@article {pmid41033729,
year = {2025},
author = {Chan, CSY and Georgakopoulos-Soares, I},
title = {From nonexistence to novel applications: Nullomers and related k-mer based concepts in bioinformatics.},
journal = {Advances in clinical chemistry},
volume = {129},
number = {},
pages = {191-206},
doi = {10.1016/bs.acc.2025.06.009},
pmid = {41033729},
issn = {2162-9471},
mesh = {*Computational Biology/methods ; Humans ; Genomics ; Proteomics ; Neoplasms/diagnosis/genetics ; },
abstract = {Underrepresented k-mer sequences, provide insights into evolutionary constraints, molecular mechanisms, and organismal fitness. Analysis of these sequences have broad applications across genomics and proteomics, such as in biomarker development, cancer diagnostics, phylogenetic analysis, synthetic biology and novel drug discovery. Absent sequences (nullomers and neomers) show promise for cancer detection and tissue-of-origin identification using nucleic acids derived from liquid biopsies, while quasi-primes serve as genomic fingerprints that offer potential for evolutionary studies for understanding trait evolution, and in metagenomics, as biomarkers of organismal presence. The chapter also discusses computational challenges associated with analyzing absent sequences and highlights available k-mer based resources and databases. With the continuous expansion of genomic and proteomic data, absent sequences present an innovative framework for addressing fundamental biological questions and advancing applications in basic and translational research.},
}

*Computational Biology/methods
Humans
Genomics
Proteomics
Neoplasms/diagnosis/genetics

@article {pmid41033716,
year = {2025},
author = {Garima, and Dhanawat, M and Wilson, K and Chaubey, P},
title = {High-throughput sequencing technologies for cancer genomics.},
journal = {Methods in cell biology},
volume = {198},
number = {},
pages = {103-133},
doi = {10.1016/bs.mcb.2025.02.018},
pmid = {41033716},
issn = {0091-679X},
mesh = {Humans ; *Neoplasms/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; Genome, Human ; Transcriptome ; },
abstract = {In investigations about transcriptomics, epigenomics, and genomics, high-throughput sequencing technologies have become indispensable. Several hundred million of DNA molecules may be sequenced at once thanks to high throughput sequencing (HTS) technologies, which can simultaneously analyze many DNA molecules. Traditionally, sequencing information has been clarified utilizing a low throughput technique known as Sanger sequencing. This added value makes it feasible to employ HTS to generate tremendous amounts of data, which enhances the comprehension of the transcriptome and genetic fingerprints of cells during various stages of evolution and pathology. By identifying somatic changes, morphological deviations, and repetitive changes across the human genome, techniques such as whole exome sequencing (WES) and whole genome sequencing (WGS) provide information about cancer formation as well as prospective therapies. Identifying tumor biology and discovering biomarkers rely on the examination of aberrant networks and variations in gene expression that RNA DNA sequencing, or RNA-Seq, offers. By identifying rare cell kinds and their function in carcinogenesis, the sequencing of one cell offers illumination on the wide range of cells observed across tumors. Metagenomics and chromatin immunoprecipitation sequencing (ChIP-Seq) delivers essential knowledge by discovering alterations that affect the epigenetic configuration and the microenvironment that accompanies tumors. Integrating these recent developments will allow the development of personalized treatments that use unique genetic traits to determine every cancer patient, offering more individualized treatments. The revolutionary implications of high-throughput genome sequencing for cancer research and treatment are addressed in this book chapter, particularly concerning cancer precision as well as effective treatment outcomes.},
}

Humans
*Neoplasms/genetics
*High-Throughput Nucleotide Sequencing/methods
*Genomics/methods
Genome, Human
Transcriptome

@article {pmid41033677,
year = {2025},
author = {Ilbağı, H and Kanakala, S and Masonbrink, R and Lozier, Z and Miller, WA},
title = {Metagenomic Sequencing of Maize Reveals Abundant Genomic RNA of a Comovirus, a Genus Previously Known to Infect Only Dicots.},
journal = {The plant pathology journal},
volume = {41},
number = {5},
pages = {656-670},
doi = {10.5423/PPJ.OA.06.2025.0077},
pmid = {41033677},
issn = {1598-2254},
support = {//The Scientific and Technological Research Council of Turkey/ ; NKUBAP.03.GA.21.289//Tekirdağ Namık Kemal University/ ; 4308//The Iowa Agriculture and Home Economics Experiment Station, Ames, IA/ ; //The Iowa State University Plant Sciences Institute/ ; //DARPA Insect Allies Program/ ; },
abstract = {To better understand the diversity of viral pathogens in Türkiye, a major exporter of cereals in Europe, we performed high-throughput sequencing of total RNA from maize plants collected in the Trakya region. Certain maize plants exhibiting mosaic and mottle symptoms, gathered from Tekirdağ province in Trakya, yielded large numbers of reads corresponding to the genome of a divergent strain of a comovirus, which corresponds to turnip ringspot virus (TuRSV), a recognized species of the genus Comovirus. This finding is unexpected because all known comoviruses infect only dicotyledonous species, and the known host range of TuRSV has been limited to plants in the Brassicaceae family. The nearly complete and partial nucleotide sequences of the bipartite genome of the maize isolate, as named TuRSVTR59, consist of 6,027 nt TuRSV-TR59 RNA1 and 3,920 nt TuRSV-TR59 RNA2, excluding poly (A) tails. RNA1 and RNA2 each encode a single ORF of 1,860 and 1,096 codons, respectively. Phylogenetic analysis demonstrated that TuRSV-TR59 from Türkiye clustered with other TuRSV isolates from diverse hosts and regions, showing highest identity to isolates from Germany, Czech Republic, and Croatia (80.56-77.77% and 92.09-90.50% nucleotide and amino acid sequence identities, respectively). The ability of TuRSV-TR59 isolate to infect maize was confirmed by reverse transcription polymerase chain reaction. Surveys in the Tekirdağ province of Türkiye, done in 2022-2025, revealed that 2 out of 145 maize samples (1.38%) and 8 out of 116 canola samples (6.89%) were found infected with TuRSV. This is the first report of a comovirus in maize from a monocotyledonous plant species.},
}

@article {pmid41033626,
year = {2025},
author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H},
title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122985},
doi = {10.1016/j.envres.2025.122985},
pmid = {41033626},
issn = {1096-0953},
abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems: (1) iron/manganese oxidation (e.g., feoB) associated with iron-manganese plaque (IP) formation; (2) sulfate reduction (e.g., dsrA) linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.},
}

@article {pmid41033498,
year = {2025},
author = {Saejung, C and Akkahat, S},
title = {Light color-based proliferation of purple phototrophic bacteria in a microbial consortium for sustainable wastewater treatment and bioproduct generation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133411},
doi = {10.1016/j.biortech.2025.133411},
pmid = {41033498},
issn = {1873-2976},
abstract = {Purple phototrophic bacteria (PPB) offer distinct advantages for wastewater treatment. However, the application of pure cultures of PPB in large-scale wastewater treatment is constrained by isolation challenges and microbial competition. Therefore, we investigated light color treatment as a tool to enrich PPB within a natural microbial consortium for integrated wastewater treatment and bioproduct generation. We used metagenomics to assess PPB population dynamics and measured bioproduct yields of pigments, protein, biomass, and polyhydroxybutyrate as well as chemical oxygen demand removal (COD). While an initial enrichment yielded low PPB abundance (12 %), subsequent exposure to specific light color greatly altered the community composition. White light (465 nm) enriched the consortium with 76 % PPB abundance, dominated by Rhodopseudomonas sp., which maximized bacterial biomass, polyhydroxybutyrate accumulation, and COD removal. Conversely, red light (616 nm) suppressed PPB proliferation but enhanced specific yields of photosynthetic pigments and protein, indicating a metabolic trade-off between growth and bioproduction. Thus, light color treatment may be a simple and powerful strategy to boost PPB abundance and performance within a microbial consortium, creating a cost-effective platform for wastewater biorefineries.},
}

@article {pmid41033373,
year = {2025},
author = {Yarim, D and Abay, S},
title = {First Comprehensive Genome Analysis and Antimicrobial Resistance Profile of Clostridium innocuum from a Domestic Cat.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108076},
doi = {10.1016/j.micpath.2025.108076},
pmid = {41033373},
issn = {1096-1208},
abstract = {This study aimed to investigate the molecular and phenotypic properties of a C. innocuum isolate from a healthy cat, which was previously misidentified as C. difficile by molecular testing (tpi-PCR). To resolve the misidentification and obtain more information on the isolate at the genetic level, whole genome sequencing (WGS) on the long-read sequencing platform Oxford Nanopore PromethION was performed. WGS data were analysed to identify virulence factors, antibiotic resistance, and hypothetical prophage genes. The isolate was identified as C. innocuum as a result of WGS. While several virulence genes, including pilM, yabQ, HrcA, and CptIN family toxins, were detected, toxin-coding genes in other Clostridium species were not detected. Four prophage regions were detected; three appeared as intact phage sites, while one was incomplete. The isolate was susceptible to ampicillin, clindamycin, vancomycin, and metronidazole but was resistant to meropenem using the E-test method. The genome also contained resistance genes such as tet(M), aph(2'')-Ia, and VanT, VanW, VanY, VanG, and VanZ. Genetic similarities between our isolate and those obtained from global human-derived metagenome-associated genomes (MAGs) and non-MAG genomes from healthy humans and animals were illustrated through WGS-SNP-based phylogenetic analyses. This study provides insights into the phenotypic and genotypic characteristics of C. innocuum, an emerging pathogen. Taken together, the isolation of this agent-possessing intrinsic resistance mechanisms and emerging after the treatment of C. difficile infections from a domestic cat highlights its potential threat to public health. Nevertheless, many clinical questions remain unanswered, underscoring the need for further research to deepen our understanding of this pathogen and to develop effective control and treatment strategies.},
}

@article {pmid41033148,
year = {2025},
author = {Luo, L and Wong, JWC and Yan, B and Xu, S and Rabaey, K},
title = {Mechanistic insights into fermentative pathway control during solid-state food waste acidogenesis under autogenic pressure.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124679},
doi = {10.1016/j.watres.2025.124679},
pmid = {41033148},
issn = {1879-2448},
abstract = {The efficiency of two-phase anaerobic digestion hinges on the acidogenic phase, where acidogenic off-gas generates autogenic pressure that alters the physicochemical environment and may affect microbial activity, pathways, and intermediates. However, its mechanistic role under solid-state conditions remains unclear. To address this knowledge gaps, we investigated the effects of autogenic pressure on solid-state food waste acidogenesis, focusing on soluble microbial product (SMP) formation and the associated metabolic responses at the molecular level. Autogenic pressure enhanced acidogenic decomposition, increasing SMP yields from 365.3 ± 10.5 g COD/kg VSadded to 407.1 ± 7.3 g COD/kg VSadded. It initially promoted lactate production, followed by enhanced conversion of lactate to butyrate and acetate functioning by Megasphaera. Metagenomic and metabolite analyses revealed that autogenic pressure increased the abundance of functional genes associated with homoacetogenesis and butyrate synthesis. Incubation experiments further confirmed that acetate, stimulated by autogenic pressure, played a key role in driving the reverse β-oxidation pathway while suppressing the acrylate pathway during lactate conversion. As a result, butyrate production increased by 25 %, while propionate decreased by 43 %. These findings provide new insights into how SMP-producing microbial communities respond to autogenic pressure and demonstrate the potential of self-regulation to enhance product yield and process controllability. This strategy advances sustainable solid waste management and promotes the development of circular bioeconomy.},
}

@article {pmid41032862,
year = {2025},
author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A},
title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.},
journal = {Journal of medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jmedchem.5c02169},
pmid = {41032862},
issn = {1520-4804},
abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.},
}

@article {pmid41032855,
year = {2025},
author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Pan, YP and Hua, ZS and Zhang, CJ and Li, M},
title = {Temporal and Spatial Dynamics of Microbial Community Composition and Functional Potential in Mangrove Wetlands over a Seven-Year Period.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01564},
pmid = {41032855},
issn = {1520-5851},
abstract = {Microbial communities are essential to sustaining ecosystem functions in mangrove wetlands, yet their long-term responses to environmental changes remain poorly characterized. Here, we conducted a seven-year multiomics investigation (2017-2023) of microbial diversity, functionality, and evolutionary dynamics in the Futian Mangrove National Nature Reserve, Shenzhen, China. This region has experienced ecological degradation followed by phased restoration efforts since 2007. By analyzing 81 metagenomes, 8474 microbial metagenome-assembled genomes (MAGs) were successfully reconstructed, representing 13 archaeal phyla, 70 bacterial phyla, and up to 95% newly identified species. Community composition was primarily influenced by sediment depth and seasonal variations. Integrating 72 metatranscriptomes revealed marked temporal shifts in gene expression linked to carbon, nitrogen, and sulfur cycling, including enhanced transcription of genes involved in organic carbon oxidation, sulfate reduction, denitrification, and nitrogen fixation during later stages restoration. Evolutionary analyses demonstrated pervasive purifying selection across microbial lineages, with environmental fluctuations and genome size acting as key determinants of selective pressures. Additionally, a new class Candidatus Shennongiarchaeia within Thermoplasmatota was proposed, exhibited anaerobic, facultatively heterotrophic characteristics and bioactive compound synthesis potential. These findings demonstrate that microbial communities in restored mangrove wetlands undergo structural and functional reorganization, characterized by the enrichment of anaerobic lineages, upregulation of key metabolic pathways, and environmentally driven selective pressures. This long-term study deepens our understanding of microbial resilience and adaptation in mangrove ecosystems, with implications for future conservation and restoration strategies in coastal wetlands.},
}

@article {pmid41032194,
year = {2025},
author = {Naderian, R and Alibabaei, F and Paraandavaji, E and Dehghan, P and Eslami, M},
title = {Phage-Microbiota Interactions in the Gut: Implications for Health and Therapeutic Strategies.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41032194},
issn = {1867-1314},
abstract = {The diversified ecology of microorganisms, including bacteria, archaea, fungi, protozoa, and viruses known collectively as the gut microbiota, which includes bacteriophages, is crucial to human health because it affects functions like immune system regulation, vitamin production, and pathogen protection. Bacteriophages are viruses that infect bacteria and are increasingly recognized as a viable treatment option for antibiotic-resistant strains, owing to their high host specificity, which enables precise targeting of drug-resistant bacteria while sparing commensal microbiota. The complex relationships between bacteriophages and gut microbiota are examined, with emphasis on their roles in maintaining health and contributing to disease. Gut microbiota homeostasis is influenced by a number of factors, including age, nutrition, and drugs. Bacteriophages, via lytic cycles and lysogenic conversion, influence the gut microbiota composition and microbial community structure. Gaining an understanding of these processes is crucial to appreciating their contribution to the stability and variety of microbes. Recent research highlights the gut phageome's potential for therapeutic interventions by demonstrating its substantial influence on immunological responses and metabolic problems. The study of phage-microbiota interactions has been transformed by cutting-edge technologies, including high-throughput sequencing, CRISPR-Cas systems, and viral metagenomics, which allow for thorough research and the creation of new therapeutics. Even though tailored medicine and pathogen management hold great potential, obstacles such as regulatory difficulties and bacterial resistance call for additional investigation. Phage-based therapeutic strategies are rapidly advancing, ranging from genetically engineered phages and phages with modified capsid proteins designed to enhance efficacy to phage cocktails that target multiple bacterial strains.},
}

@article {pmid41031628,
year = {2025},
author = {Yu, D and Kang, Y and Lu, W and Chen, B},
title = {Progress in diagnosis and treatment of primary spondylodiscitis: a systematic literature review.},
journal = {EFORT open reviews},
volume = {10},
number = {10},
pages = {815-828},
doi = {10.1530/EOR-2025-0041},
pmid = {41031628},
issn = {2058-5241},
abstract = {OBJECTIVE: Primary spondylodiscitis poses significant diagnostic and therapeutic challenges, with delayed diagnosis or improper treatment potentially resulting in severe complications. This systematic review aimed to summarize the latest diagnostic and therapeutic approaches for primary spondylodiscitis.

METHODS: Adhering to PRISMA 2020 guidelines, we conducted a systematic literature review. PubMed was comprehensively searched for English-language original studies from January 1, 1990, to October 31, 2024. Structured queries combined keywords and MeSH terms relevant to spondylodiscitis, vertebral osteomyelitis, spinal infection, and associated treatments. Two reviewers independently screened titles, abstracts, and full texts, with manual bibliography searches as a supplement. A total of 147 articles were finally included.

RESULTS: The literature indicates that diagnosis can be based on clinical suspicion, using serological, radiological, and microbiological tests. Newer methods such as metagenomics next-generation sequencing (mNGS) and positron emission tomography-computed tomography (PET-CT) can enhance diagnostic sensitivity and specificity. For confirmed cases, appropriate antibiotic therapy is crucial. Surgical treatment can benefit patients with neurological deficits, sepsis, spinal instability/deformity, epidural abscesses, or failed conservative treatment, accelerating recovery and reducing complications. Minimally invasive surgical approaches may also serve as an alternative to open surgery for select patients.

CONCLUSION: Although new technologies have improved diagnostic accuracy and treatment success rates for primary spondylodiscitis, establishing a robust staging system is vital to ensure patients receive effective, evidence-based treatment options.},
}

@article {pmid41031110,
year = {2025},
author = {Slunečko, J and Kogoj, R and Zakotnik, S and Suljič, A and Knap, N and Bosilj, M and Strle, F and Avšič-Županc, T and Bogovič, P and Korva, M},
title = {Development and performance evaluation of a clinical metagenomics approach for identifying pathogens in the whole blood from patients with undifferentiated fever.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1667422},
pmid = {41031110},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Fever ; *Bacteria/genetics/isolation & purification/classification ; *Blood/microbiology/virology ; Computational Biology ; Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; Female ; Male ; },
abstract = {INTRODUCTION: Blood culture is the cornerstone of microbiological diagnostics for patients with acute undifferentiated fever and no obvious localization of infection; however, up to 50% of cases remain undiagnosed. Infections caused by arboviruses, fastidious or even uncultivable bacteria, or parasites often go undiagnosed without the use of target-specific molecular methods. These are typically performed in a stepwise manner, increasing cost and delaying results. Metagenomic next-generation sequencing (mNGS) has recently gained recognition as a potential universal pathogen detection tool for such cases. Our study aimed to develop a streamlined mNGS workflow for simultaneous detection of intracellular and cell-free pathogens within a single sequencing library.

METHODS: Total nucleic acid was isolated separately from 200 EDTA blood samples. The plasma isolate was processed with DNase, followed by the depletion of host ribosomal and messenger RNA, reverse transcription, and sequence-independent single primer amplification (SISPA). The whole blood isolate was only reverse transcribed, with no other pre-processing manipulation. Finally, the two fractions were combined prior to library preparation and sequencing using either Oxford Nanopore Technologies or Illumina. Following established bioinformatics analysis, we developed a mathematical ranking approach (ClinSeq score) that enabled quick identification of relevant pathogens in approximately one hour.

RESULTS: The mNGS workflow reached 79.5% (159/200) overall sensitivity. For bacteria the sensitivity was 88.6% (70/79), DNA viruses, 66.7% (10/15) and for RNA viruses 73.8% (76/103). Pathogen detections by individual sequencing methods showed overall sensitivity of Illumina and ONT to be 80.0% (76/95) and 79.1% (83/105) respectively. The ClinSeq score correctly highlighted the pathogen in 126/200 (63.0%) samples effectively with a Cohen's kappa (κ) agreement of 0.61 with manual analysis.

CONCLUSION: Developed comprehensive mNGS workflow detects a wide range of pathogens in patients with acute undifferentiated fever. The unified workflow improves sensitivity for intracellular bacteria and RNA viruses, reduces time, cost and complexity by eliminating the need for separate library preparations, enabling faster turnaround suitable for clinical settings. The ClinSeq score effectively differentiates true pathogen signals from background noise, reducing false positives and manual interpretation time. Overall, the workflow demonstrates flexible, and efficient pathogen detection, supporting its potential for clinical diagnostics and improved patient management.},
}

Humans
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
*Fever
*Bacteria/genetics/isolation & purification/classification
*Blood/microbiology/virology
Computational Biology
Sensitivity and Specificity
Molecular Diagnostic Techniques/methods
Female
Male

@article {pmid41031025,
year = {2024},
author = {Waterworth, SC and Solomons, GM and Kalinski, JJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA},
title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.23.595633},
pmid = {41031025},
issn = {2692-8205},
abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, SAUL, and Tethybacterales appear to have broad host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, thus far only observed in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.},
}

@article {pmid41030903,
year = {2025},
author = {Li, Y and Jiang, X and Ji, J and Yao, B and Zhao, F and Zhang, J and Yu, Y and Fu, Y},
title = {Case report: Laboratory diagnosis methods on brain abscess pathogens caused by anaerobic species and Streptococci constellatus.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02373},
pmid = {41030903},
issn = {2214-2509},
abstract = {Brain abscess (BA) represents a severe, intracranial infection associated with high morbidity and mortality. Multiple pathogens may contribute to BA development, some of which are difficult to detect using conventional diagnostic methods alone. With the wide utilization of metagenomic next-generation sequencing (mNGS), more experiences are concluded in authenticity practice except for being regarded as a comprehensive method for detecting all pathogens. Here, we report a severe case of BA in a patient diagnosed by CT imaging, who subsequently underwent surgical removal of the abscess. To identify the causative pathogen and support anti-infection treatment, Gram staining, culture, and mNGS were performed on the abscess specimen. Interesting, we found the results were discordant: the Streptococcus constellatus was identified by culture, whereas mNGS predominantly detected anaerobic bacteria. Following additional human DNA removal, sequencing detected S. constellatus in the specimen as well. In conclusion, we highlight that a combined diagnostic strategy, leveraging both conventional culture and mNGS, is critical for comprehensive pathogen identification and informed clinical decision-making in BA.},
}

@article {pmid41030838,
year = {2025},
author = {Maqsood, S and Arshad, MT and Ikram, A and Al-Aoh, HA and Gnedeka, KT},
title = {Foodomics in Diabetes Management: A New Approach.},
journal = {Food science & nutrition},
volume = {13},
number = {10},
pages = {e71021},
pmid = {41030838},
issn = {2048-7177},
abstract = {Critical information regarding the interactions among food components, human metabolism, and disease is contained in foodomics, an interdisciplinary field that bridges food science with contemporary omics technologies (genomics, proteomics, metabolomics, and lipidomics). In order to gain a better understanding of the metabolic dysregulation in type 2 diabetes mellitus (T2DM), foodomics examines bioactive compounds derived from food (e.g., polyphenols, fibers, and lipids) alongside host molecular responses. For the enhancement of glycemic control and the prevention of diabetes-related complications, the current study is concerned with how foodomics enables personalized dietary interventions that are aligned with one's metabolic and genetic characteristics. We investigate deeper into the role of the gut microbiota in T2DM progress and how foodomics-informed methodologies, such as metabolomics and metagenomics, can be functional to discover treatments intended at the microbiota. In addition, we discover the prospective that functional foods enriched with bioactive elements, comprising β-glucans and flavonoids, may influence metabolic processes in diabetes. In addition, foodomics improves food safety by recognizing conceivable diabetes-causing contaminants (endocrine disruptors). Foodomics has incredible potential for improving precision nutrition in the prevention and treatment of T2DM, though experiments in data integration and standardization are present. Through the integration of dietary concepts, molecular biology, and clinical consequences, this method offers revolutionary strategies towards metabolic wellness.},
}

