@article {pmid42605089,
year = {2026},
author = {Wang, NL and Xu, LF and Liu, XG and Wei, XX and Chen, XP and Wang, LX and Zhou, K and Lin, YQ and Gong, YP and Xie, ZD and Wang, JS and , },
title = {[Metagenomic sequencing-based pathogen analysis in pediatric severe acute non-A-E hepatitis].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {64},
number = {9},
pages = {1041-1047},
doi = {10.3760/cma.j.cn112140-20260608-00446},
pmid = {42605089},
issn = {0578-1310},
abstract = {Objective: Metagenomic sequencing was employed to analyze the pathogen detection profile in pediatric severe acute non-A-E hepatitis. Methods: Based on the platform of the China Childhood Severe Acute Hepatitis Collaborative Group, a case series study was conducted. This study enrolled 36 children with severe acute non-A-E hepatitis, who were admitted to 17 hospitals between April and July 2022. Clinical data, including etiological test results and liver function tests, were collected, and peripheral blood and nasopharyngeal swab specimens were obtained. Metagenomic next-generation sequencing (mNGS) was performed to detect potential infectious pathogens. Results: Among 36 children, there were 24 males and 12 females, with an onset age of 3.5 (1.1, 9.0) years. Common clinical symptoms were fever in 22 cases (61%), jaundice in 13 cases (36%), vomiting in 12 cases (33%), abdominal pain in 10 cases (28%), rash in 10 cases (28%), and diarrhea in 3 cases (8%). Serum alanine aminotransferase and aspartate aminotransferase levels were 950 (826, 1 404) and 811 (498, 1 295) U/L, respectively. Using PCR, plasma Epstein-Barr virus (EBV)-DNA was tested in 31 cases (86%) and plasma cytomegalovirus (CMV)-DNA in 25 cases (69%), and all results were below 5×10[5] copies/L. Plasma mNGS was performed on all 36 patients, detecting 11 viruses. These included EBV in 14 cases, CMV in 12 cases, human adenovirus in 2 cases, herpes simplex virus type 1 in 2 cases, adeno-associated virus type 2 (AAV2) in 1 case, and 6 other viruses. No patient tested positive for both human adenovirus and AAV2 simultaneously. Plasma mNGS results showed a viral read count of 4 (2, 10) per 1×10[8] reads. Nasopharyngeal swab mNGS was performed on 8 cases (22%), detecting 7 viruses. These included human herpesvirus 7 in 4 cases, EBV in 3 cases, and CMV in 3 cases, as well as 4 other viruses. Human adenovirus and AAV2 were not detected. Among the 4 children with human herpesvirus 7, 2 cases were also positive for human herpesvirus 6B, but neither virus was detected in their plasma mNGS. Conclusions: The detection rates of human adenovirus and AAV2 are both low among children with severe acute non-A-E hepatitis, and there are no cases of co-infection with both viruses.},
}

@article {pmid42605509,
year = {2026},
author = {Xiao, L and Fu, C and Santos, IR and Duarte, CM and Liu, J and Zhou, L and Zhou, M and Dang, R and Lin, J and Xiao, K and Luo, Y and Han, G},
title = {Microbial Decomposition of Lignin to Methane Reduces Net Blue Carbon Benefit Across China's Saltmarshes.},
journal = {Global change biology},
volume = {32},
number = {8},
pages = {e71059},
pmid = {42605509},
issn = {1365-2486},
support = {2022YFF0802101//National Key Research and Development Program in China/ ; U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 41991330//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Methane/metabolism ; *Lignin/metabolism ; China ; *Wetlands ; Carbon/metabolism ; *Microbiota ; Biodegradation, Environmental ; },
abstract = {CH4 emissions from mangrove, saltmarsh, and seagrass ecosystems partially offset carbon sequestration, potentially diminishing the climate mitigation capacity of these blue carbon habitats. However, a mechanistic understanding of the processes governing CH4 production potential across large spatial scales remains limited. By integrating incubation-based measurements from 116 sites, we reveal significant ecosystem-specific differences in CH4 production potential, with saltmarshes emerging as CH4 production hotspot relative to mangroves and seagrass meadows. Using an integrated analytical approach encompassing more than 30 environmental, biogeochemical, and microbial parameters, we demonstrate that CH4 production potential converges on sediment organic carbon availability, particularly plant-derived carbon, as a key regulatory axis. Additionally, metagenome-assembled genomes (MAGs) recovered from saltmarshes show a functional bias toward lignin degradation, thereby fueling downstream CH4 production via methylotrophic pathways. Lignin-addition and stable carbon isotope experiments further provide supportive evidence that lignin decomposition enhances Chinese saltmarsh CH4 production potential, revealing a pathway that may reduce net blue carbon benefit. Together, these findings underscore that saltmarsh plant-derived lignin is less stable than conventionally assumed, as microbial processing redirects stored carbon toward CH4 production, challenging current blue carbon accounting frameworks at a continental scale within China.},
}

*Methane/metabolism
*Lignin/metabolism
China
*Wetlands
Carbon/metabolism
*Microbiota
Biodegradation, Environmental

@article {pmid42606111,
year = {2026},
author = {Hua, B and Pang, S and Li, A and Hu, Z and Wu, H and Zhang, S and Fan, Y and Wu, Y and Yang, W and Zhao, Y and Guan, Y and Ji, B and Kong, D and Zhao, Y and Goncharov, AA and Korotkevich, AY and Mao, R and Zhang, Y and Zhang, X},
title = {Rainfall Shapes the Diversity of Soil Nitrogen-Fixing Microorganisms Worldwide.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77215},
pmid = {42606111},
issn = {2198-3844},
support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; //Top-Notch Young Talents Program (to Ximei Zhang) of China/ ; },
abstract = {Soil nitrogen-fixing microorganisms naturally fertilize terrestrial ecosystems, but the primary driver of their diversity across the globe and the underlying mechanisms remain unclear. We analyzed the nifH gene in 1257 (1137 publicly available + 120 self-generated) soil metagenomes from 318 terrestrial ecosystems globally. Mean annual precipitation was identified as the key factor influencing the relative abundance, richness, and composition of the potential nitrogen-fixers. Precipitation was directly associated with nitrogen-fixers (e.g., water availability) rather than indirectly via other soil variables (e.g., pH). Lower precipitation increased the contribution of deterministic processes (e.g., interspecific competition) in driving their community assembly and selected species with larger genomes, while higher precipitation increased the contribution of stochastic processes (e.g., random birth/death) and favored smaller-genome species. A multifactorial experiment further demonstrated that precipitation increase had a larger regulatory effect on the stochastic processes than other factors (e.g., climate warming). eXtreme Gradient Boosting (XGBoost) projections under future global change scenarios indicate a general increase in their relative abundance across most regions worldwide, with declines only in specific areas. These findings reveal distinct patterns and mechanisms governing the global biodiversity and biogeography of soil nitrogen-fixers, providing valuable insights for developing region-specific management strategies aimed at maintaining ecosystem productivity.},
}

@article {pmid42606386,
year = {2026},
author = {Ghisleni, G and Dow, E and Iovino, T and Colman-Vega, PJ and Dicesare, A and Guanella, E and Bacchi, YM and Colombo, A and Leccese, M and Marzucchi, M and Gorla, ME and Caracciolo, A and Sala, A and Makarycheva, P and Rubrica, SC and Ferrier, A and Armanni, A and Fumagalli, S and Wood-Charlson, E and Bruno, A},
title = {Fantastic Microbes and Where to Find Them: evaluating learning-by-doing outcomes in a crowdfunded metagenomics workshop.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag093},
pmid = {42606386},
issn = {1574-6968},
abstract = {Metagenomics offers a powerful framework for authentic, interdisciplinary learning, yet it remains underrepresented in undergraduate education due to technical and infrastructural barriers. We hypothesized that a research-based, learning-by-doing metagenomics workshop supported by accessible bioinformatics tools could enhance students' perceived skills, self-efficacy, and conceptual understanding of metagenomic analysis. To test this hypothesis, we designed and evaluated a hybrid hands-on workshop in which undergraduate and postgraduate students analyzed real environmental shotgun metagenomic datasets generated from soil samples collected during a citizen science initiative. Using the graphical workflow platform KBase, participants completed an end-to-end metagenomic analysis, from quality control and assembly to genome reconstruction, taxonomic classification, functional annotation, and scientific presentation of results. Educational outcomes were assessed through validated retrospective pre-post questionnaires, self-efficacy scales, and an open-ended conceptual understanding task. Participants showed significant increases in perceived metagenomic skills and confidence in performing metagenomic analyses, while gains in perceived learning showed a positive trend. Conceptual understanding improved across educational levels, particularly among participants with limited prior experience. Together, these findings demonstrate that authentic, data-driven metagenomics activities can effectively lower barriers to computational biology and foster meaningful learning through hands-on research experiences.},
}

@article {pmid42607773,
year = {2026},
author = {Zhao, C and Mo, J and Peng, Z and Cheng, J and Zhan, O and Gong, Y and Mao, Y and Qin, Y and Wu, W},
title = {Combined lysine and cobalt supplementation improves semi-thermophilic anaerobic digestion performance with enhanced Methanosarcina-associated methylotrophic potential.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135647},
doi = {10.1016/j.biortech.2026.135647},
pmid = {42607773},
issn = {1873-2976},
abstract = {Protein-rich food waste challenges anaerobic digestion (AD) through rapid acidification and chronic ammonia stress. Semi-thermophilic AD (STAD, 41-49℃) offers a promising balance between mesophilic stability and thermophilic conversion efficiency, but further improvement may depend on strengthening methylotrophic methanogenesis, a route better aligned with the methylamine-forming potential of this substrate. l-lysine and cobalt were therefore selected as targeted additives to support its key methyl-transfer step. Their enhancement effects were evaluated through a series of experiments. Initial tests across different temperatures showed that STAD outperformed mesophilic and thermophilic digestion in both methane production and process stability, and combined supplementation gave the strongest enhancement. Under STAD, combined addition increased methane production by 58.0%, reduced volatile fatty acids (VFAs) and free ammonia by 24.7% and 21.9%, respectively, and strengthened Methanosarcina-linked methylotrophic signatures. Further optimization under STAD showed that intermediate doses performed best, and the predicted optimum, 45 mg·L[-1]l-lysine and 3.5 mg·L[-1] cobalt, was validated in a continuous reactor. This combination increased methane yield (314.21 ± 42.35 mL·gVS[-1]·d[-1]) by 33.3%, reduced VFAs and residual soluble chemical oxygen demand, by 29.6% and 44.8%, respectively, without aggravating ammonia stress. It also showed favorable preliminary economic potential, with a benefit-cost ratio of ∼15.0 during subsequent maintenance dosing. Mechanistically, these effects were linked to enrichment of hydrolytic, fermentative, and syntrophic bacteria, reduced competition from non-methylotrophic taxa, and more favorable conditions for Methanosarcina-centered, potentially methylamine-utilizing pathways. Overall, this study provides a practical strategy with clear engineering potential to further strengthen STAD for food-waste treatment.},
}

@article {pmid42608197,
year = {2026},
author = {Rao, X and Gu, Y and Gabriella, and Ma, J and Wang, H and Zou, Y},
title = {Promises and Pitfalls of Long-Read Sequencing for Resolving Microbial Complexity.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag087},
pmid = {42608197},
issn = {2047-217X},
abstract = {Long-read sequencing (LRS) has driven a transition in microbial genomics, overcoming the assembly fragmentation inherent to short-read sequencing. This review elucidates the impact of LRS across isolate genomics, metagenomics, and multi-omics domains. By spanning extensive repetitive regions, LRS facilitates the reconstruction of circular chromosomes and precisely resolves mobile genetic elements (MGEs). In metagenomics, LRS enables strain-level resolution, the recovery of circular metagenome-assembled genomes, and the precise localization of MGEs within host replicons. Furthermore, the single-molecule, amplification-free properties of LRS provide enhanced resolution of native epigenetic modifications and full-length transcriptomes. Despite these advancements, widespread implementation remains constrained by multidimensional challenges, including stringent high-molecular-weight DNA requirements, depth deficits, and computational overhead. Nevertheless, LRS is increasingly becoming the method of choice for isolate genomics and metagenomics. As detection technologies and algorithms progress, LRS will further improve our ability to decipher the structural and functional diversity of microbial ecosystems.},
}

@article {pmid42608979,
year = {2026},
author = {Wang, P and Wang, C and Zhang, Y and Bi, L and Zhao, H and Xu, Z and Wang, Z and Sheng, Y and Cui, Y},
title = {Topical Application of Indole-3-Acetic Acid, Present in S. epidermidis Supernatant, Alleviates Atopic Dermatitis in Mice at Least via the Aryl Hydrocarbon Receptor Signalling Pathway.},
journal = {Experimental dermatology},
volume = {35},
number = {8},
pages = {e70329},
doi = {10.1111/exd.70329},
pmid = {42608979},
issn = {1600-0625},
support = {201920102303//Peking Union Medical College/ ; 2024-ZX-019//Project of Integrated Traditional Chinese Medicine Collaboration "Flagship" Department Development/ ; ZRJY2023-GG14//China-Japan Friendship Hospital Youth Science and Technology Excellence Project/ ; 2208085Y25//Outstanding Youth Project of Natural Science Foundation of Anhui Province/ ; 2022YFC3602002//China National Key R&D Program of China/ ; 2022-NHLHCRF-LX-02-03//National High-Level Hospital Clinical Research Funding/ ; },
mesh = {Animals ; *Dermatitis, Atopic/drug therapy/metabolism/microbiology ; *Indoleacetic Acids/administration & dosage/pharmacology/therapeutic use/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism/antagonists & inhibitors ; *Staphylococcus epidermidis/metabolism ; Signal Transduction/drug effects ; Mice ; Humans ; Skin Microbiome ; Skin/metabolism/microbiology ; Keratinocytes/metabolism ; Administration, Topical ; Disease Models, Animal ; Female ; Molecular Docking Simulation ; },
abstract = {Dysbiosis of the skin microbiome, characterised by Staphylococcus aureus overgrowth and imbalance of commensals such as Staphylococcus epidermidis (S. epidermidis), is closely associated with atopic dermatitis (AD). However, the therapeutic relevance of defined S. epidermidis-associated indole metabolite, especially indole-3-acetic acid (IAA), in AD-like inflammation remains incompletely characterised. Here, we investigated the role of IAA, a tryptophan-derived metabolite enriched in the culture supernatant of the tested S. epidermidis strain, in AD-like inflammation. Public transcriptomic analyses suggested impaired AHR-associated and tryptophan-metabolism signatures in AD skin, particularly in lesional skin, while human metagenomic data indicated AD-associated staphylococcal alterations. Targeted metabolomics identified IAA as an enriched indole metabolite in S. epidermidis culture supernatant. In an MC903-induced AD-like mouse model, cutaneous IAA levels and S. epidermidis abundance were reduced. Topical IAA attenuated AD-like phenotypes, improved barrier-related proteins and reduced inflammatory indices. These protective effects were diminished by the AHR antagonist CH223191. Molecular docking predicted a possible interaction between IAA and AHR, and in vitro assays showed that IAA modulated keratinocyte AHR-associated inflammatory and barrier-related responses. Together, our findings support IAA as a microbiome-associated postbiotic candidate for AD management, at least partly through AHR-associated signalling.},
}

Animals
*Dermatitis, Atopic/drug therapy/metabolism/microbiology
*Indoleacetic Acids/administration & dosage/pharmacology/therapeutic use/metabolism
*Receptors, Aryl Hydrocarbon/metabolism/antagonists & inhibitors
*Staphylococcus epidermidis/metabolism
Signal Transduction/drug effects
Mice
Humans
Skin Microbiome
Skin/metabolism/microbiology
Keratinocytes/metabolism
Administration, Topical
Disease Models, Animal
Female
Molecular Docking Simulation

@article {pmid42609044,
year = {2026},
author = {Kudureti, A and Zhao, S and Liu, X and Wang, BZ and Tian, CY},
title = {Adaptation of Soil Viruses to Salinity Stress: Insights Into Genome Size Expansion and Functional Diversification.},
journal = {Environmental microbiology},
volume = {28},
number = {8},
pages = {e70395},
doi = {10.1111/1462-2920.70395},
pmid = {42609044},
issn = {1462-2920},
support = {2024TSYCCX0056//Tianshan Talent Program of Xinjiang/ ; 2025D01D47//Natural Science Foundation of Xinjiang/ ; 31971448//Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Genome, Viral ; *Viruses/genetics/classification/isolation & purification ; *Salt Stress ; *Genome Size ; Salinity ; Soil/chemistry ; Metagenome ; Biodiversity ; },
abstract = {Viruses are important components of soil biodiversity and ecosystem functions. However, their response to soil salinity stress, including ecological patterns and functional potential, remains poorly understood. Here, metagenomic data from 84 saline soil samples were retrieved from public databases and analysed. Viral sequences were extracted from metagenomes, and auxiliary metabolic genes (AMGs) were identified. 83.34% of the vOTUs had no detectable gene-sharing links with the RefSeq Viral database, highlighting the unexplored diversity of saline soil viromes. In soils with higher salinity, viral genomes exhibited larger genome sizes and increased GC content. The diversity of temperate viruses (3.16-7.32) was significantly higher than that of lytic viruses (2.49-6.99). Although the diversity of temperate viruses decreased with increasing salinity, no significant trend was observed for lytic viruses. Viral abundance correlated positively with host abundance, consistent with the 'piggyback-the-winner' ecological coupling hypothesis. Functional potentials varied with salinity, and structural analysis showed changes in atomic interactions in key proteins (NhaA, ACAT) across salinity gradients. Significantly positive correlations were found between viral diversity and functional potential related to salt tolerance, carbon fixation, organic phosphorus mineralisation and nitrogen metabolism. These results suggest viral traits correlate with salinity gradients and provide insights into viral responses in saline soils.},
}

*Soil Microbiology
*Genome, Viral
*Viruses/genetics/classification/isolation & purification
*Salt Stress
*Genome Size
Salinity
Soil/chemistry
Metagenome
Biodiversity

@article {pmid42609251,
year = {2026},
author = {Tang, J and Deng, J and Guo, K and Song, Y and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Fang, H and Zhuge, J},
title = {The clinical application of metagenomic next-generation sequencing for invasive pulmonary aspergillosis in neutropenic patients: a multicenter retrospective study in the ICU.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1878097},
pmid = {42609251},
issn = {2235-2988},
mesh = {Humans ; *Invasive Pulmonary Aspergillosis/drug therapy/diagnosis/microbiology/mortality ; Retrospective Studies ; *Neutropenia/complications ; Female ; Intensive Care Units ; Male ; Antifungal Agents/therapeutic use ; Middle Aged ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; Treatment Outcome ; },
abstract = {BACKGROUND: Early initiation of targeted antifungal therapy is critical for improving outcomes in neutropenic patients with invasive pulmonary aspergillosis (IPA) in the intensive care unit (ICU). Although metagenomic next-generation sequencing (mNGS) is valuable for pathogen detection, its clinical value in IPA patients with neutropenia remains unclear.

METHODS: This multicenter retrospective study included patients clinically diagnosed with invasive pulmonary aspergillosis (IPA). All patients underwent both conventional microbiological tests (CMTs) and metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Based on neutrophil status, patients were stratified into neutropenic and non-neutropenic groups and further divided into mNGS-guided and CMT-guided groups according to the antifungal treatment strategy.

RESULTS: mNGS demonstrated higher pathogen detection rate than conventional microbiological tests (CMTs) in both neutropenic and non-neutropenic patients with invasive pulmonary aspergillosis (IPA). It also identified a broader pathogen spectrum and a higher proportion of mixed infections. Overall, IPA patients in the mNGS-guided group had lower 28-day mortality compared with the CMT-guided group (23.17% vs. 43.75%, P = 0.04). Multivariate analysis indicated that mNGS-guided therapy was associated with reduced 28-day mortality (adjusted OR = 0.329, 95% CI: 0.111-0.974, P = 0.045). A significant interaction between treatment strategy and neutrophil status was observed (adjusted P = 0.002). In subgroup analysis, the survival benefit of mNGS-guided therapy was mainly observed in neutropenic IPA patients, who achieved higher rates of appropriate antifungal therapy and lower mortality, whereas no significant intergroup difference was found among non-neutropenic IPA patients.

CONCLUSION: mNGS-guided antifungal therapy significantly reduced 28-day mortality in neutropenic IPA patients, whereas no clear effect was observed in non-neutropenic patients. These findings highlight the potential clinical value of mNGS in guiding antifungal therapy in neutropenic IPA patients.},
}

Humans
*Invasive Pulmonary Aspergillosis/drug therapy/diagnosis/microbiology/mortality
Retrospective Studies
*Neutropenia/complications
Female
Intensive Care Units
Male
Antifungal Agents/therapeutic use
Middle Aged
*Metagenomics/methods
Bronchoalveolar Lavage Fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
Aged
Adult
Treatment Outcome

@article {pmid42609329,
year = {2026},
author = {Qin, P and Tuersong, W and Tao, Z and Huang, B and Tan, L and Liu, H and Zhao, J and Hu, M},
title = {Metagenomic profiling of pathogens and antibiotic resistome in influent of six municipal wastewater treatment plants: a descriptive analysis of plant-specific microbial hazards.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780611},
pmid = {42609329},
issn = {1664-302X},
abstract = {INTRODUCTION: Wastewater treatment plants (WWTPs) serve as critical nodes for monitoring urban biological hazards, yet the raw influent-the primary entry point for pathogens and antibiotic resistance genes (ARGs)-remains less characterized compared to treated effluent, particularly at the level of individual facilities, as most prior studies have pooled samples or focused on post-treatment matrices.

METHODS: In this descriptive study, we performed metagenomic sequencing on influent samples collected from six municipal WWTPs, with each plant treated as an independent unit to profile its specific microbial community, pathogen composition, and antibiotic resistome.

RESULTS: Across all samples, a total of 853 bacterial and 232 eukaryotic pathogen species were identified. An exploratory risk index, calculated by integrating species abundance with established risk group classifications, assigned the highest heuristic score to Tangxun Lake (2150), reflecting its concurrent enrichment of both enteric and respiratory pathogens. The pathogen distribution exhibited plant-specific patterns: enteric pathogens including Escherichia coli, Vibrio cholerae, and Campylobacter jejuni were predominantly detected in Huangpu road and Nantaizi Lake, whereas respiratory pathogens such as Mycobacterium tuberculosis and Legionella pneumophila were more abundant in Xinzhuang, Jinyang, and Tangxun Lake. A core set of ARGs-comprising multidrug efflux pumps, β-lactamases, and tetracycline resistance genes-was consistently present across all six facilities, collectively accounting for approximately 60% of the total ARG abundance detected. In addition, exploratory correlations between mobile genetic elements (e.g., plasmids and transposases) and clinically relevant ARGs were observed across the dataset, warranting further investigation.

DISCUSSION: By generating plant-specific hazard inventories rather than pooled averages, this study provides a descriptive baseline that enables facility-specific surveillance prioritization.},
}

@article {pmid42609485,
year = {2026},
author = {Yuan, G and Xie, X and Tang, M and Zheng, X and Luo, X and Xiong, A},
title = {Determinants of fungal infection and hospital readmission risk in interstitial pneumonia with autoimmune features: associations with vitamin D and pirfenidone.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1825951},
pmid = {42609485},
issn = {1664-3224},
mesh = {Humans ; Female ; *Pyridones/therapeutic use ; Retrospective Studies ; Male ; Risk Factors ; *Vitamin D/blood ; *Patient Readmission/statistics & numerical data ; *Lung Diseases, Interstitial/immunology/complications ; Middle Aged ; Aged ; *Mycoses ; *Autoimmune Diseases ; Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; },
abstract = {BACKGROUND: Fungal infections significantly compromise the prognosis of patients with interstitial pneumonia with autoimmune features (IPAF). However, the specific immune-related risk factors and their impact on clinical stability remain poorly defined. This study aimed to identify independent predictors for fungal infection and early readmission to optimize risk stratification.

METHODS: We conducted a retrospective analysis of 98 patients meeting the 2015 European Respiratory Society/American Thoracic Society (ERS/ATS) IPAF classification criteria. Fungal infections were confirmed through clinical manifestations, radiological findings, and metagenomic next-generation sequencing (mNGS). Logistic and Cox regression models were employed to identify factors independently associated with fungal infection and hospital readmission.

RESULTS: Fungal infection was identified in 40.8% of the cohort, with Candida albicans as the primary pathogen. Respiratory failure (odds ratio [OR]=3.76, 95% confidence interval [CI]: 1.24-11.38) and hypertension (OR = 2.94, 95% CI: 1.01-8.64) were independent associated with higher risks of fungal infection. Vitamin D (OR = 0.94, 95% CI: 0.89-0.99) and pirfenidone (OR = 0.17, 95% CI: 0.04-0.71) were independently associated with lower risks of fungal infection. Regarding prognosis, anti-Ro-52 (hazard ratio [HR]=2.23, 95% CI: 1.06-4.68) and anti-PL-12 (HR = 3.87, 95% CI: 1.11-13.44) antibody positivity independently predicted 3-month and 6-month hospital readmission, respectively.

