@article {pmid40164558,
year = {2025},
author = {Zhou, HY and Zhang, J and Weng, DD},
title = {[One case of recurrent infection with chlamydia psittaci pneumonia].},
journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases},
volume = {43},
number = {3},
pages = {237-240},
doi = {10.3760/cma.j.cn121094-20240109-00008},
pmid = {40164558},
issn = {1001-9391},
mesh = {Humans ; *Chlamydophila psittaci/isolation & purification ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; Psittacosis/microbiology ; Recurrence ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {This paper analyzed the clinical data of a patient with recurrent infection of chlamydia psittaci pneumonia within 7 months. The patient had a clear history of contact with live poultry, and the clinical manifestations were dry cough, persistent fever, and respiratory failure. Chest CT imaging changes showed lobar consolidation of infected lung lobes, ground-glass shadows, bronchial air-filling signs, and pleural effusion. The two infections were detected in bronchoalveolar lavage fluid by metagenomic next-generation sequencing (mNGS) and pathogen targeted next-generation sequencing (tNGS), respectively, to achieve early diagnosis of chlamydia psittaci pneumonia. New tetracycline drugs were used as the core of treatment for both infections, and rapid improvement was achieved after anti-infection treatment.},
}

Humans
*Chlamydophila psittaci/isolation & purification
Male
Bronchoalveolar Lavage Fluid/microbiology
Psittacosis/microbiology
Recurrence
Middle Aged
High-Throughput Nucleotide Sequencing
Anti-Bacterial Agents/therapeutic use

@article {pmid40163992,
year = {2025},
author = {Lei, H and Zhou, N and Zhang, J and Lin, R and Chen, T and Wu, J and Su, L and Liu, S and Liu, T},
title = {Salinity as a key factor affects viral structure, function, and life strategies in lakes from arid and semi-arid regions.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138075},
doi = {10.1016/j.jhazmat.2025.138075},
pmid = {40163992},
issn = {1873-3336},
abstract = {Salinity impacts lake microorganisms in arid and semiarid zones, affecting climate change. Viruses regulate community structure, facilitate gene transfer, and mediate nutrient cycling. However, studies on the diversity and functional differences of viruses in lakes of varying salinity are limited. Thus, we investigated metagenomic data from 20 lakes in Xinjiang Province, China, to determine viral distribution, virus-host linkage, function, and drivers in lakes of varying salinity. The results showed that salinity shaped the distribution of viral community composition, and Hafunaviridae was the dominant virus in high-salinity lakes. All the metagenome-assembled genomes (MAGs) belonging to Halobacteriota were predicted as hosts, with a lysogenic lifestyle predominating the life strategy, implying their potential protection in salt lakes. Moreover, some auxiliary metabolic genes (AMGs), such as cpeT and PTOX, were related to antioxidant and stress responses, which might help the host survive high salinity stress-induced peroxidation. Notably, the main antibiotic resistance genes (ARGs) carried by viruses, which conferred resistance to polymyxin and trimethoprim, related to the local use of veterinary antibiotics, suggesting that they are potential vehicles for the transmission of ARGs. Overall, these findings suggest that lake systems include unique viral varieties that may influence microbial ecosystems and host metabolism related to environmental adaptability.},
}

@article {pmid40163955,
year = {2025},
author = {Du, R and Cui, L and Feng, Y and Lv, X and Gao, Y and Li, A and Wang, Q and Ma, Y},
title = {Enhancing the decomposition and composting of food waste by in situ directional enzymatic hydrolysis: performance, ARGs removal and engineering application.},
journal = {Waste management (New York, N.Y.)},
volume = {200},
number = {},
pages = {114774},
doi = {10.1016/j.wasman.2025.114774},
pmid = {40163955},
issn = {1879-2456},
abstract = {This research utilized food waste (FW) as substrate, innovatively developed a directional multienzyme applied for accelerating FW hydrolysis and composting, and an in situ enzymatic hydrolysis combining in composting has been developed to manage FW. Results showed that the composting was achieved at 4 days and the humification index was increased by 2.60 compared with that of without enzymatic hydrolysis. FTIR analysis revealed that following multienzyme pretreatment, the primary constituents of FW, including protein, starch and lipid, underwent structural breakdown, among which protein exhibited the higher susceptibility to multienzyme action and was the first to disintegrated, and the structure also became looser. Moreover, the total antibiotic resistance gene (ARGs) was reduced more than 90 % in the proposed composting process. Analysis of microbial communities and metagenomes showed that multienzyme pretreatment reshaped microbial communities towards favoring FW hydrolysis and humification. The engineering application analysis further implied that the proposed composting approach is scale flexible, engineering applicable, economic viability and environmentally sustainability. It was anticipated that this study has the potential to trigger a paradigm shift in future in-situ treatment of FW to achieve full resource recovery towards zero solid discharge.},
}

@article {pmid40163458,
year = {2025},
author = {Vendrell-Fernández, S and Beamud, B and Abou Haydar, Y and Am de Sousa, J and Burlaud-Gaillard, J and Kornobis, E and Raynal, B and Vinh, J and Bikard, D and Ghigo, JM},
title = {Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles.},
journal = {PLoS biology},
volume = {23},
number = {3},
pages = {e3002787},
doi = {10.1371/journal.pbio.3002787},
pmid = {40163458},
issn = {1545-7885},
mesh = {*Bacteriophages/physiology/genetics ; *Virion/ultrastructure ; *Bacteroides/virology/genetics ; *Lysogeny ; Phylogeny ; Retroelements/genetics ; DNA, Viral/genetics ; Genome, Viral ; },
abstract = {Advances in metagenomics have led to the identification of new intestinal temperate bacteriophages. However, their experimental characterization remains challenging due to a limited understanding of their lysogenic-lytic cycle and the common lack of plaque formation in vitro. In this study, we investigated the hankyphage, a widespread transposable phage of prominent Bacteroides symbionts. Hankyphages spontaneously produced virions in laboratory conditions even in the absence of inducer, but virions did not show any evidence of infectivity. To increase virion production and raise the chances of observing infection events, we identified a master repressor of the hankyphage lytic cycle, RepCHP, whose silencing amplified hankyphage gene expression, and enhanced replicative transposition and virion production. However, attempts to infect or lysogenize new host cells with different capsular types remained unsuccessful. Transmission electron microscopy and capsid DNA sequencing revealed an abnormal virion morphology and incomplete DNA packaging of the hankyphage, suggesting that it cannot complete its assembly in laboratory conditions for reasons that are yet to be identified. Still, metavirome and phylogenetic analyses were suggestive of hankyphage horizontal transmission. We could also detect the activity of diversity-generating retroelements (DGRs) that mutagenize the hankyphage tail fiber, and likely contribute to its broad host range. This study sheds light on the life cycle of this abundant intestinal bacteriophage and highlights important gaps in our understanding of the factors required for the completion of its life cycle. Elucidating this puzzle will be critical to gain a better understanding of the hankyphage biology and ecological role.},
}

*Bacteriophages/physiology/genetics
*Virion/ultrastructure
*Bacteroides/virology/genetics
*Lysogeny
Phylogeny
Retroelements/genetics
DNA, Viral/genetics
Genome, Viral

@article {pmid40163416,
year = {2025},
author = {Tordoff, J and Alfonse, LE and Makarova, KS and Ornstein, A and Garrity, AJ and Yan, WX and Scott, DA and Koonin, EV and Cheng, DR},
title = {Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems.},
journal = {The CRISPR journal},
volume = {},
number = {},
pages = {},
doi = {10.1089/crispr.2024.0100},
pmid = {40163416},
issn = {2573-1602},
abstract = {Type V CRISPR systems are highly diverse in sequence, mechanism, and function. Although recent efforts have greatly expanded our understanding of their evolution, the diversity of type V systems remains to be completely explored, and many clades have not been experimentally characterized. In this work, we mined metagenomic databases to identify three new subtypes and nine new variants of Cas12, the effector of Type V systems, and provide experimental and computational characterization of their Protospacer-Adjacent Motif (PAM), interference activity, loci architecture, and tracrRNA dependence. Half of the new Cas12s are found in phages or prophages. New subtypes Cas12o and Cas12p lack the canonical RuvC catalytic residues, suggesting they interfere with the target without cleavage, possibly by blocking transcription or replication. One variant, Cas12f10, displays substantial activity on PAM-less targets. Our work expands the diversity of the functionally characterized Cas12 effectors and provides some promising candidates for genome engineering tools.},
}

@article {pmid40162776,
year = {2025},
author = {Haft, DH and Tolstoy, I},
title = {Novel selenoprotein neighborhoods suggest specialized biochemical processes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0141724},
doi = {10.1128/msystems.01417-24},
pmid = {40162776},
issn = {2379-5077},
abstract = {UNLABELLED: Prokaryotic genomes encode selenoproteins sparsely, roughly one protein per 5,000. Finding novel selenoprotein families can expose unknown biological processes that are enabled, or at least enhanced, by having a selenium atom replace a sulfur atom in some cysteine residues. Here, we report the discovery of 18 novel selenoprotein families or second selenocysteine sites in previously unrecognized extensions of protein translations. Most of these families had some confounding factors-too small a family, too few selenoproteins in the family, selenocysteine (U) too close to one end, a skew toward understudied or uncultured lineages, and consequently were missed previously. Discoveries were triggered by observations during the ongoing construction of protein family models for the National Center for Biotechnology Information's RefSeq and Prokaryotic Gene Annotation Pipeline or made by targeted searches for novel selenoproteins in the vicinity of known ones, rather than by any broadly applied genome mining method. Unrelated families TsoA, TsoB, TsoC, and TsoX are adjacent in tso (three selenoprotein operon) loci in the bacterial phylum Thermodesulfobacteriota. TrsS (third radical SAM selenoprotein) occurs strictly in the context of a molybdopterin-dependent aldehyde oxidoreductase. A short carboxy-terminal motif, U-X-X-stop (UXX-star), occurs in selenoproteins with various architectures, usually providing the second U in the protein. The multiple new selenocysteine insertion sites, selenoprotein families, and selenium-dependent operons we curated manually suggest that many more proteins and pathways remain to be discovered; once improved computational methods are applied comprehensively to the latest collections of microbial genomes and metagenomes, they may reveal surprising new biochemical processes.

IMPORTANCE: Next-generation DNA sequencing and assembly of metagenome-assembled genomes (MAGs) for uncultured species of various microbiomes adds a vast "dark matter" of hard-to-decipher protein sequences. Selenoproteins, optimized by natural selection to encode selenocysteine where cysteine might have been encoded much more easily, carry a strong clue to their function-some specialized aspect of binding or catalysis. Operons with multiple adjacent, but otherwise unrelated, selenoproteins should provide even more vivid information. In this study, efforts in protein family construction and curation, aimed at improving the PGAP genome annotation pipeline, generated multiple novel selenoprotein-containing genomic contexts that may lead to the future characterization of several systems of proteins. Past observations suggest roles in the metabolic handling of trace elements (mercury, tungsten, arsenic, etc.) or of organic compounds refractory to simpler enzymatic pathways. In addition, the work significantly expands the truth set of validated selenoproteins, which should aid future, more automated genome mining efforts.},
}

@article {pmid40162769,
year = {2025},
author = {Dickter, JK and Zhao, Y and Parekh, V and Ma, H and Modi, BG and Li, W-Y and Armenian, SH and Wu, X and Abdulla, FR},
title = {Mining metagenomes and metatranscriptomes unveils viruses associated with cutaneous squamous cell carcinoma in hematopoietic stem cell transplant recipients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0005325},
doi = {10.1128/spectrum.00053-25},
pmid = {40162769},
issn = {2165-0497},
abstract = {UNLABELLED: We investigated the presence of viral DNA and RNA in cutaneous squamous cell carcinoma (cSCC) tumor and normal tissues from nine individuals with a history of hematopoietic stem cell transplantation (HCT). Microbiome quantification through DNA and RNA sequencing (RNA-seq) revealed the presence of 18 viruses in both tumor and normal tissues. DNA sequencing (DNA-seq) identified Torque teno virus, Saimiriine herpesvirus 1, Merkel cell polyomavirus, Human parvovirus B19, Human gammaherpesvirus-4, Human herpesvirus-6, and others. RNA-seq revealed additional viruses such as Tobamovirus, Pinus nigra virus, Orthohepadnavirus, Human papillomavirus-5, Human herpesvirus-7, Human gammaherpesvirus-4, Gammaretrovirus, and others. Notably, DNA-seq indicated that tumor samples exhibited low levels of Escherichia virus in three out of nine subjects and elevated levels of Human gammaherpesvirus-4 in one subject, while normal samples frequently contained Gammaretrovirus and occasionally Escherichia virus. A comparative analysis using both DNA- and RNA-seq captured three common viruses: Abelson murine leukemia virus, Murine type C retrovirus, and Human gammaherpesvirus-4. These findings were corroborated by an independent data set, supporting the reliability of the viral detection methods utilized. The study provides insights into the viral landscape in post-HCT patients, emphasizing the need for comprehensive viral monitoring in this vulnerable population.

IMPORTANCE: This study is important because it explores the potential role of viruses in the development of cSCC in individuals who have undergone allogeneic HCT. cSCC is common in this population, particularly in those with chronic graft-versus-host disease on long-term immunosuppression. By using advanced metagenomic and metatranscriptomic next-generation sequencing, we aimed to identify viral pathogens present in tumor and adjacent normal tissue. The results could lead to targeted preventive or therapeutic interventions for these high-risk people, potentially improving their outcomes and management of cSCC.},
}

@article {pmid40162572,
year = {2025},
author = {Wu, H and Zhang, H and Dong, T and Li, Z and Guo, X and Chen, H and Yao, Y},
title = {Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2502743},
doi = {10.1002/advs.202502743},
pmid = {40162572},
issn = {2198-3844},
support = {2024YFD1700500//National Key R&D Program of China/ ; A279021901//Shaanxi Youth Thousand Talents/ ; 2024CY2-GJHX-74//Shaanxi Key R&D Program of China/ ; 2452021112//Chinese Universities Scientific Fund/ ; JCYJ20220530161408019//Shenzhen Natural Science Foundation/ ; 2023KCXTD038//Guangdong Provincial University Innovation Team Project/ ; 2022-K32//Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering/ ; Z111021902//Northwest A&F University Young Talent Project/ ; },
abstract = {High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.},
}

@article {pmid40162034,
year = {2025},
author = {Huang, L and Zheng, D and Li, T and Li, X and Kong, J and Wang, K and Wang, S and Cao, C},
title = {Disseminated Histoplasmosis Due to Anti-IFN-γ Autoantibodies-Associated Immunodeficiency.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1605-1609},
doi = {10.2147/IDR.S513750},
pmid = {40162034},
issn = {1178-6973},
abstract = {BACKGROUND: Disseminated histoplasmosis caused by the temperature-dependent dimorphic fungus Histoplasma capsulatum is an invasive fungal disease rarely reported in southern China. Here, we report a case of disseminated histoplasmosis due to anti-IFN-γ autoantibodies (AIGA)- associated immunodeficiency.

CASE PRESENTATION: We present the case of a 57-year-old HIV-negative female patient with disseminated histoplasmosis in southern China. The patient showed progressively enlarging multiple clavicular, neck, and upper chest skin nodules and dyspnea, which led to the initial suspicion of pulmonary tuberculosis or lung cancer. Bacterial cultures results were negative. Histopathology of a skin tissue showed infectious granulomas. Disseminated histoplasmosis was diagnosed via next-generation sequencing (mNGS) and fungal culture. Furthermore, enzyme-linked immunosorbent assay results from a peripheral blood confirmed that the patient had a high-titer of AIGA.

CONCLUSION: This case prompts clinicians to consider histoplasmosis an important differential diagnosis in a region where talaromycosis is highly endemic. This case report emphasizes that clinicians should be vigilant for immunodeficiency and consider testing for AIGA in HIV-negative patients who are suspected of having complex opportunistic infections.},
}

@article {pmid40161798,
year = {2025},
author = {Zeamer, AL and Lai, Y and Sanborn, V and Loew, E and Tracy, M and Jo, C and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP},
title = {Microbiome functional gene pathways predict cognitive performance in older adults with Alzheimer's disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.06.641911},
pmid = {40161798},
issn = {2692-8205},
abstract = {Disturbances in the gut microbiome is increasing correlated with neurodegenerative disorders, including Alzheimer's Disease. The microbiome may in fact influence disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby driving disease pathology along the "microbiota-gut-brain-axis". Currently, drivers of cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (age 60+) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiomes. Subjects were classified as healthy controls or as having mild cognitive impairment based on cognitive performance. Those with a diagnosis of Alzheimer's Diseases with confirmed using serum biomarkers. Using metagenomic sequencing, we found that relative species abundances correlated well with cognition status (MCI or AD). Furthermore, gene pathways analyses suggest certain microbial metabolic pathways to either be correlated with cognitive decline or maintaining cognitive function. Specifically, genes involved in the urea cycle or production of methionine and cysteine predicted worse cognitive performance. Our study suggests that gut microbiome composition may predict AD cognitive performance.},
}

@article {pmid40161742,
year = {2025},
author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B},
title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.11.642547},
pmid = {40161742},
issn = {2692-8205},
abstract = {UNLABELLED: Composition and function of the gut microbiome is associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models to recapitulate ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure and their ecological features were compared to human donors by metagenomic sequencing. HMA mice were more similar in gut composition to other mice than their respective human donors, with taxa including Akkermansia muciniphila and Bacteroides species enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse datasets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice were more like other mice than their human donor. Our data suggest that HMA mice are limited models to assess the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overwhelm ecological effects of treatment in humans that HMA models aim to recapitulate.

IMPORTANCE: Human microbiota-associated (HMA) mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effect of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, MET4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbour a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.},
}

@article {pmid40161675,
year = {2025},
author = {Secaira-Morocho, H and Jiang, X and Zhu, Q},
title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.13.643052},
pmid = {40161675},
issn = {2692-8205},
abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes evenly distributed across major microbial phyla, covering only a small fraction of gene families. And yet, most microbial diversity is found in metagenome-assembled genomes that are unevenly distributed and harbor gene families that do not fit the criteria of universal orthologous genes. To address these limitations, we systematically evaluate the phylogenetic signal of gene families annotated from KEGG and EggNOG functional databases for deep microbial phylogenomics. We show that markers selected from an expanded pool of gene families and tailored to the input genomes improve the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes. The improved accuracy of trees compared to previous markers persists even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. We introduce TMarSel, a software tool for automated, systematic, free-from-expert opinion, and tailored marker selection that provides flexibility in the number of markers and annotation databases while remaining robust against uneven taxon sampling and incomplete genomic data.},
}

@article {pmid40161639,
year = {2025},
author = {Williams, A and Ravel, J and Kaul, R and Armstrong, E and Huibner, S and Holm, JB},
title = {Temporal Dynamics of the Vaginal Microbiome and Host Immune Markers Before, During, and After Metronidazole Treatment for Bacterial Vaginosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.13.643085},
pmid = {40161639},
issn = {2692-8205},
abstract = {UNLABELLED: This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment, variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.

IMPORTANCE: Bacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections among others, is characterized by a dysbiotic vaginal microbiome associated with dominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at initiation of treatment as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during and after metronidazole treatment.},
}

@article {pmid40160274,
year = {2025},
author = {Naushad, S and Gao, R and Duceppe, MO and Dupras, AA and Reiling, SJ and Merks, H and Dixon, B and Ogunremi, D},
title = {Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1566579},
doi = {10.3389/fmicb.2025.1566579},
pmid = {40160274},
issn = {1664-302X},
abstract = {INTRODUCTION: Infections with protozoan parasites associated with the consumption of fresh produce is an on-going issue in developed countries but mitigating the risk is hampered by the lack of adequate methods for their detection and identification.

MATERIALS AND METHODS: We developed a metagenomic next-generation sequencing (mNGS) assay using a MinION sequencer for the identification of parasites in intentionally contaminated lettuce to achieve a more accurate and rapid method than the traditional molecular and microscopy methods commonly used for regulatory purposes. Lettuce (25 g) was spiked with varying numbers of Cryptosporidium parvum oocysts, and microbes washed from the surface of the lettuce were lysed using the OmniLyse device. DNA was then extracted by acetate precipitation, followed by whole genome amplification. The amplified DNA was sequenced by nanopore technology and validated with the Ion Gene Studio S5, and the generated fastq files raw reads were uploaded to the CosmosID webserver for the bioinformatic identification of microbes in the metagenome. To demonstrate the ability of the procedure to distinguish other common food and waterborne protozoan parasites, lettuce was also spiked with C. hominis, C. muris, Giardia duodenalis and Toxoplasma gondii individually or together.

