhibited strong spatial patterns in soil samples, associated with distance from fertilized zones and buffer strips. In fertilized highland soils, mobile genetic elements (MGEs), such as transposases and Insertion Sequence Common Region (ISCRs), were significantly correlated with ARG abundance, indicating active horizontal gene transfer. In unfertilized-lowland soils, ARG composition was primarily influenced by heavy metals, particularly arsenic and cadmium. Source-tracking analysis showed that up to 70.3% of microbes migrated downslope via gravitational runoff, facilitating long-distance ARG dispersal. Risk assessment revealed higher ecological than human health risks, with high-risk ARGs linked to crop pathogens. Our findings highlight the need for landscape-based ARG management strategies within the One Health framework.},
}

@article {pmid41782139,
year = {2026},
author = {Mao, K and Zang, Y and Wang, C and Yang, W and Lu, G and Qiu, Q and Ouyang, K and Zhao, X and Song, X and Liang, H and Xu, L and Qu, M and Li, Y},
title = {Rumen microbiota-associated stress alleviation by creatine pyruvate in newly received cattle: a multi-omics study.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02365-1},
pmid = {41782139},
issn = {2049-2618},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; No. 3230810//the National Natural Science Foundation of China/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
abstract = {BACKGROUND: Stress experienced by newly received cattle is a significant challenge in the beef industry, frequently resulting in weakened immune responses and impaired growth. The rumen microbiota is essential to host health, and its imbalance can exacerbate stress. This study investigates the mechanisms by which creatine pyruvate (CrPyr) mitigates stress in newly received cattle through multi-omics approaches, including metagenomics, metabolomics, in vitro and in vivo experiments, and rumen microbiota transplantation (RMT) in mice.

RESULTS: Our results revealed that CrPyr significantly reduces stress-related hormones (cortisol and adrenocorticotropic hormone) and inflammatory markers (IL-6, IL-1β, and TNF-α), and enhanced antioxidant capacity (SOD: 57.38 versus 46.93 U/mL, P < 0.05; GSH-Px: 305.87 versus 217.07 U/mL, P < 0.05; T-AOC: 9.62 versus 7.66 U/mL, P < 0.05). Metagenomic analysis demonstrated that CrPyr increased Prevotella abundance, a key rumen bacterium involved in volatile fatty acid (VFA) production, and enriches metabolic pathways associated with energy metabolism (ATP synthesis, and pyruvate metabolism) and antioxidant defense (glutathione metabolism, FC = 1.08, P < 0.05). In vitro and in vivo experiments, as well as RMT studies in mice, further validate these findings, demonstrating that CrPyr promote VFA synthesis and increased ATP production through the electron transport phosphorylation pathway.

CONCLUSIONS: CrPyr modulates the abundance of ruminal Prevotella in transport-stressed cattle to enhance glutathione and VFA metabolism and to accelerate ATP and nucleotide synthesis, thereby alleviating stress in newly received cattle. This multimodal approach established CrPyr as an effective nutritional intervention that improves rumen function and increases livestock productivity. Video Abstract.},
}

@article {pmid41781883,
year = {2026},
author = {Xie, Y and Wang, R and Liu, X and Du, Q and Mo, S and Liu, Q and Yang, G and Fan, Z and Li, J},
title = {Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04902-2},
pmid = {41781883},
issn = {1471-2180},
support = {32171607//National Natural Science Foundation of China/ ; },
}

@article {pmid41781852,
year = {2026},
author = {Eldridge, N and Spörri, L and Kreuzer, M and Haldimann, G and Zinkernagel, MS and Zysset-Burri, DC},
title = {Uncovering the relationship between the human ocular surface microbiome and gut microbiome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04878-z},
pmid = {41781852},
issn = {1471-2180},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
}

@article {pmid41780450,
year = {2026},
author = {Li, Z and Li, X and Jiao, B and Yang, Y and Wang, H and Gu, L and Ai, H and Cheng, H and Cheng, S},
title = {Redox oscillations in riparian zone stimulate carbon loss by enhancing microbial respiration.},
journal = {Water research},
volume = {296},
number = {},
pages = {125672},
doi = {10.1016/j.watres.2026.125672},
pmid = {41780450},
issn = {1879-2448},
abstract = {Redox oscillations within riparian ecosystems emerge as a critical threat to carbon sequestration, yet the mechanistic coupling between abiotic drivers and microbial metabolism remains elusive. Through controlled incubation experiments, we demonstrate that redox-oscillating conditions significantly reduce microbial carbon use efficiency (CUE), thus accelerating carbon loss compared to static oxic or anoxic conditions. Mechanistically, redox oscillations drove the cycling of iron (Fe) species, thereby reducing the amorphous Fe pool and liberating mineral-associated organic carbon (MAOC) composed of substantial biodegradable organic substrates (e.g., lipids and proteins). Concurrently, hydroxyl radicals (•OH) generated during Fe(II) oxidation depolymerize complex aromatic organic matter into labile forms. Integrated metagenomic and metabolomic analyses further demonstrated that redox oscillations significantly reshaped soil metabolite profiles and microbial community. In particular, microbial catabolic pathways such as pentose phosphate pathway and the tricarboxylic acid (TCA) cycle were activated to efficiently mineralize newly available substrate. Together, these results identify a coupled abiotic-biotic "prime and burn" mechanism in which Fe-driven substrate reorganization primes microbial differentiation toward enhanced respiration. This study highlights redox-oscillating zones as potential carbon leakage hotpots in the terrestrial carbon sink.},
}

@article {pmid41780235,
year = {2026},
author = {Xin, Y and Liu, LH and Liu, L and Chen, SH and Zheng, YM and Zhao, QB},
title = {Seasonal variation regulates the efficacy of phytoremediation strategies on the rhizosphere resistome in urban river ecosystems.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141647},
doi = {10.1016/j.jhazmat.2026.141647},
pmid = {41780235},
issn = {1873-3336},
abstract = {Phytoremediation, as a representative nature-based solution, holds significant potential for mitigating the dissemination of antibiotic resistome in urban rivers, which is vital for safeguarding public health and aquatic ecosystems. However, the performance and mechanisms of different phytoremediation strategies (hydroponic or substrate-based strategies) in influencing the rhizosphere resistome across seasonal variation remain poorly understood. This study combined in-situ plant cultivation with metagenomic sequencing and statistical modelling to elucidate rhizosphere resistome dynamics in different phytoremediation strategies. The results showed that the phytoremediation strategies exerted limited influence on the composition and diversity of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB). Instead, the above parameters were predominantly regulated by seasonal variation and generally exhibited higher abundances during winter (4.07 ×10[-4]-2.92 ×10[-2]) than summer (3.35 ×10[-4]-2.26 ×10[-2], ANOSIM: R>0.12, P < 0.05). Nonetheless, phytoremediation strategies still led to distinct patterns for the specific resistome (P < 0.05). The relative abundance of specific VFGs was also significantly higher in the substrate-based strategy (7.21 ×10[-4]-8.82 ×10[-4]) than the hydroponic strategy (5.87 ×10[-4]-7.98 ×10[-4]), particularly during summer. The key ARB, such as those belonging to Bacteroidota, showed higher relative abundance in the hydroponic strategy (2.28 ×10[-2]-6.23 ×10[-2]) than substrate-based strategy (1.12 ×10[-2]-3.65 ×10[-2]) across seasonal variation. Mechanistically, rhizosphere exudate-derived dissolved organic matter mediated ARG dynamics by regulating bacterial communities, MGEs, and VFGs (P < 0.05). This study delineates strategy-specific controls of hydroponic and substrate-based phytoremediation on ARG dissemination across seasonal variations, delivering actionable protocols for nature-based solutions optimization in urban rivers.},
}

