@article {pmid42026803,
year = {2026},
author = {Zhang, F and Hu, K and Sun, C and Chen, R and Ni, G and Liu, X and Wei, L and Su, R},
title = {Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2662690},
doi = {10.1080/19490976.2026.2662690},
pmid = {42026803},
issn = {1949-0984},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome/genetics/drug effects ; *Neoplasms/drug therapy/microbiology ; Deep Learning ; Biomarkers, Tumor/genetics ; *Bacteria/classification/genetics/isolation & purification ; Female ; Male ; Metagenomics ; },
abstract = {Targeting programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) with immune checkpoint inhibitors (ICIs) has improved survival across multiple cancer types, but the variability in patient response highlights the need for better predictive biomarkers. Existing studies rely on taxonomic abundance derived from reference genome databases, limiting the discovery and functional interpretation of uncharacterized microbes. Here, we integrated metagenomic data from multiple ICI-treated cohorts spanning diverse cancer types and geographic regions and developed a deep learning model, named BioP-VAE, that incorporates biological prior knowledge via protein sequence embeddings and uses gene-level microbial abundance features as input. Gene-level microbial abundance outperformed taxonomy abundance in predicting both ICI response and 12-month progression-free survival (PFS). In patients receiving combination immune checkpoint blockade (CICB), BioP-VAE achieved a mean AUC of 0.89 in intracohort and 0.88 in cross-cohort evaluation. Notably, in the monotherapy-treated intracohorts, BioP-VAE achieved a mean AUC of 0.97. Feature attribution analysis revealed key microbial genes. Additionally, we identified distinct predictive microbial signatures via age-stratified analysis, suggesting that host age may modulate microbiome‒immune interactions. Importantly, this is the first large-scale study to evaluate gene-level microbial abundance features for ICI response prediction across multiple cancer types by deep learning. Our findings demonstrate that incorporating biological prior knowledge into deep learning models can improve the discovery of microbial biomarkers that can be generalized across cancer types and treatment settings, offering a novel strategy for patient stratification in immunotherapy.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Microbiome/genetics/drug effects
*Neoplasms/drug therapy/microbiology
Deep Learning
Biomarkers, Tumor/genetics
*Bacteria/classification/genetics/isolation & purification
Female
Male
Metagenomics

@article {pmid42027256,
year = {2026},
author = {Lu, S and Xia, Y and Sun, Q and Sun, Y and Chen, R and Jin, H and Zhang, J and Liu, W and Huang, J},
title = {Characterization of the Gut Virome in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {581751},
pmid = {42027256},
issn = {1178-7031},
abstract = {OBJECTIVE: The dysbiosis of the gut microbiota is a well-known correlate in the pathogenesis of inflammatory bowel disease (IBD). However, the microbiome characteristics of patients with IBD who also have non-alcoholic fatty liver disease (NAFLD) are understudied, particularly the potential pathogenic mechanisms of the gut virome.

MATERIALS AND METHODS: In this study, we conducted a comprehensive gut virome correlation study, along with serum metabolomics analysis, by performing virus-like particle (VLP) and metagenomic sequencing on fecal samples from patients with inflammatory bowel disease and non-alcoholic fatty liver disease (IBD-NAFLD) and NAFLD (MASLD) controls without gastrointestinal diseases.

RESULTS: The results showed that changes in the fecal virome were associated with IBD-NAFLD (MASLD), particularly with an increase in the abundance of Caudovirales in IBD-NAFLD (MASLD) patients. Subsequent analysis of the gut virome identified Bacteroides as the top predicted host for the viruses. Additionally, we identified the pathways involved in all differential metabolites through KEGG annotation analysis, with the highest correlation being the galactose metabolism pathway.

CONCLUSION: In conclusion, by using a customized integrated gut virome catalog tailored for IBD, we revealed the fundamental changes in the gut virome of IBD-NAFLD (MASLD) patients. This study is the first to uncover the specificity of the gut virome in IBD-NAFLD (MASLD) patients and predict Bacteroides as a potential host, suggesting a microbial signature primarily influenced by intestinal inflammation.},
}

@article {pmid42027295,
year = {2026},
author = {Sangodkar, N and Gonsalves, MJ and Nazareth, DR},
title = {Methanotrophy dominated symbiosis in novel species Gigantidas niobengalensis from the cold seeps of Krishna-Godavari basin.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag014},
pmid = {42027295},
issn = {2633-6685},
abstract = {Bathymodiolus mussels, which are prominent invertebrates at cold seeps and hydrothermal vents, are known for hosting symbiotic microbes within their gills. In this study, the microbial communities associated with the gills of novel bathymodioline mussel Gigantidas niobengalensis from an active cold seep site of Krishna-Godavari (K-G) basin was investigated by 16S rRNA amplicon sequencing. The average abundance of culturable methanotrophs in the gill tissues was 3.4 ± 0.9 × 10[4] CFU g[-1] with average methane oxidation rates of 1.71 ± 0.04 to 1.89 ± 0.02 µM g[-1] d[-1] under aerobic and 1.86 ± 0.001 to 1.98 ± 0.005 µM g[-1] d[-1] under anaerobic conditions. Metagenomic analysis revealed dominance of methanotrophs within the microbial communities comprising of >55% bacterial and >28% archaeal methanotrophs; with phyla Proteobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, Euryarchaeota, and Crenarcheaota being prevalent. Functional classification highlighted methane metabolism (20%) and carbon fixation (22%) as major energy metabolism pathways. This study represents the first metagenomic characterization of gill-associated symbionts in the novel cold seep mussel G. niobengalensis from the Indian Ocean. The findings fill a knowledge gap on chemosynthetic symbioses in Indian cold seep ecosystems and provide insights into metabolic adaptation of G. niobengalensis in the cold seep ecosystem.},
}

@article {pmid42027454,
year = {2026},
author = {Chen, X and Gong, L and Lu, Y and Liu, W and Liu, F and Li, Q and Wang, L and Qiu, L and Zhang, D and Ye, X},
title = {Epidemiological characteristics and environmental surveillance of human psittacosis in Lishui City, Zhejiang Province, China (2021-2024).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1769696},
pmid = {42027454},
issn = {1664-302X},
abstract = {INTRODUCTION: Psittacosis, caused by Chlamydia psittaci, is an underdiagnosed zoonosis that can lead to severe pneumonia and fatal outcomes. In China, traditional poultry farming poses substantial risks for avian-to-human transmission, yet comprehensive epidemiological evidence is scarce. To address this gap, we aimed to define the local epidemiology, risk factors, and environmental reservoirs of human psittacosis in Lishui City, Zhejiang Province.

METHODS: We conducted a multi-source epidemiological study (2021-2024) integrating surveillance data, clinical records, contact investigations, and environmental sampling. Cases were confirmed by quantitative polymerase chain reaction (qPCR) or metagenomic next-generation sequencing (mNGS).

RESULTS: We identified 28 laboratory-confirmed cases, showing annual fluctuations in reported case numbers. Infections, mostly confirmed by mNGS, were predominantly sporadic among elderly agricultural workers (mean age 62.6 years), with 96.4% reporting recent poultry exposure. All patients presented with pneumonia; 64.3% developed severe disease, resulting in three deaths. The median diagnostic delay-from symptom onset to diagnosis-was 12 days. A household cluster of three cases was detected; however, no secondary transmission occurred among 205 close contacts outside the household. C. psittaci DNA was detected in 14.79% (21/142) of environmental samples, with the highest number of cases detected in duck manure samples, with the highest positive rate (26.7%). Phylogenetic analysis of 20 ompA gene sequences revealed a predominantly genotype A and the waterfowl-TW genotype, which are closely related to strains from southern China.

DISCUSSION: Psittacosis in Lishui presents as a sporadic but clinically severe disease in older rural residents. The high frequency of severe pneumonia and prolonged diagnostic delay underscores an urgent need to improve clinical suspicion and access to molecular diagnostics. Detection of C. psittaci nucleic acid in environmental samples suggests possible environmental contamination; however, viability and transmissibility were not assessed.},
}

@article {pmid42027830,
year = {2026},
author = {Chen, L and Ding, Y and Liu, Y and Xie, Q and Hu, J and Wang, M and Zeng, X and Zou, D},
title = {Case Report: Ultrasound guided puncture for type 2 diabetes mellitus combined with psoas abscess-a report of two cases.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1773238},
pmid = {42027830},
issn = {2296-858X},
abstract = {BACKGROUND: Psoas abscess (PA) is a rare infectious disease, with type 2 diabetes mellitus (T2DM) serving as a significant risk factor. The combination of metagenomic next-generation sequencing (mNGS) and ultrasound offers innovative approaches for the rapid and precise treatment of PA.

CASE PRESENTATION: Case 1: A 77-year-old woman presented with lumbar pain was initially misdiagnosed with lumbar disc herniation based on CT scan. Subsequent CT scan and ultrasound-guided puncture confirmed a left lumbar PA. mNGS detected the presence of Streptococcus agalactiae, which was negative on conventional culture. The patient was successfully treated with vancomycin for 5 weeks, with no recurrence at 3-year follow-up. Case 2: A 56-year-old woman with a 10-year history of T2DM presented with poor appetite and fatigue. CT imaging identified a left lumbar PA along with perirenal infection. Pus from ultrasound-guided puncture for conventional culture and mNGS detected the presence of Staphylococcus aureus. Treatment with oxacillin and vancomycin led to clinical resolution. The follow-up CT scan in 2024 indicated complete resorption of the lesion.

CONCLUSION: mNGS combined with ultrasound-guided puncture overcomes conventional culture limitations. This approach suggests clinical feasibility.},
}

@article {pmid42028026,
year = {2026},
author = {Heinzelmann, D and Reuss, F and Zeh, N and Nilson, R and Walker, E and Fieder, J and Lindner, B and Renner, B and Schulz, P and Fischer, S and Schmidt, M},
title = {Discovery of a chimeric transposase-transposon system for advanced genome engineering.},
journal = {iScience},
volume = {29},
number = {5},
pages = {115548},
pmid = {42028026},
issn = {2589-0042},
abstract = {Transposases have transformed genetic engineering, yet functional systems remain scarce. In response, an unknown transposase system from Acyrthosiphon pisum was identified by metagenomic screening. Through systematic optimization, we enhanced nuclear localization, transposon architecture, and created a hyperactive transposase variant to boost efficiency. Intriguingly, the combined application of the newly discovered transposase with inverted terminal repeat sequences from a related pea aphid species, Aphis craccivora, further enhanced transposition activity, resulting in the first chimeric transposase system reported so far. We investigated the genomic integration events following transposition in mammalian cells to understand the underlying mechanisms and optimize the efficiency of transgene integration. This optimized system can expedite the generation of recombinant protein-producing Chinese Hamster Ovary (CHO) cell lines, even surpassing the hyperactive piggyBac system with regard to cell-specific productivity. These findings introduce a significant addition to the field of semi-targeted transgene integration technologies, offering substantial potential for enhancing biologics manufacturing.},
}

@article {pmid42028145,
year = {2026},
author = {Chen, Y and Zhang, L and Wang, T and Pan, X and Chen, D and Liu, J},
title = {Characteristics of CD4[+]T-cell reduction and pulmonary infections in critically ill immunocompromised patients.},
journal = {Journal of intensive medicine},
volume = {6},
number = {2},
pages = {157-165},
pmid = {42028145},
issn = {2667-100X},
abstract = {BACKGROUND: The CD4[+]T-cell count is a key indicator for evaluating immunosuppression. Infections significantly influence the survival and prognosis of critically ill patients. This study aims to systematically evaluate the association between reduced CD4[+] T-cell counts and lung infections in immunosuppressed ICU patients, offering clinical evidence to guide the management of lung infections in this population.

METHODS: This retrospective, single-center study included 40 immunocompromised patients admitted to the ICU from January 1, 2021, to June 30, 2023. All participants underwent metagenomic next-generation sequencing. Patients with suspected lung infections based on their CD4[+]T-cell counts were divided into mild (350/µL
RESULTS: Amang these forty immunosuppressed patients, 8 were assigned to the mild group, 16 to the moderate group, and 16 to the severe group. Streptococcus pneumoniae was almost all distributed in moderate patients (75.0%), while severe patients had a higher proportion of fungi detected (25.7%). Respiratory microbiome analysis identified Acinetobacter baumannii, Human alphaherpesvirus 1, and Klebsiella pneumoniae as the most abundant species. Although no significant difference in the alpha diversity index was found among the groups, index values were lower in the severe group than in the moderate group. Beta diversity analysis showed that the microbial community structure did not significantly differ among the three groups. A total of 27 microbial markers were obtained, with multiple streptococcal species showing enrichment in moderate group and Candida tropicalis in severe group. By day 28, four patients (50.0%) in the mild group had died compared with six (37.5%) in the moderate group and nine (56.3%) in the severe group. There were no significant difference in the duration of ICU or hospital stays.

CONCLUSIONS: This study on ICU-admitted immunocompromised patients identified the prevalent pathogens and microbiome features associated with pulmonary infections, as well as their relationship with CD4[+]T-cell depletion. These findings are valuable for optimizing clinical diagnosis and treatment strategies and may contribute to improving patient outcomes.},
}

@article {pmid42028191,
year = {2026},
author = {Hariharamohan, M and Chindarkar, M and Swain, HS and Rajesh, N and Rajesh, V},
title = {Integrating physicochemical and microbial characterization of red rice broth fermented over an 18-hour period augmented with metagenomic and metabolomic approaches.},
journal = {RSC advances},
volume = {16},
number = {23},
pages = {21129-21141},
pmid = {42028191},
issn = {2046-2069},
abstract = {Fermentation enhances the nutritional properties of foods. Fermented water of Kerala red rice (Oryza sativa L. subsp. indica), traditionally consumed in South India remains underexplored scientifically. This study characterizes the nutritional, microbial, and metabolite profiles of Kerala red rice water (broth) after 18 hours of natural fermentation using biochemical assays, shotgun whole-genome metagenomic sequencing (Illumina NovaSeq X Plus), untargeted gas chromatography-mass spectrometry (GC-MS) metabolomics, and a phytase-mediated mineral release assay. Fermentation enhanced nutritional quality with increase in carbohydrates by 22.7%, protein by 163.52%, and free amino acids by 35.47% compared to unfermented controls. Phytase activity rose from negligible levels to 0.12 U mL[-1]. Metagenomics identified 50 taxa, dominated by Proteobacteria (59.63%) and Firmicutes (40.12%), with ∼34% of the community carrying phytase-encoding genes. Dominant genera included Pantoea, Saccharibacillus, and Bacillus. Fermentation also enhanced mineral release, with calcium, iron, and zinc in the fermented rice water showing increases of approximately 1190%, 566%, and 93%, respectively, relative to unfermented controls over a 360 min in vitro digestion period. These findings provide the first integrated insight bridging traditional dietary practice with modern analytical science.},
}

@article {pmid42028978,
year = {2026},
author = {Xiao, L and Liu, J and Noyce, GL and Lee, J and Duarte, CM and Zhou, M and Luo, M and Sun, R and Dang, R and Zhou, L and Zhang, L and Fu, C and Tan, Y and Yu, J and Han, G},
title = {Microbial Responses to Warming Reduce Deep Blue Carbon Storage.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70883},
doi = {10.1111/gcb.70883},
pmid = {42028978},
issn = {1365-2486},
support = {U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 42071126//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; XDA23050202//Strategic Priority Research Program of Chinese Academy/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; },
mesh = {*Soil Microbiology ; *Carbon Cycle ; *Carbon/metabolism ; *Global Warming ; Soil/chemistry ; *Carbon Sequestration ; Wetlands ; *Climate Change ; Plants/metabolism ; },
abstract = {Coastal wetlands are critical blue carbon reservoirs, yet the depth-resolved impacts of warming on belowground carbon dynamics remain poorly understood. Over the course of an 8-year in situ experiment, we investigated plant-derived carbon inputs, soil carbon losses via respiration, and microbially mediated carbon fixation across a 60 cm soil profile under a projected 2°C atmospheric warming scenario. Plant carbon fixation (above- and belowground net primary productivity) and soil respiration exhibited synchronized responses to warming, with an initial increase, followed by a decline in the mid-term, and no significant response in the later stages. Soil and microbial respiration stabilized after prolonged exposure to elevated temperatures, as these processes were constrained by substrate availability. In contrast, phospholipid fatty acid profiling, amino sugar biomarkers, and metagenome-assembled genomes consistently indicated a greater than one-third reduction in microbial carbon fixation within subsoils (40-60 cm). Our fully factorial, depth-stratified warming design reveals the particular vulnerability of deep soil microbial carbon retention to long-term climate warming, independent of shifts in plant input or respiratory carbon loss. This work highlights underappreciated pathways influencing soil blue carbon dynamics in a changing world.},
}

*Soil Microbiology
*Carbon Cycle
*Carbon/metabolism
*Global Warming
Soil/chemistry
*Carbon Sequestration
Wetlands
*Climate Change
Plants/metabolism

@article {pmid42028995,
year = {2026},
author = {Liu, M and Du, M and Xi, Z and Tastambek, KT and Bao, Y and Song, X and Zhou, A and Wang, Y},
title = {Bacillus aerius synergizes with coal gangue to enhance Medicago sativa growth via soil microbiome and gene regulation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0026826},
doi = {10.1128/aem.00268-26},
pmid = {42028995},
issn = {1098-5336},
abstract = {UNLABELLED: The extensive accumulation of coal gangue poses significant environmental threats through water contamination, soil degradation, and atmospheric pollution, necessitating the urgent development of ecological utilization strategies. This study elucidates the mechanistic basis by which the thermophilic bacterium Bacillus aerius (B. aerius) enhances plant growth in coal gangue-amended sandy soils. Through integrated analysis of nutrient dynamics, phytohormonal activities, soil enzymatic profiles, and metagenomic functional profiling, we demonstrate significant synergy between coal gangue and B. aerius. When applied together in sandy soils, the germination rate, plant height, root length, and fresh biomass of Medicago sativa (alfalfa) increased by 1.18-2.06 times. The levels of soil nitrogen, phosphorus, and potassium also significantly increased, resulting in notable improvements in soil fertility. The bacterial treatment enhanced the activities of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various soil enzyme activities while also optimizing the microbial community structure and increasing the abundance of beneficial bacteria, including Bacillus. Metagenomic analysis revealed the upregulation of growth-promoting genes such as acdS, nifK, and phnG, which collectively drive plant growth through multiple pathways, including enhanced soil nutrient availability, hormone regulation, soil enzyme activities, and nutrient cycling. Collectively, this work deciphers molecular-scale bacteria-gangue synergism, providing a theoretical foundation for sustainable coal gangue utilization and ecological restoration of degraded soils.

IMPORTANCE: The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium Bacillus aerius acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soil nutrient availability, beneficial microbial communities, and associated biological activities, with these effects supported by molecular evidence. As the first study to verify this growth-promoting mechanism, our findings address a critical knowledge gap and provide a theoretical foundation for the sustainable utilization of coal gangue in the ecological restoration of degraded soils.},
}

@article {pmid42029028,
year = {2026},
author = {Valdez-Nuñez, LF and Chávez, IJ and Sekerci, F and Ayala-Muñoz, D and Straub, D and Kappler, A and Fischer, S and Mansor, M},
title = {Desulfosporosinus and Acididesulfobacillus dominate an acidophilic sulfate-reducing bacteria consortium during acid mine drainage bioremediation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030826},
doi = {10.1128/aem.00308-26},
pmid = {42029028},
issn = {1098-5336},
abstract = {Acid mine drainage (AMD) is an environmental threat due to its low pH and high metal content. Biological treatment of AMD using acidophilic sulfate-reducing bacteria (aSRB) represents a potential solution for this problem, but their substrate specificity and low tolerance to extreme acidity (pH ≤3.0) and toxic metals limit their application. Here, we used an indigenous aSRB-containing consortium to remove metals and neutralize a synthetic AMD (sAMD) system starting at pH 2.9. The consortium was enriched from acidic sediments of an abandoned mine tunnel in Peru. A bioremediation experiment (pH 2.9) was set up with Fe[2+] (40.25 mM), Al[3+] (5.39 mM), and Zn[2+] (3.97 mM) as the main dissolved metals. Glycerol and yeast extract were used as carbon sources. Physicochemical parameters, mineral formation, microbial communities, and dissolved metals were monitored for 160-200 days. At the end of the incubation, the final pH reached 6.1 and 100% of Zn[2+], >99% of Fe[2+], and >94% of Al[3+] were removed by the aSRB consortium as X-ray diffraction-amorphous minerals. The aSRB Desulfosporosinus and Acididesulfobacillus dominated the bioremediation experiment. Two high-quality metagenome-assembled genomes taxonomically affiliated to the aforementioned aSRB showed metabolic potential related to sulfur compounds reduction as well as to organic carbon degradation (e.g., glycerol and acetate). Differences related to carbon degradation during AMD bioremediation suggest a synergy between Acididesulfobacillus and Desulfosporosinus, thus avoiding toxic waste product accumulation. Overall, we obtained a novel aSRB-containing microbial consortium that can be used for acidity neutralization and metal removal, suitable for more robust AMD treatment technologies.IMPORTANCEAcid mine drainage (AMD) remains one of the biggest environmental challenges of the mining industry. Treatment technologies based on the application of microbial consortia are gaining popularity, taking advantage of synergistic interactions between different species to widen substrate specificity and to limit toxicity. Our research work here shows two acidophilic sulfate-reducing bacteria, Desulfosporosinus and Acididesulfobacillus, working together in AMD bioremediation. Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate as the waste product. Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon source, thus avoiding acetate accumulation and cell toxicity. In the end, this synergistic interaction neutralized acidic pH and removed metals to a great extent, making it suitable for biological treatment of AMD.},
}

@article {pmid42029155,
year = {2026},
author = {Perlas, A and Reska, T and Sánchez-Cano, A and Mejías-Molina, C and Gygax, D and Martínez-Puchol, S and Rusiñol, M and Eger, E and Schaufler, K and Höfle, U and Croville, G and Le Loc'h, G and Guérin, J-L and Urban, L},
title = {Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0254325},
doi = {10.1128/aem.02543-25},
pmid = {42029155},
issn = {1098-5336},
abstract = {UNLABELLED: Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites and used environmental DNA to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces, where the health of animals, humans, and the environment are interconnected and pathogen transmission can occur across these domains.