CONCLUSION: Fungal infections in IPAF involve a complex interplay between clinical comorbidities and immune status. In this single-center retrospective cohort, vitamin D and pirfenidone were independently associated with lower risks of fungal infection and hospital readmission after adjustment for confounders. These findings should be interpreted as associations rather than evidence of causality and require validation through large-scale, multicenter prospective studies.},
}

Humans
Female
*Pyridones/therapeutic use
Retrospective Studies
Male
Risk Factors
*Vitamin D/blood
*Patient Readmission/statistics & numerical data
*Lung Diseases, Interstitial/immunology/complications
Middle Aged
Aged
*Mycoses
*Autoimmune Diseases
Anti-Inflammatory Agents, Non-Steroidal/therapeutic use

@article {pmid42609578,
year = {2026},
author = {Li, L and Wang, C and Liu, L and Xu, T and Nie, X and Liu, Y and Zhang, H and Yang, C and Di, J},
title = {Gut microbiota-derived imidazole propionate is associated with obesity.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1861257},
pmid = {42609578},
issn = {2296-861X},
abstract = {Obesity is a progressive metabolic disorder with some well-recognized markers, such as increased or elevated branched-chain amino acids (BCAAs). However, the role of gut microbiota-derived metabolites remains unknown in Asian populations. By employing an integrated multi-omics approach combining metagenomic and plasma metabolomic profiling in an Asian cohort alongside a longitudinal analysis of a bariatric surgery subgroup. We identified a distinct metabolic signature in obesity characterized by depleted circulating histidine and a concomitant elevation of Imidazole Propionate (ImP). The elevated ImP level not only positively correlated with the body mass index (BMI) but also increased progressively across obesity severity categories, and were associated with the taxonomic enrichment of ImP-producing species, such as Streptococcus mutans and Lactobacillus gasseri. Meanwhile, the ImP level showed rapid reduction within 3 months post-bariatric surgery. Collectively, our findings indicate that gut dysbiosis and histidine metabolism toward ImP production link with obesity and metabolic dysfunction.},
}

@article {pmid42609856,
year = {2026},
author = {Salmona, M and Benattia, A and Meignin, V and Marie Ferré, V and Jouenne, F and Lorillon, G and Le Goff, J and Mourah, S and Tazi, A},
title = {No detectable infectious agents in Langerhans cell histiocytosis with lung involvement.},
journal = {ERJ open research},
volume = {12},
number = {4},
pages = {},
pmid = {42609856},
issn = {2312-0541},
abstract = {Shotgun metagenomics of pulmonary and extrapulmonary Langerhans cell histiocytosis lesions revealed no infectious pathogens and no microbiome differences from control lung tissue, which does not support an infectious role in disease pathogenesis https://bit.ly/4liJHfO.},
}

@article {pmid42610730,
year = {2026},
author = {Sukkasam, N and Liu, TX and Dofher, K and Monshupanee, T and Hallam, SJ},
title = {Metagenome-assembled genomes for N2-fixing cyanobacterium Nostoc sp. TISTR 8405 and co-occurring microorganisms from a long-term laboratory culture.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0055326},
doi = {10.1128/mra.00553-26},
pmid = {42610730},
issn = {2576-098X},
abstract = {We report here metagenome-assembled genomes from a long-term laboratory culture of the nitrogen-fixing cyanobacterium Nostoc sp. TISTR 8405, originally sourced from a Thai freshwater lake. The community consists of two additional co-occurring microorganisms, Erythrobacter sp. THAI-01 and Allorhizobium sp. THAI-01, and contains putative plasmids associated with Nostoc and Allorhizobium, respectively.},
}

@article {pmid42610965,
year = {2026},
author = {Liu, ZT and Zhao, XD and Li, JQ and Li, SX and Tang, X and Zhang, SY},
title = {High molecular weight dissolved organic matter drives soil resistome proliferation by enhancing microbial competition and viral carbon metabolism.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag212},
pmid = {42610965},
issn = {1751-7370},
abstract = {Soil organic carbon is a key determinant of microbial community structure and function, yet the role of dissolved organic matter (DOM) bioavailability in shaping the soil antibiotic resistome remains poorly understood. Here, we combined previous continental-scale field sampling across 18 provinces in China (n = 141) with additional microcosm experiments to investigate how DOM molecular weight influences soil antibiotic resistance genes (ARGs) proliferation. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic analyses, we found that soils enriched in high molecular weight (HMW) DOM harbored significantly greater ARG abundance and diversity compared to low molecular weight (LMW) DOM soils. HMW DOM intensified microbial competition, as evidenced by a higher proportion of negative correlations in the co-occurrence network and lower niche breadth, favoring the enrichment of co-hosts that simultaneously carried ARGs, carbon metabolism genes, and biosynthetic gene clusters for antimicrobial compounds. Microcosm experiments confirmed that HMW DOM (lignin) addition significantly increased ARG transcript abundance (2.4-fold) and co-host relative abundance (2.3-fold), accompanied by a concurrent increase in transcribed viral auxiliary metabolic genes (2.5-fold) involved in complex carbon degradation. Structural equation modeling revealed that HMW DOM abundance and chemodiversity exerted the strongest positive effects on ARG abundance, primarily by shaping microbial community competition and metabolic potential. Collectively, our findings establish DOM bioavailability, particularly its molecular weight, as a critical yet previously overlooked driver of soil resistome development, challenging the conventional focus on total carbon content and highlighting the potential for molecular-level organic matter management to mitigate the spread of ARGs.},
}

@article {pmid42611076,
year = {2026},
author = {Irbaz, M and Hamood, Z and Shahid, S and Ghufran, A and Ajmal, A and Rafiq, I},
title = {Bacteriophage therapy for antimicrobial-resistant, biofilm‑associated diabetic foot infection: delivery routes, phage antibiotic synergy, and practical wound‑care integration.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42611076},
issn = {1432-072X},
mesh = {*Phage Therapy/methods ; *Diabetic Foot/therapy/microbiology ; *Biofilms/drug effects/growth & development ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteriophages/physiology ; *Bacterial Infections/therapy/microbiology ; Animals ; Drug Resistance, Multiple, Bacterial ; Pseudomonas aeruginosa/drug effects/virology ; Bacteria/drug effects/virology ; },
abstract = {Diabetic foot infections (DFIs) are a significant public health problem, associated with a delayed healing process and high rates of recurrence, which culminates in amputation. Two main factors, antimicrobial resistance (AMR) and biofilm formation, are responsible for the persistence and therapeutic failure of DFIs, resulting in extended healing time, infection recurrence, and an increased risk of amputation. In addition, the emergence of multidrug-resistant (MDR) pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa has made traditional antibiotic treatment less effective, necessitating alternative or adjunctive therapy. Phage therapy is an alternative approach to treat biofilm-associated and antimicrobial-resistant DFIs. Bacteriophages, viruses that infect bacteria, are highly specific to their bacterial hosts, can disrupt biofilms, and increase the activity of antimicrobial drugs used alone or in combination. This review focuses on the therapeutic potential of phage-based interventions for AMR and biofilm-related DFIs, highlighting delivery methods, phage-antibiotic synergy (PAS), incorporation into wound care regimens, and novel translational potential. Further interest in phage-based therapeutics has grown with recent advances in engineered phages, phage-derived enzymes, and precision diagnostics. Clinical and preclinical data indicate that phage therapy may be a promising strategy to improve bacterial control in specific DFI applications. Experimental studies have shown activity against MDR pathogens and biofilm-associated infections, and early clinical reports show potential for therapeutic benefit. The evidence base is currently small and is skewed towards in vitro studies, animal models, case reports, and small clinical trials. However, significant clinical evidenceis still needed before they can be widely adopted. There are several important barriers, such as the absence of large-scale randomized controlled trials, standardized treatment protocols, manufacturing consistency, and harmonized regulatory frameworks. Rigorous clinical evaluation, enhanced diagnostics (e.g., metagenomics profiling), delivery optimization, and regulatory coordination will be the key factors for further progress. Together, these advances could facilitate the integration of phage therapy into a multidisciplinary approach to DFI treatment and improve outcomes for patients with complex biofilm-related and AMR infections.},
}

*Phage Therapy/methods
*Diabetic Foot/therapy/microbiology
*Biofilms/drug effects/growth & development
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Bacteriophages/physiology
*Bacterial Infections/therapy/microbiology
Animals
Drug Resistance, Multiple, Bacterial
Pseudomonas aeruginosa/drug effects/virology
Bacteria/drug effects/virology

@article {pmid42611116,
year = {2026},
author = {Ajagbe, MA and Ahmed, SF and Ouf, A and Abdoullateef, BMT and Abdallah, RZ and Siam, R and Elbehery, AHA},
title = {Siwa spring microbiomes as reservoirs of biosynthetic gene clusters: Unlocking natural product potential.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42611116},
issn = {1573-0972},
mesh = {*Multigene Family ; *Biological Products/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota/genetics ; Metagenomics ; Metagenome ; Archaea/genetics/classification/metabolism/isolation & purification ; Phylogeny ; Biosynthetic Pathways/genetics ; Computational Biology ; },
abstract = {The rising demand for novel therapeutics, including antimicrobial, anticancer, and anti-inflammatory agents, underscores the need for new drug discovery strategies. Microbial communities represent rich reservoirs of bioactive compounds encoded by biosynthetic gene clusters (BGCs), yet traditional approaches remain limited by the inability to culture most microorganisms and the frequent rediscovery of known metabolites. Sequence-based metagenomics provides a transformative solution by directly identifying BGCs from environmental DNA. Using NovaSeq X Plus shotgun sequencing, we explored the biosynthetic potential of microbial communities in two previously unstudied brackish springs of the Siwa Oasis, Cleopatra and Fatnas. These ecosystems were dominated by bacteria (99.2%), with archaea being nearly absent (< 0.1%), and the microbial composition consisted largely of mesophilic taxa from Pseudomonadota, Bacteroidota, Actinomycetota, and Planctomycetota, which together accounted for 98.2% of the community. Our integrated bioinformatics pipeline enabled the reconstruction of 37 medium-to-high-quality metagenome-assembled genomes (MAGs), and recovered 147 BGCs mostly from Pseudomonadota, Actinomycetota, and Acidobacteriota phyla. Terpene (n = 23) and ribosomally synthesized and post-translationally modified peptide (RiPPs; n = 22) BGCs predominated within Cleopatra Spring, whereas RiPPs (n = 20) represented the dominant class recovered from Fatnas Spring. None of the recovered gene clusters mapped to experimentally validated entries in the MIBiG database (distance > 0.4), and 96.6% displayed structural divergence from the gene cluster families catalogued in the BGC Atlas. These results highlight the Siwa Oasis as a promising reservoir of unexplored biosynthetic potential and a valuable resource for natural product discovery to address global health challenges.},
}

*Multigene Family
*Biological Products/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota/genetics
Metagenomics
Metagenome
Archaea/genetics/classification/metabolism/isolation & purification
Phylogeny
Biosynthetic Pathways/genetics
Computational Biology

@article {pmid42611121,
year = {2026},
author = {Tomar, SS and Khairnar, K},
title = {SARS‑CoV‑2 Associated Shifts in the Upper Respiratory Tract Mycobiome in Non-hospitalized Cases.},
journal = {Mycopathologia},
volume = {191},
number = {5},
pages = {},
pmid = {42611121},
issn = {1573-0832},
support = {OLP-57//CSIR-NEERI/ ; },
mesh = {Humans ; *COVID-19/microbiology ; SARS-CoV-2 ; *Mycobiome ; Male ; *Fungi/classification/genetics/isolation & purification ; Female ; India ; Metagenomics ; Adult ; Middle Aged ; *Respiratory System/microbiology ; },
abstract = {SARS‑CoV‑2 infection is associated with marked changes of the upper respiratory tract mycobiome. URT mycobiome Changes in non-hospitalized patients however, remains poorly defined. We performed shotgun metagenomic sequencing of 95 upper respiratory tract swab samples from 48 symptomatic SARS‑CoV‑2-positive individuals and 47 healthy controls from central India. Fungal diversity and community structure were compared using alpha- and beta-diversity analyses, while differential taxa were identified using prevalence-based testing and a Directional Significance Score (DSS). SARS‑CoV‑2-positive samples showed significantly higher fungal alpha diversity than controls, with increased Shannon diversity (p = 0.000319) and Simpson diversity (p = 0.017). Beta-diversity analysis showed significant separation between groups for both Bray-Curtis and Jaccard distances (PERMANOVA p = 0.001), with significant dispersion effects as well (PERMDISP p = 0.001). DSS analysis showed certain fungal taxa associated with the SARS-CoV-2 group, including enrichment of Candida orthopsilosis, Malassezia furfur, Aspergillus glaucus, Aspergillus terreus, and Aspergillus niger, while Malassezia arunalokei, Aspergillus chevalieri, and Aspergillus sydowii were enriched in controls. These findings indicate that SARS‑CoV‑2 infection is associated with URT mycobiome dysbiosis and enrichment of clinically relevant opportunistic fungi in community cases.},
}

Humans
*COVID-19/microbiology
SARS-CoV-2
*Mycobiome
Male
*Fungi/classification/genetics/isolation & purification
Female
India
Metagenomics
Adult
Middle Aged
*Respiratory System/microbiology

@article {pmid42611158,
year = {2026},
author = {Vock, I and Bargetzi, A and Weisser, M and Mueller, OK and Junker, M and Mehrkens, A and Neidhoefer, C and Hamelin, B and Hosch, S and Mertz, KD and Keller, PM and Kuehl, R},
title = {Hematogenous vertebral osteomyelitis caused by vaginal microbiota: metagenomic resolution of a polymicrobial anaerobic case.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42611158},
issn = {1439-0973},
abstract = {We describe a rare case of a 35-year-old female patient suffering from polymicrobial hematogenous vertebral osteomyelitis caused by vaginal microbiota following sexual intercourse. Anaerobic blood cultures yielded Fannyhessea vaginae and Gemelliphila asaccharolytica, and intraoperative tissue cultures from decompression surgery identified Gardnerella vaginalis. Beyond Fannyhessea vaginae and Gemelliphila asaccharolytica, 16S rRNA gene Nanopore sequencing of surgical tissue also detected high amounts of Parvimonas parva, Peptostreptococcus anaerobius, Marseillibacter massiliensis, and Gemelliphila palaticanis. Antibiotic treatment with broad anaerobic coverage resulted in complete clinical resolution. Retrospective metagenomic analysis of a cervical swab obtained 9 months earlier revealed Fannyhessea vaginae and G. vaginalis to be already present in the vaginal microbiota. This case highlights the potential for hematogenous dissemination of vaginal anaerobes after sexual intercourse and underscores the diagnostic challenges posed by fastidious anaerobic bacteria. Molecular techniques are helpful tools in uncovering pathogens that may escape conventional culture methods.},
}

@article {pmid42611234,
year = {2026},
author = {Zhu, Y and Deng, X and Wang, Q and Song, H and Wang, L and Zhou, D and Gao, C and Gardea-Torresdey, JL and White, JC and Zhao, L},
title = {SiO2@CuO Nanozyme Reinforces Plant-Microbiome Synergies for Simultaneous Yield Enhancement, Nutritional Fortification, and a Beneficial Soil Legacy.},
journal = {ACS nano},
volume = {20},
number = {32},
pages = {22762-22777},
doi = {10.1021/acsnano.6c06987},
pmid = {42611234},
issn = {1936-086X},
support = {2026ZD1211704//Jing-Jin-Ji Regional Integrated Environmental Improvement-National Science and Technology Major Project/ ; CX (23)3015//Independent Innovation Fund for Agricultural Science and Technology in Jiangsu Province/ ; },
mesh = {*Microbiota/drug effects ; *Copper/chemistry/pharmacology ; *Silicon Dioxide/chemistry/pharmacology ; Soil Microbiology ; Soil/chemistry ; *Zea mays/growth & development/microbiology/drug effects/metabolism ; Rhizosphere ; Seeds ; },
abstract = {Plant associated microbes play pivotal role in promoting host fitness and health. However, modern agricultural practices, such as agrochemicals use and domestication are eroding plant-microbe partnership. Here, we show that nanoenabled seed priming strengthens plant-microbe interactions, enhancing the plant holobiont performance. We found that SiO2@CuO nanozymes (NZs) with peroxidase (POD)-like activities, as seed priming agent, initiate earlier and stronger seed respiration and boost exudates release (sugars, amino acids, and fatty acids), creating a nutrient-rich and transiently hypoxic spermosphere microenvironment. Field trials revealed that by day 40, rhizosphere microbiome diversity increased, with enrichment of functional taxa involved in carbon and nitrogen metabolism, as determined by 16S rRNA and metagenomic sequencing. Throughout the growing season, above-ground tissues in the nanopriming group consistently outperformed the hydropriming control in photosynthetic pigment content and plant height. At harvest, without additional fertilizers or other inputs, nanopriming increased maize yield by 8.1% and improved kernel nutritional quality: starch (21.0%), protein (24.5%), and iron (24.2%). Soil nutrient availability (N, P, K, Ca) and cation exchange capacity also increased, indicating the improved soil quality. Notably, the soil from nanopriming group confers the subsequent maize crop with better drought tolerance and enhanced P uptake capacity, compared to the soil from hydropriming group, indicating beneficial legacy effect. This study demonstrates that a simple seed nanopriming can steer a positive feedback loop between plant and microbe, cascading into multifaceted holobiont benefits. This offers a sustainable strategy to harness plant microbiomes and promote sustainable and climate resilient agriculture.},
}

*Microbiota/drug effects
*Copper/chemistry/pharmacology
*Silicon Dioxide/chemistry/pharmacology
Soil Microbiology
Soil/chemistry
*Zea mays/growth & development/microbiology/drug effects/metabolism
Rhizosphere
Seeds

@article {pmid42611448,
year = {2026},
author = {Xie, L and Wang, L and Lin, D and Zhou, Y and Cai, T and Wang, Y and Zhou, X and Li, X and Zhu, D and Zhang, T},
title = {Biodegradable Microplastic Diversity Drives Soil Carbon Lability via Phage-Boosted Bacterial Degradation of Recalcitrant Compounds.},
journal = {Environmental science & technology},
volume = {60},
number = {32},
pages = {22492-22504},
doi = {10.1021/acs.est.6c04389},
pmid = {42611448},
issn = {1520-5851},
support = {2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2023S011//Ningbo Public Welfare Key Science and Technology Plan Project/ ; 41977142//National Natural Science Foundation of China (NSFC)/ ; 42595623//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Carbon ; *Bacteria/metabolism ; *Soil/chemistry ; Soil Microbiology ; Bacteriophages ; Biodegradation, Environmental ; },
abstract = {Microplastic (MP) pollution threatens soil carbon stability, yet the effects of diverse MPs, particularly biodegradable MPs, on the soil carbon cycle and the associated microbial mechanisms remain poorly understood. Here, we established a gradient of MP diversity to examine its impact on soil dissolved organic matter (DOM) chemodiversity, integrating multiomics analysis to reveal coupled bacterial and viral metabolic strategies. Our results revealed that elevated MP diversity increased the proportion of low-molecular-weight compounds among newly generated DOM, reducing DOM aromaticity and stability. The enrichment of genes related to recalcitrant organic compound degradation, coupled with decreased energy metabolism gene abundance, suggested that the bioprocessing efficiency was enhanced at the expense of bacterial proliferation, facilitating DOM conversion to bioavailable forms. Accordingly, elevated MP diversity remarkably increased the diversity of soil phages and strengthened phage-host interactions, which might reflect phage-host coadaptation. Importantly, the increased abundance of phage-encoded auxiliary metabolic genes, especially those related to recalcitrant organic compound degradation, might enhance the utilization of recalcitrant DOM by the host bacteria. Collectively, these findings advance our understanding of bacterial mechanisms underlying carbon dynamics following exposure to diverse MPs, highlighting the critical role of phage-host interactions during this process.},
}

Carbon
*Bacteria/metabolism
*Soil/chemistry
Soil Microbiology
Bacteriophages
Biodegradation, Environmental

@article {pmid42611487,
year = {2026},
author = {Chase, AB and Jayarathne, JRRN and Haghighatjoo, M and Tabor, NJ and Smits, KM},
title = {A Diffusion-Driven CH4-O2 Boundary Structures Methane Oxidation and Carbon Transformation in Upland Soils.},
journal = {Environmental science & technology},
volume = {60},
number = {32},
pages = {22397-22407},
doi = {10.1021/acs.est.6c03515},
pmid = {42611487},
issn = {1520-5851},
support = {693JK32010011POTA//Pipeline and Hazardous Materials Safety Administration/ ; NA//Southern Methodist University/ ; },
mesh = {*Methane ; Oxidation-Reduction ; *Soil/chemistry ; Carbon ; Soil Microbiology ; Oxygen ; },
abstract = {Although extensive work has characterized high-affinity atmospheric methane oxidation in upland soils and sustained oxidation in chronically methane-rich environments, shallow point-source inputs introduce transient methane pulses into otherwise aerated heterotrophic soils. Whether these pulses migrate rapidly toward the atmosphere or instead create localized redox boundaries that restructure soil carbon pools and microbial metabolism remains unclear. Here, we conducted a controlled natural gas release experiment to quantify coupled geochemical and microbial responses in near-surface soils across a methane gradient. The release produced a spatial interval where measured CH4 and reconstructed O2 availability overlapped, identifying a redox transition associated with shifts in carbon geochemistry and methane-oxidation-related functional potential. Spatially resolved δ13C and C:N measurements revealed strong 13C enrichment of soil organic carbon (SOC) at the plume center, while elevated carbonate abundance and isotope composition distinguished a geochemical transition between the methane-rich plume center and distal reference soils. Within the intermediate CH4-O2 overlap zone, methane-associated monooxygenases (MMOs) and C1 assimilation genes were coordinately enriched, supporting structured C1 metabolic potential across the redox boundary. Metagenomic assembly and reconstruction linked this methane-responsive interval to Actinomycetota-affiliated genomes encoding expanded monooxygenase repertoires, including sMMO-like systems supported by operon architecture and catalytic-subunit phylogeny. This association provides a mechanistic link between transient methane exposure, redox-boundary formation, and microbial carbon transformation in aerated soils. Together, these findings show that shallow methane inputs can generate spatially constrained biogeochemical hotspots where gas transport, carbonate accumulation, and monooxygenase-associated C1 assimilation converge, and define conditions under which soil processes may influence methane transport toward the atmosphere.},
}

*Methane
Oxidation-Reduction
*Soil/chemistry
Carbon
Soil Microbiology
Oxygen

@article {pmid42611489,
year = {2026},
author = {Yuan, J and Suo, Y and Kang, D and Shapleigh, JP and Wang, B and Du, R and Peng, Y},
title = {Genome-Resolved Metagenomics Reveals Dominant Enrichment and Metabolic Adaptations of Thauera sp. in Activated Sludge under Carbon Limitation.},
journal = {Environmental science & technology},
volume = {60},
number = {32},
pages = {22680-22691},
doi = {10.1021/acs.est.6c01742},
pmid = {42611489},
issn = {1520-5851},
support = {CSTB2024NSCQ-MSX0999//Natural Science Foundation of Chongqing/ ; U23A20675//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Sewage/microbiology ; *Thauera/metabolism/genetics ; Metagenomics ; Carbon/metabolism ; Denitrification ; },
abstract = {Partial denitrification has been proposed as an alternative route to supply nitrite for anammox bacteria. The genus Thauera is frequently dominant in this process, yet the genomic basis for its ecological success within activated sludge remains unclear. Here, genome-resolved metagenomics was used to elucidate the genomic traits favoring its dominance under carbon (acetate)-limited conditions. Stable nitrite accumulation was achieved during treatment of low-strength ammonium wastewater (∼30 mg N/L) only under carbon limitation, whereas no nitrite accumulation occurred under carbon-sufficient conditions. The dominant high-quality metagenome-assembled genomes (MAGs) differed markedly between the two reactors. A near-complete MAG, affiliated with T. aminoaromatica (98.9% completeness and 0.4% contamination), dominated the carbon-limited reactor (27.0 ± 3.2%) but was rare in the carbon-sufficient reactor (0.6 ± 0.5%). The Thauera MAG encoded 4 copies of the acetate transporter genes (actP), a complete gene set for denitrification and internal carbon synthesis. Consistently, acetate limitation significantly increased both polyhydroxyalkanoate (PHA) content and the abundance of PHA-encoding microbes. Comparative genomics with 39 Thauera reference genomes further indicated selective enrichment of narG-containing Thauera lineages associated with nitrite accumulation. This study provides genomic insights into the ecological dominance of Thauera, highlighting its metabolic versatility and adaptive advantages in low-carbon wastewater treatment systems.},
}

*Sewage/microbiology
*Thauera/metabolism/genetics
Metagenomics
Carbon/metabolism
Denitrification

@article {pmid42446945,
year = {2026},
author = {Shirai, T and Kuzuya, K and Kishi, M and Ichikawa, S and Sakakibara, S and Nakai, A and Leach, S and Liu, YC and Motooka, D and Okuzaki, D and Narazaki, M and Kumanogoh, A and Kurosaki, T and Saegusa, J and Suzuki, K},
title = {Migration-dependent extrafollicular programming of preplasmablast age-associated B cells drives lupus pathogenesis.},
journal = {The Journal of clinical investigation},
volume = {136},
number = {16},
pages = {},
pmid = {42446945},
issn = {1558-8238},
mesh = {Animals ; *Lupus Erythematosus, Systemic/pathology/immunology/genetics ; Mice ; *Cell Movement/immunology ; Humans ; Autoantibodies/immunology ; *Precursor Cells, B-Lymphoid/pathology/immunology ; *B-Lymphocytes/pathology/immunology ; Female ; Receptors, G-Protein-Coupled/immunology/genetics ; Mice, Knockout ; *Plasma Cells/pathology/immunology ; },
abstract = {Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by autoantibody production. Extrafollicular (EF) B cell responses contribute to SLE pathogenesis, with age-associated B cells (ABCs) giving rise to autoantibody-secreting plasmablasts (PBs). However, the migratory cues governing this EF trajectory remain unclear. Here, we identify a distinct ABC state with PB precursor characteristics (pre-PB ABCs) and reveal a migration-dependent program underlying their generation. Single-cell analysis of patients with SLE and model mice showed that pre-PB ABCs were enriched in autoreactive clones and poised for PB differentiation. Their frequency correlated with autoantibody titers and disease activity, underscoring their pathogenic relevance. We further demonstrated that the oxysterol receptor EBI2 directed ABCs to EF niches within splenic bridging channels, promoting pre-PB ABC formation and autoreactive PB output. This process depended on the COMMD3/8 complex, a positive regulator of chemoattractant receptor signaling. Beyond EBI2-mediated ABC migration to EF niches, the COMMD3/8 complex was also required for trafficking of autoantibody-secreting cells to the bone marrow and infiltration of ABCs into the kidney. Accordingly, COMMD3/8 complex inhibition ameliorated disease in murine SLE models. These findings define a migration-dependent mechanism driving the EF differentiation of ABCs into autoreactive PBs and shaping the tissue distribution of pathogenic B cells, highlighting this program as a potential therapeutic target in SLE.},
}

