@article {pmid41574342,
year = {2025},
author = {Feng, Q and Liu, B and Liu, H and Fan, Y and Gao, S and Zhang, J and Kuang, Y and Wang, W and Liang, H and Qiu, Y and Wen, H and Feng, Z and Huang, Y and Zuo, W and Zhang, X and Zeng, J and Wu, J and Liang, Y and Gu, J},
title = {The application value and limitations of metagenomic detection technology based on cerebrospinal fluid samples in suspected central nervous system infection: a retrospective study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689253},
pmid = {41574342},
issn = {1664-302X},
abstract = {BACKGROUND: Accurately diagnosing central nervous system (CNS) infections remains challenging. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) in diagnosing suspected CNS infections and its role in facilitating rapid and accurate pathogen identification.

METHODS: This retrospective study enrolled cerebrospinal fluid specimens from 246 patients with suspected CNS infections and 20 controls with definitively ruled-out infections. Using clinical diagnoses established by an expert panel based on comprehensive criteria as the reference standard, we evaluated the diagnostic performance of mNGS relative to culture and conventional tests. Additionally, we analyzed the therapeutic guidance value of positive mNGS results and risk factors for false negatives.

RESULTS: mNGS showed 73.2% (180/246) agreement with clinical diagnosis, superior to culture (54.1%, 133/246) and conventional methods (61.4%, 151/246). For general bacteria and fungi, mNGS showed 61.9% (26/42) concordance with culture. False negatives in mNGS predominantly involved viral missed detection. Age, presence of systemic infection, headache, and cerebrospinal fluid glucose levels were likely key determinants of mNGS performance. mNGS detection of Epstein-Barr virus, Streptococcus spp., Mycobacterium tuberculosis complex, herpes simplex virus type 1, and Staphylococcus spp. suggested high pathogenic potential, whereas Torque teno virus detection more likely indicated carriage or experimental contamination.

CONCLUSION: mNGS holds significant value for the diagnosis, therapeutic management, and prognostic assessment of suspected CNS infections.},
}

@article {pmid41574341,
year = {2025},
author = {Destras, G and Sabatier, M and Bal, A and Simon, B and Semanas, Q and Regue, H and Boyer, T and Ploin, D and Gillet, Y and Lina, B and Anani, H and Josset, L},
title = {Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1685035},
pmid = {41574341},
issn = {1664-302X},
abstract = {INTRODUCTION: Omics-based studies focusing on a single kingdom, such as bacterial 16S gene sequencing, viral metagenomics, and human mRNA sequencing, are commonly used to explore the microbiome and its association with host responses. But combining these approaches is often expensive and time-consuming. Metatranscriptomics provides a snapshot of the entire active microbiome through bulk RNA sequencing in a single test, yet its performance relative to kingdom-specific methods has not been systematically assessed.

METHODS: We compared metatranscriptomics with three kingdom-specific sequencing approaches in 20 nasopharyngeal aspirates from infants 7 months of age hospitalized for bronchiolitis at the Hospices Civils de Lyon.

RESULTS: Applying specific sequencing depth thresholds (≥1,000 bacterial reads, ≥100,000 human reads, and detection of an internal RNA control), metatranscriptomics showed high detection concordance and correlated abundance for RNA viruses and human coding genes. Metatranscriptomics also detected RNA from both eukaryotic and prokaryotic DNA viruses, suggesting potential for identifying transcriptional activity. For the bacteriome, 82% of genera exceeding 0.5% relative abundance were captured, revealing distinct transcriptional profiles at the species level. Metatranscriptomics reproduced multi-omics-derived host-microbiome endotypes and revealed stronger key microbial associations, particularly for transcriptionally active microorganisms.

DISCUSSION: These findings indicate that a single metatranscriptomics run can complement or replace kingdom-specific approaches for profiling RNA viruses and the host transcriptome, while also identifying transcriptionally active bacteria and DNA viruses. Low-abundance or latent microorganisms may still require targeted assays. Metatranscriptomics thus provides a cost- and time-efficient strategy for integrated microbiome research and holds promise for clinical applications in acute infections and cases of diagnostic uncertainty.},
}

@article {pmid41574306,
year = {2025},
author = {Guo, S and Wang, L and Sai, X and Tang, S and Wang, J and Wang, A and Qiu, D and Han, S and Wu, Y and Chen, C},
title = {Effect of BALF-based mNGS on clinical outcomes of immunocompromised subjects with opportunistic pulmonary infections: a multicenter propensity score-matched study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1724935},
pmid = {41574306},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Immunocompromised Host ; Aged ; Propensity Score ; *Opportunistic Infections/diagnosis/microbiology/drug therapy/mortality ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; Treatment Outcome ; Aged, 80 and over ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a promising tool for pathogen detection. However, its clinical utility in detecting opportunistic pulmonary infections of immunocompromised patients remains controversial.

METHODS: This multicenter retrospective study involving 162 immunocompromised patients with opportunistic pulmonary infections was conducted across four respiratory centers. The enrolled patients were divided into the conventional microbiological tests (CMT) group and the mNGS group based on whether mNGS of BALF was performed after admission. Propensity score-matching (PSM) was adopted to minimize selection bias, and sensitivity analysis confirmed the robustness. The primary outcomes were >30% improvement in oxygenation index (OI) at 7 days post-admission and clinical improvement by day 14 as assessed with the WHO 7-category ordinal scale. Secondary outcomes included 21-day mortality, incidence of septic shock during hospitalization, and pathogen detection rate.

RESULTS: Among the 110 patients who underwent mNGS, the results prompted modifications to the antibiotic therapy in 89 patients (80.9%), encompassing both escalation and de-escalation of therapy. The remaining 52 patients received only CMT. After the PSM, 41 matched pairs were further analyzed. Compared to the CMT group, OI improvement >30% on day 7 was more frequent in the mNGS group (41.5% vs. 9.8%, P = 0.001). Clinical improvement on day 14 in the mNGS group was higher than in the CMT group (36.6% vs. 9.8%, P = 0.004). Additionally, BALF mNGS was associated with decreased 21-day mortality (7.3% vs. 34.1%; P = 0.003) in patients with opportunistic pulmonary infections, while showing no significant association with reduced incidence of septic shock during hospitalization. Moreover, the causative pathogen detection rate was significantly higher in the mNGS group compared to the CMT group (97.6% vs. 22.0%, P<0.001), demonstrating the superior diagnostic yield of mNGS.

CONCLUSION: Our study indicated that early BALF mNGS testing upon admission was associated with improved OI up to day 7, clinical improvement on day 14, and decreased 21-day mortality. These benefits are likely facilitated by the higher diagnostic yield of mNGS and its direct impact on guiding targeted antibiotic therapy.},
}

Humans
Retrospective Studies
Male
Female
Middle Aged
*Immunocompromised Host
Aged
Propensity Score
*Opportunistic Infections/diagnosis/microbiology/drug therapy/mortality
*Bronchoalveolar Lavage Fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Adult
Treatment Outcome
Aged, 80 and over

@article {pmid41574290,
year = {2025},
author = {Chen, J and Gong, G and Su, X and Song, X and Zhang, J and Wu, P and Wang, H and Shan, T and Zhang, W},
title = {Viral metagenomic analysis of fecal samples from Bos grunniens on the Qinghai-Tibet Plateau reveals novel picornaviruses and diverse CRESS-DNA viruses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719300},
pmid = {41574290},
issn = {2235-2988},
mesh = {*Feces/virology ; Animals ; Phylogeny ; *Metagenomics ; *DNA Viruses/genetics/classification/isolation & purification ; Tibet ; Cattle/virology ; *Virome ; *Picornaviridae/genetics/classification/isolation & purification ; Genome, Viral ; China ; },
abstract = {INTRODUCTION: The Qinghai-Tibet Plateau (QTP), one of the most extreme environments on Earth, provides a unique natural setting for exploring viral diversity and evolution under conditions of high altitude, hypoxia, and intense ultraviolet radiation. The yak (Bos grunniens), a key endemic ruminant species of the QTP, plays an essential ecological and economic role, yet its fecal virome remains poorly characterized.

METHODS: In this study, we analyzed 43 yak fecal samples collected from Yushu, Qinghai Province, and constructed nine metagenomic libraries to investigate the composition, diversity, and phylogenetic characteristics of the yak fecal virome.

RESULTS: Metagenomic sequencing generated approximately 463 million raw reads, of which 2.87 million were classified as viral. The viral reads in the sequenced libraries were primarily composed of single-stranded DNA viruses (92.46%), particularly members of Smacoviridae, Circoviridae, and Genomoviridae, whereas RNA viruses such as Picornaviridae accounted for a minor fraction (0.71%). Phylogenetic analyses revealed that several circular single-stranded DNA (CRESS-DNA) virus and picornavirus genomes share high similarity with known ruminant-associated viruses, while forming independent evolutionary clades, suggesting potential cross-species transmission among plateau animals. The large-scale divergence within Smacoviridae further reflects extensive lineage expansion under the plateau's extreme environmental pressures.

DISCUSSION: Compared with our previous yak virome study, this work provides independent and complementary insights into the genomic and evolutionary characteristics of key viral taxa. Overall, our findings expand the genomic landscape of the yak fecal virome and highlight the Qinghai-Tibet Plateau as an important reservoir for exploring viral diversity, evolution, and host-environment interactions in extreme ecosystems.},
}

*Feces/virology
Animals
Phylogeny
*Metagenomics
*DNA Viruses/genetics/classification/isolation & purification
Tibet
Cattle/virology
*Virome
*Picornaviridae/genetics/classification/isolation & purification
Genome, Viral
China

@article {pmid41574217,
year = {2026},
author = {Rulhania, A and Panigrahi, S and Swami, S and Singh, Y and Balyan, P and Singh, KP and Mir, RR and Kumar, U},
title = {Identification and expression analysis of putative genomic regions disseminating biotic stress tolerance in chickpea (Cicer arietinum).},
journal = {3 Biotech},
volume = {16},
number = {2},
pages = {81},
pmid = {41574217},
issn = {2190-572X},
abstract = {UNLABELLED: Chickpea (Cicer arietinum L.) productivity is heavily constrained by major biotic stresses, particularly Fusarium wilt, Ascochyta blight and Botrytis gray mold, which collectively cause significant annual yield losses worldwide. To develop a refined understanding of the genetic architecture underlying resistance to these pathogens, a comprehensive meta-analysis was conducted using 113 QTLs taken from 24 independent studies, including diverse mapping populations. This analysis led to the identification of 27 MQTLs, which represent both novel genomic regions and, crucially, refined positions of previously known QTLs with reduced confidence intervals. Four robust Breeders' MQTLs were identified on the basis of high phenotypic variance (PVE ≥ 10%), a low confidence interval (CI ≤ 2 cM) and the involvement of multiple initial QTLs. Among these breeder MQTLs, 229 candidate genes, including key players in plant defense, such as receptor-like kinases (RLKs), resistance gene analogues (RGAs) and genes for RML1A, HSPRO2 and endochitinase A, were identified. These genes were validated through qRT‒PCR expression profiling in contrasting genotypes (WR-315 and JG-62). These refined genomic regions and their associated markers provide a direct pathway for pyramiding multiple resistance QTLs through marker-assisted selection and provide a direct pathway to breed chickpea varieties with durable, broad-spectrum resistance to key fungal diseases. The integrated meta-genomic framework significantly enhances precision and utility and paves the way for the functional characterization of the underlying resistance mechanisms.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04698-y.},
}

