@article {pmid42229597,
year = {2026},
author = {Fard, MB and Kwon, S and Vrieze, J and Wu, D},
title = {Long-term inhibition under continuous perfluorooctanoic acid exposure during anaerobic digestion of waste microalgal-bacterial aerobic granular sludge: Metagenomic-metatranscriptomic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135056},
doi = {10.1016/j.biortech.2026.135056},
pmid = {42229597},
issn = {1873-2976},
abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but the effect of residual perfluorooctanoic acid (PFOA) on the anaerobic digestion of waste MB-AGS (WMB-AGS) remains poorly understood. This study evaluated PFOA effects (100, 500, and 1000 µg/L) on anaerobic digestion of WMB-AGS by comparing short-term single-exposure batch assays with long-term semi-continuous digestion. Under control conditions, methane production reached 76 ± 2 mL CH4/g volatile solids. Relative to the control, methane yield changed marginally in the presence of PFOA, indicating no measurable inhibition in a single-exposure biochemical methane potential (BMP) assay. In contrast, during continuous exposure in the semi-continuous digester, biogas output decreased after introducing 1000 µg/L PFOA (31 ± 1 to 19 ± 1 mL/day) and coincided with increased residual soluble chemical oxygen demand. During 3-day hydrolysis-acidogenesis tests, total volatile fatty acids increased from 82 ± 9 mg/L (control) to 122 ± 12 mg/L (1000 µg/L), suggesting greater accumulation of fermentation intermediates in the early digestion phase. The PFOA distribution showed substantial partitioning into extracellular polymeric substance fractions and sludge solids, with 28.3% remaining in supernatant, 23.2% in loosely bound extracellular polymeric substances, 16.0% in tightly bound extracellular polymeric substances, and 32.6% in sludge solids with no transformation products. Multi-omics analysis supported that dominant microbial communities remained broadly stable, whereas reduced transcription of glycolysis and pyruvate-to-acetyl-coenzyme A conversion genes was consistent with soluble organic accumulation and reduced biogas production. Overall, single-exposure BMP assays underestimated the long-term operational impact of continuous PFOA exposure during anaerobic digestion of WMB-AGS.},
}

@article {pmid42229598,
year = {2026},
author = {Dong, C and Pan, J and Li, Y and Liu, M and Li, Y and Zhao, Z and Zhang, Y},
title = {Direct interspecies electron transfer-based simplified microbial consortia for high-efficiency conversion of lignocellulose to methane: Construction, metabolic pathway and performance optimization.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135043},
doi = {10.1016/j.biortech.2026.135043},
pmid = {42229598},
issn = {1873-2976},
abstract = {Establishing direct interspecies electron transfer (DIET)-based methanogenic pathway is likely to address the technical bottlenecks involved in long periods and low rates of methanogenesis during anaerobic digestion of lignocellulose. However, the efficiency of DIET is limited by low abundance of electroactive bacteria and electron competition with conventional methanogenic pathway. Here, we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a 'top-down' selection. Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level) and increased methane production rates (ca. 32 vs 10-25 mL/gVS·d). Lowering pH dramatically increased conductivity of both DIETsimp, similar to that was found in electrically conductive pili of Geobacter sulfurreducens. Meanwhile, the intensities of characteristic peaks in electrochemical Fourier transform infrared spectra associated with c-type cytochrome in both DIETsimp dramatically increased. Metagenomic analysis showed that, Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively. The potential DIET-based methanogenic pathway during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane was proposed. At last, we optimized culture conditions (including inoculum ratio, C/N and period) to maximize the performances of both DIETsimp via combining the single-factor experiments with response surface methodology.},
}

@article {pmid42229914,
year = {2026},
author = {Li, H and Yang, L and Chen, B and Zhang, L and Zhu, J and Zhang, H and Lin, L},
title = {Pneumococcal Rib Osteomyelitis With Concurrent Lung and Chest Wall Abscess in an Infant.},
journal = {Pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1542/peds.2025-073077},
pmid = {42229914},
issn = {1098-4275},
abstract = {We present a rare case of a 7-month-old infant with a complex invasive Streptococcus pneumoniae infection involving rib osteomyelitis, a pulmonary abscess, and a chest wall abscess. The patient presented with persistent fever and no respiratory symptoms. On day 9, chest radiography was performed because of persistent fever and marked leukocytosis, consistent with the American College of Radiology Appropriateness Criteria that recommend imaging in febrile infants with high fever (≥39°C) or elevated white blood cell counts (≥20 000/mm3). On day 14, the emergence of a chest wall mass prompted escalation to ultrasonography, which provided noninvasive assessment of soft tissue involvement. Subsequent contrast-enhanced computed tomography scans were undertaken to delineate the extent of contiguous spread, evaluate rib destruction, and exclude alternative diagnoses. Microbiological cultures of sputum and aspirated pus, along with metagenomic sequencing, confirmed the presence of macrolide-resistant S. pneumoniae. Because of benzylpenicillin and cephalosporin allergy, intravenous linezolid was selected, resulting in rapid clinical improvement. A 6-week course (intravenous infusion followed by oral) led to complete resolution on imaging, with no recurrence over 5 years. This case underscores the importance of appropriate imaging modalities in febrile infants without respiratory symptoms and the need to consider extrapulmonary spread in chest wall masses. It highlights the diagnostic value of metagenomic sequencing and susceptibility testing in guiding individualized antimicrobial therapy, particularly in macrolide-resistant settings.},
}

@article {pmid42230119,
year = {2026},
author = {Alexander, JL and Mullish, BH and Thomas, L and Weersma, RK and Sokol, H and Roberts, LA and Edwards, LA and Emmanuel, A and Gerasimidis, K and Hall, LJ and Iqbal, TH and Kinross, JM and McIlroy, J and Monaghan, TM and Sergaki, C and Shawcross, DL and Stewart, CJ and Lamb, CA and Williams, HRT and Hansen, R and Hold, G},
title = {Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338252},
pmid = {42230119},
issn = {1468-3288},
abstract = {At around 10 years ago, at the time of the first publication by the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology, recognition of the gut microbiome's importance in health and disease was transitioning from fringe interest towards major global pursuit. A decade on, we appraise the considerable progress made in the field, while acknowledging ongoing challenges. Earlier human work characterising the 16S rRNA gene amplicon signature of particular conditions in small cohorts has been superseded by larger, multicentre studies with extensive metadata. Studies increasingly employ shotgun metagenomics and other 'omic' techniques-coupled with refined bioinformatic tools and disease models-to better characterise perturbation in gut microbiome functionality. The arrival of 'gold standard' pipelines for microbiome analysis and increased mechanistic validation of signals are key developments towards more clinically-translatable outcomes. Novel clinical areas where the gut microbiome has relevance have emerged, including early life and the efficacy of certain treatments (including immune checkpoint inhibitors and vaccination). Enthusiasm for 'microbiome diagnostics and treatments' has grown, but barriers to widespread adoption remain. Faecal microbiota transplant (FMT) is established for treating recurrent Clostridioides difficile infection, with donor-derived 'next generation' FMT products licensed for this condition in certain countries. Beyond FMT, other microbial therapeutic techniques-including nutritional, bacteriophage and probiotic therapies-show promise, but have not fulfilled their high expectations yet. Gut microbiome research is now well-established and shows significant translational potential; the future focus will be translational work to drive its utility in clinical diagnostics, prognostics and therapeutics.},
}

@article {pmid42230654,
year = {2026},
author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F},
title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01029-0},
pmid = {42230654},
issn = {2055-5008},
abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.},
}

@article {pmid42230804,
year = {2026},
author = {Linh, LTK and My, TN and Thi Tran, N and Song, LH and Nurjadi, D and Boutin, S and Velavan, TP},
title = {Metagenomic profiling reveals shared resistome signatures between humans and pigs in Vietnamese smallholder farms.},
journal = {npj antimicrobials and resistance},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44259-026-00223-6},
pmid = {42230804},
issn = {2731-8745},
support = {PACE-UP; DAAD Project ID: 57592343//Deutscher Akademischer Austauschdienst/ ; },
abstract = {Antimicrobial resistance (AMR) is a global health concern, yet the extent of resistant genes and microbial exchange between humans and livestock in low- and middle-income countries remains underexplored. Vietnam, an AMR hotspot, was studied using shotgun metagenomic sequencing of paired faecal samples from pigs and caretakers across 50 small-scale farms. Results revealed 10,270 antimicrobial resistance genes (ARGs) representing 550 unique types, including clinically relevant mcr, blaOXA-58, and optrA genes. Pigs showed higher total AMR abundance, while workers harboured richer resistomes. Approximately 52% (288/550) of ARGs were shared between hosts, dominated by aminoglycoside, β-lactam, and tetracycline resistance genes, often co-located with mobile genetic elements, indicating horizontal transfer potential. Closely related Escherichia coli strains were identified in both hosts, consistent with strain sharing or exposure to common sources beyond individual farms. These findings highlight the human-pig interface as an important setting for shared AMR signatures and support the need for integrated One Health surveillance and antimicrobial stewardship.},
}

@article {pmid42231385,
year = {2026},
author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N},
title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.},
journal = {Nutrition journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12937-026-01343-5},
pmid = {42231385},
issn = {1475-2891},
support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; },
abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.

METHODS: A total of 102 male Han participants was randomized to curcumin (812 mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.

RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P = 0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P < 0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P < 0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P < 0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.

CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.

TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.},
}

@article {pmid42231497,
year = {2026},
author = {Vayena, G and Giangeri, G and Gaspari, M and Ghofrani-Isfahani, P and Tsapekos, P and Kougias, PG and Angelidaki, I},
title = {Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02443-4},
pmid = {42231497},
issn = {2049-2618},
abstract = {BACKGROUND: Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.

RESULTS: Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.

CONCLUSIONS: This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.},
}

@article {pmid42231509,
year = {2026},
author = {Sarhan, MS and Samadelli, M and Zink, A and Maixner, F},
title = {The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42231509},
issn = {2049-2618},
support = {FESR1078-MummyLabs//European Regional Development Fund/ ; },
abstract = {BACKGROUND: The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.

RESULTS: By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.

CONCLUSIONS: Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.},
}

@article {pmid42231528,
year = {2026},
author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA},
title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2679516},
doi = {10.1080/19490976.2026.2679516},
pmid = {42231528},
issn = {1949-0984},
abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.},
}

@article {pmid42232316,
year = {2026},
author = {Webster, NS and Bell, SC and Luter, HM and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {211},
pmid = {42232316},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Rhopaloeides odorabile (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.42 kilobases. From the metagenome data, we recovered 162 bins, of which 96 were high-quality MAGs. R. odorabile displays a characteristic high microbial abundance sponge profile, with MAGs representing diverse phyla (i.e., Acidobacteriota, Pseudomonadota, and Chloroflexota) and candidate phyla (i.e., Ca. Latescibacteria, Ca. Poribacteria, and Ca. Tectomicrobia).},
}

@article {pmid42232360,
year = {2026},
author = {Li, Y and Yi, G and Han, Z and Fu, J and Xu, L},
title = {Comparison of mNGS microbial detection profiles between percutaneous lung aspiration biopsy and bronchoalveolar lavage fluid in infective pneumonia.},
journal = {Open medicine (Warsaw, Poland)},
volume = {21},
number = {1},
pages = {20261445},
pmid = {42232360},
issn = {2391-5463},
abstract = {OBJECTIVES: To compare the mNGS-based microbial detection profiles of percutaneous lung aspiration biopsy (PLAB) and bronchoalveolar lavage fluid (BALF) in patients with infective pneumonia under real-world clinical sampling strategies.

METHODS: The study included 166 patients with infective pneumonia, of whom 54 underwent PLAB to obtain unfixed fresh lung tissue from the lesion site, while 112 underwent fiberoptic bronchoscopy to obtain BALF.

RESULTS: In the BALF group, 3 pathogens of high concern and 5 suspected pathogens, totaling 8 types of pathogens, were detected. In contrast, in the PLAB group, 1 pathogen of high concern and 1 suspected pathogen, totaling 2 types of pathogens were detected. Cumulatively, 348 pathogens were identified in the BALF group. In the PLAB group, 96 pathogens were identified cumulatively, p<0.001. In the BALF group, the most frequently detected pathogen was Streptococcus pneumoniae, with 19 strains of Mycobacterium tuberculosis among the special pathogens. In the PLAB group, the most frequently detected pathogen was Epstein-Barr virus (EBV) (14.58 %).

CONCLUSIONS: BALF and PLAB showed different mNGS microbial detection patterns under different clinical sampling strategies. Because of the retrospective non-paired design, these findings should be interpreted as descriptive comparative data rather than proof of the superior diagnostic performance of either sampling method.},
}

@article {pmid42232489,
year = {2026},
author = {Huang, Y and Yang, M and Liu, J and Zhang, M and Penttinen, P and Zhang, L and Ge, L and Zhang, X and Zhao, N},
title = {Phage succession and putative mechanisms of microbial community regulation in Sichuan radish paocai (traditional Chinese fermented vegetable).},
journal = {Food chemistry: X},
volume = {36},
number = {},
pages = {103997},
pmid = {42232489},
issn = {2590-1575},
abstract = {Spontaneous fermentation of Sichuan paocai is shaped by complex microbial and environmental factors, yet phage communities remain understudied. This study presents integrated viromic and metagenomic analysis of radish paocai combined with metabolite profiling to elucidate phage diversity, dynamics, ecological roles, and sources. Time-series metagenomics revealed Lactiplantibacillus increasing from 11% to 71%, while viromics showed phages comprising 78% of viral contigs, with Uroviricota reaching 88% by day 5. Host prediction indicated that 89% of phages targeted Lactiplantibacillus, mainly L. plantarum. Correlation analysis suggested that core phages were associated with fermentation-related metabolites, including volatile compounds (e.g., decanal), implicating that phages might influence metabolism by modulating host activity. Functional annotation showed phage encoded amino acid and carbohydrate metabolism genes, suggesting auxiliary metabolic roles. Source analysis suggested that most phages in radish paocai may be derived from bacterial prophages. This work advances understanding of phage diversity and ecological function in fermented vegetable ecosystems.},
}

@article {pmid42232626,
year = {2026},
author = {Han, X and Zhang, L and Zhang, R and Liu, W},
title = {Case Report: Multiple organ dysfunction syndrome in a preterm infant secondary to respiratory syncytial virus and bacterial co-infection.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1825002},
pmid = {42232626},
issn = {2296-2360},
abstract = {This article reports a case of a 1-month 11-day-old preterm infant, born at 36 + 6 weeks gestation, who presented to an outside hospital emergency department with a persistent cough that had not improved over four days. During this period, the infant progressively developed respiratory distress and lethargy. The infant subsequently developed cardiopulmonary arrest, underwent cardiopulmonary resuscitation, and was transferred to our hospital under endotracheal intubation with positive pressure ventilation. Respiratory pathogen polymerase chain reaction testing of a throat swab was positive for respiratory syncytial virus (RSV), while sputum and bronchoalveolar lavage fluid culture and blood metagenomic next-generation sequencing (mNGS) detected Haemophilus influenzae and S. pneumoniae. After 22 days of hospitalization and treatment including invasive mechanical ventilation, antibiotic adjustment, intravenous immunoglobulin (IVIG), and dexamethasone, the infant was discharged without further complications. Metagenomic next-generation sequencing provides rapid diagnostic evidence for mixed infections, while integrated interventions, including IVIG, short-course corticosteroids, and nutritional support, effectively modulate immune responses.},
}

@article {pmid42232631,
year = {2026},
author = {Gao, L and Wen, Y and Jing, X},
title = {Case Report: Cervical lymphadenitis resulting from Pseudomonas aeruginosa diagnosed by metagenomic next-generation sequencing.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1795457},
pmid = {42232631},
issn = {2296-2360},
abstract = {Pediatric cervical lymphadenitis is usually caused by Staphylococcus aureus and Streptococcus pyogenes. Cases resulting from Gram-negative bacteria are rare. Herein, we report the case of an 11-year-old boy who developed cervical lymphadenitis. He was diagnosed with a Pseudomonas aeruginosa infection through metagenomics next-generation sequencing of blood and biopsy. After treatment with meropenem, the patient's condition improved and he was discharged. Lymphadenitis may be caused by Gram-negative opportunistic pathogens. Metagenomic next-generation sequencing can help identify the underlying cause.},
}

@article {pmid42232653,
year = {2026},
author = {Fan, F and Wang, B and Jia, R and Lyu, J and Han, F},
title = {Amelioration of tic disorder by Jujuboside A via gut microbiota remodeling and intestinal 5-HT signaling.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1760647},
pmid = {42232653},
issn = {1662-4548},
abstract = {BACKGROUND: Tic disorder (TD) is a common chronic neuropsychiatric condition manifesting during childhood and adolescence. Jujuboside A (JuA) may alleviate TD symptoms; however, the mechanisms underlying its therapeutic effects remain unclear.

METHODS: We established a rat model of TD and used histological techniques to evaluate the effects of JuA on pathological changes. We also measured 5-hydroxytryptamine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels and assessed tryptophan hydroxylase 1 (TPH1) mRNA expression. Finally, we analyzed the gut microbiota composition in fecal samples using 16S rRNA metagenomic sequencing.

RESULTS: JuA administration alleviated pathological changes in rats with TD, increased 5-HT and 5-HIAA levels, and upregulated TPH1 mRNA expression. Compared with no treatment, JuA treatment increased the proportion of Bacteroidia, Muribaculaceae, Bacteroidales, and Bacteroidota, while reducing that of Bacilli, Lactobacillaceae, Lactobacillus, Lactobacillales, and Firmicutes.

CONCLUSION: These findings indicate that JuA mitigates TD progression, potentially by remodeling the gut microbiota and regulating 5-HT levels.},
}

@article {pmid42232910,
year = {2026},
author = {Oskolkov, N},
title = {Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1603339},
pmid = {42232910},
issn = {1664-302X},
abstract = {Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.},
}

@article {pmid42232914,
year = {2026},
author = {Chamberlain, EJ and Boulton, W and Connors, E and Calianos, T and Bowman, JS and Creamean, JM and Mock, T and Kim, HH},
title = {From microbial diversity to functional potential using dimensionality reduction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786397},
pmid = {42232914},
issn = {1664-302X},
abstract = {The high dimensionality of microbial diversity data from 'omics observations can be reduced using Machine Learning, with many recent studies showcasing ML utility for exploratory ecological feature finding and process prediction. Here, we compare the Self Organizing Map (SOM) dimensionality reduction method to the well-documented sample-based Principal Coordinate Analysis (PCoA) and taxa-based Weighted Gene Correlation Network Analysis (WGCNA) using near daily 16S rRNA gene amplicon sequencing data from the 2019 to 2020 MOSAiC International Arctic Drift Expedition. We then map k-means clustering outputs from each method to available metagenomes, extracting functionally distinct seasonal microbial ecotypes in the surface Arctic Ocean. Our results indicate the SOM method better represented expected seasonal transitions and identified a greater number of metabolically distinct functional groups than the more traditional PCoA ordination. Ultimately, we identified four community ecotypes with distinct taxonomic and functional cut-offs driven by seasonality, water mass, and substrate turnover, highlighting the importance of succession in functional diversity for the central Arctic Ocean. These results reinforce ML dimensionality reduction as a meaningful translator in the mining of historical amplicon datasets to address modern mechanistic questions and potentially provide 'omics informed ecotype diversity to leverage in mechanistic biogeochemical models.},
}

@article {pmid42233252,
year = {2026},
author = {Hashmi, L and Rehman, SU and Jabeen, F and Kayani, MUR},
title = {GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
doi = {10.1093/database/baag029},
pmid = {42233252},
issn = {1758-0463},
support = {//Metagenomics Discovery Lab at the SINES/ ; //NUST/ ; },
abstract = {Gut dysbiosis is widely recognized as a contributor to autoimmune diseases, as it can lead to the expression of microbial antigens that disrupt immune regulation through specific molecular mechanisms. However, existing resources do not systematically link gut microbial antigen sequences to the specific autoimmune mechanisms through which they act. Here, we present GUTAID (Gut Microbes in Autoimmune Disorders), a literature-curated database of gut microbial antigens annotated with experimentally supported autoimmune mechanisms. Peer-reviewed studies published from October 1970 to September 2024 were manually screened, yielding 73 potential antigens that operate through nine molecular mechanisms, including protein citrullination, epitope spreading, molecular mimicry, and immune modulation, amongst others. The corresponding protein sequences were retrieved from UniProtKB, and redundancy was removed with MMseqs2. For the database implementation, data were delivered through a lightweight LAMP (Linux-Apache-MySQL/MariaDB-PHP) stack with server-side HTML/Bootstrap rendering, MySQL indexing, and HTTPS-secured downloads. Users can browse, keyword-search, or bulk-download sequence archives via a five-tab interface (Home, Downloads, Search, Team, and About). GUTAID thus enables mechanism-oriented exploration of gut microbial antigens and supports downstream biomarker and therapeutic discovery in autoimmune research. Database URL: https://gutaid.mgdiscoverylab.com/.},
}

@article {pmid42233644,
year = {2026},
author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M},
title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149825},
doi = {10.1128/msystems.01498-25},
pmid = {42233644},
issn = {2379-5077},
abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.},
}

@article {pmid42233648,
year = {2026},
author = {Hu, J and Zhang, H and Miao, H and Chang, W and Zheng, J and Hu, F and Zhang, D and Guo, W and Hu, P and Han, R and Wang, J and Li, L and Wang, X},
title = {Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0399325},
doi = {10.1128/spectrum.03993-25},
pmid = {42233648},
issn = {2165-0497},
abstract = {UNLABELLED: This study aimed to compare the analytical characteristics and diagnostic performance of short-read next-generation sequencing (NGS) and long-read third-generation sequencing (TGS) for metagenomic pathogen detection, using defined mock communities and clinical bronchoalveolar lavage fluid (BALF) samples. Mock evaluations included microbe-host gradient mixtures (D1/D2) and six complex microbial panels (M1-M6). Sequencing was performed on Illumina, MGI, and Oxford Nanopore Technologies (ONT) platforms. Clinical validation was conducted on 62 BALF samples. Diagnostic performance was assessed against culture, clinical microbiological tests (CMT), and a composite reference standard (CRS). Turnaround times for Illumina and MGI were approximately 18-20 h and 14-19 h, respectively, whereas the ONT workflow was completed within 4-6 h. The microbe-to-host DNA ratio significantly influenced sequencing performance. Depletion of host DNA notably enhanced ONT detection, reducing the false-negative rate for low-abundance microorganisms from 43.3% to 6.7%. For all mock samples, both the Illumina and MGI platforms demonstrated 100% sensitivity and showed highly concordant detection profiles. In clinical specimens, when evaluated against the composite reference standard, the positive percent agreement (PPA) values of NGS and TGS were 93.3% and 90.7%, respectively, with corresponding negative percent agreements (NPAs) of 77.6% and 83.3%. Both platforms identified numerous pathogens that were missed by culture, especially in polymicrobial infections. Among 22 CRS-defined polymicrobial samples, culture identified all pathogens in only 2 cases, whereas NGS and TGS achieved full pathogen recovery in 18 and 17 cases, respectively. Within the evaluated workflows, short-read sequencing showed slightly higher sensitivity and overall stability, whereas host-depleted ONT offered a substantial turnaround-time advantage and may serve as a useful complementary approach in complex or time-sensitive clinical scenarios.