@article {pmid41780079,
year = {2026},
author = {Zhao, B and Xu, Y and Li, F and Song, S and Liu, Z and Liu, J and Liu, Z and Chen, X and Zhou, M and Zhao, L and Wang, X},
title = {Cyclosporine A ameliorates ulcerative colitis by inhibiting cellular senescence, modulating the JAK2-STAT3/NF-κB signaling pathway, and regulating the gut microbiota-metabolite axis.},
journal = {International immunopharmacology},
volume = {175},
number = {},
pages = {116452},
doi = {10.1016/j.intimp.2026.116452},
pmid = {41780079},
issn = {1878-1705},
abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease characterized by immune dysregulation, compromised intestinal barrier integrity, and disruptions in the microbiota-metabolite axis. Current clinical management of UC remains limited, underscoring the need for novel therapeutic approaches. Cellular senescence is increasingly recognized as a significant contributor to the pathogenesis of this disease. Senescent cells promote inflammatory responses via the sustained release of pro-inflammatory mediators such as IL-6, IL-1β, and TNF-α. Conversely, persistent inflammation drives further cellular senescence, establishing a self-amplifying cycle that exacerbates disease progression. Additionally, gut microbiota dysbiosis (reduced Akkermansia abundance) and metabolic abnormalities (disrupted bile acid metabolism) may further compromise intestinal barrier integrity. Cyclosporine A (CsA), a classical immunosuppressant, has unclear mechanisms in UC, particularly regarding its potential effects on senescence and the microbiota-metabolite axis. In this investigation, using a dextran sulfate sodium (DSS)-induced UC model, we demonstrated that CsA significantly alleviated DSS-induced acute colitis in mice and senescence-associated pathological changes. Multi-omics analyses integrating network pharmacology, transcriptomics, metabolomics, and metagenomics demonstrated that CsA likely exerts its therapeutic effects through inhibition of the JAK2-STAT3/NF-κB signaling pathway. This leads to reduced release of pro-inflammatory cytokines, modulation of intestinal microbiota composition and metabolite profiles, and enhanced intestinal barrier function.These findings elucidate new mechanisms by which CsA improves DSS-induced colitis in mice through anti-senescence effects and microbiota-metabolic regulation, providing potential therapeutic targets for UC.},
}

@article {pmid41779028,
year = {2026},
author = {Ladd-Wilson, SG and Fawcett, RW and Park, SY and Venkatasubrahmanyam, S and Lindner, MS and Davis, S and Spry, A and Singleton, J and Karpathy, SE and Paddock, CD},
title = {Rickettsia lanei Rickettsiosis, Oregon, USA, 2025.},
journal = {Emerging infectious diseases},
volume = {32},
number = {4},
pages = {},
doi = {10.3201/eid3204.251962},
pmid = {41779028},
issn = {1080-6059},
abstract = {Using metagenomic sequencing, we identified a patient infected with Rickettsia lanei who was initially diagnosed with Rocky Mountain spotted fever (RMSF), a clinically similar disease caused by infection with R. rickettsii. Our investigation highlights the importance of clinical, epidemiologic, and laboratory partnerships to leverage the discovery of novel pathogens.},
}

@article {pmid41778823,
year = {2026},
author = {Shean, RC and Tardif, KD and Rangel, A and Dutrschi, J and Bogumil, D and Cruse, A and Hernandez, S and Iremadze, N and Pollock, S and Lipson, D and Bradley, BT},
title = {Evaluation of the Ultima Genomics UG 100 sequencer for low-cost, high-sensitivity metagenomic pathogen detection from cerebrospinal fluid.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0187425},
doi = {10.1128/spectrum.01874-25},
pmid = {41778823},
issn = {2165-0497},
abstract = {Clinical metagenomic next-generation sequencing (mNGS) is a diagnostic tool allowing near-universal pathogen detection directly from clinical specimens. Despite promising clinical data, broad adoption of mNGS has been hindered by high cost and reduced sensitivity relative to targeted nucleic acid amplification tests (NAATs). Recently, Ultima Genomics introduced the UG 100 NGS platform which advertises 10 billion reads per $2,400 sequencing wafer. By lowering costs and improving sequencing depth, the historical value proposition of mNGS may be improved. This study evaluates the UG 100 sequencer's ability to generate reads for metagenomic pathogen detection from cerebrospinal fluid specimens. Ultima reads demonstrated 93% (26/28) positive agreement with orthogonal test results and 63% (10/16) negative agreement against a syndromic panel for meningitis and encephalitis. Near full-length genomes were recovered for three organisms (human herpesvirus-1 [HSV-1], Streptococcus pneumoniae, and Haemophilus influenzae), with the ability to detect putative antimicrobial resistance genes for H. influenzae. Recovery of Borrelia burgdorferi reads (6.1 reads per million [RPM] and 9.03 RPM) was achieved from clinical samples with late cycle threshold values (39.7 and 43.0, respectively). Limit of detection (LoD) studies demonstrated detection of HSV-1 and S. pneumoniae reads at concentrations of 50 genomes/mL each, which is below the reported LoD for the orthogonal NAATs used in this study. Reducing sequencing costs and improving the analytical sensitivity remove two major hurdles for mNGS adoption by clinical laboratories. While these results are preliminary, they demonstrate a future in which mNGS may be more widely implemented.IMPORTANCEClinical metagenomic next-generation sequencing has struggled to gain wider adoption for nearly a decade, due in part to its high cost and reduced performance versus targeted molecular assays. This study demonstrates the ability of the UG100 sequencing platform to reduce per-base metagenomic sequencing costs while producing reads that maintain high positive agreement with existing molecular assays. Further improvements to cost and analytical performance may shift clinical metagenomics from an expensive test of last resort to a front-line diagnostic for identifying infections.},
}

@article {pmid41778788,
year = {2026},
author = {Lee, S and Kim, H-L and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Cho, J and Kim, H-N},
title = {Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0097125},
doi = {10.1128/spectrum.00971-25},
pmid = {41778788},
issn = {2165-0497},
abstract = {Dyslipidemia, characterized by abnormal blood lipid levels, constitutes a significant risk factor for cardiovascular disease. Emerging evidence indicates that the gut microbiota influences lipid metabolism, although findings across studies have been inconsistent. In this cross-sectional investigation, we analyzed the composition of gut microbiota, associated metabolic pathways, predicted gut metabolites, and the resistome in 1,384 participants (including 895 individuals with dyslipidemia and 489 controls) through shotgun metagenomic sequencing. Our findings demonstrated that Bacteroides caccae was enriched among dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism. Conversely, Coprococcus eutactus and Coprococcus catus, recognized producers of short-chain fatty acids (SCFAs) involved in lipid regulation, as well as Blautia obeum, known to be positively affected by SCFAs, were more prevalent in the control group. Additionally, we identified an enrichment of the gene family responsible for dTDP-beta-D-fucofuranose biosynthesis, associated with bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris serving as a major contributor. Dyslipidemia cases also exhibited depletion of glycogen and peptidoglycan biosynthesis pathways, which may compromise energy storage and immune function, alongside decreased levels of pseudouridine, a molecule involved in RNA metabolism. Furthermore, a marginal increase in abundance of antibiotic-resistance genes, tetQ, was observed in dyslipidemia cases, suggesting a potential link between the gut resistome and metabolic dysregulation. These results offer novel insights into the role of gut microbiota in the pathophysiology of dyslipidemia and underscore potential microbiome-targeted interventions for metabolic disease management.IMPORTANCEDyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. This study analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and antimicrobial resistance genes in 1,384 participants using shotgun metagenomic sequencing. Individuals with dyslipidemia exhibited an imbalance in gut bacteria, including an increase in Bacteroides caccae, a species associated with inflammation, and a decrease in short-chain fatty acid-producing bacteria such as Coprococcus eutactus and Blautia obeum, which support metabolic health. Furthermore, we identified significant changes in microbial metabolic pathways related to energy storage and immune function, as well as an increased abundance of tetracycline resistance genes (tetQ), suggesting a potential link between dyslipidemia and antimicrobial resistance. Our study provides a comprehensive overview of dyslipidemia-associated gut microbial alterations, highlighting potential mechanistic links and therapeutic targets.},
}

@article {pmid41778780,
year = {2026},
author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S},
title = {Beyond bacilli: integrating the microbiome into the TB research agenda.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638004},
doi = {10.1080/19490976.2026.2638004},
pmid = {41778780},
issn = {1949-0984},
abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.},
}

