@article {pmid40459709,
year = {2025},
author = {Quoc, NB and Nhu, LTT and Chau, NNB},
title = {Identification of diet resources of big-eyed bug Geocoris ochropterus (Fieber) (Hemiptera: Geocoridae) by multiplex PCR and shotgun metagenomic approaches.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {537},
pmid = {40459709},
issn = {1573-4978},
support = {E2022.02.1//Đại học Mở Thành phố Hồ Chí Minh/ ; },
mesh = {Animals ; *Metagenomics/methods ; Multiplex Polymerase Chain Reaction/methods ; *Hemiptera/genetics ; Diet ; Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; },
abstract = {BACKGROUND: Big-eyed bugs (Geocoris spp.) are important generalist predators in agricultural ecosystems, playing a crucial role in natural pest control.

METHODS: To better understand their dietary sources, we assessed the plant and animal food sources in the gut of Geocoris ochropterus using multiplex PCR and shotgun metagenomic analysis. The PCR assays targeted genetic markers from both animal (COI) and plant (matK and rbcL) DNA.

RESULTS: Results revealed the presence of both animal and plant-derived DNA in the gut samples, indicating that Geocoris ochropterus feeds on a mixed diet. Additionally, the results of shotgun metagenomic sequencing of the gut microbiota showed a predominance of Eukaryota, with over 80% of sequences belonging to this domain, while a diverse range of taxonomic groups were identified, including arthropods, plants, bacteria, and fungi. Arthropods particularly insects from the orders Lepidoptera, Hemiptera, Hymenoptera, Coleoptera, Phasmatodea and plants belonging to the orders Brassicales, Cucurbitales, and Poales constituted the most abundant dietary components. At the genus level, notable taxa included Maniola (family Nymphalidae), Carposina (Carposinidae), Helicoverpa (Noctuidae), and Solanum (Solanaceae). Species-level analysis confirmed the dominance of several insect species, including Maniola hyperanthus, Carposina sasakii, and Bombyx mori, alongside plant species such as Cucumis melo, Gossypium hirsutum, and Digitaria exilis.

CONCLUSIONS: These findings provide a comprehensive characterization of the diet of Geocoris ochropterus, highlighting its role as a generalist predator with a diverse diet consisting of both insect and plant food sources. This study contributes to the understanding of Geocoris ochropterus as a potential biocontrol agent in agricultural systems.},
}

Animals
*Metagenomics/methods
Multiplex Polymerase Chain Reaction/methods
*Hemiptera/genetics
Diet
Gastrointestinal Microbiome/genetics
Metagenome/genetics

@article {pmid40458954,
year = {2025},
author = {Wang, Y and Pan, Z and Shi, Y and Bai, Y and Liang, J and Wang, A and Qu, J},
title = {MnOxGeneTool: A Comprehensive Tool for Identifying and Quantifying Mn(II)-Oxidizing Genes, Revealing Phylogenetic Diversity and Environmental Drivers of Mn(II)-Oxidizers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01235},
pmid = {40458954},
issn = {1520-5851},
abstract = {Manganese (Mn) oxides are crucial for degrading organic pollutants and driving biogeochemical cycles. Microorganisms drive Mn(II) oxidation, but traditional cultivation-dependent identification methods are inefficient and error-prone. To overcome these limitations, we developed MnOxGeneTool, a bioinformatics tool for identifying and quantifying Mn(II)-oxidizing genes from genomic and metagenomic data. MnOxGeneTool consists of three main components: (1) a curated database of known Mn(II)-oxidizing proteins and their homologues, (2) a hidden Markov models (HMMs) database derived from this protein data set, and (3) a computational pipeline that integrates bioinformatics tools (e.g., HMMER and BLASTX) to identify and quantify Mn(II)-oxidizing genes. We assessed the accuracy and sensitivity of these HMMs through cross-validation, demonstrating their effectiveness in identifying Mn(II)-oxidizing genes in bacterial genomes. Using MnOxGeneTool, we explored the phylogenetic diversity of Mn(II)-oxidizers and identified 824 bacterial genera containing Mn(II)-oxidizing genes, significantly expanding previous knowledge in this field. Additionally, we analyzed metagenomic data from various environments to explore environmental drivers of Mn(II)-oxidizing genes, identifying two potential drivers: oligotrophic conditions and alkaline environments. These findings enable targeted discovery of novel Mn(II)-oxidizers and genetic determinants through identification of their ecological niches and expression optima, thereby expanding MnOxGeneTool's predictive coverage of uncatalogued Mn(II)-oxidizing proteins. By providing an innovative bioinformatics tool that enables efficient identification and quantification of Mn(II)-oxidizing genes from both genomic and metagenomic data, this study offers significant advancements in the research of biogenic Mn(II) oxidation. The tool is available at https://github.com/wyh19990121/MnOxGeneTool.},
}

@article {pmid40458218,
year = {2025},
author = {Qush, A and Assaad, N and Alkhayat, FA and Al-Kuwari, MS and Al-Khalaf, N and Bassil, M and Yassine, HM and Zeidan, A and Razali, R and Kamareddine, L},
title = {Insects in agricultural greenhouses: a metagenomic analysis of microbes in Trialeurodes vaporariorum infesting tomato and cucumber crops.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1581707},
pmid = {40458218},
issn = {1664-462X},
abstract = {INTRODUCTION: With the predicted 9-10 billion world population increase by 2050 and its accompanying need for sustainable food production, and with the harsh climate conditions challenging agriculture and food security in many countries world-wide, employing "horticultural protected cultivation practices" in farming for seasonal and off-seasonal crop production is on the rise, among which is the use of agricultural greenhouses. The importance of greenhouse farming has been, indeed, evident by the perceived increase in year-round crops production, curtail in production risks, upsurge in agricultural profits, outreaching food stability and security in many countries globally. Yet, and despite this acknowledged success of employing greenhouses in farming, many constraints, including the presence of insect pests, still chaperoned this practice over the years, significantly impacting crop quality and production.

METHODS: As such, we assessed in this study the status of "insect pests" in the greenhouse model by collecting insects from different greenhouse sectors grown with tomatoes and cucumbers and identified the collected insects using relevant identification keys. To further explore the pest paradigm in greenhouses, we then focused on particularly studying Trialeurodes vaporariorum (TRIAVA), a key insect species among the collected and identified insects in the studied greenhouse model and a significant pest with an impactful effect on many crops worldwide. To do so, we traced the abundance of TRIAVA in the tomato and cucumber grown greenhouse sectors over the period of the study, analyzed its metagenome and associated its abundance with crop yield.

RESULTS AND DISCUSSION: Our findings revealed TRIAVA hosted microbes with aptitudes to either serve as symbiotic microorganisms and protect TRIAVA against pathogens or to potentially cause damage to crops. This work provides additional insight into the insect pests paradigm in greenhouses, an upshot that could serve integrated insect pest management strategies in greenhouses for optimal agricultural practices.},
}

@article {pmid40456950,
year = {2025},
author = {Kocharovskaya, Y and Delegan, Y and Sevostianov, S and Bogun, A and Demin, DV},
title = {Metagenomic Analysis of Pulp and Paper Wastes and Prospects for Their Self-purification.},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {320},
pmid = {40456950},
issn = {1432-0991},
mesh = {*Paper ; *Metagenomics ; Lignin/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Industrial Waste/analysis ; Biodegradation, Environmental ; *Microbiota ; High-Throughput Nucleotide Sequencing ; },
abstract = {Thousands of tons of waste accumulate, as a result of the activities of the pulp and paper industry, which is often stored in the form of dumps. However, intensifying the use of lignocellulose for more efficient bioremediation remains highly challenging. Therefore, the study of microbiomes with potentially desirable characteristics for the decomposition of pulp and paper wastes is currently an important task. In this study, a comprehensive assessment of the microbiota biodiversity of these dumps was carried out using high-throughput, high-resolution sequencing. In study 472 million high-quality clean reads assembled into 6,413,337 contigs with a total length of 4306 Mb, of which 3,633,174 open reading frames (ORFs) were identified. The core microbiome was composed of four phyla from Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Representatives of phylum Proteobacteria prevailed in samples. Annotation using the KEGG database in the Metabolism category resulted in 654,234 ORFs and 5138 ORFs encoding enzymes/proteins involved in degradation of lignocellulose which formed main pool of the wastes. By use of the created database, the search for lignocellulose degradation genes showed that genera Shewanella, Achromobacter, and Delftia covered significant part of the reads. The results indicate that the established microbiome of local landfills can be considered as an important source for improving lignocellulose bioremediation, provided that lignocellulosic fungi are sufficiently active. In whole, these new data can be used as a scientific basis to form an efficient eco-biotechnology for auto-remediation of pulp and paper industry waste.},
}

*Paper
*Metagenomics
Lignin/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Industrial Waste/analysis
Biodegradation, Environmental
*Microbiota
High-Throughput Nucleotide Sequencing

@article {pmid40456770,
year = {2025},
author = {Zhou, XQ and Chen, KH and Yu, RQ and Yang, M and Liu, Q and Hao, YY and Li, J and Liu, HW and Feng, J and Tan, W and Huang, Q and Gu, B and Liu, YR},
title = {Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5102},
pmid = {40456770},
issn = {2041-1723},
support = {42425701//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methylmercury Compounds/metabolism/toxicity ; *Oryza/metabolism/microbiology ; *Soil Microbiology ; Biodegradation, Environmental ; Metagenomics ; *Soil Pollutants/metabolism/toxicity ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; },
abstract = {Toxic methylmercury (CH3Hg[+]) is produced by microbial conversion of inorganic mercury in hypoxic environments such as rice paddy soils, and can accumulate in rice grains. Although microbial demethylation has been recognized as a crucial pathway for CH3Hg[+] degradation, the identities of microbes and pathways accountable for CH3Hg[+] degradation in soil remain elusive. Here, we combine [13]CH3Hg[+]-DNA stable-isotope probing experiments with shotgun metagenomics to explore microbial taxa and associated biochemical processes involved in CH3Hg[+] degradation in paddy and upland soils. We identify Pseudarthrobacter, Methylophilaceae (MM2), and Dechloromonas as the most significant taxa potentially engaged in the degradation of [13]CH3Hg[+] in paddy soil with high mercury contamination. We confirm that strains affiliated with two of those taxa (species Dechloromonas denitrificans and Methylovorus menthalis) can degrade CH3Hg[+] in pure culture assays. Metagenomic analysis further reveals that most of these candidate [13]CH3Hg[+] degraders carry genes associated with the Wood-Ljungdahl pathway, dicarboxylate-hydroxybutyrate cycle, methanogenesis, and denitrification, but apparently lack the merB and merA genes involved in CH3Hg[+] reductive demethylation. Finally, we estimate that microbial degradation of soil CH3Hg[+] contributes to 0.08-0.64 fold decreases in CH3Hg[+] accumulation in rice grains across China (hazard quotient (HQ) decrements of 0.62-13.75%). Thus, our results provide insights into microorganisms and pathways responsible for CH3Hg[+] degradation in soil, with potential implications for development of bioremediation strategies.},
}

*Methylmercury Compounds/metabolism/toxicity
*Oryza/metabolism/microbiology
*Soil Microbiology
Biodegradation, Environmental
Metagenomics
*Soil Pollutants/metabolism/toxicity
*Bacteria/metabolism/genetics/classification
Soil/chemistry

@article {pmid40456641,
year = {2025},
author = {Wen, M and Liu, Y and Feng, CY and Ji, W and Li, ZQ},
title = {Differences of key processes in soil nitrogen cycling and their driving factors under different land-use types.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {5},
pages = {1387-1397},
doi = {10.13287/j.1001-9332.202505.036},
pmid = {40456641},
issn = {1001-9332},
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Nitrogen Cycle ; *Nitrogen/analysis/metabolism ; China ; Nitrification ; *Ecosystem ; Denitrification ; Forests ; Wetlands ; Grassland ; Agriculture ; Nitrogen Fixation ; },
abstract = {To investigate the responses and drivers of soil microbial nitrogen (N)-cycling functional genes under different land-use types, we analyzed five representative ecosystems in the Yellow River alluvial plain: Tamarix chinensis forests, Fraxinus chinensis forests, grasslands, wetlands, and farmlands. With metagenomic sequencing, we quantified the relative abundances of 22 functional genes associated with six critical N-cycling processes. Soil physicochemical properties were characterized. There were significant variations in soil nitrogen (N)-cycling functional gene abundances across land-use types. Wetlands exhibited the highest relative abundances of nitrogen fixation (1.28×10[-5]), nitrification (4.91×10[-4]), and denitrification (7.03×10[-4]) genes, but the lowest assimilatory nitrate reduction potential (1.84×10[-4]). Farmlands showed maximal assimilatory nitrate reduction gene abundance (3.31×10[-4]), while grasslands dominated in ammonification gene expression (2.35×10[-4]), significantly higher than other ecosystems. T. chinensis forests maintained the most constrained N-cycling profile, with minimal nitrification (2.77×10[-4]) and denitrification (5.25×10[-4]) relative gene abundances. Redundancy analysis identified soil total nitrogen, organic carbon, total potassium, and electrical conductivity as the key environmental drivers of these variations. Our findings demonstrated that land-use types could shape microbial N-cycling functional gene abundances by altering soil nutrient conditions, with consequence on fundamental processes of soil nitrogen transformation.},
}

*Soil/chemistry
*Soil Microbiology
*Nitrogen Cycle
*Nitrogen/analysis/metabolism
China
Nitrification
*Ecosystem
Denitrification
Forests
Wetlands
Grassland
Agriculture
Nitrogen Fixation

@article {pmid40456384,
year = {2025},
author = {Nayyar, J and Bedu-Ferrari, C and Patangia, D and Hurley, E and Feeley, L and Ross, RP and Stanton, C and Brady, P},
title = {Gut and oral microbial profile associations to oral cancer.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105848},
doi = {10.1016/j.jdent.2025.105848},
pmid = {40456384},
issn = {1879-176X},
abstract = {The human microbiome is widely known to be associated with health and disease. The oral microbiome has been linked with oral diseases and infections, though not many studies have explored the relation between oral and gut microbiome with oral cancer based on lesion histology METHODS: This study uniquely explores the oral and gut microbiota in 30 participants (n=30) divided into three groups based on histology; Benign (B) (n=15), Potentially Malignant (PM) (n=8), and Malignant (M) (n=7) oral lesions. Using shotgun metagenomic sequencing, we analysed microbiota profiles to determine their potential as biomarkers for oral malignancy RESULTS: Distinct gut microbial profiles were observed between Benign and Malignant groups and the association of specific microbes in oral saliva, such as Haemophilus parainfluenzae, Veillonella parvula, Fusobacterium nucleatum and Rothia mucilaginosa were strongly associated with malignancy CONCLUSION: The data from this exploratory study suggest that oral and gut microbiomes could act as possible biomarkers and aid in early detection and assessment of oral cancer risk. With regard to potentially malignant lesions, future research could study individual Oral Potentially Malignant Disorders (OPMDs) as distinct entities due to the wide variation in clinical and histological presentation. Further research is required to develop definitive biomarkers in both potentially malignant and malignant oral lesions CLINICAL SIGNIFICANCE: While smoking and alcohol are known risk factors for oral cancer, a biomarker such as the saliva/stool microbiome profile could help identify a risk indicator or a potential risk factor. Additionally such a biomarker could help identify patients with OPMDs that are likely to undergo malignant transformation.},
}

@article {pmid40456327,
year = {2025},
author = {Zhao, F and Yang, Z and Wang, J and Bartlam, M and Wang, Y},
title = {Enantioselective effects of chiral antibiotics on antibiotic resistance gene dissemination and risk in activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132749},
doi = {10.1016/j.biortech.2025.132749},
pmid = {40456327},
issn = {1873-2976},
abstract = {Misuse of antibiotics drives the spread of antibiotic resistance genes (ARGs). Although reducing residual antibiotic concentrations can help curb ARG proliferation, the biodegradation and transformation of antibiotic stereoisomers may exacerbate resistance development. However, the impact of antibiotic enantiomers on ARG proliferation remains poorly understood. This study employed metagenomic analysis to investigate the enantiomer-specific selection and resistance risks of chiral antibiotic ofloxacin (OFL) and its (S)-enantiomer, levofloxacin (LEV), in activated sludge. Results showed that LEV primarily promoted the enrichment of ARGs related to aminoglycoside and mupirocin resistance by selecting for pathogenic bacteria carrying virulence factors under high toxicity stress. OFL-driven ARG proliferation involved more diverse mechanisms, including increased gene mobility, co-selection with heavy metals, broader host range, and elevated pathogenicity. The antibiotic resistome risk index (ARRI) further demonstrated a higher environmental risk under OFL treatment than LEV. These findings offer critical insights into the enantioselective resistance risks posed by chiral antibiotics.},
}

@article {pmid40455595,
year = {2025},
author = {Fetters, AM and Cantalupo, PG and Robles, MTS and Pipas, JM and Ashman, TL},
title = {Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf073},
pmid = {40455595},
issn = {1557-7023},
abstract = {Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether 1) life history, floral traits, or pollination generalism were associated with viral richness, and 2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.},
}

@article {pmid40455399,
year = {2025},
author = {Qayyum, H and Raziq, MF and Manzoor, H and Zaidi, SSA and Ali, A and Kayani, MUR},
title = {Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.},
journal = {Interdisciplinary sciences, computational life sciences},
volume = {},
number = {},
pages = {},
pmid = {40455399},
issn = {1867-1462},
abstract = {De novo assembly and genome binning are fundamental steps for genome-resolved metagenomics analyses. However, the availability of limited computational resources and extensive processing time limit the broader application of these analyses. To address these challenges, the optimization of the parameters employed in these processes can improve the effective utilization of available metagenomics tools. Therefore, this study tested three sets of k-mers (default, reduced, and extended) for their efficiency in metagenome assembly and suitability in recovering metagenome-assembled genomes. The results demonstrate that the reduced set of k-mers outperforms the other two sets in computational efficiency and the quality of results. The assemblies from the default set are comparable with those from the reduced set; however, less complete and highly contaminated metagenome-assembled genomes are obtained at the expense of higher processing time. The extended set of k-mers yields less contiguous but computationally expensive assemblies. This set takes approximately 3-times more processing time than the reduced k-mers and recovers the lowest proportions of high and medium-quality metagenome-assembled genomes. Contrarily, the reduced set produces better assemblies, substantially improving the number and quality of the recovered metagenome-assembled genomes in significantly reduced processing time. Validation of the reduced k-mer set on previously published metagenome datasets further demonstrates its effectiveness not only for human metagenomes but also for the metagenomes of environmental origin. These findings underscore that the reduced k-mer set is optimal for efficient metagenome analyses of varying complexities and origins. This optimization of the k-mer set used in metagenome assemblers significantly reduces computational time while improving the quality of the assemblies and recovered metagenome-assembled genomes. This efficient solution will facilitate the widespread application of genome-resolved analyses, even in resource-limited settings, and help the recovery of better-quality metagenome-assembled genomes for downstream analyses.},
}

@article {pmid40455288,
year = {2025},
author = {Hu, J and Yu, W and Cui, J and Zhang, L and Yu, W},
title = {Recent advances in diagnostic technologies for postoperative central nervous system infections: a review.},
journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology},
volume = {},
number = {},
pages = {},
pmid = {40455288},
issn = {1590-3478},
abstract = {Postoperative central nervous system infections (PCNSIs), including meningitis, cerebral abscesses, and implant-associated infections, represent critical complications following neurosurgical procedures. These infections pose significant risks to patient outcomes due to delayed diagnosis, escalating antimicrobial resistance, and limited therapeutic efficacy. Conventional diagnostic approaches, such as cerebrospinal fluid (CSF) analysis, microbial cultures, and neuroimaging, exhibit notable limitations in sensitivity, specificity, and rapidity. This review highlights transformative technologies reshaping PCNSI diagnostics, including molecular assays (e.g., quantitative PCR, digital droplet PCR), metagenomic next-generation sequencing (mNGS), CRISPR-based pathogen detection platforms, metabolomics, and advanced molecular imaging modalities. Furthermore, we address translational challenges in clinical adoption, including cost barriers, standardization gaps, and the need for interdisciplinary collaboration. Emerging artificial intelligence (AI)-driven strategies are proposed to optimize pathogen identification, predict antimicrobial resistance profiles, and tailor personalized therapeutic regimens.},
}

@article {pmid40455149,
year = {2025},
author = {da Silva, AF and Wallau, GL},
title = {Bioinformatic Identification of Viral Genomes from High-Throughput Metagenomic Sequencing Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2927},
number = {},
pages = {1-22},
pmid = {40455149},
issn = {1940-6029},
mesh = {*Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Computational Biology/methods ; *Viruses/genetics ; Phylogeny ; },
abstract = {Virus identification has historically been performed through cell culture isolation and low-throughput methodologies that are limited often requiring previous information about the investigated viruses. These classical virological methods have been pivotal to many discoveries, but overall, they have a limited capacity for characterization of highly divergent and novel viruses. Nowadays, new technologies such as next-generation sequencing have revolutionized the virology field, enabling unbiased high-throughput viral genome characterization. But although the sequencing bottleneck has been surpassed, we could not say the same for the bioinformatics bottleneck of fishing new viral genomes from these large datasets littered with host and other microbes sequencing data. Here, we describe a bioinformatic framework to process metagenomic or metatranscriptomic data, aiming to assemble, identify, and study the evolutionary relationship of viral sequences and genomes.},
}

*Genome, Viral
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Computational Biology/methods
*Viruses/genetics
Phylogeny

@article {pmid40454874,
year = {2025},
author = {Pfister, CA and Berlinghof, J and Bogan, M and Cardini, U and Gobet, A and Hamon-Giraud, P and Hart, J and Jimenez, N and Siegel, A and Stanfield, E and Vallet, M and Leblanc, C and Rousseau, C and Thomas, F and Stock, W and Dittami, SM},
title = {Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0099624},
doi = {10.1128/msphere.00996-24},
pmid = {40454874},
issn = {2379-5042},
abstract = {UNLABELLED: Seaweeds harbor a rich diversity of bacteria, providing them with metabolic resources and a surface for attachment and biofilm development. The host's unique environment potentially shapes the bacterial genomes and promotes adaptations for a symbiotic lifestyle. To investigate whether the genomes of seaweed-associated bacteria are genetically and metabolically distinct from their close free-living relatives in seawater, we compared both the seaweed-associated and free-living counterparts of 72 bacterial genera across 16 seaweed hosts using whole-genome sequences or high-quality metagenome-assembled genomes. While taxonomic affiliation strongly influenced genome characteristics such as GC content, gene number, and size, host association had a lower effect overall. A reduced genome size was suggested only in Nereocystis luetkeana-associated microbes, while only Ascophyllum nodosum-associated bacteria had an increased GC content. Metabolic adaptations were indicated from the genomes of seaweed-associated bacteria, including enriched pathways for B vitamin production, complex carbohydrate utilization, and amino acid biosynthesis. In particular, Flavobacteriia showed the most pronounced differences between host-associated and free-living strains. We further hypothesized that bacteria associated with seaweed might have evolved to complement their host's metabolism and tested this inference by analyzing the genomes of both the seaweed Ectocarpus subulatus and its 28 bacterial associates but found no evidence for such complementarity. Our analyses of 72 paired bacterial genomes highlighted significant metabolic differences in seaweed-associated strains with implications for carbon, nitrogen, and sulfur cycling in the coastal ocean.