RESULTS: The efficient lysis of oocysts and cysts was a prerequisite for the sensitive detection of parasite DNA and was rapidly achieved within 3 min. Amplification of extracted DNA led to the generation of 0.16-8.25 μg of DNA (median = 4.10 μg), sufficient to perform mNGS. Nanopore sequencing followed by bioinformatic analysis led to the consistent identification of as few as 100 oocysts of C. parvum in 25 g of fresh lettuce. Similar results were obtained using the Ion S5 sequencing platform. The assay proved useful for the simultaneous detection of C. parvum, C. hominis, C. muris, G. duodenalis and T. gondii.

DISCUSSION: Our metagenomic procedure led to the identification of C. parvum present on lettuce at low numbers and successfully identified and differentiated other protozoa either of the same genus or of different genera. This novel mNGS assay has the potential for application as a single universal test for the detection of foodborne parasites, and the subtyping of parasites for foodborne outbreak investigations and surveillance studies.},
}

@article {pmid40160273,
year = {2025},
author = {Liu, Y and Ying, Y and Li, Y and Zhang, W and Shu, J},
title = {Symbiotic bacteria associated with different species of Curculio (Coleoptera: Curculionidae) and their host plants.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1531847},
doi = {10.3389/fmicb.2025.1531847},
pmid = {40160273},
issn = {1664-302X},
abstract = {Bacteria often play important roles in the host adaptation of phytophagous insects. Beetles of the genus Curculio (Coleoptera: Curculionidae) include pest species that bore into the seeds of trees in the family Fagaceae and damage the cotyledons. At present, there are few studies of the taxonomic diversity and functional effects of symbiotic bacteria involved in changes in host ranges and host adaptation of Curculio. Here, we used 16S rRNA gene Illumina and metagenomic sequencing to compare the composition and functions of the bacterial communities of three species of host plants and several Curculio species combinations: Curculio bimaculatus feeding on Castanopsis sclerophylla, C. bimaculatus feeding on Castanopsis tibetana, and Curculio davidi feeding on Ca. tibetana. The host plants influenced the diversity of symbiotic bacteria, while the Curculio species influenced the community structure of the symbiotic bacteria. Functional predictions showed that symbiotic bacteria contributed to the metabolism of the hosts. However, consistent with the variation in bacteria, the major metabolism-related bacterial genera varied among the treatment groups. Comparisons of metabolic enzymes based on KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation revealed differences in the enzymes involved in insect development and detoxification of plant secondary compounds among the three groups, and the patterns were influenced by the dominance of the Curculio species on the host plants. This study provides valuable insights into the possible role of symbiotic bacteria in Curculio as host insects.},
}

@article {pmid40160271,
year = {2025},
author = {Yang, B and Feng, C and Jiang, H and Chen, Y and Ding, M and Dai, H and Zhai, Z and Yang, M and Liang, T and Zhang, Y},
title = {Effects of long-term continuous cropping on microbial community structure and function in tobacco rhizosphere soil.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496385},
doi = {10.3389/fmicb.2025.1496385},
pmid = {40160271},
issn = {1664-302X},
abstract = {As is well known, continuous cropping can lead to a decrease in crop yield and quality. Despite this, continuous cropping remains prevalent in practical agricultural production, particularly in the case of tobacco cultivation, owing to its high economic value. The samples for this study were collected from a flue-cured tobacco planting base located in Huili County, Liangshan Yi Autonomous Prefecture, Sichuan Province, China. After years of continuous planting, the yield of tobacco in this base has significantly decreased. In order to explain the microecological causes of this phenomenon, we collected non-continuous cropping, continuous cropping for 5 years, and continuous cropping for 10 years of tobacco rhizosphere soil, and analyzed the effects of long-term continuous cropping on nutrients, enzyme activities, microbial community structure, and function of tobacco rhizosphere soil. The results showed that with the continuous cropping, the majority nutrients (except for phosphorus and manganese) in rhizosphere soil decreased significantly, and the rhizosphere microbial community structure changed significantly. Correlation network analysis results showed that changes in the rhizosphere microbial community of tobacco were closely related to soil urease, active organic carbon, and available iron content. The results of functional analysis based on microorganisms and genes showed that the rhizosphere microbiota may change the content of soil nutrients through iron_respiration, sulfur_respiration, and Carbon fixation in prokaryotes pathways. The results of the correlation network analysis and the functional analysis mutually confirmed each other, both emphasizing the important role of soil carbon and iron in shaping the structure of the tobacco rhizosphere microbial community. Based on the results of this study, we propose to improve the microbial community structure of tobacco rhizosphere soil by increasing the levels of readily oxidizable organic carbon, available iron, and soil urease activity in the future, so as to alleviate the negative impact of continuous cropping on crop yield. The results of this study provide theoretical support for modifying the rhizosphere microbial environment through nutrient regulation, thereby enhancing plant growth in the context of continuous tobacco cropping.},
}

@article {pmid40160267,
year = {2025},
author = {Kragh, ML and Scheel, NH and Leekitcharoenphon, P and Truelstrup Hansen, L},
title = {Repeated biocide treatments cause changes to the microbiome of a food industry floor drain biofilm model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1542193},
doi = {10.3389/fmicb.2025.1542193},
pmid = {40160267},
issn = {1664-302X},
abstract = {There is a concern about the development of microbial tolerance and resistance to biocides due to their repeated use within the food industry. This study aimed to develop a floor drain biofilm model and test whether repeated biocide treatment would result in increased tolerance to biocides. Culturomics and shotgun metagenomic analysis of 14 drains and 214 bacterial isolates from three industrial food production environments revealed microbiomes with great diversity and complexity, but with the dominance of a few highly abundant taxa, including Pseudomonas. A representative drain biofilm was created (3 days, 15°C) using 31 whole genome sequenced bacterial isolates from 24 genera. The biofilm model represented 47-58% and 76-81% of the microbial abundance observed in the metagenome and viable microbiota, respectively. The biofilm model was exposed on days 3 and 6 to water or different industrial concentrations of benzalkonium chloride (BC), peracetic acid (PAA), or sodium hypochlorite (SH). Analysis of the viable survivors using MALDI-TOF MS and the regrowing biofilms using 16S rRNA amplicon sequencing showed how the diversity of the biofilm decreased but without any change in biocide tolerance as seen in log reductions (CFU/cm[2]). The use of different biocides did, however, exert significantly different selective pressures on the microbiomes as Citrobacter, Acinetobacter, Aeromonas, and Pseudomonas dominated the biofilm after treatments with SH or PAA, while Serratia and Moraxella dominated after treatments with BC. The dominance of Serratia marcescens could be explained by the carriage of a BC efflux pump (oqxB) and the highest (20 mg/L BC) minimum inhibitory concentration (MIC) result of the drain isolates. In contrast, despite carrying a BC efflux pump (qacH), Listeria monocytogenes ST121 did not show increased survival or presence in the biofilm after BC treatments. Only the highest tested concentration of PAA was able to completely eradicate L. monocytogenes. The developed biofilm model and the repeated biocide treatments enabled a better understanding of how biocides affect the biofilm microbiome. Future research should involve testing biocide rotation strategies to control biofilm regrowth and inactivation of persistent foodborne pathogens in floor drains.},
}

@article {pmid40159059,
year = {2025},
author = {Shang, SY and Li, XP and Xu, J and Li, Y and Cao, LQ and Ye, H},
title = {[A case of acute pseudomembranous necrotizing tracheobronchitis in an adult].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {4},
pages = {385-388},
doi = {10.3760/cma.j.cn112147-20240828-00510},
pmid = {40159059},
issn = {1001-0939},
mesh = {Humans ; *Tracheitis/diagnosis/microbiology ; *Bronchitis/microbiology/diagnosis ; *Staphylococcal Infections/diagnosis ; Male ; Staphylococcus aureus/isolation & purification ; Bronchoscopy ; Influenza B virus/isolation & purification ; Adult ; Necrosis ; Influenza, Human/complications ; Middle Aged ; Linezolid/therapeutic use ; },
abstract = {This study presented a rare case of secondary Staphylococcus aureus (S. aureus) infection following influenza B virus infection, resulting in diffuse airway injury and hemorrhagic pneumonia. The patient initially underwent bronchial artery embolization (BAE) due to persistent hemoptysis refractory to conventional hemostatic therapy. Although the hemoptysis was resolved postoperatively, severe hypoxemia persisted. Bronchoscopy revealed diffuse yellow plaques with mucosal erosion and necrosis in the airways. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified S. aureus harboring the Panton-Valentine leukocidin (PVL) genes. Histopathological examination revealed severe acute inflammatory changes consistent with necrotizing airway pathology. A diagnosis of IBV-associated S. aureus infection leading to acute pseudomembranous necrotizing tracheobronchitis and hemorrhagic pneumonia was made. The patient responded favorably to linezolid therapy. Follow-up bronchoscopy revealed multiple granulation tissues in the airways, which were subsequently removed under endoscopic guidance. After ruling out persistent infection, the patient was treated with low-dose oral prednisone, which resulted in significant clinical improvement.},
}

Humans
*Tracheitis/diagnosis/microbiology
*Bronchitis/microbiology/diagnosis
*Staphylococcal Infections/diagnosis
Male
Staphylococcus aureus/isolation & purification
Bronchoscopy
Influenza B virus/isolation & purification
Adult
Necrosis
Influenza, Human/complications
Middle Aged
Linezolid/therapeutic use

@article {pmid40158829,
year = {2025},
author = {Liu, Y and Zhang, Q and Lu, L and Qian, Y and Wu, Y and Hu, D and Xu, Y and Xu, H and Ji, G},
title = {Huang-qin Decoction alleviates Deoxycholic Acid-induced Colorectal Cancer in Mice by Regulating Gut Microbiota.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119715},
doi = {10.1016/j.jep.2025.119715},
pmid = {40158829},
issn = {1872-7573},
abstract = {Huangqin Decoction (HQD), a traditional Chinese medicine (TCM) formula documented in Shang Han Lun, has demonstrated safety and efficacy in the treatment of ulcerative colitis (UC). Recent studies also suggest that HQD exerts therapeutic effects on colorectal cancer (CRC). However, the underlying mechanisms remain unclear.

AIMS OF THE STUDY: This study aimed to investigate the therapeutic effects of HQD on CRC and explore its potential mechanisms of action.

METHODS: The active ingredients and potential targets of HQD were identified through network pharmacology-based analyses. The CRC-related targets were compared with those of HQD. Shared targets were subjected to Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein-protein interaction (PPI) network was constructed. Additionally, APC[min/+] mice were treated with 0.2% deoxycholic acid (DCA) and gavaged with low or high doses of HQD. Tumor morphology was assessed using hematoxylin and eosin (HE) staining. Immunohistochemical staining was performed to evaluate the expression of Ki-67, Caspase-3, and MUC2 in the intestine. Periodic acid-Schiff (PAS) and PAS-alcian blue (PAS-AB) staining were utilized to detect mucin distribution and the number of goblet cells in the intestines of the mice. The mRNA expression levels of interleukin 6 (IL-6), mitogen-activated protein kinase 8 (MAPK8), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), albumin (ALB), and Caspase 3 (CASP3) were quantified using quantitative reverse-transcription PCR (qRT-PCR). Immunofluorescence was employed to assess the degree of apoptosis. Additionally, 16S ribosomal RNA gene sequencing, sequence curation and annotation, and metagenomic sequencing were performed to analyze changes in the composition of the mouse intestinal microbiota and related functions and signaling pathways.

RESULTS: The active ingredients of HQD were identified. GO and KEGG pathway enrichment analyses indicated that the shared targets were primarily involved in tumor suppression. HQD effectively treated DCA-induced CRC in mice. Furthermore, positive PAS and PAS-AB staining was significantly increased in the intestines of mice treated with HQD. HQD enhanced the abundance of Lachnospiraceae, Firmicutes, Fusobacteria, and Clostridium, while reducing the abundance of Eggerthellales. Additionally, HQD modulated secondary bile acid metabolism, carbohydrate synthesis, and other energy metabolism pathways, which may underlie its therapeutic effects.

CONCLUSION: HQD effectively treated CRC in mice, and its mechanisms of action may be related to the regulation of the gut microbiota.},
}

@article {pmid40158299,
year = {2025},
author = {Borkakoti, N and Ribeiro, AJM and Thornton, JM},
title = {A structural perspective on enzymes and their catalytic mechanisms.},
journal = {Current opinion in structural biology},
volume = {92},
number = {},
pages = {103040},
doi = {10.1016/j.sbi.2025.103040},
pmid = {40158299},
issn = {1879-033X},
abstract = {In this perspective, we analyse the progress made in our knowledge of enzyme sequences, structures and functions in the last 2 years. We review how much new enzyme data have been garnered and annotated, derived from the study of proteins using structural and computational approaches. Recent advances towards capturing 'Catalysis in silico' are described, including knowledge and predictions of enzyme structures, their interactions and mechanisms. We highlight the flood of enzyme data, driven by metagenomic sequencing, the improved enzyme data resources, the high coverage in Protein Data Bank of E.C. classes and the AI-driven structure prediction techniques that facilitate the accurate prediction of protein structures. We note the focus on disordered regions in the context of enzyme regulation and specificity and comment on emerging bioinformatic approaches that capture reaction mechanisms computationally for comparing and predicting enzyme mechanisms. We also consider the drivers of progress in this field in the next five years.},
}

@article {pmid40158160,
year = {2025},
author = {Zhu, M and Wang, Q and Yang, Y and Liu, X and Zhang, J and Li, G and Liu, W and Xiang, X and Chen, J},
title = {Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {50},
pmid = {40158160},
issn = {1475-2891},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Child ; Male ; Cross-Sectional Studies ; *Metabolome/physiology ; Female ; Child, Preschool ; *Feces/microbiology ; China ; *Diet/methods ; Metabolomics/methods ; Nutritional Status ; Multiomics ; },
abstract = {The gut microbiome can modulate nutrient metabolism to produce many metabolites interacting with the host. However, the intricate interactions among dietary intake, the gut microbiome and metabolites, and host metabolites need to be further explored although some studies have been devoted to it. Here, in a cross-sectional studies, 88 children aged 2-12 years were enrolled from northwestern China. The dietary intake data were collected via a designed food frequency questionnaire to calculate plant-based diet indices (PDIs). Stool and plasma samples were collected for metagenomic and broad-targeted metabolomic analysis. Spearman's rank correlation was used to describe the associations between nutrients/PDIs and the gut microbiota and metabolites. PDI was significantly positively associated with Bilophila wadsworthia, Bacteroides thetaiotaomicron, and Alistipes indistinctus, etc., but was obviously negatively correlated with Roseburia intestinalis, Faecalibacterium prausnitzii, etc. However, these species showed no significant associations with either healthy PDI (hPDI) or unhealthy PDI (uPDI). Interestingly, hPDI was significantly positively related to species, including Ruminococcus bicirculans, and was significantly negatively associated with uPDI, and vice versa. The above correlation trends were also observed between PDIs and predicted gut microbial functional pathways, microbial metabolites and the host metabolome. Notably, the significantly related pathways were focused mainly on substances and energy metabolism. PDI was significantly positively associated with the fecal contents of P-aminobenzoate, chenodeoxycholic acid, 4,6-dihydroxyquinoline, quinoline-4,8-diol, etc., but was significantly negatively associated with those of TMAO, FFA, creatine phosphate, etc. In plasma, PDI was significantly positively associated with sarcosine, ornithine, L-histidine, etc., but was distinctly negatively correlated with FFAs, carnitine C2:0, etc. Strikingly, the healthy plant-based diet index (hPDI) is correlated with increased levels of metabolites related to tryptophan metabolism, whereas the unhealthy PDI (uPDI) is linked to increased levels of metabolites associated with tyrosine and sphingolipid metabolism, which are pathways commonly associated with Western diets. Our studies provide reliable data support and a comprehensive understanding of the effects of dietary intake on the gut microbiome and microbial and host metabolites and lay a foundation for further studies of the diet-gut microbiota-microbial metabolites and host metabolism.},
}

*Gastrointestinal Microbiome/physiology
Humans
Child
Male
Cross-Sectional Studies
*Metabolome/physiology
Female
Child, Preschool
*Feces/microbiology
China
*Diet/methods
Metabolomics/methods
Nutritional Status
Multiomics

@article {pmid40158141,
year = {2025},
author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY},
title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {87},
pmid = {40158141},
issn = {2049-2618},
support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; },
mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; Bacteria/classification/genetics ; Computer Simulation ; },
abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.},
}

Humans
*Neural Networks, Computer
*Microbiota
Metagenomics/methods
Bacteria/classification/genetics
Computer Simulation

@article {pmid40157594,
year = {2025},
author = {Wang, C and Fan, S and Li, M and Ye, Y and Li, Z and Long, W and Li, Y and Huang, Z and Jiang, Q and Yang, W and Yang, R and Tang, D},
title = {A 7-year feed study on the long-term effects of genetically modified maize containing cry1Ab/cry2Aj and EPSPS genes on gut microbiota and metabolite profiles across two generations of cynomolgus macaques.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115419},
doi = {10.1016/j.fct.2025.115419},
pmid = {40157594},
issn = {1873-6351},
abstract = {The health implications of genetically modified (GM) crops remain controversial relative to their non-GM counterparts, particularly regarding long-term dietary exposure. Although the gut microbiome is a key health indicator, studies investigating the impact of GM crop consumption on intestinal microbiota remain limited. This study presents a comprehensive 7-year evaluation of GM maize expressing cry1Ab/cry2Aj and G10evo-EPSPS proteins through metagenomic and metabolomic analyses. We assessed the effects of GM maize consumption on gut microbiota diversity and metabolite profiles in cynomolgus macaques (Macaca fascicularis) compared with non-GM maize. Three diet regimens were implemented: a conventional compound feed (CK group), diet formulation containing 70% non-GM maize (Corn group), and diet formulation containing 70% GM maize (Tg group). The results demonstrated that feeding GM maize to the first (F0) and second (F1) generations of monkeys did not substantially affect the composition, community structure, or function of the intestinal microbiome, as indicated by species composition and diversity analyses. Minor differences in intestinal metabolites were observed but were not directly linked to transgenic maize consumption. Collectively, long-term intake of maize with cry1Ab/cry2Aj and g10evo-epsps genes had no adverse effects on macaques or their offspring.},
}

@article {pmid40157532,
year = {2025},
author = {Pienaar, RD and Herrero, S and Cerqueira de Araujo, A and Krupa, F and Abd-Alla, AMM and Herniou, EA},
title = {High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens).},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108322},
doi = {10.1016/j.jip.2025.108322},
pmid = {40157532},
issn = {1096-0805},
abstract = {Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.},
}

@article {pmid40157487,
year = {2025},
author = {Li, J and Zhu, L and Li, X and Han, X and Yi, J and Wu, Y and Wang, M},
title = {Characterization and Risk-quantification of Antibiotic Resistome in Grain-based and Non-grain Cropping Soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126147},
doi = {10.1016/j.envpol.2025.126147},
pmid = {40157487},
issn = {1873-6424},
abstract = {Microbial contamination in soils, encompassing human bacterial pathogens (HBPs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs), poses a significant threat to human health via the food chain. Currently, there is a lack of comprehensive assessments of microbial contamination and associated health risks of ARGs in agricultural soils. In this study, metagenomic sequencing was used to evaluate microbial contamination in grain-based cropping soils (rice cultivation) and non-grain cropping soils (vegetable cultivation and aquaculture). The results showed that the diversity and abundance of HBPs and VFGs were significantly higher in non-grain soils. Further resistome analysis revealed higher abundances of high-risk (from 0.014 to 0.018 - 0.023) and "last-resort" ARGs (from 0.007 to 0.034 - 0.046) in non-grain soils. Besides ARGs abundance, health risk quantification revealed that non-grain soils exhibited 1.49 to 2.14-fold greater ARG-related risks than grain-based soils. Additionally, stronger network associations were found between HBPs, ARGs, and mobile genetic elements (MGEs) in non-grain soils. This study indicated that the non-grain cropping pattern of soils elevated the risk of microbial contamination and ARGs health risk, which provided an important basis for accurately quantifying the risk of microbial contamination in different agricultural soils.},
}