IMPORTANCE: Rapid and accurate identification of the microbes causing pneumonia is essential for choosing effective treatment, yet current diagnostic tests are slow and often miss important pathogens. We systematically compared two major DNA sequencing strategies-established short-read platforms and newer long-read nanopore sequencing-using both carefully designed mock communities and real bronchoalveolar lavage samples from patients. We show when removal of human DNA is essential, how mixed infections are best captured, and what trade-offs exist between speed and sensitivity. Our results provide practical guidance on how hospitals can implement sequencing-based diagnostics, when rapid nanopore testing can complement conventional short-read workflows, and how to interpret sequencing read counts in day-to-day clinical decision-making.},
}

@article {pmid42233650,
year = {2026},
author = {Kane, M and Moukaha Doukanda, SF and Sankhé, S and Sow, B and Ndione, MHD and Mhamadi, M and Dieng, M and Diop, SMBS and Seye, S and Mbanne, M and Faye, O and Barry, MA and Sembene, PM and Loucoubar, C and Fall, G and Diallo, A and Diagne, CT and Dia, N and Diagne, MM},
title = {Evaluating myxovirus resistance protein A-based rapid testing combined with pathogen sequencing for arboviral and incidental viral infection surveillance in Senegal.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0339225},
doi = {10.1128/spectrum.03392-25},
pmid = {42233650},
issn = {2165-0497},
abstract = {Accurate differentiation between viral and bacterial infections remains challenging in resource-limited, arbovirus-endemic settings, leading to antibiotic misuse and diagnostic uncertainty. Myxovirus resistance protein A (MxA), an interferon-induced host biomarker, may offer a pathogen-agnostic approach to improve rapid diagnosis and clinical triage. We evaluated the performance of an MxA rapid diagnostic test (RDT) using archived samples from febrile patients collected during dengue virus (DENV) and chikungunya virus (CHIKV) outbreaks in Senegal. We tested 171 blood samples from patients with acute febrile illness using an MxA RDT and RT-qPCR for DENV and CHIKV. Samples with discordant results (MxA-positive and RT-qPCR-negative) underwent metagenomic and hybrid-capture Illumina-based sequencing to detect missed infections. Sequencing data were analyzed using maximum-likelihood phylogenetics to assess viral lineage placement. The MxA RDT demonstrated moderate-to-high sensitivity (70.0%-85.1%, depending on virus) and moderate specificity (70.2%) for detecting primary arboviral infections. Among discordant samples, sequencing revealed previously missed pathogens, including DENV serotype 3 (genotype III), Parvovirus B19 (B19V), and Torque teno virus (TTV). Detection of B19V and TTV highlights the broader clinical utility of host-response biomarkers to uncover unexpected viral pathogens in high-diversity settings. MxA's longer persistence than viral RNA enables detection of recent infections missed by PCR. Combined with sequencing, this broadens the diagnostic window, improves clinical triage, and supports identification of underdiagnosed viruses. Future research should integrate MxA testing into routine clinical care and surveillance protocols to enhance outbreak responses in resource-limited regions.IMPORTANCETimely and equitable viral diagnosis is vital in outbreak-prone regions where advanced laboratories are scarce. This study shows how a simple, rapid test for the host biomarker myxovirus resistance protein A can provide real-time detection of viral infections such as dengue and chikungunya, even in remote or frontline health centers. When paired with pathogen sequencing, the test also uncovers infections that standard PCR may miss. This integrated approach demonstrates how field-deployable diagnostics can operate both during and between epidemics, strengthening outbreak preparedness, improving patient triage, and advancing laboratory equity worldwide.},
}

@article {pmid42233654,
year = {2026},
author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H},
title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0318325},
doi = {10.1128/spectrum.03183-25},
pmid = {42233654},
issn = {2165-0497},
abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.

IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.},
}

@article {pmid42233680,
year = {2026},
author = {Grettenberger, CL and Macalady, JL and Hamilton, TL},
title = {Metabolic diversity of Ferrovaceae and potential contributions to iron oxidation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0070026},
doi = {10.1128/aem.00700-26},
pmid = {42233680},
issn = {1098-5336},
abstract = {Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovaceae are Fe-oxidizing bacteria observed in AMD globally and thus could be an asset for bioremediation strategies. To better understand the potential for Ferrovaceae to contribute to AMD bioremediation, we analyzed 240 genomes and metagenome-assembled genomes from Ferrovaceae, including sequences from AMD sites with high iron oxidation rates. Based on our analyses, the phylogenetic and physiological diversity of this group is greater than previously known. We found that while all taxa are likely capable of iron oxidation using a cyc-2 like protein, some may also be capable of iron oxidation using an Mto-like protein. We also identified Ferrovaceae that are likely capable of anoxygenic phototrophy. Our findings indicate that multiple Ferrovaceae populations co-occur and suggest that differences in physiology may promote niche differentiation along resource axes. Physiologically diverse iron oxidizer communities could support a more resilient microbial community, resulting in higher iron oxidation rates and potentially more efficient bioremediation, and thus our results also indicate that future studies that link taxonomy with iron oxidation activity are warranted.IMPORTANCEAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation because they drive biogeochemical processes in these ecosystems. In AMD streams, iron-oxidizing microbial populations remove iron from the AMD effluent by precipitating iron oxides, which absorb other metals. These communities vary across sites and differ in how rapidly they oxidize iron. The factors that contribute to iron oxidation rates are not well understood, making it difficult to design effective bioremediation strategies. Ferrovaceae populations are widespread in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovaceae to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovaceae in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovaceae as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity leads to co-occurrence of multiple Ferrovaceae species at the same sites. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.},
}

@article {pmid42233768,
year = {2026},
author = {Éles, ZB and Rahmani, L and Gyöngyösi, E and Szarka, K and Rebenku, I and Veress, G and Major, T and Kónya, J and Szalmás, A},
title = {Sublineage-Specific A45S Polymorphism Alters the Biological Function of the Human Papillomavirus 11 E7 Protein.},
journal = {Journal of medical virology},
volume = {98},
number = {6},
pages = {e70997},
doi = {10.1002/jmv.70997},
pmid = {42233768},
issn = {1096-9071},
support = {FK125038//National Research, Development and Innovation Office/ ; //Hungarian Academy of Sciences/ ; //Faculty of Medicine, University of Debrecen/ ; //Richter Gedeon Talentum Foundation/ ; },
abstract = {The E7 oncoprotein of human papillomavirus (HPV) plays a crucial role in viral pathogenesis and replication. Although it is generally highly conserved across HPV genotypes, naturally occurring E7 variants can display functional differences that may affect viral persistence, oncogenic potential, and host cellular responses. The prevalent HPV11 A2 sublineage is characterized by a distinctive amino acid substitution at position 45 (A45S) within the E7 protein. In comparative analyses of transfected primary keratinocytes and HPV-negative cancer cells, we here demonstrate that the A45S substitution enhances the interaction of HPV11 E7 with key cellular targets, including pRb family proteins and PTPN14. A further consequence is an increased ability to target both PTPN14 and pRb family proteins for degradation. Functionally, these differences are exemplified by the S45 variant's enhanced ability to activate E2F-driven gene expression, particularly resulting in elevated mRNA levels of key factors involved in homologous recombination-mediated repair of DNA double-strand breaks, a pathway critical for preserving genomic integrity. Together, these findings indicate that the A45S substitution imparts high-risk-like molecular properties to the low-risk HPV11 E7 oncoprotein. To our knowledge, this is the first report to identify a functionally significant alteration in HPV11 E7 activity resulting from a naturally occurring sequence variation. Understanding the underlying mechanisms could provide new strategies for targeting the therapeutically challenging HPV-associated conditions, such as recurrent respiratory papillomatosis.},
}

@article {pmid42234268,
year = {2026},
author = {Hoseini, R and Hoseini, Z and Heydarpour, B and Faraji, M},
title = {A systematic review of molecular signaling in the muscle-brain-gut axis: exercise-induced myokines and microbial metabolites as key mediators.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42234268},
issn = {1573-4978},
abstract = {Exercise physiology is evolving from an organ-based framework toward a systems-level understanding, where molecular interactions between muscle, brain, and the gut microbiome critically influence performance and health. This review systematically examines the genetic, molecular, and cellular bases of this triad, with a focus on translational insights for disease prevention and human optimization. A systematic search of PubMed, Embase, and Web of Science was conducted up to October 2023 to identify studies exploring molecular pathways linking skeletal muscle, cognitive/affective function, and gut microbiota in exercise contexts. Inclusion criteria were original research articles investigating at least two components of the muscle-brain-gut axis. Exclusion criteria included non-English articles, conference abstracts, and studies without molecular data. The PRISMA 2020 guidelines were followed. The search strategy is detailed in Supplementary Material. Evidence was categorized into Grades 1 through 4 based on methodological rigor, omics integration, reproducibility, and translational relevance to human physiology and disease models. Analysis included 154 studies encompassing 987 molecular associations. Among these, 59 associations (Grades 1-2) provided robust evidence for genetically and functionally validated pathways, including myokine-mediated (e.g., irisin, BDNF) and microbially derived metabolites (e.g., SCFAs, tryptophan derivatives) that modulate neuroplasticity, mitochondrial function, inflammation, and HPA axis activity. Psychobiological factors influenced microbial composition, illustrating bidirectional gut-brain-muscle signaling. Most associations (n = 952) were limited by methodological variability or insufficient mechanistic depth. The integration of multi-omics platforms (metagenomics, metabolomics, proteomics) emerges as a key tool for personalized exercise interventions and biomarker discovery. This review synthesizes molecular evidence for the muscle-gut-brain axis as an integrative determinant of exercise responsiveness and disease resilience. We highlight genetic and metabolic pathways with diagnostic and therapeutic potential, aligning with the development of molecular tools for precision medicine. Future interdisciplinary research should leverage artificial intelligence and longitudinal omics to translate these mechanisms into targeted strategies for performance enhancement and disease prevention.},
}

@article {pmid42234577,
year = {2026},
author = {Faure, R and Faure, U and Truong, T and Derzelle, A and Lavenier, D and Flot, JF and Quince, C},
title = {SNooPy: a statistical framework for long-read metagenomic variant calling.},
journal = {Nucleic acids research},
volume = {54},
number = {10},
pages = {},
doi = {10.1093/nar/gkag556},
pmid = {42234577},
issn = {1362-4962},
support = {101088572//ERC/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; },
abstract = {Current long-read single-nucleotide variant callers were designed primarily for genomic data-particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inherent complexity of metagenomic samples. To date, no long-read variant caller has been purpose-built for metagenomic applications. To address this gap, we present SNooPy, a single nucleotide polymorphism (SNP)-calling tool that implements a new statistical framework tailored to long-read metagenomic data. Unlike previous genomic methods, our approach makes no assumptions about the number of haplotypes present, their evolutionary relationships, or their sequence divergence. We demonstrate that SNooPy outperforms both traditional statistical and deep learning-based SNP callers. Our results suggest that future integration of this framework with deep learning approaches could further enhance variant-calling performance. SNooPy is freely available on github.com/rolandfaure/snoopy.},
}

@article {pmid42234710,
year = {2026},
author = {Liu, F and Lai, T and Xu, W and Li, G},
title = {ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0349393},
doi = {10.1371/journal.pone.0349393},
pmid = {42234710},
issn = {1932-6203},
abstract = {Accurate functional annotation of viral proteins is essential for genomic surveillance, yet rapid viral evolution causes "functional drift" that challenges conventional sequence-only models. These models often lack interpretability and struggle with fragmented sequences from complex environmental samples such as wastewater. We developed ViralMultiNet, a structure-aware multimodal framework that integrates multi-scale k-mer encodings (4-7-mers) with functional semantic embeddings derived from UniProt annotations. Using a curated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) dataset of 66,011 samples from wastewater metagenomics (NCBI SRA: SRX28474964), we implemented gated multimodal fusion and triple knowledge distillation to transfer structural insights from a teacher to a student model. Model performance was evaluated via 5-fold cross-validation and external validation on emerging variants. Training efficiency was optimized using Low-Rank Adaptation and Flash Attention. ViralMultiNet achieved robust classification performance with a macro F1 score of 0.921 ± 0.004, accuracy of 0.928 ± 0.003, and AUC of 0.983 in cross-validation. The distilled student model matched teacher performance within a negligible margin (<0.003 F1 difference) while reducing training time by 40.4% (from 94.3 to 56.2 minutes per epoch). Interpretability analysis revealed that model attention peaks consistently aligned with experimentally validated functional domains of the SARS-CoV-2 Spike protein, including the receptor-binding domain (residues 319-541), S1/S2 cleavage site (681-685), and fusion peptide (816-835). ViralMultiNet offers a scalable, interpretable solution for viral protein function prediction. Its ability to generalize across variants and map attention to critical biological regions supports deployment in wastewater-based early warning systems, enhancing global pandemic preparedness.},
}

@article {pmid42235107,
year = {2026},
author = {Candia-Herrera, D and Guerra, M and Carrasco-Fernández, J and Campos-Quiroz, C and Garcia-Gomez, M and Igual, JM and Carro, L and Castro, JF},
title = {Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126734},
doi = {10.1016/j.syapm.2026.126734},
pmid = {42235107},
issn = {1618-0984},
abstract = {Comprehensive phylogenomic and comparative genomic analyses were conducted to clarify the taxonomic boundaries of the genus Metabacillus. Phylogenetic trees reconstructed from a set of single-copy orthologous proteins (SCOPs) revealed that the genus, as currently defined, is polyphyletic. The type species of the genus Metabacillus and its closest relatives formed a consistent clade, herein designated as Metabacillus sensu stricto. The remaining species were grouped into three well-supported clades: Kandeliae, Indicus, and Mangrovi, and two single-taxon lineages: M. arenae and M. lacus. The phylogenomic delineation found in these divergent taxa was corroborated by either inconsistent distribution patterns or the absence of previously defined conserved signature indels (CSIs) specific to Metabacillus. Genomic metrics, including Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), and digital DNA-DNA hybridization (dDDH) further supported the taxonomic delineation proposed here. The observed genomic divergence was mirrored by phenotypic differences, including variations in GC content ranges. Based on this polyphasic evidence, we propose the reclassification of the genus Metabacillus taxa into five novel genera: Chryseobacillus gen. nov. (encompassing the Kandeliae clade), Cohnibacillus gen. nov. (M. lacus), Salimetabacillus gen. nov. (M. arenae), Pantoeobacillus gen. nov. (Indicus clade), and Lutimetabacillus gen. nov. (Mangrovi clade). The core lineage is retained as Metabacillus sensu stricto, for which an emended description of the genus Metabacillus is also provided. A novel bacterial strain, designated as MAU-250[T], was isolated from a soil sample collected on the shore of an artificial reservoir in the Andean foothills of the Maule Region in central Chile. Public metagenome screening supported a low-abundance taxon with broad ecological adaptability, preferentially associated with soil habitats. A polyphasic analysis based on phenotypic traits and genomic distances (78.0% ANIb and 19.8% dDDH against its closest relative) also supported its designation as a novel species, for which the name Chryseobacillus diguaensis sp. nov. is proposed. The type strain is MAU-250[T] (=RGM 3146[T] = IMI 507634[T]).},
}

@article {pmid42235155,
year = {2026},
author = {Zhang, YF and Li, MY and Zhang, Y and Ding, H and Yun, L and Li, ZY},
title = {Genome-resolved analysis reveals successional dynamics and functional transitions in chicken gut archaea across the broiler growth cycle.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107186},
doi = {10.1016/j.psj.2026.107186},
pmid = {42235155},
issn = {1525-3171},
abstract = {Archaea are indispensable members of the gut microbiota, playing important roles in host metabolism and gut homeostasis. Despite their ecological significance, the archaeal community within the chicken gut remains poorly understood, particularly regarding its taxonomic diversity, functional potential, and successional dynamics throughout the broiler growth cycle. In this study, we employed a metagenome-assembled genome (MAG) approach to systematically characterize the composition, phylogeny, and functional shifts of the chicken gut archaea. We constructed a genome catalog comprising 172 non-redundant archaeal MAGs, encompassing 11,796 protein clusters. Community analysis revealed that alpha diversity indices differed significantly across growth stages, suggesting that the archaeal community becomes increasingly robust and functionally complex as the host matures. Functional annotation further demonstrated broad metabolic versatility, with distinct metabolic profiles emerging across multiple functional modules at different ages. This study reveals the dynamics of chicken gut archaeal communities and their potential functional characteristics across different production stages, providing a basis for future research into their ecological roles and possible associations with host gut ecosystem stability.},
}

@article {pmid42235160,
year = {2026},
author = {Lu, T and Chen, Y and He, Q and Zheng, B and Deng, D and Xiong, X},
title = {Gut bacterial species, serum metabolites, and serum cytokines associated with broodiness in chickens.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107187},
doi = {10.1016/j.psj.2026.107187},
pmid = {42235160},
issn = {1525-3171},
abstract = {Increasing evidence suggests that the gut microbiota, serving as a "virtual endocrine organ", potentially modulates reproductive behavior in poultry via the gut-brain and gut-ovary axes. Broodiness in hens inhibits egg-laying activity and causes major economic losses in native chicken breeds, but its micro-physiological basis remains unclear. This study used shotgun metagenomic sequencing to delineate the cecal bacterial species associated with brooding status in Chinese Kangle chickens. We identified 34 cecal bacterial species exhibiting significantly varying abundances between the broodiness and control groups, including six species (e.g., Bacteroides sp. An51A and Phocaeicola barnesiae) that were significantly enriched in the broodiness group. Additionally, 28 species significantly enriched in the control group were screened. Among them, Subdoligranulum variabile and Oribacterium asaccharolyticum served as key biomarkers for distinguishing brooding status in Kangle chickens and were associated with functional shifts in the cecal microbiome. Non-targeted metabolomic analysis identified 17 differential metabolites, among which seven (e.g., (13E) -11a-hydroxy-9,15-dioxoprost-13-enoic acid and d-arabitol) were defined as metabolic markers of the broody state and were significantly associated with Subdoligranulum variabile and Oribacterium asaccharolyticum. In addition, our results suggest that serum cytokines, such as IFN-γ and IL-22, are potentially associated with the broody state and the alterations in both serum metabolites and the gut microbiota (e.g., Subdoligranulum variabile and Oribacterium asaccharolyticum). These findings provide a new insight into the mechanisms underlying reproductive behavior in poultry and offer a theoretical basis for alleviating broodiness through microecological interventions, thereby improving the reproductive efficiency of indigenous chicken breeds.},
}

@article {pmid42235395,
year = {2026},
author = {Li, Y and Zhu, T and Tao, C and Li, S and Cheng, H and Chen, W},
title = {Threshold-dependent control of ARG removal in global wastewater treatment plants: Molecular mechanisms of low-abundance functional genes deciphered via metagenomics and explainable AI.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142574},
doi = {10.1016/j.jhazmat.2026.142574},
pmid = {42235395},
issn = {1873-3336},
abstract = {Wastewater treatment plants (WWTPs) serve as critical barriers against the dissemination of antibiotic resistance genes (ARGs) from urban water environments to nature, yet the molecular mechanisms governing their biological removal remain poorly understood. By combining experimental metagenomic data from 19 Chinese WWTPs with additional data from 31 global WWTPs (50 WWTPs in total), an explainable machine learning (ML) framework was developed. The RFE-SHAP (Recursive Feature Elimination-SHapley Additive exPlanations) based on feature importance was applied to identify key biological features driving ARG removal. The study revealed that low-abundance microbial functional genes particularly those involved in DNA repair, energy metabolism, and quorum sensing exhibit threshold-dependent control over ARG attenuation. ML models (BFGs-GBDT) incorporating the RFE-SHAP-selected functional genes achieved exceptional predictive accuracy (R[2]test = 0.967), outperforming taxonomy-based models (average R[2]test = 0.805). Strikingly, these functionally critical genes, despite their low abundances (0.04 - 0.15%), exerted disproportionate influence on ARG removal efficiency, challenging the prevailing high-abundance-centric paradigm in WWTPs design. The findings not only elucidated the molecular mechanisms of ARG mitigation but also provided a predictive framework for precision engineering of microbial communities to enhance ARG elimination. This study advances wastewater treatment strategies from empirical ARG removal to mechanism-driven environmental risk control.},
}

@article {pmid42235463,
year = {2026},
author = {Lin, Q and Mei, X and Zheng, H and Meng, J and He, F and Yang, B and Ru, X and Su, M and Wang, D and Tan, N and Fang, J and Fu, S and Ouyang, N and Yang, Z and Jiang, S and Zhang, Y},
title = {Optimisation and validation of capture mNGS for predicting antimicrobial resistance.},
journal = {EBioMedicine},
volume = {129},
number = {},
pages = {106319},
doi = {10.1016/j.ebiom.2026.106319},
pmid = {42235463},
issn = {2352-3964},
abstract = {BACKGROUND: Antibiotic resistance critically compromises bacterial infection treatment. While antimicrobial susceptibility testing (AST) remains the standard for resistance assessment, its culture dependence is time-consuming. Clinical metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection and antibiotic resistance gene (ARG) profiling. However, low ARG detection sensitivity and unclear genotype-phenotype correlations limit its clinical utility.