IMPORTANCE: We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in seawater. For genome features that included the number of genes, the size of the genome, and the GC content, taxonomy was of greater importance than bacterial lifestyle. When we compared metabolic abilities, we again found a strong effect of taxonomy in determining metabolism. Although several metabolic pathways differed between free-living and host-associated bacteria, this was especially prominent for Flavobacteriia in the phylum Bacteroidota. Notably, bacteria living on seaweeds had an increased occurrence of genes for B vitamin synthesis, complex carbohydrate use, and nitrogen uptake, indicating that bacterial genomes reflect both their evolutionary history and the current environment they inhabit.},
}

@article {pmid40454811,
year = {2025},
author = {Millard, SA and Vendrov, KC and Young, VB and Seekatz, AM},
title = {Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.},
journal = {mBio},
volume = {},
number = {},
pages = {e0110825},
doi = {10.1128/mbio.01108-25},
pmid = {40454811},
issn = {2150-7511},
abstract = {UNLABELLED: Colonization resistance provided by the gut microbiota is essential for resisting both initial Clostridioides difficile infection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying the efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearing C. difficile compared to a mouse-derived microbiota, despite recovery of taxonomic diversity, compositional changes, and bacterial functions typically associated with clearance. Metabolomic analysis revealed deficits in secondary metabolites compared to those that received murine FMT, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors to consider in FMT-based recovery from rCDI.

IMPORTANCE: Clostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain underexplored. This study reveals that the effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for C. difficile infection (CDI) and other conditions.},
}

@article {pmid40454480,
year = {2025},
author = {Lynch, LE and Lahowetz, R and Maresso, C and Terwilliger, A and Pizzini, J and Melendez Hebib, V and Britton, RA and Maresso, AW and Preidis, GA},
title = {Present and future of microbiome-targeting therapeutics.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {11},
pages = {},
pmid = {40454480},
issn = {1558-8238},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Phage Therapy/trends/methods ; Bacteriophages ; Animals ; },
abstract = {A large body of evidence suggests that single- and multiple-strain probiotics and synbiotics could have roles in the management of specific gastrointestinal disorders. However, ongoing concerns regarding the quality and heterogeneity of the clinical data, safety in vulnerable populations, and the lack of regulation of products containing live microbes are barriers to widespread clinical use. Safety and regulatory issues must be addressed and new technologies considered. One alternative future strategy is the use of synthetic bacterial communities, defined as manually assembled consortia of two or more bacteria originally derived from the human gastrointestinal tract. Synthetic bacterial communities can model functional, ecological, and structural aspects of native communities within the gastrointestinal tract, occupying varying nutritional niches and providing the host with a stable, robust, and diverse gut microbiota that can prevent pathobiont colonization by way of colonization resistance. Alternatively, phage therapy is the use of lytic phage to treat bacterial infections. The rise of antimicrobial resistance has led to renewed interest in phage therapy, and the high specificity of phages for their hosts has spurred interest in using phage-based approaches to precisely modulate the microbiome. In this Review, we consider the present and future of microbiome-targeting therapies, with a special focus on early-life applications, such as prevention of necrotizing enterocolitis.},
}

Humans
*Gastrointestinal Microbiome
*Probiotics/therapeutic use
*Phage Therapy/trends/methods
Bacteriophages
Animals

@article {pmid40454439,
year = {2025},
author = {Rosam, K and Steixner, S and Bauer, A and Lass-Flörl, C},
title = {Non-conventional diagnostic methods for invasive fungal infections.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2509026},
pmid = {40454439},
issn = {1744-8352},
abstract = {INTRODUCTION: Biomarkers have revolutionized the field of fungal diagnostics by enabling early detection, risk assessment, and monitoring treatment response. Their value in clinical practice is influenced by a wide range of determinants including diagnostic performance (sensitivity and specificity), predictive value in diverse patient groups, host immune status and comorbidities, technical standardization and antifungal treatment.

AREA COVERED: This review provides a comprehensive overview of the current antigen and DNA-based methods used for the detection of invasive fungal infections (IFIs), with a particular focus on the clinically significant pathogens Aspergillus spp. Candida spp. and Mucorales. It examines the advantages and limitations of the available diagnostic tools, emphasizing their role in early detection, specificity, and clinical application.

EXPERT OPINION: The selection of fungal biomarkers should be tailored based on the patient population, the clinical setting, and the type of fungal infection suspected. Using a combination of biomarkers often improves diagnostic accuracy, particularly in high-risk populations like hematologic malignancy patients. Fungal biomarkers do not provide definitive proof of an active fungal infection; instead, they serve as indirect indicators of the presence of fungal components. Their primary role is to support the diagnosis, assess risk, and guide clinical decisions, but they must be interpreted within the broader clinical context to follow current guidelines for diagnosing fungal infections (EORTC/MSG).},
}

@article {pmid40454309,
year = {2025},
author = {Xu, J and Li, Y and Wang, X and Mu, Y},
title = {Case Report: A Case of Visceral Leishmaniasis Misdiagnosed as Brucellosis.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2673-2677},
pmid = {40454309},
issn = {1178-6973},
abstract = {Visceral leishmaniasis (VL) is an infectious disease caused by protozoan parasites of the genus Leishmania and transmitted through the bites of infected female sandflies. Due to its nonspecific clinical presentation, VL is prone to misdiagnosis and underdiagnosis. Though rare, VL is endemic in regions of Africa, South America, Asia, and parts of Europe, including the Mediterranean. This report describes a case of VL initially misdiagnosed as brucellosis due to a history of close contact with sheep. The patient tested negative for brucellosis via serum agglutination, blood culture, and bone marrow smear, and showed no improvement with a combination of omadacycline and rifampin therapy. Definitive diagnosis was achieved through metagenomic next-generation sequencing (mNGS) and confirmation with the rk39 antigen test. The patient was successfully treated with amphotericin B cholesterol sulfate complex and recovered fully. This case highlights the need to consider rare pathogens when epidemiological history and clinical response to treatment are incongruent and emphasizes the value of mNGS in timely diagnosis of VL.},
}

@article {pmid40454150,
year = {2025},
author = {Du, R and Mao, H and Li, WM and Liu, D and Wang, K},
title = {Case Report: Empyema secondary to percutaneous transthoracic needle biopsy in three cases.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1531909},
pmid = {40454150},
issn = {2296-858X},
abstract = {Percutaneous transthoracic needle biopsy (PTNB) is a widely utilized diagnostic procedure for pulmonary lesions, with the current literature predominantly documenting pneumothorax and hemorrhage as primary complications. While empyema represents a rare complication, its clinical implications warrant special attention. In this study, we report the cases of three patients with unidentified pulmonary masses who developed empyema after PTNB. All cases exhibited fever (24-48 h post-procedure) and radiographic evidence of pleural effusion progression shortly after the procedure, which was successfully managed through pleural drainage and antibiotic treatment. These findings suggest that pre-procedural infectious foci may be prone to iatrogenic pleural seeding during PTNB. This report emphasizes the necessity of monitoring infectious indicators in patients undergoing biopsy of cavitary or necrotic lesions. Physicians should exercise caution when puncturing lumps suspected of abscesses and remain vigilant for empyema secondary to PTNB if the patient shows signs of infection.},
}

@article {pmid40453877,
year = {2025},
author = {Ma, R and Yin, Y and Zhang, JP and Zhang, MX and Zhou, JR and He, Y and Gai, W and Zhang, XH and Wang, Y and Xu, LP and Liu, KY and Huang, XJ and Sun, YQ},
title = {Metagenomic Next-generation Sequencing Compared With Blood Culture as First-line Diagnostic Method for Bloodstream Infection in Hematologic Patients With Febrile Neutropenia: A Multicenter, Prospective Study.},
journal = {Open forum infectious diseases},
volume = {12},
number = {6},
pages = {ofaf288},
pmid = {40453877},
issn = {2328-8957},
abstract = {Bloodstream infection (BSI) is a frequent but lethal complication in hematologic patients with febrile neutropenia (FN). However, blood culture (BC) only detects an organism in 20%-30% of patients with FN. We aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) as a first-line diagnostic method in BSI. This study was prospectively performed in 4 Chinese hematologic centers. In patients aged ≥15 years with hematologic diseases, peripheral blood specimens were collected per patient for simultaneous BC and mNGS at the onset of FN. The clinical physician and mNGS analysis team were double-blinded, and the adjudication of the clinical diagnosis was evaluated by another expert panel of 4 specialists. The primary endpoint of this study was the diagnostic performance of mNGS. This study was registered on ClinicalTrials.gov. Three hundred FN events were enrolled, including 62 definite BSI, 61 probable BSI, 116 infectious FN other than BSI, 55 noninfectious FN events, and 6 FN of indeterminate cause. Among 62 definite BSI cases, mNGS identified causative pathogens in 59 (95.2%). Concurrent BC initially detected pathogens in 59 cases, and 3 additional pathogens consistent with mNGS were later identified in repeated BC testing. The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were 95.2%, 94.6%, 95.2%, and 94.6%, respectively. The diagnostic time of mNGS was significantly shorter than that of BC (39.7 ± 15.0 vs 119.8 ± 31.9 hours, P < .0001). The findings suggest that the mNGS approach has excellent diagnostic performance for the first-line diagnosis of BSI in patients with FN. The study will promote early diagnosis and better management of the patients.},
}

@article {pmid40453711,
year = {2025},
author = {Zhou, J and Kamau, E and Wei, Q},
title = {Editorial: Targeted metagenomics in pathogen detection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1612802},
pmid = {40453711},
issn = {2235-2988},
}

@article {pmid40452057,
year = {2025},
author = {Francioli, D and Kampouris, ID and Kuhl-Nagel, T and Babin, D and Sommermann, L and Behr, JH and Chowdhury, SP and Zrenner, R and Moradtalab, N and Schloter, M and Geistlinger, J and Ludewig, U and Neumann, G and Smalla, K and Grosch, R},
title = {Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {148},
pmid = {40452057},
issn = {1474-760X},
support = {031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Zea mays/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Stress, Physiological ; Bacillus ; Plant Roots/microbiology ; Soil Microbiology ; *Agricultural Inoculants/physiology ; },
abstract = {BACKGROUND: Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits.

RESULTS: Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores.

CONCLUSIONS: Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.},
}

*Zea mays/microbiology/growth & development
*Rhizosphere
*Microbiota
*Stress, Physiological
Bacillus
Plant Roots/microbiology
Soil Microbiology
*Agricultural Inoculants/physiology

@article {pmid40451466,
year = {2025},
author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P},
title = {Deciphering common bean (Phaseolus Vulgaris L.) microbiome assemblages reveal mechanistic insights into host-pathogen-microbiome interactions.},
journal = {Genomics},
volume = {},
number = {},
pages = {111064},
doi = {10.1016/j.ygeno.2025.111064},
pmid = {40451466},
issn = {1089-8646},
abstract = {Common bean (Phaseolus vulgaris L.) is the primary source of proteins and nutrients in most households in sub-Saharan Africa. However, production of this crop is constrained by several biotic factors. While research on common bean plant-pathogen interactions has predominantly focused on binary relationships, the diversity of microbes naturally inhabiting plant tissues and their interactions has often been overlooked. Recent findings, however, show that these resident microbes actively contribute to plant defense mechanisms, rather than merely acting as passive bystanders. This study aimed to document and explore potential interactions within the common bean microbiome assemblages through field investigations in selected locations across the western regions of Kenya. Common bean leaf samples were collected from farmer's fields along motorable roads 3-5 km apart. Shotgun metagenomic analysis identified a diverse range of microorganisms, including bacteria, fungi, yeast, phytoplasmas, viruses, and bacteriophages, across multiple taxonomic levels-spanning 4 Kingdoms, 136 Phyla, 168 Classes, 360 Orders, 792 Families, 2039 Genera, and 6130 Species-both epiphytic and endophytic, and pathogenic or non-pathogenic. Pseudomonadota consistently showed the highest taxonomic annotation for antimicrobial-resistant organisms, highlighting its central role in resistance across the studied area. The sequences obtained were mapped to the EggNOG, CAZy, and KEGG databases to explore, assign, and predict gene functions. The EggNOG database emphasized the importance of "Replication, recombination, and repair" processes in maintaining genomic stability, along with amino acid transport, energy production, and metabolism. CAZy analysis revealed a significant presence of glycosyltransferases, particularly from GT1 and GT32 families, and noted the role of enzymes like Glycoside Hydrolases in plant defense against pathogens. KEGG pathway analysis underscored the central role of metabolic processes such as energy metabolism, translation, and carbohydrate metabolism. Key pathways linked to plant defense and resilience, including 2-oxocarboxylic acid metabolism, amino acid biosynthesis, and secondary metabolite biosynthesis, were identified. These findings underscore the role of metabolic and enzymatic processes in strengthening plant defenses and stress tolerance while laying the groundwork for multidisciplinary research to advance sustainable agriculture and food safety.},
}

@article {pmid40451005,
year = {2025},
author = {Su, X and Liu, J and Chang, L and Hu, W and Fang, Y and Li, J and Huang, L and Shu, W and Dong, H},
title = {Viral insights into the acidification of sulfidic mine tailings.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138754},
doi = {10.1016/j.jhazmat.2025.138754},
pmid = {40451005},
issn = {1873-3336},
abstract = {The acidification of sulfidic mine tailings, driven primarily by sulfur- and iron-oxidizing microorganisms, can lead to severe environmental pollution and imperil human health. The role of viruses in this process and its underlying mechanisms yet remain poorly understood. In this study, we recovered 623 species-level viral genomes and 322 prokaryotic genomes from seven metagenomes of mine tailings with pH values ranging from 7.51 to 2.13. We observed that acidification drastically altered geochemical properties and degraded environmental quality, characterized by significant decreases in carbon/nitrogen ratio and heavy metal levels. The structure and function of viral communities were significantly correlated with pH and prokaryotic diversity, showing distinct dynamics across different acidification stages, similar to patterns observed in the prokaryotic community. Notably, potential sulfur-oxidizing prokaryotes increased in relative abundance as pH declined, while their virus-host abundance ratio exhibited a significant positive correlation with pH. Results indicated that viral "top-down" predation on sulfur-oxidizing prokaryotes was likely suppressed during acidification, providing a survival advantage to these organisms over iron-oxidizing counterparts. Moreover, viruses likely reprogrammed the sulfur and iron metabolism of prokaryotic hosts and enhanced their adaptability to environmental stressors through auxiliary metabolic genes. Additionally, a pH- and lifestyle-dependent evolutionary scenario for viruses revealed that frequent recombination and the accumulation of synonymous mutations in lytic viruses and chronic Inoviridae, likely increased their intrapopulation diversity and resilience. These findings provide new insights into the multifaceted roles of viruses in mine tailings acidification, deepening understanding of the underlying mechanisms and advancing potential strategies to mitigate associated environmental risks.},
}

@article {pmid40450941,
year = {2025},
author = {Wu, L and Wang, J and Jin, T and Zhou, X and Wang, L},
title = {Lignin-enhanced fungal-bacterial consortium for degradation of petroleum hydrocarbon contaminants.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {125973},
doi = {10.1016/j.jenvman.2025.125973},
pmid = {40450941},
issn = {1095-8630},
abstract = {A lignin-enhanced fungal-bacterial consortium strategy (Bau_Lignin) was proposed to promote the biodegradation of petroleum hydrocarbon contaminants (PHCs), with pyrene and n-docosane selected as representative compounds. Optimal performance was achieved by co-inoculating fungi and bacteria at a 5:5 ratio. Within 12 days, the pyrene removal efficiency of Bau_Lignin was 2.23 times and 1.67 times higher than that of the bacterial consortium (XH40) and the fungal-bacterial consortium (Bau), respectively. Lignin addition enhanced enzyme activities (e.g., ligninolytic enzymes, dioxygenases, dehydrogenases) and increased the abundance of key functional genera (e.g., Pseudomonas, Achromobacter, Stenotrophomonas). Metagenomic sequencing further revealed an enrichment of genes associated with biosurfactant production and oxygenase activity in Bau_Lignin, facilitating mass transfer, hydroxylation, and ring-cleavage processes. Thus, a potential reinforcement mechanism was proposed, highlighting the synergistic interactions among enzyme activities, functional genera, and key functional genes across multiple pathways.},
}

@article {pmid40450938,
year = {2025},
author = {Hou, Y and Jia, R and Zhou, L and Zhang, L and Wei, S and Li, B and Zhu, J},
title = {Alterations in microbial-mediated methane, nitrogen, sulfur, and phosphorus cycling within paddy soil induced by integrated rice-fish farming.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126056},
doi = {10.1016/j.jenvman.2025.126056},
pmid = {40450938},
issn = {1095-8630},
abstract = {Rice paddies are crucial ecosystems, supporting dense microbial populations and playing a significant role in global food security. Integrated rice-fish farming has been recognized as an important agricultural production pattern to enhance agro-ecosystem stability and food productivity. Using metagenomic sequencing, we compared the microbial-mediated soil CH4, N, S, and P cycles in integrated rice-fish farming versus traditional rice monoculture, exploring their potential coupling mechanisms within microbes. Integrated rice-fish farming has significantly impacted these microbial-mediated cycles in paddy soil, altering the overall functional diversity, sum abundance, and microbial host diversity for the CH4, N, S, and P cycling genes. Specifically, it suppressed the denitrification, assimilatory nitrate reduction (ANR), assimilatory sulfate reduction (ASR), thiosulfate oxidation, organic phosphoester hydrolysis, and two-component system pathways and most of their associated functional genes, while enhanced the acetoclastic methanogenesis and the reduction of tetrathionate to thiosulfate processes. Compared to traditional rice monoculture, integrated rice-fish farming resulted in metagenome-assembled genomes (MAGs) with fewer and more isolated biogeochemical cycling genes, lacking potential couplings among multi-element cycles. Additionally, this farming approach increased the soil nutrient levels including the total carbon (TC), total organic carbon (TOC), total nitrogen (TN), total sulfur (TS), and total phosphorus (TP) concentrations, which have been identified as the most crucial factors driving the alterations in microbial functional genes/pathways involved in biogeochemical cycling processes in our study. Overall, integrated rice-fish farming dynamically altered the microbial-mediated CH4, N, S, and P cycles and their potential couplings within microbes through promoting the soil nutrient levels, which could favor rice growth, thus maintaining food security and providing refined knowledge for maintaining soil sustainability.},
}

@article {pmid40450783,
year = {2025},
author = {Rajput, V and Pramanik, R and Nannaware, K and Shah, P and Bhalerao, A and Jain, N and Shashidhara, LS and Kamble, S and Dastager, S and Dharne, M},
title = {Metagenomics based longitudinal monitoring of antibiotic resistome and microbiome in the inlets of wastewater treatment plants in an Indian megacity.},
journal = {The Science of the total environment},
volume = {986},
number = {},
pages = {179691},
doi = {10.1016/j.scitotenv.2025.179691},
pmid = {40450783},
issn = {1879-1026},
abstract = {The growing threat of antimicrobial resistance (AMR) poses a significant global challenge, undermining advancements in healthcare, agriculture, and life expectancy. Despite its critical importance, data on population-level AMR trends, including seasonal and temporal variations, remain scarce. In this study, we conducted metagenomic analysis on 190 wastewater samples collected monthly from December 2022 to December 2023 in Pune, India, to assess the diversity, dynamics, and co-occurrence of AMR determinants. Using nanopore shotgun sequencing, we generated 87.86 Gbp of data, enabling the taxonomic classification of 157 bacterial phyla and 3291 genera. Proteobacteria dominated the microbial community, with notable seasonal shifts, including increased Streptococcus abundance correlating with SARS-CoV-2 viral surges in March 2023. We identified 637 distinct antimicrobial resistance genes (ARGs) associated with 29 antibiotic classes, with multidrug, macrolide-lincosamide-streptogramin, beta-lactams, and tetracyclines genes being the most prevalent, particularly within WHO priority pathogens such as Enterobacteriaceae and Pseudomonas. Temporal normalization of ARG abundance revealed significant seasonal variability, peaking during winter, potentially driven by increased antibiotic use for respiratory infections. The integration of viral load data with AMR trends highlighted complex interactions between viral outbreaks and AMR dissemination. This study demonstrates the potential of wastewater surveillance as an early warning system for AMR, providing valuable insights into environmental and community resistance dynamics. Our results underscore the importance of integrated AMR surveillance to inform public health strategies aimed at mitigating the global AMR threat.},
}

@article {pmid40450775,
year = {2025},
author = {Han, M and Li, S and Li, Z and Wang, A and Ren, N and Ho, SH},
title = {Layer-specific photo-metabolic specialization of encapsulated microalgae: A strategy for synchronous multi-nitrogen elimination from wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123926},
doi = {10.1016/j.watres.2025.123926},
pmid = {40450775},
issn = {1879-2448},
abstract = {Conventional wastewater treatment (WWT) systems face persistent challenges in simultaneous ammonium (NH4[+]-N) and nitrate (NO3[-]-N) removal due to substrate competition and energy-intensive multi-stage processes. This study presents an innovative strategy leveraging encapsulated microalgal systems to achieve synchronous 94.45 % NH4[+]-N and 98.47 % NO3[-]-N removal within a single reactor through spatial reprogramming of photosynthetic energy allocation. By exploiting the structural heterogeneity within alginate-encapsulated beads, depth-stratified metabolic zones were created that challenge the long-held dogma of microalgae's inherent NH4[+]-N preference. Multidimensional analyses, including spatial distribution mapping, molecular dynamics simulations, metagenomic profiling and photosynthetic regulation, further revealed that light-modulated oxygen gradients, polymer-mediated solute transport, and stratified photo-metabolic specialization synergistically reprogramed microalgal nitrogen metabolism, enabling co-utilization of NH4[+]-N and NO3[-]-N. The system demonstrated robust dual-nitrogen assimilation efficiencies under varying environmental conditions, transcending conventional substrate utilization hierarchies. This transformative approach not only resolves the dilemma of mixed nitrogen pollution but also advances sustainable WWT by integrating pollutant removal with biomass valorization. The findings provide mechanistic insights into microalgal metabolic plasticity and offer a scalable, energy-efficient solution to upgrade traditional denitrification technologies, aligning with urgent demands for circular economy in water resource management.},
}

@article {pmid40450375,
year = {2025},
author = {Kuhar, U and Krapež, U and Slavec, B and Račnik, J and Šenica Kavčič, P and Jamnikar-Ciglenecki, U},
title = {Virome analysis suggests deltacoronaviruses and picornaviruses as a probable cause of severe intestinal disease on three quail farms.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {54},
pmid = {40450375},
issn = {2524-4671},
support = {research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; },
abstract = {BACKGROUND: Quail farming is increasingly popular mainly due to higher market interest in meat and eggs. However, quails are susceptible to several common poultry viral infections, especially in intensive farming systems. Enteric viruses in poultry can cause significant economic losses, particularly in young birds. Mixed viral infections often exacerbate disease severity. Gamma and deltacoronaviruses are known causes of enteritis in quails, although infections with coronaviruses as well as picornaviruses may be also asymptomatic. Advanced diagnostic tools like next-generation sequencing (NGS) and metagenomics have improved understanding of these infections, yet knowledge gaps persist, and new viruses are continually being identified.