IMPORTANCE: Wetlands connect wildlife, livestock, and people, making them key places to watch for pathogens and antibiotic resistance. Yet potentially harmful microbes are easy to miss in water because they represent only a small fraction of the abundant microbial life in water, making them hard to detect. We paired 3D-printed passive torpedo-shaped samplers with a portable genetic sequencer to analyze all microbes captured. We deployed this approach at 12 wetlands in Germany, France, and Spain. It revealed local microbial communities, identified disease-causing bacteria, and linked many antibiotic resistance genes to likely bacterial hosts. By comparing locations, we observed that sites near cities, farms, or wastewater had higher levels of pathogens and resistance than protected natural sites. Our analysis also recovered all viruses present, including those from mammals, birds, fish, insects, and plants. We also specifically looked for the virus that causes avian flu, found it at several sites, and classified it as low pathogenicity. Because our method is non-invasive to wildlife, affordable, and practical to deploy, it can provide early warnings to conservation and public health agencies and guide action where risks are present.},
}

@article {pmid42029954,
year = {2026},
author = {Gao, J and Li, HL and Li, MS and Shao, ZJ and Yang, ZF and Li, CJ and Zhang, ZX and Zhu, D and Lv, ZH and Song, RH and Li, JL and Hu, W and Yin, YR},
title = {Cloning, heterologous expression, and characterization of a metagenome-derived GH10 xylanase with salt and alkali tolerance from Xinjiang saline-alkali soil.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {42029954},
issn = {1572-9699},
support = {YWLCYXZX2023300075//the Yunnan Provincial Clinical Medical Center for Emergency Traumatic Diseases/ ; 32560004//the National Natural Science Foundation of China Regional Program/ ; },
mesh = {*Metagenome ; Cloning, Molecular ; *Endo-1,4-beta Xylanases/genetics/metabolism/chemistry ; *Soil Microbiology ; *Alkalies ; Hydrogen-Ion Concentration ; *Soil/chemistry ; Enzyme Stability ; Salt Tolerance ; Escherichia coli/genetics ; Xylans/metabolism ; Recombinant Proteins/genetics/metabolism/isolation & purification ; Temperature ; Amino Acid Sequence ; China ; Sodium Chloride ; Phylogeny ; },
abstract = {Xylanases are widely used in baking, seafood processing, and paper production, but their performance is often compromised under high-salt, acidic, or alkaline conditions, limiting broader industrial deployment. Identifying robust xylanases from saline-alkali environments is therefore of practical importance. Here, we report a GH10 xylanase gene, XynE102, mined from a saline-alkali soil metagenome from Karamay, Xinjiang. The deduced amino acid sequence shares 69.17% identity with a xylanase from Cellvibrionaceae bacterium (GenBank accession HEY7885703.1). XynE102 was cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme was purified by Ni-NTA affinity chromatography. Using beechwood xylan as substrate, XynE102 exhibited optimal activity at 50 °C and pH 7.0. It retained ≥ 50% relative activity between 30 and 55 °C and pH 5.6-8.6, and ≥ 75% activity in 2.0 M NaCl. Notably, after preincubation at 40 °C for 60 and 120 min, its activity increased to 130% and 165% of the initial value, respectively. Following 24 h preincubation at pH 7-10, residual activity remained ≥ 80%, indicating pronounced alkaline stability. At 1 mM, Mn[2+], Co[2+], and Fe[3+] activated the enzyme, whereas Mg[2+], Cu[2+], and Cd[2+] inhibited it; 1% SDS had no measurable effect. XynE102 primarily hydrolyzed xylan to xylobiose and xylotetraose. It also hydrolyzed alkali-treated corn stalk and hot-water-pretreated wheat bran, yielding reducing sugar concentrations of 5.44 mM and 4.18 mM, respectively, after 24 h. Taken together, these results indicate that XynE102 is a neutral-pH xylanase with notable salt and alkali tolerance, supporting its potential for prebiotic XOS production and food-processing applications under moderate temperature conditions.},
}

*Metagenome
Cloning, Molecular
*Endo-1,4-beta Xylanases/genetics/metabolism/chemistry
*Soil Microbiology
*Alkalies
Hydrogen-Ion Concentration
*Soil/chemistry
Enzyme Stability
Salt Tolerance
Escherichia coli/genetics
Xylans/metabolism
Recombinant Proteins/genetics/metabolism/isolation & purification
Temperature
Amino Acid Sequence
China
Sodium Chloride
Phylogeny

@article {pmid42030718,
year = {2026},
author = {Chen, L and Zhong, J and Deng, N and Lin, H and Zhang, L},
title = {Spatiotemporal patterns of arsenic and its microbial arsenic transformation in the Pearl River Estuary.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142145},
doi = {10.1016/j.jhazmat.2026.142145},
pmid = {42030718},
issn = {1873-3336},
abstract = {Estuarine ecosystems are critical zones for arsenic (As) biogeochemical cycling, yet the spatiotemporal distribution and microbial transformation mechanisms of As in these dynamic environments remain poorly understood. This study integrated geochemical analyses with metagenomic and metatranscriptomic approaches to investigate As distribution and microbial transformation mechanisms in Pearl River Estuary (PRE). Our results revealed distinct spatiotemporal patterns of As in the PRE. As in sediment were significantly higher in the western region and exhibited a clear decreasing gradient from upstream to downstream. As(V) was the dominant species in both sediments and water, while organic As remained below detection limits. Seasonally, As concentrations peaked in winter and spring. Microbial community analysis showed that highly diverse microbial taxa capable of transforming As were detected, with Proteobacteria identified as the dominant phylum. Among key functional genes, arsM exhibited the highest abundance and transcription level, indicating substantial methylation potential throughout the estuary. Notably, metagenome-assembled genome (MAG) analysis uncovered a previously undocumented metabolic transition along the estuarine gradient, shifting from As(V) reduction coupled with methylation and efflux in upstream to As(III) oxidation with a more diversified strategy in mid-downstream. This systematic study clarified the distribution and microbial transformation mechanisms of As in the PRE, advancing our understanding of As biogeochemical cycling in estuarine ecosystems.},
}

@article {pmid42030844,
year = {2026},
author = {Zhao, H and Che, W and Tan, X and Shen, Y and Xu, Y and Man, Y},
title = {Distribution characteristics and potential microbial degradation mechanisms of microplastics in oyster aquaculture areas of southern China.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142136},
doi = {10.1016/j.jhazmat.2026.142136},
pmid = {42030844},
issn = {1873-3336},
abstract = {Microplastic (MP) pollution in coastal aquaculture is a growing environmental and public health concern. Despite increasing reports, the cross-regional and cross-media pollution patterns, ecological risks, and microbial degradation potentials in aquaculture ecosystems remain poorly understood. We investigated oyster farming systems in South China: Zhanjiang Bay (ZJB, semi-enclosed) and Xuwen (XW, open coast). MP abundances ranged from 20 to 54 items/L in seawater and 950-6483 items/kg in sediment, with particles < 50 μm and granular shapes dominant in both media, as determined by Laser Direct Infrared Imaging. MP spatial patterns differed markedly between regions; XW exhibited higher seawater MP levels attributed to larger farming scales, whereas ZJB showed greater sediment MP accumulation owing to weaker water exchange and a longer farming history. Source apportionment identified aquaculture facilities as the primary source (44.86%). Notably, while the overall pollution load was relatively low, the potential ecological risk index reached 866.51 (classified as "dangerous"), driven predominantly by highly toxic polymers such as polyurethane (PU) and polyvinyl chloride (PVC). The distribution of plastic-degrading genes (PDGs) and their host microbial communities was primarily determined by these aquaculture facilities and the environmental medium (sediment vs. seawater), rather than by localized water-quality conditions. Metagenomic analysis identified sediments as key metabolic hotspots, harboring diverse functional genes involved in polyethylene β-oxidation, polystyrene aromatic ring cleavage, and PU hydrolysis. These findings bridge the gap in understanding MP dynamics between diverse aquaculture habitats and highlight the potential of indigenous microbes in natural attenuation, providing critical insights for MP risk management.},
}

@article {pmid42030878,
year = {2026},
author = {Saini, K and Prajapati, A and Kumar, SS and Kumar, V and Bajar, S},
title = {Performance assessment of sulfate-reducing bacterial consortium for the treatment of real landfill leachate under anaerobic conditions.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129743},
doi = {10.1016/j.jenvman.2026.129743},
pmid = {42030878},
issn = {1095-8630},
abstract = {Landfill leachate contains complex organic pollutants, ammonia, sulfate, and toxic metals, posing major environmental challenges. This study evaluated a sulfate-reducing bacterial (SRB) consortium isolated from electroplating wastewater for the treatment of real landfill leachate under anaerobic conditions. Physicochemical characterization revealed a Leachate Pollution Index (LPI) of 63.16, confirming the high hazardous nature of the leachate. The acclimatized SRB consortium exhibited strong metabolic activity and rapidly degraded pollutants. Within 10 days of treatment, the system achieved 82.84% removal of chemical oxygen demand (COD) and 97.83% removal of biochemical oxygen demand (BOD5), demonstrating efficient biodegradation of both biodegradable and persistent organic compounds. The concentrations of heavy metals were reduced to below the detection limit (BDL), primarily due to sulfide-mediated precipitation. Thus, SRB provide dual benefits of organic degradation and metal detoxification. Metagenomic profiling (16S rRNA sequencing) revealed dominant sulfate-reducing species, including Desulfovibrio vulgaris, Desulfotomaculum nigrificans, Desulfobulbus propionicus, and Desulfosporosinus orientis. Kyoto Encyclopedia of Genes and Genomes (KEGG) based functional annotation was performed to elucidate the metabolic potential of the SRB consortium. Scanning electron microscopy (SEM) analysis before and after treatment confirmed microbial colonization and sulfide-mediated metal precipitation. Overall, SRB-based anaerobic processes demonstrate significant potential as a sustainable and efficient treatment for high-strength landfill leachate with strong potential for scale-up and integration into waste management systems. Although the treated effluent did not meet CPCB (India) and EPA COD discharge standards, this bioremediation approach provides a cost-effective alternative to conventional physicochemical treatments. Further optimization of operational parameters and microbial activity could enhance treatment efficiency and facilitate regulatory compliance.},
}

@article {pmid42030912,
year = {2026},
author = {Hua, Y and Xu, X and Chen, Y and Li, Y and Dai, X},
title = {Making waves: Wastewater sludge holds untapped antimicrobial potential.},
journal = {Water research},
volume = {300},
number = {},
pages = {125989},
doi = {10.1016/j.watres.2026.125989},
pmid = {42030912},
issn = {1879-2448},
abstract = {Wastewater treatment plants are widely recognized as critical nodes in the environmental dissemination and control of antimicrobial resistance (AMR). This risk-focused view is warranted, but incomplete. Wastewater sludge is one of the largest engineered and repeatedly accessible microbiomes on Earth, continuously shaped by diverse microbial inputs and exposure to antimicrobial compounds and other stressors. These conditions may also harbor underexplored antimicrobial functions. Here we propose framing sludge as a dual-function node within AMR stewardship: a resource for routine surveillance and risk management, and a source material for an offline, containment-first workflow to identify antimicrobial candidates, particularly antimicrobial peptides. We summarize recent advances in metagenomics and machine-learning-enabled peptide prioritization and outline an evidence ladder that links sequence signals to functional validation. A central principle is to decouple discovery from plant operations and to apply explicit decision gates early in the pipeline, including cross-resistance screening and resistance-evolution assays, to prevent inadvertently increasing selection pressure or AMR risks. Finally, we call for shared benchmarks to improve comparability across studies, including curated datasets, standardized validation panels, and routine reporting of negative findings and resistance-related outcomes. Together, these steps can help translate sludge-enabled discovery into environmentally responsible innovation aligned with AMR stewardship.},
}

@article {pmid42030968,
year = {2026},
author = {Brown, JR and Chiu, CY and López-Labrador, FX and de Vries, JJC},
title = {The impact of clinical metagenomic testing on patient management: facts versus fantasy.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(26)00106-4},
pmid = {42030968},
issn = {1474-4457},
abstract = {Clinical metagenomic testing by agnostic, unbiased next-generation sequencing is a diagnostic approach with the broad-based capacity to detect all known and novel pathogens in a single assay. After the discovery of this potentially transformative method decades ago, the availability of clinical metagenomic testing in the daily practice of the infectious disease specialist is accelerating. Prospective metagenomic studies have supplemented the substantial existing body of retrospective, exploratory literature, and these reports offer us a glimpse into the real-world use of clinical metagenomic testing for the diagnosis of infections in patients. In this Review, we examine the evidence collected from the prospective reports published to date, focusing on their impact on patient management, treatment, and outcomes.},
}

@article {pmid42031746,
year = {2026},
author = {Yang, Y and Zhang, H and Herbold, CW and Huang, Y and Wang, R and Liu, J and Zhang, D and Ou, J and Zheng, F and Mao, C and Huang, J and Yu, Y and He, J and He, Z and Yan, Q},
title = {Trophic status strongly regulates nitrous oxide but not methane production in global freshwater lake sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42031746},
issn = {2041-1723},
support = {92051120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32030015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100086//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Nitrous Oxide/metabolism/analysis ; *Methane/metabolism/analysis ; *Lakes/chemistry/microbiology ; *Geologic Sediments/chemistry/microbiology ; Denitrification ; Nitrification ; Eutrophication ; Greenhouse Gases/metabolism/analysis ; Metagenomics ; },
abstract = {Freshwater lakes are globally significant sources of potent greenhouse gases (GHGs), but how their GHGs emissions respond to changing nutrient levels remains unclear. Here, we demonstrated that nitrous oxide (N2O) production pathways in lake sediments are tightly linked to trophic state, whereas methane (CH4) production appears to be multifactorial Through global metagenomics and controlled batch experiments. In eutrophic sediments, N2O is efficiently removed through complete denitrification, with nitrification serving as the main production pathway, whereas oligotrophic sediments produce N2O primarily via incomplete denitrification. By simulating nutrient transitions using an innovative cross-inoculation experiment, we further revealed that lake sediments systematically shift between these N2O production pathways as their trophic state changes, from denitrification-driven to nitrification-dominated during eutrophication, with the inverse pattern during oligotrophication. Consequently, N2O emissions can be effectively mitigated by inhibiting nitrification in eutrophic lakes and restricting incomplete denitrification in oligotrophic ones. Our findings establish trophic status as a key driver of N2O production sources in lake sediments.},
}

*Nitrous Oxide/metabolism/analysis
*Methane/metabolism/analysis
*Lakes/chemistry/microbiology
*Geologic Sediments/chemistry/microbiology
Denitrification
Nitrification
Eutrophication
Greenhouse Gases/metabolism/analysis
Metagenomics

@article {pmid42031750,
year = {2026},
author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K},
title = {Addendum: Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42031750},
issn = {2041-1723},
}

@article {pmid42032005,
year = {2026},
author = {Gladkikh, AS and Naydenov, DD and Sharova, AA and Popova, MR and Arbuzova, TV and Klyuchnikova, EO and Sbarzaglia, VA and Gibitova, EA and Forghani, M and Tokarevich, NK and Lunina, GA and Ramsay, ES and Dedkov, VG},
title = {Metaviromic analysis of Ixodes ticks in Northwestern Russia reveals high viral diversity and novel RNA virus lineages.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50087-z},
pmid = {42032005},
issn = {2045-2322},
support = {N. 24-45-20005//RSF grant/ ; },
abstract = {Ticks of the genus Ixodes are recognized as important vectors of a wide range of viral pathogens with potential implications for public and veterinary health. Recent advances in metagenomic sequencing have uncovered an unprecedented diversity within tick-associated viromes, yet much of the global tick metavirome remains unexplored, particularly in vast and ecologically diverse regions such as Northwestern Russia. In this study, we present a comprehensive metaviromic and phylogenetic characterization of viruses detected in Ixodes persulcatus and Ixodes ricinus ticks collected from five regions in Northwestern Russia between 2021 and 2023. Using high-throughput RNA sequencing, we identified viral sequences representing families Nairoviridae, Partitiviridae, Phenuiviridae, Flaviviridae, Chuviridae, and Narnaviridae, Orthototiviridae. Putative novel viral lineages were identified. Phylogenetic analyses revealed strong geographic structuring of some viral lineages. This suggests either the presence of local genotypes, or underrepresentation of Eurasian tick-associated viromes, in current databases. In addition to TBEV, other viruses previously associated with human illness were detected in ticks in Northwestern Russia (Beiji nairovirus, Mukawa virus). Our findings provide the first high-resolution snapshot of the tick virome in Northwestern Russia. They emphasize the importance of continued viral surveillance in underrepresented biogeographic zones. These data contribute to the growing global virome map and may inform the development of region-specific vector-borne disease countermeasures.},
}

@article {pmid42032049,
year = {2026},
author = {Zhang, X and Li, W and Wu, H and Cai, T and Chen, H and Zeng, S},
title = {Enhanced pathogen identification in fungal endophthalmitis by metagenomic next-generation sequencing: a retrospective clinical evaluation.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50225-7},
pmid = {42032049},
issn = {2045-2322},
support = {LHGJ20220091//Henan Province Medical Science and Technology Key Project/ ; 2023A1515012220//Guangdong Basic and Applied Basic Research Foundation/ ; 2024ZDJS120//Guangdong Province Research Capability Improvement Project for Key Construction Disciplines/ ; 2025XSJ013；2024XK003；2021BQ011//Nanfang College Guangzhou/ ; },
abstract = {Fungal endophthalmitis (FE) is a vision-threatening emergency that requires rapid pathogen identification. Conventional microbial culture demonstrates limited sensitivity in FE, warranting improved diagnostic approaches. We evaluated the detection performance of unbiased metagenomic next-generation sequencing (mNGS) in 31 clinically diagnosed FE cases, including 16 vitreous humor (VH) and 15 aqueous humor (AH) specimens. mNGS showed a positivity rate of 90.3% (28/31, 95% CI: 74.2%-98%), outperforming culture (9.1%, 2/22, 95% CI: 1.1%-29.2%). The positivity rates were 100% for endogenous FE and 85% for exogenous FE, while VH and AH specimens achieved 100% and 80% positivity, respectively. mNGS identified polymicrobial infections in 5 exogenous cases, and a total of 15 fungal species across 9 genera, dominated by Aspergillus flavus, Candida albicans, and Aspergillus niger. Candida albicans and Aspergillus flavus were the predominant pathogens in endogenous and exogenous FE, respectively. Notably, mNGS enabled detection of rare fungal species including Aspergillus niger, Aspergillus welwitschiae, Fusarium oxysporum, Memnoniella echinata, Rhizopus oryzae, Rhizopus microsporus, Chaetomium globosum, and Debaryomyces fabryi. Sequencing results were supported or supplemented by culture, beta-D-glucan, and galactomannan testing in selected cases. Among mNGS-positive cases, 82.1% (23/28) experienced clinical management changes guided by fungal identification. We further propose a laboratory workflow integrating mNGS with conventional assays, tailored to the obtained specimen volume of intraocular fluids.},
}

@article {pmid42032279,
year = {2026},
author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G},
title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42032279},
issn = {2058-5276},
support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; },
abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .},
}

@article {pmid42032281,
year = {2026},
author = {Tonkin-Hill, G and Shao, Y and Zarebski, AE and Mallawaarachchi, S and Xie, O and Mäklin, T and Thorpe, HA and Davies, MR and Bentley, SD and Lawley, TD and Corander, J},
title = {Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42032281},
issn = {2058-5276},
support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE240100316//Department of Education and Training | Australian Research Council (ARC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
abstract = {Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmision Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.},
}

@article {pmid42032282,
year = {2026},
author = {},
title = {Benchmarking shotgun metagenomics.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42032282},
issn = {2058-5276},
}

@article {pmid42012708,
year = {2026},
author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P},
title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.},
journal = {European journal of nutrition},
volume = {65},
number = {4},
pages = {},
pmid = {42012708},
issn = {1436-6215},
abstract = {BACKGROUND: Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood.

OBJECTIVE: To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions.

METHODS: Screening participants with a positive faecal immunochemical test at ages 55–77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis.

