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Bibliography on: Metagenomics

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ESP: PubMed Auto Bibliography 27 Aug 2025 at 01:31 Created: 

Metagenomics

While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.

Created with PubMed® Query: ( metagenomic OR metagenomics OR metagenome ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2025-08-26

Gao ZQ, Su JW, Qin Y, et al (2025)

Metagenomic analysis of vitamins B and K2 biosynthesis in chicken gut microbiota across laying periods.

BMC microbiology, 25(1):553.

RevDate: 2025-08-26

Salcher MM, Layoun P, Fernandes C, et al (2025)

Bringing the uncultivated microbial majority of freshwater ecosystems into culture.

Nature communications, 16(1):7971.

Axenic cultures are essential for studying microbial ecology, evolution, and genomics. Despite the importance of pure cultures, public culture collections are biased towards fast-growing copiotrophs, while many abundant aquatic prokaryotes remain uncultured due to uncharacterized growth requirements and oligotrophic lifestyles. Here, we applied high-throughput dilution-to-extinction cultivation using defined media that mimic natural conditions to samples from 14 Central European lakes, yielding 627 axenic strains. These cultures include 15 genera among the 30 most abundant freshwater bacteria identified via metagenomics, collectively representing up to 72% of genera detected in the original samples (average 40%) and are widespread in freshwater systems globally. Genome-sequenced strains are closely related to metagenome-assembled genomes (MAGs) from the same samples, many of which remain undescribed. We propose a classification of several novel families, genera, and species, including many slowly growing, genome-streamlined oligotrophs that are notoriously underrepresented in public repositories. Our large-scale initiative to cultivate the "uncultivated microbial majority" has yielded a valuable collection of abundant freshwater microbes, characterized by diverse metabolic pathways and lifestyles. This culture collection includes promising candidates for oligotrophic model organisms, suitable for a wide array of ecological studies aimed at advancing our ecological and functional understanding of dominant, yet previously uncultured, taxa.

RevDate: 2025-08-26

Zou X, Cao H, Hong L, et al (2025)

Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection.

Signal transduction and targeted therapy, 10(1):272.

Respiratory microbial dysbiosis has been implicated in the occurrence and progression of community-acquired pneumonia (CAP). However, the dynamic variation in the respiratory microbiota and its interaction with the host response remain poorly understood. Here, we performed metagenomic analysis of respiratory and gut microbiota, along with blood transcriptomics, using longitudinally collected samples from 38 CAP patients. CAP patients presented disrupted sputum microbiota at the early, middle, and late stages of hospitalization. Microbial pathways involved in peptidoglycan biosynthesis and immune evasion, particularly contributed by the Streptococcus genus, were enriched in CAP patients. Additionally, several Streptococcus strains demonstrated correlation between respiratory and gut microbiota in CAP patients. By incorporating host response data, we revealed that Streptococcus oralis (SOR) was associated with host pathways involved in the innate immune response to infection, and this microbe‒host interaction was reproduced in a newly enrolled CAP cohort consisting of 22 patients with influenza infection. The host-SOR interaction was validated in a mouse model, where SOR demonstrated protective efficacy against influenza virus infection comparable to that of the well-established respiratory probiotic Lactobacillus rhamnosus GG. Preaspiration of SOR in mice significantly mitigated body weight loss, reduced lung inflammation, and lowered viral loads following influenza virus challenge. Host response profiling indicated that SOR priming activated a greater innate immune response at the early stage of infection and that this response resolved timely as the host began to recover. These findings suggest that respiratory commensals play an immune-protective role by inducing a timely innate immune response to prevent CAP progression.

RevDate: 2025-08-26

Ruiz-Castilla FJ, Barbudo-Lunar M, Gutiérrez MC, et al (2025)

Storage of Alperujo influences composting performance: Insights into gaseous emissions and functional metagenomics.

Journal of environmental management, 393:127015 pii:S0301-4797(25)02991-3 [Epub ahead of print].

Alperujo (AL), the primary by-product of olive oil extraction, poses a significant environmental challenge in the Mediterranean region. Understanding the AL composting process is essential for controlled aerobic revalorisation to obtain a stable and good quality organic amendment with the minimum environmental impact. Our approach assumes that full-scale pond storage duration modifies the degree of hydrolytic fermentation of AL, affecting the subsequent stages of the composting process. In this work, AL raw materials for composting were stored for 3 or 6 months. Subsequently, during pilot-scale composting, the loss of organic matter (OM) not only induced key changes in the solid mass but also in gaseous emissions, which decreased along with the storage time. Consequently, the initial C/N ratio decreased from 25.76 to 22.24, and composting yields relative to the AL initially mixed with a bulking agent (3/1, wt./wt.) were 76.4 % and 41.7 %, respectively. Phenolic compounds were effectively degraded throughout the composting process under both initial conditions, enhancing the potential value of the final products. Metagenomic analysis revealed differences in the raw material bacteriome, variations that also became evident throughout composting. The thermophilic stage fostered the selection of a range of thermotolerant microorganisms, many of them with lignocellulosic activity, which is essential for the decomposition of OM. Then, at the final mesophilic phase, a significant increase in bacterial diversity and metabolic activity was observed. This study contributes to better understand the functional role of the microbiome in AL composting, particularly regarding the bacterial community dynamics and gaseous emissions to the atmosphere.

