@article {pmid41561026,
year = {2025},
author = {Li, F and Qiu, Z and Pei, Z and Zhu, Q and Shen, S and Fan, L and Xu, L and Huang, C and Wang, J and Huang, B and Huang, L and Liu, X and Han, Q},
title = {Effects of pesticides on soil microbial community structure and nitrogen transformation in tobacco fields affected by root rot.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1733977},
pmid = {41561026},
issn = {1664-302X},
abstract = {INTRODUCTION: In tobacco planting soil infected with root rot disease, the potential impacts of prothioconazole (T1), pyrisoxazole (T2), kasugamycin combined with Paenibacillus polymyxa (T3), and cyclobutrifluram (T4) on soil microecology remain unclear. This study examined their effects on soil microbial communities and nitrogen transformation processes.

METHODS: By measuring soil nitrogen forms and enzyme activities, combined with metagenomic sequencing, we conducted a comprehensive assessment of the soil microecology, focusing on shifts in microbial community composition, xenobiotic degradation potential, and nitrogen cycling processes.

RESULTS AND DISCUSSION: The results revealed that pesticide application significantly changed the content of nitrogen forms and their transformation rate. T1 and T2 treatments significantly increased the accumulation of ammonium nitrogen (NH4 [+]-N), while T2 and T4 markedly promoted the accumulation of nitrate nitrogen (NO3 [-]-N). Microbial community analysis indicated that the T2 and T4 treatments significantly affected the microbial structure. Analysis of xenobiotic degradation pathways showed that multiple pathways were suppressed by the four pesticide treatments, with the T2 treatment exhibiting the broadest suppressive effect. Metagenomic analysis further revealed that the T2 treatment promoted the accumulation of both NH4 [+]-N and NO3 [-]-N by up-regulating the mineralization gene (gdh) and nitrification genes (hao and nxrAB), while the T4 treatment facilitated NO3 [-]-N accumulation by up-regulating nitrification genes (hao and nxrAB). Correlation network analysis uncovered relationships between key nitrogen cycle genes and microbial genera, showing that nitrification genes (hao and nxrAB) in the T2 and T4 treatment groups exhibited positive correlations with Nitrobacter and Nitrosovibrio. This research clarifies the pathways through which these four pesticides influence the soil nitrogen cycle, providing an important theoretical basis for their ecological risk assessment and rational application.},
}

@article {pmid41561024,
year = {2025},
author = {Chen, YX and Xuan, YS and Wang, MH and Li, Y and Shi, SM and Zhao, HY and Niu, YH and Chen, M and Li, SY},
title = {Research on the regulation of gut microbiota homeostasis and immune function in asthmatic mice by Huanglong Zhixiao Formula.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1726388},
pmid = {41561024},
issn = {1664-302X},
abstract = {BACKGROUND: Asthma affects approximately 334 million people worldwide. Accumulating evidence indicates that gut dysbiosis exacerbates airway inflammation through the gut-lung axis. In the present study, using an OVA-induced murine model of asthma, we investigated whether Huanglong Zhixiao Formula (HLZXF) restores gut lung homeostasis by reshaping the gut microbiota and enhancing intestinal barrier function, thereby attenuating pulmonary pathological changes.

METHODS: Female BALB/c mice were randomly assigned to three groups (n = 15 per group): Control (C), Asthma Model (MX), and HLZXF-treated (ZG) groups. Asthma was induced by OVA sensitization and challenge over a 6-week period. The ZG group received daily oral gavage of HLZXF, 1 h prior to each OVA challenge. Fecal samples were collected for metagenomic sequencing. Lung and intestinal tissues were excised for HE and IHC staining of tight junction proteins, including Claudin, Occludin, and ZO-1. Alpha and beta diversity analyses were conducted to evaluate the composition and structure of the gut microbiota.

RESULTS: We analyzed the structure of the gut microbiota, detected the expression levels of intestinal barrier-related proteins, and assessed inflammatory injury in the lungs and intestines. Results demonstrated that HLZXF significantly ameliorated gut microbiota dysbiosis in asthmatic mice, as evidenced by the significant enrichment of Heminiphilus faecis and Paramuribaculum intestinale. Additionally, certain fungal taxa, such as Piromyces finnis and Rhizopus arrhizus, were significantly enriched in the ZG group. HLZXF also significantly upregulated the expression levels of the tight junction proteins Claudin, Occludin, and ZO-1 in intestinal tissues, thereby promoting the repair of the intestinal mucosal barrier. Furthermore, HLZXF significantly attenuated inflammatory cell infiltration and tissue injury in the lungs and intestines, alleviated alveolar septal thickening, and enhanced the integrity of the intestinal mucosal barrier.

CONCLUSION: This study elucidates the potential therapeutic mechanisms of HLZXF in the treatment of asthma from the perspective of gut microbiota and intestinal barrier function. It highlights that HLZXF can attenuate pulmonary inflammation by regulating the balance of gut microbiota and enhancing intestinal barrier function.},
}

@article {pmid41560914,
year = {2025},
author = {Chevokina, E and Sibiryakina, D and Sobolev, A and Slonova, D and Demkina, A and Yurikova, D and Galivondzhyan, A and Konovalova, O and Sutormin, D and Isaev, A},
title = {Efficient recovery and DNA extraction for algae-associated microbial communities.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1693747},
pmid = {41560914},
issn = {1664-462X},
abstract = {The extraction of high-quality microbial DNA from environmental samples is critical for many downstream applications, including short- and long-read metagenomic sequencing. However, environmental DNA is prone to low recovery, degradation, and contamination by enzymatic inhibitors, with the extent of these issues largely dependent on the DNA purification method. The embedding of bacterial cells in a mucoid matrix within biofilms further complicates the process, making the study of algal symbionts particularly challenging. This study benchmarked five methods to recover microbial cells from biofilms associated with three major groups of marine macroalgae, namely: red (Palmaria stenogona), brown (Saccharina japonica), and green (Ulva lactuca). This was followed by a systematic evaluation of six widely used commercial DNA purification kits for their ability to extract high-quality DNA suitable for 16S rRNA gene and shotgun sequencing. A universal trade-off was observed between the quantity and quality of the extracted DNA. While whole-sample homogenization and manual collection of biofilms resulted in high levels of chloroplast contamination, washing microbial cells with a buffer led to low DNA recovery; however, the use of a detergent improved DNA yields. A comparison of the DNA extraction kits revealed that their efficiency varied significantly among algal species, with the GeneJET Genomic DNA Purification Kit (Thermo Scientific) identified as the most versatile. The present findings provide a comparative benchmark of methods to recover algae-associated microbial communities and extract their DNA, offering guidance in selecting procedures suited for metagenomic sequencing.},
}

@article {pmid41560360,
year = {2026},
author = {Zhang, J and Wang, Z and Li, S and Luo, C and Li, H and Ma, S and Wang, P and Liu, H and Sun, L and Yin, Y and Zhang, W and Wang, Q},
title = {Phocaeicola coprophilus-Derived 6-Methyluracil Attenuates Radiation-Induced Intestinal Fibrosis by Suppressing the IDO1-Kynurenine-AHR Axis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18502},
doi = {10.1002/advs.202518502},
pmid = {41560360},
issn = {2198-3844},
support = {JDYY15202429//Youth Development Fund of the First Hospital of Jilin University/ ; JDYY-DEP-2022006//Doctor of Excellence Program (DEP), The First Hospital of Jilin University/ ; YDZJ202402012CXJD//Department of Science and Technology of Jilin Province/ ; 82330017//National Natural Science Foundation of China/ ; 82270610//National Natural Science Foundation of China/ ; 20240484505//Beijing Nova Program/ ; 2024ZD0530100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; },
abstract = {Therapeutic options for radiation-induced intestinal fibrosis (RIF) remain limited. This study reveals that intestinal kynurenine (Kyn) is persistently elevated after radiation and correlates with fibrosis severity in both murine models and human rectal cancer samples. Exogenous Kyn exacerbated RIF, whereas inhibition of indoleamine 2,3-dioxygenase 1 (IDO1) attenuated fibrotic progression. Mechanistically, Kyn activates the aryl hydrocarbon receptor (AHR) to promote fibroblast activation and fibrosis. Antibiotic depletion of gut microbiota abrogates radiation-induced IDO1-Kyn upregulation and protects against RIF. Conversely, fecal microbiota transplantation from irradiated mice recapitulates the elevated IDO1-Kyn phenotype. Metagenomic analysis identify radiation-induced depletion of Phocaeicola coprophilus (P. coprophilus), whose abundance inversely correlates with Kyn levels. Supplementation with live P. coprophilus suppresses IDO1-Kyn signaling and ameliorates RIF. Untargeted metabolomics further show that radiation reduces 6-methyluracil, a metabolite derived from P. coprophilus. Exogenous 6-methyluracil replenishment inhibits repression of the IDO1-Kyn axis and mitigates fibrosis. Together, these findings define a microbiota-metabolite-host pathway in which radiation depletes P. coprophilus, leading to loss of 6-methyluracil and derepression of the IDO1-Kyn-AHR axis, thereby driving fibrogenesis. Restoration of either P. coprophilus or its metabolite 6-methyluracil represents a promising therapeutic strategy against RIF.},
}

@article {pmid41560354,
year = {2026},
author = {He, N and Wang, H and Yang, Z and Li, H and Liu, B and Chen, K and Wu, Z and Zhao, X and Liang, H and Wang, M and Li, X and Zhong, Y and Zhang, H and Xiao, L and Kristiansen, K and Peng, J and Zou, Y and Li, S},
title = {The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17596},
doi = {10.1002/advs.202517596},
pmid = {41560354},
issn = {2198-3844},
support = {82470615//National Natural Science Foundation of China/ ; 2024KJJ042//Shandong Provincial Youth Entrepreneurship Program for Colleges and Universities/ ; ZR2022MH217//Shandong Provincial Natural Science Foundation/ ; 2023TD52//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023TD76//Central Public-interest Scientific Institution Basal Research Fund/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; No.25-1-5-smjk-13-nsh//Qingdao Municipal Demonstration Project for Science & Technology to Benefit the People/ ; 2025YFA1310200//National Key Research and Development Program of China/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease. This study investigates the anti-MASLD effects of dietary prebiotic stachyose (STA) on disease progression identifying Butyricimonas virosa as a key bacterium boosted by STA supplementation. Oral gavage of B. virosa to high fat diet (HFD)-fed mice significantly suppresses the progression of MASLD and modulates gut microbiota composition. Integration of metagenomic and metabolomic data demonstrates that B. virosa treatment significantly enhances the production of thiamine monophosphate (TMP), as well as its conversion to thiamine and subsequent accumulation in the liver. The accumulation of hepatic thiamine further leads to elevated thiamine pyrophosphate (TPP) concentrations enhancing the activity of branched-chain α-keto acid dehydrogenase E1 subunit α (BCKDHA) associated with augmented degradation of branched chain amino acids (BCAAs). Administration of B. virosa compensates via production of gut bacterial-derived TMP for hepatic TPP deficiency in mice fed a thiamine-deficient HFD. A population-based analysis reveals an inverse correlation between plasma thiamine levels, abundances of bacterial genes involved in thiamine synthesis and metabolism, and phenotypes associated with MASLD, suggesting that key genes involved in fecal thiamine metabolism, as well as serum thiamine determination, may potentially serve as biomarkers for the diagnosis of MASLD.},
}

@article {pmid41560107,
year = {2026},
author = {Duan, JX and Jian, H and Chang, L and Teng, J and Lai, SY and Yang, QX and Che, GL and Luo, LL and Liu, F},
title = {mNGS facilitates the diagnosis of pediatric murine typhus: A case report.},
journal = {Medicine},
volume = {105},
number = {3},
pages = {e47253},
doi = {10.1097/MD.0000000000047253},
pmid = {41560107},
issn = {1536-5964},
mesh = {Humans ; *Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications ; Child ; *Rickettsia typhi/genetics/isolation & purification ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Anti-Bacterial Agents/therapeutic use ; Doxycycline/therapeutic use ; Female ; Dexamethasone/therapeutic use ; },
abstract = {RATIONALE: Murine typhus, caused by Rickettsia typhi, is a globally distributed flea-borne rickettsiosis. Although rarely recognized, it can trigger hemophagocytic lymphohistiocytosis (HLH), a life-threatening hyperinflammatory syndrome. Nonspecific febrile illness and atypical petechial eruptions frequently lead to delayed or missed diagnoses. This report aims to illustrate the diagnostic process and clinical implications of murine typhus-associated HLH in a pediatric patient, and to evaluate the utility of metagenomic next-generation sequencing (mNGS) as an unbiased detection tool for occult pathogens.

PATIENT CONCERNS: A 10-year-old child was admitted with unexplained recurrent fever and generalized petechiae, refractory to treatment at outside hospitals.

DIAGNOSES: The patient was ultimately diagnosed with murine typhus-associated HLH caused by R typhi, based on a comprehensive diagnostic work-up.

INTERVENTIONS: Empirical dexamethasone was initiated promptly to control hyperinflammation. After mNGS confirmation, oral doxycycline was added for targeted anti-rickettsial therapy.

OUTCOMES: The patient's clinical status continued to improve, culminating in discharge.

LESSONS: Murine typhus-associated HLH should be considered in febrile children with unexplained cytopenias and petechiae. Early empiric HLH-directed immunosuppression followed by pathogen-specific therapy improves prognosis. mNGS provides a rapid, unbiased method to detect rare, overlooked pathogens and guide definitive treatment when conventional tests are negative.},
}

Humans
*Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications
Child
*Rickettsia typhi/genetics/isolation & purification
*Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology/microbiology/drug therapy
*High-Throughput Nucleotide Sequencing/methods
Male
Anti-Bacterial Agents/therapeutic use
Doxycycline/therapeutic use
Female
Dexamethasone/therapeutic use

@article {pmid41559953,
year = {2026},
author = {Wu, J and Sun, D and Pan, Y and Liu, DF and Zhang, H and Zhou, JH and Gao, T and Wu, J and He, RL and Chen, YG and Li, WW},
title = {Overlooked Roles of Pharmaceutical Metabolic Products in Stimulating Microbial Metabolism and Antibiotic Resistance Gene Dissemination of Anaerobic Sludge.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70247},
doi = {10.1111/1462-2920.70247},
pmid = {41559953},
issn = {1462-2920},
support = {51878638//National Natural Science Foundation of China/ ; 52192681//National Natural Science Foundation of China/ ; 22106160//National Natural Science Foundation of China/ ; U21A20160//National Natural Science Foundation of China/ ; 202423110050028//Key R&D Project of Anhui Province, China/ ; SYG2024111//Science and Technology Program of Suzhou/ ; WK2060000099//Fundamental Research Funds for the Central Universities/ ; //Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education/ ; JYB2025XDXM909//State Key Laboratory of Advanced Environmental Technology/ ; SKLAET2025-LH01//State Key Laboratory of Advanced Environmental Technology/ ; },
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Metformin/metabolism/pharmacology ; *Bacteria/genetics/metabolism/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Biotransformation ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; },
abstract = {The roles of non-antibiotic pharmaceuticals in shaping the dissemination behaviours of antibiotic resistance genes (ARGs) in wastewater treatment systems remain poorly understood, and the influences of their transformation products have been overlooked. Here, we unveil more profound impacts of the metformin (MET) biotransformation product than the parent pollutant on the microbial community structure and ARG propagation of wastewater anaerobic sludge. The exposure to MET and its metabolic products guanylurea (GUA) at environmentally relevant concentrations both raised the methane production and resulted in up to 52.5% higher sludge ARGs abundance relative to the unexposed control. Especially, the GUA group showed up to 188-fold upregulation in several ARGs including bcrA, PmrF, acrB and mexF, enabled 3218-fold enrichment of plasmids from several bacteria. The underlying mechanisms were elucidated by integrated metagenomics, molecular dynamics simulations, and metabolic profiling analyses. MET and GUA were found to trigger coordinated cellular responses including disrupted glycerophospholipid metabolism, increased membrane permeability and broad metabolic reprogramming, which collectively boosted the ARGs dissemination. Overall, this work establishes a mechanistic link between micropollutant-induced microbial stress and ARGs propagation in anaerobic sludge, and advocates for re-evaluating the environmental risks of non-antibiotic pharmaceuticals and integrating resistance control into wastewater management framework.},
}

*Sewage/microbiology
Anaerobiosis
*Drug Resistance, Microbial/genetics
*Metformin/metabolism/pharmacology
*Bacteria/genetics/metabolism/drug effects
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Biotransformation
Wastewater/microbiology
Water Pollutants, Chemical/metabolism

@article {pmid41559841,
year = {2026},
author = {Galgano, S and Faruk, MU and Eising, I and Houdijk, JGM and Khattak, F},
title = {Dietary muramidase leads to the downregulation of peptidoglycan biosynthesis and to caecal microbial modulation in laying hens.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {7},
pmid = {41559841},
issn = {2524-4671},
}

@article {pmid41559596,
year = {2026},
author = {Liu, Y and Zhang, Q and Li, J and Wu, X and Zang, Q and Wang, Q and Huang, P and Wang, Y and Zhang, S and Liu, S and Zhu, C and Zhao, Y and Yan, T and He, Y},
title = {mNGS improves the efficiency of infection diagnosis and treatment in acute-on-chronic liver failure.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-025-04601-8},
pmid = {41559596},
issn = {1471-230X},
abstract = {INTRODUCTION: The early diagnosis of infections in acute-on-chronic liver failure (ACLF) is still difficult. mNGS(metagenomic next-generation sequencing) is a no-bias, sensitive pathogen diagnosis method, and further research on mNGS in ACLF is needed.

METHODS: A total of 275 ACLF patients with suspected or confirmed infections were recruited and divided into the mNGS group and the non-mNGS group. Differences between the two groups were assessed.

RESULTS: The 1:1 Propensity score matching (PSM) for balancing the baseline variables produced 86 patients in each group. From these 86 patients in the mNGS group, 134 samples were collected and analyzed. The overall microbiological positive rate (103/134, 76.9%) detected by mNGS was higher than that detected by culture (24/134, 17.9%), particularly for fungi (14.9% vs. 2.2%). The etiological diagnosis rates for pulmonary and thoracoabdominal infections detected by the mNGS method were higher than those of the culture method (47.9% vs. 11.4%; 52.0% vs. 18.4%, respectively). The etiological diagnosis can be confirmed 22.83 ± 26.27 h ahead of time. mNGS testing did not significantly improve 90-day transplant-free survival in the overall cohort (sHR 0.96, 95% CI 0.72-1.27; P = 0.76). In the subgroup where mNGS guided therapy, numerically higher resolution rates were observed for pulmonary (53.8% vs 37.1%), abdominal (63.2% vs 52.6%), and bloodstream infections (66.7% vs 50.0%), though these differences were not statistically significant.

CONCLUSIONS: mNGS is a valuable diagnostic tool for ACLF with infections, especially for viruses and fungi. mNGS allows for precise and earlier pathogen diagnosis, enabling timely and targeted anti-infective therapy. mNGS may be associated with improved clinical outcomes in ACLF patients with co-infections, though this potential association requires further validation.

TRIAL REGISTRATION: The study was registered on Clinicaltrials.gov (registration number: NCT05740696, release date: February22,2023). Accessible at: https://classic.