@article {pmid41030555,
year = {2025},
author = {Worku, AT and Sciarretta, A and Guarnieri, A and Falcone, M and Brancazio, N and Minwuyelet, A and Cutuli, MA and Atenafu, G and Nicolosi, D and Colacci, M and Yewhalaw, D and Di Marco, R and Petronio Petronio, G},
title = {Microbial gatekeepers: midgut bacteria in Aedes mosquitoes as modulators of arboviral transmission and targets for sustainable vector control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656709},
pmid = {41030555},
issn = {1664-302X},
abstract = {Arboviral diseases such as Dengue virus, Zika virus, Chikungunya virus, and West Nile virus pose significant global public health and economic challenges, particularly in tropical and subtropical regions. The absence of effective vaccines and sustainable vector control strategies continues to drive high morbidity and mortality rates. Symbiotic bacteria residing in the mosquito midgut can produce antimicrobial compound, stimulate the host immune response, disrupt nutrient pathways critical for pathogen development, and interfere with the pathogen's lifecycle and dissemination. Additionally, these microbes may reduce vector reproduction and shorten the lifespan of both immature and adult stages. Genetically modified symbiotic bacteria can release effector molecules that target pathogens without harming mosquitoes. Advances in genomic and metagenomic tools have deepened our understanding of the mosquito gut microbiome. This review highlights current knowledge of gut bacteria and arbovirus interactions and explores strategies to reduce arboviral transmission. Comprehensive literature searches were conducted using global databases, including PubMed, Web of Science, and Scopus, with a focus on English-language publications.},
}

@article {pmid41030552,
year = {2025},
author = {Zhang, B and Yang, T and Cheng, C and Li, T and Zhang, N and Wang, F and Chen, W and Zhong, Z and Liu, Z and Gu, G and Lin, X and Xie, X},
title = {Multi-omics analysis reveals the alleviating effect of oxidation remediation on tobacco quinclorac stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1625585},
pmid = {41030552},
issn = {1664-302X},
abstract = {The extensive use of the herbicide quinclorac has led to significant residues in agricultural soil, posing adverse effects on crop safety and high-quality production. In this study, using the tobacco variety CB-1 as material, we found that oxidizing agent K2S2O8 can significantly reduce quinclorac-induced phytotoxicity symptoms in tobacco. Furthermore, we integrated biochemical methods, metagenomics, metabolomics, and transcriptomics to investigate the effects of K2S2O8 on both quinclorac-contaminated soil and tobacco plants. Soil physicochemical properties analysis showed that the incorporation of K2S2O8-based remediation significantly mitigated the negative effects of quinclorac and largely restored the soil properties affected by quinclorac stress. Metagenomic analysis found that quinclorac significantly reduced soil species diversity, while K2S2O8-based remediation soil exhibited higher richness of microbial communities, with increased abundance of Sphingomonas and Bradyrhizobium, and decreased abundance of Alphaproteobacteria. Differential gene expression analysis showed significant up-regulation and down-regulation of genes under C10H5Cl2NO2 stress, which was partially mitigated by K2S2O8 treatment. Gene Ontology (GO) enrichment analysis indicated that these genes were mainly involved in cellular processes, metabolic pathways, and biological regulation. Metabolomic analysis further confirmed significant changes in metabolite profiles, with K2S2O8 treatment restoring many metabolites to near control levels. Integrated metabolomic-transcriptomic analysis revealed enrichment of differentially expressed genes (DEGs) and metabolites in six key pathways: (1) lysine degradation, (2) stilbenoid diarylheptanoid and gingerol biosynthesis, (3) arginine and proline metabolism, (4) phenylalanine biosynthesis, (5) tyrosine metabolism, and (6) flavonoid biosynthesis. Additionally, the levels of 4-hydroxyphenylacetylglutamic and 5-aminovaleric acid were down-regulated, along with the expression of genes associated with these metabolites, when quinclorac residual soil was treated by K2SO8. The results of this study provide a theoretical basis for the remediation of pesticide residue soil in rice tobacco rotation areas, offering valuable insights for sustainable agricultural practices.},
}

@article {pmid41030387,
year = {2025},
author = {Zheng-Qiang, L and Jun, L and Rui, A and Rui, L and Wei, D and Ping, M and Xu, Y and Rong, S and Xiao-Yan, Y and Wen, X},
title = {A probiotic for preventing microplastic toxicity: Clostridium dalinum mitigates microplastic-induced damage via microbiota-metabolism-barrier interactions.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101200},
pmid = {41030387},
issn = {2665-9271},
abstract = {Microplastics (MPs) are widely distributed and accumulated in the environment, making it nearly impossible for humans to avoid ingestion. Their toxicity can cause serious health damage and pose a threat to human health. In this context, developing strategies to prevent and restore toxic damage from their ingestion is extremely urgent. This study comprehensively employs various techniques, including metagenomics and metabolomics, to explore the pre-protective and restorative effects of Clostridium dalinum, a potential probiotic with excellent antioxidant and anti-inflammatory capabilities, on damage induced by exposure to polystyrene microplastics (PS-MPs) in mice. The results show that exposure to PS-MPs leads to significant intestinal damage in mice; preemptive intake of C. dalinum for pre-protection, or post-exposure intake of C. dalinum for restorative treatment, both significantly reduced the damage caused by MPs exposure, as evidenced by changes in intestinal length (PS-MPs exposure vs C. dalinum pre-protection vs C. dalinum restoration vs control = 36.55 vs 39.94 vs 40.12 vs 41.05 cm), barrier protein content (27.12 % vs 97.28 % vs 97.73 % vs 100.00 %), and inflammation levels (284.56 % vs 101.05 % vs 98.17 % vs 100.00 %). Mechanistically, the pre-protective and restorative effects of C. dalinum both rely on upregulating the expression of barrier proteins such as ZO-1 and Occludin and inhibiting the TLR4/NF-κB inflammatory signaling pathway. Meanwhile, the two intervention modes also exhibit specific mechanisms: in the pre-protection mode, C. dalinum enhances lipid metabolic balance and antioxidant reserves by pre-activating the PPARγ/GPR43 pathway, and enriches the ABC transporters pathway to promote toxin efflux capacity, thereby preventing PS-MPs-induced damage; in the restoration mode, C. dalinum repairs intestinal damage by enriching the beneficial bacterium Lachnospiraceae NK4A136 and inhibiting the pro-inflammatory bacterium Desulfovibrio, and regulating intestinal metabolites. In summary, this study is the first to confirm that C. dalinum can effectively prevent and restore intestinal damage caused by PS-MPs exposure through the synergistic pathway of "microbiota-metabolism-barrier". Importantly, this study is the first to reveal the potential and unique mechanisms of probiotics in preventing and restoring MPs exposure toxicity, providing a theoretical basis for the future development of probiotic-based defense strategies.},
}

@article {pmid41030376,
year = {2025},
author = {Aldeguer-Riquelme, B and Rodriguez-R, LM and Konstantinidis, KT},
title = {Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf140},
pmid = {41030376},
issn = {2730-6151},
abstract = {The importance of rarefying ecological or amplicon sequencing data to a standardized level of diversity coverage for reliable diversity comparisons across samples is well recognized. However, the importance of diversity coverage, i.e. the fraction of the genomic diversity of a sample sequenced, in comparative shotgun metagenomic studies remains frequently overlooked. Using both in silico and natural metagenomes from a wide range of environments, we demonstrate that uneven metagenome coverage can result in misleading biological conclusions, particularly for identifying differentially abundant features, i.e. groups of genes or genomes assigned to the same protein family or taxonomic rank, respectively, and for comparing diversity between samples. The main underlying cause is that not all members of a feature may be detectable, and thus counted, across such unevenly covered metagenomes depending on the sequencing effort applied and the underlying member-abundance curves. Unfortunately, 99.5% of previous comparative metagenomic studies have overlooked this metric, suggesting that their reported results might be misleading. We show that achieving high Nonpareil coverage (≥0.9), a metric that estimates metagenome diversity coverage, is the most reliable strategy to mitigate this issue. When high Nonpareil coverage is not achievable, such as for highly diverse and complex samples like soils, we show that standardizing (or subsampling) metagenomic datasets to the same Nonpareil coverage, rather than sequencing effort, prior to comparative analysis provides for more accurate results. We provide a set of practical recommendations and the corresponding Python scripts to help researchers to assess and standardize metagenome diversity coverage for their comparative analyses.},
}

@article {pmid41030375,
year = {2025},
author = {Sheridan, PO and Meng, Y and Bodington, D and Coutts, D and Williams, TA and Gubry-Rangin, C},
title = {Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf152},
pmid = {41030375},
issn = {2730-6151},
abstract = {Genome reconstruction from metagenomic samples has dramatically increased our understanding of uncultivated lineages of life. However, untargeted metagenomic sequencing is biased towards the more abundant microbes, neglecting less abundant lineages playing important ecological roles, such as the ammonia-oxidising archaea. Here, we demonstrate that separating soil molecular DNA using a bisbenzimide-CsCl guanine-cytosine (GC)-content-based DNA fractionation approach separates microbial DNA along a GC-content gradient. The fractions from both extremes of the GC-content gradient possess different 16S rRNA gene composition than the original unfractionated DNA. The high diversity in the lower GC-content fractions (< 45%) contrasts with the higher DNA abundance in the higher GC-content fractions (50%-70%), highlighting the low GC fractions as an enriched source of rare microbe DNA. Metagenomic sequencing of specific low- and high-GC fractions enabled the reconstruction of 204 taxonomically diverse metagenome-assembled genomes from 31 microbial phyla, with at least 63 of these originating from rare (< 0.1% relative abundance) or very rare (< 0.01% relative abundance) microbial families. Therefore, this approach facilitates genomic assembly of rare taxa in resulting pseudo-communities. Ultimately, this technique enables a semi-targeted metagenomic approach to recover genomes from low-abundance microbes with GC-contents that differ significantly from the environmental microbial community of interest. As mounting evidence suggests that rare microbes drive critical ecosystem functions, this approach will facilitate a deeper understanding of their metabolic potential in the environment.},
}

@article {pmid41029845,
year = {2025},
author = {Rey-Velasco, X and Auladell, A and Deulofeu-Capo, O and Lundin, D and Pinhassi, J and Ferrera, I and Sánchez, O and Gasol, JM},
title = {Decoding the genetic drivers of marine bacterial blooms through comparative genomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {198},
pmid = {41029845},
issn = {2049-2618},
support = {PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; FPU20/01625//Ministerio de Universidades/ ; },
mesh = {*Bacteria/genetics/classification/growth & development/isolation & purification ; *Genome, Bacterial ; *Seawater/microbiology ; *Genomics/methods ; *Microbiota/genetics ; Phytoplankton ; Metagenome ; Eutrophication ; Metagenomics/methods ; },
abstract = {BACKGROUND: While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as "bloomers," have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.

RESULTS: We tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.

CONCLUSIONS: In this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.},
}

*Bacteria/genetics/classification/growth & development/isolation & purification
*Genome, Bacterial
*Seawater/microbiology
*Genomics/methods
*Microbiota/genetics
Phytoplankton
Metagenome
Eutrophication
Metagenomics/methods

@article {pmid41029787,
year = {2025},
author = {Lemieux, É and Monger, XC and Saucier, L and Charette, SJ and Guay, F and Pouliot, É and Fournaise, S and Vincent, AT},
title = {Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {402},
pmid = {41029787},
issn = {1756-0500},
support = {RGPIN-2022-03321//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Swine/microbiology ; *Bacteriophages/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology/virology ; Cross-Over Studies ; },
abstract = {OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type.

RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both α- and β-diversity between sample types (digesta, feces) than between treatments. β-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. β-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.},
}

Animals
*Probiotics/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
Swine/microbiology
*Bacteriophages/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Feces/microbiology/virology
Cross-Over Studies

@article {pmid41029310,
year = {2025},
author = {Huang, J and Dong, T and Yang, C},
title = {Diagnosis of pleural aspergillosis caused by Aspergillus infection via metagenomic next-generation sequencing from a patient with unexplained pleural effusion: a case report.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {434},
pmid = {41029310},
issn = {1471-2466},
mesh = {Humans ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; *Pleural Effusion/microbiology ; *Aspergillus fumigatus/genetics/isolation & purification ; Metagenomics ; *Aspergillosis/diagnosis/drug therapy/microbiology/complications ; Antifungal Agents/therapeutic use ; Voriconazole/therapeutic use ; },
abstract = {Pleural aspergillosis is a severe pathological condition triggered by Aspergillus species and commonly affects immunocompromised individuals. This case report describes a 63-year-old man with normal immune function who was admitted to the hospital due to a 20-day history of right-sided chest pain and cough. He was diagnosed with an infection-related pleural effusion of unknown origin. Metagenomic next-generation sequencing (mNGS) identified Aspergillus fumigatus in the pleural effusion intrapleurally, and pathological examination revealed granulomatous inflammation. The patient received three months of antifungal treatment with voriconazole tablets. A six-month follow-up examination showed complete resolution of both pleural and pulmonary abnormalities. This case highlights the utility of mNGS as a diagnostic tool for detecting clinical fungal pathogens with atypical features, thereby improving diagnostic accuracy and therapeutic strategies for such conditions.},
}

Humans
Male
Middle Aged
High-Throughput Nucleotide Sequencing
*Pleural Effusion/microbiology
*Aspergillus fumigatus/genetics/isolation & purification
Metagenomics
*Aspergillosis/diagnosis/drug therapy/microbiology/complications
Antifungal Agents/therapeutic use
Voriconazole/therapeutic use

@article {pmid41029068,
year = {2025},
author = {Gao, J and Lao, C and Chen, J},
title = {Chlamydia psittacosis infection complicating cerebral infarction: A case report and literature review.},
journal = {Medicine},
volume = {104},
number = {39},
pages = {e44854},
doi = {10.1097/MD.0000000000044854},
pmid = {41029068},
issn = {1536-5964},
support = {No.2024ZL175//Chinese Medical Science and Technology Project of Zhejiang Province/ ; },
mesh = {Humans ; Female ; Middle Aged ; *Cerebral Infarction/etiology/complications/therapy/microbiology ; *Psittacosis/complications/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Chlamydophila psittaci/isolation & purification ; },
abstract = {RATIONALE: Chlamydia psittaci (CP) pneumonia is a rare zoonosis. Severe infection predisposes patients to thrombotic complications; however, only 2 documented cases of delayed cerebral infarction occurring during anticoagulant therapy exist in the literature.

PATIENT CONCERNS: A 60-year-old female with a history of hypertension and a concealed history of avian exposure presented with fever, chest tightness, and dyspnea. Examination revealed severe hypoxemia (PaO2 46.8 mm Hg), systemic inflammation (C-reactive protein 343.65 mg/L), and multi-organ dysfunction.

DIAGNOSES: CP pneumonia; cerebral infarction.

INTERVENTIONS: Following definitive diagnosis via metagenomic next-generation sequencing of bronchoalveolar lavage fluid, targeted antimicrobial therapy with omadacycline (100 mg daily) and moxifloxacin (400 mg daily) was initiated immediately. Concurrent interventions included mechanical ventilation and prophylactic anticoagulation with enoxaparin (5000 IU daily). Upon development of an acute cerebral infarction, the antithrombotic strategy was modified: anticoagulation was discontinued and dual antiplatelet therapy (aspirin 100 mg/d + clopidogrel 75 mg/d) was commenced, alongside early rehabilitation in a dedicated stroke unit.

OUTCOMES: By day 5 of antimicrobial therapy, inflammatory markers decreased significantly and oxygenation improved. Neurological function showed partial recovery by day 14 postinfarction (National Institutes of Health Stroke Scale score reduced from 8 to 3), enabling successful weaning from ventilation and hospital discharge.

LESSONS: Active screening for avian contact history and early application of metagenomic next-generation sequencing should be considered in patients with severe pneumonia. CP infection can trigger immunothrombosis, warranting vigilance for delayed stroke even during anticoagulation. Multidisciplinary management is crucial for optimizing outcomes in infection-associated cerebral infarction.},
}

Humans
Female
Middle Aged
*Cerebral Infarction/etiology/complications/therapy/microbiology
*Psittacosis/complications/diagnosis/drug therapy
Anti-Bacterial Agents/therapeutic use
*Chlamydophila psittaci/isolation & purification

@article {pmid41029053,
year = {2025},
author = {Wang, CC and Chen, Y and Li, MJ and Xie, B and Shan, Q and Guo, H and Huang, QC and Guo, BM},
title = {Acute fibrinous and organizing pneumonia presents as right lung upper lobe cavitary lesion: Case report and literature review.},
journal = {Medicine},
volume = {104},
number = {39},
pages = {e44915},
doi = {10.1097/MD.0000000000044915},
pmid = {41029053},
issn = {1536-5964},
mesh = {Humans ; Male ; Middle Aged ; Tomography, X-Ray Computed/methods ; Diagnosis, Differential ; *Cryptogenic Organizing Pneumonia/diagnosis/drug therapy/diagnostic imaging ; *Lung/pathology/diagnostic imaging ; *Pneumonia/diagnosis/drug therapy ; Methylprednisolone/therapeutic use/administration & dosage ; Organizing Pneumonia ; },
abstract = {RATIONALE: The upper lobe of the right lung, due to its unique anatomical structure that is prone to tumor occurrence, poses a challenge for the differential diagnosis of focal cavitary lesions. Cases of acute fibrinous and organizing pneumonia presenting as cavitary lesions in the upper lobe of the right lung are extremely rare in the previous literature.

PATIENT CONCERNS: This case presents a 59-year-old man who was hospitalized with a cough, phlegm, and low-grade fever after a bout of strenuous exercise and exposure to rain. A chest computed tomography (CT) revealed a cavitary lesion (lesions maximum diameter 9 cm, hollow maximum diameter of 3.5 cm) in the upper lobe of the right lung.

DIAGNOSES: Initially, he was incorrectly diagnosed with community-acquired pneumonia, and the empirical anti-infective and antiviral therapies proved ineffective. The flexible bronchoscopy lavage fluid showed negative results in metagenomic Next-Generation Sequencing (mNGS), but the pathological micrograph indicated a suspected diagnosis of acute fibrinous and organizing pneumonia.

INTERVENTIONS: He was taken off antibiotics, changed to 40 mg of methylprednisolone intravenously each day.

OUTCOMES: Six days after receiving methylprednisolone, the cough disappeared. A reexamination chest CT showed a significant reduction of the lesion. Additionally, the patient did not report any discomfort during the 6 months of follow-up.

LESSONS: This case highlights the particular characteristics of the focal cavitary lesions in the upper lobe of the right lung and emphasizes the role of liquid-based cytology in the diagnosis of acute fibrinous and organizing pneumonia, rather than mNGS.},
}

Humans
Male
Middle Aged
Tomography, X-Ray Computed/methods
Diagnosis, Differential
*Cryptogenic Organizing Pneumonia/diagnosis/drug therapy/diagnostic imaging
*Lung/pathology/diagnostic imaging
*Pneumonia/diagnosis/drug therapy
Methylprednisolone/therapeutic use/administration & dosage
Organizing Pneumonia

@article {pmid41028724,
year = {2025},
author = {Li, Z and Wei, T and He, L and Qian, H and Zhu, YG and Wang, Y},
title = {Genomic potential for mercury biotransformation in marine sediments across marginal slope to hadal zone.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8655},
pmid = {41028724},
issn = {2041-1723},
support = {42376149//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; *Mercury/metabolism ; Metagenome/genetics ; Biotransformation/genetics ; China ; Seawater/microbiology/chemistry ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; Phylogeny ; Genomics ; Methyltransferases/genetics/metabolism ; Methylation ; Ecosystem ; },
abstract = {Mercury accumulates in the deep sea, but its ecological impact on deep-sea ecosystems remains poorly understood. We conduct an analysis of 32 sediment cores, comprising 101 layers for the study of metagenomes, and additional 41 global reference sediment metagenomes. These sediment cores are collected from two deep-sea regions: the South China Sea and Mariana Trench, followed by revealing high mercury accumulation in the South China Sea. In these metagenomes, we find that the mercury methylation genes hgcAB are abundant in marginal seas but negligible in open oceans. Genomics result indicates that some Hg-methylating microorganisms affiliated with Desulfobacterota, Spirochaetota, and Zixibacteria in the deep-sea sediments encode MttB, the sole corrinoid-dependent methyltransferase identified in these taxa, which may interact with HgcA to transfer methyl groups from possibly osmolyte-derived trimethylamine for methylation. The demethylation gene merB is widely distributed and exhibits higher abundance in the open ocean. Moreover, we identify a large number of novel Hg demethylating taxa that are associated with horizontal transfer of the merB gene potentially involving methane generation. Our results expand the diversity of Hg-transforming taxa and reveal their unique ecophysiological adaptations in deep-sea sediments.},
}

*Geologic Sediments/microbiology/chemistry
*Mercury/metabolism
Metagenome/genetics
Biotransformation/genetics
China
Seawater/microbiology/chemistry
*Water Pollutants, Chemical/metabolism
Oceans and Seas
Phylogeny
Genomics
Methyltransferases/genetics/metabolism
Methylation
Ecosystem

@article {pmid41028597,
year = {2025},
author = {Maile-Moskowitz, A and Brown, CL and Rumi, MA and Moumi, NA and Majeed, H and Finkielstein, CV and Ceci, A and Gonzalez, R and Xia, K and McDaniel, L and Baffoe-Bonnie, A and Rao, J and Zhang, L and Pruden, A and Vikesland, PJ},
title = {Relating antimicrobial use to wastewater resistance gene patterns via metagenomic analysis of two neighboring treatment plants circa the COVID-19 pandemic.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {82},
pmid = {41028597},
issn = {2731-8745},
support = {1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; 2004751//National Science Foundation/ ; 2004751//National Science Foundation/ ; 2004751//National Science Foundation/ ; 1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; 1545756//National Science Foundation/ ; },
abstract = {Minimizing antimicrobial use is a recommended strategy to reduce the evolution and spread of antibiotic resistance; however, efficacy is elusive to measure. Wastewater-based surveillance provides a promising means to relate trends in microbial community antibiotic resistance profiles as a function of interventions and other factors. We examined influent sewage metagenomes for two neighboring wastewater treatment plants (WWTPs) serving a university and a nearby community. We compared antibiotic resistance gene (ARG) profiles as a function of diagnoses of COVID-19 and other illnesses, antibiotic use, antibiotic/antimicrobial and disinfectant/quaternary ammonium compound concentrations, and COVID-19-related behavioral shifts. Diversity and abundances of ARGs unique to the corresponding sewage were consistently higher for the community WWTP, but converged in 2022 when antibiotic prescriptions surged in the university zip code. Decreases in ARG diversity/abundance were not apparent during periods of decreased antibiotic usage, indicating that extended times may be required for wastewater ARG signals to attenuate following interventions.},
}

