@article {pmid42810054,
year = {2026},
author = {Ghorbani, Y and Schwenger, KJP and Maughan, H and Teterina, A and Lou, W and Comelli, EM and Fischer, SE and Jackson, TD and Okrainec, A and Allard, JP},
title = {Multi-omic profiling and pathways related to changes in liver histology after Roux-en-Y gastric bypass: a longitudinal study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106498},
doi = {10.1016/j.ebiom.2026.106498},
pmid = {42810054},
issn = {2352-3964},
abstract = {BACKGROUND: Roux-en-Y gastric bypass (RYGB) improves metabolic dysfunction-associated steatotic liver disease (MASLD). However, the impact of RYGB on hepatic transcriptome, faecal microbiome and serum/faecal metabolome remain understudied. Our objective was to investigate the change in these omics and their relationships with changes in liver histology.

METHODS: In this prospective cohort study, patients undergoing RYGB were recruited between 2013 and 2020 and followed for 12 months. Anthropometrics, biochemistry, hepatic transcriptome, faecal microbiome (shotgun metagenomics) and serum/faecal metabolomes were measured. Liver histology and NAFLD Score (NAS) were assessed.

FINDINGS: Thirty-eight patients completed the study. Anthropometrics, biochemical and histological parameters improved post-RYGB (p < 0.05). Hepatic transcriptome analysis revealed a co-expression module enriched in fatty acid metabolism which correlated with changes in NAS post-RYGB (ρ = 0.38, p = 0.019). The core enrichment genes in this pathway were involved in mitochondrial and peroxisomal β-oxidation (ACADVL, ACOX1, and EHHADH) and the tricarboxylic acid (TCA) cycle (SUCLG2, SDHC, and SERINC1). There was an increase in TCA cycle gene expression associated with the resolution of ballooning, while upregulation of β-oxidation genes correlated with less reduction in NAS, ballooning, and inflammation. Metabolomic changes related to the identified co-expression module and pathways reveal a significant increase in faecal acylcarnitines, likely due to malabsorption from RYGB, with a significant reduction in circulating acylcarnitines which correlated positively with SUCLG2 expression and resolution of ballooning. Additionally, the increase in faecal acylcarnitines positively correlated with the bacterial species utilising acylcarnitines. In network analysis, ballooning of hepatocytes was associated with faecal/serum acylcarnitines and TCA metabolites while SUCLG2 was the hub gene associated with these changes.

INTERPRETATION: These findings provide insight on how post-RYGB changes in the transcriptome, metabolome, and microbiome could be associated with improvement in liver histology and may inform the development of future strategies for MASLD management.

FUNDING: Canadian Institutes of Health Research and American College of Gastroenterology.},
}

@article {pmid42810079,
year = {2026},
author = {Chen, F and Zhao, N and Fan, Q and Tao, W and Du, E and Wei, J},
title = {Integrative metabolic and lipidomic analysis reveals microbiota-associated mechanisms of thigh meat quality variation in spent laying hens from different rearing systems.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107848},
doi = {10.1016/j.psj.2026.107848},
pmid = {42810079},
issn = {1525-3171},
abstract = {This study aims to elucidate the differences in poultry meat quality between cage-rearing (CR) and free-range (FR) rearing systems and to dissect the underlying microbiota-mediated mechanisms. A total of 200 Jianghan laying hens (50-week-old) were equally assigned to either FR or CR group. At 56 w, 10 hens from each group were selected and underwent integrated analyses of gut microbial metagenomes, muscle nutrient composition, amino acid, and lipid profiles. The results showed that the FR group had lower abdominal fat yield but higher leg muscle yield (P < 0.01). Leg muscle of FR hens exhibited lower crude fat content, drip loss, malondialdehyde levels, but higher pH24h, glutathione peroxidase (GSH-Px) activity and DPPH radical-scavenging rate (P < 0.05). Additionally, the FR group showed significant increases in glutamic acid, alanine, isoleucine, tyrosine, phenylalanine, histidine, arginine and total flavor amino acids (FAA, P < 0.05). Lipidomic profiling identified 38 differentially abundant lipids and an elevation in total fatty acyls in FR muscles. Subsequent fatty acids composition analysis revealed higher proportions of C20:4 and total polyunsaturated fatty acids (PUFA) in the FR group (P < 0.05). Cecal microbiota analysis indicated FR rearing increased the relative abundances of Ligilactobacillus aviarius, Enterococcus faecium, Corynebacterium stationis, C.glutamicum, and C.casei (P < 0.05). Correlation analyses demonstrated that L. aviarius was positively correlated with FAA content, while the three Corynebacterium species were positively correlated with GSH-Px activity, pH24h, FAA, and PUFA, and negatively with drip loss (|r| > 0.6, P < 0.05). Collectively, free-range rearing improves meat quality and nutritional traits, which may be linked to changes in the gut microbial community.},
}

@article {pmid42810185,
year = {2026},
author = {Yan, J and Lei, Z and Li, K and Zheng, M and Zhang, A and Sun, Z and Liu, Y},
title = {Far-UVC-activated calcium peroxide facilitates simultaneous antibiotic removal and carbon recovery from waste activated sludge.},
journal = {Water research},
volume = {308},
number = {Pt C},
pages = {126990},
doi = {10.1016/j.watres.2026.126990},
pmid = {42810185},
issn = {1879-2448},
abstract = {Antibiotic residues in waste activated sludge (WAS) require effective removal to reduce ecological risks and improve the safety of sludge resource recovery. This study evaluated 222 nm far-UVC-activated calcium peroxide (CaO2) pretreatment for simultaneous antibiotic removal and carbon recovery from WAS, using sulfamethoxazole (SMX) as a model antibiotic. Far-UVC and CaO2 exhibited a synergistic effect, achieving 80% apparent SMX removal within 240 min at a CaO2 dosage of 0.1 g/g TS. Mechanistically, continuous CaO2 hydrolysis induced sludge disintegration and alkalization (pH = 9.55). This dual-action not only co-released the entrapped SMX and endogenous dissolved organic matter (DOM) into the aqueous phase but also shifted SMX toward its highly photo- and radical-susceptible deprotonated state. Consequently, efficient far-UVC photolysis of slowly released H2O2 and DOM-mediated sensitization unlocked an abundant reactive species cascade (dominated by HO• and [1]O2), which efficiently degraded SMX and its intermediates to minimize potential ecological risks. From a practical standpoint, the process effectively buffered complex matrix interferences, degrading 13 indigenous multi-class antibiotics in real sludge (with removal efficiencies of up to 89%) while yielding a 1.4-fold increase in energy efficiency compared to far-UVC alone. Furthermore, far-UVC/CaO2 enhanced WAS solubilization and subsequent anaerobic fermentation, increasing volatile fatty acids (VFAs) production to 3.8 times that of the control. Metagenomic profiling indicated enrichment of hydrolytic and acidogenic microbial populations and functional genes related to substrate hydrolysis and VFA formation, supporting enhanced carbon recovery from antibiotic-containing WAS.},
}

@article {pmid42810338,
year = {2026},
author = {Yang, L and Singh, V and Gawey, BJ and Sinnwell, JP and Johnson, S and Billings, EC and Van Gorp, TM and Harrington, JJ and Slama, MQ and Till, LM and Singh, M and Samineni, TR and Zhu, M and Kalari, KR and Farrugia, G and Chen, J and Mars, RAT and Kashyap, PC},
title = {Microbiome signatures linked to cancer and treatment adverse events in a real-world cohort.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.09.009},
pmid = {42810338},
issn = {1097-4172},
abstract = {The gut microbiome has emerged as a key contributor to cancer biology. Prior studies have focused on individual cancers and often overlook comorbidities, obscuring whether reported associations are specific to a cancer type. Here, we present findings from a real-world mixed-cancer cohort (Mayo Clinic Cancer Microbiome), comprising 1,364 cancer patients and 287 healthy controls. By applying a framework to account for non-specific microbiome associations with cancer, comorbidities, and demographic and clinical variables, we identified 341 cancer-associated species across five cancer classes that represent the most plausible contributors to cancer pathogenesis. Within cancer classes, we found lower levels of fecal bile acids and C. scindens in early-onset breast cancer and elevated lactate and Veillonella parvula in early-onset colorectal cancer. Additionally, Anaerostipes hadrus encoding dihydropyrimidine dehydrogenase was protective against 5-fluorouracil-induced diarrhea. These findings demonstrate the strength of our cohort and provide a foundational resource for the discovery of cancer-specific microbiome signatures and predictive biomarkers.},
}

@article {pmid42810659,
year = {2026},
author = {Yue, Y and Liu, H and Ma, Z and Cai, L and Liu, Z and Liu, G and Cui, X},
title = {Chlorite-Mediated Regulation of Nitrite Accumulation and Nitrogen Removal in Integrated Partial Denitrification/Anammox Biofilter.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125786},
doi = {10.1016/j.envres.2026.125786},
pmid = {42810659},
issn = {1096-0953},
abstract = {Achieving stable and efficient nitrite accumulation in integrated partial denitrification/anammox (PD/A) processes is typically constrained by substrate competition among microorganisms, posing a significant challenge for large-scale engineering applications. This study proposes a novel strategy for regulating nitrogen transformation pathways using chlorite (ClO2[-]) as a bioregulator, by inducing denitrification to remain at the nitrite stage and thereby providing a stable substrate supply for the anammox process. In the continuous-flow PD/A biofilter, the increase of ClO2[-] concentration from 0 to 1.0 mg/L was associated with an increase in total nitrogen removal efficiency (Re.TN) from 62.74% to a peak value of 85.27%, accompanied by an increase in effluent nitrite accumulation rate (NAR) from 62.24% to 81.77%. [15]N stable isotope tracing further confirmed that the anammox pathway dominated the system, contributing up to 98.9% of the total N2 production and serving as the primary functional support for deep nitrogen removal. The system demonstrated exceptional process robustness across a wide hydraulic retention time (HRT) range of 5-12 h, with Re.TN consistently maintained above 80%. In addition, the system exhibited good conversion capacity for ClO2[-], with the residual concentration in the effluent maintained within the safety limits, thereby reducing the potential risk of secondary pollution. Microbial community analysis indicated that ClO2[-] regulation was associated with changes in the functional microbial community structure, accompanied by increased relative abundances of the core autotrophic anammox bacteria (Candidatus Brocadia and Candidatus Jettenia) and the succession of heterotrophic Thauera populations toward nitrite-producing subgroups. Metagenomic functional profiling revealed that the functional potential of core nitrogen metabolism changed under ClO2[-] regulation, with increased relative abundances of nitrate reduction-related genes (narG/H/I) and decreased relative abundance of the nitrite reduction-related gene (nirS), while the relative abundance of the Anammox-related marker gene hdh increased by 27.5%. This study provides new insights into optimizing the stability of the PD/A system and offers new perspectives for the further engineering application of efficient nitrogen removal processes.},
}

@article {pmid42810665,
year = {2026},
author = {Zhou, X and Chen, W and Zhao, K and Han, X and Fu, J and Chen, S and Yang, S and Yu, X and Zou, L},
title = {Thermophilic Parageobacillus toebii G12 suppresses ARG enrichment during chicken manure composting even with multidrug-resistant plasmid-harboring bacteria as a stressor.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125810},
doi = {10.1016/j.envres.2026.125810},
pmid = {42810665},
issn = {1096-0953},
abstract = {The enrichment of antibiotic resistance genes (ARGs) during composting poses a substantial risk to the safe utilization of chicken manure. However, the role of multidrug-resistant plasmid (MRP)-harboring bacteria in ARG dissemination and microbial succession during composting remains poorly understood. In this study, we investigated the regulatory effects of thermophilic Parageobacillus toebii G12 (G12) on ARG dynamics, as well as its performance under interference from MRP-harboring bacteria. Our results showed that G12 inoculation elevated compost temperature, extended the thermophilic phase, and accelerated maturation. It increased overall ARG removal to 60.9 % and 55.6 % in the conventional and MRP-contaminated systems, respectively, and reduced persistent ARG enrichment by 71.4 % and 66.3 %, respectively. Although MRP-associated stress shifted the suppression preference of G12 from protection-type to alteration/replacement-type persistent ARGs, the strain consistently suppressed efflux- and inactivation-type persistent ARGs. Moreover, G12 markedly reduced the coverage depth of MRPs after composting, thereby alleviating MRP-associated stress. Integrated analyses, including co-occurrence network, Mantel test, partial least squares path modeling, and metagenome-assembled genome approaches, revealed that G12 reshaped the microbial community by suppressing the dominant host Pseudomonadota, thereby reducing its efflux-type persistent ARGs, while directly diminishing integration/excision-type mobile genetic elements to curtail horizontal gene transfer potential. This study elucidates the core mechanisms by which G12 counteracts ARG enrichment and demonstrates its efficacy even under MRP-associated stress, providing a theoretical foundation for mitigating antimicrobial resistance risks in manure composting.},
}

@article {pmid42811263,
year = {2026},
author = {Li, L and DU, L},
title = {[Clinical value of cerebrospinal fluid metagenomic next-generation sequencing in the diagnosis of neonatal intracranial infection].},
journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences},
volume = {55},
number = {7},
pages = {675-682},
doi = {10.3724/zdxbyxb-2025-0965},
pmid = {42811263},
issn = {1008-9292},
mesh = {Humans ; Infant, Newborn ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Female ; Sensitivity and Specificity ; Male ; *Cerebrospinal Fluid/microbiology ; },
abstract = {OBJECTIVES: To investigate the diagnostic performance of cerebrospinal fluid metagenomic next-generation sequencing (mNGS) for neonatal intracranial infections and its value in clinical decision-making.

METHODS: A retrospective observational study was conducted, enrolling neonates admitted to the Children's Hospital, Zhejiang University School of Medicine from 2020 to 2025 with suspected intracranial infection who underwent cerebrospinal fluid mNGS. The sensitivity of mNGS and its concordance with cerebrospinal fluid culture-quantitative polymerase chain reaction (qPCR) were calculated. Clinical impact was evaluated using predefined criteria, and samples were categorized accordingly into positive-impact and no-impact groups to explore independent factors influencing the positive impact of mNGS on clinical decision-making.

RESULTS: Among 61 neonates with suspected intracranial infection, 48 were confirmed. Pathogens were identified in 18 cases, of which 9 were detected exclusively by mNGS, accounting for 50% of etiological diagnoses. The sensitivity of mNGS was 31.3% (95%CI: 18.7%-46.3%), higher than that of cerebrospinal fluid culture-qPCR at 18.8% (95%CI: 8.9%-32.6%), though the difference was not statistically significant (P=0.15). The positive and negative concordance rates between mNGS and cerebrospinal fluid culture-qPCR were 66.7% (95%CI: 29.9%-92.5%) and 76.9% (95%CI: 60.7%-88.9%), respectively. mNGS positively influenced clinical decisions in 23 patients: 12 cases with positive results guided etiological diagnosis and treatment adjustment, while 11 cases with negative results led to antibiotic de-escalation or discontinuation. Multivariate analysis identified a positive mNGS result as an independent factor associated with positive clinical impact (OR=22.127, P<0.01).

CONCLUSIONS: Cerebrospinal fluid mNGS provides positive support in etiological diagnosis and clinical decision-making for neonatal intracranial infection.},
}

Humans
Infant, Newborn
Retrospective Studies
*High-Throughput Nucleotide Sequencing
*Metagenomics
Female
Sensitivity and Specificity
Male
*Cerebrospinal Fluid/microbiology

@article {pmid42811337,
year = {2026},
author = {Detman-Ignatowska, A and Schiro, G and Filip, R and Samborowska, E and Karczmarski, J and Jarmakiewicz-Czaja, S and Jakubowska, K and Williams, A and Hickman, NR and Laubitz, D and Sikora, A},
title = {Fecal microbiota fermenting simple organic carbon substrates in vitro as microbial factories capable of distinguishing Crohn's disease from healthy states.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {42811337},
issn = {1475-2859},
support = {MG-2/21-18//Institute of Biochemistry and Biophysics Polish Academy of Sciences/ ; },
mesh = {Humans ; *Feces/microbiology ; Fermentation ; *Crohn Disease/microbiology/diagnosis ; Lactic Acid/metabolism ; Butyrates/metabolism ; *Gastrointestinal Microbiome ; Acetates/metabolism ; Bacteria/metabolism/classification ; Glucose/metabolism ; },
abstract = {BACKGROUND: Crohn's disease (CD) is characterized by low microbial richness and diversity of the gut microbiome, shifts in the abundance of specific taxa, reduced presence of C2-C6 organic acid producers, especially butyrate-forming bacteria, and alterations in gut metabolites. This study aimed to demonstrate differences in the dynamics and fermentation activity of the fecal microbiota of CD patients and healthy individuals (HIs) grown in vitro on glucose or a mixture of acetate and lactate (fecal microbiota batch cultures). Glucose was used as a substrate for glycolytic fermentation, whereas a mixture of acetate and lactate supported related pathways leading to the production of C2-C6 organic acids, particularly butyrate via the conversion of lactate and acetate.

RESULTS: HI fecal microbiota cultures produced butyrate mainly through lactate and acetate transformation rather than via glucose fermentation. This pathway was impaired in the CD fecal microbiota cultures, which exhibited reduced synthesis of butyrate, valerate, caproate and propionate, and excessive production of ethanol and certain amino acids. These distinct fermentation activities stemmed from differences in the original CD and HI fecal microbiota composition that were further accentuated in batch cultures. The number of beneficial commensal bacteria (e.g., Coprococcus catus, Ruminococcus torques, Gemmiger formicilis, Eubacterium rectale, Fusicatenibacter saccharivoransi, Faecalibacterium prausnitzii) were significantly lower in the CD fecal microbiota cultures and correlated with reduced butyrate, valerate and caproate levels. Conversely, an overabundance of the recognized CD dysbiosis-associated bacteria, such as Escherichia coli, was reflected in elevated ethanol and amino acid levels in post-fermentation liquids. Metabolic potential analysis further indicated an enrichment of genes encoding enzymes involved in ethanol and amino acid biosynthesis in CD fecal microbiota cultures and highlighted the metabolic versatility of E. coli.

CONCLUSIONS: Fermentation patterns of fecal microbiotas in batch cultures can distinguish CD-associated dysbiosis from a healthy microbiome, with particular emphasis on lactate and acetate conversion to butyrate as a key pathway of butyrate production. The differences are observed under standardized in vitro conditions without the need to reconstruct the intestinal environment. These findings, pending further validation, may offer novel diagnostic opportunities and have implications for strategies aimed at restoring a healthy gut microbiome.},
}

Humans
*Feces/microbiology
Fermentation
*Crohn Disease/microbiology/diagnosis
Lactic Acid/metabolism
Butyrates/metabolism
*Gastrointestinal Microbiome
Acetates/metabolism
Bacteria/metabolism/classification
Glucose/metabolism

@article {pmid42811560,
year = {2026},
author = {Wei, CJ and Cheng, ZS},
title = {[Advances in early bedside etiological diagnosis of severe pneumonia].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {49},
number = {10},
pages = {1046-1049},
doi = {10.3760/cma.j.cn112147-20260519-00286},
pmid = {42811560},
issn = {1001-0939},
support = {2026AFC0828//Joint Fund Project of Hubei Provincial Natural Science Foundation for Innovation and Development/ ; },
mesh = {Humans ; *Pneumonia/diagnosis/microbiology ; Early Diagnosis ; *Pneumonia, Bacterial/diagnosis/microbiology ; Point-of-Care Systems ; },
abstract = {The case fatality rate of severe pneumonia remains high, early and accurate etiological diagnosis is a prerequisite for precision antimicrobial therapy. Conventional culture techniques are limited by long turnaround times and low positivity rates. In recent years, novel detection systems such as microbiological rapid on-site evaluation(M-ROSE), point-of-care immunoloassays, multiplex PCR, and metagenomic sequencing have advanced rapidly, markedly shortening the time to pathogen identification. The integration of rapid detection assays for antimicrobial resistance genes has further facilitated precision antimicrobial therapy. Multi-omics analysis integrating the pathogen spectrum with host immune response status helps distinguish colonization from infection, thereby helping prevent antibiotic overuse. This article reviews techniques for pathogen and antimicrobial resistance gene detection together with strategies to distinguish colonization from infection to inform rapid bedside etiological diagnosis in severe pneumonia.},
}

Humans
*Pneumonia/diagnosis/microbiology
Early Diagnosis
*Pneumonia, Bacterial/diagnosis/microbiology
Point-of-Care Systems

@article {pmid42811876,
year = {2026},
author = {Bo, T and Liu, X and Liu, M and Shen, W and Zhang, X and Guo, H and Wen, J},
title = {Winter Caching of Artemisia frigida Is Associated With Host Physiological and Gut Microbial Variation in Brandt's Voles.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70576},
doi = {10.1111/mec.70576},
pmid = {42811876},
issn = {1365-294X},
support = {32470487//National Natural Science Foundation of China/ ; 32201278//National Natural Science Foundation of China/ ; 2023FY100305//Science & Technology Fundamental Resources Investigation Program/ ; 5242016//Natural Science Foundation of Beijing Municipality/ ; },
mesh = {Animals ; *Arvicolinae/physiology/microbiology/genetics ; Seasons ; *Artemisia ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Hypothalamus/metabolism ; Cold Temperature ; Transcriptome ; Lipid Metabolism/genetics ; },
abstract = {Seasonal variation in food resources represents a major ecological challenge for wild herbivores, yet how naturally selected dietary resources become associated with host and microbial responses remains poorly understood. During winter, Brandt's voles (Lasiopodomys brandtii) cache large amounts of Artemisia frigida, suggesting that this plant may have ecological significance beyond its nutritional value. However, the biological basis underlying this seasonal food preference remains unclear. Here, using Brandt's voles as a model system, we investigated whether the naturally selected winter food A. frigida was associated with coordinated variation in host physiology and gut microbial organization under cold conditions. By integrating physiological phenotyping, hypothalamic neuroendocrine analyses, adipose tissue transcriptomics, shotgun metagenomics and metagenomic binning, we characterized host and microbial responses across multiple biological levels. Dietary A. frigida was associated with altered hypothalamic AgRP expression, increased UCP1 expression in BAT and transcriptional changes related to lipid metabolism and thermogenic pathways during cold exposure. Supplement of A. frigida was associated with changes in gut microbial community structure, enrichment of specific bacterial taxa and shifts in predicted microbial functional potential. Genome-resolved analyses further reconstructed 277 non-redundant metagenome-assembled genomes, enabling assessment of microbial ecological variation associated with seasonal food conditions. Together, our findings provide molecular ecological evidence linking winter caching of A. frigida with coordinated variation in host physiology and gut microbial organization, highlighting seasonal dietary resources as an overlooked component of ecological variation in wildlife.},
}

Animals
*Arvicolinae/physiology/microbiology/genetics
Seasons
*Artemisia
*Gastrointestinal Microbiome/genetics
Metagenomics
Hypothalamus/metabolism
Cold Temperature
Transcriptome
Lipid Metabolism/genetics

@article {pmid42812340,
year = {2026},
author = {Nakajima, Y and Kato-Kogoe, N and Yasuda, T and Sakaguchi, S and Kamiya, K and Inubushi, J and Hamada, W and Horiuchi, M and Kudo, A and Tsuda, K and Nakano, T and Tamaki, J and Ueno, T},
title = {Serum antibody titers against Porphyromonas gingivalis are associated with oral and gut microbiota.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1956003},
pmid = {42812340},
issn = {2673-4842},
abstract = {INTRODUCTION: Porphyromonas gingivalis (P. gingivalis) is a keystone pathogen in the oral microbiota and has attracted attention for its association with periodontal as well as systemic diseases. While animal studies have suggested that P. gingivalis affects the gut microbiota and may trigger related pathologies, evidence from human studies remains insufficient. In this study, we aimed to identify characteristics of the oral and gut microbiota associated with serum antibody titers against P. gingivalis, which serve as an indicator of P. gingivalis infection.

METHODS: Serum antibody titers against P. gingivalis were measured in 149 community-dwelling older adults, who were classified by their quartile into high (PgAb_H), medium (PgAb_M), and low (PgAb_L). Simultaneously collected saliva and stool samples were subjected to 16S rRNA metagenomic analysis to compare the bacterial composition of the oral and gut microbiota between the PgAb_H and PgAb_L groups. Using Linear Discriminant Analysis Effect Size (LEfSe), we identified the bacteria whose abundance differed significantly between the groups. The prevalence of bacterial genera commonly present in both the oral and gut microbiota of the same individual was compared between the groups.

RESULTS: Significant differences were observed between the PgAb_H and PgAb_L groups regarding the bacterial composition of the oral microbiota (unweighted UniFrac distance, p = 0.001; weighted UniFrac distance, p = 0.041) and that of the gut microbiota (weighted UniFrac distance, p = 0.045). LEfSe analysis identified several bacterial genera in the oral and gut microbiota whose abundances differed between the two groups. Although the two groups did not differ in the number of bacterial genera shared between the oral and gut microbiota in the same individual, the proportion of individuals possessing Haemophilus in both the oral and gut microbiota was significantly lower in the PgAb_H group than in the PgAb_L group (p = 0.003).

CONCLUSION: This study characterized the oral and gut microbiota profiles associated with serum antibody titers against P. gingivalis. These findings deepen our understanding of how P. gingivalis infection affects the human body beyond the oral cavity, and suggest that serum antibody titers against P. gingivalis could serve as a potentially meaningful indicator for health management.},
}

@article {pmid42813064,
year = {2026},
author = {Lei, X and Zhao, L and Zhong, Z and Lin, H and Xie, Z and Guo, Y and Zhang, S and Zhang, C and Gong, T},
title = {Clinical Characteristics and Machine Learning-Based Severity Classification of Chlamydia psittaci Pneumonia: A Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {622689},
pmid = {42813064},
issn = {1178-6973},
abstract = {BACKGROUND: Chlamydia psittaci infection can cause severe community-acquired pneumonia with significant mortality. Distinguishing severe from non-severe disease remains challenging. This study used clinical data from patients with C. psittaci pneumonia and multiple machine-learning methods to develop a model for severity classification.

METHODS: We retrospectively analyzed 231 hospitalized patients with C. psittaci pneumonia, including 84 severe cases, between January 2022 and April 2025 in Jiangxi Province, China. Severe pneumonia was defined according to the IDSA/ATS and Chinese adult community-acquired pneumonia criteria. The model outcome was the composite clinical label of severe versus non-severe pneumonia rather than mortality. A comprehensive machine-learning framework incorporating 11 algorithms and six feature-selection strategies was used to develop the severity-classification model.

RESULTS: C. psittaci pneumonia cases were sporadic and widely distributed across Jiangxi Province. Elderly patients, especially those with cardiovascular disease or diabetes, had an increased risk of severe illness. Laboratory tests in severe cases showed higher neutrophils, D-dimer, CRP, PCT, IL-6, IL-8, and IL-10, with lower lymphocytes, NK cells, albumin, and serum calcium. CT commonly showed large patchy opacities in the lower lung lobes. Additional microorganisms were co-detected by mNGS in 74.03% of patients. In the internal hold-out test set (n = 69), the RF+SVM model achieved an area under the receiver operating characteristic curve (AUC) of 0.845 (95% CI, 0.754-0.935) for distinguishing severe from non-severe pneumonia. The final RF+SVM severity-classification model incorporated nine laboratory predictors.