@article {pmid40157184,
year = {2025},
author = {Qiao, X and Kong, X and Zhou, H and Fan, X and Yuan, J and Zhang, Y},
title = {Deciphering the inhibitory mechanisms of polystyrene microplastics on thermophilic methanogens from the insights of microbial metabolite profiling and metagenomic analyses.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138054},
doi = {10.1016/j.jhazmat.2025.138054},
pmid = {40157184},
issn = {1873-3336},
abstract = {Due to the utilization of food packaging bags, a substantial amount of polystyrene microplastics (PS MPs) are introduced into the food waste (FW) treatment system during the pre-treatment process, potentially impacting the subsequent biochemical treatment system. In order to investigate the mechanism by which PS MPs affect anaerobic methanogenesis metabolism in thermophilic condition, this study analyzed the characteristics of methanogenesis in thermophilic anaerobic digestion (AD) of FW under different concentrations of PS MPs (100 μm, 10-200 mg/L). The results revealed a negative correlation between PS MPs concentration and methane (CH4) yield from FW. When the concentration of PS MPs reached 200 mg/L, CH4 yield decreased by 47.8 %. Further mechanistic investigations revealed that while the presence of PS MPs at lower concentrations could alleviate its adverse impact on methanogenesis by enhancing EPS content, the accumulation of reactive oxygen species (ROS) persisted with increasing PS MPs concentration, thereby inhibiting the activities of key enzymes involved in solubilization and acidification metabolisms (e.g., acetate kinase and F420). Metagenomics analysis indicated that the presence of PS MPs down-regulate abundance of genes for quorum sensing and CH4 metabolism pathways. These findings not only unveil potential detrimental effects of PS MPs on AD systems but also provide novel insights into comprehending and controlling the impact of MPs pollution on environmental preservation and energy recovery processes.},
}

@article {pmid40157173,
year = {2025},
author = {Weiting, S and Chen, W and Xiao, L and Yanqiu, H},
title = {Enhanced acid reduction in lactic acid bacteria: Breeding through irradiation-induced mutation and functional assessment.},
journal = {International journal of food microbiology},
volume = {435},
number = {},
pages = {111161},
doi = {10.1016/j.ijfoodmicro.2025.111161},
pmid = {40157173},
issn = {1879-3460},
abstract = {High concentrations of citric acid (CA), malic acid (MA), and tartaric acids (TA) are the primary contributors to the sour taste of fruit and fruit products. However, lactic acid bacteria that are capable of efficiently degrading these organic acids are scarce. Here, three brands of sauerkraut (Xinxi, X; Yuyuan, Y; and Zou Youcai, Z) with various doses of [60]Co γ-irradiation could be treated to induce mutations in their associated lactic acid bacteria and then the abilities of the resulting microbial communities to degrade CA, MA, and TA were evaluated. Sauerkraut X treated with 0.4 kGy irradiation demonstrated the greatest ability of acid reduction. Metagenomic analyses of irradiated (0.4 kGy) and non-irradiated bacterial communities from sauerkraut X revealed a slight decrease in microbial diversity due to irradiation, with a substantial decline in the relative abundance of Lactiplantibacillus xiangfangensis. Concurrently, the relative abundance of dominant acid-reducing lactic acid bacteria such as Levilactobacillus brevis, Pediococcus ethanolidurans, and Lentilactobacillus parafarraginis increased. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed an increase in metabolism-related genes after irradiation, indicating that fatty acid synthesis and aspartate metabolism might be key pathways involved in the enhanced degradation of CA, MA, and TA. Analysis using the Carbohydrate-Active enzymes Database (CAZy) database revealed that glycoside hydrolase (GH) and glycosyltransferase (GT) genes were the most abundant carbohydrate-associated enzyme genes in the bacterial community of sauerkraut X. This finding proved that the oligosaccharides and monosaccharides produced by GH and GT might indirectly affect rates of organic acid degradation. Three highly effective acid-reducing lactic acid bacteria from the microbial community of irradiated sauerkraut X a were isolated and identified via 16S rRNA sequencing as Pediococcus ethanolidurans, Levilactobacillus brevis, and Loigolactobacillus coryniformis. The individual strains showed degradation rates as high as 92.02 % for citric acid (Pediococcus ethanolidurans), 83.04 % for malic acid (Levilactobacillus brevis), and 90.33 % for TA (Loigolactobacillus coryniformis). This study provides a theoretical basis and technical support for the development of enhanced microbial strains that can reduce the acid content of fruit materials.},
}

@article {pmid40156973,
year = {2025},
author = {Zhong, S and Li, B and Chen, Q and Zhang, J and Cai, H and An, R and Liu, G and Zhou, S},
title = {Identifying groundwater anthropogenic disturbances and their predominant impact on microbial nitrogen cycling at a former contamination site adjacent to Baiyangdian Lake.},
journal = {Water research},
volume = {280},
number = {},
pages = {123544},
doi = {10.1016/j.watres.2025.123544},
pmid = {40156973},
issn = {1879-2448},
abstract = {Groundwater ecosystems face increasing threat from declining water quality due to intensified urbanization, agricultural, and industrial activities. Accurately identifying anthropogenic disturbances remains challenging, and their effects on microbial nitrogen cycling are still largely unknown. Here, by collecting 64 groundwater samples from an aquifer beneath the Tanghe sewage reservoir in the North China Plain, we conducted a full-spectrum screening of 228 physiochemical indices, 47 nitrogen cycling genes (NCGs) and 2182 metagenome-assembled genomes (MAGs) harboring NCGs. Unmix model identified antibiotic usage, industrial manufacturing, and agricultural practices as the predominant pollution sources, explaining 49.6-92.2 % (averaged 81.0 %) of the variations in aquifer attributes. These activities were primary drivers governing distributions of groundwater NCGs and NCG-hosts, with fragmented denitrification processes being prevalent. Antibiotic usage and industrial activities were probably associated with suppressed nitrogen cycling, while agriculture had a positive effect. Notably, we observed enhanced mutualistic interactions within NCG-hosts and increased enrichment of NCG-antibiotic resistance gene (ARG), NCG-mental resistance gene (MRG), and NCG-ARG-MRG co-hosts under high anthropogenic stresses, suggesting microbial adaptation to optimize nutrient and energy metabolism. This study provided new insight into how groundwater nitrogen cycling responds to anthropogenic disturbances, offering valuable information for developing groundwater management and pollution control strategies.},
}

@article {pmid40156579,
year = {2025},
author = {Sanghani, A and Antaliya, K and Patel, R and Dave, S and Tipre, D},
title = {Revealing Microbial Functionalities and Ecological Roles in Rajpardi Lignite Mine: Insights from Metagenomics Analysis.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf048},
pmid = {40156579},
issn = {1472-765X},
abstract = {The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10,071,318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance (AMR) and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasising the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.},
}

@article {pmid40156577,
year = {2025},
author = {Kop, LFM and Koch, H and Martins, PD and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S},
title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf032},
pmid = {40156577},
issn = {1574-6941},
abstract = {Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7±15% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.},
}

@article {pmid40156536,
year = {2025},
author = {Sarker, S and Klukowski, N and Talukder, S and Athukorala, A and Uddin, MJ},
title = {Opportunistic sampling from the near-threatened Alexandrine parakeet uncovers genomes of a novel parvovirus and beak and feather disease virus.},
journal = {Australian veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/avj.13442},
pmid = {40156536},
issn = {1751-0813},
support = {DE200100367//Australian Research Council/ ; },
abstract = {Birds are known to harbour a wide range of pathogenic viruses, including the beak and feather disease virus (BFDV; species, Circovirus parrot), which poses a significant threat to the conservation of endangered avian species. This study reports the genomic identification and characterisation of a novel psittaciform chaphamaparvovirus (PsChPV-6) and BFDV, sequenced from the faecal samples of healthy Alexandrine parakeets (Psittacula eupatria). PsChPV-6 is a linear, single-stranded DNA virus consisting of 4232 nucleotides (nt) with a high A + T content and five predicted open reading frames (ORFs). Key proteins encoded by PsChPV-6, such as the nonstructural protein 1 (NS1) and major capsid protein VP1, demonstrate strong sequence similarities to other avian parvoviruses, with conserved motifs in NS1 crucial for viral replication. The presence of a previously uncharacterised ORF1 region suggests strain-specific viral features that warrant further exploration. BFDV is a circular single-stranded DNA virus in the Circoviridae family and was also identified in the samples. Phylogenetic analysis positioned PsChPV-6 within the Chaphamaparvovirus genus, closely related to parvoviruses from diverse avian species, whereas BFDV was grouped with strains from Australian cockatoos and other nonpsittacine birds, suggesting potential cross-species transmission. These findings contribute to a deeper understanding of the genetic diversity and evolutionary dynamics of these viral pathogens in bird populations, underscoring the importance of ongoing surveillance to evaluate their ecological and veterinary impacts.},
}

@article {pmid40156205,
year = {2025},
author = {Huyghe, CET and Fages, A and Ronco, F and Indermaur, A and Schedel, FDB and Kimirei, I and Makasa, L and Tschopp, P and Salzburger, W},
title = {Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17743},
doi = {10.1111/mec.17743},
pmid = {40156205},
issn = {1365-294X},
support = {189970//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterise trophic specialisations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specialisations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild-caught individuals at around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids' diet. Based on their dietary compositions, the Tanganyikan cichlids can be grouped into herbivores, invertivores, piscivores and mixed feeders. Further, we showed that trophic disparity in the radiation is shaped by rapid divergence and documented cases of dietary niche convergence. Diet composition correlated with carbon and nitrogen stable isotope values, gut length, and body morphology. Differences in diet-such as the consumption of diatoms, streptophytes and chlorophytes versus fish and arthropods-were associated with changes in body, upper oral jaw and lower pharyngeal jaw shape. Collectively, this study presents a comprehensive and detailed diet classification of the Tanganyikan cichlids, highlighting the power of metagenomic approaches in delineating dietary adaptations.},
}

@article {pmid40155949,
year = {2025},
author = {Song, J and Lin, LA and Tang, C and Chen, C and Yang, Q and Zhang, D and Zhao, Y and Wei, HC and Linghu, K and Xu, Z and Chen, T and He, Z and Liu, D and Zhong, Y and Zhu, W and Zeng, W and Chen, L and Song, G and Chen, M and Jiang, J and Zhou, J and Wang, J and Chen, B and Ying, B and Wang, Y and Geng, J and Lin, JW and Chen, L},
title = {DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {76},
pmid = {40155949},
issn = {1474-760X},
mesh = {*Metagenomics/methods ; Humans ; *Nanopore Sequencing/methods ; *Sequence Analysis, RNA/methods ; COVID-19/virology/genetics ; Gene Expression Profiling/methods ; Transcriptome ; Glioma/genetics ; High-Throughput Nucleotide Sequencing/methods ; SARS-CoV-2/genetics ; Software ; Malaria ; },
abstract = {Nanopore direct RNA sequencing (DRS) is a powerful tool for RNA biology but suffers from low basecalling accuracy, low throughput, and high input requirements. We present DEMINERS, a novel DRS toolkit combining an RNA multiplexing workflow, a Random Forest-based barcode classifier, and an optimized convolutional neural network basecaller with species-specific training. DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime. Applications include clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons, uncovering microbial diversity in COVID-19 and m[6]A's role in malaria and glioma. DEMINERS offers a robust, high-throughput solution for precise transcript and RNA modification analysis.},
}

*Metagenomics/methods
Humans
*Nanopore Sequencing/methods
*Sequence Analysis, RNA/methods
COVID-19/virology/genetics
Gene Expression Profiling/methods
Transcriptome
Glioma/genetics
High-Throughput Nucleotide Sequencing/methods
SARS-CoV-2/genetics
Software
Malaria

@article {pmid40155846,
year = {2025},
author = {Zhang, Z and Tian, L},
title = {Validation of mNGS results using extensive lab and clinical data.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {173},
pmid = {40155846},
issn = {1471-2180},
mesh = {Humans ; Retrospective Studies ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Mycoplasma pneumoniae/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Female ; Tuberculosis/microbiology/diagnosis ; Aged ; Adolescent ; Young Adult ; Child ; },
abstract = {PURPOSE: Interpreting the results of metagenomic next-generation sequencing (mNGS) presents a significant challenge in both clinical and laboratory contexts.

METHODS: A retrospective analysis was conducted to validate mNGS findings, with a particular emphasis on Mycobacterium tuberculosis, Mycoplasma pneumoniae, and Pneumocystis jirovecii as representative pathogens, examined from both clinical and laboratory perspectives.

RESULTS: Based on a comprehensive clinical analysis, the mNGS demonstrated detection accuracies for M. tuberculosis, M. pneumoniae, and P. jirovecii of 87.0% (60 out of 69; 95% confidence interval [CI], 77.04%-92.99%), 97.6% (81 out of 83; 95% CI, 91.63%-99.34%), and 78.9% (45 out of 57; 95% CI, 66.72%-87.53%), respectively. Conversely, when incorporating laboratory confirmation from a variety of detection methodologies, the accuracy rates for mNGS in identifying M. tuberculosis, M. pneumoniae, and P. jirovecii were 92.7% (51 out of 55; 95% CI, 82.74%-97.14%), 82.3% (51 out of 62; 95% CI, 70.96%-89.80%), and 83.9% (26 out of 31; 95% CI, 67.36%-92.91%), respectively. Additionally, our analysis revealed no statistically significant difference in read counts and relative abundances between mNGS results deemed clinically as false positives and those considered true positives (P < 0.05).

CONCLUSION: In contemporary clinical practice, the detection of positive results from mNGS is notably high from both laboratory and clinical standpoints. Nonetheless, the interpretation of results with low read counts presents significant challenges for both clinical and laboratory environments under current conditions.},
}

Humans
Retrospective Studies
*Mycobacterium tuberculosis/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Mycoplasma pneumoniae/genetics/isolation & purification
Male
Adult
Middle Aged
Female
Tuberculosis/microbiology/diagnosis
Aged
Adolescent
Young Adult
Child

@article {pmid40155693,
year = {2025},
author = {Refahi, M and Sokhansanj, BA and Mell, JC and Brown, JR and Yoo, H and Hearne, G and Rosen, GL},
title = {Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {517},
pmid = {40155693},
issn = {2399-3642},
support = {1936791//National Science Foundation (NSF)/ ; 1919691//National Science Foundation (NSF)/ ; 2107108//National Science Foundation (NSF)/ ; },
mesh = {*Genomics/methods ; Sequence Analysis, DNA/methods ; Base Sequence ; Algorithms ; Metagenomics/methods ; },
abstract = {Analysis of genomic and metagenomic sequences is inherently more challenging than that of amino acid sequences due to the higher divergence among evolutionarily related nucleotide sequences, variable k-mer and codon usage within and among genomes of diverse species, and poorly understood selective constraints. We introduce Scorpio (Sequence Contrastive Optimization for Representation and Predictive Inference on DNA), a versatile framework designed for nucleotide sequences that employ contrastive learning to improve embeddings. By leveraging pre-trained genomic language models and k-mer frequency embeddings, Scorpio demonstrates competitive performance in diverse applications, including taxonomic and gene classification, antimicrobial resistance (AMR) gene identification, and promoter detection. A key strength of Scorpio is its ability to generalize to novel DNA sequences and taxa, addressing a significant limitation of alignment-based methods. Scorpio has been tested on multiple datasets with DNA sequences of varying lengths (long and short) and shows robust inference capabilities. Additionally, we provide an analysis of the biological information underlying this representation, including correlations between codon adaptation index as a gene expression factor, sequence similarity, and taxonomy, as well as the functional and structural information of genes.},
}

*Genomics/methods
Sequence Analysis, DNA/methods
Base Sequence
Algorithms
Metagenomics/methods

@article {pmid40155620,
year = {2025},
author = {Kazarina, A and Wiechman, H and Sarkar, S and Richie, T and Lee, STM},
title = {Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {521},
pmid = {40155620},
issn = {2052-4463},
support = {2020-67019-31803//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2238633//National Science Foundation (NSF)/ ; OIA-1656006//National Science Foundation (NSF)/ ; },
mesh = {*Soil Microbiology ; *Metagenome ; Metagenomics ; Bacteria/genetics/classification ; Kansas ; Soil/chemistry ; Archaea/genetics ; },
abstract = {Soil contains a diverse community of organisms; these can include archaea, fungi, viruses, and bacteria. In situ identification of soil microorganisms is challenging. The use of genome-centric metagenomics enables the assembly and identification of microbial populations, allowing the categorization and exploration of potential functions living in the complex soil environment. However, the heterogeneity of the soil-inhabiting microbes poses a tremendous challenge, with their functions left unknown, and difficult to culture in lab settings. In this study, using genome assembling strategies from both field core samples and enriched monolith samples, we assembled 679 highly complete metagenome-assembled genomes (MAGs). The ability to identify these MAGs from samples across a precipitation gradient in the state of Kansas (USA) provided insights into the impact of precipitation levels on soil microbial populations. Metabolite modeling of the MAGs revealed that more than 80% of the microbial populations possessed carbohydrate-active enzymes, capable of breaking down chitin and starch.},
}

*Soil Microbiology
*Metagenome
Metagenomics
Bacteria/genetics/classification
Kansas
Soil/chemistry
Archaea/genetics

@article {pmid40155586,
year = {2025},
author = {Bebawy, AS and Saad, BT and Saad, MT and Mosaad, GS and Gomaa, FAM and Alshahrani, MY and Aboshanab, KM},
title = {Evaluation of the taxonomic classification tools and visualizers for metagenomic analysis using the Oxford nanopore sequence database.},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {40155586},
issn = {2190-3883},
abstract = {Microbial metagenomic identification is generally attributed to the specificity and type of the bioinformatic tools, including classifiers and visualizers. In this study, the performance of two major classifiers, Centrifuge and Kraken2, and two visualizers (Recentrifuge and Krona) has been thoroughly investigated for their efficiency in the identification of the microorganisms using the Whole-Genome Sequence (WGS) database and four targeted databases including NCBI, Silva, Greengenes, and Ribosomal Database Project (RDP). Two standard DNA metagenomic library replicates, Zymo and Zymo-1, were used as quality control. Results showed that Centrifuge gave a higher percentage of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica identification than Kraken2. Compared to Recentrifuge, Kraken2 was more accurate in identifying Staphylococcus aureus, Listeria monocytogenes, Bacillus subtilis, and Cryptococcus neoformans. The results of the rest of the detected microorganisms were generally consistent with the two classifiers. Regarding visualizers, both Recentrifuge and Krona provided similar results regarding the abundance of each microbial species regardless of the classifier used. The differences in results between the two mentioned classifiers may be attributed to the specific algorithms each method uses and the sequencing depth. Centrifuge uses a read mapping approach, while Kraken2 uses a k-mer-based system to classify the sequencing reads into taxonomic groups. In conclusion, both Centrifuge and Kraken2 are effective tools for microbial classification. However, the choice of classifier can influence the accuracy of microbial classification and, therefore, should be made carefully, depending on the desired application, even when the same reference database is used.},
}

@article {pmid40154870,
year = {2025},
author = {Yang, JT and Zhang, Y and Xiong, SY and Wei, HJ and Zhang, WT and Lian, XL and Xu, XL and Jiang, HX and Sun, J},
title = {Microplastics Reduced the Natural Attenuation of Antibiotic Resistance Genes in Fertilized Soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126144},
doi = {10.1016/j.envpol.2025.126144},
pmid = {40154870},
issn = {1873-6424},
abstract = {The prolonged application of mulch and manure in agriculture has led to significant microplastic (MP) pollution in fertilized soils, raising global concerns about its potential impacts on soil health and ecosystem function. However, the effects of MP exposure on antibiotic resistance genes (ARGs) and microbial communities in fertilized soils are unknown. Therefore, we comprehensively explored the trends and drivers of ARGs during their natural abatement under the stress of conventional and biodegradable MP addition in fertilized soils using a soil microcosm experiment and metagenomic. The findings indicated that the presence of polybutylene succinate MPs (PBS-MPs) reduced the natural attenuation rate of ARGs in fertilized soils while increasing the fraction of high-risk ARGs in soils. Microbial communities and mobile genetic elements (MGEs) mainly drove the inhibitory effect of MPs on ARG abatement. Interestingly, most potential hosts for the coexistence of ARGs, metal resistance genes (MRGs), and MGEs were annotated as pathogens, such as Escherichia spp., Salmonella spp., and Klebsiella spp. In addition, MP stress in fertilized soil may lead to long-term contamination by highly virulent and antibiotic-resistant Escherichia coli. MPs influence the distribution of carbon sources, which in turn reduces the diversity and stability of soil microbial communities, while simultaneously promoting the colonization of crucial ARG hosts, like Dyella spp. This ultimately prolonged the high-risk state for ARG proliferation in the soil. This study highlights the significant risk posed by MPs to the persistence and spread of ARGs in fertilized soils. These results provide valuable insights for managing MP contamination in agricultural systems, emphasizing the need for sustainable practices to mitigate the long-term environmental risks associated with MP pollution.},
}