@article {pmid41574048,
year = {2026},
author = {Ru, SS and Li, W and Hao, J and Cao, CY and Ma, L and Zhang, X},
title = {Evaluation of the diagnostic value of metagenomic next-generation sequencing for zoonotic cestode Spirometra mansoni infection.},
journal = {Food and waterborne parasitology},
volume = {42},
number = {},
pages = {e00316},
pmid = {41574048},
issn = {2405-6766},
abstract = {Metagenomic next-generation sequencing (mNGS) technology offers substantial advantages in parasite detection; however, we still know very little about its diagnostic value for Spirometra mansoni infection. In this study, mNGS technology was used to analyse faecal samples and blood samples from cats infected with S. mansoni, as well as tissue samples and blood samples from mice infected with the plerocercoid larvae of S. mansoni. Moreover, polymerase chain reaction (PCR) was employed to validate the mNGS results. The diagnostic value of mNGS for S. mansoni infection was systematically evaluated. The mNGS results revealed that the read counts of S. mansoni in the cat faeces (CF) samples were 301,497 (CF1), 1,330,549 (CF2), 1,181,162 (CF3), and 0 (CF0), with relative abundances of 3.17%, 16.64%, 13.14%, and 0%, respectively. In the mouse tissue (MT) samples, the read counts of S. mansoni were 10,791 (MT1), 438 (MT2), 3697 (MT3), and 10 (MT0), with relative abundances of 67.21%, 3.65%, 21.12%, and 0.16%, respectively. No sequences of S. mansoni were detected in the cat blood samples or mouse blood samples. The PCR results were consistent with the mNGS results, confirming the accuracy of the mNGS analysis. In addition, during the detection process, the assembly-based analysis did not detect sequences of S. mansoni in all samples. In contrast, the read-based analysis successfully detected the target sequences without fail. Finally, the analysis of microbiota diversity in the definitive host faecal samples revealed that compared with those in the control group, the elevated microbial taxa in the infected group mainly were probiotics, such as Prevotella copri and Bifidobacterium adolescentis. Conversely, the decreased microbial populations were primarily associated with certain diseases, such as Collinsella stercoris and Catenibacterium sp. In this study, the diagnostic value of mNGS for S. mansoni infection was systematically evaluated. These findings establish a foundation for the more precise application of mNGS technology in the detection of S. mansoni and related cestode infections.},
}

@article {pmid41572901,
year = {2026},
author = {Hock, L and Luiken, R and Valério, E and Vargha, M and Vierheilig, J and Börjesson, S and Pitkänen, T and Schmitt, H},
title = {Integrating AMR surveillance into wastewater monitoring systems in 2025: a position on the implementation of Article 17 of the Urban Wastewater Treatment Directive (UWWTD).},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {31},
number = {3},
pages = {},
doi = {10.2807/1560-7917.ES.2026.31.3.2500289},
pmid = {41572901},
issn = {1560-7917},
mesh = {*Wastewater/microbiology ; Humans ; *Water Purification/legislation & jurisprudence/methods ; European Union ; *Environmental Monitoring/methods ; Europe ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Public Health ; Water Microbiology ; },
abstract = {The recast Urban Wastewater Treatment Directive (UWWTD) calls for monitoring antimicrobial resistance (AMR) in wastewater of large European agglomerations (≥ 100,000 person equivalents). Guidance on scope and methods is currently in development. Two European Joint Actions share a goal to harmonise procedures and indicators: the European Union (EU)-Wastewater Integrated Surveillance for Public Health (EU-WISH), aiming to strengthen wastewater-based surveillance (WBS) for public health and the EU-Joint Action Antimicrobial Resistance and Healthcare Associated Infections (EU-JAMRAI) 2, providing among others, approaches for environmental surveillance of AMR. An EU-WISH survey in 2024, mapping WBS AMR-related activities across Europe, revealed that of 27 countries surveyed, 11 had an operative AMR WBS system and mainly employed WBS to determine AMR trends, primarily through culture-based analyses, in-depth characterisation of specific bacteria, and quantitative PCR for specific resistance genes. Occasionally metagenomics was used. We argue that prioritising AMR WBS targets should consider the intended objectives of surveillance, which could include uncovering AMR trends and emerging AMR determinants in humans, the assessment of antimicrobial/AMR environmental release, and wastewater treatment efficiency. Targets should be assessed for their public health relevance and the usefulness of complementary information they provide, while integrating measurability, resource efficiency, and expertise from different One Health domains.},
}

*Wastewater/microbiology
Humans
*Water Purification/legislation & jurisprudence/methods
European Union
*Environmental Monitoring/methods
Europe
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial
Public Health
Water Microbiology

@article {pmid41572827,
year = {2026},
author = {Xu, B and Liu, P and Yan, N and Wang, T and Liu, L and Cheng, Y},
title = {Multi-omics insights into gut microbial dysbiosis and metabolic alterations in immune checkpoint inhibitor-induced thrombocytopenia.},
journal = {Immunotherapy},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/1750743X.2026.2618937},
pmid = {41572827},
issn = {1750-7448},
abstract = {BACKGROUND: Immune checkpoint inhibitors-induced thrombocytopenia (ICIs-TCP) is a rare immune-related adverse events (irAEs). The physiological changes underlying ICIs-TCP remain incompletely elucidated.

METHODS: We performed multi-omics analysis (gut microbiome, plasma metabolomics/proteomics) comparing microbial/metabolic alterations in cancer patients with (n = 8) and without ICIs-TCP (n = 8). Fecal metagenomic shotgun sequencing was performed to assess microbial composition and function, while plasma metabolomics and proteomics analyses identified systemic metabolic and protein expression changes associated with ICIs-TCP.

RESULTS: Patients with ICIs-TCP exhibited distinct gut microbiota profiles, with an increased abundance of Segatella, Prevotella, and Clostridium, alongside a depletion of Bacteroides and Roseburia. Functional analysis revealed significant downregulation of metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism. Plasma metabolomics identified reduced arginine levels and disruptions in key amino acid and energy metabolism pathways, suggesting systemic arginine depletion. Proteomic analysis further demonstrated down-regulation of folate hydrolase 1 (FOLH1), a key enzyme in glutamate metabolism, implicating metabolic dysregulation in TCP pathogenesis.

CONCLUSION: The depletion of arginine and associated metabolic disruptions are associated with ICIs-TCP and may represent a potential therapeutic target for mitigating TCP risk in patients receiving ICIs.},
}

@article {pmid41572814,
year = {2026},
author = {Fathima, N and Mascarenhas, R and Umar, D and Rekha, PD and Shetty, S and Amin, V},
title = {Impact of removing fixed orthodontic appliances on oral microbial dysbiosis: A longitudinal study and metagenomic sequencing analysis.},
journal = {Journal of orthodontics},
volume = {},
number = {},
pages = {14653125251408048},
doi = {10.1177/14653125251408048},
pmid = {41572814},
issn = {1465-3133},
abstract = {OBJECTIVE: To investigate the impact of appliance removal on oral microbial diversity, composition, and abundance using metagenomic sequencing. It aims to identify the core microbiome and assess changes between mid-treatment and 2 weeks after debonding to better understand the relationship between orthodontic therapy and oral health.

METHODS: This longitudinal cohort study recruited 26 patients undergoing fixed orthodontic treatment between January 2022 and June 2023. Saliva samples were collected at two predefined time points: mid-treatment (T0, defined as before appliance removal) and 2 weeks after debonding (T1). Microbial DNA was extracted and the V1-V3 hypervariable regions of the 16S rRNA gene were sequenced using Illumina NovaSeq. Bioinformatics analysis was performed using QIIME and the SILVA database to evaluate microbial diversity and composition at T0 and T1. Beta diversity metrics and statistical tests, including PERMANOVA and Wilcoxon signed-rank tests, were applied to identify significant differences (P < 0.05). Effect sizes with 95% confidence intervals (CIs) were reported.

RESULTS: The analysis revealed significant shifts in microbial diversity and composition between T0 and T1. A total of 189 species across 63 genera were identified, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria as dominant phyla. Genera such as Fusobacterium periodonticum (↑ 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (↑ 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (↓ 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (↓ 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).

CONCLUSION: This study demonstrated significant microbial shifts between mid-treatment and 2 weeks after debonding, including increases in potentially pathogenic genera and alterations in the core microbiome. These findings indicate microbial changes persist for at least 2 weeks after appliance removal. Further research with pre-treatment baselines and extended follow-up is required to better define the long-term trajectory of these changes.},
}

@article {pmid41572438,
year = {2026},
author = {Maes, M and Almulla, AF and Vasupanrajit, A and Jirakran, K and Tunvirachaisakul, C and Maes, A and Chancham, P and Klomkliew, P and Payungporn, S and Zhang, Y},
title = {Functional Shotgun Metagenomic Insights into Gut Microbial Pathway and Enzyme Disruptions Linking Metabolism, Affect, Cognition, and Suicidal Ideation in Major Depressive Disorder.},
journal = {Acta neuropsychiatrica},
volume = {},
number = {},
pages = {1-47},
doi = {10.1017/neu.2026.10056},
pmid = {41572438},
issn = {1601-5215},
abstract = {BACKGROUND: Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune-metabolic processes.

AIMS: To identify gut microbial alterations in MDD and to quantify functional pathways and enzyme gene families and integrate these with the clinical phenome and immune-metabolic biomarkers of MDD.

METHODS: Shotgun metagenomics with taxonomic profiling was performed in MDD versus controls using MetaPhlAn v4.0.6, and functional profiling was conducted using HUMAnN v3.9, aligning microbial reads to species-specific pangenomes (Bowtie2 v2.5.4) followed by alignment to the UniRef90 v201901 protein database (DIAMOND v2.1.9).

RESULTS: Gut microbiome diversity, both species richness and evenness, is quite similar between MDD and controls. The top enriched taxa in the multivariate discriminant profile of MDD reflect gut dysbiosis associated with leaky gut and NIMETOX mechanisms, i.e., Ruminococcus gnavus, Veillonella rogosaem and Anaerobutyricum hallii. The top four protective taxa enriched in controls indicate an anti-inflammatory ecosystem and microbiome resilience, i.e., Vescimonas coprocola, Coprococcus, Faecalibacterium prausnitzii, and Faecalibacterium parasitized. Pathway analysis indicates loss of barrier protection, antioxidants and short-chain fatty acids, and activation of NIMETOX pathways. The differential abundance of gene families suggests that there are metabolic distinctions between both groups, indicating aberrations in purine, sugar, and protein metabolism. The gene and pathway scores explain a larger part of the variance in suicidal ideation, recurrence of illness, neurocognitive impairments, immune functions, and atherogenicity.

CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.},
}

@article {pmid41572348,
year = {2026},
author = {He, W and Yu, Z and Wu, Z and Olesen, AK and Madsen, JS and Dechesne, A and Smets, BF and Nesme, J and Sørensen, SJ},
title = {Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {39},
pmid = {41572348},
issn = {2049-2618},
support = {NNF 200C0062223//Novo Nordisk Foundation Data Science Collaborative Research Programme 2020/ ; DARWIN project #7044-00004B//Joint Programming Initiative-Antimicrobial Resistance grant/ ; },
mesh = {*Plasmids/genetics ; *Wastewater/microbiology ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Spain ; Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Denmark ; *Drug Resistance, Bacterial/genetics ; Europe ; Whole Genome Sequencing ; Humans ; },
abstract = {BACKGROUND: Urban wastewater systems (UWSs) act as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs), with plasmids playing a central role in their spread. Despite their significance, the diversity and persistence of plasmids in UWSs remain underexplored.

RESULTS: This study applies a multi-omics approach, including metagenomic and direct plasmidome sequencing, high-throughput qPCR array, and whole genome sequencing of plasmid isolates, to comprehensively profile the microbial plasmidome and resistome on 78 samples across UWSs in Denmark, Spain, and the UK. We successfully uncovered an extensive plasmid and ARG diversity that could not be fully captured by a single method, especially identified 78,574 plasmids, including 20,925 plasmids previously unreported. We also observed that plasmids carried a disproportionate share of clinically relevant ARGs, particularly beta-lactamase resistance genes; most importantly, they were preferentially located on transmissible plasmids. Furtherly, plasmids harbor ARG can enhance their persistence in wastewater ecosystems, especially harboring multiple types of ARGs. Moreover, Bacteroides emerged as a unique persistent ARG reservoir not only for harboring and disseminating diverse resistance genes especially in residential-relevant areas, but also emerged as a major driver of antimicrobial resistance dynamics across different wastewater treatment processes.