Animals
*Lupus Erythematosus, Systemic/pathology/immunology/genetics
Mice
*Cell Movement/immunology
Humans
Autoantibodies/immunology
*Precursor Cells, B-Lymphoid/pathology/immunology
*B-Lymphocytes/pathology/immunology
Female
Receptors, G-Protein-Coupled/immunology/genetics
Mice, Knockout
*Plasma Cells/pathology/immunology

@article {pmid42604162,
year = {2026},
author = {Jia, P and Zhang, W and Zhang, G and Pei, W and Wu, F and He, Z and Chen, T and Liu, G},
title = {Environmental selection shapes the ecological cascade of biofilm assembly and functional gene abundance in sandstone weathering.},
journal = {Biofilm},
volume = {12},
number = {},
pages = {100388},
pmid = {42604162},
issn = {2590-2075},
abstract = {Microorganisms are pivotal agents in the process of sandstone weathering; nevertheless, the ecological mechanisms that govern their transition from mere colonization to sustained weathering activity remain ambiguous. This study systematically elucidated microbe-mediated weathering mechanisms through amplicon and metagenomic sequencing of bacteria, fungi, and archaea across a sandstone weathering sequence-from original unweathered sandstone (OS), biofilm-covered sandstone (BS), to weathered sandstone (WS). The findings indicate that microbial communities undergo associations across a weathering gradient, with biofilms constituting a unique transitional state. Community assembly mechanisms undergo a transition from stochastic processes in original sandstone to deterministic processes during the processes of biofilm formation and weathering. Biofilm communities formed modular, tightly interconnected putative association networks enriched with keystone taxa. Metagenomic analysis revealed significant enrichment of functional pathways related to iron acquisition, organic acid metabolism, and sulfur cycling during weathering, with functional annotation directly linking these traits to pivotal microbial groups. The findings of this study, as suggested by partial least squares path modeling (PLS-PM), indicate that environmental changes are associated with deterministic processes and with increased microbial richness. These factors are further linked to the composition of putative keystone taxa along the weathering gradient. These pivotal groups subsequently influence the abundance of weathering-related functional genes, directly accelerating weathering processes. This finding unveils a distinct ecological cascade pathway, commencing with environmental selection and culminating in the enrichment of functional gene potentials. The present study proposes a universal framework demonstrating that sandstone weathering is associated with deterministic processes, putative keystone taxa, and synergistic gene networks. This mechanism is not only applicable to sandstone systems, but also offers novel insights into the understanding of microbially mediated mineral weathering in terrestrial environments. This process is fundamental in influencing global biogeochemical cycles, soil formation, and the preservation of geological and cultural heritage.},
}

@article {pmid42604235,
year = {2026},
author = {Frizzo, R and Pettenuzzo, S and Bortoletto, E and Gregori, I and Vezzi, A and Panin, M and Hemmati, S and Archetti, L and Mammi, S and Bogialli, S and Venier, P},
title = {Viral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt-marsh tidal creek sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag184},
pmid = {42604235},
issn = {2730-6151},
abstract = {Salt marshes are highly productive ecosystems where microbial communities drive key transformations of organic matter at rates often exceeding those of oceanic and inland environments. Viruses are recognized as important drivers and regulators of global biogeochemical cycling, yet their diversity, host range, and functional roles in salt marsh ecosystems remain largely unresolved. To address these gaps, we investigated how viral lysis and host reprogramming can affect microbe-mediated organic matter transformations in a salt marsh of the Venice lagoon (Italy). Focusing on tidal creek surface sediments, we reconstructed 311 metagenome-assembled genomes (MAGs), built corresponding genome-scale metabolic models (GEMs) individually constrained with 121 metabolites detected in the sediments, and identified 3537 viral populations (vOTUs) across 10 samples. To assess the impact of viral lysis, we inferred prokaryotic hosts for 243 vOTUs and analysed host metabolism through MAG pathway analysis and GEM flux modelling across 13 bacterial orders, thus highlighting a negative impact on polysaccharide degradation, organic nitrogen mineralization, and organosulphur mineralization/volatilization processes. For host metabolic reprogramming, we characterized a subset of 50 auxiliary viral genes (AVGs) by mapping them to GEM reactions and analysing their stoichiometry, directionality, and pathway context, outlining two dominant strategies: resource scavenging through nucleotide-sugar biosynthesis, amino acid utilization, and sulphate assimilation; functional host maintenance through cofactor biosynthesis, electron transport, and energy production through carbonyl-compound utilization. Our findings provide a mechanistic view of the viral influence on organic matter transformations in salt marsh sediments and confirm viruses as key players in salt marsh biogeochemistry.},
}

@article {pmid42604251,
year = {2026},
author = {Zhang, B and Jiang, X and Zhao, H and Wang, B},
title = {BileActome reveals community-assembled bile acid metabolism in the rumen microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag205},
pmid = {42604251},
issn = {2730-6151},
abstract = {Microbial bile acid metabolism is an important link between microbiomes and host physiology, but its genetic basis remains difficult to resolve from genome and metagenome data. This is largely because existing annotation resources are not designed for the high sequence diversity and functional complexity of microbial bile acid genes. Here we present BileActome, a reusable annotation resource developed specifically for microbial bile acid metabolism. BileActome defines 27 experimentally supported gene families, including bile salt hydrolases, bile acid-inducible operon genes, and microbial hydroxysteroid dehydrogenases. Its design prioritizes experimentally supported functional sites when available and conserved domain features otherwise, while also distinguishing key functional subtypes. We applied BileActome to 1693 high-quality rumen metagenome-assembled and isolate genomes and validated its performance using controlled in vitro rumen fermentations under three bile acid interventions. In metagenomic gene-catalog analyses, BileActome enabled pathway-level interpretation of microbial responses to bile acid exposure, with the most reproducible responses centered on Bai-associated gene families. At genome scale, it generated a phylogeny-informed map of bile acid metabolic potential that was broader and more informative than Kyoto Encyclopedia of Genes and Genomes (KEGG)-based annotation. Further analyses of genomes, local gene organization, and genome-level guilds showed that bile acid metabolism in the rumen is modular, phylogenetically structured, and distributed across different microbial members. Deconjugation and oxidation/epimerization-related functions were widespread, whereas complete bile acid-inducible systems were less common. Together, these findings support a community-assembled model of bile acid metabolism and establish BileActome as an open and reproducible framework for studying specialized microbial functions in complex ecosystems.},
}

@article {pmid42604392,
year = {2026},
author = {Wang, S and Shui, F and Zhou, Y and Wang, X and Zeng, Y and Shan, Y and Li, J and Zhang, L and Song, K and Wu, F},
title = {Unexpected novel clade III type nitrous oxide-reducing bacteria from incubated lake sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag194},
pmid = {42604392},
issn = {2730-6151},
abstract = {Nitrous oxide-reducing bacteria (N2ORB) play a pivotal role in regulating N2O emissions in aquatic ecosystems, with clade I and clade II nosZ-harboring microorganisms representing well-recognized contributors to microbial N2O consumption. Beyond conventional N2ORB, the recently identified clade III nosZ from soil may represent a previously overlooked potential N2O sink, yet the distribution and characterization remain largely unexplored in aquatic ecosystems. Here we established microcosm systems using sediments from five lakes and subjected them to warming temperature gradients to investigate the diversity and genomic characteristics of N2ORB. Hidden Markov model (HMM)-based analyses identified a total of 45 nonredundant nosZ sequences, including 12 affiliated with clade III nosZ. Clade III nosZ accounted for 10.2%-40.6% of total nosZ genes, indicating that clade III nosZ-harboring N2ORB is widespread and non-negligible. Reconstruction of metagenome-assembled genomes (MAGs) identified four phylogenetically novel clade III nosZ-harboring N2ORB, with these MAGs showing low average amino acid identity to their closest known reference genomes. These MAGs showed different denitrification gene inventories, with MAG33 lacking identifiable genes for upstream N2O-producing steps, suggesting a potential non-denitrifying N2O reducer. They also encoded oxygen-related stress-response genes, suggesting a potential ability to perform N2O respiration in the presence of oxygen. Unlike canonical clade I/II nosZ clusters, clade III nosZ-harboring MAGs lacked typical accessory genes and instead exhibited distinct neighboring transporter- and cytochrome-related genes. Together, our results provide evidence for the occurrence of clade III nosZ-harboring N2ORB in non-soil ecosystems and expand current understanding of their genomic traits.},
}

@article {pmid42604646,
year = {2026},
author = {Cai, L and Chen, J and Hu, W and Xi, M and Zhang, Y and Chen, X},
title = {Chronic Fibular Osteomyelitis Caused by Schaalia turicensis: A Case Report and Literature Review.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {109064},
doi = {10.1016/j.ijid.2026.109064},
pmid = {42604646},
issn = {1878-3511},
abstract = {BACKGROUND: Schaalia turicensis (previously classified as Actinomyces turicensis) may lead to actinomycosis, typically presented as a chronic, granulomatous infection marked by suppuration and sinus tract formation, with a propensity for recurrence. This report details a rare case of chronic post-traumatic osteomyelitis attributable to S. turicensis.

CASE PRESENTATION: A 57-year-old woman was presented with a four-year history of recurrent redness, swelling, and ulceration of the left lower leg after surgical intervention. Debridement of the lesion was performed by orthopedists. Metagenomic next-generation sequencing (mNGS) analysis of intraoperative tissue samples revealed S. turicensis and penicillin therapy was initiated accordingly. Subsequent culture results identified Actinomyces species and methicillin-resistant Staphylococcus epidermidis (MRSE). The antibiotic regimen was adjusted to clindamycin, leading to clinical improvement and eventual discharge.

CONCLUSION: This case underscores the diagnostic dilemma posed by indolent pathogens like S. turicensis in chronic post-surgical osteomyelitis. mNGS provided a rapid and precise microbiological diagnosis, directly informing critical therapeutic decisions.},
}

@article {pmid42604702,
year = {2026},
author = {Liang, E and Shen, J and Song, T and Liu, X and Liu, Y and Su, J and Gu, Y and Zhao, Y},
title = {A novel in-situ sludge reduction strategy: Bio-promoter assisted low-MLVSS operation for reducing sludge production while maintaining nitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135648},
doi = {10.1016/j.biortech.2026.135648},
pmid = {42604702},
issn = {1873-2976},
abstract = {Excess sludge production and subsequent treatment remain major challenges in activated sludge-based wastewater treatment. However, biological strategies for efficient in-situ sludge reduction remain limited. In this study, a composite bio-promoter was developed to support low-MLVSS operation. At 15% lower MLVSS, the bioreactor maintained 88.37% ammonia nitrogen removal, while the observed sludge yield decreased by 19.78% within a cycle. Long-term operation showed that bio-promoter addition activated the metabolic activity and key enzyme functions, thereby reducing the net sludge increase by 13.46%. The lower sludge production response was accompanied by higher biomass-specific nitrifying activity. The specific oxygen uptake rate of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria increased by 7.39% and 11.55%, respectively. The specific activities of ammonia monooxygenase and hydroxylamine oxidase increased by 13.66% and 27.71%, respectively. Metagenomics analysis revealed that Nitrosomonas and Nitrospira became the dominant functional bacteria in the community. The relative abundance of key nitrification genes amoA and hao increased by 6.25% and 40.80%, respectively, suggesting that the bio-promoter enhanced the functional activity of retained nitrifying biomass and helped maintain nitrification under reduced sludge concentration. This study created a novel bio-promoter technology scheme for in-situ sludge reduction and provided a theoretical basis and practical strategy for achieving energy-saving and efficient operation.},
}

@article {pmid42602596,
year = {2026},
author = {Xie, Z and Liu, X and Bo, B and Wei, W and Li, C and Ye, C},
title = {Effect of phosphorus fraction in shaping bacterial and archaeal community succession in the largest hydrologically connected lake of Northeast Asia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844785},
pmid = {42602596},
issn = {1664-302X},
abstract = {Microbial beta diversity and its components are key ecological indicators for understanding community assembly in lake sediments, yet their coupling with phosphorus (P) fractions remains poorly understood in hydrologically connected lake systems. In this study, sediment cores were collected from Xingkai Lake, the largest freshwater lake in Northeast Asia with a unique twin lake structure, and were analyzed using metagenomic sequencing combined with sequential P fractionation. Results showed that total beta diversity and species turnover for bacteria and archaea increased significantly with sediment depth in both lakes, with faster turnover rates in Daxingkai Lake. Nestedness was generally not significant in Daxingkai Lake but showed a significant positive trend with depth for archaea in Xiaoxingkai Lake. The dominant P fraction in the Daxingkai Lake sediments were HCl-Pi and residual P, while NaOH-Pi dominated in Xiaoxingkai lake sediments. Organic P explained the largest proportion of bacterial beta diversity variation in Daxingkai Lake, while inorganic P was the primary driver in Xiaoxingkai Lake. Conversely, inorganic P dominated the archaeal beta diversity variation in Daxingkai, whereas organic P dominated in Xiaoxingkai. These findings demonstrate that species turnover is the dominant component of beta diversity along the sediment depth gradient. The contrasting roles of organic P and inorganic P in shaping microbial beta diversity highlight the importance of P resource partitioning in driving microbial community succession and provide a basis for developing microbial beta diversity indicators to support eutrophication assessment and sediment management in hydrologically connected lake systems.},
}

@article {pmid42602688,
year = {2026},
author = {Sheng, H and Liu, J and Yu, Q and Peng, H},
title = {Comparative Analysis of Metagenomic Next-Generation Sequencing and Conventional Culture for Pathogen Detection in 218 Patients with Pulmonary Infectious Diseases: A Retrospective Study.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {625827},
pmid = {42602688},
issn = {1178-6973},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a promising technique, but comparative studies of mNGS and culture across different pulmonary diseases are limited.

METHODS: We retrospectively analyzed data from 218 patients who underwent BALF mNGS testing between November 2021 and April 2025, and patients were categorized into pneumonia, bronchiectasis, NTM, tuberculosis, and other groups based on discharge diagnoses. We compared detection rates, pathogen spectra, co-infection rates, and special pathogen distributions between mNGS and culture. We also assessed concordance (Kappa) and complementary rates.

RESULTS: The overall positive detection rate of mNGS was significantly higher than that of culture (95.4% vs 67.4%, P<0.001). The overall concordance rate was 71.1%, with a Kappa of 0.42. mNGS additionally detected pathogens in 84 cases (38.5%), primarily viruses (38), Nocardia (8), NTM (15), fungi (45), and Legionella (4). Culture additionally detected 23 cases (10.6%). Co-infection was detected by mNGS in 118 cases (54.1%), far higher than culture (42 cases, 19.3%, P<0.001). The bronchiectasis group had significantly higher detection of Pseudomonas aeruginosa (54.5%) and Nocardia (18.2%).

CONCLUSION: mNGS provides a higher detection rate than culture in this cohort, particularly for special pathogens, and is complementary to culture. Pathogen profiles varied across disease types; however, the clinical benefit of mNGS-guided therapy remains to be evaluated in prospective studies.},
}

@article {pmid42603397,
year = {2026},
author = {Geng, D and Ding, Y and Jiang, Y and Wang, Z and Chen, G and Chang, G and Bai, H},
title = {Multi-omics analysis of cecal microbiota-hypothalamus axis interactions in small-sized meat ducks with divergent residual feed intake.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107310},
doi = {10.1016/j.psj.2026.107310},
pmid = {42603397},
issn = {1525-3171},
abstract = {Residual feed intake (RFI) is an indicator of feed efficiency that reflects variation in nutrient utilization independent of growth. This study characterized physiological traits and multi-omics profiles associated with divergent RFI in small-sized meat ducks. From an initial population of 500 1-day-old ducks, a total of 420 healthy ducks were individually housed from 21 to 42 d to record feed intake, and ducks with low RFI (LRFI) and high RFI (HRFI) were identified for further analyses. During the experiment, 30 ducks per group for growth performance, 15 ducks per group for plasma biochemical and 5 per group for multi-omics. Compared with HRFI ducks, LRFI ducks showed lower feed intake, lower feed conversion ratio (FCR), and lower plasma triglyceride concentrations, whereas body weight gain did not differ between groups. Shotgun metagenomic analysis showed that LRFI ducks were enriched in Bacteroides-related lineages and had higher predicted capacities for complex carbohydrate degradation, lipid and energy metabolism, and cofactor synthesis, whereas HRFI ducks were enriched in taxa including Subdoligranulum variabile and Clostridioides difficile. Untargeted cecal metabolomics revealed distinct lipid- and bile acid-related metabolic profiles between the 2 groups, including differences in long-chain lipid species and bile acid-associated metabolites. Hypothalamic transcriptomic analysis identified differentially expressed genes related to neuropeptide signaling, serotonin biosynthesis, intracellular signaling, and inflammatory regulation, including NMUR2, TPH1, and PTK2B. Correlation analysis integrating microbial taxa, metabolites, and hypothalamic transcripts further revealed coordinated associations among these features in small-sized meat ducks with divergent RFI. Overall, variation in feed efficiency in ducks was associated with differences in cecal microbiota, metabolite profiles, and hypothalamic gene expression, and these results highlight candidate microbial taxa, metabolites, and genes for further validation.},
}

@article {pmid42603473,
year = {2026},
author = {Zhang, XM and Lai, CY and Men, Y and Zhao, HP},
title = {Aerobic biotransformation of 8:2 FTCA in activated sludge: Carbon source dependence and multiple transformation pathways.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143305},
doi = {10.1016/j.jhazmat.2026.143305},
pmid = {42603473},
issn = {1873-3336},
abstract = {8:2 fluorotelomer carboxylic acid (8:2 FTCA) has been detected in environmental matrices and biota, yet its aerobic biodegradation remains poorly understood. Here, 30-day activated-sludge microcosms were used to investigate the degradation kinetics, transformation pathways, and microbial responses of 8:2 FTCA (10 μM) under carbon-limited and carbon-amended conditions. Only 38 mol% removal occurred without external carbon, whereas acetate, butanol, and octane increased removal to 85-90 mol%, with octane producing the highest fluoride release (24 μM). Target and non-target analyses identified 8:2 FTUCA and 7:3 FTCA as major intermediates and revealed the accumulation of five perfluorocarboxylic acids (PFCAs). Detection of OH-8:2 FTCA and PFNA supported a potential α-oxidation pathway. Mechanistically, 8:2 FTUCA forms via HF elimination and 7:3 FTCA via H/F exchange, while hydroxylation, α/β-oxidation, and decarboxylation may have contributed to PFCAs formation. Metagenomic analysis showed that 8:2 FTCA exposure and carbon amendments selectively enriched microorganisms, including Tepidiforma, Ectorhizobium, and Actinocorallia, which harbored genes encoding dehalogenases, monooxygenases, and fluoride exporters. Collectively, these results suggest that carbon sources availability may influence 8:2 FTCA transformation, defluorination, and microbial functional profiles in activated sludge, providing additional insights into the potential aerobic biotransformation of FTCAs in multi-contaminant environments.},
}

@article {pmid42603474,
year = {2026},
author = {Zhang, C and Chen, J and Yang, W and Du, K and Tao, W and Lu, Q and Jiang, M and Hu, J and Zhu, Q and Elrys, AS and Cai, Z and Meng, L and Müller, C and Dan, X and Zhang, J},
title = {Small-sized biodegradable PLA microplastics inhibit plant nitrogen uptake by reshaping soil microbial communities and stimulating microbial metabolism.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143209},
doi = {10.1016/j.jhazmat.2026.143209},
pmid = {42603474},
issn = {1873-3336},
abstract = {The effects of microplastics (MPs) varying in polymer type and size on soil microbial community composition, metabolic functions, and nutrient cycling remain insufficiently understood. Here, we conducted a pot experiment using MPs differing in polymer type (non-biodegradable polyethylene [PE], and biodegradable polylactic acid [PLA]) and four particle sizes (1200-1400, 600-700, 120-150, and 25-38 μm), with amplicon sequencing, shotgun metagenomics, and nitrogen-15 ([15]N) tracing model. Our results showed that small-sized PLA-MPs (25-38 μm) reduced bacterial diversity, destabilized microbial networks, and shifted community assembly toward deterministic processes, whereas PE-MPs and larger-sized PLA-MPs exerted minimal effects. This shift was associated with enhanced depolymerization-related enzymatic potential, accompanied by greater dissolved organic carbon (DOC) availability. The resulting increase in C availability stimulated central C metabolism, promoting microbial resource acquisition and biomass synthesis. To maintain microbial C:N homeostasis, microbial N assimilation was stimulated through ammonium (NH4[+]) assimilation mediated by the glutamate dehydrogenase (GDH) and glutamine synthetase-glutamate synthase (GS-GOGAT) pathways and nitrate (NO3[-]) assimilation via assimilatory nitrate reduction to ammonium (ANRA). Consistently, the [15]N tracing model revealed that microbial assimilation rates of NH4[+]-N and NO3[-]-N increased by 10.5-fold and 12.7-fold, respectively, exceeding gross N mineralization rates, thereby depleting soil inorganic N pools and suppressing plant N uptake. Overall, our findings provide mechanistic insights into how PLA-MPs reshape soil functioning by reprogramming microbial communities and metabolism, thereby altering plant-microbe competition for N. These results highlight the potential risks of increasing biodegradable plastic inputs for cropland nutrient cycling and plant N acquisition.},
}

@article {pmid42603694,
year = {2026},
author = {Du, J and Liu, Y and Zuo, Z and Fan, S and Xu, X},
title = {Growth form controls the seasonal stability of nutrient-pollution mitigation by submerged macrophytes in shallow lakes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125499},
doi = {10.1016/j.envres.2026.125499},
pmid = {42603694},
issn = {1096-0953},
abstract = {Submerged macrophyte restoration is widely used to mitigate nutrient pollution in eutrophic shallow lakes, yet its effectiveness is often evaluated during peak plant growth rather than across the full growing season. This creates uncertainty about whether restored clear-water conditions can persist during late-season plant decline. Here, a mesocosm experiment compared a canopy-forming species, Hydrilla verticillata, with a rosette-forming species, Vallisneria natans, at vigorous- and late-growth stages. We measured overlying-water quality, sediment properties, extracellular enzyme activities, microbial community structure and metagenomic functional potential, and evaluated association patterns using Mantel analysis and partial least squares path modeling. Both species reduced nitrogen and chlorophyll-a during vigorous growth, indicating comparable short-term restoration effects. By late growth, however, H. verticillata showed biomass decline and rebound of total phosphorus and chlorophyll-a to levels similar to the unvegetated control, whereas V. natans maintained lower nutrient concentrations, stronger rhizosphere redox status and more persistent water-quality improvement. Under the shared seasonal background, this late-season divergence is more consistent with differences in growth-form strategy and late-stage plant condition than with seasonal forcing alone, and in H. verticillata may reflect senescence- and decomposition-associated nutrient rerelease. Sediment and metagenomic patterns indicated treatment- and niche-related differences in microbial functional potential for nitrogen and phosphorus cycling, although these abundance-based patterns should not be interpreted as direct process rates. The results show that submerged macrophyte restoration in nutrient-polluted shallow lakes should be assessed by full-season stability rather than peak-growth performance alone. Rosette-forming macrophytes may provide more reliable support for internal nutrient loading control where late-season persistence is a management priority.},
}

@article {pmid42603915,
year = {2026},
author = {Cherinet, MT and Bereded, NK and Van de Voorde, I},
title = {Traditional Ethiopian fermented condiments: a systematic review of microbial dynamics, nutritional transformations, and future perspectives.},
journal = {Journal of food science and technology},
volume = {63},
number = {9},
pages = {1637-1647},
pmid = {42603915},
issn = {0022-1155},
abstract = {UNLABELLED: Traditional Ethiopian fermented condiments, including Siljo, Datta, Awaze, Helbat, and Azo, are culturally significant and nutritionally valuable. Despite their importance, evidence on their microbial ecology, nutritional transformations, safety, and functional potential remains fragmented and insufficiently characterized. This systematic review, conducted in accordance with PRISMA 2020 guidelines, consolidates current knowledge on the microbial dynamics, nutritional changes, probiotic traits, and food safety of these traditional Ethiopian fermented condiments. A comprehensive literature search was carried out up to December 2025 across PubMed, Scopus, Cochrane Library, Epistemonikos, and Google Scholar. Studies consistently reported that lactic acid bacteria-particularly Lactiplantibacillus plantarum, Pediococcus pentosaceus, and Weissella spp.-dominate spontaneous fermentations, driving acidification to pH values typically between 3.6 and 4.5 and contributing to pathogen suppression. Fermentation also induced product-specific nutritional transformations, including changes in protein content and digestibility, mineral dynamics, and the formation of bioactive compounds. However, outcomes varied considerably depending on substrate composition, microbial consortia, and processing conditions. Data on antinutritional factor reduction (phytates, tannins, and trypsin inhibitors) were absent across all included studies, representing a critical knowledge gap. Despite these promising attributes, research on these condiments is largely limited by reliance on culture-dependent methods, heterogeneous fermentation practices, and inconsistent analytical approaches. The evidence base for some condiments, particularly Azo and Datta, is further constrained by reliance on grey literature and secondary data sources. To fully harness their microbial, nutritional, and commercial potential, future studies should employ integrated research methodologies based on standardized fermentation protocols, metagenomics, metabolomics, and comprehensive nutritional assessments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-026-06764-y.},
}