CLINICALTRIALS: gov/ct2/show/NCT05740696.},
}

@article {pmid41559060,
year = {2026},
author = {Ding, Z and Wen, T and Teng, X and Yang, W and Yuan, X and Liu, X and Xie, P and Zhao, X and Shen, Q and Yuan, J},
title = {Enhancing soil citrulline degrading function to mitigate soil-borne Fusarium wilt.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68606-x},
pmid = {41559060},
issn = {2041-1723},
support = {42322708//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Continuous cropping often exacerbates soil-borne diseases, particularly Fusarium wilt, yet the intricate rhizosphere relationships among phyto-derived metabolites, pathogens, and particular microbial functions remain poorly understood. Here, we observe that citrulline accumulation during continuous cropping is positively correlated with Fusarium wilt severity by enhancing fusaric acid production in Fusarium oxysporum. Metagenomic analyses reveal that citrulline turnover-related functions, represented by functional modules including M00978, are significantly enriched in healthy rhizosphere soils but are notably reduced in Fusarium-conducive soils. The functional genes, arcB and argH, are identified in Pseudomonas putida YDTA3, with arcB being essential for citrulline-degradation via knockout experiments. The inoculation of an arcB-expressing indigenous Escherichia consortium (EO-arcB) in three independent continuous cropping systems of cucurbit crops demonstrates that enhancing and maintaining the soil citrulline-degrading function mitigates soil-borne Fusarium wilt. In summary, this study advances our understanding of rhizosphere interactions underlying Fusarium wilt disease occurrence and offers a promising biocontrol strategy.},
}

@article {pmid41559018,
year = {2026},
author = {Liu, J and Li, D and Wang, S and Gao, S and Xu, B and Zhao, J and Liu, Q and Chen, M and Zhou, X and Cai, Y and He, L},
title = {Congenital babesiosis in China: first molecularly confirmed case of vertical transmission of Babesia microti.},
journal = {Emerging microbes & infections},
volume = {15},
number = {1},
pages = {2608389},
doi = {10.1080/22221751.2025.2608389},
pmid = {41559018},
issn = {2222-1751},
mesh = {Humans ; *Babesia microti/genetics/isolation & purification/classification ; *Babesiosis/transmission/drug therapy/diagnosis/parasitology ; Male ; China ; *Infectious Disease Transmission, Vertical ; Infant ; Atovaquone/therapeutic use ; Azithromycin/therapeutic use ; Female ; Proguanil/therapeutic use ; Antiprotozoal Agents/therapeutic use ; Infant, Newborn ; Drug Combinations ; },
abstract = {Congenital babesiosis is rarely reported globally. We report a 74-day-old male infant presented with fever, pallor, and severe, life-threatening haemolytic anaemia (haemoglobin: 45 g/L). The infant had 16% parasitemia with ring forms evident on peripheral blood smear. Babesia microti infection was confirmed in both the mother and infant by PCR and metagenomic next- generation sequencing. Genetic analysis revealed an identical strain in bot. Treatment with intravenous azithromycin and oral atovaquone/proguanil resulted in rapid clearance of parasitemia and resolution of anaemia. This first molecularly confirmed case of congenital B. microti transmission in China demonstrates vertical transmission from an asymptomatic mother. It underscores the need for heightened clinical suspicion in neonates with unexplained haemolytic anaemia in endemic regions and highlights critical gaps in access to essential anti-babesia therapies.},
}

Humans
*Babesia microti/genetics/isolation & purification/classification
*Babesiosis/transmission/drug therapy/diagnosis/parasitology
Male
China
*Infectious Disease Transmission, Vertical
Infant
Atovaquone/therapeutic use
Azithromycin/therapeutic use
Female
Proguanil/therapeutic use
Antiprotozoal Agents/therapeutic use
Infant, Newborn
Drug Combinations

@article {pmid41558536,
year = {2026},
author = {Kasuma, N and Fitri, H and Wulandari, RW and Ernesto, G and Juwita, DR and Effendi, MDS and Wirza, TR},
title = {Salivary Microbiome Differences in Stunted and Healthy Children: A Metagenomic Analysis.},
journal = {European journal of dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0045-1814094},
pmid = {41558536},
issn = {1305-7456},
abstract = {This study aimed to compare the composition and diversity of the salivary microbiome in stunted and nonstunted children using 16S rRNA gene sequencing to explore the relationship between nutritional status and oral microbiota.A total of 20 saliva samples were collected from children aged 6 to 10 years, comprising two groups: stunted (n = 10) and healthy controls (n = 10). Deoxyribonucleic acid was extracted, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced. Bioinformatics analysis included taxonomic assignment, calculation of relative abundance, α diversity (using Shannon and Simpson indices), β diversity (UniFrac-based principal coordinate analysis and permutational multivariate analysis of variance [PERMANOVA]), and differential abundance testing using the Mann-Whitney U test.The dominant phyla in both groups were Proteobacteria, Firmicutes, and Bacteroidota, with Proteobacteria being more prevalent in the stunted group. At the genus level, Neisseria and Veillonella were more abundant in stunted children. Notably, Veillonella was significantly elevated in the stunted group (28.6%) compared with controls (14.9%, p = 0.0376). Alpha diversity indices revealed a higher diversity trend in the stunted group, although this difference was not statistically significant (Shannon, p = 0.130; Simpson, p = 0.762). Beta diversity analysis revealed no considerable clustering between groups (PERMANOVA p > 0.05), indicating moderate interindividual variability but no clear group separation.Children with stunted growth demonstrated distinct microbial signatures in their salivary microbiota, particularly in the increased abundance of Proteobacteria and Veillonella, suggesting a potential link between chronic undernutrition and oral microbial dysbiosis. These findings underscore the need for additional studies to investigate the impact of nutritional status on oral and systemic health through the microbiome axis.},
}

@article {pmid41558481,
year = {2026},
author = {Keller, V and Calchera, A and Otte, J and Tuovinen Nogerius, V and Schmitt, I},
title = {Ubiquitous occurrence of the black fungus Melanina gundecimermaniae in the lichen Umbilicaria pustulata.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.12.046},
pmid = {41558481},
issn = {1879-0445},
abstract = {Lichen symbioses frequently include additional fungal associates beyond the canonical mycobiont (fungus) and photobiont (alga/cyanobacterium). Despite the prevalence and diversity of these lichen cohabitants, their geographic distribution and role within the lichen consortium remain poorly understood. Combining genomics, metagenomics, and advanced microscopy, we identified the black fungus Melanina gundecimermaniae as a constant cohabitant in the lichen Umbilicaria pustulata. We analyzed metagenomes from 149 individuals across 15 populations, spanning the Europe-wide range of U. pustulata. Additionally, we screened pooled metagenomes of U. pustulata and Umbilicaria phaea along five elevation gradients (Europe and North America). Genome mapping, using a near-complete reference genome of M. gundecimermaniae, revealed that the black fungus was present in 100% of the screened lichen metagenomes, with 0.85%-3.78% of reads mapping against the reference. Among all lichen-associated fungi, it was one of the most common. These findings indicate that the black fungus is widely distributed and associated with different lichen species, underscoring its potential ecological significance. Using fluorescence in situ hybridization coupled with confocal laser scanning microscopy, we confirmed the presence of M. gundecimermaniae within various structures of U. pustulata, including vegetative symbiotic propagules involved in dispersal. Elucidating its widespread occurrence across continents, consistent presence in U. pustulata, and ability to be dispersed together with the lichens' canonical partners, our findings suggest a potential interaction of M. gundecimermaniae that extends beyond incidental colonization. Our study contributes to the growing body of evidence that organismal complexity within lichens is a prevalent and largely unexplored dimension of the lichen symbiosis.},
}

@article {pmid41558447,
year = {2026},
author = {Han, Y and Wang, A and Zhang, Z and Liu, L and Chen, Q and Fan, W and Tan, E and Tang, K},
title = {Multi-omics reveal the prevalence of Thaumarchaeota and their biogeochemical roles in coastal low oxygen zones.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119293},
doi = {10.1016/j.marpolbul.2026.119293},
pmid = {41558447},
issn = {1879-3363},
abstract = {The intensification of coastal hypoxia under anthropogenic eutrophication and climate change necessitates understanding microbial adaptive mechanisms. However, the composition of microbial communities and their biogeochemical roles in response to oxygen gradients remain poorly understood. Here, we employed ‌integrated multi-omics‌ approaches to analyze microbial communities and their biogeochemical functions across oxic to low oxygen gradients off the Yangtze River Estuary in East China Sea. Results revealed that surface oxic waters hosted phytoplankton (Synechococcus) and opportunistic bacteria (Flavobacteriia, Pelagibacterales), while bottom layers enriched chemolithoautotrophs (Thaumarchaeota, Nitrospina) and facultative anaerobes (Planctomycetes, Marine Group II), with sediment resuspension further amplified particle-attached taxa. Meanwhile, a remarkable shift in microbial nitrogen metabolism was observed between oxic and low oxygen waters, with dissolved nitrogen assimilation dominated in oxic waters. Despite genomic potential for complete nitrogen reduction in low oxygen waters, our metaproteomics revealed only a significant expression of nitrate reductases. This decoupling between genomic potential and proteomic expression implies that ambient oxygen levels remain above thresholds for full pathway activation, showcasing microbial metabolic plasticity. Both metagenomic and metaproteomic have confirmed that Thaumarchaeota, particularly the genus Nitrosopumilus, emerged as keystone taxa, contributing to nitrification and dark carbon fixation, thereby coupling nitrogen‑carbon biogeochemical cycling in coastal hypoxic zones. These findings highlight redox-driven microbial niche differentiation and metabolic adaptation, providing predictive insights into biogeochemical feedbacks under expanding coastal deoxygenation.},
}

@article {pmid41558437,
year = {2026},
author = {Wang, S and Zhang, T and Shi, Y and Zhang, Y and Fan, J and Shen, Z},
title = {Immobilized exogenous proteinase K enhances mesophilic anaerobic co-digestion of polylactic acid and food waste.},
journal = {Journal of environmental management},
volume = {399},
number = {},
pages = {128634},
doi = {10.1016/j.jenvman.2026.128634},
pmid = {41558437},
issn = {1095-8630},
abstract = {Hydrolysis efficiency constraints impede anaerobic biodegradation of plastics, inducing kinetic imbalance during co-digestion with organic substrates. To address this limitation in food waste (FW) and commercial polylactic acid (PLA) biodegradable plastics (BPs), protease K (Pro K) was embedded onto BPs to leverage PLA-specific depolymerization activity. Regulatory mechanisms of enzymatic action on anaerobic microbial degradation were investigated through integration of classical model equations with metagenomic analysis. Results demonstrate that during hydrolysis, enzymatic reinforcement augmented hydrolysis rates, elevating BPs degradation from 7.3 % to 19.3 %. Throughout hydrogen/acidogenesis, microbial cascade responses were activated, enabling directional enhancement of the 'lactate-propionate-acetate' metabolic pathway. During methanogenesis, methyl oxidation was inhibited while concurrent reinforcement of hydrogenotrophic methanogenesis occurred, yielding 23.32 % (311.37 mL/g·VSadded[-1]) methane elevation. Metagenomic analysis revealed Pro K-mediated regulation of anaerobic metabolic gene pathways, establishing a novel strategy for accelerated BPs degradation and methane yield.},
}

@article {pmid41558352,
year = {2026},
author = {Xia, J and Li, C and Zhen, Y and Liu, M and Guo, J and Jiang, F},
title = {Bell-shaped response of mercury methylation to sulfate loading in urban sewer systems: Implications for source-level control.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141191},
doi = {10.1016/j.jhazmat.2026.141191},
pmid = {41558352},
issn = {1873-3336},
abstract = {Urban sewer systems act as incubators for mercury-methylating (hgcA) microorganisms, yet how sulfate-an abundant and variable sewage constituent-drives this process remains unclear. Here, we combined controlled bioreactor experiments, batch incubations, and genome-resolved metagenomics to demonstrate that Hg methylation potential follows a nonlinear, bell-shaped response to sulfate loading. The MeHg production rate peaked at moderate sulfate concentrations (75-150 mg/L), reaching levels 1.2-5.4 times higher than those observed under low sulfate conditions (6-30 mg/L). This enhancement arose from distinct community responses: at 75 mg/L, a phylogenetically diverse hgcA consortium emerged, with methanogens and fermenters complementing SRB, whereas at 150 mg/L, SRB-methylators such as Desulfobulbus dominated, indicating functional specialization. Outside this range, low sulfate (<30 mg/L) suppressed most hgcA populations due to electron acceptor scarcity, while high sulfate (>300 mg/L) favored non-methylating SRB like Desulfobacter postgatei, thereby reducing overall methylation potential. Importantly, by integrating our findings with reported sewage data, we show that sulfate concentrations in most domestic sewage fall within the optimal range for hgcA proliferation, explaining their consistently high abundances worldwide. Our results also highlight the potential basis for source-level interventions, such as substituting sulfate-free coagulants or restricting sulfate-rich industrial discharges, to reduce hgcA proliferation and mitigate downstream MeHg risks in urban water systems.},
}

@article {pmid41558305,
year = {2026},
author = {Gu, X and Yu, P and Duan, X and Chen, J and Zhou, Y and Jian, Q and Huang, M and Xue, G and Li, X},
title = {Metatranscriptomics reveals system-specific viral adaptive strategies and prokaryotic defense trade-offs across anaerobic digestion systems.},
journal = {Water research},
volume = {292},
number = {},
pages = {125401},
doi = {10.1016/j.watres.2026.125401},
pmid = {41558305},
issn = {1879-2448},
abstract = {Viruses are increasingly recognized as critical modulators of microbial community dynamics in anaerobic digestion (AD) systems, yet their ecological roles across distinct AD process types remain poorly understood. Here, we investigated viral ecology in three full-scale food waste treatment systems representing three predominant process types-dry AD (Dry-AD), wet AD (Wet-AD), and two-stage wet AD (2St-wet-AD)-through integrated metatranscriptomics and metagenomics. We recovered 4404 viral operational taxonomic units (vOTUs) and 206 metagenome-assembled genomes (MAGs). Dry-AD exhibited unique viral-prokaryotic diversity decoupling, elevated lysogeny (48.7% vs. 22.1%-26.5% in wet systems), and reduced transcriptionally active communities (viruses: 65.5% vs. 89.4% and 80.7% in wet systems; prokaryotes: 76.9% vs. 94.5% and 86.3% in wet systems). Comparative analyses revealed stronger viral endemism (55.4% system-specific vOTUs) than prokaryotes (30.6% MAGs). Virus-host networks demonstrated highly centralized infection patterns in Dry-AD with uneven transcript-based virus-host ratios (VHR) (Clostridia: 18.28 vs. Methanomicrobia: 0.15) compared to more uniform ratios (≈1.0) in wet systems. Transcriptomic profiling provided the first quantitative evidence of system-specific antiviral defense strategies: Wet-AD exhibited the highest defense gene transcriptional activity (3833 TPM), Dry-AD reduced defenses transcription (2614 TPM), while 2St-wet-AD displayed the lowest defense transcriptional activity (2455 TPM). Functional annotation revealed viral auxiliary metabolic genes exhibited distinct transcriptional patterns: enhancing host stress resilience in Dry-AD, promoting nutrient acquisition in Wet-AD, and improving metabolic efficiency in 2St-wet-AD. These findings reveal that viruses adopt distinct ecological roles across different AD process types, providing mechanistic insights for developing system-specific strategies to optimize stability and efficiency.},
}

@article {pmid41558076,
year = {2026},
author = {Zhao, M and Wu, F and Feng, S and Li, C and Liu, S and Chen, S and Liu, Y and Chen, B and Zhang, G and Han, S},
title = {Ursolic acid modulates gut microbiota and metabolites to enhance Treg/Th17 balance and intestinal health in broilers.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106427},
doi = {10.1016/j.psj.2026.106427},
pmid = {41558076},
issn = {1525-3171},
abstract = {Ursolic acid (UA), a naturally occurring pentacyclic triterpenoid abundant in various plants, possesses potent biological activities. However, its effects and mechanisms on immune competence in broilers remain unclear. In this study, 320 one-day-old Cobb broilers were randomly allocated to four groups (8 replicates of 10 birds each) for a 42-day trial: a control group (CON) and three treatment groups supplemented with 50, 200, or 400 mg/kg UA (UA 50, UA 200, or UA 400). We employed enzyme-linked immunosorbent assay (ELISA), alcian blue-periodic acid schiff (AB-PAS) staining, immunofluorescence (IF), immunohistochemistry (IHC), qRT-PCR, metagenomics, and untargeted metabolomics to analyze the effects of UA on immune factors, inflammatory cytokines, intestinal barrier function, regulatory T (Treg) cell / T helper 17 (Th17) cell balance, as well as intestinal microbial composition and metabolism in broilers. The results indicated that UA significantly increased immune factor levels while reducing pro-inflammatory cytokine concentrations in broilers. Regarding intestinal barrier function, UA supplementation effectively reduced lipopolysaccharide (LPS) and D-lactic acid levels, promoted goblet cell proliferation, and enhanced the expression of tight junction proteins (Claudin-1, ZO-1). Notably, UA also significantly modulated Treg/Th17 balance. Furthermore, UA supplementation modulated the gut microbial composition, which was marked by an increase in the beneficial Lactobacillus johnsonii and a concurrent suppression of the pathobiont Escherichia coli. Furthermore, UA reduced the enrichment of microbial pathways associated with pathogenic Escherichia coli and Salmonella infection. Further analysis indicated that UA modulated propionate and tryptophan metabolism, thereby increasing the concentrations of propionic acid and the tryptophan metabolites (5-Hydroxyindole-3-Acetic Acid (5HIAA) and Indole-3-Acetic Acid (IAA)). In summary, our findings demonstrate that UA enhances broiler immunity and intestinal barrier function. These benefits appear to be mediated by the UA-driven enrichment of Lactobacillus johnsonii, which promotes the production of propionate and tryptophan-derived metabolites (5-HIAA and IAA), thereby rebalancing the Treg/Th17 balance and ultimately reinforcing intestinal integrity. These findings underscore the potential of UA as a natural supplement for sustainable poultry production.},
}

@article {pmid41558030,
year = {2026},
author = {Fan, C and Hayase, T and Chang, CC and Glover, IK and Flores, II and McDaniel, LK and Ortega, MR and Sanchez, CA and El-Himri, RK and Brown, AN and Karmouch, JL and Jamal, MA and Ahmed, SS and Halsey, TM and Jin, Y and Tsai, WB and Prasad, R and Enkhbayar, A and Mohammed, A and Schmiester, M and Damania, AV and Ajami, NJ and Wargo, JA and Peterson, CB and Rondon, G and Al-Juhaishi, T and Alousi, AM and Molldrem, JJ and Champlin, RE and Shpall, EJ and Martens, E and Arias, CA and Jenq, RR and Hayase, E},
title = {Fecal carbohydrate-degrading bacteria are associated with reduced incidence of lower gastrointestinal GVHD.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2025016780},
pmid = {41558030},
issn = {2473-9537},
abstract = {Lower gastrointestinal graft-versus-host disease (LGI-GVHD) carries morbidity and mortality for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), with critical contributions from the intestinal microbiome. In a retrospective cohort of metagenomic sequencing of allo-HSCT patient stool (n = 90), we found that a reduction in specific Parabacteroides and Bacteroides species around the time of engraftment contributes to LGI-GVHD risk. Given the known diverse carbohydrate degrading functionality of these bacteria, we investigated gene abundances for Carbohydrate-Active enZyme (CAZyme) and found that Parabacteroides merdae, Parabacteroides distasonis and Bacteroides ovatus abundances were significantly correlated with CAZymes in patients who did not develop LGI-GVHD compared to those who did. The specific gene abundances of xylosidase, which contribute to the degradation of xylose-containing polysaccharides, were significantly associated with reduced risk of LGI-GVHD. Together, these findings show the importance of carbohydrate degrading functionality of putative beneficial bacteria in mediating risk of LGI-GVHD.},
}

@article {pmid41557799,
year = {2026},
author = {Liao, T and Chen, S and Wang, S and Huang, Y and Tsui, SKW and Stüeken, EE and Cao, Q and Luo, H},
title = {Noncanonical genetic markers resolve the pre-GOE emergence of aerobic bacteria in Earth's history.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {4},
pages = {e2515709123},
doi = {10.1073/pnas.2515709123},
pmid = {41557799},
issn = {1091-6490},
mesh = {*Bacteria, Aerobic/genetics/metabolism/classification ; Earth, Planet ; Genome, Bacterial ; Genetic Markers ; Oxygen/metabolism ; Phylogeny ; Evolution, Molecular ; Machine Learning ; Aerobiosis ; },
abstract = {The transition from anaerobic to aerobic life was a pivotal adaptation in Earth's history, yet the timing and genomic drivers remain poorly resolved. Traditional approaches relying on oxygen-utilizing genes need improvement for obligate anaerobes and fragmentary environmental genomes, where gene absence may reflect poor assembly rather than phenotype. We developed a machine learning model (GBDT40-LR) to predict microbial oxygen requirements using 40 broadly conserved genes, 35 without direct oxygen roles. This approach overcomes incompleteness biases in environmental genomes. Applied to 80,787 bacterial genomes [including metagenome-derived assemblies (MAGs)], the model classified 42,014 aerobes and 38,775 anaerobes, enabling large-scale ancestral reconstruction. Molecular clock dating indicates an emergence of aerobic bacterium prior to the Great Oxidation Event (GOE, 2.5 to 2.3 Ga), likely around ~2.7 Ga. Aerobic lineages subsequently diversified during the GOE and Neoproterozoic Oxygenation Event (NOE, 0.8 to 0.55 Ga), with persistent anaerobe diversity across Earth's oxygenation. This establishes that aerobic bacteria originated planetary oxygenation, potentially by 200 to 400 My, providing insights into phenotypic evolution and prolonged anaerobe-aerobe coexistence.},
}

*Bacteria, Aerobic/genetics/metabolism/classification
Earth, Planet
Genome, Bacterial
Genetic Markers
Oxygen/metabolism
Phylogeny
Evolution, Molecular
Machine Learning
Aerobiosis

@article {pmid41557465,
year = {2026},
author = {Ivanov, A and Popov, V and Morozov, M and Olekhnovich, E and Ulyantsev, V},
title = {MetaFX: feature extraction from whole-genome metagenomic sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag018},
pmid = {41557465},
issn = {1367-4811},
abstract = {MOTIVATION: Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers.