CONCLUSIONS: Overall, this work provides the first attempt at a holistic description of the UWSs' resistome, its structure, dynamics, and mobility and significantly expands the current knowledge. Video Abstract.},
}

*Plasmids/genetics
*Wastewater/microbiology
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
Spain
Metagenomics/methods
*Drug Resistance, Microbial/genetics
Denmark
*Drug Resistance, Bacterial/genetics
Europe
Whole Genome Sequencing
Humans

@article {pmid41572308,
year = {2026},
author = {Natalia, Z and Aleksandra, S and Egor, S and Ksenia, K},
title = {Bacteriophages in gut metagenomes: from analysis to application.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03069-6},
pmid = {41572308},
issn = {1743-422X},
support = {23-75-10125//Russian Science Foundation/ ; 23-75-10125//Russian Science Foundation/ ; 23-75-10125//Russian Science Foundation/ ; 23-75-10125//Russian Science Foundation/ ; },
abstract = {Bacteriophages constitute a major component of the human gut virome, playing very important roles in shaping of the structure and function of the gut microbiota. Moreover, bacteriophages interact with the human immune system, thereby influencing various disease processes. Recent advancements in metagenomic sequencing and computational analysis have substantially expanded our understanding of gut phage diversity and the scale of the so-called 'viral dark matter'. In this review, we summarize current bioinformatic approaches for identifying and annotating bacteriophage sequences in metagenomic data, discuss key challenges in taxonomic classification and host prediction of phages, as well as the limitations associated with the assembly and analysis of viral metagenome-assembled genomes (vMAGs). We also analyze the therapeutic potential of bacteriophages, including their application in cancer immunotherapy, inflammatory diseases, and liver diseases, and their promise as diagnostic and prognostic biomarkers.},
}

@article {pmid41572158,
year = {2026},
author = {Wijaya, SC and Richi, M and Waturangi, DE and Yulandi, A},
title = {Linking metagenomic insight to cultivable microbes: isolation of a vitamin B12-producing Sphingomonad from Indonesian tempeh.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04681-2},
pmid = {41572158},
issn = {1471-2180},
}

@article {pmid41570777,
year = {2026},
author = {Wang, Z and Lu, J and Wang, X and An, W and Zhao, Y and Han, B and Tao, H and Liu, J and Guo, J and Wang, J},
title = {Long-term pet ownership promotes resistome similarity between cats and their owners.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110074},
doi = {10.1016/j.envint.2026.110074},
pmid = {41570777},
issn = {1873-6750},
abstract = {Pet ownership offers physical and mental health benefits, but the risks of antibiotic resistance genes (ARGs) transmission between pets and humans remain underexplored. In this study, we used metagenomics analysis of fecal samples to compare resistome profiles among four groups: owned cats and their owners, and caged cats and non-cat owners. Our findings show significant similarities in gut microbial composition, ARGs, and mobile genetic elements (MGEs) between owned cats and their owners, identifying 73 shared core ARGs and 80 shared MGEs. In contrast, caged cats and non-cat owners shared only 30 ARGs and 73 MGEs. Long-term contact was positively correlated with a higher number of shared ARGs (from 20 + to 60 +) and MGEs (from 10 + to 40 +), as well as increased resistome risk (2.47- to 4.92-fold) between pet cats and owners. The gut microbiota played a key role in shaping the ARGs and MGEs profiles, with Escherichia coli and Klebsiella pneumoniae identified as primary carriers, each genome harboring 20 to 62 ARGs and 6 to 29 MGEs. ARGs transfer events were more frequent between pet cats and their owners than in other groups. These findings underscore a potential risk of shared antimicrobial resistance between companion animals and humans within the studied population in China.},
}

@article {pmid41570646,
year = {2026},
author = {Sidikjan, N and Li, Y and Chen, Y and Guo, XP and Liu, M and Huang, Y},
title = {Multimedia profiling of metal resistance genes in the Yangtze Estuary: Biofilm dominance and community-driven regulatory pathways.},
journal = {Ecotoxicology and environmental safety},
volume = {310},
number = {},
pages = {119769},
doi = {10.1016/j.ecoenv.2026.119769},
pmid = {41570646},
issn = {1090-2414},
abstract = {Biofilms are critical microbial assemblages that function as sinks and potential reservoirs of metal resistance genes (MRGs) in contaminated aquatic systems. In this study, metagenomic sequencing and environmental profiling were employed to characterize MRGs distribution, heavy metal contamination, and microbial community structure across water, sediment, and biofilm samples in the Yangtze Estuary. Biofilms exhibited significantly higher concentrations of heavy metals and MRGs than other matrices, particularly for key genes such as corS (Cu-resistance), nrsS (Ni-resistance), and pbrA (Pb-resistance). Ecological risk assessment identified cadmium as the primary risk contributor, especially in biofilms. Partial redundancy analysis revealed that microbial community composition was the dominant factor shaping MRGs distribution, rather than metal concentrations alone. Network and canonical correspondence analyses further demonstrated strong co-occurrence patterns between MRGs and antibiotic resistance genes (ARGs), regulated by eutrophication (TN, Chl-a) and heavy metals (Pb, Cd, Cu). Notably, Pb-resistance genes in biofilm communities were significantly enriched and closely associated with Cyanobacteria and Proteobacteria, reflecting a multi-stage co-occurrence pattern potentially involving pbrT, pbrA, cadD, and czcD. These findings highlight the ecological significance of biofilms in MRGs enrichment, dissemination, and risk propagation in estuarine ecosystems under combined pollution stress.},
}

@article {pmid41570514,
year = {2026},
author = {Yan, S and Ahmad, HA and Xie, Y and Liu, S and Wu, J and Cui, J and Yang, B and Su, L and Ding, T and Liu, T},
title = {Metagenomic insights into the trophic gradient influence on nitrogen cycling microbiomes in plateau lakes.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119288},
doi = {10.1016/j.marpolbul.2026.119288},
pmid = {41570514},
issn = {1879-3363},
abstract = {The increasing prevalence of nitrogen (Nr) pollution in lake ecosystems is a growing global concern. Understanding the dynamics of Nr-cycling microbial communities in these environments is crucial for assessing how ecosystem processes and functions respond to trophic gradients. This study investigates the microbial Nr-metabolism in plateau lakes with varying trophic states across a broad geographical range. A detailed metagenomic study revealed that increasing trophic status index (TSI) reduced the α-diversity of Nr-cycling microbial communities, while TSI and altitude jointly shaped the β-diversity patterns. The Nr-cycling microorganisms predominantly belonged to the phylum Proteobacteria, with the most abundant functional genes associated with organic Nr degradation and synthesis, dissimilatory/assimilatory nitrate reduction to ammonium (DNRA and ANRA), and denitrification processes (DNiF). Key Nr functional genes exhibited differential enrichment across lakes, indicating changes in Nr-metabolism strategies along the trophic gradient. A total of 126 metagenome-assembled genomes (MAGs) contributed to Nr-cycling, with the majority assigned to Proteobacteria (36) and Planctomycetes (25). Among these, MAG110 was enriched in eutrophic lakes and possessed near-complete DNiF and ANRA pathways, while MAG115, predominant in oligotrophic lakes, relied solely on ANRA. This functional divergence reflects trophic-specific ecological adaptations, that denitrification is favored in nutrient-rich, low-oxygen conditions and Nr- retention is prioritized under Nr-limited environments. Moreover, enzymes like nitronate monooxygenase (encoded by both genomes) and nitroalkane oxidase highlight a novel metabolic interaction between Nr-transformations and organic C1 compound oxidation in freshwater ecosystems. Overall, this study highlights the complex relationship among trophic status, microbial diversity, and Nr-metabolism in lake ecosystems.},
}

@article {pmid41570486,
year = {2026},
author = {Lahariya, R and Anand, G and Kumari, B and Priyadarshi, K},
title = {Postbiotics and the gut-brain axis: A mechanistic review on modulating neuroinflammation and cognitive aging.},
journal = {Journal of neuroimmunology},
volume = {413},
number = {},
pages = {578870},
doi = {10.1016/j.jneuroim.2026.578870},
pmid = {41570486},
issn = {1872-8421},
abstract = {Aging triggers gut microbiota dysbiosis that disrupts the gut-brain axis (GBA), promoting neuroinflammation and neurodegeneration. Elderly exhibit reduced microbial diversity, depleted beneficial bacteria, and expanded pathobionts, elevating neurotoxic metabolites-lipopolysaccharides (LPS), trimethylamine-N-oxide, kynurenine derivatives, and secondary bile acids. These drive "inflammaging," blood-brain barrier breakdown, microglial activation, mitochondrial impairment, and proteinopathies in Alzheimer's and Parkinson's disease. Conversely, neuroprotective metabolites from commensals-short-chain fatty acids, indole-3-propionic acid, and urolithins-preserve gut integrity, suppress inflammation, upregulate BDNF for synaptic plasticity, and enhance mitophagy. Postbiotics, stable probiotic-derived bioactives (butyrate, polyphenol metabolites, and lactate derivatives), surpass live probiotics in safety and precision. They modulate GBA via histone deacetylase inhibition, GPR41/43 signaling, NF-κB blockade, and microglial M2 shift, blocking LPS translocation and bolstering neuronal resilience. Preclinical rodent studies demonstrate robust neuroprotection, but human translation reveals challenges: inter-individual microbiota variability (diet/genetics/comorbidities), inconsistent metabolite absorption/brain penetration between species, methodological limitations (16S rRNA vs. functional metagenomics), postbiotic standardization barriers, and sparse Phase I/II trials showing biomarker benefits without cognitive endpoints. This review synthesizes gut dysbiosis-metabolite-brain aging mechanisms, positioning postbiotics as precision therapeutics. Multi-omics stratified controlled trials are essential to validate long-term efficacy for delaying neurodegeneration and extending cognitive health.},
}

@article {pmid41570402,
year = {2026},
author = {Nitert, MD and Sternes, PR and Altemani, F and Callaway, LK and McIntyre, H and Tyson, GW and Barrett, HL},
title = {Gut microbiota is different before the development of preeclampsia.},
journal = {Pregnancy hypertension},
volume = {43},
number = {},
pages = {101415},
doi = {10.1016/j.preghy.2026.101415},
pmid = {41570402},
issn = {2210-7797},
abstract = {OBJECTIVES: The gut microbiota contributes to the regulation of blood pressure during and outside pregnancy. Preeclampsia (PE) is characterised by the development of hypertension along with renal, liver or other systemic complications. In women with PE, alterations in the gut microbiota composition have been reported.

STUDY DESIGN: We investigated whether changes in the gut microbiota composition were present before the onset of symptoms in a group of 10 women who developed late-onset PE and 24 women who remained normotensive throughout pregnancy. Faecal samples were obtained at 28 weeks' gestation from a subset of participants of the Study of PRobiotics IN Gestational diabetes (SPRING) and sequenced by metagenomic sequencing.

MAIN OUTCOME MEASURES: Taxonomic and functional characteristics were compared between the groups.

RESULTS: There were no taxonomic or functional differences in alpha diversity; however, for beta diversity, women who developed PE demonstrated a different taxonomic composition compared to women who remained normotensive. Women who developed PE had lower abundance of numerous taxa and functions. Both systolic and diastolic blood pressure were correlated with the abundances of specific species, though members of the same genus did not show consistency in the direction of correlation.

CONCLUSION: Despite a limited sample size, this study demonstrates numerous taxonomic and functional alterations in the gut microbiota composition. However, a clear signature to identify women at high risk of developing late-onset PE remains to be uncovered. The species-level data indicate that the regulation of blood pressure by the gut microbiota in pregnancy is complex and needs further investigation.},
}

@article {pmid41570020,
year = {2026},
author = {Beuker, C and Schulte-Mecklenbeck, A and Wirth, T and Kleffner, I and Thomas, C and Strunk, D and Schmidt-Pogoda, A and Gross, CC and Klotz, L and Minnerup, J},
title = {Spontaneous cervical artery dissection is associated with a distinct peripheral immune cell signature.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0340592},
pmid = {41570020},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; *Leukocytes, Mononuclear/immunology ; Case-Control Studies ; *Vertebral Artery Dissection/immunology ; Killer Cells, Natural/immunology ; },
abstract = {OBJECTIVES: Despite being a major cause of ischemic stroke in young adults, the biological underpinnings of cervical artery dissection (CeAD) remain poorly defined. Recent data implicate immune activation as a potential contributor. We aimed to determine whether patients with CeAD display a distinct peripheral immune signature, which may provide insights into pathogenic inflammatory processes.