@article {pmid41028522,
year = {2025},
author = {Moon, SJ and Kim, HJ and Lim, JE and Hong, S and Won, HH and Jeong, BC and Kim, JH},
title = {HSF1-DBC1 axis drives prostate cancer progression by activating a metastatic transcriptional program.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {41028522},
issn = {2092-6413},
support = {2023R1A2C1005018//National Research Foundation of Korea (NRF)/ ; 2022R1I1A1A01064189//National Research Foundation of Korea (NRF)/ ; 2022R1I1A1A01053377//National Research Foundation of Korea (NRF)/ ; 2021R1A2C1004656//National Research Foundation of Korea (NRF)/ ; },
abstract = {Heat shock factor 1 (HSF1) is a key stress-protective transcription factor that acts as a guardian of proteostasis. HSF1 also plays multifaceted roles in tumor-associated processes including proliferation and metastasis. HSF1 is frequently overexpressed and activated in a wide range of cancers, including prostate cancer, and hijacked by cancer cells to promote their survival in harsh tumor microenvironments and during metastasis. However, mechanisms underlying the persistent activation of HSF1 and its coregulators in malignancies are largely unknown. Here we show that HSF1 is highly activated and required for metastatic spread and growth of metastatic castration-resistant prostate cancer (mCRPC) cells. The HSF1-driven transcriptional program and its genome occupancy in mCRPC cells were distinct from those of castration-resistant prostate cancer cells and massively reprogrammed during the metastatic progression of castration-resistant prostate cancer cells. In addition, we report DBC1 as a key coregulator of HSF1. DBC1 positively regulated HSF1-mediated transcription and genome-wide chromatin binding of HSF1. Moreover, DBC1 was required for super-enhancer formation and activation of super-enhancer-associated HSF1 target genes, including MMP11, involved in metastasis. Mechanistically, DBC1 activated and stabilized HSF1 by enhancing trimerization and DYRK2-mediated phosphorylation of HSF1 and inhibiting CHIP-mediated HSF1 ubiquitination, thereby increasing the transcriptional activity and genome-wide binding of HSF1. Importantly, DBC1 loss suppresses the metastatic growth of mCRPC cells, and HSF1-DBC1 double-high expression correlated with worse outcomes in patients with mCRPC. Our results highlight the critical role of HSF1 as a metastasis-promoting transcription factor and a novel regulatory mechanism of HSF1 activity and stability by DBC1. Thus, targeting the HSF1-DBC1 axis could be a promising therapeutic strategy for metastatic cancers.},
}

@article {pmid41028378,
year = {2026},
author = {Sahil, R and Jain, M},
title = {A Multi-omics Approach for Microbiome Data Analysis in Legumes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2977},
number = {},
pages = {181-196},
pmid = {41028378},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Computational Biology/methods ; Data Analysis ; Metagenome ; Multiomics ; },
abstract = {Microbiome plays a crucial role in influencing the health and function of living beings as well as in regulating the biogeochemical cycles. The plant microbiome, in particular, has garnered significant research interest aimed at exploring the microbes that play a crucial role in regulating plant growth and nutrient acquisition. Recent advancements in omics sciences have played a crucial role in uncovering the complexities of these relationships. While techniques such as amplicon and shotgun metagenomics provide taxonomic profiling up to the species level and even the strain level, metatranscriptomics further elucidates the functional roles of these microbes. These techniques are being rapidly and widely adopted to understand the influence of microbes on the host. However, the challenge lies in their integration. Most studies to date rely on only one of these techniques, which limits the scope of holistic understanding of host-microbe interactions. Additionally, there is currently no well-established workflow that effectively combines these techniques to provide comprehensive biological insights. In this work, we describe an integrated approach for microbiome data analysis to provide biologically meaningful insights.},
}

*Microbiota/genetics
*Metagenomics/methods
*Fabaceae/microbiology/genetics
*Computational Biology/methods
Data Analysis
Metagenome
Multiomics

@article {pmid41028236,
year = {2025},
author = {Ning, Z and Liu, J and Zhang, J and Zhong, W and Yang, T and Huang, Y and Qin, X and Zhang, X and Xu, X},
title = {Enhancement of short-chain fatty acids production by biochar-supported zero-valent iron in anaerobic fermentation: focusing on metabolic reactions and electron transport.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {41028236},
issn = {1615-7605},
abstract = {Carbon-based and iron-based materials have been widely reported as effective promoters in biogas fermentation due to the promotion of electron transport. However, the effect of these materials, especially in combination, on short-chain fatty acids (SCFAs) production has been scarcely reported. In this study, the production of short-chain fatty acids (SCFAs) from green cabbage waste was promoted by adding biochar (BC) and biochar-supported zero-valent iron (BC@ZVI). The underlying mechanisms, focusing on metabolic pathways and electron transport, were subsequently investigated through metagenomic analysis. The optimal SCFAs yields were achieved with BC (5 g·L[-]1) and BC@ZVI (15 g·L[-]1). While BC notably enhanced n-butyrate production (89.4-fold), BC@ZVI balancedly promoted acetate and n-butyrate. Metagenomics revealed that BC@ZVI's superiority stemmed from its enhanced ability to enrich functional microbes and facilitate electron transfer. Metagenomic analysis revealed that BC@ZVI enriched Sphaerochaeta and Herbinix, which could participate in the direct interspecies electron transfer process. The abundance of almost all functional enzymes involved in carbohydrate hydrolysis and the synthesis of acetate and n-butyrate were remarkably increased by BC@ZVI. BC and BC@ZVI lead to a notable enrichment of conductive pili genes, including pilB, pilC, and pilM. BC@ZVI enriched both conductive pili and c-type cytochromes, which could be considered a more effective selection than BC. Notably, BC@ZVI was more effective than BC in stimulating n-butyrate-type fermentation, significantly shortening the lag phase and the overall fermentation cycle, thereby exhibiting better comprehensive performance, enhancing pH buffering capacity, and strengthening electron transfer and substrate hydrolysis. The results proved the potential of BC@ZVI in SCFAs fermentation and deciphered the underlying mechanisms, which provided a new perspective to promote resource recovery of organic waste by anaerobic system.},
}

@article {pmid41028186,
year = {2025},
author = {Chen, J and Lou, H and Yao, Y and Chen, Q and Liu, C and Zhou, H},
title = {Metagenomic next-generation sequencing for concurrent diagnosis of infections and malignancies in patients with lung lesions: a single-center prospective study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33721},
pmid = {41028186},
issn = {2045-2322},
support = {2022YFC2504502//the Key R&D Plan of the Ministry of Science and Technology of China/ ; 2023C03068//the Research and Development Program of Zhejiang Province/ ; 82272338//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Lung Neoplasms/diagnosis/genetics ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Prospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; DNA Copy Number Variations ; Adult ; Sensitivity and Specificity ; Diagnosis, Differential ; },
abstract = {Metagenomic next-generation sequencing (mNGS) offers sensitive and rapid pathogen detection and has the added advantage of analyzing chromosomal copy number variations (CNVs) of the host in the same test. This study aimed to evaluate the dual diagnostic performance of mNGS in clinical cases where pulmonary infections and malignancies are difficult to be distinguished. A single-center prospective study was conducted at the First Affiliated Hospital, Zhejiang University School of Medicine. The study recruited patients with lung lesions from October 2021 to October 2022 that required differential diagnosis of infection, malignancy, or other pulmonary diseases. The mNGS was used to detect both pathogens and potential CNVs of the host chromosomes to inform presence of neoplasm, and the results were compared to conventional microbiological tests (CMTs), bronchoalveolar lavage fluid (BALF) cytology, histology, and clinical composite diagnoses. The mNGS demonstrated a significantly higher sensitivity of infection diagnosis (56.5% vs.39.1% for CMTs, P < 0.05). The CNVs analysis showed moderate sensitivity (38.9%) and high specificity (100%) for diagnosing malignancy, which helped determine lung cancer in 4 cases who were initially considered as pneumonia. Combining CNVs analysis with BALF cytology has increased the sensitivity for detecting malignancy from 38.9% to 55.6%. Furthermore, the sensitivity of CNVs analysis was higher (50%) when bronchoscopy directly found positive signs, such as neoplasm or bronchial mucosal infiltration. This study highlights the dual capacity of mNGS to simultaneously detect infections and malignancies. The integration of both pathogen and tumor detection could significantly enhance clinical decision-making, particularly for patients with overlapping symptoms of infection and cancer.},
}

Humans
*Lung Neoplasms/diagnosis/genetics
Male
*High-Throughput Nucleotide Sequencing/methods
Prospective Studies
Female
Middle Aged
*Metagenomics/methods
Aged
Bronchoalveolar Lavage Fluid/microbiology
DNA Copy Number Variations
Adult
Sensitivity and Specificity
Diagnosis, Differential

@article {pmid41028005,
year = {2025},
author = {Xu, H and Ba, W and Yu, R and He, Z and Wang, P and Gou, X and Zhang, X and Wang, F},
title = {Fructophilic Apilactobacillus kunkeei alleviates high-fructose diet-induced lipid accumulation by modulating gut microbiota and intestinal barrier function in mice.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {201},
pmid = {41028005},
issn = {2396-8370},
support = {32402039//National Natural Science Foundation of China/ ; },
abstract = {Excessive fructose consumption is strongly linked to metabolic syndrome, with gut microbiota playing a pivotal role in mediating fructose metabolism and associated metabolic disturbances. In this study, we aimed to characterize Apilactobacillus (A.) kunkeei, a fructophilic lactic acid bacterium from honey, and evaluate its probiotic function in male C57BL/6 J mice fed a high-fructose diet (HFD). Transcriptome analysis was carried out to analyze the activation of pathways under various culture conditions. Pathway inhibitors were used in cell culture and a hepatectomy mouse model to study the function of different pathways in hepatocyte growth and liver regeneration. Our results showed that A. kunkeei FM01 exhibited strong tolerance to simulated gastrointestinal stress in vitro, indicating good probiotic potential. Administration of A. kunkeei FM01 significantly reduced body weight gain, improved glucose tolerance, and attenuated hepatic and visceral (perirenal and epididymal) lipid accumulation in HFD-fed mice. Serum lipid profiling and targeted lipidomic analysis revealed that A. kunkeei FM01 lowered triglycerides, phosphatidylcholine, and lysophosphatidylcholine levels while increasing beneficial phospholipids such as phosphatidylethanolamine. Metagenomic analysis demonstrated that A. kunkeei FM01 modulated gut microbiota composition by reducing pro-inflammatory and fructose-metabolizing taxa, including Alistipes, Oscillibacter, Desulfovibrio, Lawsonibacter, and Enterococcus, while enriching beneficial species, including Kineothrix alysoides and Faecalibaculum rodentium. These microbial shifts were associated with increased abundances in genes encoding carbohydrate-active enzymes and amino acid biosynthesis pathways. Furthermore, A. kunkeei FM01 restored intestinal barrier integrity by upregulating tight junction proteins (Zonula Occludens-1 and occludin) and reduced serum lipopolysaccharide and diamine oxidase levels. Collectively, these findings suggest that A. kunkeei FM01 exerts protective effects against HFD-induced metabolic dysfunction through multi-targeted mechanisms involving lipid metabolism, gut microbiota modulation, and intestinal barrier restoration. This study identifies A. kunkeei FM01 as a promising probiotic candidate for preventing and managing fructose-associated metabolic disorders.},
}

@article {pmid41027803,
year = {2025},
author = {Blank, RB and Bu, K and Zhang, X and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Williams, FMK and Clemente, JC and Scher, JU},
title = {Short-chain fatty acids and their gut microbial pathways distinguish rheumatoid arthritis in discordant monozygotic twins.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ard.2025.08.029},
pmid = {41027803},
issn = {1468-2060},
abstract = {OBJECTIVES: Although genetic risk factors, such as HLA-DRB1 alleles, contribute to the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other factors are involved in disease development. Further, the relative contribution of nongenetic elements in identical twins has not been characterised. Here, we aimed to characterise host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multiomics approach.

METHODS: Eight pairs of MZ twins discordant for RA (N = 16) were enrolled in the United States (US). The gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and plasma proteins were measured in both plasma and faeces. Levels of short-chain fatty acids (SCFAs) from serum and faeces were quantified using gas chromatography mass spectrometry (GC-MS). Metagenomic data from a UK twin registry (TwinsUK) (N = 14) were used to validate findings in the US population.

RESULTS: Although microbiome diversity and composition did not differ between twins, we observed a significant decrease in the SCFA-producing bacteria Blautia faecis and significantly lower concentrations of faecal butyrate and propionate in affected RA twins in the US. TwinsUK showed a similar reduction in the SCFA-producers Gemmiger formicilis and Faecalicatena fissicatena, as well as bacterial SCFA metabolism pathways.

CONCLUSIONS: Multiomics biomarkers differentiate MZ twins discordant for RA. Faecal butyrate and propionate, as well as SCFA-producing bacteria, were decreased in affected twins. We found a similar decrease in SCFA-producing taxa in affected twins in a geographically distinct cohort in the UK. Our results suggest that, if further validated in larger cohorts, multiomics approaches may improve our understanding of RA pathogenesis and, potentially, contribute to more accurate diagnostics and coadjuvant therapies.},
}

@article {pmid41027356,
year = {2025},
author = {Kahwage, S and Lanzarini, NM and de Paula, BB and Saggioro, EM and Motta, ATF and Mannarino, CF and Miagostovich, MP},
title = {Viral genetic diversity in surface and groundwater at a non-operational dumpsite and its surrounding neighborhood.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180604},
doi = {10.1016/j.scitotenv.2025.180604},
pmid = {41027356},
issn = {1879-1026},
abstract = {Inappropriate municipal solid waste disposal areas lack waterproof base liners, drainage systems, treatment of waste degradation by-products, mass coverages, and vector control. Leachate is a by-product derived from water percolation through solid waste disposal sites, comprising an environmental and health contamination source when not adequately collected and treated. This study aimed to describe surface and groundwater viral diversity in a dumpsite area non-operational for over a decade and its surrounding neighborhood in the metropolitan Rio de Janeiro region employing shotgun metagenomic analysis. Between May 2021 and March 2023, 100 leachate samples (2 L each) were collected from 21 sampling points and subsequently organized into five pooled samples. Nucleic acids were extracted employing the Biopur Nucleo-mag Virus kit, followed by purification with AMpure XP beads and quantification via Qubit 4.0, Next-Generation Sequencing was performed on a NextSeq 2000 sequencer (Illumina, USA). Sequencing analysis identified 578 operational taxonomic units, of which 312 (54 %) were classified into 46 viral families, while 266 (46 %) remained unclassified, the Microviridae family was the most abundant. Viral sequences linked to pathogenic hosts were detected, including canine circovirus. Comparable viral family profiles were observed between the dumpsite and the residential area suggesting that some of the shared viral families may be influenced by groundwater flow originating from the closed dumpsite. Although irregular land use hinders precise attribution of contamination sources, the detection of potentially pathogenic viruses in waters intended for human use raises significant public health concerns. These findings support long-term virome-based surveillance of groundwater near closed dumpsite.},
}

@article {pmid41027219,
year = {2025},
author = {Li, X and Zhu, S and Wang, H and Zhen, Q and She, D},
title = {Silicon-modified lignin biochar outperforms hydrochar in heavy metal remediation: stochastic microbial assembly and functional gene reprogramming drive soil multifunctionality.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139966},
doi = {10.1016/j.jhazmat.2025.139966},
pmid = {41027219},
issn = {1873-3336},
abstract = {Heavy metal contamination severely threatened soil health, microbial stability, and food safety worldwide. While lignin-based biochar had shown potential in mitigating metal toxicity, its regulatory effects on soil microbiomes and ecosystem functions remained inadequately understood, especially across different carbonization strategies. A cross-scale remediation framework using silicon-modified lignin-based hydrochar (Si-LHB) and pyrochar (Si-LPB) was developed to restore cadmium (Cd)/zinc (Zn)-contaminated soil ecosystems. In a pot experiment combined with metagenomics and biochemical assays, metal speciation, microbial dynamics, nitrogen cycling, and soil multifunctionality were evaluated. Results showed that both Si-LHB and Si-LPB effectively enhanced metal stabilization and plant growth, yet Si-LPB outperformed Si-LHB by significantly reducing acid-soluble Cd and Zn (by 16.22 % and 48.43 %) and increasing residual fractions up to 72.70 %, primarily via silicate precipitation and microenvironment modulation. Compared to Si-LHB, Si-LPB more effectively restructured bacterial communities, enriching Pseudomonadota and increasing community stochasticity (NST＞50 %). It also selectively upregulated nitrogen transport genes (e.g., narK, nrtP) and suppressed denitrification genes (e.g., nirK, nosZ), enhancing nitrogen retention and carbon fixation. Consequently, Si-LPB improved soil multifunctionality by 72.13 % and reduced Cd/Zn accumulation in plants by up to 99.66 %. This study demonstrates that silicon-enhanced lignin biochars, particularly Si-LPB, restore soil ecological functions through functional redundancy and enrichment of keystone taxa rather than by increasing diversity, offering a promising carbon-silicon-microbe strategy for sustainable remediation.},
}

@article {pmid41027192,
year = {2025},
author = {Xu, H and Chen, C and Pang, Z and Zhang, G and Zhang, W and Kan, H},
title = {Effects of microplastics and excessive nitrogen pollution on oat growth and soil nitrogen cycling.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119119},
doi = {10.1016/j.ecoenv.2025.119119},
pmid = {41027192},
issn = {1090-2414},
abstract = {Both excessive nitrogen (N) and microplastic (MPs) pollution pose global change challenges to ecosystems and human health. The effects of MPs coexisting with excessive N on plant growth and N cycling are still largely unknown. This study employed a pot experiment to assess how polypropylene (PP) MPs influence oat (Avena sativa L.) growth and soil N cycling under conditions of excessive N fertilization. In the treatments of excessive N treatment, 2 % PP MPs significantly increased underground biomass (54.5 %). [15]N stable isotope results showed that 2 % PP MPs treatment significantly reduced the percentage of N from fertilizer in oat by 10.4 %. Compared to without N treatment, excessive N treatment reduces the Shannon index of the rhizosphere soil bacterial community. Only at the 0.5 % PP MPs level, excessive N treatment significantly reduced the diversity of bacterial communities in the bulk soil compared to the without N treatment. The Shannon index of fungal community was not affected by N treatment and MPs. Microbial biomass nitrogen (MBN) and pH were significant related to sensitive species in microbial communities. The coexistence of excess N and 2 % PP MPs significantly reduced the abundance of genes (norB, nosZ and nirB) related to denitrification process. Structural equation modeling showed that MPs could promote underground biomass, reduce soil pH, inorganic N content, and reduce N uptake efficiency, thus resisting growth damage caused by high N. In the future, the effects of different concentrations and types of MPs and different nitrogen forms on soil and crops should be further investigated.},
}

@article {pmid41027153,
year = {2025},
author = {Zhang, S and Gao, W and Gao, X and Xu, W and Liu, Y and Guo, Z and Liu, G and Zhang, P and Shi, H and Chang, X},
title = {Astragaloside VI attenuates mechanical stress-induced cardiac remodeling through piezo1-VDAC1 dependent endoplasmic reticulum unfolded protein response.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157288},
doi = {10.1016/j.phymed.2025.157288},
pmid = {41027153},
issn = {1618-095X},
abstract = {BACKGROUND: The dysregulation of protein homeostasis is a condition associated with mechanical stress-induced cardiac remodeling (CR) due to endoplasmic reticulum (ER) dysfunction and stress.

PURPOSE: This research explores the effect of Piezo1 on the ER unfolded protein response (UPR) in cardiomyocytes following hypoxic stress, specifically through its interaction with VDAC1. In addition, the study evaluates the therapeutic potential that this mechanism holds for treating CR and cardiomyocyte hypertrophy.

STUDY DESIGN: Considering the relative limitation of potential therapeutic drugs for CR, our goal is to utilize a multi-omics approach to confirm the process by which Astragaloside IV (AS) alleviates CR through the Piezo1-VDAC1 dependent UPR.

METHODS: We utilized multiple omics studies, such as single-cell sequencing, network pharmacology, and metagenomics, for the validation of AS's targets and phenotypic mechanisms. Following this, we created Piezo1/VDAC1 transgenic mice (Piezo1[TG]/VDAC1[TG]) and wild-type mice, which were then subjected to transverse aortic constriction (TAC) to induce myocardial damage. We performed assessments of cardiac function, myocardial injury staining, and cardiomyocyte hypertrophy on these animal models both before and after the drug intervention. The analysis into the interaction between Piezo1-VDAC1 and the structural integrity of cytoskeletal proteins and the ER was conducted utilizing laser confocal microscopy, immunofluorescence, and molecular biology experiments.

RESULTS: The regulation of mechanical stress-induced cardiac remodeling crucially involves Piezo1-VDAC1. Data from single-cell sequencing and network pharmacology suggest that ER damage, mitochondrial energy metabolism dysfunction, and the dysregulation of subcellular organelles are important phenotypes that mediate this process. Our animal experiments demonstrated that AS is capable of improving cardiac function after TAC, inhibiting myocardial injury and the associated inflammatory reaction, and suppressing excessive UPR stress. The therapeutic effect of the drug was eliminated by the transgenic treatment of Piezo1. In vitro experiments also offered confirmation that AS can ameliorate cardiomyocyte damage through the ER pathway. This is achieved by regulating the Piezo1-VDAC1 interaction mechanism, which restores ER structural collapse after hypoxic injury, enhances energy metabolism levels, and inhibits excessive UPR stress.