RESULTS: Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend = 0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10 g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in α- and β-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria.

CONCLUSION: Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions. Trial registration: The BCSN is registered at clinicaltrials.gov (National clinical trial (NCT) no. 01538550).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00394-026-03960-6.},
}

@article {pmid42020953,
year = {2026},
author = {Flatau, R and Bickley, CD and Altamia, MA and Gasser, MT and Distel, DL},
title = {Metabolic potential structures gill symbiont communities in two common shipworm species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag089},
pmid = {42020953},
issn = {1751-7370},
abstract = {Shipworms (Bivalvia: Teredinidae) are the most prolific wood consumers in marine environments. These wormlike marine bivalves digest wood using carbohydrate-active enzymes (CAZymes) produced by intracellular bacterial endosymbionts housed within their gills. Although several shipworm species are known to host multiple co-occurring symbiont species, the factors that influence symbiont community assembly, including the phylogenetic identity and metabolic capabilities of the symbionts, remain poorly understood. We sequenced gill symbiont metagenomes from multiple specimens of two shipworm species, Teredo bartschi (22 specimens) and Lyrodus pedicellatus (14 specimens), which have sympatric distribution in the wild, and which were reared together in laboratory co-culture. From these metagenomes, we assembled 90 metagenome-assembled genomes (MAGs) representing seven distinct symbiont species. The metagenome of each host specimen contained between 1 and 5 symbiont species, with each including at least one nitrogen-fixing symbiont. Six of the seven identified symbiont species were found in both host species, demonstrating a lack of host species specificity in these symbioses. We identified patterns of symbiont occurrence and co-occurrence in these two hosts and used these patterns to constrain the core set of CAZyme and nitrogen-fixation gene classes necessary to support host survival. Our results indicate that, in these two host species, symbiont community composition reflects the symbionts' capabilities for carbohydrate degradation and nitrogen fixation, rather than strict species-specific mechanisms of host and symbiont sorting.},
}

@article {pmid42021075,
year = {2026},
author = {Ishikawa, R and Nakamura, M and Sakurai, A and Nakayama-Imaohji, H and Kuwahara, T and Ichimura-Shimizu, M and Shishibori, M and Kataoka, K},
title = {Influences of ampicillin exposure in early life on the murine gut microbiota and steatotic liver disease associated with western diet.},
journal = {The journal of medical investigation : JMI},
volume = {73},
number = {1.2},
pages = {186-207},
doi = {10.2152/jmi.73.186},
pmid = {42021075},
issn = {1349-6867},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Ampicillin/adverse effects/pharmacology ; Mice, Inbred C57BL ; Mice ; *Fatty Liver/etiology/microbiology ; *Diet, Western/adverse effects ; Female ; *Anti-Bacterial Agents/adverse effects ; Male ; Dysbiosis/chemically induced ; },
abstract = {Dysbiosis of gut microbiota is one of the important factors associated with metabolic dysfunction-associated steatotic liver disease (MASLD). Antibiotic use, especially in early life, could profoundly disrupt an establishing process of stable gut microbiota, and the influence on gut environment may persist throughout life. In this study, we examined effects of ampicillin exposure (AMP) in early life on the temporal changes of fecal microbiota and severity of MASLD in western diet-fed C57BL/6J mice. Histological evaluation of MASLD showed that steatosis in female mice and lobular inflammation was significantly influenced with AMP, and that NAS (MASLD activity score constituting from score of steatosis, lobular inflammation, and ballooning degeneration) tended to be high in female of AMP-treated group. 16S metagenome analyses of fecal microbiota showed significant decrease of α-diversity and remarkable shift to normally minor bacterial species at 4 weeks of age in AMP-treated mice, and the influence was continuously observed even after finishing the western diet feeding period. α-Diversity at 4weeks of age negatively correlated with combined scores of steatohepatitis and fibrosis. These results suggest that AMP in early life induced dysbiosis of gut microbiota and could promote the development of western diet-associated steatotic liver disease. J. Med. Invest. 73 : 186-207, February, 2026.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Ampicillin/adverse effects/pharmacology
Mice, Inbred C57BL
Mice
*Fatty Liver/etiology/microbiology
*Diet, Western/adverse effects
Female
*Anti-Bacterial Agents/adverse effects
Male
Dysbiosis/chemically induced

@article {pmid42021418,
year = {2026},
author = {Ravi, A and Shestivska, V and Thiago Dobbler, P and Sechovcová, H and Maixnerová, M and Semerád, J and Nehasilová, A and Vadroňová, M and Odriozola, I and Šubrtová Salmonová, H and Větrovský, T and Musilová, Š and Cajthaml, T and Pěchoučková, E and Nemec, A and Kyselková, M},
title = {Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00568-3},
pmid = {42021418},
issn = {2524-4671},
}

@article {pmid42021724,
year = {2026},
author = {Batra, N and Rout, PR and Dey, P},
title = {Modulation and adaptation of gut microbial metabolic functions under probiotic and postbiotic treatment using a novel in vitro anaerobic pseudo-colon system.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04976h},
pmid = {42021724},
issn = {2042-650X},
abstract = {Probiotic and postbiotic compounds found in food influence gut microbiota to attenuate chronic metabolic diseases; however, the underlying mechanisms are not yet fully understood. This study employed a customized in vitro anaerobic pseudo-colon system (AMMR) to evaluate the impacts of Lactiplantibacillus plantarum (probiotic) and butyrate (postbiotic) on gut microbial composition and functionality, using human fecal samples. Metagenomic (16S rRNA) profiling and untargeted metabolomic (GC-MS) analysis were conducted after 48 h treatments. The results showed that butyrate supplementation markedly enhanced microbial diversity, inhibited opportunistic pathobionts (e.g., Enterococcus and Klebsiella), and selectively enriched butyrate producers (e.g., Lachnoclostridium), while diminishing the Firmicutes : Bacteroidetes ratio. It increased indole levels metabolically and redirected pathways towards amino acid synthesis and energy metabolism, while suppressing fatty acid formation. In contrast, L. plantarum exhibited modest alterations in microbial diversity while enhancing Bacteroides and Klebsiella and preserving elevated Enterococcus levels. It elevated saturated fatty acids (octanoic/capric acid) and enhanced amino acid catabolic pathways (valine/leucine) and redox regulators (taurine metabolism). Correlation analysis revealed that butyrate was associated with fiber-degrading microbes, whereas L. plantarum was associated with lactic acid bacteria, suggesting distinct ecological niches and interaction patterns. These findings collectively indicate that butyrate and L. plantarum elicit complementary microbial alterations, i.e., butyrate directly transforms the microbial structure and metabolism towards an anti-inflammatory phenotype, while L. plantarum largely influences via metabolic byproducts and niche adjustment. The complementary actions highlight the therapeutic potential of integrated probiotic-postbiotic approaches for the enhancement of gut health.},
}

@article {pmid42021875,
year = {2026},
author = {Li, H and Song, Z and Zhao, Y and Li, M},
title = {[Advances in the Application of Artificial Intelligence in Clinical Microbiological Testing].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {2},
pages = {313-318},
pmid = {42021875},
issn = {1672-173X},
mesh = {*Artificial Intelligence ; Humans ; Deep Learning ; *Microbiological Techniques/methods ; Algorithms ; Microbial Sensitivity Tests ; },
abstract = {Traditional microbiological detection methods have inherent limitations in detection speed, sensitivity, and specificity, making them increasingly unable to meet growing clinical demands. In recent years, artificial intelligence (AI) has been rapidly integrated into clinical microbiological testing, with numerous studies demonstrating its significant potential to enhance pathogen identification, predict antimicrobial susceptibility testing, and advance laboratory automation. This article systematically reviews classical AI algorithms and their latest advancements in this field. For visual data applications, deep learning-based models are used to automatically analyze microscopy images or colony morphology, significantly improving recognition efficiency and diagnostic accuracy. For non-visual data, AI has achieved breakthroughs in analyzing multi-omics data such as genomics, transcriptomics, and metagenomics, and is widely used for rapid pathogen identification and prediction of antimicrobial resistance. Despite its promising prospects, the application of AI in clinical microbiological testing remains in the early stages of transitioning from scientific research to clinical practice. This paper further discusses the key challenges and opportunities encountered during this technological translation, aiming to help clinical professionals comprehensively understand the current status, future trends, and potential impact of AI in this field, thereby promoting its development into reliable and scalable routine diagnostic methods.},
}

*Artificial Intelligence
Humans
Deep Learning
*Microbiological Techniques/methods
Algorithms
Microbial Sensitivity Tests

@article {pmid42021890,
year = {2026},
author = {Zhang, W and Zhong, S and Lu, S and Xiao, X and Xie, Y},
title = {[Diagnostic Performance of Metagenomic Next-Generation Sequencing for Mucormycosis: A Retrospective Cohort Study].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {2},
pages = {411-418},
pmid = {42021890},
issn = {1672-173X},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology ; Retrospective Studies ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Middle Aged ; Mucorales/genetics/isolation & purification ; *Metagenomics/methods ; Adult ; Aged ; ROC Curve ; Sensitivity and Specificity ; },
abstract = {OBJECTIVE: Mucormycosis is a life-threatening invasive fungal infection with high mortality, yet traditional diagnostic methods are limited by low positivity rates. This study aims to evaluate the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in mucormycosis.

METHODS: A retrospective analysis was conducted on 135 patients with mNGS results positive for Mucorales fungi at West China Hospital of Sichuan University from November 1, 2022, to October 31, 2024. Based on comprehensive clinical diagnostic criteria (including proven and probable cases), patients were classified into a confirmed mucormycosis group and a non-mucormycosis group. Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic performance of normalized read counts (lgRPM) from different specimen types. Fungal species distribution and laboratory parameters were compared between the two groups.

RESULTS: Among the 135 patients with positive mNGS results for Mucorales, 100 (74.1%) were ultimately diagnosed with mucormycosis. ROC curve analysis revealed that the diagnostic performance of mNGS varied by specimen type. For blood specimens, the area under the curve (AUC) was 0.772, with a specificity of 87.5% at the optimal cutoff value of 0.11 RPM. For bronchoalveolar lavage fluid specimens, the AUC was 0.717, with a sensitivity of 76.5% at the optimal cutoff value of 0.02 RPM. Combined analysis of all specimens showed that at the optimal cutoff value of 0.08 RPM (approximately 8 reads/100M), the sensitivity and specificity were 62.0% and 71.4%, respectively. Species distribution analysis showed that the proportions of Cunninghamella elegans (11.0% vs. 2.9%) and Rhizomucor pusillus (9.0% vs. 2.9%) were significantly higher in the confirmed group than in the non-mucormycosis group (P < 0.05). Levels of C-reactive protein and interleukin-6 were also significantly higher in the confirmed group (P < 0.05). Notably, all seven renal perfusion fluid samples yielded false-positive mNGS results.

CONCLUSION: mNGS technology can effectively improve the diagnostic yield for mucormycosis. However, results should be interpreted in conjunction with specimen type, read count, and clinical characteristics. BALF specimens offer high sensitivity, making them suitable for screening, while blood specimens demonstrate high specificity, making them valuable for confirmation. Positive results from low-biomass samples such as renal perfusion fluid warrant caution against false positivity. Fungal species identification and inflammatory markers may serve as adjunctive evidence for clinical diagnosis.},
}

Humans
*Mucormycosis/diagnosis/microbiology
Retrospective Studies
Female
*High-Throughput Nucleotide Sequencing/methods
Male
Middle Aged
Mucorales/genetics/isolation & purification
*Metagenomics/methods
Adult
Aged
ROC Curve
Sensitivity and Specificity

@article {pmid42022012,
year = {2026},
author = {Conrad, RE and Rodriguez-R, LM and Lindner, BG and Gerhardt, K and Konstantinidis, KT},
title = {An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag068},
pmid = {42022012},
issn = {2730-6151},
abstract = {Although sequence-discrete species appear to dominate microbial communities, readily distinguishing between distinct populations of a species recovered from different short-read metagenomic samples is challenging due to technical limitations associated with read length. To close this gap, we developed a novel algorithm to evaluate which reads in a metagenome belong to a target population based on the distribution of sequence identities of reads aligned to a reference sequence, which are filtered using a Kernel density estimation (KDE) as a flexible alternative to the commonly used static 95% nucleotide identity cutoff. Subsequently, we employed the average nucleotide identity of reads (ANIr) aligning above the KDE threshold, and resampling techniques for estimating the confidence intervals of ANIr values, to quantify intrapopulation sequence diversity and compare populations across globally representative marine samples. Most populations showed high ANIr in only a few samples at similar depths and decreased ANIr and increased gene-content difference between samples where a closely related population is detected (e.g. same 95% ANI-based species). Accordingly, ANIr correlated with the physical distance between the samples, and only a few truly cosmopolitan populations were identified. Among the latter, Alteromonas macleodii [97% average amino-acid identity (AAI) to the type genome] and Prochlorococcus marinus (79% AAI) showed high relative abundance in both surface (0-200 m) and deep (>1000 m) samples. These results suggest that microbial communities under different environmental conditions share very few identical and abundant populations and provide a highly needed methodology to track such populations over space and time, in marine or other habitats.},
}

@article {pmid42022013,
year = {2026},
author = {Franco, MEE and Singer, E and Roux, S and Meredith, LK and U'Ren, JM},
title = {Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome specificity.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag054},
pmid = {42022013},
issn = {2730-6151},
abstract = {Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have evolved convergently in phylogenetically distant organisms, forming eight structurally unrelated classes that share physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2 transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57 218 α-, β-, and γ-CA sequences from 24 184 metagenomes and genomes, including the first putative α-CA from an archaeal species. CA sequences formed 3859 protein clusters (1188 with three or more sequences). Sequences within a cluster were typically taxonomically conserved only at higher levels (i.e. Superkingdom, Phylum). When viewed within a phylogenetic framework, the majority of subclades for each CA class contained CAs representing multiple Superkingdoms, although numerous novel β-CA clades appear unique to Fungi. Queries of CA Hidden Markov models against all public metagenome and metatranscriptome datasets revealed that CA is a ubiquitous enzyme present in virtually all sampled environments. However, CA clusters that were taxonomically conserved also appeared more environment-specific, which may explain high CA diversity. This work represents an important contribution to our understanding of the evolution, diversity, and environmental distribution of an enzyme that is key to life and has broad environmental and industrial applications.},
}

@article {pmid42022196,
year = {2026},
author = {Yan, Z and Xie, J and Jin, L and He, T and Zhang, X and Li, X},
title = {Steam Cooking Methods Promote the Transfer of Viable Antibiotic-Resistant Pathogens from Water into Air.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {4},
pages = {730-741},
pmid = {42022196},
issn = {2833-8278},
abstract = {Steam cooking is an ancient and widely used method for sterilizing water and food globally. However, its effectiveness may be compromised by the ubiquitous presence of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in these media. Here, we combined metagenomic sequencing, quantitative PCR analysis, plate culture, and Sanger sequencing to examine the effects of steam cooking on the profiles of antibiotic resistance in cooked fish, tap water, and indoor air in real cooking environments (i.e., a canteen and a home kitchen) and a laboratory chamber. We found that while steam cooking eliminated over 92.0% of bacteria and ARGs in both tap water and fish, it significantly increased the absolute abundance of bacteria and ARGs in indoor fine particulate matter (PM2.5) across all settings. Tap water was identified as the primary contributor to the increase, transferring 14.6% of bacteria and 33.2% of ARGs into indoor PM2.5 during steam cooking. This process also elevated the relative abundance of certain putative human pathogens in indoor PM2.5, containing ARGs and heat shock proteins and mainly originating from tap water. To test if these transferred ARGs hosts were viable, we conducted plate culture experiments and identified a viable heat-resistant ARB, Bacillus cereus, transferred from water to indoor PM2.5 via water vapor. Our results highlight the cross-medium transport of ARB and ARGs via steam cooking and underscore the potential microbial safety issues to cooking personnel through inhalational exposure.},
}

@article {pmid42022320,
year = {2026},
author = {Zhang, W and Huang, R and Yuan, J},
title = {Case Report: HHV8-positive multicentric Castleman disease in an HIV-positive patient :diagnostic challenges arising from atypical histology and the role of metagenomic sequencing.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1779973},
pmid = {42022320},
issn = {2234-943X},
abstract = {BACKGROUND: Multicentric Castleman disease (MCD), especially the HHV8-positive subtype, is a rare lymphoproliferative disorder that presents considerable diagnostic and therapeutic difficulties, particularly among HIV-positive patients. The co-occurrence of other infections, such as syphilis, may further complicate its clinical picture and management.

CASE DESCRIPTION: A 65-year-old man with well-controlled HIV presented with persistent fever, fatigue, and disseminated lymphadenopathy,. Through histopathological examination, molecular testing (including mNGS for HHV8), and PET-CT imaging, HHV8-positive MCD was diagnosed, along with latent syphilis. The patient was successfully treated with R-VP16 (rituximab and etoposide) for MCD and benzathine penicillin for syphilis, showing a positive clinical response. Throughout 36 months of continuous monitoring, the patient has maintained sustained complete remission with no evidence of disease recurrence.

CONCLUSION: This case underscores the importance of considering HHV8-driven lymphoproliferative disorders in HIV patients with unexplained lymphadenopathy and systemic symptoms, particularly in HHV8-endemic regions. It also highlights the essential roles of advanced diagnostics and multidisciplinary management in such complex presentations. The favorable outcome demonstrates the effectiveness of timely and targeted treatment, though long-term follow-up remains necessary due to the potential for relapse or progression.},
}

@article {pmid42022392,
year = {2026},
author = {Abedien, ZU and Lean, IJ and Djordjevic, SP and Hick, PM and Westman, ME and Mckay-Demeler, J and Webster, J and Brito, BP},
title = {Next-generation detection in bovine respiratory and enteric diseases: metagenomic and amplicon sequencing insights into microbial diversity.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1788101},
pmid = {42022392},
issn = {2297-1769},
abstract = {Respiratory and enteric diseases are major contributors to morbidity, mortality, and economic loss in cattle production, with significant implications for animal welfare, particularly in calves. Traditional diagnostic approaches have laid the foundation for pathogen detection in cattle, providing essential tools for disease surveillance and control. However, their targeted nature limits the capacity to identify unexpected, novel, or polymicrobial infections that often underlie complex respiratory and enteric syndromes. Recent advances in molecular technologies, particularly amplicon sequencing (metataxonomics), metagenomics, and metatranscriptomics, enable untargeted, high-resolution profiling of microbial communities directly from clinical samples, offering transformative potential for research and diagnostics. This review synthesises current applications of these approaches in bovine respiratory and enteric disease research, highlighting key findings across virology, bacteriology, and parasitology. Collectively, these studies have expanded the catalogue of the microbial diversity, yet their interpretation remains challenged by the still-evolving understanding of microbial contributions to pathogenesis. Progress toward clinical integration is further hindered by the need for methodological standardisation, validation, and improved interpretive frameworks. Looking ahead, advancing these technologies will require harmonised protocols, integration of multi-omics datasets, and robust experimental and epidemiological studies to establish causal links between microbial signatures and disease outcomes. By bridging discovery and application, these approaches hold the potential to enhance diagnostic accuracy, strengthen surveillance, and support sustainable cattle production systems. As these technologies continue to evolve, they are likely to play an increasingly central role in bovine disease research and diagnostics.},
}

@article {pmid42022531,
year = {2026},
author = {Wang, Y and Fu, J and Zhan, J and Liang, Y and Chen, R and Su, L and Zhou, Q and Zhang, Y and Cong, W and Xu, F},
title = {Panax ginseng-Polygonum cuspidatum is beneficial for alleviating atherosclerosis in ApoE[-/-] mice by modulating the composition of gut microbiota and related metabolites.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1773819},
pmid = {42022531},
issn = {2297-055X},
abstract = {BACKGROUND: Atherosclerosis (AS) is a central pathological driver underlying most cardiovascular diseases. Gut microbiota and related metabolites participate in regulating atherosclerosis. Panax ginseng and Polygonum cuspidatum (GP) herb pair has traditionally been used for cardiovascular diseases. Some active compounds in GP have shown anti-atherosclerotic effects and the effects of GP still needs more evidence-based supports. Therefore, this study aims to investigate the potential effects of GP on atherosclerosis and explore the underlying mechanisms.

METHODS: Fifty C57BL/6J ApoE[-/-] mice were randomly assigned to five groups: model, statin, low-dose GP, medium-dose GP and high-dose GP. They were fed a high-fat diet (HFD) to induce atherosclerosis. Ten wild-type C57BL/6J mice were given chow diet and served as controls. After 12-week intervention, their aortic tissues were collected for Oil Red O staining, colon tissues for Alcian staining and immunofluorescence, and serum samples for measurement of lipid levels and inflammatory cytokines. Then, their fecal DNA was extracted for metagenomic sequencing, while cecum and ileocecal valves were for untargeted metabolomics. Finally, fecal microbiota transplantation was performed to assess the contribution of gut microbiota to observed effects. Twenty additional ApoE[-/-] mice were randomized to two groups: FMT-Mod and FMT-GPH, given feces from the model or high-dose GP group.