RESULTS: Here we present MetaFX-an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualised on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average.

AVAILABILITY: MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369.},
}

@article {pmid41556741,
year = {2026},
author = {Cao, L and Wang, X and Zhou, Y and Qiu, J and Zeng, Q and Zhang, C and Pan, L},
title = {Diagnosis of Paralytic Rabies by Metagenomics Next-Generation Sequencing: A Case Report and Review of the Literature.},
journal = {Veterinary medicine and science},
volume = {12},
number = {1},
pages = {e70748},
pmid = {41556741},
issn = {2053-1095},
mesh = {Animals ; Dogs ; *Dog Diseases/diagnosis/virology ; High-Throughput Nucleotide Sequencing/veterinary ; Metagenomics ; *Rabies/diagnosis/veterinary/virology ; *Rabies virus/genetics/isolation & purification ; },
abstract = {Paralytic rabies is an atypical form of the disease that is notoriously difficult to diagnose early due to the absence of classic features like hydrophobia. The case being discussed presents a patient who has altered mental status, for whom the initial diagnosis was difficult due to an absent clear bite history and typical symptoms. The final diagnosis of the case was confirmed by metagenomic next-generation sequencing (mNGS) of directly from cerebrospinal fluid, which led to the detection of the rabies virus. This case underscores the critical diagnostic value of mNGS in identifying elusive neurotropic infections.},
}

Animals
Dogs
*Dog Diseases/diagnosis/virology
High-Throughput Nucleotide Sequencing/veterinary
Metagenomics
*Rabies/diagnosis/veterinary/virology
*Rabies virus/genetics/isolation & purification

@article {pmid41556662,
year = {2026},
author = {Zhang, N and Atoni, E and Nyaruaba, R and Kibaba, P and Shadrack, K and Wang, F and Agwanda, B and Zheng, Z and Dai, J and Yuan, Z and Xia, H},
title = {Host and geography shape microbial communities in Kenyan mosquitoes: insights from metatranscriptomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0142725},
doi = {10.1128/msystems.01427-25},
pmid = {41556662},
issn = {2379-5077},
abstract = {Mosquitoes harbor diverse microbial communities that influence their potential to transmit pathogens. However, the ecological drivers shaping these microbiomes, particularly in under-sampled regions like Africa, remain poorly resolved. We conducted a large-scale metatranscriptomic survey of 3,940 Aedes and Culex mosquitoes from diverse ecological zones across Kenya. Our analyses revealed that viruses dominated the overall transcriptome, while bacteria exhibited the greatest taxonomic richness. Geographic location emerged as the primary driver of microbial community structure, whereas host genus identity shaped virome diversity at local or city-level scales. Culex mosquitoes harbored higher viral richness, particularly in coastal regions, while Aedes supported more diverse bacterial assemblages. Microbial co-occurrence networks exhibited distinct topologies across hosts: Culex networks featured cross-domain interactions and viral keystone taxa, whereas Aedes networks were more cohesive and robust, centered on bacterial hubs. We identified 102 distinct viruses from 24 families, including 31 putative novel RNA viruses. Segment-resolved phylogenies revealed cryptic clades within Bunyavirales, Picornavirales, and other lineages. Collectively, our findings highlight the scale-dependent influences of geography and host identity on mosquito microbiomes in East Africa and demonstrate the utility of metatranscriptomics in uncovering hidden microbial diversity and ecological interactions. These insights provide a foundation for ecologically informed arthropod vector surveillance and microbiome-based intervention strategies.IMPORTANCEMosquitoes are more than just flying syringes; they are complex ecosystems hosting a variety of microbes. Understanding what shapes this microbial world inside mosquitoes is key to developing new control strategies. Our study of nearly 4,000 mosquitoes from Kenya reveals that where a mosquito lives matters most for its overall microbial makeup, but its genus dictates which viruses it carries. We discovered that different mosquito types have distinct microbial social networks: one type has a fragile network centered on viruses, while the other has a resilient network built around bacteria. This means that strategies to disrupt disease transmission by targeting mosquito microbes may need to be tailored to a specific mosquito genus. Our work provides a map of these microbial ecosystems, highlighting potential new viruses and offering insights for future public health surveillance and interventions.},
}

@article {pmid41556507,
year = {2026},
author = {Cheng, S and Tang, X and Huang, X and Li, Y and Huang, S and He, D and Moreno-Jiménez, E and Xu, J and Rillig, MC and Dai, Z and Delgado-Baquerizo, M},
title = {Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70704},
doi = {10.1111/gcb.70704},
pmid = {41556507},
issn = {1365-2486},
support = {41721001//National Natural Science Foundation of China/ ; 2019YFC1803704//National Key Research and Development Program of China/ ; +226-2024-00029//The Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; Metagenomics ; *Metagenome ; *Stress, Physiological ; Biodiversity ; *Climate Change ; Ecosystem ; Bacteria/genetics/classification ; },
abstract = {Soil microorganisms constitute the largest portion of Earth's biodiversity. However, soil microorganisms are also highly sensitive to on-going global change, and the influence of an increasing number of stressors on common, rare, and unknown taxa across large environmental gradients remains virtually unknown. Here, we combined a large-scale spatial field survey across multiple different ecosystems and found that the diversity and abundance of soil rare taxa were significantly reduced under high environmental stressor number (i.e., a high number of stressors passing a 75% stressor threshold). Strikingly, the abundance of unknown soil taxa and unknown genes increased with increasing environmental stress number. We further identified the metagenome-assembled genomes (MAGs) that were considered as relatively common taxa using metagenomics. Compared to 9% of negative responders, 32% of common MAGs were resistant or positively responsive to multiple stress, displaying a reduced potential for cellular processes and an enhanced potential for environmental, genetic, and metabolic processes. Our study suggests that as stress increases, we would have less rare, but more unknown microorganisms and unique genomes of resistant common taxa, suggesting major changes in the soil microbiome in a world subjected to multiple global change stressors.},
}

*Soil Microbiology
*Microbiota
Metagenomics
*Metagenome
*Stress, Physiological
Biodiversity
*Climate Change
Ecosystem
Bacteria/genetics/classification

@article {pmid41556498,
year = {2026},
author = {Becsei, Á and Munk, P and Fuschi, A and Otani, S and Stéger, J and Visontai, D and Papp, K and Brinch, C and Kant, R and Weinstein, I and Vapalahti, O and de Graaf, M and Schapendonk, CME and Roelfsema, J and van den Beld, M and Pijnacker, R and Franz, E and Alba, P and Battisti, A and De Cesare, A and Indio, V and Troja, F and Sironen, T and Oliveri, C and Pasquali, F and Liachko, I and Auch, B and O'Cathail, C and Bányai, K and Makó, M and Pollner, P and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM},
title = {A comprehensive database for biological data derived from sewage in five European cities.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {41556498},
issn = {1758-0463},
support = {NNF16OC0021856//Novo Nordisk Foundation/ ; NNF24SA0094147//Novo Nordisk Foundation/ ; 874735//Horizon 2020/ ; INV-044643/GATES/Gates Foundation/United States ; NKKP-153428//National Research, Development and Innovation Office of Hungary/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office of Hungary/ ; },
mesh = {*Sewage/microbiology ; Europe ; Cities ; *Databases, Genetic ; *Metagenomics ; *Metagenome ; },
abstract = {Sewage metagenomics is a powerful tool for proactive pathogen surveillance and understanding microbial community dynamics. To support such efforts, we present a highly curated and accessible longitudinal dataset of 239 sewage samples collected from five European cities. The dataset, processed through metagenomic sequencing, includes rich analytical outputs such as taxonomic profiles, identified antimicrobial resistance genes, assembled contigs with annotated origins, metagenome-assembled genomes with functional gene annotations, and metadata. Given the computational intensity and time required to reproduce such analyses, we share this dataset to promote reuse and advance research. In addition to the metagenomic data, qPCR was used to identify specific pathogens, and Hi-C sequencing was performed on a subset of the samples to strengthen genomic linkage analysis. Central to this resource is a publicly available PostgreSQL database, designed to facilitate efficient exploration and reuse of the data. This comprehensive database allows users to perform targeted queries, subset data, and streamline access to this extensive resource.},
}

*Sewage/microbiology
Europe
Cities
*Databases, Genetic
*Metagenomics
*Metagenome

@article {pmid41556347,
year = {2026},
author = {},
title = {Correction to: HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {54},
number = {2},
pages = {},
doi = {10.1093/nar/gkag014},
pmid = {41556347},
issn = {1362-4962},
}

@article {pmid41556085,
year = {2026},
author = {Chen, J and Ling, D and Wang, F and Liu, L and Ren, Y and Chen, C and Su, N},
title = {Septic Shock Caused by Coinfection of Shewanella algae Bloodstream Infection and Epstein-Barr Virus: Clinical Characteristics and Genomic Analysis.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70221},
pmid = {41556085},
issn = {2045-8827},
support = {2023170//Chengdu Medical Research Project/ ; Q22080//Youth Innovation Project of Sichuan Medical Association/ ; 2024001//Youth Innovation Medical Research Project of Chongzhou People's Hospital/ ; },
mesh = {*Shewanella/genetics/isolation & purification/classification/pathogenicity ; Humans ; *Shock, Septic/microbiology/diagnosis/virology ; *Epstein-Barr Virus Infections/complications/virology/diagnosis ; *Coinfection/microbiology/virology ; Phylogeny ; *Gram-Negative Bacterial Infections/microbiology/complications/diagnosis ; *Herpesvirus 4, Human/isolation & purification/genetics ; Virulence Factors/genetics ; China ; Male ; Genome, Bacterial ; Genomics ; *Bacteremia/microbiology/complications ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; },
abstract = {Shewanella algae, a marine-origin opportunistic pathogen, has shown a significant increase in non-coastal infections, yet its environmental adaptability and synergistic pathogenic mechanisms with Epstein-Barr virus (EBV) coinfection remain unclear. This study reports a clinical case of S. algae bloodstream infection complicated by EBV reactivation leading to septic shock in Sichuan Province, China, and elucidates the molecular mechanisms through genomic analysis. Pathogen identification was performed via blood culture, antibiotic susceptibility testing, and genomic annotation. The strain harbored resistance genes (acrB, tolC, tet(35), golS) and virulence factors (bplL/bplF, clpC/clpP, tonB). Phylogenetic analysis indicated the highest genetic affinity to freshwater-derived Shewanella chilikensis, while pan-genome analysis identified 1412 unique genes, including transmembrane transporters and carbohydrate-active enzyme genes, suggesting freshwater adaptive evolution. Metagenomic next-generation sequencing (mNGS) detected a high EBV load. The patient succumbed to multi-organ failure. This study reveals that S. algae may evolve freshwater adaptability to cause inland infections, and EBV coinfection accelerates septic shock through immunosuppression and inflammatory cascades. Genomic analysis provides critical insights for precision diagnosis and treatment of polymicrobial infections.},
}

*Shewanella/genetics/isolation & purification/classification/pathogenicity
Humans
*Shock, Septic/microbiology/diagnosis/virology
*Epstein-Barr Virus Infections/complications/virology/diagnosis
*Coinfection/microbiology/virology
Phylogeny
*Gram-Negative Bacterial Infections/microbiology/complications/diagnosis
*Herpesvirus 4, Human/isolation & purification/genetics
Virulence Factors/genetics
China
Male
Genome, Bacterial
Genomics
*Bacteremia/microbiology/complications
Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests

@article {pmid41555453,
year = {2026},
author = {Orr, RJS and Brynildsrud, O and Bøifot, KO and Gohli, J and Skogan, G and Kelly, FJ and Hernandez, MT and Udekwu, K and Lee, PKH and Mason, CE and Dybwad, M},
title = {Spatial and temporal patterns of public transit aerobiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02303-7},
pmid = {41555453},
issn = {2049-2618},
abstract = {BACKGROUND: Aerobiome diversity is extensive; however, species-level community structure remains poorly resolved. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though interannual cycles remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi.

RESULTS: Air samples taken over a 3-year period (2017-2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Interannual variation had limited significance on the public transit aerobiome diversity and community structure.

CONCLUSIONS: Cities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, possible correlation between geographical distance and genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low-biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented. Video Abstract.},
}

@article {pmid41555276,
year = {2026},
author = {Zhang, J and Feng, S and Liu, Z and Xie, K and Gu, C and Shen, J and Zhang, Y and Zhou, Y},
title = {Surgical treatment of Emphysematous Osteomyelitis of the spine in malnutrition and anemia patient: a rare case report.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {82},
pmid = {41555276},
issn = {1471-2334},
abstract = {BACKGROUND: Emphysematous Osteomyelitis is a rare and potentially fatal form of severe osteomyelitis. It is characterized by gas produced by pathogenic bacteria accumulating in bone structures and surrounding soft tissues. Its rarity and severe nature pose significant challenges for diagnosis and treatment. This case report describes the diagnosis and treatment of Emphysematous Osteomyelitis of the spine in a patient with long-term malnutrition and anemia.

CASE PRESENTATION: A 72-year-old agricultural worker presented with persistent low back pain accompanied by radiating pain in both lower limbs for one month. The patient reported continuous dull pain that worsened with postural changes and improved when lying flat. Based on clinical presentation, biochemical indicators, and imaging studies, spinal infection was initially suspected. Empirical antimicrobial therapy administered for two weeks after admission proved ineffective and was complicated by an epidural abscess, leading to the decision for surgical intervention in the third week. Intraoperative tissue samples were identified through culture identification and high-throughput culture and metagenomic pathogen detection, identifying Citrobacter koseri and Staphylococcus aureus as causative pathogens. Postoperatively, based on antimicrobial susceptibility testing results, treatment was switched to intravenous meropenem and levofloxacin. One month postoperatively, the patient showed good recovery with normalized infection markers, no fever, and significant pain relief.

DISCUSSION AND CONCLUSION: In summary, this rare and severe form of Emphysematous Osteomyelitis requires prompt diagnosis and treatment in clinical practice. The diagnosis of Emphysematous Osteomyelitis of the spine relies on imaging studies. Failure to achieve accurate and timely diagnosis may lead to misdiagnosis or delayed treatment, which not only compromises therapeutic efficacy but may also result in catastrophic consequences. Timely antibiotic therapy, early detection, and aggressive surgical intervention when necessary are key to the successful management of Emphysematous Osteomyelitis of the spine.},
}

@article {pmid41554846,
year = {2026},
author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Gop, AP and Shravana, KS and Jagannivasan, A and Nair, AV and Sudarsan, KS and Santhosh, B and Ebeneezar, S and Gopalakrishnan, A},
title = {Egg disinfection improves larval survival and shapes the microbial community in snubnose pompano (Trachinotus blochii).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35646-8},
pmid = {41554846},
issn = {2045-2322},
support = {BT/AAQ/3/SP28267/2018//Department of Biotechnology, Government of India/ ; },
abstract = {Early microbial colonization is crucial for immunity and survival in aquatic animals. This study evaluated the impact of egg disinfection on microbial colonization and larval performance in Trachinotus blochii, a high-value mariculture fish. Optimal egg disinfection protocols were initially identified as 20 ppm iodophor for 10 min, 400 ppm H2O2 for 10 min, and 40 ppm glutaraldehyde for 5 min to improve hatchability. Sequential analyses included 16S rRNA amplicon sequencing of larval microbiota at 10-days post hatching (DPH) and assessment of survival and antioxidant status till 25 DPH. Disinfection significantly enhanced hatchability (up to 90.88 ± 2% with 40 ppm glutaraldehyde), larval survival (up to 34.80 ± 1.1% in glutaraldehyde and 31.18 ± 1.5% in H2O2), and catalase activity. Notably, egg disinfection reshaped the larval microbiota, enriching microbial diversity measures and beneficial bacterial taxa, such as Hyphomonadaceae, Halieaceae, Nannocystaceae, and Alteromonadaceae. Improved survival correlated with enhanced taxonomic and functional metagenomic diversity, lower Proteobacteria: Bacteroidota ratio and higher combined proportions of Fusobacteriota, Firmicutes, and Bacteroidota relative to Proteobacteria. The findings suggest that egg disinfection acts as a microbiota programming strategy to promote larval health, offering a practical approach to enhance sustainability in T. blochii aquaculture.},
}

@article {pmid41382117,
year = {2025},
author = {Wang, Y and Bai, Z and Sun, J and Gong, Q and Miao, W and Niu, Z and Li, X and Xu, J and Lai, Z},
title = {Intestinal congestion-driven gut dysbiosis: a cross-disease hemodynamic mechanism in liver cirrhosis and heart failure.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {79},
pmid = {41382117},
issn = {1479-5876},
support = {SYYYRC-2022006//First Hospital of Shanxi Medical University/ ; 202103021224408//Natural Science Foundation of Shanxi Province/ ; 202203021221248//Natural Science Foundation of Shanxi Province/ ; 202204010931008//Shanxi Provincial Science and Technology Department/ ; YDZJSX2021B012//Shanxi Provincial Science and Technology Department/ ; 82470693//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2023065//Health Commission of Shanxi Province/ ; },
abstract = {BACKGROUND: Intestinal congestion is a common pathophysiological feature of both liver cirrhosis and heart failure (HF). This study aimed to investigate whether intestinal congestion induces similar gut microbiota and metabolite alterations under both conditions, and to identify key microbial and metabolic signatures.

METHODS: We analyzed 117 cirrhosis patients (uncomplicated cirrhosis, cirrhosis with hepatocellular carcinoma, transjugular intrahepatic portosystemic shunt, and liver transplantation), 75 HF patients, and 31 healthy controls (CG). We performed 16S rRNA sequencing on all samples to assess gut microbial diversity, and subjected six representative samples per group to metagenomic sequencing. We conducted untargeted metabolomics on 30 fecal samples each from the uncomplicated cirrhosis, HF with reduced ejection fraction (HFrEF), and CG groups to profile intestinal metabolites, followed by correlation analyses among representative taxa, clinical characteristics, and key metabolites.

RESULTS: Intestinal congestion of different etiologies exhibits similar alterations in the gut microbiota, particularly in patients with uncomplicated cirrhosis and HFrEF. Alterations in Bacteroides were closely associated with the severity of congestion. Veillonella and Lactobacillales were enriched in cirrhotic patients, whereas Coprococcus was uniquely abundant in HFs. Metabolomic analysis revealed significant reductions in tripeptides, anti-inflammatory compounds, and prostaglandin analogs in patients with intestinal congestion. Musacin D and neopterin may serve as potential noninvasive biomarkers for HF and cirrhosis, respectively.