RevDate: 2025-08-26

Miao Y, Liu X, Liu M, et al (2025)

Vertical migration of antibiotics, ARGs, and pathogens in industrial multi-pollutant soils: Implications for environmental and public health.

Ecotoxicology and environmental safety, 303:118912 pii:S0147-6513(25)01257-6 [Epub ahead of print].

Urban soils accumulating multiple pollutants act as critical reservoirs for antibiotic resistance genes (ARGs) and pathogens, yet their vertical migration in industrial soils remains poorly understood. Here, we investigated antibiotics, ARGs, and pathogenic hosts in soil profiles (0-310 cm) from Shanghai's Taopu Industrial Park (China) using ultra-performance liquid chromatography tandem mass spectrometry and metagenomic sequencing. Nineteen antibiotics (0.7-113.6 ng g[-1]) decreased exponentially with depth, influenced by polycyclic aromatic hydrocarbons (PAHs). Among 1183 ARG subtypes, 437 persisted across depths, with relative abundance increasing with soil depth, primarily driven by microbial community shifts, where metabolic pathways (e.g., carbohydrate and nitrogen metabolism as network hubs) contributed substantially to ARG dissemination. Random forest modelling identified clay (38 %) and fluoranthene (21 %) as primary drivers for bacterial communities, while pathogens responded divergently: antibiotics explained 48 % of Acinetobacter abundance variation, whereas clay governed 36 % of Pseudomonas abundance. The top 30 ARG-host genera included seven pathogens enriched in middle-deep layers (20-310 cm), indicating elevated groundwater contamination risks. Our findings reveal synergistic pollutant-microbial metabolic interactions promoting deep-soil resistance propagation, advocating urgent co-pollutant mitigation to safeguard urban soil systems.

RevDate: 2025-08-26

Ji F, Yang X, Quan H, et al (2025)

Enhanced performance of algal-bacterial granular sludge in treating wastewater under PFOA stress: Synergistic effects and mechanisms.

Journal of hazardous materials, 497:139631 pii:S0304-3894(25)02550-6 [Epub ahead of print].

The ubiquitous distribution of perfluorooctanoic acid (PFOA) in wastewater poses significant challenges for wastewater treatment systems, yet its impact on granular sludge systems remains poorly understood. This study investigated the performance of aerobic granular sludge (AGS) and algal-bacterial granular sludge (ABGS) systems in terms of stability, nutrient and PFOA removal, enzyme activity, and microbial communities under PFOA stress. Both systems demonstrated tolerance and adsorptive removal of PFOA with enhanced total nitrogen (TN) and slightly decreased total phosphorus (TP) removals. Notably, ABGS showed superior performance with approximately 19 % and 80 % improved removal for TN and PFOA compared to AGS under 1 mg/L PFOA stress. Microbial community and metagenomic analyses revealed that the proliferation of nitrogen-removal bacteria (e.g., Nitrospirae increased by around 360 %) and the increased abundance of denitrification-related genes (including genes associated with electron donor pathways) boosted TN removal. Under PFOA stimulation, the synergistic interaction between bacteria and algae in the ABGS system secreted about 12 % more extracellular polymeric substances (EPS). The higher concentration and diverse composition of EPS offered abundant adsorption sites for PFOA while serving as a protective barrier that restricted its penetration into cells. This protective mechanism was further supported by the enhanced antioxidant defenses in ABGS as evidenced by the lower increase in reactive oxygen species and lactate dehydrogenase levels compared to AGS. These findings deepen our understanding of the stress responses and adaptive mechanisms of granular sludge systems under long-term per- and polyfluoroalkyl substance exposure and highlight the potential of ABGS in treating PFOA-laden wastewater.

RevDate: 2025-08-26

Ji Q, Zhu J, Hou G, et al (2025)

Antibiotic stress alters lysogeny-lysis dynamics and drives phage-mediated transfer of antibiotic resistance genes in the activated sludge process.

Journal of hazardous materials, 497:139659 pii:S0304-3894(25)02578-6 [Epub ahead of print].

The spread of antibiotic resistance genes (ARGs) in wastewater treatment systems poses a significant public health concern, yet the role of bacteriophages (phages), particularly temperate phages, in mediating horizontal gene transfer (HGT) of ARGs under antibiotic stress remains poorly understood. This study investigated the effects of escalating ciprofloxacin (CIP; 0-200 μg/L)-selected as a representative antibiotic due to its frequent occurrence and persistence in wastewater-on phage lysogeny-lysis dynamics and phage-mediated ARG transfer in a laboratory-scale activated sludge reactor. Integrating metaviromic and metagenomic analysis revealed that the phage-mediated ARG-HGT events mainly occurred at the highest CIP concentration stage (200 μg/L), indicating that high-level antibiotic stress is essential for triggering significant ARG transfer. Notably, all these HGT events were associated with temperate phages. The HGT-associated ARGs may confer host resistance to antibiotics, as supported by the ARG expression and antibiotic resistance activity experiment. Although temperate dynamics generally shifted toward lysogeny under escalating stress, most of the temperate phages involved in ARG-HGT became more active at higher CIP concentration stages, which may facilitate host survival under stress conditions.