METHODS: We developed capture mNGS approach with probe-based ARG enrichment and a host-attribution algorithm for precise ARG-bacteria linkage. Its ARG detection sensitivity was comparatively analysed against standard mNGS. Using phenotypic AST as reference, we then evaluated the clinical predictive value of capture mNGS-detected ARGs in a retrospective cohort from Sun Yat-sen Memorial Hospital (SYSMH) and an external cohort from Liuzhou Worker's Hospital (LWH). In addition, a prospective cohort from SYSMH was used to explore the clinical utility of ARG detection by mNGS.

FINDINGS: Compared to standard mNGS, capture mNGS significantly enhanced ARG detection sensitivity, achieving a 44-fold increase in sequencing depth. In our retrospective cohort, key resistance genes detected by capture mNGS accurately predicted phenotypic resistance: blaCTX-M achieved a sensitivity of 1.00 (95% CI: 0.86, 1.00) and specificity of 1.00 (95% CI: 0.59, 1.00) for ceftriaxone resistance prediction, with an area under the receiver operating characteristic curve (AUC) of 0.93 (95% CI: 0.87, 0.99). BlaKPC demonstrated a sensitivity of 0.94 (95% CI: 0.73, 1.00) and specificity of 1.00 (95% CI: 0.95, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.92, 1.00). Similarly, blaOXA-23 exhibited a sensitivity of 0.95 (95% CI: 0.82, 0.99) and specificity of 1.00 (95% CI: 0.69, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.94, 1.00), which was externally validated in the LWH cohort. In addition, mecA showed a sensitivity of 0.94 (95% CI: 0.71, 1.00) and specificity of 0.94 (95% CI: 0.81, 0.99) for oxacillin resistance (AUC = 0.94, 95% CI: 0.87, 1.00). Whereas blaTEM/blaSHV showed higher false-positive rates for cephalosporin resistance and ErmB/ErmC showed lower sensitivity (0.6, 95% CI: 0.32, 0.84) for macrolide-lincosamide-streptogramin (MLS) resistance. Capture mNGS reported results (median turnaround time (TAT): 24.71 h (IQR 22.74-41.00)) were shorter than AST (median TAT: 73.16 h (IQR 54.19-93.42)). In a prospective cohort, the time to guide antibiotic therapy based on reported positive ARGs was significantly shorter than that based on reported resistant phenotypes from AST.

INTERPRETATION: These results highlight that ARGs can be leveraged to rapidly and accurately predict bacterial resistance phenotypes with high sensitivity and specificity, thereby guiding antibiotic management in clinical practice.

FUNDING: The National Natural Science Foundation of China, the Guangdong Science and Technology Department, Science and Technology Projects in Guangzhou.},
}

@article {pmid42224761,
year = {2026},
author = {Ma, S and Zhao, B and Jing, G and Han, M and Wang, M and Shan, X and Wang, Z and Lu, S and Liu, X and Wu, F},
title = {Vertical stratification and distribution patterns of the ARG resistome in Fuxian Lake: Insights from a global baseline.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142528},
doi = {10.1016/j.jhazmat.2026.142528},
pmid = {42224761},
issn = {1873-3336},
abstract = {Deep lakes are critical reservoirs for antibiotic resistance genes (ARGs), yet global ARG dynamics and vertical mechanisms remain poorly constrained. By combining metagenomics with a global comparative analysis across 17 plateau lakes and 83 Fuxian Lake samples, this study investigates ARG distribution from macro- to micro-scales. The macro-scale analysis identified Longitude, Latitude, and Temperature (all p-values < 0.05) as dominant constraints on ARG abundance. A distinct, synergistic mechanism drives vertical stratification: ARG enrichment occurs in the deep layer (50-150 m) at the lake center, but enrichment shifts to the shallow layer (0-40 m) in the tourism area. This complex pattern is governed by a biotic-abiotic synergy. Specifically, ARG dynamics in the deep layer are jointly regulated by biotic factors and physicochemical constraints such as pH and ORP. Differences observed at the local scale, including the increase in ARG abundance and rare-to-core conversion, contrast with broader patterns observed across plateau lakes. This study provides the first global distribution spectrum of ARGs in plateau lakes and reveals crucial interactive patterns. The persistent presence of high-risk ARGs and critical priority pathogens necessitates heightened vigilance. We propose controlling anthropogenic inputs and mitigating the risk of deep sediment pollutant release as crucial strategies for these vital freshwater resources.},
}

@article {pmid42224764,
year = {2026},
author = {Sun, Y and Yu, Z and Wu, C and Wang, J and Feng, X},
title = {First insights into agricultural practice-driven mobilization and methylation of arsenic and mercury in soil with implications for groundwater risk mitigation.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142530},
doi = {10.1016/j.jhazmat.2026.142530},
pmid = {42224764},
issn = {1873-3336},
abstract = {The migration of heavy metals from soils to groundwater via karst conduits (e.g., dolines) in karst terrains threatens the safety of anthropogenic water supplies. Despite widespread recognition of contamination risks, the underlying mechanisms governing the transformation and mobilization of heavy metals, particularly those mediated by agricultural activities, remain inadequately characterized. Here, we systematically studied the impact of rice straw return (RS) on the biogeochemical transformation processes of both arsenic (As) and mercury (Hg) from a co-polluted soil in karst regions using a combination of geochemical, microbial, and spectroscopic approaches. The results indicated that RS enhanced the desorption of As from Fe(III)oxyhydroxides and methylation of As(III). Metagenomic sequencing analyses revealed that RS increased the abundance of Fe-reducing bacteria (FeRB) and As-methylating microorganisms, which collectively drive As mobilization and transformation. Furthermore, RS promoted the release of Hg from Fe(III)oxyhydroxides and stimulated methylmercury (MeHg) formation, primarily due to the increased abundance of Hg-methylating microbes and hgcAB genes, as well as enhanced Hg availability through the transformation of HgS into organic matter bound Hg and nano-HgS. These findings are essential for predicting As and Hg leaching risks from soils to groundwater under the influence of agricultural practices in karst regions worldwide.},
}

@article {pmid42224874,
year = {2026},
author = {Kenzi, M and Benbernou, M and Khelifa, H and Tbahriti, HF},
title = {Machine learning-based prediction of antibiotic resistance gene distribution in agricultural soils under different climate change scenarios.},
journal = {The Science of the total environment},
volume = {1042},
number = {},
pages = {181905},
doi = {10.1016/j.scitotenv.2026.181905},
pmid = {42224874},
issn = {1879-1026},
abstract = {Antibiotic resistance genes (ARGs) in agricultural soils represent a major public health concern, as climate change is believed to augment their dissemination and abundance. Understanding the impact of future climate change scenarios on ARG abundance is essential to implement predictive and proactive One Health strategies. In this study, a total of 2301 soil samples from 67 countries across six continents were compiled from three global metagenome databases, namely NCBI SRA, MG-RAST, and JGI IMG/M. Six machine learning models, namely LightGBM, XGBoost, Random Forest, Support Vector Machines, Deep Neural Networks, and Logistic Regression, were used to predict ARG distribution patterns in agricultural soils, and their performance was evaluated using stratified 10-fold cross-validation with metrics such as AUC-ROC, precision, recall, F1 score, and Matthews Correlation Coefficient. WorldClim 2.1 and CMIP6 models were used to project ARG distribution under three Representative Concentration Pathway scenarios, namely RCP 2.6, RCP 4.5, and RCP 8.5, for the years 2050 and 2070. The LightGBM model achieved the best predictive performance, with an AUC-ROC of 0.957 (95% CI: 0.951-0.963), substantially higher than that of the other models, while the Deep Neural Networks model achieved an AUC-ROC of 0.891. The LightGBM model demonstrated high stability across cross-validation folds, with minimal fold-to-fold variance, defined as the standard deviation of AUC-ROC scores across the 10 folds (SD = 0.008). SHAP feature importance analysis identified soil temperature, pH, and organic carbon content as the top three factors influencing ARG relative abundance, with SHAP values of 0.342, 0.287, and 0.251, respectively. Annual precipitation and soil moisture level were also identified as significant contributors to ARG distribution. SHAP dependency plots revealed critical thresholds for ARG relative abundance, with a sharp increase observed independently when soil temperature exceeds 18 °C and when soil pH drops below 6.5. Furthermore, a non-linear accelerating increase in ARG abundance risk was observed as climate change intensity worsened across scenarios. Projections for future climate change scenarios indicate a potential 34.7% increase in high-risk ARG zones by the year 2070, with the largest changes expected in South Asia, Sub-Saharan Africa, and Mediterranean regions. Paired t-tests revealed significant differences in performance among all models (p < 0.001). These findings demonstrate that gradient-boosting methods such as LightGBM outperform deep learning approaches for ARG prediction from soil microbiome data, offering higher accuracy and interpretability. As climate change is projected to increase ARG risks in a non-linear manner, the development of climate-adaptive agricultural practices and global surveillance systems is urgent. This framework provides actionable risk-mapping tools to support precision farming and region-specific policy interventions within the One Health approach.},
}

@article {pmid42225156,
year = {2026},
author = {Feng, S and Bao, Y and Zhu, X and Wu, J and Chen, W and Huang, D and Zhou, T and Meng, L and Lee, CH and Li, D and Huang, M},
title = {Biodegradable versus persistent nanoplastics reshape nitrogen metabolism and biofilm architecture in denitrifying biofilters.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135048},
doi = {10.1016/j.biortech.2026.135048},
pmid = {42225156},
issn = {1873-2976},
abstract = {The presence of nanoplastics (NPs) in biological wastewater treatment systems is an emerging concern. Nevertheless, their differential influence on critical biofilm-mediated processes has yet to be fully elucidated. In this study, denitrifying biofilters were exposed to biodegradable polylactic acid nanoplastics (PLA-NPs) and non-biodegradable polystyrene nanoplastics (PS-NPs) to simulate both typical and cumulative high-exposure scenarios. Results showed that long-term NP stress significantly reduced the denitrification performance, with a maximum inhibition of 35% in total nitrogen (TN) removal. Mechanistically, PLA and PS induced distinct biofilm remodeling strategies. PLA exposure enhanced nitrate assimilation pathways, promoting nitrogen sequestration into microbial biomass. In contrast, PS-NPs elicited concentration-dependent stress responses. Low PS exposure was associated with reduced extracellular polymeric substances (EPS) and enhanced carbohydrate degradation potential, whereas high PS concentrations were linked to altered EPS composition, decreased microbial diversity, and directional succession toward stress-tolerant genera. Metagenomic analysis revealed shifts in central carbon metabolic strategies, including enhanced gluconeogenesis and EPS precursor synthesis under NP exposure. Differences in substrate bioavailability between PLA and PS treatments further contributed to distinct carbon utilization patterns within the biofilms. Overall, this study demonstrates that NP biodegradability governs biofilm functional stability, nitrogen transformation, and denitrification performance, providing mechanistic insight into NP-biofilm interactions in engineered systems.},
}

@article {pmid42225158,
year = {2026},
author = {Wang, M and Wang, H and Liang, X and Li, J and Wang, C and Cui, L and Yang, S and Lin, J and Yang, Q and Yang, Z},
title = {Enhanced phenanthrene degradation in microalgae-bacteria systems: Mechanistic roles of exogenous and indigenous degraders.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135034},
doi = {10.1016/j.biortech.2026.135034},
pmid = {42225158},
issn = {1873-2976},
abstract = {This study investigates the synergistic mechanisms of phenanthrene (PHE) biodegradation using Chlorella vulgaris consortia with exogenous (EB) and indigenous (IB) bacteria. Results showed that both cooperative systems significantly enhanced algal growth and PHE removal, with biomass increasing by 17.2% (C.v-EB) and 75.0% (C.v-IB), and biodegradation rates reaching 75.3%-78.4%. Mechanistically, C.v-EB relied on enzymatic antioxidant responses (SOD and CAT) and a protein-rich extracellular polymeric substance (EPS) shield to mitigate oxidative stress. In contrast, C.v-IB exhibited superior resilience through non-enzymatic redox regulation (glutathione/thioredoxin systems) and the formation of a dense, biofilm-like EPS matrix supported by active transport genes (wzm/wzt). Metagenomic analysis revealed that C.v-IB possessed higher metabolic redundancy and energy production efficiency, organized into a coordinated "Degradation-Defense-Communication" genomic architecture via quorum sensing. Furthermore, both consortia expanded the metabolic landscape of PHE, effectively eliminating intermediate toxicity through divergent pathways. These findings provide a systematic framework for developing robust algal-bacterial biotechnologies for the remediation of polycyclic aromatic hydrocarbons in wastewater.},
}

@article {pmid42225249,
year = {2026},
author = {Nie, X and Qin, J and Liu, M and Wang, H and Hou, K and Duan, Y},
title = {Process-Level Design of Engineered Microalgal-Bacterial Systems for Carbon-Efficient Nitrogen Removal from Low C/N Wastewater: Carbon/Electron Redistribution Revealed by Metabolic Network Analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124883},
doi = {10.1016/j.envres.2026.124883},
pmid = {42225249},
issn = {1096-0953},
abstract = {Carbon scarcity in low carbon-to-nitrogen (C/N) wastewater limits electron donor availability and constrains biological nitrogen removal. Although microalgal-bacterial symbiosis (MBS) is a promising low-input alternative, the mechanisms that sustain nitrogen removal under carbon-limited conditions remain unclear. Here, process-level characterization and metagenomic analysis were combined to investigate community assembly and carbon/electron redistribution in engineered MBS systems. Under the tested conditions, a balanced algae-to-bacteria ratio (1:1) created the most stable niche and achieved >97% NH4[+]-N removal with minimal nitrate accumulation, indicating effective coupling of nitrification, denitrification, and assimilation. EPS dynamics showed a shift from accumulation to reutilization during prolonged carbon limitation: polysaccharides decreased in the later stage as external COD was depleted, suggesting mobilization of EPS as an internal carbon source. Consistently, TCA-cycle genes (e.g., IDH, OGDH, mdh) were enriched whereas glycolysis-related genes (e.g., GAPDH, PGK) declined, indicating a shift in metabolic potential toward greater generation of reducing equivalents. Overall, the results suggest that EPS functions as a dynamic carbon reservoir and that algae-bacteria interactions promote carbon/electron redistribution under carbon-limited conditions. This study provides a process-level basis for designing carbon-efficient wastewater treatment systems.},
}

@article {pmid42226305,
year = {2026},
author = {Grundler, F and Ducarmon, QR and Holley, A and Knufinke, M and Strathmeyer, S and Heelemann, S and Geyer, R and Martínez-Téllez, B and MacArthur, MR and Zeller, G and Wilhelmi de Toledo, F and Mesnage, R},
title = {Health benefits of a five-day at-home modified fasting program: a randomised controlled trial.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42226305},
issn = {1756-994X},
support = {ALTF 1030-2022//EMBO postdoctoral fellowship/ ; RYC2022-036473-I//MCIN/AEI/10.13039/501100011033/ ; },
abstract = {BACKGROUND: Fasting is one of the most cost-effective methods to improve cardiometabolic health. We tested a 5-day hypocaloric (~ 600 kcal/day) and ketogenic, modified fasting program (MFP) in a two-arm randomised controlled trial, where sixty-four healthy subjects were randomised to MFP or control group.

METHODS: We randomly assigned 64 participants to a group receiving the MFP or to a group of participants who were told to continue with their usual eating behaviour and lifestyle (control group). The changes in blood pressure and body weight were considered as primary endpoints. Secondary outcomes included ketosis, glucose and lipid metabolism, inflammatory markers, antioxidant capacity and well-being. Biological pathways and metabolic processes were explored with nuclear magnetic resonance blood metabolomics and gut metagenomics analyses. Outcomes were assessed at baseline, end of the MFP, after food reintroduction, and one month later.

RESULTS: MFP participants (n = 32) experienced weight loss compared to controls (- 0.52 ± 0.03 kg vs. - 0.03 ± 0.02 kg, p < 0.001). Changes in blood pressure caused by the MFP were non-significant at the end of the fasting period. However, blood pressure was significantly reduced following food reintroduction (systolic: -0.56 ± 0.12 mmHg vs. - 0.16 ± 0.12 mmHg, p < 0.05 and diastolic: -0.36 ± 0.08 mmHg vs. - 0.01 ± 0.08 mmHg, p < 0.01). Serum biochemistry showed the MFP reduced glucose levels and coagulation factors. The MFP also significantly increased physical well-being. Blood metabolomics revealed a significant decrease in chronic inflammation markers. Shotgun metagenomics of the gut microbiome showed significant changes in relative abundance of 11 bacterial species and in the genomic repertoire of 52 carbohydrate-active enzymes (CAZymes), reflecting an increase in families metabolising host-derived glycan substrates. None of these differences in gut microbiome and blood metabolome were shown to be statistically different from the control group one month after the intervention. Comparing MFP effects with a previous cohort's 5-day prolonged fasting showed similar metabolic changes.

CONCLUSIONS: This MFP is safe and transiently improves cardiometabolic health and physical well-being in healthy individuals.

CLINICAL TRIAL REGISTRATION: This trial was prospectively registered at ClinicalTrials.gov (NCT05821660) on 6 April 2023 prior to the start of patient recruitment.},
}

@article {pmid42226423,
year = {2026},
author = {Xu, Q and Zhang, X and Tian, H and Yang, X and Zhang, J and Li, H and Ma, Z and Zhang, D and Huang, K and Zhang, Y and Zhao, Y and Li, X and Zhao, L and Cheng, J and Xu, D and Li, F and Weng, X and Wu, W and Wang, W},
title = {Integrating rumen microbiome and host metabolome to investigate feed conversion ratio across different fattening stages in Hu sheep.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.260317},
pmid = {42226423},
issn = {2765-0189},
abstract = {OBJECTIVE: Feed conversion ratio (FCR) is a crucial economic trait in animal breeding and management and is also of great significance for environmental sustainability. This study aimed to investigate the potential regulatory mechanisms of FCR in sheep by integrating rumen microbiota and host metabolome through multi-omics analysis.

METHODS: FCR data were collected from 127 male Hu sheep. Extreme individuals were selected for rumen metagenomic and serum metabolomic analyses to identify key factors driving FCR across early and late fattening stages.

RESULTS: Bacteroides, Prevotella, and other genera were identified as dominant taxa in the rumen across both stages, suggesting their involvement in FCR regulation. Notably, Nocardia tengcongensis differed significantly between the highest FCR values (HF) and lowest FCR values (LF) groups at different stages, indicating its potential as a predictive biomarker of feed efficiency. Functional analysis revealed that the pentose phosphate pathway (M00004) and lysine biosynthesis via the succinyl-DAP pathway (M00016) were enriched in the LF group, whereas the methanogenesis pathway (M00357) was significantly enriched in the HF group, indicating increased methane production. Thirteen metabolites consistently differed between HF and LF across fattening stages and may serve as predictive biomarkers. In addition, the abundance of Prevotella and Bacteroides increased over time and showed significant correlations with key metabolites.