@article {pmid40154751,
year = {2025},
author = {Jiang, X and Zhao, Y and Zhang, W and Zheng, Q and Li, D and Zhang, G and Zhou, T},
title = {Chlorotetracycline-driven modulation of substrate utilization and metabolic traits in sludge anaerobic fermentation for optimized methane production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132449},
doi = {10.1016/j.biortech.2025.132449},
pmid = {40154751},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a highly efficient and promising method for treating waste activated sludge (WAS). Nevertheless, the presence of chlortetracycline (CTC) in WAS introduced uncertainty into the AD process. This study revealed thatthe cumulative methane yield was increased by 27.5 % with the CTC concentration at 50 mg/kg dry sludge by enhancing hydrolysis, acidification and methanogenesis during which specific microbial communities were enriched and related functional genes were enhanced. Subsequent investigations foundthe accumulation of extracellular polymeric substances (EPS) was improved and methane-producing microorganisms (e.g., Bacteroidetes and Euryarchaeota) were also enriched under CTC exposure. Metagenomic analysis further elucidated thatCTC significantly increased functional genes related to bacterial secretion system and metabolism of organic matter for methane production (e.g., pyruvate metabolism and methane metabolism). This study shed light on the substantial impact of CTC on the AD of WAS and provided a promising strategy for improvements in anaerobic fermentation.},
}

@article {pmid40154110,
year = {2025},
author = {Alameer, RM and Tayeb, H and Magrashi, A and Alqasabi, A and Nazmi, A and Yamani, A and Almaghrabi, RS},
title = {Diagnosis of donor-derived Malassezia restricta &Aspergillus species invasive fungal infection in renal transplant recipient using next generation sequencing - A report of 2 cases and literature review.},
journal = {Journal of infection and public health},
volume = {18},
number = {5},
pages = {102742},
doi = {10.1016/j.jiph.2025.102742},
pmid = {40154110},
issn = {1876-035X},
abstract = {Diagnosing donor-derived fungal infection in solid organ transplant recipients can be particularly challenging and is associated with high mortality. Here, we report two cases of Malassezia restricta and Aspergillus spp donor-derived fungal infection in renal transplant recipients leading to graft loss. Fortunately, both patients achieved full recovery with the administration of antifungal therapy.},
}

@article {pmid40154057,
year = {2025},
author = {Chen, H and Zhong, S and Liu, Z and Hu, Z and Wang, C and Zhou, Y and Xu, N and Zhao, F and Li, D and Hu, Y},
title = {Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation.},
journal = {Food chemistry},
volume = {481},
number = {},
pages = {143980},
doi = {10.1016/j.foodchem.2025.143980},
pmid = {40154057},
issn = {1873-7072},
abstract = {Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.},
}

@article {pmid40154039,
year = {2025},
author = {Li, J and Huang, Z and Zhang, R},
title = {Unmasking Prototheca wickerhamii: A rare case of cutaneous infection and its implications for clinical practice.},
journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases},
volume = {29},
number = {3},
pages = {104525},
doi = {10.1016/j.bjid.2025.104525},
pmid = {40154039},
issn = {1678-4391},
abstract = {Prototheca, an opportunistic pathogenic algae widely found in nature, has emerged as a potential public health concern. Most cases occur in immunocompromised individuals, with infections in immunocompetent patients being relatively rare. Due to their non-specific clinical presentation and limited awareness among clinicians, Prototheca infections are often misdiagnosed, resulting in delayed treatment. Recent advances in species identification and antifungal susceptibility testing have provided important tools for diagnosis and therapy. Here, we report a case of recurrent facial infection in a 76-year-old immunocompetent man. Skin biopsy revealed an infectious granuloma, and fungal culture identified yeast-like colonies. Fluorescence staining and scanning electron microscopy revealed abundant spores, while metagenomic sequencing confirmed the infection as Prototheca wickerhamii. The patient was successfully treated with long-term itraconazole and dipotassium glycyrrhizinate capsules. This case highlights the importance of early and accurate diagnosis in the management of Prototheca skin infections and reviews the therapeutic strategies used.},
}

@article {pmid40153957,
year = {2025},
author = {Huang, M and Mu, G and Mai, F and Zhou, Y and Li, X and Yang, Q and Shao, B and Wang, J and Tong, Y},
title = {Methane cycling in typical emerging proglacial lakes on the Tibetan Plateau: Insights into the metabolic mechanisms mediated by microorganisms.},
journal = {Water research},
volume = {280},
number = {},
pages = {123533},
doi = {10.1016/j.watres.2025.123533},
pmid = {40153957},
issn = {1879-2448},
abstract = {A large number of high-latitude emerging proglacial lakes have formed on the Tibetan Plateau (TP) due to the global warming and deglaciation. These lakes have the potential to emit methane (CH4) because of the exposure of cryopreserved organic carbon, leading to their significance in regional carbon turnover and cycling. However, previous studies have focused more on human-impacted lakes (e.g., eutrophic lakes), resulting in limited research on the mechanisms of CH4 cycling in the proglacial lakes. In this study, we demonstrated that three typical emerging high-latitude proglacial lakes (∼5500 m a.s.l.) on the TP exhibited a diffusive emission flux of 32.39 ± 11.66 μmol/m[2]/d during the summer. The δ[13]C-CH4 values (-50.10 ± 0.56‰) suggested a biogenic origin of CH4 through the acetoclastic pathway in the lakes. Metagenome sequencing further showed that microbes involved in methanogenesis were dominated by Methanosarcina (36.74 ± 0.07 % of total methanogens). Significant CH4 consumption was observed in the proglacial lakes. The microbes involved in the CH4 consumption were dominated by Methylobacter (48.50 ± 0.17 % of total methanotrophs). A Mantel test demonstrated that dissolved iron (Fe) was a key factor controlling the structure of the CH4 cycling microbial communities. Functional gene and co-occurrence network analyses indicated that members of Pseudomonadota, Bacteroidota, and Actinomycetota may be involved in CH4 cycling by providing methanogenic substrates (i.e., acetyl coenzyme A) and consuming CH4 oxidative intermediates (i.e., methanol, formaldehyde, and formic acid). This study emphasized the ecological significance of emerging proglacial lakes in CH4 releases. It broadened the current understanding of cryophilic CH4 cycling microbes and their mechanisms, that enhances our knowledge of the carbon cycle on the TP.},
}

@article {pmid40153355,
year = {2025},
author = {Klištincová, N and Koreňová, J and Rešková, Z and Čaplová, Z and Burdová, A and Farkas, Z and Polovka, M and Drahovská, H and Pangallo, D and Kuchta, T},
title = {Bacterial consortia of ewes´ whey in the production of bryndza cheese in Slovakia.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf047},
pmid = {40153355},
issn = {1472-765X},
abstract = {Whey from previous production is often used as a natural starter in the technology of traditional cheeses, including bryndza-cheese in Slovakia. Therefore, studying its bacterial community and isolating new potential natural starters is important for improving the characterisitics of final product. Composition of bacterial consortia of fresh and fermented whey in the production of raw ewes´ milk-based bryndza-cheese from 8 small or medium-sized producers was analysed. Culture-based microbiological analysis and culture-independent analysis based on 16S rRNA gene sequencing by MiSeq and MinION were used. Results showed the dominance of lactococci or streptococci, with 3 - 8 log CFU ml-[1] of Lactobacillus sensu lato in all whey samples. Potential natural starters comprising Lacticaseibacillus paracasei/casei, Lactiplantibacillus plantarum, Lentilactobacillus parabuchneri, Lactobacillus helveticus, Lactobacillus diolivorans, Levilactobacillus brevis, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus gasseri and Lentilactobacillus otakiensis were isolated. Coliforms were also present in all samples, with no consistently lower values in fermented whey samples. Some samples contained pseudomonads and/or acinetobacters. Coagulase positive staphylococci were present at relevant levels in samples from 4 producers. The results revealed that whey is a source of natural starters due to the presence of lactobacilli.},
}

@article {pmid40153196,
year = {2025},
author = {Erickson, I and Davidson, S and Choi, H and Rho, S and Guignet, M and Peagler, K and Thummel, K and Ericsson, A and Barker-Haliski, M},
title = {Intestinal dysbiosis alters acute seizure burden and antiseizure medicine activity in Theiler's virus model of encephalitis.},
journal = {Epilepsia},
volume = {},
number = {},
pages = {},
doi = {10.1111/epi.18395},
pmid = {40153196},
issn = {1528-1167},
support = {//University of Washington/ ; },
abstract = {OBJECTIVE: Brain infection with Theiler's murine encephalomyelitis virus (TMEV) in C57BL/6J mice produces an etiologically relevant model of acquired seizures. Dietary changes can modify seizure presentation following TMEV brain infection and influence intestinal microbiome diversity and composition. Intestinal dysbiosis may thus similarly affect seizure burden and antiseizure medicine (ASM) activity in this model, independent of pharmacokinetic effects. We thus sought to define the influence of antibiotic (ABX)-induced gut dysbiosis on acute seizure presentation, anticonvulsant activity of carbamazepine (CBZ), and CBZ pharmacokinetics with TMEV infection.

METHODS: Male C57BL/6J mice (4-5 weeks old) received oral ABX or saline (SAL) once daily beginning on arrival through day 7 after TMEV infection (postinfection [p.i.]). Mice were infected with TMEV or phosphate-buffered saline on day 0. Mice received intraperitoneal (20 mg/kg) CBZ or vehicle (VEH) twice daily on days 3-7 p.i. and were assessed for handling-induced seizures 30 min after treatment. Plasma was collected on day 7 p.i. at 15 and 60 min after CBZ administration for bioanalysis.

RESULTS: TMEV infection induced acute seizures, but ABX-induced gut dysbiosis altered seizure presentation. There were 75% SAL-VEH, 35% SAL-CBZ, 35% ABX-VEH, and 72% ABX-CBZ mice with seizures during the 7-day monitoring period. There was a significant pretreatment × ASM interaction (p = .0001), with differences in seizure burden in SAL- versus ABX-pretreated mice (p = .004). CBZ significantly increased latency to seizure presentation, an effect absent in ABX-CBZ mice. Plasma CBZ concentrations did not differ between SAL and ABX pretreatment groups, suggesting that ABX did not influence CBZ pharmacokinetics.

SIGNIFICANCE: ABX-induced gut dysbiosis markedly altered acute disease trajectory with TMEV-induced encephalitis, reflecting a novel contribution of the gut microbiome to seizure presentation. ABX-induced gut dysbiosis also significantly changed acute seizure control by CBZ, but did not influence plasma CBZ concentrations. The gut-brain axis is thus an underrecognized contributor to TMEV infection-induced seizures, ASM activity, and disease burden.},
}

@article {pmid40152616,
year = {2025},
author = {Yao, J and Zeng, Y and Hong, X and Wang, M and Zhang, Q and Chen, Y and Gou, M and Xia, Z-Y and Tang, Y-Q},
title = {Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoate-producing mixed microbial cultures via meta-omics study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0020025},
doi = {10.1128/msystems.00200-25},
pmid = {40152616},
issn = {2379-5077},
abstract = {The dynamics of the structure of polyhydroxyalkanoate-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, five PHA-MMCs were enriched, and biological samples were sampled temporally to study the interactions between phage and bacterial members by combining metagenomics and metatranscriptomics. A total of 963 metagenome-assembled genomes (MAGs) and 4,294 phage operational taxonomic units (pOTUs) were assembled from bulk metagenomic data. The dynamic changes in the structure of phage and bacterial communities were remarkably consistent. Structural equation modeling analysis showed that phages could infect and lyse dominant species to vacate ecological niches for other species, resulting in a community succession state in which dominant species alternated. Seven key auxiliary metabolic genes (AMGs), phaC, fadJ, acs, ackA, phbB, acdAB, and fadD, potentially contributing to PHA synthesis were identified from phage sequences. Importantly, these AMGs were transcribed, indicating that they were in an active expression state. The meta-analysis provides the first catalog of phages in PHA-MMCs and the AMGs they carry, as well as how they affect the dynamic changes in bacterial communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of open microbial systems.IMPORTANCEThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (PHA-MMCs), at extremely low cost, has the potential for expanded production. However, the dynamics of dominant species in PHA-MMCs are poorly understood. Our results demonstrate for the first time the impact of phages on the structure of bacterial communities in the PHA-MMCs. There are complex interactions between the PHA producers (e.g., Azomonas, Paracoccus, and Thauera) and phages (e.g., Casadabanvirus and unclassified Hendrixvirinae). Phage communities can regulate the activity and structure of bacterial communities. In addition, the AMGs related to PHA synthesis may hitchhike during phage-host infection cycles, enabling their dissemination across bacterial communities, and phages may act as a critical genetic reservoir for bacterial members, facilitating access to PHA synthesis-related functional traits. This study highlights the impact of phages on bacterial community structure, suggesting that phages have the potential to be used as a tool for better controlling the microbial community structure of PHA-MMCs.},
}

@article {pmid40152185,
year = {2025},
author = {Allos, H and Hasbun, R},
title = {Aseptic meningitis: a foundation review.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001105},
pmid = {40152185},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: This review addresses the multifaceted nature of aseptic meningitis, a condition with diverse infectious and noninfectious etiologies. Despite its common presentation in clinical settings, over half of the cases remain without an identified cause, necessitating a comprehensive examination of diagnostic and management strategies. The increasing availability of advanced molecular diagnostics and the challenge of distinguishing bacterial from nonbacterial cases make this an opportune time to explore its implications for clinical practice.

RECENT FINDINGS: The literature highlights the pivotal role of advanced molecular diagnostics, such as multiplex PCR and metagenomic sequencing, in improving the identification of pathogens in aseptic meningitis. Enteroviruses remain the leading cause, but pathogens like Herpesviridae, arboviruses, and nonviral agents such as fungi and spirochetes also contribute significantly. New diagnostic algorithms and clinical models are emerging to distinguish bacterial from viral meningitis, reducing unnecessary treatments.

SUMMARY: Aseptic meningitis management is evolving with advancements in diagnostic technologies that allow for earlier pathogen identification, improving patient outcomes and minimizing healthcare costs. These findings underscore the importance of timely and accurate diagnostics and tailored therapeutic strategies in both clinical and research settings. Enhanced awareness of noninfectious causes is also crucial for comprehensive care.},
}

@article {pmid40152095,
year = {2025},
author = {Wu, S and Luo, Y and Wei, F and Li, Y and Fan, J and Chen, Y and Zhang, W and Li, X and Xu, Y and Chen, Z and Xia, C and Hu, M and Li, P and Gu, Q},
title = {Lactic acid bacteria target NF-κB signaling to alleviate gastric inflammation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo06308b},
pmid = {40152095},
issn = {2042-650X},
abstract = {Helicobacter pylori (H. pylori) infection and the resulting gastric inflammation are major contributors to gastric cancer development. Probiotics, particularly Lactobacillus, are promising for their anti-inflammatory potential, yet their exact mechanisms in inhibiting H. pylori-induced inflammation are unclear. In our previous study, Lactiplantibacillus plantarum ZJ316 (L. plantarum ZJ316) demonstrated strong anti-inflammatory effects against H. pylori infection in vivo, but its precise mechanisms were not fully understood. Here, we aimed to investigate how L. plantarum ZJ316 inhibits the inflammatory response to H. pylori infection. Our results demonstrated that L. plantarum ZJ316 effectively reduced the expression of pro-inflammatory cytokines in H. pylori-infected AGS cells. Mechanistically, L. plantarum ZJ316 inhibited the NF-κB signaling pathway by preventing the degradation of IκBα, suppressing p65 phosphorylation, and blocking the nuclear translocation of phosphorylated p65. Treatment with the NF-κB inhibitor BAY 11-7082 further decreased tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interleukin-1β (IL-1β) levels, confirming the inhibitory effect of L. plantarum ZJ316 on the NF-κB pathway. In H. pylori-infected mice, oral administration of L. plantarum ZJ316 significantly alleviated inflammatory cell infiltration, reduced TNF-α and pepsinogen II (PGII) levels, and increased interleukin-10 (IL-10) levels in serum. A comparative metagenomic analysis of the gastric microbiota revealed a decrease in Prevotella and Desulfovibrio, alongside an increase in Ligilactobacillus and Akkermansia, supporting the protective effects of L. plantarum ZJ316 and correlating with their decreased inflammatory response. In summary, administration of L. plantarum ZJ316 demonstrated robust anti-inflammatory effects against H. pylori infection by suppressing NF-κB signaling and promoting favorable changes in the gastric microbiota composition. Therefore, L. plantarum ZJ316 holds promise as a novel functional food for protecting the body against H. pylori infection.},
}

@article {pmid40151642,
year = {2025},
author = {Cai, X and Cho, JY and Chen, L and Liu, Y and Ji, F and Salgado, K and Ge, S and Yang, D and Yu, H and Shao, J and Futreal, PA and Sepesi, B and Gibbons, D and Chen, Y and Wang, G and Cheng, C and Wu, M and Zhang, J and Hsiao, A and Xia, T},
title = {Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112162},
pmid = {40151642},
issn = {2589-0042},
abstract = {Understanding the effect of gut microbiota function on immune checkpoint inhibitor (ICI) responses is urgently needed. Here, we integrated 821 fecal metagenomes from 12 datasets to identify differentially abundant genes and construct random forest models to predict ICI response. Gene markers demonstrated excellent predictive performance, with an average area under the curve (AUC) of 0.810. Pathway analyses revealed that quorum sensing (QS), ABC transporters, flagellar assembly, and amino acid biosynthesis pathways were enriched between responders (R) and non-responders (NRs) across 12 datasets. Furthermore, luxS, manA, fliC, and trpB exhibited consistent changes between R and NR across 12 datasets. Follow-up microbiota transplant experiments showed that inter-species signaling by different QS autoinducer-2 (AI-2) molecules (synthesized by luxS) can act on overall community function to promote the colonization of Akkermansia muciniphila, which is associated with superior ICI responses. Together, our data highlight the role of gut microbiota function in modulating the microbiome and antitumor immunity.},
}

@article {pmid40151403,
year = {2025},
author = {Otsuki, A and Inoue, R and Imai, T and Miura, H and Nishida, A and Inatomi, O and Andoh, A},
title = {Characterization of the gut phageome of Japanese patients with ulcerative colitis under endoscopic remission.},
journal = {Journal of clinical biochemistry and nutrition},
volume = {76},
number = {2},
pages = {202-209},
pmid = {40151403},
issn = {0912-0009},
abstract = {This study aimed to analyze the gut phageome in Japanese patients with ulcerative colitis (UC) in endoscopic remission. Fecal samples were collected from 35 UC patients and 22 healthy controls. The gut microbiome was analyzed using 16S rRNA amplicon sequencing, and the phageome was profiled through shotgun metagenomic sequencing. Compared to healthy controls, UC patients showed a significant reduction in phageome richness (observed species and Chao1 index). Principal coordinate analysis revealed a significant difference in beta-diversity between UC and healthy controls (p = 0.001). The abundance of temperate phages was higher in UC (15.2%) compared to healthy controls (5.9%), although this was not statistically significant (p = 0.088). Temperate phages associated with Coprococcus sp., Bacteroides sp. KFT8, and Faecalibacterium prausnitzii, as well as virulent phages associated with Ruminococcus gnavus and Lactobacillus farciminis, were increased in UC patients. Conversely, phages associated with Thermosipho affectus, Bacteroides sp. OF03-11BH, and Odoribacter splanchnicus were decreased in UC patients. Phages associated with the genera Odoribacter (p = 0.0004), Ruminococcus (p = 0.009), and Veillonella (p = 0.013) were significantly reduced in UC patients. The gut phageome of inactive UC patients exhibited notable alterations in viral composition compared to healthy controls. These results suggest that changes in the gut phageome might be involved in the pathogenesis of UC.},
}

@article {pmid40151093,
year = {2025},
author = {Liu, D and Zhang, W and Zhu, L and Gong, J and Huang, Y and Li, Z and He, J},
title = {Autoinducer-2 Quorum Sensing Is an Active Universal Signaling System in Sociomicrobiology.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e024},
doi = {10.1002/jobm.70024},
pmid = {40151093},
issn = {1521-4028},
support = {//This study was supported by National Natural Science Foundation of China (grants 32371495 and 32171424), Hubei Province Technology Innovation Plan Project (2024BCB028), and Wuhan Science and Technology Major Project (grant 2023020302020708)./ ; },
abstract = {Autoinducer-2 (AI-2) is a bacterial quorum sensing (QS) signaling molecule that regulates inter-specific and intraspecific bacterial communication in complex ecological environments. Here, we systematically analyzed the distribution of AI-2 QS-related proteins (synthases and receptors) in the domain bacteria, explored the evolution and development of AI-2 receptors, and analyzed the AI-2 regulatory networks using human intestinal metagenomic data. The results show that AI-2 QS-related proteins are distributed in 17 bacterial phyla, accounting for approximately 36.80% of the total genomes. Based on the ability of bacteria to synthesize and receive AI-2 signals, we divided bacteria into four major categories, namely Prosumer, Producer, Monitor, and Immunizer. The Gram-positive bacteria are mainly responsible for producing the AI-2 signals, while Gram-negative bacteria are more likely to respond to AI-2. Evolutionary analysis shows that the AI-2 receptor CahR is mainly derived from the methyl-accepting chemotaxis protein (MCP). Based on the length difference of the ligand-binding domains, we further speculate that AI-2 binding activates CahR through either allostery or aggregation mode. Using human intestinal metagenomic data, we found a strong correlation between AI-2 signaling and c-di-GMP signaling. These findings will have an important impact on the AI-2 QS research and accelerate its development.},
}

@article {pmid40150979,
year = {2025},
author = {Yildirim, EA and Laptev, GY and Ilina, LA and Ponomareva, ES and Brazhnik, EA and Smetannikova, TS and Novikova, NI and Turina, DG and Filippova, VA and Dubrovin, AV and Dubrovina, AS and Kalitkina, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN},
title = {Metagenomic Composition and Predicted Metabolic Pathway Analyses of the Endometrial and Rectal Microbiota in Dairy Cows Following the Introduction of a Complex Feed Additive.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {17},
number = {1},
pages = {25725},
doi = {10.31083/FBE25725},
pmid = {40150979},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Cattle/microbiology ; Female ; *Animal Feed ; *Rectum/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; Metabolic Networks and Pathways ; Metagenomics ; Dairying ; },
abstract = {BACKGROUND: The microbiome composition in dairy cows (Bos taurus) directly impacts on health and reproductive performance. This study aimed to determine the metagenomic composition and predicted microbial community functions in the endometrium and rectal chyme of cows fed a complex feed additive (CFA). The latter included the Bacillus mucilaginosus 159 strain, a short-chain fatty acid, plus essential oils.