CONCLUSION: This study identified key clinical and laboratory differences between non-severe and severe C. psittaci pneumonia and developed a predictive model using comprehensive machine learning approaches. The model may support admission-based severity stratification and identify patients who may warrant closer monitoring. This is a single-center retrospective study, and the model needs further validation in prospective multicenter cohorts.},
}

@article {pmid42813505,
year = {2026},
author = {Huang, S and Sun, S and Zhao, Z and Gao, D and Zhang, W and Zhou, N and Jin, Y and Jin, B and Sun, D},
title = {Associations of Gut Microbiota Composition and Fecal Metabolomic Profiles in Patients With Acquired Premature Ejaculation: A Cross-Sectional Pilot Study.},
journal = {American journal of men's health},
volume = {20},
number = {5},
pages = {15579883261493263},
doi = {10.1177/15579883261493263},
pmid = {42813505},
issn = {1557-9891},
mesh = {Humans ; Male ; Pilot Projects ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Premature Ejaculation/microbiology/metabolism ; Metabolomics ; Case-Control Studies ; *Metabolome ; },
abstract = {Premature ejaculation (PE) is a prevalent male sexual disorder with an incompletely understood pathogenesis and limited effective therapeutic strategies. Although the gut microbiota has been implicated in several diseases, its association with PE remains unclear. Metabolomic analyses and metagenomic sequencing were performed to compare the intestinal microbiota profiles between 20 patients with PE and 20 healthy controls, investigating the association between PE and gut microbiota. Comprehensive analysis revealed distinct microbial signatures between PE and control groups. The PE group exhibited significantly reduced relative abundances of Bifidobacteriaceae bacterium, Blautia, Coprobacillus, Ruminococcus sp. ctHOG1, Siphoviridae, and Alistipes. Metabolomic profiling identified 150 upregulated and 73 downregulated metabolites between the two groups. Kyoto encyclopedia of genes and genomes pathway enrichment analysis indicated significant enrichment of several potential signaling pathways in the PE group. This study characterized distinct gut microbiota features in patients with PE compared with healthy controls and investigated microbiota-associated pathways potentially related to PE through integrated metabolomics analysis. The findings provide preliminary insights into microbiome-associated alterations in PE.},
}

Humans
Male
Pilot Projects
Adult
*Feces/microbiology/chemistry
Cross-Sectional Studies
*Gastrointestinal Microbiome
*Premature Ejaculation/microbiology/metabolism
Metabolomics
Case-Control Studies
*Metabolome

@article {pmid42813801,
year = {2026},
author = {Xu, J and Fan, Y and Qu, G and Li, J and Peng, Y and Wang, M and Zhang, J and Feng, Y and Liu, X and Hu, Y and Kan, B and Li, Z and Zeng, M and Lu, X},
title = {Comparative gut microbiome in diarrheal and non-diarrheal children: an individually matched case-control study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019826},
doi = {10.1128/msystems.00198-26},
pmid = {42813801},
issn = {2379-5077},
abstract = {Diarrhea, a leading cause of under-five mortality in developing countries, drives therapeutic challenges amid global antibiotic resistance. This study aimed to compare gut microbiota, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) in diarrheal and non-diarrheal children, explore reasons for asymptomatic pathogen carriage, and develop a microbiome-based model to predict the potential etiology of diarrhea. This individually matched case-control study analyzed 42 paired fecal samples (selected from 716 diarrhea/non-diarrhea cases) to compare gut microbiome profiles, ARGs, MGEs, and VFs using metagenomic sequencing and pathogen-specific PCR. Diarrheal children showed reduced alpha diversity, increased Proteobacteria, and elevated VFs and MGEs. Surprisingly, ARGs were more abundant in non-diarrheal children, suggesting ARG colonization in healthy hosts. Actinomyces was enriched in non-diarrheal pathogen carriers and may be associated with asymptomatic bacterial pathogen carriage. A random forest (RF) model incorporating non-pathogenic bacteria achieved high accuracy in predicting diarrheal status and pathogen carriage. This study reveals distinct microbial ecologies between diarrheal and healthy children. The enrichment of specific bacterial taxa in asymptomatic carriers may be associated with pathogen tolerance. The unexpected ARG abundance in healthy children highlights a hidden antimicrobial resistance reservoir. These findings inform microbiome-based diagnostics and antibiotic stewardship in pediatric diarrhea.IMPORTANCEThis study is significant because it provides robust, individually matched case-control evidence linking childhood diarrhea to gut microbiome dysbiosis and the distribution of pathogenic and resistance-related genetic elements. By integrating metagenomic sequencing with pathogen-specific polymerase chain reaction (PCR), it offers a comprehensive comparison of microbial composition, virulence factors (VFs), mobile genetic elements (MHEs), and antibiotic resistance genes (ARGs) between diarrheal and non-diarrheal children. The findings demonstrate reduced microbial diversity and enrichment of Proteobacteria, virulence factors, and mobile genetic elements in diarrheal cases, highlighting microbiome instability during infection. Importantly, the unexpectedly higher abundance of antibiotic resistance genes in non-diarrheal children underscores the underestimated role of healthy populations as reservoirs of resistance. Furthermore, the establishment of predictive models for diarrhea status and pathogen carriage enhances the translational value of the study. Overall, this work advances the understanding of pediatric diarrheal disease and informs prevention, surveillance, and treatment strategies in the context of global antimicrobial resistance.},
}

@article {pmid42813975,
year = {2026},
author = {Aitolo, GL and Rambo, IM and Weisend, RE and Mullis, MM and Tringe, S and Kosmopoulos, JC and Anantharaman, K and Kiel Reese, B and Baker, BJ and De Anda, V},
title = {Shifts in vegetation impact estuary microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0107126},
doi = {10.1128/msystems.01071-26},
pmid = {42813975},
issn = {2379-5077},
abstract = {Coastal wetlands, including mangrove-cordgrass mosaics, are among Earth's most effective carbon stores sequestering >1 Pg C/year. Rapid sea level rise, warming, and storm intensification are now reshaping these habitats. Vegetation type influences root exudates, sediment redox profiles, and organic matter quality. However, the impacts of vegetation on microbe-virus networks that mediate carbon burial and nutrient cycling remain unclear. Here, we sampled coastal sediment profiles in patches of cordgrass (dominated by Sporobolus alterniflorus), black mangrove (Avicennia germinans), and seagrass on the Texas Gulf Coast. We obtained 491 bacterial and archaeal metagenome assembled genomes (MAGs) and 1,097 viral MAGs (vMAGs) from 55 surface sediment samples spanning day and night during summer and fall. Phylogenetic and comparative analyses revealed dominant lineages across the distinct vegetation types, organized into metabolic guilds based on similar protein compositions, revealing contrasting and complementary sulfur, iron, and nitrogen cycling pathways that regulate greenhouse gas emissions and encode genes important for carbon metabolism. Inference from virus-host linkages revealed that dominant lineages were infected, and viral communities have genes for organic carbon degradation, potentially shaping the microbial community dynamics in this ecosystem. This spatio-temporal characterization of estuary ecotone microbiomes provides a framework to better understand the diversity and metabolism of these productive coastal ecosystems.IMPORTANCECoastal wetlands are among the most effective environments for storing carbon and regulating climate. As sea level rise and changing weather patterns drive shifts in coastal vegetation, these vulnerable ecosystems are undergoing rapid transformation. Yet, little is known about the microbes that regulate carbon storage and nutrient cycling. Here, we characterized microbial and viral communities associated with coastal wetland sediments along the Texas Gulf Coast. We identified key microbial groups responsible for key carbon, sulfur, nitrogen, and iron cycling and showed that vegetation type influences their distribution and ecological roles. We also found that viruses interact with dominant microbial groups and carry genes linked to carbon processing, suggesting an important role in shaping ecosystem function. These findings provide insights into the mechanisms that sustain coastal wetlands and help predict how shifts in vegetation may affect nutrient cycling and ecosystem resilience in the future.},
}

@article {pmid42814154,
year = {2026},
author = {Sivarajan, D and Pothayi, V and Devasia, SC and Ramachandran, B},
title = {Photoperiod driven modulation of behavior, gut microbiota, and brain transcriptomics in zebrafish.},
journal = {Pflugers Archiv : European journal of physiology},
volume = {478},
number = {10},
pages = {},
pmid = {42814154},
issn = {1432-2013},
support = {CSIR-UGC-JRF-905/2018//CSIR-UGC/ ; ECR/2018/002479//DST-SERB/ ; },
mesh = {Animals ; *Zebrafish/physiology ; *Brain/metabolism/physiology ; *Photoperiod ; *Gastrointestinal Microbiome/physiology ; *Transcriptome ; Circadian Rhythm/physiology ; *Behavior, Animal/physiology ; },
abstract = {Circadian rhythms regulate physiological and behavioural processes, with the light-dark cycle acting as the principal environmental cue synchronising the biological clock; disruption of this cue can affect brain function and behaviour. Using zebrafish (Danio rerio) as a translational model, we examined how chronic photoperiod alteration, applied from the larval stage to adulthood, affects exploratory activity, anxiety-like behaviour, aggression, and social preference, and whether these changes are paralleled by shifts in gut microbiota composition and brain transcriptomic profile. Zebrafish were reared under three photoperiod regimes: 14L/10D (control), 20L/4D (extended light), and 4L/20D (extended dark), followed by behavioural, gut metagenomic, and brain transcriptomic analyses. Extended darkness (4L/20D) reduced anxiety-like behaviour, whereas extended light (20L/4D) increased aggression both extended photoperiods altered social behaviour, but with distinct behavioural profiles. Gut microbiota in the 20L/4D group showed phylum-level co-dominance of Actinomycetota and Pseudomonadota, including a greater presence of potentially pathogenic taxa, while the 4L/20D group was dominated by Bacillota. Brain transcriptome profiling, based on a single pooled sample per condition, identified transcripts showing the largest expression differences in each group: in 20L/4D, transcripts linked to phototransduction (gnat1, saga, pde6ga, exorh), ribosomal function (rpl13a, rpl9, knop1), melatonin synthesis (asmt), calcium signalling (plcb4a), and glycolysis (eno1a) were elevated; in 4L/20D, transcripts linked to neuroprotection (nr4a1), DNA repair and chromatin remodelling (fance, uimc1, histh1l), synaptic plasticity (serpina10a), neurodevelopment (six6a), and cell-cycle regulation (btg2) were elevated. These findings indicate that photoperiod shapes zebrafish behaviour, gut microbial composition, and brain gene expression, providing a hypothesis-generating basis for future studies incorporating biological replication.},
}

Animals
*Zebrafish/physiology
*Brain/metabolism/physiology
*Photoperiod
*Gastrointestinal Microbiome/physiology
*Transcriptome
Circadian Rhythm/physiology
*Behavior, Animal/physiology

@article {pmid42814861,
year = {2026},
author = {Pareek, S and Wright, RD and Ballarò, R and Xue, C and Bartelli, TF and Chandra, V and Li, L and Ortiz, J and Lam, T and Patel, H and Lee, J and Shrestha, P and Savage, H and Le Roux, O and Liu, H and Vallejo-Schmidt, T and De Maleki, R and Putluri, V and Putluri, N and Petrosino, JF and Burks, JK and Gomez, JA and Guarnerio, J and Katz, MHG and Ngo-Huang, A and Prakash, LR and Parker, NH and Petzel, MQB and Tan, L and Baydogan, S and McAllister, F and Schadler, KL},
title = {Exercise Modulates Microbial Metabolites and Induces Stromal Remodeling in Pancreatic Cancer.},
journal = {Cancer research},
volume = {},
number = {},
pages = {OF1-OF17},
doi = {10.1158/0008-5472.CAN-25-5143},
pmid = {42814861},
issn = {1538-7445},
support = {1R37CA237384//National Cancer Institute (NCI)/ ; 1R01CA282786//National Cancer Institute (NCI)/ ; RP190256//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP200173//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP210227//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; 13723124//U.S. Department of War (DOW)/ ; P30CA125123//National Cancer Institute (NCI)/ ; },
abstract = {UNLABELLED: Exercise induces a variety of changes in the tumor microenvironment, with beneficial effects in several tumor types. However, a better understanding of the clinical effects of exercise and mediating mechanisms is needed to maximize the utility of exercise for patients. In this study, we analyzed tumors from patients with pancreatic ductal adenocarcinoma (PDAC) in the PancFit trial and identified an exercise-induced reduction in cells expressing α-smooth muscle actin (αSMA). Interrogation of changes in tumor stromal composition with exercise in a murine PDAC model revealed a microbially influenced reduction in αSMA+ cells and Il6-expressing inflammatory cancer-associated fibroblasts (iCAF). Cholic acid, a microbial bile acid, was increased in both patients and murine models with exercise, as a potential mediator of exercise-induced reduction in iCAFs. Consistent with these findings, patients that exercised more also exhibited fewer iCAFs and lower tumor IL6 expression, supporting a stromal remodeling effect of physical activity. In summary, this study demonstrates that the antitumor effect of exercise includes stromal remodeling, which is affected by microbial metabolites.

SIGNIFICANCE: Exercise-induced changes in cancer associated fibroblasts vary with microbiome composition, which may explain the heterogeneity in tumor responses to exercise and could guide future exercise trials in cancer patients.},
}

@article {pmid42815123,
year = {2026},
author = {Sun, Y and He, W and Yin, G and Wan, J and Yi, C and Ke, J and Shen, W and Zhang, M and Guo, R and Liu, Y and Shang, J and Chen, J and Liao, Q},
title = {Effects and mechanisms of sustained-release embedded composite biochar in carbon enhancement and acid reduction of acidified black soil.},
journal = {Journal of environmental management},
volume = {418},
number = {},
pages = {131051},
doi = {10.1016/j.jenvman.2026.131051},
pmid = {42815123},
issn = {1095-8630},
abstract = {Black soils in Northeast China are undergoing acidification and organic matter degradation, and are in urgent need of efficient and environmentally sustainable improvement technologies. In this study, a novel sustained-release embedded composite biochar material was fabricated through a ball-milling integration process, in which biochar, reduced iron powder, and polymer materials were combined. A systematic screening process was established through the optimization of biochar substrate preparation conditions, the selection of functional loading components, and the development of a sustained-release carrier process. Through physicochemical characterization and evaluation of environmental effects, Chitosan-Fe-Biochar(CS-Fe-BC) and Polyacrylamide-Fe-Biochar(PAM-Fe-BC) were ultimately identified as the optimal materials. A 180-day incubation experiment was conducted under simulated climate conditions representative of Northeast China. Within 180 days, the application of 5‰ CS-Fe-BC[5] increased soil pH by approximately 0.5 units and enhanced SOC content by about 26.88%.The application of different material treatments effectively improved the structural integrity of the soil carbon pool, leading to significant increases in POC, ROC, andMOC contents. The metagenomic sequencing results revealed that, while maintaining overall abundance stability, the composite material reshaped the soil microbial community structure, facilitated the enrichment of functional bacteria involved in carbon fixation and acid mitigation, and achieved carbon enhancement and acid reduction through differentiated metabolic pathways. These findings suggest that the material plays a pivotal role in driving the processes of carbon accumulation and acid mitigation.The research findings may offer novel materialand theoretical support for the sustainable management of black soil acidification in Northeast China.},
}

@article {pmid42815128,
year = {2026},
author = {Wang, W and Sun, J and Wang, Z and Su, Y and Zhan, M and Hong, S and Xie, B},
title = {Enzymatic valorization of food waste leachate into volatile fatty acid-rich carbon source for enhanced denitrification.},
journal = {Journal of environmental management},
volume = {418},
number = {},
pages = {131041},
doi = {10.1016/j.jenvman.2026.131041},
pmid = {42815128},
issn = {1095-8630},
abstract = {Food waste leachate (FWL) is a high-strength organic waste stream that poses increasing disposal and resource recovery challenges. This study developed an integrated enzymatic fermentation strategy to convert FWL into a volatile fatty acid (VFA)-rich carbon source for wastewater denitrification. Screening of ultrasonic, alkaline, alkaline-thermal, and enzymatic pretreatments identified the combined amylase-protease treatment as the most effective for FWL solubilization, increasing SCOD by 23.4% and promoting the release of biodegradable organic matter. During semi-continuous thermophilic anaerobic fermentation (55 ± 2°C, HRT 3 d), the enzymatically pretreated FWL showed enhanced VFAs production compared with the untreated system, with acetate and butyrate as the dominant products. The fermentation broth derived from enzyme-pretreated FWL achieved 99.5% NO3[-]-N removal within 8 h and showed nitrate-removal performance comparable to commercial sodium acetate. Metagenomic analysis indicated that enzymatic pretreatment enriched hydrolytic and acidogenic microorganisms associated with VFAs production, particularly Sporanaerobacteraceae and Tepidanaerobacter, while the VFA-rich fermentation broth promoted the enrichment of denitrifying bacteria such as Thauera and Paracoccus. Moreover, economic analysis shows that using FWL-derived fermentation carbon sources can reduce the estimated annual external carbon source cost by 34.4% compared to sodium acetate. These findings demonstrate a feasible waste-to-resource pathway for recovering intrinsic organic carbon from FWL as an alternative carbon source for wastewater denitrification.},
}

@article {pmid42815131,
year = {2026},
author = {Mu, X and Bi, J and Yu, Q and Han, Q and Wang, X and Li, H},
title = {Urban parks as potential hotspots for pathogenic determinants: A One Health perspective on environmental-human transmission risks.},
journal = {Journal of environmental management},
volume = {418},
number = {},
pages = {131067},
doi = {10.1016/j.jenvman.2026.131067},
pmid = {42815131},
issn = {1095-8630},
abstract = {Urban parks are vital public spaces, yet their role as potential reservoirs and transmission pathways for pathogenic bacteria under the "One Health" framework remains poorly understood. We gathered paired soil, water, and human fecal samples from nine parks in Lanzhou, China. Metagenomic and 16S rRNA sequencing revealed abundant pathogenic bacteria, virulence factor (VF) genes, and pathogen-host interaction (PHI) genes. Pathogenic bacteria were significantly more abundant in water than in soil, and their presence was positively correlated with key environmental nutrients (TC, TN, TP, TS). Immune modulation and motility genes dominated the VF repertoire, while PHI genes primarily mediated virulence attenuation, maintenance, or enhancement. Crucially, the profile of these virulence genes was significantly shaped by the native bacterial community and mobile genetic elements (MGEs). Metagenomic binning provided direct genomic evidence that MGEs frequently co-localize with VF and PHI genes, demonstrating a high potential for horizontal gene transfer from park environments to humans. Our findings highlight urban parks as significant environmental reservoirs for pathogenic determinants and delineate the ecological and genetic drivers of their dissemination, providing a critical basis for targeted environmental management and public health protection.},
}

@article {pmid42410522,
year = {2026},
author = {Wu, S and Wang, K and Ge, X and Yuan, S and Wu, DD and Ge, C and Jia, J and Su, Z and Dou, T},
title = {Comparative and population genomics analyses of eared pheasants inhabiting highly varying altitudes.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42410522},
issn = {1471-2164},
mesh = {Animals ; *Altitude ; *Galliformes/genetics ; *Genetics, Population ; *Genomics ; Selection, Genetic ; Adaptation, Physiological/genetics ; Genetic Variation ; *Metagenomics ; },
abstract = {BACKGROUND: Oxygen pressure varies dramatically with altitudes on Earth; however, humans and animals thrive at almost all altitudes.

RESULTS: To better understand genetic basis underlying adaptation of closely related species to varying altitudes, we annotated and compared the genome of a white eared pheasant (WT) (Crossoptilon crossoptilon) inhabiting high altitudes and the genome of a brown eared pheasant (BR) (C. mantchuricum) inhabiting low altitudes. Moreover, we compared genetic variations in populations of WT and BR as well as of blue eared pheasants (BL) (C. auritum) inhabiting intermediate altitudes, and identified thousands of selective sweeps in each species.

CONCLUSIONS: Intriguingly, the unique genes and pseudogenes in the genomes of WT and BR converge on the same set of altitude adaptation-related pathways of four functional categories as genes in selective sweeps in each species. Thus, these species appear to adapt to highly varying altitudes by diverging selection on the same traits via loss-of-function mutations and fine-tuning genes in common pathways.},
}

Animals
*Altitude
*Galliformes/genetics
*Genetics, Population
*Genomics
Selection, Genetic
Adaptation, Physiological/genetics
Genetic Variation
*Metagenomics

@article {pmid42805094,
year = {2026},
author = {Schoier, AF and de Castro, ÍMS and Dorn, M},
title = {Foundation models and taxonomy inference for metagenomics: A practical review.},
journal = {Computational biology and chemistry},
volume = {126},
number = {Pt 1},
pages = {109409},
doi = {10.1016/j.compbiolchem.2026.109409},
pmid = {42805094},
issn = {1476-928X},
abstract = {Taxonomic classification in metagenomics remains anchored in alignment-based methods and exact k-mer indexers, which provide calibrated, traceable species-level assignments at scale when reference coverage is comprehensive. This review synthesizes the progression of the field toward self-supervised, DNA-specific foundation models, clarifying where they add value and how they should be evaluated. We report a structured literature search with explicit inclusion and exclusion criteria, and then critically compare families of approaches along two axes of practical relevance: reference coverage (in-index versus open-set) and read context and quality (short and accurate versus long and noisy). Across the evidence base, classical k-mer pipelines remain preferable for routine, high-throughput species-level assignment on well-covered clades, whereas the gains reported for foundation models at the read level are mixed and highly sensitive to evaluation design. The most plausible benefits arise under conditions of novelty, for long or noisy sequences, or when a calibrated back-off to higher taxonomic ranks is acceptable; embeddings can also support sample-level augmentation and quality control. Because pretraining and long-context inference impose substantial GPU and memory requirements, practical deployments favor hybrid designs: fast, reference-based classification for the bulk of reads, combined with compact, parameter-efficient adapters or selective embedding to rescore ambiguous cases and flag off-index content. We conclude with a roadmap that emphasizes standardized open-set benchmarks, joint reporting of accuracy and computational cost, and lightweight adaptation techniques that bring foundation-model components within reach of resource-constrained laboratories.},
}

@article {pmid42805174,
year = {2026},
author = {Perl, M and Guetter, S and Shah, D and Holzinger, S and Becker, L and Tariq, M and Menauer, P and Delahais, S and Lutzny-Geier, G and Scherer, JN and Göttert, S and Herfeld, K and Heinrich, P and Kreitmeier, KG and Gebhard, C and Herr, W and Trefny, MP and Doerr, J and Sameri, S and Harrer, DC and Ziegler-Martin, K and Staudt, S and Hansmann, L and Edinger, M and Wolff, D and Weber, D and Meedt, E and Denk, A and Gessner, A and Holler, E and Wertheimer, T and Neuhaus, K and Zheng, T and Cordas Dos Santos, DM and Theurich, S and Schirmer, M and Kleigrewe, K and Schluter, J and van den Brink, M and Schmitt, M and Feuerer, M and Heuser-Loy, C and Baldwin, J and Gattinoni, L and Rehli, M and Hudecek, M and Bigenwald, C and Zitvogel, L and Subklewe, M and Blumenberg, V and Schubert, ML and Stein-Thoeringer, C and Luu, M and Kobold, S and Fante, MA and Thiele Orberg, E and Poeck, H},
title = {Opposing functions of gut immunomodulatory metabolites on CAR-T therapy.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.09.004},
pmid = {42805174},
issn = {1097-4172},
abstract = {Chimeric antigen receptor (CAR)-T cell therapy has transformed hematological cancer treatment, yet nearly half of patients still relapse or progress. Increasing evidence implicates the gut microbiome and antibiotic exposure as key modulators of clinical outcomes. In a cohort of 129 patients across three German centers, shotgun metagenomics and targeted mass spectrometry revealed that reduced short-chain fatty acids, particularly valeric acid, prior to CAR-T cell therapy correlated with increased risk of disease progression. Conversely, high levels of indole metabolites, including indole-3-carboxaldehyde and indole-3-acetic acid as well as the branched-chain fatty acid isovaleric acid, were linked to adverse outcomes. Functional validation in human and murine CAR-T cell models demonstrated that valeric acid supplementation enhanced, while indole-3-carboxaldehyde and isovaleric acid impaired, CAR-T cell efficacy. These findings reveal the opposing roles of immunomodulatory metabolites on CAR-T cell therapy, carrying significant implications for the design of metabolite-guided, microbiome-based therapeutics.},
}

@article {pmid42805386,
year = {2026},
author = {Hang, G and Sun, J and Kwok, LY and Gao, G and Li, W},
title = {An exploratory dual-platform metabolomics reveals region- and milk source-associated signatures in commercial cheeses.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-29087},
pmid = {42805386},
issn = {1525-3198},
abstract = {Commercial cheeses exhibit distinct compositional profiles shaped by milk substrate, production practices, and geographical terroir. However, the relative contribution of geographic origin versus milk source to cheese metabolomes remains poorly quantified, particularly in unstandardized commercial products. This exploratory study investigated region-associated metabolic signatures in commercially available cheeses, with a focus on comparing the relative contributions of geographic origin and milk source to metabolomic variance. We applied complementary volatile (HS-SPME-GC-MS) and non-volatile (UHPLC-MS/MS) metabolomic profiling to 32 commercial cheeses from Hungary (n = 11) and 3 Australian regions (Queensland, New South Wales, Victoria; n = 21), representing cow (n = 24) and goat/sheep (n = 8) milk sources. Multivariate ANOVA and random forest analyses revealed pronounced metabolic separation by geographic origin, which accounted for a substantially larger proportion of variance than milk source. Hungarian cheeses were enriched in citrate-derived flavor compounds (e.g., 2,3-butanedione, 2,3-butanediol), while Australian samples exhibited elevated lipid oxidation and branched-chain amino acid catabolites. Non-volatile profiles further highlighted regional differences in fatty acid composition and dipeptide abundance, with phenylalanine metabolism emerging as a consistent discriminant pathway. Correlation-based association networks revealed interconnected volatile and non-volatile metabolic modules. Since cheese variety, ripening protocols, and starter cultures were uncontrolled, observed patterns reflect region-associated metabolic signatures rather than causal terroir effects. These findings provide a preliminary metabolomic landscape for authenticity tracing and hypothesis-driven fermentation research. Future controlled trials integrating metagenomics and standardized production parameters are needed to isolate the specific contributions of geography, milk substrate, and processing technology.},
}

@article {pmid42805416,
year = {2026},
author = {Jiang, L and Li, J and Wang, H and Xie, R and Zhang, L},
title = {Single-stage autotrophic removal of thiocyanate and nitrogen from high-strength thiocyanate wastewater: start-up, performance, and metabolic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135971},
doi = {10.1016/j.biortech.2026.135971},
pmid = {42805416},
issn = {1873-2976},
abstract = {A single-stage partial nitrification and thiocyanate-driven denitrification (SPN-TDN) process offers a promising and resource-efficient route for simultaneous thiocyanate and nitrogen removal from high-strength thiocyanate (SCN[-]) wastewater. However, reliable start-up remains challenging because the establishment of this process requires coordination under contrasting oxygen and substrate conditions. Here, a sequencing batch reactor was operated for 384 cycles using a staged enrichment-optimization strategy to investigate how the synergistic process became established under increasing SCN[-] loading. During enrichment, SCN[-] removal remained above 98 %, partial nitrification was established, but total nitrogen (TN) removal stayed limited. In the optimization phase, TN removal progressively increased to 40 %, accompanied by biogenic elemental sulfur accumulation. Ex-situ batch tests confirmed SCN[-]-driven autotrophic denitrification, achieving 49 % TN removal with a nitrite/SCN[-] consumption ratio of 0.38. Community profiling showed that phase I established the dominant Thiobacillus (0.2 % to 23.0 %) and Nitrosomonas (0.99 % to 2.46 %), with the normalized stochasticity ratio indicating a greater deterministic contribution at both genus and species levels. Phase II largely retained this genus-level framework while exhibiting taxonomic-scale-dependent assembly and lineage-level turnover. Genome-resolved metagenomics further showed increased representation of cyanate-pathway lineages, a corresponding decline in the carbonyl sulfide-pathway lineages, and lineage-level turnover within ammonia-oxidizing bacteria. Collectively, successful process establishment involved multiple functional pathways during enrichment and subsequent pathway- and lineage-level reorganization under intensified constraints. These findings provide a mechanistic basis for understanding and further optimizing staged start-up of single-stage SPN-TDN for high-strength SCN[-] wastewater treatment.},
}