@article {pmid41778495,
year = {2026},
author = {Lu, J and Bi, H and Zhang, R and Liu, X and Wang, B and Wu, J and Lee, JK and Kalia, VC and Gong, C},
title = {Pesticide Biodegradation Catalyzed by a Cold-Adapted Acetylxylan Esterase Identified from a Metagenome-Assembled Genome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13419},
pmid = {41778495},
issn = {1520-5118},
abstract = {This study identified a putative cold-adapted acetylxylan esterase in Glutamicibacter soli Em07 via a metagenome-assembled genome. The gene encoding this enzyme was cloned and heterologously expressed in Escherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed that the protein has a molecular weight of 33.24 kDa. Using 1-naphthyl acetate as a substrate, the enzyme activity was optimal at 20 °C and pH 9. Furthermore, the enzyme exhibited excellent cold adaptation, alkali resistance, and salt tolerance. It demonstrated OCP pesticide-degrading activity: 66.48% degradation of carbaryl, 92.14% of cypermethrin, and 97.78% of malathion, underscoring its strong potential in environmental remediation. Notably, this esterase emerged as the first to simultaneously possess cold adaptation, alkali resistance, and salt tolerance. These results positioned the enzyme as a promising candidate for bioremediation strategies in multiextreme environments. Further research will investigate its activity on other persistent organic pollutants.},
}

@article {pmid41778161,
year = {2026},
author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z},
title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1755982},
pmid = {41778161},
issn = {1664-2392},
abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.

METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.

RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial β-oxidation of long-chain saturated fatty acids, α-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).

DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.},
}

@article {pmid41777547,
year = {2026},
author = {Maisto, L and Telegrafo, C and Rubino, F and Santamaria, M and Traka, MH and Tullo, A and Bouwman, J and Sbisà, E and Balech, B},
title = {Multifaceted human gut microbiome data associated with health and nutrition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1722500},
pmid = {41777547},
issn = {1664-302X},
abstract = {The microbiome, also considered the hidden organ, is a fundamental ecosystem directly associated with the disease and health status of the human body. With the availability of high-throughput DNA sequencing technologies, a growing number of studies from clinical and experimental (observation and intervention) samples are constantly revealing new findings on the relationship between human organs and their microbiomes. In such a context, diet and nutrition are among the key factors influencing microbiome composition, richness, and functional behavior. In this review, we illustrate how microbiome-related data and associated metadata are in recent times scattered across primary and specialized databases with different levels of curation, annotation, and standardization, limiting, to some extent, the possibility of deep data discovery, reuse, alignment, and harmonization. Therefore, we describe the way Findable, Accessible, Interoperable, and Reusable (FAIR) data principles would enhance the onset of novel scientific hypotheses and potential microbiome-targeted therapies by improving the standardization policies in data sources. Accordingly, using advanced semantic classification and data mining technologies based on suitable and comprehensive ontologies, annotations of studies present in source databases or in scientific literature would further improve the data and metadata enrichment, integration and alignment relevant to microbiome data associated with health, disease and nutrition.},
}

@article {pmid41777539,
year = {2026},
author = {Wang, M and Li, X and Liu, X and Ye, Y and Zhou, P and Liu, Y and Zhu, L and Wei, W and Li, Z and Li, Z and Wu, R and Peng, Y and Liu, Z and Lu, X and Zhao, J and Kan, B},
title = {Restaurant occupational exposure affects the profiles of oral and gut pathobiomes and resistomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771459},
pmid = {41777539},
issn = {1664-302X},
abstract = {INTRODUCTION: Restaurant occupational exposure refers to contact with food-processing environments, raw materials, and customers, which may influence the composition of the human microbiome. Differences and associations between human oral and gut pathobiome and their resistomes under restaurant occupational exposure remain unclear. We conducted a comprehensive metagenomic analysis of paired oral and fecal samples from Front-of-House (FOH) workers and Back-of-House (BOH) workers to elucidate the effects of occupational exposure in the restaurant environment on oral and gut pathobiome, antimicrobial resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs).

METHODS: We collected the oral and fecal samples from 35 FOH and 37 BOH workers across 24 Chinese restaurants in Zhengzhou, Henan, China. The diversity and relative abundances of microbial species, ARGs, VFs, and MGEs were compared. Clonal strains from paired oral and fecal samples were analyzed. The serovars of Salmonella were determined using the ucgMLST. Finally, we used the O2PLS method to explore relationships among ARG subtypes, bacterial communities (species-level), MGEs (subtype-level), and plasmids.

RESULTS: The gut microbiome acts as the primary reservoir, exhibiting greater alpha diversity and a higher burden of pathogens/resistomes (including high-risk Rank_I genes). In contrast, the oral microbiome was more sensitive to occupational differences. Significant beta diversity variations in microbiomes, antimicrobial resistance genes (ARGs), and virulence factors were observed exclusively in oral samples. Notably, Salmonella Typhimurium was significantly more prevalent in the oral cavity of BOH workers (R [2] = 0.032, p = 0.047), indicating their potential role as intermediaries in foodborne pathogen transmission. Strain-level analysis confirmed that clonal strains of the opportunistic pathogen and probiotics were shared between the oral cavity and the gut. O2PLS analysis identified plasmids as the main correlates of ARGs.

DISCUSSION: While the gut serves as the primary reservoir for pathogens/resistomes, restaurant occupational exposure distinctly shapes oral microbial/resistome profiles, underscoring the critical need for reinforced hygiene management, particularly for BOH workers, to mitigate pathogen and resistance transmission.},
}

@article {pmid41777393,
year = {2026},
author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D},
title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1685007},
pmid = {41777393},
issn = {1664-462X},
abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.},
}

@article {pmid41777069,
year = {2026},
author = {Zamperin, G and Palumbo, E and Castellan, M and Marciano, S and Fusaro, A and Monne, I},
title = {Metagenomic sequencing of zoonotic viruses: evaluation of a CRISPR-Cas-based rRNA depletion system.},
journal = {Veterinaria italiana},
volume = {62},
number = {2},
pages = {},
doi = {10.12834/VetIt.3908.38985.2},
pmid = {41777069},
issn = {1828-1427},
abstract = {Pathogen-agnostic diagnostics are crucial for the early detection of emerging viruses. Shotgun metagenomic sequencing enables unbiased detection of viral genomes but is frequently constrained by the abundance of host and microbial ribosomal RNA (rRNA), which reduces sensitivity and increases sequencing costs. CRISPR-Cas9-based rRNA depletion has emerged as an alternative to enzymatic methods; however, its performance for the characterization of zoonotic viruses across diverse animal hosts and tissues remains underexplored. We compared CRISPR-Cas9 (Jumpcode CRISPRclean™ Plus) and RNase H-based enzymatic depletion (Ribo-Zero Plus, Illumina) using 12 samples positive for rabies lyssavirus, influenza A virus, West Nile virus or norovirus, from multiple host species and tissues, including both high-quality and degraded RNA. CRISPR-Cas9 efficiently reduced rRNA content (14.5%) but recovered fewer viral reads than Ribo-Zero, which achieved up to 60.7× enrichment. Both methods produced complete viral consensus genomes when RNA quality and viral load were sufficient. However, based on the data generated here, enzymatic depletion currently remains more efficient and cost-effective for viral metagenomics. Further optimization of CRISPR-Cas9 workflows could enhance its utility for viral surveillance and diagnostics.},
}

@article {pmid41634542,
year = {2026},
author = {Sun, M and Wei, J and Wang, M and Xu, H and Ma, W and Wang, Y},
title = {Research on the process of synergistic degradation of corn straw by probiotics-enzymes based on microbiome and metabolomics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41634542},
issn = {1471-2180},
support = {CARS-39-27//National Wool Sheep Industry Technology System/ ; jytms20231736//Liaoning Provincial Department of Education General Project/ ; 2024010768-JH3/107, 2024012131-JH4/4800//Liaoning Provincial Natural Science Foundation Project/ ; S202410160014//College Student Innovation Project/ ; },
abstract = {BACKGROUND: Probiotics enzyme co-fermentation significantly improves the use efficiency and nutritional value of crop straw, although the underlying synergies are not clear.