RESULTS: Atherosclerotic plaques accumulated in the aorta and aortic sinus after HFD, while statin and high-dose GP alleviated this burden. TC, TG, LDL-C, MCP-1, MCP-3 and IL-2 showed significant increase after HFD, while statin and GP decreased LDL-C, MCP-1 and MCP-3. The goblet cells, ZO-1 and Occludin decreased after HFD, while statin and GP increased them, indicating that the intestinal barrier integrity was improved. Additionally, the composition of gut microbiota was modulated by GP. Some candidate taxa were identified, such as Bifidobacteriales, Bacteroidetes and Escherichia coli. Twenty-two metabolites were differentially abundant among the control, model and GP groups. Nineteen of them were modulated by HFD and reversed by GP, including 1-methylnicotinamide, dopamine and lysoPA (0:0/18:0). Mice given fecal transplants from the high-dose GP group showed less aortic plaques, lower levels of some lipid and inflammatory cytokines, more goblet cells, more expression of ZO-1 and Occludin, and more 1-methylnicotinamide than those given fecal transplants from the model group.

CONCLUSION: This study suggests that GP is beneficial for alleviating atherosclerosis in HFD-induced ApoE[-/-] mice, potentially by modulating the composition of gut microbiota and related metabolites.},
}

@article {pmid42022543,
year = {2026},
author = {Yang, P and Meng, Y and Ma, Y and Xu, M and Zhang, X},
title = {Fermented cotton stalks preserve colonic epithelial integrity in Hu sheep via the microbiota-metabolite-NF-κB/MLCK axis and mitigate the adverse effects of direct feeding.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1777023},
pmid = {42022543},
issn = {2296-861X},
abstract = {BACKGROUND: This study aimed to compare three cotton-stalk processing strategies-grinding (FS), steam explosion (PH), and microbial fermentation (FJ)-and to clarify whether fermented cotton stalks preserve colonic epithelial integrity through a microbiota-metabolite-NF‑κB/MLCK axis in Hu sheep.

METHODS: Fifteen clinically healthy Hu sheep (26.7 ± 1.76 kg body weight; 115 ± 4 days of age) were used after a 14‑day adaptation period and randomly assigned to one of three diets (n = 5 per treatment) containing 40% processed cotton stalks (FS, PH, or FJ) for 8 weeks.

RESULTS: PH and FJ increased final body weight compared with FS, and average daily gain increased progressively from FS to PH to FJ (206.07, 282.50, and 322.14 g/d, respectively; p < 0.05). Colonic fermentation profiles were markedly improved by FJ, evidenced by lower pH, ammonia nitrogen, free gossypol, and acetate (p < 0.05), alongside higher total VFAs with elevated propionate and butyrate (p < 0.05), whereas LPS was not different among treatments (p > 0.05). Histology and scanning electron microscopy indicated that FJ maintained intact crypt architecture and epithelial surface continuity, while FS exhibited epithelial detachment and surface erosion. Metagenomic analysis revealed distinct community structures among groups, with FJ showing higher richness and enrichment of taxa associated with carbohydrate utilization and butyrate‑producing guilds (e.g., Lachnospiraceae‑related genera such as Anaerostipes, Blautia, and Coprococcus). Consistently, FJ suppressed colonic mucosal inflammation, as reflected by reduced IL‑1β, IL‑6, IL‑8, and TNF-α at both mRNA and protein levels (p < 0.05). Mechanistically, FJ attenuated NF‑κB activation and downstream MLCK signaling, shown by decreased p‑p65/p65, p‑IκB/IκB, MLCK abundance, and p‑MLC/MLC ratio (p < 0.05), while upregulating tight‑junction proteins (ZO‑1, occludin, claudin‑1, and claudin‑4; (p < 0.05).

CONCLUSION: Fermentation‑based processing of cotton stalks enhanced growth performance and promoted a favorable hindgut fermentation and microbial-metabolic milieu, thereby reinforcing colonic barrier integrity via inhibition of NF‑κB/MLCK‑associated inflammatory signaling, supporting fermented cotton stalk as a practical strategy to valorize cotton residues for ruminant feeding while mitigating gossypol‑related hindgut stress.},
}

@article {pmid42022809,
year = {2026},
author = {Tian, YP and Li, QH and Li, YM and Zhao, JY and Wei, XX and Wang, JY and Zhou, YL and Yang, SB and Li, W and Guo, P and Wang, LX and Dai, TT and Hu, SF and Zhong, ZQ and Xie, YM and Lv, ZH},
title = {Gut microbiota and metabolome signatures in preterm infants with high versus low risk for neurodevelopmental impairment: a prospective, matched, longitudinal multi-omics study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799859},
pmid = {42022809},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Infant, Premature ; Prospective Studies ; *Metabolome ; Longitudinal Studies ; Female ; Male ; Infant, Newborn ; Feces/microbiology ; *Neurodevelopmental Disorders/microbiology ; Metagenomics ; Infant ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; Biomarkers ; Dysbiosis/microbiology ; Multiomics ; },
abstract = {Preterm birth is a leading global cause of neurodevelopmental impairment (NDI), yet early predictive biomarkers remain elusive. The gut microbiome, developing in parallel with the brain and communicating via the microbiota-gut-brain axis, holds potential as a source of such biomarkers. However, specific longitudinal multi-omics signatures predictive of NDI risk in preterm infants are poorly defined. We conducted a prospective, matched, longitudinal study of 60 preterm infants, classified at 3 months corrected age (CA) into high-risk (HR, n=30) or low-risk (LR, n=30) groups for NDI based on combined motor (TIMP) and neurological (GMs) assessments. Fecal samples from birth (meconium) and 3 months CA underwent shotgun metagenomic sequencing and untargeted metabolomics. Groups were rigorously matched for gestational age, birth weight, sex, and clinical exposures. While α- and β-diversity did not differ between groups, profound taxonomic and functional divergence emerged. At 3 months CA, the LR gut was enriched with Akkermansia muciniphila, whereas the HR gut was dominated by Klebsiella variicola. Functional metagenomics revealed a dysbiotic HR trajectory, enriching pathways for bacterial virulence, stress response, and-notably-multiple pathways annotated for human neurodegenerative diseases, contrasting with LR expansion of core biosynthesis. Metabolomics confirmed a dysfunctional HR state, showing impaired amino acid metabolism and aberrant neuroactive pathway enrichment. Critically, meconium features correlated with 3-month neurobehavioral scores, demonstrating ultra-early predictive potential. Integrated networks at 3 months directly linked Akkermansia muciniphila and co-varying glycerophospholipids to superior neurodevelopmental scores, forming a beneficial "Akkermansia-lipid" axis, while Klebsiella variicola and triterpenoids formed a dysbiotic hub. Our study defines a high-risk gut ecosystem trajectory in preterm infants, characterized by early commensal depletion, pathobiont expansion, and a functional shift towards inflammation and neuroinflammation. These signatures offer novel targets for early risk prediction and microbiome-targeted interventions.},
}

Humans
*Gastrointestinal Microbiome
*Infant, Premature
Prospective Studies
*Metabolome
Longitudinal Studies
Female
Male
Infant, Newborn
Feces/microbiology
*Neurodevelopmental Disorders/microbiology
Metagenomics
Infant
Metabolomics
Bacteria/classification/genetics/isolation & purification
Biomarkers
Dysbiosis/microbiology
Multiomics

@article {pmid42022943,
year = {2026},
author = {Fu, F and Zhang, C and Xu, Z and Ji, P and Zhang, Z},
title = {Gastric Microbiome Alterations in Sepsis-Related Gastrointestinal Bleeding: Two Case Reports and Literature Review.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {10},
number = {3},
pages = {e70318},
pmid = {42022943},
issn = {2397-9070},
abstract = {Sepsis, characterized by life-threatening organ dysfunction resulting from an uncontrolled response to infection, can impact various systems of the body, including the digestive system. Prior research has identified sepsis as a significant risk factor for gastrointestinal bleeding. However, there is limited reporting on the gastric microecology of individuals with sepsis complicated by gastrointestinal bleeding. This paper presents the cases of two patients, shedding light on this issue. The first case was a 29-year-old female who developed sepsis during perioperative liver transplantation, while the second case features a 34-year-old female with acute pancreatitis complicated by septic shock. Both patients underwent gastroscopy following gastrointestinal bleeding, revealing evident gastric mucosal injuries. Notably, the second patient exhibited suppurative gastritis. Metagenomic Next-Generation Sequencing (NGS) of gastric juice from these two patients unveiled microecological alterations in the stomach. The sequencing results indicated a substantial presence of pathogenic sequences, underscoring the role of direct gastric mucosal injury due to infection as a significant contributor to gastrointestinal bleeding. This study not only introduces a novel approach to pinpointing the causes of gastrointestinal bleeding in sepsis but also provides valuable insights for clinical diagnosis and treatment.},
}

@article {pmid42022944,
year = {2026},
author = {Zhao, Z and Ling, J and Chen, J},
title = {Oral Microbiome and Constipation: A Causal Link Revealed by Mendelian Randomization.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {10},
number = {3},
pages = {e70390},
pmid = {42022944},
issn = {2397-9070},
abstract = {BACKGROUND: Constipation affects approximately 15.3% of the global population. While the gut microbiome's role in constipation has been studied, the causal relationship between the oral microbiome and constipation remains unexplored.

METHODS: We utilized Mendelian randomization (MR) and large-scale GWAS data to investigate the causal relationship between the oral microbiome and constipation. Oral microbiome data were sourced from a metagenome-wide association study (mgGWAS) on 2984 individuals, while constipation GWAS data came from 176 629 samples in the Japan Biobank. Statistical methods included inverse variance-weighted (IVW) analysis, weighted median, and MR-Egger regression.

RESULTS: The MR analysis revealed significant associations between specific oral microbiome and constipation. Treponema denticola, found in saliva, was positively associated with an increased risk of constipation (OR = 3.961, 95% CI = 1.085-14.453, p = 0.037). Conversely, certain bacteria like Pauljensenia sp000308055 showed protective effects (OR = 0.409, 95% CI = 0.167-0.999, p = 0.0496). In the tongue coating, Neisseria sicca exhibited a significant positive association with constipation (OR = 4.864, 95% CI = 1.293-18.302, p = 0.019), while Aggregatibacter segnis demonstrated a protective effect (OR = 0.400, 95% CI = 0.188-0.854, p = 0.018).

CONCLUSION: This study is the first to explore the potential causal relationship between oral microbiome and constipation. The findings suggest that specific oral bacteria may influence the risk of constipation, highlighting the need for further research to validate these relationships and understand the mechanisms involved. Moreover, the study underscores the importance of considering both oral and gut microbiome in the context of gastrointestinal health and disease management.},
}

@article {pmid42023092,
year = {2026},
author = {Li, X and Chen, D and Xiao, Y and Lei, Z and Yang, X and Zhang, Y and Li, L and Zheng, Y and Zhang, Y and Huang, Z and Lin, B},
title = {Metagenomic next-generation sequencing improves diagnosis of Talaromyces marneffei and mixed infections in HIV/AIDS patients: a retrospective study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1800314},
pmid = {42023092},
issn = {2296-858X},
abstract = {BACKGROUND: Opportunistic infections remain a leading cause of morbidity in people living with HIV (PLWH). Talaromyces marneffei (T. marneffei) accounts for up to 15% of HIV-related hospitalizations in endemic regions. Metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection; however, its utility in diagnosing HIV-associated coinfections is uncertain.

METHODS: This retrospective study enrolled 56 hospitalized PLWH with coinfections at the Third Affiliated Hospital of Sun Yat-sen University from March 2022 to October 2024. All patients underwent pathogen detection using both mNGS and CTM, with their diagnostic performance compared. Clinical data, treatment adjustments, and outcomes were analyzed.

RESULTS: mNGS demonstrated significantly higher detection rate (84.4%, 54/64; 95% CI: 73.1-92.2%) than CTM (28.1%, 18/64; 95% CI: 17.6-40.8%; p < 0.0001), especially for T. marneffei detection (100% vs. 45.5%, p < 0.0001). mNGS identified T. marneffei in 39.3% (n = 22/56) of patients, including two rare cases (urinary and intracranial infections) missed by CTM. mNGS revealed mixed infections in 82.1% (46/56) of patients, substantially higher than the 5.4% detected by CTM. Notably, mNGS-guided therapy adjustments occurred in 74.1% of cases, compared with 22.2% for CTM (p < 0.001), correlating with clinical improvement in 90% (36/40) of adjusted regimens.

CONCLUSION: Our data demonstrated that mNGS had a higher positive detection rate than CTM for detecting coinfections among PLWH, especially for T. marneffei and mixed infections. These results highlight the clinical value of mNGS as a complementary tool for pathogen identification in this vulnerable population.},
}

@article {pmid42023515,
year = {2026},
author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y},
title = {PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag382},
pmid = {42023515},
issn = {1362-4962},
support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; //City University of Hong Kong/ ; 9667256//Institute of Digital Medicine/ ; 9678241//Institute of Digital Medicine/ ; },
abstract = {Metagenomic sequencing has transformed virus discovery; however, downstream bioinformatic analyses for viral identification, classification, and host prediction remain fragmented across multiple tools. Here, we present PhaBOX2, a major upgrade that extends the platform from a specialized bacteriophage identification tool to a comprehensive and integrated suite for viral sequence analysis. PhaBOX2 broadens its detection, taxonomic, and host prediction scope beyond phages to enable the characterization of archaeal and eukaryotic viruses. The updated workflow incorporates rigorous quality control and quantitative analyses, automatically removes host contamination, clusters sequences into viral operational taxonomic units, and performs phylogenetic analysis based on marker genes. In contrast to traditional "black-box" deep learning approaches, PhaBOX2 combines alignment-based strategies with machine-learning models under a "glass-box" design philosophy, providing interpretable intermediate evidence alongside final predictions to improve transparency and biological interpretability. Powered by a dedicated high-performance computing infrastructure, the server delivers a fully automated, end-to-end workflow, while achieving an ~80% reduction in processing time. PhaBOX2 thus provides a robust and user-friendly ecosystem for viral metagenomic analysis and is freely available at https://phage.ee.cityu.edu.hk/.},
}

@article {pmid42023591,
year = {2026},
author = {Lei, P and Qi, Z and Ma, Q and Zhao, B and Wen, B and Jiang, W and Xi, W and Liu, Y and Xun, Y and Zhang, S and Wang, Y and Guo, Y and Wang, W and Ma, X and Jia, M and Fan, Y},
title = {Gut microbiota reshapes host energy metabolism to modulate depressive behaviors.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2662556},
doi = {10.1080/19490976.2026.2662556},
pmid = {42023591},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Energy Metabolism ; Male ; Animals ; *Major Depressive Disorder/microbiology/metabolism/therapy ; Mice ; Female ; Fecal Microbiota Transplantation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Middle Aged ; Adult ; Mice, Inbred C57BL ; Disease Models, Animal ; Metabolomics ; Mitochondria/metabolism ; },
abstract = {Disturbances in energy metabolism are a key pathophysiological feature of major depressive disorder (MDD). The gut microbiota, as a critical regulator of host metabolism, may influence systemic energy homeostasis and contribute to depression. To investigate this, we performed a multi-omics analysis integrating targeted metabolomics and shotgun metagenomics on samples from 100 MDD patients and 68 healthy controls. MDD patients exhibited significant disruptions in central energy pathways (glycolysis, TCA cycle, and ornithine cycle), which correlated with symptom severity and cognitive impairment. We identified 36 bacterial species whose abundances were linked to mitochondrial fatty acid synthesis, ketogenesis, and amino acid metabolism, and were associated with altered levels of core metabolites like lactate and L-glutamic acid. Mediation analysis established a "gut microbiota-energy metabolites-depressive phenotype" axis, where metabolites mediated the effects of specific bacteria (e.g., Dorea_formicigenerans) on symptoms. To validate causality, we used a chronic social defeat stress mouse model with simultaneous autologous fecal microbiota transplantation (FMT). FMT effectively reshaped the gut microbiota, ameliorated depression-like behaviors, and reversed the stress-induced shift toward anaerobic glycolysis in serum and the central nervous system. Critically, FMT restored mitochondrial morphology and structural integrity in the prefrontal cortex and hippocampus, renormalizing the relationship between metabolism and behavior. Our findings elucidate the gut microbiota's role in MDD pathogenesis via host energy metabolism regulation and posit early autologous FMT as a novel strategy to correct central energy imbalances.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Energy Metabolism
Male
Animals
*Major Depressive Disorder/microbiology/metabolism/therapy
Mice
Female
Fecal Microbiota Transplantation
*Bacteria/classification/genetics/metabolism/isolation & purification
Middle Aged
Adult
Mice, Inbred C57BL
Disease Models, Animal
Metabolomics
Mitochondria/metabolism

@article {pmid42023670,
year = {2026},
author = {Santillan, E and Neshat, SA and Wuertz, S},
title = {Predicting microbial community responses to disturbance using genome-resolved trait-based life-history strategies.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag099},
pmid = {42023670},
issn = {1751-7370},
abstract = {Understanding how microbial communities respond to disturbance remains a fundamental question in ecology, with broad implications for biodiversity, ecosystem function, and biotechnology. Trait-based approaches offer general rules to predict community responses by linking ecological strategies to measurable traits. Whereas life-history strategy frameworks such as the competitor-ruderal-stress-tolerant (CSR) model are well established in plant and animal ecology, their application to microbial communities has been limited. Here, we experimentally tested how microbial communities shift across a gradient of disturbance frequency in replicated bioreactors treating synthetic wastewater. We applied six conditions by doubling the organic loading rate at different frequencies, from undisturbed to press disturbance, and monitored changes over 42 days using genome-resolved metagenomics, 16S rRNA gene sequencing, biomass quantification, and effluent chemistry. By integrating ordination, network analysis, and machine learning, we identified emergent community-level life-history strategies, with competitor-dominated communities under undisturbed conditions, ruderal-associated strategies at intermediate disturbance frequencies, and stress-tolerant strategies under sustained high-frequency (press) disturbance. These strategies were reflected in functional trade-offs, shifts in community composition, and genomic trait distributions. A simulation-based approach was used to generate a CSR classification of metagenome-assembled genomes, which was consistent with patterns observed in other microbial ecosystems. Our results demonstrate that life-history frameworks can capture predictable microbial dynamics across disturbance regimes. This approach provides a unifying tool for linking microbial structure, function, and traits across scales, helping to reconcile ecological theory with microbial resource management in natural and engineered ecosystems.},
}

@article {pmid42023843,
year = {2026},
author = {Olagoke, O and Zheng, X and Chung, S and Mengistie, HD and Asfaha, K and Read, TD and Dean, D},
title = {Phylogenetic diversity, functional pathways, and network interactions of ocular chlamydia-like organisms (CLOs) in trachoma-endemic Ethiopia.},
journal = {mBio},
volume = {},
number = {},
pages = {e0053426},
doi = {10.1128/mbio.00534-26},
pmid = {42023843},
issn = {2150-7511},
abstract = {Trachoma is the leading infectious cause of blindness worldwide and classically attributed to Chlamydia trachomatis (Ct). However, other members of the phylum Chlamydiae, particularly environmental chlamydia-like organisms (CLOs), may modulate ocular ecology and influence disease outcomes. Here, we investigated CLO distribution, phylogeny, and microbiome associations among 1,059 individuals from trachoma-endemic communities in Ethiopia using targeted 16S rRNA sequencing and metagenomic shotgun sequencing. CLOs were detected in 249 (23.3%) participants of all ages and sexes and were significantly less likely to be associated with Ct or trachomatous scarring (TS) and trichiasis (TT). Phylogenetic analyses revealed extensive CLO diversity with six novel phylotypes, the most abundant of which was ancestral to Sorochlamydiaceae-a family linking pathogenic Chlamydiaceae, which includes the genus Chlamydia, and symbionts of protists. CLO-positive microbiomes exhibited significantly greater species richness and evenness with distinct differences in community composition relative to CLO-negative microbiomes. These effects were most pronounced among males and older adults. Functional profiling revealed widespread depletion of biosynthetic and metabolic pathways in CLO-positive microbiomes, particularly in participants with TS/TT, suggesting reduced community biosynthetic capacity and niche modification. Species interaction network analyses demonstrated substantial reorganization of microbial associations in the presence of CLOs with increased connectivity and centrality compared to CLO-negative networks. These findings identify CLOs as prevalent, phylogenetically diverse, and ecologically influential members of the microbiome. Their inverse association with Ct and TS/TT underscores the importance of considering intracellular symbionts beyond Ct in understanding conjunctival microbial ecology, resilience, and trachoma pathogenesis and for designing novel control strategies.IMPORTANCETrachoma caused by Chlamydia trachomatis (Ct) remains the leading infectious cause of blindness globally. While control efforts focus exclusively on Ct, other members of the phylum Chlamydiae, such as chlamydia-like organisms (CLOs), inhabit mucosal surfaces but remain understudied in the eye. Using targeted 16S rRNA and metagenomic shotgun sequencing of conjunctival samples from villagers in trachoma-endemic Ethiopia, CLOs were prevalent (23.3%; 249/1,059), phylogenetically diverse, including novel Chlamydiae phylotypes, and inversely associated with both Ct infection and severe scarring disease. CLO microbiomes had increased microbial diversity, altered community composition, depleted metabolic pathway abundance, and reorganized species interaction networks compared to CLO-negative microbiomes. These findings challenge the singular focus on Ct in trachoma control and research and suggest that CLOs represent ecologically significant members of the conjunctival microbiome. Further research on their interactions with ocular microbial communities could reveal new insights into trachoma pathogenesis and inform more holistic approaches to disease control.},
}

@article {pmid42023878,
year = {2026},
author = {Conte, CA and Rivarola, M and Gonzalez, S and Milla, FH and Soria, C and Giardini, MC and Segura, DF and Handler, AM and Bourtzis, K and Ragoussis, J and Lanzavecchia, SB},
title = {De novo whole-genome assembly of the Wolbachia sp. endosymbiont from Anastrepha fraterculus using long- and short-read metagenomic data.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0042526},
doi = {10.1128/mra.00425-26},
pmid = {42023878},
issn = {2576-098X},
abstract = {A whole-genome assembly and annotation of Wolbachia sp. infecting Anastrepha fraterculus sp. 1 were generated by a metagenomic analysis of sequencing reads from a host genome project. This study contributes to the characterization of this endosymbiotic bacterium and provides valuable insights for research on host-symbiont interactions and pest management strategies.},
}

@article {pmid42024170,
year = {2026},
author = {Jiang, L and Tang, Y and Xu, L and Wei, Y and Liu, M and Che, X and Xin, R and Zhu, Y},
title = {Microbiome in adult severe caries and cross-kingdom biofilms validation.},
journal = {Clinical oral investigations},
volume = {30},
number = {5},
pages = {},
pmid = {42024170},
issn = {1436-3771},
support = {ZDXX25182//Nanjing Medical Science and Technique Development Foundation/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; 0224C010//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; },
mesh = {*Biofilms/growth & development ; Humans ; *Dental Caries/microbiology ; Candida albicans ; Adult ; Saliva/microbiology ; *Microbiota ; Streptococcus mutans ; Male ; Veillonella ; Female ; Microscopy, Electron, Scanning ; Microscopy, Atomic Force ; Microscopy, Confocal ; Metagenomics ; Middle Aged ; },
abstract = {OBJECTIVES: Adult severe caries (ASC) is a form of rampant caries that develops in adulthood, causing severe impairment of oral function and reducing quality of life. However, the pathogenic mechanism of ASC remains unclear. This study aimed to identify the core microbiota in patients with ASC and preliminarily investigate the microbial interactions and pathogenicity of key ASC-associated core microorganisms.