RESULTS: Three outbreaks of enteritis with high mortality in quail farms were investigated using NGS with a metagenomic approach. We found that coronaviruses, picornaviruses (anativiruses) and parvoviruses were highly abundant in samples from investigated outbreaks. Viruses belonging to the families Adenoviridae, Astroviridae and Flaviviridae were less abundant and not present in all samples. Coronaviruses and picornaviruses were detected in all outbreaks, while parvovirus was detected only in one. The complete genomes of three quail deltacoronaviruses, three quail anativiruses and one quail chaphamaparvovirus were determined by NGS. Phylogenetic analysis revealed that the coronavirus and anativirus strains from this study were closely related to the other relevant quail virus strains. As for chaphamaparvovirus, this is the first report of this virus in quails.

CONCLUSIONS: The data from this study indicates the presence of numerous viruses in samples from quails with enteritis that have been overlooked by standard diagnostic approaches but could have played a role in the development of enteritis. These results may support further analysis of virome in healthy quails and in those with different clinical signs.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00428-6.},
}

@article {pmid40450182,
year = {2025},
author = {Wang, C and Dong, T and Rong, X and Yang, Y and Mou, J and Li, J and Ge, J and Mu, X and Jiang, J},
title = {Microbiome in prostate cancer: pathogenic mechanisms, multi-omics diagnostics, and synergistic therapies.},
journal = {Journal of cancer research and clinical oncology},
volume = {151},
number = {6},
pages = {178},
pmid = {40450182},
issn = {1432-1335},
support = {82172230//the National Natural Science Foundation of China/ ; 21ZGY29//the Changchun Scientific and Technological Development Program/ ; 3R218FM83430//Life Spring AKY Pharmaceuticals/ ; 20240205001YY//the Jilin Scientific and Technological Development Program/ ; 2017F014//the Jilin Health Service Capacity Improvement Program/ ; },
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology ; Male ; *Microbiota ; Metagenomics/methods ; Multiomics ; },
abstract = {BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related deaths in men, with the microbiome emerging as a significant factor in its development and progression. Understanding the microbiome's role could provide new insights into PCa pathogenesis and treatment.

OBJECTIVE: This review aims to explore the interactions between the microbiome and PCa, focusing on microbial imbalances and their effects on immune responses, inflammation, and hormone levels. It also discusses advanced research techniques and the potential for microbiome modulation in PCa management.

METHODS: The review synthesizes current literature on the microbiome's role in PCa, highlighting differences in microbial composition between cancerous and healthy prostate tissues. It examines techniques such as high-throughput sequencing and metagenomics and explores the mechanisms through which the microbiome influences PCa.

CONCLUSIONS: The review reveals substantial microbial differences in prostate tissues of PCa patients compared to healthy individuals, indicating a potential link between microbiome alterations and disease progression. It highlights the promise of microbiome-based strategies for diagnosis and treatment and underscores the need for further research into personalized, microbiome-centric approaches for PCa management.},
}

Humans
*Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology
Male
*Microbiota
Metagenomics/methods
Multiomics

@article {pmid40450127,
year = {2025},
author = {Yan, P and Zhu, J and Ji, Q and Hou, G and Liang, G and Liu, X and Liu, R},
title = {Significant impact of bleaching treatment on phage-host interaction dynamics in a full-scale wastewater treatment plant.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19165},
pmid = {40450127},
issn = {2045-2322},
support = {No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; },
mesh = {*Bacteriophages/genetics/physiology ; *Wastewater/microbiology/virology ; Sewage/microbiology/virology ; *Bacteria/genetics/virology ; *Water Purification/methods ; Genome, Viral ; Metagenomics ; *Host Microbial Interactions ; },
abstract = {The temporal dynamics of phage-host interactions within full-scale biological wastewater treatment (BWT) plants remain inadequately characterized. Here, we provide an in-depth investigation of viral and bacterial dynamics over a nine-year period in an activated sludge BWT plant, where bleach addition was applied to control sludge foaming. By conducting bioinformatic analyses on 98 metagenomic time-series samples, we reconstructed 3,486 bacterial genomes and 2,435 complete or near-complete viral genomes, which were classified into 361 bacterial and 889 viral clusters, respectively. Our results demonstrate that the primary bleaching event induced significant shifts in both bacterial and viral communities, as well as in virus-host interactions, as evidenced by alterations in bacteria-virus interaction networks and virus-to-host ratio dynamics. Following bleaching, the bacteria-virus network became less interconnected but more compartmentalized. Viral communities mirrored bacterial dynamics, indicating a strong coupling in phage-host interactions. Among the identified virus-host pairs, many exhibited a decelerating rise in viral abundance relative to host abundance, with virus-to-host ratios generally displaying a negative correlation with host abundance. This trend was particularly pronounced in virus-host pairs where viruses harbored integrase genes, indicative of temperate dynamics resembling a "Piggyback-the-Winner" model. Notably, the bleaching intervention appeared to induce a transition from lysogeny to lysis in viruses associated with some foaming-related bacterial species, suggesting a potential virus-involved indirect mechanism by which bleaching mitigates sludge foaming.},
}

*Bacteriophages/genetics/physiology
*Wastewater/microbiology/virology
Sewage/microbiology/virology
*Bacteria/genetics/virology
*Water Purification/methods
Genome, Viral
Metagenomics
*Host Microbial Interactions

@article {pmid40450092,
year = {2025},
author = {Nesti, DR and Hayashida, K and Sugi, T and Artama, WT and Wijayanto, H and Kawai, N and Yamagishi, J},
title = {Development of a semicomprehensive detection method for paramyxoviruses and its validation using Indonesian bats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19154},
pmid = {40450092},
issn = {2045-2322},
support = {0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; 0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; 0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; },
mesh = {*Chiroptera/virology ; Animals ; Indonesia ; *Paramyxoviridae Infections/virology/veterinary/diagnosis ; *Paramyxoviridae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Genome, Viral ; Zoonoses/virology ; },
abstract = {An outbreak of zoonotic diseases is one of the worldwide threats. Bats were reported as important reservoir hosts for many emerging zoonotic diseases. To mitigate the risk, understanding bat virome and their distribution is indispensable. Universal detection methods that can simultaneously identify multiple viruses are some of the most promising approaches. Here, we developed a semicomprehensive detection method integrating group-wide RT-PCR for paramyxoviruses and multiplex next-generation sequencing. The RT-PCR consists of three sets of degenerative primers covering viruses from Paramyxoviridae, including Pneumoviridae, which have now been reclassified into a distinct family. Index nucleotides were added to the primers to enable cost-effective multiplex sequencing, and the length of index was optimized to increase sensitivity. The method was applied to tracheal and rectal swabs from 135 bats captured in Indonesia. A conventional RT-PCR test validated the NGS results. Collectively, seven sequences of novel paramyxovirus-like similar to Pararubulavirus, Orthorubulavirus, and Henipavirus were successfully identified from seven bat samples. Furthermore, sequences between the two different target locations detected by NGS in the virus genomes were verified by RT-PCR. The similarity of the obtained sequences to the known paramyxoviruses sequences was relatively low, ranging from 70.88 to 82.44%. It suggests that the obtained sequences from novel viruses and the zoonotic risk of those novel viruses remain unknown. This cost-affordable, semi-comprehensive, pan-paramyxovirus test can be applied to other samples for viral genome surveillance, and the same strategy can be implemented to other pathogens for zoonosis control.},
}

*Chiroptera/virology
Animals
Indonesia
*Paramyxoviridae Infections/virology/veterinary/diagnosis
*Paramyxoviridae/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/methods
Phylogeny
Reverse Transcriptase Polymerase Chain Reaction/methods
Genome, Viral
Zoonoses/virology

@article {pmid40450052,
year = {2025},
author = {Kundral, S and Giang, PD and Grundon, LR and Supper, JM and Khare, SK and Bernhardt, PV and Evans, P and Bell, SG and De Voss, JJ},
title = {Characterisation of the thermophilic P450 CYP116B305 identified using metagenomics-derived sequence data from an Australian hot spring.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {133},
pmid = {40450052},
issn = {1432-0614},
support = {FT210100812//Australian Research Council/ ; DP240101500//Australian Research Council/ ; DP240101500//Australian Research Council/ ; },
mesh = {*Cytochrome P-450 Enzyme System/genetics/metabolism/chemistry/isolation & purification ; *Hot Springs/microbiology ; Escherichia coli/genetics/metabolism ; Metagenomics ; Enzyme Stability ; Oxidation-Reduction ; Heme/metabolism ; Recombinant Proteins/genetics/metabolism/chemistry/isolation & purification ; Hot Temperature ; Australia ; Queensland ; },
abstract = {Cytochrome P450 enzymes (P450s) have gained significant attention due to their remarkable ability to oxidise unactivated C-H bonds with high regio- and stereoselectivity. Their industrial utility is often limited by challenges such as low stability, poor expression, and dependence on elusive redox partners. These issues have driven the search for more robust P450s, especially those that are inherently stable under extreme conditions typical of industrial processes. "Self-sufficient P450s" in which the P450 heme domain is naturally fused to redox domains in a single polypeptide chain eliminates the need to identify and separately express required redox partners. Furthermore, P450s from thermophilic organisms are more temperature tolerant with fewer stability issues. This study presents a self-sufficient P450, CYP116B305, identified from metagenomically assembled genomes from Innot Hot Springs (71 °C), located in North Queensland, Australia. CYP116B305 was heterologously expressed in Escherichia coli and purified using standard protocols. Investigation of the thermal stability of CYP116B305 revealed a robust heme domain with a [15]T50 value of 56.9 ± 0.1 °C, while the reductase domain exhibited slightly lower stability, with a [15]T50 value of 52.5 ± 0.5 °C. Further characterisation revealed that CYP116B305 efficiently bound to and hydroxylated 2-hydroxyphenylacetic acid (2-HPA) at the C-5 position, yielding homogentisic acid. The catalytic parameters, including the coupling efficiency and rate of electron transfer from the NADPH cofactor to the P450 heme, were shown to improve at an elevated temperature (45 °C) compared to 25 °C. The combination of the self-sufficiency and improved stability makes CYP116B305 a promising platform for biotechnological applications and biocatalyst engineering. KEY POINTS: • Hot spring metagenomics reveals thermostable P450s of biocatalytic value. • CYP116B305 shows enhanced catalytic activity at elevated temperature (45 °C). • CYP116B305 is a promising platform enzyme for diverse biotechnological use.},
}

*Cytochrome P-450 Enzyme System/genetics/metabolism/chemistry/isolation & purification
*Hot Springs/microbiology
Escherichia coli/genetics/metabolism
Metagenomics
Enzyme Stability
Oxidation-Reduction
Heme/metabolism
Recombinant Proteins/genetics/metabolism/chemistry/isolation & purification
Hot Temperature
Australia
Queensland

@article {pmid40449763,
year = {2025},
author = {Liu, W and Chen, S and Yang, J and Chen, Y and Yang, Q and Lu, L and Li, J and Yang, T and Zhang, G and Hu, J},
title = {Characterization of blood and urine microbiome temporal variability in patients with acute myeloid leukemia.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107734},
doi = {10.1016/j.micpath.2025.107734},
pmid = {40449763},
issn = {1096-1208},
abstract = {BACKGROUND: Investigating the microbiota of blood and urine from acute myeloid leukemia (AML) patients is essential to unravel the complex role of microbiota in systemic host-microbe interactions and implications.

METHODS: We conducted a longitudinal observational study to characterize the temporal dynamics of blood and urine microbiota in 27 AML patients, utilizing metagenomic analysis pipeline for microbial identification to identify disease-associated microbial signatures.

RESULTS: The composition of blood and urine microbiota of AML was dominated by Proteobacteria phylum in blood, Firmicutes phylum in urine. The species and diversity of blood and urine microbiota did not have difference between AML patients and healthy controls. Restitution of alpha and beta diversity of blood microbiota and urine microbiota to resemble that of healthy controls occurred after cessation of treatment. Temporal variation of urine microbiome was higher than blood after treatment which was closely related to pathogenic bacteria and beneficial bacteria measured by coefficient of variation (CV) of alpha diversity. The temporal variability of urine microbiota was significantly correlated with platelet and exposure of levofloxacin. The variation of microbiome of AML patients with infection was found that the relative abundance of Burkholderia significantly enriched in blood and urine which had high accuracy and sensitivity. The correlation between blood microbiota and serum amino acid metabolites was similar to that between gut microbiota and serum metabolites.

CONCLUSION: This study represents the first comprehensive investigation to quantify the longitudinal variability of blood and urine microbiota in AML patients, revealing distinct patterns compared to gut microbiota and associations with adverse clinical outcomes. Our findings highlight the potential of leveraging stabilizing taxa as a target for microbiome restoration.},
}

@article {pmid40449445,
year = {2025},
author = {Zheng, Z and Gustavsson, DJI and Zheng, D and Holmin, F and Falås, P and Wilén, BM and Modin, O and Persson, F},
title = {Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {125972},
doi = {10.1016/j.jenvman.2025.125972},
pmid = {40449445},
issn = {1095-8630},
abstract = {Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m[2]·d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m[2]·d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.},
}

@article {pmid40449443,
year = {2025},
author = {Hou, M and Gu, X and Lai, W and Fan, Y and Sun, S and Yan, P and Zhang, Y and Zheng, X and He, S},
title = {Sulfur-iron interactions forming activated FexSy pool in-situ to synergistically improve nitrogen removal in denitrification system.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126047},
doi = {10.1016/j.jenvman.2025.126047},
pmid = {40449443},
issn = {1095-8630},
abstract = {Sulfur-iron coupling has received increasing attention for improving nitrogen removal. However, the boosting mechanisms of denitrification in sulfur-iron coupling biological system are still ambiguous, and no reasonable explanation has been given for the mismatch between the amount of S[0] loss and the amount of SO4[2-] produced in the coupling system. Therefore, this study established sulfur-iron coupling denitrification systems, and investigated the nitrogen removal performances and coupling mechanisms of the systems. The research results showed that the TN removal efficiencies of the sulfur-iron coupling systems were 122.73-149.27 % higher than those of the single electron donor systems. In the process of nitrogen removal, about 26.03-35.32 % of the more leached S[0] and Fe[0] in the coupling systems co-precipitated to form activated FexSy pool in-situ, contributing about 25.41 % of the nitrogen removal and allowing the systems to remove 76.32-100 % of TN without external electron donors; moreover, the oxidation process of S[2-] provided electrons for the reduction of Fe (Ⅲ) to Fe (Ⅱ), generating more electron donors. Metagenomic sequencing results showed significant increases in the richness and diversity of functional microorganisms associated with sulfur and iron autotrophic denitrification in the coupling systems, and their contributions to the key genes in the denitrification, sulfur transformation and iron cycle processes increased substantially. In general, this study offered deeper understanding for assessing the nitrogen removal potential of the sulfur-iron coupling system, as well as investigating the interactions between S[0] and Fe[0] and elucidating nitrogen removal pathways within the system.},
}

@article {pmid40449312,
year = {2025},
author = {Xia, Z and Ng, HY and Bae, S},
title = {Synergistic microalgal-bacterial interactions enhance nitrogen removal in membrane-aerated biofilm photoreactors treating aquaculture wastewater under salt stress: Insights from metagenomic analysis.},
journal = {Water research},
volume = {283},
number = {},
pages = {123878},
doi = {10.1016/j.watres.2025.123878},
pmid = {40449312},
issn = {1879-2448},
abstract = {This study investigates the membrane-aerated biofilm photoreactor (MABPR) for treating aquaculture effluents with low C/N ratio and elevated salinity (0.5%-3.2%). The MABPR integrated biofilm reactors with microalgal-bacterial consortia, achieving superior total inorganic nitrogen (TIN) removal by leveraging counter-diffusional biofilm properties, bubbleless aeration, and enhanced microalgal productivity. The system consistently outperformed conventional reactors, achieving 84.7 ± 1.9% TIN removal at 3.2% salinity with TIN removal flux increasing from 0.82 ± 0.04 to 1.22 ± 0.07 g/m[2] d. The MABPR promoted microalgal proliferation (Chl-a/VSS: 8.08-15.04 mg/g) and higher biomass productivity (1.83 g/m[2] d) compared to SBBPR and MABR. Elevated salinity stimulated extracellular polymeric substance (EPS) production, reinforcing biofilm stability and microbial resilience. The MABPR demonstrated 22%-65% higher nitrogen removal efficiency than controls at the highest salinity. Canonical nitrification-denitrification remained the primary nitrogen removal pathway, with short-cut nitrification-denitrification contributing under salt stress. Metagenomic analysis revealed bidirectional adaptation between microalgae and bacteria, with enriched nitrogen assimilation (GS/GOGAT pathway) compensating for bacterial deficits. Microalgae facilitated pollutant removal through ammonia uptake and dissolved organic matter release, supporting denitrification. At 3.2% salinity, Nitrosomonas and Nitrobacter abundance increased by 42.6% and 35.8%, while denitrifiers Denitromonas and Hoeflea dominated, comprising 59.4% and 35.9% of the population. The MABPR further promoted the synthesis of growth cofactors (vitamins, phytohormones), enhancing microalgal productivity and stress resilience. These synergistic microalgal-bacterial interactions supported pollutant removal, showcasing the MABPR as a robust, sustainable solution for aquaculture wastewater treatment and resource recovery under salt stress.},
}

@article {pmid40449097,
year = {2025},
author = {Cañete-Reyes, Á and González, JG and Alteio, LV and Rodríguez-Lázaro, D and Hernández, M},
title = {Aetiology and environmental factors of the Watery Mouth Disease associated with neonatal diarrhoea in lambs.},
journal = {Veterinary microbiology},
volume = {306},
number = {},
pages = {110542},
doi = {10.1016/j.vetmic.2025.110542},
pmid = {40449097},
issn = {1873-2542},
abstract = {Watery Mouth Disease is the main disease in neonatal lambs, causing great economic losses. Despite this, the cause of the condition remains poorly understood. Therefore, we have analysed the main bacteria found in sick animals, their intestinal and temporal distribution, as well as the main sources of contamination. Twelve different farms were sampled, from which 331 samples were taken in total. From these samples, 184 environments were analyzed using 16S rRNA amplicon sequencing, 164 isolates were identified by whole genome sequencing and 35 bacterial counts were performed. The dominant bacterial groups at the rectal level were Escherichia-Shigella (36 %) and Clostridium (29 %), with a homogeneous distribution along the digestive tract and a maximum abundance ranging between 12 and 24 hours of lamb life. Within Escherichia-Shigella: Escherichia coli and Escherichia fergusonii and within Clostridium: Clostridium perfringens, Clostridium cadaveris, Clostridium tertium and Clostridium paraputricum were identified as the main isolates present in sick animals. The high presence of Clostridium strains, especially potentially pathogenic species like C. perfringens in sick animals, point out Clostridium as a new important protagonist of watery mouth disease and the need of their inclusion in future studies. In particular, bedding was established as the main microbial contaminating factor, reaching the highest increase 48 hours after removal and cleaning of the lambing area (i.e. 8.03 ×10[8], 1.88 ×10[6], 3.88 ×10[6], 4.85 ×10[7] and 4.00 ×10[5] CFU/g for mesophilic aerobes, coliforms, E. coli, mesophilic anaerobes and sporulates, respectively). These results highlight the need to increase cleanliness in bedding to reduce the presence of these bacteria.},
}

@article {pmid40448586,
year = {2025},
author = {Jones, LM and El Aidy, S},
title = {Electroactive ecosystem insights from corrosion microbiomes inform gut microbiome modulation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf112},
pmid = {40448586},
issn = {1751-7370},
abstract = {Electroactive microorganisms influence environmental and host-associated ecosystems through their ability to mediate extracellular electron transfer. This review explores parallels between EAM-driven microbiologically influenced corrosion systems and the human gut microbiome. In corrosion, EAMs contribute to biofilm formation, redox cycling, and material degradation through mechanisms such as direct electron transfer and syntrophic interactions. Similarly, gut-associated EAMs regulate redox balance, drive short-chain fatty acid production, and shape host-microbe interactions. Despite differing contexts, both systems share traits like anoxic niches, biofilm formation, and metabolic adaptability. Insights from well-characterized corrosion microbiomes offer valuable frameworks to understand microbial resilience, electron transfer strategies, and interspecies cooperation in the gut. Bridging knowledge between these systems can inform microbiome engineering approaches aimed at promoting gut health, highlighting the need for further functional metagenomics and exploration of archaeal contributions to biofilm stability and redox modulation.},
}

@article {pmid40448221,
year = {2025},
author = {Fan, KC and Lin, CC and Chiu, YL and Koh, SH and Liu, YC and Chuang, YF},
title = {Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {122},
pmid = {40448221},
issn = {1758-9193},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology/pathology/metabolism ; *Alzheimer Disease/microbiology/pathology/metabolism ; Male ; Female ; Aged ; Feces/microbiology ; Biomarkers ; Brain/pathology/metabolism ; Aged, 80 and over ; Dysbiosis ; tau Proteins ; Middle Aged ; },
abstract = {BACKGROUND: Emerging evidence highlights the bidirectional communication between the gut microbiota and the brain, suggesting a potential role for gut dysbiosis in Alzheimer's disease (AD) pathology and cognitive decline. Existing literature on gut microbiota lacks species-level insights. This study investigates gut microbiota alterations in mild cognitive impairment (MCI), focusing on their association with comprehensive AD biomarkers, including amyloid burden, tau pathology, neurodegeneration, and cognitive performance.

