@article {pmid42174665,
year = {2026},
author = {Nolan, S and Trego, A and Waters, N and Thorn, C and Fenton, O and Richards, KG and O'Flaherty, V and Ijaz, UZ and Abram, F},
title = {Using feeding regime as a microbial selective pressure to optimise biogas production and digestate sanitisation from slurry-based anaerobic digestion.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00902-x},
pmid = {42174665},
issn = {2524-6372},
support = {14 F847//Irish Department of Agriculture, Food and Marine/ ; },
abstract = {BACKGROUND: The urgent need to adopt sustainable agricultural practices has positioned anaerobic digestion (AD) as a pivotal technology. Indeed, slurry-based AD can mitigate agricultural pollution by capturing greenhouse gas from stored slurry and converting it into biomethane, a valuable source of renewable energy, while generating digestate that can be used as fertiliser. For such a strategy to be effectively and widely deployed however, AD must be optimised. To this end, efforts have typically focused solely on biogas yields, yet improvements in pathogen load reduction may potentially negate the need for a costly pasteurisation step. Hence, optimisation of AD for sanitisation as well as improved biogas output is desirable. To address this, we set up triplicate 10-L CSTR bioreactors, which were fed with a combination of slurry and fats, oils and grease for 216 days. An organic loading rate (OLR) of 2 g VS L[-1] d[-1] was used throughout the trial, with a retention time of 21 days. For the first 98 days, bioreactors were fed each weekday (Monday to Friday), with 3 × feedstock on Fridays to maintain the OLR over the weekend. On Day 99 and for the remainder of the trial, the feeding regime was changed to every three days, still maintaining the 2 g VS L[-1] d[-1] OLR. The change in feeding regime was prompted by a noticeable increase in E. coli removal on Mondays, indicating that feeding regime could potentially function as a controllable ecological selection pressure.

RESULTS: After an initial period of adaptation to the new operating conditions (from day 99-150), the change in feeding regime resulted in improved E. coli removal, achieving consistently the required reduction in numbers to satisfy EU sanitisation standards (< 1000 CFU g[-1]). Additionally, methane production increased significantly in all bioreactors with an average of 58% higher methane yield per gram VS fed when compared to the previous 5-day feeding regime. Interestingly, process optimisation led to a more tailored microbial community as revealed by metagenomics. Specifically, we observed selection for improved carbon oxidation, syntrophic acetate oxidation and methanogenesis, as well as overall reduced microbial richness and decreased functional diversity. This could potentially lead to a reduced ecosystem stability however the emergence of Methanosarcina prevalence, known for its robustness, together with the detection of the two main methanogenic pathways-acetoclastic and hydrogenotrophic-after process optimisation might confer some resistance against future perturbations. The impact of microbial shifts on ecosystem stability needs to be further assessed experimentally.

CONCLUSIONS: Taken together, we demonstrate that feeding regime can function as a microbial selection pressure in anaerobic digestion. The switch from a 5-day to a 3-day feeding regime led to shifts in microbial pathways, underpinning the simultaneous improvement in methane production and E. coli removal. While further research is required to assess the impact of the observed microbial community dynamics on system stability, our findings suggest that full scale on-farm AD operators could explore the effects of feeding intervals on their process performance.},
}

@article {pmid42175291,
year = {2026},
author = {Dicko, A and Barro, SG and Somda, NS and Sombie, S and Bandaogo, O and Sanou, G and Esona, MD and Bonkoungou, JIO},
title = {Application of Metagenomics and Artificial Intelligence for Pathogen Characterization in Domestic Animals and Epizootic Prediction: A Systematic Review and Meta-Analysis.},
journal = {Studies in health technology and informatics},
volume = {336},
number = {},
pages = {2095-2096},
doi = {10.3233/SHTI260622},
pmid = {42175291},
issn = {1879-8365},
mesh = {Animals ; *Metagenomics/methods ; *Artificial Intelligence ; *Animals, Domestic/microbiology ; *Disease Outbreaks/veterinary/prevention & control ; *Animal Diseases/diagnosis/microbiology ; },
abstract = {Sub-Saharan Africa suffers devastating animal health losses exceeding $20 billion each year. By combining metagenomics with artificial intelligence (AI), a promising path emerges for faster diagnostics and proactive disease prediction. Our PRISMA-guided review of 1,225 studies reveals that metagenomics achieves 94.2% diagnostic sensitivity (compared to 67.3% with conventional methods), while AI dramatically shortens turnaround from 48-72h to just 4-8h, offering a valuable 14-18 day early warning window for epizootics.},
}

Animals
*Metagenomics/methods
*Artificial Intelligence
*Animals, Domestic/microbiology
*Disease Outbreaks/veterinary/prevention & control
*Animal Diseases/diagnosis/microbiology

@article {pmid42175403,
year = {2026},
author = {Tang, R and Wang, R and Han, Y},
title = {Mycobacterium avium complex pulmonary disease in rheumatoid arthritis-associated interstitial lung disease under non-biologic immunomodulatory therapy: A case report.},
journal = {Medicine},
volume = {105},
number = {21},
pages = {e48801},
doi = {10.1097/MD.0000000000048801},
pmid = {42175403},
issn = {1536-5964},
mesh = {Humans ; Male ; *Lung Diseases, Interstitial/complications/drug therapy/etiology ; Aged ; *Arthritis, Rheumatoid/complications/drug therapy ; *Mycobacterium avium-intracellulare Infection/drug therapy/diagnosis/complications/etiology ; Mycobacterium avium Complex/isolation & purification ; },
abstract = {RATIONALE: Rheumatoid arthritis (RA) is a well-recognized risk factor for nontuberculous mycobacterial infections, especially among patients receiving glucocorticoids or biological disease-modifying antirheumatic drugs. However, cases of Mycobacterium avium complex (MAC) pulmonary disease in RA patients without such immunosuppressive therapies are rarely reported, which challenges the conventional risk stratification.

PATIENT CONCERNS: A 78-year-old male with a 3-year history of RA and interstitial lung disease (ILD) presented with progressive dyspnea and chest tightness. He had no fever, joint swelling, or typical infection flares. Before admission, he was treated with Tripterygium Glycosides and Iguratimod (non-biologic, non-glucocorticoid agents).

DIAGNOSIS: The patient had chest tightness and weight loss. Chest high-resolution computed tomography showed asymmetric progression of ILD, along with tree-in-bud signs, centrilobular nodules, and suspicious fibrocavities. Bronchoscopy revealed necrotizing granulomatous inflammation, and quantitative metagenomic sequencing of bronchoalveolar lavage fluid confirmed MAC (no drug-resistant genes detected).

INTERVENTIONS: The patient was put on a 4-drug anti-MAC regimen (rifampicin, azithromycin, ethambutol, amikacin). However, he was lost to follow-up after being transferred to a tuberculosis specialist hospital. He eventually died of unknown causes, and there were prior reports of his nonadherence to treatment.

OUTCOMES: For RA patients with ILD who show asymmetric imaging progression or discordant inflammatory markers, it is crucial to actively screen for atypical pathogens like MAC, even in the absence of glucocorticoid or biologic exposure. This case highlights the necessity of expanding nontuberculous mycobacterial infection risk assessment beyond traditional immunosuppressive therapies in RA-ILD patients.

LESSONS: For patients with autoimmune disease-associated interstitial pneumonia, particularly those with progressive interstitial lung disease (ILD) despite stable autoimmune serology, proactive screening for atypical pathogens such as nontuberculous mycobacteria is critical. When imaging shows asymmetric lesions, tree-in-bud opacities, centrilobular nodules, or fibrocavitary changes, clinicians should prioritize comprehensive etiological evaluation - including bronchoscopy and histopathology - to avoid misdiagnosing these opportunistic infections.},
}

Humans
Male
*Lung Diseases, Interstitial/complications/drug therapy/etiology
Aged
*Arthritis, Rheumatoid/complications/drug therapy
*Mycobacterium avium-intracellulare Infection/drug therapy/diagnosis/complications/etiology
Mycobacterium avium Complex/isolation & purification

@article {pmid42175735,
year = {2026},
author = {Li, J and Liu, Q and He, C and Zhu, Y and Yin, C and Pang, X},
title = {Microbial Life-History Strategies and Functional Gene Regulation Drive Soil Nitrogen and Phosphorus Bioavailability During Succession in an Arid Valley Ecosystem.},
journal = {Molecular ecology},
volume = {35},
number = {10},
pages = {e70408},
doi = {10.1111/mec.70408},
pmid = {42175735},
issn = {1365-294X},
support = {32572029//National Natural Science Foundation of China/ ; 2025ZYD0007//Sichuan Province Science and Technology Support Program/ ; XZ202501JX0012//Science and Technology Projects of Xizang Autonomous Region, China/ ; DJ-ZDXM-2024-28//Power Construction Corporation of China/ ; },
mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Phosphorus/metabolism ; *Ecosystem ; *Soil/chemistry ; Microbiota/genetics ; Tibet ; Metagenomics ; Bacteria/genetics ; },
abstract = {Arid valley ecosystems are highly vulnerable to environmental change and face accelerating degradation due to climate warming and anthropogenic disturbance. Although soil microorganisms are known to drive nutrient cycling during succession, their adaptive strategies under persistent nutrient limitation remain poorly understood. This study integrated metagenomics, enzymatic stoichiometry and co-occurrence network analysis to investigate microbial community composition, life-history strategies, and nitrogen (N) and phosphorus (P) cycling functional genes along a successional gradient in an arid valley on the southeastern Tibetan Plateau. We found that microbial communities experienced consistent N limitation throughout succession, which shaped their functional potential and biogeochemical roles. Notably, during the transition from bare soil to biological soil crusts (BSCs), shifts in microbial life-history strategies towards resource acquisition (A-strategy) were accompanied by increased network complexity. Key functional genes, particularly those involved in nitrification (nxrB, amoC), dissimilatory nitrate reduction (nirB, nifH, nirD), inorganic P solubilization (gcd, ppk) and organic P mineralization (phnJ, phoA, phnM, phnI), were significantly upregulated during the BSCs stage. These genetic traits facilitated the transformation of organic and mineral nutrients into bioavailable forms, thereby supporting ecosystem development. This is manifested as a higher bioavailability of DON (+110%) and Bio-P (+97%) in the BSCs stage compared to bare land. Our results demonstrate that microbial communities adapt to resource constraints through trait-based strategies and functional gene regulation, highlighting the BSCs stage acts as a critical biogeochemical trigger in early succession. These insights advance our understanding of microbial-mediated nutrient cycling in arid ecosystems and inform restoration strategies under global change.},
}

*Nitrogen/metabolism
*Soil Microbiology
*Phosphorus/metabolism
*Ecosystem
*Soil/chemistry
Microbiota/genetics
Tibet
Metagenomics
Bacteria/genetics

@article {pmid42175741,
year = {2026},
author = {Yuan, S and Wang, X and Chang, Z and Zhang, B and Wang, M and Yu, J and Chen, Z},
title = {Climate Change Elevates the Risk of Antibiotic Resistance in Global Surface Ocean.},
journal = {Global change biology},
volume = {32},
number = {5},
pages = {e70929},
doi = {10.1111/gcb.70929},
pmid = {42175741},
issn = {1365-2486},
support = {42277386//National Natural Science Foundation of China/ ; 24JCYBJC01900//Tianjin Natural Science Foundation/ ; },
mesh = {*Climate Change ; *Drug Resistance, Microbial/genetics ; Oceans and Seas ; *Microbiota ; Virulence Factors/genetics ; *Seawater/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Understanding how climate change affects antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in marine microbiomes is critical to safeguarding global health, yet a systematic, global-scale analysis of their responses and associated health risks remains lacking. Here, we analyzed 890 surface-ocean metagenomic samples, the largest dataset collected using a standardized sampling pipeline to date. Our analysis revealed distinct biogeographical patterns in the composition of ARGs and VFGs across spatial and temporal gradients. Using machine learning, we mapped global distributions of ARGs and VFGs across the surface ocean by leveraging their strong associations with climate-releated environmental factors, revealing clear differences between polar and low-latitude areas. We then quantified the community-level antibiotic resistance risk and identified global risk zones, finding that high-risk regions are the least extensive and occur primarily at low latitudes. Furthermore, we estimated how this risk would change under future climate scenarios, suggesting that anthropogenic climate change is projected to increase the antibiotic resistance risk index of the surface ocean by altering environmental factors, most notably carbonate concentrations. Under the SSP5-8.5 scenario, which respresents a high greenhouse gas emissions pathway, the risk index is projected to rise across 33.0% (95% CI: 32.2%-33.5%) of the surface ocean by 2100, mainly in low-latitude regions, driven by an increase in genes involved in antibiotic efflux, inactivation, and motility. In contrast, effective greenhouse-gas mitigation would limit this increase to 3.7% (95% CI: 3.4%-4.1%). This study advances our understanding of how climate shapes marine antibiotic resistome and underscores the urgency of climate mitigation.},
}

*Climate Change
*Drug Resistance, Microbial/genetics
Oceans and Seas
*Microbiota
Virulence Factors/genetics
*Seawater/microbiology
Anti-Bacterial Agents/pharmacology

@article {pmid42176010,
year = {2026},
author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E},
title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02785-4},
pmid = {42176010},
issn = {1432-184X},
abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.},
}

@article {pmid42176043,
year = {2026},
author = {Khan, I and Naeem, I and Ali, S and Gulbin, M and Iqbal, A and Shafiq, M},
title = {Metagenomic surveillance identifies a high-risk antibiotic resistance profile in community wastewater: a pilot study from Pakistan.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42176043},
issn = {1432-1912},
abstract = {Environmental antimicrobial resistance surveillance in low- and middle-income countries (LMICs) faces critical data gaps, particularly in Pakistan, where approximately 90% of municipal wastewater is discharged untreated. In the absence of systematic monitoring in regions like Khyber Pakhtunkhwa, we conducted a pilot shotgun metagenomic sequencing study on two strategically selected community wastewater sites in Mardan. To translate complex metagenomic data into actionable public health intelligence, we developed the Antibiotic Resistance Risk Index (ARRI), a novel framework integrating antibiotic resistance gene (ARG) proportional abundance, pathogen taxonomic expansion, and WHO priority weighting. Our analysis revealed that the urban site (MCW2) exhibited a "critical" resistance profile, characterized by a 54% increase in ARG allelic richness (628 unique variants) despite a 19.9% decline in total relative ARG abundance. Taxonomic compositional changes consistent with an aerobic shift, including a 34-fold decline in Thermodesulfobacteria and a 46% increase in Pseudomonadota, were observed alongside an increased proportion of WHO priority pathogens, including Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. This site served as a reservoir for last-resort resistance determinants, including blaNDM, blaIMP, blaCTX-M, and mcr, which emerged exclusively in the urban drainage environment. The resistome contained 159 ARG families and 26 MGE types. Network analysis showed that 90.8% of ARG-MGE pairs exhibited coordinated increase in relative abundance, with all carbapenemase-linked pairs showing parallel trends. Consequently, ARRI scores escalated from 8.7 (moderate risk) to 34.2 (critical risk) at the urban site. These findings reveal the environmental circulation of hospital-associated resistance through decentralized sanitation infrastructure, representing a convergence of hospital-associated and community resistance profiles in LMIC settings. This study demonstrates that risk-weighted surveillance enables high-resolution, actionable AMR monitoring, providing a baseline methodology for environmental AMR surveillance in resource-limited settings.},
}

@article {pmid42176229,
year = {2026},
author = {Cagle, GA and Baiser, B and Bernardin, JR and Bittleston, LS and Young, EB and Gray, SM and Freedman, ZB},
title = {Carbon regime structures functional trait trajectories during primary succession in microorganisms.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag134},
pmid = {42176229},
issn = {1751-7370},
abstract = {Primary succession is a foundational process in ecology, but how microbial communities shift functionally during succession, and whether these dynamics follow predictable patterns, remains unresolved. We conducted a systematic review of functional primary succession in microorganisms and applied a consistent metagenomic pipeline to evaluate functional richness, rRNA operon copy number (RRN), and average genome size (AGS) over time. We also explored the yield-acquisition-stress (Y-A-S) life-history framework using functional gene annotations. Across autotrophic systems, RRN tended to decrease and AGS tended to increase during succession, whereas heterotrophic systems exhibited more variable trajectories. These consistent shifts in autotrophic systems suggest a transition from early colonization by copiotrophic taxa with small genomes and high RRN toward later-stage communities with larger genomes, lower RRN, and greater functional versatility. In contrast, heterotrophic systems showed heterogeneous trait trajectories, likely reflecting variation in the timing and predictability of organic inputs. Topic modeling further revealed that early successional stages were enriched in stress-tolerance genes, followed by shifts toward other strategies over time. While certain trait patterns such as RRN and AGS appeared broadly conserved, changes in life-history strategies during succession were context dependent and shaped by resource dynamics and system type. These findings suggest that microbial successional trajectories are structured by differences in resource availability, particularly whether systems are driven by autotrophic inputs or constrained by externally supplied carbon sources.},
}

@article {pmid42176246,
year = {2026},
author = {Chen, Y and Wang, S and Chen, A and Lin, Z and Wang, H and Li, W and Liu, J and Yao, J and Tian, D and Lei, Y and Liu, M},
title = {Multi-omics Analysis Reveals the Protection of a Quadruple Probiotic Mixture in Experimental Autoimmune Hepatitis.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42176246},
issn = {1867-1314},
support = {2025M782000//China Postdoctoral Science Foundation/ ; 2023AB006//Shangrao Science and Technology Bureau/ ; 202303021221195//Fundamental Research Program of Shanxi Province/ ; 82270558//National Natural Science Foundation of China/ ; },
abstract = {Autoimmune hepatitis (AIH) is a chronic progressive inflammatory liver disease with a rising global incidence. The treatment of AIH remains challenging because first-line drugs show limited efficacy and systemic side effects. Gut microbiota plays a crucial role in the pathogenesis of AIH, leading to growing interest in developing probiotic-based therapies. In this study, we used multi-omics analysis to investigate the therapeutic effects of a quadruple probiotic mixture (Probiotic-quad) consisting of Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus in a well-established chronic AIH murine model. Our results showed that Probiotic-quad treatment significantly alleviated AIH progression, as evidenced by lower serum liver enzyme levels, ameliorated hepatic inflammatory infiltration and histopathological damage. Metagenomic sequencing results showed that gut dysbiosis in AIH mice was partially reversed after Probiotic-quad administration. Additionally, the integrity of the intestinal epithelial barrier was restored, accompanied by a reduction in serum lipopolysaccharide levels. Untargeted metabolomic and transcriptomic analysis revealed that Probiotic-quad treatment was linked to alterations in hepatic metabolism, including the citrate cycle and tryptophan metabolism, and was associated with reduced activation of the NF-κB and NOD-like receptor signaling pathways. These findings suggest that Probiotic-quad treatment ameliorates AIH severity and is potentially associated with changes in hepatic immune responses, metabolism, gut microbiota, and intestinal barrier function, highlighting its potential as an adjuvant therapy for AIH.},
}

@article {pmid42176375,
year = {2026},
author = {Zhang, Y and Wang, R and Su, X and Lang, T and Li, D},
title = {Freeze-thaw specifically regulates microbiome patterns and phosphorus acquisition strategies in the lake-groundwater interaction zone.},
journal = {Water research},
volume = {302},
number = {},
pages = {126129},
doi = {10.1016/j.watres.2026.126129},
pmid = {42176375},
issn = {1879-2448},
abstract = {Freeze-thaw regulates phosphorus cycling in lake-groundwater interaction zones (LIZ) of seasonally frozen regions, where microorganisms and their functional traits play indispensable roles. However, the spatiotemporal dynamics of phosphorus pools and their driving mechanisms in the LIZ remain poorly understood, especially with insufficient quantitative evidence. Using absolute quantitative metagenomics, this study investigated the LIZ of Lake Chagan, a typical eutrophic lake in the seasonally frozen region. Results showed that Losses of Fe-P (44.69%) and Res-P (35.47%) dominated sediment phosphorus dynamics. Freeze-thaw induced opposing trends in diversity and similarity of PCGs-microbial communities between sediment and the lake-groundwater. The assembly of PCGs-microbial communities shifted from stochastic to deterministic processes in lake-groundwater, while stochastic processes persisted in sediments. DIP and DOP in lake-groundwater were driven by genes involved in P-uptake and transport (r = 0.65 and 0.40, respectively, P<0.05), while phosphorus release from sediments was co-regulated by inorganic P-solubilization and organic P-mineralization genes (r = 0.89 and -0.36, respectively, P<0.05). Microbial taxa harboring complete phosphorus cycling pathways (42.2%) and organic P-mineralization genes (48.1%) were relatively rare, with Pseudomonadota as the dominant phylum (65.2% and 57.0%, respectively). This study reveals medium-specific adaptive strategies of microorganisms and PCGs-mediated phosphorus cycling mechanisms, providing scientific support for predicting eutrophication risks and managing lake ecosystems in seasonally frozen regions.},
}

@article {pmid42176511,
year = {2026},
author = {Li, K and Jin, F and Tan, S and Zeng, X and Yuan, D and Shu, F and Chen, J and Ouyang, JM and Zhang, L and Li, C and Zhu, J},
title = {Cinchonain Ia inhibits uric acid reabsorption by binding to the TRP-459 residue of the GLUT9 protein.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {157},
number = {},
pages = {158292},
doi = {10.1016/j.phymed.2026.158292},
pmid = {42176511},
issn = {1618-095X},
abstract = {BACKGROUND: Hyperuricemia, a chronic metabolic disorder resulting from purine metabolism abnormalities, imposes a substantial burden on patients, their families, and society. Consequently, discovering more efficient prevention strategies and treatment drugs is of crucial importance. Polygonum capitatum (Buch.-Ham. ex D. Don) H. Gross is a plant belonging to the Polygonaceae family and Polygonum genus. Polygonum capitatum can reduce uric acid levels and alleviate gouty arthritis; However, whether its aqueous extract contains other uric acid-lowering active components besides quercetin and gallic acid still requires further research.