MATERIALS AND METHODS: Saliva samples were collected from 7 adult patients with severe caries and 6 caries-free volunteers for metagenomic analysis. Based on microbiome profiling results, an in vitro cross-kingdom biofilm model composed of Streptococcus mutans (S. mutans), Candida albicans (C. albicans) and Veillonella parvula (V. parvula) was established to simulate a high caries-risk microenvironment. Scanning electron microscopy (SEM), crystal violet (CV) staining, and live/dead bacterial staining were used to evaluate biofilm formation. Acid production assays, acid stress challenge tests, confocal laser scanning microscopy (CLSM) and qRT-PCR were performed to analyze the acidogenicity and synthesis of extracellular polysaccharides (EPS). Additionally, atomic force microscopy (AFM) was used to assess the surface roughness of demineralized dentin slices.

RESULTS: Metagenomic analysis revealed significant enrichment of C. albicans and V. parvula in the saliva of patients with high caries susceptibility. The in vitro cultured cross-kingdom biofilms exhibited enhanced growth and EPS synthesis compared with single-species S. mutans biofilms. Moreover, cross-kingdom biofilms significantly increased surface roughness of demineralized samples, with a stronger effect than single- and dual-species biofilms.

CONCLUSIONS: Colonization by C. albicans and V. parvula increases biofilm biomass, enhances microbial survival under stress, and elevates biofilm virulence, which induces demineralization of dentin slices in vitro.

CLINICAL RELEVANCE: This study demonstrates that the interspecies interactions among caries-related microorganisms in ASC patients confer enhanced virulence and cariogenicity, providing novel insights for the investigation and prevention of high caries susceptibility.},
}

*Biofilms/growth & development
Humans
*Dental Caries/microbiology
Candida albicans
Adult
Saliva/microbiology
*Microbiota
Streptococcus mutans
Male
Veillonella
Female
Microscopy, Electron, Scanning
Microscopy, Atomic Force
Microscopy, Confocal
Metagenomics
Middle Aged

@article {pmid42025071,
year = {2026},
author = {Waseem, H and Feng, K and Zhao, B and Yang, X and Liu, M and Wang, J and Li, J and He, Q and Wang, S and Lu, Y and Örmeci, B and Deng, Y},
title = {Diversity and geographic distribution of antibiotic resistance in food waste anaerobic digestion systems.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142168},
doi = {10.1016/j.jhazmat.2026.142168},
pmid = {42025071},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) present in food waste pose a significant environmental and public health challenge, with anaerobic digestion emerging as a promising technology to reduce ARG abundance during waste treatment. In this study, we analyzed the resistomes in 64 anaerobic digestion sludge samples from seven full-scale food waste treatment facilities representing seven Chinese provinces. Across all facilities, a small core set of glycopeptide (van clusters), β-lactamase, aminoglycoside, and macrolide-lincosamide-streptogramin genes accounted for most ARG abundance (70.3%), marking them as critical targets for monitoring and post-treatment at high-risk sites such as Wenzhou. Resistome composition differed significantly among facilities and exhibited moderate correlation with bacterial taxonomic composition, with Firmicutes (Bacillota), Chloroflexota, and Proteobacteria as the major carriers associated with multiple resistance classes. ARG abundance was positively correlated with mobile genetic elements (r = 0.54, p < 0.0001), driven by integrases, transposases, and Tn916. Horizontal gene transfer was largely constrained within phylogenetic boundaries, particularly within Firmicutes (66.67%), limiting cross-phyla ARG dissemination. Resistome variation was driven predominantly by deterministic processes.; these deterministic filters together with regional differences in food-waste composition and MGEs, collectively select for a glycopeptide-dominated, Firmicutes-anchored resistome that is distinct from those in activated sludge and manure digesters.},
}

@article {pmid42025084,
year = {2026},
author = {Xu, GL and Tan, S and Hu, Y and Cheng, M and Hou, J and Cui, HL},
title = {Five novel Haloarchaeobius species from coastal tidal flats and saline-alkali soil in China using integrated culture-dependent and culture-independent approaches.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {3},
pages = {126718},
doi = {10.1016/j.syapm.2026.126718},
pmid = {42025084},
issn = {1618-0984},
abstract = {Six novel halophilic archaeal strains, DFWS5[T], DT45[T], DYHT-AS-18[T], HRN-SO-5[T], TZWSO28, and TZWWS8[T] were isolated from tidal flats and saline-alkali soil collected from the eastern coastal region of China. Amplicon sequencing and metagenomic analyses indicated that these strains were present at low abundance in their original habitats, with only three strains detected by culture-independent approaches. These six strains constituted an independent clade alongside members of the genus Haloarchaeobius based on the 16S rRNA gene phylogeny. Except for the comparison between strains DYHT-AS-18[T] and TZWSO28, the average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values among these strains and existing members of the genus Haloarchaeobius were 76.60-89.50%, 21.00-38.50%, and 67.99-88.76%, respectively, below the proposed thresholds for species delineation. In contrast, these three values between strains DYHT-AS-18[T] and TZWSO28 were 97.36%, 76.30%, and 97.25%, respectively, exceeding the proposed thresholds. Phylogenomic analysis revealed that the six strains clustered with members of the genus Haloarchaeobius, but formed distinct branches separate from the current species. The optimal growth conditions for these six strains in terms of NaCl, MgCl2, temperature, and pH were 0.9-4.8 M, 0-1 M, 20-50 °C, and 5.0-9.5, respectively. According to phenotypic differences in nutrition and biochemical activity, these six strains can be distinguished from their related species. On the basis of polyphasic taxonomic evidence, five novel species within the genus Haloarchaeobius are proposed to accommodate strains DFWS5[T], DT45[T], DYHT-AS-18[T], HRN-SO-5[T], TZWSO28, and TZWWS8[T], respectively.},
}

@article {pmid42025086,
year = {2026},
author = {Islam, A and Han, Z and Rana, ML and Qiao, W and Guruge, SK and Zhang, Y and Yang, M},
title = {Removal of protozoa, opportunistic pathogens with virulence factors in swine manure using anaerobic digestion: Full-scale investigation and lab-scale optimization.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129728},
doi = {10.1016/j.jenvman.2026.129728},
pmid = {42025086},
issn = {1095-8630},
abstract = {Swine manure serves as a significant reservoir of zoonotic protozoa and opportunistic pathogens, posing environmental and public health risks when inadequately treated. In this study, multiple molecular approaches, including quantitative PCR, nested PCR with gp60-based phylogenetic analysis, virulence factor profiling, and metagenome-assembled genome (MAG) reconstruction, were employed to investigate the abundance, diversity, and treatment responses of Cryptosporidium, Giardia, twelve opportunistic pathogens, and associated virulence factors (VFs) in swine manure. Three full-scale anaerobic digestion (AD) systems were investigated, and thermophilic and hyperthermophilic pretreatments were applied to lab-scale AD systems to evaluate the efficiency of biological risk control. Cryptosporidium parvum was identified as the dominant species, with subtype IIaA17G4R1 and related zoonotic subtypes detected in both lab-scale and full-scale samples. Phylogenetic clustering of swine-derived sequences with human and cattle isolates indicates a potential risk of zoonotic transmission through manure-associated environmental contamination. In lab-scale AD, a significant reduction in Cryptosporidium, particularly under hyperthermophilic conditions, was observed, while Giardia was undetectable in both influent and effluent samples. In full-scale systems, persistence of Escherichia coli, Clostridium perfringens, Enterococcus, Salmonella, and multiple VFs was confirmed in the effluents. The hyperthermophilic-mesophilic (70 °C-37 °C) lab-scale treatments achieved a substantial reduction in overall pathogen abundance from 3.40 × 10[8] to 1.21 × 10[8] copies/g dry weight and in virulence gene loads from 5.24 to 2.35 copies/cell (P < 0.001), along with the significant removal of pathogenic MAGs such as Enterococcus, Escherichia, Pseudomonas, and Streptococcus. These findings demonstrate the effectiveness of AD for reducing microbial risks and underscore the potential of thermophilic phase digestion as a scalable, biologically effective method for reducing microbial risks associated with livestock manure reuse.},
}

@article {pmid42025876,
year = {2026},
author = {Stamatopoulou, P and Scarborough, MJ},
title = {Impacts of organic loading rate fluctuations and division of labor on sugar-based chain elongation revealed through metatranscriptomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134687},
doi = {10.1016/j.biortech.2026.134687},
pmid = {42025876},
issn = {1873-2976},
abstract = {Medium-chain carboxylates (MCCs) can be produced using open, mixed cultures of microorganisms in a process termed "chain elongation." Chain elongating bacteria can increase ATP yield by producing six-carbon caproate rather than four-carbon butyrate. Therefore, requiring chain elongating bacteria to maximize ATP yield for cell synthesis may be a way to increase production of the more valuable caproate. To test this, duplicate bioreactors were operated, and the impact of organic loading rate (OLR) fluctuations were assessed with glucose and xylose as substrates in media that did not include amino acids, vitamins, or other growth factors. Increasing the OLR did not reliably improve caproate production despite several known caproate-producing bacteria being present. 16S rRNA gene amplicon sequencing and shotgun metagenomics revealed that the same chain-elongating and sugar-degrading species were enriched in both bioreactors, including members of the Caproiciproducens, Caproicibacter, Olegusella, and Tractidigestivibacter genera. Further, metatranscriptomic results suggest a distinct division of labor associated with critical growth factors, including amino acids, folate, and pantothenate. This division of labor, while potentially beneficial to the microbial community, may result in low caproate production.},
}

@article {pmid42026082,
year = {2026},
author = {Human, ZR and Štursová, M and Odriozola, I and Větrovský, T and Howe, A and Navrátilová, D and López-Mondéjar, R and Žifčáková, L and Brabcová, V and Mundra, S and Thoen, E and Morgado, L and Fiore-Donno, AM and Bonkowski, M and Adamczyk, B and Kohout, P and Lipton, MS and Calhoun, S and LaButti, K and Lipzen, A and Keymanesh, K and Tejomurthula, S and Pennacchio, C and Grigoriev, IV and Martin, F and Kauserud, H and Baldrian, P},
title = {Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07163-w},
pmid = {42026082},
issn = {2052-4463},
support = {240859//Norges Forskningsråd (Research Council of Norway)/ ; },
abstract = {Coniferous forest soils represent a globally important carbon sink, where the microbiome is essential for carbon flux between tree roots, rhizosphere, litter and soil. Soil habitats, such as roots, rhizosphere, bulk soil and litter differ in physicochemical properties and composition of highly specialized microbial communities, whose activity reflects the seasonality of temperature and tree activity of these mid- to high-latitude biomes. Here we present a multi-omic dataset encompassing 160 samples collected from four coniferous forest soil habitats in the Czech Republic and Norway, sampled in early summer, late summer, early winter and late winter that characterize the composition, genomic potential and activity of tree roots and microbiome. For each sample, we provide metabarcoding-based composition of bacterial, fungal and eukaryotic communities, results of shotgun DNA sequencing (metagenomes) and shotgun RNA sequencing (metatranscriptomes) illustrating the functional potential and activity within habitats. This dataset enables analyses of the temporal variation of taxonomic composition, functional potential and transcription across seasons in a temperate and boreal coniferous forest.},
}

@article {pmid42026126,
year = {2026},
author = {Miravet-Verde, S and Cacace, E and Mores, CR and Rutschmann, C and Lin, CW and Ruscheweyh, HJ and Cuénod, A and Barazzone, EC and Marrec, E and Vershynina, K and Schumann, R and Bower, DJ and Schubert, M and Egli, A and Fiebig, T and Slack, E and Sunagawa, S and Keys, TG},
title = {In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42026126},
issn = {2058-5276},
support = {51NF40_225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; CRSK- 3_228959//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40_225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 117.143 IP-LS//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 117.143 IP-LS//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; LT0050/2023-L//Human Frontier Science Program (HFSP)/ ; FN24-0000000703//Novartis Stiftung für Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; 865730//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Serotyping identifies bacterial variants based on surface antigens, traditionally using antibody-based assays, but has been increasingly replaced by in silico methods that infer serotypes from genomic sequences for faster, scalable and more reproducible analyses. However, traditional Escherichia coli capsule serotyping has largely fallen out of use since the 1990s, leaving gaps in our knowledge of capsule genetics, diversity, distribution and epidemiology. As capsules influence bacterial interactions with phages, host immune systems and the environment, this gap limits our understanding of E. coli ecology and pathogenicity as well as vaccine and diagnostic development. Here we established a definitive genotype-serotype map for 35 serologically identified and structurally characterized transporter-dependent capsules. We then surveyed 37,723 E. coli genomes, cataloguing 85 transporter-dependent capsule types (K-types), including 55 types that were not part of the reference collection. We leveraged this catalogue to develop a hidden Markov model-based in silico serotyping tool, kTYPr, and applied it to curated sets of 24,015 E. coli genomes and 2,762 metagenome-assembled genomes spanning diverse environmental and clinical sources. We found previously uncharacterized K-types enriched in undersampled environments and associated with E. coli disease. This study expands our understanding of E. coli surface structures, supporting efforts for precision targeting with phage therapy or vaccines.},
}

@article {pmid42026467,
year = {2026},
author = {Luo, C and Yao, H and Xian, Y and Yang, T and Xiao, X and Ying, L and Xu, J and Luo, X and Qiu, D and Liu, Y and Liu, B and Li, F},
title = {Functional remodeling of the gut microbiome and metabolome in primary idiopathic male infertility.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05064-x},
pmid = {42026467},
issn = {1471-2180},
support = {2024NSFSC0647//Sichuan Provincial Science and Technology Support Program/ ; 24SYJS01//Health Commission of Sichuan Province Medical Science and Technology Program/ ; SCU2025J4183//the Fundamental Research Funds for the Central Universities/ ; },
}

@article {pmid42026490,
year = {2026},
author = {Pan, J and Kong, H and Liang, M and Fang, X},
title = {Pneumonia caused by co-infection with Mycobacterium tuberculosis and Pneumocystis jirovecii leading to acute respiratory distress syndrome in an HIV-negative immunocompromised patient: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13398-0},
pmid = {42026490},
issn = {1471-2334},
}

@article {pmid41807604,
year = {2026},
author = {Santacroce, M and Baranek, J and Adamski, Z and Trzebny, A and Dabert, M and Bufo, SA and Scrano, L},
title = {Prevalence of Bacillus species in the lytic cultural heritage of Santa Lucia alle Malve Rupestrian Church.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41807604},
issn = {2045-2322},
abstract = {UNLABELLED: Santa Lucia alle Malve (SLM) is a unique rupestrian heritage site, entirely carved into limestone. This monument, which was a church in the ancient settlement of Benedictine nuns over a millennium ago in southern Italy, holds exceptional value not only from an architectural and cultural perspective but also in terms of its microbial ecology. Until now, the specific microbiota of this site had remained unexplored. In this study, the bacterial community inhabiting the interior walls of Santa Lucia alle Malve was investigated using a metagenomic approach, alongside the isolation and comprehensive characterization of cultivable strains from various sampling sites. Both methodologies consistently revealed a dominance of spore-forming bacteria from the phylum Bacillota, particularly the genus Bacillus. Notably, most of the cultivable strains belonged to the Bacillus cereus sensu lato group and the Bacillus. licheniformis clade. Despite the high genetic similarity among these microorganisms, each strain exhibited a unique set of phenotypic traits, highlighting the potential complexity of the SLM metabolome. Additionally, two isolates were identified as Bacillus thuringiensis, entomopathogenic bacteria with possible applications in biological pest management. Finally, Staphylococcus warneri, a human skin commensal found in the church, suggests human influence on the microbial landscape.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41655-4.},
}

@article {pmid42014993,
year = {2026},
author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C},
title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05043-2},
pmid = {42014993},
issn = {1471-2180},
}

@article {pmid42015023,
year = {2026},
author = {Peng, Z and He, H and Zhou, S and Qiao, L and Wang, Q and Li, M and Zhao, Y},
title = {Rhino-orbito-cerebral Rhizopus delemar infection in a patient with anti-melanoma differentiation-associated-5-positive dermatomyositis diagnosed by metagenomic next-generation sequencing: a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13359-7},
pmid = {42015023},
issn = {1471-2334},
}

@article {pmid42015434,
year = {2026},
author = {Wang, S and Deng, F},
title = {Clinical Features and Coinfection Factors of Severe Community-Acquired Pneumonia with <em>Mycoplasma Pneumoniae</em> in Children.},
journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP},
volume = {36},
number = {4},
pages = {483-488},
doi = {10.29271/jcpsp.2026.04.483},
pmid = {42015434},
issn = {1681-7168},
mesh = {Humans ; *Community-Acquired Infections/microbiology/epidemiology/diagnosis ; Male ; Female ; *Coinfection/epidemiology/microbiology/diagnosis ; Child ; Retrospective Studies ; *Pneumonia, Mycoplasma/epidemiology/diagnosis/microbiology ; *Mycoplasma pneumoniae/isolation & purification/genetics ; Child, Preschool ; China/epidemiology ; Infant ; Adolescent ; Anti-Bacterial Agents/therapeutic use ; Severity of Illness Index ; Community-Acquired Pneumonia ; },
abstract = {OBJECTIVE: To characterise the clinical features of children with severe community-acquired pneumonia (CAP) associated with Mycoplasma pneumoniae (Mp) infection and to identify factors influencing polymicrobial coinfections.

STUDY DESIGN: A descriptive study. Place and Duration of the Study: Department of Internal Medicine, Anhui Provincial Children's Hospital, Anhui, China, from January to December 2023.

METHODOLOGY: A retrospective cohort study was conducted on 207 hospitalised children aged <16 years with confirmed CAP who underwent BALF testing due to severe symptoms, antibiotic-unresponsive fever, or unclear aetiology. Those with chronic comorbidities were excluded. BALF pathogens were detected via multiplex PCR and metagenomic next-generation sequencing (mNGS). Patients were divided into Mp mono-infection and coinfection groups; demographic, clinical, and laboratory data were compared, and logistic regression analysis was performed to identify factors associated with coinfection.

RESULTS: The coinfection group was significantly younger (4.12 ± 2.83 vs. 6.56 ± 2.47 years, p = 0.013) and had longer hospital stays (11.21 ± 4.26 vs. 9.90 ± 3.68 days, p = 0.049) than the mono-infection group. Inflammatory markers differed significantly: the coinfection group had higher IL-6 (28.64 ± 8.03 vs. 15.86 ± 14.21 pg/mL, p <0.001), but lower IL-2R (1774.15 ± 104.18 vs. 2157.39 ± 382.76 U/mL, p <0.001) and ESR (30.31 ± 14.79 vs. 40.08 ± 13.66 mm/h, p <0.001). Logistic regression confirmed IL-6 (p <0.001), IL-2R (p <0.001), and complications (p = 0.0281) as independent factors associated with coinfections, while chest CT findings showed no correlation (p >0.05).