@article {pmid42805474,
year = {2026},
author = {Du, S and Shi, Y and Tong, C and Qi, X and Wen, H and Ji, B},
title = {Ferric iron enhances granule densification and pollutant removal in microalgal-bacterial granular sludge via iron-homeostatic microbial rewiring.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125791},
doi = {10.1016/j.envres.2026.125791},
pmid = {42805474},
issn = {1096-0953},
abstract = {Microalgal-bacterial granular sludge (MBGS) is a promising low-energy wastewater treatment technology, but the role of Fe[3+] concentration in regulating its structure and function remains unclear. MBGS was cultivated under four Fe[3+] concentrations (0.1, 1, 3, and 5 mg/L). At 5 mg/L Fe[3+], granules became more compact, with SVI5 decreasing from 80.0 to 60.1 mL/g and average size increasing from 1.72 to 1.90 mm. These changes were accompanied by enhanced extracellular polymeric substances (EPS) hydrophobicity despite reduced EPS production. The 5 mg/L treatment also increased dark-cycle COD and PO4[3-]-P removal, while NH4[+]-N removal remained unchanged. At 5 mg/L Fe[3+], Thauera and iron-associated Rubrivivax formed a synergistic consortium, supporting the superior dark-cycle pollutant removal. Metagenomic analysis revealed limited variation in C/N/P metabolic genes but strong iron-related regulation, with fur decreasing by 40.4% at 5 mg/L relative to the initial inoculum, suggesting a community shift toward iron-homeostatic configuration rather than a stress response. Four MAGs (Thauera mechernichensis MAG43, Rubrivivax sp. MAG118 and MAG36, and Microcoleus sp. MAG30) showed distinct C/N/P/Fe gene distributions, reflecting functional differentiation among community members. These findings provide a mechanistic basis for optimizing iron supplementation strategies to enhance the stability and performance of MBGS in practical applications.},
}

@article {pmid42805588,
year = {2026},
author = {Metris, A and Guan, R and Ampatzoglou, A and Murphy, B},
title = {Methods to Address Compositional Data Challenges in Clinical Studies for the Safety Assessment of Human Microbiome Perturbations.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100933},
doi = {10.1016/j.jfp.2026.100933},
pmid = {42805588},
issn = {1944-9097},
abstract = {Advances in sequencing technologies have enabled increasingly detailed characterisation of the human microbiome in clinical studies, but interpretation of microbiome modulation which has relevance to health and disease characterisation or safety assessments remains methodologically challenging. Taxonomic profiles generated by amplicon or shotgun sequencing are inherently compositional, sparse, and limited by detection, which complicates differential abundance analysis and may lead to unstable or misleading conclusions, especially in low-biomass settings where contamination and under-detection are concerns. Here, we review strategies used to analyse and complement sequencing-derived taxonomic count data, with the aim of obtaining more quantitative information on microbial differential abundance and viability. These include transformations for relative-abundance-based analyses and bias corrections between samples based on mathematical assumptions or additional experimental measurements such as spike-ins, broad-range qPCR and flow cytometry. We find that there is no consensus on which method best addresses compositionality and that detection level and significance of low-level microbes in health and diseases are overlooked. We discuss the limitations of sequence-based methods, such as the biases induced by the experimental and analytical process, as well as viability measurements for meaningful differential abundance assessment. We illustrate the need to integrate prevalence as well as abundance and the importance of covariates in models in the case of bacterial vaginosis. Overall, meaningful assessment of microbiome perturbations requires not only statistical correctness of differential abundance analysis, but also careful study design, appropriate measurement choices, quantitative context, and explicit recognition of the biological and analytical limits of sequencing-derived data.},
}

@article {pmid42805970,
year = {2026},
author = {Wu, Y and Su, Z and Zhang, B and Zhou, F and Xi, R and Peng, X and Li, Y and Yue, L and Wang, X and Chen, F and Lu, Y and Zhou, X and Ren, B and Li, J},
title = {Spatially resolved single cell atlas deciphers SAA1 inflammatory epithelial cells.},
journal = {International journal of oral science},
volume = {18},
number = {1},
pages = {},
pmid = {42805970},
issn = {2049-3169},
support = {81991501//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170949//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024NSFSC1584//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2025ZNSFSC1910//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; },
mesh = {Humans ; *Epithelial Cells/metabolism ; *Serum Amyloid A Protein/metabolism ; Porphyromonas gingivalis ; *Inflammation/metabolism ; Transcription Factors/metabolism ; Cell Differentiation ; Periodontitis ; Single-Cell Analysis ; Gingiva/metabolism ; },
abstract = {Disruption of epithelial integrity is a pivotal event in inflammation, disease pathogenesis, and tissue homeostasis. To investigate these processes in chronic inflammatory disease, we performed spatial transcriptomics integrated with single-cell RNA sequencing (scRNA-seq) on human gingival tissue, coupled with metagenomic analysis of matched subgingival plaque. This approach allowed in situ characterization of epithelial heterogeneity and microbiome-epithelium-connective tissue crosstalk. We identified a distinct inflammatory epithelial subpopulation (SAA1+Epi), situated within the junctional epithelium, that becomes activated through the TLR2-PITX2 axis by Porphyromonas gingivalis lipopolysaccharide. These SAA1+Epi cells secrete TGFβ, which induces an inflammatory program in the connective tissue by driving the differentiation of inflammation-associated fibroblasts (C3+FB) via the PI3K/Akt pathway. Concurrently, SAA1+Epi cells express chemotactic factors such as CXCL6 to recruit NK cells, thereby sustaining the inflammatory niche. The transcription factor PITX2 emerged as a critical regulator of SAA1+Epi differentiation; targeting PITX2 suppressed C3+FB induction and natural killer (NK) cells recruitment, ultimately attenuating periodontitis progression. Our findings position SAA1+Epi as a frontline responder to dysbiotic bacteria at the inflammatory interface and underscore its essential role in regulating epithelial-connective tissue homeostasis during inflammation.},
}

Humans
*Epithelial Cells/metabolism
*Serum Amyloid A Protein/metabolism
Porphyromonas gingivalis
*Inflammation/metabolism
Transcription Factors/metabolism
Cell Differentiation
Periodontitis
Single-Cell Analysis
Gingiva/metabolism

@article {pmid42805991,
year = {2026},
author = {Minch, B and Moniruzzaman, M},
title = {Widespread genomic islands are hotspots of genome variations and mosaicism in giant viruses.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42805991},
issn = {2041-1723},
support = {OCE-2346438//National Science Foundation (NSF)/ ; },
mesh = {*Genomic Islands/genetics ; *Genome, Viral/genetics ; *Giant Viruses/genetics ; *Mosaicism ; *Genetic Variation ; Evolution, Molecular ; Phylogeny ; Metagenome ; },
abstract = {Giant viruses in the phylum Nucleocytoviricota possess exceptionally large and mosaic genomes, yet the mechanisms underlying their remarkable plasticity remain poorly understood. Genomic islands are dynamic genomic regions that are major drivers of diversification and adaptation in bacteria. However, their contribution to giant virus evolution remains largely unexplored. Here, we characterize the genomic island landscape of giant viruses using 369 high-quality genomes spanning cultured isolates and long-read metagenome-assembled genomes. We identify 307 genomic islands across >50% of the genomes, demonstrating that these regions are pervasive across Nucleocytoviricota. These genomic islands are frequently associated with genomic hypervariability and enriched in genes involved in host interaction, particularly surface adhesion proteins, suggesting roles in host adaptation during the virus-host arms race. Comparative analyses further reveal these islands as hotspots of genome diversification, exhibiting frequent gain/loss and rearrangement even among highly similar genomes. Notably, many genomic islands are enriched in bacterial homologs, and several exhibit striking synteny with genomic regions recovered from co-occurring bacterial genomes, supporting large-scale genetic exchange between bacteria and giant viruses. Together, these findings identify genomic islands as pervasive and dynamic drivers of giant virus genome evolution, providing a framework for genome plasticity, mosaicism, and adaptive potential of giant viruses.},
}

*Genomic Islands/genetics
*Genome, Viral/genetics
*Giant Viruses/genetics
*Mosaicism
*Genetic Variation
Evolution, Molecular
Phylogeny
Metagenome

@article {pmid42806173,
year = {2026},
author = {Balasubramaniyan, M and Karthik, PA and Veeran, Y},
title = {Predicted shifts in microbial functional potential across the late glacial to holocene transition: a 16S rRNA-based inference from southeastern Arabian Sea sediments.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {10},
pages = {},
pmid = {42806173},
issn = {1572-9699},
mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; Phylogeny ; Seawater/microbiology ; *Archaea/genetics/classification/metabolism ; },
abstract = {Marine sediments preserve valuable records of ancient microbial communities. In this exploratory study, direct environmental amplicon sequencing reconstruction is often constrained by DNA degradation. In this exploratory study, we applied predictive functional profiling (PICRUSt2) to 16S rRNA gene amplicon data from five discrete sediment horizons spanning ~14.400 years (Bølling-Allerød, Younger Dryas, Early Holocene, Mid-Holocene, and Late Holocene) in the southeastern Arabian Sea. Inferred functional profiles based on Clusters of Orthologous Groups (COGs) pointed to variations in the predicted abundance of genes associated with carbon metabolism-specifically COG0183 (Acetyl-CoA acetyltransferase) and COG1024 (Enoyl-CoA hydratase/carnitine racemase)-and transport systems. Notably, the predicted potential for carbon metabolism reached its peak during the early Holocene, suggesting possible changes in carbon cycling dynamics during this warming phase. Principal component analysis accounted for 68.7% of the variance in predicted functions across time periods. While these findings are predictive and rely on amplicon-based inference, they provide a preliminary model of microbial functional reorganisation during major climate transitions, offering hypotheses for future high-resolution metagenomic validation.},
}

*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism
*Microbiota/genetics
Phylogeny
Seawater/microbiology
*Archaea/genetics/classification/metabolism

@article {pmid42806489,
year = {2026},
author = {Song, K and Qin, Y and Luo, J and Liu, L and Luo, C and Qiu, Y and Zhong, Y and Zhong, H and Wu, K and Ni, M and Wu, D and Dai, M and Zhu, S and Chen, H},
title = {Gut Microbial Topology and Metabolic Signatures Associated With Colorectal Neoplasia.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77991},
doi = {10.1002/advs.77991},
pmid = {42806489},
issn = {2198-3844},
support = {2024YFA0918500//National Key Research and Development Project of China/ ; 2022-I2M-1-003//CAMS Innovation Fund for Medical Sciences/ ; 2025ZD0551704//National Science and Technology Major Program of China/ ; BRWEP2024W034010101//Beijing Research Ward Excellence Program/ ; 82273726//National Natural Science Foundation of China/ ; 82473705//National Natural Science Foundation of China/ ; XZ202501JD0021//Science and Technology Projects of Xizang Autonomous Region, China/ ; UGG06641//PUMCH Talent Development Program (Category B Project)/ ; 2025-LYZX-C-B03//National High Level Hospital Clinical Research/ ; 2025-PUMCH-C-048//National High Level Hospital Clinical Research/ ; },
abstract = {Alterations of gut microbial communities impact health. However, the structure and function of community-level topologies related to colorectal neoplasia (CRN) remain unclear. We analyzed 3807 newly sequenced stool metagenomes from participants (2725 healthy controls, 759 non-advanced adenomas, 297 advanced adenomas, and 26 colorectal cancers) in a multicenter TARGET-C screening trial and validated our findings in multiple independent cohorts. We identified a CRN-associated network (14 species, including Clostridium symbiosum) and a negatively associated network (37 species, including Roseburia and Lachnospira), forming a "seesaw-like" microbial association pattern characterized by within-group co-occurrence and between-group co-exclusion. The structures were stable across the independent datasets. A composite score derived from the microbial topology stratified CRN risk, and diagnostic models based solely on the presence/absence status of the topological species achieved moderate accuracy across the cohorts (area under the curve ranging from 0.66 to 0.87). Functionally, changes in CRN-related microbial association patterns were associated with microbe-derived metabolites. Our findings provide novel insights into the microbial topology associated with CRN and support its potential application in non-invasive risk stratification. However, the utility of these topological features in colorectal cancer remains exploratory and requires further validation in larger colorectal cancer cohorts.},
}

@article {pmid42806510,
year = {2026},
author = {Singh, S and Sharma, VK and Shrivastav, D and Kushwaha, JM and Mishra, MK and Beg, MMA},
title = {From Rhizosphere to Resistance: Microbe-Plant Interactions in Eco-Smart Biocontrol.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70398},
doi = {10.1002/mbo3.70398},
pmid = {42806510},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Plant Diseases/prevention & control/microbiology ; Pest Control, Biological/methods ; Soil Microbiology ; Plant Roots/microbiology ; *Biological Control Agents ; Microbiota ; Multiomics ; Crops, Agricultural/microbiology ; Fungi ; *Plants/microbiology ; },
abstract = {The increasing limitations of chemical pesticides such as environmental pollution, pathogen resistance, and threats to human and ecosystem health have increased the demand for sustainable, biologically based crop protection methods. Eco-smart biocontrol has emerged as a game-changing paradigm that uses beneficial microorganisms associated with plants to suppress phytopathogens, boost plant immunity, and make agroecosystems more resilient over time. Moving beyond traditional single-strain biocontrol, eco-smart biocontrol integrates multi-omics discovery, artificial intelligence-assisted predictive microbiome design, and dynamic rhizosphere ecology. This review brings together ecological, molecular, and technological dimensions of eco-smart biocontrol, focusing on the rhizosphere as a dynamic hotspot for plant-microbe interactions. We investigate rhizosphere microbiome assembly and demonstrate the preferential recruitment of beneficial bacteria, fungi, actinomycetes, and mycorrhizal symbionts by plant root exudates. Moreover, the review highlights the impact of innovations in multi-omics techniques (metagenomics, transcriptomics, proteomics, and metabolomics), systems biology, and artificial intelligence on microbial biocontrol agent discovery, functional validation, and predictive design. Examples from cereal crops, legumes, and horticulture crops indicate that the application of beneficial microbial inoculants can significantly lower the burden of pests and diseases, enhance crop productivity, and fit perfectly within an integrated pest management system. Lastly, we critically analyze the main challenges preventing large-scale adoption, such as inconsistent field performance, limited microbial survival and competitiveness, and comparative regulatory frameworks across global markets. Ultimately, eco-smart microbial biocontrol combines mechanistic insights with omics-driven discovery, artificial intelligence (AI)- assisted prediction, advanced formulation strategies, and field-level validation, creating a strong, scalable, and environmentally friendly framework for resilient, low-input agricultural systems.},
}

*Rhizosphere
*Plant Diseases/prevention & control/microbiology
Pest Control, Biological/methods
Soil Microbiology
Plant Roots/microbiology
*Biological Control Agents
Microbiota
Multiomics
Crops, Agricultural/microbiology
Fungi
*Plants/microbiology

@article {pmid42806854,
year = {2026},
author = {Min, J and Niu, Z and Yin, J and Xu, S and Zhang, S and Mao, J and Liu, M and Li, L and Li, R and Zhang, H and Wu, X},
title = {Diagnostic value of metagenomic next-generation sequencing for bacterial and fungal detection and its role in antimicrobial therapy adjustment in critically ill patients with non-resolving pneumonia.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2740261},
doi = {10.1080/07853890.2026.2740261},
pmid = {42806854},
issn = {1365-2060},
mesh = {Humans ; Female ; Retrospective Studies ; Critical Illness ; Male ; Aged ; *Metagenomics/methods ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Intensive Care Units ; Bronchoalveolar Lavage Fluid/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Fungi/isolation & purification/genetics ; Bacteria/isolation & purification/genetics ; *Pneumonia/drug therapy/microbiology/diagnosis ; *Pneumonia, Bacterial/drug therapy/diagnosis/microbiology ; },
abstract = {INTRODUCTION: Early targeted antibiotic therapy is critical for improving outcomes in ICU patients with pneumonia unresponsive to initial treatment. Metagenomic next-generation sequencing (mNGS) is a unique diagnostic tool; however, its effectiveness for high-risk populations remains unclear.

METHODS: This retrospective study included 642 ICU patients with pneumonia unresponsive to initial treatment, categorized into single- or repeat-test groups based on mNGS testing frequency. We analyzed the results of mNGS and conventional microbiological tests (CMTs), compared microbial detection characteristics between patients with different immune statuses, assessed the impact of repeat testing on microbial detection and treatment adjustments and evaluated its association with patient prognosis using multivariable logistic regression and propensity score matching.

RESULTS: Among 642 patients, patient-level agreement between mNGS and CMTs was low (κ = 0.180, p < 0.001). First bronchoalveolar lavage fluid (BALF)-mNGS results showed a higher microbial detection rate in immunocompromised than immunocompetent patients. Among patients undergoing repeat BALF-mNGS testing, partial concordance between first and second tests was most common pattern. Antibiotic treatments were modified in 67.6% of cases based on mNGS results, with a higher adjustment rate in the repeat-test group. Although ICU mortality was higher in the repeat-test group, multivariate logistic regression analysis revealed no significant association between repeat testing and mortality risk (adjusted odds ratio = 1.15, 95% CI: 0.64-2.06, p = 0.630). After propensity score matching, no significant difference was observed between two groups (absolute risk difference: 1.12%, 95% CI: -7.43% to 9.67%, p = 0.798).

CONCLUSION: mNGS is a valuable microbial detection tool for ICU patients with pneumonia unresponsive to initial treatment and can support early antimicrobial adjustment. Repeat testing can provide information on dynamic changes in the microbial spectrum during disease but was not associated with improved patient outcomes, suggesting that repeat testing frequency should be carefully considered to avoid unnecessary testing. mNGS results should be interpreted in conjunction with CMTs, host immune status and inflammatory biomarkers to optimise its clinical value in ICU pneumonia.},
}

Humans
Female
Retrospective Studies
Critical Illness
Male
Aged
*Metagenomics/methods
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Intensive Care Units
Bronchoalveolar Lavage Fluid/microbiology
*Anti-Bacterial Agents/therapeutic use
Fungi/isolation & purification/genetics
Bacteria/isolation & purification/genetics
*Pneumonia/drug therapy/microbiology/diagnosis
*Pneumonia, Bacterial/drug therapy/diagnosis/microbiology

@article {pmid42807009,
year = {2026},
author = {Li, J and Li, X and Zhong, H and Wang, L and Yue, L},
title = {Case Report: Sequential mNGS captures fatal HSV-1 reactivation after intestinal obstruction-associated ARDS in a 91-year-old.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1910309},
pmid = {42807009},
issn = {2296-858X},
abstract = {Herpes simplex virus type 1 (HSV-1) is a ubiquitous pathogen. Nevertheless, disseminated HSV-1 infection with confirmed viremia and fatal acute respiratory distress syndrome (ARDS) following intestinal obstruction in very old individuals is exceedingly rare. Here we report a 91-year-old patient with previously intact immunity who developed ARDS after incomplete intestinal obstruction, followed by HSV-1 reactivation. Although routine microbiological tests remained negative, five consecutive metagenomic next-generation sequencing (mNGS) assays dynamically tracked the evolving pathogens throughout the disease course. Despite broad-spectrum antibiotics, antifungals, antivirals, corticosteroids, IVIG, and mechanical ventilation, the patient's refractory hypoxemia remained uncorrected, leading to multiple organ dysfunction and death. This case highlights a rare clinical scenario and provides valuable insights for the diagnosis and management of critically ill elderly patients, offering a comprehensive, longitudinal perspective on the clinical application of mNGS.},
}

@article {pmid42807220,
year = {2026},
author = {Liu, Y and Liu, Y and Huang, S and Zhao, Y and Zhu, L and Wang, T and Liang, H and Liu, M and Geng, W},
title = {Systemic lupus erythematosus complicated by refractory Mycobacterium avium complex infection involving bilateral lower extremities: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1936197},
pmid = {42807220},
issn = {2296-858X},
abstract = {BACKGROUND: Patients with systemic lupus erythematosus (SLE) receiving long-term glucocorticoids and immunosuppressants are at markedly increased risk of opportunistic infections. Mycobacterium avium complex (MAC) is a common nontuberculous mycobacterial pathogen, but MAC osteomyelitis is extremely rare in non-HIV SLE patients, posing diagnostic and therapeutic challenges.

CASE PRESENTATION: We report a 52-year-old female with SLE on long-term prednisone, azathioprine, leflunomide, and hydroxychloroquine, who developed bilateral tibial and femoral osteomyelitis complicated by soft tissue abscesses, drug-induced dermatitis, and severe malnutrition. Conventional microbiological tests remained negative. Metagenomic next-generation sequencing (mNGS) of lower-extremity secretions and pus identified MAC. She underwent five surgical debridements and prolonged multidrug antimycobacterial therapy (azithromycin, rifampicin, ethambutol, amikacin), along with nutritional support and immunosuppressant adjustment. The infection was controlled with no SLE flare, and she recovered favorably.

CONCLUSION: Disseminated MAC osteomyelitis can occur in SLE patients under sustained immunosuppression even during disease remission. mNGS enables rapid pathogen identification and is crucial for diagnosing complicated infections. Management requires combined surgical debridement, prolonged antimycobacterial therapy, and multidisciplinary care.},
}

@article {pmid42807267,
year = {2026},
author = {Xu, N and Guo, T and Yang, Z and Zheng, Y and Wang, Y and Sha, W and Yin, B and Dong, W},
title = {Effects of dietary supplementation with bacteriocin-like inhibitory substance-producing Weissella cibaria XN-2a on growth performance, immune responses, and gut microbiota in crucian carp (Carassius auratus).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1953174},
pmid = {42807267},
issn = {1664-302X},
abstract = {INTRODUCTION: The intensive farming of crucian carp (Carassius auratus) often compromises fish health and increases disease susceptibility, driving interest in probiotic interventions as sustainable alternatives to antibiotics. However, the in vivo efficacy and mechanistic basis of Weissella cibaria strains in freshwater fish remain poorly understood.

METHODS: A bacteriocin-producing strain, Weissella cibaria XN-2a, was isolated from fish viscera and supplemented in the diet of crucian carp at an initial viable dose of 2.74 × 10[10] CFU/g feed (freshly prepared and replaced every 3 days) for 30 days, followed by a challenge with Aeromonas hydrophila. Growth performance, immune parameters, intestinal histology, and gut metagenomic profiles were compared between the probiotic-fed group (XS) and the control group (XD).

RESULTS: Probiotic supplementation significantly improved weight gain (28.17% vs. 13.98%), feed conversion ratio (1.88 ± 0.32 vs. 2.58 ± 0.27, p < 0.05), and post-challenge survival (50% vs. 0%) (p < 0.001). The XS group exhibited enhanced intestinal morphology (higher mucosal fold height and FH/IFD ratio, lower inter-fold distance), elevated IgM and SOD activities, and reduced post-challenge IL-6 and MDA levels. Metagenomic analysis revealed that the probiotic reshaped the gut microbiota from a pathogen-associated virulence profile (LPS, flagella, enterobactin) toward a commensal profile enriched in T6SS/T2SS and alternative siderophores, without increasing the overall antibiotic resistance burden. The butanoate metabolism pathway showed differences consistent with increased butyrate synthesis potential, with enrichment of butyrate-synthetic enzymes (e.g., enoyl-CoA hydratase, acetolactate decarboxylase) in XS and butyrate-diverting enzymes in XD. CAZy profiling further showed enrichment of antibacterial (GH25/GH73) and antioxidant (AA4) gene families in XS, with Weissella as a major contributor.

DISCUSSION: These findings suggest that dietary Weissella cibaria XN-2a enhances growth performance, intestinal health, and disease resistance in crucian carp, potentially through a dual mechanism involving bacteriocin-mediated microbiota modulation and enhanced butyrate synthesis potential. Further investigations, including direct metabolite quantification, are warranted to validate these mechanistic inferences.},
}

@article {pmid42807290,
year = {2026},
author = {Huang, J and Xu, R and Liu, B and Liao, Q and Wang, M and Shan, Z and Zhong, H and Liao, F and Liang, H and Wang, H and Li, S and Fu, Y and Liang, H and Rong, X},
title = {Molecular confirmation of transfusion-transmitted dengue virus infection following platelet transfusion in the Chinese mainland.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1920581},
pmid = {42807290},
issn = {2235-2988},
mesh = {Humans ; *Dengue/transmission/virology/diagnosis ; *Dengue Virus/genetics/isolation & purification/immunology/classification ; *Platelet Transfusion/adverse effects ; RNA, Viral/blood/genetics ; Antibodies, Viral/blood ; China ; Immunoglobulin M/blood ; Retrospective Studies ; Immunoglobulin G/blood ; Viral Nonstructural Proteins/genetics ; Male ; Female ; Adult ; *Transfusion Reaction ; High-Throughput Nucleotide Sequencing ; Blood Donors ; Blood Donation ; East Asian People ; },
abstract = {BACKGROUND: Dengue virus (DENV) is considered an emerging threat to blood safety. While transfusion-transmitted DENV (TT-DENV) cases have been documented, TT-DENV has never been reported in Chinese mainland. In this study, a retrospective investigation was conducted after two patients developed dengue fever (DF) following apheresis platelet (PLT) transfusion from the same healthy donor.

METHODS: Blood samples from the recipients and the donor were tested for DENV RNA by nucleic acid testing (NAT). Nonstructural protein 1 (NS1) antigen and anti-DENV immunoglobulin M/G (IgM/IgG) antibodies were detected by ELISA. To confirm transmission, DENV E gene fragments were amplified, and whole-genome sequences were obtained by metagenomic next-generation sequencing (mNGS).

RESULTS: Our results revealed that the PLT donor was asymptomatic, tested positive for DENV RNA, and negative for anti-DENV IgM/IgG antibodies at donation. After donation, no dengue-like symptoms was developed. Seroconversion was observed at day 21 postdonation. After receiving the DENV-positive PLT unit, recipient 1 had DF only, while recipient 2 developed DF together with headache, joint/muscle pain, and rash. After transfusion, both recipients were positive for DENV RNA and NS1 while negative for anti-DENV IgM/IgG antibodies. Viral sequences from the donor and recipients were identical and belonged to DENV-2.