@article {pmid42604017,
year = {2026},
author = {Wu, Y and Xie, L and Li, S and Ye, J and Zhu, Z and Zhang, Y and Chen, F},
title = {Ecosystem settings and urbanization shape microbial communities and antibiotic resistance genes on coastal microplastics.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100655},
pmid = {42604017},
issn = {2666-5174},
abstract = {Coastal wetlands are increasingly contaminated by microplastics that provide long-lived substrates for microbial colonization, yet the joint effects of ecosystem settings and urbanization on plastisphere communities and their resistomes remain poorly understood. Here, we used a 2 × 2 factorial design across mangrove and sandy-beach sediments under rural and urban influence, combined with metagenomic profiling, to characterize microplastic-associated microbiota and antibiotic resistance genes (ARGs). Microbial communities on microplastics showed clear separation between mangroves and sandy shores, with additional shifts along the rural-urban gradient, indicating context-dependent plastisphere assembly. Urbanization substantially increased richness in mangrove plastispheres, whereas effects on sandy beaches were weak or inconsistent and largely confined to low-abundance taxa. In situ exposure yielded a diverse ARG repertoire (>1 000 ARGs), and ARG composition showed significant ecosystem × human-impact interactions, with urban mangrove microplastics hosting the highest ARG diversity. Genus-ARG co-occurrence networks showed denser bacteria-ARG association patterns in mangrove than in sandy-beach plastispheres, with a limited number of genera statistically associated with multiple ARGs. These results suggest that plastisphere communities and resistomes varied across ecosystem settings and urbanization contexts, with urban mangrove microplastics showing relatively higher ARG diversity and stronger bacteria-ARG co-occurrence patterns. These findings highlight the need for habitat-specific monitoring of microplastic-associated resistance.},
}

@article {pmid42599548,
year = {2026},
author = {Medeiros, WB and Hidalgo-Martinez, KJ and Penna, DDPS and Oliveira, VM},
title = {Environmental filtering shapes biosynthetic potential and resistome of antarctic microbiomes.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42599548},
issn = {1573-0972},
mesh = {Antarctic Regions ; *Microbiota/genetics ; Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Phylogeny ; Ecosystem ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental filtering is a major driver of microbial community assembly in Antarctic ecosystems, yet its influence on biosynthetic potential and antimicrobial resistance remains poorly understood. Here, we analyzed 319 medium- to high-quality metagenome-assembled genomes (MAGs) recovered from four Antarctic sites (Whalers Bay, Crater Lake, Fumarole Bay, and Hannah Point) to investigate the relationship between geochemical gradients, biosynthetic gene clusters (BGCs), and antimicrobial resistance genes (ARGs). Integrating genome-resolved metagenomics, biosynthetic mining, resistome profiling, and environmental analyses, we identified 1,197 BGCs, with terpene clusters representing more than 25% of the total. Several biosynthetic hotspots were detected, including an Acidobacteriota MAG harboring 62 BGCs. Resistome composition exhibited strong site-specific structuring and was significantly associated with geochemical variables, particularly cobalt, iron, organic carbon, and thermal variation. Network analyses revealed highly connected MAGs affiliated with Pseudomonadota and Actinomycetota, linking diverse BGC and ARG classes. At the same time, genomic co-localization of biosynthetic and resistance determinants suggests potential adaptive associations between secondary metabolism and self-resistance mechanisms. Together, these findings demonstrate that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.},
}

Antarctic Regions
*Microbiota/genetics
Multigene Family
Metagenome
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics
Phylogeny
Ecosystem
Drug Resistance, Bacterial/genetics

@article {pmid42599752,
year = {2026},
author = {Zhou, Y and Shao, Q and Liu, C and Tian, J and Guan, X and Zhang, X and Lu, J},
title = {Seasonal Dynamics of Community and Function of Gut Microbiome in Taihangshan Macaque (Macaca mulatta tcheliensis): Inferred From Metagenomic Data.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70163},
pmid = {42599752},
issn = {1749-4877},
support = {No.31672302;No.32070446//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a key regulator of host nutritional intake, growth, and health, playing an essential role in mediating host adaptation to environmental changes. The northernmost population of rhesus macaque, Taihangshan macaque (Macaca mulatta tcheliensis), faces severe survival challenges, such as food shortages and harsh temperatures during winter and early spring. Previous studies have shown that they cope with seasonal changes through behavioral adaptations, such as adjusting food resources and flexibly regulating macronutrient intake. However, the role of the gut microbiome in supporting the seasonal adaptation of Taihangshan macaques remains unclear. Herein, we investigated seasonal variations in gut microbiome alpha diversity, composition, and functions from fecal samples of Taihangshan macaques using metagenomic analysis. The results showed that: (1) totally 435 non-redundant metagenome assembled genomes (MAGs) were generated; (2) alpha diversity was significantly higher in spring and winter than in summer and autumn; and (3) in winter, pathways of fatty acid biosynthesis and essential amino acid (EAA) biosynthesis, as well as CAZymes (GH3 and GH5) involved in cellulose and hemicellulose degradation, were significantly enriched. In contrast, pathways related to carbohydrate, energy, and glycan biosynthesis and metabolism, along with CAZymes (GT8 and GH23) potentially facilitating fat synthesis and storage, were enriched in summer. These functional adjustments likely help the host cope with seasonal variations in food availability and environmental conditions. Overall, this study provides new insights into how the gut microbiome responds to seasonal changes in diet and environmental factors in mammals inhabiting temperate forests.},
}

@article {pmid42600417,
year = {2026},
author = {Kasaiyan, S and Mateo, J and Buzzanca, D and Chiarini, E and Alessandria, V and Caro, I},
title = {Technological and microbial changes in cooked sausages incorporating cooked chickpea as a meat replacer and powdered banana pseudostem.},
journal = {Meat science},
volume = {242},
number = {},
pages = {110204},
doi = {10.1016/j.meatsci.2026.110204},
pmid = {42600417},
issn = {1873-4138},
abstract = {This study investigated the quality and microbial dynamics of vacuum-packaged cooked pork sausages reformulated by partially replacing meat protein (13%) with cooked chickpea paste and incorporating powdered banana pseudostem (BPS; 0%-0.4%) as a fibre source. Four sausages: Control (CON), CCP without BPS (CCP-0), and CCP with low (0.2%) or high (0.4%) BPS (CCP-BL and CCP-BH) were analysed over 20 days of refrigerated vacuum storage (3-7 °C). Composition, liquid retention, texture profile, colour, and microbial counts were evaluated. High-resolution shotgun metagenomics was applied to characterize bacterial and fungal dynamics. Composition and cooking yield remained unaffected by the reformulations (p > 0.05). However, substituting meat with cooked chickpea increased centrifugation loss (2 percentage points) and decreased hardness (2-3N), chewiness (∼3 N), and elasticity (0.04-0.05 units). Incorporating BPS increased initial product pH (up to 0.1 units), while decreasing lightness (up to 4 units). Initial total mesophilic bacterial counts were about 1 Log CFU/g higher in sausages with BPS and reached levels near 7 Log CFU/g across all batches by day 10. Adding chickpea supported the growth and survival of Enterobacteriaceae during storage. Shotgun metagenomics revealed that Brochothrix thermosphacta dominated the spoilage microbiota in CON and CCP-0 batches, exceeding 80% relative abundance by day 20. Conversely, BPS inclusion introduces plant-associated taxa (Klebsiella michiganensis and Pantoea rwandensis), significantly elevating alpha diversity and reducing B. thermosphacta percentage (< 20% relative abundance). While cooked chickpeas alter sausage textural characteristics, BPS serves as a functional fibre that modulates vacuum-packaged spoilage ecology.},
}

@article {pmid42600516,
year = {2026},
author = {Hu, Q and Wan, T and Liu, Y and Zhong, H and Chen, Y and Ao, Z and Jin, X and Guo, S},
title = {A real-world retrospective cohort study reveals the clinical utility of metagenomic next-generation sequencing in lower respiratory tract infections.},
journal = {Journal of infection and public health},
volume = {19},
number = {10},
pages = {103332},
doi = {10.1016/j.jiph.2026.103332},
pmid = {42600516},
issn = {1876-035X},
abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are complicated by diverse pathogens, posing challenges to traditional diagnostics. However, robust evidence on LRTI pathogen spectra and metagenomic next-generation sequencing (mNGS) clinical utility remains limited.

METHODS: A retrospective analysis was conducted among 815 patients with suspected LRTIs who underwent mNGS and conventional microbiological testing(CMT) of bronchoalveolar lavage fluid. We evaluated the pathogen spectrum, the diagnostic value of mNGS across different infection categories, and its utility in guiding antibiotic therapy.

RESULT: Following exclusions, 754 patients demonstrated 84.5% mNGS positivity. mNGS detected DNA viruses (33.85%, EBV predominating), bacteria (30.83%), fungi (23.30%), mycobacteria (9.43%), and special pathogens (2.59%). Confirmed pathogens included Mycobacterium tuberculosis (n = 124), Candida albicans (n = 118), Pseudomonas aeruginosa (n = 87), Pneumocystis jirovecii (n = 65), Haemophilus influenzae (n = 50) and Aspergillus fumigatus (n = 48). mNGS showed higher positivity than CMT (84.5% vs 53.6%, P < 0.05), with sensitivities of 90.6% (LRTIs), 73.3% (bacterial), 74.7% (fungal), and 81.9% (tuberculosis); specificities were 22.6%, 56.5%, 73.5%, and 96.4%. Its high sensitivity but modest specificity necessitates cautious interpretation. mNGS guided treatment adjustments in 48.4% of patients, with higher rates in critically ill patients (60.1% vs 45.7%, P < 0.05), though clinical improvement was lower in this group (54.7% vs 79.2%, P < 0.05).

CONCLUSIONS: mNGS comprehensively detects pathogens in LRTIs, including bacteria, fungi, mycobacteria, DNA viruses, and special pathogens. While its broad diagnostic value and treatment guidance utility are significant, integration with clinical context is essential to distinguish true pathogens from colonization.},
}

@article {pmid42600761,
year = {2026},
author = {Hong, Z and Lu, Z and Shi, R and Zheng, S and Luo, J and Chen, J and Xie, Z and Zheng, JS and Chen, YM and Zhang, Z},
title = {Prospective associations of tea consumption with skeletal muscle mass and strength: Insights from the gut microbiome and proteomics.},
journal = {Pharmacological research},
volume = {231},
number = {},
pages = {108398},
doi = {10.1016/j.phrs.2026.108398},
pmid = {42600761},
issn = {1096-1186},
abstract = {Tea consumption may be associated with skeletal muscle health, but longitudinal evidence based on repeated assessments remains limited. We examined the associations of tea intake and serum biomarkers with repeated skeletal muscle measures and explored whether these associations might be partly explained by multi-omics features. In this prospective cohort, 3408 adults were followed for approximately 12 years. Skeletal muscle mass was measured by dual-energy X-ray absorptiometry, handgrip strength by digital dynamometry, gut microbial taxonomic and functional profiles by shotgun metagenomic sequencing, serum proteins by data-independent acquisition mass spectrometry, and fecal metabolites by targeted UPLC-MS/MS metabolomics. Linear mixed-effects models examined longitudinal associations, and mediation analyses estimated indirect effects. In longitudinal analyses, higher tea consumption frequency was associated with greater appendicular skeletal muscle mass, appendicular skeletal muscle index, and handgrip strength (β: 0.037-0.140; 95% CI: 0.002-0.205). Higher circulating flavan-3-ols showed similar associations with these muscle-related outcomes (β: 0.085-0.174; 95% CI: 0.007-0.254), whereas no significant associations were observed with walking speed. Exploratory multi-omics analyses identified tea-related differences in gut microbial species and functional pathways, fecal metabolites, and circulating proteins, including Gemmiger formicilis, amino acid biosynthesis pathways, fructose 1,6-bisphosphate, VTN, CFI, CNDP1, and ITIH4. Exploratory mediation analyses identified statistical indirect associations involving multi-omics features, with estimated proportions mediated ranging from 4.5% to 19.0%. Overall, higher tea consumption and circulating biomarkers were associated with greater skeletal muscle mass and strength, accompanied by distinct multi-omics features that may provide potential biological links between tea exposure and muscle-related outcomes.},
}

@article {pmid42600856,
year = {2026},
author = {Li, Y and Chen, L and Zhang, J and Zhang, Y and Wang, M and Zhang, R and Fang, W and Zhang, P and Zhang, G},
title = {Metagenomics reveals rumen residues as a superior inoculum for volatile fatty acid production in vitro.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135627},
doi = {10.1016/j.biortech.2026.135627},
pmid = {42600856},
issn = {1873-2976},
abstract = {Rumen microbiome is widely recognized as an efficient system for lignocellulose degradation. Rumen fluid (RF) has been often used as the inoculum in previous study of bioprocesses, however, the potential of rumen solids (RS) to enhance volatile fatty acid (VFA) production remains underexplored. The anaerobic fermentation performance of RS, RF, and RF + RS mixture as inocula was compared using corn stover as substrate, with RS addition at 5%, 10%, or 20% (w/w) to corn stover and RF addition at 1:2 (v/v) to buffer solution. At a corn stover content of 2.5% (w/v, based on final working volume), the highest VFA concentration of 10.05 g/L was achieved with 20% RS as inoculum, outperforming those with both RF and RF + RS. Metagenomic analysis revealed significant differences in bacterial, fungal, and archaeal community structures with 20% RS and RF. With 20% RS, hydrolytic bacteria (e.g., Enterobacter) dominated the ecological niche, microbial co-occurrence network analysis of the 2,000 most abundant genera revealed a simpler network with fewer negative associations, and functional analysis demonstrated a notable increase in relative abundance of glycosyltransferase (GT) families within carbohydrate-active enzymes (CAZymes). With 20% RS, enrichment in glycolysis-related genes was observed, indicating a preference for carbohydrate degradation, while acid-producing pathways were enriched such as pyruvate metabolism with RF. Rumen solids, as a superior inoculum for VFA production, effectively enhanced lignocellulose bioconversion by enriching specific low-abundance microbial taxa, forming a microbial network with fewer negative associations, increasing the relative abundance of GT families, and strengthening the systemic hydrolysis capacity.},
}

@article {pmid42601406,
year = {2026},
author = {Antman, T and Lewin-Epstein, O and Yerushalmi, T and Broder, YS and Zeevi, D},
title = {Global microbial DNA signatures of temperature and nutrient limitation across ecosystems.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42601406},
issn = {2058-5276},
abstract = {Microbial genomes continuously adapt to environmental conditions, but identifying universal signatures of adaptation remains challenging. Here we show that environmental temperature can be accurately predicted across ecosystems from DNA composition alone (R[2] = 0.75), using tetranucleotide frequencies from 1,235 marine and soil metagenomes and a machine learning approach. This predictive signal was also apparent within individual taxa, consistent with a fundamental temperature-associated signature. By contrast, GC content exhibited opposite correlations with temperature in soil (positive) and marine (negative) environments. This phenomenon was probably driven by differences in nutrient availability, as GC content increases with nutrients while nutrients decrease with temperature in marine samples. By integrating these observations, we identified specific tetranucleotides, with 50% GC, that displayed consistent and robust temperature correlations across environments and may have contributed to the stability of predictions. This work highlights metagenome-wide DNA-temperature associations, relevant for understanding microbial community responses to global changes.},
}

@article {pmid42601613,
year = {2026},
author = {Lotfi, M and Jalal, D and Sayed, AA},
title = {plsMD: a plasmid reconstruction tool from short-read assemblies.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {42601613},
issn = {1471-2105},
mesh = {*Plasmids/genetics ; *Software ; *Sequence Analysis, DNA/methods ; Genome, Bacterial ; Whole Genome Sequencing/methods ; },
abstract = {BACKGROUND: While whole genome sequencing has become a cornerstone of antimicrobial resistance surveillance, the reconstruction of plasmid sequences from short-read data remains a challenge due to repetitive sequences and assembly fragmentation. Current computational tools for plasmid identification and binning have limitations in reconstructing full plasmid sequences, hindering downstream analyses like phylogenetic studies and antimicrobial resistance gene tracking.

RESULTS: We present plsMD, a tool designed for full plasmid reconstruction from short-read assemblies. plsMD integrates Unicycler assemblies with replicon and full plasmid sequence databases to guide plasmid reconstruction through a series of contig manipulations. Using two datasets - an established benchmark dataset used in previous benchmarking studies and a novel dataset consisting of newly sequenced bacterial isolates - plsMD outperformed existing tools in both. In the benchmark dataset, it achieved excellent recall, precision, and F1 scores of 91.3%, 95.5%, and 92.0%, respectively. In the novel dataset, it achieved recall, precision, and F1 scores of 77.6, 88.9 and 74.5%, respectively. plsMD supports two usage modalities: single-sample analysis for plasmid reconstruction and gene annotation, and batch-sample analysis for phylogenetic investigations of plasmid transmission.

CONCLUSIONS: plsMD represents a significant advancement in plasmid analysis, offering a robust solution for utilizing existing short-read whole genome sequencing data to study plasmid-mediated antimicrobial resistance spread and evolution.},
}

*Plasmids/genetics
*Software
*Sequence Analysis, DNA/methods
Genome, Bacterial
Whole Genome Sequencing/methods

@article {pmid42601633,
year = {2026},
author = {Albastaki, A and Naji, M and Moussa, M and Smith, J},
title = {Soil Microbiomes Across Depth and Ecosystems in Dubai, UAE: Potential Environmental Signatures for Forensic Geolocation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70403},
doi = {10.1111/1758-2229.70403},
pmid = {42601633},
issn = {1758-2229},
mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Ecosystem ; Soil/chemistry ; Metagenomics ; Forensic Sciences ; Phylogeny ; },
abstract = {Soil microbial communities exhibit strong sensitivity to environmental gradients, yet their distribution across depth and land-use types in hyper-arid environments remains poorly characterised. Using whole-genome shotgun metagenomics via Oxford Nanopore Technologies long-read sequencing, we profiled soil microbial communities across six contrasting land-use sites in Dubai, UAE: urban, industrial (two locations), marine, desert and agricultural, where each sampled at three depth intervals (0-25 cm, 25-50 cm and 50-100 cm). Marine soils exhibited extreme salinity (EC 23.7-30.7 dS m[-1]) and the highest organic matter content (1.19%-1.76%), while desert soils were nutrient-poor with minimal salinity. Actinomycetota and Pseudomonadota co-dominated across all sites, collectively accounting for 77%-96% of classified sequences. Actinomycetota prevailed in undisturbed desert horizons (up to 53.4%), while Pseudomonadota dominated nutrient-enriched environments, reaching 69.4% at industrial sites. A notable compositional reversal was observed in the desert deep horizon (50-100 cm), where Pseudomonadota increased to 56.8%, departing from the expected oligotrophic depth gradient. PERMANOVA confirmed land use as the primary driver of community composition (p = 0.001), with depth exerting a secondary but significant effect (p ≤ 0.01). NMDS ordination revealed strong site-specific clustering, with each environment harbouring a distinctive microbial fingerprint with promising forensic geolocation potential.},
}

*Soil Microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Ecosystem
Soil/chemistry
Metagenomics
Forensic Sciences
Phylogeny

@article {pmid42602060,
year = {2026},
author = {Sahu, K and Yao, Q},
title = {metaIVP: an integrative metavirome focused metagenomic processing pipeline.},
journal = {BMC methods},
volume = {3},
number = {1},
pages = {37},
pmid = {42602060},
issn = {3004-8729},
abstract = {BACKGROUND: Metagenomic studies increasingly rely on complex, multi-tool pipelines to recover and characterize viral and non-viral genomes from mixed microbial communities. While these pipelines enable high-resolution genome recovery, limited functionality in downstream post-processing workflows and insufficient logging structures often hinder reproducibility, error tracing, and selective re-analysis. These challenges are particularly critical in metaviral analyses, where viral and non-viral genomes must be processed using distinct methodologies. To address these limitations, we introduce metaIVP, a modular, integrative, and flexible framework designed to systematically manage genome content purification, re-binning, quality assessment, and downstream analyses of viral and non-viral metagenomic contexts.

METHODS: The metaIVP framework is organized into hierarchical modules, each governed by dedicated log files that explicitly control execution state and re-runnability. Contig-level and bin-level analytical and purification steps are implemented as essential modules to isolate genome contents, followed by separate viral and non-viral post-processing workflows. Viral workflows incorporate contamination detection, genome quality evaluation, host prediction, and virus-specific binning. Non-viral analyses include genome binning, alignment and mapping statistics, genome quality assessment, and replication rate estimation. Checkpoints are explicitly defined such that deletion of selected module- or sub-module-level logs enables targeted re-execution of specific analytical steps without rerunning the full pipeline. All analyses are integrated to depict a comprehensive system in the metagenomic samples, with focus on the metaviromic information.

RESULTS: The usage of metaIVP was demonstrated using both a well-controlled human gut virome dataset and a geographically structured environmental metavirome dataset, showing its broad applicability across host-associated and environmental systems. The pipeline effectively separates viral and non-viral genomic content, improves viral bin purity, and preserves sample-specific functional, taxonomic, and host-association features after virome enrichment. Compared with recent state-of-the-art approaches, metaIVP achieves comparable performance, particularly when optional re-binning with vRhyme is applied, while maintaining a higher fraction of high-confidence viral bins.

DISCUSSION: The metaIVP addresses a key gap in metavirome analysis by jointly characterizing viral and non-viral genomic components and supporting integrative downstream analyses within a single framework. Its user-friendly, modular, and controllable design allows flexible execution and provides a foundation for incorporating additional downstream analytical tools as metavirome methodologies continue to evolve.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s44330-026-00090-7.},
}

@article {pmid42602126,
year = {2026},
author = {Ortúzar, M and Formariz, V and Suescún-Sepúlveda, JA and González-Hernández, M and Riesco, R and Garrido-Oter, R and Trujillo, ME},
title = {From natural assemblages to synthetic communities in the Lupinus microbiome.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1891479},
pmid = {42602126},
issn = {1664-462X},
abstract = {INTRODUCTION: Plant roots harbour complex microbial communities that enhance nutrient acquisition, stress tolerance, and pathogen defence, yet their assembly and functional dynamics remain incompletely understood.

RESULTS: In this work, we isolated over 700 bacterial strains from wild Lupinus angustifolius across multiple compartments and soil types, capturing both dominant and rare bacterial taxa. Using co-occurrence network analysis, we selected representative strains to assemble synthetic communities (SynComs) of varying complexity, which were inoculated under sterile and non-sterile conditions. Plants were inoculated with SynComs of increasing complexity under both non-sterile soil and gnotobiotic conditions. SynCom inoculation reshaped root-associated microbiota, moderately influenced the rhizosphere, and had limited impact on bulk soil communities. Increasing SynCom complexity enhanced plant growth and triggered host transcriptional responses involving hormone signaling, defence pathways, and metabolic reprogramming.

DISCUSSION: These findings indicate that soil-driven filtering and microbial interactions govern microbiome assembly and plant responses. Incorporating taxa with distinct ecological roles, including low-abundance members, improves SynCom functionality and advances understanding of plant-microbe interactions in natural and agricultural systems.},
}

@article {pmid42602195,
year = {2026},
author = {Maitray, A and Rishi, P and Conrady, CD and Binkley, E and Williams, BK and Yeh, S and Nicola, MD and Finger, PT},
title = {Vitreoretinal Lymphoma: A Comprehensive Clinical Review and Current Standards in Management.},
journal = {Journal of vitreoretinal diseases},
volume = {},
number = {},
pages = {24741264261474159},
pmid = {42602195},
issn = {2474-1272},
abstract = {PURPOSE: To summarize current evidence on clinical features, multimodal imaging findings, diagnostic techniques, and management strategies for vitreoretinal lymphoma.

METHODS: A literature review was performed to provide updated information on available treatment options for vitreoretinal lymphoma.

RESULTS: Diagnosis of vitreoretinal lymphoma requires vitreous biopsy, with or without retinal/subretinal tissue, for cytology and immunohistochemistry, along with ancillary tests such as flow cytometry, cytokine profiling (interleukin-10/interleukin-6 ratio >1), immunoglobulin heavy chain gene rearrangement analysis, and detection of the MYD88 L265P mutation. Optical coherence tomography and other multimodal imaging techniques have become increasingly useful in raising suspicion, guiding biopsy, and monitoring treatment response. No standardized treatment protocol exists for isolated vitreoretinal lymphoma. Management options include intravitreal chemotherapy (methotrexate and/or rituximab), radiation therapy, and systemic chemotherapy, often showing a good initial response, but relapse and subsequent central nervous system (CNS) involvement are common, resulting in poor overall prognosis and survival. For vitreoretinal lymphoma with CNS disease, current strategies favor high-dose methotrexate-based systemic chemotherapy, with or without intrathecal chemotherapy; whole-brain radiation is generally reserved as rescue therapy. Emerging directions for earlier diagnosis include metagenomic deep sequencing, and chimeric antigen receptor T-cell (CAR-T) therapy has shown promise for treatment of selected relapsed/refractory cases of primary CNS lymphoma with a potential to prolong survival.