CONCLUSION: The abnormal activation of the UPR, which is mediated by Piezo1-VDAC1, constitutes the pathological mechanism behind mechanical stress-induced cardiac remodeling. By regulating the Piezo1-VDAC1 interaction, AS inhibits excessive UPR stress and improves the breakdown of ER structure and functional abnormalities. These actions further normalize ER function and ameliorate cardiac function and myocarditis-related injury. This work offers a promising strategy for utilizing natural medicine to treat mechanical stress-induced cardiac remodeling.},
}

@article {pmid41026933,
year = {2025},
author = {Greco, M and Coculo, D and Conti, A and Agresti, S and Pontiggia, D and Mélida, H and Favaro, L and Lionetti, V},
title = {Biorefining of Anaerobic Digestates for the Recovery of Biostimulants and Bioelicitors for Immune Priming and Plant Protection.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03321},
pmid = {41026933},
issn = {1520-5851},
abstract = {Olive oil production is a major global agricultural industry that generates significant waste, particularly olive pomace, which poses environmental and economic challenges. Anaerobic digestion emerges as a promising solution for its valorization into biogas. However, the resulting digestate remains underutilized and its long-term environmental impact is uncertain. Traditional disposal methods are costly and inefficient, underscoring the need for more sustainable approaches. In this study, olive pomace digestate was biorefined, and its components were upcycled into soil amendments and plant immunostimulants. Metagenomic analysis revealed a diverse microbial community in the liquid fraction. A microbial-enriched protein extract (MIPE) was obtained, containing precursors of microbe- and damage-associated molecular patterns, including Flagellin, Elongation Factor Tu, and the plant phytocytokine Golven. Plant treatment with MIPE triggered a rapid immune response, characterized by oxidative burst, mitogen-activated protein kinase activation, and the upregulation of defense-related genes such as CYP81F2, FRK1, and WRKY53. MIPE-induced priming enhanced Arabidopsis and tomato resistance to Botrytis cinerea and Pseudomonas syringae. Our findings highlight olive pomace digestate as a valuable growth biostimulant, with its liquid fraction also representing a promising resource of immunity bioelicitors. This refinement valorizes olive mill waste, providing a sustainable alternative to chemical fertilizers and pesticides and supporting sustainable agriculture.},
}

@article {pmid41026643,
year = {2025},
author = {Wu, D and Van Goethem, MW and Graham, DW and Zhang, X and Li, Z and Shi, G},
title = {Antarctic Environmental Resistomes Closely Associated with Human and Animal Waste Releases.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06023},
pmid = {41026643},
issn = {1520-5851},
abstract = {Antarctica harbors a diverse spectrum of antibiotic resistance genes (ARGs) across lake, soil, and seawater environments. However, linkages between resistomes in waste-impacted and pristine settings are not well understood in polar settings, especially how phage, plasmids, and microbial community assembly influence the spatial distribution of ARGs. Metagenomic sequencing of 85 Antarctic samples showed 10-fold greater ARG abundances near animal and human waste-impacted sites compared with more remote settings, including glacial, lake, soil, and offshore seawater sites (-1.9 to -0.1 log10(ARGs/cell), P < 0.01), although (except for glaciers) resistome compositions were broadly similar. Based on metagenomic data, plasmids appear to be more associated with ARGs than phages in the Antarctic samples, with Pseudomonas, Staphylococcus, Bacillus, and Mycobacterium being primarily associated with ARG prevalence because they dominate local microbial assemblages. These primary taxa exhibit wide cross-setting prevalence and are not significantly impacted by local environmental selection (P > 0.05, SNPs-RDA). As such, human- and animal-waste-impacted locations, which have higher microbial migration rates (m = 10.8, NCM), are primary sources of ARG-containing and assembly predominant bacteria in Antarctic settings. Thus, better management of waste releases from human settlements must be central to retaining "pristine" Antarctic environments against the globally expanding resistomes.},
}

@article {pmid41026231,
year = {2025},
author = {Qian, M and Zhou, J and Chen, P and Jiang, N and Wang, T and Chen, X and Xu, H and Zhou, F and Yang, Y and Lin, X and Yang, Q and Shao, L and Ruan, Q and Zhang, W},
title = {A Novel Compound Heterozygous Mutation in the IL12RB1 Gene Causes Susceptibility To Mycobacterium Tilburgii Infection.},
journal = {Journal of clinical immunology},
volume = {45},
number = {1},
pages = {133},
pmid = {41026231},
issn = {1573-2592},
support = {82271794//National Natural Science Foundation of China/ ; KY2024-664//Clinical Research Project of Huashan Hospital, Fudan University./ ; },
mesh = {Humans ; Female ; *Receptors, Interleukin-12/genetics ; *Genetic Predisposition to Disease ; Adult ; Heterozygote ; *Mycobacterium Infections/genetics/diagnosis/drug therapy/immunology ; *Mutation ; *Mycobacterium ; Interferon-gamma ; },
abstract = {Mendelian susceptibility to mycobacterial disease (MSMD) is a rare clinical syndrome that is characterized by selective vulnerability to intracellular pathogens. Deficiency in IL12RB1 is the most common type of MSMD but the heterogeneity of its clinical Manifestation Makes precise diagnosis difficult. Here, we report a previously healthy 29 year-old woman who had suffered from disseminated infection with Mycobacterium tilburgii, which is a rare, unculturable environmental mycobacteria, for over 2 years. We used whole exome sequencing to detect a novel compound heterozygous variant in the IL12RB1 gene. Immunological analysis of the patient's peripheral lymphocytes showed a barely detectable level of IL-12Rβ1, a reduced population of follicular helper T (Tfh) cells and impaired production of IFN-γ in response to IL-12/IL-23 stimulation. Metagenomic next-generation sequencing was used to identify the causative pathogen and to analyze drug susceptibility. The infection was contained by a combination of anti-mycobacterial drugs and IFN-γ supplementary treatment. An RNA-seq analysis, using follow-up blood samples, revealed the limited success of these treatments over 6 months. Our findings support the screening for inherited immunological problems in patients with difficult-to-treat mycobacterial infections. The suboptimal response to prolonged anti-mycobacterial drugs and IFN-γ supplementation warrants the development of novel therapeutic strategies for MSMD patients.},
}

Humans
Female
*Receptors, Interleukin-12/genetics
*Genetic Predisposition to Disease
Adult
Heterozygote
*Mycobacterium Infections/genetics/diagnosis/drug therapy/immunology
*Mutation
*Mycobacterium
Interferon-gamma

@article {pmid41026172,
year = {2025},
author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y},
title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {98},
pmid = {41026172},
issn = {1432-184X},
support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; },
abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.},
}

Animals
*Gastrointestinal Microbiome
*Bacteriophages/genetics/classification/physiology/isolation & purification
*Bacteria/classification/genetics/isolation & purification/virology
*Ecosystem
RNA, Ribosomal, 16S/genetics
*Antelopes/microbiology/virology
Metagenome
Feces/microbiology

@article {pmid41026152,
year = {2025},
author = {Nassirnia, S and Scherz, V and Greub, G and Caruana, G and Taffé, P and Jaton, K and Papis, S and Posfay-Barbe, KM and Mornand, A and Rochat-Guignard, I and Bertelli, C and Asner, SA},
title = {Concordance between upper and lower airway microbiota in children with cystic fibrosis.},
journal = {Journal of medical microbiology},
volume = {74},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002079},
pmid = {41026152},
issn = {1473-5644},
mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Sputum/microbiology ; *Microbiota ; Child ; *Pharynx/microbiology ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Adolescent ; Longitudinal Studies ; *Respiratory System/microbiology ; Metagenomics ; Infant ; },
abstract = {Introduction. Sputum is the most used sample type to monitor the lower respiratory tract microbiota in cystic fibrosis (CF), but young patients often cannot expectorate.Hypothesis. We hypothesized that throat swabs could reflect lower airway colonization and assessed the concordance of bacterial community composition between paired sputum and throat swab samples from children with CF.Aim. We aimed to compare bacterial community diversity and composition between sputum and throat swabs in the full cohort and in patients with paired samples from the same visit.Methodology. The prospective longitudinal multicentre MUCOVIB cohort included 379 samples from 61 CF children. Using V3-V4 16S rRNA amplicon metagenomics, we compared bacterial community diversity and composition between sputum and throat swabs in the full cohort and in 11 patients with paired samples from the same visit.Results. Sputum and throat swabs exhibited similar bacterial diversity, regardless of the exacerbation status, and presented a substantial agreement for detecting pathogens (Cohen's kappa: 0.6). Differences in bacterial abundance were observed (P=0.001), but not presence/absence (P=0.098). Community typing revealed three distinct community types, with 86% of paired samples falling into the same cluster, highlighting the homogeneity between sputum and throat swab microbiota. Network analysis demonstrated slight, non-random similarities in microbial interactions between sample types (adjusted Rand index=0.08 and 0.10). The average beta-diversity distances between samples collected from the same visit were shorter (0.505±0.056 95% confidence interval), compared with sputum (0.695±0.017) or throat swab (0.704±0.045) from the same patient collected during different visits.Conclusion. Throat swabs can provide representative information on lower respiratory microbiota. Clinicians should collect throat swabs rather than relying on sputum samples from previous visits to guide antibiotic prescriptions in CF children unable to expectorate.},
}

Humans
*Cystic Fibrosis/microbiology
*Sputum/microbiology
*Microbiota
Child
*Pharynx/microbiology
Male
Female
*Bacteria/classification/genetics/isolation & purification
Prospective Studies
RNA, Ribosomal, 16S/genetics
Child, Preschool
Adolescent
Longitudinal Studies
*Respiratory System/microbiology
Metagenomics
Infant

@article {pmid41026097,
year = {2025},
author = {Patyka, M and Wang, R and Honchar, A and Patyka, T and Khablak, S},
title = {Modulation of the rhizosphere microbiome structure and optimization of beneficial functions in winter wheat induced by Bacillus subtilis: a metagenomic and phenotypic study.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf097},
pmid = {41026097},
issn = {1574-6941},
abstract = {The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in above-ground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.},
}

@article {pmid41025937,
year = {2025},
author = {Garvey, SM and Blonquist, TM and Brutscher, LM and Walsh, DM and Kaden, VN and Beckman, DB and Zeng, M and Bruno, RS and Cook, CM and Spears, JL},
title = {Dietary Supplementation with the Probiotic Bacillus velezensis BV379 Decreases Abdominal Bloating Without Perturbing the Commensal Gut Microbiota: A Randomized, Double-Blind, Placebo-Controlled Trial in Healthy Adults.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/27697061.2025.2563894},
pmid = {41025937},
issn = {2769-707X},
abstract = {OBJECTIVE: Various bacterial Bacillaceae and Bacillus strains have demonstrated health benefits, but less is known about probiotic characteristics of strains of Bacillus velezensis. In this randomized, double-blind, placebo-controlled clinical trial, we investigated the safety and efficacy of B. velezensis BV379 supplementation for 8 weeks (2 × 10[9] colony-forming units (CFU)/day).

METHODS: During the baseline and final weeks, GI symptoms were recorded daily using the 8-item Gastrointestinal Tolerance Questionnaire (GITQ). The primary outcome was the proportion of participants showing an improvement from baseline to week 8 in the 7-day, 3-item composite score for abdominal distention/bloating, burping, and gas/flatulence. Plasma chemistry, hematology, intestinal permeability, and fecal metagenomes were also investigated.

RESULTS: Eighty participants (54% female; age: 50.3 ± 10.1 years) were randomized to BV379 (n = 39) or placebo (n = 41). At end of study, no significant difference was observed in the percentage of participants with improvement in the 3-item composite GITQ score (BV379: 36.1%; placebo: 28.2%; p = 0.46). Analysis of individual GI symptoms showed that more participants experienced improvement in abdominal distention/bloating with BV379 compared to placebo (38.9% vs 17.9%; p = 0.044). There were no clinically meaningful changes in plasma chemistry, hematology, or intestinal permeability between groups. Fecal metagenomic analyses showed no overall shifts in microbial composition between groups. In addition to B. velezensis, a few commensal species such as Lacticasei bacillus casei were significantly enriched in the BV379 group.

CONCLUSION: Despite not significantly improving the composite GITQ score of distention/bloating, burping, and gas/flatulence, BV379 supplementation was a well-tolerated approach to specifically lower abdominal bloating.},
}

@article {pmid41025824,
year = {2025},
author = {Li, Z and Li, S and Han, C and Chen, Y and Zhen, H and Sun, Y and Zhou, X and Chen, Y and Zheng, Y and Han, L and Krutmann, J and Nie, C and Wang, J and Xia, J},
title = {A comprehensive reference catalog of human skin DNA virome reveals novel viral diversity and microenvironmental influences.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0117825},
doi = {10.1128/spectrum.01178-25},
pmid = {41025824},
issn = {2165-0497},
abstract = {UNLABELLED: Human skin serves as a dynamic habitat for a diverse microbiome, including a complex array of viruses whose diversity and roles are not fully understood. A total of 2,760 skin metagenomes from 6 published skin studies were collected. A skin virome catalog was constructed using standard methods in the viromics field. Viral characteristics were identified through cross-cohort meta-analysis and used to characterize viral features across different skin environments. We identified 20,927 viral sequences, which clustered into 2,873 viral operational taxonomic units (vOTUs), uncovering a substantial breadth of viral diversity on human skin. The results also highlight significant differences in viral communities that are associated with varying skin microenvironments. The oily skin is enriched in Papillomaviridae, the dry skin area is enriched in Autographiviridae and Inoviridae, and the moist skin is enriched in Herelleviridae. We also investigated the relationship between bacteriophages and bacteria on the skin surface. We found that skin bacteria such as Pseudomonas, Klebsiella, and Staphylococcus are predicted to be infected by phages from the class Caudoviricetes. This comprehensive skin DNA viral catalog significantly advances our understanding of the virome's role within the skin ecosystem.

IMPORTANCE: This study presents a comprehensive reference catalog of the human skin DNA virome, constructed from 2,760 metagenomic datasets collected globally. It identified 20,927 viral sequences, with 90.85% representing previously unknown viruses, greatly expanding our understanding of skin viral diversity. The findings reveal significant differences in viral communities between distinct skin microenvironments (oily, dry, and moist) and highlight close interactions between bacteriophages and their bacterial hosts, suggesting a potential role for the virome in maintaining microbial balance and skin health. This extensive skin viral catalog constitutes a crucial resource for future epidemiological and therapeutic research, potentially facilitating the development of novel phage therapies and diagnostic markers for skin disorders.},
}

@article {pmid41025799,
year = {2025},
author = {Buckner, AM and Glendinning, L and Palma Hidalgo, JM and van Munster, JM and Stevens, M and Watson, M and Newbold, CJ},
title = {The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0056325},
doi = {10.1128/spectrum.00563-25},
pmid = {41025799},
issn = {2165-0497},
abstract = {Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.},
}

@article {pmid41025782,
year = {2025},
author = {Boyd, AI and Kafer, LA and F Escapa, I and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP},
title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0049325},
doi = {10.1128/msphere.00493-25},
pmid = {41025782},
issn = {2379-5042},
abstract = {UNLABELLED: Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. Human nasal epithelial organoids (HNOs) differentiated at air-liquid interface (ALI) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. Due to their natural stem-like properties, HNO lines are a long-term experimental resource that offers genetic diversity based on the different donors. To develop HNOs as a new model system for bacterial nasal colonization, we reproducibly monocolonized HNOs differentiated at ALI with S. aureus, S. pneumoniae, or Dolosigranulum pigrum for up to 48 h with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, which is consistent with colonization rather than infection. Only live S. aureus colonization robustly induced epithelial cell production of interleukin-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a new model system for uncovering microbe-epithelial cell dynamics at the human nasal mucosa.

IMPORTANCE: Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and drug-resistant Streptococcus pneumoniae. Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum. Learning how these microbionts interact with the nasal epithelium and identifying new means to reduce pathobiont colonization are key goals in the field. As a tool to advance this research, we developed human nasal epithelial organoids (HNOs) differentiated at an air-liquid interface as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages, enabling exploration of bacterial-epithelial interactions, which is important since the epithelium is an instigator of the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria, setting the stage for future research.},
}

@article {pmid41025644,
year = {2025},
author = {Saito, D and Saito, CPB and Cannavan, FDS and Tsai, SM},
title = {Draft genome sequences of six Rothia mucilaginosa strains assembled from the human oral microbiome.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0050825},
doi = {10.1128/mra.00508-25},
pmid = {41025644},
issn = {2576-098X},
abstract = {We report draft metagenome-assembled genomes (MAGs) of six Rothia mucilaginosa strains recovered from the oral microbiome of distinct human subjects. MAGs were retrieved according to a species-specific genome mapping approach, displaying high average nucleotide identities (≥95.85%) to R. mucilaginosa ATCC 25296's genome and minimal contamination levels (≤3.75%).},
}

@article {pmid41025564,
year = {2025},
author = {Zeng, S and Wang, H and Zhang, L and Li, S and Yuan, Y and Tian, M and Qu, Y and Ying, J and Zhou, M and Hu, Y and Huang, J and Zou, R and Zhao, F and Su, X and Liu, Q and He, Y and Feng, J and Huang, W and Luo, Y and Zhou, Z and Shen, W and Mu, D and Wang, S},
title = {The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e05154},
doi = {10.1002/advs.202505154},
pmid = {41025564},
issn = {2198-3844},
support = {2021YFC2701704//National Key Research and Development Program/ ; 2021YFC2701700//National Key Research and Development Program/ ; 82402025//National Natural Science Foundation of China/ ; 82241036//National Natural Science Foundation of China/ ; 82271749//National Natural Science Foundation of China/ ; 82371717//National Natural Science Foundation of China/ ; 82201905//National Natural Science Foundation of China/ ; 82571980//National Natural Science Foundation of China/ ; 82530056//National Natural Science Foundation of China/ ; 2025ZNSFSC1677//Department of Science and Technology of Sichuan Province/ ; SCU2023D006//Fundamental Research Funds for the Central University/ ; SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; },
abstract = {The accelerating threat from antimicrobial resistance (AMR) has become a global health issue. The properties of AMR in the gut microbiome of preterm infants and its clinical relevance with necrotizing enterocolitis (NEC) remain unknown. In-depth integrative analyses of 5,684 gut metagenomes are performed to build an AMR genes (ARGs) landscape. A subset of 107 preterm infants who developed NEC is sampled to examine the trajectory and predictive potential of ARGs preceding NEC onset. The variation and core set of ARGs, their higher burden and diversity, and potential ARGs-enriched gut bacteria in preterm infants compared to full-term infants are comprehensively discovered, reflecting a strain shift in genomic functions. Moreover, the gut resistome converged over 9 days before NEC onset is observed, which is driven by 24 ARGs. Machine learning analysis reveals potential usage of the gut resistome as an indicator for predicting NEC onset in an external validation preterm birth cohort (the area under the receiver operating characteristic curve, AU-ROC = 0.823), which is significantly higher than that based on the bacterial species (AU-ROC = 0.727). Overall, the findings can be referenced to mitigate the burden and spread of ARGs, and specific ARGs have potential for disease risk stratification to improve clinical management.},
}

@article {pmid41025248,
year = {2025},
author = {Park, YJ and Lim, JK and Lee, YJ and Kwon, KK},
title = {Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {9},
pages = {e2507003},
doi = {10.71150/jm.2507003},
pmid = {41025248},
issn = {1976-3794},
support = {EA0311//Ministry of Oceans and Fisheries/ ; KIMST 20210469//Ministry of Oceans and Fisheries/ ; },
mesh = {Animals ; *Microbiota/genetics ; *DNA, Bacterial/isolation & purification/genetics ; *Aquatic Organisms/microbiology ; *Bacteria/genetics/isolation & purification/classification ; *Porifera/microbiology ; Symbiosis ; Republic of Korea ; *Invertebrates/microbiology ; Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; },
abstract = {Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts' immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.},
}

Animals
*Microbiota/genetics
*DNA, Bacterial/isolation & purification/genetics
*Aquatic Organisms/microbiology
*Bacteria/genetics/isolation & purification/classification
*Porifera/microbiology
Symbiosis
Republic of Korea
*Invertebrates/microbiology
Anthozoa/microbiology
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
Polymerase Chain Reaction

@article {pmid41024883,
year = {2025},
author = {Abdelwahab, MM and Ghattas, AS and Tawheed, A},
title = {Implications of gut microbiota in hepatic and pancreatic diseases: Gut-liver-pancreas axis.},
journal = {World journal of hepatology},
volume = {17},
number = {9},
pages = {109965},
pmid = {41024883},
issn = {1948-5182},
abstract = {The gut-liver-pancreas axis (GLPA) is a critical network shaped by gut microbiota (GM) and their metabolites, essential for maintaining metabolic and immune balance. Disruption of this microbial equilibrium, known as dysbiosis, contributes to the development and progression of various hepatic and pancreatic diseases. Through mechanisms such as increased intestinal permeability and exposure to microbial products-including lipopolysaccharide, trimethylamine-N-oxide, and secondary bile acids-dysbiosis promotes inflammation, oxidative stress, insulin resistance, and carcinogenesis. These changes are linked to conditions including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cirrhosis, hepatocellular carcinoma, pancreatitis, pancreatic ductal adenocarcinoma, and diabetes. Emerging tools like stool metagenomics and serum metabolomics help identify microbial biomarkers for diagnosis and risk stratification. While interventions such as probiotics, dietary changes, and fecal microbiota transplantation aim to restore microbial balance, their success remains inconsistent. This work aims to highlight the pathogenic role of GM across the GLPA, with special emphasis on the underexplored gut-pancreas connection. Advancing our understanding of the GLPA can unlock novel microbiota-targeted approaches for early diagnosis and treatment of hepatopancreatic diseases.},
}

@article {pmid41024767,
year = {2025},
author = {Ezzat, WM},
title = {Machine learning as an artificial intelligence application in management of chronic hepatitis B virus infection.},
journal = {World journal of gastroenterology},
volume = {31},
number = {35},
pages = {109776},
pmid = {41024767},
issn = {2219-2840},
mesh = {Humans ; *Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology ; *Machine Learning ; *Gastrointestinal Microbiome ; *Hepatitis B virus/pathogenicity ; Algorithms ; Artificial Intelligence ; Antiviral Agents/therapeutic use ; Supervised Machine Learning ; },
abstract = {Let's review the role of gut microbiota in pathogenesis of chronic hepatitis B infection as addressed in by Zhu et al. Zhu et al used high-throughput technology to characterize the microbial ecosystems, which led to an explosion of various types of molecular profiling data, such as metagenomics, metatranscriptomics, and metabolomics. To analyze such data, machine learning (ML) algorithms have shown to be useful for identifying key molecular signatures, discovering potential patient stratifications, and, particularly, for generating models that can accurately predict phenotypes. Strong evidence suggests that such gut microbiome-based stratification could guide customized interventions to benefit human health. Supervised learning includes designing an algorithm to fix a pre-identified problem. To get an answer, ML software must access data that have been nominated. On the other hand, unsupervised learning does not address any pre-defined problems. Bias should be eliminated as much as possible. In unsupervised learning, an ML algorithm works to identify data patterns without any prior operator input. This can subsequently lead to elements being identified that could not be conceived by the operator. At the intersection between supervised and unsupervised learning is semi-supervised ML. Semi-supervised learning includes using a partially labeled data set. The ML algorithm utilizes unsupervised learning to label data (that has not yet been labelled) by drawing findings from the labeled data. Then, supervised techniques can be used to solve defined problems involving the labeled data. Reinforcement learning, which is similar to supervised learning in the meaning, is goal-oriented. Reinforcement learning does not need labeled data, instead, it is provided with a set of regulations on a problem. An algorithm will carry out operations to try to answer questions involving the problem. Based on obtained data of gut microbiota, various therapeutic modalities can be applied: Prebiotics, probiotics, postbiotics, engineered bacteria, bacteriophage, and novel microbe-materials therapeutic system and fecal transplantation. In conclusion, ML is an artificial intelligence application that helps in providing new perspectives on tailored therapy. Furthermore, assessing the impact of gut microbiota modification is a critical step in advanced liver disease management. These new artificial intelligence techniques although promising, still require further analysis and validation in future studies.},
}

Humans
*Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology
*Machine Learning
*Gastrointestinal Microbiome
*Hepatitis B virus/pathogenicity
Algorithms
Artificial Intelligence
Antiviral Agents/therapeutic use
Supervised Machine Learning

@article {pmid41024212,
year = {2025},
author = {Wang, Y and Gong, L and Dong, D and Li, X},
title = {Metagenomic binning reveals community and functional characteristics of sulfur- and methane-oxidizing bacteria in cold seep sponge ground.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {122},
pmid = {41024212},
issn = {2524-6372},
support = {KEXUE2020GZ01//The Senior User Project of R/V Kexue/ ; 42176114//The National Natural Science Foundation of China/ ; ZR2023MD100//Natural Science Foundation of Shandong Province/ ; },
abstract = {BACKGROUND: Cold seep sponges typically reside in the carbonate rock areas surrounding the vents, often comprising only a few individuals of a limited number of species. Previous limited studies have indicated that sponges living in seeps or vents host chemolithotrophic microorganisms, including sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), regardless of their feeding habits. This suggests that they may utilize compounds from their environment. However, when multiple sponge species are found co-occurring in a single sponge ground sharing identical environmental and material conditions, it remains unclear how their symbiotic community structure will behave. Specifically, it is uncertain whether the community will exhibit greater similarity or, as seen in most studies, demonstrate host specificity.