RevDate: 2025-08-26

Jin L, Yuan L, Bürgmann H, et al (2025)

Wastewater treatment plant effluent drives coupled changes of viral and bacterial community structure and function in impacted rivers.

Environment international, 203:109737 pii:S0160-4120(25)00488-X [Epub ahead of print].

The discharge of wastewater treatment plant (WWTP) effluent containing bacteria and viruses has significant ecological and public health implications for aquatic ecosystems. While viruses infecting bacterial hosts are abundant and diverse in wastewater, their environmental fate, host association, and functional impact in affected river ecosystems remain poorly understood. Using a metagenomic approach, we characterized double-stranded DNA viral communities across nine WWTPs and impacted riverine habitats, including water, suspended particles, sediment, and epilithic biofilm. River water was the most affected habitat by WWTP effluent, with viral diversity increasing by 22 % (±15 %) downstream. In contrast, no significant differences were observed in either viral or bacterial community structures across locations in biofilm or sediment. Among 38,826 viral operational taxonomic units (vOTUs) recovered from 148 metagenomes, 18 % were shared exclusively between effluent and downstream habitats, primarily with river water (99 % of the vOTUs). These wastewater-associated vOTUs were predicted to infect key bacterial taxa involved in carbon and nitrogen cycling (e.g., Nitrosomonas and Methylomonadaceae) and potential human pathogens (e.g., Vibrio and Ralstonia). Additionally, WWTP effluent increased the diversity of virus-encoded auxiliary metabolic genes, especially those involved in carbon, nutrient, and drug metabolism, suggesting potential roles in shaping host fitness and environmental adaptation. Overall, our findings demonstrate that WWTP effluent drives coupled changes in viral and bacterial communities in river water, highlighting the potential ecological consequences of virus-host interactions in wastewater-impacted aquatic environments.

RevDate: 2025-08-26

Zou Y, Chen W, Wang L, et al (2025)

Microbial metabolic functions, rather than taxonomic composition, predominantly shape the distribution of antibiotic resistance genes in an effluent-impacted hyporheic zone.

Water research, 287(Pt B):124455 pii:S0043-1354(25)01359-4 [Epub ahead of print].

Discharge of wastewater treatment plant effluent into rivers introduces substantial loads of emerging pollutants; however, the distribution and drivers of antibiotic resistance genes (ARGs) in subsurface areas such as the hyporheic zone (HZ) remain poorly understood. Using metagenomic and bioinformatic approaches, this study examined ARG profiles and identified the dominant factors shaping their distribution in the HZ of a river where treated sewage serves as the primary water source. ARG abundances were higher in winter and in surface sediment samples (0-10 cm). On average, 53.5 % of detected ARGs conferred resistance to more than one antibiotic, reflecting disturbance caused by effluent discharge. Microbial communities were characterized in terms of both taxonomic diversity and metabolic functions related to elemental cycling. The results showed that Bray-Curtis dissimilarities based on functional profiles were lower than those based on taxonomic compositions. Moreover, physicochemical properties of the HZ exerted opposite effects on microbial metabolic functions (path coefficient:0.41) and taxonomic structure (0.75), indicating a clear decoupling between metabolic function and taxonomy. Compared with microbial composition, ARG composition exhibited stronger correlations with the profiles of carbon and phosphorus cycle genes. Furthermore, 46.1 % of the recovered metagenome-assembled genomes (MAGs) carried ARGs, with detection frequencies exceeding 60.0 % in MAGs associated with elemental cycling. Notably, both network analysis and co-localization patterns on contigs demonstrated positive and physical linkages between ARGs and functional genes for carbohydrate metabolism and organic phosphorus release. These findings revealed that in effluent-dominated rivers with minimal base flow, microbial metabolic functions dominate ARG distribution dynamics in the HZ.

RevDate: 2025-08-26

Liang A, Wu X, Zhu Y, et al (2025)

Targeted next-generation sequencing (tNGS): An upcoming application for pathogen identification in clinical diagnosis.

Journal of infection and public health, 18(10):102936 pii:S1876-0341(25)00285-0 [Epub ahead of print].

Rapid and efficient detection of pathogens is a goal for clinical laboratories. Traditional methods such as post-culture identification, smear microscopy, antigen-antibody detection, and polymerase chain reaction cannot perform hundreds of high-throughput tests simultaneously. With the development of genetic engineering, next-generation sequencing technology has gradually been introduced into clinical testing. The new technology of targeted next-generation sequencing (tNGS) has the advantages of high sensitivity, high efficiency, and relatively low cost. This review of articles on tNGS published in the past two decades summarizes tNGS workflow and clinical applications, compares it with traditional culture and metagenomic next-generation sequencing (mNGS), and highlights its role in detecting multiple pathogens in mixed infections and drug-resistance genes. It also elaborates on the latest guidelines and the quality control process. By highlighting the practical clinical use of tNGS, it offers insights for optimizing the detection of multiple pathogens in polymicrobial infections to enhance diagnostic accuracy and efficiency.

RevDate: 2025-08-26

Yue Y, Mao Y, Read TD, et al (2025)

Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency in testing differential abundance.

Journal of the American Statistical Association [Epub ahead of print].