METHODS: We analyzed fecal samples from 119 individuals with MCI and 320 cognitively normal controls enrolled in the Taiwan Precision Medicine Initiative on Cognitive Impairment and Dementia cohort. Shotgun metagenomic sequencing was conducted with taxonomic profiling using MetaPhlAn4. Amyloid burden and plasma pTau181 were quantified via PET imaging and Simoa assays, respectively, while APOE genotyping was performed using TaqMan assays. Microbial diversity, differential abundance analysis, and correlation mapping with neuropsychological and neuroimaging measures were conducted to identify gut microbiota species signatures associated with MCI and AD biomarkers.

RESULTS: We identified 59 key microbial species linked to MCI and AD biomarkers. Notably, species within the same genera, such as Bacteroides and Ruminococcus, showed opposing effects, while Akkermansia muciniphila correlated with reduced amyloid burden, suggesting a protective role. Functional profiling revealed microbial pathways contributing to energy metabolism and neuroinflammation, mediating the relationship between gut microbes and brain health. Co-occurrence network analyses demonstrated complex microbial interactions, indicating that the collective influence of gut microbiota on neurodegeneration.

CONCLUSIONS: Our findings challenge genus-level microbiome analyses, revealing species-specific modulators of AD pathology. This study highlights gut microbial activity as a potential therapeutic target to mitigate cognitive decline and neurodegeneration.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognitive Dysfunction/microbiology/pathology/metabolism
*Alzheimer Disease/microbiology/pathology/metabolism
Male
Female
Aged
Feces/microbiology
Biomarkers
Brain/pathology/metabolism
Aged, 80 and over
Dysbiosis
tau Proteins
Middle Aged

@article {pmid40447717,
year = {2025},
author = {Lai, LM and Dai, QB and Cao, ML and Liu, Y and Zhao, R and Yuan, L},
title = {Clinical utility of metagenomic next-generation sequencing in pathogen detection for lower respiratory tract infections.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19039},
pmid = {40447717},
issn = {2045-2322},
support = {2024B1362//the Science and Technology Plan of Jiangxi Provincial Health Commission/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commission/ ; 20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; },
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Retrospective Studies ; Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; },
abstract = {Identifying pathogens in patients with lower respiratory tract infections (LRTIs) has always been a major challenge. Metagenomic next-generation sequencing (mNGS) technology is a new diagnostic tool that can assist clinicians in the etiological diagnosis of LRTIs. This study focuses on the clinical value of mNGS in the diagnosis of suspected LRTIs. A total of 400 patients with suspected LRTIs admitted at the First Affiliated Hospital of Nanchang University from July 2020 to February 2023 were enrolled in this retrospective study. Bronchoalveolar lavage fluid (BALF) samples were analyzed using both mNGS and culture methods. The diagnostic accuracy of two approaches was systematically compared against the final clinical diagnosis, which served as the gold-standard reference. Of the 400 enrolled cases, 82.3% (329/400) were diagnosed with LRTIs. From these cases, mNGS identified 76.8% (307/400) truepositive cases, 8.0% (32/400) falsepositive cases, 9.8% (39/400) truenegative cases, and 5.5% (22/400) falsenegative cases. mNGS demonstrated significantly higher sensitivity [93.3% (307/329) vs. 55.6(183/329)%] alongside greater negative predictive values [63.9% (39/61) vs.25.9%(51/197)], whereas culture offered higher specificity [54.9%(39/71) vs. 71.8%(51/71)]. The area under the receiver-operating curve (AUC) of mNGS[0.744(95%CI: 0.67-0.82)]was significantly higher than that of cultures[0.636(95%CI: 0.57-0.71)]. Specifically, mNGS detected more Streptococcus pneumoniae (7.0% vs. 0%), Haemophilus influenzae (6.7% vs. 0%), Aspergillus (9.4% vs. 3.5%), Pneumocystis jirovecii (11.9% vs. 0%) and other intracellular pathogens. Of the 329 patients with LRTIs, antibiotic treatment was modified based on the mNGS results in more than half of the patients(50.5%,166/329), including 20 cases of adjusted antimicrobial regimens, 70 cases de-escalated the empirical antibiotic treatment, and 76 patients escalated the treatment by increasing dosage or medication. 60.8%(101/166) of patients responded to modified antibiotic treatment. Significant benefits of mNGS have been shown in pathogen identification and antimicrobial treatment stewardship in patients with LRTIs. For those with suboptimal therapeutic responses, physicians should be alert to some emerging intracellular pathogens, including Chlamydia psittaci, Mycobacterium tuberculosis, and Pneumocystis jirovecii.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
Female
Male
*Metagenomics/methods
Middle Aged
Retrospective Studies
Aged
Adult
Bronchoalveolar Lavage Fluid/microbiology
Sensitivity and Specificity

@article {pmid40447596,
year = {2025},
author = {Wang, X and Jiang, Q and Tian, X and Chen, W and Mai, J and Lin, G and Huo, Y and Zheng, H and Yan, D and Wang, X and Li, T and Gao, Y and Mou, X and Zhao, W},
title = {Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {92},
pmid = {40447596},
issn = {2055-5008},
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Metagenomics/methods ; China ; *Lactobacillus/genetics/isolation & purification/classification/physiology ; Adult ; Gardnerella vaginalis/growth & development ; Microbiota ; Vaginosis, Bacterial/microbiology ; Biofilms/growth & development ; Asian People ; Pregnant People ; Young Adult ; },
abstract = {This study investigated the relationship between vaginal microbiota and women's health conditions in 95 Chinese pregnant women in their third trimester. We conducted vaginal metagenomic analysis, examining species, functional pathways, and genes, and utilized correlation and LEfSe analyses to link microbiota to health conditions. Results revealed that healthy participants exhibited higher levels of Lactobacillus iners, with its abundance associated with tetrahydrofolate biosynthesis pathways. They also possessed more glycosyltransferase and ErmB antibiotic resistance genes compared to women with diagnosed conditions. Comparative genomics demonstrated that L. iners strains linked to bacterial vaginosis (BV) possessed more genes encoding biofilm-associated YhgE/Pip domain-containing proteins than healthy-associated strains. Notably, three BV-associated L. iners strains exhibited stronger biofilm formation abilities than four healthy-associated strains isolated in this study. Also, four out of seven L. iners strains inhibited the growth of Gardnerella vaginalis. Overall, L. iners may help maintain vaginal ecosystem stability in Chinese pregnant women.},
}

Humans
Female
*Vagina/microbiology
Pregnancy
*Metagenomics/methods
China
*Lactobacillus/genetics/isolation & purification/classification/physiology
Adult
Gardnerella vaginalis/growth & development
Microbiota
Vaginosis, Bacterial/microbiology
Biofilms/growth & development
Asian People
Pregnant People
Young Adult

@article {pmid40447587,
year = {2025},
author = {Paluoja, P and Vaher, M and Teder, H and Krjutškov, K and Salumets, A and Raime, K},
title = {Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {91},
pmid = {40447587},
issn = {2396-8370},
support = {616219790085//European Agricultural Fund for Rural Development/ ; 616219790085//European Agricultural Fund for Rural Development/ ; 616219790085//European Agricultural Fund for Rural Development/ ; },
abstract = {Honey's DNA mixture originates from various organisms like plants, arthropods, fungi, bacteria, and viruses. Conventional methods like melissopalynological analysis and targeted honey DNA metabarcoding offer a limited view of honey's biological composition. We conducted a honey bulk DNA metagenomic analysis to characterize the honey's taxonomic composition and identify honey bee-related pathogens and parasites based on 266 Estonian and 103 foreign honey samples. 70.4% of the DNA in Estonian honey was derived from green plant families like Brassicaceae, Rosaceae, Fabaceae, and Pinaceae. Geographical distribution analysis revealed distinct botanical compositions between Estonian mainland and island samples. The bacterial family Lactobacillaceae was prevalent overall, reflecting the honey bee microbiota in honey. We detected 12 honey bee pathogens and parasites, including Paenibacillus larvae, Nosema ceranae, Varroa destructor, and Aethina tumida. In conclusion, the study underscores the potential of bulk DNA-based non-targeted metagenomic approaches for monitoring honey bee health, environment, and honey composition, origin, and authenticity.},
}

@article {pmid40447574,
year = {2025},
author = {Rodríguez Del Río, Á and Scheu, S and Rillig, MC},
title = {Soil microbial responses to multiple global change factors as assessed by metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5058},
pmid = {40447574},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects ; Metagenome ; Soil/chemistry ; Droughts ; Microbiota/genetics ; Salinity ; *Climate Change ; Global Warming ; },
abstract = {Anthropogenic activities impose multiple concurrent pressures on soils globally, but responses of soil microbes to multiple global change factors are poorly understood. Here, we apply 10 treatments (warming, drought, nitrogen deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides and insecticides) individually and in combinations of 8 factors to soil samples, and monitor their bacterial and viral composition by metagenomic analysis. We recover 742 mostly unknown bacterial and 1865 viral Metagenome-Assembled Genomes (MAGs), and leverage them to describe microbial populations under different treatment conditions. The application of multiple factors selects for prokaryotic and viral communities different from any individual factor, favouring the proliferation of potentially pathogenic mycobacteria and novel phages, which apparently play a role in shaping prokaryote communities. We also build a 25 M gene catalog to show that multiple factors select for metabolically diverse, sessile and non-biofilm-forming bacteria with a high load of antibiotic resistance genes. Finally, we show that novel genes are relevant for understanding microbial response to global change. Our study indicates that multiple factors impose selective pressures on soil prokaryotes and viruses not observed at the individual factor level, and emphasizes the need of studying the effect of concurrent global change treatments.},
}

*Soil Microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/drug effects
Metagenome
Soil/chemistry
Droughts
Microbiota/genetics
Salinity
*Climate Change
Global Warming

@article {pmid40446767,
year = {2025},
author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A},
title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.},
journal = {Water research},
volume = {284},
number = {},
pages = {123887},
doi = {10.1016/j.watres.2025.123887},
pmid = {40446767},
issn = {1879-2448},
abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.},
}

@article {pmid40446617,
year = {2025},
author = {Rono, JK and Zhang, Q and He, Y and Zhao, L and Wang, S and Lyu, Y and Li, C and Ngigi, AN and Yang, ZM and Feng, Z},
title = {Identification and characterization of halotolerant multifunctional GH6 endoglucanases ZFEG1605 and ZFEG1663 from Mt. Everest soil metagenome.},
journal = {Carbohydrate research},
volume = {554},
number = {},
pages = {109549},
doi = {10.1016/j.carres.2025.109549},
pmid = {40446617},
issn = {1873-426X},
abstract = {Environmental microorganisms express enzymes with unique hydrolytic activity, stability, and kinetic parameters, which are of great interest for biotechnological applications. In this study, two novel endoglucanases, ZFEG1605 and ZFEG1663, were cloned from Mt. Everest soil metagenomic library, heterologously expressed in E. coli BL21(DE3), and characterized. Both enzymes exhibited high activity on konjac glucommanan (KG) and sodium carboxymethylcellulose (CMC), while ZFEG1605 also exhibited activity towards guar gum (GG). The optimal pH for both enzymes was slightly shifted toward acidic range (pH 5/6). The optimal reaction temperatures for ZFEG1605 and ZFEG1663 were 50 and 40 °C, respectively. ZFEG1605 was more thermostable than ZFEG1663 as it remained stable up to 50 °C, compared to 40 °C for ZFEG1663. Both enzymes showed broad pH stability, although they retained more mannanase activity than CMCase activity within the same pH range. The endoglucanases exhibited remarkable salt tolerance, retaining over 70 % of their enzymatic activity in the presence of 2.5 M NaCl. The purified enzymes hydrolyzed alkali-pretreated rice straw to release reducing sugars, demonstrating their potential usage for biomass saccharification.},
}

@article {pmid40445840,
year = {2025},
author = {Ricci, L and Selma-Royo, M and Golzato, D and Servais, C and Nabinejad, A and Marchi, P and Punčochář, M and Trenti, F and Garcia-Aloy, M and Armanini, F and Marconi, R and Asnicar, F and Pinto, F and Guella, G and Tamburini, S and Segata, N},
title = {Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.006798},
pmid = {40445840},
issn = {1466-5034},
mesh = {*Phylogeny ; *Feces/microbiology ; Humans ; Base Composition ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Genome, Bacterial ; Adult ; Fatty Acids/analysis ; Phospholipids/analysis ; },
abstract = {A recent metagenomic survey has revealed an unknown bacterial clade within the Catenibacterium mitsuokai species to be significantly more prevalent in non-urbanized populations, compared to urbanized ones. We isolated and characterized a strain of this clade from the stool of a healthy adult volunteer. Strain CMD8551[T] is strictly anaerobic, appears as long chains of Gram-positive rods and produces acetate in the presence of glucose. The lipidomic profile showed a higher proportion of saturated lipid species amongst the detected phospholipids. The whole genome is 2,320,430 bp long and has a G+C content of 33.7 mol% with 2,239 CDSs. A phylogenetic analysis comparing the sequences of the strain CMD8551[T] with publicly available reference genomes from the Catenibacterium genus revealed that the CMD8551[T] isolate, together with other isolate genomes, forms a distinct subspecies of C. mitsuokai and has an average nucleotide identity lower than 94% with respect to the previously described C. mitsuokai subsp. mitsuokai. Given the phenotypic, chemotaxonomic and phylogenetic characteristics of the newly isolated CMD8551[T] (=DSM 118469[T]=LMG 33725[T]=CIP 112509[T]) that clearly differ from those of the C. mitsuokai subsp. mitsuokai type strain RCA14-39[T], we propose it as the type strain of a novel subspecies of C. mitsuokai, with the name C. mitsuokai subsp. tridentinum subsp. nov.},
}

*Phylogeny
*Feces/microbiology
Humans
Base Composition
DNA, Bacterial/genetics
Bacterial Typing Techniques
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Genome, Bacterial
Adult
Fatty Acids/analysis
Phospholipids/analysis

@article {pmid40445833,
year = {2025},
author = {Li, W and Huang, B and Guo, M and Zeng, Z and Cai, T and Feng, L and Zhang, X and Guo, L and Jiang, X and Yin, Y and Wang, E and Huang, X and Zheng, J},
title = {Unveiling the evolution of antimicrobial peptides in gut microbes via foundation-model-powered framework.},
journal = {Cell reports},
volume = {44},
number = {6},
pages = {115773},
doi = {10.1016/j.celrep.2025.115773},
pmid = {40445833},
issn = {2211-1247},
abstract = {Antimicrobial resistance poses a major threat to public health, prompting the development of alternative therapies such as antimicrobial peptides (AMPs). Protein language models (PLMs) have advanced protein structure and function predictions, facilitating AMP discovery. We developed antimicrobial peptide structural evolution miner (AMP-SEMiner), an AI-driven framework that integrates PLMs, structural clustering, and evolutionary analysis to systematically identify AMPs encoded by small open reading frames and AMP-containing proteins in metagenome-assembled genomes. AMP-SEMiner identified over 1.6 million AMP candidates across diverse environments. Experimental validation showed antimicrobial activity in 9 of the 20 tested candidates, with 5 surpassing antibiotic effectiveness; variant peptides derived from these candidates similarly demonstrated strong antimicrobial efficacy. AMPs from human gut microbiomes revealed both conserved and adaptive evolutionary strategies, reflecting their dynamic ecological roles. AMP-SEMiner thus represents a valuable tool for expanding AMP discovery and has significant potential to inform the development of alternative antimicrobial treatments.},
}

@article {pmid40445752,
year = {2025},
author = {Xing, Y and Hernandez Santos, HJ and Qiu, L and Ritter, SR and Zulk, JJ and Lahowetz, R and Patras, KA and Terwilliger, AL and Maresso, AW},
title = {Phage-induced protection against lethal bacterial reinfection.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {22},
pages = {e2423286122},
doi = {10.1073/pnas.2423286122},
pmid = {40445752},
issn = {1091-6490},
support = {U19AI157981//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U19AI144297//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 5F31DK136201//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; 5359//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation (Kleberg Foundation)/ ; },
mesh = {*Phage Therapy/methods ; Animals ; *Bacteriophages/physiology ; *Reinfection/prevention & control/therapy/microbiology ; Mice ; *Bacterial Infections/therapy/prevention & control ; },
abstract = {Bacteriophages, or phages, are viruses that target and infect bacteria. Due to a worldwide rise in antimicrobial resistance (AMR), phages have been proposed as a promising alternative to antibiotics for the treatment of resistant bacterial infections. Up to this point in history, phage use in preclinical animal studies, clinical trials, and emergency-use compassionate care cases has centered around the original observation from 1915 showing phage as lytic agent, and thus a treatment that kills bacteria. Here, we describe an activity associated with phage therapy that extends beyond lytic activity that results in long-term protection against reinfection. This activity is potent, providing almost complete protection against a second lethal infection for animals treated with phage therapy. The activity also reduced infection burden an astounding billion-fold over the control. Reinfection protection requires phage lytic killing of its target bacterium but is independent of additional phage therapy. The effect is not driven by phage alone, lingering phage resistors, or a sublethal inoculum. In vitro phage-lysed bacteria provide partial protection, suggesting a combination of phage-induced lytic activity and immune stimulation by phage treatment is responsible for the effect. These observations imply certain phages may induce host adaptive responses following the lysis of the infecting bacteria. This work suggests phage therapy may contain a dual-action effect, an initial treatment efficacy followed by a long-term protection against reoccurring infection, a therapeutic-vaccination mechanism of action.},
}

*Phage Therapy/methods
Animals
*Bacteriophages/physiology
*Reinfection/prevention & control/therapy/microbiology
Mice
*Bacterial Infections/therapy/prevention & control

@article {pmid40445195,
year = {2025},
author = {Schuele, L and Masirika, LM and Cassidy, H and Clausen, PTLC and Zaeck, LM and Boter, M and Ndishimye, P and Udahemuka, JC and de Vries, RD and Otani, S and Molenkamp, R and Nieuwenhuijse, DF and Mbiribindi, JB and Siangoli, FB and Koopmans, M and Aarestrup, FM and Oude Munnink, BB},
title = {Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0051225},
doi = {10.1128/spectrum.00512-25},
pmid = {40445195},
issn = {2165-0497},
abstract = {Mpox is an emerging zoonotic disease that caused two public health emergencies of international concern within two years. Less is known about the interplay of microbial organisms in mpox lesions which could result in superinfections that exacerbate outcomes or delay recovery. We utilized a unified metagenomic sequencing approach involving slow-speed centrifugation and differential lysis on 19 mpox lesion swabs of hospitalized patients in South Kivu province (eastern DRC) to characterize bacteria, antimicrobial resistance genes, mpox virus (MPXV), and viral co-infections. High-quality MPXV whole-genome sequences were obtained until a Ct value of 27. Furthermore, co-infections with other clinically relevant viruses, such as varicella zoster virus and herpes simplex virus-2, were detected and confirmed by real-time PCR. In addition, metagenomic sequence analysis of the bacterial content showed the presence of bacteria associated with skin and soft tissue infection in 10 of the 19 samples analyzed. These bacteria had a high abundance of resistance genes, with possible implications for antimicrobial treatment based on the predicted antimicrobial resistance. In conclusion, we report the presence of bacterial and viral pathogens in mpox lesions and detection of widespread resistance genes to the standard antibiotic treatment. The possibility of a co-infection, including antimicrobial resistance, should be considered when discussing treatment options, along with the determination of the case-fatality ratio.IMPORTANCEThe mpox virus clade Ib lineage emerged in the eastern Democratic Republic of the Congo owing to continuous human-to-human transmission in a vulnerable patient population. A major challenge of this ongoing outbreak is its occurrence in regions with severely limited healthcare infrastructure. As a result, less is known about co-infections in affected patients. Identifying and characterizing pathogens, including their antimicrobial resistance, is crucial for reducing infection-related complications and improving antimicrobial stewardship. In this study, we applied a unified metagenomics approach to detect and characterize bacterial and viral co-infections in mpox lesions of hospitalized mpox patients in the eastern DRC.},
}