CONCLUSIONS: To our knowledge, this is the first TT-DENV case reported in the Chinese mainland, revealing the necessity of revising current donor deferral policies and testing strategies that predominantly rely on symptoms and travel history.},
}

Humans
*Dengue/transmission/virology/diagnosis
*Dengue Virus/genetics/isolation & purification/immunology/classification
*Platelet Transfusion/adverse effects
RNA, Viral/blood/genetics
Antibodies, Viral/blood
China
Immunoglobulin M/blood
Retrospective Studies
Immunoglobulin G/blood
Viral Nonstructural Proteins/genetics
Male
Female
Adult
*Transfusion Reaction
High-Throughput Nucleotide Sequencing
Blood Donors
Blood Donation
East Asian People

@article {pmid42807808,
year = {2026},
author = {Struillou, A and Deschamps, P and Moreira, D and López-García, P},
title = {Phylogeny-guided curation reveals widespread misannotation of Asgard archaeal 16S rRNA gene sequences in public databases.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag253},
pmid = {42807808},
issn = {2730-6151},
abstract = {Accurate taxonomic assignment of 16S rRNA gene sequences is essential for the reliable interpretation of microbial community studies based on amplicon sequence data. Yet, it critically depends on the reliability of reference databases such as the Genome Taxonomy Database (GTDB) and the SILVA ribosomal RNA database. Here, we evaluate the consistency of taxonomic annotations within the Asgardarchaeota phylum, a lineage of major evolutionary and ecological interest. Using a phylogenetically curated set of GTDB-derived 16S rRNA gene sequences, we show that most of the affiliations of these sequences were consistent with the phylogenomic placement of their corresponding metagenome-assembled genomes (MAGs), although a small fraction of them exhibited clear inconsistencies likely resulting from erroneous binning to MAGs. In contrast, phylogenetic analyses of SILVA-derived 16S rRNA gene sequences including curated reference sequences revealed widespread taxonomic misannotation and/or limited resolution of taxon assignment. Specifically, many sequences annotated as Odinarchaeales robustly clustered within Lokiarchaeia, Heimdallarchaeia, Hermodarchaeia, or Sifarchaeia, leading to an artificial inflation of Odinarchaeales assignments and potentially biased ecological interpretations. To mitigate these issues, we constructed a curated reference dataset of Asgardarchaeota 16S rRNA gene sequences and generated phylogenetically validated taxonomic assignments across clustered entries, providing a resource for improved classification of environmental sequences. Our results demonstrate that widely used reference databases can contain systematic annotation errors that propagate across studies and distort ecological inference. Although illustrated using Asgard archaea, these limitations are likely pervasive across understudied microbial diversity, highlighting the need for routine phylogenetic validation and systematic curation of reference datasets.},
}

@article {pmid42808285,
year = {2026},
author = {Wang, X and Patel, RH and Li, Q and Ching, CB and Schwartz, L and Rosado, JDR and Spencer, JD and Becknell, B},
title = {Leveraging Bioinformatic Strategies to Advance Care of Children With Urinary Tract Infections.},
journal = {Journal of paediatrics and child health},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpc.70607},
pmid = {42808285},
issn = {1440-1754},
support = {1R03DK140423-01A1/DK/NIDDK NIH HHS/United States ; LRP 2L40DK130152-02//NIH/ ; },
abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections and pose a significant global health challenge in children. UTIs can cause a range of conditions from cystitis and pyelonephritis to bacteraemia. Current methods for diagnosing UTI lack adequate sensitivity and specificity and are time-consuming, driving demand for improved approaches. Although most UTIs resolve with antibiotic therapy, some children develop recurrent UTIs due to multidrug-resistant organisms and progressive chronic kidney disease. Currently, there are no reliable methods to identify which children are at risk for adverse outcomes, representing a critical gap in paediatric UTI management. This review explores how bioinformatic approaches can offer a comprehensive framework to harness scientific discoveries and meet clinical challenges posed by paediatric UTI. Recent advances in high-throughput sequencing and proteomics have generated extensive datasets, enabling detailed analysis of microbial and host responses during UTI. We summarize how computational and multi-omics approaches, including metagenomics, bulk and single-cell transcriptomics, proteomics, epigenetics and integrative frameworks, have deepened our understanding of UTI pathogenesis and the foundational determinants of a successful host response. We consider the collective potential of these discoveries and technologies to transform future UTI management.},
}

@article {pmid42809026,
year = {2026},
author = {Akanmu, AM},
title = {Beyond the Rumen: Current Evidence and Knowledge Gaps in Microbial Diversity and Function Across the Bovine Gastrointestinal Tract.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42809026},
issn = {1432-0991},
mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Tract/microbiology ; Rumen/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; Biodiversity ; },
abstract = {The bovine gastrointestinal tract (GIT) is a spatially organised microbial ecosystem, but the evidence supporting a whole-tract interpretation is highly uneven. This critical review distinguishes well-established rumen biology from emerging observations in the reticulum, omasum, abomasum, small intestine and hindgut. Comparative studies show strong regional filtering of microbial communities, yet most available datasets are cross-sectional, use digesta rather than mucosa, and infer function from DNA. Consequently, the presence of genes or taxa cannot be equated with active metabolism. Early life provides an important developmental dimension: microbial succession during the milk-to-solid-feed transition accompanies rumen maturation and region-specific immune development, although durable effects on adult productivity remain incompletely demonstrated. Across adult cattle, foregut fermentation supplies most microbially derived energy, whereas downstream compartments support residual fermentation, epithelial interactions and barrier-related processes whose quantitative contributions are less certain. Methanogenesis is therefore treated as one outcome among nutrition, immune function, pathogen resistance and gut integrity. Metagenomics, metatranscriptomics, metaproteomics and metabolomics are complementary rather than interchangeable; coordinated sampling is required to connect functional potential to activity and host phenotype. Priority should be given to longitudinal, multi-compartment, mucosa-and-digesta studies with absolute microbial measurements, metabolite fluxes and transparent causal inference. A tract-wide framework is valuable not because all compartments are equally understood, but because it makes the present evidence imbalance explicit and identifies where microbiome-targeted nutrition can be tested responsibly.},
}

Animals
Cattle/microbiology
*Gastrointestinal Tract/microbiology
Rumen/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
Biodiversity

@article {pmid42809384,
year = {2026},
author = {Shen, Q and Shi, W and Liu, C and Cao, Z and Fu, Y and Ndjekadom, A and Wang, X and Liu, Y and Yang, S and Ji, L and Li, H and Zhou, C and Liu, J and Zhang, W},
title = {AI-Empowered Viral Metagenomics for Clinical Diagnosis: Advances, Bottlenecks, and Translational Pathways.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag239},
pmid = {42809384},
issn = {1365-2672},
abstract = {Viral metagenomics, leveraging high-throughput sequencing technologies, provides comprehensive, hypothesis-free characterization of viral communities in clinical specimens, establishing itself as a pivotal tool for clinical diagnosis, pathogen discovery, and epidemiological surveillance of viral infectious diseases. The integration of artificial intelligence (AI) has demonstrated transformative potential in viral metagenomic data analysis, significantly enhancing sequence classification, feature extraction, pattern recognition, and result interpretation, thereby improving analytical efficiency, accuracy, and automation. Machine-learning and deep-learning approaches have shown potential for detecting low-abundance viral signals and mitigating background noise in complex clinical samples, and facilitating pathogen identification in complex clinical samples, substantially augmenting the clinical utility of viral metagenomics. Nevertheless, routine clinical implementation faces persistent challenges, including high host nucleic acid background, low viral titers, contamination control, limited reference databases, absence of standardized analytical pipelines, and limited interpretability and generalizability of some predictive models. Furthermore, clinical validation, result reproducibility, ethical compliance, and data security represent critical translational barriers that impede widespread adoption. This review comprehensively summarizes recent advances and clinical applications of AI-empowered viral metagenomics, highlighting its transformative potential in pathogen detection, diagnosis of challenging infections, infectious disease surveillance, and precision medicine. We comprehensively address major technical bottlenecks and translational barriers that must be overcome to facilitate standardized development and clinical implementation of this emerging paradigm.},
}

@article {pmid42809394,
year = {2026},
author = {Chen, M and Liu, J and Tsai, HY and Li, CY and Batucan, JD and Eckhardt, CW and Pham, THD and Ellis, EK and Ratnayake, R and Paul, VJ and Bruner, SD and Donia, MS and Luesch, H and Ding, Y},
title = {Biosynthetic origin of anticancer dolastatin 15 reveals a noncanonical NRPS architecture enabling 2-keto acid activation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {40},
pages = {e2615454123},
doi = {10.1073/pnas.2615454123},
pmid = {42809394},
issn = {1091-6490},
support = {RM1GM145426//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM128742//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; AWD13127-2236414//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {*Depsipeptides/biosynthesis/chemistry/genetics ; *Peptide Synthases/metabolism/genetics/chemistry ; Multigene Family ; *Antineoplastic Agents/metabolism/chemistry ; *Cyanobacteria/genetics/metabolism ; Biosynthetic Pathways ; Phylogeny ; Genome, Bacterial ; },
abstract = {Elucidating the biological origins and biosynthetic pathways of marine natural products remains a major challenge, particularly for compounds derived from microbial consortia. Here, we identify the marine cyanobacterial genus Dapis as the source of the potent anticancer natural product dolastatin 15 using genome-resolved metagenomics. Reconstruction of two complete and two near-complete genomes provides genome-resolved characterization of the genus Dapis, revealing extensive biosynthetic potential. Genome mining identified the dolastatin 15 biosynthetic gene cluster. Subsequent analyses reconstructed its pathway and uncovered a noncanonical five-domain nonribosomal peptide synthetase module containing an embedded 2-keto acid-activating domain, revealing an unexpected architectural solution for incorporating 2-keto acid-derived hydroxy acid building blocks. Comparative and evolutionary analyses support a model in which this architecture may have arisen through recruitment of keto acid-activating domains and reduction of canonical adenylation domain features. We further biochemically and structurally characterize an O-methyltransferase that catalyzes formation of the characteristic methoxy pyrrolinone moiety, thereby validating a key terminal tailoring step in the proposed biosynthetic pathway. Together, these findings define the biosynthetic logic of dolastatin 15 and expand understanding of substrate activation and assembly-line diversification in nonribosomal peptide biosynthesis.},
}

*Depsipeptides/biosynthesis/chemistry/genetics
*Peptide Synthases/metabolism/genetics/chemistry
Multigene Family
*Antineoplastic Agents/metabolism/chemistry
*Cyanobacteria/genetics/metabolism
Biosynthetic Pathways
Phylogeny
Genome, Bacterial

@article {pmid42801164,
year = {2026},
author = {Ye, Q and Liu, Y and Zhang, K and Tian, M and Zhang, Z and Lin, M and Zheng, Y},
title = {Recent Advances and Future Perspectives in the Detection of Carbapenem-Resistant Acinetobacter Baumannii.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {612634},
pmid = {42801164},
issn = {1178-6973},
abstract = {Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major global public health threat. The World Health Organization (WHO) has classified CRAB as a critical priority pathogen. This threat is mainly attributed to its multidrug resistance, efficient nosocomial transmission, and limited therapeutic options. Timely and accurate detection is essential for early diagnosis, targeted antimicrobial therapy, and effective infection control. This review summarizes recent advances in CRAB detection technologies, including conventional phenotypic methods, nucleic acid amplification-based assays, genomic and AI-assisted diagnostics, mass spectrometry-based methods, and biosensor platforms. Conventional antimicrobial susceptibility testing (AST) remains the reference standard. However, it requires bacterial culture and isolation before testing, and the process usually takes 18-24 h after bacterial colony growth. This delay may limit its value for early therapeutic decision-making. Phenotypic carbapenemase assays provide complementary information on carbapenemase activity and resistance mechanisms, but their sensitivity, specificity, and clinical applicability vary across methods. Molecular methods substantially shorten turnaround times, with PCR and qPCR generally producing results within approximately 2-3 h. Isothermal amplification platforms further accelerate detection. LAMP-based assays report turnaround times of approximately 21-60 min, whereas RPA-based assays complete detection within approximately 40-90 min, supporting their potential application in point-of-care testing (POCT). Emerging genomic approaches, including whole-genome sequencing, nanopore sequencing, and metagenomic sequencing, enable comprehensive resistance profiling, outbreak investigation, and surveillance, while AI-assisted diagnostics may enhance resistance prediction and clinical interpretation. Mass spectrometry-based methods enable high-throughput species identification and can support resistance profiling in selected assay formats, with some assays detecting resistance-associated features within 15-90 min. Biosensor-based and CRISPR-integrated platforms offer highly sensitive, rapid, and portable detection, although challenges remain in multiplexing, standardization, cost, and clinical validation. Overall, this review highlights the transition of CRAB diagnostics from culture-based susceptibility testing toward integrated, automated, and clinically adaptable platforms, emphasizing the need to balance analytical performance, turnaround time, cost, and suitability for POCT.},
}

@article {pmid42801199,
year = {2026},
author = {Zhou, F and Cao, L and He, Y and Bai, J and Wang, Y},
title = {ViTax-RAG: a retrieval-augmented language modeling tool for viral contig taxonomic classification.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag247},
pmid = {42801199},
issn = {2635-0041},
abstract = {MOTIVATION: Taxonomic classification of viral metagenomic contigs remains difficult for short or divergent sequences. Reference-based methods are precise when close homologs exist, whereas representation-based models can generalize beyond direct matches but lack explicit biological evidence.

RESULTS: Here, we present ViTax-RAG, a retrieval-augmented framework that integrates alignment-derived evidence with learned sequence representations for robust viral classification. ViTax-RAG reformulates BLAST as a domain-specific retrieval module and integrates retrieved homology information into a sequence modeling framework, thereby enabling the complementary use of alignment-based and representation-based signals. We evaluated ViTax-RAG on in-distribution (ID) and within-genus out-of-distribution (OOD) datasets, where it consistently outperformed current viral taxonomy methods at comparable taxonomic endpoints and supported fragment lengths. The pipeline processed all 195 728 GOV 2.0 contigs; 87.2% of predictions terminated at class, demonstrating hierarchical backoff rather than fine-rank accuracy on data without ground truth.

ViTax-RAG is implemented in Python and is freely available at GitHub (https://github.com/Ying-Lab/ViTax-Rag) under an open-source license. Documentation and example workflows are provided to facilitate integration into metagenomic analysis pipelines.},
}

@article {pmid42801217,
year = {2026},
author = {Shen, F and Hu, L and Xin, C and Du, F and Zhang, S},
title = {Gut Microbiota and SCFA Changes After Alendronate-Calcitriol Therapy in Postmenopausal Osteoporosis.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {636595},
pmid = {42801217},
issn = {1179-1411},
abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO) is driven primarily by estrogen deficiency, and gut microbiota-derived metabolites may participate in bone remodeling. The intestinal effects of conventional anti-osteoporosis therapy remain unclear. We investigated gut microbial and short-chain fatty acid (SCFA) changes associated with alendronate-calcitriol therapy in PMO.

METHODS: Forty-one postmenopausal women were enrolled, including 21 healthy controls and 20 patients with PMO. PMO patients received oral alendronate plus calcitriol for six months, with paired fecal samples collected before and after treatment. Shotgun metagenomic sequencing was used to assess microbial taxonomy, KEGG pathways, and CAZy profiles. Fecal SCFAs were quantified by gas chromatography-mass spectrometry.

RESULTS: After treatment, lumbar spine BMD T-score improved from -2.98 to -2.65, and femoral neck BMD T-score increased from -2.40 to -2.12, and all measured bone turnover markers (BALP, TRACP-5b, PINP and osteocalcin) decreased significantly (P < 0.05). Global microbial diversity did not differ significantly among groups, but treatment was accompanied by shifts in specific taxa. Roseburia, Megamonas, Dialister, and unclassified Lactobacillaceae increased, whereas Enterobacter, Salmonella, Raoultella, Serratia, and Rahnella decreased. Functional profiles showed treatment-associated shifts in propanoate metabolism, pyruvate metabolism, the TCA cycle, and selected carbohydrate-active enzyme patterns. Overall fecal SCFA composition remained relatively stable; however, propionic acid concentration increased significantly after treatment (FDR-adjusted P = 0.021). Correlation analyses linked selected commensal taxa and SCFAs with BMD and bone turnover markers.

CONCLUSION: Alendronate-calcitriol therapy was associated with improved bone metabolism and treatment-associated shifts in gut microbial composition, microbial functional potential, and propionate-related SCFA profiles. These findings provide preliminary evidence for microecological changes accompanying conventional PMO therapy.},
}

@article {pmid42801568,
year = {2026},
author = {Zhu, H and Chen, X and Li, Q and Sun, C and Xia, H and Huang, Y and Wang, C and Chen, P and Gao, C},
title = {Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77591},
pmid = {42801568},
issn = {2198-3844},
support = {XDA28030401//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2025YFF0512900//National Key R&D Program of China/ ; 32322053//National Natural Science Foundation of China/ ; },
abstract = {Community-level average genome size (AGS) is a key trait linking microbial diversity, functional potential, and eco-evolutionary strategy, yet estimates of AGS diverge markedly among common methods. Here, we introduce and validate a framework that adjudicates conflicting AGS estimates by testing which estimate yields a gap between scaled functional diversity and scaled taxonomic diversity that is consistent with the expected positive association between genome size and gene functional breadth. Across independent environmental gradients, metagenomic AGS estimates align with this framework and expectations from metagenome-assembled genome (MAG) dynamics and gene co-occurrence network module sizes, whereas 16S rRNA metabarcoding-based AGS estimates deviate, particularly in extreme environments with sparse reference coverage. Applying this validated framework, we reveal a U-shaped relationship between soil pH and AGS across a broad pH range, unifying prior findings of decreasing AGS from acidic to neutral soils with a newly observed increase along an alkaline gradient. Applying the same framework to a saline-gradient dataset, we further suggest that conclusions of a recent study regarding eco-evolutionary trade-offs under salt stress may stem from method biases. This work identifies a potentially pervasive conflict in AGS estimation, provides a framework to resolve it, and clarifies and expands relationships between AGS and the environment.},
}

@article {pmid42802002,
year = {2026},
author = {Li, H and Wang, J and Li, Y and Chen, X and Chen, L and Jin, X and Jin, P},
title = {Enriched multifunctional microbes coupling antibiotic resistance risk and nitrogen metabolic potential in eutrophic lakes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125764},
doi = {10.1016/j.envres.2026.125764},
pmid = {42802002},
issn = {1096-0953},
abstract = {Lakes are facing increasing threats from the dual challenges of eutrophication and antibiotic contamination, yet how microorganisms respond to these concurrent threats remains poorly understood. Here, we conducted a metagenomic binning investigation into the co-occurrence patterns of antibiotic resistance genes (ARGs) and nitrogen cycling functional genes (NFGs) within resistant microbes across three lakes with distinct eutrophic levels. We found a significant increase in the abundance and diversity of ARGs along the trophic gradient. Meanwhile, ARG hosts tended to show a transition pattern from carrying combinations of ARGs, virulence factor genes (VFGs), and NFGs to possessing highly integrated complexes encompassing ARGs, mobile genetic elements (MGEs), VFGs, and NFGs. This reflected the coupling between antibiotic resistance and nitrogen metabolism, and contributed to the survival of resistant microbes that cope with environmental stress. Furthermore, multifunctional hosts (accounting for 57.55%), dominated by Limnohabitans_A, CAISIP01, and RFTU01, could play important roles in linking ecological functions and biosafety risks under highly eutrophic conditions. These findings present a framework centered on multifunctional microbes for elucidating resistome evolution across varying trophic levels, thus guiding host-based strategies to inform ARG risk assessment and eutrophication management in lakes.},
}

@article {pmid42802107,
year = {2026},
author = {Beeby, N and Rasoanarimalala, C and Rasoavolandrainy, MF and Rothman, JM and Higham, JP and Sardaro, MLS and Amato, KR and Webster, TH and Baden, AL},
title = {Microbial and Metabolic Flexibility in Response to Habitat Disturbance in an Ecologically Specialist Primate.},
journal = {Molecular ecology},
volume = {35},
number = {18},
pages = {e70562},
doi = {10.1111/mec.70562},
pmid = {42802107},
issn = {1365-294X},
mesh = {Animals ; *Ecosystem ; Diet ; Forests ; *Gastrointestinal Microbiome/genetics ; *Strepsirhini/microbiology/metabolism/physiology ; RNA, Ribosomal, 16S/genetics ; Energy Metabolism ; Lemuridae ; },
abstract = {In the Anthropocene, understanding what renders a species prone to extinction is critical to wildlife management. Ecological specialists are hypothesised to be at particular risk, given that morphological, physiological, and/or behavioural constraints are expected to impede their responses to rapid habitat degradation. Nevertheless, studies have found mixed support for this hypothesis, raising the question, 'how resilient are specialists to environmental change?' Here, we test the hypothesis that ecological specialists, limited by behavioural and physiological constraints, may be at an energetic disadvantage in degraded habitats. Specifically, we tested whether Critically Endangered dietary specialist primates, black-and-white ruffed lemurs (Varecia variegata), living in secondary forests suffered nutritional and energetic deficits compared to those in primary forest habitats over a 12-month period. To do this, we used mixed modelling approaches to examine relationships among behaviour, nutritional chemistry, 16S sequencing, metagenome functional predictions, metabolite profiles, and energetic outcomes. Compared to primary forest-living conspecifics, we found that animals in the degraded forest consumed slightly fewer calories from less diverse diets. These animals exhibited less diverse gut microbiota, reduced microbial functional potential, and altered metabolomic profiles. Nevertheless, despite apparent nutritional constraints, energetic outcomes were broadly similar across habitats. These findings suggest that an organism's gut microbiome may be able to regulate microbial metabolic potential to facilitate resilience under suboptimal conditions. These findings highlight host-microbiome interactions as an important component of resilience in ecological specialists, with broad implications for predicting species persistence amid ongoing environmental change.},
}

Animals
*Ecosystem
Diet
Forests
*Gastrointestinal Microbiome/genetics
*Strepsirhini/microbiology/metabolism/physiology
RNA, Ribosomal, 16S/genetics
Energy Metabolism
Lemuridae

@article {pmid42802256,
year = {2026},
author = {Wang, Y and Huang, S and Pei, Y and Ma, H and Ji, L and Guo, S and Wei, B and Cai, S and Xue, Y and Lv, Z and Zhang, W and Yang, S},
title = {Identification and characterization of a novel Taupapillomavirus strain in lymphoid tissue of a stray dog.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {42802256},
issn = {1572-994X},
support = {2023YFD1801300//the National Key Research and Development Programs of China/ ; },
abstract = {In this study, viral metagenomic approach was employed to identify a novel canine papillomavirus (CPV) strain in the lymphoid tissue of a stray dog. The complete circular genome (8,297 bp) of a novel papillomavirus strain, designated canpapil01, was characterized and taxonomically assigned to the genus Taupapillomavirus. The genome encodes five early genes (E1, E2, E4, E6, E7) and two late genes (L1 and L2), lacking the E5 gene. Conserved motifs essential for viral replication and host interaction were identified, including ATP-binding and cyclin interaction sites in E1, DNA-binding domains in E2, and zinc-binding domains in E6 and E7. Notably, the pRb-binding motif (LXCXE) was absent in E7. The long control region (LCR) contained predicted E1 and E2-binding sites, indicating regulatory functions. Phylogenetic analysis based on the L1 gene revealed that canpapil01 clustered with Taupapillomavirus 2 strains, which were isolated from nasal swab or blood samples of dogs and wolves in the Switzerland and the USA, forming a separate branch. Genome-wide comparisons showed 71.4% amino acid identity with the Taupapillomavirus 2 reference strain (NC_040578), confirming it as a novel strain within this species. These findings expand the known genetic diversity of canine papillomaviruses and provide valuable genomic data for future research into CPV-associated diseases.},
}

@article {pmid42803159,
year = {2026},
author = {Merkesvik, J and Langa, J and Pietroni, C and Alberdi, A and Poulsen, LL and Bojesen, AM and Meuronen, T and Turunen, S and Kärkkäinen, O and Westereng, B and Pope, PB and Hvidsten, TR},
title = {Integrative holo-omic data analysis predicts interactions across the host-microbiome axis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0026326},
doi = {10.1128/spectrum.00263-26},
pmid = {42803159},
issn = {2165-0497},
abstract = {Understanding the interplay between host organisms and their microbiomes is central to the development of sustainable food systems. However, high dimensionality and spurious associations remain major obstacles to extracting meaningful biological insight from multi-omic host-associated microbiome data; a challenge further exacerbated when "holo-omic" analyses across the host-microbiome boundary are considered. Here, we show that a computational method designed for multi-omic analysis in eukaryotes can be leveraged to integrate and analyze five layers of holo-omic data from porcine hosts and their gut microbiomes. We collected caecal tissue and digesta samples during a feeding trial that tested the impact of microbiota-directed fibers (acetylated galactoglucomannan) at critical developmental stages. From 800,000 features including microbial and host genes, metagenome-assembled genomes, and metabolites from caecal tissue and digesta, we used multiset correlation and factor analysis to select the most relevant features for capturing coordinated patterns across omic layers. From these features, we predicted over 2,000 putative host-microbiome interactions based on co-occurrence. Some interactions reflected previously known relationships between animal and microbiome features, such as microbial genes for carbohydrate metabolism being linked to glycoside abundances in host tissue. Other predicted co-occurrences included features that were not detected in single-omic analysis and offer new hypotheses of host-microbiome interactions that warrant future investigation. Hence, we showcase an application of holo-omic analysis that avoids common pitfalls in high-dimensional data analysis, identifies known interactions as a form of validation, and most importantly, predicts new leads for understanding host-microbiome symbiosis.IMPORTANCEWhile study systems involving mammalian hosts and their microbiomes are inherently complex, multi- and holo-omic analyses promise to provide interpretable results with translational value for the animal production industry. Unfortunately, computational methods capable of this kind of integration are currently scarce, as most existing multi-omics approaches have been developed for analysis of data layers within a single multicellular organism. We propose to adapt existing multi-omic methods for holo-omics by combining feature selection and interaction inference. This two-step analysis approach addresses common challenges in data-driven studies and can be implemented with a variety of tools for feature selection and interaction modeling. Through this holistic approach, we show that both known and novel relationships across the holobiont axis can be identified in a data-driven manner, offering new targets for the continued study and experimental validation of host-microbiome interactions and the effect of dietary interventions on production animals.},
}

@article {pmid42803189,
year = {2026},
author = {Aplakidou, E and Baltoumas, FA and Chasapi, MN and Lamari, E and Chasapi, IN and Georgakopoulos-Soares, I and Karatzas, E and Iliopoulos, I and Aydin Buluç, and Finn, RD and Camargo, AP and Kyrpides, NC and Pavlopoulos, GA},
title = {"Quadrupling" the protein family space with global metagenomics.},
journal = {Nucleic acids research},
volume = {54},
number = {18},
pages = {},
doi = {10.1093/nar/gkag938},
pmid = {42803189},
issn = {1362-4962},
support = {23592-EMISSION//Foundation for Research and Innovation/ ; //Hellenic Foundation for Research and Innovation/ ; 28787-VIROMINE//Research Project to support Postdoctoral Researchers'/ ; 945405//Marie Skłodowska-Curie Grant agreement/ ; DE-AC02-05CH11231//University of Texas at Austin/ ; DE-AC02-05CH11231//Advanced Scientific Computing Research/ ; //US Department of Energy/ ; DE-AC02-05CH11231//US Department of Energy Office of Science/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; *Proteins/genetics/classification/chemistry ; Open Reading Frames ; Multigene Family ; },
abstract = {The known universe of protein families represents only a small fraction of nature's molecular diversity. From 40.3 billion predicted open reading frames across 40 446 metagenomes, 9540 metatranscriptomes, and 539 million proteins from 167 415 reference genomes, we identified 608 258 previously uncharacterized putative protein families with ≥100 members and 6.5 million families with ≥25 members, none matching known Pfam domains or reference proteins. This effort doubles the known repertoire of large families and quadruples that of smaller families. Integration of AlphaFold2-based structural predictions with gene-neighborhood and taxonomic analyses enables the characterization of these previously unannotated proteins, revealing candidates for both novel and known biological functions in understudied microbial lineages and biomes. This expanded repertoire provides insights into microbial adaptation and broadens the molecular toolkit available for biotechnology, highlighting the power of global metagenomics to uncover hidden protein diversity.},
}