The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Surprisingly, many microbiome studies have performed both experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, suggesting that an integrative analysis of both datasets could enhance the testing power for these signatures. However, differential experimental biases, partially overlapping samples, and uneven library sizes pose tremendous challenges when combining the two datasets. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two datasets for testing differential abundance at the genus level as well as the community level while overcoming these difficulties. Our simulation studies demonstrate that Com-2seq substantially enhances statistical efficiency over analysis of a single dataset and outperforms two ad hoc approaches to integrative analysis. In analysis of real microbiome data, Com-2seq uncovered scientifically plausible findings, namely, the association of Butyrivibrio, Gemella and Ignavigranum with prediabetes status, which would have been missed by analyzing a single dataset. Butyrivibrio failed to reach the significance level in the analysis of each dataset despite showing a consistent trend; Gemella and Ignavigranum failed to produce adequate data in the 16S experiment.

RevDate: 2025-08-26
CmpDate: 2025-08-26

Umair M, Yasir M, Jamal Z, et al (2025)

Whole-Genome sequencing of Chikungunya Virus (CHIKV) from Pakistan: Detection of the East/Central/South African (ECSA) genotype during the 2024 outbreak in Mansehra.

PloS one, 20(8):e0329856 pii:PONE-D-25-13287.

The 2024 chikungunya virus (CHIKV) outbreak in Mansehra, Khyber Pakhtunkhwa, Pakistan, marked a significant public health event, providing a unique opportunity to investigate the genomic diversity and evolutionary dynamics of circulating strains. Using metagenomic next-generation sequencing (mNGS), we analyzed serum samples from patients presenting with acute febrile illness and joint pain, identifying 16 CHIKV-positive cases, six of which yielded near-complete genomes. Phylogenetic analysis revealed that all isolates belonged to the East/Central/South African (ECSA) genotype, closely related to strains from India (2020-2024) and China (2017). Notably, this study represents the first comprehensive whole-genome sequencing of CHIKV in Pakistan, uncovering unique mutations in structural (E1: I28V, V290I; E2: Y39H, D54E) and non-structural proteins (NSP1: I167V, M376T; NSP4: G27R, P52S, I403V), suggesting potential viral adaptations to local environmental and vector conditions. The absence of the E1-A226V mutation, associated with enhanced transmission by Aedes albopictus, highlights the need for continued genomic surveillance to monitor emerging variants. Additionally, the detection of a GB virus-C co-infection in one case underscores the utility of mNGS in identifying co-circulating pathogens. This study provides critical insights into the genomic landscape of CHIKV in Pakistan, emphasizing the importance of enhanced surveillance, diagnostics, and vector control strategies to mitigate future outbreaks. The findings underscore the necessity of regional collaboration and genomic monitoring to address the evolving threat of CHIKV in South Asia.

RevDate: 2025-08-26
CmpDate: 2025-08-26

Pushkareva E, Keilholz L, Böse J, et al (2025)

Genetic Diversity and Potential of Cyanobacteria and Fungi Living on Arctic Liverworts.

Microbial ecology, 88(1):90.

Liverworts often form symbiotic associations with fungi and cyanobacteria, yet the distribution and specificity of these relationships remain largely unexplored, particularly in Arctic environments. This study used metagenomic sequencing to investigate fungal and cyanobacterial communities associated with Arctic liverworts, analyzing photosynthetic parts of gametophytes and their rhizoids with attached soil separately. The results revealed that Ascomycota dominated the fungal community. The cyanobacterial community was primarily composed of heterocytous Nostoc and non-heterocytous filamentous Leptolyngbya, with Nostoc showing evidence of nitrogen fixation, especially in gametophytes, suggesting a potential role in enhancing nitrogen availability for the host. These findings underscore the ecological significance of liverwort-associated microorganisms in Arctic ecosystems, with microbial composition differing between upper and lower parts of plants, as well as between leafy and thalloid liverworts, indicating possible functional specialization.

RevDate: 2025-08-26
CmpDate: 2025-08-26

Sharma P, Iqbal MZ, R Chandra (2025)

Bacterial allies in chromium hyperaccumulation: native rhizobacterial dynamics of profusely growing Dactyloctenium aegyptium in highly tainted tannery sludge.

World journal of microbiology & biotechnology, 41(9):314.

Tannery sludge has highly toxic heavy metals like chromium (Cr), posing environmental and health risks. This research investigates the potential of Dactyloctenium aegyptium (L.) Willd. and the associated rhizobacterial communities for bacterial-assisted phytoremediation of tannery sludge, having 6403.16 ± 0.71 mg/kg Cr. The analyses of culturable bacterial communities resulted in the exploration of two highly potent plant growth-promoting strains (CRB2 and CRB5), out of the six culturable strains obtained. SEM imaging depicted robust bacterial colonization on the plant root surface, confirming active plant-microbe interaction. D. aegyptium showed significant Cr accumulation (4936 ± 1.34 mg/kg) within the tissues, followed by substantial translocation to shoots and leaves (TF = 1.01). With a BCF of 1.66 for Cr, D. aegyptium bespeaks evident hyperaccumulation potential. TEM imaging revealed the granular metal deposition in the plant tissues. Post-plant growth, the sludge exhibited an 80.3% reduction in Cr concentration, alongside enhanced physicochemical properties (reduced pH, increased organic matter, reduced metal content). Furthermore, metagenomics analyses showed that the growth of D. aegyptium drastically changed rhizobacterial communities, decreasing species richness and increasing functional pathways associated with stress responses and metal tolerance. Important genes (copA, czcA, nirA), enzymes (dioxygenases, trimethylamine-N-oxide reductase), and proteins (CsgE, DsbG), essential for the nitrogen cycle, chromium detoxification, and plant-microbe associations, were found to be involved in metabolic pathways. The study amalgamates morphophysiological and advanced metagenomic approaches to put forth an understanding of species-specific plant-microbe interactions for the development of scalable and sustainable remediation and engineering of rhizospheric microbiomes for eco-restoration of heavy metal-polluted industrial sites.