PURPOSE: This study aims to investigate the protective effects and potential mechanisms of Polygonum capitatum aqueous extract on liver and kidney function, while also identifying new potential pharmacologically active components for hyperuricemia within the extract.

METHODS: This study established a hyperuricemia rat and mice model and a uric acid-induced renal injury cell model. Liquid chromatography-tandem mass spectrometry was employed to analyze the active components of Polygonum capitatum aqueous extract. The target was analyzed by proteomics. Metagenomics and spatial metabolome were used to analyze gut microbes and metabolites associated with liver and kidney injury. Finally, SPR, DARTS, and CETSA were used to assess the binding potential of active components to targets. Additionally, mutant plasmids were constructed to analyze the binding sites between pharmacologically active components and their targets.

RESULTS: The aqueous extract of Polygonum capitatum significantly reduced serum uric acid levels and alleviated renal injury in the hyperuricemia rat model, with no apparent damage on liver tissue morphology or hepatic function indicators. Metagenomic and spatial metabolomics analyses demonstrated that the extract increased the relative abundance of beneficial gut microbiota and decreased that of harmful bacteria. It also modulated the levels and distribution of renal metabolites such as l-arginine and N-acetylglucosamine, reduced lipid oxidation in the kidney. Proteomics analysis suggests that renal GLUT9 may be one of the action targets of this extract. LC-MS/MS analysis indicated that the chemical composition of the extract underwent significant changes after entering rat blood and undergoing renal metabolism. Specifically, serves as a new active component in Polygonum capitatum aqueous extract, Cinchonain Ia was found to bind to the TRP-459 residue of GLUT9, inhibiting its expression and thereby reducing uric acid reabsorption in vivo and in vitro, and alleviated oxidative stress, inflammation, and tissue damage. However, overexpression of GLUT9 markedly reversed the inhibitory effects of Cinchonain Ia on inflammation and injury.

CONCLUSIONS: The aqueous extract of Polygonum capitatum prevents liver damage and alleviates kidney injury by regulating gut microbiota and renal metabolites. Furthermore, Cinchonain Ia, as one of its active components, can bind to the TRP-459 residue of the GLUT9 protein and inhibit its expression, thereby suppressing uric acid reabsorption and lowering serum uric acid levels.},
}

@article {pmid42176589,
year = {2026},
author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q},
title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128552},
doi = {10.1016/j.micres.2026.128552},
pmid = {42176589},
issn = {1618-0623},
abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.},
}

@article {pmid42176630,
year = {2026},
author = {Wu, Y and Ma, W and Sun, Y and Tang, J and Xu, X and Zhu, J and Miao, J and Li, M and Zeng, J and Gou, K and Song, Y and Zou, J},
title = {From active defense to cross-kingdom alarm: Rhizosphere microenvironment remodeling in soybean under polylactic acid nanoplastics and cadmium Co-stress.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142470},
doi = {10.1016/j.jhazmat.2026.142470},
pmid = {42176630},
issn = {1873-3336},
abstract = {As foundational components of the food web, plants face significant environmental threats caused by the coexistence of micro/nanoplastics (MNPs) and heavy metals. This study investigates the combined effects of cadmium and biodegradable polylactic acid nanoplastics on soybean. Under co-exposure conditions, toxicity progressively diminishes from the roots to the leaves of soybeans. By integrating root transcriptomics, root exudate metabolomics, rhizosphere soil metagenomics, and soil physicochemical analyses within a Bayesian structural equation modeling framework, we identified the Flavonoid biosynthesis pathway as a central mediating hub in the rhizosphere microenvironment under combined stress. Soybean roots modulated this pathway as a response strategy, which concurrently served as a signal for rhizosphere microbes to downregulate energy-intensive processes such as Methane metabolism, facilitating microbial adaptation. The down-regulation of the Flavonoid biosynthesis pathway in root exudates further altered rhizosphere soil properties, creating a feedback loop that amplified the expression of stress-related genes in soybean roots.},
}

@article {pmid42176697,
year = {2026},
author = {Yao, J and Zhu, T and Tian, W and Xu, J and Nie, M and Wan, J},
title = {Artificial reefs alter viral communities and functional traits in coastal waters.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108131},
doi = {10.1016/j.marenvres.2026.108131},
pmid = {42176697},
issn = {1879-0291},
abstract = {Artificial reefs (ARs) are widely deployed as engineered coastal structures to enhance habitat complexity and support marine resource management, yet their impacts on marine viral ecology remain poorly understood. Viruses regulate microbial communities and biogeochemical processes, and their functional traits are sensitive to environmental change. Here, we investigated how artificial reefs influence viral community composition, functional gene profiles, and virus-environment interactions across paired reef and non-reef sites in coastal shelf systems. Using an integrated viromic and metagenomic approach, we compared viral assemblages in both seawater and sediments under artificial reef influence. ARs significantly modified seawater physicochemical conditions, including pH, sulfate concentration, dissolved oxygen, and salinity, whereas sediment properties remained largely unchanged. These environmental differences coincided with distinct virus-environment association patterns across habitats. Notably, artificial reefs were associated with viral functional profiles characterized by a reduced genomic representation of lysis-related genes and an increased representation of genes involved in DNA replication and nucleotide metabolism. Network analyses further showed differences in the balance of positive and negative virus-host correlations between AR and non-AR sites. Together, these results indicate that engineered coastal structures are linked to habitat-specific patterns in viral functional traits and virus-host associations. Our findings highlight viruses as sensitive indicators of anthropogenic habitat modification and underscore the importance of incorporating viral dynamics into assessments of microbial and biogeochemical responses in engineered coastal ecosystems.},
}

@article {pmid42176766,
year = {2026},
author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM},
title = {Neuronutrition In Asd: Involvement Of Gut Microbiota, Oxidative Stress And Inflammatory Markers.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106775},
doi = {10.1016/j.neubiorev.2026.106775},
pmid = {42176766},
issn = {1873-7528},
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.},
}

@article {pmid42176818,
year = {2026},
author = {Dorofeev, A and Pelevina, A and Gruzdev, E and Beletsky, A and Berestovskaya, Y and Litti, Y and Mardanov, A and Pimenov, N},
title = {Development of an Azonexus- and Competibacter-enriched phosphate-accumulating community in the anaerobic/anoxic sequencing batch reactor: Cooperative denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134959},
doi = {10.1016/j.biortech.2026.134959},
pmid = {42176818},
issn = {1873-2976},
abstract = {Denitrifying polyphosphate-accumulating organisms (DPAOs) enable simultaneous N and P removal, however, reliable strategies for enriching stable DPAO communities and their metabolic interactions remain insufficiently understood. In this study, DPAO-enriched cultures were developed in a sequencing batch reactor operated under anaerobic/anoxic conditions with acetate as C source. For three independent experiments, activated sludge, collected at different times, was used as the inoculum. Within 0.5-2 months, all experiments exhibited definitive DPAO phenotype dynamics. After 100-200 days of operation, the microbial community was consistently co-dominated by two genera: Azonexus (19-35 %), representing DPAOs, and Competibacter (23-31 %), representing denitrifying glycogen-accumulating organisms (DGAOs). Metagenomic reconstruction revealed that neither Azonexus nor Competibacter harbored the full complement of denitrification genes. The Azonexus metagenome-assembled genome encoded napAB (nitrate reductase), nirS (nitrite reductase), and nosZ (nitrous oxide reductase), while the Competibacter MAG possessed only norBC (nitric oxide reductase) genes. This genomic complementarity provides evidence that complete denitrification in this system could be achieved through cooperation between DPAOs and DGAOs. Consequently, the observed lower phosphorus removal efficiency, compared to anaerobic/aerobic systems, is attributed to the reduced biomass yield of DPAOs and the high essential abundance of DGAOs. These results clarify the ecological role of Azonexus as a DPAO dependent on partnership with DGAOs. Furthermore, the selective conditions favoring Azonexus development in enhanced nutrient removal systems, are evaluated. This work reveals a possible mechanism of syntrophic cooperation between DPAO and DGAO, which has direct implications for the development of resource-saving biological processes for nutrient removal.},
}

@article {pmid42176923,
year = {2026},
author = {Pi, D and Zhou, F and Huang, S and Yan, H and Pan, J and Yang, Q and Pan, M and Zhang, Y},
title = {Atractylodes lancea (Thunb.) DC polysaccharide alleviates MASH by regulating the 1‑carbon cycle through intestinal flora remodelling.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152668},
doi = {10.1016/j.ijbiomac.2026.152668},
pmid = {42176923},
issn = {1879-0003},
abstract = {Metabolic-associated steatohepatitis (MASH) is a severe stage of Metabolic-associated fatty liver disease (MAFLD). Currently, effective pharmacological therapies for MASH are extremely limited. An Atractylodes lancea (Thunb.) DC polysaccharide (ALP) was isolated from Atractylodes lancea (Thunb.) DC, and its preventive effect on MASH and the potential mechanism were investigated. Mice were fed a high-fat, high-cholesterol, high-fructose diet (HFMCD) to induce MASH. MASH model mice were then treated with ALP at low (50 mg/kg/d) or high (100 mg/kg/d) dosages. Faecal metagenomics, nontargeted metabolomics sequencing, biochemical and pathological analyses, ELISAs, western blotting and other detection techniques were conducted to elucidate the mechanism by which ALP alleviates MASH. The research results indicate that both the low-dose (50 mg/kg/d) and high-dose (100 mg/kg/day) of ALP can effectively alleviate MASH, but the high-dose has a more significant effect. ALP effectively reduced liver lipid accumulation and inflammation in MASH model mice by regulating the 1‑carbon cycle through intestinal flora remodelling. ALP may be a promising natural candidate for the treatment of MASH.},
}

@article {pmid42177038,
year = {2026},
author = {Strobel, KM and Leibel, SL and Bhute, S and Aja, E and Jacobs, JP and Calkins, K},
title = {Gut microbial differences and function in infants with gastroschisis: a pilot prospective cohort study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-14},
doi = {10.1163/18762891-bja00121},
pmid = {42177038},
issn = {1876-2891},
abstract = {Newborns with gastroschisis hospitalised in the neonatal intensive care unit (NICU) are at risk for a disrupted gut microbiome. Infants with gastroschisis are particularly vulnerable to a dysbiotic microbiome; they require prolonged parenteral nutrition (PN) due to intestinal dysmotility, which often leads to growth faltering (GF). This pilot study's goals were to (1) compare the gut microbiome in infants with gastroschisis to infants admitted to the NICU without congenital anomalies, (2) identify differences in the gut microbiome between infants with gastroschisis requiring prolonged PN and those who do not, and (3) compare the microbiome in infants with gastroschisis with GF to those without GF. This was a multi-site prospective cohort study including 17 infants born with gastroschisis and 16 infants with a gestational age greater than 34 weeks admitted to the NICU without congenital anomalies (controls). Prolonged PN was defined as more than 28 days. GF was defined as a decline in weight or length z-score from birth to discharge of ≤-0.8. Stool samples were collected weekly during hospitalisation and analysed by shotgun metagenomics to assess bacterial composition, diversity, and function. Gestational age and birth weight were similar in the gastroschisis group and the control group. Infants with gastroschisis showed increased Staphylococcus aureus and decreased Bifidobacterium longum. Those requiring prolonged PN had a reduced abundance of genes in the glucosidase pathway compared to those who did not. Infants with GF showed a lower abundance of genes involved in the NAD-diphosphatase pathway compared to those without GF. Infants with gastroschisis display a distinct microbial composition and function compared to NICU infants without this condition. Among infants with gastroschisis, differences in bacterial functional capacity were observed in those who required prolonged PN and developed GF.},
}

@article {pmid42177062,
year = {2026},
author = {Adamek, M and Yılmaz, TM and Erdogmus, S and Moore, S and Ziemert, N},
title = {The ARTS toolset: Resistance-based genome mining for systematic prioritization of bioactive gene clusters.},
journal = {Methods in enzymology},
volume = {730},
number = {},
pages = {35-60},
doi = {10.1016/bs.mie.2025.08.023},
pmid = {42177062},
issn = {1557-7988},
mesh = {*Multigene Family ; *Software ; Genome, Bacterial ; Genome, Fungal ; Fungi/genetics/metabolism ; *Bacteria/genetics/metabolism ; *Computational Biology/methods ; Biological Products/metabolism ; Data Mining/methods ; Genomics/methods ; Metagenome ; },
abstract = {Natural products, especially those produced by bacteria and fungi, have been a rich source of antibiotics and other medically important compounds. Advances in genome sequencing have revealed that many microorganisms harbor far more biosynthetic potential than previously known, but identifying which gene clusters are most likely to produce bioactive compounds remains a major challenge. One promising strategy is to look for genes that protect the producing organism from its own toxic products-so-called resistance genes-which often appear near the biosynthetic genes. In this chapter, we introduce the ARTS toolset, a collection of computational tools designed to identify such resistance-linked biosynthetic gene clusters in microbial genomes. ARTS 2.0 allows users to analyze bacterial genomes and metagenomes, ARTS-DB provides access to precomputed results from tens of thousands of genomes, and FunARTS adapts the approach for fungal genomes. We describe how each tool works and provide examples to guide their use, with additional online tutorial videos provided by the authors.},
}

*Multigene Family
*Software
Genome, Bacterial
Genome, Fungal
Fungi/genetics/metabolism
*Bacteria/genetics/metabolism
*Computational Biology/methods
Biological Products/metabolism
Data Mining/methods
Genomics/methods
Metagenome

@article {pmid42171933,
year = {2026},
author = {Xu, Y and Sun, X and Xu, S and Deng, S and Zhang, Y},
title = {Clinical profile of microsporidial keratoconjunctivitis in healthy individuals of China -new species and neglected risk factors.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12348-026-00596-9},
pmid = {42171933},
issn = {1869-5760},
abstract = {OBJECTIVE: To characterize microsporidial keratoconjunctivitis (MKC) in immunocompetent individuals in Mainland China, including novel etiologies and risk factors.

METHODS: A prospective analysis of 20 MKC patients in 2025, including clinical features, pathogens (via corneal scrapings and metagenomic sequencing), risk factors and etc. RESULTS: All patients were misdiagnosed for a median of 1 month. Patients (mean age 28.5 years, 13 F) showed Encephalitozoon hellem (65.0%), E. bieneusi (15.0%, first reported in MKC), and Vittaforma corneae (15.0%). Key risks included bird contact (70.0%, mostly psittacines), contact lens use (40.0%), and water exposure (15.0%). The most common symptom was redness (85.0%); limbal fluorescein positivity occurred in 65.0%. Topical 0.02% PHMB cured 90.0% of 20 cases; one recurrence followed treatment stop. Some E. hellem cases linked to parrots showed potential zoonotic transmission.

CONCLUSION: MKC in China involves E. bieneusi and parrot-associated E. hellem. Limbal staining aids diagnosis; PHMB is effective. Zoonotic risks related to Psittacine birds and contact lens use require clinical attention.},
}

@article {pmid42172047,
year = {2026},
author = {Delgado, LF and Sunyer, JO and Laczny, CC and Hickl, O and May, P and Wilmes, P},
title = {PathoFact 2.0: An Integrative Pipeline for the Prediction of Antimicrobial Resistance Genes, Virulence Factors, Toxins and Toxin-associated Proteins, and Biosynthetic Gene Clusters in Metagenomes.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag062},
pmid = {42172047},
issn = {2047-217X},
abstract = {BACKGROUND: Antimicrobial resistance genes (ARG) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections.

FINDINGS: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGC) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting biosynthetic gene clusters.