METHODS: Peripheral blood mononuclear cells (PBMCs) from patients with spontaneous CeAD (n = 7 without and n = 11 with ischemic stroke) and ten age-matched healthy controls were analyzed via multi-color flow cytometry. Immune cell composition and activation markers were assessed, and sparse partial least squares discriminant analysis (sPLS-DA) was employed to identify CeAD-associated immune features. A secondary comparison with ischemic stroke controls was included to assess the specificity of identified immune alterations.

RESULTS: Compared to healthy controls, CeAD patients displayed increased frequencies of CD4 ⁺ T cells and decreased natural killer T (NKT) cells. sPLS-DA demonstrated clear separation of CeAD and control immune profiles, driven by increased CD28 expression on naïve CD8 ⁺ T cells, NKp46 on NK cells, and IL-2Rα (CD25) on myeloid dendritic cells (mDC2). Elevated granzyme K in naïve CD8 ⁺ T cells indicated enhanced cytotoxic potential, while regulatory T cells were diminished. These alterations were largely preserved when compared to ischemic stroke controls, suggesting CeAD-specific immune activation. No microbial pathogens were detected by untargeted metagenomic sequencing.

DISCUSSION: CeAD is associated with a distinct peripheral immune signature characterized by enhanced cytotoxic activity and reduced regulatory features. These alterations may reflect a post-infectious autoimmune mechanism triggering CeAD or a secondary immune-inflammatory response to vascular injury. Larger, longitudinal studies are needed to clarify causality and assess whether immune modulation could serve as a therapeutic target in CeAD.},
}

Humans
Male
Female
Middle Aged
Adult
*Leukocytes, Mononuclear/immunology
Case-Control Studies
*Vertebral Artery Dissection/immunology
Killer Cells, Natural/immunology

@article {pmid41569365,
year = {2026},
author = {Duarte, M and Mansilha, C and Melo, A and Sobral, D and Ferreira, R and Gomes, JP and Rebelo, H and Veber, A and Puskar, L and Schade, U and Jordao, L},
title = {Detection of polycyclic aromatic hydrocarbons, microplastic presence and characterization of microbial communities in the soil of touristic zones at Alqueva's edges (Alentejo, Portugal).},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41569365},
issn = {1614-7499},
abstract = {Environmental pollution is a growing concern. Here, we assessed the occurrence of two groups of persistent organic pollutants (POPs-polycyclic aromatic hydrocarbons (PAHs) and microplastics (MPs)) and bacterial populations in the topsoil of three tourist spots located at the Alqueva's edges during 1 year, once per season. Soil chemical analysis revealed low content of total organic carbon, pH close to neutrality, and nitrogen and phosphorus levels consistent with acquisition of these nutrients only by atmospheric deposition. PAH's concentrations were in the range of ng/kg, being significantly below the "reference values" for contaminated soils. Nevertheless, potentially carcinogenic PAHs, detected at all locations, raise ecotoxicological concerns. Polyamide, polyester, polystyrene, and styrene acrylonitrile resin MPs were found. Six bacterial phyla constitute the core microbiome in the three locations and include genera of bacteria reported as plastic degraders, such as Bacillus, Exiguobacterium, Paenibacillus, and Pseudomonas. The presence of POPs, even at low levels, in the soil at the edges of a water reservoir should be monitored. The identification of bacteria reported as plastic degraders in the soil, and previously in the water, is promising, and their ability to spontaneously ensure the detoxification of the ecosystem should be further investigated.},
}

@article {pmid41569097,
year = {2026},
author = {Ayala-Montaño, S and Afolayan, AO and Kociurzynski, R and Loeber, U and Reuter, S},
title = {Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001609},
pmid = {41569097},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; Humans ; Computational Biology/methods ; *DNA Contamination ; *Metagenome ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Infant, Newborn ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; },
abstract = {Metagenomic sequencing of clinical samples has significantly enhanced our understanding of microbial communities. However, microbial contamination and host-derived DNA remain a major obstacle to accurate data interpretation. Here, we present a methodology called 'Stop-Check-Go' for detecting and mitigating contaminants in metagenomic datasets obtained from neonatal patient samples (nasal and rectal swabs). This method incorporates laboratory and bioinformatics work combining a prevalence method, coverage estimation and microbiological reports. We compared the 'Stop-Check-Go' decontamination system with other published decontamination tools and commonly found poor performance in decontaminating microbiologically negative patients (false positives). We emphasize that host DNA decreased by an average of 76% per sample using a lysis method and was further reduced during post-sequencing analysis. Microbial species were classified as putative contaminants and assigned to 'Stop' in nearly 60% of the dataset. The 'Stop-Check-Go' system was developed to address the specific need of decontaminating low-biomass samples, where existing tools primarily designed for short-read metagenomic data showed limited performance.},
}

*Metagenomics/methods
Humans
Computational Biology/methods
*DNA Contamination
*Metagenome
Microbiota/genetics
Sequence Analysis, DNA/methods
Infant, Newborn
High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification

@article {pmid41568738,
year = {2026},
author = {Warren, A and Wynia, Z and Corr, PG and Devin, MF and Celikkol, Z and Gordon, L and Farah, M and Karam, M and Villarreal, D and Jackson, SA and Frame, LA},
title = {The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e71023},
pmid = {41568738},
issn = {1552-5279},
support = {//TMCity/ ; },
mesh = {Humans ; *Cognitive Dysfunction/microbiology ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; *Brain ; },
abstract = {Alzheimer's disease (AD) is projected to become the highest-burden neurological disorder globally. Mounting evidence implicates the gut microbiome in AD pathogenesis. This scoping review of gut microbiomes in mild cognitive impairment (MCI) and AD included dietary and probiotic interventions. We included original research and systematic reviews/meta-analyses. Animal and non-English studies were excluded. We searched PubMed, Scopus, and Cochrane Library through February 2023. Using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-Extension for Scoping Reviews (ScR) checklist, we screened 4751 articles, with 58 meeting predefined inclusion criteria. Our results demonstrated that gut dysbiosis was frequently reported in MCI and AD, including increased Pseudomonadota and Actinomycetota in AD and reduced diversity in some cases. Probiotic and dietary interventions showed promise in modulating cognition and microbiota, inconsistently. Emerging evidence links dysbiosis to cognitive decline; however, methodological heterogeneity and limited follow-up impede causal inference. Research should prioritize standardized protocols, functional microbiome analysis, and longitudinal human studies to clarify therapeutic potential. HIGHLIGHTS: Gut dysbiosis is a common feature of MCI and AD, with phylum-level microbial shifts frequently observed. Pseudomonadota and Actinomycetota are enriched in AD across multiple human studies. Beneficial genera like Faecalibacterium and Roseburia are consistently reduced in MCI and AD in a small number of studies. Probiotic and dietary interventions are promising to modulate the microbiota-cognition axis. More longitudinal human studies are needed to assess causal microbiome relationships.},
}

Humans
*Cognitive Dysfunction/microbiology
*Alzheimer Disease/microbiology
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
Probiotics/therapeutic use
*Brain

@article {pmid41568321,
year = {2026},
author = {Yahyapour, A and Najafi, A and Ahmadi, A and Salarizadeh, N},
title = {Immunoprotective and neuroprotective properties of gut microbiome in psoriasis.},
journal = {Journal of translational autoimmunity},
volume = {12},
number = {},
pages = {100348},
pmid = {41568321},
issn = {2589-9090},
abstract = {Psoriasis impacts nearly 100 million people globally and is associated with neuropsychiatric comorbidities such as depression and anxiety. With gut microbiome dysbiosis serving as a primary pathophysiological factor, the gut-brain-skin axis provides a crucial framework for understanding this relationship. This review evaluates the mechanisms of the gut-brain-skin axis in psoriasis pathophysiology and assesses the therapeutic potential of microbiome-based treatments, combining preclinical, clinical, and multi-omics data. Patients with psoriasis show specific gut dysbiosis patterns, including reduced microbial diversity, lower SCFA-producing bacteria (especially Faecalibacterium and Akkermansia), and increased pro-inflammatory bacteria. This microbial imbalance damages intestinal barrier integrity, triggers systemic inflammation, activates cutaneous Th17 pathways, and induces neuroinflammation through blood-brain barrier disruption. Axis communication occurs through immune-inflammatory mechanisms mediated by SCFAs and neuroendocrine pathways involving microbially-derived neurotransmitters (GABA, serotonin, dopamine). Metagenomic research indicates functional deficiencies in neurotransmitter and SCFA synthesis pathways are more significant than taxonomic alterations. Machine learning models can utilize these functional features to identify patients at risk for neuropsychiatric comorbidities and predict treatment response. Recent randomized controlled trials demonstrate that targeted interventions (probiotics, prebiotics, postbiotics, fecal microbiota transplantation) significantly improve Psoriasis Area and Severity Index scores, inflammatory markers, and microbiota composition. The evidence supports a shift toward integrated microbiome strategies, emphasizing functional approaches including mitochondrial therapies, psychobiotics, precision nutrition, and multi-omics-guided therapies.},
}

@article {pmid41568044,
year = {2025},
author = {Kan, Y and Ma, XY and Wang, YL and Sun, B and Wang, S},
title = {A comprehensive comparison of web-based tools for amplicon-metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1711000},
pmid = {41568044},
issn = {1664-302X},
abstract = {Amplicon sequencing provides a suitable approach for microbiome profiling, supported by a variety of R-based and web-based tools. In this review, we systematically evaluated eight freely accessible web-based tools suitable for users without scripting experience, comparing their performance across modules including alpha and beta diversity, taxonomic composition, differential comparison, network and correlation analysis, functional profiling, machine learning, tree-plot and user experience. While all tools exhibit limited data filtering and normalization options, performance varied considerably across modules. Mian and MicrobiomeAnalyst 2.0 excelled in alpha diversity analysis and taxonomic composition analysis, METAGENassist outperformed others in beta diversity, and MicrobiomeAnalyst 2.0 achieved the highest score in differential comparison and functional analysis. Namco and Mian outperform in network analysis and correlation analysis, respectively. Machine-learning functions were comparable across animalcules, MicrobiomeAnalyst 2.0 and METAGENassist, with the best treeplot visualization in animalcules and MicrobiomeAnalyst 2.0. And, user experience was highest for animalcules and Mian. Overall, MicrobiomeAnalyst 2.0 achieving the highest overall performance, followed by Mian and Namco. Several limitations among evaluated tools include inconsistent accessibility, diverse input data formats, restricted feature sets, and incomplete retention of key information in exported figures. Future development should integrate preprocessing, interactive visualization and figure export, alongside advanced statistical methods, multi-omics integration and meta-analytical capabilities, to enhance flexibility, reproducibility and interpretability. This comprehensive assessment provides a practical reference for researchers in selecting the most suitable web-based tools for specific microbiome analysis tasks, highlighting the importance of both module-specific performance and overall tool capabilities.},
}

@article {pmid41568034,
year = {2025},
author = {Yu, F and Song, J and Qi, L and Liu, J and Yang, Y and Li, W and Li, L and Ma, ZS},
title = {Gene and function diversity-area relationships in the inflammatory bowel disease fecal and mucosal microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1660973},
pmid = {41568034},
issn = {1664-302X},
abstract = {The diversity-area relationship (DAR), an extension of the classic species-area relationship (SAR), provides a powerful framework for understanding how biodiversity scales across space. In this study, we applied DAR and its metagenomic counterpart (m-DAR) to investigate the spatial scaling of metagenomic genes (MGs) and metagenomic functional gene clusters (MFGCs) of seven functional databases in the gut microbiomes of individuals with inflammatory bowel disease (IBD) and healthy cohorts. Using shotgun sequencing data from 42 mucosal and 22 fecal samples from both healthy and IBD cohorts, we modeled how this MGs and MFGCs accrues with area (samples), estimating diversity scaling parameters (z), pair-wise diversity overlap (PDO), and maximal accrual diversity (MAD), which reflects the total potential diversity. We found that mucosal communities exhibited greater dissimilarity (less pair-wise diversity overlap) between individuals than fecal cowmmunities at the levels of gene richness and evenness (q = 1, 2), whereas fecal communities showed a stronger influence from dominant, abundant genes (q = 2, 3). Furthermore, healthy gut microbiomes showed greater similarity than those of IBD at the level of gene richness (q = 0), but showed greater dissimilarity at the level of abundant genes and dominant genes. Healthy gut microbiomes generally demonstrated a higher potential total diversity compared to those from IBD patients. Notably, fecal samples captured a broader range of microbial diversity than mucosal samples. Additionally, mucosal communities showed greater dissimilarity than fecal communities in almost all the MFGCs of the seven databases except ARDB, which showed the same trend as MGs. We also identified that specific functional clusters related to antibiotic resistance, such as genes for chloramphenicol and vancomycin resistance, displayed distinct scaling behaviors, suggesting their potential role in IBD pathogenesis. These findings demonstrate that the gut microbiome in IBD is not merely less diverse but is fundamentally restructured in its spatial architecture. The application of DAR provides a novel, quantitative insight to diagnose and understand this dysbiosis, moving beyond simple diversity metrics to capture the spatial diversity scaling of microbial genes and functions.},
}