RESULTS: We utilize metagenomics and binning analysis to characterize six new sponge species belonging to two classes and two distinct dietary habits, all discovered in the same cold seep. Our findings reveal that their associated microbial communities, primarily composed of SOB and MOB from the phylum Proteobacteria, exhibit a high abundance of groups with the same chemosynthetic functions. Binning recovered diverse, novel MAGs (metagenome-assembled genomes) primarily dominated by order PS1 (SOB) and order Methylococcales (MOB). This similarity extends beyond the dietary habits and higher taxonomic levels of the sponge hosts. Phylogenetic and abundance difference analyses of MAGs indicate significant host specificity in the selection of symbiotic microbial species among different sponge species. Notably, these MOB and SOB exhibit potential novelty within their clade compared to known taxa. Furthermore, the genomes of these SOB and MOB contain abundant functions related to their adaptation to the chemoautotrophic environment and symbiotic lifestyle within the cold seep.

CONCLUSIONS: The chemosynthetic environment shapes the high relative abundance of key functional groups that dominate the symbiotic community, while the species differences among host sponges determine the strain selection within these groups. The metabolic functions expressed by this "convergence with divergence" community structure collectively endow the holobionts with the ability to adapt to the cold seep environment.},
}

@article {pmid41024198,
year = {2025},
author = {Altalhi, S and Schultz, J and Jamil, T and Diercks, I and Sharma, S and Follmann, J and Alam, I and Raman, K and Augustin, N and van der Zwan, FM and Rosado, AS},
title = {Decoding microbial diversity, biogeochemical functions, and interaction potentials in red sea hydrothermal vents.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {118},
pmid = {41024198},
issn = {2524-6372},
support = {BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; FCC/1/1973-43-01//King Abdullah University of Science and Technology/ ; FCC/1/1973-43-01//King Abdullah University of Science and Technology/ ; BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; },
abstract = {BACKGROUND: Hydrothermal vents along mid-ocean ridges host diverse microbial communities and are crucial to global elemental cycling. The Red Sea, known for its unique environmental conditions-including low nutrient levels, high year-round temperatures, bottom-water temperatures of 21 °C, and elevated salinity-hosts recently discovered active low-temperature hydrothermal vent fields at the axial Hatiba Mons volcano. These vents, characterized by large iron oxide mounds and abundant microbial mats, offer an extreme environment for studying the diversity and functions of prokaryotes involved in elemental cycling in this system. In this study, we used 16S rRNA sequencing and shotgun metagenomics to examine the microbial diversity and metabolic capabilities of precipitates and microbial mats from five vent sites.

RESULTS: We recovered 314 non-redundant metagenome-assembled genomes (MAGs), including 250 bacterial and 64 archaeal MAGs, representing 34 bacterial and 11 archaeal phyla. Functional annotations revealed diverse nutrient and metal cycling potentials, with notable enrichment in iron redox genes. Key players include Bathyarchaeia and Chloroflexi in the precipitates (contributing to carbon, nitrogen, sulfur, and metal cycling potentials) and Pseudomonadota members in the microbial mats and upper precipitates (involved in iron and sulfur metabolism and carbon fixation through the CBB cycle). Carbon fixation in precipitate potentials primarily occurs through the Wood-Ljungdahl pathway. Sulfur and nitrogen cycling genes are distributed across various genomes, indicating collaborative cycling.

CONCLUSION: Our genome-resolved analysis positions the Hatiba Mons vents as an iron-rich system that provides new insights into oligotrophic hydrothermal environments, with potential relevance for understanding novel metabolic pathways, extremophilic adaptations, and their roles in element cycling and biotechnological applications.},
}

@article {pmid41024077,
year = {2025},
author = {Zhang, Y and Guo, S and Lu, L and Li, Y and Wu, Y},
title = {Metagenomic next-generation sequencing for pathogen detection of pulmonary infections in persons living with HIV.},
journal = {AIDS research and therapy},
volume = {22},
number = {1},
pages = {95},
pmid = {41024077},
issn = {1742-6405},
support = {kq2403197//Natural Science Foundation of Changsha/ ; 2025JJ80470//Natural Science Foundation of Hunan Province/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; *HIV Infections/complications/virology ; Retrospective Studies ; *Metagenomics/methods ; Middle Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology/virology ; CD4 Lymphocyte Count ; *Lung Diseases/diagnosis/microbiology/virology ; Sensitivity and Specificity ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; },
abstract = {BACKGROUND: This study aimed to evaluate the diagnostic utility of metagenomic next-generation sequencing (mNGS) in detecting pulmonary infections in persons living with HIV(PLWH).

METHODS: We conducted a retrospective study involving 246 PLWH with pulmonary infections. Bronchoalveolar lavage fluid (BALF) specimens were collected from all patients. mNGS and traditional microbial cultures were performed in parallel to compare the differences in pathogen identification. Patients were stratified by immune status based on CD4[+] T cell counts, and the association between pathogen profiles and immunodeficiency severity was analyzed.

RESULTS: mNGS demonstrated a significantly higher pathogen detection sensitivity (98.0%) compared to traditional cultures (32.1%). The spectrum of pathogens detected by mNGS and culture methods differed significantly. mNGS identified 123 pathogenic microorganisms, whereas cultures detected only 17. mNGS detected additional pathogens, including viruses (e.g., Epstein-Barr virus and cytomegalovirus) and fastidious microorganisms (e.g., Pneumocystis jirovecii). Furthermore, mNGS revealed a significant correlation between PLWH-associated immunodeficiency and pathogen profiles. The diversity of pathogens, particularly fungi and viruses, increased with declining CD4[+] T cell counts (p < 0.05).

CONCLUSION: mNGS comprehensively characterizes the complex pathogen spectrum in PLWH-associated pulmonary infections, significantly enhancing detection sensitivity for mixed and fastidious infections, thereby guiding targeted anti-infective therapy. Immunosuppression severity strongly correlates with opportunistic pathogen profiles and the risk of specific pathogen detection, highlighting the importance of immune status-guided clinical strategies. mNGS serves as a valuable adjunct to conventional diagnostic methods, enhancing the detection and prognostic assessment of infectious complications in PLWH.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Male
Female
*HIV Infections/complications/virology
Retrospective Studies
*Metagenomics/methods
Middle Aged
Adult
Bronchoalveolar Lavage Fluid/microbiology/virology
CD4 Lymphocyte Count
*Lung Diseases/diagnosis/microbiology/virology
Sensitivity and Specificity
*Respiratory Tract Infections/diagnosis/microbiology/virology

@article {pmid41023882,
year = {2025},
author = {Luo, Y and Zhao, C and Chen, H and Lin, Z and Xia, J and Liu, X and Li, X},
title = {Clinical value of metagenomic next-generation sequencing in diagnosis of Coxiella burnetii infection.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1219},
pmid = {41023882},
issn = {1471-2334},
support = {No. 2023A1515220226//Basic and Applied Basic Research Foundation of Guangdong Province/ ; No. 2420004000311//Science and technology plan project in the field of social development of ZhuhaiScience and technology plan project in the field of social development of Zhuhai/ ; },
mesh = {Humans ; *Q Fever/diagnosis/microbiology/drug therapy ; *Coxiella burnetii/genetics/isolation & purification ; Adult ; Male ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Aged ; Young Adult ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a new pathogen detection technique, but the current experience of clinical application in Coxiella burnetii infection is relatively limited. This study aimed to investigate the clinical application value of mNGS in diagnosis of Coxiella burnetii infection.

METHODS: We conducted a retrospective study that included patients with Coxiella burnetii infection detected by mNGS from December 2018 to August 2024. Their clinical information and mNGS test results were retrieved for analysis.

RESULTS: A total of 70 patients with Coxiella burnetii infection were included in this study. The mean age of these patients was 43.5 years and the common clinical manifestations were fever (67/70, 95.7%), followed by headache (43/70, 61.4%), weakness (36/70, 51.4%), and muscle and joint pain (27/70, 38.6%). The mean length of hospitalization was five days. 92.9% (65/70) patients were discharged with improvement, and one patient died. The median duration of fever for these patients was seven days. Most patients temperatures returned to normal within 2-3 days after receiving targeted antibiotic therapy. No correlation was observed between the duration of fever and the reads of mNGS in febrile patients. The specimens tested by mNGS were mainly blood specimens. The reads of mNGS detected fluctuated from one to 826, with the range of one to 50 being the most frequent. 43 (61.4%) samples of mNGS detected only Coxiella burnetii. Pathogens detected along with Coxiella burnetii include viruses, bacteria, and fungi. None of the 63 patients followed up for six months had clinical manifestations of chronic Q fever.

CONCLUSIONS: Q fever is a disseminated infectious disease that deserves attention for its nonspecific clinical symptoms. mNGS emerges as a powerful novel tool for pathogen detection, demonstrating significant value in diagnosing Q fever, particularly in where conventional serological and PCR testing is unavailable or inconclusive.},
}

Humans
*Q Fever/diagnosis/microbiology/drug therapy
*Coxiella burnetii/genetics/isolation & purification
Adult
Male
Female
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
Middle Aged
*Metagenomics/methods
Aged
Young Adult

@article {pmid41023790,
year = {2025},
author = {Cao, L and Sun, H and Wang, Y and Wei, Z and Zhang, J and Wang, Y and Yan, J and Zhu, Y and Cheng, N and He, S and Liu, X and Li, T and Wang, M and Li, E},
title = {Comparative analysis of metagenomics between high- and medium-temperature daqu, and microbial succession in Jiang-Nong Jianxiang Baijiu fermentation.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {852},
pmid = {41023790},
issn = {1471-2164},
mesh = {*Fermentation ; *Metagenomics/methods ; *Alcoholic Beverages/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Temperature ; Phylogeny ; },
abstract = {BACKGROUND: The mixture of high-temperature Daqu and medium-temperature Daqu can be used to produce Chinese Jiang-Nong Jianxiang Baijiu. This study used metagenomic sequencing and physicochemical analysis to investigate the microbial community and functionality of high-temperature Daqu and medium-temperature Daqu. In addition, exploring the changes of microbial communities during the Jiang-Nong Jianxiang Baijiu fermentation process.

RESULTS: The results showed that Lichtheimia ramose and Saccharopolyspora rectivirgula were the significantly different species in high-temperature Daqu. However, Paecilomyces variotii, Aspergillus chevalieri, and Rasamsonia emersonii were the significantly different species in medium-temperature Daqu. The medium-temperature Daqu had higher saccharifying power (101.20 ± 1.85 U/g) than high-temperature Daqu (60.00 ± 0.58 U/g). And the protease activity of high-temperature Daqu (62.47 ± 5.84 U/mg) was significantly higher than medium-temperature Daqu (36.10 ± 1.13 U/mg). The community structure analysis results of the stack fermentation stage showed that the mixture of high-temperature Daqu and medium-temperature Daqu inherited the community advantages of both high-temperature Daqu and medium-temperature Daqu. With Jiang-Nong Jianxiang Baijiu fermentation, the significantly different species changed from Pichia sp., Acetobacter sp., and Lactobacillus sp. to Pediococcus sp., Lactobacillus sp., Lentilactobacillus sp., Saccharomyces sp., Thermoactinomyces sp., and Saccharopolyspora sp., implying the importance of acid-resistant and ethanol-resistant microorganisms for the production of flavor substances in the late Baijiu fermentation.

CONCLUSIONS: Our research revealed the difference in microbial communities between high-temperature Daqu and medium-temperature Daqu, and demonstrated the shifts and functionality of microbiota during Jiang-Nong Jianxiang Baijiu fermentation. This study provides a theoretical reference for utilizing core synergistic microbiota and their functional traits in Baijiu fermentation starters to improve Baijiu quality.},
}

*Fermentation
*Metagenomics/methods
*Alcoholic Beverages/microbiology
*Microbiota
*Bacteria/genetics/classification
Temperature
Phylogeny

@article {pmid41023748,
year = {2025},
author = {Soto-López, JD and García-Martín, JM and Lizana-Ciudad, D and Lizana, M and Hernández-Tabernero, L and Fernández-Soto, P and Velásquez-González, OE and Aragón, SL and Belhassen-García, M and Muro, A},
title = {Taxonomic and functional profiling of bat guano microbiota from hiking trail-associated tunnels: a potential risk for human health?.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {123},
pmid = {41023748},
issn = {2524-6372},
support = {Orden EDU/1868/2022//Predoctoral Fellowship Program of Junta de Castilla y Leon - Fondo Social Europeo Plus (FSE +)/ ; },
abstract = {Metagenomic studies have significantly expanded our understanding of the bacterial communities present in bat guano. Several studies have reported the presence of common human pathogenic bacteria, including enteric foodborne species, zoonotic pathogens, unusual Gram-negative bacteria, and multidrug-resistant strains. These findings have reinforced the perception of bat guano as a potential reservoir of pathogens. Despite this, research conducted in sites with frequent human contact remains limited. Caves and tunnels such as those along the Camino del Hierro in northeastern Spain represent environments with regular human exposure, making them areas of particular interest from a public health perspective. In this study, we conducted an extensive analysis of the guano microbiome during both the breeding season and hibernation period in bats inhabiting this touristic site, using shotgun metagenomics and a comprehensive bioinformatic pipeline. Our results revealed marked differences in the relative microbial composition across samples from fresh and desiccated bat guano. The most abundant viral order detected was Herpesvirales, while among bacterial genera, Bacillus, Burkholderia, Lactobacillus, Pseudomonas, Salmonella and Streptococcus were dominant. The presence of these taxa in the tunnels poses a potential risk not only to visitors but also to park staff who are regularly exposed to bat guano, particularly due to the presence of species associated with various human viral and bacterial diseases. No significant differences were observed in the overall abundance of detected organisms between seasons. However, distinct seasonal patterns emerged when analyzing metabolic pathways and virulence factors. During the breeding season, there was a notable predominance of metabolic pathways related to cell proliferation, along with virulence factors associated with strategies for surface attachment and biofilm formation. Overall, our findings highlight an underrecognized and unmonitored risk of pathogen transmission for both visitors and personnel at this tourist site, underscoring the need for increased awareness and further investigation into the health implications of human-bat interactions in such environments.},
}

@article {pmid41023693,
year = {2025},
author = {Yang, M and Zhang, HX and Zhou, YL and Selvarajan, R and Xu, PK and Gao, ZM and Wang, Y},
title = {Viral ecogenomics across oxic and anoxic zones of the Yongle Blue Hole.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {119},
pmid = {41023693},
issn = {2524-6372},
support = {ZDKJ2021028//Major Science and Technology Plan Project of Hainan Province/ ; 2022YFC2805304//National Key Research and Development Program of China/ ; 42376149//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Deep ocean blue holes are characterized by distinct physicochemical gradients and complex biological processes, and Yongle Blue Hole (YBH) in the South China Sea (SCS) is the world's deepest (301 m) underwater cavern with unique environmental characteristics. So far, studies investigated the bacterial community structure with different lifestyles of the YBH; however, our understanding of viruses in the YBH remains limited. Here, we utilized a metagenomic approach to investigate viral communities in both the "viral fraction" and "cellular fraction" of seawater samples in oxic and anoxic zones within YBH.

RESULTS: A total of 1,730 viral operational taxonomic units (vOTUs) were identified, with over 70% affiliated with the classes Caudoviricetes and Megaviricetes, particularly within the families Kyanoviridae, Phycodnaviridae and Mimiviridae. Gene-sharing network analyses indicated that the deeper anoxic layers contain a high proportion of novel viral genera, while the oxic layer's viral genera overlap with those found in the open water samples from SCS. Virus-linked prokaryotic hosts predominantly belong to the phyla Patescibacteria, Desulfobacterota, and Planctomycetota. Notably, the detected putative auxiliary metabolic genes (AMGs) suggest that these viruses may influence photosynthetic and chemosynthetic pathways, as well as methane, nitrogen, and sulfur metabolisms, especially with several high-abundance AMGs potentially involved in prokaryotic assimilatory sulfur reduction.

CONCLUSIONS: Together, these findings highlight the potential ecological roles and diversity of viral communities within YBH and shedding light on niche-separated viral speciation.},
}

@article {pmid41023631,
year = {2025},
author = {Lan, Q and Deng, Z and Li, C and Huang, H and Zhou, Z and Jiang, L and Li, F and Wu, D and Zheng, M and Zhou, M and Chen, Q and Xu, F},
title = {Evaluation of hybrid capture-based targeted and metagenomic next-generation sequencing for pathogenic microorganism detection in infectious keratitis.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1211},
pmid = {41023631},
issn = {1471-2334},
support = {2025GXNSFDA069056//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; Z2016623//Guangxi Medical Health Appropriate Technology Development and Application Project/ ; 2020036//Science and Technology Plan Project of Qingxiu District in Nanning City/ ; AD19245193//Guangxi clinical ophthalmic research center/ ; 20233071//Nanning City Science Research and Technology Development Program/ ; },
}

@article {pmid41023192,
year = {2025},
author = {Vishal, V and Thakur, P and Tigga, SS and Lal, S},
title = {A metagenomic assessment of overburden dump of coal mine soil bacterial consortium from Jharkhand, India.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1161},
pmid = {41023192},
issn = {1573-2959},
mesh = {*Soil Microbiology ; India ; *Bacteria/classification/genetics ; *Coal Mining ; *Environmental Monitoring ; *Soil Pollutants/analysis ; Metagenomics ; Soil/chemistry ; *Microbial Consortia ; Biodegradation, Environmental ; RNA, Ribosomal, 16S ; Coal ; },
abstract = {Overburden dump (OBD) of coal mine waste soils is arguably a major source of heavy metals and metalloids, leading to both public health and ecological consequences. This study employed hypervariable V3-V4 region of 1.5 kbp 16S rDNA gene-based amplicon metagenomic sequencing to analyze unexplored bacterial diversity and its phenotypical and hypothetical functions, emphasizing the significance of these studies for assessing the potential of bioremediation. Triplicate coal OBD soil samples were collected from the coal dumping yard of Sarubera Colliery from Atna-Chainpur and agricultural soils from Ramgarh Cantonment, Jharkhand. There were 30 phyla And 320 operational taxonomic units (OTUs) recorded in coal OBD soil, while agricultural soil had 26 phyla And 240 OTUs. Proteobacteria were the predominant phylum in both environments. Firmicutes, Actinobacteria, and Bacteroidetes were the most prevalent phyla in the coal OBD soil, whereas Acidobacteria, Planctomycetes, and Nitrospirae were most frequently found in agricultural soil. Alphaproteobacteria and Gammaproteobacteria was the most abundant classes, and whereas the mesophilic Acinetobacter were the most abundant genus detected in coal OBD soil. The PICRUSt2 pipeline predicted hypothetical functional categories, identifying 2404 EC numbers, 7813 KO terms, And 442 MetaCyc pathways. The most enriched categories were RNA polymerase sigma-70 factor, ABC transporters, And 3-oxoacyl-[acyl-carrier-protein] reductase, aerobic respiration pathways, and pyruvate fermentation biosynthesis pathways. Taxonomy-to-phenotypic mapping was used to record phenotypic categories like oxygen requirement, temperature range, energy sources, biotic relationships, and Gram stain nature between the two habitats. The presence of nitrogen-fixing and phosphate-solubilizing bacteria in coal OBD soil offers their key roles of biodegrading polycyclic aromatic hydrocarbons (PAHs), speeding mineralization, and ameliorating environmental issues that threaten plant viability.},
}

*Soil Microbiology
India
*Bacteria/classification/genetics
*Coal Mining
*Environmental Monitoring
*Soil Pollutants/analysis
Metagenomics
Soil/chemistry
*Microbial Consortia
Biodegradation, Environmental
RNA, Ribosomal, 16S
Coal

@article {pmid41022942,
year = {2025},
author = {Halifu, S and Deng, X and Yang, L and Qian, L and Yang, L},
title = {Metagenomic analysis of pathogenicity of puccinia xanthii on invasive plant xanthium italicum.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33530},
pmid = {41022942},
issn = {2045-2322},
support = {KX031042//PhD research startup foundation of Shihezi University/ ; KX6107//a program of Shihezi University/ ; },
mesh = {*Plant Diseases/microbiology ; Plant Leaves/microbiology ; *Xanthium/microbiology ; *Metagenomics/methods ; *Puccinia/genetics/pathogenicity ; Introduced Species ; Photosynthesis ; China ; },
abstract = {Biological invasion refers to the establishment and proliferation of non-indigenous species in previously unoccupied areas, where they form wild populations. Xanthium italicum, an invasive species in Xinjiang, China, negatively affects local ecosystems, agriculture, and animal husbandry. In this study, we investigated the pathogenicity of Puccinia xanthii on the leaves of X. italicum by exploring the morphological characteristics of the pathogenic fungi, leaf enzyme activity measurement, photosynthesis measurement, and metagenomic sequencing. This study showed that P. xanthii infects the leaves of X. italicum, significantly reducing the activities of lyase, oxidoreductase, and antioxidant enzymes, including phenylalanine ammonia-lyase (PAL), superoxide dismutase (SOD), polyphenol oxidase (PPO), and catalase (CAT), as well as impairing photosynthesis. Furthermore, metagenomic analysis indicated that P. xanthii infection reduced the homogeneity and richness of phyllosphere microorganisms and increased the abundance of P. xanthii in the phyllosphere. Functional analysis also revealed that P. xanthii infection altered the diversity of microbial functions and eventually led to the development of disease symptoms and the demise of leaves through activated oxidative phosphorylation.},
}

*Plant Diseases/microbiology
Plant Leaves/microbiology
*Xanthium/microbiology
*Metagenomics/methods
*Puccinia/genetics/pathogenicity
Introduced Species
Photosynthesis
China

@article {pmid41022717,
year = {2025},
author = {Song, K and Xiao, Y and Wang, Y and Deng, M and Zhou, S and Huang, Y and Yeerken, S and Li, L and Wu, F},
title = {Electron shuttling promotes denitrification and mitigates nitrous oxide emissions in lakes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8564},
pmid = {41022717},
issn = {2041-1723},
support = {42222709//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42307505//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42107277//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Nitrous Oxide/metabolism/analysis ; *Denitrification/physiology ; *Lakes/microbiology/chemistry ; Electron Transport ; Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; Electrons ; Eutrophication ; },
abstract = {Eutrophication is an emerging global issue that is becoming increasingly severe due to the rising nutrient inputs and limited availability of electron donors for nitrogen removal. In sediments where redox conditions fluctuate dramatically, extracellular electron transfer (EET) critically supports microbial metabolism. However, the biogeochemical significance of EET-coupled denitrification and its EET mechanisms remain unclear. Here, through field investigations and laboratory [15]N isotope experiments, we reveal that humic substance (HS)-mediated electron shuttling significantly enhances denitrification primarily by stimulating bacterial outer membrane c-type cytochrome. Specifically, EET mitigates the emission of greenhouse gas nitrous oxide by enriching nosZII-type reducers. Notably, the efficacy of exogenous HS amendment attenuates in sediment with high native HS concentration. Metagenomic binning further reveals multiple cytochromes forming a complete EET-coupled denitrification electron transport chain. Our findings elucidate the microbial mechanisms underlying electron shuttling-driven denitrification in lakes, thereby expanding the understanding of biogeochemical cycles.},
}

*Nitrous Oxide/metabolism/analysis
*Denitrification/physiology
*Lakes/microbiology/chemistry
Electron Transport
Geologic Sediments/microbiology/chemistry
Bacteria/metabolism/genetics
Oxidation-Reduction
Electrons
Eutrophication