CONCLUSIONS: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems.},
}

@article {pmid42172141,
year = {2026},
author = {Long, K and Gravel-Pucillo, K and Waldron, L and Davis, S and Oh, S},
title = {Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42172141},
issn = {1758-0463},
support = {/CA/NCI NIH HHS/United States ; U24CA289073/NH/NIH HHS/United States ; 3U24CA180996-10S1/NH/NIH HHS/United States ; },
mesh = {*Metadata/standards ; Humans ; *Data Curation/methods ; *Neoplasms/genetics ; *Databases, Genetic ; *Metagenomics ; *Genomics ; },
abstract = {Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminologies, and quality issues that severely limit data reusability and cross-study integration. While prospective metadata standards exist, the majority of published omics data remain in non-standardized formats requiring retrospective harmonization. We performed comprehensive manual curation and harmonization of metadata, such as participant characteristics and study conditions, from 212 027 omics samples across 468 studies in two repositories: curatedMetagenomicData (93 studies, 22 588 samples) and cBioPortal (375 studies, 189 438 samples). Through systematic ontology mapping, we consolidated redundant, dispersed information into far fewer harmonized columns, reduced unique values, and increased the completeness of major attributes. This curation process revealed common metadata quality issues, including typos, inconsistent terminologies, misplaced values, conflicting annotations, and inappropriately merged information across attributes. We document the challenges, decisions, and solutions during this large-scale metadata harmonization. The harmonized metadata, accessible through the OmicsMLRepoR Bioconductor package, enables repository-wide queries and cross-study analyses previously challenging with heterogeneous metadata. Our experience provides practical guidance for similar curation efforts and demonstrates the value of investing in retrospective metadata improvement for existing public omics resources.},
}

*Metadata/standards
Humans
*Data Curation/methods
*Neoplasms/genetics
*Databases, Genetic
*Metagenomics
*Genomics

@article {pmid42172324,
year = {2026},
author = {Freschlin, CR and Yang, KK and Romero, PA},
title = {Scalable and cost-efficient custom gene library assembly from oligopools.},
journal = {Science advances},
volume = {12},
number = {21},
pages = {eady2279},
pmid = {42172324},
issn = {2375-2548},
mesh = {*Gene Library ; Software ; *Oligonucleotides/genetics ; Computational Biology/methods ; },
abstract = {Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost and scalability of DNA synthesis. Here, we present OMEGA (Oligo-based Multiplexed Efficient Gene Assembly), a low-cost, accessible method for assembling hundreds to thousands of full-length genes in parallel using standard laboratory techniques. OMEGA computationally fragments target genes into short, high-fidelity Golden Gate-compatible oligonucleotides that can be ordered as a pooled library and assembled across multiplexed subpools. We systematically optimized the number of fragments per gene and orthogonal ligation sites per reaction and determine that OMEGA can assemble up to 2.6-kilobase constructs using as many as 70 Golden Gate sites. To validate the approach, we assembled and functionally screened a library of 810 natural and synthetic green fluorescent protein variants, recovering 94 to 97% of target sequences with high uniformity. OMEGA enables precision library construction at scale, with per-gene costs as low as $1.50, and offers a broadly applicable solution for bridging computational protein design with high-throughput experimental validation. We have developed OMEGA as an open-source software package and an easy-to-use Colab notebook to facilitate community adaptation.},
}

*Gene Library
Software
*Oligonucleotides/genetics
Computational Biology/methods

@article {pmid42172586,
year = {2026},
author = {Singh, R and Gupta, P and Singh, R and Basant, N},
title = {Environmental Antibiotic Contamination and AMR: Integrating Pathways, Impacts, and AI-Driven Mitigation.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/etojnl/vgag115},
pmid = {42172586},
issn = {1552-8618},
abstract = {The widespread contamination of the environment with antibiotic residues is a significant factor contributing to the global crisis of antimicrobial resistance. Antibiotics from various sources, such as effluents from municipal and hospital wastewater treatment plants, agricultural runoffs, discharges from pharmaceutical manufacturing and improper disposal of expired or unused medicines, create selective pressures in the spread of antibiotic resistance genes. These environmental reservoirs act as hotspots for horizontal gene transfer, facilitating the emergence of multidrug-resistant pathogens. Conventional detection methods including culture-based assays, chromatographic quantification, and molecular diagnostics, provide essential insights but are limited by low throughput, reduced sensitivity to new Antibiotic Resistance Genes, and challenges in real-time monitoring across complex environments. Recent advances, such as whole-genome sequencing, metagenomics, and biosensor-based detection, help to address these gaps by enabling more comprehensive surveillance of the resistome. Artificial intelligence further enhances these approaches by improving data interpretation and pattern recognition, thus complementing traditional and molecular methods rather than replacing them. This review examines the pathways of environmental antibiotic contamination, ecological and health impacts of Antimicrobial Resistance (AMR), and limitations of conventional detection methods. It aims to clarify how these pathways contribute to the AMR crisis, assess the effectiveness of existing surveillance techniques, and identify gaps in current research.},
}

@article {pmid42172842,
year = {2026},
author = {Chen, X and Tan, QG and Pan, K and Xiao, A and Cheng, H and Wang, X},
title = {Vegetation of exotic fast-growing species Sonneratia apetala increases the potential of methylmercury production: Insights from carbon bioavailability, microbial metabolism and mercury methylators.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142469},
doi = {10.1016/j.jhazmat.2026.142469},
pmid = {42172842},
issn = {1873-3336},
abstract = {Mangrove sediments are hotspots for neurotoxic methylmercury (MeHg) production, with litter-derived organic carbon strongly affecting mercury (Hg) methylation. However, the specific role of carbon bioavailability in regulating net MeHg production remains unclear. This study investigated sediments vegetated by exotic fast-growing Sonneratia apetala (SA) and native Kandelia obovata (KO) in southern China. Contrary to the expectation that larger carbon pools enhance methylation, MeHg levels were 2.1-2.6 times higher in SA sediments despite KO containing 1.2-4.2 times more total organic carbon. This disparity was driven by carbon bioavailability: SA sediments exhibited a significantly higher proportion of available carbon (34-50%) compared to KO (28-36%), which stimulated microbial activity and enriched Hg-methylating microbes (1.4-3.3 times higher in hgcAB gene abundance). Metagenomics showed that SA not only promoted key Hg-methylating taxa (e.g., Desulfobacterales, Syntrophobacteria) but also upregulated their metabolic pathways for labile carbon use and methyl transfer to Hg. Our results demonstrate that carbon bioavailability, governed by species-specific litter chemistry, is the key driver of net MeHg production. The findings provide an in-depth understanding of Hg biogeochemistry by linking soil carbon quality to microbial metabolic networks, and offer novel insights for evaluating the ecological risks associated with exotic species in mangrove restoration.},
}

@article {pmid42172844,
year = {2026},
author = {Xu, Y and Xie, T and Zhong, W and Yang, G and Zhang, W},
title = {Probable disseminated Mycobacterium avium complex infection in an apparently immunocompetent patient: A case report and literature review.},
journal = {Journal of infection and public health},
volume = {19},
number = {7},
pages = {103245},
doi = {10.1016/j.jiph.2026.103245},
pmid = {42172844},
issn = {1876-035X},
abstract = {Disseminated Mycobacterium avium complex (MAC) infection is rare in immunocompetent hosts. This often leads to diagnostic delays. We report a challenging case of an apparently immunocompetent patient with pulmonary lesions, osteomyelitis, and skin ulcers. While routine cultures were pending, metagenomic next-generation sequencing (mNGS) rapidly identified MAC, enabling timely treatment. Subsequent culture and species identification confirmed the pathogen as Mycobacterium colombiense. Systematic reviews since 2000 have shown that skeletal and pulmonary involvement are common in this population. Diagnosis has gradually incorporated molecular biological techniques, and with timely treatment, patient outcomes are generally favorable. Our findings highlight the limitations of traditional microbiology and demonstrate that mNGS is a vital adjunctive tool for slow-growing pathogens. We conclude that disseminated MAC should be considered in refractory multifocal infections, even without recognized immunodeficiencies. Early molecular diagnosis, individualized multidrug therapy, and rigorous follow-up are essential for clinical remission.},
}

@article {pmid42172850,
year = {2026},
author = {Li, Y and Shi, B and Li, D and Li, YA and Yuan, M and Luo, J and Dong, S and Wen, W and Zhao, R},
title = {Microbial community shift and functional reorganization from influent to effluent in wastewater treatment plants on the Qinghai-Tibet Plateau.},
journal = {Journal of environmental management},
volume = {409},
number = {},
pages = {130036},
doi = {10.1016/j.jenvman.2026.130036},
pmid = {42172850},
issn = {1095-8630},
abstract = {Wastewater treatment plants (WWTPs) on the Qinghai-Tibet Plateau play a critical role in safeguarding fragile high-altitude aquatic ecosystems. However, microbial community structure and functional characteristics in the influent and effluent in high-altitude WWTPs remain poorly understood. Here, we integrated 16S rRNA gene amplicon sequencing with metagenomic gene-centric profiling and genome-resolved reconstruction to investigate influent and final effluent microbiomes from 18 municipal WWTPs across five cities in Qinghai Province. The results showed that alpha diversity was comparable between influent and effluent, whereas microbial community composition differed significantly. Co-occurrence networks revealed a simplified and more modular interaction pattern in effluent, accompanied by fewer keystone taxa compared with influent. Metagenomic analyses showed that major metabolic pathways were retained across treatment stages, but their relative abundances declined toward effluent. Genome-resolved analyses further indicated this treatment-associated functional reorganization primarily reflected shifts in the taxa and genomic coverage supporting these pathways, rather than replacement of pathway categories. Pseudomonadota accounted for the largest proportion of metabolic contributions across carbon, nitrogen, and sulfur transformation pathways, while multiple pathways persisted in effluent but were encoded by fewer genomes with lower coverage. Denitrification-associated steps, particularly nitric oxide and nitrous oxide reduction, constituted major genome-level contributions to nitrogen removal potential. Notably, Patescibacteria were significantly enriched in effluent and exhibited highly simplified genomes dominated by energy-conserving traits. These results reveal treatment-associated microbial and functional reorganization in plateau WWTPs and provide a genome-resolved framework for interpreting microbial metabolic potential in high-altitude wastewater systems.},
}

@article {pmid42172982,
year = {2026},
author = {Yan, S and Zhang, Y and Fan, Q and Jia, W and Dai, Y and Li, X and Lu, S and Sheng, Y and Sun, S and Lin, R and Tang, Y and Zhao, C},
title = {Evodiamine targets ZO-1 to ameliorate cholestatic liver disease: Intestinal homeostasis as the core mediator of gut-liver axis repair and bile acid metabolism remodeling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {157},
number = {},
pages = {158288},
doi = {10.1016/j.phymed.2026.158288},
pmid = {42172982},
issn = {1618-095X},
abstract = {BACKGROUND: Cholestatic liver disease (CLD) is a complex and multifactorial chronic disorder that requires a systematic and integrative management. Evodiamine (EVO), a natural alkaloid derived from Evodiae Fructus, has demonstrated significant therapeutic potential in ameliorating digestive diseases. However, the beneficial effects of EVO on CLD and the underlying mechanisms remain poorly understood.

OBJECTIVE: This study aims to elucidate the mechanisms through which EVO modulates the progression of CLD, with a particular focus on the regulation of gut-liver axis homeostasis.

METHODS: The therapeutic efficacy of EVO in bile duct ligation (BDL)- and α-naphthyl isothiocyanate (ANIT)-induced CLD rat models was systematically evaluated. An integrative approach combining network pharmacology with multi-omics analyses (transcriptomic, metagenomic sequencing, targeted bile acid metabolomics) was employed to identify significantly altered molecular networks. Fecal microbiota transplantation (FMT) was conducted to validate the functional role of gut microbiota in the hepato-intestinal protective effects. Direct molecular targets as well as the functional validation were confirmed through molecular docking, pull-down assays, surface plasmon resonance and cellular thermal shift assay.

RESULTS: EVO achieved significant synchronous hepato-intestine protection in both CLD rats: it markedly ameliorated hepatic injury and hepatic fibrosis, downregulated pro-inflammatory cytokine levels, while preserving intestinal barrier integrity and alleviating intestinal inflammation. Mechanistically, EVO exerted these protective effects by directly targeting the tight junction protein ZO-1 and enhancing its expression and stability. Furthermore, EVO restored intestinal microbial homeostasis, corrected dysregulated BA metabolism-specifically normalizing deoxycholic acid (DCA) levels. FMT experiments demonstrated that the synchronous hepato-intestinal beneficial effects of EVO were partially mediated by gut microbiota.

CONCLUSION: EVO exerts a protective effect against CLD by directly targeting ZO-1 to strengthen intestinal barrier function, thereby restoring gut microbial balance and rebalancing BAs metabolism (especially DCA levels) in the gut-liver axis. This study uncovers a novel ZO-1-dependent mechanism of EVO in CLD, highlighting EVO as a promising candidate for the treatment of CLD and providing new insights into gut-liver axis-targeted therapies.},
}

@article {pmid42173380,
year = {2026},
author = {Du, S and Ding, S and Zhao, Y and Wang, Y and Ju, F and Wu, D},
title = {Maintaining oxygen above a critical threshold prevents acetate-driven phytotoxicity in industrial-scale aerobic composting: metagenomic, MAG, and enzyme-activity evidence.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134949},
doi = {10.1016/j.biortech.2026.134949},
pmid = {42173380},
issn = {1873-2976},
abstract = {Aerobic composting is a key route for organic-waste valorization, yet product utilization is often constrained by phytotoxicity and low germination index (GI), particularly under oxygen-limited operation. Here, we developed an actionable oxygen-control window (O2 ≥ 10% v/v) to mitigate acetate-associated GI inhibition by integrating process monitoring with inhibitor profiling of GI extracts, metagenomics/metagenome-assembled genomes (MAGs), and pyruvate dehydrogenase (PDH) activity measurements. Three composting modes were implemented to create contrasting oxygen regimes: mechanical composting (MC; well-aerated), forced aeration composting (FC; intermittently oxygen-limited), and static composting (SC; ventilation-supported static aerobic). Chemical profiling and mixed-effects/regression analyses identified acetate as the dominant GI-inhibiting compound relative to other candidates (e.g., ammonium, formate, chloride). A bench-scale oxygen-gradient validation experiment (0-21% O2) confirmed an oxygen dose-response of acetate accumulation: acetate reached 1163.5 and 865.4 mg/L at 0% and 5% O2, but remained near baseline at ≥ 10% O2 (85.8 and 80.2 mg/L at 10% and 21% O2, respectively; 24 h), defining an oxygen window for suppressing acetate build-up. To probe mechanism, KEGG-based pathway mapping showed that acetate-linked functions were dominated by pyruvate metabolism, and high-acetate states were associated with reduced PDH-related functional gene abundance (PDHA/B) and lower PDH activity. MAG co-occurrence and correlation analyses further linked acetate-associated states to specific MAG-level contributors (including Thermobifida fusca). Together, these results support a PDH-linked metabolic constraint under oxygen limitation that promotes acetate persistence and GI inhibition, and provide operational guidance to maintain in-pile O2 ≥ 10% (v/v) to reduce acetate-driven phytotoxicity in industrial composting of readily acidogenic wastes.},
}

@article {pmid42173516,
year = {2026},
author = {Ogasawara, K and Uno, K and Tamahara, T and Asano, N and Sudo, K and Kusano, K and Tanabe, M and Kaise, Y and Shindo, T and Shimoyama, Y and Kanno, T and Koike, T and Shimizu, R and Masamune, A},
title = {Antibiotics treatment promotes squamocolumnar junction tumor progression via tumor immune evasion in K19-Wnt1/C2mE mice fed high-fat diet and acidic bile salts.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00056.2026},
pmid = {42173516},
issn = {1522-1547},
support = {19K08434//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 23K07368//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 24K13105//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; },
abstract = {Clinical studies suggested that antibiotics (ABx) administration might increase esophagogastric junction adenocarcinoma risk, but the underlying mechanisms remain unclear. We previously demonstrated that the administration of a high-fat diet (HFD) and acid bile salts (ABS) to K19-Wnt1/C2mE mice might promote the metabolic-driven tumor growth at the squamocolumnar junction (SCJ) cooperatively with gut dysbiosis. To clarify whether ABx-induced dysbiosis promotes the tumorigenesis, we evaluated the effects of HFD+ABS ± ABx treatment on tumor immune evasion in mice. In HFD+ABS+ABx-treated mice, SCJ tumor growth with increased tumor cell proliferation and infiltration of inflammatory cells positive for CD8, programmed cell death protein 1 and programmed cell death-ligand 1 (PD-L1) were observed along with apoptosis suppression. Protein expressions of interferon-gamma (IFN(?)) and phosphorylated signal transducer and activator of transcription (p-STAT) 3 were upregulated in the tumors of the HFD+ABS+ABx group, whose p-STAT1 expression was equivalent to that of the control group. The mice exhibited insulin resistance and metabolic endotoxemia, and metagenomic analysis of their ileal excrement revealed dysbiosis with a decrease in butyrate-producing bacteria and bacterial butanoate metabolism activity. Moreover, IFN(?) stimulation of human-derived NUGC-4 cells increased the protein expression of PD-L1, p-STAT1 and p-STAT3, all of which decreased in response to STAT inhibitors. Transfection with small interfering RNA targeting STAT1 or STAT3 did not attenuate PD-L1 induction, which was inhibited by the combined knockdown. Therefore, oral HFD+ABS+ABx administration to K19-Wnt1/C2mE mice may promote SCJ tumors through tumor immune evasion via IFN(?)-STAT1/STAT3-PD-L1 signaling, along with metabolic endotoxemia.},
}

@article {pmid42173938,
year = {2026},
author = {van Beek, N and Bargheet, A and Jian, C and Noordzij, HT and Ponsero, A and Pettersen, VK and Korpela, KE},
title = {Metagenomic survey of pathogen prevalence in the infant gut.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47440-7},
pmid = {42173938},
issn = {2045-2322},
support = {101039583//ERC Starting Grant/ ; },
abstract = {The human microbiota impacts our health and well-being from infancy throughout our lives. Besides mutualistic and commensal strains, it also contains opportunistic pathogens. Infants may be especially vulnerable to opportunistic pathogen colonisation due to their immature immune systems and low microbial diversity.The study aims to examine associations between opportunistic pathogen prevalence and factors such as breastfeeding, antibiotic use, birth-mode, and the presence of other bacterial taxa. This study analysed 3981 publicly available shotgun metagenomes collected from 1275 infants and 415 mothers across ten countries to identify species that may be considered opportunistic pathogens in the infant gut. The prevalence of C. difficile was decreased in breastfed infants and in those carrying Faecalibacterium and Dorea spp. S. aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding. K. pneumoniae was acquired later in life and was more prevalent in premature infants, and less commonplace in vaginal deliveries without antibiotics. Our findings indicate that opportunistic pathogen prevalence in the infant gut is influenced by medical and caregiving practices and may be modifiable through targeted interventions. Reducing the spread of these opportunistic pathogens could contribute to global efforts against early life infections.},
}

@article {pmid42174003,
year = {2026},
author = {Kumari, R and Ghosh, C and Kumar, R and Shakya, R and Kumar, S and Saini, AK},
title = {Assessment of water quality and microbial contamination in institutional water resources: a necessity to understand health risks.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53672-4},
pmid = {42174003},
issn = {2045-2322},
support = {project grant MH-32/2024//R&D cell, Miranda House, University of Delhi, India/ ; },
abstract = {Lack of regular monitoring of water sources may lead to undetected contamination, posing serious health risks and necessitating regular water quality assessments. Sampling for physicochemical, microbial analyses, and online surveys across three higher education institutions was done to evaluate water quality. Spatiotemporal variations among physicochemical parameters showed that the pH, EC, and TDS decreased during the wet season, reflecting the dilution effect of rain. However, DO increased from 0.67 to 4.83 ppm, indicating better aeration. PCA showed seasonal variability, whereas the correlation matrix highlighted both positive and negative interrelationships between temperature-pH (- 0.25), DO-ORP (0.11), and TDS-EC (1.00). Potentially toxic metals were either negligible or not detected. Metagenomics revealed the presence of 29 bacterial phyla, 61 classes, 124 orders, 241 families, and 457 genera. Canonical correspondence analysis showed the influence of Mo, EC, salinity, and TDS on Bacteroidota, Chloroflexota, Cyanobacteriota, and Planctomycetota, whereas Verrucomicrobiota, Acidobacteriota, Chlamydiota, Candidatus Melainabacteria, Bdellovibrionota, and Deinococcota were affected by Ni, pH, and COD. Pathogen mapping revealed the presence of Vibrio, Pseudomonas, Enterobacter spp., etc., responsible for diseases such as cholera, diarrhea, and typhoid. Also, occupants' perception about the water quality emphasizes the need for better management of drinking water in HEIs.},
}

@article {pmid42174021,
year = {2026},
author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W},
title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53556-7},
pmid = {42174021},
issn = {2045-2322},
abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.},
}

@article {pmid42174437,
year = {2026},
author = {van Bemmelen, J and Nika, I and Baaijens, JA},
title = {Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12874-w},
pmid = {42174437},
issn = {1471-2164},
abstract = {BACKGROUND: Over the past decades, genome databases have expanded exponentially, often incorporating highly similar genomes at the same taxonomic level. This redundancy can hinder taxonomic classification, leading to difficulties distinguishing between closely related sequences and increasing computational demands. While some novel taxonomic classification tools address this redundancy by selecting a subset of genomes as references, insights regarding the impact of different reference genome selection methods across taxonomic classification tools are lacking.

RESULTS: We systematically evaluate genome selection and dereplication methods on bacterial and viral datasets using simulated metagenomic samples and a bacterial mock community. For bacterial species-level profiling, incorporating all available genomes generally yields the highest accuracy, while having a limited impact on computational resource usage. In contrast, for highly similar bacterial strain-level and SARS-CoV-2 lineage-level datasets we find that selection significantly improves abundance estimation accuracy. Incorporating location-based metadata further enhances viral profiling performance by prioritizing locally relevant genomes. Across viral experiments, smaller reference sets significantly reduce memory and runtime requirements during both indexing and profiling, although this comes at an additional pre-processing cost.