METHODS: The experiment used corn straw as the raw material. It was treated with a 0.2% composite enzyme preparation containing cellulase, xylanase, lignin peroxidase, manganese peroxidase, and laccase. A composite microbial inoculant was also added at a total inoculum level of 1 × 10⁸ CFU/g, using a ratio of Lactobacillus, yeast, and Bacillus subtilis of 3:2:1. After thorough mixing, the solution was sprayed evenly onto the straw surface. Fermentation proceeded under room temperature conditions. Multipoint random sampling was carried out on days 7, 14, 21, and 28. By integrating metagenomic, metabolomic, and conventional analytical approaches, this study systematically investigated microbial community structure, dynamic metabolic pathways, and fermentation quality during the process.

RESULTS: The application of a probiotics-enzyme composite led to a clear improvement in fermentation quality. It also reduced the cellulose content of corn stover compared to the untreated control. The results showed that major microbial taxa, such as Proteobacteria and Firmicutes, are influenced by environmental factors like pH and lactic acid. These microbes significantly degraded fibre components (p < 0.05) by secreting extracellular enzymes and organic acids. This process encouraged the accumulation of raw proteins and dipeptides. Key metabolic pathways, such as pyrimidine metabolism and the TCA cycle, were significantly enhanced. This led to the synthesis of valuable metabolites, including mevalonate and biopterin, which have increased antioxidant and metabolic properties.

CONCLUSION: The research results demonstrate that the “microbiota structure—metabolic function—fermentation quality” relationship constitutes a complex and mutually influential system, providing important theoretical support for targeted microbial community regulation and optimization of fermentation processes in straw.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04776-4.},
}

@article {pmid41776697,
year = {2026},
author = {Shi, X and Chen, F and Dai, M and Tang, Y and Wang, J and Lin, Y and Shi, M and Lan, T and Liu, H and Jin, X and Xiao, L and Kristiansen, K and Li, X},
title = {Comprehensive catalog of gut microbial genomes in Asian elephants: insights from shotgun metagenomics.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00533-0},
pmid = {41776697},
issn = {2524-4671},
}

@article {pmid41776502,
year = {2026},
author = {Tümmler, B and Schulz, A and Minso, R and Alfeis, N and Tamm, S and Rademacher, J and Ringshausen, FC},
title = {CFTR activity in nasal potential difference of adults with idiopathic bronchiectasis.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03599-1},
pmid = {41776502},
issn = {1465-993X},
}

@article {pmid41776310,
year = {2026},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {41776310},
issn = {2662-8465},
support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}

@article {pmid41776033,
year = {2026},
author = {Yu, Q and Liu, H and Shi, H and Abdrakhmanov, Y and Shen, J and Zhang, C and Dong, Z and Zong, L and Si, L and Dai, L and Li, Y},
title = {Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models.},
journal = {Nature biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {41776033},
issn = {2157-846X},
abstract = {Identifying evolutionarily remote antimicrobial peptides (AMPs) is crucial for discovering underexplored clinical candidates to combat antibiotic resistance. Existing experimental and computational methods are limited by their reliance on sequence identity to known AMPs, missing distant homologues. Here we introduce HMD-AMP, a protein language model-based approach for AMP discovery. HMD-AMP outperforms previous methods in identifying evolutionarily distant AMPs and enables the discovery of unknown and highly potent AMPs from metagenomic data. Applied to host and gut microorganism genomes of nine mammals, HMD-AMP revealed over 37 million predicted AMPs. Of 91 high-confidence sequences experimentally validated, 74 showed strong antibacterial activity and 48 were evolutionarily remote from known AMPs. Four of these AMPs exhibited broad-spectrum antibacterial activity at low effective concentrations and showed low toxicity, with the most potent peptide demonstrating therapeutic efficacy in a mouse model of peritoneal Escherichia coli infection. This study introduces an effective strategy to uncover AMPs.},
}

@article {pmid41775849,
year = {2026},
author = {Plewnia, A and Hildwein, T and Quezada Riera, AB and Terán-Valdez, A and Crawford, AJ and Heine, C and Franco-Mena, D and Székely, D and Armijos-Ojeda, D and Siavichay, FR and Arpi, JD and Salazar, J and Erens, J and Páez-Vacas, MI and Székely, P and Böning, P and Stassen, R and Carvajal-Endara, S and Lötters, S and Guayasamin, JM},
title = {Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41937-x},
pmid = {41775849},
issn = {2045-2322},
}

@article {pmid41775798,
year = {2026},
author = {Nearman, A and Lamas, ZS and Niño, EL and Fine, J and Mayack, C and Seshadri, A and Boncristiani, D and Huang, WF and Evans, JD and Chen, YP},
title = {Metagenomic and gene expression patterns in declining commercial honey bee colonies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42605-w},
pmid = {41775798},
issn = {2045-2322},
support = {FSA25IRA0012292//Farm Service Agency/ ; 8130-0960//Animal and Plant Health Inspection Service/ ; },
}

@article {pmid41775707,
year = {2026},
author = {Wang, J and Wang, S and Li, T and Hou, W and Deng, Y},
title = {A watershed-scale potential pathogenic bacteria dataset from the Yangtze River Basin.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06983-0},
pmid = {41775707},
issn = {2052-4463},
support = {42277104//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbial safety is fundamental to ensuring water quality, particularly in the Yangtze River Basin, China's most critical drinking water source. Despite its ecological and economic importance, the basin faces significant anthropogenic pressures, including wastewater discharge, which may elevate the risk of pathogenic contamination. However, fragmented sampling efforts and limited coverage have hindered a systematic understanding of pathogenic microbial diversity and distribution across this vast ecosystem. A novel bioinformatic pipeline leveraging Genome-Specific Markers to accurately identify and quantify potential pathogenic taxa in metagenomic data was applied to 625 publicly available metagenomes, spanning water, sediments, and riparian soils along the 6,300 km Yangtze River continuum. We reconstructed a potential pathogen catalog comprising 403 taxa, largely expanding the pathogen diversity in the large river ecosystem. We also generate the Richness distribution maps of potential pathogens for water, sediments and soils along Yangtze River. The basin-scale pathogen inventory not only establishes a baseline for potential pathogenic bacteria communities in the Yangtze Basin but also serves as a reference library for quick biosurveillance and risk management from genomic resolution.},
}

@article {pmid41775307,
year = {2026},
author = {Li, Y and Pan, J and Li, Y and Zhao, Z and Zhang, Y},
title = {Direct interspecies electron transfer-based methanogenic aggregate: A survival strategy to overcome defensive attack from type VI secretion system during syntrophic cooperation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134329},
doi = {10.1016/j.biortech.2026.134329},
pmid = {41775307},
issn = {1873-2976},
abstract = {Physically tight structure of methanogenic aggregates formed by syntrophic microbes that exchange electrons via interspecies hydrogen/formate transfer (IHT/IFT) can activate defensive attack from type VI secretion system (T6SS), which has been recognized as the primary cause for poor stability. Direct interspecies electron transfer (DIET) may alleviate the technical bottleneck of proximity-triggered defensive attack from T6SS, since syntrophic microbes function long-distance electron transfer via electrically conductive pili (e-pili) or its displayed c-type cytochromes. Here, three up-flow anaerobic sludge blanket reactors, respectively with ethanol, propionate, and butyrate as a sole substrate, were used to culture DIET- and IHT/IFT-based aggregates. DIET-based aggregates were generally larger and exhibited a looser, porous structure compared to IHT/IFT-based aggregates. However, rheological behavior showed that they possessed higher rigidity and toughness, attributed to the structural support of the conductive pili network. 3D reconstruction and imaging of a single DIET-based aggregate by nano-industrial computed tomography showed that syntrophic microbes did not display a pronounced localized aggregation pattern. Conductivity-temperature/pH response showed that the DIET-based aggregates exhibited a metallic-like conductance similar to that found in e-pili. Meanwhile, the surface-enhanced Raman spectra showed that the intensities of characteristic peaks associated with c-type cytochromes in DIET-based aggregates were higher than those in IHT/IFT-based aggregates. Analysis of metagenomic and metaproteomic data showed that in DIET-based aggregates expression of key proteins of T6SS was suppressed. These results demonstrated that in DIET-based aggregates syntrophic microbes did not aggregate to form a physically tight structure, eluding defensive attack from T6SS and strengthening their stabilities.},
}