CONCLUSION: These findings suggest strong interactions between rumen microbiota and host metabolites that may collectively influence FCR, providing new insights into microbial and metabolic regulation of feed efficiency and a theoretical basis for optimizing feeding strategies in sheep.},
}

@article {pmid42227278,
year = {2026},
author = {Li, W and Wang, Z and Fu, H and Ma, YR and Gu, Y and Zhuang, JL and Zhao, YX and Liu, YD and Yang, Q and Shapleigh, JP and Jin, RC and Guo, J and Kartal, B and Rittmann, BE},
title = {A Novel Freshwater Anammox Species of Candidatus Loosdrechtia Thriving Under Dual Salinity and Sulfate Stresses.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c03295},
pmid = {42227278},
issn = {1520-5851},
abstract = {Anaerobic ammonium oxidation (anammox) bacteria are key players in the global nitrogen cycle and are widely applied in energy-efficient nitrogen removal processes. However, their activity is often inhibited in saline and sulfate-rich environments. Here, we report the discovery and characterization of Candidatus Loostrechtia thiotolerans (HSAMX1), a novel nonmarine anammox species that became dominant under combined high salinity (3% by weight) and high sulfate concentrations (∼86 mM). Through integrated metagenomic and metatranscriptomic analyses, we reveal the physiological and molecular strategies enabling HSAMX1 to thrive under dual-stress conditions. In response to osmotic stress, HSAMX1 activated ion export systems and subsequently synthesized organic osmoprotectant solutes to maintain cellular homeostasis. It also encoded and strongly expressed the sulfide:quinone oxidoreductase (SQR) gene, which accounted for over 90% of the total community SQR transcription. Intriguingly, HSAMX1 did not emerge under either salinity or sulfate stress alone, suggesting a previously unrecognized niche shaped by the interactions of these two stressors. These findings expand our understanding of nonmarine anammox diversity and identify a promising candidate for nitrogen removal in sulfate-laden, saline wastewater.},
}

@article {pmid42227352,
year = {2026},
author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT},
title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70190},
pmid = {42227352},
issn = {1365-2591},
support = {//European Society of Endodontology/ ; },
abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.

METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (< 3 mm) or large (> 7 mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p < 0.05 was considered as significant.

RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p = 0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.

CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.},
}

@article {pmid42227741,
year = {2026},
author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD},
title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0018826},
doi = {10.1128/msystems.00188-26},
pmid = {42227741},
issn = {2379-5077},
abstract = {Studies of whole viral populations-the "virome"-are yielding exciting new insights into biological systems, but methods are still being optimized. Here, we describe generation and use of a synthetic viral community and its use to evaluate technical challenges arising in virome analysis. We spiked the mock community into different human sample types, then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared with direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from stool and saliva. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1,000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC) and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced compared with T4 genomes with unmodified cytosine. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.IMPORTANCEA challenge in characterizing the human virome in health and disease is identifying optimal methods for enriching the viral content of samples. Due to the tremendous abundance and diversity of viruses, capturing as broad of a range of viruses as possible for analysis is difficult and potentially complicated by unrecognized biases. This report presents the use of a synthetic viral community for methods optimization in virome studies and illustrates the feasibility and challenges of current virus enrichment strategies for high-throughput virome analysis of different human sample types.},
}

@article {pmid42227750,
year = {2026},
author = {Becker, DJ and Dyer, KE and Olbrys, BL and Hightower, MG and Allira, M and Demory, B and Lock, LR and Taylor, KN and Bhata, NN and Hernandez, SM and Lawson, PA and Youssef, NH and Miller, SL and Elshahed, MS and Verrett, TB and Clark, KL},
title = {Molecular detection of relapsing fever Borrelia puertoricensis in migratory Mexican free-tailed bats.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0008526},
doi = {10.1128/msphere.00085-26},
pmid = {42227750},
issn = {2379-5042},
abstract = {UNLABELLED: Bats have been increasingly recognized to host relapsing fever borreliae as well as borreliae that form novel clades adjacent to the Lyme borreliosis group. However, the genetic diversity and zoonotic potential of bat-borne borreliae remain poorly understood, in part because most work to date has focused on bats in the tropics. Fewer bat-borne Borrelia surveys have been conducted in temperate zones, where many bats undertake seasonal migrations that may facilitate pathogen dispersal. We surveyed blood from nearly 400 Mexican free-tailed bats (Tadarida brasiliensis) during their seasonal occupancy in Oklahoma, USA, during 2022 and 2023, for Borrelia spp. Targeted PCR of the 16S rRNA and flaB genes revealed high nucleotide identity to Borrelia puertoricensis, and shotgun metagenomics further demonstrated high amino acid identity to strains isolated from argasid ticks and human blood. This represents the first detection of Borrelia puertoricensis in bats and only the second detection within wild vertebrate hosts. Infection prevalence was low but comparable to that of other borreliae in bats. Our findings suggest that Mexican free-tailed bats may contribute to the dispersal of this emerging tick-borne bacterial pathogen in North America.

IMPORTANCE: Bacteria in the genus Borrelia are primarily spread by ticks and cause either Lyme borreliosis or relapsing fever. Substantial work has demonstrated the degree to which rodents and songbirds can contribute to the enzootic cycles and dispersal of these human diseases, but comparatively less attention has been paid to the role of wild bats, particularly in temperate regions. We here report human-relevant findings from a two-year, seasonal survey of migratory Mexican free-tailed bats (Tadarida brasiliensis) in Oklahoma, USA. We tested nearly 400 bats and identified Borrelia puertoricensis, a relapsing fever species that could infect humans. Importantly, this represents the first detection of Borrelia puertoricensis in bats and only the second detection in wild vertebrate hosts, expanding the known host range of this emerging tick-borne pathogen. Given the known migratory routes of Mexican free-tailed bats, our results have implications for the role that bats may play in tick-borne pathogen dispersal in North America.},
}

@article {pmid42227946,
year = {2026},
author = {Wang, H and Wang, X and Xiu, Z and Wei, H and Cai, H and Chen, J and Zhang, T and Yang, Y},
title = {Substrate-driven microbial specialization and cooperative dechlorination of chlorinated pollutants in estuarine ecosystems.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0023526},
doi = {10.1128/aem.00235-26},
pmid = {42227946},
issn = {1098-5336},
abstract = {Organohalide-respiring bacteria (OHRB) are globally distributed, yet their ecological roles in marine environments remain poorly understood, with few isolates characterized from these systems. Here, we describe a stable anaerobic consortium from estuarine sediments that performs sustained dechlorination of 1,1,2-trichloroethane (1,1,2-TCA) to vinyl chloride (VC) at a rate of 126.3 ± 0.9 µM d[-1]. This activity was associated with the stable co-enrichment of two key populations, Dehalogenimonas and Desulfitobacterium, which increased to dominate the community at 49.7% and 32.5%, respectively. Metagenome-assembled genomes confirmed both populations represent novel species with distinct genomic adaptations. Dehalogenimonas sp. strain H harbors 24 putative reductive dehalogenase genes and complete ectoine biosynthesis pathways (ectABC) essential for osmotolerance, while Desulfitobacterium sp. strain Y represents the first cultivated marine-associated member of this genus. Proteomic analysis confirmed active expression of multiple reductive dehalogenases from strain H, strongly supporting its role as the primary dechlorinator. Concurrently, physiological and genomic data suggest that strain Y is strongly co-selected under 1,1,2-TCA-amended conditions and likely occupies a crucial supportive niche. Alongside its extensive metabolic versatility that likely buffers the consortium against environmental fluctuations, its complete de novo corrinoid biosynthesis pathway implies a complementary role as a vitamin B12 provider for the extreme corrinoid-auxotrophic strain H. This study provides evidence for a stable co-enrichment consistent with nutritional niche differentiation within native microbial communities and suggests a potential cooperative interaction between novel Dehalogenimonas and Desulfitobacterium species, advancing our understanding of halogen cycling in coastal ecosystems.IMPORTANCEEstuaries serve as critical interfaces between terrestrial and marine ecosystems, yet the microbial processes governing chlorinated pollutant fate in these vulnerable zones remain largely unexplored. Our discovery of a novel partnership between Dehalogenimonas and Desulfitobacterium species challenges the conventional understanding that Desulfitobacterium is restricted to terrestrial habitats. Integrative multi-omic and physiological analyses reveal that Dehalogenimonas strain H serves as the highly specialized primary dechlorinator, while Desulfitobacterium strain Y is stably co-enriched and exhibits genomic potential to sustain the consortium by providing essential corrinoid cofactors. The identification of genomic determinants underlying salt tolerance in Dehalogenimonas, including ectoine and mannosylglycerate biosynthesis pathways, provides mechanistic insights into OHRB adaptation to fluctuating salinity. These findings have direct implications for developing bioremediation strategies for contaminated coastal sites and highlight the importance of characterizing microbial diversity in transitional ecosystems.},
}

@article {pmid42228562,
year = {2026},
author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N},
title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.},
journal = {Cell reports},
volume = {45},
number = {6},
pages = {117478},
doi = {10.1016/j.celrep.2026.117478},
pmid = {42228562},
issn = {2211-1247},
abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.},
}

@article {pmid42229136,
year = {2026},
author = {Delgado, N and Fernández, KG and Zambrano-Alegría, C and Espinosa, ZYD and Ramos-Cabrera, E},
title = {Physiological and microbial alterations induced by pesticides in agricultural systems: A bioassay- and 16S rRNA-based approach.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142560},
doi = {10.1016/j.jhazmat.2026.142560},
pmid = {42229136},
issn = {1873-3336},
abstract = {The extensive use of pesticides in agricultural production systems has increased interest in understanding their potential impacts on soil environmental dynamics. This study evaluates the effects of pesticide application on Lactuca sativa L. and soil microbiota. An initial field survey identified the main active ingredients commercial pesticides, followed by bioassays assessing germination and early development of Lactuca sativa, as well as soil microbial structure through physiological assessments and metagenomic analyses based on 16S rRNA gene sequencing, during a three-week soil experiment. Thirty active ingredients were identified in 92 agricultural products. Chlorpyrifos was identified as one of the most commercialized insecticides, where insecticides represented 69% of marketed phytosanitary products, mainly organophosphates (18%) and pyrethroids (21%), despite its hazardous classification and ban in several countries. Germination assays showed a hormetic response at low dose (2200 mg/L), reaching 70% germination compared with 51% in the control, while the germination index decreased to 75% at the recommended dose (4400 mg/L). Statistical analyses revealed inhibition of hypocotyl elongation (p = 0.001) and cotyledon development (p = 0.029). Soil microbiome analysis showed that high chlorpyrifos concentrations reduced microbial richness and diversity, while beta diversity analyses explained 99% of the variance among treatments. Proteobacteria, Burkholderiales, and Sphingomonadales increased under pesticide exposure, indicating microbial adaptation and biodegradation potential. Functional prediction using PICRUSt2 revealed enrichment of genes K03381, K00446, K01048, and K01560 associated with potential organophosphate degradation pathways. These findings demonstrate that chlorpyrifos induces ecological and seedling alterations even at agronomically recommended concentrations. highlighting the need to strengthen sustainable pesticide management and environmental monitoring strategies.},
}

@article {pmid42229568,
year = {2026},
author = {Dang, R and Xiao, L and Zhou, L and Liu, J and Liang, Z and Wang, Y and Song, W and Wang, X and Chu, X and Zhang, X and Song, Y and Song, W and Han, G},
title = {Asymmetric microbial community reassembly under 7-year experimental precipitation decouples soil carbon storage in a coastal wetland.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124851},
doi = {10.1016/j.envres.2026.124851},
pmid = {42229568},
issn = {1096-0953},
abstract = {Climate-driven extremes in precipitation are fundamentally altering the hydrological regimes of wetland ecosystems. However, the mechanistic understanding of how soil microbial communities and their metabolic functions respond to precipitation change, and how these responses regulate soil organic carbon (SOC) dynamic, remains limited. Here, we leveraged a 7-year precipitation manipulation experiment (± 40%) in a coastal wetland and applied genome-resolved metagenomics to systematically examine microbial community structure, ecological networks, and key biogeochemical functions (carbon fixation and degradation). We found that although microbial community structure showed no pronounced response to increased precipitation, decreased precipitation reorganized the community, as evidenced by higher β-diversity and more complex co-occurrence networks with strengthened positive interactions. Compared with dominant species, rare species played a more important role in maintaining the stability of microbial networks. Functional potential for carbon degradation and fixation remained relatively stable under decreased precipitation. In contrast, increased precipitation concurrently suppressed degradation of polysaccharides and aromatic compounds, and some carbon fixation pathways, such as Acetyl-CoA (rAcCoA) pathway. Collectively, decreased and increased precipitation induced asymmetric responses in microbial communities, with decreased precipitation primarily reshaping community composition but having little effect on functional potential, whereas increased precipitation predominantly altered functional profiles without substantially changing community structure. We further found microbial community reassembly decoupled SOC content. Together, this study highlights that prolonged precipitation extremes shape coastal wetland microbiomes through divergent ecological trajectories; however, these microbial shifts may not necessarily translate directly into changes in soil carbon storage.},
}

@article {pmid42229596,
year = {2026},
author = {Lou, D and Duan, J and Zhou, B and Zhou, H and Wang, Y and Yang, J and Cui, J and Ma, X and Tan, J and Duan, H},
title = {Characterization and activity enhancement of a novel thermostable 3-quinuclidinone reductase through modulating the microenvironment of catalytic residues.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135058},
doi = {10.1016/j.biortech.2026.135058},
pmid = {42229596},
issn = {1873-2976},
abstract = {The biocatalytic synthesis of chiral alcohols offers a sustainable alternative to traditional chemical catalysis, yet the lack of robust, high-efficiency enzymes remains an industrial bottleneck. Here, a novel thermostable 3-quinuclidinone reductase (SdQR) was discovered via metagenomic mining of hot spring environments and biochemically characterized. Among the candidates, the H161Q variant, situated proximal to the conserved catalytic triad, emerged as a high-potential lead. Experimental validation revealed that the H161Q mutation yielded a 16-fold increase in catalytic efficiency (kcat/Km) over the wild-type enzyme while preserving its exceptional thermostability. Molecular dynamics (MD) simulations and MM-PBSA calculations elucidated the mechanistic basis for this enhancement: the mutation establishes a "structurally rigid yet physicochemically fluid" microenvironment. This subtle shift optimizes the hydrophobic landscape within the active pocket and modulates cofactor binding thermodynamics, lowering the desolvation energy barrier without compromising the robust structural scaffold. This study provides a highly potent biocatalyst for the asymmetric synthesis of (R)-3-quinuclidinol, and highlights a sophisticated engineering paradigm for the precise physicochemical fine-tuning of catalytic microenvironments in industrial enzymes.},
}

@article {pmid42218514,
year = {2026},
author = {Fabre, V and Robinson, ML and Martino, F and Monge, R and Forastiero, A and Corso, A and Pasteran, F and Karyakarte, R and Randive, B and Singh, S and Naik, M and Prasad, HB and Schwab, KJ and Simner, PJ and Berman, Y and Foy, WI and Salinas, AB and Gupta, A and Lu, J and Vasquez, AM and Noble-Wang, J and Moser, KA and Perry-Dow, KA and Patrick, M and Rock, C},
title = {Environmental reservoirs of carbapenem-resistant organisms in the intensive care unit: a multicenter longitudinal study in two middle-income country hospitals.},
journal = {Antimicrobial resistance and infection control},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13756-026-01768-x},
pmid = {42218514},
issn = {2047-2994},
support = {75D30121D12750/CC/CDC HHS/United States ; },
abstract = {BACKGROUND: There is limited data regarding environmental reservoirs of carbapenem-resistant organisms (CRO) during non-outbreak settings in resource-limited hospitals, or the role of these reservoirs in healthcare transmission.

METHODS: Prospective longitudinal study in which sinks and high-touch surfaces (HTS) were sampled prior to room cleaning in intensive care units (ICUs) in two hospitals (hospital A, Argentina, and hospital B, India), July 2023-February 2024. Selective media was used to recover CROs. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) pairwise analysis were performed on environmental and clinical isolates to evaluate bacterial transmission dynamics. Metagenomic sequencing was performed to evaluate bacterial diversity of environmental samples.

RESULTS: Of 541 environmental samples collected, 47.9% in hospital A and 97.5% in hospital B grew at least one CRO. Most CROs tested for the presence of a carbapenemase were positive (63.9-91.0% for hospital A and B isolates, respectively). Carbapenemase producer (CP)-Acinetobacter baumannii and CP-Pseudomonas spp. predominated in HTS and sinks samples, respectively, in hospital A; while CP-Klebsiella pneumoniae predominated in hospital B samples. WGS of 113 CRO isolates and SNP analysis demonstrated certain lineages established enduring reservoirs in the ICUs environment (e.g., blaVIM-36 P. aeruginosa ST395 isolates with 2-9 SNP difference were detected in sinks over 7 months). Several clusters involving environmental and clinical isolates that shared an epidemiological link and displayed ≤ 10 SNP difference were identified (e.g., blaOXA-23 A. baumannii ST195 isolated from three unique patients who stayed in the same private room on sampling months 4, 5, 6 and 7, and from HTS of that room on sampling month 5 displayed 0-3 SNP difference). Metagenomic analysis identified additional AMR genes of clinical importance.

CONCLUSIONS: CROs were abundant and persisted in the ICU environment in countries with high prevalence of MDROs. Our data suggests movement of clones between the environment and patients.},
}

@article {pmid42218533,
year = {2026},
author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY},
title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01680-4},
pmid = {42218533},
issn = {1756-994X},
support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; },
abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.

METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.

RESULTS: Durable disease control (PFS ≥ 24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.

CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).},
}

@article {pmid42218921,
year = {2026},
author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X},
title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108650},
doi = {10.1016/j.ympev.2026.108650},
pmid = {42218921},
issn = {1095-9513},
abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.

METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.

PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.

CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.},
}

@article {pmid42219044,
year = {2026},
author = {Shil, S and Dutta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A},
title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107565},
doi = {10.1016/j.mimet.2026.107565},
pmid = {42219044},
issn = {1872-8359},
abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.},
}

@article {pmid42219122,
year = {2026},
author = {Wang, X and Huang, Y and Xu, J and Lin, B and Chen, X and Li, ZH},
title = {Exogenous floc-granule replacement stabilizes aerobic granular sludge via quorum sensing/quorum quenching-mediated ecological reorganization.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135039},
doi = {10.1016/j.biortech.2026.135039},
pmid = {42219122},
issn = {1873-2976},
abstract = {Aerobic granular sludge (AGS) operation remains constrained by excessive granule enlargement, particle-size redistribution, and structural instability. In this study, exogenous floc-granule replacement was evaluated as a chemical-free, in situ particle-size management strategy for AGS. A conventional granulation reactor (R1) and an exogenous floc-granule replacement reactor (R2) were operated in parallel to compare granulation dynamics, reactor performance, extracellular polymeric substances (EPS), extracellular acyl-homoserine lactones (AHLs), respiration, bacterial partitioning, metagenomic functional gene profiles, and microbial co-occurrence patterns. During the first replacement window, R2 maintained smaller and more uniform granules than R1, with mean particle size of 220 μm on Day 83 compared with 378 μm in R1. R2 also maintained comparable chemical oxygen demand and NH4[+]-N removal performance and showed lower nitrite accumulation during rapid granulation. Particle-size regulation was accompanied by lower extracellular AHL accumulation, altered EPS composition, and distinct respiratory allocation, reflecting higher autotrophic-to-heterotrophic respiration ratio in R2 than in R1 on Day 82 (0.10 vs. 0.07). Comparative characterization indicated that exogenous flocs represented a distinct biomass fraction with smaller particle size, lower protein-to-polysaccharide ratio, and lower extracellular AHL accumulation than endogenous flocs and mature granules. Metagenomic and co-occurrence network analyses showed higher abundance of quorum quenching (QQ)-related genes and greater representation of QQ- or combined quorum sensing /QQ-associated taxa in R2. Overall, exogenous floc-granule replacement represents a tunable structure-based strategy for regulating AGS particle-size distribution, but its effectiveness should be further evaluated according to application scenario.},
}

@article {pmid42219517,
year = {2026},
author = {Velando, F and Molina, L and Hurtado, I and van Dillewijn, P and Segura, A},
title = {Aeonium decorum as a microbial recruitment platform for atmospheric polycyclic aromatic hydrocarbons mitigation in urban gardens.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00914-7},
pmid = {42219517},
issn = {2524-6372},
abstract = {BACKGROUND: In the context of the Sustainable Architecture, green roofs, green walls, green belts or urban farms are becoming popular infrastructures in cities and have been proposed as promising elements to ameliorate air pollution. Atmospheric contaminants are deposited not only on the foliar surface of plants, but also in soils. Plants may interact with pollutants, but their associated microbiomes (epiphytic, endophytic and rhizospheric) may harbor contaminant-degrading bacteria which could play an important role in pollutant mitigation. Therefore, we explored the effects of atmospheric contaminants, using naphthalene as a model compound, on some of the living elements of urban gardens (plants and microbiomes).

RESULTS: Exposure to gaseous naphthalene had weak effects on Aeonium decorum and Trifolium repens plants (measured as efficiency of photosystem II), and on soil bacterial diversity. Although the presence of naphthalene is not the major driver of soil bacterial community structure, metagenomic and qPCR analysis revealed an increase in polycyclic aromatic hydrocarbon (PAH)-ring hydroxylating dioxygenases in Aeonium planted soils, suggesting a positive effect of this plant species for the selection of potential contaminant-degrading microbes. We have also observed an increment in Pseudomonas (known for their capacity to degrade contaminants) and Solimonas in response to naphthalene. Validation of tools designed to evaluate the exposure of plants to atmospheric contaminants was performed creating urban gardens planted with A. decorum plants and exposed to environmental conditions.