@article {pmid41567631,
year = {2025},
author = {Wang, S and Hu, Y and Li, X and Ou, Y and Chen, J and Chen, Y and Chen, J and Bai, K and Xu, F and Wang, X and Du, H and Yuan, D and Yang, Z and Yuan, J and Niu, H},
title = {Gut microbiota-dependent anti-inflammatory mechanisms of berberine in ameliorating hypertension: role of SCFAs, LPS reduction, and STAT3 signaling.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1696934},
pmid = {41567631},
issn = {1663-9812},
abstract = {BACKGROUND: Hypertension is a chronic disease closely related to vascular remodeling, inflammatory response and intestinal flora disorders. Traditional Chinese medicines, especially Rhizoma Coptidis, are becoming increasingly popular as a possible cardioprotective drug. Berberine, the main active ingredient of Rhizoma Coptidis, has various pharmacological activities, but its specific mechanism of regulating blood pressure through intestinal flora is not clear.

METHODS: In this study, the potential targets of berberine were predicted using network pharmacology, and its antihypertensive mechanism was validated in spontaneously hypertensive rats (SHR). A comprehensive evaluation integrating non-invasive blood pressure measurement, echocardiography, histological analyses (H&E and Masson staining), immunohistochemistry, qPCR, metagenomic sequencing, and untargeted metabolomics was performed to investigate the effects of berberine on cardiovascular remodeling, intestinal barrier integrity, gut microbial composition, and metabolic profiles.

RESULTS: Network pharmacology screened 160 common targets of berberine and hypertension, among which STAT3 may play a key role. Animal experiments confirmed that berberine significantly reduced SHR blood pressure and improved aortic fibrosis and cardiac function. In addition, berberine repaired intestinal barrier damage, upregulated ZO-1 and Occludin expression, and significantly altered the structure of the intestinal flora, increasing the abundance of Short-chain fatty acids (SCFAs) - producing bacteria (e.g., Marvinbryantia, Bacteroides), while decreasing pro-inflammatory bacteria (e.g., Mycoplasma, Treponema). Metabolomics analysis showed that berberine increased fecal SCFAs levels and decreased serum Lipopolysaccharide (LPS). Molecular docking and experimental validation showed that berberine attenuated the inflammatory response by inhibiting STAT3 activation and decreasing colonic IL-6 expression.

CONCLUSION: Berberine exerts antihypertensive effects by regulating the gut flora-SCFAs-LPS-IL6-STAT3 axis, improving intestinal barrier function, and reducing systemic inflammation. This study provides a new mechanistic basis for berberine treatment of hypertension.},
}

@article {pmid41567008,
year = {2026},
author = {Zhao, S and Rogers, MJ and Ding, C and He, J},
title = {Stable Function, Dynamic Phylotypes: Microdiversity as a Reservoir for Resilience in Dehalococcoides.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c14525},
pmid = {41567008},
issn = {1520-5851},
abstract = {Organohalide-respiring bacteria (OHRB) are key contributors to global halogen cycling and mitigation of anthropogenic halogenated pollutants, yet their persistence is challenged by slow growth and restricted metabolic capacity. The mechanisms supporting long-term functional stability remain unclear. As a key OHRB, Dehalococcoides faces similar constraints, including declining abundance and loss or divergence of functional genes in bioaugmentation. Here we demonstrate that strain-level microdiversity within Dehalococcoides supports the resilience of community-scale dehalogenation. In AEDhc, a reconstructed consortium derived from eight Dehalococcoides-containing enrichment cultures, sequencing of a Dehalococcoides-specific marker gene revealed 30 distinct Dehalococcoides phylotypes coexisting within the community. Despite fluctuations in phylotype abundance over successive transfers, AEDhc consistently debrominated tetra- and pentabrominated diphenyl ethers (0.39 ± 0.06 - 0.45 ± 0.05 μM Br[-]/d), producing no detectable accumulation of intermediates. Proteomics analyses revealed that among 71 putative reductive dehalogenase (RDase) genes identified in metagenomic analysis, expression was consistently dominated by PcbA1-like and TceA-like RDases across transfers. These findings demonstrated that Dehalococcoides phylotypes can coexist and fluctuate dynamically even under constant cultivation conditions, with genetic variation serving as a reservoir of metabolic potential. Such microdiversity enhances functional stability and ecological resilience, highlighting the need to consider strain-level heterogeneity in bioremediation strategies.},
}

@article {pmid41566339,
year = {2026},
author = {Fernández-Trapote, E and Cobo-Díaz, JF and Oliveira, M and Puente, A and Berdejo, D and Puente, H and Cordero-García, R and López, M and Prieto, M and Argüello, H and Alvarez-Ordóñez, A},
title = {Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02288-3},
pmid = {41566339},
issn = {2049-2618},
support = {FPU21/03421//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; PRE2021-098910//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; CNS2022-136066//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; No 818368//European Commission under the European Union´s Horizon 2020/ ; PID2020-118813GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {BACKGROUND: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing.

RESULTS: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found.

CONCLUSIONS: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.},
}

@article {pmid41565819,
year = {2026},
author = {Ricci, L and Heidrich, V and Punčochář, M and Armanini, F and Ciciani, M and Nabinejad, A and Fazaeli, F and Piperni, E and Servais, C and Pinto, F and Valles-Colomer, M and Asnicar, F and Segata, N},
title = {Baby-to-baby strain transmission shapes the developing gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41565819},
issn = {1476-4687},
abstract = {The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life[1-3], but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic survey to model microbiome transmission in the nursery setting among babies attending the first year, their educators and their families (n = 134 individuals). We performed dense longitudinal microbiome sampling (n = 1,013 faecal samples) during the first year of nursery and tracked microbial strain transmission within and between nursery groups across 3 different facilities. We detected extensive baby-to-baby microbiome transmission within nursery groups even after only 1 month of nursery attendance, with nursery-acquired strains accounting for a proportion of the infant gut microbiome comparable to that from family by the end of the first term. Baby-to-baby transmission continued to grow over the nursery year, in an increasingly intricate transmission network with single strains spreading in some classes, and with multiple baby-acquisition and species-transmissibility patterns. Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers, while antibiotic treatment was the condition that most accounted for the increased influx of strains. This study shows that microbiome transmission between babies is extensive during the first year of nursery, and points to social interactions in infancy as crucial drivers of infant microbiome development.},
}

@article {pmid41565669,
year = {2026},
author = {Schneeberger, PHH and Dommann, J and Rahman, N and Hürlimann, E and Sayasone, S and Ali, S and Coulibaly, JT and Keiser, J},
title = {Profound taxonomic and functional gut microbiota alterations associated with trichuriasis: cross-country and country-specific patterns.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00911-1},
pmid = {41565669},
issn = {2055-5008},
support = {101019223/ERC_/European Research Council/International ; },
abstract = {The human gut microbiota is vital for immune function, metabolism, and resistance to pathogens. Soil-transmitted helminths like Trichuris trichiura can disrupt this microbial community, but the extent and functional significance of these disruptions across diverse regions remain unclear. We investigated the impact of T. trichiura infection on gut microbiota composition and function in three endemic regions-Côte d'Ivoire, Laos, and Tanzania-using standardized, high-resolution metagenomic profiling. Our findings reveal consistent depletion of key short-chain fatty acid (SCFA) producers, including Blautia sp. MSJ 9 and Holdemanella biformis, and enrichment of mucin-degrading genera such as Ruminococcus and Bacteroides. These changes coincided with increased microbial utilization of host-derived carbohydrates and destabilization of microbial networks, notably with the emergence of Segatella copri in infected individuals. Although taxa-level responses varied by region, similar trends in SCFA depletion and mucin degradation were observed across sites, pointing to a potentially shared metabolic response to infection. These alterations suggest compromised gut barrier function and immune modulation, potentially promoting parasite persistence. Our results underscore the potential of microbiome-based strategies, such as targeted probiotics or dietary interventions, to support helminth control by restoring microbial balance and improving host resilience.},
}

@article {pmid41565402,
year = {2026},
author = {Zhou, Y and Wang, H and Guo, L and Liu, X and Wang, X and Liu, Y and Shang, M and Zheng, B and Li, K and Liu, L and Li, J and Ding, G},
title = {Human umbilical cord MSC-derived exosomes attenuate radiation-induced pulmonary fibrosis via remodeling the gut-lung axis in mice.},
journal = {Life sciences in space research},
volume = {48},
number = {},
pages = {204-215},
doi = {10.1016/j.lssr.2025.11.011},
pmid = {41565402},
issn = {2214-5532},
mesh = {*Exosomes/metabolism ; Humans ; Animals ; Mice ; *Mesenchymal Stem Cells/cytology/metabolism ; *Pulmonary Fibrosis/etiology/therapy ; *Umbilical Cord/cytology ; Gastrointestinal Microbiome ; *Lung/radiation effects/metabolism/pathology ; Male ; Mice, Inbred C57BL ; },
abstract = {OBJECTIVE: To investigate whether human umbilical cord mesenchymal stem cell-derived exosomes (hUC-MSC-Exos) attenuate radiation-induced pulmonary fibrosis (RIPF) through modulation of the gut-lung axis.

METHODS: The therapeutic efficacy of hUC-MSC-Exos was evaluated in a mouse model of RIPF through histopathology and western blot analysis of fibrosis markers (α-SMA, Vimentin, and E-cadherin). Gut barrier integrity (ZO-1, Occludin) and intestinal inflammation (IL-6, IL-1β) were examined using immunohistochemistry, RT-qPCR, and ELISA. Gut microbial composition and metabolic profiles were characterized via metagenomics and untargeted metabolomics, followed by integrated bioinformatics analyses to identify key pathways and metabolites.

RESULTS: hUC-MSC-Exos significantly reduced pulmonary collagen deposition and restored fibrosis markers expression, concomitant with enhanced gut barrier function and attenuated intestinal inflammation. Multi-omics analysis revealed restoration of gut microbiota homeostasis and metabolic reprogramming, with the alanine, aspartate, and glutamate pathway being notably co-regulated. L-Glutamic acid was the most significantly altered metabolite and correlated significantly positively with the severity of pulmonary fibrosis and gut dysfunction. Gut microbiota associated with L-Glutamic acid (e.g., Duncaniella, Ruminococcus) were also significantly restructured.