@article {pmid40445192,
year = {2025},
author = {Mullinax, SR and Darby, AM and Gupta, A and Chan, P and Smith, BR and Unckless, RL},
title = {A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {40445192},
issn = {2050-084X},
support = {AI139154/NH/NIH HHS/United States ; 2330095//National Science Foundation/ ; CMADP COBRE P20-GM103638/NH/NIH HHS/United States ; },
mesh = {Animals ; *Alleles ; Female ; Male ; *Drosophila Proteins/genetics/immunology ; *Selection, Genetic ; Providencia/immunology ; *Drosophila/genetics/immunology/microbiology ; Gastrointestinal Microbiome ; *Drosophila melanogaster/genetics/immunology/microbiology ; *Antimicrobial Peptides/genetics/immunology ; },
abstract = {The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.},
}

Animals
*Alleles
Female
Male
*Drosophila Proteins/genetics/immunology
*Selection, Genetic
Providencia/immunology
*Drosophila/genetics/immunology/microbiology
Gastrointestinal Microbiome
*Drosophila melanogaster/genetics/immunology/microbiology
*Antimicrobial Peptides/genetics/immunology

@article {pmid40445060,
year = {2025},
author = {Gao, H and Guo, Z and Xu, R and He, X and Fernio, JU and Li, S and Liu, X and Liu, H and Xue, W},
title = {Chemolithoautotrophic Antimonite Oxidation Coupled Nitrogen Fixation in the Rhizosphere of Local Plant in Antimony Tailing Area.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03872},
pmid = {40445060},
issn = {1520-5851},
abstract = {Antimony (Sb) tailings pose a significant environmental challenge. N-fixing microorganisms are essential for nutrient accumulation and plant colonization in degraded habitats. However, the oligotrophic conditions of tailings often inhibit the energy-intensive N-fixing process. This study identified a chemolithoautotrophic Sb(III) oxidation-coupled nitrogen fixation (SbNF) pathway in the rhizosphere of local plants. SbNF integrates biological detoxification and nutrient accumulation, enabling plant colonization and ecological restoration of degraded habitats. Multi-omic analyses reveal that Sb content strongly shapes the composition of Sb-oxidizing and N-fixing bacterial communities in the rhizosphere. Abundant marker genes for carbon fixation (cbbL), Sb(III) oxidase (aioAB/anoA), and nitrogenase (nifH) were consistently detected in SbNF metagenome-assembled genomes. Positive correlations between gene abundances associated with autotrophic potential (aioA-cbbL) and coupling potential (aioA-nifH) were observed in the rhizoplane but not in the endosphere. In addition to genetic potentials, high-throughput cultivation of native SbNF-isolates (e.g., Pseudomonas, Arthrobacter, and Sphingomonas) confirmed their rapid Sb(III) oxidation coupling autotrophic growth and nitrogen fixation. Isolates also exhibited plant growth-promoting traits, including indole-3-acetic acid production, phosphate solubilization, and siderophore secretion, providing multiple benefits to host plants. Co-cultivation of these isolates revealed minimal antagonism, suggesting the potential for designing synthetic microbial communities for sustainable phytoremediation. Cross-validation further suggests that SbNF is widespread in the rhizosphere of various local plants. These findings uncover a novel biogeochemical process in the rhizosphere, linking mineral oxidation, autotrophic growth, and nitrogen fixation, highlighting its importance for the ecological restoration of degraded tailing area.},
}

@article {pmid40445001,
year = {2025},
author = {Andréani, J and Smiljkovic, M and Lametery, E and Khedimallah, S and Court, N and Jardin, H and Arata-Bardet, J and Truffot, A and Germi, R and Morand, P and Cappy, P and Rodriguez, C and Lupo, J and Larrat, S},
title = {Metagenomics Diagnosis of a Parvovirus B19-Associated Encephalomyelitis in an Epidemic Context.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004780},
pmid = {40445001},
issn = {1532-0987},
abstract = {In the context of increasing parvovirus B19 (B19V) infections, we describe a case of B19V encephalomyelitis without any usually associated clinical features. Etiology was identified by metagenomics and confirmed by PCR and whole-genome sequencing. This case highlights the need to consider the diagnosis of B19V infection in patients presenting with neurological symptoms.},
}

@article {pmid40444981,
year = {2025},
author = {Harrison, K and Rapp, JZ and Jaffe, AL and Deming, JW and Young, J},
title = {Chemoautotrophy in subzero environments and the potential for cold-adapted Rubisco.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0060425},
doi = {10.1128/aem.00604-25},
pmid = {40444981},
issn = {1098-5336},
abstract = {The act of fixing inorganic carbon into the biosphere is largely facilitated by one enzyme, Rubisco. Beyond well-studied plants and cyanobacteria, many bacteria use Rubisco for chemolithoautotrophy in extreme environments on Earth. Here, we characterized the diversity of autotrophic pathways and chemolithoautotrophic Rubiscos from two distinct subzero, hypersaline Arctic environments: 40-kyr relic marine brines encased within permafrost (cryopeg brines) and first-year sea ice. The Calvin-Benson-Bassham (CBB) cycle was widely found in both environments, although with different predominant Rubisco forms. From cryopeg brine, reconstructions of metagenome-assembled genomes (MAGs) uncovered four MAGs with the potential for chemolithoautotrophy, of which the CBB-containing genus Thiomicrorhabdus was most abundant. A broader survey of Thiomicrorhabdus genomes from diverse environments identified a core complement of three Rubisco forms (II, IAc, IAq) with a complex pattern of gain and loss, with form II constitutively present in genomes from subzero environments. Using representative kinetic data, we modeled carboxylation rates of Rubisco forms II, IAc, and IAq across CO2, O2, and temperature conditions. We found that form II outcompetes form I at low O2, but cold temperatures minimize this advantage. Inspection of form II from genomes from cold environments identified signals of potential thermal adaptation due to key amino acid substitutions, which resulted in a more exposed active site. We argue that subzero form II from Thiomicrorhabdus warrants further study as it may have unique kinetics or thermal stability. This work can help address the limits of autotrophic functionality in extreme environments on Earth and other planetary bodies.IMPORTANCEAutotrophy, or the fixation of inorganic carbon to biomass, is a key factor in life's ability to thrive on Earth. Research on autotrophy has focused on plants and algae, but many bacteria are also autotrophic and can survive and thrive under more extreme conditions. These bacteria are a window to past autotrophy on Earth, as well as potential autotrophy in extreme environments elsewhere in the universe. Our study focused on dark, cold, saline environments, which are likely to be found on Enceladus and Europa, as well as in the Martian subsurface. We found evidence for potential cold adaptation in a key autotrophic enzyme, Rubisco, which could expand the known boundaries of autotrophy in rapidly disappearing icy environments on Earth. We also present a novel model framework that can be used to probe the limits of autotrophy not only on Earth but also on key astrobiological targets like Enceladus and Europa.},
}

@article {pmid40444423,
year = {2025},
author = {Yi, H and Zhang, S and Wang, J and Xu, C and Yang, D and Lin, Q and Wang, X and Feng, S},
title = {CT Features for Prognostic Assessment of Pulmonary Mucormycosis in Patients With Hematological Diseases.},
journal = {Journal of thoracic imaging},
volume = {},
number = {},
pages = {},
doi = {10.1097/RTI.0000000000000832},
pmid = {40444423},
issn = {1536-0237},
support = {2021-I2M-1-017 and 2023-I2M-2-007//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; },
abstract = {PURPOSE: To explore the CT features in prognostic evaluations for pulmonary mucormycosis in patients with hematological diseases.

MATERIALS AND METHODS: A retrospective analysis of clinical data and chest CT features of 53 HD patients with PM was conducted. Univariate and multivariate logistic regression analyses were used to determine the risk factors for death. The Cox regression model was used to analyze the factors affecting the survival rate.

RESULTS: A total of 30 patients with proven PM and 23 with probable PM were included. All 30 patients with proven PM underwent bronchoscopy-guided biopsy, among which 9 cases underwent surgical resection. Of the 23 patients with probable PM, 5 cases had positive results in sputum smear microscopy, 4 cases in sputum culture, 13 cases in bronchoalveolar lavage fluid (BALF) microscopy, and 1 case in BALF culture. All identification of pathogen genera and partial species was conducted by metagenomic next-generation sequencing (mNGS) testing. In the multivariate regression analysis, the CT feature of multiple lesions (≥2) on the initial CT scan was an independent risk factor for mortality (P=0.019). Cox survival analysis demonstrated a significantly lower survival rate (P=0.043) in patients exhibiting the CT feature of multiple lesions on the initial CT scan.

CONCLUSIONS: The CT feature of multiple lesions (≥2) on the initial CT may serve as an independent risk factor for mortality in patients with hematologic disorders with pulmonary mucormycosis.},
}

@article {pmid40444400,
year = {2025},
author = {Burdon, I and Bouras, G and Fenix, K and Yeo, K and Connell, J and Cooksley, C and Barry, E and Vreugde, S and Wormald, PJ and Psaltis, AJ},
title = {Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {e23617},
doi = {10.1002/alr.23617},
pmid = {40444400},
issn = {2042-6984},
support = {//Garnett Passe and Rodney Williams Memorial Foundation/ ; APP1196832//National Health and Medical Research Council/ ; },
}

@article {pmid40444000,
year = {2025},
author = {Pacheco-Dorantes, C and Tovar-Pedraza, JM and Ochoa-Martínez, DL and González-Garza, R and Diaz-Lara, A},
title = {Unleashing the potential of high-throughput sequencing for plant virus and viroid detection in Mexico.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1603010},
pmid = {40444000},
issn = {1664-302X},
abstract = {High-throughput sequencing (HTS) has revolutionized plant virology in Mexico by enhancing the detection and characterization of plant viruses and viroids. This technology has contributed to identifying previously neglected pathogens affecting key crops such as corn, beans, and tomato. The use of HTS has also revealed the presence of mixed viral infections, highlighting the complexity of plant viromes within agricultural ecosystems. Furthermore, metagenomic studies have demonstrated the role of water sources as reservoirs for plant viruses, underscoring the urgent need for improved management strategies. Despite its advantages, the widespread adoption of HTS faces challenges, including high costs, the need for bioinformatics expertise, and infrastructure limitations. Supporting collaborations between research institutions and regulatory agencies is crucial to integrating HTS into routine phytosanitary programs. Future research should aim to expand HTS applications to include epidemiological monitoring, resistance breeding, and the development of sustainable management strategies to mitigate the impact of emerging plant viruses in Mexico.},
}

@article {pmid40443674,
year = {2025},
author = {Wang, Y and Ma, X and Ma, C and Sun, T and Zhao, D and Li, H and Yan, Y and Guo, J},
title = {Case Report: Anti-NMDAR encephalitis associated with neurobrucellosis: causality or coexistence?.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1536740},
pmid = {40443674},
issn = {1664-3224},
mesh = {Humans ; Male ; *Brucellosis/complications/diagnosis/immunology/drug therapy/microbiology ; Adult ; *Anti-N-Methyl-D-Aspartate Receptor Encephalitis/diagnosis/etiology/immunology/drug therapy ; *Brucella melitensis/immunology ; Autoantibodies/immunology ; },
abstract = {Human brucellosis, caused by Brucella, is an infectious disease with specific endemic regions, especially in pastoral areas, and may affect multiple organ systems. Neurological involvement, namely neurobrucellosis, occurs in very few of these patients. Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is the most frequent type of autoimmune encephalitis and is usually associated with tumors or herpes simplex virus infections. However, the link between the two disease entities is unknown. In this report, we present a rare case of a 29-year-old Chinese man with anti-NMDAR encephalitis associated with neurobrucellosis, with the detection of anti-NMDAR antibodies by cell-based assay and Brucella melitensis by metagenomic next-generation sequencing in his cerebrospinal fluid sample. The patient improved after antimicrobial treatment and immunotherapies, including steroids and intravenous immunoglobulin. This case implicates Brucella infection as a possible trigger for the production of anti-NMDAR antibodies, and prospective studies should reveal whether there is a casual relationship between brucellosis and anti-NMDAR antibodies.},
}

Humans
Male
*Brucellosis/complications/diagnosis/immunology/drug therapy/microbiology
Adult
*Anti-N-Methyl-D-Aspartate Receptor Encephalitis/diagnosis/etiology/immunology/drug therapy
*Brucella melitensis/immunology
Autoantibodies/immunology

@article {pmid40443669,
year = {2025},
author = {Zhang, C and Xu, Y and Zhang, M and Li, J and Sun, Z and Wang, Y and Lin, P},
title = {An exploratory study on the metagenomic and proteomic characterization of hypothyroidism in the first half of pregnancy and correlation with Th1/Th2 balance.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1500866},
pmid = {40443669},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/immunology/microbiology/metabolism ; Adult ; Proteomics/methods ; *Th2 Cells/immunology/metabolism ; *Th1 Cells/immunology/metabolism ; Metagenomics/methods ; *Gastrointestinal Microbiome/immunology ; *Pregnancy Complications/immunology/metabolism/microbiology ; *Proteome ; Cytokines/metabolism ; },
abstract = {OBJECTIVE: To explore the gut microbiota and proteomic characteristics of hypothyroidism in the first half of pregnancy (referred to as hypothyroidism in the first half of pregnancy) and its association with Th (T helper cells, Th)1/Th2 balance using metagenomics combined with proteomics.

METHODS: Stool and blood samples were collected from 20 hypothyroid (hypothyroidism group) and normal pregnant women (normal group) in the first half of pregnancy. Flora and proteomic characteristics were analyzed using metagenomics sequencing and 4D-DIA proteomics. Th1 and Th2 cells were quantified, and cytokine levels were measured using cellular micro-bead arra. The enzyme-linked immunosorbent test (ELISA) was utilized to assess differential proteins.

RESULTS: (1) Metagenomic sequencing revealed distinct microbial profiles: The β-diversity of gut microbiota was diminished in the hypothyroidism group (p < 0.05). LEfSe analysis identified Phocaeicola vulgatus and Bacteroides fragilis enriched in the hypothyroidism group (p<0.05), and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis showed significant enrichment in pathways related to peptidoglycan biosynthesis and glycerol ester metabolism.(2) Proteomic analysis demonstrated downregulation of Diacylglycerol Kinase Kappa (DGKK) and P05109|S10A8(S10A8) proteins in the hypothyroidism group, with marked enrichment in the KEGG pathways for vascular smooth muscle contraction and phosphatidylinositol signaling. (3) ELISA validation confirmed that the proteins DGKK and S10A8 were downregulated in pregnant women in the hypothyroidism group.

CONCLUSION: Increased P. vulgatus and B. fragilis, decreased DGKK and S10A8 proteins, and a left shift in the Th1/Th2 balance in patients with hypothyroidism in the first half of pregnancy may be associated with the development of the disease.},
}

Humans
Female
Pregnancy
*Hypothyroidism/immunology/microbiology/metabolism
Adult
Proteomics/methods
*Th2 Cells/immunology/metabolism
*Th1 Cells/immunology/metabolism
Metagenomics/methods
*Gastrointestinal Microbiome/immunology
*Pregnancy Complications/immunology/metabolism/microbiology
*Proteome
Cytokines/metabolism

@article {pmid40442718,
year = {2025},
author = {Pivrncova, E and Bohm, J and Barton, V and Klanova, J and Borilova Linhartova, P},
title = {Viable bacterial communities in freshly pumped human milk and their changes during cold storage conditions.},
journal = {International breastfeeding journal},
volume = {20},
number = {1},
pages = {44},
pmid = {40442718},
issn = {1746-4358},
support = {LM2023069//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; 857560//Horizon 2020 Framework Programme/ ; },
mesh = {Humans ; *Milk, Human/microbiology ; Female ; *Bacteria/isolation & purification/genetics/classification ; *Food Storage/methods ; Adult ; RNA, Ribosomal, 16S ; *Microbiota ; Freezing ; Refrigeration ; Azides ; Propidium/analogs & derivatives ; },
abstract = {BACKGROUND: Human milk harbors diverse bacterial communities that contribute to infant health. Although pumping and storing milk is a common practice, the viable bacterial composition of pumped milk and the impact of storage practice on these bacteria remains under-explored. This metagenomic observational study aimed to characterize viable bacterial communities in freshly pumped human milk and its changes under different storage conditions.

METHODS: In 2023, twelve lactating mothers from the CELSPAC: TNG cohort (Czech Republic) provided freshly pumped milk samples. These samples were stored under various conditions (refrigeration for 24 h, 48 h, or freezing for six weeks) and treated with propidium monoazide (PMA) to selectively identify viable cells. The DNA extracted from individual samples was subsequently analyzed using 16S rRNA amplicon sequencing on the Illumina platform.

RESULTS: The genera Streptococcus, Staphylococcus, Diaphorobacter, Cutibacterium, and Corynebacterium were the most common viable bacteria in fresh human milk. The median sequencing depth and Shannon index of fresh human milk samples treated with PMA (+ PMA) were significantly lower than in untreated (-PMA) samples (p < 0.05 for all), which was true also for each time point. Also, significant changes in these parameters were observed between fresh human milk samples and their paired frozen samples (p < 0.05), while no differences were found between fresh human milk samples and those refrigerated for up to 48 h (p > 0.05). Of specific genera, only + PMA frozen human milk samples showed a significant decrease in the central log-ratio transformed relative abundances of the genera Diaphorobacter and Cutibacterium (p < 0.05) in comparison to + PMA fresh human milk samples.

CONCLUSIONS: The study demonstrated that the bacterial profiles significantly differed between human milk samples treated with PMA, which represent only viable bacteria, and those untreated. While storage at 4 °C for up to 48 h did not significantly alter the overall diversity and composition of viable bacteria in human milk, freezing notably affected both the viability and relative abundances of some bacterial genera.},
}

Humans
*Milk, Human/microbiology
Female
*Bacteria/isolation & purification/genetics/classification
*Food Storage/methods
Adult
RNA, Ribosomal, 16S
*Microbiota
Freezing
Refrigeration
Azides
Propidium/analogs & derivatives

@article {pmid40442502,
year = {2025},
author = {Tzlil, G and Marín, MDC and Matsuzaki, Y and Nag, P and Itakura, S and Mizuno, Y and Murakoshi, S and Tanaka, T and Larom, S and Konno, M and Abe-Yoshizumi, R and Molina-Márquez, A and Bárcenas-Pérez, D and Cheel, J and Koblížek, M and León, R and Katayama, K and Kandori, H and Schapiro, I and Shihoya, W and Nureki, O and Inoue, K and Rozenberg, A and Chazan, A and Béjà, O},
title = {Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40442502},
issn = {2058-5276},
support = {3131/20//Israel Science Foundation (ISF)/ ; JPMXP1323015482//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMXP1323015482//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {Aquatic bacterial rhodopsin proton pumps harvest light energy for photoheterotrophic growth and are known to contain hydroxylated carotenoids that expand the wavelengths of light utilized, but these have not been characterized in marine archaea. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes, we show light energy transfer from diverse hydroxylated carotenoids to heimdallarchaeial rhodopsins (HeimdallRs) from uncultured marine planktonic members of 'Candidatus Kariarchaeaceae' ('Candidatus Asgardarchaeota'). These light-harvesting antennas absorb in the blue-light range and transfer energy to the green-light-absorbing retinal chromophore within HeimdallRs, enabling the use of light that is otherwise unavailable to the rhodopsin. Furthermore, we show elevated proton pumping by the antennas in HeimdallRs under white-light illumination, which better simulates the light conditions encountered by these archaea in their natural habitats. Our results indicate that light-harvesting antennas in microbial rhodopsins exist in families beyond xanthorhodopsins and proteorhodopsins and are present in both marine bacteria and archaea.},
}

@article {pmid40442233,
year = {2025},
author = {Li, X and Tang, C and Zhou, M and Mi, J and Liu, J and Han, L and Yu, X and Zhang, X},
title = {Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18923},
pmid = {40442233},
issn = {2045-2322},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; 23DX1900300//Shanghai Targeted Biomedical Emergency Project/ ; },
mesh = {Humans ; *COVID-19/virology/epidemiology ; *SARS-CoV-2/genetics/isolation & purification/classification ; Aged ; Female ; Male ; *Coinfection/virology/microbiology/epidemiology ; Middle Aged ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Phylogeny ; Retrospective Studies ; Hospitalization ; Adult ; Aged, 80 and over ; },
abstract = {Metagenomic next-generation sequencing (mNGS) is widely used to diagnose complex infections in hospitalized patients, particularly those associated with COVID-19 which has garnered significant concern over the past five years. To investigate the molecular epidemic of the viral variant and the potential co-infection pathogens, we conducted retrospective mNGS analysis of 254 SARS-CoV-2-positive specimens collected from 200 hospitalized patients between March and September 2023. Phylogenetic analysis of the identified Omicron subvariants showed minimal evolutionary divergence, with no association between sub-lineages and pneumonia severity. Notably, mNGS demonstrated enhanced detection of polymicrobial coinfections, identifying bacterial, fungal, and viral co-pathogens in 92.5% (185/200) of cases. Pneumonia severity was associated with advanced age (proportion of elderly patients: 61.1 vs 78.3%; p = 0.032) and comorbid conditions, particularly diabetes mellitus (OR 2.03, 95% CI 1.03-4.02, p = 0.041), but showed no correlation with SARS-CoV-2 sub-lineages or coinfecting pathogens. While mNGS enhances coinfection diagnosis, COVID-19 outcomes are predominantly driven by host factors rather than Omicron subvariant evolution. Prioritized monitoring of elderly and comorbid individuals remained critical for severe pneumonia management.},
}