CONCLUSIONS: Our results suggest that Pseudomonas and Solimonas could be used as markers for biodegradation. A. decorum is proposed as a good candidate for amelioration of atmospheric contaminants and gardens constructed with these plants carried PAH degrading bacteria on leaf surfaces indicating that they have the capacity to respond to the presence of contaminants.},
}

@article {pmid42219665,
year = {2026},
author = {Recio, MI and de la Torre, J and Rocha-Martin, J and de la Mata, I and Ramos, JL},
title = {A Biotechnological Approach to Enzyme-Based Fertilisers: Immobilisation of Acid Phosphatases.},
journal = {Microbial biotechnology},
volume = {19},
number = {6},
pages = {e70385},
doi = {10.1111/1751-7915.70385},
pmid = {42219665},
issn = {1751-7915},
support = {PID2021-123469OB-IOO//Agencia Estatal de Investigación/ ; MICIU/AEI/10.13039/501100011033//Agencia Estatal de Investigación/ ; PREDOC_01447//Consejería de Conocimiento, Investigación y Universidad, Junta de Andalucía/ ; },
mesh = {*Acid Phosphatase/metabolism/chemistry ; *Enzymes, Immobilized/metabolism/chemistry ; Hydrogen-Ion Concentration ; Enzyme Stability ; Clay ; *Fertilizers/analysis ; Aluminum Silicates/chemistry ; *Biotechnology/methods ; Temperature ; Soil/chemistry ; },
abstract = {We explore enzyme-based technologies as sustainable alternatives to conventional chemical fertilisers, addressing the challenges associated with using enzymes in free or immobilised form for agricultural applications. We use the metagenome-derived Class A acid phosphatase M2-32, selected for its high activity, broad pH tolerance and thermophilic properties, and evaluated its immobilisation on clay minerals to enhance stability and applicability in soils. Several clays were tested as immobilisation supports. Bentonite caused complete enzyme inactivation, while kaolin formed aggregates and was unsuitable. In contrast, palygorskite, sepiolite and agrozeolite adsorbed more than 99% of the added enzyme. However, only a fraction of the immobilised enzyme retained catalytic activity, with optimal performance observed at moderate protein loading (40-80 μg protein). Among the tested supports, palygorskite consistently provided the highest specific activity (22,000 ± 2200 U/mg), followed by sepiolite (11,000 ± 730 U/mg), whereas agrozeolite (2250 ± 40 U/mg) showed comparatively low activity. ATR-FTIR spectroscopy confirmed successful enzyme immobilisation without significant alteration of the clay structures. Immobilised M2-32 preserved a broad pH range (between 4 and 8.5) and thermophilic behaviour similar to the free enzyme, remaining active up to 50°C. Immobilisation increased substrate affinity while reducing Vmax relative to the free enzyme. To assess environmental compatibility, the effects of free and palygorskite-immobilised M2-32 on soil microbial communities were evaluated using corn rhizosphere microcosms with different organic matter contents. Metabarcoding high-throughput sequencing revealed that microbial diversity and community structure were primarily shaped by soil type, plant presence and incubation time. Enzyme application, whether free or immobilised, did not significantly alter microbial diversity or composition. Overall, these results support palygorskite-immobilised M2-32 as a promising, environmentally compatible candidate for enzyme-based fertiliser development.},
}

*Acid Phosphatase/metabolism/chemistry
*Enzymes, Immobilized/metabolism/chemistry
Hydrogen-Ion Concentration
Enzyme Stability
Clay
*Fertilizers/analysis
Aluminum Silicates/chemistry
*Biotechnology/methods
Temperature
Soil/chemistry

@article {pmid42219690,
year = {2026},
author = {Zhu, P and Yuan, X and Wang, X and Shi, Y},
title = {Application of Nano Silica Is Associated With Enhanced Wheat Resistance to Fusarium Crown Rot via Regulation of Metabolic Pathways and Soil Microbial Community.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70343},
doi = {10.1111/1462-2920.70343},
pmid = {42219690},
issn = {1462-2920},
support = {SDAIT0107//Shandong Modern Agricultural Technology & Industry System/ ; SDNYXTTG-2023-30//Agricultural Major Technology Collaborative Promotion Plan Project in Shandong Province/ ; },
mesh = {*Triticum/microbiology ; *Fusarium/physiology ; *Soil Microbiology ; *Silicon Dioxide/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention & control ; *Disease Resistance/drug effects ; Lignin/metabolism ; *Nanoparticles ; },
abstract = {Nano silica (NS) has promising agricultural applications, yet its effects and mechanisms in enhancing wheat resistance to Fusarium crown rot (FCR) caused by Fusarium pseudograminearum (FP) remain underexplored. Here, we conducted a pot experiment with 200 mg/L NS, integrating soil metagenomics, plant physiology, and metabolomics to investigate this process. Soil metagenomic analysis revealed that NS was associated with reshaped microbial community structure and distinct functional pathway variations (GO/KEGG annotations). In wheat, NS treatment was linked to activated fructose/mannose metabolism and phenylpropanoid biosynthesis, increasing SOD and POD activities by 14.5% and 169.9% and reducing MDA content by 37.0%. It was also associated with upregulated lignin-related enzymes (PAL, C4H, and 4CL) and their encoding genes, thus promoting lignin accumulation, enhancing stem strength, and restoring cellulose content. Our findings suggest a potential dual mechanism: NS-associated soil microbiome changes coincide with improved plant antioxidant capacity and defence gene expression, reinforcing stem integrity to alleviate FCR, providing new insights for eco-friendly FCR management.},
}

*Triticum/microbiology
*Fusarium/physiology
*Soil Microbiology
*Silicon Dioxide/pharmacology
Metabolic Networks and Pathways/drug effects
*Microbiota/drug effects
*Plant Diseases/microbiology/prevention & control
*Disease Resistance/drug effects
Lignin/metabolism
*Nanoparticles

@article {pmid42219901,
year = {2026},
author = {Yang, J and Shi, T and Du, Z and Wang, Y and Shen, J and Wu, C and Fu, B},
title = {Sub-inhibitory polyether ionophores enhance resistance plasmid transfer and transiently perturb the broiler gut resistome.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {6},
pages = {},
doi = {10.1093/jac/dkag190},
pmid = {42219901},
issn = {1460-2091},
support = {32141002//National Natural Science Foundation of China/ ; 81991535//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Ionophores/pharmacology/administration & dosage ; *Plasmids/genetics ; Chickens/microbiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; *Drug Resistance, Bacterial/genetics/drug effects ; Polyether Compounds ; Cecum/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Bacteria/drug effects/genetics ; Polyether Polyketides ; Conjugation, Genetic/drug effects ; Pyrans ; },
abstract = {BACKGROUND: Chronic sub-inhibitory antimicrobial exposures may shape antibiotic resistance (AMR) dissemination at the animal, food and environment interface. Polyether ionophore coccidiostats remain widely used in poultry production, yet their influence on AMR dissemination at sub-inhibitory exposure is unclear.

OBJECTIVES: To determine whether sub-minimum inhibitory concentration (MIC) polyether ionophores enhance resistance plasmid transfer in vitro and to characterize their effects on gut microbiota and resistome dynamics in vivo during and after administration.

METHODS: We investigated the effects of representative polyether ionophores at sub-MICs on resistance spreading phenotypes in vitro and gut resistome dynamics in VREfm-challenged broilers. In vitro plasmid conjugation and related phenotypes were quantified, and in vivo caecal microbiota and resistome were profiled by 16S rRNA gene sequencing and shotgun metagenomics.

RESULTS: Sub-MIC polyether ionophores increased plasmid conjugation, copy number and biofilm formation in Enterococcus spp., whereas no comparable effects were observed in Escherichia coli. In vivo, salinomycin temporarily disrupted caecal microbiota development and, at Day 20, suppression of indigenous taxa (e.g. Faecalibacterium) was accompanied by a transient surge in VREfm colonization and vanA abundance; resistome expansion was non-persistent. After salinomycin cessation, recovery of beneficial genera like Akkermansia was associated with reduction of the total resistance gene burden towards pre-treatment baseline by Day 42.

CONCLUSIONS: Polyether ionophores can promote resistance dissemination phenotypes in vitro, but gut ecological resilience may limit long-term impacts after cessation of exposure under recommended dosing conditions. The transient resistome surge during the treatment suggests increased shedding and potential environmental dissemination via manure, warranting surveillance and risk assessment.},
}

Animals
*Ionophores/pharmacology/administration & dosage
*Plasmids/genetics
Chickens/microbiology
Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/drug effects
*Drug Resistance, Bacterial/genetics/drug effects
Polyether Compounds
Cecum/microbiology
*Gene Transfer, Horizontal/drug effects
*Bacteria/drug effects/genetics
Polyether Polyketides
Conjugation, Genetic/drug effects
Pyrans

@article {pmid42221085,
year = {2026},
author = {Liu, F and Yang, K and Wu, M and Li, P and Luo, L},
title = {Case Report: Basal ganglia brain abscess caused by Nocardia farcinica.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1798434},
pmid = {42221085},
issn = {2296-858X},
abstract = {We report a rare case of Nocardia farcinica brain abscess in the basal ganglia, detailing its diagnosis, management, and rehabilitation. Diagnosing brain abscess based solely on clinical and imaging findings remains extremely challenging. Fortunately, metagenomic next-generation sequencing (mNGS) proved valuable in this case by rapidly identifying the pathogen, thereby facilitating targeted antibiotic therapy. This case highlights the importance of differentiating brain abscess from ischemic stroke and intracranial tumors. After completing a full course of anti-infective therapy and comprehensive rehabilitation, the patient achieved significant recovery in activities of daily living (ADL).},
}

@article {pmid42221483,
year = {2026},
author = {Yang, H and Liu, S and Chen, X and Yin, C and Xiao, L and Xu, W and Lv, S and Xie, L and Yin, C},
title = {Gut microbiota-associated immunomodulation contributes to the protective effects of fluvastatin against endometriosis in a mouse model, accompanied by increased Akkermansia muciniphila abundance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762444},
pmid = {42221483},
issn = {1664-302X},
abstract = {BACKGROUND: Endometriosis (EMs) is a chronic inflammatory disease characterized by tumor-like growth behavior and limited therapeutic options. Increasing evidence suggests that gut microbiota may contribute to EMs progression by promoting chronic inflammation and immune dysregulation. Fluvastatin, a lipid-lowering agent, exhibits anti-inflammatory, anti-tumor, and immunomodulatory effects and has also been reported to influence microbial homeostasis. However, the relationship among fluvastatin treatment, gut microbiota, and EMs progression remains unclear. This study aimed to investigate this relationship.

MATERIALS AND METHODS: A mouse model of EMs was established by autologous uterine tissue transplantation, followed by oral fluvastatin administration for 3 weeks. Lesion growth, inflammatory responses, and immune characteristics were evaluated by histology, quantitative PCR, flow cytometry, immunofluorescence, and immunohistochemistry. Gut microbiota involvement was assessed using antibiotic-mediated microbiota depletion and fecal microbiota transplantation (FMT). Microbial composition was analyzed by metagenomic sequencing. The role of Akkermansia muciniphila was evaluated by direct oral supplementation.

RESULTS: Fluvastatin significantly reduced the volume and mass of ectopic lesions and decreased the mRNA expression of pro-inflammatory cytokines. It was also associated with changes in macrophage polarization-related markers and reduced abnormal activation of splenic immune cells. Antibiotic-induced gut microbiota depletion attenuated the protective effects associated with fluvastatin treatment, whereas FMT from fluvastatin-treated mice partially transferred similar protective changes. Metagenomic analysis revealed that fluvastatin reshaped gut microbiota composition and increased the abundance of Akkermansia muciniphila. Moreover, oral supplementation with Akkermansia muciniphila attenuated EMs progression and was associated with anti-inflammatory and immune-related changes similar to those observed after fluvastatin treatment.

CONCLUSION: These findings suggest that the protective effects associated with fluvastatin treatment are accompanied by changes in gut microbiota composition, including increased abundance of Akkermansia muciniphila. Gut microbiota may contribute to the beneficial effects of fluvastatin in EMs. These results support the potential value of microbiota-informed therapeutic strategies for EMs.},
}

@article {pmid42221497,
year = {2026},
author = {Taussig, R and Peralta, R and Bustamante, JP},
title = {A pilot proof-of-concept study of microbial and botanical diversity in honey samples from Necochea, Argentina.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1833002},
pmid = {42221497},
issn = {1664-302X},
abstract = {INTRODUCTION: Honey is a complex biological matrix containing plant-derived, microbial, and viral components that reflect both environmental and hive-associated processes. Traditional methods for determining botanical origin, such as melissopalynology, have limitations in resolution and scope. In this context, untargeted shotgun metagenomics emerges as a promising integrative approach for comprehensive honey characterization.

METHODS: This pilot study explored the feasibility of applying an untargeted shotgun metagenomic approach to honey samples from Necochea, Buenos Aires province, Argentina. Two honey samples and a pollen control sample from Rosa chinensis were subjected to DNA extraction, shotgun library preparation, and sequencing on an Illumina NextSeq 500 platform.

RESULTS: The control sample showed exclusive assignment to Rosa chinensis, supporting the validity of the analytical workflow. In both honey samples, plant-derived sequences were predominantly assigned to Helianthus annuus (common sunflower) and Eucalyptus grandis (rose gum), consistent with the regional flora. Key bacterial taxa included Paenibacillus larvae in one sample, Acinetobacter johnsonii in the other, and Apilactobacillus kunkeei, Bradyrhizobium sp., Sphingobium yanoikuyae, and Stutzerimonas stutzeri in both. Apis mellifera filamentous virus was detected in both samples.

DISCUSSION: Given the limited sample size, these findings should be interpreted as exploratory and hypothesis-generating. Nevertheless, this proof-of-concept supports the potential of untargeted metagenomics as an integrated tool for the simultaneous characterization of botanical origin, microbial communities, and viral content in honey, offering advantages over targeted amplicon-based approaches. Future studies with larger and systematically designed cohorts will be necessary to validate and extend these observations.},
}

@article {pmid42221499,
year = {2026},
author = {Chang, N and Li, N and Li, W and Xue, J and Zheng, Y and Zhao, C and Zhang, S and Zhang, Y and Yin, G and Bao, M and Shen, W},
title = {Control efficacy and groundwater risk of antibiotic resistance genes in semi-arid landfill leachate treatment: seasonal insights and engineering implications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1807935},
pmid = {42221499},
issn = {1664-302X},
abstract = {Landfill leachate is a critical reservoir of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), posing prominent risks to groundwater, especially in semi-arid regions. This study focused on the performance of landfill leachate treatment system in Hohhot (Inner Mongolia, semi-arid region), investigating the seasonal variation across three seasons (spring, summer, and autumn), migration characteristics, and control effect of ARGs/MGEs through process optimization-oriented monitoring. Metagenomic sequencing was employed to analyze four key matrices (raw leachate, ultrafiltration effluent, treated leachate, and adjacent groundwater) across three seasons. The treatment system achieved efficient removal of conventional pollutants but failed to eliminate ARGs, MGEs, and antibiotic-resistant bacteria. Instead, it enriched high-risk hosts (e.g., Pseudomonas_E) and transposases (e.g., tnpA), exacerbating horizontal gene transfer potential. ARGs abundance showed pronounced peaks in summer and autumn among the sampled seasons. Notably, the resistome profile of treated leachate was highly similar to that of groundwater, indicating incomplete ARG containment and hydrological connectivity between the treatment system and groundwater. A dual-track health-environmental risk framework was applied to the detected ARG subtypes, revealing that overall risk burden was concentrated in a small set of high-priority determinants. The top contributors were dominated by mobility- and co-selection-linked markers (intI1, tnpA, IS6100, IS26, and qacE△1) together with clinically relevant resistance genes (sul1, aacA, and aadA), underscoring the coupling between resistance functions and genetic mobility in the leachate-groundwater continuum. Collectively, these findings indicate that semi-arid landfill systems can act as both sinks and sources of high-risk resistance determinants, and they highlight the need to integrate ARGs/MGEs-targeted treatment upgrades, seasonally adaptive operational strategies, and risk-based dual-track monitoring into leachate management. This study therefore provides actionable engineering insights for optimizing leachate treatment performance and mitigating cross-media contamination in water-scarce environments.},
}

@article {pmid42221583,
year = {2026},
author = {David Hanna, LB and Steinig, E and Bond, K and Lim, CK and Ramachandran, PS},
title = {Enrichment techniques for clinical metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1723747},
pmid = {42221583},
issn = {2235-2988},
mesh = {*Metagenomics/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Polymerase Chain Reaction/methods ; CRISPR-Cas Systems ; },
abstract = {Metagenomic next-generation sequencing (mNGS) offers a powerful, hypothesis-free approach for pathogen detection in clinical samples, allowing the identification of both known and novel microorganisms. However, the predominance of host nucleic acid in most samples poses a significant challenge, often overshadowing low-abundance pathogen sequences and increasing the cost of mNGS due to the high sequencing depth required. Enrichment techniques which selectively amplify pathogen-specific sequences can help to overcome this challenge, improving the sensitivity, specificity, and overall efficiency of mNGS - albeit while compromising the hypothesis-free nature and breadth of shotgun mNGS. As such, they can augment the use of mNGS in clinical scenarios where a more targeted approach is needed. This review provides a comprehensive analysis of the main enrichment techniques currently employed in the field, including PCR-based enrichment, CRISPR-Cas9 enrichment, molecular inversion probes (MIP), nanopore adaptive sequencing (AS), and hybridisation capture-based methods. We evaluate each method on a range of metrics including methodology, cost, sensitivity, specificity, and ease of integration into clinical workflows, as well as describing their application to date for purposes including pathogen detection, antimicrobial resistance profiling, and whole-genome sequencing across diverse clinical sample types. Current limitations and future directions for refinement and implementation of these techniques are also discussed. By summarising the current landscape and latest advancements in mNGS enrichment strategies, this review aims to guide the optimisation of mNGS workflows in clinical diagnostics and highlight key areas for future research.},
}

*Metagenomics/methods
Humans
*High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity
Polymerase Chain Reaction/methods
CRISPR-Cas Systems

@article {pmid42221911,
year = {2026},
author = {Gazulla, CR and Ferrera, I and Balagué, V and Marín-Vindas, C and González-Vega, A and Escánez-Pérez, J and Fraile-Nuez, E and Arrieta, JM and Gasol, JM and Sánchez, O},
title = {Diversity and community structure of aerobic anoxygenic phototrophic bacteria are shaped by the deep chlorophyll maximum.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag076},
pmid = {42221911},
issn = {2730-6151},
abstract = {The surface ocean exhibits strong vertical gradients in light irradiance, nutrients, and temperature, shaping the phytoplankton distribution, which often defines a deep chlorophyll maximum (DCM). Aerobic anoxygenic phototrophic (AAP) bacteria inhabit the euphotic zone, with their abundances generally following the chlorophyll a variability. While AAP bacterial communities are known to differ across regions with contrasting environmental conditions, their vertical distribution remains poorly understood. We hypothesized that the diversity and community structure of AAP bacteria vary across the vertical gradient, in relation to changes in environmental variables and following the DCM profile. To test this hypothesis, we studied the composition of AAP communities at different depths along the DCM structure in the South and Central Atlantic Ocean, by means of amplicon sequencing of the pufM gene. The results show significant differences in richness, community structure, and taxonomic composition of samples from different layers of the DCM, highlighting the dependence of AAP bacteria on its structure. Remarkably, the use of primers with broad phylogenetic coverage enabled the recovery of several AAP phylogroups previously detected only through metagenomics. We show that they represent a significant fraction of marine AAP communities, provide clues about their ecological preferences, and confirm their association with the family Candidatus Luxescamonaceae.},
}

@article {pmid42222018,
year = {2026},
author = {Ye, J and Ye, L and Sun, W and Xie, S and Lai, Z},
title = {A case of infective endocarditis caused by Streptococcus gordonii complicated with bacterial meningitis and cerebral infarction -- Application of metagenomic next-generation sequencing (mNGS).},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02608},
pmid = {42222018},
issn = {2214-2509},
abstract = {This study reports a case of infective endocarditis (IE) caused by Streptococcus gordonii. The patient presented with cerebral infarction as the initial manifestation, complicated by bacterial meningitis and mitral regurgitation. The diagnosis of Streptococcus gordonii-induced infective endocarditis was facilitated by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). Streptococcus gordonii was detected by CSF mNGS within 40 h after admission, which was 30 h earlier than the positive result of blood culture. During anti-infective therapy, the patient experienced recurrent thromboembolic events and underwent emergency mechanical thrombectomy due to occlusion of the left vertebral artery. Despite aggressive treatment, the patient eventually died of heart failure. This case indicates that Streptococcus gordonii is a rare pathogen of infective endocarditis, and its clinical presentation complicated by cerebral infarction and bacterial meningitis is distinctive; particularly, complex cases requiring mechanical thrombectomy are extremely rare in clinical practice. As an important complement to conventional bacterial culture, mNGS can shorten diagnostic delay, especially in patients with negative blood or CSF cultures. For patients with concurrent cerebral infarction and meningitis, the possibility of infective endocarditis should be highly suspected, and indications for valve replacement surgery should be evaluated as early as possible in high-risk cases.},
}

@article {pmid42222019,
year = {2026},
author = {Wang, F and Xie, C and Zhao, M and Pan, Y and Xie, Y and Wang, X and Zhu, W and Xie, Y},
title = {VV-ECMO-supported management of severe ARDS secondary to melioidosis sepsis: A case report and concise review.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02612},
pmid = {42222019},
issn = {2214-2509},
abstract = {Melioidosis, caused by Burkholderia pseudomallei (B. pseudomallei), is a life-threatening tropical infection that is frequently underdiagnosed because of its heterogeneous and nonspecific clinical presentation. We report a critically ill patient from an endemic area who developed fulminant pneumonia that progressed to septic shock and severe acute respiratory distress syndrome. Despite empirical broad-spectrum antimicrobial therapy, respiratory failure worsened, prompting early etiologic investigation with metagenomic next-generation sequencing, which identified B. pseudomallei and was subsequently confirmed by culture. The patient required early venovenous extracorporeal membrane oxygenation (ECMO) for refractory hypoxemia. Management included a targeted antimicrobial therapy in accordance with current guidelines and CT-guided drainage of a pulmonary abscess as definitive source control. The patient achieved full recovery without recurrence at follow-up. Early identification of the causative pathogen and timely source control were central to the management of melioidosis-associated severe ARDS. Advanced supportive measures, including ECMO, may be considered in selected patients with refractory hypoxemia as part of management involving multiple specialties.},
}

@article {pmid42222035,
year = {2026},
author = {Liu, YH and Fang, SR and Chen, W and Wu, YF and Liu, DK and Li, T},
title = {Comparative Study of Confirmed versus Suspected Cases of Vibrio vulnificus Infection in Chaoshan District, Guangdong, China.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {613123},
pmid = {42222035},
issn = {1178-6973},
abstract = {OBJECTIVE: To compare the epidemiological, clinical, and laboratory data of patients with confirmed and suspected Vibrio vulnificus infection in Chaoshan District, Guangdong.