METHODS: Clinically healthy cows were divided into two groups (n = 15 in each): (I) a control group fed the standard diet, and (II) an experimental group. CFA was introduced into the diet of Group II during the entire transit period at a dose of 50 g per animal per day; moreover, all animals received Pen-Strep 400 antibiotics to prevent endometritis and other pathologies. The microbial community composition from the endometrium and rectal chyme biotopes was assessed using targeted next-generation sequencing.

RESULTS: Significant changes were observed in the composition and predicted metabolic pathways due to the CFA administration, with the endometrial microbiota being more responsive to CFA than the intestinal chyme microbiome. Remarkably, the Actinobacteriota representatives disappeared in the endometrium of Group II animals compared to controls, whose content ranged from 0.34 to 3.3%. The use of CFA also resulted in a less pronounced effect in four predicted metabolic pathways for microbial degradation of catechol in the endometrium compared to controls (p < 0.05).

CONCLUSIONS: Our findings support the concept of a relationship between the gut microbiome and the reproductive system microflora of cows, as we observed changes in the composition and predicted metabolic pathways of the endometrial microbiota after orally administering CFA. This emphasizes the need for an integrated approach combining the correction of microecological disorders in the intestines and the reproductive system simultaneously.},
}

Animals
Cattle/microbiology
Female
*Animal Feed
*Rectum/microbiology
*Endometrium/microbiology/metabolism
*Microbiota
Metabolic Networks and Pathways
Metagenomics
Dairying

@article {pmid40150359,
year = {2025},
author = {Liu, Y and Dong, X and Sun, L and Cui, H and Kang, J and Bu, N and Zhang, Y and Qi, Z and Li, Z and Zhang, Z and Zhao, L},
title = {Analysis of the Microbial Community Structure of Ixodes persulcatus at Each Developmental Stage.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/ani15060830},
pmid = {40150359},
issn = {2076-2615},
support = {32260887//National Natural Science Foundation of China/ ; },
abstract = {Ticks are the second most significant vector of pathogens worldwide. Ixodes persulcatus is one of the dominant tick species in Inner Mongolia that can carry and transmit various pathogenic microorganisms. However, only one specific pathogen has been detected in a particular developmental stage of I. persulcatus, moreover metagenomic analysis has been conducted only in the adult tick stage. In this study, we used I. persulcatus at different developmental stages (first-generation female adult ticks, eggs, larval ticks, engorged larval ticks, nymphal ticks, engorged nymphal ticks, and second-generation adult ticks) from Inner Mongolia as materials for nucleic acid extraction. Subsequently, we constructed Illumina PE250 and Illumina PE150 libraries and sequenced them on the Illumina NovaSeq 6000 platform. Finally, we used molecular biology software and sequence analysis platform to analyze microbial community structures. Illumina PE250 sequencing revealed that the seven developmental stages of I. persulcatus were annotated to 21 phyla, 43 classes, 104 orders, 188 families, 391 genera, and 556 species of bacteria. Among them, 4 phyla and 14 genera were present at all developmental stages, with Proteobacteria being the dominant phylum and Rickettsia spp. being the dominant genus. In addition, Rickettsia had the highest relative abundance in the seven developmental stages. All developmental stages were annotated to a certain abundance of Brucella spp. Illumina PE150 sequencing revealed that the three samples (X-I-YDCP: first-generation adult ticks; X-I-MIX: mixed samples of eggs, larval ticks, and nymphal ticks; X-I-EDCP: second-generation adult ticks) of I. persulcatus were annotated to six orders, 28 families, 72 genera, and 158 species of viruses, of which 46 genera and 80 species were found in all three sample species. To the best of our knowledge, this is the first study that comprehensively analyzed the microbial community composition of I. persulcatus at different developmental stages. Based on the study outcomes, certain abundance of Rickettsia japonica, bovine viral diarrhea virus, and African swine fever virus were annotated to I. persulcatus.},
}

@article {pmid40149936,
year = {2025},
author = {Zhan, J and Cheng, J and Chang, W and Su, Y and Yue, X and Wu, C},
title = {Absolute Quantitative Metagenomic Analysis Provides More Accurate Insights for the Anti-Colitis Effect of Berberine via Modulation of Gut Microbiota.},
journal = {Biomolecules},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/biom15030400},
pmid = {40149936},
issn = {2218-273X},
mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Metagenomics/methods ; Colitis, Ulcerative/microbiology/drug therapy ; Mice ; Bacteria/drug effects/genetics/classification ; Male ; Butyric Acid/pharmacology ; Disease Models, Animal ; },
abstract = {Current gut microbiota studies often rely on relative quantitative sequencing. However, under certain circumstances, while the relative quantitative abundance of these bacteria may remain stable, the absolute quantities of specific bacteria can vary considerably. Since the function of bacteria is directly linked to their total numbers, absolute quantification is crucial. This study aims to identify the optimal method for microbiome analysis by comparing relative and absolute quantitative sequencing. Using ulcerative colitis, which is closely associated with gut microbiota, as a disease model and berberine (which affects microbiota) versus sodium butyrate (which does not) as drugs, relative and absolute quantitative methods were used to evaluate the varying effects of the different drugs on the regulation of gut microbiota in UC-affected animals. The regulatory effects of BBR on gut microbiota were further synthesized as identified in earlier studies using an individual-based meta-analysis, and we compared these findings with our absolute sequencing results. The results from absolute sequencing were more consistent with the actual microbial community, suggesting that relative abundance measurements might not accurately reflect the true abundance of microbial species. Moreover, meta-analysis results were only partially consistent with absolute quantitative sequencing and sometimes directly opposed, suggesting that relative quantitative sequencing analyses are prone to misinterpretation and incorrect correlation of results. This study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.},
}

*Berberine/pharmacology
*Gastrointestinal Microbiome/drug effects/genetics
Animals
*Metagenomics/methods
Colitis, Ulcerative/microbiology/drug therapy
Mice
Bacteria/drug effects/genetics/classification
Male
Butyric Acid/pharmacology
Disease Models, Animal

@article {pmid40149684,
year = {2025},
author = {Zhao, X and Xu, J and Wu, D and Chen, N and Liu, Y},
title = {Gut Microbiota in Different Treatment Response Types of Crohn's Disease Patients Treated with Biologics over a Long Disease Course.},
journal = {Biomedicines},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/biomedicines13030708},
pmid = {40149684},
issn = {2227-9059},
support = {(No. RDJP2022-15 to X.Z., No. RDJP2023-22 to J.X.)//Scientific Research Development Funds of Peking University 401 People's Hospital/ ; No. CFH2024-4-4089 to J.X.//the Capital Health Research and Development of Special/ ; (82370555 to J.X., 400 No. 82370537, 82341228 to Y.L.)//the National Natural Science Foundation of China/ ; (No. XZ2024ZR-ZY012(Z) to X.Z.//the Xizang Autono- 402 mous Region Natural Science Foundation Group Medical Aid Project/ ; },
abstract = {Background and Aims: Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) with a globally increasing prevalence, partially driven by alterations in gut microbiota. Although biological therapy is the first-line treatment for CD, a significant proportion of patients experience a primary non-response or secondary loss of response over time. This study aimed to explore the differences in gut microbiota among CD patients with divergent long-term responses to biological therapy, focusing on a long disease course. Methods: Sixteen CD patients who applied the biological agents for a while were enrolled in this study and were followed for one year, during which fecal specimens were collected monthly. Metagenomic analysis was used to determine the microbiota profiles in fecal samples. The response to biological therapy was evaluated both endoscopically and clinically. Patients were categorized into three groups based on their response: R (long-term remission), mA (mild active), and R2A group (remission to active). The differences in the gut microbiota among the groups were analyzed. Results: Significant differences in fecal bacterial composition were observed between the groups. The R2A group exhibited a notable decline in gut microbial diversity compared to the other two groups (p < 0.05). Patients in the R group had higher abundances of Akkermansia muciniphila, Bifidobacterium adolescentis, and Megasphaera elsdenii. In contrast, Veillonella parvula, Veillonella atypica, and Klebsiella pneumoniae were higher in the R2A group. Conclusions: Gut microbial diversity and specific bacterial significantly differed among groups, reflecting distinct characteristics between responders and non-responders.},
}

@article {pmid40149628,
year = {2025},
author = {Kaczka, A and Błońska, A and Chojnacki, C and Gąsiorowska, A and Błasiak, J and Popławski, T and Chojnacki, J},
title = {Periodic Changes in the Gut Microbiome in Women with the Mixed Type of Irritable Bowel Syndrome.},
journal = {Biomedicines},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/biomedicines13030652},
pmid = {40149628},
issn = {2227-9059},
abstract = {Background: The mixed type of irritable bowel syndrome (IBS-M) is characterized by recurrent constipation and diarrhea. The cause of the variability of these symptoms is not sufficiently understood. The aim of this study was to perform metagenomic and metabolic assessment of the gut microbiome in constipation and diarrheal period of IBS-M. Methods: This study included 30 women, aged 28-47 years old, with the symptoms which aligned with those of IBS-M, according to the Rome IV Criteria. Results: In both periods of the disease, the dysbiosis index (DI), the Shannon diversity index (SDI), the hydrogen-methane and ammonia breath tests, as well as the selected bacterial metabolites (-p-hydroxyphenyl acetic acid (HPA), 3-indoxyl sulfate (Indican, 3-IS)), and hippuric acid (A) in urine, were determined. The dysbiosis index (DI) in the period of constipation was 3.73 ± 0.90 points, and in the diarrheal period it did not change significantly 3.93 ± 0.75 points (p > 0.05). During the diarrheal period, the diversity of bacteria increases from 2.16 ± 0.59 to 2.74 ± 0.50 points on the Shannon dietary index (p < 0.001). The gut microbiome profile also changed, especially during the diarrheal period where an abundance of Bifidobacterium spp. and Lactobacillus spp. decreased significantly. In addition, during this period, the levels of hydrogen and ammonia in breath air increased, while the methane level decreased. The differences also concern the results of urinary metabolites, especially related to hippuric acid and indican. During the diarrheal period, the levels of hydrogen and ammonia ions increased, while the methane level decreased. The differences also concern the results of urinary metabolites, especially related to hippuric acid and indican. Conclusions: In patients with IBS-M, periodic changes in the profile and metabolism of the gut microbiome occur, which coexist with recurrent symptoms such as constipation and diarrhea.},
}

@article {pmid40149502,
year = {2025},
author = {Hailu, G and Legesse, M and Mulu, A and Medhin, G and Tsegaye, MM and Alemayehu, DH and Ayele, A and Gebreegziabxier, A and Tayachew, A and Aguine, A and Dejene, H and Tessema, SK and Onywera, H and Stanislas, AE and Abate, E and Marcello, A and Bitew, M},
title = {SARS-CoV-2 Genetic Variants Identified in Selected Regions of Ethiopia Through Whole Genome Sequencing: Insights from the Fifth Wave of COVID-19.},
journal = {Genes},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/genes16030351},
pmid = {40149502},
issn = {2073-4425},
mesh = {Humans ; Ethiopia/epidemiology ; *COVID-19/virology/epidemiology/transmission ; *SARS-CoV-2/genetics/pathogenicity ; Male ; Female ; Adult ; *Whole Genome Sequencing/methods ; *Genome, Viral ; Middle Aged ; Phylogeny ; Genetic Variation ; Young Adult ; Adolescent ; },
abstract = {BACKGROUND: The COVID-19 pandemic highlighted SARS-CoV-2 variants with increased transmissibility and immune evasion. In Ethiopia, where cases surged, the understanding of the virus's dynamics was limited. This study analyzed SARS-CoV-2 variants during the fifth wave, crucial for guiding vaccines, therapeutics, diagnostics, and understanding disease severity.

METHOD: From June to August 2022, 150 SARS-CoV-2-positive samples were randomly selected from the Ethiopian Public Health Institute repository. Sixty-three high-quality genome sequences were analyzed.

RESULTS: Of the 63 sequences, 70% were from males and 30% from females, with a median age of 34. Omicron dominated (97%, 61/63), primarily clade 22A (64%, 40/63), followed by 22B (18%, 11/63) and 21K (14%, 9/63). Delta accounted for 3.2% (2/63). Omicron was identified in all (25) vaccinated study participants. Ethiopian sequences showed limited evolutionary divergence and lower genetic diversity compared to global sequences.

CONCLUSION: Omicron was the predominant variant during Ethiopia's fifth wave, indicating recent community transmission. Despite minor genetic diversity differences, ongoing surveillance remains critical for tracking variants and informing public health interventions.},
}

Humans
Ethiopia/epidemiology
*COVID-19/virology/epidemiology/transmission
*SARS-CoV-2/genetics/pathogenicity
Male
Female
Adult
*Whole Genome Sequencing/methods
*Genome, Viral
Middle Aged
Phylogeny
Genetic Variation
Young Adult
Adolescent

@article {pmid40149437,
year = {2025},
author = {Alharbi, SM and Al-Sulami, N and Al-Amrah, H and Anwar, Y and Gadah, OA and Bahamdain, LA and Al-Matary, M and Alamri, AM and Bahieldin, A},
title = {Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems.},
journal = {Genes},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/genes16030285},
pmid = {40149437},
issn = {2073-4425},
mesh = {*Rhizosphere ; *Soil Microbiology ; Mycorrhizae/genetics/classification ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics/methods ; Metagenome ; Ecosystem ; Microbiota/genetics ; Plant Roots/microbiology ; Fungi/genetics/classification ; },
abstract = {Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.},
}

*Rhizosphere
*Soil Microbiology
Mycorrhizae/genetics/classification
Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics/methods
Metagenome
Ecosystem
Microbiota/genetics
Plant Roots/microbiology
Fungi/genetics/classification

@article {pmid40149106,
year = {2025},
author = {Olsen, NS and Riber, L},
title = {Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/antibiotics14030296},
pmid = {40149106},
issn = {2079-6382},
support = {NNF23OC0086264//Novo Nordisk Foundation/ ; },
abstract = {Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.},
}

@article {pmid40148934,
year = {2025},
author = {de Campos, GM and Clemente, LG and Lima, ARJ and Cella, E and Fonseca, V and Ximenez, JPB and Nishiyama, MY and de Carvalho, E and Sampaio, SC and Giovanetti, M and Elias, MC and Slavov, SN},
title = {Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {88},
pmid = {40148934},
issn = {1743-422X},
support = {2022/00910-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/11944-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/11944-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/11944-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/23205-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 403075/2023-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Anelloviridae/genetics/classification/isolation & purification ; *Torque teno virus/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; DNA Virus Infections/virology/blood ; Plasma/virology ; Algorithms ; Metagenome ; Genome, Viral/genetics ; },
abstract = {BACKGROUND: Viral metagenomics has expanded significantly in recent years due to advancements in next-generation sequencing, establishing it as the leading method for identifying emerging viruses. A crucial step in metagenomics is taxonomic classification, where sequence data is assigned to specific taxa, thereby enabling the characterization of species composition within a sample. Various taxonomic classifiers have been developed in recent years, each employing distinct classification approaches that produce varying results and abundance profiles, even when analyzing the same sample.

METHODS: In this study, we propose using the identification of Torque Teno Viruses (TTVs), from the Anelloviridae family, as indicators to evaluate the performance of four short-read-based metagenomic classifiers: Kraken2, Kaiju, CLARK and DIAMOND, when evaluating human plasma samples.

RESULTS: Our results show that each classifier assigns TTV species at different abundance levels, potentially influencing the interpretation of diversity within samples. Specifically, nucleotide-based classifiers tend to detect a broader range of TTV species, indicating higher sensitivity, while amino acid-based classifiers like DIAMOND and CLARK display lower abundance indices. Interestingly, despite employing different algorithms and data types (protein-based vs. nucleotide-based), Kaiju and Kraken2 performed similarly.

CONCLUSION: Our study underscores the critical impact of classifier selection on diversity indices in metagenomic analyses. Kaiju effectively assigned a wide variety of TTV species, demonstrating it did not require a high volume of reads to capture diversity. Nucleotide-based classifiers like CLARK and Kraken2 showed superior sensitivity, which is valuable for detecting emerging or rare viruses. At the same time, protein-based approaches such as DIAMOND and Kaiju proved robust for identifying known species with low variability.},
}

*Metagenomics/methods
Humans
*Anelloviridae/genetics/classification/isolation & purification
*Torque teno virus/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods
DNA Virus Infections/virology/blood
Plasma/virology
Algorithms
Metagenome
Genome, Viral/genetics

@article {pmid40148927,
year = {2025},
author = {Feng, Z and Lorenc, N and O'Brien, B and Sun, G and Li, Z and Jung, D and Ronholm, J},
title = {Deep culturing the fecal microbiota of healthy laying hens.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {32},
pmid = {40148927},
issn = {2524-4671},
abstract = {BACKGROUND: The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.

RESULTS: In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.