CONCLUSION: Intestinal congestion is associated with gut microbiota dysbiosis and metabolic disturbances in cirrhosis and HFs, with specific microbes and metabolites showing potential predictive value for distinguishing underlying diseases.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07547-3.},
}

@article {pmid41554738,
year = {2026},
author = {Zheng, J and Zhang, C and Xiang, S and Li, M and Wang, H and Shi, K and Tondrob, D and Han, Y},
title = {Integrated metabolomics and metagenomics uncover pathogenic mechanisms of Fusarium wilt and faba bean defense responses.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-025-00673-8},
pmid = {41554738},
issn = {2396-8370},
support = {31901929//National Natural Science Foundation of China/ ; cstc2021jcyj-msxmX1021//Natural Science Foundation of Chongqing Municipality/ ; },
abstract = {Fusarium wilt diseases pose a huge threat to faba bean (Vicia faba L.) production globally, with significant outbreaks in Chongqing, China. Symptomatic plants showed wilting leaves and rotten roots, ultimately perishing in the advanced stage. Morphological features, multilocus phylogenetic analyses, and pathogenicity tests demonstrated that the primary causal agent was Fusarium oxysporum. Untargeted metabolomics of faba beans revealed substantial metabolic differences in the infected faba bean roots. Plants responded to fungal biotic stress by reprogramming key metabolic pathways, including alanine, aspartate, and glutamate metabolism, the citrate cycle, arginine biosynthesis, and jasmonic acid metabolism, which collectively underscore activated defense responses. Metagenome sequencing showed that Fusarium wilt significantly reshaped the structure of the rhizosphere microbiota and affected the abundance of genes encoding element cycling in soil. This work elucidates the pathogenic mechanisms of F. oxysporum by integrating pathogen identification, host metabolism, and microbiome ecology. Our findings offer biomarkers for disease diagnosis and targets for biocontrol, advancing sustainable management of Fusarium wilt diseases in legumes.},
}

@article {pmid41552949,
year = {2026},
author = {Dani, M and Beszteri, S and Castellanos, AB and Schimani, K and Skibbe, O and Zimmermann, J and Soares, AR and Griesdorn, L and Probst, AJ and Kahlert, M and Beszteri, B},
title = {Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70124},
pmid = {41552949},
issn = {1529-8817},
support = {CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; ZI 1628/2-1//Deutsche Forschungsgemeinschaft/ ; Dnr. 18/171//Swedish EPA, Swedish Agency for Marine and Water Management/ ; },
abstract = {The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.},
}

@article {pmid41552936,
year = {2026},
author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y},
title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04604a},
pmid = {41552936},
issn = {2042-650X},
abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.},
}

@article {pmid41552860,
year = {2026},
author = {Wang, F and Xiong, W and Huang, X and Li, S and Zhan, A},
title = {Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70102},
pmid = {41552860},
issn = {1755-0998},
support = {2025ZD1207600//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2025ZD1200800//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2024ZY0128//Guiding Funds of Central Government for Supporting the Development of Local Science and Technology/ ; 32471608//National Natural Science Foundation of China/ ; },
mesh = {*DNA, Environmental/isolation & purification/genetics ; *Biodiversity ; *Deoxyribonucleases/metabolism ; *DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/classification/genetics ; Rivers/chemistry ; *Metagenomics/methods ; },
abstract = {Environmental RNA (eRNA) metabarcoding has rapidly emerged as a powerful tool for assessing contemporary biodiversity patterns across diverse ecosystems. However, the potential for false positive detections caused by co-extracted environmental DNA (eDNA) remains unquantified. Distinguishing true signals from false positives caused by residual eDNA is a technical challenge in eRNA-based metabarcoding. To address this issue, we employed a freshwater river receiving treated effluent from a wastewater treatment plant as a model system. In such settings, eDNA in the treated effluent can lead to the detection of non-local species (e.g., marine taxa). Treated effluent typically contains minimal or no eRNA, making it well-suited for evaluating the influence of eDNA carryover. By comparing DNase-treated and untreated eRNA samples, we assessed the impact of residual eDNA on fish species richness and community composition. Our results showed that omitting DNase treatment significantly inflated taxonomic richness, with untreated samples detecting a conservative estimate of over 25% more taxa per site. Fold-change analysis revealed that residual eDNA inflated taxon abundances in both high- and low-abundance taxa, with some showing over 10-fold increases. Community composition analyses revealed clear clustering between treated and untreated samples, highlighting substantial shifts driven by residual eDNA. These findings demonstrate that co-extracted eDNA can severely distort eRNA-based biodiversity estimates, leading to false positives and misrepresented contemporary community profiles. We recommend further evaluation of DNase treatment parameters, including enzyme concentration, incubation time and treatment times, and the adoption of optimised protocols to standardise and improve the accuracy of eRNA-based biodiversity monitoring.},
}

*DNA, Environmental/isolation & purification/genetics
*Biodiversity
*Deoxyribonucleases/metabolism
*DNA Barcoding, Taxonomic/methods
Animals
*Fishes/classification/genetics
Rivers/chemistry
*Metagenomics/methods

@article {pmid41552431,
year = {2026},
author = {Buonaccorsi, A and McMullen, BN and Builder, B and Drummond, K and Halteman, S and See, JC and Thomas, E and Viands, A and Worley, S and Wright, JR and Keeney, J and Lamendella, R},
title = {Metagenomic surveillance of tick-borne pathogens and microbiomes in Huntingdon County, Pennsylvania.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101305},
pmid = {41552431},
issn = {2352-7714},
abstract = {The rise in tick populations across the United States has contributed to a surge in tick-borne diseases, with Pennsylvania ranking among the highest in reported cases. To better understand local pathogen prevalence and microbial community structure, an integrative study of ticks collected from ten recreational trails in Huntingdon County, Pennsylvania during the summer of 2023 was conducted. A total of 96 ticks were sampled, with 33 PCR-positive specimens selected for shotgun metagenomic sequencing. Pathogen screening via qPCR detected Borreliella burgdorferi, Borrelia miyamotoi, Babesia spp., and Anaplasma phagocytophilum. Shotgun metagenomics revealed a broader diversity of tick-borne pathogens, including Rickettsia and Ehrlichia spp., and demonstrated increased sensitivity by detecting low-abundance pathogens in samples that were PCR-negative. Co-infections were common, and multivariate statistical analysis identified significant associations between environmental variables (e.g., humidity, time of day, land cover) and microbial diversity and predicted gene function. Notably, diversity was higher in ticks collected during early afternoon and from northern sites. Co-occurrence network analysis showed Rickettsia as a central taxon with multiple significant positive associations with other microbes while other pathogens were largely absent or peripheral. These findings underscore the enhanced resolution of metagenomic approaches for pathogen detection and the value of combining molecular surveillance with ecological metadata. Our study provides critical insights into local tick microbiomes and pathogen prevalence, which may inform public health interventions and vector management strategies in central Pennsylvania.},
}

@article {pmid41551931,
year = {2026},
author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I},
title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {1},
pages = {lqaf172},
pmid = {41551931},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Workflow ; *Computational Biology/methods ; Microbiota ; },
abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.},
}

*Metagenomics/methods
*Software
Workflow
*Computational Biology/methods
Microbiota

@article {pmid41551812,
year = {2026},
author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Zhang, Z and Xie, F and Ai, L},
title = {Docynia delavayi polyphenols enhance short-chain fatty acid synthesis via the chlorogenic acid-caffeic acid-protocatechuic acid pathway: insights from in vitro digestion-fermentation.},
journal = {Food chemistry: X},
volume = {33},
number = {},
pages = {103416},
pmid = {41551812},
issn = {2590-1575},
abstract = {Docynia delavayi fruit polyphenols (DDP) demonstrate potential for enhancing short-chain fatty acid (SCFA) synthesis; however, underlying mechanisms remain poorly understood. This study utilized an in vitro digestion-fermentation model combined with multi-omics analyses to explore these mechanisms. The in vitro model revealed notable alterations in both 1,1'-diphenyl-2-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical-scavenging capacities, as well as in total phenolic and flavonoid content, accompanied by increased production of acetic, propionic, and butyric acids. Metagenomic indicated that DDP stimulated Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Bifidobacterium longum, and Bifidobacterium bifidum growth. Metabolomics demonstrated enrichment of SCFA-associated metabolic pathways, including propanoate and butyrate metabolism, and identified caffeic acid and protocatechuic acid as primary bioactive metabolites produced from DDP. Multi-omics analysis suggested that DDP modulated gut microbiota by enriching the chlorogenic acid-caffeic acid-protocatechuic acid metabolic pathway (r > 0.95, p < 0.01), ultimately boosting SCFA biosynthesis. This study offers new insights into the mechanisms by which polyphenols regulate health.},
}

@article {pmid41551788,
year = {2026},
author = {Song, Q and Li, J and Liu, Y and Li, W and Li, M and Zhang, B and Guo, B},
title = {Metagenomics and volatile metabolomics reveal microbial succession and its correlations with fruity flavor volatile compounds during Mianhua industrial processing.},
journal = {Food chemistry: X},
volume = {33},
number = {},
pages = {103446},
pmid = {41551788},
issn = {2590-1575},
abstract = {Mianhua, a traditional fermentation-type staple food popular in northern China, undergoes dynamic microbial and volatile compound changes during industrial processing. 848 volatile compounds were identified using volatile metabolomics dominated by esters (18.51 %), notably hexanoic acid ethyl ester and octanoic acid ethyl ester, which confer fruity flavors. Metagenomics analysis revealed Proteus (25.93 %), Fructilactobacillus (16.63 %), Lactobacillus (10.16 %) and Companilactobacillus (7.14 %) as dominant genera. Mixing with traditional starters was critical for flavor development, driven by microbial succession and synergistic interactions between Lactobacillaceae (e.g., Fructilactobacillus sanfranciscensis and Lactobacillus helveticus) and Kazachstania during fermentation. Notably, F. sanfranciscensis and L. helveticus were significantly correlated with the formation of key esters with fruity characteristics, elucidating their roles in substrate conversion via carbohydrate metabolism and the esterification pathways. This study clarifies the microbial contributions to fruity flavor and provides insights into volatile-microbiota correlations, laying a foundation for future flavor-oriented research and industrial applications of microbiota regulation in Mianhua production.},
}

@article {pmid41551588,
year = {2026},
author = {Arnold, CB and Kelder, A and Woltemate, S and Geffers, R and von Felde, A and Knudsen, KEB and Visscher, C and Vital, M},
title = {Uncovering differences in rye and wheat degradation by human gut microbiota applying a quantitative multi-metaOmics in vitro approach.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100532},
pmid = {41551588},
issn = {2666-5174},
abstract = {While wheat is the most common grain used in bread-making worldwide, rye is popular in many European countries too. Rye is associated with several health benefits, which is attributed to its comparatively higher dietary fiber content (primarily fructans and arabinoxylans) that promote production of short chain fatty acids (SCFA) by gut microbiota, in particular butyrate. Intervention studies revealed bacterial alterations upon rye administration, however, the detailed mechanisms involved in its degradation are not understood. We grew fecal communities (n = 20) on pre-digested rye and wheat, respectively, demonstrating that rye was yielding higher cell and SCFA concentrations in almost all samples along with distinct abundances of many taxa. A multi metaOmics (metagenomics/metatranscriptomics) approach (n = 5 donors) showed higher bacterial growth rates for most taxa on rye compared to wheat. The higher growth rate of rye was accompanied by increased expression of genes involved in growth and energy generation suggesting higher carbon substrate accessibility. The carbohydrate active enzyme repertoire was greatly distinct between communities growing on the two substrates with several specific glycoside hydrolases increasingly expressed in rye containing cultures. Agathobacter faecis was revealed as the key butyrogenic species for rye degradation and its expression pattern based on metagenome assembled genomes showed adaptation to growth on rye via expression of genes involved in arabinoxylan degradation and fructose (major monomer of fructans) uptake. Our study verifies higher SCFA production from rye over wheat and gives detailed insights into molecular mechanisms involved. It suggests that the observed health benefits of rye are mediated by gut microbiota.},
}

@article {pmid41551583,
year = {2026},
author = {Chen, T and Huang, R and Huang, Y and Wang, J and Wang, Z and Zhang, X},
title = {Shared signatures of alcohol-associated dysbiosis in humans and non-human primates.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100534},
pmid = {41551583},
issn = {2666-5174},
abstract = {Alcohol use disorder (AUD) is a chronic brain disease with limited therapeutic options. Increasing evidence suggests that the gut microbiome contributes to AUD via the microbiome-gut-brain axis. Here, we conducted a cross-species investigation of gut microbiota alterations in patients with clinically diagnosed AUD and in non-human primates (NHPs) subjected to long-term alcohol (ethanol) self-administration, using metagenomic sequencing. Both cohorts showed reduced microbial diversity and conserved dysbiosis, with consistent depletion of Verrucomicrobia, Actinobacteria, Faecalibacterium, Akkermansia, Intestinibacter, Phascolarctobacterium, and Ruminococcus, alongside increased Blautia and Coprococcus. These microbial shifts correlated with liver function indices, notably positive associations between Ruminococcus and bilirubin levels in both species, suggesting a potential role in liver injury. Functional analyses revealed conserved microbial adaptations, including upregulated DNA repair pathways, fermentative energy metabolism, and downregulated glutamate/glutamine biosynthesis. Together, these results identify evolutionarily conserved microbial and metabolic alterations linking alcohol consumption, gut dysbiosis, and hepatic dysfunction. Our cross-species evidence highlights the gut microbiome as a potential biomarker and therapeutic target for AUD.},
}

@article {pmid41551517,
year = {2025},
author = {Wang, Y and Zhang, X},
title = {Rapid diagnosis of Lemierre's syndrome by metagenomic next-generation sequencing: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1730031},
pmid = {41551517},
issn = {2296-858X},
abstract = {Lemierre's syndrome, also known as postopharyngeal septicaemia or necrobacillosis, is a rare, fatal opportunistic infection, often caused by Fusobacterium necrophorum invading the throat. Bacterial culture is a conventional method to establish a diagnosis, but is time-consuming and insensitive in some cases. Metagenomic next-generation sequencing (mNGS), as an emerging technique, has become an important supplementary detection method for infectious diseases. It greatly favors the rapid, precise diagnosis and treatment of Lemierre's syndrome through accurately obtaining etiological information. We reported a case of Lemierre's syndrome that was rapidly and accurately diagnosed by mNGS.},
}

@article {pmid41551358,
year = {2026},
author = {Wu, X and Yin, Y and Guo, Y and Sun, L and Shi, Q and Ji, T and Wang, H},
title = {A case of atypical cat scratch disease with bone and joint infection diagnosed through clinical metagenomics.},
journal = {IDCases},
volume = {43},
number = {},
pages = {e02482},
pmid = {41551358},
issn = {2214-2509},
abstract = {Cat scratch disease (CSD) is a common zoonotic infection caused by Bartonella henselae (B. henselae) and typically presents with fever and regional lymphadenopathy. However, skeletal involvement, including osteomyelitis and arthritis, is rare. We report a 28-year-old immunocompetent female who presented with a five‑month history of persistent right knee swelling without fever or lymphadenopathy. She had previously undergone distal femoral tumor resection with prosthetic joint replacement, and this episode of chronic knee swelling together with the imaging findings was highly suggestive of prosthetic joint infection. Approximately one month before the onset of knee swelling, she had sustained a scratch from a cat. Conventional microbiological tests, including joint effusion and drainage fluid cultures, were negative. Metagenomic next‑generation sequencing (mNGS) of joint effusion identified B. henselae with 27 specific sequence reads, 0.1 % genome coverage and an RPM ratio of 1.9. This result was subsequently confirmed by a quantitative PCR assay targeting the nuoG gene. The patient underwent surgical debridement followed by oral minocycline and rifampin for 8 weeks, resulting in marked clinical improvement. This case underscores that B. henselae infection should be considered in culture‑negative bone and joint, particularly prosthetic joint, infections with a history of cat exposure, and that mNGS can provide valuable etiological evidence in atypical CSD.},
}

@article {pmid41551289,
year = {2025},
author = {Zhang, J and Thomas Backet, RV and Sekela, JJ and Zeller, MJ and Sellers, RS and Redinbo, MR and Gulati, AS and Bhatt, AP},
title = {Commercially Purchased and In-House Bred C57BL/6 Mice with Different Gut Microbiota Exhibit Distinct Indomethacin-Induced Toxicities.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {},
pmid = {41551289},
issn = {2993-3935},
support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R35 GM155168/GM/NIGMS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK122042/DK/NIDDK NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R35 GM152079/GM/NIGMS NIH HHS/United States ; },
abstract = {Non-steroidal anti-inflammatory drug (NSAID)-induced toxicities are a significant clinical problem, yet the factors influencing these outcomes remain incompletely understood. Here, we investigated the impact of mouse vendor on indomethacin-induced injury using C57BL/6 mice from different breeding facilities (in-house "Tar Heel" and commercial Charles River). We found that Tar Heel mice exhibited significantly enhanced susceptibility to indomethacin toxicity, characterized by greater body weight loss, increased ileal ulceration, elevated fecal lipocalin-2 levels, and higher goblet cell numbers in ileum compared to Charles River mice. Importantly, whole genome metagenomic analysis revealed distinct baseline gut microbiomes between the two types of mice. Notably, Tar Heel mice showed higher abundances of β-glucuronidase (GUS)-producing bacteria, particularly those expressing Loop-1 GUS enzymes, and elevated levels of mucolytic enzyme-encoding bacteria. These differences suggest that enhanced indomethacin toxicity observed in Tar Heel mice may be related to functional changes in their gut microbiome, which may predispose to an exaggerated response to NSAID exposure. Together, our findings demonstrate that vendor-specific differences significantly influence NSAID-induced intestinal toxicity and highlight the importance of considering mouse sources and gut microbial compositions in experimental design. Moreover, we highlight potential functional roles that gut microbes play in host-indomethacin interactions.},
}

@article {pmid41551178,
year = {2026},
author = {Esposito, A and Valentino, V and Tagliamonte, S and Sequino, G and Vitaglione, P and Ercolini, D and De Filippis, F},
title = {Development of a synbiotic dietary supplement containing potential Next Generation Probiotics for modulation of the gut microbiome and metabolome.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101289},
pmid = {41551178},
issn = {2665-9271},
abstract = {The term Next Generation Probiotics (NGPs) refers to microbial strains positively impacting on human health, but do not belong to common probiotic species (e.g., lactic acid bacteria, LAB). We characterized genomically and phenotypically 14 strains isolated from the gut microbiome of healthy individuals, to evaluate their ability to produce urolithins, equol and short-chain fatty acids (SCFA). The 4 most promising strains (namely Bacteroides uniformis A4, Bacteroides thetaiotaomicron A14, unclassified Bacteroidaceae A26 and unclassified Lachnospiraceae A49) were used for the production of a synbiotic formulation, containing the strains and the precursors of health-promoting molecules. This dietary supplement was administered for 2 weeks to a continuous mucosal-Simulator of the Human Intestinal Microbial Ecosystem (mSHIME) model inoculated with a faecal sample from a low fiber-consuming donor. We performed Shotgun Metagenome Sequencing on a total of 204 samples collected from lumen and mucosa compartments, and determined the concentration of SCFA, equol and urolithin. Our results highlighted that the potential NGP strains contained in the supplement persisted in the gut ecosystem during 2 weeks of washout (Wilcoxon's rank sum test, p-value <0.05). In addition, the treatment led to an enrichment in beneficial taxa and to an increase in the production of SCFAs (p-value <0.05). This study demonstrated that feeding the gut microbiota with NGPs and dietary prebiotics can modulate both the gut microbiome and metabolome, suggesting a potential beneficial impact on human health. However, further in vivo studies are needed to confirm these results.},
}

@article {pmid41551170,
year = {2026},
author = {Chang, CC and Pak, J and Bae, S and Kim, GD and Son, HS},
title = {Impact of low aging temperature on the microbial and metabolic dynamics of rice wine during long-term storage.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101294},
pmid = {41551170},
issn = {2665-9271},
abstract = {This study investigated the effects of aging temperature and microbial inoculation on the physicochemical, microbiological, and metabolic properties of Korean rice wine (makgeolli) during long-term storage. Samples were aged at three different temperatures (4 °C, -1 °C, and -5 °C) for 180 days and were inoculated with Lactiplantibacillus plantarum or Saccharomyces cerevisiae to examine their respective influences on metabolite shifts during cold storage. Microbial communities were analyzed using amplicon (16S rRNA) and shotgun metagenomic sequencing, and metabolite profiles were determined by GC-MS to provide an integrative understanding of microbial and metabolic stability during long-term cold storage. Lower aging temperatures reduced fluctuations in metabolic and microbial activities, particularly among LAB, thereby contributing to a more stable physicochemical profile and extended shelf life. During rice wine aging, LAB exerted a more pronounced effect on metabolite dynamics than yeast, particularly for pyruvate, γ-aminobutyric acid, and lactic acid, underscoring their role in the aging process. Additionally, sub-zero aging temperatures preserved the initial microbial composition, limited enzymatic degradation, and stabilized organic acid profiles, reflecting enhanced chemical stability of the product during aging. While such chemical stability may have implications for sensory outcomes, this remains a hypothesis that requires direct sensory evaluation in future studies. Overall, the findings suggest that controlled storage temperatures and targeted microbial inoculation can improve the chemical and microbiological stability of rice wine during long-term storage.},
}

@article {pmid41551013,
year = {2025},
author = {Wang, C and Chang, K and Chen, M and Zou, X and Ni, Y and Zhang, Q and Zhao, L and Xing, B and Guo, L and Chen, W and Cao, B},
title = {Enrichment of the commensal microbiome in the lower respiratory tract is associated with improved outcomes following lung transplantation.},
journal = {Chinese medical journal pulmonary and critical care medicine},
volume = {3},
number = {4},
pages = {308-318},
pmid = {41551013},
issn = {2772-5588},
abstract = {BACKGROUND: Alterations in the respiratory microbiome are common following lung transplantation; however, the complex relationship between microbial composition and posttransplant clinical outcomes remains insufficiently characterized. This study aimed to delineate microbial signatures within the lower respiratory tract and to elucidate their associations with posttransplant outcomes in lung transplant recipients (LTRs).

METHODS: Metagenomic sequencing was performed on 138 bronchoalveolar lavage fluid (BALF) samples collected in 2023 from patients who had undergone lung transplantation between 2017 and 2023 at the China-Japan Friendship Hospital. Lung function indices, hematologic parameters, and serum cytokine levels were assessed, and patients were prospectively followed to record adverse clinical events.