CONCLUSIONS: Treatment of vitreoretinal lymphoma requires a multidisciplinary, individualized approach that integrates multimodal imaging, cytologic and molecular diagnostics, CNS evaluation, and tailored local or systemic therapy. Prospective multicenter studies are needed to refine diagnostic algorithms and standardize management.},
}

@article {pmid42594461,
year = {2026},
author = {Lu, D and Chen, B and Nie, E and Lian, S and Li, R and Guo, R and Fu, S},
title = {Indole inhibits anaerobic digestion by disrupting AHLs-mediated quorum sensing.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143267},
doi = {10.1016/j.jhazmat.2026.143267},
pmid = {42594461},
issn = {1873-3336},
abstract = {The emerging understanding highlights indole as a disruptive factor to quorum sensing (QS) mechanisms, prompting further investigation into its role in anaerobic digestion (AD) system inhibition. However, relevant studies are still scarce and the potential mechanism linking indole and AD inhibition remains unclear. This study showed that indole (1, 2, and 3 mM) significantly reduced cumulative methane production by 8.47-51.89% and extended the lag phase by 1.34-6.68 days. Time-series AHLs quantification, metagenomics, and circular clustering heatmaps analysis revealed that indole might disrupt microbial communication between hydrolysis-acidification bacteria and acetoclastic methanogens by reducing the AHLs level (C6-HSL, 3-oxo-C8-HSL, C10-HSL, C12-HSL, 3-oxo-C10-HSL, and C18-HSL). Notably, indole degradation alleviated the inhibition of C10-HSL, C18-HSL, and 3-oxo-C10-HSL, which might restore hydrolysis and acidification and mitigate AD inhibition. Exogenous AHLs (1 and 5 µM) restored methane production by 48.44-55.59% in 3 mM indole-inhibited reactors (p < 0.05), while the quorum quenching agent vanillin further reduced methane production by 72.55%, suggesting that AHLs play an important role in helping microorganisms resist indole stress. These findings highlight the importance of AHLs-mediated inter-microbial communication in counteracting indole-inhibited methanogenesis inhibition, suggesting potential practical strategies to enhance AD stability and efficiency in challenging conditions.},
}

@article {pmid42595035,
year = {2026},
author = {Mao, H and Deng, Y and Wang, X and Yu, Q and Zhao, Z and Zhang, Y},
title = {Two-phase anaerobic digestion with sub-thermophilic hydrolysis: Regulating metabolites to accelerate electron transfer and enhance methanogenesis.},
journal = {Environmental research},
volume = {307},
number = {},
pages = {125448},
doi = {10.1016/j.envres.2026.125448},
pmid = {42595035},
issn = {1096-0953},
abstract = {Sub-thermophilic anaerobic digestion accelerates the hydrolysis and acidogenesis of complex substrates to improve methane production, but methanogens may be inhibited under such condition. Two-phase anaerobic digestion (TPAD) system can decouple the hydrolytic-acidogenic and methanogenic phases to optimize microbial activity in each phase. Therefore, in this study, a novel temperature-phased strategy combining a 45°C hydrolytic-acidogenic phase with a 37°C methanogenic phase (TPAD45°C/37°C) was developed to accelerate the degradation of agricultural waste and avoid the sub-thermophilic temperature-induced inhibition of methanogenesis. Results showed that 45°C hydrolytic phase increased ethanol and acetate production, and decreased propionate production compared to the 37°C control. Consequently, at a solid retention time of 20 days, the methane yield in the TPAD45°C/37°C group was 31.8% and 13.0% higher than that in the TPAD37°C/37°C and TPAD45°C/45°C groups, respectively. Mechanistically, the TPAD45°C/37°C group exhibited the highest McrA activity and coenzyme F420 content, indicating superior methanogenic activity. Furthermore, Tafel polarization and temperature-dependent conductivity analyses revealed that the higher levels of ethanol from 45°C hydrolysate provided a stronger thermodynamic driving force to minimize the energy barrier and improve intrinsic electron transfer rates, thereby enhancing methanogenesis. Additionally, the TPAD45°C/37°C group exhibited the highest overall metabolic potential. Microbial community analysis revealed that this system enriched the methanogens, which in turn promoted the degradation of complex substrates and increased methane production. This study provided an economically viable, energy-positive, and highly resilient technological strategy for the sustainable valorization of agricultural waste.},
}

@article {pmid42595117,
year = {2026},
author = {Hashimoto, M and Oki, H and Kawahara, K and Fujii, KK and Koide, T},
title = {Molecular basis of collagen triple helix recognition by VWF A-like domain 2 of collagen VII: Implications for interlaced anchoring fibril formation.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {113448},
doi = {10.1016/j.jbc.2026.113448},
pmid = {42595117},
issn = {1083-351X},
abstract = {Anchoring fibrils formed by collagen VII play a critical role in stabilizing the dermal-epidermal junction. The N-terminal non-collagenous (NC1) domain of collagen VII binds firmly to basement membrane components including collagen IV and has also been reported to interact with mesenchymal fibrillar collagens via its von Willebrand factor A-like domain 2 (A2 domain). To elucidate how collagen VII recognizes fibrillar collagen, we performed yeast two-hybrid screening using a triple-helical random peptide library, which resulted in the identification of a Met-Gly-Φ (Φ; aromatic amino acid residue) motif. Biochemical analysis with synthetic triple-helical peptides revealed a binding preference of Trp > Phe as the Φ residue by the A2 domain despite Trp being absent in native collagens. The crystal structure of the A2 domain in complex with the Nle (Met surrogate)-Gly-Trp-containing peptide revealed a unique mechanism by which two distinct hydrophobic pockets of the A2 domain accommodate the Nle and Trp residues corresponding to the Met-Gly-Φ motif, engaging all three chains of the triple helix. Subsequent molecular dynamics simulations demonstrated that the A2 domain recognizes the corresponding native Met-Gly-Phe motif in a similar manner, but with lower affinity, implying a transient interaction with mesenchymal collagens. The findings obtained in this work suggest models in which transient A2-triple helix interaction promotes the recruitment of collagen I and III fibrils into the arc-shaped structure of anchoring fibrils. This also provides a foundation for linking structural understanding to skin fragility diseases caused by collagen VII dysfunction.},
}

@article {pmid42595349,
year = {2026},
author = {Yang, Z and Ramakrishnan, M and Wang, B and Wei, Q and Ahmad, Z},
title = {Optimized Controlled-Release Fertilization Improves Productivity and Reshapes the Rhizosphere Microbiome in Lei Bamboo: A Metagenomic Assessment.},
journal = {Environmental microbiology},
volume = {28},
number = {8},
pages = {e70401},
pmid = {42595349},
issn = {1462-2920},
support = {2018YFD060010403//National Key Research and Development Program of China/ ; 2021F1065-10//Special Project of Zhejiang Provincial Scientific Research Institutes/ ; },
mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Poaceae/microbiology/growth & development ; Nitrogen/metabolism ; Metagenomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Soil/chemistry ; Urea/metabolism ; },
abstract = {Intensive nitrogen fertilization in Lei bamboo (Phyllostachys praecox) plantations has increased productivity but has also reduced nitrogen-use efficiency (NUE), accelerated nutrient losses, and contributed to soil degradation. How nutrient-release strategies influence rhizosphere microbiome assembly and ecosystem functioning remains poorly understood. Here, we developed a bamboo shoot-specific controlled-release fertilizer (CRF) and evaluated different urea-CRF blending ratios to identify sustainable fertilization strategy for Lei bamboo production. Mixed CRF-urea treatments outperformed both sole-fertilizer applications and the unfertilized control. T2 (30% urea + 70% CRF) achieved the highest shoot yield, whereas T3 (50% urea + 50% CRF) enhanced NUE. Optimized fertilization improved soil nutrient availability and organic matter accumulation without significantly affecting soil pH. Metagenomic analysis revealed the enrichment of taxa associated with nutrient transformation, organic matter turnover, and plant growth. However, pathway-level analysis revealed shifts in carbon, nitrogen, and sulfur cycling activities under optimized nutrient-release regimes. Our results demonstrate that synchronizing nitrogen release with plant and microbial demand enhances rhizosphere function, productivity and NUE. T2 delivered the strongest overall agronomic performance by maximizing shoot yield while maintaining improved nutrient retention and ecological stability. These findings provide a mechanistic link between fertilization strategy, rhizosphere microbial dynamics, and ecosystem function, supporting sustainable Lei bamboo production.},
}

*Fertilizers/analysis
*Rhizosphere
*Microbiota
*Soil Microbiology
*Poaceae/microbiology/growth & development
Nitrogen/metabolism
Metagenomics
Bacteria/classification/genetics/isolation & purification/metabolism
Soil/chemistry
Urea/metabolism

@article {pmid42595408,
year = {2026},
author = {McQueen, AD and Calomeni-Eck, AJ and Cicerrella, AS and Chung, SH and Malmfeldt, MP and Lindsay, DL and Gong, P},
title = {Enhancing early-season detection of harmful algal blooms caused by sediment-borne overwintering cyanobacteria using metagenomic and qPCR tools.},
journal = {Harmful algae},
volume = {158},
number = {},
pages = {103160},
doi = {10.1016/j.hal.2026.103160},
pmid = {42595408},
issn = {1878-1470},
mesh = {*Harmful Algal Bloom ; *Cyanobacteria/genetics/classification/physiology ; *Geologic Sediments/microbiology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics/analysis ; Seasons ; Lakes/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Polymerase Chain Reaction ; },
abstract = {To better inform adaptive management strategies for harmful algal blooms (HABs), there is a critical need to improve detection capabilities of bloom risks earlier in the growing season. Emerging molecular tools such as metagenomic Next-Generation Sequencing (NGS) and amplification-based quantitative polymerase chain reaction (qPCR) can accurately identify the taxonomy of cyanobacteria and akinetes of which the latter are particularly challenging to distinguish morphologically and estimate their abundance. This study aimed to evaluate the contribution of these advanced molecular tools to assessing the presence, density, and planktonic growth potential of overwintering cyanobacterial cells in sediments from historically HAB-impacted waterbodies in the USA. We conducted 14-day incubation experiments using field-collected lake sediments and characterized cyanobacterial taxonomy and abundance in the sediments (pre-incubation) and overlying water (post-incubation) using light microscopy, genus-specific qPCR, and 16S rRNA amplicon sequencing. By analyzing qualitative and quantitative results, we not only identified the prevailing cyanobacterial genera that moved from sediment to water column over the incubation but also determined their relative abundance and the cyanobacterial genera consistent between sediment and water column. This study demonstrated that metagenomic and qPCR tools provided additional lines of evidence to augment traditional microscopy and improved taxonomic identification and quantification. Our approach can better inform planktonic growth potential of problematic cyanobacteria to enhance early detection capabilities, and guide targeted countermeasures taken to improve preventative or remedial HAB management, reducing environmental and public health impacts.},
}

*Harmful Algal Bloom
*Cyanobacteria/genetics/classification/physiology
*Geologic Sediments/microbiology
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics/analysis
Seasons
Lakes/microbiology
Real-Time Polymerase Chain Reaction/methods
Polymerase Chain Reaction

@article {pmid42595551,
year = {2026},
author = {Wang, L and Yang, J and Li, D and Zhang, F and Yan, JA and Wang, YY and Sun, J and Cao, H},
title = {[Tremella fuciformispolysaccharide retards the progression of colorectal cancer by regulating the gut microbiota-metabolome axis].},
journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]},
volume = {48},
number = {8},
pages = {975-982},
doi = {10.3760/cma.j.cn112152-20250925-00485},
pmid = {42595551},
issn = {0253-3766},
support = {MS2024064//Jiangsu Province Science and Technology Development Program of Traditional Chinese Medicine (General Project)/ ; YJZ202305//the Jiangnan University Affiliated Hospital Research-Oriented Hospital Medical Research Project (General Project)/ ; KX-25-C166//Wuxi City 2025 Soft Science Research Project/ ; },
mesh = {Animals ; *Colorectal Neoplasms/pathology/metabolism/microbiology/drug therapy/chemically induced ; Humans ; Mice ; HT29 Cells ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Polysaccharides/pharmacology ; NF-kappa B/metabolism ; Male ; *Basidiomycota/chemistry ; *Metabolome/drug effects ; Azoxymethane ; Apoptosis/drug effects ; Dextran Sulfate ; Cell Proliferation/drug effects ; Feces/chemistry/microbiology ; Disease Progression ; Colon/pathology/metabolism ; },
abstract = {Objective: To investigate the anti-colorectal cancer effect of tremella fuciformis polysaccharides (TFP) via the gut microbiota-metabolite axis. Methods: Colorectal cancer was induced in C57BL/6J mice using azoxymethane/dextran sulfate sodium. TFP or distilled water was administered by gavage for 3 weeks. Disease activity index (DAI), colon length, tumor burden, histopathology, gut microbiota (metagenomics), fecal metabolites (untargeted metabolomics), and colonic protein expression (Western blot) were assessed. Pyridoxic acid's effect on HT-29 cells was tested in vitro. Results: TFP significantly reduced DAI [2.0(1.8, 3.3) vs. 3.5(2.8, 4.5), P＜0.01], increased colon length [(7.2±1.1) vs. (5.5±0.5) cm, P＜0.05], lowered pathological score [6(3, 8) vs. 9(8, 10), P＜0.05], and decreased tumor number [2(1, 3) vs. 4(3, 4), P＜0.05] and volume [(11.02±7.88) vs. (24.99±3.38), P＜0.01]. Metagenomics revealed that TFP significantly reshaped gut microbiota (R[2]=0.173, P=0.027), enriching Candidatus Amulumruptor, Helicobacter, and Akkermansia. Metabolomics showed distinct profiles (R[2]=0.159, P=0.004), with pyridoxic acid elevated 1.20 fold (P＜0.001). Pyridoxic acid suppressed HT-29 cell viability and migration, and correlated positively with several upregulated bacteria, suggesting a microbiota-metabolite axis underlying its anti-tumor effect. TFP downregulated nuclear factor-κB (NF-κB) (P＜0.01) and upregulated phosphorylated AMP-activated protein kinase alpha (p-AMPKα) (P＜0.001), BAX (P＜0.001), and cleaved caspase-3 (P＜0.05). Conclusion: TFP inhibits colorectal cancer progression by modulating gut microbiota, elevating pyridoxic acid, suppressing NF-κB, and activating AMPK-mediated apoptosis.},
}

Animals
*Colorectal Neoplasms/pathology/metabolism/microbiology/drug therapy/chemically induced
Humans
Mice
HT29 Cells
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Polysaccharides/pharmacology
NF-kappa B/metabolism
Male
*Basidiomycota/chemistry
*Metabolome/drug effects
Azoxymethane
Apoptosis/drug effects
Dextran Sulfate
Cell Proliferation/drug effects
Feces/chemistry/microbiology
Disease Progression
Colon/pathology/metabolism

@article {pmid42595815,
year = {2026},
author = {Vasquez, YM and Nardi, T and Terasaki, GM and Byl, P and Brůna, T and Villada, JC and Romero-Gutiérrez, MF and Mock, T and James, TY and , and Woyke, T and Schulz, F},
title = {Genomic catalogue of giant viruses reveals expanded diversity and functional potential.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42595815},
issn = {2058-5276},
support = {Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Nucleocytoplasmic large DNA and Mirusviricota viruses exhibit taxonomic richness which continually expands due to metagenomic sequencing. Here we curate a database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level representatives from 18,727 GVMAGs, a sixfold increase from the previous giant virus phylogenetic frameworks. Phylogenomics revealed 712 previously undescribed genera, 13 previously unknown viral families and an order we propose named Mycodnavirales. By accounting for alternative and custom genetic codes, we improved gene calling in over 1,300 GVMAGs, enabling more accurate identification of protein-coding genes. Database mining uncovered putative endogenous viral elements in hosts spanning algae, fungi and parasitic protists, highlighting that giant virus integration is widespread and evolutionarily persistent. Protein-level analysis revealed enriched genes for pollutant degradation in Algavirales and widespread biosynthetic gene clusters linked to antimicrobial-like and antibiotic resistance gene-like activity. This public resource will serve as a foundation for expanding giant virus diversity, uncovering virus-host interactions and exploring viral evolution.},
}

@article {pmid42595818,
year = {2026},
author = {Cumbo, F and Blankenberg, D},
title = {Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42595818},
issn = {1546-1696},
support = {U24HG006620//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; U24CA231877//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Accurately characterizing metagenome-assembled genomes remains a substantial challenge due to the presence of sequencing errors, incomplete assembly and contamination. Here, we present MetaSBT, a tool for organizing, indexing and characterizing microbial reference genomes and metagenome-assembled genomes, demonstrated in this study using viruses. MetaSBT identifies clusters of genomes across all seven taxonomic levels using the Sequence Bloom Tree data structure, which relies on Bloom filters to index large amounts of genomes based on their k-mer composition. We built an initial set of databases composed of over 190,000 viral genomes from public sources, grouped into sequence-consistent clusters at different taxonomic levels. We defined over 40,000 candidate species, ~80% of which, to our knowledge, do not match viral species in reference databases to date. Furthermore, we showed that our databases are useful to existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. The open-source framework and databases are fully integrated into the Galaxy platform.},
}

@article {pmid42595876,
year = {2026},
author = {Knuth, D and Mäder, P and Boekhorst, J and Poll, C and Kandeler, E and Alaoui, A and Pasković, I and Polić Pasković, M and Baldi, I and Bureau, M and Alcon, F and Contreras, J and Glavan, M and Abrantes, N and Campos, I and Norgaard, T and Huerta Lwanga, E and Geissen, V and Harkes, P},
title = {Beneath the surface: non-target effects of multiple pesticides on the soil microbiome in organic and conventional agricultural European fields.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42595876},
issn = {1614-7499},
support = {862568//HORIZON EUROPE Framework Programme/ ; },
abstract = {Previous studies have shown that diverse cocktails of pesticide mixtures are omnipresent in agricultural soils yet miss a clear link to the effects on the soil microbiome. In this study, we linked the occurrence of pesticides in conventional and organic agricultural soils of the SPRINT (Sustainable plant protection transition) projects' Case Study Sites to the composition and function of soil microbial communities. Metagenomic sequencing, phospholipid fatty acids analysis and enzyme activity measurements were used to characterize the soil microbiome and effects of site-specific parameters such as pH and SOC, and pesticide residues. Differences in the soil microbiome were strongly influenced by the geographic origin of the samples, with the pH value as dominant driver. Against our hypothesis, effects of the investigated management systems were limited, yet significant at the European level. Notably, an association between some pesticides could still be observed after accounting for the variation explained by the environmental factors. Among these, especially fungicides, with modes of action that aim to interfere with processes in microorganisms, seemed to affect the soil microbiome. This might occur either by directly affecting these processes in non-target organisms or by changing co-dependencies between fungi and bacteria. Next to fungicides, aminomethylphosphonic acid showed a significant effect on the soil microbial composition and an interactive, possibly synergistic effect with the persistent pesticide hexachlorobenzene. The latter raises concerns about a possible interaction of recently applied pesticides and persistent "legacy" pesticides. This work highlights that even though environmental parameters can overshadow the effects of pesticides, especially the identity of the pesticides present, can have an influence on the soil microbiome.},
}

@article {pmid42597171,
year = {2026},
author = {Wang, T and Liang, H and Wu, Y and Zhang, X and Zhang, S and Wei, Z and Li, W and Song, W and Luo, Z and Al-Dalali, S},
title = {Multi-omics profiling of microbial ecology and non-volatile compounds across fermentation stages of spontaneous litchi (Litchi chinensis Sonn.) fermented vinegar-like beverage.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1908193},
pmid = {42597171},
issn = {2296-861X},
abstract = {INTRODUCTION: Litchi fruit vinegar-like beverages (LVBs) are notable processed products derived from litchi fruit, yet few studies have focused on the systematic characterization of microbial and metabolic dynamics during their natural fermentation process.

METHODS: This work employed a comprehensive methodology integrating metagenomics and untargeted metabolomics based on UHPLC-MS/MS (Orbitrap Q Exactive HF-X) to elucidate the dynamic profiles of the microbial community and non-volatile metabolites, as well as their interrelations, across the various spontaneous fermentation stages of LVBs.

RESULTS: Metagenomic analysis indicated reduced microbial diversity and substantial structural changes within the community. Bacteria dominated the fermentation, accounting for 69.16 - 99.04% of the microbial community based on the taxonomically classified reads at the kingdom level. During the preliminary stage, Leuconostoc, Enterobacter, and Klebsiella were the prevalent genera. During the mid-fermentation stage, Komagataeibacter and Lactiplantibacillus emerged as the predominant genera in acid production. In the final stage, the microbial community was dominated primarily by Zymomonas and the Acetobacteriaceae family, including Acetobacter and Komagataeibacter. The non-targeted metabolomics study identified 2,382 metabolites through comprehensive database matching (in-house library, HMDB, KEGG, and metDNA algorithm) and stringent quality filtering (identification score > 0.5 and QC CV < 0.5), which were categorized into 20 distinct groups. Thirty seven metabolites, including amino acids, organic acids, and benzene derivatives, were identified as probable distinct differential metabolites based on a p-value threshold of p < 0.05, VIP > 1.0, and a fold change (FC ≥ 2 or ≤ 0.5) between consecutive fermentation stages in pairwise OPLS-DA of litchi vinegar-like beverage fermentation. Spearman correlation analysis revealed a highly organized ecological interaction network among dominant bacteria, physicochemical parameters, and non-volatile taste metabolites in the LVB fermentation system. Zymomonas mobilis, Acetobacter pasteurianus, Leuconostoc suionicum, and Lactiplantibacillus plantarum facilitated fermentation through metabolic synergy. Meanwhile, stage-specific enrichment of distinct Enterobacteriaceae species (Enterobacter hormaechei, and Enterobacter quasiroggenkampii) reflected species-level niche differentiation and resource competition, rather than a unified family-wide competitive behavior.

DISCUSSION: These findings provide a theoretical framework for engineering synthetic consortia and bioaugmentation approaches, informing the selection of starters and co-cultures to enhance LVB sensory and bioactive properties, alongside facilitating sfruit valorization.},
}

@article {pmid42597276,
year = {2026},
author = {Ding, Y and Li, Q and He, F and Zheng, Q and Zhao, G and Wan, J and Fang, Y and Yang, T and Zou, L and Yu, W and Dai, J},
title = {The Impact of Human Immunodeficiency Virus Co‑Infection on the Pathogen Spectrum and Outcomes of Severe Community‑Acquired Pneumonia: Insights from Metagenomic Next‑Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {599541},
pmid = {42597276},
issn = {1178-6973},
abstract = {PURPOSE: Severe community-acquired pneumonia (SCAP) causes high morbidity and mortality. Metagenomic next-generation sequencing (mNGS) data comparing pathogen profiles in SCAP between people living with human immunodeficiency virus (HIV) (PLWH) and HIV-uninfected individuals remain scarce.

PATIENTS AND METHODS: We retrospectively enrolled 72 SCAP patients at Kunming Third People's Hospital. We compared alpha diversity of respiratory microbiota, pathogen spectrum and healthcare resource utilization (HRU) between the two groups. We also assessed whether HIV infection was an independent risk factor for 30-day mortality.

RESULTS: mNGS detected pathogens in 70 of 72 patients (97.2%). PLWH showed higher detection rates of Pneumocystis jirovecii (p < 0.001), Human gammaherpesvirus 4 (EBV) (p = 0.013), and Human betaherpesvirus 5 (CMV) (p < 0.001). Among the 54 SCAP patients who survived 30 days, HRU metrics did not differ between groups. Elevated D-dimer level was an independent risk factor for 30-day mortality in SCAP patients (hazard ratio [HR]: 1.02, 95% confidence interval [CI]: 1.004-1.030; p = 0.0127).