CONCLUSIONS: hUC-MSC-Exos attenuate RIPF through a comprehensive remodeling of the gut-lung axis, in which L-Glutamic acid and its associated microbiota serve as potential mediators. These findings highlight the gut-lung axis as a promising therapeutic target for RIPF.},
}

*Exosomes/metabolism
Humans
Animals
Mice
*Mesenchymal Stem Cells/cytology/metabolism
*Pulmonary Fibrosis/etiology/therapy
*Umbilical Cord/cytology
Gastrointestinal Microbiome
*Lung/radiation effects/metabolism/pathology
Male
Mice, Inbred C57BL

@article {pmid41564978,
year = {2026},
author = {Yuan, C and Jin, P and He, Z and Guo, J and Xiong, M and Sun, J and Wang, L and Wang, Z and Han, N and Feng, W and Hou, Y and Qi, H and Jia, Z},
title = {Maxing Shigan Decoction serves as a Key component of Lianhua Qingwen in Alleviating Lung and Gut Injury by Restoring Gut Microbiota Homeostasis and Inhibiting Inflammation via TLR4/NF-κB and JAK2/STAT3 dual Regulation.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108285},
doi = {10.1016/j.micpath.2026.108285},
pmid = {41564978},
issn = {1096-1208},
abstract = {Lianhua Qingwen (LHQW), a clinically validated herbal medicine containing Maxing Shigan Decoction (MXSGT) and others, shows broad efficacy in various respiratory disease. However, its regulatory role on the gut-lung axis, particularly the contribution of its MXSGT components, remains unexplored. This study employed a formula-disassembled approach to decipher this mechanism. Three preparations, including the complete LHQW prescription, LHQW excluding MXSGT components (LHQW-MXSGT), and MXSGT along, were administered to LPS-induced acute lung injury and DSS-induced ulcerative colitis to evaluate their therapeutic effects via the gut-lung axis. Pathological changes, mucosal barrier integrity, inflammatory cell infiltration and pro-inflammatory cytokine levels were evaluated by H&E staining, histochemical staining, immunofluorescence, ELISA, RT-qPCR and western blot. Metagenomic analysis (16S rDNA sequencing) was conducted to examine their regulatory role of gut microbiota. Network pharmacology analysis and cellular validation was employed to explore their underlying mechanisms. Our analyses demonstrated that LHQW and MXSGT, but not LHQW-MXSGT, significantly attenuated lung/intestinal pathology damage, reduced pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), and restored gut barrier proteins (ZO-1, Occludin, MUC2). LHQW/MXSGT suppressed pathogenic bacteria (Escherichia coli, Salmonella, Klebsiella pneumoniae) while enriching Akkermansia muciniphila, correlating with decreased systemic LPS. Network pharmacology and subsequent validation identified dual inhibition of TLR4/NF-κB and JAK2/STAT3 pathways as key mechanism of MXSGT. In conclusion, MXSGT serves a pivotal pharmacologically active component of LHQW for its gut-lung axis regulation, acting through gut microbiota homeostasis restoration, intestinal barrier integrity maintenance, and anti-inflammatory signaling pathways, providing compelling scientific evidence supporting LHQW's potential therapeutic application in managing diseases characterized by comorbid gut and lung inflammation.},
}

@article {pmid41564676,
year = {2026},
author = {Liu, J and Zhang, W and Wang, R and Wu, S and Bai, X and Wang, X and Zhu, W and Ding, C},
title = {Functional decoupling between plant remediation efficacy and microbial metal resistance in iron tailings: A Robinia pseudoacacia-driven paradox.},
journal = {Ecotoxicology and environmental safety},
volume = {310},
number = {},
pages = {119760},
doi = {10.1016/j.ecoenv.2026.119760},
pmid = {41564676},
issn = {1090-2414},
abstract = {Mining-derived iron tailings pose severe ecotoxicological risks through soil degradation and persistent heavy metal contamination. This study evaluates the ecorestoration potential of three tree species-Populus davidiana, Robinia pseudoacacia, and Rhus typhina-in iron tailings from China's Huluyu Iron Mine. Using an integrated assessment combining soil quality index (SQI), enzymatic activities, metagenomics, and partial least squares path modeling (PLS-PM), we demonstrate that Robinia pseudoacacia achieved the highest SQI (0.68) by significantly mitigating metal stress, which was associated with a marked reduction in soil pH (to 6.29). This acidification is consistent with the well-documented role of root exudates in legumes, alongside enhancing nutrient accumulation (total carbon: 24.8 g/kg; total nitrogen: 1.5 g/kg), and stimulating sucrase and phosphatase activities. Paradoxically, Robinia pseudoacacia soils exhibited minimal enrichment of microbial metal resistance genes, challenging the prevailing "Rhizosphere Synergy Hypothesis." Instead, Robinia pseudoacacia's efficacy relied on functional decoupling from microbial metal detoxification pathways, favoring metabolic optimization of carbon/nitrogen cycling and organic acid-driven pH regulation. PLS-PM confirmed soil chemical properties (pH, total carbon, nitrogen) and enzymatic activities as direct positive drivers of SQI (p < 0.05), while heavy metal content exerted significant negative effects (r = -0.55, p < 0.001). These findings establish RP as an optimal species for iron tailings restoration, reconciling soil fertility enhancement with a potential reduction in metal bioavailability mediated by soil acidification. We propose a predictive SQI framework for selecting remediation species in metalliferous environments, offering critical insights into sustainable management of mining-associated ecotoxicological risks.},
}

@article {pmid41564537,
year = {2026},
author = {Asokan, S and Damilare, II and Kumar, S and Pandey, RK and Verma, G and Banerjee, N and Radhamanalan, G and Vijayan, S and Jacob, T and Rajeswary, D},
title = {From pandemic influenza to novel coronaviruses: emerging infectious diseases of the 21st century.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {4},
pages = {117277},
doi = {10.1016/j.diagmicrobio.2026.117277},
pmid = {41564537},
issn = {1879-0070},
abstract = {Emerging infectious diseases have risen significantly in the twenty-first century as ecological disruption, climate change, expanding human-animal interfaces, and global mobility intensify opportunities for pathogen transmission. This review synthesizes historical and contemporary evidence across viral, bacterial, fungal, and parasitic threats to characterize how diverse pathogens emerge and spread. Foundational events such as the 1918 influenza pandemic, mid-century influenza pandemics, the emergence of HIV/AIDS, and the eradication of smallpox provide context for understanding modern disease dynamics. In recent decades, coronaviruses including SARS, MERS, and SARS-CoV-2, pandemic H1N1, avian influenza subtypes, and major arboviruses such as dengue, chikungunya, Zika, West Nile virus, and yellow fever have demonstrated the rapidity with which zoonotic pathogens can disseminate globally. Viral hemorrhagic fevers including Ebola, Marburg, Lassa, and Crimean-Congo hemorrhagic fever remain critical threats, especially in regions with limited health-care capacity. Concurrently, antimicrobial resistance, the emergence of Candida auris, and the climate-driven expansion of endemic mycoses involving Histoplasma, Coccidioides, and Blastomyces highlight the increasing importance of fungal pathogens. Parasitic diseases such as artemisinin-resistant malaria, zoonotic trypanosomiasis, and expanding Leishmania transmission reflect shifting ecological conditions. These patterns are shaped by intersecting drivers including deforestation, wildlife trade, agricultural intensification, urban crowding, conflict, and rapid microbial evolution that enable spillover and sustained transmission. Although advances in genomic surveillance, metagenomic diagnostics, mRNA vaccines, monoclonal antibodies, and broad-spectrum antivirals have strengthened global response capacity, substantial gaps persist in equity, surveillance, and access to countermeasures. Strengthening One Health systems and resilient public health infrastructures is essential to anticipate and mitigate emerging infectious threats.},
}

@article {pmid41564488,
year = {2026},
author = {Huang, Z and Shen, J and Wang, J and Wang, C and Liu, H and Tian, C and Feng, J and Wang, X},
title = {Seasonal dynamics of sedimentary dissolved organic matter in plateau lakes: Driving effects on microbial community and functional genes in elements cycling.},
journal = {Journal of environmental management},
volume = {399},
number = {},
pages = {128688},
doi = {10.1016/j.jenvman.2026.128688},
pmid = {41564488},
issn = {1095-8630},
abstract = {Plateau lakes, as sensitive zones to global climate change and critical hubs for land-water carbon exchange, remain understudied in terms of the seasonal dynamics of their sedimentary dissolved organic matter (DOM) and its interactions with microbial ecological function. This study employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic techniques to unravel the seasonal variations of DOM and their regulatory roles in microbial community and elements cycling. During the dry season, low water temperature (WT), dissolved oxygen (DO), and high electrical conductivity (EC) promoted accumulation of lignin-like and carboxyl-rich aliphatic molecules (CRAMs), with Fuxian Lake exhibiting the strongest sequestration. The subsequent wet period raised microbial biomass carbon (MBC) and easily oxidizable organic carbon (EOC), lowered average mass-to-charge ratios and increased both nominal hydrogen-to-carbon ratios (H/C) and the molecular lability index (MLB%). Labile sugars and peptides enhanced microbial α-diversity, whereas refractory compounds selected for specialist taxa and intensified community differentiation. Random forest identified sugars, peptides, O3S + O5S, biological index (BIX), and WT as core drivers of element cycling genes expression. Functional gene modules diverged along trophic status. The oligotrophic deep lake underwent seasonal turnover, whereas the eutrophic shallow lake preserved stable supermodules integrating multiple metabolic pathways to buffer perturbations. Anthropogenic disturbances elevated sulfur/nitrogen-containing heteroatomic compounds and threatened sediment carbon sinks and element cycling balance. This study advances the understanding of DOM-driven biogeochemical cycles and provides a scientific framework for managing multi-element interactions in climatically sensitive plateau lakes.},
}

@article {pmid41563943,
year = {2026},
author = {Xiong, HF and Zhang, WT and Liu, Y and Hou, F and Liu, B and Cui, TT and He, ZY and Zhang, X and Zhao, R and Sun, LY},
title = {Successful Use of Sulbactam-Durlobactam in Treating Carbapenem-Resistant Acinetobacter baumannii Pneumonia and Sepsis After Liver Transplantation: A Case Report.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e949738},
doi = {10.12659/AJCR.949738},
pmid = {41563943},
issn = {1941-5923},
mesh = {Humans ; Female ; *Liver Transplantation/adverse effects ; *Acinetobacter Infections/drug therapy ; *Acinetobacter baumannii/drug effects ; *Sulbactam/therapeutic use ; *Sepsis/drug therapy/microbiology ; Young Adult ; Carbapenems/pharmacology ; *Postoperative Complications/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/drug therapy/microbiology ; },
abstract = {BACKGROUND Orthotopic liver transplantation is the primary treatment for end-stage liver disease; however, postoperative infections, especially those caused by carbapenem-resistant Acinetobacter baumannii (CRAB), remain a major cause of mortality due to limited therapeutic options. Sulbactam-durlobactam (SUL-DUR), a novel b-lactam/b-lactamase inhibitor combination, has shown potent activity against CRAB. This report describes the first reported use of SUL-DUR in a liver transplant recipient with CRAB pneumonia and sepsis. CASE REPORT A 22-year-old woman with acute liver failure underwent auxiliary liver transplantation. Postoperatively, she developed CRAB pneumonia and septicemia confirmed by imaging, bronchoscopy, and metagenomic next-generation sequencing. She received combination therapy with SUL-DUR (1 g/1 g every 8 h), meropenem, eravacycline, and neutralized polymyxin B. Blood and sputum cultures confirmed CRAB susceptibility to SUL-DUR. Following treatment, inflammatory markers (CRP, IL-6, PCT) and pathogen loads markedly decreased, leading to complete clinical resolution without significant adverse effects. The patient was successfully discharged after rehabilitation. CONCLUSIONS SUL-DUR demonstrated excellent efficacy and safety in treating CRAB pneumonia and sepsis after liver transplantation. This case supports Phase III trial data and suggests the potential for use in high-risk, immunocompromised populations. Further studies are warranted to validate its clinical role and inform future guidelines for multidrug-resistant infections.},
}

Humans
Female
*Liver Transplantation/adverse effects
*Acinetobacter Infections/drug therapy
*Acinetobacter baumannii/drug effects
*Sulbactam/therapeutic use
*Sepsis/drug therapy/microbiology
Young Adult
Carbapenems/pharmacology
*Postoperative Complications/drug therapy/microbiology
*Anti-Bacterial Agents/therapeutic use
*Pneumonia, Bacterial/drug therapy/microbiology

@article {pmid41563008,
year = {2026},
author = {Karatzas, E and Beracochea, M and Baltoumas, FA and Aplakidou, E and Richardson, L and Yates, JAF and Lundin, D and , },
title = {nf-core/proteinfamilies: A scalable pipeline for the generation of protein families.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag009},
pmid = {41563008},
issn = {2047-217X},
abstract = {The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterised sequences with the few experimentally characterised ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.},
}