*Metagenomics/methods
*Metagenome
*Proteins/genetics/classification/chemistry
Open Reading Frames
Multigene Family

@article {pmid42803406,
year = {2026},
author = {Saeed, M and Huang, X and Mustafa, G and Li, M and Yang, P},
title = {Rhizosphere Microbiome-Mediated Drought Resilience in Cereals: Implications for Grain Nutrition, Yield, and Tolerance.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70901},
pmid = {42803406},
issn = {1365-3040},
support = {2024BBB001//Hubei Provincial Key Research and Development Projects/ ; 2023AFB614//Hubei Provincial Natural Science Foundation/ ; 2023AFA016//Hubei Provincial Natural Science Foundation/ ; },
abstract = {Drought-mediated declines in grain nutritional quality and cereal yield put global food security at risk, yet the rhizosphere microbiome provides an alternative solution for improving crop tolerance. Our review synthesised existing knowledge on how soil microbiomes, particularly arbuscular mycorrhizal fungi (AMF) and plant-growth-promoting rhizobacteria (PGPR), simultaneously regulate three interlinked pillars of crop performance (stress tolerance, grain nutrient uptake, and yield) under drought. Our in-depth analysis showed that such relationships were governed by synergies (improved root architecture improves all three traits) and trade-offs (i.e., ABA-induced stomatal closure improves water efficiency but restricts carbon assimilation). Furthermore, these relationships were governed at different biological layers through multi-omics (metagenomics, transcriptomics, proteomics, and metabolomics) to identify biomarkers and pathways. With the application of an integrated framework through bioinformatics, it is now possible to reveal the hidden molecular layout between cereals and their underground partners, identify drought-responsive pathways, and discover biomarkers (nutrient transporter gene, microbial abundance, osmolyte accumulation, and root exudates). Despite advancements, critical technical gaps hinder data integration and standardised pipelines to identify complex traits through heterogeneous databases of omics. Our review proposes an integrated framework linking multi-omics tools, microbiome traits, and crop outcomes. Furthermore, we provide a research roadmap prioritising drought biofortification, synthetic communities (SynComs), microbial consortia, and spatial omics. Such research directly supports hidden hunger and food security agendas, while progressing climate-resilient agriculture.},
}

@article {pmid42803537,
year = {2026},
author = {Watts, TD and Jirapanjawat, T and Perlaza-Jiménez, L and Ricci, F and Tudor-Matthew, E and Chiri, E and Bay, SK and Grinter, R and Lappan, R and Lithgow, T and Woods, LC and Greening, C},
title = {Integrated cross-sectoral surveillance of antimicrobial resistance genotypes and phenotypes across disparate reservoirs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0074126},
doi = {10.1128/msystems.00741-26},
pmid = {42803537},
issn = {2379-5077},
abstract = {Antimicrobial-resistant (AMR) bacteria and genes are continually exchanged among humans, animals, and environmental reservoirs. Disparate and siloed surveillance methods present a major challenge for tracing and disrupting AMR transmission, with clinical monitoring focusing on detecting specific pathogens or specific genes of interest, and environmental surveys often relying on inferences drawn from indicator organisms. Here, we demonstrate that, following sample-specific pre-processing, common surveillance approaches can be applied consistently to profile AMR abundance, distribution, and phenotypes across diverse reservoirs in both urban and agricultural settings. Across all sample types, three core methods provided complementary insights: (i) quantitative PCR (qPCR) arrays to measure multiple AMR genes, (ii) gene- and genome-centric metagenomics for comprehensive resistome profiling, and (iii) culture-based genomics with susceptibility testing to link genotypes to phenotypes. We applied this approach to profile 1,032 metagenome-assembled genomes, 66 bacterial isolate genomes, and 78 and 6,642 AMR genes/reference sequences via qPCR and metagenomics, respectively. This integrated framework revealed the prevalence and diversity of resistance mechanisms in both putative pathogens and non-pathogenic bacteria with potentially transmissible genes, with wastewater especially enriched in AMR genes. We detected mismatches between genotype and phenotype predictions and a prevalence of intermediate resistance phenotypes, highlighting how many mechanisms of environmental resistance remain poorly understood. Overall, this study demonstrates that unified, field-leading surveillance methods can be used in diverse environmental and animal samples while highlighting that multiple methods are needed to capture the diverse AMR genotypes and phenotypes in these settings to enable comprehensive monitoring and adaptive solutions to restrict transmission.IMPORTANCEAntimicrobial resistance (AMR) is driven by the exchange of resistant bacteria and genes across interconnected human, animal, and environmental reservoirs, yet fragmented surveillance limits our ability to track transmission and intervene effectively. We demonstrate that widely used surveillance methods can be applied cohesively across diverse sample types, including wastewater, soil, water, agricultural environments, and fecal samples, to generate comparable insights into AMR abundance, diversity, and phenotype. By integrating qPCR, metagenomics, and culture-based genomics, we reveal resistance in both pathogenic and non-pathogenic bacteria, reaffirm wastewater as a major AMR reservoir, and uncover frequent mismatches between genetic predictions and observed susceptibility. The prevalence of intermediate resistance further suggests that many environmental resistance mechanisms remain poorly understood. These findings show that no single method captures AMR complexity and highlight the need for unified, multi-method surveillance to support comprehensive monitoring and strategies to control the spread of resistance.},
}

@article {pmid42803564,
year = {2026},
author = {Wolfe, MK and North, D and Jaffe, AL and Zulli, A and Duong, D and Shelden, B and Goldman, M and Richardson, M and Thana, P and Chan-Herur, V and Kheradpour, P and Bidwell, AL and Hilton, SP and Conforti, S and Paulos, AP and Boehm, AB},
title = {Prospective metagenomic sequencing of wastewater across the United States yields robust viral enrichment and concordance with digital PCR measurements.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0102026},
doi = {10.1128/aem.01020-26},
pmid = {42803564},
issn = {1098-5336},
abstract = {Metagenomic sequencing is increasingly applied to wastewater to characterize the diversity, dynamics, and relative abundance of human and animal viruses. Among these sequencing approaches are those that enrich viral nucleic acids from the wastewater matrix, aiming to increase the viral read fraction for analysis. However, the feasibility of scaling targeted viral sequencing to diverse sewersheds across large geographic scales is currently unknown. In this study, we apply hybrid capture metagenomic sequencing to nearly 450 weekly wastewater samples collected during the respiratory virus season in the United States and evaluate sequencing performance for generating public health-relevant data. Analysis of data from 15 wastewater treatment plants demonstrates that our approach enabled efficient capture of pathogens of interest, achieving a median viral read fraction over 19%. Importantly, relative abundance estimates of common pathogens correlated with direct quantification of viral targets using reverse transcription digital droplet PCR. Together, our results demonstrate that hybrid capture sequencing of wastewater is a viable tool to monitor both common and rare pathogens across geographically diverse sewersheds.IMPORTANCEWastewater testing is commonly used to identify and quantify human pathogens at a community scale. However, the most commonly used approaches rely on targeted, PCR-based methods that are highly specific to a single virus. Metagenomic sequencing provides an opportunity to detect and quantify the relative abundance of a wide range of viruses that are important for human health from wastewater, and hybrid capture approaches work by first enriching samples for these extremely rare targets to increase sensitivity. We demonstrate that hybrid capture metagenomic sequencing successfully enriches wastewater samples from diverse locations across the United States and that data derived from sequences are associated with detections of 11 key viruses using standard RT-ddPCR methods. This work suggests that scaling hybrid capture metagenomics for viruses in wastewater is a feasible way to generate data critical for public health to support infectious disease outbreak response.},
}

@article {pmid42803581,
year = {2026},
author = {Lim, S and Murali, R and Speth, DR and Szabo, RE and Cordero, OX and Orphan, VJ},
title = {Activity and diversity of sulfate- and methane-based pathways of anaerobic chitin and N-acetylglucosamine degradation in marine sediments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0128026},
doi = {10.1128/aem.01280-26},
pmid = {42803581},
issn = {1098-5336},
abstract = {UNLABELLED: Sulfate reduction is estimated to account for half of the organic carbon respiration in anoxic, organic-rich ocean sediments. Sulfate-reducing microorganisms (SRMs) typically oxidize simple carbon compounds, such as primary alcohols, or small fatty acids. However, much of the organic input to the seafloor is complex, driving interactions between terminal respirers, such as SRMs and methanogens, and primary degraders that initiate the breakdown of complex organic carbon. To explore how these interactions shape sediment microbiomes, we conducted multi-month microcosm experiments using serially diluted sediments in deep 96-well plates. Sediments from a former deep-sea whalefall site were amended with either the insoluble polymer chitin or its soluble monomer N-acetylglucosamine. The high replication in these experiments allowed us to evaluate the effects of complex versus labile carbon on degradation activity, microbial diversity, community structure, and functional redundancy over time. Geochemical analysis, combined with 16S rRNA gene sequencing and metagenomics, revealed that chitin addition preserved higher microbial diversity and increased predicted interactions among microorganisms. Despite anaerobic chitin degradation producing N-acetylglucosamine, microbial communities enriched by these substrates showed low nestedness over the 7-month experiment. Complex carbon inputs fostered unique microbial assemblages and functional interactions, including the emergence of diverse methanogenic lineages at medium to high dilutions-less apparent in monomer treatments. In microoxic sediments, methanogens and other rare biosphere members co-exist with SRM and dynamically respond to complex carbon inputs. Our results highlight the contribution of carbon complexity and recalcitrance in stimulating metabolically diverse community members in sediments, driving the assembly of functional microbial networks.

IMPORTANCE: Deep-sea sediments cover over 60% of the planet's surface and harbor diverse microbial communities that are important contributors to the carbon and nitrogen budget of the ocean. Despite their importance, the mechanisms by which these communities maintain diversity are poorly understood. In this work, we discuss the contribution of complex carbon to the community structure of marine sediment microbial consortia through the establishment of highly replicated anaerobic incubations provided with either the complex cosmopolitan carbon source chitin or its monomer N-acetylglucosamine.},
}

@article {pmid42803773,
year = {2026},
author = {Ettinger, CL and Eisen, JA and Stajich, JE},
title = {Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001845},
pmid = {42803773},
issn = {2057-5858},
mesh = {*Zosteraceae/microbiology/genetics ; *Metagenome ; Phylogeny ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Chytridiomycota/genetics/classification ; Genome, Fungal ; Diatoms/genetics/classification ; },
abstract = {Fungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associated with the seagrass, Zostera marina, have revealed an abundance of potentially novel chytrids. In this study, we employed deep metagenomic sequencing to extract metagenome-assembled genomes (MAGs) from these chytrids and other microbial eukaryotes associated with Z. marina leaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Lobulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte alga in the genus Prymnesium (40% BUSCO completeness). Whole-genome phylogenomic assessment of these MAGs suggests they all largely represent undersequenced and possibly novel eukaryotic lineages. Of particular interest, the chytrid MAG was placed within the order Lobulomycetales, consistent with the identity of the dominant chytrid from previous Z. marina amplicon survey results. Annotation of this MAG yielded 5,650 gene models, of which 77% shared homology with current databases. Within these gene models, we predicted 121 carbohydrate-active enzymes (CAZymes) and 393 secreted proteins (103 cytoplasmic effectors, 30 apoplastic effectors). Exploration of orthologs between the Lobulomycetales MAG and existing Chytridiomycota genomes has revealed a landscape of high-copy gene families related to host recognition and interaction. Further machine learning analyses based on CAZyme composition classified this MAG's CAZyme profile as most consistent with a symbiotic lifestyle. Overall, these five eukaryotic MAGs represent substantial genomic novelty and valuable community resources, contributing to a deeper understanding of the roles of fungi and other microbial eukaryotes in the larger seagrass ecosystem.},
}

*Zosteraceae/microbiology/genetics
*Metagenome
Phylogeny
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
*Chytridiomycota/genetics/classification
Genome, Fungal
Diatoms/genetics/classification

@article {pmid42803857,
year = {2026},
author = {Ali, S and Ali, B and Shaukat, A and Alghamdi, S and Kabrah, A and Ahmed, MA and Zhang, L},
title = {From dysbiosis to disease: the role of gut microbial communities in Toxoplasma gondii pathogenesis, zoonotic transmission, diagnostic innovation, and therapeutic outcomes.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42803857},
issn = {1573-7446},
mesh = {Animals ; *Dysbiosis/veterinary/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Toxoplasma/physiology ; *Zoonoses/transmission/parasitology/microbiology ; Humans ; *Toxoplasmosis, Animal/transmission/microbiology/diagnosis ; *Toxoplasmosis/transmission/therapy/microbiology/diagnosis/parasitology ; },
abstract = {Toxoplasma gondii, an obligate intracellular protozoan infecting approximately one-third of the global human population, causes substantial morbidity in immunocompromised individuals, congenital complications, neuropsychiatric sequelae, and considerable economic losses in livestock production. Gut microbial communities critically modulate T. gondii infection susceptibility, disease progression, and clinical outcomes, positioning the microbiome as a central axis in toxoplasmosis pathogenesis. This review examines the bidirectional relationship between gut microbiota and T. gondii, wherein dysbiosis functions simultaneously as a consequence and driver of disease severity. Protective commensal taxa reinforce intestinal barrier integrity, produce short-chain fatty acids, and stimulate anti-parasitic immunity through IFN-γ, IL-12, and tryptophan-aryl hydrocarbon receptor signaling, while pathobionts exacerbate immunopathology via TLR4 and inflammasome activation. Conversely, acute infection drives rapid microbial community collapse with persistent Proteobacteria expansion, butyrate-producing taxa depletion, neuroinflammation, and cognitive impairment in chronic infection. Across the One Health spectrum, host-specific microbiome signatures in felids, livestock, wildlife, and environmental reservoirs modulate zoonotic transmission dynamics and population-level susceptibility. Diagnostically, emerging microbiome-based approaches including metagenomics and multi-omics platforms offer promising biomarker discovery opportunities, though validated clinical signatures remain absent. Microbiome-targeted therapeutic strategies including probiotics, prebiotics, fecal microbiota transplantation, and postbiotics show preclinical promise, although human clinical trial validation is critically lacking. Critical research gaps and interdisciplinary One Health priorities are identified to advance microbiome-informed surveillance, diagnosis, and treatment of toxoplasmosis.},
}

Animals
*Dysbiosis/veterinary/parasitology/microbiology
*Gastrointestinal Microbiome
*Toxoplasma/physiology
*Zoonoses/transmission/parasitology/microbiology
Humans
*Toxoplasmosis, Animal/transmission/microbiology/diagnosis
*Toxoplasmosis/transmission/therapy/microbiology/diagnosis/parasitology

@article {pmid42804018,
year = {2026},
author = {Ren, G and Yang, W and Wang, J and Zhang, J and Gao, H and Gao, X and Chen, X and Wang, T and Cao, L and Wang, Z and Xiao, W},
title = {Longxue tongluo capsule enhances ischemic stroke recovery via microbiota-metabolite-gene interactions.},
journal = {Metabolic brain disease},
volume = {41},
number = {1},
pages = {},
pmid = {42804018},
issn = {1573-7365},
support = {JCYJ2326//Lianyungang Science and Technology Bureau/ ; JSTJ-2025-858//Young Elite Scientists Sponsorship Program by Jiangsu Province/ ; LYG06521202221//The sixth phase of the 521 Project scientific research funding project of Lianyungang/ ; BK20232014//Basic Research Program Natural Science Fund -Frontier Leading Technology Basic Research Special Project of Jiangsu Province/ ; },
mesh = {Animals ; *Ischemic Stroke/drug therapy/metabolism/genetics ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Recovery of Function/drug effects ; Male ; Brain/drug effects/metabolism ; *Brain Ischemia/drug therapy/metabolism ; Rats ; },
abstract = {The gut-brain axis represents an emerging therapeutic target. This study seeks to investigate the regulatory effects of LXTL on the brain-gut axis and to elucidate its mechanism of action during the ischemic stroke recovery period. This study investigated the effects of LXTL on a middle cerebral artery occlusion and reperfusion model. The assessment of recovery effects was conducted through the evaluation of brain injury scores, Y-maze performance, open field tests. Furthermore, comprehensive analyses were conducted on the gut microbiota, damaged brain tissue, cecal contents, and brain samples using metagenomic sequencing, transcriptomic sequencing, and non-targeted metabolomics. And the selected targets were verified. Integrated analyses were conducted by constructing correlation networks and performing joint pathway enrichment to elucidate the connections between microbial alterations, metabolite changes, and gene expression modifications. LXTL improved cognitive and exploratory behaviors, reduced brain damage and neuron loss, and enhanced gut health by increasing beneficial bacteria like Eubacterium and Kurthia. It boosted SCFAs, neuroactive metabolites, and altered nucleotide metabolism. LXTL is linked to genes involved in neurorepair and immune homeostasis, correlates with microglial polarization, and is associated with genes such as Ngfr, Card9, Chat, Nkg7, and Gch1 within the pertinent pathways. The integrated network linked LXTL-enhanced microbiota, gut and brain metabolites, and repair genes, facilitating recovery through a neurorepair-immune-metabolic triad. LXTL aids ischemic stroke recovery by altering gut microbiota and gut-brain metabolite profiles, while regulating brain gene networks related to neuroplasticity, inflammation, and metabolism. This demonstrates LXTL's multi-target effects through the gut-brain axis, underscoring the potential of herbal medicine in stroke rehabilitation.},
}

Animals
*Ischemic Stroke/drug therapy/metabolism/genetics
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Recovery of Function/drug effects
Male
Brain/drug effects/metabolism
*Brain Ischemia/drug therapy/metabolism
Rats

@article {pmid42804444,
year = {2026},
author = {Kirtane, A and van der Loo, E and Doppmann, Z and Deiner, K},
title = {Distinct Environmental DNA States Reveal Biodiversity and Transport Patterns Across Alpine Watersheds.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70207},
doi = {10.1111/1755-0998.70207},
pmid = {42804444},
issn = {1755-0998},
support = {852621//H2020 European Research Council/ ; },
mesh = {*DNA, Environmental/genetics/isolation & purification ; *Biodiversity ; Animals ; Extrachromosomal DNA ; Lakes ; *Rivers/chemistry ; Plants/genetics/classification ; DNA Barcoding, Taxonomic ; Metagenomics/methods ; },
abstract = {Environmental DNA (eDNA) exists in three states: membrane-bound, adsorbed and dissolved. These states differ in persistence and degradation, strongly influencing the interpretation of eDNA data. Despite this, they have rarely been separated and analyzed independently from environmental samples. We developed a state-sorting workflow to isolate and analyze them, applying it to samples from 221 sites from 58 streams across eight lake watersheds with COI and ITS metabarcoding, targeting metazoans and plants, respectively, to reveal differences in biodiversity content and transport dynamics. Our results show that all three states contain both shared and unique taxonomic diversity of metazoan eDNA. However, the plant eDNA was only detected in the membrane-bound state. For metazoans, membrane-bound eDNA contained 87.8% of observed ASVs, far exceeding the adsorbed (37.2%) and dissolved (20.5%) states. Only membrane-bound eDNA showed evidence of downstream transport, but its extent varied among watersheds due to local hydrology. While upstream eDNA was transported to stream-lake confluences, lake surface samples showed a turnover in community composition. Clarifying the fate of membrane-bound eDNA within lakes will enhance catchment-level detection from lake samples and understanding of lake hydrodynamics. Of the environmental parameters assessed, water temperature was most strongly aligned with changes in community composition between sites. Most previous studies have likely captured the majority of the eDNA diversity within their samples by inadvertently targeting the membrane-bound state. This study demonstrates the utility of eDNA state-sorting, but the methods require further refinement. Analyzing states independently improves the interpretation of eDNA data and elucidates the processes governing eDNA fate and transport.},
}

*DNA, Environmental/genetics/isolation & purification
*Biodiversity
Animals
Extrachromosomal DNA
Lakes
*Rivers/chemistry
Plants/genetics/classification
DNA Barcoding, Taxonomic
Metagenomics/methods

@article {pmid42804599,
year = {2026},
author = {Hensen, T and Khatib, L and Patel, L and McDonald, D and González, A and MahmoudianDehkordi, S and Blach, C and Knight, R and Kaddurah-Daouk, R and Thiele, I},
title = {Personalized whole-body modeling links gut microbiota to metabolic perturbations in Alzheimer's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2732659},
doi = {10.1080/19490976.2026.2732659},
pmid = {42804599},
issn = {1949-0984},
mesh = {Humans ; *Alzheimer Disease/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Aged ; Bacteria/classification/isolation & purification/genetics/metabolism ; Cognitive Dysfunction/metabolism/microbiology ; Aged, 80 and over ; Metabolome ; },
abstract = {The human gut microbiome has been linked to metabolic disturbances in Alzheimer's disease (AD). However, the mechanisms by which gut microbes might influence metabolic dysfunction in AD remain poorly understood. Previously, gut microbiome-personalized whole-body models of human metabolism have been applied to predict how altered gut microbiome compositions may influence metabolites in the blood of healthy aging individuals with increased risk of AD. However, these previous results have not been validated in AD. In this study, we aimed to test these prior predictions in a cohort of AD dementia patients and individuals with mild cognitive impairment (MCI) and a probable AD diagnosis. Therefore, we created gut microbiome-personalized whole-body metabolic models for 34 AD dementia patients, 51 MCI patients, and 298 healthy controls. These in silico models were profiled to predict the metabolic influences of gut microbiomes on blood metabolites with previously reported alterations in AD. We found increased capacities of the in silico host-microbiome co-metabolism to produce S-adenosyl-L-methionine, L-arginine, creatine, taurine, and formate in the blood of AD patients. The metabolic predictions were then linked to key microbial taxa using a novel method that combines modeling-informed prediction sensitivity to alternative microbial abundances with LASSO-based taxonomic stability selection and elastic net regressions. This method found that increased relative abundances of Bacteroides uniformis and Bacteroides thetaiotamicron in AD were major factors driving the predicted metabolic changes. Furthermore, the metabolic predictions were associated with allelic variations in the APOE risk gene in healthy individuals, confirming our previous findings. In conclusion, we identified blood metabolites with known links to AD that were differentially influenced by gut microbiota in AD, and identified possible microbial drivers of these predicted shifts in host-microbiome interactions. These findings may facilitate the development of microbiome-informed treatments of AD.},
}

Humans
*Alzheimer Disease/microbiology/metabolism/blood
*Gastrointestinal Microbiome
Male
Female
Aged
Bacteria/classification/isolation & purification/genetics/metabolism
Cognitive Dysfunction/metabolism/microbiology
Aged, 80 and over
Metabolome

@article {pmid42804827,
year = {2026},
author = {Chen, S and Zhang, S and Liu, C and Wang, K and Xu, L and Cao, Z},
title = {Fermented agricultural by-products improve growth performance in indigenous chickens in association with altered ileal microbiota, microbial functional potential, and mucosal responses.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107839},
doi = {10.1016/j.psj.2026.107839},
pmid = {42804827},
issn = {1525-3171},
abstract = {Fermented agricultural by-products may improve poultry health through microbiota-host interactions, but the underlying microbial and transcriptional responses remain incompletely understood. We assigned 160 Wuliangshan black-bone chickens to diets containing 0%, 5%, 10%, or 15% fermented feed from 8 to 120 d of age. The fermented feed was produced from soybean hulls, rapeseed meal, and vegetable waste by sequential fermentation with Bacillus subtilis, Lactiplantibacillus plantarum, and Limosilactobacillus reuteri. Ileal microbial communities were profiled by 16S rRNA gene sequencing, followed by shotgun metagenomics and ileal mucosal transcriptomics in the control and 10% groups. Fermented feed increased average daily gain (ADG) and ileal villus height and reduced feed conversion ratio (FCR). The 10% diet increased the relative abundance of Lactiplantibacillus from 1.05% to 74.47%, while reducing Enterococcus, Streptococcus, Staphylococcus, and Escherichia-Shigella. Metagenomic analysis revealed enrichment of microbial pathways and carbohydrate-active enzymes associated with starch and plant cell-wall polysaccharide degradation. Ileal butyrate concentration increased, whereas predicted virulence determinants, including cereulide, β-hemolysin/cytolysin, and LPS/LOS-related factors, decreased. The resistome shifted toward efflux-related determinants without broad enrichment of antimicrobial resistance genes. Ileal mucosal transcriptomics revealed lower expression of proinflammatory and innate immune genes and higher expression of genes involved in growth signaling and nutrient transport. Spearman correlation analysis showed that Lactiplantibacillus abundance and butyrate concentration were associated with higher ADG, villus height, and expression of growth-related genes and with lower FCR. Lactiplantibacillus abundance was also positively correlated with selected nutrient transport genes and negatively correlated with selected immune-related genes, whereas the depleted potentially opportunistic genera generally showed opposite correlation patterns. Collectively, fermented feed improved growth performance and intestinal health in association with Lactiplantibacillus enrichment, reduced predicted microbial virulence potential, attenuated mucosal immune activation, and enhanced host responses related to growth and nutrient transport.},
}

@article {pmid42805071,
year = {2026},
author = {Hui, J and Ren, J and Yang, X and Jia, Z and Zhang, Y and Wan, T and Wang, M and Cheng, W},
title = {Hydrodynamic regulation drives azo dye transformation and hydrolysis acidification by reshaping microbial metabolism in the micro-aerobic hydrolysis acidification reactor.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143745},
doi = {10.1016/j.jhazmat.2026.143745},
pmid = {42805071},
issn = {1873-3336},
abstract = {Acid Red GR is a representative sulfonated azo dye frequently detected in dyeing wastewater, yet the role of hydrodynamic conditions in regulating its biodegradation in micro-aerobic hydrolysis acidification (MAHA) systems remains unclear. This study investigated how hydrodynamic conditions drive Acid Red GR transformation, hydrolysis acidification, and microbial metabolic responses in the MAHA reactor. The results showed that a moderate stirring speed of 120 rad/min (R2) balanced turbulence intensity and flow uniformity, with relatively high oxygen transfer, a favorable micro-aerobic niche, and the highest biodegradability (0.50) and volatile fatty acid (VFA) production (140.38 mg/L). This hydrodynamic condition enriched hydrolytic, facultative, and fermentative genera, including Klebsiella, Enterobacter, Bacteroides, Propionivibrio, and Bacillus, and was associated with higher abundances of genes encoding enzymes involved in azo reduction, aromatic intermediate transformation, pyruvate generation, and acidogenic metabolism. Integrated metagenomic, metabolomic, and functional group evidence further indicated that Acid Red GR degradation proceeded through azo reduction, deamination, desulfonation, aromatic ring cleavage, and subsequent acidogenesis. These findings demonstrate that hydrodynamic optimization regulates MAHA performance by coordinating oxygen transfer, microbial niche formation, and metabolic functional potential, providing a mechanistic basis for enhancing the biodegradability and treatment efficiency of dyeing wastewater.},
}