CONCLUSION: HIV co‑infection in SCAP patients is associated with a distinct pathogen spectrum but does not affect HRU or 30‑day mortality. Elevated D‑dimer level is an independent risk factor for 30‑day mortality in SCAP patients.},
}

@article {pmid42597328,
year = {2026},
author = {Wu, B and Lu, S and Liu, H},
title = {Precision diagnostics in bronchiectasis: current advances in imaging, microbiology, biomarkers, and digital health.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1907636},
pmid = {42597328},
issn = {2296-858X},
abstract = {Bronchiectasis is a complex, chronic airway syndrome driven by a vicious cycle of irreversible bronchial dilatation, impaired mucociliary clearance, recurrent infection, and tissue-destructive inflammation. Reflecting its profound clinical heterogeneity, patients with identical structural damage on high-resolution computed tomography (HRCT) often exhibit divergent profiles in airway microbiology, inflammatory endotypes, exacerbation frequencies, and therapeutic responses, indicating that static anatomical classification fails to capture disease complexity. Sole reliance on visual CT inspection, standard sputum cultures, and subjective symptom tracking misses the driving mechanisms of individual disease progression. Emerging modalities-artificial intelligence (AI)-driven quantitative imaging, molecular microbiology, high-throughput biomarker profiling, and digital remote monitoring-aim to address these gaps. Our analysis shows that while these tools cannot substitute for bedside clinical acumen, they clarify obscure phenotypes, expose actionable treatable traits, and enable earlier, preemptive strategies. This review evaluates these contemporary diagnostic frameworks in non-cystic fibrosis bronchiectasis, dissecting their clinical utility, evidentiary maturity, and the economic and logistical barriers to routine adoption. Given that current evidence remains fragmented, advancing the field demands standardized imaging protocols, transparent algorithmic pipelines, clinically actionable metagenomic reporting, and robust validation in underrepresented Asian and Chinese cohorts. The real challenge lies not in generating more data, but in integrating these heterogeneous, high-dimensional datasets into pragmatic, point-of-care decision pathways that improve patient outcomes without widening disparities in global healthcare delivery.},
}

@article {pmid42597565,
year = {2026},
author = {Okonta, EO and Nnadi, CO and Paul-Chima, UO},
title = {The gut microbiome as a plausible but unproven moderator of cinnamon trial outcomes in type 2 diabetes: toward phytochemical standardization and precision nutraceuticals.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1874182},
pmid = {42597565},
issn = {2296-861X},
abstract = {Cinnamon (Cinnamomum spp.) has been widely investigated as an adjunctive nutraceutical for glycemic management in type 2 diabetes mellitus, yet clinical findings remain inconsistent. This variability is commonly attributed to differences in cinnamon species, dosage, intervention duration, baseline glycemic status and phytochemical standardization, alongside methodological factors such as trial quality, dietary patterns, medication use, adherence and endpoint selection. One potential contributor that has received limited attention is the gut microbiome. We propose a testable hypothesis that a substantial proportion of the marked inter-trial heterogeneity observed in cinnamon meta-analyses (I[2] > 75%) may reflect underlying gut-microbial metabotypes differing in their ability to convert cinnamon polyphenols and procyanidins into bioactive metabolites. Type 2 diabetes is associated with altered microbial composition, reduced butyrate-producing taxa and disrupted metabolic pathways. Cinnamon phytochemicals, including polyphenols, cinnamaldehyde, procyanidins and coumarin, undergo microbial biotransformation that may influence their bioavailability and metabolic effects. Because cinnamaldehyde is rapidly absorbed in the proximal gastrointestinal tract, colon-targeted delivery systems may be required to rigorously evaluate microbiome-mediated mechanisms. No randomized controlled trial has directly examined whether microbiome composition modifies cinnamon's glycemic effects in type 2 diabetes. Future studies should therefore incorporate microbiome-informed designs, including phytochemical fingerprinting, safety monitoring and, where feasible, metagenomic and metabolomic profiling, to distinguish true biological non-response from intervention heterogeneity and advance precision nutraceutical approaches for diabetes management.},
}

@article {pmid42597686,
year = {2026},
author = {Annaswamy, V and Mikesh, M and Dinkeloo, K},
title = {The Microbiome of Nurdles: Life on the Primary Microplastics of the Texas Gulf Coast.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {42597686},
issn = {2578-9430},
abstract = {Nurdles are small, pre-production plastic pellets. Globally, nurdles are the second largest source of microplastic pollution due to release during manufacture and transport. As these nurdles persist in the environment, they undergo weathering-a process that significantly increases surface area and colonization by microbes. To gain an understanding of the composition of the microbiome found on nurdles, full-length 16S targeted metagenomic sequencing was performed on DNA extracted from nurdles collected from the Texas Gulf Coast. Sequencing data showed a greater amount and diversity of microbes found to be associated with nurdles than with the sand from which the nurdles were collected.},
}

@article {pmid42597889,
year = {2026},
author = {Ren, S and Ren, S and Chen, H and Zhang, W and Zhang, T and Chong, H and Wang, Z and Cao, W and Yong, X and Zhou, J},
title = {SuSha: A multi-model ensemble learning framework for predicting microbial salinity adaptation.},
journal = {Engineering microbiology},
volume = {6},
number = {3},
pages = {100292},
pmid = {42597889},
issn = {2667-3703},
abstract = {Current research on microbial salinity adaptation faces substantial challenges, including the limited predictive accuracy of traditional single-gene models and difficulty in dissecting systemic biological responses to salinity stress in complex natural habitats. To overcome these bottlenecks, the multi-model ensemble learning tool SuSha, which leverages genome-wide amino acid composition features, was developed. By extracting features from the whole-genome data of 123 bacterial and archaeal species with well-defined salinity adaptations, a 24-dimensional feature vector was constructed, comprising the frequencies of 20 standard amino acids and four aggregated functional categories. Based on this, an ensemble model was developed by integrating algorithms such as random forest, bagging, and extra trees. Five-fold cross-validation demonstrated that this 24-dimensional feature-based ensemble model achieved a global accuracy of 0.765 and an area under the curve of 0.941, significantly outperforming individual baseline models. Furthermore, the model was externally validated using 2678 metagenomic samples from six global regions, encompassing freshwater, marine, and hypersaline habitats. SuSha exhibited high robustness, ecological consistency across diverse salinity gradients, and a classification accuracy of over 90% for extreme halophiles, particularly within the extreme halophilic range. By enabling high-precision genotype-to-phenotype predictions using a habitat-adaptive algorithm-switching strategy, SuSha provides a robust computational framework for inferring the physiological potential of uncultivated microorganisms and mining microbial resources in extreme environments.},
}

@article {pmid42598143,
year = {2026},
author = {Mollick, SA and Khual, GK and Ghosh, A and Patel, SK and Bhattacharyya, S and Roy, CS and Maile, A and Nagarajaram, HA and Longkumer, M and Babu, MN and Kundapur, AR and Uniyal, S and Chattterjee, A and Mitra, M and Sikdar, M and Urade, BP and Pulamaghatta, VN},
title = {Gut microbial diversity and candidate keystone taxa in Indian tribes: Insights across lifestyle-ecological continuum and health associations.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100650},
pmid = {42598143},
issn = {2666-5174},
abstract = {Despite the critical role of the gut microbiome in host physiology and health, it remains poorly characterized in Indigenous populations undergoing rapid acculturation. This study presents high-resolution, whole-genome metagenomic profiling of gut microbiota from five Particularly Vulnerable Tribal Groups (PVTGs) of Southern India, Irula, Jenu Kuruba, Kurumba, Chenchu, and Konda Savara, spanning distinct ecological zones and cultural transitions. Using an ecology-lifestyle continuum framework, we investigated taxonomic and functional diversity with a focus on identifying computationally inferred candidate keystone taxa, defined by their association with variation in community ordination structure. A leave-one-taxon-out ordination framework identified 121 candidate keystone taxa, many of which were population-specific and have not been widely reported. Functional analyses revealed a conserved core of metabolic pathways, including glycolysis and folate biosynthesis, alongside group-specific enrichment in xenobiotic degradation, amino acid biosynthesis, mucin metabolism, and lipid processing, associated with differences in dietary and environmental exposures across populations. Large-scale disease-association mapping (n = 5,625) linked 50 candidate keystone taxa to 14 conditions, with 44 associated with health and 6 with disease. While Fusicatenibacter saccharivorans and Alistipes shahii were enriched in healthy states, Ruminococcus gnavus, Bifidobacterium longum, Flavonifractor plautii, and Blautia wexlerae were enriched in disease-associated profiles. Cross-cohort validation against an independent set of traditional metagenomes (n = 119) further showed that a subset of Indian tribal core candidate keystone taxa was consistently identified across geographically distinct populations, with partial conservation of community associations and health associations, indicating reproducible context-dependent microbial association patterns across traditional populations. Alpha diversity was highest in minimally acculturated groups, with higher degrees of acculturation associated with reduced microbial diversity and greater enrichment of disease-associated taxa. Overall, this study provides a context-aware framework for understanding gut microbiome dynamics in culturally transitioning populations, emphasizing the conservation of microbial heritage and informing population-specific microbiome-based interventions.},
}

@article {pmid42598172,
year = {2026},
author = {Udahemuka, JC and Cassidy, H and Schuele, L and Uwibambe, E and Ngabo, MG and Masirika, LM and Sindayiheba, R and Otani, S and Gashegu, M and Twizere, JC and Aarestrup, F and Ndayisenga, F and Oude Munnink, BB and Koopmans, MPG and Ndishimye, P},
title = {Persistent circulation of Rift Valley fever virus lineage C in Rwanda, 2022-2025.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101529},
pmid = {42598172},
issn = {2352-7714},
abstract = {Rwanda has experienced recurrent Rift Valley fever virus outbreaks in the last decade. In this study, we investigated whether these outbreaks resulted from repeated introductions or sustained local circulation. We generated RVFV whole-genome sequences from livestock samples collected between 2022 and 2025 using Nanopore sequencing. Genomic analyses indicated the outbreaks resulted from sustained local circulation of lineage C rather than repeated introductions, suggesting ongoing transmission likely driven by sporadic spillover. This study underscores the importance of continuous genomic One Health surveillance in endemic settings.},
}

@article {pmid42598412,
year = {2026},
author = {Wang, X and Chen, W and Zhang, H and Cao, D and Sun, J and Hu, H},
title = {Gut microbial biomarkers for major depressive disorder: a cross-sectional study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1690285},
pmid = {42598412},
issn = {2235-2988},
mesh = {Humans ; *Major Depressive Disorder/microbiology/diagnosis/virology ; *Biomarkers/analysis/blood ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Female ; Adult ; Male ; Metagenomics ; Bacteria/genetics/classification/isolation & purification ; Middle Aged ; Viruses/genetics/classification/isolation & purification ; Feces/microbiology/virology ; },
abstract = {BACKGROUND: Alterations in the gut microbiota have been associated with a variety of psychiatric disorders, including major depressive disorder (MDD). However, the relationship between MDD and gut microbial communities remains incompletely understood. Most previous studies have primarily focused on gut bacteria, with relatively limited attention to other microbial components.

METHODS: In this study, we analyzed gut microbial profiles from 36 patients with MDD and 36 healthy controls using metagenomic sequencing data. The MaAsLin2 algorithm was applied to identify potential microbial biomarkers associated with MDD.

RESULTS: A total of 6 bacterial biomarkers and 7 viral biomarkers were identified. The models based on these features demonstrated strong predictive performance, with area under the curve (AUC) values of 0.891 for bacteria and 0.878 for viruses. Notably, the combined bacterial-viral model achieved an AUC of 0.946. These findings were further evaluated through external testing in two unrelated research cohorts. In the Shanxi cohort, the AUC values were 0.825 (bacteria), 0.803 (viruses), and 0.972 (combined model). In the Wuhan cohort, the AUC values were 0.683 (bacteria), 0.693 (viruses), and 0.784 (combined model).

CONCLUSION: In summary, our results highlight the potential of gut bacterial and viral biomarkers as candidate biomarkers and potential auxiliary tools for MDD assessment and suggest that integrating multi-domain microbial features may improve prediction accuracy.},
}

Humans
*Major Depressive Disorder/microbiology/diagnosis/virology
*Biomarkers/analysis/blood
Cross-Sectional Studies
*Gastrointestinal Microbiome
Female
Adult
Male
Metagenomics
Bacteria/genetics/classification/isolation & purification
Middle Aged
Viruses/genetics/classification/isolation & purification
Feces/microbiology/virology

@article {pmid42598558,
year = {2026},
author = {Abbasi, H and Hawn, SE and Javanbakht, A and Seedat, S and Bourassa, K and Sinnott, SM and Seligowski, AV and Hemmings, S and Kimbrel, NA and Wolf, E and Smith, AK and Brick, L and Mehta, D},
title = {From molecules to minds: Integrative multi-omics in psychiatry.},
journal = {Journal of mood and anxiety disorders},
volume = {15},
number = {},
pages = {100194},
pmid = {42598558},
issn = {2950-0044},
abstract = {Psychiatric disorders are biologically complex conditions arising from interactions across genomic, epigenomic, transcriptomic, proteomic, metabolomic, and metagenomic layers. Single-omics approaches rarely capture more than a fraction of the variance in complex conditions, underscoring the importance of integrative multi-omics frameworks. This mini-review summarizes key methodologies and their application in psychiatric research, with a focus on systems-level integration of genomic risk scores, transcriptomic networks, and neuroimaging data to advance biological understanding of disorders such as depression, schizophrenia, and Alzheimer's disease. We also outline the infrastructural requirements for effective multi-omics research, including standardized biobanking, Laboratory Information Management Systems, adherence to FAIR data principles, and federated learning approaches for privacy-preserving analysis. Importantly, we highlight the need for greater global inclusivity in psychiatric genomics. Current datasets are heavily biased toward relatively high-resourced and predominantly White, non-Hispanic populations, limiting generalizability. Initiatives such as the Psychiatric Genomics Consortium-Africa and H3ABioNet demonstrate how locally led efforts can strengthen capacity, promote data sovereignty, and support equitable research practices. Advancing multi-omics psychiatry will require coordinated investment in infrastructure, training, and inclusive international collaboration. This mini-review serves primarily as a conceptual roadmap, highlighting what integrative approaches have demonstrated so far and future directions for the field.},
}

@article {pmid42598885,
year = {2026},
author = {Baidya, AK and Aich, P},
title = {Serum-Cecal Metabolome Integration Predicts Gut Microbial Communities and Reveals Pathway-Level Host-Microbe Crosstalk Under Disease-Induced Dysbiosis.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261479266},
doi = {10.1177/15578100261479266},
pmid = {42598885},
issn = {1557-8100},
abstract = {The gut microbiome shapes systemic physiology through metabolites that enter circulation, yet most computational approaches focus on predicting metabolite profiles from microbial features rather than inferring microbial composition from host metabolomes. Here, we investigate whether host-derived metabolomic profiles can be leveraged to predict gut microbial community structure and to determine how disease-associated dysbiosis reshapes metabolite-microbe interactions and gut-to-systemic metabolic communication. We developed an integrative multi-omics framework combining serum and cecal metabolomics with 16S rRNA-based microbiome profiling. Supervised learning models demonstrated that cecal metabolites carry predictive signals for microbial abundances across conditions. Regularized canonical correlation analysis (rCCA) revealed cross-compartment metabolite-microbe networks. These analyses showed both conserved and condition-specific interaction patterns, indicating substantial network reorganization under disease-associated dysbiosis. Pathway-level integration further identified metabolic pathways linking the gut microbiome, the cecal environment, and the systemic circulation, representing coordinated gut-to-systemic communication axes. Together, our results establish a multi-omics strategy for predictive inference of gut microbial composition from host metabolomes and provide a framework for identifying pathway-level mechanisms underlying host-microbe metabolic crosstalk.},
}

@article {pmid42599000,
year = {2026},
author = {Wang, W and Jiang, L and Niu, T and Zhang, M and Chen, L and Jia, X and Yuan, L and Tian, K and Li, X},
title = {Resolving the Phylogenetic Placement of the FSfaCV/PCV5-Related Viruses Within the Genus Macochavirus.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {1},
pages = {e8481347},
doi = {10.1155/tbed/8481347},
pmid = {42599000},
issn = {1865-1682},
support = {2023YFD1800500//National Key Research and Development Program of China/ ; 32500538//National Natural Science Foundation of China/ ; D18007//111 Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
mesh = {Animals ; *Phylogeny ; Genome, Viral ; Swine ; *Swine Diseases/virology/epidemiology ; China/epidemiology ; *DNA Viruses/genetics/classification ; Circovirus/genetics ; },
abstract = {Metagenomic analysis of fecal samples from diarrheic pigs in China identified 10 complete circular single-stranded DNA viral genomes previously designated as putative porcine circovirus 5 (PCV5)-like viruses. Genome characterization revealed a typical cressdnavirus organization with bidirectionally oriented Rep and Cap genes. Phylogenetic analyses based on complete genomes and encoded proteins showed that these viruses do not cluster with members of Circoviridae but instead form a distinct lineage within the family Pecoviridae, closely related to the genus Macochavirus. Sequence identity, genetic distance, and nucleotide diversity analyses supported their classification as a coherent viral group. Comparative analyses indicated greater sequence divergence in the Rep region than in the Cap region. These findings support reclassification of putative PCV5 as a porcine-associated lineage within the genus Macochavirus, designated porcine Macochavirus (PMV), thereby resolving their long-standing taxonomic ambiguity and expanding the recognized diversity of cressdnaviruses within the family Pecoviridae.},
}

Animals
*Phylogeny
Genome, Viral
Swine
*Swine Diseases/virology/epidemiology
China/epidemiology
*DNA Viruses/genetics/classification
Circovirus/genetics

@article {pmid42599081,
year = {2026},
author = {Buddhasiri, S and Singhla, T and Pengpanun, S and Eiamsam-Ang, T and Thiennimitr, P},
title = {Shotgun metagenomic sequence data from milk and fecal samples of dairy cattle in Thailand.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0056426},
doi = {10.1128/mra.00564-26},
pmid = {42599081},
issn = {2576-098X},
abstract = {We report shotgun metagenomic sequence data from milk and fecal samples of dairy cattle in Thailand. This data set captures microbial genetic profiles from mammary- and gut-associated sample types and provides a resource for future comparative microbiome, functional, and antimicrobial resistance gene analyses in dairy cattle.},
}

@article {pmid42599332,
year = {2026},
author = {Lee, SY and Hwang, S and Cho, I and Lee, H and Lee, J and Koo, D and Kim, JW and Cho, KS},
title = {Functional dynamics and interactions within the bacterial community responsible for biodegradable plastic degradation during aerobic composting.},
journal = {Biodegradation},
volume = {37},
number = {4},
pages = {},
pmid = {42599332},
issn = {1572-9729},
support = {RS-2025-02311604 & RS-2025-07902968//Ministry of Trade, Industry and Energy/ ; },
mesh = {*Composting ; Biodegradation, Environmental ; Aerobiosis ; *Bacteria/metabolism/genetics/classification ; *Biodegradable Plastics/metabolism ; Polyesters/metabolism ; Polyhydroxybutyrates ; Sewage/microbiology ; *Plastics/metabolism ; },
abstract = {Though biodegradable plastics have been widely developed as sustainable alternatives to petroleum-based plastics, their degradation behavior and microbial interactions in composting environments remain insufficiently understood. In this study, the degradation characteristics of polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), and polybutylene succinate (PBS), and the interactions between bacterial communities and functional genes, were evaluated in a 41-day aerobic composting system using anaerobically digested sewage sludge as substrate. Composting parameters were similarly affected by all biodegradable plastics, and the final compost reached a Solvita compost maturity index of 8.0 with no detectable pathogenic bacteria and a CO2 index of 7.83, indicating stable composting. After 41 days of composting, microcracks and microbial attachment were observed on all biodegradable plastic surfaces, with PHB and PBAT showing the most pronounced structural damage and biofilm formation, whereas microbial attachment to PLA was limited. Although biodegradable plastic addition did not greatly alter the overall bacterial community structure, it selectively promoted specific bacterial genera (Symbiobacterium, Paenibacillus, and Psychrobacillus). PICRUSt2-based functional gene prediction revealed that PHB degradation-related genes exhibited the highest predicted abundance, whereas PLA- and PBS-related genes showed low abundance, indicating differences in functional degradation potential among plastic types. Positive correlations among esterase- and hydrolase-related genes under biodegradable plastic-amended conditions suggest that coordinated microbial functional responses to biodegradable plastic addition. Network analysis further indicated that biodegradable plastic addition influenced interactions between specific bacterial genera and degradation-related functional genes. Overall, this study provides insights into bacterial functional adaptation during biodegradable plastic degradation under aerobic composting conditions.},
}

*Composting
Biodegradation, Environmental
Aerobiosis
*Bacteria/metabolism/genetics/classification
*Biodegradable Plastics/metabolism
Polyesters/metabolism
Polyhydroxybutyrates
Sewage/microbiology
*Plastics/metabolism

@article {pmid42586034,
year = {2026},
author = {Ibarbalz, FM and Pierella Karlusich, JJ},
title = {Genes from the deep: Evolution's untapped biotechnology.},
journal = {Cell host & microbe},
volume = {34},
number = {8},
pages = {1486-1488},
doi = {10.1016/j.chom.2026.07.004},
pmid = {42586034},
issn = {1934-6069},
mesh = {*Biotechnology ; Metagenomics/methods ; Evolution, Molecular ; *Bacteria/genetics ; },
abstract = {The deep sea, Earth's largest yet least-explored biome, harbors vast microbial diversity. In this issue of Cell Host & Microbe, Guo et al. uncover its hidden functional potential through metagenomics guided by AI-predicted protein folds, while Eriksson et al. reveal how microbial diversity is structured across latitude and depth.},
}

*Biotechnology
Metagenomics/methods
Evolution, Molecular
*Bacteria/genetics

@article {pmid42586263,
year = {2026},
author = {Zhou, Y and Guo, Q and Zhao, X and Zhang, W and Zhang, H and Huang, S and He, Z and Xie, Y and Zhang, W and Gu, J and Pan, S and Li, W},
title = {Blood and gut virome remodeling in gastric cancer: Anellovirus expansion and novel virus discovery.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.08.010},
pmid = {42586263},
issn = {1995-820X},
abstract = {Gastric cancer (GC) is a prevalent malignancy worldwide, yet effective early diagnostic tools remain lacking, and the role of the virome, a key component of the tumor microenvironment, in GC progression is largely unknown. This study aimed to characterize the virome landscapes in peripheral blood and feces of GC patients versus healthy controls, and to identify viral signatures associated with GC onset and metastasis. We performed viral metagenomic sequencing on pooled libraries from 100 GC patients (45 non-metastatic, 55 metastatic) and 50 healthy controls, followed by taxonomic annotation, diversity assessment, LEfSe differential abundance testing, and co-occurrence network analysis. In blood, the GC virome shifted from a bacteriophage-dominated profile in controls to one overwhelmingly dominated by Anelloviridae (> 80%), with significantly decreased alpha diversity. In contrast, the gut virome of GC patients showed increased alpha diversity and coexistence of diverse bacteriophages. LEfSe identified betatorquevirus in blood as a key discriminatory taxon for GC. Network analysis revealed negative correlations between Anelloviridae and multiple bacteriophage families, suggesting niche competition. We also discovered 67 provisional novel anellovirus species and one novel gemykibivirus in GC patient blood. Collectively, our findings indicate that GC is associated with compartment-specific virome remodeling in blood and gut, and that expansion of blood anelloviruses holds promise as a non-invasive biomarker. This study provides a foundational resource for understanding the virome's role in GC.},
}

@article {pmid42586379,
year = {2026},
author = {Zhuo, Q and Wei, R and Su, Y and Shao, H and Han, L and Huang, G},
title = {Responses of biogeochemical cycles to polyethylene microplastics exposure during aerobic fermentation of dairy manure.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135605},
doi = {10.1016/j.biortech.2026.135605},
pmid = {42586379},
issn = {1873-2976},
abstract = {Microplastics (MPs) are emerging contaminants that may disrupt Earth's biogeochemical cycles of elements, yet their effects on multi-element cycling during aerobic fermentation of livestock manure remain unclear. This study evaluated how polyethylene (PE) MPs and fermentation strategy affected multi-element functional potential during aerobic fermentation of dairy manure solids by integrating metagenomic functional profiling, co-occurrence networks, and other complementary approaches. Fermentation time dominated functional gene succession, with treatment separation becoming most evident on day 30. Biomarkers were confined to the C cycling and detected only in the low concentration treatments, with none at the higher concentration. Network analysis revealed predominantly positive associations among genes involved in different elemental cycles. The membrane-covered treatment at the lower concentration formed the most connected network. The pathway profiles and network topology in the membrane-covered treatment at the higher concentration were similar to those of the blank control. This suggests that, under high MPs exposure, the membrane-covered treatment retained a functional profile similar to the blank control, likely in association with the more stable fermentation conditions in the membrane-covered treatment. Physicochemical properties, process variables, and gas emissions jointly explained 78% of functional gene variation. Mantel tests and structural equation modelling further linked fermentation conditions, gas emissions, and multi-element functional potential. Overall, multi-element functional responses to MP exposure varied with fermentation stage, strategy, and PE MP concentration. These findings highlight the importance of fermentation management when assessing multi-element functional responses to MP exposure during manure valorization.},
}

@article {pmid42586589,
year = {2026},
author = {Carsello, EA and Liston, K and Maust, B and Deutsch, G and Wright, J and Wong, S and Morgan, L and Vora, S},
title = {Balamuthia mandrillaris presenting as central nervous system vasculitis in a young child.},
journal = {BMJ case reports},
volume = {19},
number = {8},
pages = {},
doi = {10.1136/bcr-2026-275051},
pmid = {42586589},
issn = {1757-790X},
mesh = {Humans ; *Vasculitis, Central Nervous System/parasitology/diagnosis ; Male ; *Balamuthia mandrillaris/isolation & purification/genetics ; *Amebiasis/diagnosis/parasitology/complications/drug therapy ; Brain/pathology/parasitology ; Diagnosis, Differential ; },
abstract = {Balamuthia mandrillaris is a rare and difficult-to-diagnose infection with high mortality. We present the case of an immunocompetent toddler presenting with central nervous system (CNS) vasculitis. He was initially diagnosed with Takayasu arteritis and had an initial period of improvement following immunosuppressive therapy. Subsequently, he had rapid decompensation with diffuse intracranial lesions progressing to severe neurological injury and compassionate extubation. Metagenomic sequencing of the CSF and pathology and PCR from brain biopsy were positive for B. mandrillaris To our knowledge, this is the first case of Balamuthia presenting as a mixed vessel CNS vasculitis and highlights the importance of consideration of this infection in cases of vasculitis, particularly in mixed vessel disease. It further demonstrates the potential use of newer diagnostics, namely CSF metagenomic testing and amoeba PCR, in earlier diagnosis and treatment.},
}

Humans
*Vasculitis, Central Nervous System/parasitology/diagnosis
Male
*Balamuthia mandrillaris/isolation & purification/genetics
*Amebiasis/diagnosis/parasitology/complications/drug therapy
Brain/pathology/parasitology
Diagnosis, Differential