CONCLUSIONS: Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.},
}

@article {pmid40148567,
year = {2025},
author = {Austin, GI and Brown Kav, A and ElNaggar, S and Park, H and Biermann, J and Uhlemann, AC and Pe'er, I and Korem, T},
title = {Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40148567},
issn = {2058-5276},
support = {R01HD106017//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD114715//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T15LM007079//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; U54DK104309//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
abstract = {Every step in common microbiome profiling protocols has variable efficiency for each microbe, for example, different DNA extraction efficiency for Gram-positive bacteria. These processing biases impede the identification of signals that are biologically interpretable and generalizable across studies. 'Batch-correction' methods have been used to address these issues computationally with some success, but they are largely non-interpretable and often require the use of an outcome variable in a manner that risks overfitting. We present DEBIAS-M (domain adaptation with phenotype estimation and batch integration across studies of the microbiome), an interpretable framework for inference and correction of processing bias, which facilitates domain adaptation in microbiome studies. DEBIAS-M learns bias-correction factors for each microbe in each batch that simultaneously minimize batch effects and maximize cross-study associations with phenotypes. Using diverse benchmarks including 16S rRNA and metagenomic sequencing, classification and regression, and a variety of clinical and molecular targets, we demonstrate that using DEBIAS-M improves cross-study prediction accuracy compared with commonly used batch-correction methods. Notably, we show that the inferred bias-correction factors are stable, interpretable and strongly associated with specific experimental protocols. Overall, we show that DEBIAS-M facilitates improved modelling of microbiome data and identification of interpretable signals that generalize across studies.},
}

@article {pmid40147547,
year = {2025},
author = {Liu, H and Sun, R and Wu, Y and Feng, J and Fan, G and Chen, S and Li, L},
title = {Molecular detection and identification of goose astrovirus in GuangDong Province, China.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105745},
doi = {10.1016/j.meegid.2025.105745},
pmid = {40147547},
issn = {1567-7257},
abstract = {In recent years, Goose Astrovirus (GAstV) has become a major pathogen in China, afflicting geese with significant clinical manifestations like gout and urate deposits in organs. Notably, similar symptoms have emerged in ducks. From 2023 to 2024, 126 liver samples were collected from ducks in Guangdong Province, where farms reported emaciation, paralysis, and deaths. Metagenomic analysis pinpointed GAstV as the primary pathogen, with a 43.65 % confirmed positive rate via qPCR. A new strain, GD2406, was identified, showing 97.5 %-98.8 % similarity to 30 GAstV-2 strains in GenBank. GD2406 displayed 98.3 % and 97.7 % identity with the duck strains HNNY0620 and SDTA, and 98.3 % and 98.4 % identity with highly virulent GAstV strains HNKF-1 and HNSQ-6. Phylogenetic analysis indicated a genetic closeness between GD2406 and the goose strain HB01. There were 13 amino acid mutations, mainly within ORF2, and a single mutation differing from HNKF-1 and HNSQ-6, hinting at significant pathogenic potential for both ducks and geese. This study is the first to report GAstV causing severe symptoms and mortality in Muscovy ducks in Guangdong Province, suggesting ducks could be key hosts and underscoring the risk of cross-species transmission.},
}

@article {pmid40147421,
year = {2025},
author = {Goswami, P and Ji, R and Shen, J and Roberts, AP and Lin, W},
title = {Genomic and metabolic characterisation of a novel species Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov. from an acidic peatland.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {3},
pages = {126605},
doi = {10.1016/j.syapm.2025.126605},
pmid = {40147421},
issn = {1618-0984},
abstract = {Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe3O4) and/or greigite (Fe3S4) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the Nitrospirota phylum (previously known as the Nitrospirae phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce Magnetominusculus dajiuhuensis DJH-1[Ts], a newly discovered Nitrospirota MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus Magnetominusculus, family Magnetobacteriaceae, order Thermodesulfovibrionales, class Thermodesulfovibrionia according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of Magnetominusculus dajiuhuensis DJH-1[Ts] provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.},
}

@article {pmid40147302,
year = {2025},
author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD},
title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.},
journal = {Water research},
volume = {280},
number = {},
pages = {123511},
doi = {10.1016/j.watres.2025.123511},
pmid = {40147302},
issn = {1879-2448},
abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.},
}

@article {pmid40147232,
year = {2025},
author = {Wang, J and Ge, Y},
title = {Unveiling the latitudinal dependency of global patterns in soil prokaryotic gene content.},
journal = {The Science of the total environment},
volume = {974},
number = {},
pages = {179224},
doi = {10.1016/j.scitotenv.2025.179224},
pmid = {40147232},
issn = {1879-1026},
abstract = {Prokaryotic genomic traits offer insights into their functional roles, evolutionary processes, and ecological interactions, but global patterns in soil microbial genomes remain poorly understood. In this study, we examined 6436 metagenome-assembled genomes (MAGs) from global soil environments to explore the driving factors of prokaryotic gene content. Through random forest analysis, we found that, among numerous potential influencing factors such as climate, soil physicochemical properties, and human activities, geographic latitude was the primary factor affecting prokaryotic gene content. Our results showed a marked decrease in gene content from the tropics to the poles, with polar MAGs containing 10.4 % and 13.3 % fewer genes than those in tropical and temperate zones, respectively. This decline correlates with shifts in key metabolic processes, such as nitrogen fixation and energy conversion. Furthermore, we assessed interspecies metabolic interactions using Metabolic Resource Overlap (MRO) and Metabolic Interaction Potential (MIP) metrics. Our analysis revealed significantly lower MRO in high-latitude microbial communities, yet comparable MIP values to those in lower latitudes, indicating that reduced competition may contribute to genomic streamlining. These findings highlight the significant influence of latitude and interspecies interactions on microbial genomic characteristics, advancing our comprehension of microbial ecological adaptations.},
}

@article {pmid38630846,
year = {2024},
author = {Phan, HV and Tsitsiklis, A and Maguire, CP and Haddad, EK and Becker, PM and Kim-Schulze, S and Lee, B and Chen, J and Hoch, A and Pickering, H and van Zalm, P and Altman, MC and Augustine, AD and Calfee, CS and Bosinger, S and Cairns, CB and Eckalbar, W and Guan, L and Jayavelu, ND and Kleinstein, SH and Krammer, F and Maecker, HT and Ozonoff, A and Peters, B and Rouphael, N and , and Montgomery, RR and Reed, E and Schaenman, J and Steen, H and Levy, O and Diray-Arce, J and Langelier, CR},
title = {Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.},
journal = {Science translational medicine},
volume = {16},
number = {743},
pages = {eadj5154},
pmid = {38630846},
issn = {1946-6242},
support = {U19 AI090023/AI/NIAID NIH HHS/United States ; U19 AI118608/AI/NIAID NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; S10 OD026880/OD/NIH HHS/United States ; U19 AI077439/AI/NIAID NIH HHS/United States ; U19 AI118610/AI/NIAID NIH HHS/United States ; U19 AI167891/AI/NIAID NIH HHS/United States ; U19 AI167903/AI/NIAID NIH HHS/United States ; U19 AI128913/AI/NIAID NIH HHS/United States ; R01 AI132774/AI/NIAID NIH HHS/United States ; S10 OD030463/OD/NIH HHS/United States ; R01 AI135803/AI/NIAID NIH HHS/United States ; U19 AI089992/AI/NIAID NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; U19 AI128910/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Aged ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged, 80 and over ; *COVID-19 ; SARS-CoV-2 ; Prospective Studies ; Multiomics ; Chemokines ; },
abstract = {Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.},
}

Humans
Aged
Adolescent
Young Adult
Adult
Middle Aged
Aged, 80 and over
*COVID-19
SARS-CoV-2
Prospective Studies
Multiomics
Chemokines

@article {pmid40146796,
year = {2025},
author = {Li, J and Zhu, Y and Chang, Q and Gong, Y and Wan, J and Xu, S},
title = {Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.},
journal = {Polish journal of microbiology},
volume = {74},
number = {1},
pages = {71-81},
doi = {10.33073/pjm-2025-006},
pmid = {40146796},
issn = {2544-4646},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; Middle Aged ; Female ; *Bacteria/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Aged ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; },
abstract = {Alteration of the gut microbiota (GM) is associated with various diseases, including colorectal cancer (CRC). With the development of next-generation sequencing techniques, metagenomic sequencing, along with metabolic function and antibiotic-resistant gene analyses, has been used to investigate differences in GM between CRC patients and healthy controls. Fecal samples were obtained from seven CRC patients and six healthy subjects, and the sequencing data were analyzed for similarity, a-diversity, principal component analysis (PCA), and linear discriminant analyses (LDA). Regarding Actinobacteria, 3 orders, 5 families, 9 genera, and 19 species were identified with no differences between the CRC and control groups, while the levels of Bifidobacterium bifidum and Bifidobacterium dentium were higher, and the level of Bifidobacterium breve was lower in the CRC group compared to the healthy controls (p = 0.053). Otherwise, 2 genera (Leuco-nostoc and Salmonella) and 7 species of bacteria (Parabacteroides merdae, Alistipes shahii, Alistipes finegoldii, Clostridium nexile, Salmonella enterica, unclassified Salmonella, Enterobacter cloacae) were found to be significantly differently distributed between CRC patients and healthy controls. PCA-LDA successfully classified these 2 groups with satisfactory accuracy (84.52% for metabolic function and 77.38% for resistant genes). These findings underscore the potential of GM as a diagnostic tool for CRC, offering a promising avenue for non-invasive screening and risk assessment. The identification of specific microbial signatures, particularly those linked to metabolic functions and resistance traits, could open new doors for understanding the role of the microbiome in CRC progression and treatment resistance.},
}

Humans
*Colorectal Neoplasms/microbiology
Male
Middle Aged
Female
*Bacteria/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
Feces/microbiology
Aged
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Adult

@article {pmid40146759,
year = {2025},
author = {Guan, Y and Guo, H and Xia, D and Liu, Y and Wang, X},
title = {Migration of heavy metals and microbial metabolic regulation mechanisms in the co-fermentation of coal slime and sawdust.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/09593330.2025.2482966},
pmid = {40146759},
issn = {1479-487X},
abstract = {Heavy metals (HMs) significantly affect the anaerobic fermentation of coal slime (CS), while sawdust serves as a promising substrate for methane bioconversion and an effective adsorbent for HMs. To explore the migration of HMs and improve the conversion efficiency of CS and sawdust to biomethane, experiments were conducted on the co-fermentation of CS and sawdust with different mass ratios. FT-IR, ICP-MS, SEM-EDS, and metagenomic sequencing were employed to elucidate the regulation mechanism of microorganisms after adding sawdust in altering the toxicological environment. The results revealed that the optimum mass ratio of CS to sawdust was 2:1. Oxygen-containing functional groups in CS were removed, and the fatty structure was degraded. Addition of sawdust promoted the further degradation of CS and migration of various HMs. Metal elements such as Fe, Mg, Co, and Cd had also been detected on its surface. Bacillota (39.05%) was significantly enriched, which effectively improved the microbial community structure. The abundance of species with metal detoxification functions increased. The types and abundance of transporters related to toxic metal ions increased in families such as ATP-binding Cassette Superfamily (ABC) and Resistance-Nodulation-Cell Division Superfamily (RND), which would further aid in cellular homeostasis. Moreover, the addition of sawdust promoted the expression of metal resistance genes (MRGs). Multi-MRGs were primarily linked to Cu, As, and Zn, with an increased abundance of bacterial species contributing to key MRGs such as copA, ziaA, and actP. These findings offer valuable insights that support the clean and efficient utilization of CS and sawdust.},
}

@article {pmid40145240,
year = {2025},
author = {Zhou, Y and Oba, K and Xu, T and Kuroiwa, M and Hori, T and Terada, A},
title = {Actively N2O-Reducing Oxygen-Tolerant Microbial Consortium Attained by Using a High-Dilution-Rate Chemostat Fed with Methanol.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12732},
pmid = {40145240},
issn = {1520-5851},
abstract = {Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB consortium under intermittent oxygen and N2O supplies. [15]N tracer analysis showed that the N2O consumption activity of the enriched consortium was higher than its N2O production activity in the presence of either a single or multiple electron acceptors (i.e., nitrogen oxides). The observed maximum N2O consumption was 80.7 μmol·g-biomass[-1]·h[-1]. Quantitative PCR results showed that clade I nosZ bacteria overwhelmed clade II nosZ bacteria at high (0.41 mmol·min[-1]) and low (0.08 mmol·min[-1]) N2O loading rates. The dilution rate and N2O loading rate affected the microbial community composition and activity. A higher N2O loading rate stimulated active and oxygen-tolerant N2ORB that boosted N2O consumption by approximately 50% in the presence of oxygen. Metagenomic analysis unraveled the predominance of a novel methylotrophic N2ORB, possessing entire denitrifying genes and high-affinity terminal oxidase genes, from the reactor with a high N2O loading rate. The unique physiological traits of the consortium enriched by methanol shed light on a novel function─aerobic N2O consumption by N2ORB─and pave the way for innovative N2O mitigation strategies applying powerful N2O sinks in engineered systems.},
}

@article {pmid40144527,
year = {2025},
author = {Wang, J and Ren, W and Sun, Z and Liu, S and Han, Z and Wang, Y and Zeng, Y and Meng, J and Yao, X},
title = {Impact of intragastric administration of donkey milk on mouse immunity utilizing gut microbiomics and plasma metabolomics.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1486406},
pmid = {40144527},
issn = {2297-1769},
abstract = {INTRODUCTION: Donkey milk demonstrates closer compositional resemblance to human milk compared to bovine milk, positioning it as an optimal nutritional substitute for infants with cow's milk allergy. Furthermore, its rich profile of bioactive compounds suggests potential immunomodulatory properties. This study systematically investigated the effects of donkey milk supplementation on murine immune function and gut microbiome dynamics, thereby providing mechanistic insights to support its clinical development in functional food applications.

METHODS: Following daily intragastric administration of 10 mL/kg of body weight of donkey milk (DM) or distilled water (DW) to the mice for 28 consecutive days, liver tissues were harvested for immunological profiling, with concurrent collection of blood samples for plasma metabolomic analysis and fecal specimens for gut microbiome characterization. Subsequently, the modulatory effects of donkey milk supplementation on immune parameters, intestinal microbiota composition, and plasma metabolic profiles were systematically evaluated.

RESULTS: Immunity analysis revealed that intragastric administration of DM raised the levels of IL-6 and TNF-α cytokines in mouse liver. In addition, DM modulated the composition of both the murine gut microbiome and plasma metabolites. One-hundred and forty-five differentially-produced metabolites were identified, most prominently nicotinamide, L-valine, and β-estradiol, that are primarily associated with valine, leucine, and isoleucine biosynthesis and degradation, nicotinate and nicotinamide metabolism, and unsaturated fatty acid biosynthesis. Alterations at phylum, genus, and species levels were evident in the fecal microbiota of mice after intragastric administration of DM. In particular, an increased abundance of the Lactobacillus bacterium was observed. Correlation analysis of differential metabolites and microbiomes indicated a correspondence between Falsiroseomonas and Salipiger species and the antioxidant coenzyme Q that has the potential to activate the immune system.

CONCLUSION: The data collectively suggest that DM may adjust the murine gut microbiome and plasma metabolites thereby potentially improving immunity in mice.},
}

@article {pmid40144403,
year = {2025},
author = {Li, Z and Zou, D and Liu, R and Pan, J and Huang, J and Ma, J and Huang, L and He, J and Fu, L and Zheng, X and Wang, M and Fang, J and Dong, H and Li, M and Huang, L and Dai, X},
title = {A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf042},
pmid = {40144403},
issn = {2730-6151},
abstract = {Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.},
}

@article {pmid40143870,
year = {2025},
author = {Hu, Y and Zhou, J and Lin, X},
title = {Akkermansia muciniphila helps in the recovery of lipopolysaccharide-fed mice with mild intestinal dysfunction.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1523742},
pmid = {40143870},
issn = {1664-302X},
abstract = {BACKGROUND: Mild intestinal dysfunction, linked to subtle yet significant health issues, can be induced by lipopolysaccharide (LPS), a Gram-negative bacterial component that disrupts gut function and triggers inflammation. Akkermansia muciniphila has shown promise as a probiotic for gut health due to its roles in mucin degradation and short-chain fatty acid production. This study explores the therapeutic effects of Akkermansia muciniphila on LPS-induced mild intestinal dysfunction in mice.

METHODS: Thirty-eight 6-week-old C57BL/6 mice were split into control (n = 19) and LPS-treated (n = 19) groups. LPS-treated mice received 300 μg/kg/day of LPS for 4 weeks, followed by Akkermansia muciniphila supplementation at 41 mg/kg/day (Akk1) or 82 mg/kg/day (Akk2) for another 4 weeks. Gut microbiota was analyzed via metagenomic sequencing, and gene expression was evaluated through transcriptomics.

RESULTS: LPS significantly altered gut microbiota, reducing diversity and increasing pathogenic genera like Lachnoclostridium. Akkermansia muciniphila supplementation, particularly at higher doses, partially restored gut microbiota by increasing beneficial genera such as Muribaculum. Transcriptomics showed that LPS induced immune and inflammatory responses, while Akkermansia muciniphila reduced these effects by modulating pathways like TNF and NF-kappa B signaling.

CONCLUSION: Akkermansia muciniphila mitigates LPS-induced gut dysfunction by restoring microbiota balance and modulating immune responses, highlighting its potential as a therapeutic agent for gut health.},
}

@article {pmid40143862,
year = {2025},
author = {Sujatha, S and Sindhura, KAV and Koti, PS and Hiremath, S and Muttappagol, M and Vinay Kumar, HD and Shankarappa, KS and Venkataravanappa, V and Reddy, KMS and Reddy, CNL},
title = {Influence of weather and seasonal factors on whitefly dynamics, associated endosymbiotic microbiomes, and Begomovirus transmission causing tomato leaf curl disease: insights from a metagenomic perspective.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1555058},
pmid = {40143862},
issn = {1664-302X},
abstract = {INTRODUCTION: Bemisia tabaci (Gennadius) is a globally significant agricultural pest, responsible for transmitting over 120 plant viruses, including those from the Begomovirus genus, which contribute to considerable crop losses. The species complex comprises cryptic species, associated with a diverse array of bacterial endosymbionts that play essential roles in host nutrition, virus transmission, and overall host adaptability. These endosymbionts are classified into primary and secondary categories, with primary endosymbionts forming obligatory, long-term associations, and secondary endosymbionts influencing factors such as biotype differentiation and vector competency. Notably, these microbial communities enhance B. tabaci's capacity to transmit viruses, including the tomato leaf curl virus (ToLCuV), which poses a significant threat to tomato production.

METHODS: In this study, we examined the population dynamics of B. tabaci across three major tomato-growing regions in Karnataka, South India, focusing on their seasonal associations with endosymbionts and the incidence of tomato leaf curl disease (ToLCuD). Multiple regression analysis was employed to assess the influence of weather parameters on whitefly populations and disease prevalence. Additionally, we constructed a metagenomic profile to evaluate the effects of geographical location, seasonality, environmental factors, and agricultural practices on the bacterial communities associated with B. tabaci. Species-specific primers were used to validate the presence and diversity of these bacterial communities.

RESULTS: Meteorological data revealed a positive correlation between temperature and B. tabaci populations, which corresponded with an increased incidence of ToLCuD. Genetic characterization of the whitefly identified Asia II-5 and Asia II-7 cryptic species as the dominant forms in the surveyed regions, with Portiera emerging as the most prevalent endosymbiont. A more in-depth analysis of the microbial communities associated with B. tabaci, utilizing 16S rRNA metagenomic sequencing, revealed a dominance of the Proteobacteria phylum. The endosymbiotic bacterial consortium was primarily composed of Candidatus Portiera, Candidatus Hamiltonella, Candidatus Rickettsia, and Candidatus Arsenophonus.