@article {pmid41022706,
year = {2025},
author = {Füssy, Z and Lampe, RH and Arrigo, KR and Barry, K and Brisbin, MM and Brussaard, CPD and Decelle, J and de Vargas, C and DiTullio, GR and Elbourne, LDH and Frischer, ME and Goodstein, DM and Grigoriev, IV and Hayes, RD and Healey, AL and James, CC and Jenkins, JW and Juery, C and Kumar, M and Kustka, AB and Maumus, F and Novák Vanclová, AMG and Oborník, M and Paulsen, IT and Probert, I and Saito, MA and Schmutz, J and Skalický, T and Tec-Campos, D and Tomelka, H and Věchtová, P and Venepally, P and Wilson-Mortier, B and Zengler, K and Zheng, H and Allen, AE},
title = {Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8559},
pmid = {41022706},
issn = {2041-1723},
support = {NA15OAR4320071//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NA19NOS4780181//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NSF OCE-1756884//National Science Foundation (NSF)/ ; 970820//Simons Foundation/ ; },
mesh = {Phylogeny ; *Haptophyta/genetics/classification/metabolism ; Phylogeography ; Gene Transfer, Horizontal ; Metagenome ; Oceans and Seas ; Genome ; Genomics ; },
abstract = {Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.},
}

Phylogeny
*Haptophyta/genetics/classification/metabolism
Phylogeography
Gene Transfer, Horizontal
Metagenome
Oceans and Seas
Genome
Genomics

@article {pmid41021050,
year = {2025},
author = {Kishk, M and Rahmeh, R and Asiri, F and Karam, H and Al-Muhanna, K and Hejji, AB and Shajan, A and Al-Salem, SM},
title = {Substrate-specific microbial community shifts during mesophilic biodegradation of polymers in compost amended soil.},
journal = {Biodegradation},
volume = {36},
number = {5},
pages = {93},
pmid = {41021050},
issn = {1572-9729},
support = {FB187K//Kuwait Institute for Scientific Research/ ; },
mesh = {Biodegradation, Environmental ; *Soil Microbiology ; *Soil/chemistry ; *Polymers/metabolism ; *Composting ; *Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Fungi/metabolism/genetics/classification ; Starch/metabolism ; },
abstract = {Plastics are widely utilized across various industries, but their persistent accumulation in the environment has become a major ecological concern. Biodegradable alternatives offer a potential solution to plastic pollution; however, their degradation behavior under environmentally relevant conditions remains underexplored. This study evaluates the aerobic biodegradation of four polymer materials: starch, commercial thermoplastic starch of polyester origin (TPS1), linear low-density polyethylene (LLDPE), and a co-polyester thermoplastic starch (TPS2), over 180 days at 25 °C in a compost-soil matrix using the testing protocols of ASTM D5988-18 for carbon dioxide (CO2) evolution. Microbial community dynamics were profiled using 16S rRNA and ITS2 amplicon sequencing. TPS2 reached complete mineralization (~ 100%) in 28 days, followed by starch at 71.1% by day 180. TPS1 showed partial mineralization of 38.6%, while LLDPE showed minimal mineralization (21.9%) as expected. Alpha diversity revealed higher bacterial richness in starch treatments and a marked reduction in fungal diversity in TPS1 and LLDPE. Differential abundance testing revealed significant microbial shifts between treatments. Linear discriminant analysis Effect Size (LEfSe) identified polymer-specific microbial biomarkers, including Paenibacillus and Botryotrichum for starch, Acrophialophora and Mycothermus for TPS2, and the Mycobacterium for LLDPE. Subgroup 10 Acidobacteria was uniquely enriched in TPS2-treated samples. These taxa reflect substrate-driven microbial selection. Coupling CO2 mineralization with microbial profiling offers a practical framework to evaluate polymer biodegradability and guide the design of soil-degradable bioplastics. Overall, these findings demonstrate that polymer composition significantly influences microbial community structure and mineralization performance under mesophilic conditions.},
}

Biodegradation, Environmental
*Soil Microbiology
*Soil/chemistry
*Polymers/metabolism
*Composting
*Bacteria/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics
*Microbiota
Fungi/metabolism/genetics/classification
Starch/metabolism

@article {pmid41020900,
year = {2025},
author = {Aziez, M and Yanat, B and Rodriguez-Diaz, C and Suharoschi, R and Vulturar, R and Heghes, SC and Guenaoui, N and Ali, AM and Garcia-Fuentes, E and Bribi, N},
title = {Pharmacological Potential of Arthrospira platensis in Mitigating Sub-Chronic Colitis: Redox Homeostasis and Gut Microbiota Modulation.},
journal = {Current issues in molecular biology},
volume = {47},
number = {9},
pages = {},
doi = {10.3390/cimb47090778},
pmid = {41020900},
issn = {1467-3045},
abstract = {Inflammatory bowel diseases (IBDs) are complex disorders involving interconnected immune, oxidative, and microbial dysregulations. Arthrospira platensis (Spirulina) is a rich source of bioactive compounds with antioxidant, anti-inflammatory, and immunomodulatory properties. This study investigates the pharmacological efficacy of its aqueous extract (APA) in mitigating 2,4-Dinitrobenzene Sulfonic Acid (DNBS)-induced sub-chronic colitis with a focus on restoring redox balance and modulating gut microbiota composition. APA's antioxidant capacity was assessed in vitro by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulphonic) acid (ABTS) radical scavenging, and metal chelation assays. In vivo, BALB/c mice received two DNBS inductions to establish sub-chronic colitis and were treated with APA (50, 100, and 200 mg/kg). Therapeutic efficacy was assessed through clinical scoring, histopathological assessment, biochemical analysis, and gut microbiota profiling based on 16S rRNA gene sequencing. APA exhibited strong antioxidant activity and significantly attenuated colitis severity, as evidenced by reduced Disease Activity Index (DAI) scores, decreased colon inflammation, suppression of Myeloperoxidase (MPO)-mediated neutrophil infiltration, and modulation of redox biomarkers. Moreover, metagenomic profiling revealed APA-induced modulation of the gut microbiota, mainly through a decreased abundance of pathogenic genera such as Staphylococcus and Enterobacteriaceae. APA demonstrates potent antioxidant, anti-inflammatory, and microbiota-modulating activities, supporting its potential as a complementary therapy for IBDs and encouraging further clinical studies.},
}

@article {pmid41020604,
year = {2025},
author = {Mohr, J and Albers, A and Schaumburg, F and Paulus, W and Brokinkel, B and Stummer, W and Spille, DC and Thomas, C},
title = {Deep 16S rDNA Sequencing of Chronic Subdural Hematomas Suggests Involvement of Bacterial Infection in Recurrences.},
journal = {Neurosurgery},
volume = {},
number = {},
pages = {},
doi = {10.1227/neu.0000000000003754},
pmid = {41020604},
issn = {1524-4040},
support = {TH222202//Medizinische Fakultät, Westfälische Wilhelms-Universität Münster/ ; },
abstract = {BACKGROUND AND OBJECTIVES: Chronic subdural hematoma (CSDH) is an encapsulated blood collection between the dura mater and arachnoid that often follows mild head trauma. It involves pronounced inflammation and angiogenesis, and recurrence remains common despite advances in surgical management. Subclinical bacterial involvement has been hypothesized as a potential factor in these recurrent cases. We aimed to determine whether bacteria are present in CSDH outer membranes and to define accompanying histological and transcriptomic changes.

METHODS: A total of 39 Formalin-fixed paraffin-embedded outer-capsule specimens from 19 patients (17 primary, 22 recurrent) underwent: (1) ultra-deep Nanopore 16S rDNA profiling; (2) histomorphology with Gram staining, lipopolysaccharide immunohistochemistry and quantitative immune-cell counts; and (3) RNA-seq of 3 matched primary-recurrent pairs, followed by differential-expression and pathway analysis.

RESULTS: Gram staining revealed bacteria in 2 recurrent samples (5%) from a single patient, whereas lipopolysaccharide immunohistochemistry was negative in all cases. Notably, 16S rDNA sequencing detected bacterial DNA exclusively in recurrent lesions (6 samples from 4 patients), with none in primary cases (P = .02, χ2 test). The identified bacterial genera included Staphylococcus, Neisseria, Prevotellamassilia, and Paracoccus. Histopathological evaluation showed no significant differences in eosinophils, myeloperoxidase-positive cells, CD3-positive T-cells, or CD20- positive B-cells when comparing primary with recurrent lesions, or infected to uninfected membranes. Unsupervised clustering of matched primary and recurrent CSDH samples revealed distinct transcriptomic profiles, identifying 184 differentially expressed genes (including consistent Toll-like receptor 4 upregulation) and highlighting pathways related to development, protein biosynthesis, and wound healing.

CONCLUSION: These findings suggest that bacterial DNA is present in a subset of recurrent CSDH, suggesting that bacteria could be involved in recurrences. Further research with larger cohorts is needed to determine whether antimicrobial or anti-inflammatory strategies might help reduce recurrence.},
}

@article {pmid41020558,
year = {2025},
author = {Diallo, D and Sene, O and Ngom, D and Khoulé, A and Faye, ET and Dieng, I and Ndione, MHD and Faye, O and Simon-Lorière, E and Diagne, MM and Diallo, M and Sakuntabhai, A and Fall, G},
title = {Detection and genetic characterization of arboviruses and other viruses from mosquitoes collected in southeastern and central Senegal, October 2022.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70017},
pmid = {41020558},
issn = {1365-2915},
support = {U01AI151758//National Institute of Allergy and Infectious Diseases, National Institues of Health/ ; },
abstract = {The knowledge of the distribution of viruses and their associated mosquito species is still incomplete in Senegal. Additionally, data on the genetic characterization of these viruses are limited. The aim was to update knowledge on the diversity, distribution and genetic relationships of mosquito-associated viruses in Senegal through entomological and molecular surveillance. Mosquitoes were collected in October 2022 across 10 districts in Senegal. Samples were identified morphologically and processed for virome characterization using qRT-PCR and next-generation sequencing. The most common species were Culex cinereus Theobald, 1901, Culex quinquefasciatus Say, 1823, Culex neavei Theobald, 1904, and Culex poicilipes Theobald, 1904 (Diptera: Culicidae). The number of mosquitoes collected varied by habitat and district. We detected 42 isolates of 7 viruses, including Bagaza (BAGV), Barkedji, Sindbis (SINV), Usutu (USUV), Dezidougou, Densovirus and Pestivirus A (PESVA), in 6 mosquito species (Mansonia uniformis, Cx. neavei Theobald, 1901, Anopheles coustani, Cx. cinereus Laveran, 1900, Aedes aegypti Linnaeus, 1762 and Aedes vexans Meigen, 1830) (Diptera: Culicidae). The viruses were mainly detected in mosquitoes collected near ponds (92.9%). BAGV and SINV were detected for the first time in southeastern Senegal. This is also the first association of PESVA with mosquitoes in the field. Phylogenetic analyses revealed that PESVA clustered with strains from Asia and Egypt, BAGV with strains from Senegal and Spain, USUV with strains from Senegal and SINV with strains from Spain and Kenya. This study expands the understanding of mosquito-virus associations in Senegal, revealing new geographic distributions and vectors for several viruses, with implications for arbovirus emergence and surveillance strategies.},
}

@article {pmid41020500,
year = {2025},
author = {Yang, Y and Kang, D and Mihalache, B and Vexler, S and Jain, S and Peng, H and Annabi, N and Yang, S and Chen, IA},
title = {Metagenome-inspired libraries to engineer phage M13 for targeted killing of Gram-negative bacterial species.},
journal = {Nucleic acids research},
volume = {53},
number = {18},
pages = {},
doi = {10.1093/nar/gkaf984},
pmid = {41020500},
issn = {1362-4962},
support = {R35GM148249/GF/NIH HHS/United States ; T32GM145388/GM/NIGMS NIH HHS/United States ; UL1TR001881/TR/NCATS NIH HHS/United States ; 32201100//National Natural Science Foundation of China/ ; //UCLA/ ; },
mesh = {*Metagenome ; *Bacteriophage M13/genetics ; Pseudomonas aeruginosa/virology/drug effects ; Anti-Bacterial Agents/pharmacology ; *Gram-Negative Bacteria/virology/drug effects ; Humans ; *Peptide Library ; Phage Therapy ; },
abstract = {Given concerning trends in antibiotic resistance, phages have been increasingly explored as promising antimicrobial agents. However, a major problem with phage therapy is the overly high specificity of phages for their hosts, which is currently addressed by a personalized approach involving screening a bank of wild-type phages against each clinical isolate. To shorten this process, we propose that a focused library of synthetic phages could be rapidly selected for a member binding to a given clinical isolate. We created libraries of recombinant M13 phages expressing receptor-binding proteins based on the collective metagenome of inovirus phages, a diverse group whose members appear to infect nearly all bacterial phyla. Using two rounds of a pull-down selection, phage variants were identified against several Gram-negative pathogens, including a variant (M13PAB) that bound to several Pseudomonas aeruginosa strains, including clinical isolates. To confer bactericidal activity to the nonlytic phage, a last-line but nephrotoxic lipopeptide, colistin, was cross-linked to the M13PAB virions. The colistin-M13PAB phage conjugate lowered the minimal inhibitory concentration of colistin by 1-2 orders of magnitude for multiple strains of P. aeruginosa and showed a lack of hemolytic or cytotoxic activity in vitro, suggesting high potency combined with low toxicity. Thus, a metagenome-inspired library displayed on the M13 phage scaffold, when subjected to a short selection for binding to a bacterial clinical isolate, could yield a phage variant that targets the specified strain. This approach may improve the speed, consistency, and cost-effectiveness of personalized phage therapy.},
}

*Metagenome
*Bacteriophage M13/genetics
Pseudomonas aeruginosa/virology/drug effects
Anti-Bacterial Agents/pharmacology
*Gram-Negative Bacteria/virology/drug effects
Humans
*Peptide Library
Phage Therapy

@article {pmid41020266,
year = {2025},
author = {Back, F and Sandoval, A and Vu, LM and Hong, VM and Bhaskara, A and Rodriguez, SR and O'Brien, JT and Kolber, BJ and Kroener, S and Ploski, JE},
title = {Adeno-associated viral vector resource for the RNA-targeting Cas13d: A comparison of high-fidelity variants, DjCas13d and hfCas13d.},
journal = {Molecular therapy. Methods & clinical development},
volume = {33},
number = {4},
pages = {101565},
pmid = {41020266},
issn = {2329-0501},
abstract = {RNA-targeting CRISPR-Cas systems have emerged as alternatives to RNA-interference technology to knock down specific RNA transcripts. In particular, Cas13d derived from Ruminococcus flavefaciens (CasRx, RfxCas13d) has generated interest due to its superior knockdown efficiencies; however, accumulating evidence indicates that CasRx is prone to inducing transcriptome alterations due to its tendency to cleave bystander RNAs. High-fidelity Cas13d (hfCas13d) derived from CasRx and DjCas13d, an ortholog of Cas13d derived from Ruminococcus sp. UBA7013 (gut metagenome), are two recently identified variants that are superior to CasRx, as they both show a reduced tendency to cleave bystander RNAs. In this study, we created a resource of adeno-associated viral (AAV) vectors designed to deliver Cas13d, including hfCas13d and DjCas13d. We directly compared hfCas13d and DjCas13d for their on- and off-target potential in 293FT and neuro 2A cells. Specifically, we examined their ability to knockdown several endogenous and ectopically expressed transcripts using several different guide RNAs (gRNAs), and we examined knockdown specificity using a combination of reporter assays, RNA integrity analysis, and RNA sequencing (RNA-seq). We report that while both of these enzymes exhibit generally similar levels of knockdown potential, with DjCas13d sometimes outperforming hfCas13d, hfCas13d consistently caused significantly fewer transcriptome alterations when targeting highly expressed genes compared to DjCas13d.},
}

@article {pmid41020244,
year = {2025},
author = {Yang, YM and Guo, J and Dang, NN},
title = {Case Report: Diagnosis of Nocardia asteroides infection using metagenomic next-generation sequencing of lymph node puncture tissue.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1626685},
pmid = {41020244},
issn = {2296-858X},
abstract = {The Nocardia genus is an aerobic, Gram positive, opportunistic pathogen that primarily affects cell-mediated immunosuppressed patients. The clinical manifestation of nocardiosis varies widely, making it challenging to diagnose. In this report, we describe a 48 year old woman with a muscular abscess caused by Nocardia asteroides. Venous blood, skin biopsy specimen, muscle tissue, and inguinal lymph node puncture tissue cultures yielded negative results. Using metagenomic next-generation sequencing (mNGS), the pathogen was identified as Nocardia asteroides. Whole-exome sequencing of the peripheral blood showed that the patient had a monoallelic mutation in the lipopolysaccharide-responsive beige-like anchor protein (LRBA) gene. The mNGS detected Nocardia asteroides in the patient, and the administration of accurate treatment led to her complete recovery.},
}

@article {pmid41020144,
year = {2025},
author = {Tan, Y and Li, X and Xie, Y and Zhang, Z and Liu, J and Zhou, G and Liu, M},
title = {A Rare Case of Yersinia Pseudotuberculosis Infection with Septic Shock and Splenic Infarction.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5057-5065},
pmid = {41020144},
issn = {1178-6973},
abstract = {Yersinia pseudotuberculosis is a Gram-negative bacterium of the family Yersiniaceae, primarily transmitted via the gastrointestinal tract. Progression to sepsis is uncommon, and the combination of septic shock and splenic infarction is exceedingly rare. We report a 40-year-old male who initially presented with fever, abdominal pain, and distension, which rapidly progressed to sepsis and multi-organ dysfunction. Definitive diagnosis of Y. pseudotuberculosis infection was established by blood culture and metagenomic next-generation sequencing, supported by imaging evidence of splenic infarction. The patient was managed with stepwise antimicrobial regimens (including piperacillin-tazobactam, meropenem, levofloxacin, linezolid, and daptomycin), plasma exchange, continuous renal replacement therapy, and organ function support. Following comprehensive treatment, the patient recovered and was discharged in stable condition. This case highlights the importance of considering Y. pseudotuberculosis in atypical sepsis presentations and demonstrates that timely diagnosis and multidisciplinary management are crucial to improving outcomes in such rare and life-threatening infections.},
}

@article {pmid41019955,
year = {2025},
author = {Hajjar, J and Voigt, AY and Conner, ME and Swennes, AG and Fowler, S and Calarge, C and Mendonca, DD and Armstrong, D and Chang, CY and Walter, JE and Butte, MJ and Savidge, T and Oh, J and Kheradmand, F and Petrosino, JF},
title = {Gut dysbiosis patterns in CVID patients with noninfectious complications observed in a germ-free mouse model through fecal microbiota transplantation.},
journal = {Journal of human immunity},
volume = {1},
number = {1},
pages = {},
pmid = {41019955},
issn = {3065-8993},
abstract = {Patients with common variable immunodeficiency (CVID) who develop noninfectious complications (NIC) have worse clinical outcomes than those with infections only (INF). While gut microbiome aberrations have been linked to NIC, reductionist animal models that accurately recapitulate CVID are lacking. Our aim in this study was to uncover potential microbiome roles in the development of NIC in CVID. We performed whole-genome shotgun sequencing on fecal samples from CVID patients with NIC, INF, and their household controls. We also performed fecal microbiota transplants from CVID patients to germ-free mice. We found potentially pathogenic microbes Streptococcus parasanguinis and Erysipelatoclostridium ramosum were enriched in gut microbiomes of CVID patients with NIC. In contrast, Fusicatenibacter saccharivorans and Anaerostipes hadrus, known to suppress inflammation and promote healthy metabolism, were enriched in gut microbiomes of INF CVID patients. Fecal microbiota transplant from NIC, INF, and their household controls into germ-free mice revealed gut dysbiosis patterns only in recipients from CVID patients with NIC, but not in those from INF CVID or household controls recipients. Our findings provide a proof of concept that fecal microbiota transplant from CVID patients with NIC to germ-free mice recapitulates microbiome alterations observed in the donors.},
}

@article {pmid41019762,
year = {2025},
author = {Vazzana, R and Mularoni, A and Vaiana, C and Cona, A and Mulè, G and Amato, C and Ranucci, G and Conaldi, PG and Agnese, V and Cuscino, N and Gallo, A},
title = {Shotgun metagenomics detects the human pegivirus complete genome in a pediatric patient with acute hepatitis of unknown etiology: a case report.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1653082},
pmid = {41019762},
issn = {1664-8021},
abstract = {Human pegivirus (HPgV) is a positive-sense, single-strand RNA virus belonging to the Flaviviridae family. Although not conclusively linked to a specific disease, an increasing number of studies have recently reported an association between this virus and different human pathologies. In this study, we present a 6-month-old female infant admitted to the hospital for severe acute hepatitis. Her clinical history started with a one week of fever and diarrhea treated with paracetamol and amoxicillin-clavulanate for a total of 4 days. The persistence of the symptoms, high levels of transaminases, coagulopathy, increased lymphocytosis, and C-reactive protein (CRP) in the blood suggested an acute hepatitis episode. Serological and molecular biology tests for hepatotropic and non-hepatotropic viruses, including hepatitis B virus (HBV), hepatitis A virus (HAV), hepatitis C virus (HCV), hepatitis E virus (HEV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), herpes simplex virus (HSV), enterovirus, and adenovirus, were negative. Metabolic and genetic alterations, deficiency of alpha-1 antitrypsin, and Wilson's disease were ruled out following negative results. The child was thus treated with supportive therapy. Metagenomic next-generation sequencing (mNGS) performed to identify other possible infective agents undetected with the classical tests, showed the presence of the complete genome of human HPgV-1. This case provides further evidence supporting the hypothesis of the pathogenic role of HPgV-1 and warrants particular attention, especially in the pediatric population. Moreover, here we confirmed the diagnostic power of metagenomic-NGS in the detection of unusual pathogens.},
}

@article {pmid41019524,
year = {2025},
author = {Shang, KM and Liu, R and Ni, HB and Ma, H and Su, JW and Yu, HL and Guo, L and Chen, BN and Zhang, XX and Yang, X},
title = {Bile acid pathways in Caprinae gut microbiota: adaptive shifts in microbial metabolism and community structure.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1648896},
pmid = {41019524},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiota plays a central role in host metabolism and immunity, in part through bile acid (BA) biotransformation. In Caprinae animals such as goats and sheep, this process is critical for nutrient absorption, immune regulation, and intestinal homeostasis, yet the microbial taxa and functional pathways involved remain poorly characterized.

METHODS: By leveraging 7,530 high-quality non-redundant metagenome-assembled genomes (MAGs) from Caprinae gut microbiomes, this study systematically characterized microbial diversity, taxonomic composition, and bile acid (BA)-related metabolic pathways through genome annotation, phylogenetic inference, and statistical analyses.

RESULT: The results revealed a diverse gut microbiota across 28 phyla, with Bacillota_A being the most dominant. A significant number of genes (8,290) from 5,217 genomes were identified to be involved in BA transformation pathways, including deconjugation, oxidation, and dehydroxylation. Bacteria from the Bacillota_A phylum were the primary carriers of BA-related genes. Among the MAGs, 1,845 encoded bile salt hydrolase (BSH), an enzyme crucial for the initial step of BA metabolism. Comparative analysis with human and pig gut microbiota highlighted a distinct BA metabolic profile in Caprinae animals, characterized by a higher proportion of BSH-related genes. Functional profiling of BSH-carrying MAGs within the genus Alistipes revealed significant differences in carbohydrate-active enzymes (CAZymes), indicating distinct metabolic repertoires that may reflect divergent ecological roles in the intestinal environment. Microbial taxonomic composition and bile acid (BA)-metabolizing potential varied markedly across the ten intestinal segments of Ovis aries, with the colon, cecum, and rectum showing the highest microbial diversity and functional gene abundance. Key BA-transforming enzymes (BSH, 7α-HSDH, and baiB) were widely distributed, with particularly high abundances in the jejunum and ileum, indicating region-specific specialization in BA metabolism.