@article {pmid42586639,
year = {2026},
author = {Humayun, S and Justine, EE and Rjabovs, V and Lee, HJ and Darko, CNS and Reile, I and Kim, YJ and Tuvikene, R},
title = {Gut-protective efficacy of red algal galactans: The role of structure and molecular weight.},
journal = {Carbohydrate polymers},
volume = {389},
number = {},
pages = {125609},
doi = {10.1016/j.carbpol.2026.125609},
pmid = {42586639},
issn = {1879-1344},
mesh = {Molecular Weight ; Humans ; *Galactans/chemistry/pharmacology/isolation & purification ; *Rhodophyta/chemistry ; Animals ; Caco-2 Cells ; Oxidative Stress/drug effects ; Rheology ; Mice ; },
abstract = {Linking structure, rheology, and bioactivity, this study demonstrates how red algal galactans can be tailored as functional food ingredients with gut-protective potential. Funoran and furcellaran were isolated from Gloiopeltis furcata and Furcellaria lumbricalis, respectively, and characterized using chromatographic and NMR spectroscopic techniques. Funoran was identified as a highly sulfated, methoxylated agaran (22.7% sulfate), whereas furcellaran exhibited a hybrid κ-/β-carrageenan structure (17.4% sulfate). High molecular weights (3955 and 2966 kDa) were observed and reduced via controlled autohydrolysis without sulfate loss. Structural variations governed rheological behavior, with furcellaran showing ion-dependent gelation and funoran forming weaker networks. Both native and depolymerized galactans were non-cytotoxic to Caco-2 cells, maintained tight junction integrity, and reduced oxidative stress. In a DSS-induced colitis model, treatments alleviated clinical symptoms, decreased pro-inflammatory cytokines and MPO activity, and restored barrier-related proteins. Metagenomic analysis revealed partial correction of dysbiosis, including enrichment of short-chain fatty acid producing taxa, particularly in depolymerized funoran. Overall, structural features and molecular weight critically determine both rheological and biological functions. Depolymerization enhances fermentability while preserving bioactivity, highlighting red-algal galactans as promising multifunctional hydrocolloids for food and gut health applications.},
}

Molecular Weight
Humans
*Galactans/chemistry/pharmacology/isolation & purification
*Rhodophyta/chemistry
Animals
Caco-2 Cells
Oxidative Stress/drug effects
Rheology
Mice

@article {pmid42586789,
year = {2026},
author = {Deas, G and Macgregor, K and Kite, D and Ward, H and May, A and Powell, M and Jenkins, M},
title = {HIV-associated CD8 encephalitis: role of metagenomics in complex CNS presentations.},
journal = {Practical neurology},
volume = {},
number = {},
pages = {},
doi = {10.1136/pn-2026-005308},
pmid = {42586789},
issn = {1474-7766},
abstract = {We describe a 54-year-old woman living with HIV who presented with a tonic-clonic seizure and rapidly progressive encephalitis. Despite an undetectable plasma viral load while taking Biktarvy, initial investigations revealed cerebrospinal fluid escape with an HIV viral load of 474 copies/mL. Extensive testing for opportunistic infections and autoantibodies was negative. Brain biopsy and metagenomic next-generation sequencing identified frequent CD8+ T-cell infiltration and human pegivirus, though the latter was deemed a bystander. The patient's condition improved significantly, notably without the high-dose corticosteroids typically required for CD8+ encephalitis. This recovery suggests a moderate, self-limiting phenotype of the disease. The case highlights the diagnostic utility of metagenomics in complex presentations while cautioning against the misinterpretation of non-pathogenic commensals.},
}

@article {pmid42587158,
year = {2026},
author = {Sinha, T and Brushett, S and Fernández-Pato, A and Garmaeva, S and Andreu-Sánchez, S and Spreckels, JE and Mallon, CA and Kuzub, N and Gois, MB and Wu, J and Kruk, M and Jankipersadsing, SA and Dekens, JAM and Gacesa, R and Vila, AV and Bang, C and Perenboom, C and Franke, A and Tytgat, HLP and Mottaz, SC and Peters, L and de Jonge, A and Verkade, HJ and Swertz, MA and Wijmenga, C and Kuipers, F and Scherjon, S and Sikkema, J and Sprikkelman, AB and de Kroon, MLA and Prins, JR and Gordijn, SJ and Koppelman, GH and Reijneveld, SA and , and Fu, J and Yassour, M and Kurilshikov, A and Zhernakova, A},
title = {Maternal influences on infant gut microbiome and health.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42587158},
issn = {1476-4687},
abstract = {The establishment of the infant gut microbiome is critical for later health[1,2], yet how it is shaped by maternal and early-life factors remains unclear. Here we metagenomically sequenced 4,526 longitudinal faecal samples from 714 mother-infant pairs in the Dutch birth cohort Lifelines NEXT, spanning 12 weeks of pregnancy to 1 year postpartum. We integrated these data with 474 clinical and exposure variables, and with ultra-deep sequencing of breast milk and vaginal microbiomes. We observe that the maternal gut microbiome undergoes only subtle changes during pregnancy and postpartum, influenced by diet, infections and pre-pregnancy smoking. The maternal gut microbiome is a major reservoir for infant gut strains, with only occasional transmission from vaginal and breast milk microbiomes. Mother-infant gut strain sharing is time dependent, and higher maternal gut species abundance increases the likelihood of strain transmission. We find that the maternal gut microbiome is a predictor of infant eczema. Mode of delivery and feeding mode primarily shaped the infant gut microbiome and its functional profiles, with maternal exposures also having a role. Of 585 vaginally delivered infants, 155 were born at home, but home delivery was only moderately associated with infant gut microbiome composition, similar to other birth parameters such as duration of pushing and ruptured membranes. Overall, we highlight the central role of the mother and her microbiome in shaping the infant gut ecosystem and early health outcomes.},
}

@article {pmid42587419,
year = {2026},
author = {Chang, H and Yang, Y and Zhang, P and Lei, Z and Zhang, Y and Li, S and Wang, L and Wang, Y and Jiang, J and Li, L and Shi, H and Shi, A},
title = {Disrupted Gut Viral-Bacterial Ecology of Patients With Liver Cirrhosis.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {46},
number = {9},
pages = {e70836},
pmid = {42587419},
issn = {1478-3231},
support = {2025JC-YBQN-1179//Natural Science Basic Research Program of Shaanxi Province/ ; 2025SCIPT-63//Scientific Research Supporting Fund of the Second Affiliated Hospital of Xi'an Jiaotong University/ ; },
mesh = {Humans ; *Liver Cirrhosis/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/genetics ; Case-Control Studies ; Metagenome ; Metagenomics ; Male ; },
abstract = {BACKGROUND: The gut microbiota contributes to liver cirrhosis (LC), yet the gut virome and its cross-kingdom ecology with bacteria are less well defined.

METHODS: To characterize LC-associated virome alterations and assess their clinical relevance, we reanalyzed publicly available faecal metagenomes from patients with LC and healthy controls. After quality control and removal of human reads, sequences were mapped to the Chinese Gut Viral Catalogue at 95% nucleotide similarity, viral operational taxonomic units (vOTUs) were annotated using the latest ICTV framework, and viral functions were inferred by KEGG annotation. Differential vOTUs and bacterial species, virus-bacteria networks and random forest classifiers were constructed with internal and external validation.

RESULTS: LC showed reduced viral richness and Shannon diversity, and a distinct Bray-Curtis separation from controls. Ten viral families and 473 vOTUs differed between groups (59 LC-enriched). KEGG-based profiling highlighted functional shifts in LC-enriched viruses, including increased K01185 (lysozyme) and K02172 (blaR1). Virus-bacteria networks were markedly sparser in LC than in controls (130 vs. 509 significant correlations). A virome-based random forest model distinguished patients from controls with high accuracy in internal (optimal AUC = 0.911) and external (optimal AUC = 0.773) validation cohorts, and the model combining viral and bacterial features achieved similarly robust performance.

CONCLUSIONS: LC is associated with disrupted gut viral-bacterial ecology, and virome features show promise as non-invasive biomarkers, warranting longitudinal and mechanistic follow-up.},
}

Humans
*Liver Cirrhosis/microbiology/virology
*Virome
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Bacteria/genetics
Case-Control Studies
Metagenome
Metagenomics
Male

@article {pmid42587714,
year = {2026},
author = {Becherucci, V and Romano, F and Russo, E},
title = {Artificial Intelligence for Integrated Analysis of Non-Blood Biological Fluids: From Biomarker Discovery to Clinical Decision-Support Systems.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {15},
pages = {},
doi = {10.3390/diagnostics16152478},
pmid = {42587714},
issn = {2075-4418},
abstract = {The analysis of non-blood biological fluids, including cerebrospinal fluid (CSF), serous effusions, and synovial fluid, plays a central role in laboratory medicine by providing essential diagnostic and prognostic information for neurological, infectious, inflammatory, and neoplastic diseases. However, the interpretation of these specimens remains challenging because it requires the integration of heterogeneous biochemical, cytological, microbiological, molecular, and clinical data, often in the absence of standardized analytical workflows. Artificial intelligence (AI), particularly Machine Learning (ML) and Deep Learning (DL), is emerging as a powerful approach for extracting clinically relevant information from complex multidimensional datasets beyond the capabilities of conventional analytical methods. AI-driven Clinical Decision-Support Systems (CDSSs) can integrate laboratory findings with clinical, demographic, imaging, and multi-omics data, supporting diagnostic interpretation, patient stratification, and personalized clinical decision-making. At the same time, the convergence of AI with proteomics, metabolomics, metagenomics, and other omics technologies is accelerating biomarker discovery and advancing precision laboratory medicine. Current evidence indicates different levels of maturity across biological fluids. AI-assisted interpretation of CSF biomarkers and digital cytology of serous effusions currently show the strongest clinical evidence, whereas applications involving synovial fluid and integrated multi-omics remain largely exploratory. Although important technical, methodological, and regulatory challenges still limit widespread clinical implementation, AI has the potential to improve diagnostic accuracy, reduce interpretative variability, and support more integrated diagnostic workflows. This mini-review summarizes current and emerging AI applications in non-blood biological fluid analysis, with particular emphasis on biomarker discovery, CDSS, multi-omics integration, current evidence, existing limitations, and future perspectives for precision laboratory medicine.},
}

@article {pmid42587989,
year = {2026},
author = {Zhang, X and Sun, L and Yang, L and Li, X and Cao, Z and Pan, C},
title = {Identification of Key Microorganisms and Metabolic Pathways Associated with the Formation of Off-Flavour Compounds in the Pit Mud of Strong-Flavour Baijiu.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
doi = {10.3390/foods15152731},
pmid = {42587989},
issn = {2304-8158},
support = {231111112000//Henan Province/ ; },
abstract = {Off-flavours represent one of the most prevalent and severe causes of deteriorating pit mud quality in Strong-Flavour Baijiu production. However, the key compounds responsible for these off-flavours and their formation mechanisms remain poorly understood, thereby limiting quality control in the production process of Strong-Flavour Baijiu pit mud. To investigate the origin of off-flavours in pit mud, this study employed gas chromatography-mass spectrometry coupled with metagenomic methods to compare samples from normal and off-flavoured pit mud. The results show that the main cause of off-flavours in pit mud is the abnormal accumulation of acids such as heptanoic acid and hexanoic acid due to imbalanced nutrient ratios, along with insufficient synthesis of key esters including ethyl hexanoate, ethyl butyrate, and ethyl lactate; microorganisms such as Fermentimonas, Methanoculleus, Hortaea and Proteiniphilum, which are non-strictly anaerobic and acid-sensitive in the pit mud, are key microbes associated with these odour compounds. Furthermore, based on the annotation from the KEGG database, this study further inferred the possible microbial metabolic pathways that could lead to the formation of these off-flavour compounds, including starch and cellulose degradation pathways, biosynthesis pathways of valine, leucine, and isoleucine, pyruvate metabolism pathways, and butyric acid metabolism pathways. In summary, the study systematically analysed the key substances related to the odour of the pit mud of strong-flavour Chinese Baijiu and its microbial sources, providing a theoretical basis for the quality regulation of the pit mud during production and developing high-quality artificial pit mud.},
}

@article {pmid42587998,
year = {2026},
author = {Lefèvre, H and Fadhlaoui, K and Guez, JS and Lainé, E and Beyssac, E},
title = {Resistance of Bamboo Fibers to Gastrointestinal Digestion and Their Nutrient-Dependent Fermentation by Human Gut Microbiota.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
doi = {10.3390/foods15152740},
pmid = {42587998},
issn = {2304-8158},
abstract = {Bamboo fibers are increasingly incorporated into food products as sustainable dietary fiber ingredients, yet their gastrointestinal digestion resistance and fermentative behavior by human gut microbiota remain insufficiently characterized. This study combined an INFOGEST-based in vitro digestion protocol with colonic fermentation using fecal microbiota from three healthy donors as an exploratory donor panel. Bamboo fibers were resistant to salivary, gastric, and intestinal enzymatic hydrolysis, as demonstrated by the absence of structural modifications in FTIR spectra, preserved morphology observed by scanning electron microscopy, and negligible release of reducing sugars (<0.1 g/L across all digestive phases), in contrast to extensively hydrolyzed wheat starch used as a positive control. During in vitro colonic fermentation, microbial responses were strongly dependent on substrate availability. In nutrient-limited minimal medium, bamboo fiber supplementation increased gas production, acidification, and SCFA formation compared with control conditions. Concomitantly, SCFA concentrations increased under minimal-medium conditions, although the magnitude of the response varied among donors, with the strongest changes observed for donor 1 (acetate reaching 5.4 vs. 3.3 g/L and propionate 1.48 vs. 0.76 g/L). These effects were markedly attenuated in nutrient-rich medium, indicating competition with readily fermentable substrates. Beta-diversity analyses and metagenomic profiling revealed that microbial community composition clustered primarily according to donor identity rather than experimental conditions. SEM further showed surface erosion and microbial attachment on fermented fibers, supporting partial structural alteration. Overall, bamboo fibers are resistant to upper gastrointestinal digestion but display context-dependent fermentative activity by human gut microbiota under carbohydrate-limited conditions, highlighting the importance of inter-individual variability, dietary context and substrate availability in determining their fermentative potential.},
}

@article {pmid42588064,
year = {2026},
author = {De Sales-Millan, A and Reyes-Ferreira, P and González-Cervantes, RM and Luna-Álvarez, M and Guillén-López, S and Cobo-Díaz, JF and Ramos, S and Aguirre-Garrido, JF and Velázquez-Aragón, JA},
title = {Clinical Improvement and Taxonomic-Functional Gut Microbiome Remodeling After Six Months of Multi-Strain Synbiotic Supplementation in Mexican Children with Autism Spectrum Disorder.},
journal = {Nutrients},
volume = {18},
number = {15},
pages = {},
doi = {10.3390/nu18152441},
pmid = {42588064},
issn = {2072-6643},
support = {E022 Program Recursos Fiscales para la Investigación//Instituto Nacional de Pediatria/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Mexico ; Longitudinal Studies ; *Synbiotics/administration & dosage ; Child ; Feces/microbiology ; Child, Preschool ; Probiotics/administration & dosage ; Dietary Supplements ; Treatment Outcome ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; },
abstract = {Background/Objectives: Gut dysbiosis in children with autism spectrum disorder (ASD) has been associated with alterations in microbial ecology and metabolic function that may contribute to gastrointestinal dysfunction and the severity of clinical manifestations. Synbiotic and probiotic supplementation has emerged as a promising microbiome-targeted strategy for ASD; however, its effects on gut microbiome composition, functional potential, and clinical outcomes remain incompletely understood. We conducted a longitudinal study of Mexican children diagnosed with ASD to analyze changes in the composition, diversity, and functional potential of the gut microbiome during six months of multi-strain synbiotic supplementation. Methods: Stool samples were collected from 25 children with ASD at baseline and after 3 and 6 months of multi-strain synbiotic supplementation. Gut microbiome composition and diversity were analyzed by 16S rRNA gene sequencing, whereas whole metagenome sequencing (WMS) was performed in a subset of samples to evaluate the functional potential of the fecal microbiome. Gastrointestinal symptoms were assessed using the Rome IV criteria, and ASD severity was evaluated with the Childhood Autism Rating Scale (CARS). Results: Twenty-five children with ASD completed the 6 months of synbiotic supplementation. Overall, ASD severity decreased, reflected by a reduction in total CARS score, and improvements in several CARS domains. Gastrointestinal symptoms also decreased significantly. Longitudinal microbiome profiling revealed significant taxonomic and diversity changes over the supplementation period, while WMS identified changes in microbial metabolic potential, including enrichment of tryptophan biosynthesis pathways and reduced L-rhamnose degradation. Conclusions: This exploratory research provides proof-of-concept evidence supporting multi-strain synbiotic supplementation in children with ASD. Larger controlled studies are needed to confirm these findings and clarify their relevance to microbiota-gut-brain axis interactions. The observed concordance between clinical improvements and microbiome remodeling supports further investigation of microbiome-targeted interventions according to ASD severity and duration of supplementation.},
}

Humans
*Autism Spectrum Disorder/microbiology/therapy
Male
*Gastrointestinal Microbiome/genetics
Female
Mexico
Longitudinal Studies
*Synbiotics/administration & dosage
Child
Feces/microbiology
Child, Preschool
Probiotics/administration & dosage
Dietary Supplements
Treatment Outcome
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology

@article {pmid42588960,
year = {2026},
author = {Kiss, J and Libisch, B and Ozoaduche, CL and Fébel, H and Rasschaert, G and Lambrecht, E and Heyndrickx, M and Szabó, M and Keresztény, T and Posta, K and Olasz, F},
title = {Genetic Elements Associated with the Acquired Resistome of the Gut Microbiota in a Broiler Rooster Flock in Hungary.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {15},
pages = {},
doi = {10.3390/ani16152322},
pmid = {42588960},
issn = {2076-2615},
support = {TKP2020-NKA-24//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00007//National Research, Development and Innovation Office/ ; 2019-2.1.11-TÉT-2020-00141//National Research, Development and Innovation Office/ ; GINOP_PLUSZ-2.1.1-21-2022-00221//National Research, Development and Innovation Office/ ; },
abstract = {Antibiotic resistance in Gram-negative bacteria poses a global health threat, and poultry farming provides an important reservoir for multidrug-resistant pathogens. Our study aimed to characterize the faecal microbiota and acquired resistome of Ross-308 roosters in Hungary. Amplicon and shotgun metagenomics revealed a faecal microbiota dominated by the Firmicutes, Bacteroidota, and Proteobacteria and a diverse faecal resistome, including qnrB and an aadA1-bearing integron. Culture-based screening of an antibiotic-free rooster yielded the MDR Escherichia coli strain K1G, displaying resistance also to third-generation cephalosporins and fluoroquinolones. Whole-genome sequencing classified K1G as a serotype O23:H16-ST453 avian pathogenic E. coli (APEC) strain featuring a set of chromosomal virulence factors (including astA, hlyE, lpfA, and iss) and three plasmids: a phage-like plasmid, a mosaic virulence plasmid (carrying blaTEM-1b, hlyF, iutA, ompT, iucD, and cvaC), and an IncC type 1 resistance plasmid harbouring blaCMY-2. The detection of identical or closely related ST453 E. coli strains also in broiler meat in Hungary highlights a potential risk of transmission to humans through the food chain. Moreover, the carriage of multiple acquired antibiotic resistance genes in E. coli K1G indicates that individual chickens can harbour or transmit antibiotic resistance even in the absence of direct antibiotic exposure.},
}

@article {pmid42589241,
year = {2026},
author = {Wang, Q and Wang, BY and Wilus, D and Xie, H},
title = {Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156584},
pmid = {42589241},
issn = {1422-0067},
support = {R16GM149359/GM/NIGMS NIH HHS/United States ; U54MD007586/MD/NIMHD NIH HHS/United States ; },
mesh = {Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; Female ; Male ; Adult ; Middle Aged ; *Periodontitis/microbiology/therapy ; Metagenome ; Dental Scaling ; Root Planing ; Metagenomics/methods ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting approximately 40% of U.S. adults aged 30 years and older, is characterized by dysbiosis of the dental plaque microbiome. However, although scaling and root planing (SRP) is the cornerstone of periodontal treatment, its effects on the taxonomic composition and functional potential of the dental plaque microbiome remain incompletely understood. In this study, we used whole-metagenome shotgun sequencing to characterize taxonomic composition and functional potential in dental plaque microbiomes collected from 39 patients with Stage II or III generalized periodontitis before and 3-4 months after SRP. Consistent with clinical improvement, periodontal therapy significantly reduced probing depth, clinical attachment level, bleeding on probing, and plaque index. Whole-metagenome shotgun sequencing identified 3.18 million non-redundant genes and 12,353 microbial species across 78 samples, revealing increased gene and species richness after treatment, along with a significant restructuring of the microbial community. Established periodontal pathogens, including Porphyromonas gingivalis, as well as the emerging pathogens Escherichia coli and Burkholderia multivorans, decreased following treatment. Tannerella forsythia also showed a marked reduction after treatment, although this decrease was not significant after false discovery rate (FDR) correction. In contrast, health-associated early colonizers, including multiple Actinomyces species and Streptococcus cristatus, increased. Functional annotation using the Carbohydrate-Active Enzymes (CAZy) database identified significant treatment-associated differences in carbohydrate-active enzymes, including multiple glycosyltransferases, indicating remodeling of the predicted functional potential of the dental plaque microbiome. These findings demonstrate that successful SRP promotes coordinated taxonomic and predicted functional remodeling of the dental plaque microbiome and highlight the value of shotgun metagenomic sequencing for characterizing both taxonomic and functional recovery following periodontal therapy.},
}

Humans
*Dental Plaque/microbiology
*Microbiota/genetics
Female
Male
Adult
Middle Aged
*Periodontitis/microbiology/therapy
Metagenome
Dental Scaling
Root Planing
Metagenomics/methods

@article {pmid42589351,
year = {2026},
author = {Shen, H and Huang, S and Wang, Z and Zhou, S and Huang, L and Zhang, H and Han, Y and Jiang, J and Guo, H},
title = {Glycyrrhizic Acid Alleviates Atherosclerosis in ApoE[-/-] Mice via Microbial Indole-3-Lactic Acid-Mediated AhR-p65 Interaction in the Endothelium.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156694},
pmid = {42589351},
issn = {1422-0067},
support = {No. 3332025150//Fundamental Research Funds for the Central Universities/ ; No. 2025-I2M-KJ-016//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Animals ; *Atherosclerosis/drug therapy/metabolism/microbiology/etiology/pathology ; Mice ; *Glycyrrhizic Acid/pharmacology/therapeutic use ; *Receptors, Aryl Hydrocarbon/metabolism ; *Indoles/metabolism ; Male ; *Transcription Factor RelA/metabolism ; *Apolipoproteins E/deficiency/genetics ; Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Humans ; Fecal Microbiota Transplantation ; Endothelium, Vascular/metabolism/drug effects ; Mice, Knockout ; },
abstract = {Glycyrrhizic acid (GL), a natural triterpenoid glycoside extracted from the "medicine food homology" herb Glycyrrhiza glabra L., exhibits potent anti-atherosclerotic effects; yet its underlying mechanisms remain unclear due to its poor oral bioavailability. The gut microbiota plays a pivotal role in the development of atherosclerosis (AS). In this study, the microbiota-dependent anti-AS effects of GL were evaluated in high-fat diet (HFD)-fed ApoE[-/-] mice using antibiotic depletion and fecal microbiota transplantation (FMT). Integrated metagenomic and metabolomic analyses were performed to identify the key bioactive microbial metabolite. Further in vivo and in vitro experiments, including co-immunoprecipitation and dual-luciferase reporter assays, were utilized to elucidate the underlying molecular mechanisms. It was demonstrated that oral administration of GL alleviated AS in a microbiota-dependent manner by reversing gut dysbiosis, improving intestinal barrier function, and reducing pro-inflammatory lipopolysaccharide (LPS) levels. GL shifted intestinal tryptophan metabolism toward bacterial-derived indole-3-lactic acid (ILA) production, suppressing LPS-induced vascular endothelial adhesion dysfunction by activating the aryl hydrocarbon receptor (AhR). Mechanistically, ILA-activated AhR interacted with the NF-κB subunit p65 in the cytoplasm, effectively preventing the nuclear translocation of p65 and suppressing the promoter activities of adhesion molecules (VCAM1 and ICAM1), resulting in the amelioration of HFD-induced AS. These findings elucidate the microbiota-dependent mechanism of orally administered GL against AS, and highlight the therapeutic potential of targeting the ILA-AhR-p65 axis in the vascular endothelium as a strategy for AS.},
}

Animals
*Atherosclerosis/drug therapy/metabolism/microbiology/etiology/pathology
Mice
*Glycyrrhizic Acid/pharmacology/therapeutic use
*Receptors, Aryl Hydrocarbon/metabolism
*Indoles/metabolism
Male
*Transcription Factor RelA/metabolism
*Apolipoproteins E/deficiency/genetics
Gastrointestinal Microbiome/drug effects
Diet, High-Fat/adverse effects
Mice, Inbred C57BL
Humans
Fecal Microbiota Transplantation
Endothelium, Vascular/metabolism/drug effects
Mice, Knockout