DISCUSSION: The metagenomic analysis revealed a highly diverse array of bacterial communities, with 92% of sequences classified under Proteobacteria, representing a spectrum of microbial types associated with B. tabaci ranging from parasitic and pathogenic to mutualistic. Within this phylum, Alphaproteobacteria were predominant, known for their role as facultative symbionts, while Gammaproteobacteria provided essential nutrients to arthropods, enhancing their survival and fitness. The interplay of continuous and intensive tomato cultivation, elevated temperatures, favorable host plants, and abundant viral inoculum creates an ideal environment for the proliferation of B. tabaci and the widespread transmission of ToLCuD. The presence of diverse cryptic species of B. tabaci, which are efficient viral vectors, further complicates the situation. These findings underscore the urgent need for integrated management strategies globally to control both whitefly populations and ToLCuD, ensuring the protection of tomato crops and the sustainability of farmer livelihoods.},
}

@article {pmid40143285,
year = {2025},
author = {Popov, N and Sonets, I and Evdokimova, A and Molchanova, M and Panova, V and Korneenko, E and Manolov, A and Ilina, E},
title = {AliMarko: A Pipeline for Virus Identification Using an Expert-Guided Approach.},
journal = {Viruses},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/v17030355},
pmid = {40143285},
issn = {1999-4915},
support = {122030900069-4//Russian State/ ; },
mesh = {*Phylogeny ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; *Feces/virology ; Animals ; *Genome, Viral ; Humans ; Metagenome ; Chiroptera/virology ; Computational Biology/methods ; Software ; Sequence Analysis, RNA/methods ; },
abstract = {Viruses are ubiquitous across all kingdoms of cellular life, posing a significant threat to human health, and analyzing viral communities is challenging due to their genetic diversity and lack of a single, universally conserved marker gene. To address this challenge, we developed the AliMarko pipeline, a tool designed to streamline virus identification in metagenomic data. Our pipeline uses a dual approach, combining mapping reads with reference genomes and a de novo assembly-based approach involving an HMM-based homology search and phylogenetic analysis, to enable comprehensive detection of viral sequences, including low-coverage and divergent sequences. We applied our pipeline to total RNA sequencing of bat feces and identified a range of viruses, quickly validating viral sequences and assessing their phylogenetic relationships. We hope that the AliMarko pipeline will be a useful resource for the scientific community, facilitating the interpretation of viral communities and advancing our understanding of viral diversity and its impact on human health.},
}

*Phylogeny
*Metagenomics/methods
*Viruses/genetics/classification/isolation & purification
*Feces/virology
Animals
*Genome, Viral
Humans
Metagenome
Chiroptera/virology
Computational Biology/methods
Software
Sequence Analysis, RNA/methods

@article {pmid40143275,
year = {2025},
author = {Sarana da Silva, A and de Campos, GM and Altizani, GM and de Carvalho, E and Barros, AC and Cella, E and Kashima, S and Sampaio, SC and Elias, MC and Giovanetti, M and Scrideli, CA and Slavov, SN},
title = {Utilizing Viral Metagenomics to Characterize Pathogenic and Commensal Viruses in Pediatric Patients with Febrile Neutropenia.},
journal = {Viruses},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/v17030345},
pmid = {40143275},
issn = {1999-4915},
support = {17/23205-8; 21/11944-6; 2022/10278-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 403075/2023-8; 305111/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Humans ; *Metagenomics/methods ; Child ; Male ; Female ; Child, Preschool ; *Febrile Neutropenia/virology ; Adolescent ; Viruses/classification/genetics/isolation & purification ; Infant ; Herpesviridae/genetics/classification/isolation & purification ; Oropharynx/virology ; Neoplasms/virology/complications ; Metagenome ; },
abstract = {Febrile neutropenia (FN) is one of the most common complications in pediatric oncology patients. It has a complex etiologic nature, which in the majority of cases remains unclear. Intervention often follows empirical treatment protocols, mainly using broad-spectrum antibiotics. To evaluate potential viral etiologic agents, this study applied viral metagenomics to paired plasma and oropharyngeal samples obtained from pediatric patients with oncological diseases diagnosed with FN. Metagenomic sequencing was performed on 15 pediatric patients with oncological diseases and FN at the outpatient clinic of Pediatric Oncology at the University Hospital of the Faculty of Medicine of Ribeirão Preto, University of São Paulo. As a control group, we included 15 pediatric patients with oncological diseases in remission or undergoing treatment. Clinically relevant viruses identified by metagenomics in FN patients predominantly included herpesviruses and viruses found in the respiratory tract, like adenoviruses. Direct molecular confirmation was performed on all of them. Anelloviruses, represented by various genera and species in all groups, were also highly prevalent. The data obtained in this study show that viruses might also have possible implications for the etiology of FN. However, due to the complex nature of this disease, more studies are necessary to evaluate their causal relationship. The results obtained in our study may serve to improve patient treatment and ensure adequate management.},
}

Humans
*Metagenomics/methods
Child
Male
Female
Child, Preschool
*Febrile Neutropenia/virology
Adolescent
Viruses/classification/genetics/isolation & purification
Infant
Herpesviridae/genetics/classification/isolation & purification
Oropharynx/virology
Neoplasms/virology/complications
Metagenome

@article {pmid40142589,
year = {2025},
author = {Chen, X and Gao, L and Kou, Y and Wang, X and Li, X and He, H and Wang, M},
title = {Composition, Distribution and Mobility Potential of the Antibiotic Resistome in Sediments from the East China Sea Revealed by Metagenomic Analysis.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030697},
pmid = {40142589},
issn = {2076-2607},
support = {41806131//National Natural Science Foundation of China/ ; 42120104006//National Natural Science Foundation of China/ ; ZR2024QD036//Natural Science Foundation of Shandong Province/ ; },
abstract = {Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the antibiotic resistome in these sediments using metagenomic analysis. Overall, we detected eighty ARG subtypes and nineteen ARG types. Beta-lactams were the dominant ARG type, and Gammaproteobacteria was the main ARG host in this study. Mobile genetic elements (MGEs) were not major drivers of ARG profiles. Although the ARG host communities significantly differed between the spring and autumn (p < 0.05), the antibiotic resistome remained stable across the two seasons. The assembly of ARGs and their hosts was governed by stochastic processes, and a high ratio of stochastic processes implied its crucial role in the assembly and stabilization of the antibiotic resistome. Co-occurrence network analysis revealed an important role of Deltaproteobacteria in the stabilization of ARG profiles across seasons. Environmental parameters (e.g., temperature and density) played certain roles in the stabilization of the antibiotic resistome between spring and autumn. Moreover, nine human pathogen bacteria (HPB) were detected in this study. We also found that the health risks caused by ARGs were relatively higher in the spring. Our results will provide a strong foundation for the development of targeted management strategies to mitigate the further dissemination and spread of ARGs in marine sediments.},
}

@article {pmid40142582,
year = {2025},
author = {Peng, Y and Jiang, L and Wu, J and Yang, J and Guo, Z and Miao, M and Peng, Z and Chang, M and Miao, B and Liu, H and Liang, Y and Yin, H and He, Q and Liu, X},
title = {Red Mud Potentially Alleviates Ammonia Nitrogen Inhibition in Swine Manure Anaerobic Digestion by Enhancing Phage-Mediated Ammonia Assimilation.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030690},
pmid = {40142582},
issn = {2076-2607},
support = {Grant No. 2018YFC1800400//the National Key Research and Development Program of China/ ; Grant No. 51909282//the National Natural Science Foundation of China/ ; Grant No. 2022JJ40583//the Natural Science Foundation of Hunan Province of China/ ; Grant No. 2022WK2017//the Hunan Provincial Key Research and Development Plan/ ; Grant No. 2023NK2030//the Hunan Provincial Key Research and Development Plan/ ; },
abstract = {Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria-phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure.},
}

@article {pmid40142572,
year = {2025},
author = {Yi, Q and Zhang, G and Wang, T and Li, J and Kang, W and Zhang, J and Liu, Y and Xu, Y},
title = {Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030682},
pmid = {40142572},
issn = {2076-2607},
support = {2022-PUMCH-B-074//National High Level Hospital Clinical Research Funding/ ; },
abstract = {Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens.},
}

@article {pmid40142491,
year = {2025},
author = {Kioukis, A and Camargo, AP and Pavlidis, P and Iliopoulos, I and Kyrpides, NC and Lagkouvardos, I},
title = {Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030598},
pmid = {40142491},
issn = {2076-2607},
support = {710//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; },
abstract = {The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the 'Global Archaea Diversity' (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.},
}

@article {pmid40142462,
year = {2025},
author = {Hadian, S and Smith, DL and Supronienė, S},
title = {Modulating the Plant Microbiome: Effects of Seed Inoculation with Endophytic Bacteria on Microbial Diversity and Growth Enhancement in Pea Plants.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030570},
pmid = {40142462},
issn = {2076-2607},
abstract = {Understanding plant microbe interactions is crucial for achieving sustainable agriculture. This study investigated the effects of inoculating pea plants (Pisum sativum) with two endophytic Bacillus strains, AR11 and AR32, isolated from Artemisia species and characterized by phosphate solubilization, nitrogen fixation, and pathogen antagonism. Utilizing cutting-edge methods such as rarefaction curves, rank abundance modeling, and metagenomic analysis, this research provides a detailed understanding of how these bacterial strains influence plant associated microbiomes. AR11 significantly enhanced microbial diversity, while AR32 showed a moderate effect. Beta diversity analyses revealed distinct shifts in microbial community composition, with AR11-treated samples enriched with beneficial taxa such as Paenibacillus, Flavobacterium, and Methylotenera, known for their roles in nutrient cycling, pathogen suppression, and plant health promotion. This innovative methodological framework surpasses traditional approaches by offering a comprehensive view of ecological and functional microbiome shifts. The study highlights the potential of nonhost bacteria as biostimulants and their role in developing microbiome engineering strategies to enhance plant resilience. These findings contribute to sustainable agriculture by demonstrating how microbial inoculants can be employed to enhance crop productivity and environmental resilience in diverse agricultural systems.},
}

@article {pmid40142456,
year = {2025},
author = {Zhu, S and Guo, Z and Liu, L and Gao, Y and Bai, L and Chen, Y and Zha, M},
title = {Complex Probiotics Relieve Constipation Through Regulation of the Intestinal Microbiota in Kittens.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030563},
pmid = {40142456},
issn = {2076-2607},
support = {2024LHMS03043//The Natural Science Foundation of Inner Mongolia, China/ ; 2022 - Science and Technology Xing Meng - Quality improvement - 02//Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; SPYQ202001//The Cultivation Project for Excellent Youth of Inner Mongolia Agricultural University/ ; },
abstract = {The early developmental phase is a critical window for feline growth, during which immature digestive systems are susceptible to microbiome imbalances caused by environmental stressors. Our research employed macrogenomic analysis to evaluate how complex probiotic formulations influence growth metrics and gastrointestinal flora in juvenile felines. Two dozen healthy kittens were equally divided into the control group and the probiotics group following a 5-day environmental adaptation phase. Fecal scores were recorded daily for all kittens. Fresh fecal samples were collected on days 1 and 14 for macrogenomic analysis. The results showed a significantly lower rate of constipation in the probiotics group compared to the control group (p < 0.05). However, no significant differences were observed in intestinal microbial diversity or structure between the two groups. Metagenomic analysis revealed a higher relative abundance of Bifidobacterium animalis in the probiotics group compared to the control group (p < 0.05). Additionally, the probiotics group exhibited lower relative abundances of Lachnospiraceae bacterium 2 1 58FAA, Lachnospiraceae bacterium 1 1 57FAA, and Acidaminococcus intestini compared to the control group (p < 0.05). These results suggest that complex probiotics can regulate the intestinal microbiota, improve constipation, and promote intestinal health in kittens.},
}

@article {pmid40142431,
year = {2025},
author = {Aires, C and Maioto, R and Inês, A and Dias, AA and Rodrigues, P and Egas, C and Sampaio, A},
title = {Microbiome and Microbiota Within Wineries: A Review.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030538},
pmid = {40142431},
issn = {2076-2607},
abstract = {The main goal of this work is to review the winery's microbiota, from the grape to the winery's microbial niches (fermentation tanks, surfaces, air), and their risks to wine and human health. The impact of climate change on the winery microbiome and related challenges are also discussed. Microbial diversity in wineries depends on several factors, such as the grape variety and its ripeness, temperature, relative humidity and the diverse activities of the winemaking process. Winery surfaces and equipment allow the establishment of a microbial community that can impact wine quality, the health of winery workers and visitors and even wine consumers. In the context of climate change, changes in the sugar content, phenolic compounds and the profile of hexoses and amino acids are already evident. These changes interfere with the fermentation microbiota and the quality of the wines, which are more alcoholic and less acidic. Furthermore, periods of drought or heavy rain favor species associated with berry diseases, including some capable of producing mycotoxins or harmful biogenic amines. In order to understand the impact of these changes on microbial communities, the use of various techniques will be discussed, such as flow cytometry, fluorescence in situ hybridization (FISH), quantitative polymerase chain reaction (qPCR) and metagenomic methods.},
}

@article {pmid40142426,
year = {2025},
author = {Needle, DB and Reboul, G and Mitchell, PK and Rothenheber, D and Marra, NJ and Cronk, BD and Patel, NG and Goodman, LB},
title = {Application of Amplicon Metagenomics to Identify Fungal Pathogens in Formalin-Fixed Paraffin-Embedded Samples: Proof of Concept in Animals with Fungal Pathologies.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030533},
pmid = {40142426},
issn = {2076-2607},
support = {1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN)/ ; 1R03DE033304-01A1/NH/NIH HHS/United States ; },
abstract = {The identification of fungal pathogens in formalin-fixed paraffin-embedded (FFPE) tissues is an unmet need in human and animal medicine, and sequence-agnostic approaches are needed to identify emerging pathogens. Eleven FFPE biopsy specimens with etiologic diagnoses of fungal disease based on standard testing of paired fresh tissue samples were utilized here to evaluate metabarcoding approaches. The cases included tissues from three dogs, three cats, one box turtle, one goat, one common loon, and one gray tree frog. The diagnoses from the fresh tissues in these cases were Microsporum canis, Penicillium sp., Exophiala sp. (likely E. jeanselmei), Verticillium sp., Rhizopus sp., atypical Cryptococcus neoformans, Conidiobolus spp., Aspergillus fumigatus, Cryptococcus neoformans var grubii, Batrachochytrium dendrobatidis, Fusarium solani, Blastomyces dermatitidis, Coccidiodes immitis, and Histoplasma capsulatum. We compared the ITS1 and 28S D1 rRNA gene genetic markers in combination with several bioinformatic strategies to identify fungal pathogens in the FFPE tissue samples, with a success rate of 9/11. These methods could allow diagnosticians who receive only FFPE tissues and see fungal pathogens to speciate the pathogens and could be of value in retrospective studies wherein FFPE tissue is the only archived tissue. Furthermore, these techniques could be of use to researchers investigating polymicrobial communities where DNA preservation is suboptimal.},
}

@article {pmid40142417,
year = {2025},
author = {Chao, S and Chen, Y and Wu, J and Zhang, Y and Song, L and Li, P and Sun, Y and Hu, Y and Wang, H and Jiang, Y and Lv, B},
title = {Exserohilum turcicum Alters Phyllosphere Microbiome Diversity and Functions-Implications for Plant Health Management.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030524},
pmid = {40142417},
issn = {2076-2607},
support = {2024-02-08-00-12-F00021//Shanghai Agriculture Applied Technology Development Program, China/ ; 32302635//National Natural Science Foundation of China/ ; 22ZR1442500//Natural Science Foundation of Shanghai/ ; SAAS Application Basic Study 2025(08)//2025 SAAS Project on Agricultural Science and Technology Innovation Supporting Area/ ; 016//Shanghai Academy of Agricultural Sciences 2022/ ; 20DZ2255300//Shanghai Engineering Research Center of Specialty Maize/ ; 2023ZD04062//the Science and Technology Innovation 2030 Biological Breeding-Major Projects/ ; 23DZ2290700//Shanghai "Science and Technology Innovation Action Plan" Professional Technical Service Platform Project/ ; },
abstract = {The phyllosphere represents the largest biological surface on Earth and serves as an untapped reservoir of functional microbiota. The phyllosphere microbiome has the potential to mitigate plant diseases; however, limited information exists regarding its role in maintaining plant health. In this study, metagenomic sequencing was employed to analyze the microbiomes of the adaxial and abaxial leaf surfaces of healthy (CKWT) and diseased (EWT) maize, with the aim of dissecting the influence of Exserohilum turcicum on phyllosphere microbiome function. E. turcicum altered the alpha and beta diversity of the phyllosphere microbiome, with the Shannon diversity and Chao1 index values significantly reduced in EWT. More beneficial microbes accumulated in the CKWT phyllosphere, whereas pathogenic microbes decreased. E. turcicum may have altered the balance between commensal and pathogenic microorganisms. The species and abundances of microorganisms on the two sets of leaf surfaces were also altered after inoculation with E. turcicum. Further analysis of disease-resistance-related metabolic pathways and abundances of antibiotic-resistance genes revealed that E. turcicum altered the abundance of the functional microbiome and modified the microbiome differences between adaxial and abaxial leaf surfaces. In conclusion, the results reveal that microbial diversity in the maize phyllosphere can influence the microbiome and regulate microbial functions to support plant health. These findings enhance our understanding of how E. turcicum affects the phyllosphere microbiome and provide a theoretical basis for biological control of E. turcicum.},
}

@article {pmid40142410,
year = {2025},
author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL},
title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030518},
pmid = {40142410},
issn = {2076-2607},
support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; },
abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).},
}

@article {pmid40141768,
year = {2025},
author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM},
title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/life15030423},
pmid = {40141768},
issn = {2075-1729},
support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; },
abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.},
}

@article {pmid40140988,
year = {2025},
author = {Yan, Q and Huang, L and Li, S and Zhang, Y and Guo, R and Zhang, P and Lei, Z and Lv, Q and Chen, F and Li, Z and Meng, J and Li, J and Wang, G and Chen, C and Ullah, H and Cheng, L and Fan, S and You, W and Zhang, Y and Ma, J and Sha, S and Sun, W},
title = {The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {30},
pmid = {40140988},
issn = {1756-994X},
mesh = {Humans ; *Virome/genetics ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; China ; Female ; Feces/virology ; Male ; Metagenomics/methods ; Genome, Viral ; Asian People/genetics ; East Asian People ; },
abstract = {BACKGROUND: The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.

METHODS: In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.

RESULTS: The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.698) and high-risk patients from controls (AUC = 0.761), and its predictive ability was also validated in external cohorts.

CONCLUSIONS: Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.},
}

Humans
*Virome/genetics
*Viruses/genetics/classification
*Gastrointestinal Microbiome/genetics
*Metagenome
China
Female
Feces/virology
Male
Metagenomics/methods
Genome, Viral
Asian People/genetics
East Asian People

@article {pmid40140753,
year = {2025},
author = {Yan, Z and Wang, Y and Zeng, W and Hui, J and Yang, B and Xu, J and Miao, Y and Xia, R},
title = {Antibiotic-driven pathogen replacement events in a kidney transplant recipient with ADPKD: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {423},
pmid = {40140753},
issn = {1471-2334},
support = {82270784//National Natural Science Foundation of China/ ; 2023A1515012276//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2024CL-GX03//Clinical High-tech and Major Technology Projects in Guangzhou Area/ ; },
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Polycystic Kidney, Autosomal Dominant/complications/surgery ; *Anti-Bacterial Agents/therapeutic use ; Male ; Transplant Recipients ; Middle Aged ; Nephrectomy ; Enterococcus faecium/isolation & purification/drug effects ; },
abstract = {BACKGROUND: Retaining the native bilateral kidneys after transplantation is a common treatment for patients with end-stage autosomal dominant polycystic kidney disease. However, this strategy poses the risks of potential complications from polycystic kidney infection. The efficiency of antibiotic therapy and the optimal time for native nephrectomy in managing these infections remain uncertain.

CASE PRESENTATION: We report a case of a kidney transplant recipient with retained bilateral polycystic kidneys who experienced recurrent cyst and bloodstream infections, accompanied by antibiotic-driven pathogen replacement. After multiple failed attempts at antibiotic therapy, the patient subsequently underwent unilateral polycystic kidney resection. Subsequently, a new infection episode occurred, leading to the other native nephrectomy. Cystic tissue and fluid samples were collected from both shallow and deep layers of the polycystic kidneys, along with peripheral blood and urine samples. These samples were analyzed using microbial culture, metagenome sequencing, and digital polymerase chain reaction to identify infectious pathogens. Pathogen replacement occurred across different infection episodes, with the dominant bacterial species being Escherichia coli, Klebsiella aerogenes, and Enterococcus faecium, in succession.

CONCLUSIONS: This case highlights the replacement of dominant pathogens under antibiotic selection pressure in polycystic kidney infections, primarily involving gram-negative bacilli. When initial and subsequent antibiotic therapy fail, re-evaluation of the cyst infection definition is necessary, and preemptive native nephrectomy should be considered.},
}

Humans
*Kidney Transplantation/adverse effects
*Polycystic Kidney, Autosomal Dominant/complications/surgery
*Anti-Bacterial Agents/therapeutic use
Male
Transplant Recipients
Middle Aged
Nephrectomy
Enterococcus faecium/isolation & purification/drug effects

@article {pmid40140741,
year = {2025},
author = {Zhao, X and Liu, X and Wang, Z and Wei, S and Wu, Z},
title = {Metagenomic next-generation sequencing for the diagnosis of Corynebacterium striatum meningitis: case report and literature review.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {127},
pmid = {40140741},
issn = {1471-2377},
support = {20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; 20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; 20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; [2023]14-73//Shanxi Provincial Department of Education/ ; },
mesh = {Humans ; Male ; Aged ; *Corynebacterium/isolation & purification/genetics ; *Corynebacterium Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Meningitis, Bacterial/diagnosis/drug therapy/microbiology ; },
abstract = {OBJECTIVE: To report a case of Corynebacterium striatum meningitis and conduct a comprehensive literature review to determine the clinical presentation, microbiology, and treatment approaches for these patients.

MATERIALS AND METHODS: A 75-year-old male patient presented with headache and fever; however, bacterial cultures of cerebrospinal fluid (CSF) yielded negative results. Metagenomic next-generation sequencing (mNGS) of CSF subsequently identified Corynebacterium striatum meningitis as the causative agent for meningitis. A systematic search was performed across various databases encompassing systematic reviews, cohort studies, case series, and case reports involving patients diagnosed with Corynebacterium striatum meningitis regardless of age. Clinical presentation characteristics and the most frequently employed diagnostic technologies were obtained. A narrative summary of the findings is presented.