RevDate: 2025-08-26

de-Dios T, Bonucci B, Barbieri R, et al (2025)

Bone adhered sediments as a source of target and environmental DNA and proteins.

Molecular biology and evolution pii:8241204 [Epub ahead of print].

In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.

RevDate: 2025-08-26

Wei L, Wu H, Wen L, et al (2025)

Rice protein peptides alleviate lipid accumulation via modulating liver metabolism and remodeling the gut microbiota in HFD-induced mice.

Food & function [Epub ahead of print].

Hyperlipidemia is a significant risk factor for lipid metabolism disorder and gut health impairment. Rice protein peptides (RPs) have emerged as promising interventions for hyperlipidemia management, owing to their safety profile, bioavailability, and cost-effectiveness. However, comprehensive investigations into their anti-hyperlipidemic effects and underlying mechanisms remain insufficiently explored. This study aimed to investigate the efficacy of RPs in alleviating hyperlipidemia and hepatic lipid accumulation by lipidomic and microbiome analyses. Results revealed that RP administration significantly ameliorated lipid metabolism disorders by reducing fat accumulation, normalizing blood lipid levels, and inhibiting lipase activity. Additionally, RPs exhibited hepatoprotective effects by increasing antioxidant enzyme activity and decreasing pro-inflammatory cytokines. Lipidomic analysis further revealed that RPs altered lipid metabolic patterns, identifying 10 differentially regulated lipid species that may serve as potential biomarkers for hyperlipidemia. Furthermore, RP supplements significantly regulated the mRNA levels of gene expression (HMGR, SREBP2, CYP7A1, LDLR, PPARα, PPARγ, FAS, and ACS) involved in hepatic lipid metabolism. Metagenomic analysis demonstrated that RPs reversed gut microbiota dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and increasing the abundance of beneficial genera such as Akkermansia, Muribaculaceae, Clostridia_UCG-014, and Blautia. Furthermore, RP intervention significantly elevated fecal short-chain fatty acid (SCFA) content, particularly butyrate, isobutyrate, and isovalerate, suggesting a link between microbial modulation and metabolic improvement. These findings suggested RPs as an effective strategy for improving lipid metabolism and the gut microbiota composition, offering a promising dietary intervention for hyperlipidemia management.

RevDate: 2025-08-26
CmpDate: 2025-08-26

Babalola OO, Ogundeji FO, AO Akanmu (2025)

Dataset of 16S rRNA and ITS gene amplicon sequencing of celery and parsley rhizosphere soils.

BMC genomic data, 26(1):60.

OBJECTIVES: This amplicon metagenomic study examines the relative abundance, taxonomic profiles and community structure of bacterial and fungal communities associated with the roots of parsley (Petroselinum crispum) and celery (Apium graveolens) under monocropping and intercropping systems. The study aims to provide a baseline understanding of how intercropping influences rhizosphere microbial dynamics.

DATA DESCRIPTION: The dataset provides insight into the effects of parsley-celery intercropping system on soil microbial richness, diversity and community structure. Amplicon metagenomic sequencing was performed on the DNA samples, targeting the 16S rRNA gene (V3-V4 region) and the ITS region for bacterial and fungal communities, respectively. The quantified libraries were pooled and sequenced using Illumina platforms, and the raw sequences were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.) pipeline. The resulting Amplicon Sequence Variant (ASV) profiles revealed Actinobacteria and Protobacteria as the most predominant bacteria phyla, followed by Bacteroidota, Gemmatimonadota and Acidobacteriaota. The most predominant taxonomic distribution of fungi at the phylum level includes Ascomycota and Mortierellomycota. The dataset includes raw sequence reads in FASTQ format (.fastq.gz), which have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the Bioproject Accession numbers; SRP540554 (16S rRNA) and SRP540675 (ITS).

RevDate: 2025-08-26
CmpDate: 2025-08-26

Graeber E, Tysha A, Nisar A, et al (2025)

Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.

BMC microbiology, 25(1):544.

BACKGROUND: The vaginal microbiome plays an important role in female health; it is associated with reproductive success, susceptibility to sexually transmitted infections, and, importantly, the most prevalent vaginal condition in reproduction-age women, bacterial vaginosis (BV). Traditionally, 16S rRNA gene sequencing-based approaches have been used to characterize the composition of vaginal microbiomes, but shallow shotgun metagenomic sequencing (SMS) approaches, in particular when implemented with the Oxford Nanopore Technologies, have important potential advantages with respect to cost effectiveness, speed of data generation, and the availability of flexible multiplexing schemes.