RESULTS: The lung microbiome of stable LTRs formed four distinct clusters, exhibiting marked heterogeneity in both α- and β-diversity. The most prevalent cluster, enriched with oral-origin commensals, such as Neisseria subflava (N. subflava), Prevotella melaninogenica, and Streptococcus mitis (S. mitis), demonstrated the highest microbial diversity, and was associated with the lowest C-reactive protein levels, fewest adverse events, and the longest complication-free postoperative duration. In contrast, a virus-enriched cluster characterized by reduced diversity and high abundance of Torque teno virus and Cytomegalovirus human betaherpesvirus 5 was associated with poorer outcomes. BALF samples from infected LTRs exhibited more severe dysbiosis than those from immunocompetent individuals, with reduced diversity and pathogen dominance. Concurrent infections aggravated antibody-mediated rejection-related lung function decline, indicating complex microbiome-immune interactions. Integrative modeling of microbiome, hematologic, and pulmonary function data yielded superior diagnostic performance for infection detection (area under the receiver operating characteristic curve = 0.93).

CONCLUSION: The composition of the lung microbiome may serve as a prognostic biomarker for clinical outcomes after lung transplantation. The presence of diverse, commensal-dominated communities was associated with improved outcomes, whereas viral enrichment correlated with adverse events. These findings underscore the clinical importance of microbiome monitoring in posttransplant management and suggest that targeted modulation of microbial communities could improve long-term graft stability and patient prognosis.},
}

@article {pmid41550607,
year = {2025},
author = {Zhang, W and Zhang, L and Liu, H},
title = {Correction: Necrotizing enterocolitis in a neonate with severe congenital pulmonary valve stenosis complicated by a postoperative right atrial thrombus: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1760028},
doi = {10.3389/fped.2025.1760028},
pmid = {41550607},
issn = {2296-2360},
abstract = {[This corrects the article DOI: 10.3389/fped.2025.1594899.].},
}

@article {pmid41550372,
year = {2025},
author = {Tenea, GN and Jarrin-V, P and Lin, L},
title = {Editorial: Trigger the microbiome changes in foods via metagenomic technologies: from diagnostic to potential changes in product safety or quality risk profiles.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1766291},
doi = {10.3389/fbioe.2025.1766291},
pmid = {41550372},
issn = {2296-4185},
}

@article {pmid41549319,
year = {2026},
author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Chen, J and Fang, H},
title = {The impact of the timing of mNGS-guided antibiotic adjustment on clinical outcomes in ICU patients with severe community-acquired pneumonia: a retrospective study.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12941-026-00848-5},
pmid = {41549319},
issn = {1476-0711},
support = {No. 2023KY1296//Zhejiang Provincial Department of Health/ ; No. 2022K71//the Quzhou Bureau of Science and Technology/ ; },
abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) remains a major cause of intensive care unit (ICU) admission and mortality. Prompt pathogen identification and timely administration of appropriate antimicrobial therapy are essential for improving patient outcomes. Although metagenomic next-generation sequencing (mNGS) enables rapid pathogen detection, the prognostic impact of the timing of mNGS-guided antibiotic adjustment remains unclear.

METHODS: We conducted a multicenter retrospective study of ICU patients diagnosed with SCAP who underwent both bronchoalveolar lavage fluid (BALF) mNGS and conventional microbiological tests (CMTs). Patients were categorized into early (≤ 72 h) and late (> 72 h) antibiotic adjustment groups based on the interval from ICU admission to the time of antibiotic adjustment guided by mNGS results. Subgroup analyses were performed according to immune status.

RESULTS: In our study, mNGS significantly outperformed conventional microbiological tests (CMTs) in pathogen detection (92.70% vs. 57.18%, P < 0.001), with a particularly higher yield for mixed infections (51.63% vs. 19.14%, P < 0.001). Early mNGS-guided antibiotic adjustment was associated with a significantly reduced 28-day mortality compared to late adjustment (41.98% vs. 53.76%, P = 0.037). Furthermore, multivariate logistic regression analysis confirmed early adjustment as an independent protective factor for 28-day mortality (adjusted OR = 0.44, 95% CI: 0.23-0.83, P = 0.011). In the immunocompromised subgroup, early mNGS-guided adjustment was associated with significantly lower 28-day mortality than late adjustment (39.29% vs. 60.00%, P = 0.029), with a significant interaction observed between timing and immune status (P = 0.042).

CONCLUSION: Early mNGS-guided antibiotic adjustment is associated with improved survival among ICU patients with SCAP. This benefit is more pronounced in immunocompromised patients, underscoring the importance of early mNGS application to guide antimicrobial decision-making in this vulnerable population.},
}

@article {pmid41549294,
year = {2026},
author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC},
title = {Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {139},
pmid = {41549294},
issn = {1432-0991},
mesh = {*Lakes/virology ; *Metagenomics ; *Viruses/genetics/classification/isolation & purification ; *Virome ; Genome, Viral ; India ; Phylogeny ; Ecosystem ; Biodiversity ; Fresh Water/virology ; Bacteriophages/genetics/classification/isolation & purification ; },
abstract = {The virus communities of inland aquatic ecosystems have typically received less attention from the research perspective than those of marine ecosystems. In this study, we compared the viromes of an estuarine creek (Santana Creek) belonging to the khazan ecosystem and an agriculturally relevant freshwater lake (Verna Lake), both located in Goa, India. Taxonomically, the viral realm Duplodnaviria predominated in both the lake and creek communities, Varidnaviria had a minor presence in both, and Monodnaviria was exclusively present in the lake community. Sequences identified in the creek virome bore a greater resemblance to those of marine ecosystems than those in the lake virome. Functional annotation confirmed the taxonomic findings, indicating most proteins were involved in the infective and replicative functions of bacteriophages. Predicted complete viral genomes included those of Synechococcus and Proteus phages in the creek dataset, and of Gokushovirinae phages in the lake dataset. Viral communities of the khazan ecosystem and similar ecosystems worldwide are understudied, and hence the present virome analysis offers a valuable reference for further studies on these ecosystems.},
}

*Lakes/virology
*Metagenomics
*Viruses/genetics/classification/isolation & purification
*Virome
Genome, Viral
India
Phylogeny
Ecosystem
Biodiversity
Fresh Water/virology
Bacteriophages/genetics/classification/isolation & purification

@article {pmid41549250,
year = {2026},
author = {Ye, L and Cao, L and Du, Q and Xu, R and Han, Y and Liu, J},
title = {Fecal metagenome and plasma metabolome analyses reveal changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-025-04582-8},
pmid = {41549250},
issn = {1471-230X},
support = {No:2023MW35//This work was supported by the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16) and Minhang District Health Commission of Shanghai Municipality(No:2023MW35)./ ; mwyjyx16//the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16)/ ; },
}

@article {pmid41548675,
year = {2026},
author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A},
title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: comparative performance of endogenous vs. exogenous consortia.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134038},
doi = {10.1016/j.biortech.2026.134038},
pmid = {41548675},
issn = {1873-2976},
abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.},
}

@article {pmid41548597,
year = {2026},
author = {Zhao, M and Yu, X and Zhao, M and Zhang, G},
title = {Structured framework for the application of metagenomic next-generation sequencing in the whole-process management of lower respiratory tract infections.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102910},
doi = {10.1016/j.jiac.2026.102910},
pmid = {41548597},
issn = {1437-7780},
abstract = {OBJECTIVES: This study aims to assess the impact of metagenomic next-generation sequencing (mNGS) on optimizing diagnostic-therapeutic pathways for lower respiratory tract infections (LRTIs).

METHODS: This retrospective observational study analyzed 42 consecutive LRTI patients at Jiading Branch of Shanghai General Hospital (June 2023-October 2024). Comprehensive clinical data were evaluated including demographic features, laboratory result, radiological findings, mNGS interpretation, treatment modifications, and outcomes.

RESULTS: The mNGS detected pathogens in 37/42 patients (88.1%), despite the fact that 38 patients (90.5%) had received ineffective empirical antibiotic therapy prior to mNGS testing. More than half the patients(22/42, 52.4%) had comorbidities and about half the cases were within the normal range in the level of inflammatory biomarker. Pathognomonic CT features suggesting specific pathogens were observed in 33.3% (14/42) of cases. With regard to the interpretation of mNGS reports combaining the clinical characteristics, the results were consistent with the final diagnosis in 30 (30/42, 71.4%) patients. Crucially, 92.9% (39/42) underwent treatment modifications: 66.7% (28/42) transitioned to targeted/narrower-spectrum antibiotics and 26.2% (11/42) discontinued antimicrobial therapy following infection exclusion. Patients receiving targeted regimens demonstrated universal clinical improvement with radiological resolution, particularly in complex infections.

CONCLUSION: While mNGS provides robust pathogen detection, its clinical application requires integration with multidimensional patient data. The standardized protocol proposed in this study has the potential to enhances diagnostic efficiency and resource utilization in LRTI management.},
}

@article {pmid41548304,
year = {2026},
author = {Mao, C and Zhao, A and Chen, Z and Ge, F and Tang, T and Qiao, Z and Wu, Z and Zhang, Y and Liu, G and Wang, H and Li, Q and Li, T},
title = {Spatiotemporal transmission mechanisms of resistance genes in the Chishui River: Perspectives from environmental drivers and microbial interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141134},
doi = {10.1016/j.jhazmat.2026.141134},
pmid = {41548304},
issn = {1873-3336},
abstract = {The accelerating spread of antimicrobial resistance in natural ecosystems, driven principally by the dissemination of antibiotic resistance genes (ARGs), represents an escalating challenge for both environmental integrity and public health security. Aquatic systems contaminated with ARGs alongside associated virulence factors (VFs) and metal resistance elements (MRGs) have emerged as critical reservoirs of resistance propagation. This study employed metagenomic approaches to analyze microbial communities and functional diversity in the Chishui River, which spans three distinct regions under significant anthropogenic influence. The results revealed that microbial communities exhibit distinct spatiotemporal variations predominantly governed by temperature, DO, TP, and TN. In addition, variations in land use types across different regions also directly shaped microbial diversity patterns, subsequently exerting direct and indirect effects on mobile genetic elements (MGEs), ARGs, and VFs, ultimately leading to the enrichment and dissemination of high-risk resistance genes. Both microbial communities and ARGs exhibited short-distance migration patterns. Notably, a synergistic covariation pattern was observed between antibiotic resistance genes (ARGs) and dissimilatory nitrate reduction to ammonium (DNRA) functional genes, indicating a potential ecological linkage between these two genetic traits. A total of 138 metagenome-assembled genomes have been identified as potential vectors for ARG dissemination. We further revealed a novel synergistic link between ARG abundance and the DNRA process, and the class Gammaproteobacteria was identified as the primary vector of resistance dissemination, functioning as dominant co-hosts for ARGs, MRGs, VFs, and DNRA genes in the Chishui River. These findings offer new insights into river ecosystems, underscoring the importance of monitoring the fate of ARGs to enhance our understanding of how river ecosystems respond to human activities.},
}

@article {pmid41547908,
year = {2026},
author = {Kim, YC and Won, SY and Jeong, BH},
title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-025-01699-2},
pmid = {41547908},
issn = {1297-9716},
support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; },
abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.},
}

@article {pmid41547860,
year = {2026},
author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA},
title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {25},
pmid = {41547860},
issn = {2049-2618},
mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.

RESULTS: Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.

CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.},
}

Animals
Dogs/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41547817,
year = {2026},
author = {Xiao, Y and Tang, Y and Yan, Y and Cheng, Q and Chen, X and Wang, L and Li, X},
title = {Targeted next-generation sequencing has comparable clinical value to metagenomic NGS for pulmonary infections in hematological malignancy patients: a real-world propensity score-matched study.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-026-03893-0},
pmid = {41547817},
issn = {2047-783X},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is widely recognized in immunocompromised populations due to its unbiased ability to identify pathogens, while targeted next-generation sequencing (tNGS) combines PCR amplification with high-throughput sequencing technology, with advantages of lower costs and shorter turnaround times. However, it remains unclear whether tNGS can be applied in the same way as mNGS for immunodeficient patients with hematologic malignances (HM).

METHODS: This retrospective study analyzed clinical data from 245 HM patients suspected of pneumonia between April 2019 and April 2024. Bronchoalveolar lavage fluid (BALF) samples were tested using either tNGS or mNGS. Propensity score matching (PSM) (1:1) balanced the groups.

RESULTS: tNGS and mNGS showed comparable sensitivity, specificity, and accuracy for pathogen detection (97.3% vs 94.2%, 26.3% vs 26.1%, 82.6% vs 77.2%; all P > 0.05), with similar accuracy across immunodeficiency states (severe immunodeficiency: 80.0% vs 81.8%; non-severe immunodeficiency: 64.7% vs 86.7%; both P > 0.05). For non-severe pneumonia, tNGS was comparable to mNGS (accuracy: 77.9% vs 86.3%, P > 0.05), but mNGS was significantly superior in severe cases (accuracy: 50.0% vs 100.0%, P = 0.002). Both groups improved rate of correct antibiotic use (tNGS: 50.9% to 84.3%; mNGS: 57.1% to 77.8%, P < 0.01) and reduced overuse rates (tNGS: 25.9% to 2.8%; mNGS: 4.8% to 25.4%; P < 0.01), with no difference in chemotherapy intervals (37.5 ± 22.9 days vs 41.0 ± 38.4 days; P = 0.89).

CONCLUSION: In HM patients suspected of pulmonary infection, BALF-tNGS showed comparable diagnostic efficacy as BALF-mNGS, with similar clinical value across varying immunodeficiency states. tNGS is a viable alternative for non-severe pneumonia, while mNGS is superior in severe cases. Collectively, the findings of this study highlight tNGS as an alternative diagnostic approach for HM patients.},
}

@article {pmid41547254,
year = {2026},
author = {Li, C and Liu, Z and Zhao, N and Pan, H and Wang, H and Zhang, Y},
title = {Hidden oral-joint-lung axis: Porphyromonas gingivalis Infection promotes the EMyT of RA-ILD by inhibiting the JUN-regulated palmitoylation balance.},
journal = {International immunopharmacology},
volume = {172},
number = {},
pages = {116210},
doi = {10.1016/j.intimp.2026.116210},
pmid = {41547254},
issn = {1878-1705},
abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a major cause of mortality among patients with rheumatoid arthritis (RA), yet the pathological mechanism linking joint and lung involvement remains poorly understood. The pathogenic role of Porphyromonas gingivalis (P.g) in RA has been established. This study investigated how P.g infection drives RA-ILD through palmitoylation-mediated epithelial-myofibroblast transition (EMyT), thereby uncovering a mechanistic basis for the oral-joint-lung connection.

METHODS: Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and 16S rRNA sequencing of fecal samples from patients with RA-ILD were analyzed to assess the association between P.g and RA-ILD. A collagen-induced arthritis (CIA) mouse model and human lung epithelial cell lines (A549 and BEAS-2B) infected with P.g were established. Palmitoylation dynamics, EMyT marker expression, and the function of the hub gene JUN were evaluated using immunopathology, qPCR, western blotting (WB), single-cell sequencing, and molecular docking. Mechanistic studies employed the JUN activator c2-ceramide, the JUN inhibitor pterostilbene, and the palmitoylation inhibitor 2-BP to determine how P.g regulates palmitoylation in promoting RA-ILD.

RESULTS: Both mNGS and 16S rRNA analyses revealed a strong association between Porphyromonas spp. infection and RA/RA-ILD. P.g infection significantly increased EMyT marker expression (collagen I, fibronectin, and vimentin) in vitro and induced pulmonary fibrosis in CIA-ILD mice, with palmitoylation playing a central role. Mechanistically, JUN was identified as a key regulator of palmitoylation. P.g suppressed JUN level, activated ZDHHC3, and inhibited PPT1, leading to palmitoylation imbalance. Activation of JUN by c2-ceramide, combined with inhibition of palmitoylation by 2-BP, effectively suppressed EMyT progression in RA-ILD.

CONCLUSION: This study identifies a novel "oral-joint-lung axis" in which P.g infection promotes EMyT and fibrosis in RA-ILD by disrupting JUN-regulated palmitoylation homeostasis. Modulation of this axis provides a promising therapeutic strategy for RA-ILD.},
}

@article {pmid41547203,
year = {2026},
author = {Zhi, C and Wang, D and He, B and Hou, G and Gao, M and Mu, H and Wei, R and Wu, X and Bai, J and Jiao, Y and Hu, X},
title = {Metabolic coupling of arsenic, carbon, nitrogen, sulfur and iron in high-salinity groundwater in the Yellow River Delta: Insights from metagenomic analyses.},
journal = {Water research},
volume = {292},
number = {},
pages = {125368},
doi = {10.1016/j.watres.2026.125368},
pmid = {41547203},
issn = {1879-2448},
abstract = {Arsenic (As) mobilization in deltaic aquifers is regulated by tightly linked C-N-S-Fe-As biogeochemical processes, yet the influence of salinity on these interactions remains poorly resolved. Here, we investigated high-salinity groundwater from the Yellow River Delta, where total dissolved solids range from 1 to 35 g/L and As concentrations reach 303 μg/L. By integrating metagenomic sequencing, metagenome-assembled genomes (MAGs), and nitrogen and sulfur isotopic measurements, we characterized how salinity and redox gradients restructure microbial functional potential and regulate As cycling. Functional-gene profiles show a transition from nitrate- and Fe(III)-coupled metabolisms in low-salinity groundwater to sulfate- and sulfite-driven anaerobic pathways under high-salinity conditions, consistent with δ[15]N-NH4[+], δ[15]N-NO3[-], and δ[34]S-SO4[2-] signatures. Genome-resolved analyses further reveal that Pseudomonadota and Desulfobacterota dominate carbon oxidation, nitrogen and iron reduction, and sulfur-intermediate reduction, while Muiribacteriota and Planctomycetota specialize in sulfite reduction and anammox/Feammox, respectively. Together, these results show that microbial communities reorganize along the salinity gradient, with arsenic mobilization associated with nitrogen- and iron-coupled reductive processes in low-salinity groundwater and with sulfur-driven reduction under high-salinity conditions. By linking microbial metabolic interactions to salinity-related redox environments, this study provides a process-based basis for anticipating how arsenic mobility may change as coastal aquifers undergo salinization.},
}

@article {pmid41547150,
year = {2026},
author = {Liu, J and Huang, X and Wang, Y and Wang, Y and Luo, R and Lu, X and Cao, K and Xing, J and Tu, Y and Zheng, W},
title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111622},
doi = {10.1016/j.ijfoodmicro.2026.111622},
pmid = {41547150},
issn = {1879-3460},
abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), while LAB inoculation significantly reduced these (p < 0.05). Bacillota was the dominant microbial group in different samples. Compared to naturally fermented and raw mare milk, LAB-inoculated fermentation significantly altered microbial community structure (p < 0.05). This not only reduced or eliminated certain harmful bacteria but also decreased the abundance of total ARGs and multiple ARG subtypes by reducing host bacteria and MGEs. Microbes and MGEs jointly drove ARG transmission, with microbes being key. Transposon, Bacteroidota, and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation can effectively inhibit the spread of 11 ARG types, including β-lactam and multidrug resistance, by weakening the co-occurrence network among microbes, ARGs, and MGEs. This study enhances understanding of resistance genes in diverse equine dairy products, elucidates the impact of LAB fermentation on ARG distribution and transmission pathways in mare milk, and provides valuable data references and theoretical guidance for safer equine dairy processing.},
}

@article {pmid41546704,
year = {2026},
author = {Ramadoss, R and Siddique, A and Rashid, N and Liberski, AR and Vincent, AS and Mackey, HR},
title = {Effects of nitrogen and phosphorous concentrations on PHA synthesis by PNSB enriched phototrophic mixed microbial culture.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {41546704},
issn = {1615-7605},
support = {NPRP11-S-0110-180245//Qatar National Research Fund/ ; },
abstract = {Global economic burden due to plastic pollution is estimated to be over $3 trillion annually. Bioplastics derived from bacteria-synthesized biopolymers like polyhydroxyalkanoates (PHAs), are a remarkably versatile sustainable alternative. Research on optimal growth-conditions for microbial PHA-synthesis fed-on sustainable substrates, particularly by phototrophic-mixed-cultures (PMC) enriched with purple non-sulphur bacteria (PNSB) is essential. This study intends to understand the effect of nitrogen and phosphorus concentrations on PHA-production by PMC grown using fuel synthesis wastewater (FSW) (organic by-product of Fischer-Tropsch process) as substrate. Stoichiometric quantification and 16 S metagenomic sequencing followed by statistical and bioinformatic analysis were done. High PHA-production (65-82% of biomass) is observed to be induced by Low-Nitrogen conditions enriching Rhodopseudomonas, Paludibacter and Pleomorphomonas and a Low-Phosphorus condition enriching Rhodopseudomonas, Rhodoplanes and Lentimicrobium. Analysis of metabolic-potential revealed 16 enzymes (of 8 different PHA-synthesis-pathways) inherent within the genomes of bacteria enriched by these culture conditions. This study identifies optimal nitrogen and phosphorus concentrations and the corresponding microbial-composition of FSW substrate-grown PMC-system to maximize PHA-production in a laboratory-scale bioprocess.},
}