@article {pmid41775298,
year = {2026},
author = {Luo, J and Yang, S and Feng, Q and Zou, X and Wu, Y and Wang, F},
title = {Triazine-induced extracellular polymeric substance disruption drives metabolic reprogramming and enhanced volatile fatty acid production in anaerobic sludge fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134322},
doi = {10.1016/j.biortech.2026.134322},
pmid = {41775298},
issn = {1873-2976},
abstract = {The accumulation of antimicrobial contaminants in waste-activated sludge (WAS) posed challenges to anaerobic fermentation processes, with mechanistic impacts on volatile fatty acids (VFAs) production remaining poorly understood. 1,3,5-triazine (triazine), a widely detected triazine-based antimicrobial agent, paradoxically enhanced VFAs production in a concentration-dependent manner, achieving maximum yields of 1771 mg COD/L (18.4-fold increase compared with control). Enhanced production was accompanied by a distinct metabolic shift from propionate to acetate dominance (from 38.7 to 54.3%), driven by systematic disruption of extracellular polymeric substances (EPS), especially proteins. Molecular docking revealed that triazine induced conformational instability and structural damage in proteins through hydrogen bonding and hydrophobic interactions. Meanwhile, the increase in ammonium nitrogen concentration under triazine stress provided further confirmation of the hydrolysis of proteins, providing readily fermentable substrates for VFAs production (particularly acetate). High-throughput 16S rRNA sequencing uncovered concentration-dependent microbial community restructuring, characterized by enrichment of proteolytic bacteria (Petrimonas) and acetate producers (Anaerovorax), concurrent with the suppression of methanogens. Functional metagenomic analysis using PICRUSt2 revealed upregulation of proteolytic enzymes (e.g., EC:3.4.16.4) and acetyl-CoA synthesis genes (e.g., PDHA), facilitating enhanced protein hydrolysis and acetate biosynthesis. Critically, triazine stress activated quorum sensing and two-component regulatory systems, with luxS expression increasing 5.7-fold, promoting metabolic coordination and stress resilience rather than community collapse. Partial least squares path modeling confirmed that substrate availability (λ = 0.459) served as the primary driver of VFAs accumulation, mediated by microbial community adaptation (λ = 0.560). These findings unveil how antimicrobial stress enhanced resource recovery via EPS-mediated metabolic reprogramming.},
}

@article {pmid41775266,
year = {2026},
author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J},
title = {Competition and compromise between exogenous probiotics and native microbiota.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101516},
doi = {10.1016/j.cels.2025.101516},
pmid = {41775266},
issn = {2405-4720},
abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.},
}

@article {pmid41775198,
year = {2026},
author = {Xiao, J and Wang, Y and Chen, H and Bu, F and Xu, W and Qiu, S and Kang, Y and Wang, D and Wu, H and Hu, Z and Zhang, J and Guo, Z},
title = {Overlooked fate and associated pathogens of antimicrobial resistance in the Yellow River Delta, China.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141645},
doi = {10.1016/j.jhazmat.2026.141645},
pmid = {41775198},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) within terrestrial inputs and marine dispersal in estuarine deltas has posed significant environmental challenges, exacerbated by diverse microbial habitats, estuarine eutrophication, and other anthropogenic impacts. However, the precise mechanisms governing persistence and associated risks of ARGs in this region remain poorly understood. In this study, the distribution, mobility, removal and hosts of ARGs in wetlands and rivers of the Yellow River Delta (YRD) region were systematically investigated through metagenomic approaches. A total of 23 antibiotics were detected in water (0.07-4.67 ng/L) and 14 antibiotics in sediment (0.0042-0.4768 ng/g). Following wetland treatment, despite a 67.5% reduction in antibiotic concentrations, the relative abundance of antibiotic resistance genes decreased by only 7.60%, indicating substantial persistence of genetic resistance. Moreover, Proteobacteria were identified as primary hosts for ARGs. ARGs carried by resistant pathogens, especially ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), also showed a significant reduction in the abundance and diversity throughout the wetland. Notably, total nitrogen in water (Water-TN) greatest shaped the composition of the resistome and microbiome, while the presence of antibiotics exerted stronger selective pressure on ARGs in wetland than in river. Collectively, this study highlights the associated risks of ARGs in YRD, offering insights for controlling antimicrobial resistance in deltas.},
}

@article {pmid41775197,
year = {2026},
author = {Lin, L and Su, Z and Yang, X and Yang, F and Zhang, L and Adyari, B and Yang, X and Liu, S and Hu, A},
title = {Impacts of tributaries and sewage effluents on antibiotic resistance genes and pathogens in an urban river.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141641},
doi = {10.1016/j.jhazmat.2026.141641},
pmid = {41775197},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) within urban rivers presents an increasingly public health threat. This study utilized shotgun metagenomics to assess the distribution, drivers, and risks associated with ARGs and ARG-carrying pathogens (APs) in the Xiaoqing River, focusing on impacts from sewage treatment plant (STP) effluents and tributaries. Results demonstrated significantly elevated ARG and AP abundance and diversity in urban segments and STP effluents relative to upstream and downstream areas. Macrolide-lincosamide-streptogramin resistance genes dominated the urban river resistome. Tributaries were characterized by elevated concentrations of ARGs and identified as important reservoirs. STP effluents introduced APs, including Acinetobacter johnsonii, Enterobacter asburiae and Escherichia coli. Although overall ARG pollution decreased downstream, 44.8% of ARG subtypes and clinically relevant APs persisted, with downstream E. coli strains notably carrying an 8-fold higher ARG load. Mobile genetic elements showed a strong correlation with ARG propagation (R[2] > 0.60, P < 0.001), which may be facilitated by erythromycin and clarithromycin. Semi-quantitative source tracking analysis indicated that tributaries and STP effluents likely represent nonnegligible contributors to ARGs and APs in the urban river. This study demonstrates that sustained urban and tributary discharges drive resistome dissemination, posing persistent risks that require integrated riverine antimicrobial resistance management.},
}

@article {pmid41775186,
year = {2026},
author = {Geromino, P and LeMoine, CM and Drahun, I and Cassone, BJ},
title = {Co-supplementation of a polyethylene diet for improved fitness of Galleria mellonella larvae.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141617},
doi = {10.1016/j.jhazmat.2026.141617},
pmid = {41775186},
issn = {1873-3336},
abstract = {A growing number of plastivore insects have been discovered that readily consume and biodegrade various petro plastics, including LDPE. The caterpillar larvae of Galleria mellonella are capable of breaking down the polymers at expedited rates; however, feeding on LDPE as a sole nutrient source is inefficient and detrimentally impacts larval survival, growth, and development. The objective of our study was to improve fitness parameters and feeding activities of LDPE-fed larvae through the addition of various macro- and micronutrients. Each co-supplementation recovered fitness and consumption to some extent in comparison to pure LDPE; however, artificial sources produced outcomes that were well below those of the caterpillar's natural diet, regardless of the combination. Co-supplementation of LDPE, honeycomb, and corn syrup was the most successful, with larval fitness and consumption approximating their natural diet. To provide mechanistic insights into this recovery, qPCR and metagenomics analyses indicated the co-supplementation promoted greater gut bacterial abundance and species richness and evenness. In addition, GC-MS analyses identified notable differences in their fat body metabolic profiles that may contribute to slower developmental rates. We also assessed the capability of the larvae to eliminate food wastes, which showed promise and could represent a potential co-supplement source for LDPE biodegradation.},
}