CONCLUSION: Younger age, elevated IL-6 levels, reduced IL-2R levels, and the presence of complications are closely correlated with polymicrobial coinfections in children with severe Mp-associated CAP.

KEY WORDS: Pneumonia, Mycoplasma pneumoniae, Paediatrics, Coinfection, Metagenomic sequencing, Clinical characteristics.},
}

Humans
*Community-Acquired Infections/microbiology/epidemiology/diagnosis
Male
Female
*Coinfection/epidemiology/microbiology/diagnosis
Child
Retrospective Studies
*Pneumonia, Mycoplasma/epidemiology/diagnosis/microbiology
*Mycoplasma pneumoniae/isolation & purification/genetics
Child, Preschool
China/epidemiology
Infant
Adolescent
Anti-Bacterial Agents/therapeutic use
Severity of Illness Index
Community-Acquired Pneumonia

@article {pmid42015472,
year = {2026},
author = {Song, M and Zhang, Z and Huang, H and Zou, Z and Wen, S and Cui, Y and Liu, S},
title = {Spinal Tuberculosis Diagnosed by Metagenomics Capture (MetaCAP) in a Patient Undergoing Maintenance Hemodialysis: A Case Report.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e951840},
doi = {10.12659/AJCR.951840},
pmid = {42015472},
issn = {1941-5923},
mesh = {Humans ; Female ; Middle Aged ; *Tuberculosis, Spinal/diagnosis/drug therapy ; *Renal Dialysis ; *Metagenomics/methods ; *Kidney Failure, Chronic/therapy/complications ; *Mycobacterium tuberculosis/genetics/isolation & purification ; },
abstract = {BACKGROUND Spinal tuberculosis is difficult to diagnose in patients undergoing maintenance hemodialysis (MHD) because of immunosuppression, atypical clinical manifestations, and the limited sensitivity of conventional microbiological assays. Rapid and accurate pathogen identification is essential to distinguish spinal tuberculosis from other causes of vertebral destruction, including metastatic malignancy and bacterial spondylitis. This report aims to illustrate the diagnostic value of capture-based targeted sequencing for detecting Mycobacterium tuberculosis in extrapulmonary infection when routine tests and metagenomic next-generation sequencing (mNGS) yield inconclusive or misleading results. CASE REPORT A 64-year-old woman with end-stage renal disease secondary to IgA nephropathy, receiving long-term MHD, presented with progressive low back pain. Imaging revealed multilevel vertebral involvement with pathological fractures, raising suspicion of metastatic disease or infectious spondylitis. Histopathological examination demonstrated granulomatous inflammation, while acid-fast staining and routine cultures were negative. Initial mNGS of spinal tissue identified Staphylococcus aureus, leading to targeted antibacterial therapy. Although inflammatory markers declined, the patient's symptoms worsened and pancytopenia developed. Subsequent analysis of spinal pus using metagenomic capture (MetaCAP)-based targeted sequencing detected the Mycobacterium tuberculosis complex with high confidence. Anti-tuberculosis therapy was promptly initiated, resulting in rapid clinical improvement and radiological resolution. CONCLUSIONS This case shows the limitations of conventional microbiological methods and unbiased mNGS in diagnosing extrapulmonary tuberculosis in immunocompromised patients. Capture-based targeted sequencing offers enhanced sensitivity for Mycobacterium tuberculosis detection and may facilitate timely diagnosis and appropriate treatment of spinal tuberculosis in patients undergoing MHD.},
}

Humans
Female
Middle Aged
*Tuberculosis, Spinal/diagnosis/drug therapy
*Renal Dialysis
*Metagenomics/methods
*Kidney Failure, Chronic/therapy/complications
*Mycobacterium tuberculosis/genetics/isolation & purification

@article {pmid42016528,
year = {2026},
author = {Xu, H and Guo, J and Chen, C and Pang, Z and Zhang, G and Zhang, W and Kan, H and Shao, X},
title = {Metagenomics reveals the functional profiles of soil microorganisms and nutrient cycling under long-term grass vegetation cropping.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100583},
pmid = {42016528},
issn = {2666-5174},
abstract = {Soil microbes are crucial for biogeochemical cycles and their functional potential is greatly affected by ecosystem management. Yet, how does grass vegetation affect the composition of soil microbial communities and the abundance of key nutrient-cycling functional genes? In this study, based on an experimental plot built for 7 years, the long - term influence of two grass vegetation types (Carex breviculmis and Festuca arundinacea Schreb) on soil microbial community structure and C, N, P, and S cycles were explored by metagenomics. The results showed that both plants significantly increased the diversity and richness of soil bacteria and fungi, and the abundance of Pseudomonadota and Ascomycota in Carex breviculmis increased significantly, while those of Actinomycetota and Mucoromycota decreased. Microbial network analysis shows that Carex breviculmis forms a highly modular, low - complexity microbial interaction network, indicating specialized and stable microbial community functions. Conversely, Festuca arundinacea Schreb has a more complex and less modular network, suggesting enhanced microbial interactions. Carex breviculmis significantly increased the abundance of genes related to carbon fixation (fumA/B, pps, ppc) and phosphorus mineralization (phoR/P/B, phnF/P), and also enhanced soil denitrification potential. In contrast, Festuca arundinacea Schreb showed a enrichment of soil nitrogen fixation genes (nifh). Additionally, growing Carex breviculmis and Festuca arundinacea Schreb induced the growth of sulfur - oxidizing bacteria (e.g., Thiobacillus), enriching the abundance of sulfur - metabolism - related genes (apr, sox). Genes related to microbial C, N, P, and S cycles are positively correlated with soil pH, available P, and alkali-hydrolyzed nitrogen. Overall, this study reveals how different grass vegetation types regulate microbial community structure and functional gene abundance to drive nutrient cycling differentiation in grassland ecosystems, thereby providing a theoretical basis for optimizing grass vegetation configuration in managed and restored grasslands to enhance soil ecological functions.},
}

@article {pmid42016568,
year = {2026},
author = {Liu, L and Xu, C and Liu, Y and Yang, J and Ye, Y and Yao, Z and Lin, D and Qiu, H and Ruan, D and Qiu, Y and Wang, S and Lin, M and Zhang, Z and Huang, S and Meng, F and Zheng, E and Cai, G and Wu, Z and Wu, JJ},
title = {Restoring low-fiber diets-induced Lachnospiraceae bacterium loss partially recovers fiber digestion and immune function in mammals.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101401},
pmid = {42016568},
issn = {2665-9271},
abstract = {Mammals rely on their gut microbiota to degrade cellulose, the major component of dietary fiber. Westernized populations harbor a depleted microbiome with reduced fiber-digesting capacity and impaired immune regulation due to prolonged consumption of low-fiber diets. Comparable patterns are evident in other mammals, including Western commercial pigs raised on high-energy, low-fiber diets, exhibiting reduced diversity and abundance of fiber-degrading bacteria. In contrast, semi-free-ranging Chinese indigenous pigs consuming fiber-rich diets retain a more diverse and functionally resilient microbiota, reflecting divergent trajectories of host-microbiota co-evolution. However, the specific cellulose-degrading species lost and strategies to restore these functions remain unclear in mammals. By analyzing 473 human stool metagenomes spanning non-westernized and westernized diets, together with 251 fecal 16S rRNA datasets and 95 metagenomes from Western commercial pigs, Chinese indigenous pigs, and their crossbred progeny, we identified the Lachnospiraceae bacterium as a key symbiont enriched in non-westernized guts. This bacterium possesses an extensive Carbohydrate-Active Enzymes repertoire conferring strong fiber-degrading capacity. Notably, low-fiber diets leave a genetic signature on this keystone gut symbiont, which cannot be reversed by short-term dietary interventions alone. Reintroduction of Lachnospiraceae bacterium to germ-free mice improved feed efficiency and increased acetic acid production. Intestinal transcriptomics and peripheral blood flow cytometry revealed that it activates a broad adaptive immune response, promoting CD4[+] T cell accumulation, B cell activation, and anti-inflammatory cytokine induction. Reintroduction of this bacterium also alleviated dextran sodium sulfate-induced colitis. These findings highlight the preclinical functional potential of this Lachnospiraceae bacterium in mitigating low-fiber diets-induced dysfunction in mammals.},
}

@article {pmid42016597,
year = {2026},
author = {Srinivas, M and O'Sullivan, O and Cotter, PD and van Sinderen, D and Kenny, JG},
title = {Investigating the role of bacterial raw milk community members in chlorate reduction.},
journal = {Access microbiology},
volume = {8},
number = {4},
pages = {},
pmid = {42016597},
issn = {2516-8290},
abstract = {Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study identified chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for mitigating chlorate. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4 °C and after 24 h when incubated at 25 °C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4 °C and 25 °C, respectively. High abundances of ydeP and narG genes were observed for 4 °C samples and were attributed to Pseudomonas and various low-abundance genera, respectively. High abundances of the napA gene were noted in 25 °C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterized genes, such as ydeP, belonging to the DMSO reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasizing the need for further biochemical characterization of these genes to better understand the pathways involved in chlorate reduction in milk.},
}

@article {pmid42016660,
year = {2026},
author = {Qu, Y and Liu, Y and Zhou, X and Xu, P and Wang, L},
title = {Polymicrobial Pasteurella multocida-Anaerobic Coinfection Followhing a Cat Bite: Limb Salvage Through Metagenomic Next-Generation Sequencing-Guided Diagnosis and Multidisciplinary Management.},
journal = {Clinical case reports},
volume = {14},
number = {3},
pages = {e72304},
pmid = {42016660},
issn = {2050-0904},
abstract = {Successful management of a Pasteurella multocida and polymicrobial infection following a cat bite on the left leg entailed debridement, split-thickness skin grafting with vacuum-sealing drainage, and targeted antibiotic treatment. This approach enabled successful incorporation of the skin graft, preserving the limb and eliminating the necessity for amputation.},
}

@article {pmid42016731,
year = {2026},
author = {Chen, G and Tang, S and Wang, H and Liang, Z and Lv, X and Han, J and Ni, L},
title = {Integration of volatile flavor metabolomics and metagenomics reveals microbial-enzymatic pathways governing key aromatic volatile compound biosynthesis in Hongqujiu fermentation.},
journal = {Food chemistry: X},
volume = {35},
number = {},
pages = {103811},
pmid = {42016731},
issn = {2590-1575},
abstract = {The anabolic pathways of key volatile flavor compounds (VFCs) in Hongqujiu (HQJ) remain insufficiently elucidated. In this study, dynamic changes in volatile flavor profiles and microbial communities throughout HQJ brewing, were systematically investigated using an integrated multi-omics strategy combining metabolomics, flavoromics and metagenomics. The results demonstrated that the ethanol content, titratable acidity, amino nitrogen and higher alcohols increased progressively throughout fermentation. Quantitative flavor metabolomic profiling identified 18 key VFCs, maining comprising ethyl esters, acetate esters and higher alcohols. Metagenomic sequencing revealed that Weissella, Lactobacillus, Saccharomyces, Aspergillus, Talaromyces and Monascus were the predominant microbal genera throughout HQJ fermentation. Functional gene annotation further indicated that key enzymes involved in flavor metabolism are primarily associated with Lactobacillus, Aspergillus, Talaromyces, Saccharomyces, Cyberlindnera and Monascus. Overall, this study elucidates the microbial-enzymatic basis of VFC biosynthesis and establishes a comprehensive flavor metabolic framework for HQJ fermentation, providing a theoretical foundation for aroma quality improvement.},
}

@article {pmid42016742,
year = {2026},
author = {Funada Barbosa, MR and Ramos, EDSF and Villanova, F and Oliveira Silva, RL and Garcia, SC and de Araújo, RS and Mendes-Correa, MC and Tozetto-Mendoza, TR and Zhang, W and Pandey, RP and Luchs, A and Sato, MIZ and da Costa, AC and Leal, E},
title = {Exploring the Genomics of Marnaviridae Family: Identification, Characterization, and Taxonomic Implications.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {7188239},
pmid = {42016742},
issn = {1687-918X},
abstract = {In this study, we characterized sequences similar to Marnaviridae obtained from water samples in the state of São Paulo, Brazil. Sixteen complete or nearly complete genomes were determined, all of them positive-sense single-stranded RNA, with lengths between 7074 and 10,198 base pairs, containing one or two open reading frames (ORFs). The amino acid sequences derived from the ORFs showed similarity and protein domains typical of the Marnaviridae family. Phylogenetic analysis based on RNA-dependent RNA polymerase (RdRp) revealed clusters closely related to viruses that have not yet been classified by the International Committee on Taxonomy of Viruses (ICTV). Some sequences showed proximity to established genera such as Salicharnavirus, Locarnavirus, and Labynarvirus, while others formed three distinct clades, suggesting the presence of new genera. Furthermore, one sequence displayed an RdRp identity of less than 90% and a capsid identity of less than 75%, indicating that it represents a novel species related to Marnaviridae. These findings expand current knowledge of Marnaviridae diversity, contributing to a better understanding of evolutionary relationships and emphasizing the need for taxonomic reorganization.},
}

@article {pmid42016964,
year = {2026},
author = {Sun, X and Peng, Y and Hao, X and Dong, R and Wang, Z and Wang, L and Wang, C and Wu, X and Chen, Z and Zhang, W and Tang, X},
title = {Safeguarding a Flagship Species: Integrated Surveillance of Cross-Species Pathogen Transmission in Giant Panda Ecosystems.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73260},
pmid = {42016964},
issn = {2045-7758},
abstract = {Emerging infectious diseases, driven by increasing interactions among humans, wildlife, and livestock, pose an escalating threat to global health, biodiversity, and economies. As a flagship endangered species, the giant panda (Ailuropoda melanoleuca) plays a pivotal role in biodiversity conservation in China. This review synthesizes current knowledge on pathogens threatening giant panda health, including viruses, bacteria, and parasites alongside their potential transmission pathways within nature reserves. We emphasize the roles of domesticated animals, sympatric wildlife, and ectoparasites as reservoir hosts or vectors. Special focus is placed on cross-species transmission dynamics and the critical need for integrated monitoring systems utilizing metagenomics and viromics. We propose a framework for establishing early warning systems and surveillance networks at the domestic-wild animal interface to enhance pathogen detection, disease prevention, and biodiversity conservation.},
}

@article {pmid42016980,
year = {2026},
author = {De Panis, D and Priotto, O and Padró, J},
title = {Mitogenomic and Metabarcoding Resources for the Study and Conservation of Keystone Neotropical Raptors.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73262},
pmid = {42016980},
issn = {2045-7758},
abstract = {Neotropical raptors are among the most threatened birds, facing increasing extinction risks due to habitat loss and human persecution. Despite their importance for ecosystem stability, basic data on their distribution, abundance, and genetic diversity remain scarce. To address these gaps, we assembled and annotated the mitochondrial genomes of nine high-priority raptors from the Neotropics, including the threatened Chaco Eagle (Buteogallus coronatus), Black-and-Chestnut Eagle (Spizaetus isidori), Rufous-tailed Hawk (Buteo ventralis), and Harpy Eagle (Harpia harpyja), as well as the Near Threatened Orange-breasted Falcon (Falco deiroleucus), Crested Eagle (Morphnus guianensis), Ornate Hawk-Eagle (Spizaetus ornatus), Plumbeous Hawk (Cryptoleucopteryx plumbea), and Solitary Eagle (Buteogallus solitarius). Mitogenome sizes ranged from 17,848 to 20,449 bp, with consistent gene content and a Control Region architecture common in Falconidae and Accipitridae. Phylogenetic analyses provided strong support for most relationships, highlighting the value of mitogenomic data for phylogeographic studies. We further designed metabarcoding primers for environmental DNA applications. Primers targeting the 12S rRNA gene and a mini-barcode for the Harpy Eagle's Control Region showed high resolution using short, conserved sequences ideal for combining degraded DNA with next-generation sequencing. Our study provides essential molecular tools for monitoring and protecting these ecologically vital yet threatened raptors across the Americas.},
}

@article {pmid42017035,
year = {2026},
author = {Yang, Y and Ren, Y and Ma, T and An, J and Jin, S and Dong, Y},
title = {Research advances in the role of circulating microorganisms in gastrointestinal tumors (Review).},
journal = {Molecular and clinical oncology},
volume = {24},
number = {6},
pages = {40},
pmid = {42017035},
issn = {2049-9469},
abstract = {Gastrointestinal tumors are common malignant tumors of the digestive system, which globally threaten human health. Notably, it has been discovered that blood and other circulating body fluids are not completely sterile; instead, they harbor complex and dynamic microbial DNA and signatures [circulating microorganisms (CM)]. These microorganisms primarily originate from the microbial translocation (including bacterial fragments, DNA and metabolites) through a compromised intestinal barrier, and are closely associated with the initiation and progression of gastrointestinal tumors, thus providing novel perspectives for early tumor diagnosis and prognosis. Although there is currently no evidence that CM can directly cause cancer, their metabolites and exosomes may contribute to tumor microenvironment remodeling. On one hand, they activate pattern recognition and inflammatory signaling pathways, such as Toll-like receptor/signal transducer and activator of transcription, potentially inducing and maintaining low-grade chronic inflammation. On the other hand, they may facilitate immune evasion, potentially promoting the 'inflammation-cancer' transition. With the development of metagenomic technologies and the maturation of next-generation high-throughput sequencing technologies, CM have shown potential as liquid biopsy biomarkers for the early diagnosis of gastrointestinal tumors. Interventions targeting specific CMs have also shown prospects for enhancing efficacy in early clinical trials. However, the field still faces numerous challenges, including insufficient depth of mechanistic validation and a lack of standardized detection protocols. Future efforts should aim to conduct further systematic research to clarify the biological functions and clinical translational value of CM in gastrointestinal tumors.},
}

@article {pmid42017731,
year = {2026},
author = {Su, DM and Ni, T and Yu, XL},
title = {Invasive streptococcus pneumoniae infection in the hip joint and thigh muscle group of an adult diagnosed by Q-mNGS: a case report.},
journal = {JPMA. The Journal of the Pakistan Medical Association},
volume = {76},
number = {3},
pages = {451-454},
doi = {10.47391/JPMA.22494},
pmid = {42017731},
issn = {0030-9982},
mesh = {Humans ; Male ; Adult ; Thigh ; *Hip Joint/microbiology ; *Pneumococcal Infections/diagnosis/therapy/microbiology ; *Streptococcus pneumoniae/isolation & purification/genetics ; Debridement ; *Soft Tissue Infections/microbiology/therapy/diagnosis ; *Abscess/microbiology/therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; *Myositis/microbiology ; *Arthritis, Infectious/microbiology/diagnosis ; Muscle, Skeletal/microbiology ; Drainage ; },
abstract = {Joint infections and myositis due to S. pneumoniae are rare. We report the case of a young adult male presenting with right hip joint infection complicated by thigh muscle abscess, successfully treated by surgical debridement, drainage tube placement, and aggressive antimicrobial therapy. A 38-year-old male presented with right buttock and thigh swelling, pain, night sweats, and limited mobility for 45 days. Imaging examination indicated soft tissue infection around the right hip joint with abscess formation. Quantitative meta-genomic next-generation sequencing (Q-mNGS) of joint fluid confirmed S. pneumoniae as the pathogen. Surgical intervention was performed due to lack of significant improvement after six days of anti-inflammatory therapy. The patient recovered well post-operatively and was discharged with medication after a total hospital stay of 31 days. This case highlights the importance of considering S. pneumoniae as a potential pathogen in joint and soft tissue infections in adults.},
}

Humans
Male
Adult
Thigh
*Hip Joint/microbiology
*Pneumococcal Infections/diagnosis/therapy/microbiology
*Streptococcus pneumoniae/isolation & purification/genetics
Debridement
*Soft Tissue Infections/microbiology/therapy/diagnosis
*Abscess/microbiology/therapy/diagnosis
Anti-Bacterial Agents/therapeutic use
*Myositis/microbiology
*Arthritis, Infectious/microbiology/diagnosis
Muscle, Skeletal/microbiology
Drainage

@article {pmid42018084,
year = {2026},
author = {Han, D and Pan, X and Pan, F and Han, B and Wu, Q and Zhou, Y and Liu, H and Xu, H and Sun, W and Cheng, H and Liu, W and Wan, R and Weng, W and Zhang, H},
title = {Translating Host-Derived Signals from Cerebrospinal Fluid Metagenomic Sequencing into a Diagnostic Tool for Autoimmune Encephalitis in Children.},
journal = {Journal of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10875-026-02023-z},
pmid = {42018084},
issn = {1573-2592},
support = {82471882//National Natural Science Foundation of China/ ; 21ZR1452900//Natural Science Foundation of Shanghai Municipality/ ; GWVI-3//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025)/ ; shslczdzk06902//Shanghai Municipal Key Specialty/ ; },
}

@article {pmid42018438,
year = {2026},
author = {Sun, X and Jiang, X and Zhang, L and Li, M},
title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.},
journal = {Cell reports},
volume = {45},
number = {5},
pages = {117284},
doi = {10.1016/j.celrep.2026.117284},
pmid = {42018438},
issn = {2211-1247},
abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.},
}