RESULTS: Based on a study cohort of n = 52 women, of which 23 were diagnosed with BV, we evaluated the applicability of Nanopore-based SMS for the characterization of vaginal microbiomes in direct comparison to Illumina 16S-based sequencing. We observed perfect agreement between the two approaches with respect to detecting the dominance of individual samples by either Lactobacilli, vaginosis-associated, or other taxa; very high concordance (92%) with respect to community state type (CST) classification; and a high degree of concordance with respect to the overall clustering structures of the sequenced microbiomes. Comparing the inferred abundances of individual species in individual samples, we observed significant differences (Wilcoxon signed-rank test p < 0.05) between the two approaches for 12 of the 20 species most abundant in our cohort, indicating differences in the fine-scale characterization of vaginal microbiomes. Higher overall abundance of Gardnerella vaginalis, associated with an increased number of CST IV detections, in the Nanopore shallow SMS data indicated potentially increased sensitivity of this approach to dysbiotic states of the vaginal microbiome. Nanopore shallow SMS also enabled the methylation-based quantification of different human cell types in the characterized samples as well as the detection of non-prokaryotic species, including Lactobacillus phage and Candida albicans in study participants with microscopically detected Candida. One important potential limitation of the evaluated Nanopore-based SMS approach was marked variation in sequencing yields.

CONCLUSION: Our study demonstrated the successful application and potential advantages of Nanopore-based shallow SMS for the characterization of vaginal microbiomes and paves the way for its application in larger-scale research or diagnostic settings.

RevDate: 2025-08-26

Mousa AA, Zhang H, Duan H, et al (2025)

Correction: Metagenomic analysis reveals rumen microbiome enrichment and functional genes adjustment in carbohydrate metabolism induced by different sorting behavior in mid-lactation dairy cows.

Animal microbiome, 7(1):90.

RevDate: 2025-08-26
CmpDate: 2025-08-26

Enciso Garcia JS, Chignola M, Ragionieri L, et al (2025)

High-Throughput Amplicon Sequencing for Analyzing Microbial Communities of Insects.

Methods in molecular biology (Clifton, N.J.), 2935:237-258.

Insects represent more than 80% of all described species on the planet. This diversity is a result of millions of years of evolution, during which insects have colonized nearly every habitat. Their success is partly due to their ability to form symbiotic relationships with a wide variety of other organisms, especially microorganisms. Identifying and characterizing associated microorganisms are crucial to understanding the complexity and dynamics of these symbiotic relationships. To date, advancements in sequencing technologies that provide large sequence data sets have become ideal tools for characterizing insect microbiomes, including information about non-cultivable microorganisms commonly found in insects. Despite the growing number of studies focused on insect microbiome characterization, there are few protocols detailing methodological procedures for fieldwork, DNA extraction, and data processing. Here, we present an overview of the characterization of insect-associated bacterial communities. We cover best practices for data interpretation and visualization, including alpha and beta diversity analyses, community composition profiling, and statistical testing to identify microbial associations of insects.

RevDate: 2025-08-25

Haro-Moreno JM, Roda-Garcia JJ, Molina-Pardines C, et al (2025)

The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.

Environmental microbiome, 20(1):110.

RevDate: 2025-08-25

Kaelin EA, Mitchell C, Soria J, et al (2025)

Longitudinal cervicovaginal bacteriome and virome alterations associate with discordant shedding and ART duration in women living with HIV in Peru.

Nature communications, 16(1):7904.

Despite successful suppression of plasma HIV replication by antiretroviral therapy (ART), some women living with HIV (WLHIV) can still experience genital HIV shedding (discordant shedding). Female genital tract (FGT) bacterial and viral microbiome (bacteriome and virome) community dynamics during long-term ART in WLHIV are poorly understood but might contribute to discordant HIV shedding, as the bacteriome and virome are known to influence FGT health. Here, using metagenomic next-generation sequencing, we characterize the bacteriome and virome in 125 cervicovaginal specimens collected over two years from 31 WLHIV in Lima, Peru, and show that FGT bacteriome instability is associated with discordant HIV shedding, while longitudinal changes in FGT virome composition are associated with ART duration. Intrapersonal bacteriome variation is higher in discordant HIV shedders compared to non-shedders. Cervicovaginal virome composition changes over time, particularly in non-shedders. Specifically, anellovirus relative abundance is inversely associated with ART duration and CD4 counts. Our results suggest that discordant HIV shedding is linked with FGT bacteriome instability, and immune recovery during ART influences FGT virome composition.

RevDate: 2025-08-25

Ahmed OY, Boucher C, B Langmead (2025)

Robust 16S rRNA classification based on a compressed LCA index.

Genome research pii:gr.279846.124 [Epub ahead of print].