CONCLUSIONS: Reference genome selection influences both accuracy and computational efficiency in taxonomic profiling, but its benefits seem context- and resolution-dependent. Our results demonstrate that reference set design does not have a one-size-fits-all solution, and that selection strategies should be adapted based on the biological and computational setting.},
}

@article {pmid42167521,
year = {2026},
author = {Wolacewicz, M and Decewicz, P and Valdes, ME and Iaconi, OS and Todiras, M and Ferdohleb, A and Rodriguez-Mozaz, S and Borrego, CM and Dziewit, L},
title = {The occurrence and removal of antibiotic residues and antibiotic resistance genes in the largest European constructed wetland at Orhei (Moldova).},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128381},
doi = {10.1016/j.envpol.2026.128381},
pmid = {42167521},
issn = {1873-6424},
abstract = {Constructed wetlands (CWs) are increasingly promoted as low-cost, nature-based solutions for wastewater treatment, particularly in low- and middle-income countries (LMICs), yet their performance in removing pharmaceutical compounds, antibiotic resistance genes (ARGs), and bacterial pathogens remains insufficiently characterized under real-field-scale conditions. Here, we investigated the fate of pharmaceutical compounds (including antibiotic residues), wastewater bacterial communities, and the associated ARGs in the largest European passive treatment system, the vertical-flow CW of Orhei (Moldova), serving nearly 26,000 inhabitants. Metagenomic profiling revealed 783 bacterial families, with a reduction from 33 families in raw sewage to 25 in the final effluent and clear enrichment of autochthonous wetland taxa. A total of 150 ARG types conferring resistance to 16 antibiotic classes were detected. The cumulative ARG load decreased by approximately 78% from influent to effluent. ARGs conferring resistance to fosfomycin, nitroimidazoles, rifamycins, streptothricin, oxazolidinones, and pleuromutilins were not detected in the final effluent, suggesting effective removal to below the detection limit of the applied metagenomic method, while sulfonamide resistance genes (sul1, sul2) persisted across all stages. Out of 29 antibiotic residues analyzed, 13 (including two sulfamethoxazole metabolites) were detected, together with 14 non-antibiotic pharmaceuticals (out of 30 residues analyzed). The removal of individual antibiotics ranged between 85 and 100%, and for other pharmaceuticals between 34 and 100%, although some compounds (e.g., carbamazepine, 10,11-epoxycarbamazepine, alprazolam) showed negative removals. Environmental risk assessment (risk quotients, RQ) indicated no significant risk to freshwater biota (RQ < 0.1) for all detected compounds in the treated effluent. Results demonstrated that a large-scale CW in the LMIC context can substantially reduce antibiotic residues and ARGs, supporting its role as an effective, nature-based component of One Health-oriented wastewater management.},
}

@article {pmid42167540,
year = {2026},
author = {Wang, W and Liu, H and Jiang, K and Posum, W and Lu, Z and Chen, X},
title = {A rare case of Porphyromonas endodontalis lung abscess mimicking lung cancer on imaging: The diagnostic value of postoperative metagenomic next-generation sequencing.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108821},
doi = {10.1016/j.ijid.2026.108821},
pmid = {42167540},
issn = {1878-3511},
abstract = {This case highlights the diagnostic challenge of a Porphyromonas endodontalis lung abscess mimicking lung cancer. A 67-year-old male presented with a right lower lobe mass suggestive of malignancy. Following wedge resection, pathology confirmed an abscess. Metagenomic next-generation sequencing (mNGS) of the tissue revealed a microbial profile dominated by oral anaerobes of Porphyromonas endodontalis. Postoperative mNGS identified the oral origin of infection and prompted periodontal treatment, leading to full recovery. This report reveals the decisive value of postoperative mNGS in correcting a diagnosis of infection mimicking lung cancer. It emphasizes that oral anaerobic infections can present as "tumor-like" pulmonary lesions. This case suggests that oral infection sources should be considered in the differential diagnosis of challenging pulmonary lesions and highlights the potential value of a multidisciplinary approach that includes dental evaluation.},
}

@article {pmid42167986,
year = {2026},
author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S},
title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.},
journal = {Journal of the World federation of orthodontists},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ejwf.2026.03.003},
pmid = {42167986},
issn = {2212-4438},
abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.

METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.

RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri‑implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).

CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri‑implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.},
}

@article {pmid42168196,
year = {2026},
author = {Bowie, KR and Luhung, I and Burke, TR and Roberts, SC and Martinello, RA and Gerstein, M and Peccia, J and Healy, HG},
title = {Disinfection of hospital sink drains enriches pseudomonadota and efflux pump-mediated antibiotic resistance in reestablished biofilms.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73533-y},
pmid = {42168196},
issn = {2041-1723},
support = {1S10OD030363-01A1//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Antimicrobial resistant pathogens and associated infections represent major public health threats affecting healthcare facilities, with sink drain biofilms serving as reservoirs for many of these bacteria. Despite attempts at sink drain biofilm disinfection and removal, drain biofilms inevitably regrow, and disinfection may shape the returning microbial communities and their resistance profiles. We applied culture-based and metagenomic approaches to study these drain disinfection effects on microbial community abundance, taxonomy, and antimicrobial resistance in operational hospital sinks. Drain biofilms regrew to baseline densities in approximately four days. Regrown biofilms contained more viable carbapenem-resistant bacteria and were dominated by Pseudomonadota, including Cupriavidus and Pseudomonas. Long-read sequencing revealed an increase in multidrug efflux pump genes after disinfection, which confer broad resistance to antibiotics and disinfectants. This work provides mechanistic insights into how disinfection influences sink drain biofilm ecology and the enrichment of antimicrobial resistance, with implications for infection prevention strategies in healthcare environments.},
}

@article {pmid42168704,
year = {2026},
author = {Zhang, X and Mallick, H and Rahnavard, A},
title = {Meta-analytic microbiome target discovery for immune checkpoint inhibitor response in advanced melanoma.},
journal = {Communications medicine},
volume = {6},
number = {1},
pages = {},
pmid = {42168704},
issn = {2730-664X},
support = {2109688//National Science Foundation (NSF)/ ; 2109688//National Science Foundation (NSF)/ ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors have transformed melanoma therapy, yet only a subset of patients achieve durable responses. Gut microbes have been linked to response, but reported biomarkers vary across studies. We aim to identify reproducible microbial features and test their generalizability across cohorts and treatment settings.

METHODS: We reprocessed stool metagenomic sequencing data from 15 melanoma cohorts (763 samples from 484 individuals), including 12 cohorts treated with immune checkpoint inhibitors alone and 3 trials combining immune checkpoint inhibitors with fecal microbiota transplantation. Using a unified analysis pipeline, we profiled microbial species, metabolic pathways, and biosynthetic gene clusters, and analyzed their associations with treatment response using Tweedie regression, random-effects meta-analysis, and multimodal integration with leave-one-dataset-out validation.

RESULTS: Here, we show that responders in immune checkpoint inhibitor-only cohorts are enriched for several short-chain fatty acid-producing commensals, whereas non-responders show higher abundance of taxa associated with disrupted gut communities. In fecal microbiota transplantation plus immune checkpoint inhibitor trials, response associates with distinct communities and shifts in amino-acid, nucleotide and cofactor metabolism. Across cohorts, multiview prediction models repeatedly select gene clusters linked to antimicrobial peptides and surface polysaccharides, but cross-study discrimination remains modest.

CONCLUSIONS: Microbiome signatures of response are treatment-context dependent and are not captured by a single universal species. These harmonized findings prioritize microbial taxa and functions for mechanistic studies and future microbiome-informed interventions.},
}

@article {pmid42168837,
year = {2026},
author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T},
title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05157-7},
pmid = {42168837},
issn = {1471-2180},
support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; },
abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.},
}

@article {pmid42168845,
year = {2026},
author = {Zhao, Q and Zuo, S and Liu, S and Wang, J and Tang, J and Zou, X and Leng, Y and Li, X and Zhou, M and Tian, J and Wang, P},
title = {Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05168-4},
pmid = {42168845},
issn = {1471-2180},
support = {2023AFD045//Hubei Provincial Natural Science Foundation / Joint Fund Project Cultivation Project/ ; 2023BCB140//Hubei Provincial plan of science and technology key research project/ ; 2023XKQT1//The Advantages Dicipline Group (Medicine) Project in Higher Education of Hubei Province (2021-2025)/ ; },
abstract = {Alterations in the gut microbiome have been increasingly implicated in Parkinson's disease (PD), but the associated metabolic changes remain incompletely understood. Here, we applied an integrative multi-omics approach combining shotgun metagenomic sequencing and untargeted LC-MS-based plasma metabolomics to investigate host-microbiome alterations in PD. Fecal and plasma samples were collected from 30 PD patients and 30 healthy spouse controls. Significant differences in microbial diversity and taxonomic composition were observed between the two groups. Taxonomic profiling revealed marked gut microbial dysbiosis in PD, including altered abundances of Phocea massiliensis, Bacteroides sp900766005, and Alistipes_A indistinctus. Metabolomic analysis identified 86 significantly altered plasma metabolites, including glycerophospholipids, indoleacetic acid, and kynurenic acid. Integrative pathway analysis suggested links between microbial functional alterations and host metabolic changes. Machine-learning analyses identified three biomarker panels that distinguished PD patients from controls in validation datasets, with the highest area under the curve (AUC) reaching 0.92. In silico molecular docking further suggested potential interactions between several metabolite biomarkers and alpha-2-macroglobulin (A2M) or the human B[act] spliceosome. Overall, these findings provide an integrative view of host-microbiome metabolic alterations associated with PD and highlight candidate biomarkers and exploratory host-metabolite associations for further investigation.},
}

@article {pmid42169289,
year = {2026},
author = {Li, Y and Liu, X and Li, C and Xu, X and Tang, C and Zhou, G and Liu, Y and Blank, I},
title = {Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {237},
number = {},
pages = {119324},
doi = {10.1016/j.foodres.2026.119324},
pmid = {42169289},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Meat Products/microbiology/analysis ; *Odorants/analysis ; Fermentation ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; *Pea Proteins/metabolism ; Animals ; Gas Chromatography-Mass Spectrometry ; Taste ; Food Microbiology ; Humans ; Microbiota ; Swine ; Tandem Mass Spectrometry ; },
abstract = {Hybrid dry-fermented sausage analogues with texturized pea proteins (TPPs) are emerging, yet flavor formation mechanisms remain unclear. We combined quantitative descriptive analysis with complementary HS-SPME-GC-MS/HS-GC-IMS volatilomics, UHPLC-MS/MS untargeted metabolomics, and marker-gene microbiome sequencing across sausages with different fermentation and ripening stages to map key aroma and their potential microbial and metabolic drivers. Sensory data showed rising fruity, cocoa-chocolate and nutty notes. In total, 47 volatiles were identified by GC-MS and 40 by GC-IMS. Screening of odorants based on relative odor activity value (rOAV) consistently highlighted seven odorants, with a shift from hexanal-dominated raw profiles to linalool-dominated processed profiles, indicating suppression of aldehyde-derived off-notes and enrichment of terpene/ester notes. Metabolomics detected 2467 metabolites, dominated by lipids and organic acids, and short-peptide enrichment suggested intensified proteolysis supplying aroma precursors. Bacterial succession exceeded fungal variation, with Latilactobacillus and Staphylococcus as core taxa. The integrated dataset provides practical markers and microbial/process cues to enhance flavor quality of sustainable hybrid fermented meats.},
}

*Metabolomics/methods
*Meat Products/microbiology/analysis
*Odorants/analysis
Fermentation
*Metagenomics/methods
Volatile Organic Compounds/analysis
*Pea Proteins/metabolism
Animals
Gas Chromatography-Mass Spectrometry
Taste
Food Microbiology
Humans
Microbiota
Swine
Tandem Mass Spectrometry

@article {pmid42169351,
year = {2026},
author = {Yang, S and Fu, X and Yang, Z and Zhang, T and Lu, C and Yi, L and Zhao, Q and Gu, Y and Wang, S},
title = {Metagenomic sequencing reveals the similarities and differences in microbial community structure and diversity between fermented whey and Rubing cheese, a fresh goat milk cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {237},
number = {},
pages = {119400},
doi = {10.1016/j.foodres.2026.119400},
pmid = {42169351},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; *Metagenomics/methods ; Fermentation ; *Whey/microbiology ; *Food Microbiology ; Biogenic Amines/analysis ; China ; Milk/microbiology ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {Rubing cheese is a traditional handmade goat milk cheese in Yunnan, China, and the fermented whey used in its production affects its quality and safety. This study employed metagenomic sequencing to systematically characterize the microbial communities in fermented whey and Rubing cheese and to quantitatively analyze their biogenic amine (BA) contents. Metagenomic analysis revealed that Rubing cheese had higher microbial diversity than fermented whey. Approximately 403 microbial species were identified in Rubing cheese, and 209 were identified in fermented whey. Notably, fermented whey was rich in lactic acid bacteria (LAB), such as Lactobacillus delbrueckii (L. delbrueckii), Lentilactobacillus hilgardii (Le. hilgardii), and Lacticaseibacillus paracasei (La. paracasei). In contrast, Rubing cheese contained a high abundance of Escherichia coli (E. coli). The total BA content was low in both fermented whey (20.25 mg·kg[-1]) and Rubing cheese (4.69 mg·kg[-1]). These findings provide a scientific basis for establishing standardized production processes for developing functional starter cultures in the industrialization of Rubing cheese production.},
}

*Cheese/microbiology/analysis
Animals
Goats
*Metagenomics/methods
Fermentation
*Whey/microbiology
*Food Microbiology
Biogenic Amines/analysis
China
Milk/microbiology
*Microbiota
Bacteria/genetics/classification

@article {pmid42169753,
year = {2026},
author = {Song, D and Zhong, X and Zhang, G and Chen, J and Xue, Y and Yang, L},
title = {Linking geographic flavor signatures to microbial origin in high-temperature Daqu: An integrated metaproteomics and metabolomics approach.},
journal = {Food chemistry: X},
volume = {36},
number = {},
pages = {103952},
pmid = {42169753},
issn = {2590-1575},
abstract = {Elucidating the molecular architecture of microbial terroir is vital for precision fermentation, yet functional decoupling between taxonomic abundance and in situ expression remains a fundamental challenge. To resolve this "abundance-activity paradox," we integrated metaproteomics, metabolomics, and metagenomics across the Chishui River gradient. We identified distinct chemosensory fingerprints: upstream thermotolerant consortia (Bacillus and Oceanibacillus) specialize in 2,3,5,6-tetramethylpyrazine biosynthesis mediated by bacterial acetolactate decarboxylase, while downstream microbiota (Weissella and Debaryomyces) prioritize alcohol and ester formation. Crucially, metaproteomic profiling unmasked the "rare biosphere" as a primary driver of core metabolic fluxes. While Bacillus was genomically dominant, keystone functional taxa-specifically low-abundance fungi like Hyphopichia and Paecilomyces-were the actual executors of rate-limiting starch hydrolysis. Furthermore, functional resilience was uniquely maintained through robust fungal co-occurrence networks despite geographic constraints. This study challenges abundance-centric paradigms, providing an activity-based framework for the rational design of synthetic microbial consortia to standardize flavor while preserving regional identity.},
}

@article {pmid42169756,
year = {2026},
author = {Chen, Y and Yu, K and Sun, Y and Yan, Y and Yin, G and Wang, J and Li, X and Tang, S and Pronyk, P and Xia, Y},
title = {Plastic leachates drive conjugative transfer of antibiotic resistance genes.},
journal = {Environmental science and ecotechnology},
volume = {31},
number = {},
pages = {100705},
pmid = {42169756},
issn = {2666-4984},
abstract = {Plastic pollution pervades aquatic ecosystems worldwide, releasing leachates that interact intimately with microbial communities. Antibiotic resistance genes (ARGs) disseminate rapidly through horizontal gene transfer via plasmid conjugation, posing a severe and accelerating threat to public health and environmental stability. While microplastic particles are known to promote ARG exchange within biofilms, the influence of soluble chemical leachates derived from degrading plastics has remained unclear. Here we show that photodegraded leachate from polyvinyl chloride (PVC)-a widely used material in water infrastructure-substantially enhances conjugative transfer of ARGs in both laboratory model systems and natural aquatic microbiomes. Exposure increased transconjugant abundance up to 26.4-fold and conjugation efficiency up to 44.6-fold, with non-monotonic responses modulated by leachate concentration and microbial community diversity. Characterization of the leachate revealed high proportions of biolabile dissolved organic matter alongside additives; mechanistic assays demonstrated that these effects arise through elevated intracellular reactive oxygen species (21% increase), activation of the SOS response and DNA-repair pathways, increased extracellular protein production facilitating cell-cell contact, and compensatory adjustments in the electron transport chain that maintain ATP homeostasis. These results demonstrate that plastic leachates act as potent but previously overlooked facilitators of ARG dissemination beyond the physical effects of microplastics. Our findings reveal a critical synergy between plastic pollution and the global antimicrobial-resistance crisis, underscoring the urgent need for targeted regulations on plastic additives and degradation products in aquatic systems.},
}

@article {pmid42170025,
year = {2026},
author = {Higashi, K and Ishikawa, H and Kurokawa, K and Mori, H},
title = {PZLAST-MAG: full length protein sequence similarity search server of large-scale MAG proteins.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag129},
pmid = {42170025},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary analysis. However, despite the explosive growth of MAG-derived protein data, tools enabling fast and accurate similarity searches against large-scale MAG protein datasets remain limited.

RESULTS: We present PZLAST-MAG, a web server for ultra-fast sequence similarity searches against 0.4 billion MAG-derived protein sequences (0.1 trillion amino acids) from over 210 000 MAGs indexed in Microbiome Datahub. Implemented on PEZY-SC3 MIMD many-core processors, PZLAST-MAG achieves high accuracy and speed, with performance comparable to widely used tools such as DIAMOND and MMseqs2 based on our benchmark analyses. In addition to tabular alignments, PZLAST-MAG provides interactive visualizations of phylogenetic and environmental distributions and co-occurrence patterns of homologous proteins across MAGs. This combination enables rapid homolog mining of functionally important genes across diverse microbial lineages while simultaneously revealing their taxonomic and ecological contexts. Two use case analyses indicate its utility for homolog mining of metabolic enzyme genes and plasmid-derived genes.