METHODS: This retrospective study analyzed 25 confirmed cases and 23 suspected cases of V. vulnificus infection at the First Affiliated Hospital of Shantou University Medical College from January 2014 to December 2025. A confirmed case was defined by the presence of a positive result from culture and/or mNGS and a suspected case by the experience of a clear marine trauma followed by rapidly progressive soft tissue manifestations, but without etiological confirmation of V. vulnificus infection after exclusion of other infectious etiologies. The epidemiological history, early clinical manifestations, routine blood parameters, and in-hospital outcomes of the two groups were compared.

RESULTS: The confirmed group had a greater severity of soft tissue infection (84.0% vs 26.0%, P<0.01) and more involved sites (88.0% vs 47.8%, P<0.01). The laboratory data indicated the confirmed group had more abnormalities in markers of tissue injury (creatinine kinase, lactate dehydrogenase), coagulation function (platelets, prothrombin time, international normalized ratio), liver function (aspartate transaminase, total bilirubin), renal function (serum creatinine), and lipid and nutritional markers (all P<0.05). The confirmed group also had significantly higher rates of in-hospital mortality (32.0% vs 0%), multi-organ dysfunction syndrome (36.0% vs 0%), and surgical intervention (60.0% vs 30.4%), and a greater economic burden (all P<0.001).

CONCLUSION: There are significant differences in the early clinical manifestations, routine blood parameters, and in-hospital outcomes for patients with confirmed and suspected V. vulnificus infection.},
}

@article {pmid42222136,
year = {2026},
author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC},
title = {Protist community sites and structure under two barn management systems at a commercial dairy.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1803341},
pmid = {42222136},
issn = {2813-4338},
abstract = {INTRODUCTION: Investigations into the location and load of protists in the environment arounddairies are scarce but are essential to maintaining the health of livestock.Moreover, the design of dairy barns has fluctuated over the decades to maximizecattle health and milk production without regard to influences on environmentalmicrobiomes. Beyond cost, the major emphasis of barn design is the managementof appropriate temperature and comfort for cattle. However, there havebeen no corresponding investigations into whether these design changes affect protist communities within barns.

METHODS: In this study, community shotgun metagenomic analysis was used to define the spatial composition and relative abundance of protist communities from 118 samples of manure, lagoons, troughs, and house and stable flies at a commercial dairy implementing two free-stall management systems: flow-through and cross-vent. Sequence reads were mapped to the CosmosID database. Viability was not assessed; therefore, results reflect DNA detection only not viability or disease occurrence.

RESULTS: The protist composition differed significantly between dairy components. Ecological findings showed that troughs and lagoons harbored high protist diversity, including the possible pathogen Neobalantidium coli and potential carriers Paramecium biaurelia and Acanthamoeba. Manure had the lowest protist diversity. Stable flies carried more protist taxa than house flies. Both fly species uniquely carried the non-pathogenic alveolate parasite Hammondia hammondi. The water mold plant pathogen Pseudoperonospora cubensis was identified in all sample types. Of the total relative abundance of protists, 2.10% were amoebas, 7.63% alveolate parasites, 62.71% water molds, 23.31% ciliates, 1.74% foraminifera, and 2.50% diatoms.

DISCUSSION: These results describe preliminary spatial overlaps and possible avenues of dissemination, providing a basis for assessing appropriate management systems and identifying protist reservoir sites within dairy operations.},
}

@article {pmid42222213,
year = {2026},
author = {Zhou, Y and Lai, Y and Zhou, F and Wang, X and He, X and Jin, J and Zhang, R},
title = {Morphological analysis of bronchoalveolar lavage fluid in diagnosing pulmonary aspergilloma in a patient with rheumatoid arthritis: A case report.},
journal = {Experimental and therapeutic medicine},
volume = {32},
number = {1},
pages = {191},
pmid = {42222213},
issn = {1792-1015},
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disorder that primarily affects the joints and may be associated with systemic complications. Patients with RA have an increased susceptibility to opportunistic infections, attributable to inherent immune dysregulation as well as immunosuppressive therapies, including tocilizumab, particularly among those with comorbidities or high disease activity. Notably, the use of tumor necrosis factor inhibitors, such as adalimumab and etanercept, has been associated with a higher incidence of invasive pulmonary aspergillosis and chronic pulmonary aspergillosis. The present study reports a rare case of pulmonary aspergilloma in a 75-year-old female RA patient with prior tuberculosis and long-term tocilizumab use. The patient was diagnosed via bronchoalveolar lavage fluid morphology, fungal culture, Aspergillus galactomannan assay, metagenomic next-generation sequencing and pathology, and the patient achieved symptom resolution and improved imaging after 6 months of treatment with voriconazole. These findings underscore the need for vigilant monitoring and individualized management strategies in this patient population.},
}

@article {pmid42222492,
year = {2026},
author = {Tran, TTT and Nguyen, OTK and Hoang, PH and Nguyen, NP and To, HTM and Nguyen, HQ},
title = {Metagenomic and metabolomic analyses of fecal samples from civet-digested coffee in Vietnam.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21262},
pmid = {42222492},
issn = {2167-8359},
mesh = {*Feces/microbiology/chemistry ; Vietnam ; *Coffee/metabolism/microbiology ; *Metabolomics ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; Fermentation ; Humans ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism ; Animals ; },
abstract = {BACKGROUND: Civet-digested coffee originates from the feces of civets that consume coffee cherries, where microbial fermentation in the gastrointestinal tract imparts distinctive flavor attributes, thereby enhancing its global reputation and market value. Gut microbiota is considered important drivers of coffee-bean fermentation, potentially shaping the unique and region-specific flavor characteristics of civet-digested coffee. To address this context, the present study integrated metagenomic and metabolomic analyses to compare the gut microbiota and secondary metabolites involved in coffee-bean fermentation inside Vietnamese civets.

METHODS: Fecal samples were collected under two dietary conditions: a standardized one containing 20% protein, 6% fiber, and 0.4-1.5% lysine, and the same diet supplemented with coffee cherries. Metagenomic 16S rRNA sequencing and untargeted ultra-performance liquid chromatography quadrupole time-of-flight (UPLC-QTOF) revealed clear differences between the two groups.

RESULTS: Integrated metagenomic and metabolomic analyses revealed clear distinctions between the two groups. Civets on the coffee-cherry diet exhibited higher microbial diversity at the family and genus levels. Specifically, among 31 classified bacterial genera showing a trend toward significant differences in abundance, Enterococcus and Escherichia/Shigella decreased, whereas Gluconobacter, and Pseudomonas increased following the diet shift. Metabolomic profiling identified 46 metabolites across both ionization modes, and strong correlations were observed between microbial genera and metabolite profiles. Specifically, 6-hydroxyangolensic acid methyl ester, 4-aminobenzoic acid and caffeine were more abundant in civets on a coffee-cherry diet, meanwhile the other nine metabolites were more prevalent in the normal diet. Overall, the findings demonstrate that civet gut microbiota and metabolic output were highly responsive to dietary inputs, and that coffee cherries promoted a unique fermentation environment. This represents the first integrative metagenomic and metabolomic study of civets consuming coffee in Vietnam, providing valuable insights into microbial contributions to coffee fermentation.},
}

*Feces/microbiology/chemistry
Vietnam
*Coffee/metabolism/microbiology
*Metabolomics
*Metagenomics
*Gastrointestinal Microbiome/genetics
Fermentation
Humans
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/metabolism
Animals

@article {pmid42222536,
year = {2026},
author = {Yang, H and Zhao, L},
title = {Clinical characteristics and prognostic analysis of patients with herpesvirus meningitis/encephalitis based on cerebrospinal fluid mNGS positivity.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1808867},
pmid = {42222536},
issn = {1664-2295},
abstract = {BACKGROUND: Herpes viruses are a major cause of meningitis/encephalitis in adults. However, their individual clinical phenotypes and outcomes remain incompletely delineated. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) offers a powerful tool for precise pathogen identification, facilitating the comparison of distinct herpes virus infections.

METHODS: This retrospective cohort study analyzed 66 patients with CSF-mNGS confirmed herpes virus meningitis/encephalitis at a single center between October 2019 and August 2025. The cohort was stratified into five etiological groups: herpes simplex virus type 1 (HSV-1, n = 10), herpes simplex virus type 2 (HSV-2, n = 5), varicella-zoster virus (VZV, n = 27), Epstein-Barr virus (EBV, n = 15), and human herpesvirus 7 (HHV-7, n = 9). Demographic, clinical, laboratory, and neuroimaging data were collected. Outcomes were assessed using the Glasgow Outcome Scale (GOS) at 3 months post-discharge.

RESULTS: Distinct clinical phenotypes were observed. HSV-1 encephalitis typically presented with psychiatric symptoms, seizures, and temporal lobe involvement on MRI. HSV-2 infection manifested primarily as a febrile headache syndrome with minimal brain parenchymal involvement. VZV infection was associated with the most intense CSF inflammatory response (highest WBC and protein), a higher incidence of hypoglycorrhachia (25.9%) and hypochloridia (40.7%), and unique complications like cranial neuritis and vasculopathy. EBV infections occurred in older patients and showed features overlapping with HSV-1. HHV-7 infected a significantly younger population and was strikingly associated with elevated intracranial pressure (ICP ≥ 330 mmH2O in 33.3%). Multivariate analysis identified a longer interval from symptom onset to hospitalization (OR: 1.118, p = 0.025) and an abnormal EEG (OR: 0.066, p < 0.001) as independent predictors of an unfavorable outcome (GOS < 5). Antiviral or steroid therapy was not significantly associated with prognosis in this cohort.

CONCLUSION: CSF-mNGS reveals distinct and clinically significant phenotypic differences among various herpesvirus meningitis/encephalitis. VZV is characterized by a vigorous CSF inflammatory response and vascular complications, while HHV-7 predominantly affects younger adults and is significantly associated with intracranial hypertension. These findings underscore the value of mNGS in enabling pathogen-directed diagnosis and management, moving beyond syndromic approaches.},
}

@article {pmid42222738,
year = {2026},
author = {Park, JH and Chung, J and Lee, HJ and Na, HS},
title = {Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2679807},
pmid = {42222738},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease driven by a dysbiotic subgingival microbiome. While 16S rRNA gene amplicon sequencing is widely used, whole-genome shotgun (WGS) metagenomics is increasingly applied for higher taxonomic and functional resolution.

OBJECTIVE: The aim of this study was to directly compare 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomic sequencing using matched subgingival plaque samples from patients with periodontitis.

METHODS: Subgingival plaque samples from 28 patients with periodontitis were analyzed using both 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomics. Taxonomic composition, microbial diversity, differential abundance and functional analysis were compared across platforms.

RESULTS: WGS generated markedly higher read counts than 16S rRNA gene amplicon but showed wide variability in non-human reads, whereas 16S rRNA gene amplicon yielded a consistent proportion of non-chimeric reads. High taxonomic overlap was observed at the phylum level but declined at higher taxonomic ranks. WGS preferentially detected taxa such as Actinomyces, Corynebacterium and Olsenella, while the 16S rRNA gene amplicon more frequently captured Saccharibacteria (TM7) and low-abundance taxa. Core genera, including Rothia, Neisseria and Cardiobacterium showed comparable abundance patterns across platforms. When patients were grouped depending on probing pocket depth (PPD), LEfSe analysis resulted in platform-specific enrichment patterns. Functional analyses revealed shared central pathways, such as pyruvate metabolism, while 16S-based PICRUSt2 emphasized reductive and degradative pathways and WGS-based HUMAnN highlighted oxidative and biosynthetic pathways. Notably, WGS-based functional profiles were strongly influenced by microbial read depth.

CONCLUSIONS: This comparative analysis demonstrates that 16S rRNA gene amplicon (V1-V2) sequencing and WGS both robustly capture core subgingival microbial signatures. While WGS provides higher species-level and functional resolution, the resolution was strongly constrained by microbial read depth in host-rich subgingival samples. These findings provide practical guidance for selecting appropriate sequencing strategies and optimizing sample preparation when designing WGS-based periodontal microbiome studies.},
}

@article {pmid42222901,
year = {2026},
author = {Dong, Y and Hu, D and Yang, R and Xin, T and Guan, Y and Zhu, X and Ding, Y and Cui, S and Wang, R and Wang, X and Niu, Y and Kong, X},
title = {Early-Life Obesity Leaves a Metabolic Memory That Accelerates Aging-Related Decline Through the Gut Microbiota-GABA Axis.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {11},
pages = {e70513},
doi = {10.1002/mnfr.70513},
pmid = {42222901},
issn = {1613-4133},
support = {2024YFF1106004//National Key Research and Development Program/ ; PL2025H095//Natural Science Foundation of Heilongjiang Province/ ; },
mesh = {Animals ; *gamma-Aminobutyric Acid/metabolism/pharmacology ; *Aging/metabolism/physiology ; *Obesity/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; Diet, High-Fat/adverse effects ; Male ; Oxidative Stress ; Rats ; Lipid Metabolism ; },
abstract = {Childhood obesity is a critical public health concern. Whether diet-induced transient obesity during development negatively impacts later-life health remains unclear, and mechanisms are poorly understood. This study investigates whether these effects persist into aging and employs integrated omics to explore underlying mechanisms. Using a high-fat diet (HFD) to induce transient developmental obesity in post-weaning rats and larval Drosophila, we examined the long-term effects on aging metabolic health in both species. Transient developmental obesity in rats was linked to accelerated aging, weight loss, worsened metabolism, colonic inflammation, and oxidative stress. Metabolomics revealed persistent gamma aminobutyric acid (GABA) dysregulation associated with intestinal ammonia levels, and gut metagenomics showed a reduction in Lactobacillales, correlating with adverse health outcomes. In Drosophila, exogenous GABA extended HF-diet lifespan. It reduced trehalose, triglycerides (TG), and oxidative stress; concurrently, it restored intestinal Lactobacillus and activated the phosphotransferase system (PTS), thereby improving metabolic homeostasis and redox status. Transient developmental obesity is associated with reduced gut Lactobacillus abundance, which may contribute to decreased GABA levels and subsequent disruption of glucose (GLU) metabolism, potentially involving the PTS pathway. These interconnected alterations may ultimately lead to systemic dysregulation of GLU and lipid metabolism and redox homeostasis in later life, compromising overall health and longevity.},
}

Animals
*gamma-Aminobutyric Acid/metabolism/pharmacology
*Aging/metabolism/physiology
*Obesity/metabolism/microbiology/etiology
*Gastrointestinal Microbiome/physiology
Diet, High-Fat/adverse effects
Male
Oxidative Stress
Rats
Lipid Metabolism

@article {pmid42223080,
year = {2026},
author = {An, SY and Kim, I and Hong, SH and Kim, EH and Suh, JY},
title = {AcrIIA8 is a putative phage structural protein of the HTJ2 family that does not inhibit Streptococcus pyogenes Cas9.},
journal = {Protein science : a publication of the Protein Society},
volume = {35},
number = {7},
pages = {e70651},
doi = {10.1002/pro.70651},
pmid = {42223080},
issn = {1469-896X},
support = {RS-2025-23525174//National Research Foundation of Korea/ ; RS-2024-00440614//National Research Foundation of Korea/ ; BDB-2025-04-04230007//Korea Institute of Marine Science & Technology Promotion/ ; },
mesh = {*Streptococcus pyogenes/enzymology/genetics/virology ; *CRISPR-Associated Protein 9/antagonists & inhibitors/chemistry/metabolism ; *Viral Structural Proteins/chemistry/metabolism/genetics ; *Bacteriophages/chemistry ; },
abstract = {Anti-CRISPR (Acr) proteins are phage-encoded anti-defense factors that suppress CRISPR-Cas immunity in bacteria. AcrIIA8 was previously identified as an inhibitor of Streptococcus pyogenes Cas9 (SpyCas9) through functional assays of metagenomic libraries. Here, we report that AcrIIA8 does not inhibit SpyCas9 in biochemical assays under a range of buffer conditions and temperatures. The solution structure and dynamics of AcrIIA8 reveal a six-stranded β-barrel fold with flexible β1-β2 and β2-β3 loops, characteristic of phage virion-assembly proteins. In addition, genomic context analysis places AcrIIA8 and its homologs within conserved prophage morphogenetic regions at the position expected for type II head-tail joining (HTJ2) proteins. We further detected no interaction between AcrIIA8 and SpyCas9 in NMR titration experiments, suggesting that they do not specifically associate. Taken together, these findings argue against assigning AcrIIA8 as a SpyCas9 inhibitor and instead support its annotation as a putative phage structural protein of the HTJ2 family.},
}

*Streptococcus pyogenes/enzymology/genetics/virology
*CRISPR-Associated Protein 9/antagonists & inhibitors/chemistry/metabolism
*Viral Structural Proteins/chemistry/metabolism/genetics
*Bacteriophages/chemistry

@article {pmid42223254,
year = {2026},
author = {Petricciuolo, M and Carnevali, A and Torboli, A and Postinghel, M and Guasticchi, A and Foladori, P and Cadonna, M and Federici, E},
title = {Wastewater-Based Assessment of Antimicrobial Resistance and Bacterial Communities in Urban and Rural Areas in the Province of Trento (Italy).},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70319},
doi = {10.1002/mbo3.70319},
pmid = {42223254},
issn = {2045-8827},
support = {//CINECA/ ; //Ministero dell'Università e della Ricerca/ ; },
mesh = {Italy ; *Bacteria/drug effects/genetics/isolation & purification/classification ; *Anti-Bacterial Agents/pharmacology ; *Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rural Population ; Sewage/microbiology ; },
abstract = {Wastewater-based epidemiology (WBE) can supplement clinical surveillance for assessing the spread of antimicrobial resistance (AMR) across the population. We have analyzed sewage samples from seven wastewater treatment plants in the Province of Trento (Italy) using both culture-based and metagenomic DNA methods to investigate the prevalence of antimicrobial-resistant bacteria (ARBs) and resistance genes in urban and rural areas. ESBL-Escherichia coli prevalence was higher in urban areas than in rural ones. As determined by qPCR and dPCR, intI1 and genes associated with widespread resistances, namely, to tetracyclines (tetA), sulfonamides (sul1), and fluoroquinolones (qnrS), were abundant regardless of the area of origin. Among the genes coding for clinically relevant resistances, only that related to macrolides resistance (ermB) was abundant, while the others, namely, those to third-generation cephalosporins (blaCTX-M), carbapenems (blaKPC), vancomycin (vanA), and methicillin (mecA), were detected at much lower concentrations. Further, the abundances of ermB, blaKPC, and vanA were significantly higher in urban areas. 16S rRNA amplicon sequencing showed the occurrence of complex bacterial communities and the abundance of Acinetobacter, Pseudomonas, and Streptococcus, genera that may include ARBs reported in the WHO Bacterial Priority Pathogens List, with the latter showing higher prevalence in urban areas. Taken together, our data highlights the importance of implementing WBE studies across geographical areas with different characteristics in terms of vocation, number of municipalities, and population size, such as urban and rural ones. By providing a comprehensive understanding of AMR at the population level, this approach can inform and support more effective public health interventions.},
}

Italy
*Bacteria/drug effects/genetics/isolation & purification/classification
*Anti-Bacterial Agents/pharmacology
*Wastewater/microbiology
*Drug Resistance, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Rural Population
Sewage/microbiology

@article {pmid42223272,
year = {2026},
author = {Borton, MA and Oliverio, AM and Narrowe, AB and Villa, JA and Rinke, C and Hoyt, DW and Liu, P and McGivern, BB and Bechtold, EK and Ellenbogen, JB and Daly, RA and Smith, GJ and Angle, JC and Flynn, RM and Freiburger, AP and Louie, KB and Stemple, B and Northen, TR and Henry, C and Miller, CS and Morin, TH and Bohrer, G and Wrighton, KC},
title = {Mapping the soil microbiome functions shaping wetland methane emissions.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0068025},
doi = {10.1128/msystems.00680-25},
pmid = {42223272},
issn = {2379-5077},
abstract = {Accounting for only 8% of Earth's land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.IMPORTANCESoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single-lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.},
}

@article {pmid42223530,
year = {2026},
author = {Pokharel, SK and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, DC},
title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag140},
pmid = {42223530},
issn = {1751-7370},
abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Time-lapse microscopy revealed that Archangium exhibited reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate) but maintained robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.},
}