@article {pmid41562608,
year = {2026},
author = {Kos, D and Warr, B and Suchan, DM and Wadt, D and Russell, JN and Norfield, M and Liang, J and Jelinski, M and Cameron, ADS and Ruzzini, A},
title = {Survey of bacteria associated with septic arthritis in beef feedlot cattle.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0167525},
doi = {10.1128/aem.01675-25},
pmid = {41562608},
issn = {1098-5336},
abstract = {Septic arthritis (SA) is a cause of lameness in cattle attributed to bacterial infections. Mycoplasmopsis bovis is the best known and characterized etiological agent of SA; however, cases caused by diverse bacteria have been reported. Accordingly, we surveyed bacteria associated with septic and healthy joints from animals in western Canadian feedlots. Microbial community profiling showed that M. bovis was the most frequently detected pathogen in septic joints, followed by Metamycoplasma alkalescens and Trueperella pyogenes. In most cases, disease was ostensibly caused by a single pathogen, though polymicrobial infections and complex communities were also observed in DNA isolated from septic joints. The application of enhanced metagenomics by target DNA hybridization capture sequencing (CapSeq) provided more robust pathogen detection and characterization. CapSeq revealed resistance determinants that escaped detection using a conventional shotgun metagenomic approach. Notably, a series of nucleotide polymorphisms to M. bovis rrs, rrl, gyrA, and parC gene sequences were observed that confer resistance to macrolides and oxytetracycline-resistant T. pyogenes were also apparent in the CapSeq data. Complementary pathogen isolation, whole-genome sequencing, and phenotyping efforts were focused on the two most prominent pathogens, M. bovis and M. alkalescens, and corroborated metagenomic data sets.IMPORTANCEInformed antimicrobial use for the treatment of septic arthritis (SA) has been limited by overlooking the potential diversity of causative agents and our knowledge of their antimicrobial resistance (AMR) profiles. This survey begins to provide epidemiological insights, offering renewed appreciation of Metamycoplasma alkalescens as an etiological agent of SA and highlighting the prominence of important AMR determinants. Finally, the survey suggests that our knowledge of even the identities of the causative agents of SA is incomplete.},
}

@article {pmid41562434,
year = {2026},
author = {Jasilionis, A and Sivakumar, P and Dobruchowska, JM and Fjermedal, S and Guðmundsson, H and Adalsteinsson, BT and Hreggviðsson, GÓ and Meyer, AS and Nordberg Karlsson, E},
title = {Characterisation of a phylogenetically distinct PL25 family ulvan lyase from a seaweed biomass enriched metagenome.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.70390},
pmid = {41562434},
issn = {1742-4658},
support = {//European Commision/ ; },
abstract = {Ulvan is a polysaccharide most abundant in green macroalgae biomass. Investigation of ulvan confirmed the potential of the polysaccharide for food, pharmaceutical and chemistry applications, emphasising the beneficial properties of ulvan oligosaccharides. Efficient production of oligosaccharides requires action of ulvan lyases capable of ensuring polysaccharide enzymatic depolymerisation. The armoury of available ulvan lyases was expanded by characterisation of SH2L_Ulv3 ulvan lyase, which was found to be phylogenetically distinct from previously characterised lyases attributed to PL25 family. A gene encoding a novel ulvan lyase was identified among sequences from a seaweed biomass metagenome enriched in an intertidal coastal hot spring. Identified ulvan lyase was most similar to a hypothetical protein from a Bacteroidales bacterium. Recombinant SH2L_Ulv3 was heterologously (over)produced in Escherichia coli at a high yield, remaining soluble in the expression host as well as after affinity purification. Ulvan lyase active as a 48.6 kDa monomer with evaluated activity optimum pH 7.5 and 200 mm NaCl at 25 °C demonstrated broad substrate specificity. SH2L_Ulv3 degraded ulvan from blade-thallus as well as tubular-thallus morphology algae species, efficiently producing three different DP4 and DP2 unsaturated oligosaccharides. The kinetic parameters of SH2L_Ulv3 were KM 3.63 ± 0.12 mg·mL[-1], Vmax 1.78 ± 0.04 μmol·min[-1]·mL[-1] and kcat 1.46 ± 0.04 s[-1]. Magnesium ion stimulated SH2L_Ulv3 activity. The characterised enzyme was not thermostable, displaying Tm 42 °C. The computationally modelled structure of SH2L_Ulv3 revealed structural organisation and active site architecture as well as ligand substrate binding and zinc ion coordinating residues typical for PL25 lyases; however, with a larger central active site cleft facilitating ulvan polysaccharide degradation.},
}

@article {pmid41562342,
year = {2026},
author = {Winkler, M and Seel, W and Kornblum, C and Simon, MC and Reimann, J},
title = {The MicroIBioM study: the gut microbiome in inclusion body myositis.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/1b8sv1},
pmid = {41562342},
issn = {0392-856X},
abstract = {OBJECTIVES: Inclusion body myositis (IBM) is a disorder with features of both inflammation and degeneration yet without effective treatment. Influences of the gut microbiome on degenerative as well as inflammatory disorders and immune treatments are known. We sought to investigate whether the gut microbiome might influence the development or recalcitrance of IBM.

METHODS: We appealed to IBM patients and their unaffected spouses/cohabitants for stool samples and data on clinical symptoms, gathering questionnaire data (modified Gastrointestinal Symptom Rating Scale (mGSRS), IBM Functional Rating Scale (IBMFRS) and Bristol Stool Scale) and stool samples for 16S rRNA V3V4 metagenomic analysis from 21 IBM and 20 control probands. Bioinformatic analyses used QIIME2 and MicrobiomeAnalyst software packages. LEfSe and Random Forest analysis aimed to identify group specific biomarkers. PICRUSt was used to perform pathway analysis.

RESULTS: No overall differences of alpha and beta diversity were found between IBM and control group. No impact of immune treatments was found, but a reduction in alpha diversity was identified comparing older (≥ 72 years) IBM and control probands. Increased abundances of some genera, in particular Bacteroides, were detected in the IBM group. Bacteroides, Clostridium CAG 352, and Eggerthella were identified as IBM biomarkers at genus level. Gastrointestinal symptoms (mGSRS) correlated with disease severity (IBMFRS).

CONCLUSIONS: General differences of gut microbiome seem unlikely to play a role in the genesis of IBM. Whether the late occurring or the more specific differences detected are part of the disease course needs to be addressed by investigations of further biosamples.},
}

@article {pmid41562259,
year = {2026},
author = {Stuart, KC and Oomen, RA and Tigano, A and Wellenreuther, M and Wold, J and Field, DL and Mérot, C},
title = {A Beginner's Guide to Structural Variants in Eco-Evolutionary Population Genomics.},
journal = {Molecular ecology},
volume = {35},
number = {2},
pages = {e70216},
doi = {10.1111/mec.70216},
pmid = {41562259},
issn = {1365-294X},
support = {UOA1911//Royal Society Te Apārangi/ ; MFP-PAF2301//Royal Society Te Apārangi/ ; //Genomics Aotearoa ECR Grant/ ; RGPIN-2024-06892//Natural Sciences and Engineering Research Council of Canada Discovery Grant/ ; TRF-0000000175//New Brunswick Innovation Foundation/ ; 2021-05580//Swedish Research Council Starting Grant/ ; CAWX2304//New Zealand Ministry of Business, Innovation and Employment, Smart Ideas Grant/ ; PFR2430//New Zealand Ministry of Business, Innovation and Employment, Smart Ideas Grant/ ; //Fisheries and Oceans Canada/ ; 101115983(EVOL-SV)/ERC_/European Research Council/International ; },
mesh = {*Genetics, Population/methods ; *Genomics/methods ; *Evolution, Molecular ; DNA Transposable Elements ; Animals ; Genetic Variation ; Whole Genome Sequencing ; *Genomic Structural Variation ; *Metagenomics/methods ; *Biological Evolution ; Humans ; },
abstract = {Whole-genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence. This has paved the way to study the eco-evolutionary dynamics of SVs across the tree of life and within a population genomics framework. In this review, we provide the necessary fundamentals to help researchers generate and analyse population-level SV data. We discuss the unique properties of different SV groups and how these fundamental differences interact with important biological and evolutionary processes using both empirical results and theory. This includes discussion of unresolved issues around SVs, such as technical difficulties in identification, accounting for diversity and evaluating functional effects. We explicitly integrate into this discussion transposable elements, which are an important component of SVs often identified in population-level variant data. Finally, we focus on the practical side of SV analysis, offering a framework for SV identification and data analysis. In particular, we examine the heterogeneous nature of SV properties (type, length, sequence identity) that should be considered when studying them in ecology and evolution. This review aims to provide resources and guidelines to help researchers navigate the complexities of a relatively new field of eco-evolutionary genomics research.},
}

*Genetics, Population/methods
*Genomics/methods
*Evolution, Molecular
DNA Transposable Elements
Animals
Genetic Variation
Whole Genome Sequencing
*Genomic Structural Variation
*Metagenomics/methods
*Biological Evolution
Humans

@article {pmid41562140,
year = {2026},
author = {Assenmacher, CA and Mou, K and Li, G and Hsu, K and Sahin, O and Cole, SD},
title = {Actinomyces sp. detected by next-generation sequencing in paraffin-embedded, formalin-fixed tissues of a dog with severe panophthalmitis and periocular cellulitis.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {},
number = {},
pages = {10406387251410586},
doi = {10.1177/10406387251410586},
pmid = {41562140},
issn = {1943-4936},
abstract = {A 9-mo-old, castrated male Saint Bernard dog was presented for evaluation of periorbital swelling, severe uveitis, and secondary glaucoma. Concurrently, chest radiographs had evidence of pneumonia. Enucleation was performed after failure of aggressive medical management. Histopathology of the globe confirmed severe necrosuppurative panophthalmitis and periocular cellulitis with myriad intra- and extracellular bacteria forming long filamentous chains. The bacteria were gram-positive and GMS-positive but acid-fast-negative. Next-generation sequencing (NGS) was performed on formalin-fixed, paraffin-embedded (FFPE) tissue from the eye. We identified a bacterium in the Actinomycetaceae family with a 100% BLAST match, suggestive of the previously described Actinomyces catuli strain (CCUG 41709). Clinical improvement followed enucleation and continued medical management, leading to reduction of the periocular swelling and resolution of the lung disease. Uveitis is common in dogs and is the most common cause of glaucoma. In many cases of bacterial uveitis, the exact bacterial organisms remain unknown if culture is not performed before fixation. Actinomyces sp. should be considered in patients with severe endophthalmitis or panophthalmitis, especially with evidence of systemic disease. NGS on FFPE samples may be a useful tool for identifying infectious organisms, especially in cases in which culture is not an option.},
}

@article {pmid41562094,
year = {2025},
author = {Tang, K and Zhang, Y and Meneses, C and Rogerio, LA and Willen, L and Iniguez, E and Kamhawi, S and Valenzuela, JG and Oliveira, F and Cecilio, P},
title = {Phlebotomus duboscqi gut microbiota dynamics in the context of Leishmania infection.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1717935},
pmid = {41562094},
issn = {1664-3224},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Phlebotomus/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; *Leishmaniasis/parasitology ; *Insect Vectors/microbiology/parasitology ; Bacteria/genetics/classification ; },
abstract = {INTRODUCTION: The manipulation of the gut microbiota of disease vectors has emerged as a new approach to use in the integrated control of vector-borne diseases. For this purpose, a deep knowledge of their gut microbial communities is essential. To our knowledge, to date, no study has documented the gut microbiome dynamics of Phlebotomus duboscqi sand flies over the entire time-period required for the maturation of a Leishmania infection. Here, we address this limitation.

METHODS: P. duboscqi midguts were dissected both before and at different days after L. major infection and subjected to genomic DNA extraction followed by amplification of the V3-V4 hypervariable regions of the 16S rRNA, sequencing, and metagenomics analysis.