@article {pmid42018637,
year = {2026},
author = {Reynolds, RC and Weiss, ACB and James, CC and Kojima, CY and Weissman, JL and Thrash, JC and Levine, NM},
title = {Defining metabolic niches for marine microbial heterotrophs.},
journal = {Science advances},
volume = {12},
number = {17},
pages = {eadz0537},
doi = {10.1126/sciadv.adz0537},
pmid = {42018637},
issn = {2375-2548},
mesh = {Phytoplankton/metabolism ; *Heterotrophic Processes ; Ecosystem ; Carbon Cycle ; *Microbiota ; *Aquatic Organisms/metabolism ; Biomass ; *Seawater/microbiology ; Metagenomics ; },
abstract = {Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, will enable us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.},
}

Phytoplankton/metabolism
*Heterotrophic Processes
Ecosystem
Carbon Cycle
*Microbiota
*Aquatic Organisms/metabolism
Biomass
*Seawater/microbiology
Metagenomics

@article {pmid42019101,
year = {2026},
author = {Ramírez-Arenas, PJ and López-Cortés, A and Martínez-Mercado, MA},
title = {Novel Methanosarcinaceae species Methanohalophilus methylutens sp. nov., Methanolobus methylotrophicus sp. nov., and Methanococcoides guerreronegronense sp. nov. from Guerrero Negro hypersaline microbial mats in accordance with the SeqCode.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {3},
pages = {126716},
doi = {10.1016/j.syapm.2026.126716},
pmid = {42019101},
issn = {1618-0984},
abstract = {The Methanosarcinaceae family is the most versatile among methanogenic archaea, utilizing a wide variety of substrates for methanogenesis. It includes all known halophilic, methylotrophic methanogens. Despite evidence of their presence and even dominance over other methanogenic taxa in Guerrero Negro hypersaline microbial mats, no archaeal species have been cultured or described to date. Consequently, a significant gap remains in our understanding of their metabolic potential and diversity. In this study, seven high-quality metagenome-assembled genomes (MAGs) affiliated with the Methanosarcinaceae family were reconstructed. Three MAGs (E22BA4_117[TS], E22_A5_bin58[TS], and E22bin_1538[TS]) serve as the nomenclatural type for the novel proposed species Methanohalophilus methylutens, Methanolobus methylotrophicus, and Methanococcoides guerreronegronense, according to the SeqCode rules and representing the first Methanosarcinaceae species described from microbial mats of Guerrero Negro. Based on genomic content and phylogenetic features, we infer that these MAGs are cytochrome-containing methanogens supported by the presence of core methanogenesis genes (fwd/fmd, ftr, mch, mtd, mer, mtr and mcr). They exhibit distinct metabolic strategies: E22BA4_117[TS] is a generalist with broad substrate versatility, E22_A5_bin58[TS] is an expanded methylotrophic specialist, and E22bin_1538[TS] is a narrow-range methylotroph. All three MAGs encode the complete set of genes for the methylotrophic pathway, multiple Na[+]/H[+] antiporters and both transport and biosynthesis genes for compatible solutes, collectively indicative of their adaptations to hypersaline conditions. These novel species enrich the phylogenomic resolution of Methanosarcinaceae and expand current understanding of the diversity and ecological relevance of these methanogenic archaea in hypersaline ecosystems, while providing genomic evidence that clarifies their metabolic potential and adaptations.},
}

@article {pmid42019198,
year = {2026},
author = {Zhang, C and Geng, H and Li, X and Dai, X and Xu, Y},
title = {Magnetically controlled non-conductive microbial carrier-mediated anaerobic digestion of sewage sludge.},
journal = {Water research},
volume = {300},
number = {},
pages = {125963},
doi = {10.1016/j.watres.2026.125963},
pmid = {42019198},
issn = {1879-2448},
abstract = {Magnetic porous microspheres (MPMs) have been used to enhance the anaerobic digestion (AD) of sludge. However, the feasibility of using MPMs as magnetically controlled microbial carriers in long-term AD remains unclear. Herein, without replenishment of MPMs, the methanogenic performance, main physicochemical properties of sludge and methanogenic metabolomics in 150-day MPM-mediated AD were comprehensively investigated. A substantial highly active anaerobes were found to adhere to MPMs, which maintained strong magnetic controllability and structural stability and significantly enhanced methane production (P < 0.001) and the methane proportion in biogas (P < 0.05) from AD at different hydraulic retention times (HRTs). The significant positive correlations between the interfacial Lewis acid-base (AB) interaction (R[2] > 0.79, P < 0.01) and daily methane production (R[2] > 0.52, P < 0.01) with water-mediated proton-coupled electron transfer (PCET) indicate that MPM-enhanced AB interactions can accelerate electron transfer by promoting proton movement in interfacial water molecules, thus enhancing methanogenesis during AD. Statistical analyses of variations in activities or contents of key bioenergetic substances on and within anaerobic cell membranes in AD confirmed this observation and simultaneously indicated that MPMs significantly enhanced the bioenergetics of CO2-reduction methanogenesis by promoting intracellular water-mediated PCET. Microbial community changes show that during the AD under different HRTs, MPMs significantly enriched bacteria capable of decomposing complex organics into acetate and hydrogen in an attached state, as well as free acetotrophic methanogens and attached hydrogenotrophic and hydrogen-dependent methylotrophic methanogens, thereby optimising the spatial distribution of methanogenic consortia. Metagenomics and genome-centric metagenomic analyses confirmed that MPMs significantly enhanced the hydrogen-dependent methanogenesis pathways of the attached methanogenic consortia and promoted energy-conserving metabolic cooperation between free and attached methanogenic consortia, reducing resource competition. Basic economic and environmental analyses revealed that the annual economic benefit increased by 112.2% and carbon emissions decreased by approximately 1.34 × 10[5] tons CO2/year with MPM-mediated AD relative to conventional AD. These findings can provide an important reference for the development of exogenous material-mediated AD technology.},
}

@article {pmid42019199,
year = {2026},
author = {Liu, S and Wei, W and Wang, C and Ni, BJ and Zhu, S},
title = {Persulfate-driven sludge biorefinery toward value-added medium-chain fatty acids.},
journal = {Water research},
volume = {300},
number = {},
pages = {125935},
doi = {10.1016/j.watres.2026.125935},
pmid = {42019199},
issn = {1879-2448},
abstract = {Transforming waste activated sludge (WAS) into high-value biofuels is a key pathway toward sustainable waste management and carbon neutrality, yet the recalcitrance of extracellular polymeric substances (EPS) and microbial cell walls severely limits medium-chain fatty acids (MCFAs) production during anaerobic fermentation. Here, we propose a persulfate (PDS)-based pretreatment strategy that enhances MCFAs synthesis by driving sludge disintegration and substrate transformation. Treatment with 7.5 mM PDS increased MCFAs yield by ∼50%, reaching 13,341.4 mg COD/L. Mechanistic investigations reveal that SO4·[-] and ·OH radicals preferentially degrade tightly bound EPS, reducing protein and polysaccharide content by 38% and 46%, respectively, and increasing soluble chemical oxygen demand (SCOD) 5.05-fold. This transformation produces nitrogen-rich, low-molecular-weight dissolved organic matter (DOM). The resulting DOM exhibited high H/C ratios, low O/C ratios, and low aromaticity indices (AImod), significantly enhancing its bioavailability during anaerobic fermentation. Integrated metagenomic functional annotation and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed that EPS-derived DOM reshaped the microbial metabolic network, stimulating glycolysis, amino acid metabolism, and carbon chain elongation. Moreover, the formation of unsaturated and aromatic-like fermentation products indicated enhanced DOM humification, which facilitated carbon chain elongation and microbial metabolic activity. Life cycle assessment and techno-economic analysis confirmed the environmental sustainability and economic feasibility of this radical-driven strategy. By elucidating the radical-EPS-DOM-metabolism cascade, this study provides mechanism-guided strategies for efficient sludge biorefinery, advancing the field from empirical operation toward targeted, high-efficiency design.},
}

@article {pmid42019232,
year = {2026},
author = {Xu, B and Zhou, H and Xu, S and Wang, R and Xu, Q and Wu, X and Mu, D and Li, X},
title = {AI-2-mediated quorum sensing marks the ecological transition from collective cooperation to individual survival during Daqu storage.},
journal = {International journal of food microbiology},
volume = {456},
number = {},
pages = {111785},
doi = {10.1016/j.ijfoodmicro.2026.111785},
pmid = {42019232},
issn = {1879-3460},
abstract = {Quorum sensing (QS) is a central system reflecting microbial collective behavior; however, its role in shaping functional microbial communities within complex solid-state fermentation matrices such as Daqu remains insufficiently understood. Here, we integrated amplicon sequencing, metagenomics, proteomics, and metabolomics to investigate autoinducer-2 (AI-2)-mediated quorum sensing dynamics during Daqu storage. Storage induced a directional succession of the microbial community, revealing two distinct ecological stages. The rapid adjustment stage (0-2 months) was characterized by strong homogeneous selection and rapid species turnover, whereas the slow stabilization stage (3-9 months) was dominated by gradual shifts in microbial relative abundances. Notably, the LuxS/AI-2 pathway, the only QS system detected during Daqu storage, declined rapidly and then stabilized, coinciding with the transition between the two ecological stages. During the early stage, the core QS protein LuxS was tightly associated with the dominant taxon Lactobacillaceae and the methyl donor S-adenosylmethionine, forming a synergistic functional module. In contrast, during the late stage, LuxS became decoupled from stress-tolerant taxa and showed weakened associations with resistance-related metabolic networks. This shift was accompanied by a metabolic transition, with carbon flux gradually redirected from active glycolysis toward the pentose phosphate pathway and amino acid biosynthesis during later stages. Collectively, these findings demonstrate that temporal modulation of the LuxS/AI-2 quorum sensing system represents a critical regulatory node reflecting the transition of the Daqu microbial community from cooperative growth to stress-resilient survival, ultimately shaping metabolic phenotypes and ecosystem functions during storage.},
}

@article {pmid42019335,
year = {2026},
author = {Sabatino, R and Pulina, S and Sbaffi, T and Kamburska, L and Titocci, J and Cherchi, M and Pittalis, C and Piscia, R and Vaccarelli, I and Rosati, I and Padedda, BM and Allemanno, F and Casiddu, P and Di Cesare, A},
title = {Lakes and lagoons used for drinking water supply and fisheries as sources of potentially pathogenic bacteria and antimicrobial resistance.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129718},
doi = {10.1016/j.jenvman.2026.129718},
pmid = {42019335},
issn = {1095-8630},
abstract = {Drinking water supplies and water basins used for fisheries represent two essential water sources for humans. Despite the growing accessibility of metagenomic approaches, their routine use for water quality monitoring is still limited. Many key water resources have yet to be fully characterized in terms of microbiome, pathobiome, and antimicrobial resistome. In this study, surface water samples were collected over one year from the artificial Lake Bidighinzu (drinking water supply) and the coastal lagoon Cabras (fisheries) located in the western Mediterranean area. Samples were analyzed for physical and chemical properties, and 16S rRNA gene amplicon and shotgun sequencing were used to characterize bacterial communities, pathobiomes, and antimicrobial resistomes. Physical and chemical properties were generally similar between sites, except for higher salinity in Cabras Lagoon. In Cabras Lagoon, richness of the bacterial community and pathobiome was generally higher in the largest trophic fraction (>20 μm), while in both sites the abundance of potentially pathogenic bacteria (PPB) increased at this fraction. PPB, including ESKAPE pathogens, were more abundant in Lake Bidighinzu. The overall antimicrobial resistome was similar across sites, with high-risk antimicrobial resistance genes (ARGs) such as emrB prevalent. Lake Bidighinzu also had more contigs where ARGs co-occurred with mobile genetic elements. This study highlights microbiological risks in two aquatic systems, particularly Lake Bidighinzu, and underscores the need to integrate metagenomic approaches, possibly with cultivation-based methods, to monitor water quality and assess health risks in drinking water supplies and fisheries.},
}

@article {pmid42019341,
year = {2026},
author = {Zhao, Y and Chen, Y and Dang, Z and Li, K and Zhu, Y and Xu, C and Wan, X and Jia, B and Cao, G and Shen, Q and Zhao, Z},
title = {Metagenomic and transcriptomic insights into microbial activity maintenance strategies in a pilot-scale biosorption-biodegradation system for in situ sewer overflow treatment.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129750},
doi = {10.1016/j.jenvman.2026.129750},
pmid = {42019341},
issn = {1095-8630},
abstract = {Sewer overflow is a widely recognized issue in urban water environment pollution. Traditional in situ treatment technologies based on filtration and flocculation often fail to remove soluble pollutants effectively. Conventional in situ biological systems also struggle to maintain activity under fluctuating and nutrient-imbalanced influent conditions. Here, a compact in situ biological treatment process based on biosorption-biodegradation technology with a shortened hydraulic retention time (HRT) is proposed. During a 180-day pilot-scale experiment integrating ballasted flocculation, the system achieved average removal efficiencies of 75-94% for CODCr, NH4[+]-N, TP, BOD5, and SS. Effluent concentrations met Chinese surface water quality standards. The system maintained stable performance during wet weather events and after multiple dry periods of up to 30 days, demonstrating effective microbial activity maintenance. Based on the metagenomic and transcriptomic analyses, this stability is potentially related to nutrient supplementation through carbon metabolism of mixotrophic organisms and pollutant adsorption by biosorption sludge. Additionally, the reduced HRT prevents endogenous respiration and sludge degradation. The compact biosorption-biodegradation process offers an efficient and space-saving strategy for maintaining microbial activity during dry periods. It provides a promising solution for mitigating sewer overflow pollution in high-density urban areas.},
}

@article {pmid42019423,
year = {2026},
author = {Xu, C and Feng, Y and He, S and Wu, M and Hu, S},
title = {Mining of FDRs-carrying microbes involved in aflatoxin B1 degradation.},
journal = {Food chemistry},
volume = {515},
number = {},
pages = {149316},
doi = {10.1016/j.foodchem.2026.149316},
pmid = {42019423},
issn = {1873-7072},
abstract = {Aflatoxin B1 (AFB1), a potent hepatocarcinogenic mycotoxin commonly found in food and feed, poses significant threats to food safety and public health. Microbes reduce AFB1 via biotransformation, so mining degrading strains is key. In this study, a novel AFB1 degrader, Mycobacterium sp. strain HM-7, was isolated from an AFB1-degrading bacterial consortium (designated A-2). Genomic analysis of the reconstructed metagenome-assembled genome (MAG) 12 and strain HM-7 revealed six putative F420H2-dependent reductases (FDRs), which are essential for the biotransformation of AFB1. When strain HM-7 was applied to animal feed, it achieved a significant reduction in AFB1 levels. Furthermore, bioinformatics mining based on the Genome Taxonomy Database (GTDB) identified a wide diversity of FDRs-carrying microbes involved in AFB1 degradation, mainly those belonging to the phylum Actinomycetota, highlighting their potential for bioremediation applications. This study provides valuable insights into the diversity of FDRs-carrying microbes involved in AFB1 degradation.},
}

@article {pmid42019451,
year = {2026},
author = {Wei, ZW and Li, HQ and Wang, XH and Yang, XR and Su, JQ},
title = {Non-biodegradable microplastics amplify antibiotic resistance and pathogen spread in bay plastisphere.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142147},
doi = {10.1016/j.jhazmat.2026.142147},
pmid = {42019451},
issn = {1873-3336},
abstract = {Microplastics (MPs) serve as reservoirs that facilitate the dissemination of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), posing significant threats to public health. However, quantitative evaluations of high-risk ARGs in the plastisphere and comprehensive assessments of their associated health implications are still scarce. In this study, we employed in-situ incubation combined with high-throughput quantitative PCR and metagenomic sequencing to systematically compare the prevalence of ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and HBPs between biodegradable and non-biodegradable MPs. Our findings revealed a marked enrichment of ARGs, VFGs, MGEs, and HBPs in non-biodegradable MPs (polypropylene, polyethylene, and polystyrene) relative to the biodegradable MPs (polyhydroxyalkanoates, polylactic acid, and polybutylene adipate terephthalate). Furthermore, an integrated risk assessment combining high-risk ARGs quantification with a Projection Pursuit Regression model revealed significantly elevated microbial risks associated with non-biodegradable MPs. Taxonomic analysis further indicated that Pseudomonas and Aeromonas act as key HBP vectors carrying ARGs and VFGs in the plastisphere, underscoring their role in facilitating the spread of antimicrobial resistance and virulence. These results highlight how plastic properties mediate microbial colonization patterns under complex field conditions, providing a robust framework for environmental risk evaluation and the targeted management of plastic-associated biological hazards.},
}

@article {pmid42019469,
year = {2026},
author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH},
title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106914},
doi = {10.1016/j.psj.2026.106914},
pmid = {42019469},
issn = {1525-3171},
abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.},
}

@article {pmid42019695,
year = {2026},
author = {Liu, X and Wang, H and Zhou, S and Xie, Y and Wang, J and Wang, X and Xu, S and Wang, L and Jiang, C and Zhuang, X},
title = {Nanobubbles drive advanced anaerobic treatment of swine wastewater for efficient methane recovery: Performance gains and multi-pathway enhancement.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134692},
doi = {10.1016/j.biortech.2026.134692},
pmid = {42019695},
issn = {1873-2976},
abstract = {Swine wastewater contains recoverable energy, but anaerobic digestion is often limited by complex organics and slow hydrolysis. To overcome this limitation, this study introduced nanobubble technology using three gas media (air, O2, and O3) and systematically studied their effects on methane recovery during the anaerobic digestion of swine wastewater. Batch experiments showed that O3 nanobubbles achieved the strongest enhancement, increasing cumulative methane production by 87.5% compared with the control. This improvement may result from the strong oxidative capacity of O3 nanobubbles to degrade recalcitrant organics, as indicated by the second methane production peak observed only in the O3 nanobubbles. In contrast, O2 nanobubbles provided the weakest improvement, potentially because excess dissolved oxygen stimulated facultative aerobic respiration, converting substrates to CO2 and lowering availability for methanogenesis. Further analysis revealed that all nanobubble treatments accelerated volatile fatty acid turnover and enriched key hydrolytic and acidogenic microbes, particularly under O3 nanobubbles. The enrichment of Methanothrix and downregulation of the energy-intensive PilA gene suggest promoted electron transfer. Negatively charged nanobubbles may act as abiotic mediators that facilitate direct interspecies electron transfer. Metabolic analysis indicated enhanced hydrogenotrophic, methylotrophic, and acetoclastic methanogenesis, implying strengthened synergy among pathways. Overall, O3 nanobubbles show promise for resource recovery from organic waste.},
}

@article {pmid42019770,
year = {2026},
author = {Xie, M and Kong, L and Hou, L and Chen, Y and Hou, J},
title = {Atopic Dermatitis: Multi-omics Insights into Microbiota-Driven Modulation of the Gut-Skin Axis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108504},
doi = {10.1016/j.micpath.2026.108504},
pmid = {42019770},
issn = {1096-1208},
abstract = {Atopic dermatitis (AD) is a heterogeneous inflammatory skin disease resulting from complex interactions among host genetics, immune dysregulation, and microbial imbalance. Recent advances in multi-omics technologies have revealed distinct AD endotypes characterized by specific genetic variants, microbial enterotypes, and metabolite profiles. Emerging evidence highlights the gut-skin axis as an important regulatory pathway, in which alterations in gut microbiota influence the production of key microbial metabolites, including short-chain fatty acids (SCFAs) and tryptophan-derived aryl hydrocarbon receptor (AHR) ligands, thereby modulating Th2-dominant inflammatory responses. Integrated analyses combining metagenomics, metabolomics, and single-cell transcriptomics have further identified endotype-specific signatures, such as Bacteroides-enriched profiles associated with lipopolysaccharide-driven inflammation and Prevotella-dominant clusters linked to enhanced AHR activation and epithelial barrier repair. These findings provide a basis for precision stratification and the development of targeted therapeutic strategies, including genotype-guided biologics, microbiota modulation, engineered probiotics, phage therapy, and fecal microbiota transplantation. This review summarizes current evidence integrating host genetics, microbiota networks, and multi-omics biomarkers to provide a comprehensive framework for understanding AD endotypes and to highlight potential avenues for precision diagnosis and targeted interventions.},
}

@article {pmid42020064,
year = {2026},
author = {Peters, BA},
title = {Evidence grows for the gut-kidney axis, but questions still remain.},
journal = {Kidney international},
volume = {109},
number = {5},
pages = {832-834},
doi = {10.1016/j.kint.2026.02.015},
pmid = {42020064},
issn = {1523-1755},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Kidney/microbiology/metabolism ; Metabolomics ; Cross-Sectional Studies ; Metagenomics ; },
abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.},
}

Humans
*Gastrointestinal Microbiome
*Kidney/microbiology/metabolism
Metabolomics
Cross-Sectional Studies
Metagenomics