PZLAST-MAG is provided as a web-based service and is freely available at https://pzlast.nig.ac.jp/pzlast/mag without requiring registration.},
}

@article {pmid42170880,
year = {2026},
author = {Ershova-Menze, E and Westgaard, JI and Hjellnes, H and Falkenhaug, T},
title = {Optimising Zooplankton DNA Metabarcoding: Methodological Considerations for Large-Scale Monitoring.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70149},
doi = {10.1111/1755-0998.70149},
pmid = {42170880},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Zooplankton/genetics/classification ; Animals ; Biodiversity ; DNA/genetics/isolation & purification ; *Metagenomics/methods ; Electron Transport Complex IV/genetics ; },
abstract = {DNA metabarcoding is becoming an increasingly common approach in ecological monitoring of marine and freshwater planktonic communities, yet methodological choices along the metabarcoding workflow and data post-processing approaches remain highly inconsistent across studies, limiting the ability to track biodiversity trends, detect range shifts, or integrate datasets across monitoring programs. This study addresses this methodological bottleneck by combining controlled experimental comparisons with a comprehensive literature synthesis to identify how protocol decisions-from sample preservation and DNA extraction to sequencing platforms and taxonomic assignments-affect the results of COI metabarcoding and its interpretation. Overall biodiversity and community patterns were recovered by all combinations of tested methods, supporting the notion that patterns identified through DNA metabarcoding are robust and comparable across studies. We identify TES (Tris-EDTA-SDS) buffer, optionally paired with at-sea homogenisation, as a practical alternative to ethanol preservation for large-scale monitoring surveys. We show that integrating several classification methods and reference databases for taxonomic assignment improves diversity estimates and confidence in the assignments, and advocate for increased use of tools like BOLDigger that facilitate manual curation of ambiguous/erroneous references. Finally, we demonstrate that introducing stricter filtering thresholds reduces the effect of false positives, pseudogenes and lab-specific contamination, and make comparisons of data generated by different laboratories and methodological configurations more robust, although potentially at the expense of excluding rare taxa. While we intentionally refrain from recommending a universal best practices protocol, this study aims to provide a practical roadmap to help enhance the reliability and reproducibility of marine zooplankton monitoring via DNA metabarcoding.},
}

*DNA Barcoding, Taxonomic/methods
*Zooplankton/genetics/classification
Animals
Biodiversity
DNA/genetics/isolation & purification
*Metagenomics/methods
Electron Transport Complex IV/genetics

@article {pmid42171141,
year = {2026},
author = {Tagliamonte, S and Neill, HR and Murphy, BÓ and Pourshahidi, KL and De Filippis, F and Ercolini, D and Gill, CIR and Natalia, K and Curran, B and Nicole, M and Mary, S and Dobani, S and Fontana, M and Vitaglione, P},
title = {Dietary N-acylethanolamines are bioaccessible in the small intestine and modulate postprandial hormonal responses: a randomized crossover trial in subjects with ileostomy.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03328d},
pmid = {42171141},
issn = {2042-650X},
abstract = {N-Acylethanolamines (NAEs) are bioactive lipid mediators involved in the regulation of appetite, inflammation, and gut-brain signaling. This study investigated the metabolic fate of dietary NAEs following the consumption of two test meals with differing NAE contents in subjects with ileostomy and evaluated their effects on gastrointestinal hormones, glycaemia, and appetite regulation. An acute, double-blind, randomized, crossover postprandial study was conducted in ileostomy patients who consumed either a high-NAE meal (HNM) or a low-NAE meal (LNM) on two separate occasions. Ileal fluid and plasma samples were collected over an 8-hour postprandial period for analysis of NAEs and endocannabinoids (ECs). Baseline ileal microbiota composition was assessed. At the end of the 8-hour period, participants completed a buffet meal test to evaluate ad libitum energy intake. Dietary NAEs were significantly recovered in ileal fluids after HNM intake, with concentrations approximately 3-fold higher than those after LNM, suggesting partial digestion and release from the food matrix. No significant differences in postprandial plasma NAE concentrations were observed between meals. HNM consumption led to higher postprandial levels of plasma insulin, C-peptide, and glucose-dependent insulinotropic polypeptide, despite no differences in glycemic response or subsequent ad libitum energy intake. Metagenomic analysis identified clusters of ileal microbial taxa associated with circulating lipid profiles, suggesting a role of the small intestinal microbiota in the metabolism of NAEs and ECs. Dietary NAEs reach the small intestine at active concentrations and may influence local signaling via GPR119, with microbiota composition influencing their release from food.},
}

@article {pmid42171373,
year = {2026},
author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE},
title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0030526},
doi = {10.1128/msystems.00305-26},
pmid = {42171373},
issn = {2379-5077},
abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.},
}

@article {pmid42171625,
year = {2026},
author = {Paietta, EN and Johnston, RA and Kraberger, S and Randrianarisoa, SF and Razanamahenina, TT and Ramboninarimalala, A and Velontsara, JB and Raherinirina, TG and Raveloson, L and Finley, NL and Baitchman, E and McAdoo, BG and Yoder, AD and Varsani, A},
title = {Mammal-infecting DNA viruses identified in lemurs and rodents in Madagascar mirror the evolutionary history of their hosts.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001728},
pmid = {42171625},
issn = {2057-5858},
mesh = {Animals ; Madagascar ; *Lemur/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Rodentia/virology ; Rats/virology ; Metagenomics ; Genome, Viral ; },
abstract = {Given that some DNA viruses have been found to exhibit virus-host co-evolution and establish lifelong infection, mammals with unique evolutionary histories in island ecosystems likely host exceptionally diverse viruses. Madagascar is inhabited by endemic non-human primate and rodent lineages interacting with expansive populations of introduced non-native rodents across the island. Using a viral metagenomic workflow on 189 oral swabs of lemurs and rodents in southeastern Madagascar, we characterized genomic sequences of DNA viruses in the families Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, Parvoviridae and Polyomaviridae and assessed their phylogenetic relationships to known viruses. Endemic lemurs and tufted-tailed rats displayed particularly novel DNA viral diversity mirroring the geographic isolation and subsequently rich evolutionary history of their hosts. Notably, we provide the first coding-complete sequences in lemurs of herpesviruses, polyomaviruses, adeno-associated viruses and circoviruses. In contrast, the DNA viral communities of black rats in Madagascar were similar to those found in globally distributed black and brown rat populations, given their broad geographic spread and relatively recent introduction to the island. Given the scarcity of viral research in natural populations of lemurs and rodents in Madagascar despite the island's exceptional biodiversity and escalating anthropogenic pressures, this study provides a genomic and phylogenetic foundation for DNA viruses infecting Malagasy lemurs and rodents.},
}

Animals
Madagascar
*Lemur/virology
*DNA Viruses/genetics/classification/isolation & purification
Phylogeny
*Rodentia/virology
Rats/virology
Metagenomics
Genome, Viral

@article {pmid42171661,
year = {2026},
author = {Goodall, T and Busi, SB and Jones, B and Thorpe, A and Griffiths, RI and Redhead, J and Hulmes, L and Hulmes, S and Ridding, L and Peyton, J and Pereira, G and Gweon, HS and Read, DS and Pywell, R},
title = {Taxonomic filtering accompanies functional expansion during long-term soil restoration.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag131},
pmid = {42171661},
issn = {1751-7370},
abstract = {The restoration of species-rich calcareous grasslands is a critical conservation objective, yet the recovery of the invisible below-ground microbiome remains poorly quantified compared to above-ground vegetation. Using a unique 143-year land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly across arable, regenerating (23 and 67 years), and ancient grasslands. By integrating vegetation surveys with soil physiochemistry, microbial profiling, and shotgun metagenomics, we identified a decoupling between floral and edaphic recovery. While the diversity of vegetation recovered relatively rapidly, approaching ancient grassland levels within 23-67 years, soil properties exhibited persistent legacy effects and slow convergence. Bacterial richness decreased with restoration age; this taxonomic contraction was conversely matched by an expansion in inferred metagenomic functional potential. This was reflected in increased functional gene richness and shifts in the relative abundance of specific SEED-annotated functions toward metabolic pathways associated with complex carbon cycling and stress tolerance. These shifts were congruent with the emergence of specific, unnamed genera belonging to Pseudomonadota and Actinomycetota, and the Bacillota species Pristimantibacillus. The soil ecosystem remained distinct from the 143-year stage even after 67 years of recovery, characterised by persistent legacy phosphorus and a slow accumulation of soil organic matter. These findings suggest that passive regeneration alone may be insufficient for full soil functional recovery, and that strategies targeting microbial assembly and long-term carbon dynamics warrant further evaluation.},
}

@article {pmid42159601,
year = {2026},
author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y},
title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42159601},
issn = {2057-5858},
mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/metabolism ; *Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis ; Female ; Male ; Child, Preschool ; Child ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Infant ; Severity of Illness Index ; Microbiota ; Machine Learning ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.},
}

Humans
*Mycoplasma pneumoniae/genetics/pathogenicity/metabolism
*Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis
Female
Male
Child, Preschool
Child
*Metagenomics/methods
*Metabolomics/methods
Prospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Infant
Severity of Illness Index
Microbiota
Machine Learning
Anti-Bacterial Agents/pharmacology

@article {pmid42159642,
year = {2026},
author = {Ortigoza, PYA and Luiz, FN and Ghellere, GJ and Meyer, RF and Rosa, LH and Passarini, MRZ},
title = {Biogas production using the microbial community present in the soil from Deception Island, maritime Antarctica.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42159642},
issn = {1614-7499},
support = {118/2024//Institutional Program to Support Research Groups/ ; 440218/2023-3//CNPq PROANTAR/ ; },
abstract = {The current energy crisis is increasing the production of sustainable energy, such as biogas, a fuel generated by the anaerobic digestion of organic waste. The use of oat, an agricultural waste, makes the anaerobic digestion more sustainable. Antarctic microbial communities can utilize a wide range of substrates and adapt to different temperatures. Thus, this study evaluated methane production through an innovative approach, using microbial enrichment, and assessed archaeal diversity through metagenomic techniques in Antarctic soils, Deception Island, Maritime Antarctica. Metagenomic analyses showed low archaeal diversity and abundance. The Euryarchaeota (95.2%) and Methanobrevibacter were the most abundant and frequent phylum and genus, respectively. The average biogas production values were 595 LN kg VS[-][1] and 561 LN kg VS[-][1] in tests with individual oat (IO) and oat with enriched mixed culture (O + MC), respectively. However, O + MC showed a higher methane production, 4% (319 LN kg VS[-][1]) more than the results from the IO test with inoculum. Soils from Deception Island may represent a promising source of methanogenic communities capable of producing methane using agricultural waste as an alternative for energy production. Future studies are needed to understand the methane production using soil samples from cold environments.},
}

@article {pmid42159838,
year = {2026},
author = {Dos Santos Miranda, T and Cosentino, MAC and Moreira, FRR and Schiffler, FB and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Lima, M and de Oliveira, TH and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and D'arc, M and Dos Santos, AFA},
title = {Fecal virome of paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) in Rio de Janeiro, Brazil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42159838},
issn = {1678-4405},
mesh = {Animals ; *Feces/virology ; *Porcupines/virology ; Brazil ; *Virome ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Viruses/classification/genetics/isolation & purification ; },
abstract = {The Paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) is a rodent species (Rodentia, Erethizontidae) widely distributed in the Brazilian Atlantic forest. However, little is known about their viral diversity. In this study, we aimed to evaluate, using high-throughput sequencing (HTS), the virome of the feces of seven healthy adult free-living porcupines from Silva Jardim, Rio de Janeiro, Brazil. Total viral nucleic acid was extracted and used for the library preparation for HTS using the Illumina MiSeq platform. The bioinformatics pipeline included quality control, with taxonomic assignments by Kraken2 and Diamond. Unclassified RNA viruses were investigated for viral genome characterization. A total of 41 viral families were classified, of which only seven were validated by both taxonomic analysis tools, including bacteriophages, vertebrate viruses, and unclassified RNA viruses. The most abundant bacterial reads identified belonged to the phylum Proteobacteria. In addition, in-depth analyses of RNA viruses revealed the presence of the Tombusviridae family, a group of plant-infecting viruses possibly associated with the host's diet. This study provides new insights into the fecal virome of Paraguayan hairy dwarf porcupines, contributing to the knowledge of microbial diversity in Erethizontidae and supporting non-invasive virome studies in wildlife.},
}

Animals
*Feces/virology
*Porcupines/virology
Brazil
*Virome
Genome, Viral
Phylogeny
High-Throughput Nucleotide Sequencing
*Viruses/classification/genetics/isolation & purification

@article {pmid42159959,
year = {2026},
author = {Zhang, Z and Jiang, F and Li, Z and Lin, L and Qi, B and Han, D and Ran, C and Mao, S and Wang, J and Zhou, Z and Wang, M and Li, J and Wang, G and Kang, S and Zhang, T},
title = {Animal gut microbes and microbiomes in the 21st century and beyond.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42159959},
issn = {1869-1889},
abstract = {Animal gut microbiomes-comprising bacteria, archaea, fungi, viruses, and protozoa-are fundamental to host evolution, physiology, and ecosystem resilience. This review synthesizes 21st-century advances in their diversity, spatiotemporal dynamics, and functional roles across the animal kingdom. Although high-throughput metagenomics has transformed the field, major biases remain: most studies still focus on domesticated vertebrates and fecal samples, leaving substantial "microbial dark matter" in wild hosts, invertebrates, and non-bacterial domains unexplored. We highlight how gut microbiomes mediate adaptation to environmental extremes, including hypoxia, temperature stress, and toxins, and how industrialization disrupts these communities, contributing to biodiversity loss and disease risk. We further integrate eco-evolutionary theory, multi-omics, and spatial modeling to clarify cross-kingdom interactions and functional networks. Finally, we discuss translational applications-including probiotics, fecal microbiota transplantation (FMT), phage therapy, and synthetic consortia-and emphasize the need for global collaborative initiatives, artificial intelligence (AI)-driven discovery, and standardized databases to unlock the full potential of animal gut microbiomes for biodiversity conservation, climate resilience, and planetary health in the coming decades.},
}

@article {pmid42160933,
year = {2026},
author = {Geng, C and Deng, T and Ren, K and Chen, X and Xue, S and Chen, L and Huang, C and Xu, M},
title = {Divergent structure but convergent metabolic organization of tetrabromobisphenol A degrading microbial consortia from aerobic and anaerobic conditions.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142454},
doi = {10.1016/j.jhazmat.2026.142454},
pmid = {42160933},
issn = {1873-3336},
abstract = {Microbial consortia drive the degradation of persistent pollutants through complex metabolic interactions. However, how these interactions are reconfigured under contrasting redox conditions to maintain functional efficiency remains a fundamental question in microbial ecology. Here, we used a top-down enrichment approach to investigate the collaborative degradation of tetrabromobisphenol A (TBBPA) under both aerobic and anaerobic conditions, integrating sequential transfer cultivation, metagenomics, network analysis, pure culture experiments, and predictive modeling. Sequential transfers significantly (p < 0.05) enhanced TBBPA degradation efficiencies under both regimes, driving distinct structural successions in the microbial communities. Specialist taxa such as Sphingopyxis (aerobic) and Novosphingobium (anaerobic) were phase-specifically enriched, whereas generalists like Pseudomonas and Comamonas emerged as highly interconnected keystone taxa under both conditions. Pure culture experiments and genomic reconstruction indicated functional partitioning among different taxa, where specialists might mediate debromination and β-scission by haloalkane dehalogenase and cytochrome P450, respectively. Furthermore, generalists harbored genetic modules for downstream ring-cleavage pathways, collectively forming a metabolic network that partitions degradation steps across the community. Partial least squares (PLS) regression and random forest analysis supported this functional partitioning and indicated that the overall TBBPA degradation is an emergent community property driven by community‑level interactions. This study suggests a principle of structure-divergent but convergent metabolic organization in collaborative TBBPA-degrading consortia, providing a mechanistic basis for designing synthetic communities to optimize bioremediation of brominated pollutants across diverse environmental settings.},
}

@article {pmid42161086,
year = {2026},
author = {Ziliani, A and Bovio-Winkler, P and Pabst, M and Cabezas, A and Etchebehere, C and Garcia, HA and López-Vázquez, CM and Brdjanovic, D and van Loosdrecht, MCM and Rubio-Rincón, FJ},
title = {Glycine-mediated microbial interactions in biological phosphorus removal systems.},
journal = {Water research},
volume = {302},
number = {},
pages = {126057},
doi = {10.1016/j.watres.2026.126057},
pmid = {42161086},
issn = {1879-2448},
abstract = {Amino acids are less studied substrates in enhanced biological phosphorus removal (EBPR) systems. Glycine, a prevalent amino acid in wastewater, was used in this study to evaluate its role in EBPR processes. We operated a sequencing batch reactor (SBR) for over three months with glycine as the sole carbon source to investigate phosphorus removal performance and microbial dynamics using chemical and molecular analyses. The reactor supported EBPR activity, with glycine enabling anaerobic phosphorus release followed by aerobic uptake. The dissolved organic carbon to phosphorus (DOC:P) removal ratio of 100:9.9 closely matched values reported for systems dominated by polyphosphate-accumulating organisms (PAOs), and net phosphorus removal (20 mg PO4-P L[-1]) fell within the range reported for laboratory-scale EBPR systems fed with mixed carbon sources. Community analyses showed enrichment of Saccharimonadales alongside putative PAOs, including Ca. Phosphoribacter and Ca. Propionivibrio. Genome-resolved analyses indicate distinct but complementary metabolic potentials, including glycine transformation and lactate-related pathways, suggesting distributed carbon processing within the community. Together, these findings expand the understanding of amino acid utilization in EBPR systems and identify potential metabolic linkages that influence phosphorus removal under glycine-fed conditions.},
}

@article {pmid42161088,
year = {2026},
author = {Liu, Q and Zhang, Y and Gong, H and Zhou, S and Yang, J and Zhu, D and Huang, Z and Zhu, Y and Niu, H and Dai, X},
title = {Microbial-driven molecular transformation of dissolved organic matter in water-jet loom wastewater reclamation: An integrated FT-ICR MS and metagenomic investigation.},
journal = {Water research},
volume = {302},
number = {},
pages = {126124},
doi = {10.1016/j.watres.2026.126124},
pmid = {42161088},
issn = {1879-2448},
abstract = {Water-jet loom wastewater, a major textile effluent in China, contains recalcitrant dissolved organic matter (DOM) derived from synthetic sizing agents and lubricants, whose incomplete removal constrains high-quality water reuse. Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics provide high-resolution molecular and genetic insights, optimizing treatment efficacy remains hindered by a fragmented understanding of the intricate links between molecular transformations and their microbial drivers. This study established a reactomic-genomic paradigm coupling potential mass difference (PMD)-based molecular network analysis with metagenomic enzyme annotation in a full-scale membrane bioreactor (MBR) system (10000 m[3]·d[-1]). Over 8,000 molecular formulae were resolved across the treatment train. The results revealed that the dissolved air flotation unit prior to MBR selectively removed hydrophobic lipids and aliphatic/peptide-like compounds, leading to the relative enrichment of lignins/CRAM-like recalcitrant matter. The bioreactor served as the major zone of molecular turnover, with oxidation and depolymerization identified as the dominant transformation classes. These transformations were consistent with the enrichment of a Sphingomonadaceae-associated functional guild and abundant oxygenase-related genes, highlighting the role of microbial oxidation in aromatic transformation. Furthermore, a source-oriented framework revealed MBR effluent DOM as a spatially assembled mixture of three components. The recalcitrant influent-derived fraction dominated total effluent intensity (74.3%), while the bioreactor-emergent fraction constituted a consistent biogenic baseline (12.0%). In contrast, the membrane-associated emergent fraction contributed to molecular diversity (45.4% of unique formulae) but weakly to total intensity (9.7%). These findings indicate that the key challenge for high-quality reuse lies in controlling persistent and compositionally complex DOM. This framework provides a molecular basis for targeted process optimization and supports the transition of textile wastewater treatment from discharge compliance toward chemistry-informed reuse.},
}

@article {pmid42161089,
year = {2026},
author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S},
title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.},
journal = {Placenta},
volume = {181},
number = {},
pages = {168-174},
doi = {10.1016/j.placenta.2026.05.010},
pmid = {42161089},
issn = {1532-3102},
abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.

METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n = 6), (2) delivered by emergency caesarean section (n = 6), and (3) complicated by preeclampsia (n = 5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.

RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.

CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.},
}

@article {pmid42161263,
year = {2026},
author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G},
title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.04.019},
pmid = {42161263},
issn = {1934-6069},
abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.},
}

@article {pmid42161874,
year = {2026},
author = {, and , },
title = {[Expert consensus on laboratory diagnosis of inflammatory bowel disease (2026)].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {},
pages = {1-17},
doi = {10.3760/cma.j.cn112150-20260413-00324},
pmid = {42161874},
issn = {0253-9624},
support = {82472361//Natural Science Foundation of China/ ; },
abstract = {In recent years, the incidence of inflammatory bowel disease (IBD) in China has shown a significant upward trend. The invasive nature of colonoscopy limits its widespread application in population screening and long-term follow-up, while conventional laboratory parameters still suffer from insufficient sensitivity and specificity. A single test is inadequate for comprehensively assessing the complex pathophysiological processes of IBD. To enhance diagnostic efficacy, it is necessary to establish a multi-index combined evaluation system, integrating comprehensive assessments across dimensions such as inflammatory activity, nutritional metabolism, coagulation function, and infection risk. This consensus integrates relevant hematological and fecal laboratory markers, establishes a stratified application pathway covering initial screening, differential diagnosis, activity monitoring, and efficacy evaluation, and standardizes the clinical application scenarios of indicators such as fecal calprotectin (FC), the anti-Saccharomyces cerevisiae antibody (ASCA)/perinuclear anti-neutrophil cytoplasmic antibody (pANCA) panel, CRP (C-reactive protein)/ESR (erythrocyte sedimentation rate), and NLR (neutrophil-to-lymphocyte ratio). Furthermore, this consensus systematically reviews the clinical potential of cutting-edge technologies, including 16S amplicon sequencing, metagenomic sequencing, and microRNA detection, highlighting their significant prospects in analyzing microbial community structure, identifying occult pathogens, and assessing host regulation. This consensus aims to optimize non-invasive testing strategies for IBD, reduce misdiagnosis and improper treatment, and provide a standardized framework for tiered diagnosis and treatment as well as precision prevention and management.},
}

@article {pmid42162115,
year = {2026},
author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, ÅV and Walter, S and Simon, R},
title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42162115},
issn = {2045-2322},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; Feces/microbiology ; *Metagenome ; Case-Control Studies ; },
abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.},
}

Humans
*Irritable Bowel Syndrome/microbiology
*Gastrointestinal Microbiome/genetics
Female
*Metagenomics/methods
Adult
Middle Aged
Feces/microbiology
*Metagenome
Case-Control Studies

@article {pmid42162191,
year = {2026},
author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y},
title = {Author Correction: Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.},
journal = {NPJ digital medicine},
volume = {9},
number = {1},
pages = {},
doi = {10.1038/s41746-026-02769-1},
pmid = {42162191},
issn = {2398-6352},
}

@article {pmid42162287,
year = {2026},
author = {Svanella-Dumas, L and Marais, A and Faure, C and Bergey, B and Comte, R and Candresse, T},
title = {Repeated identification of plant-associated polerovirus 3 (PaPV3) and of a novel polerovirus in the virome of French grain cereals.},
journal = {Archives of virology},
volume = {171},
number = {6},
pages = {},
pmid = {42162287},
issn = {1432-8798},
support = {ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; },
mesh = {*Edible Grain/virology ; Genome, Viral ; Phylogeny ; *Hordeum/virology ; *Luteoviridae/genetics/classification/isolation & purification ; *Plant Diseases/virology ; France ; *Virome/genetics ; Metagenomics ; },
abstract = {Two novel poleroviruses were repeatedly identified by metagenomics in French barley over the 2018-2023 period. One showed ~ 98.5% nucleotide (nt) identity with plant-associated polerovirus 3 (PaPV3) identified by metagenomics in Slovenia, while the second represents a novel species for which the name barley virus H (BVH) is proposed. Both viruses show a typical polerovirus genome organization but do not have ORF6 or ORF7. In French cereals samples, the most prevalent polerovirus was barley virus G (6.4%) followed by BVH (2.3%), cereal yellow dwarf virus RPV (CYDV-RPV, 1.8%) and PaPV3 (0.9%) suggesting the novel poleroviruses to be as prevalent as CYDV.},
}

*Edible Grain/virology
Genome, Viral
Phylogeny
*Hordeum/virology
*Luteoviridae/genetics/classification/isolation & purification
*Plant Diseases/virology
France
*Virome/genetics
Metagenomics

@article {pmid42162448,
year = {2026},
author = {Bharadava, K and Makarani, N and Kaushal, RS},
title = {Co-selection of antimicrobial and heavy metal resistance in aquatic microbial communities at the water interface.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {8},
pages = {},
pmid = {42162448},
issn = {1573-2983},
mesh = {*Metals, Heavy/pharmacology/toxicity ; *Water Microbiology ; *Drug Resistance, Bacterial ; *Water Pollutants, Chemical ; Wastewater/microbiology ; *Drug Resistance, Microbial ; Humans ; *Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; },
abstract = {Antimicrobial resistance (AMR) and heavy metal resistance (HMR) in aquatic ecosystems are increasing global health concerns driven by anthropogenic pollution of water systems. Municipal wastewater, hospital effluents, industrial discharge, agricultural runoff, and aquaculture activities contribute to the persistence and dissemination of resistant microorganisms and resistance genes in aquatic environments. Clinically important waterborne pathogens, including Escherichia coli, Salmonella Typhi, Shigella spp., and Vibrio cholerae, readily acquire resistance under continuous environmental stress conditions. Heavy metals further enhance AMR persistence through co-selection and cross-resistance mediated by mobile genetic elements carrying both antimicrobial and heavy metal resistance genes. This review summarizes the major environmental drivers, molecular mechanisms, and dissemination pathways associated with AMR-HMR interactions in aquatic systems. Recent advances in wastewater-based epidemiology, metagenomic surveillance, and resistance monitoring are highlighted as emerging tools for environmental and public health assessment. Current mitigation approaches, including advanced oxidation processes, membrane bioreactors, nanomaterial-based filtration, and microbial bioremediation, are also evaluated. A multidisciplinary One Health framework is essential for limiting environmental resistance dissemination and protecting human, animal, and ecosystem health.},
}

*Metals, Heavy/pharmacology/toxicity
*Water Microbiology
*Drug Resistance, Bacterial
*Water Pollutants, Chemical
Wastewater/microbiology
*Drug Resistance, Microbial
Humans
*Anti-Bacterial Agents/pharmacology
Bacteria/drug effects/genetics

@article {pmid42162574,
year = {2025},
author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E},
title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.},
journal = {Asian journal of anesthesiology},
volume = {63},
number = {1},
pages = {20-29},
doi = {10.6859/aja.202503_63(1).0003},
pmid = {42162574},
issn = {2468-824X},
mesh = {Animals ; *Sevoflurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Female ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced/microbiology ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; },
abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.

METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.

RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.},
}

Animals
*Sevoflurane/pharmacology
*Gastrointestinal Microbiome/drug effects
Male
Mice
Female
*Anesthetics, Inhalation/pharmacology
*Dysbiosis/chemically induced/microbiology
*Metagenomics/methods
Feces/microbiology
Longitudinal Studies
Sex Factors

@article {pmid42162897,
year = {2026},
author = {Wang, C and Liu, X and Wan, S and Xie, F and Dai, J and Chen, W and Qu, L and Zhang, L and Li, N and Du, X and Zhu, H and Hua, J},
title = {BLOS1 overexpression enhances goat immune response to Brucella LPS through augmented autophagy with associated gut microbiota remodeling.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106706},
doi = {10.1016/j.tvjl.2026.106706},
pmid = {42162897},
issn = {1532-2971},
abstract = {Biogenesis of lysosome-related organelles complex 1 subunit 1 (BLOC1S1, also known as BLOS1) is a key gene involved in phagosome-lysosome maturation, transport, and autophagosome fusion, and it plays a crucial role in host resistance to Brucella infection. This study aimed to examine the effects of BLOS1 overexpression (oeBLOS1) on the stress response of goat macrophages and on intestinal microbiota composition. Peripheral blood mononuclear cells (PBMCs) were isolated from oeBLOS1 and wild-type (WT) goats and differentiated into macrophages. These macrophages were then stimulated with Brucella LPS to assess cytokine secretion and autophagy levels. Metagenomic sequencing was also performed to analyze the structural and functional profiles of the rectal fecal microbiota in these goats. After Brucella LPS stimulation, oeBLOS1 goat macrophages rapidly activated the NF-κB and TLR4 signaling pathways, promoting the synthesis and secretion of cytokines such as TNF-α (P < 0.05). Brucella LPS challenge also significantly increased the transcription of autophagy-related genes such as LAMP2 and BECN1, enhancing autophagic activity and bacterial clearance (P < 0.05). Furthermore, oeBLOS1 altered the intestinal microbiota, significantly enriching pathways linked to membrane transport and cell motility, and reducing the abundance of virulence factors and opportunistic pathogens, which may contribute to intestinal immune homeostasis. In summary, oeBLOS1 may help counteract Brucella LPS-induced infection by promoting the immune response, enhancing autophagy. In addition, it is associated with remodeling gut microbial function, suggesting a potential role in disease resistance.},
}

@article {pmid42163161,
year = {2026},
author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM},
title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.},
journal = {BMC psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12888-026-08132-8},
pmid = {42163161},
issn = {1471-244X},
abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.

METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.

RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p < 0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.

CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.

CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).},
}

@article {pmid42163620,
year = {2026},
author = {Lu, D and Lu, J and Yang, P and Lou, L and Li, W and Zhou, Y},
title = {Microbiome and Lipidomics Reveal the Mechanism of Eight Zhes Decoction on MAFLD.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113862073460107260407065758},
pmid = {42163620},
issn = {1875-5402},
abstract = {INTRODUCTION: The therapeutic potential of Eight Zhes Decoction (EZD) against metabolic dysfunction-associated fatty liver disease (MAFLD) is well-recognized; however, the underlying biological pathways are not well understood. To address this gap, an integrated investigation using both lipidomics and metagenomics was conducted to reveal the mechanistic rationale behind the effects of EZD.

METHODS: A MAFLD mouse model was established using a Methionine-Choline-Deficient (MCD) diet combined with CCl₁. The mice were treated with EZD for four weeks. Hepatic injury was assessed via H&E, Oil Red O, and Masson staining. Untargeted hepatic lipidomics and shotgun metagenomics were employed to profile lipid species and the gut microbiota composition, respectively.

RESULTS: Histopathological analysis confirmed that EZD significantly alleviated hepatic steatosis, ballooning degeneration, and fibrosis. Lipidomics identified 277 differential lipids; EZD treatment notably downregulated 24 TGs and modulated pathways related to arachidonic acid metabolism and bile secretion. Metagenomics revealed that EZD reshaped the gut microbiota, significantly increasing the abundance of Alistipes sp. while reducing the abundance of Faecalibaculum rodentium.

DISCUSSION: Correlation analysis demonstrated that the restored Alistipes sp. was negatively correlated with multiple hepatic TGs, whereas Faecalibaculum rodentium was positively correlated with lipid accumulation.

CONCLUSION: EZD mitigates MAFLD in mice by synergistically regulating hepatic lipid metabolism and gut microbiota. Specifically, the therapeutic effect involves restoring Alistipes sp. and modulating the gut-liver axis, providing experimental evidence for the clinical application of EZD.},
}

@article {pmid42164149,
year = {2026},
author = {Scutari, R and Fox, V and Mastropaolo, M and Fini, V and Mussa, M and Bigliano, P and Colagrossi, L and Vrenna, G and Perinzano, A and Scabini, S and Perno, CF and Calcagno, A},
title = {Case Report: Beyond conventional diagnostics: mNGS support in a complex immunocompromised patient diagnosis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1791094},
pmid = {42164149},
issn = {2296-858X},
abstract = {Next-generation metagenomic sequencing (mNGS) enables the direct and unbiased detection of pathogens from clinical samples, overcoming the limitations of standard methods. It is particularly valuable in immunocompromised patients and in cases of complex infections. We report the case of a man in his 40s, born in North Africa, who was admitted with progressive skin and soft-tissue lesions after a minor foot trauma. The initially localized infection rapidly worsened, leading to bilateral pneumonia, acute respiratory failure, disseminated intravascular coagulation, and death. Histopathological examination revealed granulomatous inflammation with alcohol-resistant bacilli and an undiagnosed cutaneous T-cell lymphoma associated with hemophagocytic syndrome. Conventional microbiological tests identified multiple pathogens, including influenza A virus, herpes simplex virus 1 (HSV-1), Candida albicans, Enterococcus faecalis, Proteus mirabilis, and Pseudomonas aeruginosa; however, their heterogeneous distribution and isolation from non-sterile sites hindered etiological interpretation. Cultures and molecular assays for Mycobacterium species were negative despite findings of histological examination suggestive of granulomatous inflammation with alcohol-resistant bacilli. To clarify the diagnosis, mNGS was performed on blood, serum, and lymph node samples using host DNA depletion and Illumina sequencing. Bioinformatic analysis revealed a diverse microbial landscape, with the detection of Fusarium pseudograminearum, Mycobacterium canettii, and Ralstonia sp., alongside low-level viral sequences [Epstein-Barr virus (EBV) and HSV-1]. These results reflected the patient's severe immune deficiency, characterized by a marked depletion of CD8[+] T cells and NK cells. Although the results became available too late to influence treatment, mNGS provided crucial diagnostic insights, demonstrating its ability to uncover hidden or rare pathogens. Early application of mNGS could significantly improve diagnostic precision and therapeutic decisions in critically ill immunocompromised patients.},
}

@article {pmid42164154,
year = {2026},
author = {Wang, S and Wang, X and Sun, K and Jin, Z and Ma, J},
title = {Pulmonary sarcoidosis complicated with pulmonary cryptococcosis: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1822801},
pmid = {42164154},
issn = {2296-858X},
abstract = {Pulmonary sarcoidosis is an idiopathic granulomatous disorder primarily affecting the lungs and mediastinal lymph nodes. Pulmonary cryptococcosis, an opportunistic mycosis caused by Cryptococcus species, may occur concurrently with sarcoidosis, presenting substantial diagnostic challenges, particularly in treatment-naïve patients. A 63-years-old previously healthy female presented with insidious-onset dyspnea and low-grade fever. Chest computed tomography (CT) showed mediastinal and hilar lymphadenopathy, accompanied by small nodules in the right lower lobe. She was diagnosed with pulmonary sarcoidosis at a local hospital and started on prednisone, with symptomatic improvement. However, follow-up imaging showed enlargement and cavitation of the right lower lobe nodules. Admission laboratory tests, including inflammatory markers and fungal serology, were all unremarkable. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) identified sequences of Cryptococcus neoformans. Histopathological examination of mediastinal lymph node specimens confirmed the presence of non-necrotizing granulomas, which is consistent with a diagnosis of sarcoidosis. Meanwhile, the right lower lobe lung biopsy revealed positive staining for Cryptococcus. The patient was treated with fluconazole, resulting in radiological resolution. This case highlights the importance of considering pulmonary cryptococcosis as a potential complication in treatment-naïve sarcoidosis patients who present with abnormal chest shadows. Underlying immune dysregulation in sarcoidosis may obscure both clinical and radiological findings, thereby complicating the diagnostic process.},
}

@article {pmid42164315,
year = {2026},
author = {O'Connor, BRW and Allen, D and Quinn, M and Kozey, M and Léveillé, RJ and Whyte, LG},
title = {Bipolar investigation of near-surface glacial ice reveals an active microbial ecosystem driven by photosynthesis and chemolithoautotrophy.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag105},
pmid = {42164315},
issn = {2730-6151},
abstract = {Despite extreme conditions including freezing temperatures, low water activity, and few nutrients, active microorganisms are thought to inhabit glacial ice, yet little is known about their identities and methods of survival. We used flow cytometry, cultivation, metagenomics, and metatranscriptomics to characterize viable and active microbial communities from near-surface englacial ice from White Glacier in the Canadian High Arctic and Johnsons Glacier on Livingston Island, Antarctica. The ice, though low in microbial biomass (10[4] cells/ml), harbors communities capable of growth at subzero temperatures (-5°C), high salinity (12% NaCl), and low pH (pH 3). The communities of both poles were different, with metagenome-assembled genomes (MAGs) from White Glacier belonging to Cyanobacteriota and novel phyla and MAGs from Johnsons Glacier belonging to Pseudomonadota and Actinomycetota. Despite this, both glacial communities shared key metabolic functions, including aerobic respiration, aerobic carbon monoxide oxidation, sulfide oxidation, and denitrification. Metatranscriptomics from White Glacier revealed dominant Cyanobacteriota, performing oxygenic photosynthesis and carbon fixation and accompanied by active lithoautotrophs performing metabolisms such as carbon fixation via the 3-hydroxyproprionate cycle, anoxygenic photosynthesis, sulfide oxidation, and nitrate reduction/denitrification. These metabolisms appear to support an active heterotrophic community performing aerobic respiration and aerobic carbon monoxide oxidation. This study highlights the distinct but functionally similar microbial communities in Arctic and Antarctic glaciers, hinting that there may be a core set of metabolisms required for surviving in englacial ice and suggesting that similar communities could persist in glacial ice on Mars or the icy outer moons, Europa and Enceladus.},
}

@article {pmid42164317,
year = {2026},
author = {Domínguez-Huerta, G and Cabello, AM and Santos-Bruña, JJ and Mercado, JM and Ferrera, I},
title = {Ecology of prokaryotic DNA viruses in a highly impacted coastal lagoon revealed through comparative and temporal metagenomics.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag110},
pmid = {42164317},
issn = {2730-6151},
abstract = {Coastal lagoons are highly productive ecosystems, yet their prokaryotic viruses remain poorly studied. The Mar Menor, a hypersaline coastal lagoon in south-eastern Spain, is under strong anthropogenic pressure from continuous agricultural runoff, leading to severe eutrophication. To assess the impact of these unique conditions on viral assemblages, we analyzed a 3-year metagenomic time series of picoplankton communities. We reconstructed the lagoon's prokaryotic DNA viral communities and compared them with their counterparts in open Mediterranean Sea waters to reveal how environmental variability shapes their structure. Viral communities in the Mar Menor showed higher viral operational taxonomic unit relative abundances and diversities and were distinct from those offshore. Temporally, community structure was correlated with water transparency and silicate concentration. The putative hosts of the lagoon viruses were copiotrophic rather than oligotrophic compared to the open sea, and their composition shifted in response to episodic environmental disturbances. Temperate virus levels did not consistently support either the piggyback-the-winner or refugium models, spatially or temporally, indicating that viral replication strategies are governed by factors more complex than trophic status or environmental variability alone. Auxiliary viral genes (AVGs) encoding 2-oxoglutarate/Fe(II)-dependent oxygenase and DNA methyltransferase emerged as potentially relevant functions in the lagoon, as they were more frequent than in the Mediterranean Sea. Similar to targeted hosts, AVG-specific temporal relative abundance patterns were strongly shaped by local disturbances. This study provides the first metagenomic insight into viruses of the Mar Menor, revealing viral ecology in a dynamic, eutrophic lagoon, with implications for predictive models of nutrient cycling.},
}

@article {pmid42164318,
year = {2026},
author = {Aizpurua, O and Brenner, E and Martin-Bideguren, G and Garin-Barrio, I and Cabido, C and Alberdi, A},
title = {Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag106},
pmid = {42164318},
issn = {2730-6151},
abstract = {Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (Calotriton asper) inhabiting two distinct environments: Pyrenean subalpine brooks and Atlantic montane streams. From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes, respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. Although alpha diversity remained similar across environments, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community-shared across environments and accounting for over 85% of reads-that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not associated with broad-scale dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.},
}

@article {pmid42164663,
year = {2026},
author = {Glapa-Nowak, A and Nowak, JK and Kurek, S and Walkowiak, J},
title = {What a pickle-a metagenomic perspective on the cucumber fermentation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809866},
pmid = {42164663},
issn = {1664-302X},
abstract = {Food fermentation involves an interplay between multiple strains and species. This delicate composition during fermentation has been investigated so far using both classical and molecular methods; however, the results remain difficult to interpret. In this perspective article, we discuss the spontaneous fermentation of cucumber from organic and commercial cultivation (from 1st day to 90th day) based on our preliminary data from a nanopore sequencing study. The present study is the first to report the occurrence of coagulase-negative cocci in cucumber fermentation [Staphylococcus saprophyticus (0.01%) and Staphylococcus schleiferi (0.03%)]. Furthermore, we conclude that own-cultivation cucumbers may exhibit a lower incidence and diversity of phages, which have practical implications for designing future studies as well as for direct consumers. Our data also show that, even in the absence of phages (own-cultivation cucumbers <1%), lactic acid bacteria dominance occurs, which contrasts with previous conclusions and contributes to the discussion on the role of phages in maintaining the balance between Enterobacteriaceae and lactic acid bacteria in plant fermentation. The powerful metagenomic approach provides a broader understanding of the day-to-day and sample-to-sample diversity within microbiome communities. The maturity of the fermentation product may play a significant role in exerting specific biological actions. This should be accounted for before planning an intervention study.},
}