@article {pmid41546695,
year = {2026},
author = {Zhang, T and Liu, H and Huang, Z and He, Z and Fan, Y and Liu, F and Su, E and Ming, Y and Zhu, W and Wang, C and Yu, X and Niu, M and Wu, K and Sun, X and Yang, Y and He, Z and Yan, Q},
title = {Microbially Driven Organic Carbon Degradation and Nutrient Cycling during Macroalgal Decomposition.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09758},
pmid = {41546695},
issn = {1520-5851},
abstract = {The release of labile organic carbon (OC) and nutrients during seasonal macroalgal blooms can undermine blue carbon sequestration in coastal ecosystems. Although marine microorganisms mediate OC degradation during macroalgal decay, the underlying mechanisms remain poorly defined. This study employed an integrated multiomics approach (amplicon sequencing, metagenomics, and metatranscriptomics) to investigate microbial regulation of OC degradation and coupled nutrient cycling in coastal sediments with and without decomposing Sargassaceae. Total carbon in sediments increased by over 33% in the Sargassaceae area. Microbial α-diversity in the Sargassaceae area decreased significantly (p < 0.05), while processes linked to OC degradation, carbohydrate metabolism, nitrate (NO3[-]) reduction, inorganic phosphorus utilization, and sulfur metabolism were significantly upregulated (p < 0.05). Accordingly, gene expression and extracellular hydrolase activities targeting key biopolymers (i.e., cellulose, hemicellulose, starch, and chitin) were significantly upregulated (p < 0.05) in the area with Sargassaceae. Metabolism reconstruction of metagenome-assembled genomes identified Vibrio, Pseudoalteromonas, Alteromonas, and Exiguobacterium_A as primary OC degraders, with genomic capacities enriched in NO3[-] reduction and assimilatory sulfate reduction. Key environmental drivers─including the C/N ratio, dissolved organic carbon, total dissolved nitrogen (DON), and NO3[-]─shaped microbial metabolic activities during macroalgal decomposition. Our finding demonstrates that microbially driven OC degradation is a pivotal process coupled with nutrients cycling, advancing the mechanistic understanding of microbial carbon processing and its biogeochemical linkages during macroalgal decomposition in coastal ecosystems.},
}

@article {pmid41546513,
year = {2026},
author = {Yang, YY and Bueno de Mesquita, CP and Lawrence, CR and Weyman, PD and Dores, D and Timmermann, T and Fierer, N and Fuenzalida-Meriz, GA},
title = {Synergistic Effects of a Microbial Amendment and Crushed Basalt: Soil Geochemical and Microbial Responses.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70705},
pmid = {41546513},
issn = {1365-2486},
support = {//Andes Ag, Inc./ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacillus subtilis/physiology/metabolism ; *Silicates/chemistry/metabolism ; Carbon Dioxide/metabolism ; Glycine max ; },
abstract = {Over geologic timescales, the natural weathering of silicate minerals in soils and regolith regulates atmospheric CO2. Although this process is slow relative to anthropogenic emissions, several strategies have been proposed to accelerate this process for climate mitigation. These include the application of finely-ground silicate rock to increase mineral surface area (enhanced weathering, EW) and the use of microbes that catalyze mineral dissolution and CO2 biomineralization (microbial carbon dioxide mineralization, MCM). While both approaches show promise, their combined application has rarely been tested. Here, we examined how soil chemistry and bacterial communities respond to a basalt feedstock rich in silicate minerals, a Bacillus subtilis strain (MP1) previously shown to enhance weathering, and their combination. In a 91-day soybean mesocosm experiment with slightly acidic soil (pH 6.6), MP1 persisted where applied, indicating successful inoculation via seed treatment. Basalt amendments had the strongest effect on soil bacterial community composition, whereas inoculation with MP1 exerted a smaller but detectable influence. Biogeochemical indices of weathering indicated that co-application of basalt and MP1 enhanced carbonate alkalinity beyond basalt alone. Soil carbonate alkalinity increased with MP1 treatment both with and without basalt, while soil pH and cation exchange capacity (CEC) increased with basalt in both MP1 and non-MP1 treatments. Total carbon was highest in the combined MP1 + basalt treatment, suggesting that MP1 may mitigate short-term organic carbon losses associated with basalt-driven priming. Overall, these results provide new insights into interactions between biological and mineral-based carbon dioxide removal (CDR) strategies, suggesting that co-application of MP1 with basalt in slightly acidic soil may enhance carbonate alkalinity while reducing organic carbon losses relative to basalt alone. Thus, pairing B. subtilis MP1 with enhanced weathering deployments emerges as a promising strategy to improve CDR efficiency.},
}

*Soil Microbiology
*Soil/chemistry
*Bacillus subtilis/physiology/metabolism
*Silicates/chemistry/metabolism
Carbon Dioxide/metabolism
Glycine max

@article {pmid41546385,
year = {2026},
author = {Chang, H and Qin, X},
title = {Red Complex Bacteria as a Hidden Cause of Chronic Lung Abscess: A Case Report.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e949102},
doi = {10.12659/AJCR.949102},
pmid = {41546385},
issn = {1941-5923},
mesh = {Humans ; *Lung Abscess/microbiology/diagnostic imaging/diagnosis/drug therapy ; Chronic Disease ; Male ; *Chronic Periodontitis/complications/microbiology ; Tomography, X-Ray Computed ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Hemoptysis/etiology ; },
abstract = {BACKGROUND Common oral pathogens such as Treponema denticola, Porphyromonas gingivalis, and Tannerella forsythia, which form biofilms in the periodontal pockets, are classified together as Red Complex bacteria in Socransky's subgingival cluster model and are key pathogenic bacteria in periodontitis. Oral pathogens play a critical role in pulmonary infections, particularly in the pathogenesis of lung abscesses. Lung abscesses caused by Red Complex bacteria have rarely been described; to our knowledge, few cases have been reported to date. CASE REPORT We present the first documented case of chronic lung abscess caused by Red Complex bacteria, with recurrent hemoptysis as the main symptom. The patient had chronic periodontitis and uncontrolled diabetes, and exhibited an indolent clinical course with consistently negative bacterial cultures. Chest computed tomography (CT) demonstrated a thick-walled cavity with minimal liquefactive changes in the right upper lobe. Red Complex bacteria in the bronchoalveolar lavage fluid and the lung tissue were identified by metagenomics next-generation sequencing (mNGS). The patient underwent intravenous penicillin therapy. The hemoptysis resolved completely coupled with improvement in clinical status and inflammatory markers. The chest CT demonstrated near-complete resolution of the lung abscess during follow-up. CONCLUSIONS Red Complex bacteria are rare pathogens in patients with periodontitis who develop culture-negative chronic lung abscesses accompanied by recurrent hemoptysis. This case report highlights this rare etiology and reveals a critical diagnostic limitation, as routine cultures frequently fail to detect these fastidious organisms. The incorporation of mNGS into the diagnostic algorithm for such cases can facilitate a definitive diagnosis and guide precise antimicrobial therapy.},
}

Humans
*Lung Abscess/microbiology/diagnostic imaging/diagnosis/drug therapy
Chronic Disease
Male
*Chronic Periodontitis/complications/microbiology
Tomography, X-Ray Computed
Middle Aged
Anti-Bacterial Agents/therapeutic use
Hemoptysis/etiology

@article {pmid41545847,
year = {2026},
author = {Xu, Z and Gao, L and Chen, Z and Tang, L and Wang, Y},
title = {Metagenomic next-generation sequencing for the diagnosis and evaluation of pediatric pleural effusion: a case series.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04117-1},
pmid = {41545847},
issn = {1471-2466},
support = {2023C03009//the "Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
}

@article {pmid41545588,
year = {2026},
author = {Buddle, S and Brown, LK and Morfopoulou, S and Torres Montaguth, OE and Scoto, M and Herder, V and Dhawan, A and Brown, JR and Atkinson, L and Kopec, A and Davis, D and Storey, N and Campos, L and Sebire, N and Macpherson, H and Lee, J and Orton, R and Baranello, G and Asamaphan, P and Ilia, G and Karda, R and Belfield, H and , and Counsell, J and Waddington, SN and Thomson, EC and Muntoni, F and Breuer, J},
title = {Contaminating plasmid sequences and disrupted vector genomes in the liver following adeno-associated virus gene therapy.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41545588},
issn = {1546-170X},
abstract = {Adeno-associated viruses (AAVs) are common vectors in gene therapy but can frequently cause liver complications in patients. The mechanisms underlying AAV-related liver toxicity remain poorly understood, posing challenges for effective prevention and intervention. Here we conducted a case study of a child with spinal muscular atrophy type 1 experiencing substantial hepatitis after receiving onasemnogene abeparvovec, undertaking long- and short-read metagenomic sequencing of liver tissue. We identified manufacturing plasmid sequences with complex structures and recombination. Vector genomes had extensive disruption and concatemerization as well as numerous vector-human fusion junctions. We also identified human betaherpesvirus 6B in the liver. Further work and investigation of more patients is needed to establish whether the presence of manufacturing plasmid sequences or helper viruses contribute to the formation of these complex concatemeric DNA structures in the liver, and whether these are a factor in the development of liver toxicity after AAV gene therapy.},
}

@article {pmid41545429,
year = {2026},
author = {Maharaj, SD and Nkuna, R and Matambo, TS},
title = {Shotgun metagenomic and physicochemical profiling of municipal wastewater treatment plants using activated sludge and trickling filters.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35157-6},
pmid = {41545429},
issn = {2045-2322},
abstract = {In this study, which aimed to evaluate wastewater treatment and provide data to support improved wastewater treatment plant (WWTP) design, operation and ongoing monitoring strategies, mixed liquor, return activated sludge, primary effluent and secondary effluents of two WWTPs (n = 15) and five of the industries they service (n = 15) in Emfuleni municipality, Gauteng Province, South Africa, were characterised following a 5-month monitoring study. Following physical and chemical analysis, the parameters, including the Chemical Oxygen Demand (COD), were higher than local limits (75 mg/L) for both WWTPs and extremely high for the abattoir industry (13400 mg/L). In particular, high ammonia levels were recorded in both WWTPs. Following Illumina high-throughput sequencing and analysis using the Whole Metagenome Sequencing Assembly-based (WGSA2) pipeline on the Nephele platform, Bacteria was the dominant domain in the WWTPs. The dominant phyla were Proteobacteria (87.7%), followed by Firmicutes (8.25%), Actinobacteria (2.71%) and Bacteroidetes (0.68%). Aeromonas (39.86%) was the most dominant genus, with Acinetobacter (9.29%), Pseudomonas (6.78%), Bacillus (5.99%), and Thauera following (4.78%). Total Suspended Solids (TSS), pH, Total Dissolved Solids (TDS), and DO have influenced the diversity and distribution of the microbiome. Krona charts elucidated the xenobiotics degradation and metabolism distribution potential of the microbiome of each sampled site. This study reiterates the need for constant monitoring of WWTPs due to the high pollution parameters recorded from the WWTP effluent. The metagenomic data generated in this study provides insight into the diversity and functionality of the microbiome present in WWTPs of different process configurations which can inform existing WWTP configurations and future designs.},
}

@article {pmid41544986,
year = {2026},
author = {Liu, X and Zhang, J and Niu, Y and Bai, Y and Jia, X and Cai, S and Wang, Y and Zhang, X and Shi, B and Hu, J and Zhang, C and Zhao, Z},
title = {Rumen fermentation, microbial flora, and their metabolite interaction patterns: A comparison between non-pregnant and gestational Ashidan yaks.},
journal = {Genomics},
volume = {},
number = {},
pages = {111205},
doi = {10.1016/j.ygeno.2026.111205},
pmid = {41544986},
issn = {1089-8646},
abstract = {Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2-3-year-old Ashidan yaks during the non-pregnant period (NP; 11-30 days pre-mating) and the gestational period (GP; 112-148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3-N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.},
}

@article {pmid41544844,
year = {2026},
author = {Wei, Y and Hu, Y and Shi, Q and Su, N and Chen, X and Chong, L and Cui, X},
title = {Successful Treatment of Probable Disseminated Mucormycosis Using Liposomal Amphotericin B and Isavuconazole in Myelodysplastic Syndrome: A Case Report and Literature Review.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108394},
doi = {10.1016/j.ijid.2026.108394},
pmid = {41544844},
issn = {1878-3511},
abstract = {BACKGROUND: Mucormycosis is a rare, aggressive, and life-threatening fungal infection that predominantly affects immunocompromised individuals and is associated with a high mortality rate.

CASE PRESENTATION: We treated a 72-year-old woman with myelodysplastic syndrome (MDS) who developed disseminated mucormycosis involving the lungs, skin, and central nervous system (CNS). Diagnosis was supported by metagenomic next-generation sequencing (mNGS), and she received combination antifungal therapy with liposomal amphotericin B and isavuconazole. Her clinical status stabilized after 4 weeks of treatment. She later died approximately 2 weeks after discharge because of carbapenem-resistant Pseudomonas aeruginosa bacteremia.

CONCLUSIONS: Our case highlights the importance of prompt diagnosis and timely initiation of therapy for mucormycosis and indicates that combination antifungal therapy may be an effective approach to managing severe disseminated mucormycosis in immunocompromised patients.},
}

@article {pmid41544592,
year = {2026},
author = {Zheng, Z and Lyu, H and Li, Z and Tang, J and He, J},
title = {Unraveling water depth dependent microplastic aging driven by functional microbial community interaction in a real urban river.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141133},
doi = {10.1016/j.jhazmat.2026.141133},
pmid = {41544592},
issn = {1873-3336},
abstract = {Microplastic (MPs) biofilms are dynamic microhabitats that regulate substance transformation processes. However, the influence of natural urban water depth gradients on the biofilm functions and subsequent aging of MPs remains poorly understood. Herein, we characterized the aging process of MPs in different depths of a real urban river, and the biofilm driven aging mechanism was illustrated. Surface characterization of the MPs showed an increase in oxygen-containing functional groups (CO, C-O) and O/C in polylactic acid (PLA) during aging, which indicated oxidation and hydrolysis reactions, especially at 2.0 m deep water depth. In polyvinyl chloride (PVC) MPs, carbonyl index (CI) was 2 times higher at 2.0 m as compared to 0.1 m water depth and lower chlorine content was found, indicating higher oxidative degradation and dechlorination processes in deeper water. Moreover, biofilms may regulate the synergism between oxygenase and hydrolases in PLA biofilms and oxygenase and dehalogenase in PVC biofilms. Microorganisms with both denitrification and MPs degradation functions, such as Acidovorax, Comamonas, Dechloromonas, were enriched in MPs biofilm. In addition, a positive correlation was found between MPs degradation genes (TGL2, katG, ncd2) and denitrification genes (napA, nirS, norB) in PLA biofilms at deeper water depth, suggesting a potential effect of denitrification functions on MPs aging (45 d incubation). This research challenges the conventional thoughts of higher MPs aging in shallow water, emphasizing the significant role of moderate depth gradients water in regulating the ecological function of microplastic biofilm, which is essential for evaluating the fate of MPs in real urban rivers.},
}

@article {pmid41544536,
year = {2026},
author = {Chen, R and Li, Z and Li, D and Mao, X and Xu, Z},
title = {Clinical utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing in the etiological diagnosis of community-acquired pneumonia in children.},
journal = {International journal of medical microbiology : IJMM},
volume = {322},
number = {},
pages = {151701},
doi = {10.1016/j.ijmm.2026.151701},
pmid = {41544536},
issn = {1618-0607},
abstract = {CAP is a major cause of pediatric hospitalization on a global scale, particularly in developing countries where the morbidity and mortality rates remain high. The etiological diagnosis of CAP in children is challenging, particularly for children with severe and high-risk conditions, such as immunodeficiency. This is primarily due to the nonspecific distribution of the causative agent and the limitations of traditional detection methods. As an emerging molecular diagnostic technology, BALF mNGS has been shown to detect the nucleic acid sequences of bacterial, viral, fungal, and atypical pathogens directly from clinical samples. This is attributed to the technology's unbiased, high throughput, and high sensitivity, which significantly improves the detection rate of pathogens. Furthermore, BALF mNGS also improves the detection of mixed infections. This capacity for precise analysis is of significant value, as it facilitates the identification of drug-resistant genes and rare pathogens. Consequently, this enhanced diagnostic capability provides a reliable foundation for the precise treatment of childhood CAP. Nevertheless, its clinical application continues to encounter challenges, including high cost, invasive sampling methods, complex data analysis processes, and insufficient standardization of pre-analytical sample processing. The technical principles, clinical value and optimization strategies of BALF mNGS are systematically reviewed in this paper, with the aim of providing a reference for improving the pathogenetic diagnosis of CAP in children.},
}

@article {pmid41544440,
year = {2026},
author = {Yang, L and Ru, J and Guo, S and Yang, X and Li, P and Deng, L and Wang, X},
title = {Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106373},
doi = {10.1016/j.psj.2026.106373},
pmid = {41544440},
issn = {1525-3171},
abstract = {This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.},
}

@article {pmid41543328,
year = {2026},
author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L},
title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70375},
doi = {10.1002/mnfr.70375},
pmid = {41543328},
issn = {1613-4133},
support = {2023BCF01028//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Male ; *Lactiplantibacillus plantarum/physiology ; *Probiotics/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice, Inbred C57BL ; *Liver Diseases, Alcoholic/therapy/microbiology ; Liver/metabolism ; Mice ; Dysbiosis ; NF-E2-Related Factor 2/metabolism/genetics ; Oxidative Stress ; Bile Acids and Salts/metabolism ; Disease Models, Animal ; },
abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.},
}

Animals
Male
*Lactiplantibacillus plantarum/physiology
*Probiotics/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects/physiology
Mice, Inbred C57BL
*Liver Diseases, Alcoholic/therapy/microbiology
Liver/metabolism
Mice
Dysbiosis
NF-E2-Related Factor 2/metabolism/genetics
Oxidative Stress
Bile Acids and Salts/metabolism
Disease Models, Animal

@article {pmid41543271,
year = {2026},
author = {Yamazaki, K and Yamaguchi, T and Yokoyama, Y and Tonosaki, Y and Kursanbaeva, K and Motooka, D and Akeda, Y and Kashimoto, T},
title = {Nutrient acquisition drives Edwardsiella tarda pathogenesis in necrotizing soft tissue infection.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0165725},
doi = {10.1128/msystems.01657-25},
pmid = {41543271},
issn = {2379-5077},
abstract = {Necrotizing soft tissue infections (NSTIs) are rapidly progressive and life-threatening diseases caused by diverse bacterial pathogens. While classical virulence factors, such as toxins and secretion systems, have been extensively characterized, the role of metabolic fitness in supporting bacterial survival within the nutrient-restricted host environment remains underexplored. Edwardsiella tarda, a human-pathogenic bacterium implicated in NSTIs, represents an emerging model for studying non-canonical pathogenic strategies. Here, we employed transposon-directed insertion site sequencing (TraDIS) to identify genes critical for E. tarda survival in a murine soft tissue infection model. A genome-wide screen revealed 41 genes significantly depleted during the infection, including those involved in iron and zinc acquisition (fetB, zupT), vitamin biosynthesis (pdxK, cobA), and polyamine metabolism (speB). Functional assays using defined minimal media demonstrated that supplementation with vitamin B6 or putrescine enhanced bacterial growth, validating their contribution to fitness under nutrient-limited conditions. Our findings indicate that E. tarda pathogenesis is driven not solely by classical virulence factors but also by its ability to acquire essential nutrients and adapt metabolically to host-imposed nutritional stress. This study provides the first genome-wide fitness map for E. tarda during soft tissue infection and reveals new targets for therapeutic intervention that disrupt nutrient acquisition systems. These results also emphasize the broader relevance of metabolic adaptation as a determinant of virulence in invasive bacterial infections.IMPORTANCENecrotizing soft tissue infections (NSTIs) are severe, rapidly progressing bacterial infections with high morbidity and mortality. Although classical virulence factors such as toxins have been widely studied, much less is known about how pathogens adapt metabolically to survive within the nutrient-restricted environment in host tissues. This study uses Edwardsiella tarda, an emerging NSTI pathogen, as a model to identify genes required for in vivo fitness using transposon insertion sequencing. By revealing the critical roles of nutrient acquisition and metabolic adaptation, rather than toxin production alone, this work challenges conventional paradigms of bacterial virulence. Our findings suggest that targeting bacterial nutrient acquisition pathways may offer a novel therapeutic approach to control invasive infections. Furthermore, this study provides the first genome-wide fitness map of E. tarda during soft tissue infection, offering a valuable resource for future research into polymicrobial wound infections and host-pathogen nutrient competition.},
}