@article {pmid42589520,
year = {2026},
author = {Dima, V and Calomfirescu Avramescu, A and Mirea, A and Toma, AI and Bohiltea, RE and Bivoleanu, A and Stewart, DL},
title = {Ureaplasma Species in Perinatal Disease: From the Age of Innocence to the Missing Villain.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156865},
pmid = {42589520},
issn = {1422-0067},
mesh = {Humans ; *Ureaplasma Infections/microbiology ; *Ureaplasma/pathogenicity/physiology ; Female ; Pregnancy ; Infant, Newborn ; Chorioamnionitis/microbiology ; Animals ; },
abstract = {Ureaplasma urealyticum and Ureaplasma parvum occupy an odd place in perinatal medicine: dismissed for decades as harmless residents of the female genital tract, they are now recognized as pathogens with real consequences for preterm newborns. This review traces that paradigm shift, from organisms once dismissed as harmless colonizers to pathogens now implicated in chorioamnionitis, preterm birth, and a range of serious neonatal morbidities, and describes the molecular mechanisms that underlie their pathogenicity: Toll-like receptor (TLR1/2/6/9)-mediated NF-κB and MyD88/IRAK4/TRAF6 signaling, NLRP3 inflammasome activation and pyroptosis, and blood-brain barrier disruption via claudin-5/occludin downregulation and MMP-mediated tight junction cleavage. We also review the evidence for biofilm-conferred antibiotic tolerance and the clinical associations between Ureaplasma colonization and intraventricular hemorrhage (pooled OR 1.62, 95% CI 1.23-2.13), bronchopulmonary dysplasia (pooled OR 2.30, 95% CI 1.65-3.20), late-onset sepsis, and neurodevelopmental impairment. Diagnosis remains a weak point: culture sensitivity is below 10% compared with polymerase chain reaction (PCR) testing, and no randomized trial has yet shown that microbiological eradication translates into better clinical outcomes-a gap we examine critically. Whether these organisms cause disease seems to depend on gestational age, bacterial load, serovar-specific virulence, and host immune competence. We argue that this conditionality calls for risk stratification rather than dismissal whenever Ureaplasma is identified in clinical specimens, and that the field needs a paradigm shift toward Ureaplasma screening in high-risk pregnancies and targeted neonatal PCR testing, backed by adequately powered interventional trials.},
}

Humans
*Ureaplasma Infections/microbiology
*Ureaplasma/pathogenicity/physiology
Female
Pregnancy
Infant, Newborn
Chorioamnionitis/microbiology
Animals

@article {pmid42589527,
year = {2026},
author = {Coppini, M and Mauceri, R and Vacca, D and Bertolazzi, G and Caponio, VCA and Rodolico, V and Belmonte, B and Campisi, G},
title = {Longitudinal Exploratory Analysis of Salivary Microbiota Profiles in Patients with Oral Squamous Cell Carcinoma Before and After Surgery: A Pilot Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156873},
pmid = {42589527},
issn = {1422-0067},
mesh = {Humans ; *Saliva/microbiology ; Pilot Projects ; *Mouth Neoplasms/microbiology/surgery ; Female ; Male ; *Microbiota ; *Carcinoma, Squamous Cell/surgery/microbiology ; Middle Aged ; Aged ; Longitudinal Studies ; Metagenomics/methods ; Bacteria/genetics/classification ; Adult ; Metagenome ; },
abstract = {Salivary microbiome profiling may represent a promising non-invasive approach for characterizing OSCC-associated microbial patterns and longitudinal microbiome dynamics during patient management. This exploratory pilot study aimed to longitudinally assess salivary microbiota profiles in patients with oral squamous cell carcinoma (OSCC) before and after tumor resection using Oxford Nanopore Technology. Unstimulated saliva samples were collected from 16 patients with OSCC at two time points (before and after tumor resection) and from 10 OSCC-free reference subjects. Microbial DNA was extracted using the QIAamp DNA Blood Kit (QIAGEN GmbH, Hilden, Germany) and subjected to long read metagenomic sequencing using the Oxford Nanopore MinION platform (v. 20.06.4, Oxford Nanopore Technologies, Oxford, UK). Taxonomic profiling was performed to longitudinally characterize salivary microbiota composition within patients and to provide descriptive comparisons with the OSCC-free reference cohort. Longitudinal analysis identified differences in salivary microbiota profiles between pre- and post-resection samples. Before surgery, an increased relative abundance of Neisseria subflava and Leptotrichia buccalis was observed. Post-surgical samples showed higher levels of Glaesserella parasuis, Streptomyces anulatus, and Lactobacillus species. Distinct microbial patterns were also descriptively observed between OSCC patients and OSCC-free controls, suggesting disease-associated dysbiosis. This exploratory longitudinal pilot study suggests differences in salivary microbiota profiles between samples collected before and after tumor resection in patients with OSCC, including changes in taxonomic composition and reduced alpha diversity. Given the limited sample size and the potential influence of unmeasured perioperative factors, these findings should be considered hypothesis-generating. Larger, well-controlled longitudinal studies incorporating standardized oral health assessment and detailed perioperative metadata are required to clarify the biological and clinical relevance of these observations.},
}

Humans
*Saliva/microbiology
Pilot Projects
*Mouth Neoplasms/microbiology/surgery
Female
Male
*Microbiota
*Carcinoma, Squamous Cell/surgery/microbiology
Middle Aged
Aged
Longitudinal Studies
Metagenomics/methods
Bacteria/genetics/classification
Adult
Metagenome

@article {pmid42589560,
year = {2026},
author = {Valenzuela, B and Navarrete-Diaz, I and Cayo, M and Solís-Cornejo, F and Zamorano, P},
title = {Genome-Resolved Metagenomics Reveals Thermophilic Microbial Diversity and Putative Hydrolase-Encoding Genes in the El Tatio Geothermal Field.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156905},
pmid = {42589560},
issn = {1422-0067},
support = {Fondo para el Desarrollo en Investigación: en artes, ciencias y/o tecnología para actividades de titulación de pregrado": "Bioprospección de Genes de Enzimas Hidrolíticas mediante Análisis Metagenómico en el Campo Geotermal El Tatio"//University of Antofagasta/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Phylogeny ; *Archaea/genetics/classification/enzymology ; *Hydrolases/genetics ; *Hot Springs/microbiology ; *Bacteria/genetics/classification/enzymology ; Chile ; },
abstract = {Geothermal ecosystems constitute important reservoirs of thermophilic microorganisms and their associated metabolic functions; however, the genome-resolved diversity and enzymatic potential of high-altitude geothermal systems remain poorly characterized. Here, we applied shotgun metagenomics and genome-resolved approaches to investigate thermophilic microbial communities inhabiting geothermal sediments from the El Tatio geothermal field, a polyextreme hydrothermal system located at ~4300 m above sea level in the Andean Altiplano of northern Chile. Genome reconstruction yielded 657 metagenome-assembled genomes (MAGs), including 190 near-complete and 273 high-quality genomes, providing a comprehensive genome-resolved view of microbial diversity in this environment. Taxonomic analyses revealed diverse archaeal and bacterial communities dominated by members of Thermoproteota, Methanobacteriota, Deinococcota, and Actinomycetota. Functional screening identified 612 high-confidence putative hydrolase-encoding genes distributed across multiple thermophilic lineages, including genes associated with esterases, lipases, proteases, and glycoside hydrolases. Notably, several candidates were recovered from archaeal MAGs affiliated with Thermoproteus, Sulfolobales, Pyrobaculum, and Acidilobaceae, expanding the genomic repertoire of putative hydrolytic functions in thermophilic archaea. Sequence-based thermostability prediction identified proteins with estimated melting temperatures exceeding 80 °C, with the highest predicted value reaching 87.6 °C. Collectively, these results expand current knowledge of microbial diversity and functional potential in high-altitude geothermal ecosystems and identify El Tatio as a rich source of putative hydrolase-encoding genes for future biochemical and biotechnological exploration.},
}

*Metagenomics/methods
*Metagenome
Phylogeny
*Archaea/genetics/classification/enzymology
*Hydrolases/genetics
*Hot Springs/microbiology
*Bacteria/genetics/classification/enzymology
Chile

@article {pmid42589672,
year = {2026},
author = {Zeng, C and Chen, J and Yong, X and Xie, Y},
title = {Convergent Gut Microbiome Remodeling Across Ischemic Stroke, Myocardial Infarction, and Longevity Reveals a Shared Ecological Signature of Aging and Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27157020},
pmid = {42589672},
issn = {1422-0067},
support = {cstc2021jcyj-msxmx0848//Natural Science Foundation of Chongqing/ ; BSKJ2022006//Bishan District Science and Technology Bureau/ ; 81773954//National Natural Science Foundation of China (NSFC)/ ; 202310617015//National College Student Innovation and Entrepreneurship Program/ ; X2024160170123, X2026106170029//Chongqing College Students' Innovation and Entrepreneurship Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Aging ; *Myocardial Infarction/microbiology ; *Longevity ; *Ischemic Stroke/microbiology ; Male ; Female ; Aged ; Dysbiosis/microbiology ; },
abstract = {Gut microbiota dysbiosis has been associated with ischemic stroke (IS), myocardial infarction (MI), and aging, but whether these contexts share reproducible microbial features remains unclear. We conducted an exploratory and hypothesis-generating descriptive study of genus-level microbiota patterns across an internal IS cohort and publicly available external IS, MI, and age-stratified or longevity-associated datasets. Analyses were performed within predefined age strata and interpreted cautiously because of the small internal cohort, cross-cohort heterogeneity, and the absence of direct metabolite, intestinal barrier, inflammatory, or microbial activity measurements. No taxon in the internal cohort remained statistically significant after false-discovery-rate correction; therefore, all taxonomic observations were treated as descriptive. Candidate overlapping features included repeated detection of Escherichia-Shigella and Klebsiella and non-uniform patterns among genera previously associated with short-chain fatty acid metabolism, including Faecalibacterium, Blautia, and Roseburia. Lachnoclostridium and Bacteroides showed opposite abundance gradients in selected cross-dataset comparisons. These observations suggest possible ecological overlap across ischemic disease and age-associated microbiome contexts, but they do not establish causality, disease-specific biomarkers, or shared microbial function. The mechanistic models discussed in this manuscript are literature-informed hypotheses based on exploratory compositional data and require future validation in larger, harmonized longitudinal cohorts using metagenomic, metabolomic, clinical, and experimental measurements.},
}

Humans
*Gastrointestinal Microbiome
*Aging
*Myocardial Infarction/microbiology
*Longevity
*Ischemic Stroke/microbiology
Male
Female
Aged
Dysbiosis/microbiology

@article {pmid42590140,
year = {2026},
author = {Guo, F and Zhang, L and Liu, Z and Zhou, B and Fan, H and Zhang, D and Yang, Q and Li, T and Ge, Y},
title = {Clinical Utility of Metagenomic Next-Generation Sequencing in Adult Patients with Fever of Unknown Origin: A Retrospective Real-World Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {15},
pages = {},
doi = {10.3390/jcm15156038},
pmid = {42590140},
issn = {2077-0383},
support = {2022-PUMCH-B-043.//Peking Union Medical College Hospital/ ; },
abstract = {Background: Fever of unknown origin (FUO) remains a major diagnostic challenge due to its heterogeneous etiologies and nonspecific clinical manifestations. Although metagenomic next-generation sequencing (mNGS) represents a promising diagnostic tool, its clinical utility in adult patients with FUO remains incompletely characterized. Methods: In this study, we retrospectively analyzed adult FUO patients who underwent mNGS testing at Peking Union Medical College Hospital between March 2022 and April 2024. Clinically meaningful diagnostic contribution was determined according to the final clinical diagnosis following multidisciplinary adjudication. Diagnostic performance, pathogen spectrum, therapeutic impact, specimen type, and predictors of clinically meaningful mNGS results were evaluated. Results: A total of 127 FUO patients were included in the study. Infectious diseases accounted for 53.5% of final diagnoses, followed by noninfectious inflammatory diseases (11.0%), malignancies (10.2%), and undiagnosed conditions (19.7%). mNGS made a clinically meaningful diagnostic contribution in 31.5% (40/127) of patients, despite an overall positivity rate of 56.7% (72/127), and showed a higher sensitivity than conventional culture for infectious etiologies (69.1% vs. 16.9%), though with a lower specificity (57.6% vs. 96.0%). Diagnostic contribution varied significantly by specimen type, with drainage fluid/abscess samples showing the highest diagnostic yield (90.9%). Lower white blood cell count was independently associated with clinically meaningful mNGS results (OR 0.87, 95% CI 0.77-0.98). Conclusions: mNGS provides clinically meaningful diagnostic value in adult patients with FUO, particularly for identifying occult infectious etiologies. Lesion-directed sampling, whenever feasible, and careful interpretation of sequencing results in the clinical context are essential to maximize the diagnostic utility of this approach. A lower white blood cell count was independently associated with clinically meaningful mNGS results, although this finding requires validation in larger prospective studies.},
}

@article {pmid42591141,
year = {2026},
author = {Szeitz, A and Pinto, J and Pieters, A},
title = {Editorial: Advances in mass spectrometry: transforming analytical chemistry in molecular and spatial biology, multimodal omics, and bioanalysis.},
journal = {Frontiers in molecular biosciences},
volume = {13},
number = {},
pages = {1926838},
pmid = {42591141},
issn = {2296-889X},
}

@article {pmid42591156,
year = {2026},
author = {Kütahya, C and Pániker, CC and Ly, F and Jerath, A and Little, E and Gali, R and Haimi, MZBD and Malek, AHBA and Muhamad, KB and Supian, SB and Young, TB and Lawrence, S and Bell, T and Nee, TY and Jiménez, JI and Huynh, F},
title = {Masterbatch-enabled acceleration of polyolefin biodegradation under open air terrestrial environmental conditions.},
journal = {Npj Materials degradation},
volume = {10},
number = {1},
pages = {90},
pmid = {42591156},
issn = {2397-2106},
abstract = {Polyolefins, commonly used in packaging and single-use products, are notoriously persistent in the environment, contributing significantly to environmental pollution. In scientific literature to date, polyolefins have not been reported to fully biodegrade. This study examines the biodegradation potential of polyolefin materials, specifically polyethylene (PE) and polypropylene (PP), enhanced through the incorporation of Biotransformation Masterbatch technology. The inclusion of the Biotransformation Masterbatch accelerated and enabled the full biodegradation of PE and PP, as demonstrated by laboratory weathering, and biodegradation studies in soil at mesophilic temperatures. Ecotoxicity tests revealed no adverse effects on test organisms in both soil and water environments, while metagenomics analysis demonstrated that biodegradation of these polyolefins did not significantly change the soil microbiota composition, which showed higher metabolic activity compared to virgin plastic controls. These findings demonstrate that Biotransformation technology provides an effective solution for delivering polyolefin-based materials with reduced environmental impact. It offers a sustainable alternative to conventional plastics, preserving the performance characteristics of traditional polyolefins while addressing the problem with fugitive plastic waste in the environment.},
}

@article {pmid42591585,
year = {2026},
author = {Chen, G and Pan, Y and Bai, Z and Zheng, Y and Wei, Y},
title = {Synergistic algae-bacteria interactions in a novel membrane aeration biofilm system: performance and microbial function.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1900925},
pmid = {42591585},
issn = {1664-302X},
abstract = {Low carbon-to-nitrogen (C/N) ratio wastewater poses a major challenge to biological nitrogen removal due to insufficient electron donors for denitrification. In this study, an algae-bacteria membrane-aerated biofilm reactor (AB-MABR) was established to enhance nitrogen removal under carbon-limited conditions, and its performance was compared with that of a conventional bacterial MABR (B-MABR). The results showed that the AB-MABR achieved superior pollutant removal performance, with COD, NH4 [+]-N, and TN removal efficiencies being 4.0, 21.9, and 12.3% higher, respectively, than those of the B-MABR. Overall, AB-MABR outperformed B-MABR in pollutant removal. The removal efficiencies of COD, NH4 [+]-N, and TN were 92.3, 77.2, and 66.6%, respectively, which were markedly higher than those achieved by B-MABR (88.8, 55.3, and 54.3%). The incorporation of microalgae significantly enhanced microbial metabolic activity, as evidenced by higher ATP content, electron transport system activity (ETSA), and cytochrome c (Cyt-c) levels. Meanwhile, EPS production increased by 25% in the AB-MABR, accompanied by greater accumulation of protein-like and humic-like substances. SEM and CLSM analyses revealed that microalgae promoted the formation of a denser and more stratified biofilm with higher biomass and stronger structural stability. Metagenomic analysis further demonstrated that pathways associated with microbial metabolism, secondary metabolite biosynthesis, and environmental adaptation were enriched in the AB-MABR system, indicating enhanced metabolic potential and ecological resilience. Overall, microalgal incorporation strengthened electron transfer, stimulated EPS secretion, improved biofilm development, and enhanced microbial metabolic functions, thereby promoting nitrogen transformation and removal under low C/N conditions. These findings provide new insights into the synergistic mechanisms of algae-bacteria biofilms and demonstrate the potential of AB-MABR technology for sustainable nitrogen removal from carbon-limited wastewater.},
}

@article {pmid42591617,
year = {2026},
author = {Mukhedkar, D and Stosic, MS and Székely, AJ and Avershina, E and Arroyo Mühr, LS},
title = {Strong catchment-specific structuring of Swedish wastewater microbiomes in a paired two-timepoint metagenomic survey.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1907599},
pmid = {42591617},
issn = {1664-302X},
abstract = {INTRODUCTION: Wastewater microbial communities integrate signals from human populations, environmental inputs, and sewer infrastructure, but the extent to which these communities vary between wastewater catchments compared with individual sampling occasions remains incompletely understood.

METHODS: We analyzed influent wastewater from 16 wastewater treatment plant sites across Sweden, collected at two paired within-year timepoints, Week 3 and Week 21, using shotgun metagenomic sequencing and compositional data analysis.

RESULTS: Classified genus-level profiles were dominated by bacteria (96.54%), with smaller contributions from viruses (2.03%), eukaryota (1.05%) and archaea (0.40%). Genus-level alpha diversity increased between the two sampled timepoints, with median within-site changes of +10 genera in richness and +0.21 in Shannon diversity (p < 0.003). In contrast, overall community composition was primarily structured by wastewater treatment plant site: site explained 58.3% of total variance (p = 0.0003), whereas sampling timepoint explained 3.7% and was not significant (p = 0.106). Within-site compositional change between the two timepoints was nevertheless evident (p = 4.8 × 10[-4]), but the magnitude and direction of change varied across sites, indicating heterogeneous local shifts rather than a synchronized national temporal pattern. Genera detected in at least 75% of sites at both sampled timepoints accounted for most classified community abundance, whereas most measured within-site Aitchison turnover was accounted for by genera outside the high-prevalence shared fraction. Geographic distance and the number of connected inhabitants showed no significant association with genus-level community composition.

DISCUSSION: These findings indicate that Swedish influent wastewater microbiomes are strongly catchment-specific across paired sampling timepoints and support the use of site-specific reference profiles when interpreting wastewater metagenomic data. Denser temporal sampling and additional catchment metadata will be needed to assess seasonality, long-term stability, and the local drivers of wastewater microbiome variation.},
}

@article {pmid42591668,
year = {2026},
author = {Dell'Alma, M and Cesana, M and Kenny, P and Peron, G and Cafarella, C and Rigano, F and Mondello, L and Mangieri, N and Pizzi, S and Russo, P and Mora, D and Gargari, G},
title = {Multi-omic characterization of microbial dynamics during spontaneous fermentation of sweet wine Picolit variety.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1857803},
pmid = {42591668},
issn = {1664-302X},
abstract = {INTRODUCTION: Spontaneous wine fermentation is driven by the ecological succession of vineyard-derived microorganisms, yet little is known about how this process unfolds in Picolit, a grape variety characterized by acinellatura (berry millerandage) and elevated sugar concentration. This study aimed to characterize the microbial and metabolic dynamics of spontaneous Picolit fermentation and to identify the ecological and functional transitions occurring throughout the process.

METHODS: An integrated multi-omic approach combining shotgun metagenomics and untargeted metabolomics was applied to spontaneous fermentations of Picolit grapes produced at Aquila del Torre, an organic and biodynamic winery located in Savorgnano del Torre (Friuli-Venezia Giulia, Italy), within the newly established "Friuli Colli Orientali Sottozona Savorgnano D.O.C." Five fermentation stages were sampled and analyzed to investigate microbial succession, functional pathways and metabolomic changes.

RESULTS: The initial must displayed high microbial richness dominated by non-Saccharomyces yeasts, oxidative bacteria and Botrytis cinerea. An atypical persistence and increasing abundance of B. cinerea suggested a strong interaction between grape physiology and fungal activity. Early fermentation stages were characterized by diverse non-Saccharomyces taxa, including Lachancea, Pichia, Torulaspora and Schizosaccharomyces, which were associated with acid modulation, aromatic precursor release and phenolic turnover. From mid-fermentation onward, a multi-species Saccharomyces consortium established functional dominance, coinciding with a marked reduction in bacterial diversity and a transition from aroma-related metabolic pathways to stress adaptation functions. Multi-omic network analyses revealed a progressive loss of modularity as fermentation progressed and the system became more stable.

DISCUSSION: These findings demonstrate that spontaneous Picolit fermentation follows a distinctive ecological trajectory shaped by grape physiology, terroir and native microbial diversity. The persistence of B. cinerea, together with the succession of non-Saccharomyces and Saccharomyces populations, highlights unique microbial interactions that may contribute to wine identity. Overall, the results support the enological value of spontaneous fermentation and provide a microbial and functional framework for understanding and valorizing wines produced under the Savorgnano Bianco D.O.C.},
}

@article {pmid42591980,
year = {2026},
author = {Zhao, X and Ming, X and Shang, Z and Zhou, M and Xiao, Y},
title = {Epstein-Barr Virus-Positive B-Cell Lymphoproliferative Disorder Complicated by Septic Shock in Activated PI3Kδ Syndrome: A Pediatric Case Report and Literature Review.},
journal = {Case reports in hematology},
volume = {2026},
number = {},
pages = {3644513},
pmid = {42591980},
issn = {2090-6560},
abstract = {Activated phosphoinositide 3-kinase delta syndrome (APDS) is a rare inborn error of immunity caused by gain-of-function variants in PIK3CD and characterized by recurrent infections, lymphoproliferation, and impaired viral control. We report a 17-year-old male with a heterozygous PIK3CD c.3061G > A (p.E1021K) variant who presented with progressive edema, extensive hypermetabolic lymphadenopathy, splenomegaly, and Epstein-Barr virus (EBV) DNAemia. A core needle biopsy of the right inguinal lymph node demonstrated an immunodeficiency-associated EBV-positive B-cell lymphoproliferative disorder with extensive monotypic plasmacytoid differentiation. Because the biopsy contained limited mature B-cell tissue, the pathological findings favored a polymorphic B-LPD although EBV-positive diffuse large B-cell lymphoma with plasmacytic differentiation could not be excluded. The patient received anti-B-cell-directed therapy and supportive treatment. He was subsequently readmitted with septic shock and acute respiratory distress syndrome. Blood metagenomic next-generation sequencing detected Escherichia coli and Klebsiella pneumoniae, together with antimicrobial-resistance genes including blaNDM. Despite intensive antimicrobial and organ-supportive treatment, the patient remained critically ill and was discharged at his family's request for transfer to a local hospital; his subsequent outcome was unavailable. This case highlights the diagnostic difficulty of classifying EBV-positive B-cell proliferations using limited biopsy tissue in APDS and the competing risks of lymphoproliferative disease and severe infection. Adequate tissue sampling and pathological characterization, close microbiological surveillance, and individualized multidisciplinary management are essential in this setting.},
}

@article {pmid42592599,
year = {2026},
author = {Tao, G and Tang, W and Zhao, Y and Ma, Y and Xu, Y},
title = {A case report of ocular infection caused by Aspergillus fumigatus.},
journal = {AME case reports},
volume = {10},
number = {},
pages = {154},
pmid = {42592599},
issn = {2523-1995},
abstract = {BACKGROUND: Aspergillus fumigatus (A. fumigatus) can cause invasive infections in various sites of the body, including invasive pulmonary, hematogenous disseminated, and intracranial infections, posing substantial challenges for diagnosis and treatment. The methods of identification in this laboratory are worthy of study.

CASE DESCRIPTION: A 44-year-old male was admitted to our hospital with a 1.5-month history of bilateral scleral icterus accompanied by progressive visual deterioration. The patient was previously diagnosed with acute liver failure [hepatitis B e-antigen (HBeAg)-negative chronic hepatitis B] at another hospital. During hospitalization, his vision in the left eye decreased. Slit-lamp examination during ophthalmologic consultation suggested left endophthalmitis, with concurrent suspicion of retinal detachment. Examinations at admission confirmed the presence of hepatitis B virus (HBV) DNA, acute liver failure (Child-Pugh Class C), moderate anemia. The levels of the inflammatory markers were significantly elevated, including interleukin (IL-6, IL-8, IL-1β), and interferon-gamma (IFN-γ). After obtaining informed consent, emergency vitrectomy of the left eye was performed, retinal detachment repositioning and laser photocoagulation for retinal lesions, cryotherapy for retinal lesions, and vitreous silicone oil implantation in the left eye. The vitreous was cultured, then identified using next-generation metagenomic sequencing (mNGS) technology, enabling the detection of Aspergillus within a short period of time. This enabled a rapid diagnosis of Aspergillus endophthalmitis, guiding subsequent clinical management. After undergoing anti-infection and liver-protective treatment, the patient's condition stabilized and he was discharged from the hospital.

CONCLUSIONS: mNGS is a technology that can directly perform high-throughput sequencing of all the genetic material (DNA and/or RNA) of microorganisms in clinical samples (such as blood, bronchoalveolar lavage fluid, cerebrospinal fluid, etc.). The combination of mNGS and conventional detection methods effectively improves the detection rate of fungi.},
}