@article {pmid42799756,
year = {2026},
author = {Westerbeke, FHM and Warmbrunn, MV and Rios-Morales, M and Li, XS and Tian, MY and Novak, MA and Williams, AM and Hazen, SL and Attaye, I and Nieuwdorp, M},
title = {Plasma indole-3-propionic acid is a gut-derived metabolite and is associated with type 2 diabetes and cardiometabolic outcomes: Evidence from a human antibiotic intervention.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2736321},
doi = {10.1080/19490976.2026.2736321},
pmid = {42799756},
issn = {1949-0984},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/blood/metabolism/drug therapy ; *Indoles/blood ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Male ; Female ; Middle Aged ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Adult ; Propionates ; },
abstract = {The gut microbiota influences host metabolism through diverse metabolites, many of which have been linked to glucose homeostasis and type 2 diabetes (T2D). Understanding microbial contributions to metabolite biosynthesis is essential for developing dietary and microbiota-targeted T2D prevention and treatment strategies. We performed targeted plasma metabolomics in individuals with T2D and healthy controls, all receiving histidine supplementation, before and after gut microbiota suppression using 7-day broad-spectrum antibiotic treatment. Associations between pre-antibiotic metabolite levels and fecal metagenomics-derived gut microbiota composition were examined using co-abundance network analysis and Random Forest modeling. Indole-3-propionic acid (IPA) was the only gut-derived metabolite differing between groups before antibiotics, with lower levels in T2D and higher levels associated with reduced T2D odds. Antibiotic treatment reduced IPA to near-undetectable levels in both groups, confirming its predominantly microbial origin. Beyond established inverse associations with BMI and glycemic markers, we found a novel inverse correlation between IPA and glycemic variability, consistent with a protective association with T2D. Plasma IPA was associated with gut microbiota beta diversity. IPA-associated species clustered within a single co-abundance module, but did not include known IPA producers, suggesting plasma IPA is influenced by broader microbial community composition rather than IPA-producing capacity of individual taxa alone. This study provides direct human evidence that plasma IPA is virtually exclusively gut microbiota-derived in individuals with T2D, extending prior findings in healthy populations. It highlights IPA's relevance to metabolic health and T2D, and guides future research on dietary and microbiota-targeted strategies to modulate IPA, advancing T2D prevention and treatment.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/blood/metabolism/drug therapy
*Indoles/blood
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Male
Female
Middle Aged
Feces/microbiology
Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
Adult
Propionates

@article {pmid42799757,
year = {2026},
author = {Zhang, J and Cao, X and Baniakina, LFT and Chai, L},
title = {Exploring biochar-mediated remediation of tetracycline-contaminated soil via a metagenomic approach: insights into soil microbial community and potential functions.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42799757},
issn = {1432-072X},
mesh = {*Charcoal/chemistry ; *Soil Microbiology ; *Tetracycline/pharmacology/metabolism ; Metagenomics ; *Bacteria/genetics/classification/drug effects/isolation & purification/metabolism ; *Soil Pollutants/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects/genetics ; Biodegradation, Environmental ; Soil/chemistry ; },
abstract = {Biochar is widely used as a soil amendment; however, information regarding its effects on soil microbial communities under tetracycline (TET) stress remains limited. In this study, metagenomic sequencing was employed to investigate the effects of TET contamination and biochar amendment on soil microbial community profiles, the abundance of antibiotic resistance genes (ARGs), and carbohydrate-active enzymes (CAZymes) genes through a pot experiment. Results showed that TET exposure reduced microbial diversity and evenness, and significantly altered the relative abundance of dominant microbes (e.g., Acidobacteriota and Candidatus_Rokubacteria) whereas biochar amendment especially at 0.5% application significantly increased both diversity and evenness, facilitated the recovery of dominant microbes, and improved community stability. TET exposure also enriched glycopeptide resistance genes and shifted CAZyme gene profiles. Overall, the metagenomic results demonstrated that reed biochar can regulate soil microbial responses under TET stress, providing insights into its role in alleviating antibiotic-induced microbial disturbance and supporting soil ecological resilience.},
}

*Charcoal/chemistry
*Soil Microbiology
*Tetracycline/pharmacology/metabolism
Metagenomics
*Bacteria/genetics/classification/drug effects/isolation & purification/metabolism
*Soil Pollutants/metabolism
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects/genetics
Biodegradation, Environmental
Soil/chemistry

@article {pmid42799847,
year = {2027},
author = {Ruiz-Padilla, A and Rodríguez-Romero, JL and Chiapello, M and Ayllón, MA},
title = {Identification of Mycoviral Infections.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3076},
number = {},
pages = {81-109},
pmid = {42799847},
issn = {1940-6029},
mesh = {*Fungal Viruses/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; *Botrytis/virology/genetics ; Computational Biology/methods ; RNA, Viral/genetics/isolation & purification ; Genome, Viral ; Metagenomics/methods ; },
abstract = {High-throughput sequencing of total RNA has permitted the detection of novel mycoviruses in fungi with different types of genomes, including mycoviruses with double-stranded RNA, single-stranded positive- or negative-stranded RNA, or single-stranded DNA genomes. However, in silico detection of mycoviruses is not always sufficient to guarantee their presence in sequenced samples, especially in the case of the discovery of unique mycoviruses, and additional analyses are required to validate in vivo the data obtained by bioinformatics analysis. This chapter provides comprehensive protocols for the extraction of total RNA from the plant pathogenic fungus Botrytis cinerea for next-generation sequencing (NGS), outlines the bioinformatics pipeline designed and followed to detect mycoviruses in the sequenced samples, and details the detection in vivo and the complete molecular characterization of the mycoviruses identified in silico.},
}

*Fungal Viruses/genetics/isolation & purification
High-Throughput Nucleotide Sequencing/methods
*Botrytis/virology/genetics
Computational Biology/methods
RNA, Viral/genetics/isolation & purification
Genome, Viral
Metagenomics/methods

@article {pmid42800338,
year = {2026},
author = {Gui, Y and Yu, W and Shi, Y and Li, Y and Yang, X and Zhang, H and Yan, W and Liu, Q and Jiang, G},
title = {Microbial filtering and functional reprogramming in soil exposed to spent NCM battery black powder.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120847},
doi = {10.1016/j.ecoenv.2026.120847},
pmid = {42800338},
issn = {1090-2414},
abstract = {Spent lithium-ion battery black powder is an emerging complex contaminant, which contains transition metals, residual electrolyte salts, and compounds derived from organic electrolytes or binders. Its ecological effects on soil microbiomes remain poorly understood. Here, we designed a soil microcosm experiment with using red soil exposed to a concentration gradient of black powder derived from nickel-cobalt-manganese (NCM) lithium-ion batteries. Samples were collected at two incubation time points and analyzed by shotgun metagenomic sequencing. Black powder exposure produced a nonlinear taxonomic response, with species-level alpha diversity increasing under intermediate exposure, while rare-taxon abundance distributions shifted markedly under medium and high exposure. The LEfSe and PLS-DA analyses identified concentration- and time-dependent indicator taxa, including enrichment of Actinomycetota-related taxa and depletion of Nitrospira and Candidatus Methylomirabilis under high exposure. Community structure diverged significantly along the concentration gradient, and PERMANOVA attributed 23.2% of taxonomic variation to treatment. Structural equation modeling showed no significant direct path from black powder concentration to functional potential; instead, the model was consistent with a possible indirect association through community restructuring. Functional alpha diversity generally declined with increasing black powder concentration. High concentration exposure was associated with reduced relative abundance of KEGG Orthology entries (KOs) related to nitrogen cycling and increased stress-response and organic-matter-decomposition signatures. Overall, these results suggest that NCM-derived black powder can alter soil microbial functional profiles by reshaping community composition.},
}

@article {pmid42800367,
year = {2026},
author = {Shen, S and Zhou, Y and Qian, J and Li, T and Hu, X and Ji, X and Zhang, X and Zhou, D},
title = {An intestine-centric view of neurodegeneration: How intestine-derived signals mediate the intestine-brain axis to impact Alzheimer's disease.},
journal = {Journal of neuroimmunology},
volume = {421},
number = {},
pages = {579102},
doi = {10.1016/j.jneuroim.2026.579102},
pmid = {42800367},
issn = {1872-8421},
abstract = {Alzheimer's disease (AD) has emerged as an increasingly prevalent and burdensome public health challenge with global aging, underscoring the urgent need to clarify the key factors involved in its pathogenesis for effective prevention and management. Mounting evidence suggests that disrupted crosstalk between the intestine and brain may contribute to aging-related neurodegeneration, including AD. Acting as a peripheral modulatory hub of the intestine-brain axis, the intestine releases a variety of bioactive substances that regulate brain function. This narrative review synthesizes current evidence on intestine-derived signaling molecules and immune mediators implicated in AD pathogenesis, with a focus on two primary communication routes: the vagus nerve and systemic circulation. In addition, intestine-targeted interventions-including dietary modification, probiotic supplementation, and fecal microbiota transplantation-are summarized. Notably, metagenomics-based intestinal microbiota aging clocks represent an emerging non-invasive strategy for AD risk prediction. Although preclinical findings are encouraging, the translational limitations and heterogeneity of current intestine-brain research remain noteworthy. In summary, this narrative review integrates substantial evidence on the correlation between intestine-derived mediators and AD and provides potential insights for the development of intestine-targeted preventive strategies.},
}

@article {pmid42800459,
year = {2026},
author = {Hui, H and Huang, W and Song, T and Song, Y and Zhang, X and Wang, R and Yang, J and Wu, S and Li, X and Peng, J},
title = {Modified citrus pectin orchestrates hepatic redox homeostasis through an Alistipes dispar-nicotinamide-sirtuin 1 axis to mitigate metabolic dysfunction-associated steatotic liver disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158817},
doi = {10.1016/j.phymed.2026.158817},
pmid = {42800459},
issn = {1618-095X},
abstract = {BACKGROUND: Modified citrus pectin (MCP) is a bioactive functional component with potential metabolic benefits, but its therapeutic mechanisms in metabolic dysfunction-associated steatotic liver disease (MASLD) remain unclear.

PURPOSE: To determine whether MCP alleviates MASLD through gut microbiota remodelling and to identify the key microbial and metabolic mediators involved.

STUDY DESIGN: MASLD mouse models, multi-omics analyses, fecal microbiota transplantation (FMT), bacterial supplementation, and pharmacological inhibition were integrated to establish microbiota-metabolite-host causality.

METHODS: MCP efficacy was evaluated by assessing hepatic steatosis, inflammation, oxidative stress, and lipid metabolism. Metagenomics and metabolomics were used to identify MCP-responsive microbes and metabolites. FMT, administration of live or heat-killed Alistipes dispar, validation in db/db mice, and SIRT1 knockdown and inhibition with EX-527 were performed to verify causality and mechanism.

RESULTS: MCP markedly reduced hepatic lipid accumulation, inflammation, and oxidative stress. Metagenomics identified enrichment of A. dispar as a key microbial signature associated with MCP efficacy. Live, but not heat-killed, A. dispar reproduced the protective effects of MCP and improved metabolic abnormalities in db/db mice. Mechanistically, MCP promoted A. dispar proliferation and increased nicotinamide levels, activating hepatic nicotinamide salvage and the SIRT1/PGC-1α/PPARα/CPT1A axis to enhance fatty acid oxidation. This response also suppressed COX-2/HMGB1-mediated inflammation and activated Nrf2/HO-1 antioxidant defence. EX-527 abolished the beneficial effects of MCP and A. dispar.

CONCLUSION: MCP alleviates MASLD through an A. dispar-nicotinamide-SIRT1 axis that restores metabolic, inflammatory, and redox homeostasis.},
}

@article {pmid42800885,
year = {2026},
author = {Feng, X and Wang, LY and Li, NJ and Lin, ZQ and Huang, HM and Xie, YL and Liang, J and Yao, L and Zhuo, XY and Li, Y and Qiu, Y},
title = {Pulmonary Actinomycosis Diagnosed via BALF mNGS in a 53-Year-Old Nonsmoking Man With Pneumoconiosis and Penicillin-Induced Thrombocytopenia: A Case Report.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e953438},
doi = {10.12659/AJCR.953438},
pmid = {42800885},
issn = {1941-5923},
mesh = {Humans ; Male ; *Actinomycosis/diagnosis/drug therapy ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Actinomyces/isolation & purification/genetics ; *Thrombocytopenia/chemically induced ; *Pneumoconiosis/complications ; *Penicillins/adverse effects ; *Anti-Bacterial Agents/adverse effects ; },
abstract = {BACKGROUND Pulmonary actinomycosis is an uncommon infection with nonspecific clinical and radiologic features that can be difficult to distinguish from lung malignancy, tuberculosis, and other chronic pulmonary diseases. This report describes a patient with pneumoconiosis in whom bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) provided important microbiologic evidence to support the diagnosis of pulmonary actinomycosis after inconclusive conventional evaluation. CASE REPORT A 53-year-old nonsmoking presented with a 1-month history of cough and hemoptysis. Chest computed tomography showed bilateral upper-lung masses, multiple nodules, and lymphadenopathy; he initially underwent right upper lobectomy because malignancy was suspected. Histopathologic examination showed necrotizing granulomatous inflammation with carbon deposition, but no specific pathogen was identified. Empirical antituberculosis treatment was ineffective. After transfer to our hospital, bronchoscopy was performed. Routine BALF culture and staining results were negative, whereas mNGS detected Actinomyces israelii. Intravenous ampicillin/sulbactam led to clinical and radiologic improvement, but severe thrombocytopenia developed. Platelet counts decreased again after subsequent penicillin exposure, supporting probable penicillin-induced thrombocytopenia. After discontinuation of penicillin and joint evaluation by respiratory physicians and clinical pharmacists, omadacycline was administered, followed by oral doxycycline. The patient displayed clinical improvement, platelet counts normalized, and follow-up imaging showed lesion absorption. CONCLUSIONS This case illustrates the diagnostic difficulty of pulmonary actinomycosis in a patient with pneumoconiosis and suggests that BALF mNGS can be helpful when routine studies are unrevealing. It also indicates that omadacycline is a feasible alternative when penicillin-associated thrombocytopenia prevents continuation of first-line therapy.},
}

Humans
Male
*Actinomycosis/diagnosis/drug therapy
Middle Aged
*Bronchoalveolar Lavage Fluid/microbiology
Actinomyces/isolation & purification/genetics
*Thrombocytopenia/chemically induced
*Pneumoconiosis/complications
*Penicillins/adverse effects
*Anti-Bacterial Agents/adverse effects

@article {pmid42801092,
year = {2026},
author = {Derrick, E and Barbosa da Costa, N and Barrett, RDH and Shapiro, BJ},
title = {Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton species.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag201},
pmid = {42801092},
issn = {2730-6151},
abstract = {Bacterial populations evolve rapidly in the lab when faced with experimentally applied selective pressures. Yet how bacteria evolve in nature, in more complex multi-species communities, is both challenging to study and essential to our understanding of ecosystem responses to rapid anthropogenic change. To track bacterial evolution in a semi-natural context, we applied Roundup, a glyphosate-based herbicide (GBH) that interferes with aromatic amino acid synthesis, as a selective pressure to 1000 L ponds containing bacterioplankton communities from a pristine lake. We show that both ecological and evolutionary changes can occur on short timescales after a strong selective pressure. Using metagenome-assembled genomes as a proxy for species, we found that GBH treatment substantially affected community diversity but did not purge within-species genetic diversity over the 4 weeks of the experiment. We identified several functional categories of genes consistently targeted by GBH selection across seven different species of bacteria. Genes involved in amino acid transport and metabolism were more likely to experience GBH-driven changes in allele frequency, including the gene aroA targeted by glyphosate, along with other potentially novel targets of selection. Together, these results show how environmental change can rapidly affect bacterial community structure and select for specific genetic targets without purging genetic diversity genome-wide.},
}

@article {pmid42801100,
year = {2026},
author = {Robinson, DM and Li, W and Breitbart, M and Takacs-Vesbach, C and Priscu, JC},
title = {Bacteriophages in Antarctic subglacial lakes reveal novel biodiversity and biogeochemical potential.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag252},
pmid = {42801100},
issn = {2730-6151},
abstract = {Of the more than 600 subglacial lakes identified in Antarctica thus far, Whillans Subglacial Lake and Mercer Subglacial Lake are the only lakes to have been directly and cleanly sampled. Although hydrologically isolated from direct marine contact for approximately 6.3 ± 1.0 ka, both lakes periodically discharge into the Ross Ice Shelf marine cavity. We present the first direct characterization of bacteriophages in Antarctic subglacial lakes, combining microscopy, metagenomics, and gene-sharing network analyses with bacteriophages found in the Ross Ice shelf marine cavity. The data reveal that bacteriophages are less abundant than their microbial hosts, with virus to prokaryote ratios below those of typical oligotrophic environments. Eight hundred sixty-one double-stranded DNA viral contigs were recovered forming 66 distinct viral clusters; only 18.4% could be identified at ≥85% sequence similarity in the IMG/VR database, showing high genetic novelty. The data showed 114 putative auxiliary metabolic genes involved in nutrient cycling and DNA methylation, and we predicted hosts spanning 13 prokaryotic classes. Several genetic clusters were shared with Antarctic subglacial lakes and Ross Ice Shelf cavity, indicating ecological connectivity that may extend the influence of subglacial phages to carbon and nutrient cycling in downstream Antarctic coastal ecosystems.},
}

@article {pmid42801158,
year = {2026},
author = {Song, Y and Xu, C and Zu, F and Dong, R and Yang, H},
title = {Diagnostic Performance of Bronchoalveolar Lavage Fluid Metagenomic Next‑generation Sequencing versus Conventional Microbiological Tests in Immunocompromised and Immunocompetent Patients with Pulmonary Infection.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {632502},
pmid = {42801158},
issn = {1178-6973},
abstract = {PURPOSE: Pulmonary infection in immunocompromised patients is challenging to diagnose. This study evaluated the detection performance of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in these patients.

PATIENTS AND METHODS: A total of 86 patients with confirmed pulmonary infection (48 immunocompromised, 38 immunocompetent) were retrospectively enrolled. BALF samples were tested by both mNGS and conventional microbiological tests (CMTs). Pathogen detection rates and pathogen spectrum were compared between the two groups.

RESULTS: The positive rate of mNGS was significantly higher than that of CMTs in overall patients (87.21% vs 50.00%, P < 0.001), with a more prominent advantage in the immunocompromised group (97.92% vs 43.75%, P < 0.001). Detection rates of fungi (39.58% vs 5.26%, P < 0.001) and viruses (54.17% vs 28.95%, P = 0.018) were significantly higher in the immunocompromised group. Opportunistic pathogens including Pneumocystis jirovecii, cytomegalovirus, and Epstein-Barr virus were detected exclusively in the immunocompromised group. The mixed infection rate was also significantly higher in this group (72.92% vs 36.84%, P < 0.001).

CONCLUSION: BALF‑mNGS is a reliable supplementary tool for conventional detection. It effectively identifies missed opportunistic pathogens and complex mixed infections, especially in immunocompromised patients. Combined application of mNGS and conventional tests improves pathogen detection and may help inform anti-infective treatment decisions.},
}

@article {pmid42789300,
year = {2026},
author = {Li, M and Mao, J and Liu, S and Yu, H and Qin, H and Liu, X and Tu, R and Chen, S and Liu, Z and Zhang, S and Mao, J},
title = {Ethanol exposure is associated with spatial and taxon-specific gut microbiota remodeling characterized by ecological adaptation rather than broad activation of microbial ethanol metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734657},
doi = {10.1080/19490976.2026.2734657},
pmid = {42789300},
issn = {1949-0984},
mesh = {Animals ; *Ethanol/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; *Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; Acetaldehyde/metabolism ; Metagenomics ; },
abstract = {Alcohol-associated diseases are linked to gut microbiota disruption, but how ethanol intake is associated with microbial functional remodeling remains unclear. Here, using male C57BL/6J mice, we integrated spatiotemporal quantification of ethanol and acetaldehyde across the gastrointestinal tract with 16S rRNA sequencing, metagenomics, metaproteomics, and metabolomics. Our results showed that small-intestinal communities were enriched in taxa and functions related to bile acid tolerance/utilization, whereas cecal communities exhibited pronounced remodeling of multiple core functions associated with ecological adaptation. Although the abundance of several ethanol metabolism-related genes increased, this genetic potential was not broadly translated into detectable protein-level activation. Ethanol metabolism-related proteins were mainly derived from Lachnospiraceae, whose metabolic activity was suppressed. In contrast, Muribaculaceae, Desulfovibrionaceae, and Barnesiellaceae gained functional advantages in substrate acquisition, energy metabolism, oxidative stress defense, and proteostasis. These findings provide a region-resolved functional map indicating that ethanol-associated microbiota remodeling is characterized by ecological adaptation, rather than uniform activation of direct microbial ethanol metabolism.},
}

Animals
*Ethanol/metabolism
Male
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Mice
*Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
Adaptation, Physiological
Acetaldehyde/metabolism
Metagenomics

@article {pmid42790038,
year = {2026},
author = {Wang, X and Zhang, Y and Zhang, L and Han, Y and Liu, J and Bi, X and Huang, S and Yang, T},
title = {Aeration change from horizontal brush to fine bubble substantially reduces the emission of inhalable antibiotic resistome from wastewater to air.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143712},
doi = {10.1016/j.jhazmat.2026.143712},
pmid = {42790038},
issn = {1873-3336},
abstract = {Aeration-mediated aerosolization in wastewater treatment plants (WWTPs) poses considerable sanitary menaces. However, the effect of aeration patterns on the emission of inhalable antibiotic resistome in WWTPs remains poorly understood. Herein, we analyzed seasonal metagenomics of fine particulate matter (PM2.5) and wastewater under two aeration patterns, with consistent inflow condition, aeration efficiency, and location background in the same WWTP. PM2.5-borne antibiotic resistance genes (ARGs) exhibited higher occurrence, mobile potential, pathogen involvement, and resistome risks under horizontal brush aeration than under fine bubble aeration. And the airborne resistome risks peaked in winter. Regardless of aeration patterns, mobile ARGs in PM2.5 were mainly carried by integrases and resistant to macrolide-lincosamide-streptogramin. Totally, 6 pathogenic antibiotic resistant bacteria (PARB), including Klebsiella pneumoniae and Pseudomonas aeruginosa, expressed ARG mobility in aeration environments. Horizontal brush aeration drove 74.52% of the ARGs and 75.00% of the PARB from wastewater into the air, which were higher than the 57.53% of ARGs and 50.00% of PARB driven by fine bubble aeration. For aeration-related PM2.5 resistome, aeration patterns were the principal inducement through regulating bacterial community and PM2.5 concentration. These distinguish the aerosolization response of wastewater resistome to aeration patterns that can help process selection and hygiene protection.},
}

@article {pmid42790042,
year = {2026},
author = {Feng, J and Li, SL and Chen, C and Zhang, L and Dai, XY and Chen, X and Wu, H and Smets, BF and Graham, DW and Wu, D and Chen, M},
title = {Potential dissemination of multidrug-resistant pathogens into local watersheds via aircraft wastewater from overseas aviation network.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143695},
doi = {10.1016/j.jhazmat.2026.143695},
pmid = {42790042},
issn = {1873-3336},
abstract = {Cross-border air travel contributes to antimicrobial resistance (AMR) spread, yet evidence linking aircraft wastewater to local environmental contamination remains limited. Metagenomic sequencing revealed that aircraft wastewater harbors approximately 10-fold higher levels of antibiotic resistance genes (ARGs) compared to municipal wastewater treatment plant (WWTP) influents (∼2.5 ARGs/cell) and effluent-receiving water (∼ 0.35 ARGs/cell). Furthermore, distinct resistome signatures and microbial assembly patterns were identified in aircraft wastewater relative to those in domestic wastewater sources. Notably, throughout this continuum, closely related Escherichia coli strains (ST2, with ≤10 core-genome single-nucleotide polymorphism differences) were isolated from WWTP samples receiving aircraft wastewater, whereas no such isolates were found in non-related samples. These strains consistently exhibited polymyxin resistance (carrying the mcr-1 gene) and extended-spectrum β-lactam (multidrug) resistance, a trait maintained under environmental selection (iCAMP, R[2] fit = 0.23), as confirmed by fluorescence-based bacterial tracing assays. Source-tracking further revealed that aircraft wastewater from regions with higher microbial community similarity, rather than geological proximity, contributed more substantially to domestic wastewater-borne multidrug resistant genes composition. Our findings suggest a potential route by which multidrug-resistant bacteria and ARGs associated with last-resort antibiotics may disseminate from the overseas aviation network into domestic WWTPs and effluent-receiving water, supporting integrated oversea-to-local surveillance.},
}

@article {pmid42790581,
year = {2026},
author = {Yin, J and Zhang, Y and Luo, W and Ma, Y and Sun, Y},
title = {Temperature shapes a modular division of labor among soil fungi to facilitate antibiotic dissipation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129241},
doi = {10.1016/j.envpol.2026.129241},
pmid = {42790581},
issn = {1873-6424},
abstract = {The antibiotics used in veterinary medicine accumulate in agricultural soils, where their persistence selects for antibiotic-resistance genes (ARGs). Soil fungi possess diverse metabolic enzyme systems and substantial potential for antibiotic biodegradation, but how temperature shapes fungal community succession and the functional pathways involved in antibiotic removal remains poorly understood. Herein, soils with histories of no fertilizer and organic fertilizer application (UF and OF, respectively) were spiked with 21 tetracyclines, quinolones and sulfonamides at approximately 2 mg kg[-1] per compound and incubated for 18 months at natural (NT; monthly mean of approximately 15 °C, ranging from -5.6 °C to 28.1 °C), constant (CT, 20 °C), and low (LT, 4 °C) temperatures. Dissipation kinetics were combined with fungal community and metagenomic profiling, co-occurrence networks, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway-residual correlations. Dissipation was slower in OF (total-antibiotic half-life [DT50] of 22-58 d) than in UF (DT50 of 18-44 d). Temperature exerted a stronger effect, with dissipation fastest at NT (DT50 of 18-22 d) and slowest at LT (DT50 of 44-58 d); ARGs followed the same trend, declining less than the parent compounds and least of all at LT. Temperature restructured the fungal community (PERMANOVA, P ≤ 0.018), chiefly by replacing taxa rather than by nested loss. Fungal-assigned KEGG pathways were inversely correlated with residual antibiotic concentrations (Spearman's ρ = -0.34 to -0.54, P < 0.05) and fell into three candidate functional modules: antibiotic capture and transport, oxidative transformation, and intracellular transformation. Across all temperatures the community retained a capture-and-transport core, for which no significant temperature contrast was detected, whereas oxidative and intracellular transformation were both less abundant at LT. Temperature therefore influences soil antibiotic dissipation by reshaping fungal community structure and redistributing annotated potential among complementary fungal functions. Accounting for this temperature dependence can improve bioremediation strategies for antibiotic-contaminated agricultural soils.},
}

@article {pmid42791078,
year = {2026},
author = {Gottesdiener, LS and DeLaurentis, C and Pereira, MR},
title = {A Case of Disseminated Encephalitozoon cuniculi in a Lung Transplant Recipient: Microsporidiosis in the Era of Molecular Diagnostics.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70325},
doi = {10.1111/tid.70325},
pmid = {42791078},
issn = {1399-3062},
support = {T32 AI007613//National Institute of Allergy and Infectious Diseases/ ; KL2 TR002385/TR/NCATS NIH HHS/United States ; },
}

@article {pmid42791132,
year = {2026},
author = {Bastón-Paz, N and García-Durán, C and Bayraktar, D and Palacios, E and Moreno-Blanco, A and Top, J and Garriga, M and Máiz, L and Vicente-Santamaría, S and Oliver, A and Oteo-Iglesias, J and Cantón, R and Gil, C and Schürch, AC and Del Campo, R and de Dios Caballero, J},
title = {Functional and Compositional Shifts in Lung and Gut Microbiota after One Year of Treatment with Highly Effective CFTR Modulators in Cystic Fibrosis.},
journal = {Archivos de bronconeumologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arbres.2026.08.007},
pmid = {42791132},
issn = {1579-2129},
abstract = {BACKGROUND: Highly effective CFTR modulator therapy with elexacaftor-tezacaftor-ivacaftor (ETI) has revolutionized clinical outcomes in cystic fibrosis (CF), yet its effects on gut and lung microbiota, especially at the functional level, are poorly understood.