Taxonomic sequence classification is a computational problem central to the study of metagenomics and evolution Advances in compressed indexing with the r-index enable full-text pattern matching against large sequence collections. But the data structures that link pattern sequences to their clades of origin still do not scale well to large collections. Previous work proposed the document array profiles, which use O(rd) words of space where r is the number of maximal-equal letter runs in the Burrows-Wheeler transform and d is the number of distinct genomes. The linear dependence on d is limiting, since real taxonomies can easily contain 10,000s of leaves or more. We propose a method called cliff compression that reduces this size by a large factor, over 250× when indexing the SILVA 16S rRNA gene database. This method uses Θ(r log d) words of space in expectation under a random model we propose here. We implemented these ideas in an open source tool called Cliffy that performs efficient taxonomic classification of sequencing reads with respect to a compressed taxonomic index. When applied to simulated 16S rRNA reads, Cliffy's read-level accuracy is higher than Kraken2's by 11-18%. Clade abundances are also more accurately predicted by Cliffy compared to Kraken2 and Bracken. Overall, Cliffy is a fast and space-economical extension to compressed full-text indexes, enabling them to perform fast and accurate taxonomic classification queries. Cliffy's accuracy underscores the advantages of full-text indexes, which offer a more precise solution compared to k-mer indexes designed for a specific k value.

RevDate: 2025-08-25

Silvederio GXL, Javellana TF, Genciana ABN, et al (2025)

Gut microbiome composition and diversity of wild-caught and hatchery-bred milkfish (Chanos chanos) fry.

Journal, genetic engineering & biotechnology, 23(3):100520.

Milkfish is the most produced finfish in the Philippines, with approximately 75 % of its fry sourced from hatcheries. Despite numerous studies on gut microbiota of wild and cultured fish species, the diversity and functional roles of the milkfish fry gut microbiome remain poorly understood. This study presents the first gut microbiome profiles of wild and hatchery-bred milkfish fry using 16S rRNA amplicon analysis. A total of 437 OTUs were recovered and significant differences in gut bacterial communities among fry from different sources was observed, indicating that habitat is a key determinant of gut microbiome diversity. The core gut microbiota analysis identified Vibrionaceae and Roseobacteraceae as the most common and abundant bacterial families across fry sources. However, Paenibacillaceae and Bacillaceae under Phylum Bacillota were dominant in wild fry sources, particularly Hamtic and Kirayan, whereas families belonging to Phyla Cyanobacteriota, and Thermodesulfobacteria were more prevalent in Dumagas and Kirayan hatchery fry sources. Functional predictions of the gut bacterial microbiome revealed 26 differentially abundant pathways between wild-caught and hatchery-bred fry, including those related to metabolism, organismal systems, cellular processes, environmental and genetic information processing. These findings highlight significant variations in gut microbiome composition, diversity, and functional potential across different sources of wild-caught and hatchery-bred fry. Understanding these source-specific microbial communities could provide insight into the development of interventions that can improve gut health and enhance milkfish hatchery practices. It can also generate information on ideal fry selection across local milkfish sources that will enhance larval productivity and survival in the succeeding nursery and grow-out culture stages.

RevDate: 2025-08-25

Zhang B, Yin R, Quan X, et al (2025)

Synergistic sulfur-iron redox in novel composite biofilm carriers drives efficient mixotrophic denitrification and phosphate removal: Metagenomic insights into nitrogen/sulfur metabolic networks and microbial interactions.

Bioresource technology pii:S0960-8524(25)01161-7 [Epub ahead of print].

Multifunctional biofilm carriers were developed through encapsulating acetate starch or FeCl3 using paraffin and sulfur (Paraffin-Sulfur-Acetate Starch and Paraffin-Sulfur-FeCl3), aimed at enhancing nitrate removal via mixotrophic denitrification and phosphate removal via controlling Fe[3+] release. A sequencing batch biofilm reactor with these composite carriers attained efficient nitrogen removal (99.9 % for NO3[-]-N, 98.7 ± 2.2 % for total nitrogen, 24 h cycle) and phosphate removal (98.5 %) over 60 days. The composite carriers provided multiple electron donors (S[0], acetate starch, and paraffin) to sustain mixotrophic denitrification, with sulfur autotrophic denitrification contributing 65.5 %-83.7 % of total nitrogen removal. Metagenomic analysis revealed diverse nitrogen metabolism pathways, including sulfur (S[0]/S[2-]/Sn[2-]) and Fe[2+]-based autotrophic denitrification, acetate starch/paraffin-based heterotrophic denitrification, and ammonium oxidation via Fe[3+] (Feammox). Synergistic sulfur-iron redox cycling was established through coupled biotic-abiotic reactions. This study presents a novel and sustainable strategy for nitrogen and phosphate removal from low carbon/nitrogen ratio wastewater.

RevDate: 2025-08-25

Liu L, Wang C, Zhang SJ, et al (2025)

Underlying Mechanisms of Pollutant Removal Enhancement through the Formation of Low Levels of Granular Sludge in an Innovative Continuous-flow Reactor.

Environmental research pii:S0013-9351(25)01930-9 [Epub ahead of print].