@article {pmid42164669,
year = {2026},
author = {Yuan, B and Li, C and Wang, Q and Yao, Q and Guo, X and Wang, Z},
title = {Maize stover mulching combined with an optimized fertilization strategy reshapes rhizosphere microbial communities and functions in greenhouse potato.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1670904},
pmid = {42164669},
issn = {1664-302X},
abstract = {Protected cultivation systems offer opportunities for improving potato productivity but are often constrained by inefficient maize stover utilization and suboptimal fertilization practices. In this study, a 4 × 4 factorial experiment was conducted using the potato cultivar 'Jishu No. 1' to decode the rhizosphere microbial mechanisms underpinning plant growth and yield enhancement under greenhouse conditions. We hypothesized that integrated management (the synergy between stover mulching and fertilization) would modify the soil microenvironment, thereby reshaping microbial community assembly patterns and functional gene distributions. The results showed that while split fertilization combined with moderate stover mulching (F2S2, 8,500 kg·hm[-2] stover mulching) was most effective in enhancing plant physiological status, full topdressing combined with the same mulching level (F3S2) achieved the highest agronomic productivity, increasing total yield to 42.33 t·hm[-2]. Metagenomic analysis revealed that the F3S2 strategy significantly reshaped the rhizosphere microbiome, characterized by higher α-diversity and the enrichment of pathways related to carbon metabolism and carbohydrate processing. Notably, F3S2 promoted the recruitment of copiotrophic taxa, particularly Actinobacteriota, whose relative abundance was significantly and positively correlated with soil organic phosphorus (r = 0.623, p < 0.05). In contrast, oligotrophic groups like Acidobacteriota were relatively less abundant in nutrient-rich treatments. These findings demonstrate that moderate stover mulching combined with dynamic fertilization provides a high-resource niche that favors functional microbial groups, thereby driving rhizosphere nutrient cycling to support potato performance. This study underscores the importance of optimized stover and fertilizer management strategies in protected cultivation.},
}

@article {pmid42165181,
year = {2026},
author = {Zhang, B and Zhang, J and Duan, F and Xuan, Z and Sun, T and Lu, L},
title = {Enzymatic Galactosylation of Erythritol Enhances Antibacterial Activity against Cariogenic Streptococcus mutans.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14195},
pmid = {42165181},
issn = {1520-5118},
abstract = {Erythritol is a widely used sweetener with beneficial properties and bioactivities, including the inhibition of Streptococcus mutans, a bacterium that induces dental caries. Galactosylation of compounds is an attractive method for improving antimicrobial activity. In this study, a novel metagenomic β-galactosidase gene, bga7, was successfully expressed in Escherichia coli. The recombinant enzyme was used to galactosylate erythritol, generating a high yield (93.6%) of galactoside product at a concentration of 2 U/mL upon incubation with 20 mM o-nitrophenyl-β-d-galactopyranoside and 0.5 M erythritol at 40 °C and pH 9.0 for 4 h. The product was confirmed to be β-galactosyl-erythritol by MS and NMR analysis. This galactoside demonstrated significantly enhanced inhibition of both the planktonic growth of S. mutans and biofilm formation compared to erythritol alone. Further investigation into the mechanism revealed that the galactoside suppressed the transcriptional levels of four important genes (gtfB, ftf, srtA, and spaP) associated with bacterial adhesion and biofilm formation.},
}

@article {pmid42165232,
year = {2026},
author = {Nap, B and Thinnes, CC and Thiele, I},
title = {Whole-body metabolic modelling and its prospects in precision nutrition.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-19},
doi = {10.1017/S0029665126103061},
pmid = {42165232},
issn = {1475-2719},
abstract = {Nutrition has long been investigated with respect to its influence on human health. With the availability of various omics data, such as metagenomics and metabolomics, novel insights have been obtained into the influence of nutrition, particularly concerning the gut microbiome. The gut microbiome plays an important role in the breakdown of food-derived compounds and in producing essential bioactive metabolites required for human health. However, this wealth of information made the interactions between nutrition and human health increasingly intricate, and unravelling these links is complex. This review covers the concepts of genome-scale metabolic modelling as a tool to understand the links between nutrition, the gut microbiome and human metabolism and its applications. Genome-scale metabolic modelling treats metabolism as a mathematical problem which was used to develop models of human metabolism that incorporate physiology and organ-specific metabolism, known as whole-body metabolic models (WBMs). WBMs can incorporate physiological data, such as sex, weight, and body fat percentage, as well as nutrition in the form of its metabolite constituents. Finally, the gut microbiome can also be incorporated through a mathematical representation of the species present, based on stool metagenomics. WBMs have already been applied to understand gut microbiome-host co-metabolism in various non-communicable diseases. However, challenges remain, as metabolites measured in food items in public databases typically cover only common metabolites, and engagement with end-users such as nutritionists and policymakers is limited. Nevertheless, WBMs represent a promising step towards digital metabolic twins and thus personalised nutrition and medicine.},
}

@article {pmid42165805,
year = {2026},
author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM},
title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001731},
pmid = {42165805},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/physiology ; *Colon/microbiology/virology ; Escherichia coli/virology/genetics ; Bacteria/genetics/virology/classification ; Phage Therapy ; Feces/microbiology ; },
abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteriophages/genetics/physiology
*Colon/microbiology/virology
Escherichia coli/virology/genetics
Bacteria/genetics/virology/classification
Phage Therapy
Feces/microbiology

@article {pmid42165964,
year = {2026},
author = {Chen, S and Hua, Y and Chen, D and Jiang, X},
title = {Laboratory diagnosis of brucellosis: evolving synergy between serological testing and next-generation sequencing.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42165964},
issn = {1435-4373},
abstract = {BACKGROUND: Brucellosis is an animal‑to‑human infection that is hard to identify in practice; its signs are vague and the laboratory tools used in routine care have clear limits. Bacterial culture is regarded as the reference test; the procedure is slow and has modest sensitivity, and in many hospitals clinicians rely mainly on serologic assays when they make a diagnosis. Over the past decade clinical microbiology laboratories have increasingly used next‑generation sequencing (NGS) as a tool for pathogen identification, especially metagenomic NGS (mNGS). In patients with suspected bru-cellosis clinicians and laboratory staff often see a mismatch between test results, with serological assays suggesting infection but NGS reports failing to detect Brucella, a gap between serology and sequencing that remains a frequent and unresolved problem in routine diagnosis.

OBJECTIVE: This review brings together available data on how serological tests and sequencing-based methods in both metagenomic and targeted formats contribute to the laboratory diagnosis of human brucellosis and where they fall short.

CONCLUSION: It describes biological and technical sources of false-positive serology and false-negative sequencing and sets out a practical integrated way to judge and confirm mismatched findings so that laboratories and clinicians can use conventional and molecular tools together and reach sound decisions when brucellosis is suspected.},
}

@article {pmid42166146,
year = {2026},
author = {Besteman, MS and Alaux, E and Doloman, A and Tahon, G and Ettema, TJG and Sousa, DZ},
title = {Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular AD sludges.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag052},
pmid = {42166146},
issn = {1574-6941},
abstract = {Syntrophic microbial interactions are fundamental to the degradation of organic matter (e.g. fatty acids), playing a central role in natural anoxic ecosystems and engineered systems such as anaerobic digestion (AD). Despite their ecological and biotechnological importance, only a limited number of (obligate) syntrophic fatty-acid oxidizers have been successfully isolated. In this study, microbial communities from suspended and granular sludge samples were characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Network analysis of the 16S rRNA gene amplicon data revealed strong positive associations between methanogens and known syntrophic fatty-acid oxidizers, particularly in granular sludge samples. 743 High-Completion Metagenome Assembled Genomes (HC-MAGs) were recovered. This comprehensive HC-MAGs dataset provides a valuable resource for identifying novel microorganisms with genomic potential for syntrophic oxidation of butyrate, propionate and acetate. This analysis identified multiple interesting novel targets, including Syntrophomonadia families DTU052 and CALXsZ01 as potential butyrate oxidizers; Syntrophia families UBA6807, PHBD01, FEN-1087, and FEN-1099 as potential propionate oxidizers; and, Thermacetogeniaceae genus DTU068 together with Chloroflexota family 4572-78 as potential acetate oxidizers. These findings highlight granular sludges as a reservoir for previously uncharacterized syntrophic microorganisms. The recovered HC-MAG dataset also provides a framework to further elucidating fatty-acid oxidizing bacterial lineages within complex anaerobic communities.},
}

@article {pmid42166340,
year = {2026},
author = {Sato, M and Kanaly, RA and Mori, JF},
title = {Genomic and transcriptomic insights into Achromobacter-Sphingobium co-colonization within polycyclic aromatic hydrocarbon-exposed bacterial communities.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
doi = {10.1099/mic.0.001712},
pmid = {42166340},
issn = {1465-2080},
mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Sphingomonadaceae/genetics/metabolism/growth & development ; Biodegradation, Environmental ; Genome, Bacterial ; *Transcriptome ; *Achromobacter/genetics/metabolism/growth & development ; Soil Microbiology ; *Achromobacter denitrificans/genetics/metabolism ; Phylogeny ; Genomics ; Soil Pollutants/metabolism ; Gene Expression Profiling ; Microbial Consortia ; },
abstract = {Efficient and complete biodegradation of polycyclic aromatic hydrocarbons (PAHs), which are persistent and genotoxic petroleum hydrocarbon pollutants, is often considered to require the cooperative activities of multiple bacterial groups, and bacterial (meta)genomic investigations of PAH-exposed ecosystems have contributed to elucidating such interactions. In this study, two bacterial isolates representing dominant genera within a PAH-grown soil bacterial consortium, Achromobacter xylosoxidans strain KK8 and Sphingobium barthaii strain KK22, were utilized as model organisms to investigate the relationship between these bacterial genera during PAH biodegradation. Strain KK8 has previously been characterized as incapable of biodegrading PAHs; thus, Achromobacter in the consortium appears to grow under metabolic dependence on PAH biodegradation products (i.e. salicylic acid) provided by the pioneer PAH-degrading Sphingobium. This metabolic relationship was evidenced through complete genome sequencing and functional gene analysis of strain KK8 conducted in the present study. To further elucidate potential interactions between Achromobacter and Sphingobium, cell-free filtrate-exchange experiments were performed using these isolates, revealing that strain KK8 exhibited a significantly shortened growth lag phase in the presence of the filtrate of strain KK22. Subsequent transcriptomic profiling of strain KK8 indicated that exposure to the Sphingobium filtrate up-regulated functional genes likely associated with Achromobacter colonization, including genes involved in biofilm formation (pga genes) or cell division (fts genes). Enhanced biofilm formation of strain KK8 in response to strain KK22 filtrate was additionally evidenced by biofilm assays. Taken together, these results suggest that the high abundance of Achromobacter within the consortium may be stimulated by Sphingobium when they are present together, potentially via extracellular signalling molecule(s). As the co-occurrence of Achromobacter and Sphingobium has been repeatedly documented in PAH-degrading bacterial communities, elucidating the mechanisms underlying their specific interspecies co-colonization during PAH biodegradation shall be valuable for the future biotechnological applications utilizing these bacteria.},
}

*Polycyclic Aromatic Hydrocarbons/metabolism
*Sphingomonadaceae/genetics/metabolism/growth & development
Biodegradation, Environmental
Genome, Bacterial
*Transcriptome
*Achromobacter/genetics/metabolism/growth & development
Soil Microbiology
*Achromobacter denitrificans/genetics/metabolism
Phylogeny
Genomics
Soil Pollutants/metabolism
Gene Expression Profiling
Microbial Consortia

@article {pmid42166940,
year = {2026},
author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM},
title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.},
journal = {Pathology, research and practice},
volume = {285},
number = {},
pages = {156543},
doi = {10.1016/j.prp.2026.156543},
pmid = {42166940},
issn = {1618-0631},
abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.},
}

@article {pmid42166998,
year = {2026},
author = {Wu, Q and Zheng, Y and Xia, Y and Ge, C and Deng, H and Zhao, Y and Luo, J and Feng, D},
title = {Decoding the seagrass plastisphere: Metagenomic insights into biogeochemical cycling of biogenic elements and ecological consequences.},
journal = {Environment international},
volume = {212},
number = {},
pages = {110311},
doi = {10.1016/j.envint.2026.110311},
pmid = {42166998},
issn = {1873-6750},
abstract = {Seagrass meadow, a crucial blue carbon ecosystem, is increasingly threatened by plastic pollution. Plastic debris in this sensitive ecosystem creates a new microbial habitat known as "plastisphere". However, the functional role of plastisphere, particularly in driving the cycling of key biogenic elements, remains poorly understood. This knowledge gap raises concerns over potential disruptions to elemental fluxes and subsequent ecological consequences. Here, metagenomic analysis was employed to investigate the metabolic profile of in-situ plastisphere in seagrass meadow, with particular focus on carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) biotransformation. The obtained results revealed that plastisphere microbes were taxonomically distinct from those in natural environments of the seagrass meadow, and these inhabitants were capable of driving diverse metabolic pathways. However, >75% functional gene similarity indicated a significant functional overlap between the plastisphere and natural environments. This niche enriched genes related to heterotrophic organic C degradation (27.71% ± 3.28%) and oxidation (17.86% ± 2.04%) pathways, organic N metabolism (62.18% ± 8.57%) mainly through GS-GOGAT pathways and denitrification (8.70% ± 4.06%), polyphosphate degradation (22.89% ± 2.20%) and organic P mineralization (17.50% ± 1.70%), as well as assimilatory/dissimilatory sulfate reduction (30.60% ± 3.49%) and thiosulfate disproportionation (13.57% ± 2.89%) metabolic pathways. Metabolic linkage within seagrass plastisphere was facilitated by highly connected taxa including Silicimonas and Erythrobacter, which linked electron-donating processes (including organic C degradation and S oxidation) to electron-accepting pathways (e.g., sulfate/nitrate reduction, C fixation). These interactions established the plastisphere as a potential biogeochemical hotspot, potentially amplifying the risks of CO2/N2O emission, H2S accumulation, nutrient competition with seagrass and potential eutrophication from imbalanced P mobilization, ultimately threatening the health and stability of seagrass ecosystem.},
}

@article {pmid42167281,
year = {2026},
author = {Bambakidis, T and Liu, S and Wettengel, AM and Holmes, RM and Dinga, BJ and Koning, AA and McIntyre, PB and Borton, MA and Mann, PJ and Crump, BC},
title = {Congo River Bacterioplankton Genomic Diversity Reflects Water Travel Time, Wetland Habitats, and Greenhouse Gases.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70327},
doi = {10.1111/1462-2920.70327},
pmid = {42167281},
issn = {1462-2920},
support = {DEB-1840243//National Science Foundation/ ; OCE-0851101//National Science Foundation/ ; OCE-0851015//National Science Foundation/ ; DGE-0718123//National Science Foundation/ ; DEB-1501836//National Science Foundation/ ; 52379057//China Natural Science Foundation/ ; //David and Lucile Packard Foundation/ ; //U.S. Geological Survey/ ; 10.46936/10.25585/60001289//Joint Genome Institute/ ; },
mesh = {*Wetlands ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Greenhouse Gases/analysis/metabolism ; Congo ; RNA, Ribosomal, 16S/genetics ; *Plankton/genetics/classification ; Ecosystem ; Methane/metabolism ; Phylogeny ; Carbon Cycle ; Biodiversity ; Metagenome ; },
abstract = {Tropical rivers are major contributors to global carbon cycling, yet the microbial communities driving these transformations remain largely uncharacterized. We investigated bacterioplankton communities along the northwest Congo watershed using 16S rRNA and metagenomic sequencing, paired with hydrological, biogeochemical, and greenhouse gas data. In large rivers, community composition correlated with temperature and water travel time, while smaller streams were shaped by nutrient chemistry and landscape. Most sites were dominated by Burkholderiales, but composition varied, especially in DOC-rich Cuvette Centrale wetland streams that hosted distinct communities associated with high methane and CO2, and low oxygen. Indicator species analysis identified specific taxa and metagenome-assembled genomes (MAGs) strongly associated with long travel times, wetlands, and methane, including methanotrophs (Methylcoccaceae, Methylophilaceae, Methylomonas) and MAGs encoding diverse carbon-processing metabolisms. For global context, Congo and northern Thailand river bacterioplankton were more similar to each other than to temperate Connecticut River communities, possibly reflecting shared tropical features such as high precipitation, temperature, and travel time. As in temperate systems, bacterioplankton in large tropical rivers are shaped by temperature and hydrology, while smaller tropical streams reflect localized environmental drivers. The striking similarity of tropical river bacterioplankton from Africa and Asia suggests the primacy of environmental controls on river bacterioplankton.},
}

*Wetlands
*Rivers/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
*Greenhouse Gases/analysis/metabolism
Congo
RNA, Ribosomal, 16S/genetics
*Plankton/genetics/classification
Ecosystem
Methane/metabolism
Phylogeny
Carbon Cycle
Biodiversity
Metagenome

@article {pmid41975257,
year = {2026},
author = {Tang, Z and Zhuang, D and Duan, X and Gong, Q and Tian, C and Jiang, P and Yu, J and Li, F and Zhao, F and Shi, G and Yang, H and Du, Q and Li, T and Ye, Z and Zhang, Z},
title = {MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {41975257},
issn = {1471-2105},
abstract = {BACKGROUND: Network analysis is a fundamental tool for elucidating microbial interactions, which are crucial for understanding the mechanisms that shape ecosystem structure and function. However, aggregated co-abundance/co-occurrence network approaches that infer pairwise relationships among biological entities from large sample collections often overlook sample-specific interaction patterns. To address this limitation, we developed MicroSSNet, an R package designed for analyzing microbial networks, including both aggregated and single-sample networks.

RESULTS: We designed MicroSSNet primarily to fill the current gap in bioinformatics tools for constructing single-sample networks (SSNs) from microbiome data, and we evaluated both the performance and limitations of ssPCC-based SSNs using simulated and real datasets. Through Monte Carlo simulations, we assessed the statistical behavior of ssPCC and highlighted scenarios in which ssPCC is less powerful. We then applied MicroSSNet to two distinct datasets: a human gut metagenomic dataset and a soil 16S rRNA gene dataset. In the human gut dataset, SSNs revealed unique edges not detected in the aggregated network. In the soil dataset, SSN features showed some predictive value for group classification. However, SSN-derived patterns should be interpreted cautiously, as they may not exclusively reflect true interaction changes. MicroSSNet additionally implements a full aggregated-network workflow, including bipartite networks and extensive topological property analysis.