@article {pmid41775040,
year = {2026},
author = {Liu, T and Sun, X and Huang, D and Kong, T and Huang, W and Lin, Z and Wang, Z and Li, B and Sun, W},
title = {Differential patterns of antibiotic resistance, virulence, and dissemination risks in floating and sedimented plastispheres.},
journal = {Water research},
volume = {296},
number = {},
pages = {125644},
doi = {10.1016/j.watres.2026.125644},
pmid = {41775040},
issn = {1879-2448},
abstract = {The plastisphere, a unique ecological niche on plastic surfaces, enriches microbial antibiotic resistance genes (ARGs) and virulence factors (VFs), posing environmental and health risks. Although aquatic sediment is a major sink for plastic contaminants, the resistance, virulence and dissemination potentials of sedimented plastispheres remain poorly characterized compared to floating plastics. Through investigation of metagenomes from two sites in the Pearl River in China, one of the world's plastic pollution hotspots, we report that water plastisphere showed 2.4 and 3.6 times more ARG and VF genes than those in sediment plastisphere and surrounding environments, together with higher mobile genetic element (MGE) abundances and a denser ARG-VF co-occurrence network (5,879 vs. 2,874 edges; density 0.043 vs. 0.025), indicating enhanced horizontal gene transfer potential. These differences coincide with contrasting ARG/VF assembly mechanisms, with deterministic and stochastic assembly processes dominating ARG/VF profiles in water and sediment plastispheres, respectively. Genome-resolved analyses further revealed that dominant plastisphere populations harbored multiple ARGs and VFs, with 41 MAGs predicted with pathogenicity capacities, most of which belonged to the families Mycobacteriaceae, Aeromonadaceae, Moraxellaceae, and Pseudomonadaceae. Notably, these taxa have been repeatedly reported as common plastisphere members across diverse ecosystems, suggesting that elevated resistance and virulence in floating plastispheres may be a widespread phenomenon across aquatic ecosystems. Together, our findings demonstrate that floating plastics act as dynamic vectors of antimicrobial resistance and pathogenicity, as well as their dissemination potentials, highlighting water-sediment transition may reduce these ecological risks within the plastisphere.},
}

@article {pmid41775000,
year = {2026},
author = {Mammeri, M and Obregon, D and Chevillot, A and Abuin-Denis, L and Skičková, Š and Kratou, M and Wu-Chuang, A and Maitre, A and Christine, J and Polack, B and Cabezas-Cruz, A and Adjou, KT},
title = {Yeast probiotic protects gut microbiota diversity and metabolic potential against Cryptosporidiosis-induced disruption in goat kids.},
journal = {Veterinary parasitology},
volume = {343},
number = {},
pages = {110729},
doi = {10.1016/j.vetpar.2026.110729},
pmid = {41775000},
issn = {1873-2550},
abstract = {Cryptosporidiosis, caused by Cryptosporidium parvum, is a major cause of enteric disease and gut microbiota disruption in neonatal ruminants. It can lead to impaired growth, increased susceptibility to pathogens, and long-term gut dysfunction. In this study, we investigated whether supplementation with a live yeast probiotic (Saccharomyces cerevisiae Sc47) could help preserve gut microbiota resilience and functional homeostasis during an experimental C. parvum oral infection in goat kids. Thirty male French Alpine goat kids were assigned to three groups: uninfected control (healthy), infected, and infected with yeast supplementation. Longitudinal 16S rRNA gene sequencing, network analysis, and functional metagenomic predictions were used to assess microbial diversity, community composition, co-occurrence patterns, and metabolic potential, with a focus on short-chain fatty acid (SCFA) biosynthesis. Infection induced marked dysbiosis, characterised by a substantial reduction in microbial richness and a widespread loss of SCFA-producing commensals and metabolic functions. In contrast, yeast supplementation significantly reduced oocyst excretion by more than 84% throughout the experiment, attenuated pathogen-induced community shifts, and maintained beneficial genera such as Butyricicoccus and members of the Oscillospiraceae family. Furthermore, network analysis revealed that probiotic treatment preserved microbial association structures and reduced community fragmentation. Consistent with these findings, functional profiling showed the retention of pathways involved in carbohydrate metabolism, amino acid biosynthesis, and SCFA production, suggesting enhanced microbiota resilience. These findings demonstrate that S. cerevisiae supplementation can mitigate infection-associated dysbiosis by controlling pathogenic overgrowth while sustaining commensal bacterial stability and functional capacity. This highlights its potential as a microbiota-targeted strategy to support gut health in neonatal ruminants.},
}

@article {pmid41774281,
year = {2026},
author = {Kapoor, V and Sanchez-Vicente, S and Donovan, W and Park, J and Nagapurkar, A and Gokden, A and Shrivastava, P and Horn, E and Briese, T and Lipkin, WI and Tokarz, R},
title = {Adaptation of custom capture sequencing panels to the Oxford Nanopore MinION platform.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41774281},
issn = {1573-4978},
support = {75A50122C00012//Biomedical Advanced Research and Development Authority/ ; },
abstract = {BACKGROUND: Next generation sequencing (NGS) remains underutilized in clinical microbiology applications despite providing broad pathogen spectrum detection superior to other molecular methods. This is primarily because of lower sensitivity of metagenomic NGS (mNGS) compared to PCR, lengthy turn-around times, cost, and complexity of data analysis. Capture sequencing is a technique that can mitigate some of the limitations of mNGS. Using probes that are engineered to selectively bind and pull down desired nucleic acids, capture sequencing enriches for targets of interest and can result in up to a 10,000-fold increase in sensitivity compared to mNGS. In this study, we describe the application of capture sequencing on Oxford Nanopore Technology's portable sequencer, the MinION MK1C.

METHODS: We examined the performance of VirCapSeq-VERT and TBDCapSeq, two distinct capture sequencing assays that target vertebrate viruses and tick-borne pathogens, respectively. Both assays were originally established on the Illumina platform. To enable sequencing on the MinION instrument, we developed a modified hybrid workflow using our established library preparation and capture protocol for Illumina, followed by the addition of the ONT sequencing adaptor. In tests using contrived and clinical samples, we compared sensitivity thresholds and sequencing output, including pathogen genome coverage and relevant read counts.

RESULTS: The addition of capture enrichment to MinION NGS provided significant improvement in pathogen detection when compared to mNGS. Assessment of assay performance on pathogen-positive samples revealed equivalent sensitivity on the MinION MK1C and Illumina NextSeq. We found that the elevated read counts and sequencing depth generated by Illumina NGS were offset by the greater read length obtained on the MinION MK1C and resulted in comparable pathogen genome coverage between the two platforms.

CONCLUSION: This study demonstrates the utility for employment of VirCapSeq and TBDCapSeq on different sequencing platforms and suggest the potential of the MinION platform for broad-spectrum clinical diagnostics.},
}

@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}

@article {pmid41773858,
year = {2026},
author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M},
title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0222025},
doi = {10.1128/spectrum.02220-25},
pmid = {41773858},
issn = {2165-0497},
abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.

IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.},
}

@article {pmid41773588,
year = {2026},
author = {Sun, S and Subramaniyan, S and Ranjani, G and Cid Gomes, L and Bernin, D and Bayer, T and Bornscheuer, UT and Hakkarainen, M and Syrén, PO},
title = {Polyurethane Cascade Depolymerization by a Combination of Thermal Pretreatment and Enzymatic Hydrolysis.},
journal = {ChemSusChem},
volume = {19},
number = {5},
pages = {e202502633},
doi = {10.1002/cssc.202502633},
pmid = {41773588},
issn = {1864-564X},
support = {CTS 23:2626//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 2021-02509//Svenska Forskningsrådet Formas/ ; NNF23OC0086236//Novo Nordisk Fonden/ ; NNF25OC0100562//Novo Nordisk Fonden/ ; },
abstract = {Enzymatic depolymerization of postconsumer polyurethanes (PURs) offers a promising route for sustainable plastic waste management. However, the complex chemistry of PURs containing carbamate, ether, and ester bonds poses a challenge for such a biotechnological process. Here, we explored the deconstruction of a commercial polyether-polyester-PUR through a cascade depolymerization approach, in which a low-temperature thermal pretreatment (180°C, 4 h) was combined with tandem enzymatic hydrolysis. Heat treatment modified the polymer's physicochemical properties, enabling the cutinase HiC from Humicola insolens to cause more than 8% weight loss of the treated PUR films, versus less than 2% of the untreated control after 48 h incubation. Furthermore, the addition of the metagenomic urethanase SP2 completed the one-pot enzymatic cascade, achieving not only depolymerization to the constituent monomer, 4,4'-methylenedianiline (MDA), but also a nearly 3-fold increase in MDA yield compared to using SP2 alone. Docking studies highlighted HiC's specificity toward ester bonds in the PUR polymeric units, and two HiC variants further enhanced degradation within 24 h. Altogether, this work lays the foundation for future investigation and process design for the depolymerization of polyether-polyester-PURs and related materials by cascade enzymatic reactions.},
}