@article {pmid42224759,
year = {2026},
author = {Xu, M and Qi, S and Yu, X and Han, S and Xiao, R and Guo, J and Wang, C and Zhu, N and Lu, H},
title = {Resistome risks of biological wastewater treatment communities: A global dataset of activated sludge, anaerobic digestion, and anammox.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142561},
doi = {10.1016/j.jhazmat.2026.142561},
pmid = {42224759},
issn = {1873-3336},
abstract = {Activated sludge (AS), anaerobic digestion (AD), and anammox (AMX) systems are widely used for wastewater treatment. Their microbial communities harbor resistomes, including but not limited to antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), which may pose potential risks to human and ecological health if they are mobilized or transferred to pathogenic hosts. However, cross-process comparisons of resistome risks are limited at a global scale. This study analyzed 225 metagenomic datasets (210 public: 70 each for AS, AD, AMX; plus 15 in-house AMX) to assess resistome risks and identified key influential factors. Overall, within the constraints of current data availability, North America, Europe and Asia systems exhibited comparable risk levels. AD systems exhibited more than 2-fold higher human health resistome risks (potentials for human pathogens of acute resistance concern to acquire ARGs) than AS and AMX systems. Mesophilic and co-digestion AD systems posed 30-90% higher risks than thermophilic and mono-digestion systems with higher abundance of pathogens, ARGs, and MRGs. AMX systems, otherwise, showed higher ecological resistome risks (overall mobility of ARGs/MRGs and potentials for pathogen acquisition) than AS and AD. The conservative AMX communities contained core taxa that harbor 19.8% more ARGs/MRGs per genome and exhibit 31.4% higher horizontal gene transfer potential than non-core taxa. Key operating factors influencing resistome risks included temperature for AD, and organic loading, influent antibiotics and heavy metals for AMX. These findings provide insights into future wastewater treatment towards improved efficacy and reduced resistome risks.},
}

@article {pmid42215825,
year = {2026},
author = {Lv, J and Wang, JH and Wang, YY and Huang, J and Chen, FR and Fang, S and Wang, XJ and Li, ZT and Shi, YP and Guo, L},
title = {Gut microbial alterations and functional shifts in patients with hypertriglyceridemia: insights from a northwestern Chinese metagenomic study.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42215825},
issn = {1618-1905},
support = {2025JC-YBMS-916//Shaanxi Natural Science Foundation of China/ ; No. 81702067 and 82560411//National Natural Science Foundation of China/ ; },
abstract = {Although hypertriglyceridemia (HTG) is a significant contributor to lipid-associated pathologies such as atherosclerotic cardiovascular disease, its regulation by host‒microbiome interactions remain insufficiently characterized. While the gut microbiota (GM) is known to influence cholesterol metabolism, its specific role in systemic triglyceride (TG) homeostasis, particularly in non-Western populations, is poorly defined. This study aimed to identify preliminary robust GM signatures associated with HTG and to assess their translational potential using integrated multiomics and explainable machine learning approaches. In a cross-sectional investigation of 50 well-phenotyped adults from Northwest China, we combined 16S rRNA sequencing, shotgun metagenomics, and ensemble machine learning (LightGBM/XGBoost) to elucidate the associations between the GM and TGs. Microbial features were rigorously linked to serum lipid profiles through dual-algorithm validation and SHAP interpretability analysis, while functional potential was assessed via KEGG pathway mapping. Subjects with HTG exhibited a distinct gut microbial configuration, marked by consistent enrichment of Faecalibacterium and Bacteroides coprocola (positively correlated with serum TG levels) and depletion of Bifidobacterium pseudocatenulatum and Lactobacillus salivarius (inversely correlated). Machine learning converged on five exploratory consensus biomarker taxa, three of which were independently confirmed by LEfSe analysis (Faecalibacterium). Functional profiling further revealed the upregulation of microbial starch and sucrose metabolism pathways in the HTG cohort. Our findings establish a preliminary gut microbial signature for HTG patients and suggest context‑dependent associations of butyrate-producing taxa such as Faecalibacterium. By integrating multiomics with explainable artificial intelligence, this work addresses key challenges in reproducibility and mechanistic inference in microbiome research. These results pave the way for novel microbiota-targeted therapeutic strategies, including precision probiotics and dietary interventions, to modulate lipid metabolism, pending further validation in expanded cohorts and functional studies.},
}

@article {pmid42215894,
year = {2026},
author = {Russell, T and Formiconi, E and Murphy, A and Hortion, J and McElroy, M and Casey, M and Cuartero, LG and Mee, JF and Jahns, H and Kelly, C and Byrne, J and Feeney, ER and Mallon, PW and Gautier, VW},
title = {One health viral metagenomics for pathogen surveillance: robust mNGS workflows for viral detection and genome recovery from swab and tissue specimens.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05105-5},
pmid = {42215894},
issn = {1471-2180},
support = {101132970, EU4H-2022-DGA-MS-IBA3//European Commission/ ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is an untargeted approach that enables detection of pathogens directly from samples without prior knowledge of their genetic sequences. In the context of pandemic preparedness and One Health surveillance, there is a pressing need for robust viral mNGS workflows that perform reliably across diverse hosts sample types and pre-analytical conditions.

RESULTS: The study evaluated two shotgun mNGS workflows, one for swabs and one for complex tissue matrices, using a reference repository of clinical and post-mortem samples. The panel comprised swabs and tissue samples positive for 18 DNA and RNA viruses (including 12 species) from nine host species and nine anatomical sites, encompassing a range of transport media, storage temperatures and processing timelines. Quality control metrics were embedded throughout nucleic acid extraction, library preparation and sequencing to monitor performance and support interpretation. Overall, 88.9% of 18 DNA and RNA viruses previously detected by PCR were identified, including from samples with low nucleic acid concentrations (< 1 ng/µl) and variable integrity and purity. The workflows identified viral co-infections that had not been detected by prior targeted testing, as well as Phocid herpesvirus 7 (PHV7) for which no complete reference genome was initially available.

CONCLUSIONS: These results demonstrate the feasibility and robustness of the swab and tissue mNGS workflows for virus identification across a range of complex clinical specimens supporting their use in investigations of suspected viral diseases of unknown aetiology and is currently being evaluated for early detection of emerging viral threats at the animal-human interface.},
}

@article {pmid42216070,
year = {2026},
author = {Liu, LM and Zhang, YL and Zhou, JT and Yu, QQ and Zhang, WY and Wang, WF and Pang, SD and Miao, H and Zhao, YY},
title = {Ureic clearance granule ameliorates chronic kidney disease by reshaping microbial dysbiosis via modulating bile acid metabolism.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {42216070},
issn = {1749-8546},
support = {82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Shaanxi Key Science and Technology Plan Project/ ; },
abstract = {BACKGROUND: Chronic kidney disease (CKD) is a highly prevalent global public health problem that inevitably leads to renal failure. Although renin-angiotensin system blockers, as first-line therapy, can reduce proteinuria, they cannot prevent the progression to end-stage renal disease. Therefore, the development of new treatment strategies is urgently required. The uremic clearance granule (UCG) was widely used in patients with CKD. However, the underlying molecular mechanisms of UCG for CKD treatment remain unclear.

METHODS: Fecal gut microbiota and serum metabolites were analyzed using metagenomics and metabolomics, respectively. The expression of extracellular matrix components, Takeda G protein-coupled receptor 5 (TGR5), glucagon-like peptide-1 receptor (GLP-1R), and nuclear factor kappa B (NF-κB) p65 was examined by in adenine-induced CKD rats.

RESULTS: UCG improved renal function and alleviated kidney fibrosis in adenine-induced CKD rats. Mechanistically, significantly altered gut bacteria, including Helicobacter hepaticus, Gemella hemolysans, Bacteroides ovatus, Lactococcus cremoris, Bacteroides fragilis, Alistipes finegoldii, and Eubacterium limosum, showed strong linear correlations with serum creatinine levels in CKD rats. UCG treatment improved aberrant changes in these gut bacteria, indicating that UCG can reshape gut microbiota dysbiosis. Microbial-derived metabolites act as a bridge between gut microbiota and host. Further analysis showed that serum bile acids, including ursodeoxycholic acid (UDCA), taurodeoxycholic acid, and hyodeoxycholic acid (HDCA), were strongly correlated with serum creatinine levels in CKD rats, and these aberrant metabolites were reversed by UCG treatment. Notably, both UDCA and HDCA showed strong linear correlations with Bacteroides ovatus, Lactococcus cremoris, Bacteroides fragilis, and Eubacterium limosum, suggesting that UCG regulates microbial-derived metabolites. Moreover, UCG treatment upregulated protein expression of TGR5, GLP-1R, and downregulated NF-κB p65 protein expression in the kidney tissues of CKD rats, indicating that renoprotective effects of UCG are associated with modulation of microbial dysbiosis, regulation of bile acid metabolism and improvement of TGR5, GLP-1R, and NF-κB signaling.

CONCLUSIONS: This study is the first to demonstrate that UCG ameliorates CKD and renal fibrosis by reshaping microbial dysbiosis and microbial-derived bile acid metabolism. Altered gut microbiota and metabolites may serve as biomarkers to evaluate efficacy of UCG. UCG may exert its renoprotective effects by enhancing TGR5, GLP-1R, and NF-κB p65 expression through regulating microbial dysbiosis-mediated bile acid metabolism.},
}

@article {pmid42216221,
year = {2026},
author = {Zhang, K and Duan, C and Chen, J and He, Q and Jin, Y and Liu, J and Lin, R and Han, C},
title = {Bone marrow mesenchymal stem cells synergize with fusobacterium nucleatum to drive colorectal tumorigenesis via gut microbiome dysbiosis.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00839-z},
pmid = {42216221},
issn = {1757-4749},
support = {2024M761069//Postdoctoral Research Foundation of China/ ; 82470679//National Natural Science Foundation of China/ ; 2023YFC2307001//National Natural Science Foundation of China/ ; 82170570//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The oncogenic role of F. nucleatum (Fn) in colorectal cancer (CRC) is increasingly recognized, yet its interaction with host stromal components, such as bone marrow mesenchymal stem cells (BMSCs), remains poorly understood. Building on our previous discovery that BMSC-derived Wnt3a promotes Fn-driven tumorigenesis, this study aims to investigate the synergistic interplay between BMSCs and F. nucleatum in CRC pathogenesis via the gut microbiome.

METHODS: Based on the established Apc[Min/+] mouse model of CRC, animals were randomly assigned to four experimental groups: control, Fn-only, BMSCs-only, and Fn+BMSCs co-treatment group. Gut microbiota composition was continuously analyzed over 8 weeks by metagenomic sequencing. Metagenomic functions were predicted using PICRUSt2.

RESULTS: The Fn+BMSCs co-treatment group exhibited the highest enrichment of F. nucleatum and the greatest reduction in microbial diversity. Fn+BMSCs co-treatment induced a distinct pro-tumorigenic shift, marked by a decline in symbiont Lactobacillus and an increase in pathobiont Escherichia-Shigella. Metagenomic analysis revealed a unique enhancement of butanoate metabolism in the Fn+BMSC co-treatment group. Furthermore, a profoundly elevated LPS level was discovered in the Fn+BMSCs co-treatment group, indicating hyperactivation of the pro-inflammatory and proliferative TLR4/NF-κB pathway.

CONCLUSIONS: Our findings demonstrate that BMSCs synergize with F. nucleatum to create a tumorigenicmicroenvironment by driving microbial dysbiosis, reprogramming metabolic pathways, and amplifying pro-inflammatory signaling. Our findings reveal that BMSCs fuel CRC progression via multiple mechanisms: by altering the gut microbiome ecology and, as previously discovered, by providing oncogenic Wnt3a signals. Targeting the synergistic BMSC-Fn axis may thus offer a novel therapeutic strategy for CRC.},
}

@article {pmid42216275,
year = {2026},
author = {Wong, ELY and Otte, J and Schmitt, I},
title = {Chloroplast and mitochondrial genomes of the lichen-symbiotic green alga Trebouxia illuminate evolutionary relationships and climate associations, and yield new phylogenetic markers.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag129},
pmid = {42216275},
issn = {1759-6653},
abstract = {The green-algal genus Trebouxia (Trebouxiophyceae, Chlorophyta) is the most common photosynthetic symbiont of lichens, displaying high phylogenetic diversity, and worldwide distribution across all climate zones. These single-celled terrestrial algae are valuable systems to study diversification, environmental adaptation and species interactions, yet genomic resources remain limited. We present over 30 new chloroplast and mitochondrial genomes of Trebouxia species, extracted from PacBio metagenomes of diverse Umbilicaria lichens from multiple climate zones. The genomes represent previously identified operational taxonomic units (OTUs) T. jamesii (A03), T. sp. (A04), T. incrustata (A06), T. vagua (A10), T. sp. (S02), T. sp. (S03), T. sp. (S04), T. suecica (S05), T. sp. (S08), T. angustilobata (S09), T. simplex (S10), T. sp. (S20), T. barrenoae (S28), a newly designated OTU A57, and several Single-Occurrence Sequences (SOS) from Clade A, I and S. Up to four Trebouxia OTUs were found within a single thallus. Organelle genomes vary considerably in size and structure. The consensus phylogenies from chloroplast (77 genes) and mitochondrial genes (32 genes) are largely congruent with the nuclear ITS tree, differing mainly in the derived clade S sections. All genes are under purifying selection, with mitochondrial genes exhibiting higher nucleotide diversity and hence phylogenetic resolution than chloroplast genes. Certain gene and protein features correlate with temperature variability, and some (such as GC content, arginine and valine content) mirror findings in mycobiont nuclear genomes from the same samples, and highlighting shared signatures of environmental adaptation. We designed primers for new, variable phylogenetic markers, including chloroplast genes ftsH and rpoC1, and mitochondrial genes ATP1, ATP6 and ND6. Overall, this study advances our understanding of organelle genome evolution in Trebouxia, and provides valuable resources for future ecological and evolutionary research.},
}

@article {pmid42216291,
year = {2026},
author = {Zwartjes, MSZ and de Jonge, PA and van de Laar, AW and Bruin, SC and Meijnikman, AS and Groen, AK and Gerdes, VEA and Nieuwdorp, M},
title = {Adipose Tissue Inflammation, Oxidative Stress, and Altered Adipogenesis Are Associated With Dyslipidemia in Obesity: A Multiomics Profiling Study.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e047397},
doi = {10.1161/JAHA.125.047397},
pmid = {42216291},
issn = {2047-9980},
abstract = {BACKGROUND: Obesity is an important risk factor for cardiometabolic disease, including dyslipidemia and atherosclerotic cardiovascular disease. Although the role of the liver in dyslipidemia is established, the contribution of adipose tissue is less clear. This study aims to clarify the role of adipose tissue in lipid metabolism and dyslipidemia.

METHODS: We conducted a cross-sectional analysis of 125 patients from the BARIA (The Immune System and Microbial Tone in Relation to NAFLD/NASH Before and After Bariatric Surgery in the Morbidly Obese in Amsterdam) longitudinal cohort study undergoing bariatric surgery. Comprehensive phenotyping included fasting untargeted plasma metabolomics, lipid, lipoprotein, adipokine profiling, RNA sequencing, and fecal shotgun metagenomics. Tissue transcriptomic and plasma metabolites were compared between individuals with and without dyslipidemia.

RESULTS: Dyslipidemia was present in 43 of 125 individuals (34.4%), with higher triglycerides (1.62 versus 1.24 mmol/L), apoB (apolipoprotein B; 93.15 versus 81.81 mg/dL), and lower high-density lipoprotein (1.02 versus 1.35 mmol/L) and apoAI (136.40 versus 161.35 mg/dL). Plasma adipokines showed limited differences: leptin concentrations were lower in dyslipidemia in unadjusted analysis but reduced after adjustment for age, sex, and body weight (adjusted P=0.057). RNA sequencing identified altered gene expression of liver, jejunum, visceral and subcutaneous adipose tissue, most pronounced in subcutaneous adipose tissue. Dyslipidemia was associated with adipose tissue pathways related to inflammation, oxidative stress, and adipogenesis. Plasma metabolomics revealed associations with endocannabinoid-like, secondary bile acid, plasmalogen, butyrate, and sphingolipid metabolites. Gut metagenome analysis found modest differences.

CONCLUSIONS: Dyslipidemia in obesity is associated with transcriptomic alterations in adipose tissue, including subcutaneous adipose tissue, involving inflammation, oxidative stress, and adipogenesis. These findings support a role of adipose tissue in lipid regulation beyond hepatic pathways.},
}

@article {pmid42217053,
year = {2026},
author = {Ortiz-Gasca, A and Aguirre-Noyola, JL and Ruiz-Rivas, M and de Los Santos-Villalobos, S and Trejo-Aguilar, D and Gómez-Godínez, LJ},
title = {Molecular markers for the study of arbuscular mycorrhizal fungi.},
journal = {Archives of microbiology},
volume = {208},
number = {8},
pages = {},
pmid = {42217053},
issn = {1432-072X},
mesh = {*Mycorrhizae/genetics/classification/isolation & purification ; Genetic Markers ; DNA, Fungal/genetics ; Metagenomics/methods ; DNA, Ribosomal/genetics ; Soil Microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are central components of terrestrial ecosystems and agroecosystems. However, their accurate identification remains methodologically challenging due to their complex biology and the limitations of traditional morphological approaches. Over the past three decades, molecular tools have profoundly reshaped AMF research, shifting from spore-based identification and Sanger sequencing of ribosomal markers toward high-throughput amplicon sequencing and, more recently, metagenomic frameworks that enable community-level and functional analyses. This review critically examines the conceptual and technical evolution of AMF identification strategies, comparing morphological characterization, ribosomal DNA markers (SSU, ITS, LSU), multilocus approaches, metabarcoding, and whole-genome metagenomics. We analyze their taxonomic coverage, resolution, and methodological biases, including primer specificity, intragenomic rDNA variation, database limitations, and bioinformatic pipeline effects. Attention is given to how marker selection influences ecological interpretation, cross-study comparability, and functional inference. Finally, we propose practical guidelines for aligning marker choice with study objectives and outline validation strategies-such as mock communities, curated reference databases, and multi-marker integration-to improve reproducibility and taxonomic robustness. By integrating historical perspective, methodological evaluation, and applied recommendations, this review provides a decision-oriented framework to support more accurate and comparable assessments of Glomeromycota diversity.},
}

*Mycorrhizae/genetics/classification/isolation & purification
Genetic Markers
DNA, Fungal/genetics
Metagenomics/methods
DNA, Ribosomal/genetics
Soil Microbiology

@article {pmid42217383,
year = {2026},
author = {Kong, T and Du, Z and Zhou, J and Zheng, Z and Zhang, J and Zhang, S and Jiang, F and Sun, X and Huang, W and Zhang, R and Li, F and Lin, W and Lan, X and Cao, Y and Yan, G and Sun, W},
title = {Assimilatory sulfate reduction potential in the plastisphere microbiome is linked to plastic mineralization in sulfur-rich mining-impacted river sediments.},
journal = {Water research},
volume = {303},
number = {},
pages = {126182},
doi = {10.1016/j.watres.2026.126182},
pmid = {42217383},
issn = {1879-2448},
abstract = {Microbial communities colonizing plastic surfaces are shaped by environmental factors, yet the role of sulfur in plastisphere assembly and plastic fate remains poorly understood. Here, we collected plastic debris from sulfur-rich, mining-impacted river sediments to characterize plastisphere microbiomes and evaluate their potential roles in plastic transformation. Paenibacillus spp. were identified as core plastisphere members, and their distribution was strongly associated with total sulfur concentrations. Metagenomic binning suggested that Paenibacillus harbored genomic potential associated with plastic transformation/mineralization and sulfate assimilation. An isolate of Paenibacillus provided further laboratory-based evidence that sulfate amendment may support plastic mineralization, although the precise in situ mechanism remains to be clarified. Because both the metagenome-assembled genome and the isolate genome encoded an almost complete assimilatory sulfate reduction pathway but lacked a complete dissimilatory sulfate reduction pathway, the observed sulfate depletion is more conservatively interpreted as sulfate uptake coupled with assimilatory sulfate reduction and subsequent sulfur assimilation into biomass rather than canonical sulfate respiration. Together, these findings suggest that sulfate availability and assimilatory sulfur metabolism may represent underappreciated controls on plastic turnover in sulfur-rich environments by supporting plastic-associated carbon transformation. This study links plastic-carbon fate to local sulfur cycling and provides new insight into microplastic persistence in sulfur-rich aquatic ecosystems.},
}

@article {pmid42217591,
year = {2026},
author = {Zhang, J and Liu, J and Tian, Y and Jia, W and Zhang, G and Lyu, A and Lyu, H},
title = {Metabolic interactions of host-gut microbiota: Shaping the future of precision diagnosis and therapeutic discovery in gastrointestinal cancers.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108273},
doi = {10.1016/j.phrs.2026.108273},
pmid = {42217591},
issn = {1096-1186},
abstract = {This collection of reviews and research articles highlights the diagnostic and therapeutic potential of gut microbial metabolites across various gastrointestinal cancers, including but not limited to hepatobiliary and pancreatic cancers, gastric cancer, and cholangiocarcinoma. Numerous gut microbial metabolites have been observed to mechanistically regulate cancer cell proliferation and development, supporting their utility as molecular biomarkers for clinical diagnosis and as targets for precision interventions. However, most functional metabolites derived from both host cancer tissues and the gut microbiota remain structurally unidentified; their functional features are largely unexplored due to limitations in conventional measurement technologies. To address these challenges, we propose a transformative functional metabolomics approach-S[2]M[2]ART (Single-Cell Spatial Metabolomics Metagenomics-Artificial Intelligence Recombinational Toolkit)-which will leverage AI-powered multimodal omics and single-cell, spatially-resolved analyses to decode the molecular functions and mechanisms of these metabolites in gastrointestinal cancer development. Collectively, this innovative technique will substantially enhance the applicability and translational potential of microbial metabolites in gastrointestinal cancers and beyond.},
}