Humans
*COVID-19/virology/epidemiology
*SARS-CoV-2/genetics/isolation & purification/classification
Aged
Female
Male
*Coinfection/virology/microbiology/epidemiology
Middle Aged
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Phylogeny
Retrospective Studies
Hospitalization
Adult
Aged, 80 and over

@article {pmid40442154,
year = {2025},
author = {Seong, HJ and Park, YM and Kim, BS and Yoo, HJ and Kim, T and Yoon, SM and Kim, JH and Lee, SY and Lee, YK and Lee, DW and Nam, MH and Hong, SJ},
title = {Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {91},
pmid = {40442154},
issn = {2055-5008},
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Bifidobacterium longum/genetics/isolation & purification/classification/metabolism ; Female ; Male ; Metabolomics ; Metagenomics/methods ; Feces/microbiology ; *Host Microbial Interactions ; Clostridium/genetics/isolation & purification ; Transcriptome ; Multiomics ; },
abstract = {The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.},
}

Humans
*Dermatitis, Atopic/microbiology
*Gastrointestinal Microbiome
Infant
*Bifidobacterium longum/genetics/isolation & purification/classification/metabolism
Female
Male
Metabolomics
Metagenomics/methods
Feces/microbiology
*Host Microbial Interactions
Clostridium/genetics/isolation & purification
Transcriptome
Multiomics

@article {pmid40441146,
year = {2025},
author = {Yang, Y and Duan, Y and Lang, S and Fondevila, MF and Schöler, D and Harberts, A and Cabré, N and Chen, S and Shao, Y and Vervier, K and Miyamoto, Y and Zhang, X and Chu, H and Yang, L and Tan, C and Eckmann, L and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Bataller, R and Stärkel, P and Lawley, TD and Schnabl, B},
title = {Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.003},
pmid = {40441146},
issn = {1934-6069},
abstract = {Alcohol-associated liver disease poses a global health burden with high mortality. Imbalances in the gut microbiota are important for disease progression. Using metagenomic sequencing of fecal samples from a multicenter, international cohort of patients with alcohol-associated hepatitis, we found that the presence of virulence factor KpsM, encoded in the genome of Escherichia coli (E. coli), correlated with patient mortality. Functional studies using gnotobiotic mouse models and genetic manipulation of bacteria demonstrated that kpsM-positive E. coli exacerbate ethanol-induced liver disease. The kpsM gene mediates the translocation of capsular polysaccharides to the cell surface. This enables kpsM-positive E. coli to evade phagocytosis by the scavenger receptor Marco on Kupffer cells in the liver, leading to bacterial spread. Importantly, inhibiting kpsM-dependent capsules with the small molecule 2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid (C7) attenuated ethanol-induced liver disease in mice. We show that precision targeting of the virulence factor KpsM is a promising approach to improve outcomes of patients with alcohol-associated hepatitis.},
}

@article {pmid40440847,
year = {2025},
author = {Shirai, T and Motooka, D and Ushikai, Y and Komano, J and Shioda, T and Iida, T and Sakon, N},
title = {Molecular epidemiology of human sapovirus based on the surveillance of wastewater and patients with acute gastroenteritis in Osaka, Japan.},
journal = {The Science of the total environment},
volume = {985},
number = {},
pages = {179622},
doi = {10.1016/j.scitotenv.2025.179622},
pmid = {40440847},
issn = {1879-1026},
abstract = {Wastewater-based epidemiology has recently emerged as a promising tool for determining the prevalence of infectious diseases in a community. In the present study, human sapoviruses (HuSaVs) detected in wastewater collected weekly from January 2023 to March 2024 were analyzed using qPCR and next-generation sequencing (NGS), and the results were compared with those from clinical surveillance samples obtained from patients with acute gastroenteritis (AGE) in Osaka Prefecture, Japan. The detection trend of HuSaV in wastewater agreed with the clinical surveillance data in that HuSaV genomes increased in the cold season. In wastewater surveillance, five genotypes were detected, including GI.1, GI.2, GII.3, GII.5, and GV.1. GI.2 was not detected in the clinical surveillance. In the phylogenetic analysis, VP1 gene sequences obtained from wastewater were positioned in close proximity to those obtained from clinical samples. It is suggested that the results of wastewater surveillance reflect the status of ongoing HuSaV infection in a community. Interestingly, GV.1 was detected less frequently than GI.1 in clinical surveillance samples, but was predominantly detected in wastewater at nearly all time points, accounting for up to 94.5 % of all reads in November 2023. In particular, in November 2023, most gastroenteritis outbreaks and pediatric AGE cases were attributable to GI.1, but GV.1 was present at a higher proportion in the wastewater surveillance than GI.1. Wastewater surveillance was shown to complement clinical surveillance in that the former might be able to cover asymptomatic carriers. Our results demonstrate the importance of systematic clinical and wastewater surveillance in epidemiological analyses of HuSaV.},
}

@article {pmid40440727,
year = {2025},
author = {Ning, J and Du, Y and Wang, J and Liu, W and Deng, Y and Gan, Y and Wang, Y},
title = {Contribution of Microbial Metabolism to Geogenic Phosphorus Enrichment in Groundwater: Insights from Metagenomic Sequencing and Organic Molecular Characterization.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c02169},
pmid = {40440727},
issn = {1520-5851},
abstract = {Microbial mediation in the enrichment of geogenic phosphorus (P) is often mentioned but rarely explored, especially in P enrichment processes through the mineralization of dissolved organic matter (DOM) containing natural P. To bridge the theoretical gap, this study investigated the mechanisms of P enrichment through microbially mediated mineralization of natural P-containing DOM by adopting an approach combining comprehensive field investigation with hydrochemical and molecular biological analyses. The co-analysis of the dominant microbial community compositions and genomics revealed that the microbial metabolism pathways involved in the biodegradation of P-containing DOM were associated with the enrichment level of dissolved inorganic phosphorus (DIP). Specifically, dephosphorylation was more pronounced under conditions of limited DIP, while C-P bond cleavage was the primary metabolic pathway under sufficient DIP. Co-occurrence network analysis further indicated that the substrates for DIP enrichment differed between dephosphorylation and C-P bond cleavage, namely CHONSP1 compounds in the region of highly unsaturated-low O compounds (AI ≤ 0.5, H/C < 1.5, and O/C < 0.4) and CHOP1 compounds in the region of highly unsaturated-high O compounds (AI ≤ 0.5, H/C < 1.5, and O/C ≥ 0.4), respectively. These findings provide new insights into geogenic P enrichment in groundwater from the perspective of microbial metabolism and have potential implications for the bioremediation of P-contaminated groundwater at different contamination levels.},
}

@article {pmid40440710,
year = {2025},
author = {Zhu, Y and Sun, M and Chen, B and Liu, X and Yang, G and Li, X},
title = {Diagnostic Value of Cerebrospinal Fluid Metagenomics Next-generation Sequencing in Neurobrucellosis in Children.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004845},
pmid = {40440710},
issn = {1532-0987},
support = {No. 2021GG0209//Science and Technology Project of the Inner Mongolia Department of Science and Technology/ ; },
abstract = {OBJECTIVE: To explore the clinical characteristics of neurobrucellosis in children and the diagnostic value of metagenomics next-generation sequencing (mNGS) of cerebrospinal fluid and traditional microbial detection methods.

METHODS: Three patients in the pediatrics department from April 2022 to October 2023 were diagnosed with brucellosis, and 5 mL of cerebrospinal fluid was taken and sent for routine biochemical, bacterial Gram-stained smear, antacid-stained smear, ink staining, bacterial culture and second-generation sequencing of the microgeneration of the cerebrospinal fluid, respectively (Beijing AJiAn Genetics Medical Laboratory). Cranial magnetic resonance imaging, blood culture and blood Brucella antibody test were also performed to summarize the clinical features and pathogenic analysis.

RESULTS: The chief presentations were fever, headache, vomiting, somnolence and positive signs of meningeal irritation in all patients. Case 3: persistent hemiparesis of the left limb and cerebral infarction. Brucella was detected by cerebrospinal fluid mNGS in all cases, with sequence numbers of 5252, 162 and 59 Brucella and relative abundances of 80.26%, 6.14% and 1.06%, respectively. Cerebrospinal fluid cultures were negative, and blood cultures were positive in case 3.

CONCLUSIONS: The clinical characteristics of neurobrucellosis in children are variable, and meningoencephalitis is common. Traditional microbiological tests are difficult to detect Brucella, whereas cerebrospinal fluid mNGS can provide a precise diagnosis.},
}

@article {pmid40440092,
year = {2025},
author = {Lawniczak, MKN and Kocot, KM and Astrin, JJ and Blaxter, M and Sotero-Caio, CG and Barker, KB and Childers, AK and Coddington, J and Davis, P and Howe, K and Johnson, WE and McKenna, DD and Wideman, JG and Pettersson, OV and Ras, V and Santos, BF and , },
title = {Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40440092},
issn = {2047-217X},
support = {//Science for Life Laboratory/ ; //Swedish Research Council/ ; 1846174//National Science Foundation/ ; 2138994//National Science Foundation/ ; 2321308//National Science Foundation/ ; 2001303//National Science Foundation/ ; 2110053//National Science Foundation/ ; 1937815//National Science Foundation/ ; DBI-2119963//National Science Foundation/ ; U24HG006941/HG/NHGRI NIH HHS/United States ; /NH/NIH HHS/United States ; //Agricultural Research Service/ ; },
mesh = {*Genome ; *Genomics/standards/methods ; *Metagenomics/standards/methods ; Earth, Planet ; *Specimen Handling/standards/methods ; },
abstract = {The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Life. Currently in its first phase, the project is targeting family-level representatives and is progressing rapidly. Here we outline recommended standards and considerations in sample acquisition and processing for those involved in biodiverse reference genome creation. These standards and recommendations will evolve with advances in related processes. Additionally, we discuss the challenges raised by the ambitions for later phases of the project, highlighting topics related to sample collection and processing that require further development.},
}

*Genome
*Genomics/standards/methods
*Metagenomics/standards/methods
Earth, Planet
*Specimen Handling/standards/methods

@article {pmid40439988,
year = {2025},
author = {Davidson, IM and Nikbakht, E and Haupt, LM and Dunn, PJ},
title = {Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {40439988},
issn = {1573-7330},
abstract = {PURPOSE: Rising demand for assisted reproductive technologies (ART) with limited improvements in success rates has driven interest in the impact of the vaginal microbiome on fertility outcomes. In order to fully examine the relationship between the vaginal microbiome and fertility outcomes, methodologies and technological developments must be standardised and benchmarked to provide the most accurate assessment of microbial population representation.

METHODS: This study sought to investigate the utility of 16S sequencing and bioinformatic approaches using nanopore sequencing to characterize core vaginal microbiota in a healthy Australian cohort of reproductive-age women.

RESULTS: Optimisation and comparison of different PCR strategies for whole 16S amplification was undertaken, along with the generation of bioinformatic analysis strategies. Initial qPCR identified the 27F-YM (MIX) primer as the most sensitive for C. trachomatis. However, nanopore sequencing revealed no detectable C. trachomatis across all six samples. Among the bioinformatic tools, Porechop with NanoCLUST most accurately identified microbial presence. Community state type (CST) I-characterised by Lactobacillus crispatus dominance-was identified as the most common CST (66%), aligning with patterns of a healthy vaginal microbiome.

CONCLUSION: The findings highlight a Lactobacillus-rich microbiome as the most common among healthy females; however, further refinement-potentially through a metagenomics approach-is recommended to address 16S rRNA primer limitations to enable improved accuracy of microbial detection for the vaginal microbiome.},
}

@article {pmid40439829,
year = {2025},
author = {Wu, C and Han, X and Yang, F and Zhang, G and Zhao, C},
title = {Misdiagnosis of autoimmune glial fibrillary acidic protein astrocytopathy as infectious meningitis: a case report.},
journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology},
volume = {},
number = {},
pages = {},
pmid = {40439829},
issn = {1590-3478},
abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein astrocytopathy (A-GFAP-A) is a rare autoimmune central nervous system disorder associated with anti-GFAP IgG, presenting with meningoencephalitis or myelitis. Differential diagnosis from infectious causes, such as tuberculous meningitis (TBM), is challenging due to overlapping clinical and radiological features.

CASE PRESENTATION: A 24-year-old Chinese female presented with acute headache, fever, and vomiting. The cerebrospinal fluid (CSF) analysis showed lymphocytic pleocytosis, elevated protein and decreased glucose level. Brain magnetic resonance imaging (MRI) showed diffuse leptomeningeal enhancement. She was initially diagnosed with infectious meningitis and emperically treated with antibiotics and anti-tuberculosis therapy. However, her symptoms progressed with seizures, urinary retention, and tremor. Subsequent MRI revealed the involvement of the whole spinal cord. CSF analysis identified anti-GFAP IgG (titer 1:32). Bacterial, viral and tuberculous infection were excluded through bacterial culturing, metagenomic next-generation sequencing and Xpert MTB/RIF assay. The patient responded well to intravenous immunoglobulin and corticosteroids, achieving full remission. Finally, the diagnosis of A-GFAP-A was confirmed.

CONCLUSION: A-GFAP-A mimics infectious meningitis such as TBM due to similar CSF abnormalities and neuroimaging findings. This case underscores the importance of GFAP-IgG testing in differential diagnosis of patients with meningitis who have negative microbiological studies and atypical symptoms such as urinary retention and tremor.},
}

@article {pmid40439813,
year = {2025},
author = {Biktasheva, L and Galitskaya, P and Kuryntseva, P and Shipaeva, M and Selivanovskaya, S},
title = {Challenges and distortions in microbial community analysis of oil reservoirs: a case study with heavy crude oil from the Romashkino field.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40439813},
issn = {1618-1905},
support = {075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {The study of the microbial community of wells is a methodologically complex, but urgent problem. In the course of our work, five samples of oil wells were selected from one deposit of the Romashkino field. The samples were subjected to nucleic acid extraction using three methods-direct DNA extraction, and after enrichment using aerobic and anaerobic cultivation methods. In three samples from wells W1-W3, extraction after anaerobic enrichment was successful. Effective aerobic cultivation was possible in all five samples. All three of these samples represented the aqueous part of the produced fluid; samples from wells W4 and W5, where extraction was difficult, represented the oil part. During the analysis of the microbial community in enrichment cultures from wells W1-W3, exogenous microorganisms such as Desulfovibrio, Acetobacterium, Bacillus, and Georgenia were discovered, which can be explained by the long-term exploitation of this section of the field. In one sample from well W1, community information was obtained using direct extraction and anaerobic enrichment. It was found that the microbial community changed significantly after enrichment, and its diversity decreased. At the same time, however, the functional profile of microorganisms has not changed, and sulfate-reducing microorganisms dominate in both samples. Thus, the results of the work allow us to make an assumption about the physicochemical parameters of samples in which the study of the microbial community is possible. In addition, it became known that well W1 needs to control the process of biological acidification and has a high risk of equipment corrosion.},
}

@article {pmid40439791,
year = {2025},
author = {Gigliucci, F and Barbieri, G and Veyrunes, M and Chiani, P and Marra, M and Carollo, M and Knijn, A and Brambilla, G and Morabito, S},
title = {Characterization of the resistome and antibiotic-resistant bacteria in top soil improvers and irrigation waters devoted to food production: a case study from Italy.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40439791},
issn = {1614-7499},
support = {RF-2019-12369714//Ministero della Salute/ ; },
abstract = {Biosolids and reclaimed waters are valuable resources for reintroducing organic matter into agricultural soils and reducing the water footprint of intensive agricultural food system. While the circular economy is a sustainable practice, it may introduce vulnerabilities in the food chain, by exposing crops to zoonotic agents and antimicrobial resistance determinants. This option is far from being a speculation and evidence start to accumulate indicating that the risk is tangible. This study provides further evidence that the circular economy practices of reusing biomass and reclaimed waters in agricultural setting may be vectors for the spreading of antibiotic resistance genes (ARGs) targeting molecules used to treat human bacterial infections. We screened biosolid and water samples for ARGs presence using shotgun metagenomic sequencing. We demonstrated that the identified ARGs are present in live bacterial organisms, harbouring multidrug-resistant gene clusters, confirmed through phenotypic testing and whole-genome sequencing of isolated bacteria. Additionally, we observed that most of the antibiotic-resistant bacteria identified belonged to environmentally widespread species, which were not expected to be exposed to the antimicrobials, suggesting that inter-species transfer of resistance genes.},
}

@article {pmid40439580,
year = {2025},
author = {Bondeelle, L and Cheng, GS and Bergeron, A},
title = {What's new in the management of pulmonary complications in allogeneic stem cell transplantation?.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2513519},
pmid = {40439580},
issn = {1747-6356},
abstract = {INTRODUCTION: As survival increases after allogeneic hematopoietic stem cell transplantation (allo-HCT), several organ complications have emerged, including those involving the lung, which require a multidisciplinary management approach. The constant evolution of allo-HCT procedures, advances in diagnostic tools for infections and pulmonary disease, as well as new treatment approaches, require frequent updating of knowledge in this field.

AREAS COVERED: We review the multiple infectious and noninfectious lung complications that occur both early and late after allo-HCT. This includes an updated description of these complications, risk factors, diagnostic approach and outcome. A literature search was performed using PubMed-indexed journals.

EXPERT OPINION: The diagnosis of pulmonary complications after allo-HCT remains challenging, further complicated by the frequent association of co-infections and/or links between infection and noninfectious complications. The development of metagenomic next-generation sequencing (mNGS) should enhance the diagnostic yield of bronchoalveolar lavage but its clinical relevance remains to be evaluated. A better understanding of the pathophysiology of the lung chronic graft-versus-host disease (GVHD) and improved phenotyping are essential for advancing its diagnostic and therapeutic management. This requires a revision of diagnostic criteria and the identification of new biomarkers of early disease.},
}

@article {pmid40439559,
year = {2025},
author = {Rouse, N and Buttler, J and Pabilonia, K and Weller, C and Respicio-Kingry, L and Dietrich, E and Petersen, J and Kovalenko, G and Bortz, E and Huntington, KB},
title = {Francisella tularensis Subspecies holarctica in Stranded Beluga Whales, Cook Inlet, Alaska, USA.},
journal = {Emerging infectious diseases},
volume = {31},
number = {6},
pages = {1247-1250},
doi = {10.3201/eid3106.250033},
pmid = {40439559},
issn = {1080-6059},
mesh = {Animals ; *Francisella tularensis/genetics/classification/isolation & purification ; Alaska/epidemiology ; *Tularemia/veterinary/microbiology/epidemiology/diagnosis ; *Beluga Whale/microbiology ; Multilocus Sequence Typing ; Phylogeny ; },
abstract = {We report fatal tularemia in stranded beluga whales in Cook Inlet, Alaska, USA. Francisella tularensis was detected by nanopore metagenomics, confirmed by quantitative PCR and immunohistochemistry, and characterized as F. tularensis subspecies holarctica by multilocus sequence typing. Our findings should be considered when assessing biosecurity and marine mammal health in the North Pacific.},
}

Animals
*Francisella tularensis/genetics/classification/isolation & purification
Alaska/epidemiology
*Tularemia/veterinary/microbiology/epidemiology/diagnosis
*Beluga Whale/microbiology
Multilocus Sequence Typing
Phylogeny

@article {pmid40439405,
year = {2025},
author = {Scribano, FJ and Gebert, JT and Engevik, KA and Hayes, NM and Villanueva, J and Pham, S and Kaundal, S and Dave, JJ and Prasad, BVV and Estes, MK and Ramani, S and Hyser, JM},
title = {BTP2 restricts Tulane virus and human norovirus replication independent of store-operated calcium entry.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0044425},
doi = {10.1128/jvi.00444-25},
pmid = {40439405},
issn = {1098-5514},
abstract = {Human norovirus is the leading cause of viral gastroenteritis across all age groups. While there is a need for human norovirus antivirals, therapeutic development has been hindered by a lack of cell culture systems and animal models of infection. Surrogate viruses, such as Tulane virus (TV), have provided tractable systems to screen potential antiviral compounds. Our previous work demonstrated that TV encodes a viral ion channel, which dysregulates cytosolic calcium signaling. We set out to investigate whether host pathways triggered by viral ion channel activity, including store-operated calcium entry (SOCE), play a role in virus replication. Using pharmacologic inhibitors and genetically engineered cell lines, we establish that the SOCE inhibitor, BTP2, reduces TV replication in an SOCE-independent manner. We observed a significant reduction in TV replication, protein expression, and RNA synthesis in cells with both pre- and post-infection BTP2 treatment. By serial passage and plaque isolation, we demonstrate that TV quasi-species have mixed susceptibility and resistance to BTP2. Sequence comparison of the quasi-species revealed that amino acid changes in the structural proteins were associated with drug resistance. We utilized reverse genetics to generate TV with the resistance-associated VP1 and VP2 amino acid changes and found that amino acid changes in both proteins conferred BTP2 resistance. Together, this supports that TV structural proteins are the targets of BTP2. Finally, using human intestinal organoids, we demonstrate that BTP2 significantly reduces human norovirus replication.IMPORTANCEOur work identifies BTP2 as a potential human norovirus antiviral pharmacophore and highlights the utility of targeting calicivirus structural proteins to restrict viral replication. Furthermore, we establish a system whereby Tulane virus (TV) can be used to screen novel antiviral candidates and establish their mechanism of action. Together, this will facilitate rapid preclinical validation of other novel human norovirus therapeutics.},
}