@article {pmid41543249,
year = {2026},
author = {Beals, DG and Carper, DL and Hochanadel, LH and Jawdy, SS and Klingeman, DM and Piatkowski, BT and Weston, DJ and Doktycz, MJ and Pelletier, DA},
title = {Genomic signatures in Variovorax enabling colonization of the Populus endosphere.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160525},
doi = {10.1128/msystems.01605-25},
pmid = {41543249},
issn = {2379-5077},
abstract = {Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.IMPORTANCEPlants often depend on diverse microbial partners to support their growth, resilience, and adaptation to changing environments. Among these microbes, some bacteria inhabit the rhizosphere (the narrow zone around roots where microbes interact with the plant) while others are able to enter and persist within root tissues. The traits that distinguish these two lifestyles remain poorly understood. In this study, we examined a group of related Variovorax strains from poplar tree root microbiomes to ask why some rhizosphere-associated strains also become successful endosphere colonizers. We found that strains appear to succeed through different strategies: some may benefit from rapid growth on plant-derived carbon sources, while others may rely on stress tolerance or fine-tuned regulation. These results suggest that there is no single path from the rhizosphere into the root interior, but rather multiple strategies shaped by the host environment. Understanding this diversity can inform efforts to design resilient plant-microbe communities.},
}

@article {pmid41543189,
year = {2026},
author = {Hasan, GM and Mohammad, T and Zaidi, S and Shamsi, A and Sohal, SS and Hassan, MI},
title = {<p>Klebsiella pneumoniae and pyogenic liver abscess: Emerging clinical threats, virulence mechanisms and therapeutic strategies (Review)</p>.},
journal = {Molecular medicine reports},
volume = {33},
number = {3},
pages = {},
doi = {10.3892/mmr.2026.13800},
pmid = {41543189},
issn = {1791-3004},
mesh = {Humans ; *Klebsiella pneumoniae/pathogenicity/drug effects/genetics ; *Liver Abscess, Pyogenic/microbiology/drug therapy/diagnosis/epidemiology/therapy ; Anti-Bacterial Agents/therapeutic use/pharmacology ; *Klebsiella Infections/drug therapy/microbiology/epidemiology/diagnosis ; Virulence ; Drug Resistance, Multiple, Bacterial ; Animals ; },
abstract = {

Klebsiella pneumoniae has emerged as a leading cause of pyogenic liver abscess (PLA), driven by hypervirulent and multidrug‑resistant (MDR) strains that pose major diagnostic and therapeutic challenges. This organism exhibits extensive capsular diversity (K1‑K80), with serotypes K1, K2, K5, K20, K54 and K57 being the most associated with invasive infections and severe clinical outcomes. Increasing convergence between hypervirulence and MDR determinants threatens effective management worldwide. Pharmacological and safety limitations of current antibiotics, including nephrotoxicity of colistin, hepatotoxicity of tigecycline and poor drug penetration into abscess cavities, further complicate treatment and encourage exploration of non‑traditional strategies such as anti‑virulence or immunomodulatory approaches. Recent advancements in rapid diagnostic tools such as metagenomic sequencing, MALDI‑TOF and point‑of‑care PCR assays offer promising prospects for early detection and antimicrobial optimization. Pharmacokinetic challenges at the abscess site and the emergence of hybrid hvKp‑MDR strains emphasize the urgency of precision‑guided therapy and robust global surveillance. K. pneumoniae‑associated PLA thus represents an evolving global health threat and understanding serotype diversity, antibiotic limitations and diagnostic innovations is essential for developing more effective preventive and therapeutic strategies. The present review provides current insights into the epidemiology, pathogenesis and therapeutic challenges of K. pneumoniae‑associated PLA, while highlighting translational opportunities and research priorities to counter the escalating dual threat of hypervirulence and resistance.

Humans
*Klebsiella pneumoniae/pathogenicity/drug effects/genetics
*Liver Abscess, Pyogenic/microbiology/drug therapy/diagnosis/epidemiology/therapy
Anti-Bacterial Agents/therapeutic use/pharmacology
*Klebsiella Infections/drug therapy/microbiology/epidemiology/diagnosis
Virulence
Drug Resistance, Multiple, Bacterial
Animals

@article {pmid41542367,
year = {2026},
author = {Sladký, O and Veselý, P and Břinda, K},
title = {FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT).},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbaf290},
pmid = {41542367},
issn = {2635-0041},
abstract = {MOTIVATION: The growing volumes and heterogeneity of genomic data call for scalable and versatile k-mer-set indexes. However, state-of-the-art indexes such as SBWT and SSHash depend on long non-branching paths in de Bruijn graphs, which limits their efficiency for small k, sampled data, or high-diversity settings.

RESULTS: We introduce FMSI, a superstring-based index for arbitrary k-mer sets that supports efficient membership and compressed dictionary queries with strong theoretical guarantees. FMSI builds on recent advances in k-mer superstrings and uses the Masked Burrows-Wheeler Transform, a novel extension of the classical Burrows-Wheeler Transform that incorporates position masking. Across a range of k values and dataset types-including genomic, pangenomic, and metagenomic-FMSI consistently achieves superior query space efficiency, using up to 2-3× less memory than state-of-the-art methods, while maintaining competitive query times. Only a space-optimized version of SBWT can match the FMSI's footprint in some cases, but then FMSI is 2-3× faster. Our results establish superstring-based indexing as a robust, scalable, and versatile framework for arbitrary k-mer sets across diverse bioinformatics applications.

FMSI is developed in C++ and released under the MIT license, with source code provided at https://github.com/OndrejSladky/fmsi and an installable package available through Bioconda. The datasets used in the experiments are deposited at Zenodo (https://doi.org/10.5281/zenodo.14722244).},
}

@article {pmid41542089,
year = {2025},
author = {Zhang, D and Hu, J and Gu, B and Cao, B and Lu, J and Chen, Q and Wang, L and Pei, G and Liu, ZX and Cheng, MG and Gao, S and Li, X},
title = {BodyMeta: A comprehensive database for microbes under various pathological and physiological conditions.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {3685-3692},
pmid = {41542089},
issn = {2001-0370},
abstract = {Microorganisms residing in the gut and other anatomical sites exhibit substantial alterations under both physiological and pathological conditions, which are intricately linked to human health. Consequently, the establishment of a comprehensive metagenomic database encompassing diverse body sites under both pathological and physiological conditions is highly important. In this study, we developed BodyMeta (Body Metagenome Database), an upgraded version of the gutMEGA (gut Metagenome Atlas database), and we expanded the included studies considerably from 182 to 1261. These studies were classified into two categories: 600 literature-based studies without raw data (comprising 107 whole-genome sequencing and 493 16S amplicon sequencing studies) and 661 studies containing 663 raw datasets. We systematically categorized 1842 conditions derived from the 1261 studies into 966 pathological and 879 physiological conditions spanning 31 body sites, with the pathological conditions organized according to MeSH (Medical Subject Headings) terms. We comprehensively annotated the microbial contents, diversities, biomarkers and functional differences of the curated raw 16S amplicon sequencing data. In total, 59010 microbial taxa from literature sources and 40657 from raw datasets were mapped to the NCBI Taxonomy database. Additionally, related information about literature and experiments were compiled within BodyMeta. Collectively, the BodyMeta database provides a comprehensive resource for metagenomic investigations related to both physiological and pathological conditions, which can be freely accessed at https://bodymeta.omicsbio.info/.},
}

@article {pmid41542073,
year = {2025},
author = {Kapoor, S and Mehta, P and Patial, V and Pandey, R and Padwad, YS},
title = {Phloretin-induced modulation in gut microbiome, mitigates colonic inflammation and alleviates colitis-associated colorectal cancer in mice.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {2730-2746},
pmid = {41542073},
issn = {2001-0370},
abstract = {Colitis associated colorectal cancer (CAC) is the fourth common cancer known to cause significant mortalities worldwide. Phloretin is a dihydrochalcone naturally found in apple, pear and strawberry. It exhibited different biological activities, namely anti-inflammatory, anticancer and anti-microbial. In the present study, the role of phloretin towards alleviating colonic inflammation and regulating gut microbiota was explored. The treatment of phloretin led to the reduction in the intestinal inflammation and maintained colon length-weight ratio by decreasing the total number of tumor nodules. We registered reduction in the colonic inflammatory cytokines levels namely TNFα, IL1β, IFNγ, and IL6 as well as expression of HSP90, Cox2, and Src found decreased. Results highlighted the restoration in the levels of tight junction proteins and the expression of Muc2 and Muc3. Further, role of phloretin in inducing apoptosis of tumor cells and the deregulation β-catenin pathway was studied. The histopathological analysis revealed normal colonic structure by decreasing leukocyte infiltration, as well as, circumvention in the reduction of the numbers of goblet cell, crypt abscess and ulceration in phloretin and 5-ASA (5-aminosalicylic acid) treated animals, compared to the diseased group. Metagenomic analysis of the gut microbiome in CAC mice revealed that phloretin significantly increased the abundance of Lactobacillus species, which exert probiotic effects and inhibit synchronous colon tumor growth by modulating β-catenin signaling. The increased abundance of L. reuteri and L. murinus was associated with regulated cellular proliferation, reduced TNF-α production, and decreased expression of COX-2, cyclin D1, and Bcl-2. In conclusion, the results obtained signify the nutraceutical potential of phloretin in restoring the intestinal barrier, maintaining the beneficial gut microbial population, and amelioration of CAC in mice.},
}

@article {pmid41541500,
year = {2025},
author = {Broedlow, CA and Swanson, E and Cherenack, EM and Basting, C and Nogueira, NF and France, M and Yue, P and Chakrawarti, A and Salazar, A and Acosta, L and Raccamarich, P and Gale, M and Ravel, J and Fein, LA and Holm, J and Alcaide, ML and Klatt, NR},
title = {Common cervicovaginal sequencing methods result in discordant molecular diagnoses of bacterial vaginosis and reveal strain level effects of Gardnerella vaginalis.},
journal = {npj women's health},
volume = {3},
number = {},
pages = {},
pmid = {41541500},
issn = {2948-1716},
support = {P30 AI073961/AI/NIAID NIH HHS/United States ; R01 AI138718/AI/NIAID NIH HHS/United States ; },
abstract = {Bacterial vaginosis (BV) is associated with HIV transmission and pre-term birth, yet the etiology of BV remains unknown. Our analysis addressed that knowledge gap by comparing diagnostic techniques and using Bayesian inference to find species-specific associations with clinical indicators. We also assessed the effect of sequencing methodology on the results of molecular BV profiling. We observed significant differences in microbial diversity within BV-associated CSTs based on clinical diagnosis. CST assignments were substantially influenced by sequencing methodology, with concordance between methods as low as 59% for metatranscriptomic and metataxonomic-based CST assignment. We also found that Gardnerella has a strain-dependent association with individual Amsel's criteria, and that Dialister micraerophilus and Parvimonas micra are positively associated with Amsel's criteria while Lactobacillus is negatively associated. These results highlight the challenge of characterizing a condition without a single etiological agent, reinforcing the need for more granular diagnoses and treatments that are sensitive to BV variability.},
}

@article {pmid41541065,
year = {2025},
author = {Zhang, X and Liu, C and Han, Y and She, J and Wu, W and Wang, L and Song, J and Gao, GF and Xu, Z and Liang, H and Liu, J},
title = {Sustained circulation of Aedes albopictus-derived novel almendraviruses in the urban parks.},
journal = {Biosafety and health},
volume = {7},
number = {6},
pages = {369-376},
pmid = {41541065},
issn = {2590-0536},
abstract = {The Rhabdoviridae family comprises a diverse range of negative-sense single-stranded ribonucleic acid (RNA) viruses, including significant human and mammalian viruses transmitted by various arthropod species. Herein, using Aedes albopictus (Ae. albopictus) samples collected in two urban parks during 2023 and 2024, through metagenomics sequencing, 16 sequences were identified as putative novel viruses, showing closest homology to insect-specific viruses, mycoviruses, or plant-associated viruses. Notably, two novel viruses, Aedes albopictus almendravirus GCCDC15 (Aealb-AlmV GCCDC15) and Aedes albopictus almendravirus GCCDC16 (Aealb-AlmV GCCDC16) were identified and successfully isolated. Both of these viruses belong to the genus Almendravirus within the Rhabdoviridae family. Phylogenetic analysis revealed that Aealb-AlmV GCCDC15 and GCCDC16 are distantly related to Coot Bay virus (the United States of America, 2013) and Menghai rhabdovirus (Yunnan Province, China, 2017). The genetic distances between these two viruses and their most similar viruses are marked by 59.85 % and 87.20 % of amino acid identity in the L protein, respectively, supporting their classification as two new species in the Rhabdoviridae family. Cytopathic effects and rod-like virions were observed in mosquito cells (C6/36) after inoculating with supernatants from the Ae. albopictus samples. To investigate the natural distribution and persistence of the novel almendraviruses, we conducted a specific reverse transcription-polymerase chain reaction (RT-PCR) screening of Ae. albopictus mosquitoes collected from two urban parks across different time points. The assays confirmed the presence of both Aealb-AlmV GCCDC15 and GCCDC16 in mosquito populations. Critically, these viruses were detected repeatedly over successive sampling periods and in mosquitoes from geographically distinct sites within the urban environment. In summary, our study delineates the virome characteristics of Aedes mosquitoes in the urban ecosystem and successfully isolated two novel rhabdoviruses. The recurrent detection provides clear evidence for the sustained circulation of Ae. albopictus-derived almendraviruses in urban parks, highlighting their ongoing transmission and establishment in these habitats.},
}

@article {pmid41540749,
year = {2026},
author = {Kong, L and Xu, H and Wang, Y and Tao, Y and Xiao, P and Wang, Z and Zhang, M and Zheng, X and Zhang, C and Cui, S and Xu, T and Pang, Z and Wang, A and Ren, N and Zheng, C},
title = {Single-Cell Profiling Reveals Hidden Drivers of Sediment Phosphorus Release.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15684},
pmid = {41540749},
issn = {1520-5851},
abstract = {As external phosphorus inputs are progressively brought under control, microbe-mediated release of legacy phosphorus from sediments to the overlying waters has become a primary contributor to persistent eutrophication and recurrent algal blooms in global freshwater ecosystems. However, inherent challenges exist in capturing the in situ metabolic activity of phosphorus-solubilizing bacteria (PSB) due to intrinsic cultivation biases and the disconnect between bulk metagenomic profiles and the functions of viable cells. Furthermore, a lack of research into the coupling the phenotypic activity and adaptive genetic strategies of PSB in heterogeneous sedimentary environments has led to limited understanding of the mechanisms underlying endogenous phosphorus release. Here, using single-cell Raman spectroscopy coupled with deuterium oxide labeling (Raman-D2O), distinct in situ phosphorus-solubilizing activities of PSB inhabiting eutrophic, mesotrophic, and oligotrophic sediments were quantified. Inorganic PSB dominated in all sediment types but exhibited the highest activity in nutrient-rich eutrophic sites. Their activities correlated strongly with phosphorus speciation and release fluxes at the sediment-water interface of their habits. In contrast, organic PSB prevailed in oligotrophic sediments. Raman-activated cell sorting conbined with metagenomic sequencing uncovered that low-abundance taxa (e.g., Bacillus and Acinetobacter) acted as disproportionate drivers of phosphorus mobilization. PSB from eutrophic sediments were enriched in genes encoding phosphatases and organic acid hydrolysis pathways, whereas their oligotrophic counterparts favored genes related to high-affinity transporters and polyphosphate storage. These findings elucidate how nutrient regimes shape PSB metabolic traits, advancing mechanistic insights into microbial phosphorus dynamics in aquatic ecosystems and providing a theoretical basis for optimizing lake management strategies to mitigate endogenous pollutant-driven eutrophication risks.},
}

@article {pmid41540332,
year = {2026},
author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L},
title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04699-6},
pmid = {41540332},
issn = {1471-2180},
abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.},
}

@article {pmid41540059,
year = {2026},
author = {St John, E and Reysenbach, AL},
title = {Global deep-sea hydrothermal deposit metagenomes and metagenome-assembled genomes over time and space.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06612-w},
pmid = {41540059},
issn = {2052-4463},
support = {DEB-2409507//National Science Foundation/ ; },
abstract = {Actively venting high temperature deep-sea hydrothermal vent deposits along tectonic spreading centers and in backarc basins harbor a rich diversity of thermophilic Bacteria and Archaea, many of which have no representatives in cultivation nor any genomic representation in databases. Here, in order to produce a global-scale time series metagenomic resource for studying the microbial functional and genomic diversity in these high temperature ecosystems, we obtained 70 metagenomes from collections across spatial and temporal gradients from 21 different vent fields spanning 16 years (1993-2009). The dataset (Deep-Sea Hydrothermal Vent dataset (DSV70)) includes 3.56 Tbp of raw DNA sequence reads, that have been assembled to produce 7,422 medium- to high-quality (based on CheckM2) metagenome-assembled genomes (MAGs) of Bacteria (6,063 MAGs) and Archaea (1,359 MAGs). Collectively, this DSV70 dataset and the published 40 metagenomes from more recent deep-sea collections (2004 to 2018), represent a valuable resource for exploring the functional and phylogenomic diversity of the deep-sea hydrothermal microbiomes, and provide many reference genomes for studies in the taxonomy and systematics of poorly studied microbial lineages. Further, with the interest in mining the mineral resources at deep-sea vents, the DSV70 provides a genomic legacy for monitoring impacts on the microbial communities in these systems.},
}

@article {pmid41539958,
year = {2026},
author = {Chen, D and Luo, LL and Yang, M and Wang, Y and Zhang, HY and Liu, ZQ and Qiao, LN},
title = {[Clinical characteristics of Pneumocystis jirovecii pneumonia in non-human immunodeficiency virus infected children].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {64},
number = {2},
pages = {204-209},
doi = {10.3760/cma.j.cn112140-20250811-00740},
pmid = {41539958},
issn = {0578-1310},
support = {2021YFC2701704//National Key Research and Development Program of China/ ; },
abstract = {Objective: To analyze the clinical characteristics of Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus (HIV) infected children, aiming to provide a basis for early diagnosis, timely treatment, and improved prognosis. Methods: A single-center retrospective case series study was conducted to analyze the general information, laboratory indicators, imaging features, treatment, and outcomes of 59 pediatric patients with non-HIV-infected PJP admitted to the Department of Pediatrics, West China Second Hospital, Sichuan University, from February 2022 to June 2025.These patients were categorized into two groups based on the presence or absence of underlying diseases.Comparative analysis was performed to assess differences in hospitalization duration, intensive care unit (ICU) admission rate, mechanical ventilation rate, mortality, and other relevant aspects between the 2 groups.The rank sum test, χ[2] test, or Fisher's exact test was employed for intergroup comparisons. Results: The age at presentation of 59 patients: 0.5 (0.3, 2.5) years, including 40 males and 19 females. Among the underlying diseases, there were 12 cases (20%) of primary immunodeficiency, 4 cases (11%) each of autoimmune diseases, hematologic malignancies, and organ transplantation 30 cases (51%) had received treatment with glucocorticoids and immunosuppressants before diagnosis. The main clinical symptoms were cough in 57 cases (97%), dyspnea in 51 cases (86%) and, fever in 35 cases (59%). The peripheral white blood cell count was 9.2 (6.3, 13.9)×10[9]/L, with neutrophils 4.4 (1.8, 7.4)×10[9]/L and lymphocytes 3.4 (2.0, 6.1)×10[9]/L. C-reactive protein (CRP) 1.4 (0.5, 11.6) mg/L, procalcitonin 0.2 (0.1, 0.6) μg/L, the lactate dehydrogenase was (582±49) U/L. Fifty-three percent (16/30) of fungal G-test results were positive, 27% (11/41) of the children had CD4[+] T-cell counts <0.5×10[9]/L, and 32% (13/41) had CD4[+]/CD8[+] ratios <1.0.The main imaging findings included consolidation or patchy opacities in 48 cases (81%), diffuse ground-glass opacities in 29 cases (49%), and decreased transparency in 20 cases (34%). Pneumocystis was detected via metagenomic next-generation sequencing (mNGS) in all cases. Co-infections were present in 57 cases (97%). Among the 59 pediatric patients, 34 cases (58%) were treated with trimethoprim-sulfamethoxazole monotherapy, 19 cases (32%) received combination therapy with micafungin, and 7 cases (12%) received combination therapy with clindamycin. Fifty-three cases (90%) required varying degrees of respiratory support. Concurrent glucocorticoid therapy was administered in 70% (41/59) of cases at anti-PJP treatment initiation. Fifty-five cases (93%) improved, and 4 cases (7%) died.There were 36 cases in the group with underlying diseases and 23 cases in the group without underlying diseases. No statistically significant differences were observed between the two groups in terms of length of hospital stay, ICU admission rate and length of ICU stay, mechanical ventilation rate, or mortality rate (all P>0.05). Conclusions: Non-HIV-infected children with PJP tend to occur in infants under 3 years old. It is often complicated by underlying diseases such as immunodeficiency, with most patients having a history of glucocorticoid or immunosuppressant use. Clinical manifestations and imaging findings lack specificity, and mNGS facilitates early diagnosis. The core treatment is trimethoprim-sulfamethoxazole, most children require respiratory support, and combination with low-dose glucocorticoids may improve prognosis.},
}

@article {pmid41539854,
year = {2026},
author = {Choi, S and Kwon, H and Kim, WK and Ko, G},
title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510017},
doi = {10.4014/jmb.2510.10017},
pmid = {41539854},
issn = {1738-8872},
mesh = {*Clostridium Infections/microbiology/therapy/prevention & control ; Animals ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; *Clostridioides difficile ; Disease Models, Animal ; Feces/microbiology ; Metagenomics ; },
abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.},
}

*Clostridium Infections/microbiology/therapy/prevention & control
Animals
*Clostridium/physiology/genetics
Gastrointestinal Microbiome
Mice
*Clostridioides difficile
Disease Models, Animal
Feces/microbiology
Metagenomics

@article {pmid41539847,
year = {2026},
author = {Kong, M and Zhou, W},
title = {Clinical characteristics and outcomes of Rickettsia japonica infection: A retrospective case series of five patients.},
journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)},
volume = {44},
number = {1},
pages = {503047},
doi = {10.1016/j.eimce.2025.503047},
pmid = {41539847},
issn = {2529-993X},
mesh = {Humans ; Retrospective Studies ; Middle Aged ; Male ; Aged ; Female ; *Rickettsia Infections/diagnosis/drug therapy/microbiology ; *Rickettsia/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; },
abstract = {OBJECTIVE: To characterize the clinical manifestations of Rickettsia japonica (R. japonica) infection and to generate evidence facilitating early diagnosis and targeted treatment.