RESULTS: Corynebacterium striatum meningitis patients do not exhibit any specific age or sex predisposition or distinctive symptoms or signs. In patients with Corynebacterium striatum meningitis, CSF tests typically reveal an increased number of white blood cells (predominantly polymorphonuclear cells), elevated protein levels, and decreased glucose levels. Notably, the prevalence of antibiotic-resistant strains of Corynebacterium striatum has increased in recent years, leading to a gradual rise in antibiotic treatment failure rates. It is predicted that by 2030, vancomycin may be the sole effective drug available.

CONCLUSION: The possibility of Corynebacterium striatum infection should be considered during clinical diagnosis and laboratory testing procedures for bacterial meningitis. mNGS can serve as a supplementary gold standard in the diagnosis of bacterial meningitis, effectively enhancing the detection rate of rare pathogens.},
}

Humans
Male
Aged
*Corynebacterium/isolation & purification/genetics
*Corynebacterium Infections/diagnosis/microbiology/drug therapy
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Meningitis, Bacterial/diagnosis/drug therapy/microbiology

@article {pmid40140706,
year = {2025},
author = {Best, L and Dost, T and Esser, D and Flor, S and Gamarra, AM and Haase, M and Kadibalban, AS and Marinos, G and Walker, A and Zimmermann, J and Simon, R and Schmidt, S and Taubenheim, J and Künzel, S and Häsler, R and Franzenburg, S and Groth, M and Waschina, S and Rosenstiel, P and Sommer, F and Witte, OW and Schmitt-Kopplin, P and Baines, JF and Frahm, C and Kaleta, C},
title = {Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40140706},
issn = {2058-5276},
support = {859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; FOR5042//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 416 418087534//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Aging is accompanied by considerable changes in the gut microbiome, yet the molecular mechanisms driving aging and the role of the microbiome remain unclear. Here we combined metagenomics, transcriptomics and metabolomics from aging mice with metabolic modelling to characterize host-microbiome interactions during aging. Reconstructing integrated metabolic models of host and 181 mouse gut microorganisms, we show a complex dependency of host metabolism on known and previously undescribed microbial interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome accompanied by reduced beneficial interactions between bacterial species. These changes coincided with increased systemic inflammation and the downregulation of essential host pathways, particularly in nucleotide metabolism, predicted to rely on the microbiota and critical for preserving intestinal barrier function, cellular replication and homeostasis. Our results elucidate microbiome-host interactions that potentially influence host aging processes. These pathways could serve as future targets for the development of microbiome-based anti-aging therapies.},
}

@article {pmid40140705,
year = {2025},
author = {Garrido-Sanz, D and Keel, C},
title = {Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40140705},
issn = {2058-5276},
abstract = {Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.},
}

@article {pmid40140473,
year = {2025},
author = {Brown, AA and Widdowson, M and Brandt, S and Mohammadzadeh, P and Rosenberg, JB and Jepsen, JRM and Ebdrup, BH and Hernández-Lorca, M and Bønnelykke, K and Chawes, B and Stokholm, J and Thorsen, J and Ibrahimi, P and Li, X and Sørensen, SJ and Rasmussen, MA},
title = {Associations of the gut microbiome and inflammatory markers with mental health symptoms: a cross-sectional study on Danish adolescents.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {10378},
pmid = {40140473},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Adolescent ; Cross-Sectional Studies ; Female ; Denmark/epidemiology ; *Inflammation/metabolism ; *Attention Deficit Disorder with Hyperactivity/metabolism/microbiology ; *Biomarkers ; *Depression/metabolism ; Anxiety/microbiology ; Mental Health ; Stress, Psychological/metabolism ; Feces/microbiology ; },
abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder that often persists into adulthood and is accompanied by comorbid mental health problems. This cross-sectional cohort study analyzed 411 18-year-olds from the Danish COPSAC2000 birth cohort to investigate the relationship between the gut microbiome, fasting and postprandial systemic inflammation, ADHD symptoms, and symptoms of anxiety, stress, and depression. ADHD was assessed using the Adult ADHD Self-Report Scale (ASRS), while depression, stress, and anxiety were evaluated with the Depression, Anxiety, and Stress Scale 21 (DASS-21). Fecal metagenomic data and inflammation levels, measured as glycosylated protein A (GlycA), were analyzed following a standardized meal challenge. In males, higher ADHD symptom scores correlated significantly with increased abundance of a tryptophan biosynthesis pathway (MetaCyc Metabolic Pathways Database) and elevated fasting and postprandial GlycA levels (p < 0.05). While the severity of depression, anxiety, and stress symptoms showed weak associations with GlycA and the gut microbiome, our findings indicate a significant link between ADHD symptoms and postprandial inflammation, warranting further investigation into underlying mechanisms.},
}

Humans
*Gastrointestinal Microbiome
Male
Adolescent
Cross-Sectional Studies
Female
Denmark/epidemiology
*Inflammation/metabolism
*Attention Deficit Disorder with Hyperactivity/metabolism/microbiology
*Biomarkers
*Depression/metabolism
Anxiety/microbiology
Mental Health
Stress, Psychological/metabolism
Feces/microbiology

@article {pmid40140149,
year = {2025},
author = {Ananda, A and Brigiyanti, LN and Widhiastuty, MP and Haryati, T and Suharti, and Ma'ruf, IF and Akhmaloka, },
title = {Characterization and molecular dynamics simulation of Lk2 lipase expressed in Pichia pastoris.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {342},
pmid = {40140149},
issn = {1573-4978},
support = {12/II.7/HK/2023//RIIM Research Project Program, National Research and Innovation/ ; },
mesh = {*Lipase/genetics/metabolism/chemistry/isolation & purification ; *Molecular Dynamics Simulation ; Substrate Specificity ; Pichia/genetics/metabolism ; Hydrogen-Ion Concentration ; Fungal Proteins/genetics/metabolism/chemistry ; Recombinant Proteins/metabolism/genetics/isolation & purification/chemistry ; Molecular Docking Simulation ; Hydrolysis ; Saccharomycetales ; },
abstract = {BACKGROUND: Lipase is a versatile enzyme that serves as a biocatalyst in various industries. lk2 was successfully isolated from household waste compost through a metagenomic approach.

MATERIALS AND METHODS: lk2 from plasmid pPICZαA- lk2 was integrated into chromosomes of Pichia. pastoris GS115 using the electroporation method. Lk2 was expressed on Pichia. pastoris by methanol induction. The enzyme was purified through Ion Metal Affinity Chromatography Ni-NTA. The purified enzyme was characterized based on hydrolytic activity and in silico analysis.

RESULTS: Lk2 was successfully expressed as an extracellular protein in Pichia pastoris. The cell-free supernatant exhibited hydrolysis activity to para-nitro phenyl laurate. The purified protein showed 15 times activity compared to cell-free supernatant and the size at around 35 kDa following gel electrophoresis. The enzyme showed optimum activity at 60[o]C and pH 8. Lk2 preferred para nitro phenyl laurate as substrate. The enzyme's preference for medium-long carbon chains was corroborated by in silico analysis, which revealed favorable interactions between the enzyme and substrate, including affinity binding energy and optimal orientation of catalytic pocket to the substrate. Furthermore, the radius of gyration analysis of the Lk2 showed that the best structural compactness of Lk2 was at 60[o]C. This is in line with the optimal temperature of Lk2 activity. In addition, docking analysis found important substrate binding residues, including Tyr30, Ser85, Leu121, Leu163, Leu166, Leu 233, and Leu254 beside Ser85, Asp231, and His253 as triad catalytic.

CONCLUSION: Lk2 belongs to a thermotolerant and alkaline lipase, prefers a medium-length carbon chain as substrate and is confirmed by in silico analysis. Several amino acid residues were probed to be important for substrate binding residues. The data give valuable information to develop the possibility of Lk2 as an industry's enzyme.},
}

*Lipase/genetics/metabolism/chemistry/isolation & purification
*Molecular Dynamics Simulation
Substrate Specificity
Pichia/genetics/metabolism
Hydrogen-Ion Concentration
Fungal Proteins/genetics/metabolism/chemistry
Recombinant Proteins/metabolism/genetics/isolation & purification/chemistry
Molecular Docking Simulation
Hydrolysis
Saccharomycetales

@article {pmid40139349,
year = {2025},
author = {Bilton, TP and Hickey, SM and Jonker, A and McRae, K and Hess, MK and Perry, BJ and Bryson, B and Henry, H and Bain, W and Booker, F and Veenvliet, B and Peers-Adams, J and Pile, G and Waller, E and Janssen, PH and Tiplady, KM and Reid, P and Muetzel, S and Agnew, M and Dodds, KG and McEwan, JC and Rowe, SJ},
title = {Milk fatty acids and rumen composition as proxy measures of enteric methane.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25876},
pmid = {40139349},
issn = {1525-3198},
abstract = {Genomic selection is a powerful tool to reduce methane emissions in ruminants. However, it requires large-scale on-farm phenotypic measures of methane. Current technologies to measure methane emissions have several limitations and may not be suitable for lactating animals. Because enteric methane is closely linked to the fermentation process in the rumen, which in turn affects milk composition, breeding for low-methane ruminants may change the rumen microbial and milk composition. Consequently, these compositions may provide proxy measures of methane for use in selective breeding of low-methane ruminants. We investigated the effect on rumen and milk composition in sheep bred for divergent methane yield and the potential for generating proxy measures of methane emissions from rumen or milk samples in lactating ewes. Four hundred genotyped lactating ewes from a sheep research flock bred specifically for high and low-methane emissions had methane measured and rumen and milk samples collected approximately 6 wk post-lambing across 4 lactation years. Rumen samples were processed to generate VFA and metagenomic profiles of the rumen microbial community, and fatty acid profiles and mid-infrared spectra were generated for the milk samples. Although no differences in total fat, protein, and lactose percentages in the milk were found, the milk fatty acid profiles differed between methane selection lines, with higher PUFA and branched-chain fatty acids levels, and lower total SFA contents in ewes from the low-methane line. Higher proportions of acetate relative to propionate were found in the rumen samples from the low-methane ewes. Predictions of methane were obtained from the rumen VFA and metagenomic profiles and the fatty acid profiles and mid-infrared spectra from milk. These predictions formed the proxy methane measures and were heritable (between 0.12 to 0.36) and correlated (between 0.29 and 0.42) with the measured methane values. The genetic correlation between proxies and measured methane was between 0.52 and 0.71. The estimated efficiency of indirect selection for methane was higher for the milk sample proxies (49%-75%) than the rumen metagenomic profiles (45%-47%) and rumen VFA profiles (12%-38%). These results suggest that milk fatty acid, MIR spectroscopic, and rumen microbial composition phenotypes have the potential to be used as proxy measures of methane in lactating ruminants, with the milk-based proxies showing greater promise. Results show that the number of animals with methane proxy measures could be increased substantially and will enable access to breeding technology in countries with limited methane measurement infrastructure.},
}

@article {pmid40139294,
year = {2025},
author = {Hou, Y and Jia, R and Zhou, L and Zhang, L and Sun, W and Li, B and Zhu, J},
title = {Integrated rice-fish farming dynamically altered the metal resistances and microbial-mediated iron, arsenic, and mercury biotransformation in paddy soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126107},
doi = {10.1016/j.envpol.2025.126107},
pmid = {40139294},
issn = {1873-6424},
abstract = {Given the global concern over heavy metal contamination in agricultural soil, comprehensive and in-depth investigations into the microbial ecological impacts of different agricultural practices on soil heavy metals and their biotransformation processes are both urgent and necessary. We employed metagenomic sequencing to investigate the impacts of integrated rice-fish farming on metal concentrations, metal resistance genes (MRGs), and microbial-mediated Fe, As, and Hg biotransformation processes within rice field. Our findings revealed that integrated rice-fish farming significantly reduced both the diversity and total abundance of MRGs. It also reduced the soil Al, Cd, Cu, Fe, Hg, Ni, Se, V, and Zn levels, with a marked correlation observed between metal concentration and MRGs profiles. Furthermore, integrated rice-fish farming markedly altered the microbial-mediated biotransformation processes for Fe, As, and Hg. It notably upregulated the abundance of Fe biotransformation genes, particularly those involved in the Fe gene regulation, oxidation, reduction, and storage. Biotransformation genes responsible for the As (III) oxidation and As methylation also exhibited increased abundances, along with mercury methylation and demethylation genes. Through metagenome assembled genomes (MAGs), we identified the Mycobacterium aubagnese from paddy soil which contained As oxidation genes and other multiple MRGs, exhibiting strong As remediation potential. Our findings demonstrated the potential of integrated rice-fish farming to reduce soil metal concentrations and mitigate soil metal pollution.},
}

@article {pmid40139249,
year = {2025},
author = {Taylor, JT and Lee, V and Dearlove, T and Jolly, M and Wierenga, JR and Dubrulle, J and Hodgkinson-Bean, J and Hunter, S and Gartrell, B and Morgan, K and McInnes, K and French, N and Holmes, EC and Geoghegan, JL},
title = {A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode.},
journal = {Journal of wildlife diseases},
volume = {},
number = {},
pages = {},
doi = {10.7589/JWD-D-24-00115},
pmid = {40139249},
issn = {1943-3700},
abstract = {Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions, lichenification, and feather loss. Swab samples and full-thickness skin biopsies were collected during a survey of affected kiwi in 2023 for a metatranscriptome-based, total infectome investigation to identify any possible microbial agents associated with the disease. Our approach identified novel viruses as well as a species of nematode in high relative abundance. We found a highly abundant hepacivirus within the Flaviviridae, but only in some mild cases of dermatitis across all sample types, and in both active and chronic infections. In addition, we found a significant shift in the taxonomic composition of the nonviral microbiome within severe chronic dermatitis cases, particularly an increased abundance of transcripts from a Eucoleus sp. parasitic. Although determining the primary cause of disease in critically endangered wildlife such as Rowi remains challenging, our detection of novel and highly abundant microorganisms opens new lines of inquiry to investigate their potential association with dermatosis in this nationally iconic species.},
}

@article {pmid40139192,
year = {2025},
author = {Munneke, MJ and Yuan, Y and Preisner, EC and Shelton, CD and Carroll, DT and Kirchoff, NS and Dickson, KP and Cantu, JO and Douglass, MV and Calcutt, MW and Gibson-Corley, KN and Nicholson, MR and Byndloss, MX and Britton, RA and de Crécy-Lagard, V and Skaar, EP},
title = {A thiouracil desulfurase protects Clostridioides difficile RNA from 4-thiouracil incorporation, providing a competitive advantage in the gut.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.03.001},
pmid = {40139192},
issn = {1934-6069},
abstract = {Nucleotides are essential building blocks for major cellular macromolecules and are critical for life. Consequently, bacterial pathogens must acquire or synthesize nucleotides during infection. Clostridioides difficile is the most common hospital-acquired gastrointestinal infection, and nutrient acquisition is critical for pathogenesis. However, the impact of nucleotide metabolism on C. difficile infection remains unclear. Here, we discover that 4-thiouracil (4-TU), a pyrimidine analog present in the human gut, is toxic to commensal bacteria. 4-TU hijacks the uracil salvage pathway for incorporation into RNA through the uracil phosphoribosyltransferase activity encoded by PyrR and Upp. C. difficile can salvage 4-TU as a pyrimidine source through the enzymatic action of a thiouracil desulfurase (TudS), thereby contributing to C. difficile fitness in mice fed 4-TU or MiniBioreactor models of infection containing exogenous 4-TU. Collectively, these results reveal a molecular mechanism for C. difficile to utilize a poisonous pyrimidine analog in the vertebrate gut to outcompete commensal microbes.},
}

@article {pmid40138989,
year = {2025},
author = {Uprety, T and Swan, M and Kennedy, L and Bryant, U and Cassone, L and Loynachan, A and Janes, J and Evely, MM and Calvaruso, FC and Quick, M and Morgan, J and Abdelrazek, S and Lahmers, K and Carter, C and Erol, E},
title = {Retrospective investigation of 43 necropsy cases of Tyzzer disease in foals and partial genome sequence of Clostridium piliforme by shotgun metagenomics.},
journal = {Veterinary microbiology},
volume = {304},
number = {},
pages = {110489},
doi = {10.1016/j.vetmic.2025.110489},
pmid = {40138989},
issn = {1873-2542},
abstract = {Clostridium piliforme is an obligate intracellular filamentous bacterium that causes Tyzzer disease (TD) in many animals. The disease manifests as severe, multifocal necrotizing hepatitis, with a high fatality rate in foals. Through retrospective investigation, we detected C. piliforme in 43 equine necropsy cases from 2012 to 2024. Positive cases were diagnosed from February to July, peaking in May. The age of affected foals ranged from 4 days to 2 months. Histologically, all cases had necrotizing hepatitis with multifocal, coalescing pinpoint, tan or reddish foci. Since only a partial 16S rRNA gene sequence was available for the horse strain of C. piliforme, we used shotgun metagenomics to obtain its genome sequence from the liver of a necropsied foal with TD. The sequences obtained were compared against the NCBI NT/NR database with the highest number of reads and contigs aligning to Clostridium species. A complete 16S rRNA gene was obtained, showing the highest identity to a 16S rRNA gene of the horse strain of C. piliforme (99.05 %), followed by 98.02-96.71 % identities to rabbit and rodent strains of C. piliforme, indicating cross-species variation. Additional identified genes included alveolysin, exo-α-sialidase, flagellar and spore formation/vegetation, providing the first genetic evidence of virulence factors for C. piliforme. Furthermore, presence of genes encoding multidrug export and multidrug resistance proteins suggested C. piliforme could develop resistance to beta-lactams and fluoroquinolones. This study provides the first partial genome sequence of C. piliforme using a shotgun metagenomics hepatic sampling approach on a foal with TD.},
}

@article {pmid40138908,
year = {2025},
author = {Díaz-García, C and Sánchez-Osuna, M and Serra-Compte, A and Karakatsanidou, I and Gómez-Sánchez, I and Fidalgo, B and Barbuzana-Armas, C and Fittipaldi, M and Rosselli, R and Vinyoles, J and González, S and Pich, OQ and Espasa, M and Yáñez, MA},
title = {Mapping antimicrobial resistance landscape at a city scale sewage network.},
journal = {The Science of the total environment},
volume = {974},
number = {},
pages = {179127},
doi = {10.1016/j.scitotenv.2025.179127},
pmid = {40138908},
issn = {1879-1026},
abstract = {Wastewater is a valuable source for monitoring contaminants of biotic or abiotic origin. Antimicrobial resistance (AMR) has emerged as a public health threat that consists of the ability of microorganisms to resist the effects of antimicrobial compounds, rendering them very difficult or impossible to eradicate in case of infection. Considering the dissemination of antimicrobial resistance genes (ARGs) to a wide number of ecosystems, there is a need for the identification of hotspots that concentrate antimicrobial resistance determinants. A comprehensive investigation conducted at a city-scale in Sabadell (Barcelona, Spain) has integrated both phenotypic and genotypic methodologies, including metagenomics and culture-based techniques coupled with whole-genome sequencing (WGS), to monitor ARG presence in seven different spots of the sewage system. Metagenomics approach identified 262 ARG variants across analyzed sampling sites, grouped into 15 resistance categories. The most prevalent ARGs were macrolides-lincosamides-class B streptogramins (MLSB) (35.1 %) and beta-lactams (28.7 %), including carbapenems (5.9 %) and cephalosporins (5.3 %). MLSB resistance featured dominant msr(E) and mph(E) genes, the most abundant ARGs in our study. ARGs conferring resistance to beta-lactam were dominated by blaOXA-464, blaOXA-491, and blaNPS. Key genes for carbapenem (blaOXA-372, blaKPC-2) and cephalosporin (blaOXA-10, blaOXA-1) resistance were identified. The hospital sector exhibited the highest relative abundance of ARGs, dominated by beta-lactams, MLSB, and aminoglycosides. Wastewater treatment plant (WWTP) entrance points and residential areas displayed similar ARG profiles, while WWTP effluent and industrial zones had the lowest ARG levels. WWTP significantly reduced ARG presence (93.3 %). The characterization of antibiotic-resistant bacterial isolates found that most abundant ARGs were predominantly plasmid-borne, favoring ARG spread across bacterial genera. This finding confirmed the significant role of plasmids in ARG dissemination, increasing both diversity and prevalence within waterborne bacterial communities. City-scale surveillance programs can play a pivotal role in guiding effective measures to reduce the dissemination of AMR and mitigate their environmental impact.},
}