DISCUSSION: This study provides new insights into the ecological and metabolic functions of gut microbiota in Caprinae animals, emphasizing the unique BA metabolic profiles and the functional potential of BSH-carrying MAGs, which have broader implications for understanding host-microbiota interactions in health and disease.},
}

@article {pmid41019405,
year = {2025},
author = {Song, H and Li, X and Luo, J and Wang, J and Wu, F and Jiang, J and Chen, J and Cheng, Y and Yong, Y and Duan, M and Zhu, G},
title = {The Influence of Diet on the Composition and Function of Gut Microbiota in Four Snake Species.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72204},
pmid = {41019405},
issn = {2045-7758},
abstract = {Diet plays an important role in shaping the intestinal flora, especially as demonstrated in non-mammalian studies. However, the precise associations underlying the interaction between the snake gut microbiota and diet remain poorly understood. Our findings indicate that the gut microbiomes of four snake species exhibit distinct characteristics influenced by their dietary preferences. Significant variations in gut microbial composition were observed among snakes with different diets. Similarities were noted between the gut microbiomes of Jerdon's pitviper (Protobothrops jerdonii: PJ) and Black-browed ratsnake (Elaphe taeniura: ET), which share similar food preferences. Chinese slug-eating snake (Pareas chinensis: PC), which primarily feeds on snails and slugs, displayed the highest gut microbiota diversity, suggesting a higher level of functional specificity associated with its specialized diet. Chiwen keelback (Rhabdophis chiwen: RC), which consumes fireflies and earthworms, exhibited a significantly higher abundance of antimicrobial resistance genes (ARGs) compared to other snake groups. Opportunistic pathogens such as Plesiomonas, Aeromonas, and Salmonella were relatively abundant in RC, ET, and PJ. The results of this study provide comprehensive data to differentiate the gut microbiota composition structures among four snake species with distinct dietary preferences, explore their potential functions, and identify possible correlations between gut microbial composition and diet. Furthermore, it provides a foundation for the analysis of the influence of genetic and environmental factors on the evolution of gut microbial communities.},
}

@article {pmid41019383,
year = {2025},
author = {Qu, D and Wang, Y and Cao, L and Hou, Q and Liu, Z and Zhong, J and Guo, Z},
title = {Combined microbiome and metabolome analysis of Dacha and Ercha fermented grains of Fen-flavor Baijiu.},
journal = {Food chemistry. Molecular sciences},
volume = {11},
number = {},
pages = {100298},
pmid = {41019383},
issn = {2666-5662},
abstract = {Fen-flavor Baijiu is produced via two fermentation rounds (Dacha and Ercha), and quality is shaped by microbes in fermented grains. We hypothesized that the two rounds select distinct lactic acid bacteria (LAB) consortia with different metabolic potentials that associate with stage-specific metabolites and flavor compounds. We profiled 24 fermented-grain samples using shotgun metagenomics and untargeted metabolomics. Ercha showed lower alpha-diversity and a composition distinct from Dacha. Lactobacillus acetotolerans dominated Dacha, whereas Acetilactobacillus jinshanensis dominated Ercha. We detected 225 differential metabolites; 12 involved in flavonoid biosynthesis were higher in Dacha, while pyrimidine metabolism was more prominent in Ercha. Several LAB species-including L. acetotolerans, Lentilactobacillus hilgardii, Lactobacillus amylovorus, and Lactobacillus amylolyticus-showed positive correlations with these flavonoids. Genes encoding L-lactate dehydrogenase and acetate kinase were mainly carried by L. acetotolerans and associated with acetic acid and ethyl acetate in fermented grains. These outcomes supported our hypothesis and suggested actionable levers for production: stage-targeted monitoring of marker taxa/genes and rational starter design to steer flavor formation in Fen-flavor Baijiu.},
}

@article {pmid41019081,
year = {2025},
author = {Liu, M and Cheng, Y and Wang, X and He, Z and Yang, K and Chen, K and Fan, Y and Wang, W},
title = {Diagnosing Rickettsia felis infection with Metagenomic Next-Generation Sequencing (mNGS) in a patient with ankylosing spondylitis: a case report and literature review.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1643599},
pmid = {41019081},
issn = {1664-3224},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Spondylitis, Ankylosing/complications/diagnosis ; *Rickettsia felis/genetics ; *Metagenomics/methods ; *Rickettsia Infections/diagnosis/microbiology/drug therapy ; Male ; },
abstract = {Rickettsia felis, an emerging flea-borne pathogen with global distribution potential, is a neglected cause of undifferentiated febrile illness, although reported human cases remain sparse. The development of molecular diagnostic methods, along with the application of metagenomic next-generation sequencing (mNGS), has improved the diagnostic accuracy of infectious fevers. A case of Rickettsia felis infection was diagnosed by mNGS in a 55-year-old patient with pre-existing ankylosing spondylitis. Five previously reported cases of Rickettsia felis infection were systematically reviewed, with a comprehensive analysis of their epidemiological characteristics, clinical manifestations, and therapeutic regimens. This study highlights the clinical features and diagnostic approaches of the disease through a case report and literature review.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Middle Aged
*Spondylitis, Ankylosing/complications/diagnosis
*Rickettsia felis/genetics
*Metagenomics/methods
*Rickettsia Infections/diagnosis/microbiology/drug therapy
Male

@article {pmid41018968,
year = {2025},
author = {Dai, Q and He, Y and Wu, J and Zhou, L and Jiang, G and Chen, F},
title = {Effects of neutral detergent fiber levels on apparent nutrient digestibility and intestinal microbiota composition and function in forest musk deer.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1658189},
pmid = {41018968},
issn = {2297-1769},
abstract = {This experiment was conducted to explore the effects of different neutral detergent fiber (NDF) levels on nutrient apparent digestibility and intestinal microbiota composition and function in adult male forest musk deer (FMD) (Moschus berezovskii). A total of 18 adult male forest musk deer (FMD) (aged 4-10 years) with an initial average body weight of 7.09 ± 0.82 kg were selected and randomly divided into three groups with different NDF levels: L: 21.60%, M: 25.14%, and H: 28.47%. The FMD were used in a 50-day trial. The results showed that the apparent digestibility of NDF and acid detergent fiber (ADF) first increased and then decreased as NDF levels rose, with the M group showing the highest digestibility (p < 0.05). The H group exhibited significantly higher (p < 0.05) Chao1 and ACE indices compared to the L group. In addition, at the phylum level (the relative abundance > 0.5%), no significant differences were observed among the three groups, except for Mycoplasmatota, which showed higher (p < 0.05) relative abundance in the M group compared to the L group. At the genus level (the relative abundance > 1%), the three groups did not change (p > 0.05) significantly. In the KEGG function analysis, differentially expressed genes were primarily enriched in pathways related to organismal systems and human diseases. In the CAZy functional analysis, significant differences (p < 0.05) were observed in glycoside hydrolases (GHs) and carbohydrate-binding modules (CBMs), with the M group showing clear enrichment in fiber-degrading enzymes. Overall, the M group demonstrated superior NDF apparent digestibility and enhanced fiber degradation capacity. Therefore, a dietary NDF level of approximately 25% is recommended as optimal for adult male FMD.},
}

@article {pmid41018817,
year = {2025},
author = {Zhou, X and Li, Q and Zhang, S and Wang, W and Wang, R and Zhang, X and Tan, Z and Wang, M},
title = {GCompip: a pipeline for estimating the gene abundance in microbial communities.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf207},
pmid = {41018817},
issn = {2635-0041},
abstract = {MOTIVATION: Gene abundance in metagenome datasets is commonly represented in terms of Counts or Copies Per Million. However, above term lack the consideration of the size of the microbial communities. To reflect the gene abundance in the microbial communities (GAM), GCompip, a comprehensive pipeline for estimating GAM, was developed based on specialized universal single copy genes (USCG) database, stringent alignment parameters, and rigorous filtering criteria.

RESULTS: GCompip showed high specificity without compromising computational efficiency, and improved the precision of downstream GAM estimations across diverse six ecological environments (i.e. human gut, rumen, freshwater, marine, hydrothermal sediment, and glacier). In contrast, the comparative annotation tools (i.e. KofamScan, eggNOG-mapper and HUMAnN3) showed larger error intervals, higher susceptibility to false positives, or overestimation of USCG abundance, primarily due to more relaxed thresholds, multifamily matches, or less stringent alignment settings. To facilitating the applicability of GCompip, we provided both Linux command line and R package versions. Overall, this GCompip presented an accurate, robust, user-friendly, and efficient computational pipeline designed to calculate GAM using metagenomic sequencing data. The developed pipeline makes it accessible to researchers seeking to evaluate the metabolic capabilities of microbial communities, and improve the capacity of interpreting metagenomic data related to microbial communities.

GCompip package source code and documentation are freely available for download at https://github.com/XiangZhouCAS/GCompip. A separate Linux command line version is available at https://github.com/XiangZhouCAS/GCompip_onlinux.},
}

@article {pmid41018532,
year = {2025},
author = {Wang, J and Yu, C and Qiu, M and Xiong, X and Peng, H and Zhu, S and Chen, J and Song, X and Hu, C and Xia, B and Xiong, Z and Du, L and Yang, C and Zhang, Z},
title = {Whole-genome Metagenomic Sequencing Reveals Gut Microbiota Composition and Function Associated with Differential Growth Performance in Two Chicken Breeds.},
journal = {The journal of poultry science},
volume = {62},
number = {},
pages = {2025028},
pmid = {41018532},
issn = {1349-0486},
abstract = {Growth performance, an important trait in the broiler industry, is defined by both the host genome and gut microbiota. At present, it is not known how gut microbiota contribute to the growth of Dahen broilers, a commercially important breed in China. In this study, we used metagenome sequencing to compare the taxonomic composition and functional implications of cecal microbiota in fast-growing Dahen broilers and slow-growing Tibetan chickens. A total of 2,207,811 unique genes were assembled in the non-redundant set, and 99% of them were taxonomically annotated as having a bacterial origin. The fast-growing group displayed a higher alpha diversity than the slow-growing group in terms of ACE, Chao1, and Good's coverage statistics. The two groups presented also significantly different (P < 0.05) relative abundances of the genera Collinsella, Olsenella, Pyramidobacter, Basidiobolus, and Mieseafarmvirus, along with that of eight species (e.g., Olsenella timonensis and Victivallis sp. Marseille Q1083). Although not statistically significant, we found a higher expression of several energy metabolism-related eggNOG terms in the fast-growing group. In summary, the present study identifies gut microbiota associated with growth performance in Dahen broilers and offers new tools for gut microbiome-related intervention in this breed.},
}

@article {pmid41017911,
year = {2025},
author = {Devarajalu, P and Attri, SV and Kumar, J and Dutta, S and Kabeerdoss, J},
title = {Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1649384},
pmid = {41017911},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant, Premature ; India/epidemiology ; Infant, Newborn ; *Enterocolitis, Necrotizing/microbiology/epidemiology ; Feces/microbiology ; *Metagenomics/methods ; Male ; Female ; Enterobacteriaceae/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is an inflammatory bowel disease that primarily affects preterm infants. Predisposing risk factors for NEC include prematurity, formula feeding, anemia, and sepsis. To date, no studies have investigated the gut microbiota of preterm infants with NEC in India.

METHOD: In the current study, shotgun metagenomic sequencing was performed on fecal samples from premature infants with NEC and healthy preterm infants (n = 24). Sequencing was conducted using the NovaSeq X Plus platform, generating 2 × 150 bp paired-end reads. The infants were matched based on gestational age and postnatal age.

RESULT: The median time to NEC diagnosis was 9 days (range: 1-30 days). Taxonomic analysis revealed a high prevalence of Enterobacteriaceae at the family level, with the genera Klebsiella and Escherichia particularly prominent in neonates with NEC. No statistically significant differences in alpha or beta diversity were observed between stool samples from infants with and without NEC. Linear regression analysis demonstrated that Enterobacteriaceae were significantly more abundant in stool samples from infants with NEC than without NEC (q < 0.05). Differential abundance analysis using Linear Discriminant Analysis Effect Size (LEfSe) identified Klebsiella pneumoniae and Escherichia coli as enriched in the gut microbiota of preterm infants with NEC. Functional analysis revealed an increase in genes associated with lipopolysaccharide (LPS) O-antigen, the type IV secretion system (T4SS), the L-rhamnose pathway, quorum sensing, and iron transporters, including ABC transporters, in stool samples from infants with NEC.

CONCLUSION: The high prevalence of Enterobacteriaceae and enrichment of LPS O-antigen and T4SS genes may be associated with NEC in Indian preterm infants.},
}

Humans
*Gastrointestinal Microbiome/genetics
Infant, Premature
India/epidemiology
Infant, Newborn
*Enterocolitis, Necrotizing/microbiology/epidemiology
Feces/microbiology
*Metagenomics/methods
Male
Female
Enterobacteriaceae/genetics/isolation & purification/classification

@article {pmid41017909,
year = {2025},
author = {Maan, S and Batra, K and Rajendhran, J and Joseph, R and Singh, VK and Chaudhary, D and Sindhu, S and Kadian, V and Kumar, A and Maan, NS and Mor, S},
title = {Exploring viral diversity in diarrheic porcine feces: a metagenomic analysis from an Indian swine farm.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1653342},
pmid = {41017909},
issn = {2235-2988},
mesh = {Animals ; Swine ; *Feces/virology ; *Swine Diseases/virology/epidemiology ; *Metagenomics ; India/epidemiology ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Diarrhea/veterinary/virology ; Farms ; Genome, Viral ; Virome ; *Virus Diseases/veterinary/virology ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Pig husbandry is a vital sector in India, providing nutritional security and employment for marginalized communities. Pigs are advantageous due to high reproduction rates and fecundity, shorter generation intervals, and efficient feed conversion, requiring minimal housing. However, the swine industry encounters significant disease challenges, particularly viral gastroenteritis, which poses serious public health risks, especially in developing countries. Pigs serve as natural reservoirs and amplifiers for numerous viruses with zoonotic potential, making disease surveillance essential.

MATERIALS: In this study, we conducted a metagenomic analysis of 15 fecal samples from diarrheic pigs on a farm in India, marking the first exploration of the fecal virome diversity in this region. Our next-generation sequencing approach has enabled the unbiased detection of multiple viral agents in the porcine fecal samples, detecting both known and novel viral agents without prior target knowledge.

RESULTS: The key and novel viruses obtained in our study were porcine circovirus, porcine parvovirus 7, porcine mamastrovirus 3, porcine sapelovirus A, and porcine enterovirus G. This work resulted in the generation of full genomes for multiple porcine viruses, including Circovirus, Enterovirus, Sapelovirus, and Mamastrovirus, along with partial genomes of Parvovirus, Picobirnavirus, Porcine stool-associated RNA virus (Porcine Posavirus), Kobuvirus, and Rotavirus, all subjected to phylogenetic analysis.

CONCLUSION: Our survey indicates frequent co-infections with diverse viruses, creating conducive environments for viral recombination and reassortment. Continuous surveillance of viral pathogens in animal populations is essential for understanding the dynamics of both known and novel viruses and for detecting emerging pathogens, along with their zoonotic and pathogenic potential.},
}

Animals
Swine
*Feces/virology
*Swine Diseases/virology/epidemiology
*Metagenomics
India/epidemiology
*Viruses/genetics/classification/isolation & purification
Phylogeny
*Diarrhea/veterinary/virology
Farms
Genome, Viral
Virome
*Virus Diseases/veterinary/virology
High-Throughput Nucleotide Sequencing

@article {pmid41017724,
year = {2025},
author = {Zhang, Y and Mo, C and He, X and Xiao, Q and Yang, X},
title = {Gut microbial community of patients with Parkinson's disease analyzed using metagenome-assembled genomes.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-25-00420},
pmid = {41017724},
issn = {1673-5374},
abstract = {Previous investigations into gut microbiota dysbiosis in patients with Parkinson's disease have relied on 16S rRNA amplicon sequencing and assembly-free metagenomic approaches. However, there is an urgent need to study the function of the gut microbiome at the genome level using metagenome-assembled genomes. Here, we conducted single-sample metagenomic binning analysis using shotgun metagenomic sequencing data and retrieved 2837 metagenomeassembled genomes to explore the gut microbiota profile at the genome level. Reconstructing microbial genomes from metagenomic sequences greatly enriched the diversity and number of microbial genomes, especially those of uncultivable strains. By integrating the analysis of metagenome-assembled genomes with clinical parameters, we observed higher α-diversity indexes and a very different composition of microbial communities in patients with Parkinson's disease. We also identified microbial species and metagenome-assembled genomes that were significantly associated with clinical characteristics, including disease severity, medication, motor complications, and non-motor symptoms. The genes of Parkinson's disease severity-associated metagenomeassembled genomes were distributed across multiple pathways, such as carbon metabolism, phosphonate metabolism, carbohydrate metabolism, amino acid metabolism, fatty acid metabolism, bile acid metabolism, metabolism of cofactors and vitamins, neuroprotective molecules, immunogenic components, toxic metabolites, translation, and bacterial secretion. Our work provides a comprehensive resource for investigating the gut microbiota-Parkinson's disease relationship at the genome level, which may enhance our comprehension of the underlying mechanisms of this disease.},
}

@article {pmid41017070,
year = {2025},
author = {Guo, C and Pan, Y and Yu, J and Yao, L and He, Y and Cui, J and Gao, M and Pang, Y},
title = {Disseminated Blastomycosis Mimicking Tuberculosis, China.},
journal = {Emerging infectious diseases},
volume = {31},
number = {10},
pages = {2046-2048},
doi = {10.3201/eid3110.250671},
pmid = {41017070},
issn = {1080-6059},
mesh = {Humans ; Male ; *Blastomyces/genetics/isolation & purification ; *Blastomycosis/diagnosis/drug therapy/microbiology ; China ; Diagnosis, Differential ; Tomography, X-Ray Computed ; *Tuberculosis/diagnosis ; Adult ; },
abstract = {Blastomycosis is endemic in central and southern North America but rare in China. It can mimic community-acquired pneumonia, tuberculosis, or cancer. We describe a patient who initially had tuberculosis diagnosed and later had blastomycosis diagnosed through metagenomic detection, which aided diagnosis and treatment. Clinicians should consider blastomycosis in differential diagnoses for respiratory diseases.},
}

Humans
Male
*Blastomyces/genetics/isolation & purification
*Blastomycosis/diagnosis/drug therapy/microbiology
China
Diagnosis, Differential
Tomography, X-Ray Computed
*Tuberculosis/diagnosis
Adult

@article {pmid41016664,
year = {2025},
author = {Dong, Y and Zheng, JS and Yang, Y and Wang, T and Li, F and Wu, P and Lai, Y and Wang, Y and He, X and Zhang, P and Zhang, S and Wu, N and Li, S and Yuan, J and Shan, D and Liu, X and Liu, G and Hu, Y and Pan, A and Pan, XF},
title = {Associations between Combined Healthy Lifestyle and Adverse Birth Outcomes in Two Prospective Cohorts: Roles of Gut Microbiota and Serum Metabolites.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.09.036},
pmid = {41016664},
issn = {1938-3207},
abstract = {BACKGROUND: Maternal lifestyle factors are reported to be associated with adverse birth outcomes (ABOs). These factors may also dynamically influence gut microbiota composition and serum metabolic profiles.

OBJECTIVE: To investigate the associations between combined healthy lifestyle and ABOs, and the mediating roles of gut microbiota and serum metabolites.

METHODS: This study was conducted based on the Tongji-Huaxi-Shuangliu Birth Cohort (THSBC), comprising 1086 participants with repeated multi-omics data collected at three time points. An independent validation was performed using 161 participants from the Huaxi Birth Cohort (HBC), with available multi-omics data at five time points. Participants were classified into three lifestyle categories (unhealthy, low healthy, and highly healthy) according to diet, physical activity, smoking, drinking, sleep, and body mass index. Gut microbiota were characterized using 16S rRNA gene sequencing in the THSBC and metagenomics in the HBC, while serum metabolites were profiled using untargeted liquid chromatography-mass spectrometry. Clinical data on birth outcomes, such as gestational age, birth weight, and sex were collected in the THSBC.

RESULTS: A highly healthy lifestyle was associated with lower risks of macrosomia (MAC) (odds ratio: 0.43; 95% confidence interval: 0.33, 0.57), preterm birth (PTB) (0.60; 0.46, 0.79), and large for gestational age (LGA) (0.44; 0.35, 0.56). Among the identified mediators, gut microbiota and serum metabolites, including Eisenbergiella, Tyzzerella, Megamonas, pro-Ile, and 1-amino-1-cyclobutane-carboxylic acid were negatively associated with a healthy lifestyle, while Lachnospiraceae NK4A136 group, 4-methoxyestrone, and LPC (0:0/18:3) were positively associated. Mediation analyses showed that Eisenbergiella and 4-methoxyestrone explained 11.4% and 13.0% of the inverse association between a highly healthy lifestyle and PTB, respectively, while the other microbiota and metabolites mediated 5%-7% of the associations with MAC and LGA.

CONCLUSION: Maternal healthy lifestyle was associated with lower risks of ABOs, with gut microbiota and serum metabolites serving as important mediators in these relationships.},
}

@article {pmid39345108,
year = {2025},
author = {Yu, L and Mu, C and Lan, X and Cheng, L and Li, H and Li, Z and Feng, Y and Cui, Z},
title = {A Patient With Cryptococcal Meningitis Accompanied With Acute Intracranial Hypertension Treated by Ventricular Abdominal-wall Drainage.},
journal = {The Journal of craniofacial surgery},
volume = {36},
number = {2},
pages = {e109-e111},
doi = {10.1097/SCS.0000000000010699},
pmid = {39345108},
issn = {1536-3732},
mesh = {Humans ; *Meningitis, Cryptococcal/complications ; *Intracranial Hypertension/etiology/therapy/surgery ; *Drainage/methods ; Male ; Antifungal Agents/therapeutic use ; *Abdominal Wall/surgery ; Tomography, X-Ray Computed ; Acute Disease ; Adult ; },
abstract = {Intracranial hypertension is considered a common and severe complication of cryptococcal meningitis (CM), contributing to early mortality and neurological sequelae. Timely and effective control of elevated intracranial pressure is crucial for the management of CM. Herein, the authors present a case of ventricular abdominal wall drainage for CM accompanied with acute intracranial hypertension. Notably, the patient has a history of taking immunosuppressants for thoracic and abdominal diffuse lymphangiomatosis. After continuous drainage of cerebrospinal fluid combined with standardized antifungal treatment, the patient recovered well.},
}

Humans
*Meningitis, Cryptococcal/complications
*Intracranial Hypertension/etiology/therapy/surgery
*Drainage/methods
Male
Antifungal Agents/therapeutic use
*Abdominal Wall/surgery
Tomography, X-Ray Computed
Acute Disease
Adult

@article {pmid41019634,
year = {2023},
author = {McCulloch, JA and Badger, JH and Cannon, N and Rodrigues, RR and Valencia, M and Barb, JJ and Fernandes, MR and Balaji, A and Crowson, L and O'hUigin, C and Dzutsev, A and Trinchieri, G},
title = {JAMS - A framework for the taxonomic and functional exploration of microbiological genomic data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.03.03.531026},
pmid = {41019634},
issn = {2692-8205},
abstract = {Shotgun microbiome sequencing analysis presents several challenges to accurately and consistently depict sample composition and functional potential. Here we present a two-part framework - JAMS (Just a Microbiology System) - whereby with raw fastq files and metadata as input, meaningful analysis within a sample and between a sample can be performed with ease for either shotgun or 16S sequences. JAMS is the first package to provide seamless deconvolution of functions into their taxonomic contributors. We validated our JAMS framework on two human gut shotgun metagenome test datasets against the popular tool MetaPhlAn 4. We further demonstrate the application of the JAMS package, particularly the plotting functions, on a mouse shotgun dataset.},
}

@article {pmid41016593,
year = {2025},
author = {Ma, S and Li, Y and Chen, C and Dong, Y and Huang, P and Tu, R and Liu, X and Zhou, R and Wu, C},
title = {Metabolic interactions drive microbial community succession and functional expression of Nongxiangxing (Strong-flavor) daqu.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.09.052},
pmid = {41016593},
issn = {2090-1224},
abstract = {INTRODUCTION: Nongxiangxing daqu is a wheat-based fermentation starter used in the production of Baijiu (a traditional Chinese distilled spirit), whose fermentation process during storage directly affects its quality. However, the dynamics of microbial succession and metabolism during daqu storage, particularly the functional contributions of specific microorganisms to enzyme formation and their metabolic interactions, remain unclear.