METHODS: We retrospectively reviewed the clinical data of five patients with R. japonica infection who were treated in the Emergency Department, Xiling Campus, Yichang Central People's Hospital, between January 2023 and December 2024.

RESULTS: All patients were residents of Yichang City, Hubei Province, aged 58-70 years, and 80% (4/5) were farmers. The onset of illness occurred exclusively between May and September, and all patients reported a definite history of outdoor exposure. The predominant clinical manifestations were fever, rash, and eschar. Laboratory findings revealed thrombocytopenia, elevated aspartate aminotransferase (AST) and creatine kinase (CK), as well as increased inflammatory markers including C-reactive protein (CRP), procalcitonin (PCT), and interleukin-6 (IL-6). R. japonica nucleic acid was detected in all patients by metagenomic next-generation sequencing (mNGS) of blood samples. Three patients initially received empirical doxycycline therapy, which was subsequently adjusted to a standard regimen after diagnostic confirmation. Defervescence occurred at a median of two days (range, 1-7 days), followed by gradual resolution of rash and alleviation of systemic symptoms. All patients achieved complete clinical recovery and were discharged without complications.

CONCLUSION: This study highlights the importance of heightened clinical awareness of R. japonica infection, emphasizing the integration of epidemiological context with hallmark clinical features - particularly fever, rash, and eschar - during peak transmission seasons in endemic areas. Early recognition allows the timely initiation of doxycycline therapy, which is essential for achieving favorable outcomes. Moreover, metagenomic next-generation sequencing (mNGS) provides the definitive identification of pathogens and guides targeted antimicrobial therapy.},
}

Humans
Retrospective Studies
Middle Aged
Male
Aged
Female
*Rickettsia Infections/diagnosis/drug therapy/microbiology
*Rickettsia/isolation & purification
Anti-Bacterial Agents/therapeutic use
Treatment Outcome

@article {pmid41539810,
year = {2026},
author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C},
title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118184},
doi = {10.1016/j.foodres.2025.118184},
pmid = {41539810},
issn = {1873-7145},
mesh = {*Fermentation ; *Moringa oleifera/microbiology/chemistry ; *Taste ; *Plant Leaves/microbiology/chemistry ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Amino Acids/analysis ; *Food Microbiology ; Flavoring Agents ; *Fermented Foods/microbiology ; Bacteria/metabolism/classification/genetics ; Microbiota ; Metagenomics ; Multiomics ; },
abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.},
}

*Fermentation
*Moringa oleifera/microbiology/chemistry
*Taste
*Plant Leaves/microbiology/chemistry
Gas Chromatography-Mass Spectrometry
Volatile Organic Compounds/analysis
Odorants/analysis
Amino Acids/analysis
*Food Microbiology
Flavoring Agents
*Fermented Foods/microbiology
Bacteria/metabolism/classification/genetics
Microbiota
Metagenomics
Multiomics

@article {pmid41539628,
year = {2026},
author = {Peng, Y and Liu, H and Xing, T and Zhen, F and Wu, D and Sun, Y},
title = {Instability mechanisms of overloaded anaerobic digestion: Insights from volatile fatty acid metabolism.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {134006},
doi = {10.1016/j.biortech.2026.134006},
pmid = {41539628},
issn = {1873-2976},
abstract = {To clarify the mechanisms driving process instability under overload stress, a long-term semi-continuous overload instability simulation experiment was conducted. High-throughput sequencing and metagenomics were used to determine the response of the process parameters, community composition, and volatile fatty acid (VFA)-related metabolic functional genes to the organic loading rate (OLR). When the OLR increased to 12.5 kg VS/m[3]/d, the methane yield remained low at 226.40 ± 10.78 mL CH4/g VS. Further increasing the OLR to 20 kg VS/m[3]/d completely destabilized the reactor, resulting in a final methane yield as low as 0.29 mL CH4/g VS, a hydrogen partial pressure as high as 357.37 Pa, and concentrations of butyrate, propionate, and acetate of 4328.49 ± 538.18, 1036.13 ± 75.48, and 9939.67 ± 427.68 mg/L, respectively. Organic overload stress caused reactor instability mainly by blocking VFA metabolism. When the OLR was ≥ 11 kg VS/m[3]/d, the relative abundances of key genes (aceE, buk, ptb, atoD) in the butyrate and propionate metabolic pathways decreased, resulting in the accumulation of butyrate and propionate. Despite a shift in syntrophic acetate oxidation metabolism from the methyl to the carbonyl branch under overload, the latter's recovery was insufficient to compensate for the severe impairment of the methyl branch, ultimately leading to acetate accumulation. VFA accumulation caused severe inhibition of acetogens and some methanogens, while hydrolytic and acidogenic bacteria dominated the microbiome (relative abundance: 94.18 %). As a result, the microbial metabolic balance was broken. Our results provide new insights into the mechanisms driving process instability under overload stress.},
}

@article {pmid41539627,
year = {2026},
author = {Wang, Z and Yang, Y and Qiu, B},
title = {Synergistic improvement of methane production and phosphorus recovery from anaerobic digestion of waste activated sludge by Fe2O3-assisted electroactive microorganisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134004},
doi = {10.1016/j.biortech.2026.134004},
pmid = {41539627},
issn = {1873-2976},
abstract = {Conductive materials and electroactive microorganisms (EAM) are key factors on enhancing methane production in anaerobic digestion of waste actived sludge via the direct interspecies electron transfer (DIET). However, their combined impact on simultaneous methane production and phosphorus recovery remains unclear. The Fe2O3 and EAM were added together to synergistically improve anaerobic processes, resulting in a 1.53-fold increase in methane production and a remarkable 12.03-fold enhancement in phosphorus removal. The co-additon of Fe2O3 and EAM promoted Fe(III/II) redox cycling, increased enzyme activity, and enhanced electron transport system (ETS) functionality while enriching DIET-associated bacteria (e.g., Brooklawnia, Anaerolineae) and methanogens (Methanosarcina). Metagenomic analysis revealed the upregulated genes related to phosphorus and iron metabolism, ETS, and DIET-coupled electron bifurcation. Notably, Fe2O3 may act as an alternative to cytochromes and pili in mediating DIET in electron transfer processes.},
}

@article {pmid41539626,
year = {2026},
author = {Vijande, C and Balboa, S and Lazzari, M and Lema, JM and Pabst, M},
title = {Multi-omics reveals wastewater sludge bacteria with genomic potential to degrade poly(ethylene) terephthalate.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134003},
doi = {10.1016/j.biortech.2026.134003},
pmid = {41539626},
issn = {1873-2976},
abstract = {Plastic pollution is a growing concern, especially poly(ethylene terephthalate) (PET), one of the most produced plastic polymers. Although several microorganisms capable of degrading PET have been identified, little is known about those present in wastewater treatment plants (WWTPs). This study explores their ability to degrade PET and the enzymes involved. Activated sludge from two facilities-one urban WWTP and one industrial WWTP-was cultivated with PET of different crystallinities. The inoculum source primarily determined differences in microbial community composition. Metagenomics revealed more than 300 genes homologous to PET-degrading enzymes in all biofilms; however, metaproteomics confirmed expression of only a few of these enzymes in industrial WWTP-derived biofilms. This inoculum demonstrated the ability to degrade PET breakdown products within 24 h. In addition, FTIR analysis revealed initial signs of surface alteration. In conclusion, this study reveals the presence of microorganisms in industrial wastewater treatment sludge that possess the genetic potential to degrade PET.},
}

@article {pmid41539600,
year = {2026},
author = {Li, W and Guo, H and Wang, Q and Peng, D and Wang, Y and Lu, Z},
title = {Phocaeicola vulgatus promote growth rate via tryptophan metabolism pathway mediated gut sIgA production in Taihe Silky fowl.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.022},
pmid = {41539600},
issn = {2090-1224},
abstract = {INTRODUCTION: Taihe Silky Fowl (TSF) has a long growth cycle and slow growth rate, how to effectively improve the growth rate of TSF has become the primary concern for breeders. Currently, extensive research has established the gut microbiota's role in modulating growth rate of commercial chicken breeds, while the specific microbial mechanisms influencing TSF growth rate remain poorly understood.

OBJECTIVES: Therefore, this study aimed to identify growth rate-associated key microbial species in TSF through multi-omics approaches, experimentally validate their growth-promoting roles via controlled interventions, and elucidate the species-metabolite-host interaction mechanisms.

METHODS: Cecal metagenome and metabolome was used to search for differential key microbiota and metabolites of TSF with different growth rate, the whole genome of key microbiota was used to identify the relationship between microbiota and metabolites, and gavage key microbiota to TSF was used to demonstrate the effectiveness of probiotics and preliminarily explore their mechanisms of action.

RESULTS: Cecal metagenome analysis demonstrated a significant enrichment of Phocaeicola vulgatus (P. vulgatus) in high-growth-rate fowls, Erysipelotrichaceae bacterium was significantly enriched in low-growth-rate fowls. The differential metabolites between the two groups were significantly enriched in tryptophan metabolism pathway. Subsequently, gene analysis revealed that P. vulgatus encoded tryptophan biosynthesis genes. In feeding experiment, oral gavage P. vulgatus improved the TSF final body weight, average growth rate and average daily gain, increased cecal P. vulgatus abundance, enriched the metabolites in tryptophan metabolism pathway both in the cecum and serum, and upregulated cecal tissue gene expression in the 'intestinal immune network for IgA production' pathway resulting in the higher secretory IgA (sIgA) concentrations in cecal tissue and luminal content than the control group.

CONCLUSION: P. vulgatus promoted the growth rate of TSF by optimizing the cecal microbiota, elevating cecal tryptophan metabolites and stimulating sIgA production via sIgA gene upregulation in cecal tissues, thereby enhancing host immune modulation. These findings elucidated the microbiota-metabolite-host axis governing TSF growth regulation, providing both mechanistic insights and practical applications for probiotic-based strategies to enhance growth performance and gut health in this valuable poultry breed.},
}

@article {pmid41539598,
year = {2026},
author = {Wei, S and Li, W and Ran, S and Zhang, J and Zhang, Z and Yang, Z and Tian, F and Chen, L and Hu, P and Yuan, J and Lin, H},
title = {Multi-organ metabolic dysregulation and cecal microbiota alterations following black carbon exposure.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.027},
pmid = {41539598},
issn = {2090-1224},
abstract = {BACKGROUND: Black carbon (BC) has been linked to adverse health outcomes, yet underlying mechanisms remain unclear. Integrating metabolomic and metagenomic data across tissues may clarify BC-induced biological pathways.

METHODS: We performed human epidemiology and mice experimental approaches. We included 248,288 participants with annual BC exposure estimates and plasma metabolomic profiles. Elastic net regression identified BC-associated metabolites. Male C57BL/6J mice were exposed to filtered air or BC (1 mg/m[3], 1 h/day, 5 days/week, 12 weeks). Multi-tissue metabolomics and cecal contents microbiota sequencing were conducted, with histology and gene expression measurements.

RESULTS: In humans, long-term BC exposure significantly altered plasma metabolites, notably increasing saturated fatty acids (β = 0.048), while decreasing docosahexaenoic acid (β = -0.002). Amino acid metabolism was broadly disrupted, involving elevated valine (β = 0.011) and reduced glutamine (β = -0.006). In mice, metabolomic profiling showed organ-specific shifts, including increased glutathione and cortisol in the liver (2.88-fold and 2.06-fold), increased PC(16:0/18:1(9Z)) in the heart (3.22-fold), elevated anandamide and arachidonic acid in the kidney (2.35-fold and 1.48-fold), and decreased multiple fatty acids and lysophospholipids across organs. Cecal microbiota exhibited reduced alpha-diversity (Shannon: 3.67 vs. 4.50, P < 0.05) and taxonomic shifts, including an increased abundance of g_Akkermansia and decrease in g_Bacteroides. Multi-omics integration revealed significant microbiota-metabolome correlations in the cecum and plasma (Mantel r = 0.276, P = 0.012). Histological examination confirmed organ injuries, notably lung inflammation, cardiac edema, and neuronal condensation. Gene expression analysis showed increased Il-6 in the lung (5.35-fold, P = 0.047), increased Mb in the heart (5.18-fold, P = 0.010), and increased Igfbp7 in the kidney (3.03-fold, P = 0.001), while Tjp1 expression in cecum was reduced (0.42-fold, P = 0.004).

CONCLUSIONS: Our findings suggest that BC exposure may alter systemic metabolism and gut microbiota, potentially contributing to tissue injury and inflammation. The gut-organ axis could be a target for mitigating BC-related health effects.},
}

@article {pmid41539568,
year = {2026},
author = {Farhat, I and Kaminski, H and Woerther, PL and Rodriguez, C and Pierre, C and Cheval, J and Korbi, S and Couzi, L and Merville, P and Jambon, F and Moreau, K},
title = {Spiroplasma infection complicated by macrophage activation syndrome and fulminant hepatitis in a kidney transplanted patient.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2026.01.008},
pmid = {41539568},
issn = {1600-6143},
abstract = {A 65-year-old kidney transplant recipient was admitted with isolated fever. Initial tests revealed pancytopenia and elevated C-reactive protein levels but failed to detect any pathogen. A bone marrow aspirate was performed because of signs suggestive of hemophagocytic lymphohistiocytosis (HLH), but results were negative. The patient subsequently developed fulminant hepatitis. Liver biopsy showed severe acute cytolytic hepatitis with a neutrophil-rich infiltrate, suppurative hepatocytic necrosis, and hemophagocytosis. Etoposide, N-acetylcysteine, and piperacillin-tazobactam were initiated. However, the patient died from hemorrhagic complications of the biopsy. Posthumous shotgun metagenomics (SMg) on liver samples identified Spiroplasma ixodetis.},
}

@article {pmid41539526,
year = {2026},
author = {Uddin, G and Song, J and Lu, Z and Chaofie, Z and Sajjad, W and Li, P and Fan, Q},
title = {Microbial Taxonomic and Functional Responses to Heavy Metal Gradients in Mining-Impacted Stream Sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123778},
doi = {10.1016/j.envres.2026.123778},
pmid = {41539526},
issn = {1096-0953},
abstract = {Legacy heavy metal pollution from historical mining restructures sediment microbial composition and function directly impacting contaminant fate and ecosystem health. The Dongdagou stream (Baiyin, China) possesses a pronounced geochemical gradient caused by long-term discharge of potentially toxic metals including Cd, Cu, Pb, and Zn. We employed this natural gradient to characterize microbial taxonomic and functional responses to metal stress. Sediment samples from four zones along the contamination gradient were analyzed for geochemistry, metal concentrations, and microbial composition (bacteria, archaea, and fungi) via high-throughput amplicon sequencing, with functional potential inferred using PICRUSt2. We found that microbial community structure and function were primarily shaped by metal concentration, with db-RDA explaining 18.1%, 12.4%, and 12.9% of the variance for bacteria, archaea, and fungi, respectively. Cadmium was identified as the strongest individual predictor for both bacterial (r[2] = 0.50, p = 0.001) and fungal (r[2] = 0.38, p = 0.001) communities. Bacterial diversity increased significantly downstream as contamination declined, with Shannon diversity increasing from 5.17 in the Source Zone to 6.28 in the Distal Zone (Tukey's multiple comparison test, p < 0.05). Upstream sediments were dominated by metal-tolerant taxa such as Sulfurifustis (17.4%) and Acidithiobacillus (5.0%), while downstream taxa shifted to heterotrophic genera like Gallionella (4.8%) with diverse metabolic capabilities. Despite cadmium being a key predictor, archaeal and fungal communities demonstrated greater compositional stability than bacteria, as shown by their lower beta-dispersion (ANOSIM R = 0.3152 and 0.5762, respectively, compared to 0.7222 for bacteria), indicating potential functional redundancy. Metagenomic predictions revealed a significant enrichment of genes for metal detoxification, anaerobic respiration, and oxidative stress response in polluted zones. These findings establish that microbial communities are both sensitive bioindicators and key mediators of contaminant dynamics, providing a framework for using microbial signatures to assess sediment health and monitor remediation efficacy.},
}

@article {pmid41539415,
year = {2026},
author = {Liu, P and He, G and Guo, Z and Tang, Y and Tan, Z and Song, Y and He, T and Lee, SL},
title = {Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer.},
journal = {Genomics},
volume = {},
number = {},
pages = {111204},
doi = {10.1016/j.ygeno.2026.111204},
pmid = {41539415},
issn = {1089-8646},
abstract = {Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78,p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.},
}

@article {pmid41539238,
year = {2026},
author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K},
title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106371},
doi = {10.1016/j.psj.2026.106371},
pmid = {41539238},
issn = {1525-3171},
abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.},
}

@article {pmid41539094,
year = {2026},
author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z},
title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157804},
doi = {10.1016/j.phymed.2026.157804},
pmid = {41539094},
issn = {1618-095X},
abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.

PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.

METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.

RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.

CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.},
}

@article {pmid41538947,
year = {2026},
author = {Zhang, X and Feng, Y and Jiang, X and Sun, W and Zhang, C and Han, J and Hou, Y and You, X and Zhang, H and Wang, X and Wu, X and Wang, J},
title = {Unveiling hidden risks of chiral fungicide benzovindiflupyr: Stereoselectivity in soil antibiotic resistance gene transmission.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141088},
doi = {10.1016/j.jhazmat.2026.141088},
pmid = {41538947},
issn = {1873-3336},
abstract = {Antibiotic resistance gene (ARG) dissemination is closely associated with modern agricultural practices. However, the stereoselective effects of widely applied chiral pesticides on resistance evolution remain insufficiently investigated. This study systematically explored the differential effects of benzovindiflupyr enantiomers on transmission of ARGs through long-term soil incubation experiments combined with metagenomic and in vitro studies. Results demonstrated that 1S,4R-enantiomer exhibited significantly longer half-life than 1 R,4S-enantiomer. 1 R,4S-enantiomer induced extreme enrichment of a few ARGs. 1S,4R-enantiomer persistently increased abundance of multiple ARGs. Compared with 1 R,4S-enantiomer, 1S,4R-enantiomer more consistently enhanced abundance of mobile genetic elements (MGEs) related to conjugative transfer. Moreover, 1 R,4S-enantiomer primarily enriched specific genera within Pseudomonadota. 1S,4R-enantiomer simultaneously promoted abundance of multiple genera across both Pseudomonadota and Bacteroidota, driving cross-phylum genera to correlate with shared ARGs. Genomic analysis confirmed that Pseudomonadota under 1S,4R-enantiomer treatment carried more ARGs and MGEs. In vitro transformation experiments ultimately validated that 1S,4R-enantiomer significantly enhanced transformation efficiency across multiple ARGs consistently, substantially exceeding 1 R,4S-enantiomer effects. Overall, 1S,4R-enantiomer poses more significant risks for horizontal transfer of ARGs. This study elucidates enantioselective effects of chiral pesticides on transmission of ARGs, providing a foundation for improving chiral agrochemical risk assessment.},
}