@article {pmid41773475,
year = {2026},
author = {Ma, H and Dai, Y and Xu, C and Geng, H and Li, R and Wang, S and Yang, M},
title = {Correction to "Identification of Three Novel Umami Peptides from Metagenomics of Traditional Fermented Fish, Suanyu, and Receptor Binding Mechanism via the Graph Neural Network-Based Model and Molecular Dynamics Simulation".},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01914},
pmid = {41773475},
issn = {1520-5118},
}

@article {pmid41773424,
year = {2026},
author = {Valdés-Varela, L and Goyache, I and Virto, R and Sáinz, N and López-Yoldi, M and Sánchez-Vicente, A and López-Giral, N and Gil, AG and Milagro, FI and Aranaz, P},
title = {Companilactobacillus alimentarius CNTA 209 alleviates diet-induced obesity in mice through adipose tissue browning and gut barrier modulation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04242a},
pmid = {41773424},
issn = {2042-650X},
abstract = {The use of probiotics with health-promoting effects has emerged as a promising therapeutic strategy for managing obesity and metabolic syndrome. In this study, we characterized the probiotic properties of a novel strain, Companilactobacillus alimentarius CNTA 209, and investigated its potential anti-obesity effects and safety in rodent models. C. alimentarius exhibited sensitivity to all tested antibiotics, resistance to simulated gastric and intestinal conditions in vitro, and functional activities including β-galactosidase activity and short-chain fatty acid (SCFA) production. C. alimentarius supplementation mitigated liver damage induced by a high-fat, high-fructose diet and significantly reduced adiposity in obese C57BL/6 mice by enhancing brown adipose tissue metabolic activity. Metagenomic analysis revealed a beneficial modulation of gut microbiota composition, associated with improved intestinal barrier function. A comprehensive toxicological assessment conducted in Wistar rats confirmed the safety of the strain at a dose of 1 × 10[9] CFU per animal per day for oral administration. This study provides the first documented evidence of anti-obesity and metabolic benefits conferred by a strain of C. alimentarius, positioning CNTA 209 as a novel and safe candidate for the development of probiotic-based interventions targeting obesity and related metabolic disorders.},
}

@article {pmid41773230,
year = {2026},
author = {Li, X and Feng, Q and Yu, H},
title = {A Rare Case of Concurrent Tropheryma Whipplei and Pneumocystis Jirovecii Pneumonia in a Patient During Endocrine Therapy for Breast Cancer.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {580235},
pmid = {41773230},
issn = {1178-6973},
abstract = {Tropheryma whipplei (TW), a rare Gram-positive bacterium, is an uncommon cause of pulmonary infection, typically being reported in the context of gastrointestinal or neurological Whipple's disease. We present a case of a patient receiving endocrine therapy and ovarian suppression for breast cancer who developed a concurrent pulmonary infection with both Pneumocystis jirovecii (PJ) and TW. The diagnosis was secured through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, which successfully identified both pathogens. Following the initiation of targeted antimicrobial therapy, the patient exhibited significant clinical and radiological improvement.},
}

@article {pmid41772733,
year = {2026},
author = {Buscaglia, M and Castillo-Inaipil, W and Schulz, F and Guajardo-Leiva, S and Iriarte, JL and Aparicio-Rizzo, P and Masotti, I and Díez, B},
title = {Unveiling the viral frontier in a warming world: temperature as a key ecological driver of viral diversity in subantarctic Chilean Patagonia fjords.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00869-9},
pmid = {41772733},
issn = {2524-6372},
support = {21190726//ANID/ ; AUB1900003//ANID/ ; DG_06-20//INACH/ ; 151500003//ANID-FONDAP/ ; 1523A0002//ANID-FONDAP/ ; CIMAR25F//CONA-SHOA/ ; ICN2021_044//ANID - Millennium Science Initiative Program/ ; },
abstract = {BACKGROUND: The fjords of Chilean Patagonia (~ 41.5-55.9 °S) lie at the forefront of global warming, where rising temperatures threaten to disrupt microbial processes central to ocean productivity and carbon cycling. Despite their ecological relevance, the diversity and environmental drivers of viral communities, both giant viruses and prokaryotic viruses, remain poorly understood in high-latitude fjords.

RESULTS: Here, we leveraged metagenomics across a 500 km latitudinal gradient in Chilean Patagonia (4-10 °C; salinity 18-33 PSU) to decode the structure and distribution of marine viral communities. We recovered 126 giant viruses (polB sequences dereplicated at 100% average nucleotide identity) and 9213 prokaryotic viruses (viral contigs dereplicated at 95% average nucleotide identity), primarily affiliated with Prasinoviridae (proposed genus g177, order Algavirales) and Caudoviricetes, respectively. Consistent with global-scale studies, temperature emerged as the strongest driver structuring viral communities, outpacing the effects of salinity, depth, dissolved oxygen, chlorophyll-a, and geography. Viral diversity was consistently higher in the northern warmer waters (7.5-10.4 °C), while southern colder sites (4.0-7.4 °C) harbored less diverse and compositionally distinct communities. Giant viruses shift from Pandoravirales and AG_04 (Algavirales) at lower temperatures to increasing dominance of IM_01 (Imitervirales) and Prasinoviridae (AG_01) in warmer habitats. Prokaryotic virus communities also displayed strong temperature structuring, with additional influence from salinity.

CONCLUSIONS: Together, our findings underscore the environmental sensitivity of viral communities in subpolar marine systems and highlight their vulnerability to climate-driven changes. Given the critical role of viruses in microbial turnover, nutrient cycling, and ecosystem resilience, shifts in their diversity and structure may have far-reaching consequences for biogeochemical fluxes and food web dynamics in the fjords of Chilean Patagonia.},
}

@article {pmid41772715,
year = {2026},
author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD},
title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02362-4},
pmid = {41772715},
issn = {2049-2618},
support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.

RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.

CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.},
}

@article {pmid41771902,
year = {2026},
author = {Qian, Y and Xu, S and He, X and Lai, Y and Zhang, Y and Mo, C and Ai, P and Yang, X and Xiao, Q},
title = {Gut ecosystem dysfunction in parkinson's disease: deciphering faecal metabolome-metagenome links for novel diagnostic panels.},
journal = {NPJ Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41531-026-01299-7},
pmid = {41771902},
issn = {2373-8057},
support = {81901283//National Natural Science Foundation of China/ ; 81801254//National Natural Science Foundation of China/ ; 82171246//National Natural Science Foundation of China/ ; 22YF1440200//Shanghai Sailing Program/ ; 22QA1405700//the Shanghai Rising-Star Program/ ; 2018B030337001//Key Field Research and Development Program of Guangdong Province/ ; SHDC2020CR3012A//Clinical Research Plan of SHDC/ ; 2022YFE0210100//National Key Research and Development Program of China/ ; },
abstract = {Gut ecosystem dysfunction is implicated in Parkinson's disease (PD), but integrative faecal metabolome-metagenome links are undefined. We explored these interactions in Chinese PD patients to develop diagnostic panels. Targeted faecal metabolomics (LC‒MS/MS) was performed on 132 PD and 113 healthy controls (HCs) and shotgun metagenomics was integrated for 39 PD/HC pairs. We identified 33 significantly altered faecal metabolites in PD (FDR-P < 0.05). A novel 12-metabolite panel could distinguish PD from HCs. Multi-omic integration revealed gut ecosystem dysfunction manifests via co-disruptions in microbial genes (e.g., amino acid metabolism genes) and metabolites. Critically, a combinatorial diagnostic panel integrating faecal metabolites and microbial gene markers achieved exceptional PD detection (AUC = 0.961, 95% CI = 0.923-0.998). This study deciphers metabolome-metagenome links driving gut dysfunction in PD, identifying amino acid metabolism as a core perturbed pathway. The novel diagnostic panels provide mechanistic insights and clinical tools for PD precision diagnosis.},
}

@article {pmid41771597,
year = {2026},
author = {Payne, T and Shaw, A and Hanjani, LS and Homes, R and Giddens, F and Ravuri, HG and Yap, CX and Walsh, J and Kumar, V and Garton, FC and Rhee, H and Huang, A and Francis, RS and Reid, N and McAdams-DeMarco, M and Gordon, E and Midwinter, M and Hubbard, R},
title = {ReFIT study (reversing frailty in transplantation): protocol for a longitudinal study to assess clinical and biomedical changes in frailty through kidney transplantation.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e100158},
doi = {10.1136/bmjopen-2025-100158},
pmid = {41771597},
issn = {2044-6055},
abstract = {INTRODUCTION: Losses of functional reserve across multiple physiological systems have been identified in frail patients, yet the exact aetiology of frailty remains unclear. Although strongly associated with chronological age, frailty often develops at a younger age in patients with organ failure. Frailty is prevalent in patients with kidney failure; however, individuals experience improvements in physical frailty measures following kidney transplantation. This makes younger patients with kidney failure a unique population for studying both the accelerated onset of frailty and its reversal. This research project aims to test the hypothesis that frailty secondary to organ failure and age-related frailty are associated with similar molecular and physiological measures.