METHODS: In a 12-month prospective study, we enrolled 35 clinically stable CF patients initiating ETI. Paired fecal and sputum samples, collected at baseline and after 12 months, were analyzed using shotgun metagenomics, metaproteomics, and short-chain fatty acid (SCFA) quantification. Multi-omics data were integrated with clinical parameters assessing lung, hepatic, pancreatic, and intestinal function.

RESULTS: ETI drove significant clinical improvements, including increased ppFEV1, higher fecal elastase, and better nutritional status, despite persistent major lung pathogens and minimal changes in liver or intestinal inflammation markers. Microbiota composition showed limited shifts: alpha diversity was stable, and beta diversity changes accounted for only small variance in both compartments. However, butyrate-producing genera enriched in feces, while oropharyngeal taxa increased in sputum. Metaproteomics revealed broad downregulation of host neutrophil-driven inflammatory proteins; sputum additionally showed increased abundance of extracellular matrix-related proteins. Microbial proteins linked to carbohydrate/lipid metabolism, particularly butanoate pathways, increased in feces alongside a trend for higher butyrate. In sputum, formaldehyde dehydrogenase enzymes rose, indicating enhanced oxidative microbial metabolism.

CONCLUSIONS: ETI is associated with minimal compositional but substantial functional reprogramming in CF microbiota. These changes are accompanied by an increase in butyrate-producing taxa, attenuation of host pro-inflammatory pathways, and a shift in lung metabolism toward oxidation. Despite ongoing pathogenic colonization, these changes suggest CFTR modulation is associated with a less inflammatory, more stable host-microbiota ecosystem.},
}

@article {pmid42791821,
year = {2026},
author = {Liu, W and Yang, Y and La, Y and Ma, X and Wu, X and Chu, M and Guo, X and Yan, P and Liang, C},
title = {Effects of Eucommia ulmoides Leaf Extract on Growth Performance, Serum Biochemistry, Rumen Microbiota, and Metabolic Profiles in Yaks.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/ani16182965},
pmid = {42791821},
issn = {2076-2615},
support = {CARS-37//National Beef Cattle Industrial Technology System/ ; },
abstract = {This study aimed to investigate the effects of adding Eucommia ulmoides leaf extract (ELE) to the diet on the growth performance, serum biochemical parameters, rumen fermentation parameters, rumen microorganisms and metabolites of yaks. Ten male yaks (two years old) were selected and randomly divided into two groups (n = 5). The control group (C, 153.48 ± 7.48 kg) was fed the basal diet, while the experimental group (H, 146.72 ± 1.87 kg) was fed the basal diet supplemented with 1.0 g/kg feed dry matter (DM) of ELE for 75 days. The results showed that the average daily gain, the serum total antioxidant capacity, catalase, and superoxide dismutase were significantly higher in the H group than in the C group (p < 0.01), while the serum total cholesterol, creatinine, alkaline phosphatase, blood urea nitrogen, and malondialdehyde were significantly lower than those of the C group (p < 0.05); in contrast, low-density lipoprotein cholesterol was significantly elevated in the H group (p < 0.01). Furthermore, the concentrations of acetate, butyrate, and hexanoic acid increased significantly compared with the C group (p < 0.05); 2-Hydroxypropanoic acid, butanedioic acid, and pentanedioic acid decreased significantly in the H group compared with the C group (p < 0.05). The metagenomic analysis revealed that ELE not only promoted the growth of cellulose-degrading bacteria but also significantly reduced the abundance of the virulence factors and carbohydrate-active enzymes (p < 0.05). In the experimental and control groups, the dominant microorganisms were Bacillota and Prevotellaceae, respectively. Metabolomics analysis further revealed that the differential metabolites were significantly enriched in pathways including purine metabolism, β-alanine metabolism, glutathione metabolism, and cGMP-PKG. The Pearson correlation analysis revealed that there were interactions among various microorganisms and metabolites, which can promote the growth and health of yaks. In conclusion, ELE can promote the growth and health of yaks by regulating the serum biochemical parameters, rumen fermentation, rumen microbial flora, and metabolism.},
}

@article {pmid42791967,
year = {2026},
author = {Shouqair, D and Verma, S and Alghafri, R and Nassar, R and Mohamed, L and Dhaheri, FA and Everett, D and Shibl, AA and Rodríguez, J and Moradigaravand, D and Khan, M and Goering, R and Senok, A},
title = {Source-Resolved Wastewater Metagenomics Reveals Distinct Resistome and Virulome Landscapes Across an Urban Wastewater Continuum.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090817},
pmid = {42791967},
issn = {2079-6382},
support = {Grant# AJF-NIH-1-MBRU//This work was funded by Grant# AJF-NIH-1-MBRU as part of the UAE-NIH Collaborative Re-search Initiative (UAE-NIH-CRI) which comprises four collaborating UAE institutes: Al Jalila Foundation, Mohammed Bin Rashid University of Medicine and Health Sciences,/ ; },
abstract = {BACKGROUND/OBJECTIVES: Wastewater-based antimicrobial resistance (AMR) surveillance typically relies on treatment plant influent as a single integrated matrix, obscuring source-specific signals. In arid settings where treated effluent is reused, understanding how resistomes and virulomes are structured across wastewater compartments is essential for One Health monitoring.

METHODS: Shotgun metagenomic sequencing was applied to 57 wastewater samples collected in Dubai, United Arab Emirates, between October 2024 and January 2025. Samples represented nine community sewer nodes, two tertiary-care hospital outflows, and influent and effluent from two wastewater treatment plants (WWTP). Datasets were used for taxonomic, resistome, and virulome profiling. Alpha diversity was compared using Wilcoxon rank-sum tests, beta-diversity differences were assessed using permutational multivariate analysis of variance, and source-associated AMR genes were identified using linear discriminant analysis effect size analysis.

RESULTS: A total of 1470 bacterial species, 822 antimicrobial resistance genes (ARGs), and 1554 virulence factor genes were identified. Bacterial diversity was significantly lower in WWTP effluent than in other compartments. Hospital wastewater was enriched for class D β-lactamases, including multiple blaOXA variants, whereas community wastewater and WWTP influent shared dominant macrolide and aminoglycoside resistance genes including msr(E), mph(E), strB and aadA1. Despite marked reductions in bacterial diversity after treatment, no significant difference in ARG diversity was observed between WWTP influent and WWTP effluent (p = 0.558), with resistance genes such as blaVEB, msr(E), mph(E) detected in the latter. Virulome profiles shifted from fimbrial gene dominance in untreated sources toward biofilm- and persistence-associated genes in WWTP effluent. ARG alpha diversity varied over time, whereas taxonomic and virulome diversity remained stable.

CONCLUSIONS: Community and influent wastewater capture population-level AMR carriage, hospital outflows concentrate clinically relevant resistance determinants, and WWTP effluent retains resistance markers despite microbial biomass reduction. Compartment-resolved metagenomic surveillance provides a practical One Health framework for identifying high-value monitoring points.},
}

@article {pmid42791995,
year = {2026},
author = {Mware, B and Kibet-Rono, G and Mwangi, K and Lugano, D and Osiany, S and Kiritu, E and Dobi, PO and Muli, C and Juma, J and Njeru, R and Machuka, EM and Bett, B and Ogwell, A and Abworo, EO and de Oliveira, T and Muloi, DM and Tessema, SK and Oyola, SO},
title = {Wastewater Metagenomic Surveillance Reveals Socioeconomic Patterns of Pathogen Diversity and Antimicrobial Resistance in Nairobi, Kenya.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090845},
pmid = {42791995},
issn = {2079-6382},
support = {BMZ001201//Federal Ministry of Economic Cooperation and Development/ ; HTH 017//Rockefeller Foundation/ ; 101103171//Global Health EDCTP3 Joint Undertaking, its members, and the Bill & Melinda Gates Foundation/ ; TF0B8412//World Bank Group/ ; SAMVAC//South African Medical Research Council/ ; },
abstract = {Background: Wastewater and Environmental Surveillance (WES) has become a useful public health tool as an early-warning system revealing emergence/re-emergence of pathogenic diseases and spread of antimicrobial resistance (AMR). We characterized the taxonomic composition, relative abundance, and antibiotic resistance genes (ARGs) of wastewater-identified bacterial pathogens across socioeconomically and epidemiologically diverse sewerage catchments in Nairobi, Kenya-a key East African urban city representing a low- and middle-income country (LMIC). Results: Metagenomic analysis of Nairobi's wastewater revealed distinct bacterial and antimicrobial resistance (AMR) profiles. Campylobacteraceae (52.5% ± 17.9%) and Bacteroidaceae (19.8% ± 9.9%) dominated the communities. While Arcobacter cryaerophilus was ubiquitous, Bacteroides fragilis and A. suis abundances varied by neighborhood socioeconomic status. We detected critical clinical pathogens-including Escherichia coli, Vibrio cholerae, Mycobacterium tuberculosis, and the ESKAPE species-alongside 207 distinct ARGs conferring resistance to 11 antibiotic classes. Both taxonomic and ARG compositions showed high spatial heterogeneity, with maximum variation in low-income areas. Temporal analysis captured shifting pathogen dynamics, and metagenomic abundances for Vibrio cholerae and Klebsiella pneumoniae were validated via qPCR. Conclusions: Our findings underscore the utility of WES as a scalable, non-invasive public health tool. By capturing community-level pathogen composition and AMR dynamics, WES bypasses the limitations of clinical diagnostic access, providing a vital early-warning system for underserved urban populations. To maximize its public health utility, environmental genomic signals must serve as actionable triggers for coordinated One Health responses, including targeted clinical diagnostics, localized antimicrobial stewardship reviews, proactive risk communication, and prioritized sanitation infrastructure upgrades.},
}

@article {pmid42792000,
year = {2026},
author = {Timoteo, FD and Di Giulio, E and Di Domenico, M and Secondini, B and Marotta, F and Matteucci, G and Zilli, K and Romualdi, T and Palmieri, D and Garofolo, G and Janowicz, A},
title = {Integrated qPCR and Shotgun Metagenomics for Surveillance of Antimicrobial Resistance in Municipal Wastewater from Central Italy.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090850},
pmid = {42792000},
issn = {2079-6382},
support = {SG-2021-12375470//Ministero della Salute/ ; },
abstract = {Background/Objectives: Wastewater-based epidemiology (WBE) has emerged as a valuable One Health approach for monitoring antimicrobial resistance (AMR) at the population level. Although quantitative PCR (qPCR) and shotgun (SG) metagenomics are widely used for wastewater surveillance, studies integrating these complementary approaches remain limited. This study aimed to investigate the occurrence, seasonal dynamics, and diversity of antimicrobial resistance genes (ARGs) in municipal wastewater from Central Italy by combining targeted qPCR and SG metagenomic sequencing. Methods: Influent wastewater samples were collected monthly from eight municipal wastewater treatment plants in Central Italy between April 2025 and March 2026. Clinically relevant antimicrobial resistance genes were quantified by quantitative real-time PCR, while SG metagenomic sequencing was used to characterize resistome composition, resistance gene families, and ARG sequence diversity using bioinformatic pipelines. Results: All investigated ARGs were detected in every sample. Significant seasonal variation was observed for all investigated markers, including qnrS, blaKPC, blaCTX-M and intI1. Metagenomic analysis revealed broadly similar resistome profiles across sampling sites and time points, dominated by resistance genes to macrolide-lincosamide-streptogramin, aminoglycosides, β-lactams, and fluoroquinolones. High sequence diversity was observed within the dominant ARG families, highlighting the complementary value of SG metagenomics for comprehensive resistome characterization. Conclusions: The integration of targeted qPCR and SG metagenomics provided a comprehensive characterization of antimicrobial resistance in municipal wastewater. While qPCR enabled sensitive quantification of clinically relevant ARGs and revealed seasonal trends, metagenomics expanded resistome characterization by identifying dominant resistance classes, gene families, and sequence variants. These findings support the implementation of integrated molecular approaches for routine wastewater-based AMR surveillance within a One Health framework.},
}

@article {pmid42792028,
year = {2026},
author = {Morikwe, UC and Kiki, LC and Ezeanowai, FC and Hall, S and Bhatia, S and Maswanganye, TN and Jeje, O and Hill, MS and Graves, JL and Deng, D and Jeffers-Francis, L},
title = {Building-Scale Wastewater Metagenomics Reveals Temporal Patterns in Resistance and Virulence Genes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antibiotics15090878},
pmid = {42792028},
issn = {2079-6382},
support = {EEC-2133504//U.S. National Science Foundation/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) and virulence represent co-evolving dimensions of microbial pathogenic potential whose ecological organization in building-scale wastewater systems remains poorly understood. Methods: Using shotgun metagenomic sequencing, we characterized the temporal dynamics and ecological associations of antimicrobial resistance genes (ARGs) and virulence factors (VFs) in 12 wastewater grab samples (2 per semester) collected from a university residence hall designated for COVID-19 quarantine between 2021 and 2023. Results: The wastewater microbiome was anchored by a stable core of gut-associated anaerobic bacteria, with community composition exhibiting significant Spring-versus-Fall structuring and a year × semester interaction that explained 60% of the community variation. A marked shift toward opportunistic taxa, particularly Acinetobacter, during Fall 2023 represented the most pronounced temporal perturbation. Total ARG abundance remained stable across semesters, while resistome composition shifted significantly, indicating that temporal dynamics were driven by compositional turnover rather than changes in overall resistance burden. VF functional categories were broadly conserved across sampling periods, consistent with their structural embedding within the persistent fecal core microbiome. Correlation and network analyses revealed modular ecological coupling between resistance and virulence functional categories, with metal/co-resistance and fosfomycin classes showing the strongest associations with virulence functions. At the community level, a Benjamini-Hochberg-corrected co-occurrence network resolved into taxa-anchored resistance modules and separate virulence-function clusters, with Acinetobacter and fluoroquinolone resistance as the principal connectors. Conclusions: These findings indicate that building-scale wastewater metagenomics can capture ecologically structured functional gene dynamics, highlighting its potential as a surveillance tool for monitoring AMR and virulence in built environments.},
}

@article {pmid42792243,
year = {2026},
author = {Tang, W and Wang, Z and Dong, Y and Cao, J and Chen, Y},
title = {Monochromatic Blue Light Enhances Antioxidant Status and Remodels the Gut Microbiome in Association with Increased Plasma Melatonin in Broiler Chickens.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/antiox15091204},
pmid = {42792243},
issn = {2076-3921},
support = {32172801//National Natural Science Foundation of China/ ; 32372954//National Natural Science Foundation of China/ ; 32573308//National Natural Science Foundation of China/ ; },
abstract = {The intestinal microbiome of broiler chickens has potential to regulate host health and growth performance. Although previous studies have revealed that the intestinal microbiota composition is affected by different factors including monochromatic light, the underlying mechanisms remain poorly understood, particularly regarding the causal role of light-sensitive hormones such as melatonin. To address this gap, a 2 × 4 factorial design was adopted in the present study, with two surgical treatments (sham-operation or pinealectomy) and four light conditions (white, blue, green, and red light), to investigate whether blue light modulates gut microbiota and antioxidant status through melatonin-dependent pathways. Broilers were reared under different monochromatic light conditions. On day 3 post-hatching, we ablated circulating melatonin production by conducting a pinealectomy or control sham-operation model. Accordingly, the broilers were assigned to eight groups: white light + sham-operation (WL), white light + pinealectomy (WP), blue light + sham-operation (BL), blue light + pinealectomy (BP), green light + sham-operation (GL), green light + pinealectomy (GP), red light + sham-operation (RL), and red light + pinealectomy (RP). On day 35, blue light was found to most effectively elevate plasma melatonin, which activated the Mel 1a/Nrf2/NQO1 pathway to reduce oxidative stress and remodel the jejunal microbiota. Metagenomic analysis identified Akkermansia muciniphila, Bifidobacterium longum and Ligilactobacillus aviarius as key bacteria enriched in blue light. Consequently, classes of microbiota-derived metabolites like stearidonic acid and indole propionic acid triggered the variation of tryptophan, bile acid and lipid metabolism, which contributed to broiler growth promotion. Moreover, pinealectomy accompanied by plasma melatonin deprivation significantly nullified the blue-light-induced effects. These insights confirm blue light is more effective in microbiota modulation by inducing melatonin secretion and providing a new strategy for light management in the broiler industry.},
}

@article {pmid42792532,
year = {2026},
author = {Cupples, AM and Richards, J and Basaldua Del Cid, M},
title = {Data Mining of Groundwater Genomes for Metagenome-Assembled Genomes (MAGs) Containing Monooxygenase Operons Associated with Contaminant Biodegradation.},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181586},
pmid = {42792532},
issn = {2079-7737},
support = {2413523//U.S. National Science Foundation/ ; },
abstract = {This study examined freely available whole genome sequencing (WGS) data for genes associated with contaminant biodegradation. Thirteen WGS datasets (>600 individual samples) involving more than 12,000 Gbases from multiple countries were examined. The Department of Energy Systems Biology Knowledgebase (KBase) was used to create metagenome-assembled genomes (MAGs) containing the operons of interest. The arrangement and length of subunits for each operon were compared. Phylogenetic trees were created for common biomarkers (tmoA, pmoA, prmA, mmoX, dmpN). MAGs were uploaded into publicly available KBase narratives. Thirty-four MAGs, within the phyla Actinomycetota, Pseudomonadota and Chloroflexota, were identified with the full propane monooxygenase operon (prmABCD). Twenty-six MAGs, within the classes Gammaproteobacteria and Alphaproteobacteria, contained the full operon for soluble methane monooxygenase (mmoXYBZDC). More than 100 MAGs contained the full operon for ammonia/particulate methane monooxygenase (pmoCAB) and were classified within the Gammaproteobacteria and Alphaproteobacteria groups, as well as other phyla. Fifty-five MAGs, within Burkholderiales (Gammaproteobacteria) and Alphaproteobacteria, contained the full operon for toluene-4-monooxygenase (tmoABCDEF). From the MAGs containing the full operon for toluene monooxygenase, thirty-three also contained the full operon for phenol monooxygenase (dmpKLMNOP). The MAGs generated and their associated functional gene sequences have the potential to improve molecular detection methods for site bioremediation.},
}

@article {pmid42792542,
year = {2026},
author = {Ong, CJN and Cabalbag, JN and Cruz, JTP and Valderama, TT and Roslin, CR and Magtibay, CM and Lonogan, JKK and Libres, AC and Matamis, JG and Mamaat, JER and Mortel, FA and Bacalzo, GD and Cabuhat, KSP and de Leon, CS and Nuevo, JJM and Aguilan, JR and Fortaleza, JAG},
title = {Mapping Bacteriophage-Based Antimicrobial Research in Southeast Asia: A Bibliometric Analysis of Scientific Productivity, Knowledge Structure, and Emerging Research Pathways.},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181596},
pmid = {42792542},
issn = {2079-7737},
abstract = {Southeast Asia faces a substantial burden of antimicrobial resistance (AMR), creating increasing interest in bacteriophage-based antimicrobial strategies. However, the regional development, contributors, collaboration patterns, and evolving research priorities of this field remain insufficiently characterized. This study conducted a bibliometric analysis of Scopus-indexed publications on bacteriophage-based antimicrobial research affiliated with Southeast Asian countries from 1981 to 2025. Bibliometrix/Biblioshiny and VOSviewer were used to evaluate scientific production, citation patterns, leading contributors, collaboration networks, and conceptual and thematic development. A total of 862 publications were analyzed, with scientific output accelerating markedly after 2019 and reaching its highest level in 2025. Thailand emerged as the dominant regional contributor, with Vongkamjan (n = 21) and Surachat (n = 20) as the two most prolific authors. Mahidol University (n = 182), Prince of Songkla University (n = 142), and Universiti Putra Malaysia (n = 139) were the leading institutions, demonstrating a concentration of research capacity in Thailand and Malaysia. Scientific Reports was the most productive journal (30 publications), whereas Frontiers in Microbiology recorded the highest citation count among the leading sources (963 citations). Collaboration mapping revealed increasingly interconnected regional and international research networks. Thematic analyses demonstrated a transition from foundational and pathogen-specific investigations toward AMR, bacteriophage therapy, biofilm control, aquaculture, genomic and comparative genomic analysis, wastewater and public-health applications, and One Health-oriented research. Emerging topics included endolysins, quorum sensing, CRISPR-associated approaches, metagenomics, and genome-informed phage characterization. These findings demonstrate the rapid expansion and thematic diversification of bacteriophage-based antimicrobial research in Southeast Asia while highlighting persistent geographic concentration and the need for stronger regional infrastructure, collaboration, and translational capacity.},
}

@article {pmid42792603,
year = {2026},
author = {Yang, X and Yu, J and Wang, Y and Zhao, Y and Wang, K and Lu, X and Zhang, L},
title = {Study on the Risk of Phosphorus Leaching in Dryland from Typical Purple-Soil Regions and Its Control Mechanisms.},
journal = {Biology},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/biology15181658},
pmid = {42792603},
issn = {2079-7737},
support = {No.2022YFC3204004//the National Key Research and Development Program/ ; },
abstract = {Phosphorus (P) leaching from dryland from purple soils poses a significant risk to water quality, yet effective mitigation strategies and their underlying microbial mechanisms remain poorly understood. This study aimed to evaluate the efficacy of biochar (B), a silicon-based conditioner (Si), and their combination (BSi) in controlling P leaching, hypothesizing that B would immobilize P while Si would mobilize it. The indoor soil column leaching experiments were conducted with four treatments (CK, B, Si, BSi), measuring leachate P fractions and soil P forms, and employed metagenomic sequencing combined with partial least-squares path modeling (PLS-PM) and Bayesian structural equation modeling (BSEM) to explore microbial functional mechanisms. Results showed that B alone reduced cumulative leaching of inorganic P (IP), organic P (OP), and total P (TP) by a range of 5.4-6.3%, while increasing available phosphorus (Olsen-P) by 39.4% in the surface layer. Si and BSi promoted leaching, with BSi reducing available P sharply, despite raising TP. Metagenomic analysis revealed that B suppressed subsurface IP solubilization genes (e.g., gcd, ppx) and optimized OP mineralization, whereas Si inhibited mineralization via reducing key microbial taxa. BSEM further identified water-soluble P (Water-P) and total nitrogen (TN) as direct positive drivers of inorganic P dissolution. Collectively, the key biological mechanisms for leaching reduction involve inhibiting subsurface IP solubilization, optimizing surface OP mineralization, and enhancing P transport/starvation responses. Collectively, biochar applied alone offers the optimal balance between P retention and crop-available P supply in dryland purple soils, and provides mechanistic insights-through functional gene profiling-that can inform the design of more sustainable P fertilization and leaching control practices.},
}

@article {pmid42792653,
year = {2026},
author = {Azamfirei, L and Bica, D and Mihai, MA and Beata, B and Banescu, C},
title = {Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.},
journal = {Biomedicines},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biomedicines14091910},
pmid = {42792653},
issn = {2227-9059},
abstract = {Background: Precision diagnostics are more and more important in intensive care units (ICUs), where rapid identification of infectious agents and antimicrobial resistance determinants is crucial for timely and appropriate treatment. Conventional microbiological methods are frequently limited by long turnaround times and reduced sensitivity, which may delay appropriate treatment. Nanopore sequencing allows rapid, direct, and long-read sequencing of DNA/RNA molecules without the need for amplification, avoiding biases introduced by NGS during amplification and library preparation and generating data in real time. Objectives: This narrative review aims to summarize current knowledge of nanopore technology in the ICU, discuss nanopore principles and current clinical applications in intensive care medicine, highlight its advantages and limitations, and explore future perspectives for integrating nanopore-based diagnostics into precision critical care. Methods: A literature search was performed using PubMed and Web of Science. The literature search was conducted with no lower restriction, covering English-language publications. Results: Nanopore sequencing enables real-time, long-read, single-molecule analysis of native nucleic acid molecules, rapid pathogen identification, antimicrobial resistance profiling, metagenomic analysis, and direct sequencing without amplification. Recent studies have proved the clinical utility of nanopore sequencing in critically ill patients with sepsis, bloodstream infections, hospital-acquired pneumonia, ventilator-associated pneumonia, and fungal and viral infections. Its portability, rapid turnaround time, and potential for point-of-care implementation make it particularly attractive for ICU settings. Conclusions: Nanopore sequencing technology represents a promising molecular diagnostic tool, but wider clinical implementation warrants further larger studies with clinical outcome endpoints, standardized bioinformatic pipelines, and clearer validation pathways.},
}

@article {pmid42792947,
year = {2026},
author = {Du, Q and Xing, L and Zhu, C and Li, P},
title = {Gut Microbiota and Metabolic Pathway Signatures for Inflammatory Bowel Disease Identified via Subject-Stratified Random Forest Based on the Longitudinal HMP2 Cohort.},
journal = {Genes},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/genes17091053},
pmid = {42792947},
issn = {2073-4425},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Random Forest ; *Metabolic Networks and Pathways/genetics ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Feces/microbiology ; Female ; Machine Learning ; },
abstract = {Background: Inflammatory bowel disease (IBD) is characterised by severe intestinal microbial dysbiosis. Most machine learning diagnostic models built on the longitudinal HMP2 cohort suffer serious data leakage from random sample-level cross-validation splitting, which leads to artificially inflated AUC values. Additionally, incomplete reporting of microbial preprocessing, random forest hyperparameters and multi-dimensional evaluation metrics reduces the reproducibility of existing research. Methods: We re-analysed the public HMP2 (IBDMDB) longitudinal metagenomic dataset containing 130 unique subjects (103 IBD/27 healthy controls) and 1627 longitudinal faecal samples. Raw 585 species were filtered by a minimum relative abundance of 1 × 10[-5] and sample prevalence ≥20%, retaining 89 taxa; all 1135 metabolic pathways were retained. CLR transformation was applied to compositional abundance data. We performed Wilcoxon differential testing with Benjamini-Hochberg FDR correction, alpha/beta diversity analysis, and three random forest models (filtered species, all FDR-significant pathways, strictly filtered pathways). Critical improvements included subject-ID-stratified 5-fold cross-validation repeated 5 times, within-fold training-set-only feature importance calculation, and class weighting to balance unbalanced IBD/control samples. PERMANOVA with subject stratification and PERMDISP dispersion test were implemented with 999 fixed-seed permutations. Results: All four alpha diversity indices were significantly lower in IBD patients (all p < 0.0001). Subject-stratified PERMANOVA showed disease status only explained 1.18% of total Bray-Curtis community variance (R[2] = 0.0118, p = 1); PERMDISP detected significant group dispersion heterogeneity (p = 0.027). We identified 63 differentially abundant species and 695 perturbed pathways at FDR < 0.05. Canonical butyrate producers Faecalibacterium prausnitzii and Roseburia hominis showed no significant inter-group differences. Bootstrap 1000-resampling AUC 95% CIs indicated moderate classification performance: species model (0.626-0.705, mean AUC = 0.665), all-significant-pathway model (0.645-0.712, mean AUC = 0.679), strict-pathway model (0.620-0.685, mean AUC = 0.654). Alistipes putredinis and peptidoglycan biosynthesis I were the top taxonomic and pathway biomarkers, respectively. Conclusions: This study established a leakage-free machine learning pipeline for longitudinal microbiome cohorts via subject-level cross-validation splitting. The moderate AUC values eliminate false high performance caused by sample leakage, and we provide reliable candidate microbial and metabolic biomarkers for IBD. Restricted by single-cohort internal validation and unadjusted medication confounders, these markers still require independent multi-centre external verification before clinical translation.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Random Forest
*Metabolic Networks and Pathways/genetics
*Gastrointestinal Microbiome/genetics
Longitudinal Studies
Feces/microbiology
Female
Machine Learning