@article {pmid42217781,
year = {2026},
author = {Kim, S and Kang, MG and Oh, S and Jang, KB and Kim, Y},
title = {Genome-based characterization of flavor development via metabolic interactions between Lentilactobacillus kefiri and Kluyveromyces marxianus during milk kefir fermentation.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28435},
pmid = {42217781},
issn = {1525-3198},
abstract = {Kefir, a fermented milk product comprising complex consortia of bacteria and yeasts, develops its characteristic flavor through coordinated microbial interactions. In this study, we investigated flavor compound biosynthesis and development by kefir-derived lactic acid bacteria and yeast during kefir fermentation, integrating genome-based predictions with metabolite validation. Metagenomic analysis identified Lactobacillus and Kluyveromyces as predominant genera in both kefir grains and fermented milk kefir. Lentilactobacillus kefiri SLAM023B and Kluyveromyces marxianus SLAM005Y were isolated and subjected to hybrid genome sequencing on Illumina and Nanopore platforms. Functional annotation via KEGG pathway mapping revealed featured pathways including amino acid and fatty acid metabolism, as well as interconversion of alcohol, aldehyde, and acid, contributing to the formation and generation of flavor compounds. Notably, K. marxianus SLAM005Y produced fruity fusel alcohols, whereas L. kefiri SLAM023B contributed fatty acid-derived precursors. The coculture of the 2 strains significantly enhanced ester synthesis, particularly ethyl acetate and isoamyl acetate, imparting fruity and creamy sensory notes to the fermentation profile. In addition, increases in ethyl octanoate and C6/C8 fatty acids introduced fruity and cheese-like characteristics, while levels of grassy aldehydes were reduced. Correlation analysis supported the complementary metabolic roles and potential cross-feeding mechanisms between the strains, which help explain the development of kefir flavor. Taken together, this study provides a genomic and functional framework to examine cooperative metabolism in kefir and identifies molecular targets for improving the sensory properties of fermented dairy products.},
}

@article {pmid42217859,
year = {2026},
author = {Qin, W and Zhang, H and Wang, H and Zhou, J and Wang, F},
title = {Pharmaceutical-driven disinfection by-products formation and antibiotic resistance gene enrichment under intensified chlorination during pandemic.},
journal = {Journal of environmental sciences (China)},
volume = {165},
number = {},
pages = {1-10},
doi = {10.1016/j.jes.2025.06.056},
pmid = {42217859},
issn = {1001-0742},
mesh = {Halogenation ; *Disinfection/methods ; *Drug Resistance, Microbial/genetics ; Pandemics ; *Disinfectants ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis ; *Chlorine ; Anti-Bacterial Agents ; Wastewater/chemistry ; },
abstract = {Intensified chlorine disinfection during pandemic is widely implemented in hospital and municipal wastewaters to inactivate pathogens. However, high concentrations of residual chlorine in treated wastewaters might bring secondary environmental risks. This study investigated the impacts of intensified chlorine disinfection on disinfection by-product (DBP) formation from six commonly used pandemic-related drugs and antibiotic resistance gene (ARG) enrichment in sewage. Results showed that high chlorine dosage of 2000 µmol/L led to DBP yields and estimated toxicity that were 1-2 orders of magnitude higher than those under normal chlorine dosage of 40-100 µmol/L. Intensified chlorine disinfection and drug overuse during the pandemic evidently increased the contribution of drugs as precursors to DBPs formation (29.2 %-78.8 %) in sewage. Two antibiotics emerged as major dichloroacetonitrile precursors, two bromine expectorants dominated haloacetic acids and Br-DBP formation, while two ICMs were critical precursors of iodinated acetamides. These DBPs were the main contributors to the estimated toxicity of the chlorinated drugs. Bromine expectorants produced DBPs with yields and estimated toxicity 1-2 orders of magnitude greater than other drugs. Metagenomic sequencing results showed that low chlorine up-regulated ARGs and related mobile genetic elements, driving ARGs enrichment and horizontal transfer. High chlorine in short term inhibited the total ARGs, but enriched the multidrug resistance gene subtypes related to the efflux/mutation pathway and transfer, thereby selected highly chlorine-resistant bacteria with strong antibiotic resistance. These findings reveal the environmental risks of intensified chlorine disinfection and suggest that optimizing chlorine dosage is crucial to mitigate these environmental risks and protect public health.},
}

Halogenation
*Disinfection/methods
*Drug Resistance, Microbial/genetics
Pandemics
*Disinfectants
*Waste Disposal, Fluid/methods
*Water Pollutants, Chemical/analysis
*Chlorine
Anti-Bacterial Agents
Wastewater/chemistry

@article {pmid42217876,
year = {2026},
author = {Xiao, Y and Ouyang, Q and Wen, X and Tong, H},
title = {Coupling mechanisms between microbial arsenic metabolism and carbon cycling in arsenic-contaminated groundwater.},
journal = {Journal of environmental sciences (China)},
volume = {165},
number = {},
pages = {269-276},
doi = {10.1016/j.jes.2025.10.032},
pmid = {42217876},
issn = {1001-0742},
mesh = {*Arsenic/metabolism/analysis ; *Groundwater/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/analysis ; *Carbon Cycle ; China ; Bacteria/metabolism ; *Water Microbiology ; Carbon/metabolism ; },
abstract = {Microorganisms in groundwater play a critical role in global carbon (C) cycling. However, how arsenic (As) contamination influences microbially mediated As cycling and its coupling with C metabolism remains poorly understood. Herein, we investigated the associative coupling of microbial function genes between As and C cycling in groundwater from a typical As-contaminated industrial site in southern China. Metagenomic analyses revealed that As concentrations governed microbial community assembly, leading to distinct community structures and dominant taxa. Key microbial groups, including Pseudomonadota and Euryarchaeota, exhibited dual metabolic capabilities for both As and C transformation. Compared to the Safe group (As < 10 μg/L), the Toxic group (As > 10 μg/L) displayed greater dissimilarities in the distribution of As- and C-related functional genes. A strong correlation between As- and C-cycling genes suggests a potential trade-off mechanism between microbial As resistance and organic C utilization. Furthermore, microbial function gene-based co-occurrence networks demonstrated more complex and stable network structures in the Toxic group. The enhanced coupling between As-C functional genes likely increased microbial community resilience against environmental stressors. While observed As-C coupling mechanisms may extrapolate to chemically analogous groundwater systems, their quantitative contribution to global C budgets requires validation across diverse biogeographic contexts. This study offers novel insights into the complex coupling network between As and C metabolic pathways in groundwater microbial communities and underscores their broader implications for global biogeochemical C cycling.},
}

*Arsenic/metabolism/analysis
*Groundwater/chemistry/microbiology
*Water Pollutants, Chemical/metabolism/analysis
*Carbon Cycle
China
Bacteria/metabolism
*Water Microbiology
Carbon/metabolism

@article {pmid42217938,
year = {2026},
author = {Dwivedi, S and Agnihotri, R and Kumar, V and Mishra, S and Tiwari, RK and Adhikari, D and Sharma, P and Kumar, S and Verma, T and Gupta, A and Sinam, G and Pandey, V},
title = {Scientific evidence validating spiritual beliefs for controlling pathogenic microbes in the Ganga river.},
journal = {Journal of environmental sciences (China)},
volume = {165},
number = {},
pages = {93-106},
doi = {10.1016/j.jes.2026.01.083},
pmid = {42217938},
issn = {1001-0742},
mesh = {*Rivers/microbiology ; Archaea ; Bacteria ; *Water Microbiology ; Microbiota ; Bacteriophages ; Biodiversity ; },
abstract = {During the Kumbh, the Ganga at the Sangam in Prayagraj, where it meets the Yamuna, showed greater microbial diversity than either river before their confluence. Mass bathing altered the density and diversity of archaea, bacteria, phages and viruses, while fungi, protozoans, cyanobacteria, green algae and diatoms remained largely unaffected. Notably, this study was the first to report archaeal phages, cyanophages and mycophages in the river system. Archaea species richness was higher in the Yamuna (127 spp. during Pre Kumbh), whereas bacterial diversity was greater in the Ganga (2764 spp.). The Ganga exhibited a higher relative abundance of skin, oral and gut archaea and bacteria, except for gut bacteria, which were more prevalent in the Yamuna. Skin and gut archaea showed strong positive correlations with the number of devotees (r = 0.818 and r = 0.870, respectively), while oral archaea were less affected. Pathogenic microbes with high fatality rates were more common in the Yamuna. Variations in archaeal, bacterial, phage and viral communities were influenced by physico-chemical parameters, ion levels, nutrient content and devotee's load. The Ganga exhibited higher phage diversity and a greater phage-to-bacteria ratio than the Yamuna. Hence, phages regulate the pathogenic bacteria through predator-prey dynamics, consequently reducing infection risks. Despite mass bathing by over 100 million devotees, which sharply increased nutrient and pollution levels, no endemic or epidemic outbreaks were reported.},
}

*Rivers/microbiology
Archaea
Bacteria
*Water Microbiology
Microbiota
Bacteriophages
Biodiversity

@article {pmid42218119,
year = {2026},
author = {Fessler, JL and Olm, MR and Engleman, EG and Sonnenburg, JL},
title = {Integration of donor microbiota following FMT correlates with anti-PD-1 response in melanoma.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73465-7},
pmid = {42218119},
issn = {2041-1723},
support = {R21CA290426//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Fecal microbiota transplantation (FMT) has shown promise in improving anti-PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. We performed a strain-resolved metagenomic meta-analysis across three independent FMT plus anti-PD-1 melanoma trials (n = 41). Across cohorts, therapeutic benefit was linked to successful integration of donor microbiota, rather than increased diversity or engraftment of specific species. Responders acquired more donor-derived strains, exhibited greater post-FMT similarity to their donor, and maintained a more stable microbiome. Following FMT, non-responders' microbiomes showed greater taxonomic instability, larger fluctuations in estimated microbial load, and increased abundance of pathogen-associated secretion system genes, whereas responders showed enrichment for microbial functions involved in community-level metabolism and communication. Finally, shifts in tumor-infiltrating immune profiles tracked with clinical outcomes and microbiome changes. Together these findings highlight that distinct patterns of microbiome restructuring, including stable community transitions and altered functional capacity, are associated with anti-PD-1 response following FMT.},
}

@article {pmid42218218,
year = {2026},
author = {Zhu, G and Yang, G},
title = {Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01030-7},
pmid = {42218218},
issn = {2055-5008},
support = {32571054 and 82371350//National Natural Science Foundation of China/ ; C7014-24GF//Research Grant Council of the Government of Hong Kong SAR/ ; Institute Digital Medicine internal grant (9229501-13-YG)//City University of Hong Kong/ ; },
abstract = {Emerging evidence suggests a role for the gut bacteria in the pathogenesis of multiple sclerosis (MS); however, the role of other microorganisms and their diagnostic potential for MS remain poorly explored. Here, we analyzed large-scale metagenomic data derived from fecal samples (discovery cohort n = 1152; total n = 1306 across 3 geographically diverse cohorts). Subsequently, we utilized multikingdom gut microbiome data to develop machine learning models to distinguish MS patients from healthy controls. Our analysis identified distinct microbiome alterations, revealing 90 bacterial, 3 fungal, 2 viral species, 119 KEGG orthology genes, and 17 metabolic pathways significantly associated with MS. Machine learning models integrating multikingdom taxonomic and functional features achieved the area under the receiver operating characteristic curves (AUCs) of 0.977 for males and 0.978 for females. On external validation datasets, the ensemble models yielded AUCs of 0.813 in males and 0.745 in females, while the 30-marker models reached AUCs of 0.849 and 0.763, respectively. Notably, the accuracy of the model was associated with Faecalibacterium spp. and L-methionine biosynthesis pathways, which were less abundant in MS patients. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiome markers as non-invasive biomarkers for MS.},
}

@article {pmid42215210,
year = {2026},
author = {Chen, L and Wang, G and Hu, Z and Teng, M and Cao, Q and Qin, X and Du, H and Yang, F and Tu, H and Wang, L},
title = {From diversity to stability: Acidification, antagonism, and resistance driven by Acetilactobacillus jinshanensis during jiang-flavor baijiu fermentation.},
journal = {Food microbiology},
volume = {139},
number = {},
pages = {105130},
doi = {10.1016/j.fm.2026.105130},
pmid = {42215210},
issn = {1095-9998},
mesh = {Fermentation ; Hydrogen-Ion Concentration ; Metagenomics ; *Wine/microbiology/analysis ; Microbiota ; Microbial Consortia ; Metabolomics ; },
abstract = {As a quintessential pillar of Chinese traditional industry, Baijiu relies on solid-state fermentation, a complex ecological succession process driven by highly diverse microbial consortia. While such systemic complexity often introduces stochasticity and uncertainty, baijiu solid-state fermentation is typically dominated by specific keystone species that exhibit remarkable resilience, maintaining high abundance while exerting top-down control over community structure and function. However, the mechanisms enabling these species to emerge from intensely competitive environments remain poorly understood. In this study, we employed Acetilactobacillus jinshanensis, a predominant species in the Moutai-flavor Baijiu microbiome, as a model to address these ecological questions. By integrating shotgun metagenomics, metatranscriptomics, and a pH-dependent generalized Lotka-Volterra model, we demonstrate that A. jinshanensis not only orchestrates environmental acidification but also reshapes the community landscape through active competitive inhibition. Leveraging comparative genomics and AlphaFold3-based structural predictions, we identified a unique GH25-LysM antibacterial module in A. jinshanensis predicted to target peptidoglycan with high specificity, potentially contributing to the suppression of acid-tolerant competitors. Furthermore, targeted metabolomics revealed a novel acid-resistance mechanism centered on an intra- and extracellular choline cycle, which significantly bolsters the organism's fitness under extreme acidic stress via metabolic modulation. Overall, we pinpoint a coupled mechanism set that explains the diversity-to-stability transition driven by A. jinshanensis in fermentation microbial community, offering process-relevant rules for improving reproducibility.},
}

Fermentation
Hydrogen-Ion Concentration
Metagenomics
*Wine/microbiology/analysis
Microbiota
Microbial Consortia
Metabolomics

@article {pmid42215376,
year = {2026},
author = {Kiguchi, Y and Suzuki, Y},
title = {Giants within: a new class of microbial mobile elements.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2026.05.004},
pmid = {42215376},
issn = {0168-9525},
abstract = {Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field has focused on relatively small ECEs, such as plasmids. However, the advent of long-read sequencing has revealed that prokaryotes also harbor various types of giant ECEs, spanning hundreds of kilobases to over 1 Mb, that were not hitherto recognized. In this review, we describe how long-read sequencing has enabled the discovery of giant ECEs and compare the genetic architectures and functional repertoires of several recently characterized examples. The functions of most genes in these ECEs remain uncharacterized, and current computational tools frequently misclassify or overlook them. We further discuss how the discovery of these giant ECEs challenges existing classification frameworks that attempt to distinguish megaplasmids, chromids, and chromosomes. Together, these findings highlight giant ECEs as a largely unexplored layer of microbial genetics, whose characterization will have broad implications for our understanding of microbial adaptation and horizontal gene transfer.},
}

@article {pmid41998666,
year = {2026},
author = {Yang, F and Du, Y and Ji, J and Zhang, P},
title = {Eosinophilic granulomatous inflammation and multi-organ involvement probable caused by Paragonimus heterotremus infection in a pediatric patient: a rare case report.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41998666},
issn = {1471-2431},
abstract = {BACKGROUND: Paragonimus heterotremus is a parasitic flatworm endemic to Southeast Asia that causes pulmonary and extrapulmonary infections. While more common in adults, pediatric cases are rare and often present atypically, posing diagnostic challenges. Eosinophilic granulomatous inflammation due to parasitic infection is especially difficult to identify in children.

CASE PRESENTATION: A 9-year-old female child initially exhibited subcutaneous swelling and notable peripheral blood eosinophilia, resulting in two hospital stays without a conclusive diagnosis. Upon admission to our center, laboratory results showed increased white blood cell count, hemoglobin, platelets, and persistent eosinophilia, along with a significantly increased total IgE levels. Imaging revealed granulomatous inflammation in the skin and lungs with mild pleural effusion. Despite negative parasitic serology, a newly developed umbilical mass during hospitalization was surgically excised. Anatomopathological examination and metagenomic next-generation sequencing (mNGS) supported a probable diagnosis of P. heterotremus infection.

CONCLUSIONS: This case highlights the diagnostic challenges of pediatric eosinophilic granulomatous inflammation due to rare parasitic infections, particularly in non-endemic areas. It highlights the need for heightened clinical awareness, thorough evaluation, and advanced diagnostic tools for timely and accurate identification of uncommon parasitic diseases in children.},
}

@article {pmid42206864,
year = {2026},
author = {Zhao, R and Biddle, JF},
title = {Community structure and methylation of microbes in an artificially forced sediment core.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0353325},
doi = {10.1128/spectrum.03533-25},
pmid = {42206864},
issn = {2165-0497},
abstract = {Epigenetic modifications, such as DNA methylation, may be used in prokaryotes for the adaptation of microbes to external environmental changes. In this study, we examined the microbial community structure, recovered the genomes of the dominant microbes, and tracked methylation in several dominant microbes in a 23-cm artificial sediment core formed in a settling tank that mimics the sediment formation process. Our results indicated that the prokaryotic communities only showed minor variations with depth and were dominated by bacteria (especially taxa of Deltaproteobacteria, Gammaproteobacteria, and Bacteroidota), while archaea (dominated by Bathyarchaeia) accounted for <5% of the total communities throughout the core. We detected methylation by analyzing metagenome sequencing data of methyl-specific enzyme-digested and undigested DNA. We recovered 72 high- or medium-quality metagenome-assembled genomes for the dominant taxa, for 7 of which we detected distinct downcore methylation patterns. This work highlights the diverse processes of epigenetic modification in response to the sediment burial process, which may have a long-term impact on the overall community fitness in the evolving energy-limited conditions in marine sediments.IMPORTANCEThis work reports changes in the epigenetic profiles of microbes buried in a sediment column formed under a controlled, artificially created environment. This approach removes confounding variables of bioturbation and changes in sediment flux. We also use an approach that is accessible for low amounts of DNA to determine methylation status.},
}

@article {pmid42207030,
year = {2026},
author = {Ren, P and Kan, Z and Wei, B and Qin, W and Lu, S},
title = {Yellow tea extract ameliorates dexamethasone-induced hepatic steatosis by modulating the gut-liver axis and reshaping microbial metabolites: a multi-omics insight.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo01620k},
pmid = {42207030},
issn = {2042-650X},
abstract = {Long-term glucocorticoid therapy, exemplified by dexamethasone (DEX), frequently induces hepatic steatosis, posing a significant clinical challenge. Yellow tea (YT), a lightly fermented tea, is rich in polyphenols and polysaccharides, yet its protective effects against DEX-induced liver injury remain underexplored. This study investigated the hepatoprotective mechanisms of a yellow tea water extract (YT) using a DEX-induced mouse model, integrated with transcriptomic, metagenomic, and metabolomic analyses. YT intervention (500 mg[-1] kg[-1] day[-1] for 6 weeks) significantly attenuated DEX-induced hepatocellular injury, as evidenced by reduced serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, decreased hepatic triglyceride (TG) and total cholesterol (TC) accumulation, and suppressed systemic inflammation (lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-α)). Hepatic transcriptomics and subsequent reverse transcription quantitative PCR (RT-qPCR) validation revealed that YT upregulated the antioxidant genes nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) while downregulating the lipogenic gene sterol regulatory element-binding protein 1c (SREBP-1c) and upregulating the fatty acid oxidation gene peroxisome proliferator-activated receptor alpha (PPAR-α). Gut microbiota analysis showed that YT reshaped the microbial community, notably enriching beneficial taxa such as Bifidobacterium pseudolongum and members of the Muribaculaceae family. Serum metabolomics indicated that this microbiota remodeling was associated with the restoration of perturbed metabolic pathways, notably tryptophan metabolism. Correlation analysis further linked specific microbial shifts with improved metabolic and inflammatory markers. Collectively, these integrated transcriptomic, metagenomic, and metabolomic findings demonstrate that YT alleviates DEX-induced hepatic steatosis through dual mechanisms involving direct hepatic antioxidant and lipid metabolic regulation and systemic modulation via the gut-liver axis, positioning it as a promising dietary strategy against glucocorticoid-associated metabolic complications.},
}

@article {pmid42207032,
year = {2026},
author = {Giani, N and John, J and Campbell, B},
title = {Shotgun metagenomics and metatranscriptomics of soil microbial communities under monoculture and polyculture cover crops.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0030926},
doi = {10.1128/mra.00309-26},
pmid = {42207032},
issn = {2576-098X},
abstract = {Here, we present 30 metagenomes, 21 metatranscriptomes, and 334 metagenome-assembled genomes collected from soils under different cover crop species. This data set will be useful for studying microbial interactions, especially functional redundancy, with relevance to agricultural management and sustainability.},
}