CONCLUSIONS: Together, MicroSSNet offers a framework for constructing and analyzing both single-sample and aggregated microbial networks. In this work, we also highlight the potential and limitations of single-sample network approaches, supporting their application as exploratory tools in microbiome research across individual and population levels. The package is freely available on GitHub (https://github.com/TangZecheng622/MicroSSNet).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-026-06444-w.},
}

@article {pmid42156652,
year = {2026},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Computational Microbial and Viral Ecology Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {83-141},
pmid = {42156652},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; },
abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.},
}

*Metagenomics/methods
*Computational Biology/methods
Metagenome
*Microbiota/genetics
*Viruses/genetics/classification
Virome
Bacteriophages/genetics
Bacteria/genetics
Archaea/genetics

@article {pmid42156658,
year = {2026},
author = {Roma Pi, J and Heinken, A},
title = {Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {233-260},
pmid = {42156658},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; Precision Medicine/methods ; Software ; *Microbiota/genetics ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Systems Biology/methods ; },
abstract = {High-throughput metagenomic sequencing techniques such as 16S rRNA and shotgun sequencing have enabled an unprecedented understanding of the structure and function of microbiome communities such as the human gut microbiome. Tailored dietary or therapeutic interventions targeting the microbiome could advance personalized medicine; however, predicting such interventions requires predictive systems biology methods. Constraint-Based Reconstruction and Analysis (COBRA) is a mechanistic systems biology approach that relies on detailed genome-scale reconstructions of a target organism's metabolism. A resource of genome-scale reconstructions of human microbes, AGORA, and its expansion in size and scope, AGORA2, have been developed through a semi-automated refinement pipeline, DEMETER. A user-friendly analysis pipeline, mgPipe, allows building and interrogating personalized models of microbiome communities from AGORA and AGORA2. Through sample-specific simulations, mgPipe can stratify patients and controls by the distinct metabolic capabilities of their microbiomes, starting from the processed metagenomic sequencing data. Building on this functionality, the protocol provides a comprehensive workflow for the contextualization of metagenomics data through personalized, mechanistic modeling. Comprehensive tutorials for the DEMETER and mgPipe workflows are presented, which will enable both systems biologists and microbiome scientists to contextualize metagenomic data and perform mechanistic simulations of diet-microbiome-host interactions.},
}

*Metagenomics/methods
Humans
*Gastrointestinal Microbiome/genetics
Precision Medicine/methods
Software
*Microbiota/genetics
*Metagenome
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods
RNA, Ribosomal, 16S/genetics
Systems Biology/methods

@article {pmid42156769,
year = {2026},
author = {Chen, R and Luo, S and Feng, Y and Maestre, FT and Sáez-Sandino, T and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and García-Gómez, M and Valencia, E and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Abades, S and Alfaro, F and Barrett, M and Berdugo, M and Pastor, JLB and Blaum, N and Boldgiv, B and Bowker, M and Castro, H and Chu, H and Cutler, NA and Dai, Z and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fan, K and Foronda, A and Fraser, LH and Geissler, K and Grebenc, T and Moltanvan, EG and Hart, SC and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Munson, SM and Muñoz-Rojas, M and Nair, GR and Neuhauser, S and Nunes, A and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and Ríos, AL and Rodríguez, A and Lozano, BR and Roman, R and Ruppert, JC and Salah, A and Singh, J and Throop, HL and Travers, S and Nahberger, TU and Uuganbayar, M and Valkó, O and Wang, L and Williams, MA and Xiong, C and Xu, J and Zaady, E and Ma, B and Singh, BK and Delgado-Baquerizo, M},
title = {Functional restructuring of the global soil microbiome under multiple stressors.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73231-9},
pmid = {42156769},
issn = {2041-1723},
support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbes, as the planet's most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.},
}

@article {pmid42156772,
year = {2026},
author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and , and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E},
title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73193-y},
pmid = {42156772},
issn = {2041-1723},
support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.},
}

@article {pmid42157110,
year = {2026},
author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F},
title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08962-4},
pmid = {42157110},
issn = {1471-2229},
support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; },
abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.

RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.

CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype × microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.},
}

@article {pmid42157119,
year = {2026},
author = {Li, QX and Luo, LZ},
title = {Cutaneous MAC infection in an immunocompetent patient: a case report confirmed by mNGS.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13549-3},
pmid = {42157119},
issn = {1471-2334},
abstract = {BACKGROUND: Cutaneous infections caused by non-tuberculous mycobacteria (NTM) are rare. Atypical clinical manifestations and the need for precise microbiological identification often result in misdiagnosis and underdiagnosis.

CASE PRESENTATION: A 65-year-old immunocompetent female initially presented with papular urticaria. Her symptoms improved transiently after anti-inflammatory treatment, but the lesions rapidly progressed to generalized erythematous nodules and ulcers accompanied by fever and lymphadenopathy. Routine microbiological culture and histopathological examination yielded negative results, while metagenomic next-generation sequencing (mNGS) identified Mycobacterium avium complex (MAC) as the causative pathogen.Triple antimicrobial therapy (clarithromycin, doxycycline, and levofloxacin) a favorable clinical response. This case indicates that cutaneous non-tuberculous mycobacterial (NTM) infection has atypical clinical manifestations and is frequently misdiagnosed as common cutaneous eruptions. mNGS can serve as a key diagnostic tool for suspected cutaneous NTM infection, effectively reducing misdiagnosis and missed diagnosis and providing a reliable basis for clinical diagnosis and treatment.

CONCLUSION: Cutaneous MAC infection, though rare, may occur in immunocompetent individuals. Clinicians should suspect NTM infection in treatment-refractory skin lesions. mNGS is valuable for etiological diagnosis when conventional tests are negative.},
}

@article {pmid42157131,
year = {2026},
author = {Ji, T and Cheng, R and Lu, M},
title = {mNGS and IL-5: potential early diagnostic clues for clonorchiasis before eosinophil rise - a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13612-z},
pmid = {42157131},
issn = {1471-2334},
support = {2022YFC2303203-01//National Key R&D Program of China/ ; Z-2017-24-2202//Specialized Research Fund for Pathogenic Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; },
abstract = {Clonorchiasis, caused by Clonorchis sinensis, often evades early diagnosis in non-endemic regions due to its nonspecific presentation and the delayed appearance of eosinophilia. We report an informative case of a 56-year-old male with acute fever, abdominal pain, and hepatitis, where conventional diagnostics and initial antimicrobial therapy failed. In this case, metagenomic next-generation sequencing (mNGS) of blood identified C. sinensis-specific reads, and cytokine profiling revealed a marked elevation in interleukin-5 (IL-5) before the onset of peripheral eosinophilia. Targeted treatment with praziquantel led to rapid clinical resolution. This case suggests the potential of integrating mNGS and IL-5 monitoring as early diagnostic tools for clonorchiasis, which can allow for intervention prior to classical biomarker emergence.},
}

@article {pmid42157143,
year = {2026},
author = {Sheng, G and Zhao, C and Jiang, L and Zhang, X and Gao, F},
title = {Talaromyces marneffei infection of central nervous system in an immunocompetent child in a nonendemic area: a case report and literature review.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-026-06996-z},
pmid = {42157143},
issn = {1471-2431},
abstract = {BACKGROUND TALAROMYCES MARNEFFEI: (T. marneffei, formerly Penicillium marneffei) is a rare fatal fungus endemic in Southeast Asia and southern China. T. marneffei infections mainly occur in HIV-infected adults, and commonly involves the skin, lung, and reticuloendothelial system. T. marneffei infections of isolated central nervous system (CNS) in immunocompetent pediatric patients in nonendemic areas have rarely been reported. CASE PRESENTATION: We report a rare case of T. marneffei-induced disseminated encephalomyelitis in an immunocompetent girl from a nonendemic area of Eastern China. The main clinical manifestations were abdominal pain with distension and abnormal gait. Contrast-enhanced magnetic resonance imaging (MRI) revealed both brain and spinal cord lesions. The infection status of T. marneffei was quickly determined via the metagenomic next-generation sequencing (mNGS) of spinal cord biopsy tissue. T. marneffei induced disseminated encephalomyelitis was diagnosed. Following successful antifungal treatment with amphotericin B liposomes and voriconazole, the child recovered gradually. To date, only 3 cases of T. marneffei infection of the central nervous system in non-HIV-infected pediatric patients have been reported in the literature. Among them, one child had inborn errors of immunity, and the other two children were from endemic areas. Moreover, the clinical manifestations of those 3 reported cases were disseminated with common infection sites in the lungs. our patient represents a unique case of an immunocompetent child from a nonendemic area with isolated CNS infection. CONCLUSIONS: We report this rare case and aim to promote pediatric clinicians' recognition of T. marneffei isolated CNS infection in immunocompetent pediatric patients from nonendemic regions. Furthermore, the early use of mNGS is recommended when non-HIV-infected pediatric patients present with unexplained clinical manifestations and poor response to conventional treatments. Timely diagnosis and appropriate antifungal therapy can improve patient prognosis.},
}

@article {pmid42157342,
year = {2026},
author = {Jing, Y and Liu, S and Leng, L and He, J and Wang, T and Guan, Y and Su, Z and Zhang, W and Li, Y and Luan, P and Cheng, B and Wang, N and Li, H},
title = {Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42157342},
issn = {1674-9782},
support = {No. 2022YFF1000201//National Key Research and Development Program of China/ ; No. NK20221001//National Major Agricultural Science and Technology Project/ ; No. 32272863//National Natural Science Foundation of China/ ; No. CARS-41//The earmarked fund for CARS-41/ ; },
abstract = {BACKGROUND: Emerging evidence highlights strong correlations between the cecal microbiome and abdominal fat deposition (AFD) in chickens. However, the specific microbial species driving this process remain unclear. This study aims to identify the key microbe and elucidate its underlying mechanism in regulating chicken AFD.

RESULTS: First, cecal microbiota transplantation confirmed a causal relationship between the cecal microbiota and AFD. Subsequently, metagenomic and metatranscriptomic integrations identified Alistipes communis as a key microbe implicated in AFD. Finally, in vivo gavage integrated with multi-omics revealed that A. communis enhances AFD by disrupting host tryptophan and histidine metabolism. This was evidenced by the elevated concentrations of amino acid metabolism-related metabolites, including L-phosphoarginine and spermine in the cecum.

CONCLUSIONS: This study provides direct evidence that the cecal microbiome serves as a key driver in chicken AFD and identifies A. communis as a critical AFD regulator, offering valuable insights into the gut microbiome's role in host obesity.},
}

@article {pmid42157352,
year = {2026},
author = {Pérez-Pérez, L and Galisteo, C and Castillo-Peinado, LLS and Tomé-Rodríguez, S and Priego-Capote, F and Carvajal, A and Arguello, H},
title = {Metabolomic signatures of colonic infection by Brachyspira hyodysenteriae.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {},
pmid = {42157352},
issn = {1297-9716},
support = {PRE2020-093762//Spanish Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; },
mesh = {Animals ; Swine ; *Brachyspira hyodysenteriae/physiology ; *Swine Diseases/microbiology/metabolism ; *Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism ; *Metabolome ; Colon/metabolism/microbiology ; Gastrointestinal Microbiome ; *Dysentery/veterinary/microbiology/metabolism ; Feces/microbiology ; Metabolomics ; },
abstract = {Despite swine dysentery's relevance in the pork industry, there are still gaps in our understanding of its pathogenesis and the impact of the infection in the gut. This study aimed to characterize the in vivo colonic metabolome of pigs experimentally infected with Brachyspira hyodysenteriae at the onset of fecal shedding (Early_inf group, n = 6) and during acute clinical disease characterized by mucohemorrhagic diarrhea (Acute_inf group, n = 8) compared with non-infected controls (n = 16). The metabolic profile of the colonic contents changed progressively with disease severity, showing an intermediate pattern in the Early_inf group between the control and the Acute_inf groups (p < 0.05). In acute disease, the metabolome was defined by increased concentrations of amino acids, carnitine derivatives, arachidic acid, 1,2-butanediol, and lactic acid, along with decreased levels of anti-inflammatory compounds. In the Early_inf group, increases were observed in amino acids, organic acids, amines, myo-inositol, quinoline, and 1,2-butanediol, whereas linolenic acid and oxalic acid decreased. Integrated analysis of the colonic metabolome and metagenome revealed a strong correlation between metabolic and microbial profiles, particularly in the Acute_inf group, where differential metabolites were associated with B. hyodysenteriae, Campylobacter hyointestinalis, and Velocimicrobium ethanolgignens. Metabolites showed high predictive potential for the disease stage, with lactic acid and arachidic acid being key markers of acute infection and dihydroxyacetone and leucine distinguishing early infection. Overall, this study reveals significant alterations in the colonic metabolome and its association with the microbiota during swine dysentery, providing new insights into the pathophysiology of the disease and contributing to the development of improved prevention and treatment strategies.},
}

Animals
Swine
*Brachyspira hyodysenteriae/physiology
*Swine Diseases/microbiology/metabolism
*Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism
*Metabolome
Colon/metabolism/microbiology
Gastrointestinal Microbiome
*Dysentery/veterinary/microbiology/metabolism
Feces/microbiology
Metabolomics

@article {pmid42157462,
year = {2026},
author = {Singh, HW and Gutleben, J and Bogdanov, A and Chase, AB and Demko, A and Podell, S and Haley, B and Jensen, PR},
title = {Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70320},
doi = {10.1111/1462-2920.70320},
pmid = {42157462},
issn = {1462-2920},
support = {R01GM085770/NH/NIH HHS/United States ; },
mesh = {*Geologic Sediments/microbiology ; *Polyketides/metabolism ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics/metabolism ; Metagenome ; Seawater/microbiology ; Biodiversity ; Multiomics ; },
abstract = {Microbially-derived polyketides include some of today's most valuable medicines, yet their discovery has focused on a narrow subset of Earth's microbial biodiversity. Although understudied biomes such as marine sediments have been targeted, these efforts have focused on samples collected from shallow waters. In contrast, abyssal marine sediments (4000-6000 m), which comprise > 80% of the ocean floor, remain poorly explored. This leaves foundational gaps in our understanding of deep-sea microbial diversity and its relationship to biosynthetic potential. Here, we used culture-independent approaches to characterise microbial taxonomic and biosynthetic diversity in abyssal sediments collected from three geochemically distinct plains along an 880 km transect. Sediment communities varied in both taxonomic (16S rRNA gene) and biosynthetic (ketosynthase domain) composition across sites and relative to nearshore sediments, suggesting they harbour unique opportunities for natural product discovery. Ketosynthase phylogenies revealed abyssal clades that diverged from experimentally characterised polyketide synthase pathways, further supporting biosynthetic novelty. Metagenome-assembled genomes linked unique ketosynthase domains to the poorly studied phylum Gemmatimonadota. Sediment metabolomes provided evidence of chemical novelty, with < 10% of the features detected matching previously reported spectra. These baseline findings indicate that abyssal sediments represent reservoirs of unexplored polyketide biosynthetic diversity.},
}

*Geologic Sediments/microbiology
*Polyketides/metabolism
Phylogeny
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota
RNA, Ribosomal, 16S/genetics
Polyketide Synthases/genetics/metabolism
Metagenome
Seawater/microbiology
Biodiversity
Multiomics

@article {pmid42158361,
year = {2026},
author = {Louise Jespersen, M and Kjærgaard Munk, K and Fjermedal, S and Pilgaard, B and Meyer, AS and Aarestrup, FM and Otani, S},
title = {A Hadza-enriched Prevotella/Segatella xyloglucanase shows sequence conservation and functional specialization.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2673265},
pmid = {42158361},
issn = {2993-3935},
abstract = {Bacteria can adapt to their environment through changes in their genetic material. A large proportion of gut bacteria are shaped by host-specific diet, including complex carbohydrates. The bacterial abundance, genetic content within the same bacterial species, and sequence-level variation in genes encoding similar carbohydrate-processing enzymes may therefore vary across hosts with different diets. We previously found that the abundance of diet-degrading genes varies between hominid host populations from Tanzania. We therefore hypothesized that, in addition to these abundance differences, selective pressure could act on individual gene sequences. Here, we investigated Tanzanian hominid gut microbiome differences at the taxonomic, genetic, structural, and functional levels. We analyzed 15,146 metagenome-assembled genomes (MAGs) spanning 1563 species and identified one species with striking host-associated separation. In particular, sequence variation in a xyloglucanase-encoding gene correlated strongly with the host population. This gene was highly conserved in the Hadza population, suggesting a role in the processing of diet-associated polysaccharides. Sequence differences and structural modeling revealed amino acid substitutions near the catalytic site, and biochemical assays using xyloglucan showed that representative variants differed in activity under identical assay conditions. Collectively, our findings suggest that host lifestyle and diet contribute to population-associated sequence variation in genes encoding enzymes involved in degrading polysaccharides.},
}

@article {pmid42158572,
year = {2026},
author = {Wong, E and England, J and Jagadeesan, V},
title = {Scedosporium apiospermum Infective Endocarditis With Brain Abscesses in a Lung Transplant Recipient: Review of the Literature and Evaluating the Use of Next-Generation Sequencing.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {8041837},
pmid = {42158572},
issn = {2090-6625},
abstract = {Scedosporium apiospermum is an emerging cause of invasive mold infection in immunocompromised hosts, often with central nervous system involvement and limited susceptibility to amphotericin B. We describe a 36-year-old lung transplant recipient who presented with fever, meningismus, and multiple enhancing brain lesions nine months post-transplant. Cerebrospinal fluid studies, including metagenomic next-generation sequencing (mNGS), were negative. Cardiac imaging revealed a pedunculated right ventricular septal mass, and plasma cell-free DNA (cfDNA) testing (Karius) identified S. apiospermum. Subsequent brain biopsy and thrombectomy confirmed the diagnosis by histopathology and culture. Following surgical removal of the cardiac mass and treatment with voriconazole, the patient improved with near resolution of brain lesions. This case highlights disseminated S. apiospermum endocarditis diagnosed by plasma cfDNA despite negative CSF mNGS, underscoring that site-specific mNGS may be falsely negative in compartmentalized infections. Plasma cfDNA testing can complement conventional and tissue-based diagnostics for early detection of disseminated mold infections in transplant recipients.},
}

@article {pmid42158968,
year = {2026},
author = {Shi, Z and Huang, F and Luo, C and Yang, L and Chen, Y and Qiao, C and Wang, R and Wang, Y and Yan, Y and Wang, L and Fan, L and Shen, W},
title = {Gut Microbiota Alterations in Myelodysplastic Neoplasms Are Associated With Immune Dysfunction and the Therapeutic Mechanism of Hypomethylating Agents.},
journal = {Cancer medicine},
volume = {15},
number = {5},
pages = {e71946},
doi = {10.1002/cam4.71946},
pmid = {42158968},
issn = {2045-7634},
support = {82200151//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Myelodysplastic Syndromes/drug therapy/immunology/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Dysbiosis/immunology ; Case-Control Studies ; DNA Methylation/drug effects ; Feces/microbiology ; Aged, 80 and over ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Adult ; },
abstract = {BACKGROUND: Myelodysplastic neoplasms (MDS) represent a group of heterogeneous clonal disorders characterized by immune dysregulation in their pathogenesis. Gut microbiota dysbiosis plays a critical role in immune modulation.

METHODS: We collected the fecal samples of 23 newly diagnosed MDS, 10 hypomethylating agents (HMA) treated MDS and 13 age and sex matched healthy controls (HC), and analyzed the gut microbiota compositions and functional pathways using metagenomic next-generation sequencing (mNGS).

RESULTS: Distinct microbial compositions were observed between newly diagnosed MDS and HC. Notably, the Veillonellaceae family was significantly enriched in MDS patients. Specific bacteroid species demonstrated significant correlations with lymphocyte subtypes, functional activation status, and serum inflammatory cytokines. Functional profiling revealed altered metabolic pathways in newly diagnosed patients, particularly in amino acid metabolism and ATP synthesis. Notably, glutamine/glutamate and tryptophan metabolism pathways were hyperactive in untreated MDS but downregulated following HMA treatment.

CONCLUSIONS: The gut microbiota altered in MDS patients and was associated with immune dysregulation and inflammation, which may contribute to MDS pathogenesis and mediate therapeutic effects of HMA treatment, highlighting the gut microbiota-metabolism axis as a potential therapeutic target for MDS management.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Myelodysplastic Syndromes/drug therapy/immunology/microbiology
Male
Female
Aged
Middle Aged
*Dysbiosis/immunology
Case-Control Studies
DNA Methylation/drug effects
Feces/microbiology
Aged, 80 and over
High-Throughput Nucleotide Sequencing
Metabolic Networks and Pathways
Adult