@article {pmid40439403,
year = {2025},
author = {Pang, Y and Qiu, J and Yang, H and Zhang, J and Mo, J and Huang, W and Zeng, C and Xu, P},
title = {Application value of metagenomic next-generation sequencing based on protective bronchoalveolar lavage in nonresponding pneumonia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0313824},
doi = {10.1128/spectrum.03138-24},
pmid = {40439403},
issn = {2165-0497},
abstract = {This study aims to explore the application value of metagenomic next-generation sequencing (mNGS) of protective bronchoalveolar lavage fluid in the differential diagnosis and pathogenetic identification of nonresponding pneumonia. This study analyzed patient symptoms, auxiliary examinations including pathogen detection, and treatment response to identify the reasons for the lack of response to initial treatment and the pathogenetic diagnosis of pulmonary infections. The diagnostic efficacy of pathogen culture and mNGS was statistically analyzed and compared based on the clinical diagnosis criteria. (1) The two most common reasons for the ineffectiveness of initial treatment in nonresponding pneumonia cases are that (i) the initial treatment did not cover the pathogenic bacteria in pulmonary infection cases and that (ii) non-infectious pulmonary diseases were responsible. The most common pathogens in pulmonary infection cases of nonresponding pneumonia are Mycobacterium tuberculosis (MTB), Pneumocystis jirovecii, Aspergillus, and Pseudomonas aeruginosa. (2) In pulmonary infectious cases, mNGS demonstrated a higher detection sensitivity for pathogenic bacteria than pathogen cultures. mNGS combined with protective bronchoalveolar lavage has good clinical application value in the accurate diagnosis of pathogens and identification of non-infectious diseases.IMPORTANCEThe combination of mNGS and the protective BAL technique demonstrates significant utility in accurately diagnosing pathogens and identifying non-infectious diseases. Misdiagnosis of non-infectious lung diseases as infectious lung diseases is a common factor contributing to the lack of response to initial treatment in nonresponding pneumonia patients. The most common pathogens in pulmonary infection cases of nonresponding pneumonia are MTB, Pneumocystis jirovecii, Aspergillus, and Pseudomonas aeruginosa.},
}

@article {pmid40439232,
year = {2025},
author = {McGivern, BB and Ellenbogen, JB and Hoyt, DW and Bouranis, JA and Stemple, BP and Daly, RA and Bosman, SH and Sullivan, MB and Hagerman, AE and Chanton, JP and Tfaily, MM and Wrighton, KC},
title = {Polyphenol rewiring of the microbiome reduces methane emissions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf108},
pmid = {40439232},
issn = {1751-7370},
abstract = {Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens-either through direct toxic effects or by diverting their substrates and energy-to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.},
}

@article {pmid40438915,
year = {2025},
author = {Rivas-Santisteban, J and Martínez, JM and Escudero, C and Hernández-Antolín, R and Cid-Barrio, L and Ellis, GJ and Domingo, E and Sánchez, C and Sobrino, F and Amils, R},
title = {Metagenomic analysis of heavy water-adapted bacterial communities.},
journal = {Microbial genomics},
volume = {11},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001414},
pmid = {40438915},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Water Microbiology ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenome ; DNA Transposable Elements ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Micro-organisms can survive and thrive in unusual and extreme environments. Here, we present a metagenomic analysis of living bacteria found in highly pure, deleterious heavy water (>99% D2O), stored in sealed plastic containers for more than 30 years, without any external supply. Deep DNA sequencing analyses have revealed that the most abundant genetic signatures were primarily associated with Pseudomonadota and Bacteroidota. These bacteria exhibited shorter gene lengths and depletion of polar and metabolically costly amino acids compared to the related species from light water environments. Genes related to DNA transposition, repair and modification were notably abundant, particularly mutant forms of the IS3 transposable elements family. We also explore potential carbon and energy sources and discuss the evolutionary implications of bacteria capable of surviving in such an extreme human-made environment.},
}

*Metagenomics/methods
*Water Microbiology
*Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing
Metagenome
DNA Transposable Elements
Phylogeny
Sequence Analysis, DNA

@article {pmid40438350,
year = {2025},
author = {Peng, H and Fu, J},
title = {Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf128},
pmid = {40438350},
issn = {2053-714X},
}

@article {pmid40438301,
year = {2025},
author = {Marra, PS and Marra, AR and Chen, E and Kobayashi, T and Celeghini, PD and Gutfreund, MC and Pardo, I and Lopes, GOV and Hsieh, MK and Boodhoo, NA and Fu, D and Torres-Espinosa, MA and Li, Y and Deliberato, RO and Algain, SMA and Salinas, JL and Edmond, MB and Amgarten, DE and de Mello Malta, F and Dos Santos, NV and Pinho, JRR and Louine, M and Wilson, MR},
title = {Metagenomic Next-generation Sequencing in Patients With Infectious Meningoencephalitis: A Comprehensive Systematic Literature Review and Meta-analysis.},
journal = {Open forum infectious diseases},
volume = {12},
number = {5},
pages = {ofaf274},
pmid = {40438301},
issn = {2328-8957},
abstract = {BACKGROUND: We aimed to assess the accuracy, clinical efficacy, and limitations of metagenomic next-generation sequencing (mNGS) for diagnosing infectious meningoencephalitis.

METHODS: We performed a systematic literature review and meta-analysis of studies that evaluated the performance of mNGS to determine the cause of infectious meningoencephalitis. We explored PubMed, Cumulative Index to Nursing and Allied Health, Embase, Cochrane Central Register of Controlled Trials, ClinicalTrials.gov, and Web of Science up to 12 November 2024. To perform a meta-analysis, we calculated the pooled diagnostic odds ratio (DOR) for mNGS and for conventional microbiological tests (CMTs) compared to the clinical diagnosis.

RESULTS: Thirty-four studies met the inclusion criteria, with mNGS-positive rates ranging from 43.5% to 93.5% for infectious meningoencephalitis. The meta-analysis included 23 studies with 1660 patients. The pooled sensitivity was 0.70 (95% confidence interval [CI], .67-.72), and its specificity was 0.93 (95% CI, .92-.94). The DOR for mNGS was 26.7 (95% CI, 10.4-68.8), compared to 12.2 (95% CI, 3.2-47.0) for CMTs. For tuberculosis meningoencephalitis, mNGS demonstrated a pooled sensitivity of 0.67 (95% CI, .61-.72) and specificity of 0.97 (95% CI, .95-.99), with a DOR of 43.5 (95% CI, 7.4-256.6).

CONCLUSIONS: Our review indicates that mNGS can be a valuable diagnostic tool for infectious meningoencephalitis, offering high sensitivity and specificity. mNGS's superior DOR compared to that of CMTs highlights its potential for more accurate diagnoses and targeted interventions. Further research is needed to optimize which patients and at what point in the diagnostic process mNGS should be used.},
}

@article {pmid40438215,
year = {2025},
author = {Hanna, A and Abbas, H and Yassine, F and AlBush, A and Bilen, M},
title = {Systematic review of gut microbiota composition, metabolic alterations, and the effects of treatments on PCOS and gut microbiota across human and animal studies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549499},
pmid = {40438215},
issn = {1664-302X},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is an endocrine disorder affecting around 12% of women globally, associated with infertility and various comorbidities. Emerging evidence suggests a crucial role of gut microbiota in PCOS pathophysiology, prompting research to investigate alterations in gut microbial composition in patients with PCOS.

METHODS: This systematic review aims to analyze human and animal studies that compare gut microbiota composition, gut-derived metabolites, and treatment interventions in PCOS patients versus healthy controls. A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science, yielding studies examining gut microbiota, metabolomic shifts, and treatment responses in PCOS models and human populations.

RESULTS: Our analysis revealed decreases in alpha diversity in PCOS patients, with more pronounced changes in beta diversity in animal models. Specific bacterial taxa, such as Bacteroides vulgatus, Escherichia-Shigella and Lactobacillus, showed implication in PCOS pathogenesis, suggesting potential microbial markers. Furthermore, discrepancies between human and animal studies show the need for humanized mouse models to bridge this gap. Interventions like probiotics and fecal microbiota transplantation (FMT) showed varying levels of efficacy, with FMT emerging as a more promising but invasive option, offering live bacteriotherapy as a potential therapeutic alternative. Alterations in gut-derived metabolites, including short-chain fatty acids and bile acids, highlighted the multifaceted nature of PCOS, with implications extending to metabolic, hormonal, and gut-brain axis disruptions.

DISCUSSION: In conclusion, PCOS exhibits complex interactions between gut microbiota and metabolic pathways, necessitating further research with standardized methods and larger sample sizes to elucidate the microbiome's role in PCOS.},
}

@article {pmid40438118,
year = {2025},
author = {Diallo, D and Sun, S and Somboro, AM and Baya, B and Koné, A and Diarra, B and Nantoumé, M and Koloma, I and Diakite, M and Holl, J and Maiga, AI and Seydi, M and Theron, G and Hou, L and Fodor, A and Maiga, M},
title = {Metabolic and immune consequences of antibiotic related microbiome alterations during first-line tuberculosis treatment in Bamako, Mali.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1561459},
pmid = {40438118},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Adult ; Mali ; *Dysbiosis/chemically induced/immunology ; Middle Aged ; *Tuberculosis/drug therapy/microbiology/immunology/metabolism ; Cytokines/blood ; Longitudinal Studies ; *Antitubercular Agents/therapeutic use/adverse effects ; Young Adult ; Metabolomics ; },
abstract = {BACKGROUND: Individuals with a history of tuberculosis (TB) treatment are at a higher risk of experiencing a recurrent episode of the disease. Previous cross-sectional studies identified a connection between dysbiosis (alterations) in the gut microbiota composition and the administration of first-line TB antibiotics. However, these studies have not successfully elucidated this dysbiosis's resulting metabolic and immune consequences.

METHODS: In a longitudinal assessment, we studied the antituberculosis drug-related changes in the gut microbiota's composition and the resulting functional consequences. Sputum for TB culture, peripheral blood for metabolomics and cytokines analysis, and stool for shotgun metagenomics were collected from TB participants at Month-0, Month-2, Month-6 of treatment, and 9 Months after treatment (Month-15). Healthy controls were sampled at Month-0 and Month-6.

FINDINGS: We found notable differences in gut microbiota between individuals with TB and healthy controls. While gut microbiota tended to resemble healthy controls at the end of TB treatment, significant differences for many taxa persisted up to Month-15. Concurrently, disturbances in plasma metabolites, including tryptophan, tricarboxylic acids, and cytokine levels were observed. Certain fatty acids associated with inflammation pathways negatively correlated with the abundance of several taxa.

CONCLUSION: We observed alterations in the gut microbiota composition and function during treatment and at Month-15. Numerous changes in bacterial taxa abundances and inflammation-linked metabolites did not reverse at Month-15. This study suggests potential influences of anti-TB drugs and the gut microbiome on the disease outcome, response to treatment, and resistance to future TB infections.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
Male
Female
Adult
Mali
*Dysbiosis/chemically induced/immunology
Middle Aged
*Tuberculosis/drug therapy/microbiology/immunology/metabolism
Cytokines/blood
Longitudinal Studies
*Antitubercular Agents/therapeutic use/adverse effects
Young Adult
Metabolomics

@article {pmid40437943,
year = {2025},
author = {Franzin, M and Lagatolla, C and Forgiarini, SS and Haag, M and Neef, SK and Comar, M and Schaeffeler, E and Bellich, B and Bramuzzo, M and Decorti, G and Lucafò, M and Hofmann, U and Schwab, M and Stocco, G},
title = {Klebsiella pneumoniae contributes to altered cytotoxicity of thiopurines in vitro: Possible implications of biotransformation and bacterial metabolism.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70089},
pmid = {40437943},
issn = {1476-5381},
support = {RC 07/22//Italian Ministry of Health, through the contribution given to the Institute for Maternal and Child Health IRCCS Burlo Garofolo/ ; //Robert Bosch Stiftung/ ; },
abstract = {BACKGROUND AND PURPOSE: Thiopurines are used in paediatric inflammatory bowel disease (IBD), but some patients do not respond. Because the gut microbiota influences drug efficacy and IBD-patient microbiota presents increased bacterial abundance, we investigated the impact of candidate Enterobacteriaceae on drug cytotoxicity, metabolism and efficacy.

EXPERIMENTAL APPROACH: Thiopurines were exposed in vitro to bacteria for 4 h at 37°C and drug concentrations measured by UV spectrophotometry. Cytotoxic effects and drug metabolite concentrations on NALM6 and JURKAT cells were determined after treatment with thiopurines exposed or not to bacteria. Drugs were measured in Klebsiella pneumoniae lysates and bacterial conditioned media were used for metabolomic analyses. Shotgun metagenomic sequencing was performed on eight IBD-patient faecal stools.

KEY RESULTS: Incubation of thiopurines with K. pneumoniae, but not Escherichia coli and Salmonella enterica, reduced thiopurine concentrations and cytotoxicity on NALM6 and JURKAT cells. Thiopurine metabolites were lower in cells treated with drugs previously exposed to K. pneumoniae. Internalisation of drugs was demonstrated by their detection in lysates after bacterial incubation. Untargeted metabolomics revealed biotransformation of thiopurines by K. pneumoniae, as reactions of deconjugation, reduction, glycosylation, acetylation or conjugation with propionic acid. Incubation with thiopurines led to changes in the secretion of endogenous bacterial metabolites. K. pneumoniae faecal abundance was associated with lower thiopurine metabolite concentrations in erythrocytes of paediatric IBD-patients.

CONCLUSIONS AND IMPLICATIONS: K. pneumoniae decreases the cytotoxicity of thiopurines through internalisation of MP and TG. We revealed potential bacterial drug biotransformation, as well as negative correlations between bacterial abundance and drug metabolites.},
}

@article {pmid40437611,
year = {2025},
author = {Zhang, P and Tuo, X and Jiang, J and Zhang, Y and Zhao, J and Deng, C and Zhao, G and Cheng, Y and Song, L and Yang, Y and Guo, R and Zhang, H and Zhao, H and Ma, S and Li, L and Shi, H},
title = {Characteristics of the gut virome in patients with premalignant colorectal adenoma.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {597},
pmid = {40437611},
issn = {1479-5876},
support = {No.S2024-JC-QN-1554//Natural Science Basic Research Program of Shaanxi Province/ ; },
mesh = {Humans ; *Virome ; *Colorectal Neoplasms/virology/microbiology ; *Adenoma/virology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Precancerous Conditions/virology/microbiology ; Case-Control Studies ; Aged ; Reproducibility of Results ; },
abstract = {BACKGROUND: The multi-kingdom gut microbiota (e.g., bacteriome, mycobiome, and virome) characteristics of colorectal cancer have been extensively studied, yet there is still an insufficient description of the microbiota features in its early-stage, colorectal adenoma, particularly in the gut virome aspect.

METHODS: Based on the Metagenomic Gut Virus catalogue (MGV) containing 54,118 non-redundant gut viral genomes, this study characterized the virome composition and diversity using publicly available metagenomic sequencing data from 419 individuals with premalignant colorectal adenoma and 552 healthy controls. Furthermore, we identified and assessed the reliability and classification performance of adenoma-associated microbial signatures through comparative analysis and the random forest model.

RESULTS: Our results revealed a notable shift in the gut virome structure of patients compared to healthy controls, characterized by a significant increase in viral families such as Microviridae, Podoviridae_crAss-like, and Quimbyviridae. At the viral operational taxonomic unit (vOTU) level, we identified 479 vOTU signatures showing significant differences in relative abundances between patients and controls, including some patient-enriched vOTUs tending to infect Bacteroidaceae and Lachnospiraceae. Correlation network analysis revealed specific bacterial species correlated with adenoma-associated viruses, suggesting frequent interactions between them. Moreover, random forest models trained on gut viral and bacterial signatures demonstrated area under the curve (AUC) scores of 0.68, 0.82, and 0.76 for classifying healthy individuals versus patients with tubular adenomas, patients with sessile serrated adenomas, and patients with both conditions, respectively. In three independent validation cohorts, the classification performance achieved AUC scores ranging from 0.61 to 0.65.

CONCLUSIONS: Our study provides insights into the gut virome in premalignant colorectal adenoma, highlighting its potential role in disease development and diagnosis. Further investigations are warranted to elucidate the underlying mechanisms of gut virus-bacteria interactions and validate diagnostic models in larger populations.},
}

Humans
*Virome
*Colorectal Neoplasms/virology/microbiology
*Adenoma/virology/microbiology
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Precancerous Conditions/virology/microbiology
Case-Control Studies
Aged
Reproducibility of Results

@article {pmid40437401,
year = {2025},
author = {Unrug-Bielawska, K and Sandowska-Markiewicz, Z and Pyśniak, K and Piątkowska, M and Czarnowski, P and Goryca, K and Mróz, A and Żeber-Lubecka, N and Wójcik-Trechcińska, U and Bałabas, A and Dąbrowska, M and Surynt, P and Radkiewicz, M and Mikula, M and Ostrowski, J},
title = {Western Diet and fecal microbiota transplantation alter phenotypic, liver fatty acids, and gut metagenomics and metabolomics in Mtarc2 knockout mice.},
journal = {Genes & nutrition},
volume = {20},
number = {1},
pages = {13},
pmid = {40437401},
issn = {1555-8932},
support = {2018/29/B/NZ7/00809//Narodowe Centrum Nauki/ ; },
}

@article {pmid40436871,
year = {2025},
author = {Zeng, L and Yu, B and Zeng, P and Duoji, Z and Zuo, H and Lian, J and Yang, T and Dai, Y and Feng, Y and Yu, P and Yang, J and Yang, S and Dou, Q},
title = {Mediation effect and metabolic pathways of gut microbiota in the associations between lifestyles and dyslipidemia.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {90},
pmid = {40436871},
issn = {2055-5008},
support = {723B2017//National Natural Science Foundation of China/ ; XZ202201ZD0001G//Science and Technology Major Project of Tibetan Autonomous Region of China/ ; XZ202303ZY0007G//Science and Technology Plan Projects of Tibet Autonomous Region/ ; CQFYJB01005//Chongqing Maternal and Child Health Hospital/ ; 2023YFC3604702//National Key Research and Development Program of China/ ; 2023YFC3604701; 2020YFC2008005; 2018YFC2002405//National Key Research and Development Program of China/ ; 2023YFS0251//Key R&D Project of Sichuan Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dyslipidemias/microbiology/epidemiology ; Male ; Cross-Sectional Studies ; Female ; *Life Style ; Middle Aged ; Adult ; *Metabolic Networks and Pathways ; Feces/microbiology/chemistry ; China ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenome ; Metabolomics ; Triglycerides/blood ; Aged ; },
abstract = {Whether the role of gut microbial features lies in the pathways from lifestyles to dyslipidemia remains unclear. In this cross-sectional study, we conducted a metagenome-wide association analysis and fecal metabolomic profiling in 994 adults from the China Multi-Ethnic cohort. A total of 26 microbial species were identified as mediators between lifestyle factors and risk for dyslipidemia. Specifically, the abundance of [Ruminococcus] gnavus mediated the associations between lifestyles and risks for dyslipidemia, elevated low-density lipoprotein cholesterol, elevated total cholesterol, and elevated triglycerides. [Ruminococcus] gnavus, Alistipes shahii, and Lachnospira eligens were replicated to be associated with dyslipidemia in an external validation cohort. The potential metabolic pathways included arachidonic acid, bile acid, and aromatic amino-acid metabolism.},
}

Humans
*Gastrointestinal Microbiome
*Dyslipidemias/microbiology/epidemiology
Male
Cross-Sectional Studies
Female
*Life Style
Middle Aged
Adult
*Metabolic Networks and Pathways
Feces/microbiology/chemistry
China
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenome
Metabolomics
Triglycerides/blood
Aged

@article {pmid40436643,
year = {2025},
author = {Li, J and Wu, Y and Yang, Y and Chen, L and He, C and Zhou, S and Huang, S and Zhang, X and Wang, Y and Gui, Q and Lu, H and Zhang, Q and Yang, Y},
title = {Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.},
journal = {Journal of Zhejiang University. Science. B},
volume = {26},
number = {5},
pages = {477-492},
doi = {10.1631/jzus.B2400341},
pmid = {40436643},
issn = {1862-1783},
support = {82101665, 82271588, 82200665 and 82100795//the National Natural Science Foundation of China/ ; LY22H030009//the Zhejiang Provincial Natural Science Foundation of China/ ; 2023ZL480//the Zhejiang Provincial Science and Technology Program of Traditional Chinese Medicine/ ; 2023RC153//the Medical and Health Research Project of Zhejiang Province/ ; },
mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Bacteroides ; China ; Diabetes Mellitus, Type 2/microbiology ; *Escherichia coli/genetics/isolation & purification/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; East Asian People ; },
abstract = {Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.},
}

Aged
Aged, 80 and over
Female
Humans
Male
Middle Aged
Bacteroides
China
Diabetes Mellitus, Type 2/microbiology
*Escherichia coli/genetics/isolation & purification/classification
*Gastrointestinal Microbiome/genetics
*Metagenomics
East Asian People