@article {pmid42020421,
year = {2026},
author = {Shahzadi, I and Xue, W and Ubaid Ullah, H and Maddamsetti, R and You, L and Wang, T},
title = {Integrating theory and machine learning to reveal determinants of plasmid copy number.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72303-0},
pmid = {42020421},
issn = {2041-1723},
support = {12401660//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470701//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pathogenicity. Despite their importance and immense diversity, the ecological, evolutionary and molecular factors determining PCN remain poorly understood. Here, we present a theoretical model to explain the empirical power-law relationship between plasmid size and copy number, one of the fundamental quantitative principles governing PCN control. However, this relationship alone has limited predictive power. To improve PCN prediction, we introduce a data-driven approach incorporating diverse features. Trained and tested on 11,051 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct a large-scale analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, revealing putative niche specific taxonomic PCN hotspots and hypothesis-generating ecological trends. These results provide valuable insights into plasmid ecology, antibiotic resistance genes (ARGs) surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome.},
}

@article {pmid42020426,
year = {2026},
author = {Seki, D and Pollak, S and Kujawska, M and Kiu, R and Acuna-Gonzalez, A and Crouch, LI and Bakshani, CR and Chivers, PT and Mommers, M and van Best, N and Penders, J and Hall, LJ},
title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42020426},
issn = {2041-1723},
support = {220876/Z/20/Z//Wellcome Trust (Wellcome)/ ; },
mesh = {*Milk, Human/chemistry/metabolism ; Humans ; *Oligosaccharides/metabolism ; *Escherichia coli/physiology/growth & development/genetics/metabolism ; *Symbiosis/physiology ; Female ; *Bifidobacterium bifidum/physiology/genetics/metabolism/growth & development ; Gastrointestinal Microbiome ; Feces/microbiology ; Infant, Newborn ; Infant ; Breast Feeding ; Trisaccharides/metabolism ; Male ; Metagenomics ; Adult ; },
abstract = {Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.},
}

*Milk, Human/chemistry/metabolism
Humans
*Oligosaccharides/metabolism
*Escherichia coli/physiology/growth & development/genetics/metabolism
*Symbiosis/physiology
Female
*Bifidobacterium bifidum/physiology/genetics/metabolism/growth & development
Gastrointestinal Microbiome
Feces/microbiology
Infant, Newborn
Infant
Breast Feeding
Trisaccharides/metabolism
Male
Metagenomics
Adult

@article {pmid42020430,
year = {2026},
author = {Zhou, L and Li, D and Huang, Y and Kang, J and Lu, Y and Zhang, L and Liu, SQ},
title = {Lactiplantibacillus plantarum-mediated modulation of volatile flavor and quality in low-salt spontaneously fermented yellow capsicum sauce.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00854-z},
pmid = {42020430},
issn = {2396-8370},
support = {32302036//National Natural Science Foundation of China/ ; NHXXRCXM202312//'Nan Hai Xin Xing' Science and Technology Innovation Talent Platform Project Funding of Hainan Province, China/ ; 202407560053//China Scholarship Council/ ; KYQD(ZR)-21122//Scientific Research Foundation of Hainan University, China/ ; },
abstract = {Yellow capsicum sauce (YCS) is a special fermented condiment in Hainan province, China, and its fermentation typically occurs in a high-salt environment. In this study, the effects of different salt contents (5, 10, 15, and 20%, w/w) on microbial communities and volatile flavor profiles in YCS were systematically investigated by metagenomic approach and HS-SPME-GC-MS. The results revealed that Lactiplantibacillus (54.66%) was the dominant genus in low-salt samples (SF5), while its abundance was less than 6% in higher salinity levels (SF15 and SF20). A total of 48 volatile flavor compounds (VFCs) were detected in the naturally fermented YCS, with alcohols and esters being the primary VFCs. Low-salt fermentation facilitated the accumulation of VFCs, and the total VFCs content in SF5 was the highest. Aroma compounds showed a strong correlation with Lactiplantibacillus plantarum. To further validate the findings, L. plantarum MA1 isolated from SF5 was inoculated into the low-salt YCS substrate for bioaugmented fermentation. This strain significantly increased key aroma components, such as cis-3-hexenyl isovalerate, hexyl 3-methylbutanoate, and ethyl acetate. Moreover, it significantly increased the lactic acid content while reducing the nitrite content, thereby more effectively preserving the fresh yellow color of capsicum sauce and the stability of its spiciness.},
}

@article {pmid42020464,
year = {2026},
author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH},
title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37419-9},
pmid = {42020464},
issn = {2045-2322},
support = {5850.0109317.18.9 and 21167-2//Petróleo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.},
}

@article {pmid42020750,
year = {2026},
author = {Grieshop, MP and Behr, AA and Bowden, S and Lin, JD and Molari, M and Reynolds, GZ and Brooks, EF and Doyle, B and Moore, AA and Rodriguez-Nava, G and Salinas, JL and Banaei, N and Bhatt, AS},
title = {Transposable elements are driving rapid adaptation of Enterococcus faecium.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42020750},
issn = {1476-4687},
abstract = {Bacterial pathogens adapt rapidly to clinical and within-host selective pressures[1]. Insertion sequences (IS) are transposable elements that can contribute to pathogenic adaptation[2], but their activity and consequences in contemporary clinical populations are not well characterized. Here, combining large-scale genomic surveys with long-read sequencing of clinical isolates and longitudinal gut metagenomes, we quantify pathogen IS dynamics from global patterns to within-host evolution. Across 19,485 publicly available high-contiguity ESKAPEE pathogen genomes, Enterococcus faecium genomes are the most IS dense, dominated by replicative ISL3 family elements, which have proliferated in clinical lineages over the past 30 years. We find extensive chromosomal structural variation, largely involving ISL3, within a new single-hospital collection of bloodstream isolates. Long-read metagenomic sequencing of 28 longitudinal stool samples from 12 haematopoietic cell transplantation (HCT) recipients demonstrates within-host IS dynamics and their regulatory consequences. In one patient, an ISL3 insertion upstream of a folate transporter formed a strong promoter, increasing transcription and improving relative fitness under folate limitation. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse, which is common in HCT and other critically ill patients[3]. Together, these results show that a recent ISL3 expansion is driving rapid evolution in healthcare-associated E. faecium, with consequences for its metabolic fitness that may help explain its increasing clinical burden. Several other pathogens also show elevated IS loads in our survey, which suggests that IS expansion-mediated evolution might be more broadly relevant.},
}

@article {pmid41814236,
year = {2026},
author = {Xiao, H and Zhang, Y and Zhu, L and Guo, M and Yao, K and Dong, F and Duan, X and Liu, G},
title = {Meningitis and subdural empyema caused by group A streptococcal infection.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41814236},
issn = {1471-2431},
support = {2024-1-2092//Capital's Funds for Health Improvement and Research/ ; 2-1-2-6-15//2022 Beijing Major Epidemic Prevention and Control Specially Construction Project/ ; },
abstract = {BACKGROUND: Group A streptococcus (GAS) could lead to various disease types in children, but central nervous system (CNS) infections are uncommon. In this paper, we analyzed the clinical features of a GAS case with meningitis and subdural empyema, and characterized the GAS clone.

CASE PRESENTATION: A thirteen-year-old boy complained of fever, headache, and left hemiplegia. Physical examination also showed central facial palsy of left side. The examinations of blood and cloudy cerebrospinal fluid (CSF) showed bacterial meningitis. Blood cultures and metagenomic sequencing (mNGS) of CSF showed GAS, and GAS antigen of throat swab was positive. The first anti-streptolysin (ASO) was negative, but increased obviously after 2 weeks. The examination of emm type showed emm 12.0 isolate. The head MRI showed restricted diffusion in the right frontal lobe, subdural empyema in the right side of cerebral falx, and meningitis. The CT revealed rhinosinusitis and mastoiditis. Bacterial meningitis, subdural empyema, sepsis, and sinusitis were diagnosed, and vancomycin and ceftriaxone were given. The patient also received dexamethasone in the beginning. Gradual improvement was seen in the patient’s clinical status, laboratory parameters (blood/CSF), and radiographic manifestations.

CONCLUSIONS: The contiguous spread from rhinosinusitis could lead to meningitis and intracranial abscess in adolescent. GAS infection could be the pathogen for subdural empyema in patients with an abrupt onset of symptoms and rapidly deteriorating clinical course.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12887-026-06722-9.},
}

@article {pmid41814258,
year = {2026},
author = {Zhou, Y and Yu, D and Li, S and Ruan, S and Ye, J and Zhou, D and Chen, Q and Jin, J and Song, K},
title = {Case Report: diagnosis of mixed Scedosporium apiospermum infection assisted by bronchoalveolar lavage fluid morphology.},
journal = {BMC pulmonary medicine},
volume = {26},
number = {1},
pages = {},
pmid = {41814258},
issn = {1471-2466},
support = {2025HZZD01//The Construction Fund of Key Medical Disciplines of Hangzhou, Laboratory Diagnostics/ ; 2025JK256//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; },
abstract = {BACKGROUND: Scedosporium apiospermum is a highly aggressive opportunistic pathogen, widely distributed in natural environments. Infections predominantly occur in immunocompromised individuals but may also affect immunocompetent individuals with predisposing factors such as trauma, drowning, exposure to contaminated water, diabetes, or malnutrition.

CASE PRESENTATION: In the reported case, morphological abnormalities were initially identified in bronchoalveolar lavage fluid (BALF). Subsequent microbial culture identification and metagenomic next-generation sequencing (mNGS) confirmed a mixed infection involving S. apiospermum.

CONCLUSIONS: This case highlights the importance of improving laboratory personnel’s morphological recognition of S. apiospermum in routine examinations. The combined use of multiple diagnostic methods enhances detection rates, shortens the time to identification, ensures timely and effective treatment for patients, and ultimately reduces mortality.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-026-04215-0.},
}

@article {pmid41814359,
year = {2026},
author = {Lai, C and Zhang, J and Xiong, Y and Wang, Y and Liu, Z and Shi, M and Ye, S and Zeng, J},
title = {Multi-omics analysis reveals the association of cesarean delivery with altered gut microbial profiles and a Th2-biased immune response in neonates.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41814359},
issn = {1479-5876},
support = {Z-A20241044//Guangxi Zhuang Autonomous Region Health Department/ ; Z20210019//Guangxi Zhuang Autonomous Region Health Department/ ; Z-A20240946//Guangxi Zhuang Autonomous Region Health Department/ ; 2024GXNSFBA010112//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
abstract = {BACKGROUND: The gut microbiota plays a crucial role in providing essential stimulatory signals for the development of the immune system during the early stages of life. Cesarean delivery is associated with altered vertical microbial transmission and may affect early immune priming. Currently, only a limited number of studies have investigated the interactions among gut microbiota, fecal metabolites, and immune function in neonates delivered by cesarean section, which underscores the necessity for further research.

METHODS: We performed metagenomic sequencing and untargeted metabolomics to compare the gut microbiota and fecal metabolites of neonates born through cesarean delivery (n = 18) and vaginal delivery (n = 20). RNA sequencing (RNA-Seq) was utilized to identify differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMCs). Immune profiling involved flow cytometry analysis to determine the proportions of Th1 and Th2 cells, ELISA-based quantification of plasma IFN-γ, IL-12p70, IL-4, and IL-10, and assessment of STAT4 and STAT6 expression via ELISA and Western blot. Multi-omics integration was applied to elucidate the systemic impact of cesarean delivery on the neonatal gut microbiome, metabolome, and immune system.

RESULTS: The composition and functional features of the gut microbiota, and fecal metabolite profile, were significantly altered in Cesarean group. PBMC gene expression also showed marked differences, presenting a Th2-biased immune response and enrichment of genes associated with systemic lupus erythematosus and primary immunodeficiency. Flow cytometry and ELISA confirmed a Th1/Th2 imbalance, while Western blot revealed decreased STAT4 and increased STAT6 expression in the Cesarean group. Multi-omics analysis indicates that Bacteroides sp. is associated with alterations in fecal metabolite in neonates delivered via cesarean section. The reduced abundance of Bacteroides sp. and Bacteroides fragilis correlated with Th1/Th2 dysregulation. Additionally, gut microbiota changes were correlated with variations in the host oxidative phosphorylation pathway via fecal phosphate levels.

CONCLUSIONS: This multi-omics study reveals an association between the mode of delivery and distinct gut microbiota structure, fecal metabolite profiles, and immune development during early life. This provides a framework for investigating the potential connection between early-life immune programming and mode of delivery.

CLINICAL TRIAL NUMBER: Not applicable.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07988-4.},
}

@article {pmid42007817,
year = {2026},
author = {Chen, M and Kang, Y and Cheng, M and Li, X and Keng, J and Zhao, P and Sui, H and Dong, J and Sun, L and Liu, B and Hu, Y and Jiang, J and Yang, F},
title = {Co-circulation of multiple arboviruses in acute febrile patients in Yunnan, China, identified by metagenomic sequencing.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0167025},
doi = {10.1128/jcm.01670-25},
pmid = {42007817},
issn = {1098-660X},
abstract = {UNLABELLED: Arboviruses such as dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) are transmitted by Aedes mosquitoes and mainly circulate in tropical and subtropical regions. With global warming, their geographic range is expanding, increasing their threat to public health. Yunnan Province, China, bordering Southeast Asia, is a hotspot for viral importation due to intensive cross-border mobility. However, systematic surveillance for these arboviruses among acute febrile patients remains insufficient. We performed metagenomic sequencing on serum specimens from 990 acute febrile patients at the China-Myanmar border between 2017 and 2023. The pathogens were confirmed by PCR and viral isolation. Phylogenetic and spatiotemporal analyses were used to infer viral origins and transmission dynamics. In this study, a CHIKV outbreak was confirmed in 2019, with strains closely related to those from Myanmar and Thailand. Four DENV serotypes 1-4 were identified, with the predominant serotype varying annually. ZIKV was detected and closely related to strains from Myanmar. Co-infections were identified, including one case each of CHIKV with DENV-1, CHIKV with DENV-3, CHIKV with ZIKV, and DENV-1 with DENV-2. Bayesian spatiotemporal analysis of CHIKV reconstructed global transmission routes, indicating that the 2019 outbreak in China likely originated in India and spread sequentially through Bangladesh, Thailand, and Myanmar. In addition, we also detected enterovirus, hepatitis virus, Saffold virus, and rhinovirus. This study reveals a comprehensive spectrum of pathogens, including the co-circulation of DENV, CHIKV, and ZIKV, and underscores the potential risk of arbovirus importation into China, highlighting the need for strengthened border surveillance.

IMPORTANCE: Arboviruses, including dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV), are expanding their range and threatening global public health. Yunnan, situated along the China-Southeast Asia border, is highly susceptible to viral introduction. By applying viral metagenomic sequencing to acute febrile patients, this study uncovered a comprehensive spectrum of pathogens and the co-circulation of DENV, CHIKV, and ZIKV. Phylogenetic analyses revealed that arboviruses were closely related to strains from Myanmar and Thailand, indicating possible frequent cross-border viral introductions. Meanwhile, we reconstructed the global transmission pathways of CHIKV through Bayesian spatiotemporal analysis, providing valuable insights for regional prevention and control of arboviruses. These findings demonstrate that Yunnan serves as a critical interface for viral importation and underscore the urgent need to strengthen border surveillance and early warning systems to mitigate the spread of arboviruses.},
}

@article {pmid42008001,
year = {2026},
author = {Hu, C and Yu, J and Chu, T and Wang, Q and Chen, L and Yu, Y and Wang, Y},
title = {Uncovering novel virophages and giant viruses in high-altitude Lake Namtso: diversity and evolution of host-virus-virophage tripartite interaction systems.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42008001},
issn = {1432-072X},
}

@article {pmid42008944,
year = {2026},
author = {Liu, J and Li, Y and Wang, H and Wang, L and Wu, G and Zhao, B},
title = {Biphasic dynamics of N-nitrosodimethylamine precursors in effluent-receiving rivers: Insights from multi-omics into microbial nitrogen metabolism regulation.},
journal = {Water research},
volume = {300},
number = {},
pages = {125933},
doi = {10.1016/j.watres.2026.125933},
pmid = {42008944},
issn = {1879-2448},
abstract = {Wastewater effluent introduces substantial dissolved organic nitrogen into rivers, thereby increasing the risk of carcinogenic N-nitrosodimethylamine (NDMA) formation from its precursors. However, the microbial metabolic mechanisms governing dynamics of these precursors along receiving rivers remain unclear. Here, through a 21-day time-series incubation of sediments from upstream, outfall, and downstream areas of a representative wastewater treatment plant, combined with multi-omics analyses i.e., 16S rRNA gene sequencing, metagenomics, and metabolomics, the transformation of precursors and microbially mediated nitrogen metabolism were elucidated. A biphasic pattern of NDMA precursors measured as formation potential (FP) was observed during incubation, characterized by a rapid formation from days 0 to 3 followed by a remarkable degradation until day 7 and subsequent stabilization. Nitrate peaked paralleling NDMA FP, with nitrite accumulation following the onset of precursors degradation. Multi-omics analysis revealed that this turnover was driven by strong functional coupling between key nitrogen-cycling taxa and specific metabolites, particularly short-chain peptides. Community structure in the early phase was dominated by r‑strategists e.g., Bacillota, which promoted organic nitrogen degradation and nitrification, resulting in the accumulation of NDMA precursors. As anoxia developed, the community shifted toward K‑strategists such as Pseudomonadota and Chloroflexota, which likely degraded precursors through co-metabolism and consumption of ammonia source. Metabolomics revealed the conversion of precursors into short-chain peptides and amino acid analogues. Notably, effluent exposure established a functionally specialized legacy effect in downstream sediments, stabilizing into a microbial metabolic hotspot with a peak NDMA FP of 1285 ng/L, 158% and 80.7% higher than those in the upstream and outfall area, respectively. This study establishes a mechanistic framework for evaluating the transformation and risk of NDMA precursors in river systems, with direct implications for monitoring strategies and designing of the wastewater outfall location.},
}

@article {pmid42010118,
year = {2026},
author = {Menozzi, E and Ren, Y and Geiger, M and Macnaughtan, J and Avenali, M and Toffoli, M and Gilles, M and Calabrese, R and Mitrotti, P and Gallo, L and Famechon, A and Del Pozo, SL and Mezabrovschi, R and Koletsi, S and Loefflad, N and Yalkic, S and Limbachiya, N and Clasen, F and Yildirim, S and Shoaie, S and Blottière, H and Morabito, C and David, A and Quinquis, B and Pons, N and Le Chatelier, E and Valzania, F and Cavallieri, F and Fioravanti, V and Toschi, G and Blandini, F and Almeida, M and Ehrlich, SD and Meslier, V and Schapira, AHV},
title = {Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {42010118},
issn = {1546-170X},
support = {MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research (Programi i Përbashkët i BE-së për Kërkimet mbi Sëmundjet Neuro-degjeneruese)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; },
abstract = {Parkinson's disease (PD) is a major cause of disability. GBA1 variants are the most common genetic risk factor for PD and increase the risk up to 30-fold. Why only approximately 20% of GBA1 variant carriers develop PD remains unknown. Here, by combining clinical and fecal metagenomics data from 271 patients with PD, from 43 carriers of GBA1 variants not manifesting PD symptoms (GBA-NMC) and from 150 healthy controls, and using an innovative microbiome analysis, combining differential abundance of species and coherence of differential abundance variation between the groups as assessed by Cliff's delta (δ), we show that the composition of a large component of the gut microbiome (approximately 25%) in GBA-NMC is intermediate between healthy controls and patients with PD. This component is strongly correlated with disease progression in patients and prodromal symptoms suggestive of future development of PD in both GBA-NMC and healthy individuals. We found microbiome alterations similar to those described here in three independent cohorts from the United States, Korea and Turkey, totaling 638 patients with PD and 319 healthy controls, and we conclude that gut microbiome alterations can identify both genetically and non-genetically at-risk individuals in the general population who may be progressing toward PD, thus serving as an early marker of disease development in the premanifest phase.},
}

@article {pmid42010313,
year = {2026},
author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Feng, XY and Pan, YP and Zhang, CJ and Liu, Y and Li, M},
title = {A seven-year metagenomic genome catalogue of mangrove and mudflat sediments from the Futian Reserve, China.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07291-3},
pmid = {42010313},
issn = {2052-4463},
support = {42430707//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32225003, 32393970, 92251306//National Natural Science Foundation of China/ ; JCYJ20230808105711023//General Program supported by Shenzhen Natural Science Foundation in Basic Research Fund/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; 2024T001//Shenzhen University Special Funding Initiative/ ; },
abstract = {Mangrove wetlands are ecologically and biogeochemically important "blue-carbon" ecosystems, yet long-term genomic resources for their microbial communities remain scarce. Here we present a seven-year (2017-2023) metagenomic dataset from the Futian Mangrove National Nature Reserve, China, comprising 65 sediment samples collected from paired habitats (mangrove forest and adjacent mudflat) across multiple depths. Sequencing produced ~5.3 Tbp of data, from which 6,922 metagenome-assembled genomes (MAGs) were reconstructed and dereplicated into 3,404 representative genomes (336 Archaea and 3,068 Bacteria). Quality control ensured that all genomes achieved medium- or high-quality standards, with assembly statistics and read recruitment rates supporting robustness and representativeness. Taxonomic annotation revealed broad phylogenetic diversity spanning 13 archaeal and 69 bacterial phyla, with many lineages lacking formal nomenclature and representing potential novel taxa. All raw sequences, genome assemblies, and detailed metadata have been deposited in public repositories, providing a standardized, time-resolved resource for comparative genomics, microbial ecology, and ecosystem restoration studies in coastal wetlands.},
}