RESULTS: We observed a decrease in the number of Amplicon Sequence Variants (ASVs) early after infection, at D2, and late after infection, at D12. More so Sphingomonas, Ochrobactrum, and Serratia emerged as the most prevalent genera in relative terms, before, early after, and late after infection, respectively. These results translated into a separation between the 3 groups in the context of a beta diversity analysis, with statistical relevance. Importantly, we were able to establish Corynebacterium spp. and Enterococcus spp. as potential markers of non-infected and infected sand flies, respectively, as well as Streptococcus spp., Sphingomonas spp., Ralstonia spp., and Abiotrophia spp. as potential specific markers of late infections (ANCOM-BC analysis).

DISCUSSION: Overall, we show that the composition of the gut microbiota of P. duboscqi sand flies changes significantly over the course of an infection with L. major parasites.},
}

*Gastrointestinal Microbiome
Animals
*Phlebotomus/microbiology/parasitology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
*Leishmaniasis/parasitology
*Insect Vectors/microbiology/parasitology
Bacteria/genetics/classification

@article {pmid41562034,
year = {2026},
author = {Sanchez-Cid, C and Vrchovecká, S and Dehon, E and Wacławek, S and Vogel, TM},
title = {Environmental Consequences of Anthropogenic Pollution: Non-antibiotic-Drug-Driven Antibiotic Resistance Selection in a Model Aquatic Ecosystem.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {1},
pages = {132-143},
pmid = {41562034},
issn = {2833-8278},
abstract = {Non-antibiotic drugs (NADs) used in human therapy may induce antibiotic resistance selection and dissemination in vitro. However, the potential risks of antibiotic resistance emergence associated with environmental NAD pollution have not been addressed. Here, we conducted a multidisciplinary study on river water microcosms using growth kinetics, qPCR, metagenomics, 16S rRNA sequencing, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to determine whether NADs alter river bacterial ecology and select for antibiotic resistance genes (ARGs). Four NADs with different mechanisms of action were included at a high (mg/L) and low (μg/L) dose to establish dose-response relationships: chlorpromazine (antipsychotic), diclofenac (anti-inflammatory), diphenhydramine (antihistamine), and fluoxetine (antidepressant). Although the community response to NAD pollution was compound-specific and dose-dependent, all NADs and doses were stable in the environment, altered the composition and activity of bacterial communities, and selected for several ARGs, mostly β-lactamases and aminoglycoside resistance genes, some of which were associated with horizontal gene transfer genes. Pseudomonas (including some ARG-harboring subpopulations) was identified as a key player in the response to NAD pollution. Here, we demonstrate NAD-driven antibiotic resistance selection in complex aquatic communities, raising concerns about the collateral effects on human and environmental health due to the extensive anthropocentric use of NADs.},
}

@article {pmid41561899,
year = {2026},
author = {Labbancz, J and Birnbaum, A and Dhingra, A},
title = {Long-read metagenomic dataset from domestic rabbit manure and domestic rabbit manure-derived vermicompost.},
journal = {Data in brief},
volume = {64},
number = {},
pages = {112425},
pmid = {41561899},
issn = {2352-3409},
abstract = {This dataset describes samples collected from two Domestic Rabbit manure sources and three Domestic Rabbit manure-derived vermicompost bins. Three samples were taken from each and total DNA was isolated. Nanopore sequencing was used to collect data from all isolated DNA samples. After length and quality filtering, 181.5 gigabases (Gb) of sequencing data was collected across 15 samples. Streptomyces, Bradyrhizobium, Mesorhizobium, and Microbacterium were in the top 5 genera for all vermicompost samples, but two vermicompost samples had very high proportions of Escherichia and Mycobacterium. Vermicomposting can enable the development of beneficial microbial communities, but often lacking a thermophilic phase, may also allow for the growth of potentially pathogenic microbes. The vermicomposts described by this dataset contains both beneficial and potentially harmful microbial communities and may be used to support comparisons between composts and vermicomposts of different backgrounds for safety and utility.},
}

@article {pmid41561308,
year = {2026},
author = {Mei, Z and He, C and Balcazar, JL and Fu, Y and Dou, Q and Liu, Y and Dercon, G and Jiang, X and Elsner, M and Wang, F},
title = {Antibiotic-degrading bacteria shape resistome dynamics and horizontal gene transfer potential in soils with contrasting properties.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf246},
pmid = {41561308},
issn = {2730-6151},
abstract = {Soils act as both reservoirs and filters of antimicrobial resistance genes (ARGs); however, the ecological and genetic traits of antibiotic-degrading bacteria (ADB) and their interactions with nondegrading bacteria (NADB) across soil types remain poorly understood. In particular, the role of ADB in ARG dynamics and their potential contribution to horizontal gene transfer (HGT) are still underexplored. Here, we applied [13]C-DNA stable isotope probing (DNA-SIP) combined with metagenomic sequencing to resolve active ADB from NADB in two contrasting soils: Ultisol and Mollisol. ADB harbored significantly more abundant and diverse chromosomal ARGs - especially multidrug and tetracycline resistance genes - often co-localized with mobile genetic elements (MGEs) and degradation genes, suggesting robust and regulated resistance strategies. In contrast, NADB relied more on plasmid-borne ARGs, reflecting flexible but potentially transient adaptation. Soil properties shaped both resistome composition and host taxa. Mollisol enriched enzymatic degraders such as Lysobacter and Nocardioides, while Ultisol favored stress-tolerant Burkholderia, which carried up to 34 ARGs and exhibited membrane-associated resistance. Notably, 89 ARGs or MGEs were found co-localized with degradation genes on assembled contigs, highlighting a strong potential for HGT. In addition, 24 high-potential ARG hosts were identified, including Ralstonia pickettii and Saccharomonospora viridis. These findings reveal that antibiotic degradation is embedded within complex, soil-specific resistome networks. This work enhances our understanding of ARG ecology and supports targeted mitigation strategies based on soil microbiome characteristics.},
}

@article {pmid41561096,
year = {2025},
author = {Wan, L and Huang, C and Kong, W and Li, M and Lu, C},
title = {The analysis of gut microbiota characteristics in children with global developmental delay.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1606453},
pmid = {41561096},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Female ; Feces/microbiology ; Male ; *Developmental Disabilities/microbiology ; Child, Preschool ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Child ; DNA, Bacterial/genetics ; Infant ; Biodiversity ; China ; },
abstract = {OBJECTIVE: To explore the composition and functional changes of gut microbiota in children with Global Developmental Delay(GDD),and to explore the role of gut microbiota in the pathogenesis of GDD using high-throughput sequencing.

METHODS: A prospective study was conducted to select 26 children diagnosed with GDD at Longgang District Maternal and Child HealthCare Hospital of Shenzhen City from January 2024 to December 2024 as the disease group(GDD), and 59 healthy children of the same age were selected as the healthy group(HC).General information of the children was collected through a questionnaire survey, and fecal samples from all participants were collected. Total DNA was extracted and amplified, and high-throughput sequencing of the 16S rRNA gene was performed for biological analysis of the sequencing results.

RESULTS: The alpha diversity analysis revealed a significant reduction in microbial diversity in the GDD group (Chao1 index, P = 0.007), while the beta diversity showed significant segregation between groups (R² = 0.067, P = 0.001);At the phylum level, the relative abundance of Actinobacteria was significantly increased (P < 0.01), while the abundance of Bacteroidetes was significantly decreased (P < 0.05) in the GDD group;At the genus level, the abundance of Bifidobacterium, Fusicatenibacter, and Erysipelatoclostridium were significantly increased in the GDD group (all P < 0.001), while the abundance of Faecalibacterium, Phascolarctobacterium, and Alistipes were significantly reduced (all P < 0.001);Functional prediction based on 16S rRNA data suggested potential differences in microbial metabolic pathways, including mRNA surveillance, proteasome, and atrazine degradation, in the GDD group. These findings hypothesize a functional shift in the gut microbiome associated with GDD, which requires validation by direct metagenomic or metabolomic methods.

CONCLUSION: Children with GDD have significant differences in gut microbiota composition and diversity compared to HC,and the abundance and abnormal metabolic pathway may be closely related to the neuroinflammatory process, suggesting that intestinal microecological regulation may become a new intervention target for GDD.},
}

Humans
*Gastrointestinal Microbiome/genetics
Prospective Studies
RNA, Ribosomal, 16S/genetics
Female
Feces/microbiology
Male
*Developmental Disabilities/microbiology
Child, Preschool
*Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Child
DNA, Bacterial/genetics
Infant
Biodiversity
China

@article {pmid41561086,
year = {2025},
author = {Zhang, MY and Chen, SY and Lin, YH and Yuan, XX},
title = {Gut microbiota modulation in gastrointestinal disorders: current evidence and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1740322},
pmid = {41561086},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Gastrointestinal Diseases/therapy/microbiology ; Probiotics/therapeutic use ; Animals ; Fecal Microbiota Transplantation ; Gastrointestinal Tract/microbiology ; Phage Therapy ; Dysbiosis/therapy ; },
abstract = {Gut microbiome medicine is a promising field in functional medicine, offering personalized treatment strategies for gastrointestinal disorders. Advanced metagenomic and metabolomic technologies have revealed the gut microbiome's systemic influence, extending to distant organs like the brain and lungs. While small molecules and genes facilitate these effects, the gut microbiota's greatest abundance and activity are concentrated in the gastrointestinal tract, particularly in the distal regions. The balance of microbial communities in the small and large intestines is crucial for gastrointestinal health. However, the dominance of pathogenic bacteria can disrupt this balance, leading to tissue damage and contributing to gastrointestinal disorders. Emerging interventions, such as probiotics, fecal microbiota transplantation, and dietary enrichment with short-chain fatty acids, show potential in restoring microbial balance, enhancing immune function, and potentially protecting against carcinogenesis. Current evidence from clinical trials and animal models supports the therapeutic role of gut microbiome modulation in reversing gastrointestinal disorders. However, variability in study outcomes highlights the need for further research to standardize these approaches for clinical practice. This review underscores the gut microbiome's pivotal role in gastrointestinal health and the therapeutic promise of functional medicine in addressing these disorders. This review also explores emerging interventions, such as phage therapy and engineered microbes, and provides comparative analyses of microbiota signatures and therapeutic approaches across different gastrointestinal disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Gastrointestinal Diseases/therapy/microbiology
Probiotics/therapeutic use
Animals
Fecal Microbiota Transplantation
Gastrointestinal Tract/microbiology
Phage Therapy
Dysbiosis/therapy

@article {pmid41561037,
year = {2025},
author = {Zhang, S and Mo, Y and Yang, J and Chen, X and Gao, M and Su, Y and Qiu, Q and He, Q},
title = {Vertical stratification of P pools in subtropical plantation soils under fertilization and dry-season irrigation: multiomics regulatory strategies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1714023},
pmid = {41561037},
issn = {1664-302X},
abstract = {The rapid expansion of fast-growing plantations in subtropical regions is closely linked to silvicultural practices, however, improper practices often lead to soil acidification and reduced nutrient bioavailability. Phosphorus (P), one of the most critical elements for plantation tree growth, shows complex spatial distribution patterns in soil that are influenced by multiple factors, directly affecting plantation productivity. This study investigated the effects of long-term fertilization and dry-season irrigation on the vertical distribution of phosphorus in an 8-year-old subtropical Eucalyptus plantation. This study employed stratified sampling (0-30 cm topsoil, 30-60 cm subsoil, 60-90 cm substratum) during dry seasons, coupled with metagenomics, metabolomics, and environmental factor analysis, to reveal vertical phosphorus cycling patterns and multiomics regulatory networks. Key findings: (1) Fertilization and dry-season irrigation had a limited influence on labile phosphorus and the diversity of P-cycling microorganisms. The topsoil presented significantly greater P availability than did the subsoil, manifested as elevated acid phosphatase activity (ACP), significant enrichment of the tryptophan metabolic pathway, and greater microbial diversity. (2) pH and the C:P ratio represent critical factors of vertical stratification in soil P cycling. Under acidic conditions, topsoil microorganisms facilitate P release via diverse metabolic pathways, whereas oligotrophic constraints in the substratum limit enzymatic activities. (3) Potential cross-stratum microbial functional coordination exists in acidic soil P cycling, with linkages to tryptophan metabolism and polyphosphate, synthesis/degradation. Our study provides theoretical multiomics insights for optimizing the management of soil P pools in subtropical plantations under fertilization and dry-season irrigation.},
}

@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