METHODS AND ANALYSIS: This longitudinal study will recruit 150 patients in three groups. Group A (kidney transplant recipients aged ≥40 years; n=50) and Group B (patients aged ≥40 years active on the kidney transplant waitlist; n=50) will comprise younger adults with frailty from organ failure. Group C (adults aged ≥65 years (or ≥55 years for Aboriginal and Torres Strait Islander patients); n=50) will comprise older community dwellers. The primary outcome is the Frailty Index (FI). Secondary outcomes include the change in FI over time, and at baseline when considering various clinical metadata, immune parameters, kidney function and nutrition intake which will be measured at baseline and 12-month time points. Longitudinal changes in frailty will be analysed using linear mixed models with multiple testing corrections for false discovery rates.Endocrine profiles and metabolomics, measures of immune function and microcirculatory dysfunction, will be measured by liquid chromatography-mass spectrometry and/or gas chromatography-mass spectrometry. The gut microbiome will be sequenced via shotgun metagenomics (Illumina NextSeq500, 150 bp paired-end, [3]Gbp/sample). Circulating cell-free DNA/mitochondrial DNA will be quantified through droplet digital PCR. Microcirculation will be assessed via sublingual dark field videomicroscopy with glycocalyx markers measured by ELISA.

ETHICS AND DISSEMINATION: This study will be conducted with all stipulations of this protocol, and the conditions of the ethics committee approval. Ethical principles have their origin in the Declaration of Helsinki, all Australian and local regulations and in the spirit of the standard of Good Clinical Practice (as defined by the International Conference on Harmonisation). Organs/tissues will be sourced ethically and will not be sourced from executed prisoners or prisoners of conscience or other vulnerable groups.Ethics approval was received by the Metro South Health Research Ethics Committee (HREC/2023/QMS/95392) and ratified by the University of Queensland.Results will be disseminated through peer-reviewed publications, academic conferences, participant newsletters and health organisation collaboration.},
}

@article {pmid41771407,
year = {2026},
author = {Zhao, Y and Zhang, X and Chen, X and Zhu, Z and Jiao, P and Ma, L and Li, Y},
title = {Evidence for Propioniciclava as a novel polyphosphate-accumulating organism and construction of its metabolic profile.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134320},
doi = {10.1016/j.biortech.2026.134320},
pmid = {41771407},
issn = {1873-2976},
abstract = {Enhanced biological phosphorus removal (EBPR) relies on polyphosphate-accumulating organisms (PAOs). This study identifies Propioniciclava as a novel putative PAO. High phosphorus release and uptake rates were achieved in two lab-scale Propioniciclava-dominated sequencing batch reactors (SBRs), reaching up to 2.37 and 2.10 mmolP/(gVSS·h), respectively. Metabolic pathway reconstruction for Propioniciclava was based on its most abundant metagenome-assembled genome (bin70), which accounted for 28.8% in SBR1 and 45.5% in SBR2. Functional annotation of bin70 revealed genes for phosphorus and glycogen metabolism but not for polyhydroxyalkanoate synthesis, suggesting a distinct storage strategy. Fluorescence in situ hybridization combined with 4',6'-diamidino-2-phenylindole (FISH-DAPI) staining provided evidence for intracellular polyphosphate granules. Metatranscriptomic analysis further highlighted genes related to phosphorus and glycogen synthesis being actively transcribed by Propioniciclava. The enrichment of Propioniciclava was crucially dependent on glucose. These findings expand the known diversity of PAOs and elucidate the metabolic profile of Propioniciclava, enhancing our understanding of EBPR microbiology.},
}

@article {pmid41771404,
year = {2026},
author = {Zhang, C and Zheng, L and Zhang, Q and Zhang, Y and Zheng, X},
title = {Synergistic removal of methanethiol and other odorant gases by a metabolically complementary synthetic consortia isolated from food waste.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134313},
doi = {10.1016/j.biortech.2026.134313},
pmid = {41771404},
issn = {1873-2976},
abstract = {Methanethiol (MeSH), a typical volatile sulfur compound, contributes significantly to environmental malodor and poses ecological risks. In this study, three bacterial strains capable of MeSH removal efficiencies exceeding 40% were isolated from food waste. These strains were taxonomically identified asAgrobacterium cavarae,Mycolicibacterium neoaurum, andPseudomonas qingdaonensis. Metagenomic annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that all strains possess key enzymes for the methionine and cysteine metabolism pathway, suggesting potential for MeSH degradation. In binary consortia, the combination of A. cavarae R1 and P. qingdaonensis CF (5:1 ratio) exhibited the optimal degradation performance, achieving removal efficiency of 87.2% for MeSH, 98.7% for H2S, and complete NH3 elimination (100%) after a 6-day cultivation. Among ternary consortia, the A. cavarae R1/M. neoaurum CD/ P. qingdaonensis CF combination at 3:2:1 and 3:1:2 ratios demonstrated superior removal efficiency for all three target odorants. Specifically, the 3:2:1 ratio consortium achieved 94.7% MeSH degradation, while the 3:1:2 ratio showd 91.7% NH3 removal efficiency. These results demonstrate the feasibility of using composite microbial agents for odor control in waste management systems.},
}

@article {pmid41770401,
year = {2026},
author = {Han, T and Yang, T and Liu, Y and He, Z and Hao, Y and Cao, W and Ren, J and Wang, G and Gong, C and Hou, J},
title = {Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.},
journal = {Fish physiology and biochemistry},
volume = {52},
number = {2},
pages = {},
pmid = {41770401},
issn = {1573-5168},
support = {2025JNZ-C01//the earmarked fund of Hebei Agricultural S&T Achievements Transformation/ ; 21326307D//the Key R&D Program of Hebei Province, China and the National Marine Genetic Resource Center/ ; },
abstract = {Allicin, a bioactive sulfur compound from garlic known for its antimicrobial and immunomodulatory properties, was evaluated in this study for its effects on growth, antioxidant activity, gut microbiota, and antibiotic resistance genes (ARGs) in Trachidermus fasciatus. Fish were administered allicin at concentrations of 100 mg/kg, 200 mg/kg, and 300 mg/kg. The 200 mg/kg allicin group had significantly higher WGR, LGR, and SGR than the control group. Hepatic SOD and LZM activities were also higher in the 200 mg/kg group. Metagenomics showed that allicin altered the gut microbiota composition, decreased the diversity, and altered the community structure. Allicin-treated fish had significantly reduced levels of potentially damaging bacteria, including Pseudomonas and Vibrio species. The ARGs showed that genes associated with multidrug resistance, including specific subtypes, were markedly reduced in the 200 mg/kg allicin-treated fish. The control group had a markedly decreased number of genes resistant to β-lactam antibiotics. Allicin reduced the number of genes resistant to rpoB2 and mdtC, suggesting the potential for antibiotic resistance. Network analysis of co-occurrence patterns showed that genes resistant to multiple drugs, tetracyclines, and peptides were prevalent, with most possible potential host taxa belonging to Ascomycota and Firmicutes. These results indicate the importance of allicin for fish health as a sustainable alternative to antibiotic resistance and provide a viable alternative to antibiotic resistance for fish farming.},
}