@article {pmid40436596,
year = {2025},
author = {Tan, G and Lin, K and Hu, M and Wang, Y and Li, X and Li, X and Chen, S and Zhang, Q and Zheng, Z},
title = {Uncovering the resistome and mobilome across different types of ready-to-eat fermented foods.},
journal = {Food research international (Ottawa, Ont.)},
volume = {213},
number = {},
pages = {116577},
doi = {10.1016/j.foodres.2025.116577},
pmid = {40436596},
issn = {1873-7145},
mesh = {*Fermented Foods/microbiology ; *Food Microbiology ; *Fast Foods/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Dairy Products/microbiology ; Vegetables/microbiology ; },
abstract = {Antimicrobial resistance in food poses a significant threat to public health, and the persistence of antibiotic resistance genes (ARGs) in ready-to-eat fermented foods (RTE-FFs) is a growing concern. However, information on the diversity, origins, and transferability of ARGs in RTE-FFs is limited. This study investigated the distribution of ARGs and mobile genetic elements (MGEs) in four types of RTE-FFs: soybean, dairy, meat, and vegetable products. Using whole metagenomic sequencing, we identified significant variations in the bacterial diversity, ARG profiles, and MGE profiles among these food types. Bean-based RTE-FFs exhibited the highest diversity of ARGs and MGEs, while dairy products showed the lowest diversity (p < 0.05). Eight types of ARGs were significantly more prevalent in bean-based foods than in the other food categories (p < 0.05). Several ARGs were highly abundant in the RTE-FFs, including aphA2, blaTEM-116, PBP1a, PBP1b, OqxA, OqxBgb, lsa(A), tet(34), and tet(58). Plasmids carried the highest number of ARGs among all MGEs, particularly those associated with beta-lactam, macrolide-lincosamide-streptogramin, tetracycline, and aminoglycoside resistance, suggesting a higher risk with plasmid-mediated transfer, especially in bean-based RTE-FFs. Metagenomic binning analysis recovered 76 high-quality metagenome-assembled genomes (MAGs), including four novel species. A total of 13 types of ARGs, encompassing 95 subtypes, were identified across the MAGs; Bacillus paranthracis, Enterococcus casseliflavus, and Enterococcus gallinarum had the most ARGs (16, 12, and 14, respectively). Dairy RTE-FFs (yogurt and cheese) contained a high abundance of Streptococcus thermophilus resistant to beta-lactams (PBP1b) and tetracycline (tetB(60)), raising concerns about ARG transfer in these food products. Bean RTE-FFs (sufu) harbored two pathogenic Acinetobacter species carrying carbapenem resistance genes (blaOXA-180, blaOXA-211, and blaOXA-230). No ARGs were found in the MGEs (prophages, insertion sequences, or transposons) within the MAGs. Overall, our results provide valuable insights into the antibiotic resistome and mobilome of various RTE-FFs to inform food production and management practices.},
}

*Fermented Foods/microbiology
*Food Microbiology
*Fast Foods/microbiology
Interspersed Repetitive Sequences
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Metagenomics
Dairy Products/microbiology
Vegetables/microbiology

@article {pmid40436373,
year = {2025},
author = {Vosough, M and Drees, F and Sieber, G and Stach, TL and Beisser, D and Probst, AJ and Boenigk, J and Schmidt, TC},
title = {Integrative Analysis of Nontargeted LC-HRMS and High-Throughput Metabarcoding Data for Aquatic Environmental Studies Using Combined Multivariate Statistical Approaches.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c00539},
pmid = {40436373},
issn = {1520-6882},
abstract = {Significant progress in high-throughput analytical techniques has paved the way for novel approaches to integrating data sets from different compartments. This study leverages nontarget screening (NTS) via liquid chromatography-high-resolution mass spectrometry (LC-HRMS), a crucial technique for analyzing organic micropollutants and their transformation products, in combination with biological indicators. We propose a combined multivariate data processing framework that integrates LC-HRMS-based NTS data with other high-throughput data sets, exemplified here by 18S V9 rRNA and full-length 16S rRNA gene metabarcoding data sets. The power of data fusion is demonstrated by systematically evaluating the impact of treated wastewater (TWW) over time on an aquatic ecosystem through a controlled mesocosm experiment. Highly compressed NTS data were compiled through the implementation of the region of interest-multivariate curve resolution-alternating least-squares (MCR-ALS) method, known as ROIMCR. By integrating ANOVA-simultaneous component analysis with structural learning and integrative decomposition (SLIDE), the innovative SLIDE-ASCA approach enables the decomposition of global and partial common, as well as distinct variation sources arising from experimental factors and their possible interactions. SLIDE-ASCA results indicate that temporal variability explains a much larger portion of the variance (74.6%) than the treatment effect, with both contributing to global shared space variation (41%). Design structure benefits include enhanced interpretability, improved detection of key features, and a more accurate representation of complex interactions between chemical and biological data. This approach offers a greater understanding of the natural and wastewater-influenced temporal patterns for each data source, as well as reveals associations between chemical and biological markers in an exemplified perturbed aquatic ecosystem.},
}

@article {pmid40435904,
year = {2025},
author = {Liu, Z and Yan, K and Li, J and Zhang, C and Xu, D and Wang, Y and Xie, X and Li, H and Qie, J and Li, J and Dong, X and Dong, L and Cui, H},
title = {Acute appendicitis in children: Two microbial states associated with clinical indicators and severity.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116925},
doi = {10.1016/j.diagmicrobio.2025.116925},
pmid = {40435904},
issn = {1879-0070},
abstract = {BACKGROUND: Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.

METHODS: A total of 74 pediatric intra-abdominal pus samples from appendectomy cases (aged 3-15) were collected for AA at Tianjin Children's Hospital (Feb 2022-Sep 2023). The samples were categorised into two groups based on pathological findings: SA (n = 27) and CA (n = 47). Metagenomic profiling was employed to characterized the microbial composition and function in both groups. Additionally, clinical parameters associated with the microbiota were analysed.

RESULTS: The SA group exhibited higher levels of Burkholderia, Mycobacterium, and Klebsiella, while the CA group demonstrated higher levels of Porphyromonas, Bacteroides, Fusobacterium, Prevotella, and Tannerella. Additionaly, there were significant differences in clinical parameters, including C-reactive protein (CRP), procalcitonin (PCT), fibrinogen, sodium, potassium, phosphorus, complement C3, and chloride, between two groups. Furthermore, functional profiling revealed alterations in microbial metabolism and antibiotic resistance, highlighting the complex interplay between microbial communities and host inflammatory responses in appendicitis.

CONCLUSIONS: This study identifies unique microbial and serum biomarkers and their correlates in varying severities of acute appendicitis, highlighting the role of the microbiome in the aetiology of acute appendicitis.},
}

@article {pmid40435848,
year = {2025},
author = {Jung, H and Park, S and Park, SA and Kim, H and Lee, M and Park, CH and Jegal, J and Shin, G and Kim, HJ},
title = {FDA-hydrolysis activity: A pre-screening tool for optimizing compost selection in standardized plastic biodegradation testing.},
journal = {Waste management (New York, N.Y.)},
volume = {204},
number = {},
pages = {114907},
doi = {10.1016/j.wasman.2025.114907},
pmid = {40435848},
issn = {1879-2456},
abstract = {Current ISO 14855-1 standards for assessing plastic biodegradability under composting conditions rely on physicochemical parameters, such as pH and volatile solids, to select compost inocula. However, these indicators do not directly reflect microbial activity, which is central to biodegradation processes. This study proposes fluorescein diacetate hydrolase (FDA-H) activity as a rapid, integrative biological indicator to pre-screen composts before standardized biodegradation testing. FDA-H activity was measured in five composts and showed a strong correlation with early CO2 evolution (r = 0.93), reflecting initial microbial metabolic potential. Moderate correlations were also observed with final biodegradation rates of cellulose and polybutylene succinate (PBS), suggesting that microbial community shifts and substrate-specific adaptation influence long-term outcomes. Metagenomic analysis supported this by revealing distinct microbial succession patterns during degradation, especially for synthetic polymers. We also compared FDA-H with standardized microbial activity assays, including respiration and dehydrogenase activity. Unlike these methods, FDA-H captures extracellular hydrolytic enzyme activity relevant to polymer breakdown and offers advantages in speed and operational simplicity. While FDA-H does not replace ISO/OECD biodegradation standards, it complements them by providing early-stage insight into compost suitability. Integrating FDA-H into existing testing frameworks could enhance the reliability, efficiency, and biological relevance of compost selection, ultimately improving standardized biodegradation assessments.},
}

@article {pmid40435563,
year = {2025},
author = {García-Pérez, P and Tomas, M and Giuberti, G and Capanoglu, E and Callegari, ML and Lucini, L and Patrone, V},
title = {Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128226},
doi = {10.1016/j.micres.2025.128226},
pmid = {40435563},
issn = {1618-0623},
abstract = {Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible microgreen metabolites and human gut bacteria. To this end, in vitro gastrointestinal digestion and large intestine fermentation were performed on eight different microgreens, which were further subjected to a dual high-throughput approach that combined fecal metagenomics and untargeted metabolomics. Data reveal a significant correlation between Parabacteroides merdae and two isothiocyanates in arugula fermentates, suggesting a high bioaccessibility of these bioactive compounds. Meanwhile, two species of Roseburia were correlated with pseudooxynicotine, an anti-inflammatory catabolite of nicotine in Brassica oleracea fermentates (such as broccoli, Brussels sprouts, and red cabbage), coupled with an increase in short-chain fatty acid production. These findings confer evidence on the nutritional impact of microgreens consumption, revealing the most bioaccessible metabolites with associated health-promoting properties together with their participation in the shaping of gut microbial populations, possibly leading to prebiotic effects.},
}

@article {pmid40434915,
year = {2025},
author = {Kuntz, TM and Liu, L and Wang, K and Everett, C and Eliassen, AH and Willett, WC and Sinha, R and Chan, AT and Rimm, EB and Garrett, WS and Segata, N and Piccinno, G and Huttenhower, C and Morgan, X and Song, M},
title = {Comparing the metagenomic performance of stools collected from custom cards and 95% ethanol in epidemiologic studies.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-25-0157},
pmid = {40434915},
issn = {1538-7755},
abstract = {Background Stool cards have been used for microbiome assessment in epidemiological studies. Methods We compared shotgun metagenomic sequencing from 32 participants who self-collected stool samples from the same bowel movement using a custom stool card vs. a collection tube with 95% ethanol fixative in the Nurses' Health Study II. We evaluated the agreement between methods at both the whole-community and individual species levels. To contextualize the comparison for disease association studies, we assessed the performance of the two collection methods for differentiating colorectal cancer-associated taxa. Results Overall, metagenomes from cards and 95% ethanol were highly correlated within individuals. No difference was found in alpha diversity and only ~1% of variation in beta diversity was explained by the collection method. At the species level, while the relative abundances were highly correlated between card and ethanol sample pairs (Spearman rho = 0.96), 10 (out of 239) species showed a differential abundance in paired samples, including overrepresentation of Escherichia coli and underrepresentation of three Streptococcus species in cards compared with ethanol. Among a set of 99 colorectal cancer-associated species, 4 showed differential abundances between collection methods; however, this number was consistent with what would be expected by chance. Conclusions Metagenomic sequencing using stool samples self-collected using stool cards or 95% ethanol yielded largely consistent results, although differential abundances were observed for a small number of individual species. Impact Stool cards can be a cost-effective alternative to collect stool samples for metagenomic sequencing in epidemiologic studies but warrant additional considerations for data analysis.},
}

@article {pmid40434822,
year = {2025},
author = {Berelson, MFG and Heavens, D and Nicholson, P and Clark, MD and Leggett, RM},
title = {From air to insight: the evolution of airborne DNA sequencing technologies.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {5},
pages = {},
doi = {10.1099/mic.0.001564},
pmid = {40434822},
issn = {1465-2080},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Sequence Analysis, DNA/methods ; *DNA, Environmental/genetics/analysis/isolation & purification ; Humans ; Environmental Monitoring/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.},
}

*High-Throughput Nucleotide Sequencing/methods
*Air Microbiology
*Sequence Analysis, DNA/methods
*DNA, Environmental/genetics/analysis/isolation & purification
Humans
Environmental Monitoring/methods
Computational Biology/methods
Biodiversity

@article {pmid40434093,
year = {2025},
author = {Koldaş, SS and Sezerman, OU and Timuçin, E},
title = {Exploring the role of microbiome in cystic fibrosis clinical outcomes through a mediation analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019625},
doi = {10.1128/msystems.00196-25},
pmid = {40434093},
issn = {2379-5077},
abstract = {UNLABELLED: Human microbiome plays a crucial role in host health and disease by mediating the impact of environmental factors on clinical outcomes. Mediation analysis is a valuable tool for dissecting these complex relationships. However, existing approaches are primarily designed for cross-sectional studies. Modern clinical research increasingly utilizes long follow-up periods, leading to complex data structures, particularly in metagenomic studies. To address this limitation, we introduce a novel mediation framework based on structural equation modeling that leverages linear mixed-effects models using penalized quasi-likelihood estimation with a debiased lasso. We applied this framework to a 16S rRNA sputum microbiome data set collected from patients with cystic fibrosis over 10 years to investigate the mediating role of the microbiome in the relationship between clinical states, disease aggressiveness phenotypes, and lung function. We identified richness as a key mediator of lung function. Specifically, Streptococcus was found to be significantly associated with mediating the decline in lung function on treatment compared to exacerbation, while Gemella was associated with the decline in lung function on recovery. This approach offers a powerful new tool for understanding the complex interplay between microbiome and clinical outcomes in longitudinal studies, facilitating targeted microbiome-based interventions.

IMPORTANCE: Understanding the mechanisms by which the microbiome influences clinical outcomes is paramount for realizing the full potential of microbiome-based medicine, including diagnostics and therapeutics. Identifying specific microbial mediators not only reveals potential targets for novel therapies and drug repurposing but also offers a more precise approach to patient stratification and personalized interventions. While traditional mediation analyses are ill-equipped to address the complexities of longitudinal metagenomic data, our framework directly addresses this gap, enabling robust investigation of these increasingly common study designs. By applying this framework to a decade-long cystic fibrosis study, we have begun to unravel the intricate relationships between the sputum microbiome and lung function decline across different clinical states, yielding insights that were previously unknown.},
}

@article {pmid40434086,
year = {2025},
author = {Nieves-Morales, R and Paez-Diaz, JA and Rodriguez-Carrio, SM and Melendez Martinez, G and Rivera-Lopez, EO and Rodríguez-Ramos, J and García-Arrarás, JE and Rios-Velazquez, C},
title = {Intestinal microbiome profile of the brown rock sea cucumber (Holothuria glaberrima) using ITS and 16S rDNA amplicons from direct mechanical, enzymatic, and chemical metagenomic extraction.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0029325},
doi = {10.1128/mra.00293-25},
pmid = {40434086},
issn = {2576-098X},
abstract = {Using direct mechanical, enzymatic, and chemical extraction methods, the intestinal microbiome of the marine invertebrate Holothuria glaberrima was obtained. ITS and 16S rDNA regions were sequenced to enrich and investigate the prokaryotic and fungal diversity profiles from different anatomical regions within the sea cucumber's intestinal biology.},
}

@article {pmid40434078,
year = {2025},
author = {Weisse, L and Martin, L and Moumen, B and Héchard, Y and Delafont, V},
title = {Environmental diversity of Candidatus Babelota and their relationships with protists.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0026125},
doi = {10.1128/msystems.00261-25},
pmid = {40434078},
issn = {2379-5077},
abstract = {Ca. Babelota is a phylum of strictly intracellular bacteria whose representatives are commonly detected in various environments through metagenomics, though their presence, ecology, and biology have never been addressed so far. As a group of strict intracellular, we hypothesize that their presence, occurrence, and abundance heavily depend on their hosts, which are known as heterotrophic protists, based on few described isolates. Here, we conducted a sampling campaign allowing to characterize protists and associated bacterial communities, using high-throughput sequencing. In parallel, a systematic enrichment of protists from samples was performed to attempt characterization and isolation of new Ca. Babelota within native hosts. We found that Ca. Babelota are among the most widespread phylum among the rare ones. Protist enrichments are allowed in certain cases to enrich as well for Ca. Babelota, which could be visualized in vivo infecting protist cells. Though cosmopolitan, Ca. Babelota diversity was highly site-specific. Cooccurrence analyses allowed to retrieve well-known as well as new putative associations involving numerous protists of various trophic regimes. The combination of approaches developed in this study enhances our understanding of Ca. Babelota ecology and biology, while paving the way for future isolation of new members of this elusive phylum, which could have huge impact on protists-and ecosystems-functioning.IMPORTANCEOur understanding of microbial diversity surrounding us and colonizing the environment has been dramatically impacted by the advent of DNA-based analyses. Such progress helped shine a new light on numerous lineages of yet-to-be-characterized microbes, whose ecology and biology are basically unknown. Among those uncharacterized clades is the Candidatus Babelota, a bacterial phylum for which parasitism seems to be an ancestral trait. All known Ca. Babelota thrive by infecting phagotrophic protist hosts, thereby impacting this basal link of the trophic chain. The Ca. Babelota constitutes a model that stands out, as phylum-wide conserved parasitism has only been described in one previous occurrence for Bacteria, with the Chlamydiota. Thus, exploring the intricate interplay between Ca. Babelota and their protist hosts will advance our knowledge of bacterial diversity, their ecology, and global impact on ecosystem functioning.},
}

@article {pmid40434009,
year = {2025},
author = {Chen, ZY and Gao, FZ and Bai, H and Zhang, M and He, LY and Liu, YS and Ying, GG},
title = {Key Contribution and Risk of Airborne Antibiotic Resistance: Total Suspended Particles or Settled Dust?.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11038},
pmid = {40434009},
issn = {1520-5851},
abstract = {The atmosphere is an important environmental medium in spreading antimicrobial resistance (AMR) in animal farming systems, yet the exposure risks associated with airborne pathways remain underexplored. This study employed metagenomic sequencing to investigate the airborne transmission of AMR in chicken farms (i.e., chicken feces, total suspended particles (TSP), and dust) and its exposure risks on the gut and nasal cavities of workers, office staff, and nearby villagers. Results revealed that TSP exhibited greater abundance, diversity, and transfer potential of antibiotic resistance genes (ARGs) compared to dust. The abundance of airborne resistome decreased with distance from the chicken house, and ARGs were estimated to spread up to 9.48 km within 1 h. While the gut resistome of workers and villagers showed limited differences, emerging tet(X) variants and high-risk dfrA remain future concerns. More nasal resistome was attributable to TSP compared to dust. Workers faced significantly higher inhalable exposures to antibiotic-resistant bacteria (ARB) and human pathogenic antibiotic-resistant bacteria (HPARB), exceeding those of office staff and villagers by an order of magnitude. We also compiled lists of high-risk and potential-risk airborne ARGs to inform monitoring. These findings highlight the need for regular air disinfection in animal farms and better protective measures for workers.},
}

@article {pmid40433987,
year = {2025},
author = {Zhou, Z and Yang, M and Fang, H and Zhang, B and Ma, Y and Li, Y and Liu, Y and Cheng, Z and Zhao, Y and Si, Z and Zhu, H and Chen, P},
title = {Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium nucleatum-infected Colorectal Cancer via Ecological Control.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e14232},
doi = {10.1002/advs.202414232},
pmid = {40433987},
issn = {2198-3844},
support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27//Lanzhou Municipal Science and Technology Program/ ; 2024-8-30//Lanzhou Municipal Science and Technology Program/ ; 2024-4-2//Lanzhou Municipal Science and Technology Program/ ; 20250260006//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260016//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260020//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; },
abstract = {Polymorphic microbiomes play important roles in colorectal cancer (CRC) occurrence and development. In particular, Fusobacterium nucleatum (F. nucleatum) is prevalent in patients with CRC, and eliminating it is beneficial for treatment. Here, multiple metagenomic sequencing cohorts are combined with multiomics to analyze the microbiome and related functional alterations. Furthermore, local human metagenome and metabolomics are used to discover commensal consortia. A synthetic microbial community (SynCom) is then designed by metabolic network reconstruction, and its performance is validated using coculture experiments and an AOM-DSS induced mouse CRC model. The sequencing result shows that F. nucleatum is more abundant in both the feces and tumor tissues of CRC patients. It causes alterations through various pathways, including microbial dysbiosis, lipid metabolism, amino acid metabolism, and bile acid metabolism disorders. The designed SynCom contains seven species with low competition interrelationship. Furthermore, the SynCom successfully inhibits F. nucleatum growth in vitro and achieves colonization in vivo. Additionally, it promotes F. nucleatum decolonization, and enhances tryptophan metabolism and secondary bile acid conversion, leading to reduced lipid accumulation, decreased inflammatory reaction, and enhanced tumor inhibition effect. Overall, the bottom-up designed SynCom is a controllable and promising approach for treating F. nucleatum-positive CRC.},
}

@article {pmid40433668,
year = {2025},
author = {von Ameln Lovison, O and Zempulski Volpato, FC and Weber, LG and Barth, AL and Simon Coitinho, A and Martins, AF},
title = {Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1531084},
pmid = {40433668},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology/pathology/virology ; Cross-Sectional Studies ; Disease Susceptibility ; *Microbiota ; SARS-CoV-2 ; Female ; Male ; Severity of Illness Index ; Middle Aged ; *Respiratory System/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Adult ; Biomarkers ; Aged ; },
abstract = {It is argued that commensal bacteria in the upper respiratory tract (URT) protect against pathogen colonization and infection, including respiratory viruses. Given that the microbiome can mediate immune modulation, a link between the URT microbiome (URTM) and COVID-19 susceptibility and severity is expected. This 16S metagenomics cross-sectional study assessed URTM composition, metabolic prediction, and association with laboratory biomarkers in non-COVID-19 pneumonia (NO-CoV), moderate (M-CoV), severe (S-CoV) COVID-19 patients, as well as COVID-19-negative, asymptomatic (NC) patients. The S-CoV group exhibited reduced URTM diversity, primarily due to a decreased abundance of eubiotic taxa. Some of these taxa (e.g., Haemophilus sp., Neisseria sp.) were also associated with inflammatory biomarkers. Multiple metabolic pathways (e.g., short-chain fatty acids, vitamin B12) linked to immune response, antiviral activity, and host susceptibility showed decreased abundance in S-CoV. These pathways could suggest potential alternatives for the therapeutic arsenal against COVID-19, providing reassurance about the progress in understanding and treating this disease.},
}

Humans
*COVID-19/microbiology/pathology/virology
Cross-Sectional Studies
Disease Susceptibility
*Microbiota
SARS-CoV-2
Female
Male
Severity of Illness Index
Middle Aged
*Respiratory System/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification
Adult
Biomarkers
Aged

@article {pmid40433443,
year = {2025},
author = {Dahal, U and Bansal, A},
title = {Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.},
journal = {Current genomics},
volume = {26},
number = {2},
pages = {81-94},
pmid = {40433443},
issn = {1389-2029},
abstract = {Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.},
}