OBJECTIVES: This study aimed to investigate the temporal dynamics of microbial community structure, function, and enzymatic activity in daqu during storage, with a focus on metabolic interactions such as cross-feeding and metabolic division of labor (MDOL).

METHODS: Metagenomic and metaproteomic analyses were integrated to profile microbial taxa, functional genes, and protein expression across storage time points. Weighted gene co-expression network analysis (WGCNA) linked gene modules to storage time. Genome-scale metabolic models (GEMs) were constructed to infer metabolic interaction networks among microbes.

RESULTS: Paecilomyces variotii, Rasamsonia emersonii, Rhizopus microsporus, Rhizopus delemar, Kroppenstedtia eburnea, and Weissella confusa were dominant species. In total, 14,588 protein groups were identified, including 6,801 enzymes enriched in carbohydrate, amino acid, and energy metabolism. Glucosidase activity was primarily attributed to Rasamsonia, Thermoascus, Aspergillus, Thermomyces, and Paecilomyces. Functional genes and enzymes declined sharply after month 1, reached a nadir at month 3, and partially rebounded by month 4. WGCNA identified 16 gene modules associated with storage (maximum r = 0.97, P < 0.01). Cross-feeding patterns were identified among Weissella confusa, Kroppenstedtia eburnea, Saccharopolyspora rectivirgula, and Enterobacteriaceae. The MDOL model revealed cooperative metabolic roles among Actinomycetota, Bacillota, Ascomycota, and Mucoromycota in converting raw materials into flavor compounds.

CONCLUSION: These findings improve the understanding of microecological dynamics during daqu storage and provide a theoretical basis for regulating and optimizing the fermentation process during the storage period.},
}

@article {pmid41016209,
year = {2025},
author = {Zhao, Q and Yu, C and Liu, X and Hu, X and Yang, Q},
title = {Multi-omics reveals the systematical influence of composite heavy metal(loid)s on soil microbial function: Elemental cycling and microbial adaptation mechanisms.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139973},
doi = {10.1016/j.jhazmat.2025.139973},
pmid = {41016209},
issn = {1873-3336},
abstract = {As the core of soil material cycling, soil microecosystems contaminated by combined heavy metal(loid)s have attracted widespread concern. Previous studies mostly focused on community-level ecological functions, neglecting genomic-level investigations and comprehensive microbial adaptation mechanisms. Here, we integrated multi-omics (metagenomics, genome assemblies, comparative genomics) with field and lab studies to explore responses from community to genomic scales. We found that metal(loid)s altered the assembly of microbial functional genes and weakened functional networks linking carbon, nitrogen, phosphorus, and sulfur cycling. They reduced the potential of carbohydrate metabolism, carbon fixation, and sulfur metabolism involved in protein synthesis and disrupted normal organic matter decomposition (via certain CAZymes). Conversely, they increased the potential of methanogenesis, denitrification, and organic phosphorus mineralization, as well as stimulating dissimilatory sulfate reduction and sulfur disproportionation. Microbes employed multi-level strategies to combat persistent heavy metal(loid)s stress, including reducing metal ion uptake, facilitating intracellular detoxification, and activating efflux pathways. They underwent adaptive evolution through mechanisms such as enhancing the synthesis and transportation of siderophores, strengthening DNA damage repair, and promoting genome streamlining. Notably, our analysis revealed that horizontal gene transfer, mediated by mobile genetic elements, drives the acquisition of resistance genes. This study provides systematic genomic evidence for such adaptive mechanisms in functional microbes, greatly advancing our understanding of their bioremediation potential.},
}

@article {pmid41016077,
year = {2025},
author = {Wirth, R and Pap, B and Szuhaj, M and Bagi, Z and Farkas, Z and Kovács, KL and Maróti, G},
title = {Functional resistomes in municipal wastewater treatment plants pose challenges to public health.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124663},
doi = {10.1016/j.watres.2025.124663},
pmid = {41016077},
issn = {1879-2448},
abstract = {Wastewater treatment plants (WWTPs) are essential for controlling antimicrobial resistance, but also serve as hotspots for resistance gene persistence and dissemination. In this study, a novel combinatory approach using genome-resolved metagenomics and metatranscriptomics was employed to examine the resistome of a full-scale municipal WWTP across treatment stages and seasons. Results reveal that although human-associated, potentially pathogenic, antibiotic resistance gene (ARG)-harbouring metagenome-assembled genomes (ARBMAGs) declined in abundance during treatment, many ARGs remained transcriptionally active, particularly efflux, beta-lactam, and macrolide-lincosamide-streptogramin genes conferring resistance against fluoroquinolones, cephalosporins, and macrolides. Environment and treatment-adapted microbes become increasingly dominant, with plasmids identified as major vectors of mobile resistance. Dominant potential pathogenic human-associated ARBMAGs were abundant during spring and summer, whereas environmental ARBMAGs predominated in colder seasons. Fluoroquinolone resistance genes displayed varying expression levels across ARBMAG types, with the lowest levels observed during the anaerobic phase of treatment. Although clinically relevant ARGs were detected at low relative abundance and expression levels, one of the carriers was Citrobacter freundii ARBMAG, a human-associated potential pathogen. These findings underscore the value of integrating genomic and transcriptomic data to assess site-specific and ARBMAG-type-specific resistance and to strengthen antibiotic resistance monitoring in engineered systems.},
}

@article {pmid41015769,
year = {2025},
author = {Sheppard, SK and Arning, N and Eyre, DW and Wilson, DJ},
title = {Machine learning and statistical inference in microbial population genomics.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {313},
pmid = {41015769},
issn = {1474-760X},
support = {088786/C/09/Z//Wellcome/ ; 101237/Z/13/B//Wellcome/ ; MR/L015080/1//UK Research and Innovation/ ; BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101237/Z/13/B//Royal Society/ ; },
mesh = {*Machine Learning ; *Genomics/methods ; *Metagenomics/methods ; *Genome, Microbial ; },
abstract = {The availability of large genome datasets has changed the microbiology research landscape. Analyzing such data requires computationally demanding analyses, and new approaches have come from different data analysis philosophies. Machine learning and statistical inference have overlapping knowledge discovery aims and approaches. However, machine learning focuses on optimizing prediction, whereas statistical inference focuses on understanding the processes relating variables. In this review, we outline the different aspirations, precepts, and resulting methodologies, with examples from microbial genomics. Emphasizing complementarity, we argue that the combination and synthesis of machine learning and statistics has potential for pathogen research in the big data era.},
}

*Machine Learning
*Genomics/methods
*Metagenomics/methods
*Genome, Microbial

@article {pmid41015602,
year = {2025},
author = {Nazrin, MRR and Pavan, JS and Gouda, MNR and Kumaranag, KM and Suroshe, SS and Kamil, D and Subramanian, S},
title = {Host-Driven Functional Divergence in Gut Microbiota of Honeybees Apis cerana and Apis mellifera: Implications for Pollination, Nutrition, and Sustainable Apiculture.},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {531},
pmid = {41015602},
issn = {1432-0991},
mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Pollination ; },
abstract = {Honeybees are indispensable in sustaining natural ecosystems and global crop production by pollinating key food crops. Understanding their gut microbiota is crucial for insights into their health, nutrition, and behavior, with broader ecological and agricultural relevance. This study compares the gut microbiota of Apis cerana and Apis mellifera, focusing on bacterial composition, diversity, and functional roles. Using culture-dependent and metagenomic methods, core bacteria such as Lactobacillus, Fructobacillus, Gilliamella apicola, Bartonella apis, and Snodgrassella alvi were identified, linked to carbohydrate and nitrogen metabolism, immune modulation, and polysaccharide degradation. A. mellifera exhibited greater microbial and functional diversity, reflected in higher Shannon (1.22 vs. 1.08) and Simpson (0.675 vs. 0.655) indices. Strong intraspecies correlations and weaker interspecies correlations (Pearson's r = 0.6486) indicated distinct microbial profiles, supported by PCA (75.3% variation) and Adonis test (P = 0.04, R[2] = 0.723). Functional analysis via MG-RAST and UniFrac-based PCoA showed species-specific differences in key metabolic pathways. Enzymatic profiling revealed Fructobacillus fructosus with high invertase activity (7.31 ± 0.30) and Apilactobacillus apinorum with strong pectinolytic activity (4.707 ± 0.36), enhancing honeybee nutrition. These findings have significant implications for pollination efficiency, probiotic development, and sustainable apiculture, ultimately supporting conservation strategies and the resilience of honeybee populations.},
}

Bees/microbiology/physiology
Animals
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Pollination

@article {pmid41015591,
year = {2025},
author = {Raziq, K and Saleem, R and Zafar, S and Sanaullah, T and Nazir, MM and Ummara, UE and Abbasi, A},
title = {Environmental resistomes and antimicrobial resistance: integrating the One Health framework.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41015591},
issn = {1432-1912},
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global health challenge, exacerbated by the interconnected dynamics of human, animal, and environmental health systems. The "One Health" approach, which integrates these domains, offers a comprehensive framework for addressing AMR at its roots. This review explores the environmental dimension of AMR by examining the role of environmental microbiomes as reservoirs and transmission vectors of antimicrobial resistance genes (ARGs). It highlights emerging evidence, transmission pathways, detection methodologies, and policy gaps, with an emphasis on low- and middle-income countries (LMICs). An in-depth literature synthesis was conducted across environmental, clinical, and molecular microbiology studies to understand the eco-evolutionary dynamics of resistance, routes of ARG transmission, and effectiveness of current surveillance models. Emphasis was placed on novel detection technologies and integrated policy frameworks. Environmental resistomes present in soil, water, air, and waste play a pivotal yet underappreciated role in ARG dissemination via horizontal gene transfer, mobile genetic elements, and co-selectors like heavy metals and biocides. The complexity of microbial communities in diverse ecological matrices fosters the persistence and evolution of resistance. Current surveillance systems often neglect environmental inputs, particularly in LMICs, limiting the effectiveness of AMR mitigation efforts. A paradigm shift is required to recognize the environmental microbiome as a central component of AMR. Integrated "One Health" strategies, improved environmental surveillance, policy reforms, and novel technological interventions are critical for global AMR control. Bridging the research-policy gap and empowering local surveillance infrastructure can significantly enhance resistance management and public health outcomes.},
}

@article {pmid41015495,
year = {2025},
author = {Castells-Nobau, A and Fumagalli, A and Del Castillo-Izquierdo, Á and Rosell-Díaz, M and de la Vega-Correa, L and Samulėnaitė, S and Motger-Albertí, A and Arnoriaga-Rodríguez, M and Garre-Olmo, J and Puig, J and Ramos, R and Burokas, A and Coll, C and Zapata-Tona, C and Perez-Brocal, V and Ramio, L and Moya, A and Swann, J and Martín-García, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Gut microbial modulation of 3-hydroxyanthranilic acid and dopaminergic signalling influences attention in obesity.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336391},
pmid = {41015495},
issn = {1468-3288},
abstract = {BACKGROUND: Obesity-related alterations in the gut microbiota have been linked to cognitive decline, yet their relationship with attention remains poorly understood.

OBJECTIVE: To evaluate the possible relationships among gut metagenomics, plasma metabolomics and attention.

DESIGN: We conducted faecal shotgun metagenomics and targeted plasma tryptophan metabolomics across three independent cohorts (n=156, n=124, n=804) with functional validations in preclinical models, including three faecal microbiota transplantation (FMT) experiments in mice and Drosophila melanogaster.

RESULTS: Obesity was consistently associated with reduced attention. Metagenomics analyses identified Proteobacteria species and microbial functions related to tryptophan biosynthesis from anthranilic acid (AA) as negatively associated with attention in obesity. Plasma tryptophan metabolic profiling and machine learning revealed that 3-hydroxyanthranilic acid (3-HAA) was positively associated with attention, particularly in obesity, while AA showed a negative association. Bariatric surgery improved attention and enriched microbial species linked to attention. In mice, diet-induced obesity (DIO) and microbiota depletion reduced 3-HAA and 5-hydroxy-indole acetic acid (5-HIAA) concentrations in the prefrontal cortex (PFC), which were restored by FMT. Global metabolic profiling (>600 metabolites) of PFC from the FMT group identified 3-HAA and the tryptophan and tyrosine pathways among the most significant in mice receiving microbiota from high-attention donors. A second FMT experiment also revealed a consistent enrichment of the tryptophan and tyrosine metabolism at the transcriptional level in the PFC, with Haao (3-hydroxyantrhanilic acid dioxygenase) and Aox4 (aldehyde oxidase 4), key in 3-HAA and 5-HIAA degradation, among the significantly regulated genes. In a third FMT study, attentional traits were transmitted from humans to mice alongside modulation of serotonergic and dopaminergic pathways. In Drosophila, mono-colonisation with Enterobacter cloacae and DIO induced attention deficit-like behaviours, which were mitigated by 3-HAA supplementation.

CONCLUSIONS: We have identified the microbiota and 3-HAA as potential therapeutic targets to improve attention, especially in obesity.},
}

@article {pmid41015376,
year = {2025},
author = {Zhao, JX and Wang, XY and Zhang, X and Tang, LY and Xie, SC and Lv, YH and Zheng, Z and Gao, YQ and Jiang, J and Zhang, XX and Ma, H},
title = {Toxoplasma gondii alters gut microbiota and systemic metabolism in cats: A multi-omics approach.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106455},
doi = {10.1016/j.tvjl.2025.106455},
pmid = {41015376},
issn = {1532-2971},
abstract = {Toxoplasma gondii (T. gondii) is an obligate intracellular parasite with a complex life cycle that culminates in cats-its only definitive host. While its immunological impact is well studied, how T. gondii shapes the feline gut microbiota and systemic metabolism remains largely unexplored. To investigate host-parasite-microbiome interactions, we performed a multi-omics study combining metagenomic sequencing and untargeted serum metabolomics in cats before and after T. gondii infection. Fecal samples were used to construct a comprehensive microbial gene catalog and assess functional shifts, while serum samples were analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS) to capture systemic metabolic changes. Infection with T. gondii, particularly during its sexual replication phase, significantly disrupted gut microbial diversity, composition, and function. Functional annotation revealed downregulation of microbial genes involved in vitamin, cofactor, and energy metabolism, alongside upregulation of carbohydrate metabolism pathways. Concurrently, metabolomic profiling showed marked alterations in lipid profiles, amino acid pathways, and folate-mediated one-carbon metabolism. Integrated analysis uncovered strong correlations between specific microbial taxa-such as Bifidobacterium adolescentis and Ligilactobacillus animalis-and host metabolites, underscoring a tight link between microbial function and host metabolic responses to infection. To our knowledge, this is the first study to comprehensively map the microbiome and metabolic landscape of T. gondii infection in the feline host. Our findings reveal profound parasite-induced shifts in microbial function and systemic metabolism, offering new insights into the molecular interplay between host, parasite, and microbiota. These insights may inform future strategies for therapeutic modulation of host responses in toxoplasmosis.},
}

@article {pmid41015315,
year = {2025},
author = {Miao, H and Zeng, W and Zhan, M and Hao, X and Wang, R and Peng, Y},
title = {Overcoming elemental sulfur bioavailability limitations with sponge iron coupling for enhanced nitrate removal: Novel perspective on electron transfer and iron-nitrogen-sulfur metabolism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133390},
doi = {10.1016/j.biortech.2025.133390},
pmid = {41015315},
issn = {1873-2976},
abstract = {This study developed a novel sponge iron (sFe[0]) and elemental sulfur (S[0]) coupled autotrophic denitrification biofilter (S[0]-sFe[0]AD). At the ratio Fe[0] to S[0] of 0.5 and a hydraulic retention time of 1.5 h, the system achieved high nitrate and phosphate removal rates of 969.7 mgN·L[-1]·d[-1] and 56.1 mgP·L[-1]·d[-1], with efficiencies over 98.5 %. Activated biochemical sulfidogenic pathways enabled in situ regeneration of highly bioavailable FeS. This process not only expanded electron donor pool but also reduced sulfate production by facilitating multi-pathway denitrification. Moreover, FeS-mediated direct extracellular electron transfer promoted iron-sulfur redox cycling. Metagenomic analysis further revealed enhanced iron and energy metabolism within the coupled system. The enriched iron-sulfur redox bacteria (Thiobacillus, Desulfurivibrio and Geothrix) and genes (narB, mtrC, sox, fccAB and sir) facilitated the establishment of a self-sustaining iron-sulfur cycle, thereby extending system longevity. This study provides novel insights for developing efficient iron-sulfur coupled autotrophic denitrification technology for sustainable wastewater treatment.},
}

@article {pmid41015306,
year = {2025},
author = {Hou, DJ and Guo, WL and Yang, HW and Liu, QR and Fan, NS and Jin, RC},
title = {Behaviors and adaptive strategies of anammox microbiota in response to typical ionic liquid: Metabolic compensation and gene regulation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133395},
doi = {10.1016/j.biortech.2025.133395},
pmid = {41015306},
issn = {1873-2976},
abstract = {Ionic liquids (ILs) have been used to replace organic solvents, thereby causing challenges for wastewater treatment. Anaerobic ammonium oxidation (anammox) had been recognized to treat high-strength ammonium wastewater, but its response to ILs remains unclear. Metagenomic sequencing, granule characterization and molecular docking simulation were employed to investigate the comprehensive effects of 1-ethyl-3-methylimidazolium acetate ([EMIM][Ac]) on anammox consortia. [EMIM][Ac] of 2 mg L[-1] reduced the specific anammox activity (SAA) by 46.0 %. [EMIM][Ac] also induced oxidative stress. The higher abundance of denitrifying bacteria and functional genes (nirK and nirS) compensated for the reduced nitrogen removal efficiency. In P2, the total abundance of nirK and nirS in R1 was 16.2 % higher than its initial value, and also 9.6 % higher than that in R0. This study elucidated how anammox microbiota resisted ILs via metabolic regulation and EPS secretion, providing a theoretical support for improving the feasibility and efficiency of anammox-based wastewater treatment systems.},
}

@article {pmid41015263,
year = {2025},
author = {Moore, CM and Secor, EA and Fairbanks-Mahnke, A and Everman, JL and Elhawary, JR and Witonsky, JI and Pruesse, E and Chang, CH and Contreras, MG and Eng, C and Canales, K and Rosado, T and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Lopez, N and Valentin, AM and Medina, V and Montanez-Lopez, CA and Morin, A and Nieves, NA and Oh, SS and Otero, RA and Colon, R and Rodriguez, L and Sajuthi, SP and Salazar, S and Serrano, G and Morales, EV and Vazquez, G and Morales, NV and Williams, BJM and Zhang, P and Sheppard, D and Santana, JRR and Seibold, MA},
title = {Independent and interactive effects of viral species on early-life lower respiratory tract illness.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106616},
doi = {10.1016/j.jinf.2025.106616},
pmid = {41015263},
issn = {1532-2742},
abstract = {OBJECTIVES: To determine the association between viral species and odds of severe lower respiratory tract illnesses (sLRI) versus upper respiratory illness (URI) among children under 2 years of age.

METHODS: Infants (n=2,061) enrolled in the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes were surveilled for respiratory illnesses until age 2 years (March 2020 to April 2024). Nasal swabs from 1,363 illnesses (774 participants) were screened for 21 pathogens.

RESULTS: RSV infections occurred in 23% of sLRIs and increased odds of sLRI vs URI (OR=9.28; 95% CI, 5.43-15.85). Metapneumovirus, parainfluenza, and non-SARS-CoV-2 coronavirus also increased odds of sLRIs, while SARS-CoV-2 was associated with lower risk of sLRIs. Rhinovirus (43%) and bocavirus (16.1%) were commonly detected, but were not associated with sLRI risk. Co-infection with multiple viral species was associated with 2.92-fold greater odds of sLRI (95% CI, 2.05-4.16) compared to single viral species infections. Rhinovirus-bocavirus was the most common co-infection, and interaction between these viruses was associated with increased odds of sLRI.

CONCLUSIONS: Diverse viral pathogens drive early-life sLRIs. Some (e.g. RSV and metapneumovirus) have intrinsic propensity to cause sLRIs, while other viruses' lower airway pathogenicity depends on other factors, including co-infection.},
}

@article {pmid41015172,
year = {2025},
author = {Luo, S and Yuan, J and Song, Y and Qi, J and Zhu, M and Feng, H and Zhao, Y and Mei, W and Fu, F and Li, X and Song, C},
title = {Bacterial network complexity drives carbon, nitrogen and phosphorus metabolism potential under short-term soil water content changes in wetlands.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122952},
doi = {10.1016/j.envres.2025.122952},
pmid = {41015172},
issn = {1096-0953},
abstract = {Wetland soil microbial communities play pivotal roles in biogeochemical cycling; however, how their network complexity mediates carbon (C), nitrogen (N), and phosphorus (P) metabolism in response to soil water content (SWC) changes remains unclear. In this study, soil samples from the Zhalong, Momoge and Xianghai wetlands in Songnen Plain of China were incubated under natural (CK), drought (10% SWC), and high SWC (50% SWC) conditions, followed by metagenomic sequencing to evaluate the impact of SWC changes on bacterial community structure and function. The results showed that soil bacterial diversity and network complexity decreased under drought but recovered under high SWC, with Proteobacteria and Actinobacteria displaying divergent responses. C fixation pathways (rTCA and DC-HB cycles) were significantly enriched under 50% SWC, which correlated strongly with enhanced bacterial interactions. The abundance of denitrification genes (norBC, nosZ) decreased under drought but increased under high SWC. P metabolism (purine metabolism and two-component systems) showed strong SWC dependence, with key genes (PstS, phnDC) increased in abundance under 50% SWC. Notably, bacterial network complexity tightly coupled with metabolic pathways, indicating SWC driven community restructuring regulates wetland soil C, N and P cycling. These findings underscore the critical importance of hydrological management in maintaining bacterial-mediated nutrient cycling functions of wetland ecosystem under climate change.},
}