@article {pmid42793803,
year = {2026},
author = {Kim, SY and Lee, JE and Lee, DH and Kim, HY and Kim, KH and Jeong, H and Chung, C},
title = {Diagnostic Reassessment of a Pulmonary Mass Initially Suspected to Represent IgG4-Related Lung Disease: The Complementary Role of Tissue Metagenomic Sequencing.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/diagnostics16183018},
pmid = {42793803},
issn = {2075-4418},
support = {no. 2022R1A2C2010148//National Research Foundation of Korea/ ; no. HR20C0025//Korea Health Industry Development Institute/ ; },
abstract = {Background/Objectives: Pulmonary mass-like lesions may mimic malignancy, infection, or inflammatory disease, complicating diagnosis when radiologic, histopathologic, and microbiologic findings overlap. This case illustrates the importance of diagnostic reassessment when the clinical course and treatment response are not fully consistent with the initial diagnosis. Methods: A 69-year-old man with diabetes mellitus and mild emphysema presented with chronic cough, purulent sputum, and a recurrent left upper lobe mass. Computed tomography-guided biopsy revealed dense lymphoplasmacytic infiltration with eosinophils, fibrosis, and increased IgG4-positive plasma cells, leading to a presumptive diagnosis of IgG4-related lung disease. Limited improvement with steroid therapy and recurrent hemoptysis prompted multidisciplinary reassessment, including tissue metagenomic next-generation sequencing (mNGS). Results: Imaging findings were compatible with subacute invasive aspergillosis, although conventional fungal staining, culture, antigen testing, serologic studies, and bronchial washing analyses were negative. Tissue mNGS detected 348 low-abundance Aspergillus-derived reads, accounting for 0.03% of non-host reads. Following initiation of voriconazole, the lesion decreased from 47 mm to 32 mm within six weeks and regressed further thereafter. Symptoms resolved, and hemoptysis did not recur. Conclusions: This case highlights the importance of diagnostic reassessment when findings and treatment response do not fully support the initial diagnosis. Tissue mNGS may provide complementary evidence for probable subacute invasive aspergillosis when interpreted alongside radiologic findings, exclusion of alternative diagnoses, and treatment response.},
}

@article {pmid42794458,
year = {2026},
author = {Carini, F and Sorce, A and Ciuppa, ME and David, S and Giammanco, M and Di Carlo, P and Evola, S and Tomasello, G and Mulè, G and Carollo, C},
title = {Gut, Oral, and Fungal Microbiota in Hypertension: A Multi-Compartment Systematic Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188029},
pmid = {42794458},
issn = {1422-0067},
mesh = {Humans ; *Hypertension/microbiology ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; *Mycobiome ; *Microbiota ; *Fungi ; },
abstract = {The gut microbiota is an established modulator of blood pressure, but the oral bacteriome and the fungal mycobiome have been examined largely in isolation from it and from each other. No previous synthesis has evaluated all three compartments within one analytical framework, or treated sex and ethnicity as primary analytical axes rather than adjustment covariates. Systematic review reported according to PRISMA 2020 and, for the synthesis, the SWiM guideline. PubMed/MEDLINE, Embase, Scopus, and Web of Science were searched from inception to 30 June 2026. Observational human studies in adults reporting gut, oral, or fungal microbiota data stratified by blood pressure status were eligible, together with Mendelian randomisation studies and studies with a nested experimental causal component. Two reviewers screened and extracted independently, with a third resolving disagreement. Risk of bias was assessed with the Newcastle-Ottawa Scale and certainty of evidence with GRADE adapted for exposure-outcome questions. Increased abundance of the Ruminococcus gnavus group was the most convergent taxon-level finding, replicated in three independent populations on two continents, including one prospective multi-ethnic cohort with full adjustment and correction for multiple comparisons (OR 1.07, 95% CI 1.01-1.14 for incident hypertension). In the oral compartment, depletion of the nitrate-reducing commensal Neisseria subflava converged across a United States prospective cohort and an Italian case-control study using unrelated methods, and salivary nitric oxide was approximately three-fold lower in hypertensive subjects. Depletion of the short-chain fatty acid producers Faecalibacterium and Roseburia and enrichment of Klebsiella were convergent but geographically restricted. Mycobiome evidence was contradictory: two studies reported fungal dysbiosis, one of them already at the pre-hypertensive stage, while a cross-cohort metagenome-wide study on two independent cohorts from Beijing and Dalian (N = 159 hypertensive patients, 101 healthy controls) identified 61 gut bacterial species with consistent altered abundance across both cohorts while finding no replicable mycobiome signal. Recurring across compartments and kingdoms was the collapse of microbial co-correlation networks in hypertension, alongside a dissociation between null alpha diversity and significant beta diversity. Associations differed by ethnicity within a single multi-ethnic cohort and were generally stronger in women. Certainty of evidence, assessed per individual convergent finding, was very low for every taxon-level finding and low for salivary nitric oxide; these ratings concern the attribution of hypertension to specific organisms, not the existence of a microbiota-hypertension association, which is supported at community level in every compartment examined and by experimental transfer models. That the microbiota differs in hypertension is well supported; which organisms are responsible is not. The most reproducible signal is structural rather than taxonomic, and conventional differential-abundance analysis is not designed to detect it. No individual microbial taxon is currently ready to serve as a marker of hypertension or to inform clinical practice.},
}

Humans
*Hypertension/microbiology
*Mouth/microbiology
*Gastrointestinal Microbiome
*Mycobiome
*Microbiota
*Fungi

@article {pmid42794824,
year = {2026},
author = {Kim, M and Song, WH and Ju, HJ and Koh, YK and Kim, SJ and Lee, YB and Lee, M},
title = {Shotgun Metagenomic Characterization of Skin Microbiome Shifts in Human Scabies Before and After Scabicidal Treatment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188397},
pmid = {42794824},
issn = {1422-0067},
mesh = {Humans ; *Scabies/drug therapy/microbiology ; *Skin Microbiome ; *Metagenomics/methods ; Male ; Female ; *Skin/microbiology ; Shotgun Sequencing ; Sarcoptes scabiei ; Metagenome ; Adult ; *Microbiota ; },
abstract = {Scabies, caused by Sarcoptes scabiei, is a globally prevalent ectoparasitic infestation associated with intense pruritus and secondary bacterial infection, yet the molecular composition of the skin microbiome during active infestation remains poorly characterized. We performed shotgun metagenomic sequencing of 41 skin samples collected from 18 patients at dry and moist anatomical sites before and after scabicidal treatment. In exploratory group-level comparisons, pretreatment moist-site samples had lower alpha diversity and higher bacterial and viral read-based burdens than post-treatment moist-site samples. Pretreatment dry and moist samples did not differ significantly in diversity, and Staphylococcus was the predominant genus. No genus- or species-level taxon or predicted pathway remained statistically significant after Benjamini-Hochberg false discovery rate correction at a threshold of 0.05. Nominal differences in predicted purine biosynthesis pathways were interpreted as exploratory observations. These findings provide a shotgun metagenomic characterization of the skin microbiome during active scabies and describe exploratory treatment-associated patterns that require confirmation in larger, paired longitudinal studies.},
}

Humans
*Scabies/drug therapy/microbiology
*Skin Microbiome
*Metagenomics/methods
Male
Female
*Skin/microbiology
Shotgun Sequencing
Sarcoptes scabiei
Metagenome
Adult
*Microbiota

@article {pmid42795339,
year = {2026},
author = {Carissimi, C and De Angelis, F and Laudadio, I and Fulci, V and Stronati, L and Manella, S and Alvaro, D and D'Andrea, G and Silecchia, G and Cardinale, V},
title = {Bile Microbiota Profiling in Obese and Non-Obese Patients: A Comparison of Shotgun Metagenomics and 16S rRNA Amplicon Sequencing.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/life16091474},
pmid = {42795339},
issn = {2075-1729},
support = {PNC1221852F49EDDD//Grant Piano Nazionale Complementare Salute/ ; },
abstract = {Recent advances in metagenomics have expanded our ability to detect low-abundance microbial communities. While the gut remains the most densely populated microbial habitat, emerging evidence has proposed that microorganisms might also inhabit anatomical sites once considered sterile, such as the biliary system. We apply next-generation DNA sequencing to characterize the bacterial community of bile in obese and non-obese patients with symptomatic gallstones. Bile samples were collected from 64 patients (32 obese, 32 non-obese) undergoing elective cholecystectomy. We incorporated negative (sterile tubes) and positive (mock microbial community standard) controls to evaluate contamination risks. We applied both 16S rRNA gene amplicon and shotgun metagenomic sequencing. Both sequencing methods detected extremely low bacterial biomass in bile. Specifically, shotgun metagenomic sequencing identified bacterial DNA traces in only eight samples, displaying minimal community similarity. In the positive controls, our measurements confirmed the expected microbial community composition, and in the negative controls, no bacterial DNA was detected. In contrast, 16S rRNA gene sequencing showed bacterial DNA in all bile samples as well as in negative controls, suggesting a higher susceptibility to contamination. Our findings suggest that bile may not be consistently colonized by bacterial communities in uncomplicated gallstone disease.},
}

@article {pmid42795462,
year = {2026},
author = {Szili, K and Dézsi, C and Gulyás-Oldal, V and Sallai, D and Patay, G and Paschali, E and Nagy, S},
title = {Toward AI-Driven Detection of Asymptomatic Chronic Conditions from Stool Metagenomics and Dietary Data: A Multimodal Deep Learning Framework for T1DM, T2DM, MOS/PCOS, Cancer, and Autoimmune Disease.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091880},
pmid = {42795462},
issn = {2076-2607},
abstract = {Chronic non-communicable conditions-type 1 and type 2 diabetes mellitus (T1DM, T2DM), metabolic obesity syndrome (MOS), polycystic ovary syndrome (PCOS), colorectal and extra-intestinal cancers, and systemic autoimmune disease-share a prolonged asymptomatic phase during which conventional screening is invasive, insensitive, or resource-intensive. This review synthesizes the 2021-2026 literature on fecal microbiome-based artificial intelligence (AI) diagnostics across these conditions, extracting reported discrimination, validation strategy, microbial and short-chain fatty acid (SCFA) biomarkers, and cross-cohort reproducibility. Across the primary classifier studies tabulated here, reported areas under the curve (AUCs) span 0.76-0.99 under internal validation but 0.69-0.91 under external or cross-population validation; in the four studies reporting both, the median AUC falls from 0.875 to 0.810. Verified external-validation values include 0.82 for colorectal cancer, 0.79 for T2DM and 0.792 for discrimination of systemic lupus erythematosus from rheumatoid arthritis and controls. Clinical readiness turns on this internal-to-external gap more than on the headline AUC. We propose a multimodal deep learning architecture coupled with explainable AI; no component has been implemented or evaluated on data, and it is presented as a design proposal. Fecal-microbiome-based multimodal AI is technically feasible but clinically unvalidated, pending prospective, harmonized cross-cohort trials.},
}

@article {pmid42795487,
year = {2026},
author = {Che, M and Zhang, J and Kudelaiti, K and Zhang, J and Liusui, Y and Dong, Z},
title = {Effects of Co-Application of γ-Polyglutamic Acid and Chemical Fertilizer on Rhizosphere Microbial Community Structure and Function of Cotton at Different Growth Stages in an Arid Cotton Field.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091905},
pmid = {42795487},
issn = {2076-2607},
support = {2024D01A82//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {Long-term excessive nitrogen application in arid cotton fields increases nitrate leaching risk during fallow and disrupts rhizosphere microecology. To clarify the cross-growth-stage regulatory effects of the biostimulant γ-polyglutamic acid (γ-PGA) combined with chemical fertilizer on rhizosphere microbial communities, we compared chemical fertilizer alone (NK) and γ-PGA plus chemical fertilizer (GT) using rhizosphere soils collected at boll-setting (August) and fallow (October), with physicochemical measurements and metagenomic sequencing technology. At boll-setting, GT lowered pH by 0.74 units compared with NK and increased NH4[+]-N, NO3[-]-N, and TN by 339.3%, 491.4%, and 23.0%, respectively. By fallow, GT increased TOC by 70.6% and maintained NH4[+]-N at 18.38 mg/kg, while NK accumulated 66.85 mg/kg NO3[-]-N. GT buffered post-harvest fungal community disturbance (Shannon: GT 4.06 vs. NK 2.80) and shifted bacterial communities toward oligotrophic taxa and archaea toward ammonium-preferring taxa. A metagenomic LEfSe analysis showed that GT was enriched in functional genes related to [Q]: Secondary metabolite biosynthesis, transport and catabolism, [T]: Signal transduction mechanisms, and [V]: Defense mechanisms, indicating a shift from resource acquisition to conservative maintenance. Mantel tests revealed that microbial functional profiles showed the strongest association with NH4[+]-N (r = 0.828 in August, r = 0.883 in October, p < 0.001). Thus, γ-PGA with chemical fertilizer stabilizes fallow rhizosphere microbial communities, reduces nutrient leaching, and promotes carbon-nitrogen co-retention.},
}

@article {pmid42795512,
year = {2026},
author = {Pan, S and Zheng, W and Feng, Z and Ouyang, Z and Ma, M and Huang, L and Wang, L and Wang, X and Quan, C},
title = {A Butyrate-Producing Probiotic, Clostridium butyricum DMZ-SG06, Improves Growth Performance, Immune Function and Gut Microbiota in Largemouth Bass (Micropterus salmoides).},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091931},
pmid = {42795512},
issn = {2076-2607},
support = {2022020332-JH2/1013//Department of Science and Technology of Liaoning Province/ ; },
abstract = {Intensive aquaculture and antibiotic overuse have rendered largemouth bass (Micropterus salmoides) prone to frequent mass mortalities and economic losses. Probiotics are promising antibiotic alternatives for improving intestinal health and immunity. This study evaluated a novel butyrate-producing strain Clostridium butyricum DMZ-SG06 to elucidate its growth-promoting and immunomodulatory mechanisms. Three dietary treatments were used: control (Con, basal diet), T1 (basal diet supplemented with 1 g C. butyricum powder containing 5 × 10[8] CFU per 10 g diet), and T2 (basal diet supplemented with 1 mL C. butyricum suspension containing 5 × 10[8] CFU per 10 g diet). A total of 270 healthy juvenile largemouth bass (5.63 ± 0.03 g) were randomly allocated to three groups (90 fish per group), with each group divided into three replicate tanks (60 × 40 × 34 cm) (30 fish per tank). Fish were fed the corresponding diets to apparent satiation for a 60-day rearing period. Results showed that T2 increased weight gain rate (WGR) by 11.35% compared with control (p < 0.05, 213.90 ± 12.30% vs. 192.10 ± 10.20%) and significantly improved the specific growth rate (SGR, p < 0.05), with T2 performing best. Probiotic treatments markedly improved intestinal morphology, nonspecific immune indices, and antioxidant status (p < 0.05), with T2 exerting the most prominent effects. C. butyricum DMZ-SG06 significantly reduced the levels of pro-inflammatory cytokines. For instance, TNF-α levels in T2 decreased 1.39-fold compared with the control group (128.57 ± 4.97 pg/g vs. 178.67 ± 7.80 pg/g, p < 0.05). Meanwhile, the levels of anti-inflammatory cytokines were upregulated. For example, IL-10 levels in T2 increased 1.32-fold relative to the control group (321.89 ± 15.03 pg/g vs. 244.31 ± 7.57 pg/g, p < 0.05). Metagenomic analysis revealed reduced Acinetobacter abundance, enriched beneficial genera (Lactobacillus, Parabacteroides, p < 0.05), and enhanced microbial functions related to the phosphotransferase system and galactose metabolism (p < 0.05). In conclusion, C. butyricum DMZ-SG06 promotes largemouth bass growth and intestinal health via butyrate metabolism, immune modulation, and microbiota remodeling. Notably, the liquid bacterial suspension formulation exerts a more significant effect on enhancing the fish's growth performance and intestinal health than the powder counterpart, supporting its application as a safe probiotic in antibiotic-free aquaculture.},
}

@article {pmid42795518,
year = {2026},
author = {Yang, J and Wang, Z and Wang, C and Li, Y and Niu, Y and Feng, J and Xie, S and Li, X},
title = {Metagenomic Insights into the Functional Profiles of Carbon, Nitrogen, and Phosphorus Cycles in Yuncheng Salt Lake Under Different Salinity Gradients.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091937},
pmid = {42795518},
issn = {2076-2607},
support = {202204051001035//the Special Fund for Science and Technology Innovation Teams of Shanxi Province/ ; 202303021222246; 202303021212258//the Fundamental Research Program of Shanxi Province/ ; YHYJ-2023003//the "Listed and Commanded" Project from Yuncheng Salt Lake Protection and Utilization Research Institute of Shanxi Province/ ; YQ-2023003//the Doctoral Research Start-up Project/ ; 32300111//the National Natural Science Foundation of China/ ; YCKJ-2024022//the Yuncheng City Science and Technology Program Project/ ; },
abstract = {Salinity is a key driver of microbial community structure and function in salt lake ecosystems, yet how it shapes functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling remains poorly understood. We collected metagenomic samples along a natural salinity gradient in Yuncheng Salt Lake and examined how salinity was associated with microbial taxonomic and functional diversity and with C, N, and P cycling genes. Both diversity metrics decreased significantly with increasing salinity and were positively correlated with each other. The composition and abundance of C, N, and P cycling genes differed significantly among the low-, medium-, and high-salinity groups. In carbon cycling, most carbon fixation genes were more abundant at higher salinity, whereas most carbon degradation genes were less abundant; within carbon fixation, reductive tricarboxylic acid (rTCA) cycle and Calvin cycle gene abundances were higher. In nitrogen cycling, nitrogen mineralization and assimilation genes were significantly more abundant. In phosphorus cycling, transporter and pyrimidine metabolism genes were more abundant, whereas the relative contribution of purine metabolism genes declined. Co-occurrence network analysis revealed dense positive co-occurrence associations among C, N, and P cycling genes, with mer, GLU, and ppk1 as highly connected genes. Mantel tests identified salinity and pH as the primary environmental factors associated with functional gene variation. These results suggest that salinity may regulate C, N, and P cycling genes partly by reshaping microbial community structure in salt lake ecosystems.},
}

@article {pmid42795531,
year = {2026},
author = {Zhang, YX and Wang, LX and Zhang, JG and Li, C and Wu, LF and Jiang, XF and Chun, Y},
title = {Sexual Propagation Enhances Tea Quality Through Rhizosphere Microbiome Assembly and Metabolic Reprogramming in Camellia sinensis.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091949},
pmid = {42795531},
issn = {2076-2607},
support = {32460785//National Natural Science Foundation of China，Grant No. 32460785/ ; 20241ZDD02045//Jiangxi Provincial Key Laboratory of Plantation and High-Valued Utilization of Specialty Fruit Trees and Tea/ ; 202301//Open Research Project of Jiangxi Intelligent Agricultural Machinery Equipment Engineering Research Center/ ; 202558-22380//Yingtan Municipal Science and Technology Plan Project/ ; YCTY202508//Integrated Pilot Project for Research, Development, Manufacturing, Promotion, and Application of Agricultural Machinery Equipment in Jiangxi Province/ ; },
abstract = {Tea quality is largely determined by the accumulation of specialized metabolites in fresh leaves, yet the effects of the propagation method on tea quality and its belowground ecological basis remain insufficiently understood. In this study, sexually propagated (SR) and asexually propagated (AR) tea plants were compared by integrating soil physicochemical analysis, leaf quality and physiological measurements, widely targeted metabolomics, and rhizosphere metagenomic profiling. Compared with AR, SR plants exhibited more favorable rhizosphere nutrient conditions, with soil organic matter, total nitrogen, alkali-hydrolyzable nitrogen, and available phosphorus increasing by 23.1%, 18.2%, 27.8%, and 161.5%, respectively, although available potassium decreased by 24.4%. SR leaves also contained higher dry matter, tea polyphenol, and soluble sugar contents, which increased by 11.5%, 58.8%, and 8.6%, respectively. In addition, superoxide dismutase, peroxidase, and indole-3-acetic acid oxidase activities were 30.4%, 92.0%, and 21.7% higher under SR, whereas hydrogen peroxide content remained unchanged. Metabolomic profiling revealed marked differences in leaf metabolic composition between the two propagation types, with differentially accumulated metabolites mainly enriched in flavonoid biosynthesis, phenolic acid metabolism, caffeine metabolism, carotenoid biosynthesis, plant hormone signaling, and α-linolenic acid metabolism. Rhizosphere metagenomic analysis further showed that SR was characterized by higher relative abundances of Actinomycetota, Pseudomonadota, Planctomycetota, Alphaproteobacteria, and Streptomycetales, together with distinct microbial functional profiles related to glycolysis, the tricarboxylic acid cycle, and pyruvate metabolism. Significant correlations were identified between several SR-enriched microbial taxa and quality-related metabolites, particularly flavonoids and phenolic acids. Overall, under the present field conditions, sexual propagation was more favorable than asexual propagation for tea quality formation, as reflected by improved nitrogen and phosphorus availability, greater accumulation of quality-related metabolites, higher antioxidant enzyme activities, and distinct rhizosphere microbial carbon-metabolic potential. These findings provide an integrated soil-microbiome-metabolome perspective for understanding propagation-related differences in tea quality.},
}

@article {pmid42795541,
year = {2026},
author = {Li, Q and Wang, J and Wang, Z and Cheng, C and Bao, S and Chai, S and Dai, D and Wang, X and Song, Q and Chen, Y and Lv, J and Ma, Y and Sonam, T and Qiu, J and Wang, S},
title = {Segment-Specific Gut Microbiome and Bile Acid Profiles in Grazing and Stall-Fed Yaks.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091960},
pmid = {42795541},
issn = {2076-2607},
abstract = {The yak is an iconic ruminant of the Qinghai-Tibet Plateau, yet segment-specific variation in its intestinal microbial functional potential and bile acid profiles under different feeding systems remains insufficiently characterized. Six healthy adult male yaks with similar body weights (320 ± 30 kg) were assigned to grazing (G) or stall-feeding (S) systems, with three animals per group, for a 90-day trial comprising a 10-day adaptation period and an 80-day formal experimental period. The individual yak was considered the experimental unit, and intestinal segments sampled from the same animal were treated as repeated observations. Liver tissue and digesta from the duodenum, ileum, cecum, and colon were analyzed using targeted bile acid metabolomics and shotgun metagenomics. Principal coordinate analysis based on Bray-Curtis dissimilarities showed segment-associated clustering of microbial communities, with PCo1 and PCo2 explaining 65.5% and 18.9% of the total variation, respectively. ANOSIM identified a significant intestinal-segment effect on microbial community composition (R = 0.2208, BH-FDR = 0.0144), whereas the overall feeding-system effect was not significant (R = 0.3747, BH-FDR = 0.1200). No statistically significant feeding-system differences were detected in Shannon, Simpson, Chao1, or ACE indices within individual intestinal segments (BH-FDR ≥ 0.800), and PERMDISP detected no significant differences in within-group dispersion (BH-FDR ≥ 0.1682). Bacillota and Bacteroidota were the dominant phyla. Descriptive functional profiling showed higher mean ileal abundances of GH2 (0.0035 vs. 0.0026), GH3 (0.0029 vs. 0.0024), and GH43 (0.0021 vs. 0.0013) in grazing yaks, whereas the starch-associated GH13 family showed its highest mean abundance in the colon of stall-fed yaks. These metagenomic patterns represent predicted genomic functional potential rather than gene expression, enzyme activity, or metabolic flux. Cecal total bile acid concentration showed a nominal between-group difference (unadjusted Welch's p = 0.0109), but this difference did not remain significant after correction across the five anatomical sites (BH-FDR = 0.0545). In the colon, stall-fed yaks had a lower conjugated-to-unconjugated bile acid ratio and a higher secondary-to-primary bile acid ratio than grazing yaks (BH-FDR < 0.05). Feeding-system-associated descriptive patterns were observed in predicted microbial functional profiles, whereas statistically supported between-group differences were limited mainly to selected colonic bile acid ratios. Given the limited animal-level replication, these findings should be considered exploratory.},
}

@article {pmid42795547,
year = {2026},
author = {Yuan, L and Zhang, C and Li, W and Yi, J and Liu, C and Jin, W and Li, G and Wang, B and Li, S and Wang, H},
title = {Intestinal Microbiota Structure of Xichuan Black-Bone Chickens and Preliminary Evaluation of a Probiotic-Based Fecal Microbiota Substitute.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091966},
pmid = {42795547},
issn = {2076-2607},
support = {2026ZC75//Henan Academy of Agricultural Sciences/ ; 2026BX54//Henan Academy of Agricultural Sciences/ ; 2025XMYG04//Henan Academy of Agricultural Sciences/ ; },
abstract = {In this study, we aimed to explore the intestinal microbiota structure of Xichuan black-bone chickens (XBCs) and evaluate the effect of fecal microbiota substitute transplantation (FMST) by comparing it with traditional fecal microbiota transplantation (FMT). Metagenomic sequencing was used to analyze the microbiota composition and diversity of different intestinal segments (duodenum, jejunum, ileum, cecum, and rectum) of adult XBCs. Probiotic strains were subsequently isolated and screened from the cecal contents under anaerobic conditions to prepare FMST preparations. In total, 90 1-day-old XBCs were randomly divided into the FMT group, FMST group and control group (CK) for the transplantation experiment. The results revealed that the cecum had the highest species richness among all intestinal segments, with a mean species number of 7593.2. Three probiotic strains, namely, Lactobacillus crispatus, Weissella paramesenteroides and Bacillus amyloliquefaciens, were successfully screened and identified. In the transplantation experiment, the FMT group exhibited optimal α diversity of the cecal microbiota, while compared with the FMT group, the FMST group had significantly reduced expression of pro-inflammatory cytokines (IL-6, TNF-α, and IL-1β) and increased expression of intestinal tight junction proteins (claudin-1 and ZO-1). In conclusion, the cecum of XBCs has the most abundant microbial resources. Under the short-term intervention model tested herein, the custom FMST formulation delivers superior intestinal protective effects and shows promising potential as a standardized alternative to conventional FMT, which is highly important for the standardized application of fecal microbiota transplantation in poultry production.},
}