In situ cultivation and long-term stabilization of continuous-flow aerobic granular sludge (AGS) pose significant challenges for the sustainable advancement of wastewater technology. Herein, we demonstrated the successful 330-day operation of a novel continuous-flow self-circulating AcOA-Zier reactor. Aeration-driven liquid recirculation achieved recirculation-to-influent (R/I) ratios of 26-70, optimizing dissolved oxygen gradients and enabling exceptional contaminant removal of 96% for chemical oxygen demand (COD) and 95% for total inorganic nitrogen (TIN). High hydrodynamic shear promoted granulation, yielding an average particle size of 369.7 μm, with >83% of the granules in the optimal 200-600 μm range being used to ensure operational stability. Microbial community profiling revealed Proteobacteria (80%), Chloroflexi (7.1%) and Bacteroidota (10.2%) as keystone taxa underpinning granule formation, structural integrity, and pollutant degradation. Metagenomics identified narG, nirK, norBC, nosZ and nxrB as core nitrogen cycling genes, with Methylotenera and unclassified_c_Betaproteobacteria serving as the dominant functional microorganisms. In this work, we established granulation dynamics and particle stability as pivotal factors for scalable AGS systems, providing a framework for optimizing energy-efficient, high-performance wastewater treatment processes.

RevDate: 2025-08-25

Nieves-Morales R, Paez-Diaz JA, Rivera-Lopez EO, et al (2025)

Prokaryotic communities profile from metagenomic libraries of the brown rock sea cucumber (Holothuria glaberrima) intestinal system.

Microbiology resource announcements [Epub ahead of print].

Environmental rDNA profiling enables the identification of unculturable microbial communities. To access prokaryotic diversity in the metagenomic libraries of sea cucumber's intestinal environment, 16S rDNA sequencing was performed to provide insight into the libraries' taxonomic composition, unraveling microbial groups potentially associated with biomedical, environmental, and biotechnological applications.

RevDate: 2025-08-25

Philip M, Nilsen T, Majaneva S, et al (2025)

A Targeted Reference Database for Improved Analysis of Environmental 16S rRNA Oxford Nanopore Sequencing Data.

Molecular ecology resources [Epub ahead of print].

The Oxford Nanopore Technologies (ONT) sequencing platform is compact and efficient, making it suitable for rapid biodiversity assessments in remote areas. Despite its long reads, ONT has a higher error rate compared to other platforms; necessitating high-quality reference databases for accurate taxonomic assignments. However, the absence of targeted databases for underexplored habitats, such as the seafloor, limits ONT's broader applicability for exploratory analysis. To address this, we propose an approach for building environmentally targeted databases to improve 16S rRNA gene (16S) analysis using Oxford Nanopore Technologies (ONT), using seafloor sediment samples from the Norwegian coast as an example. We started by using Illumina short-read data to create a database of full-length or near full-length 16S sequences from seafloor samples. Initially, amplicons are mapped to the SILVA database, with matches added to our database. Unmatched amplicons are reconstructed using METASEED and Barrnap methodologies with amplicon and metagenome data. Finally, if the previous strategies did not succeed, we included the short-read sequences in the database. This resulted in AQUAeD-DB, which contains 14,545 16S sequences clustered at 95% identity. Comparative database analysis reveals that AQUAeD-DB provides consistent results for both Illumina and Nanopore read assignments (median correlation coefficient: 0.50), whereas a standard database showed a substantially weaker correlation. These findings also emphasise its potential to recognise both high and low abundance taxa, which could be key indicators in environmental studies. This work highlights the necessity of targeted databases for environmental analysis, especially for ONT-based studies, and lays the foundations for future extension of the database.

RevDate: 2025-08-25

O'Kane C, Johnson NS, Scribner KT, et al (2025)

Development of PCR Blocking Primers Enabling DNA Metabarcoding Analysis of Dietary Composition in Hematophagous Sea Lamprey.

Ecology and evolution, 15(8):e71999.

Conventional dietary assessments are challenging in hematophagous species, particularly in sea lamprey (Petromyzon marinus). However, recent technological developments and molecular approaches have provided an attractive alternative through the use of DNA metabarcoding. While DNA metabarcoding has been used for dietary analyses in numerous species, including lampreys, applications of universal primers that detect a diverse set of prey items can be limited by the amplification of predator DNA. In this study, we designed and tested eight blocking primers designed to suppress the amplification of sea lamprey DNA with vertebrate-universal primers targeting the mitochondrial 12S rRNA gene. This approach allowed for the use of a single marker to amplify a taxonomically diverse suite of host species, in contrast to previous studies that used multiple taxon-specific primer pairs (e.g., Salmonidae, Cyprinidae, and Catostomidae). Candidate blocking primers evaluated in this study differed in base pair length, end sequence modification, and purification method. Samples with different sea lamprey-to-host DNA ratios were subjected to multiple detection methods including gel electrophoresis, quantitative PCR, and DNA metabarcoding to assess the ability of each blocking primer to selectively suppress amplification of the sea lamprey 12S gene region. All blocking primers tested performed well and demonstrated high effectiveness, suppressing sea lamprey reads by > 99.9% in mock communities and improving host DNA sequence recovery across various sample types, including wild-caught lamprey. Results show that the blocking primers evaluated can facilitate molecular diet analysis in sea lamprey, allowing the amplification of a taxonomically diverse range of host fish species with universal primers.

RevDate: 2025-08-25

Yan B, Wang Y, Wang Z, et al (2025)

Potential role of gut bacteria in the development of hepatocellular carcinoma.

Access microbiology, 7(8):.

Liver cancer is the fourth most deadly cancer, and early detection and timely treatment apparently play a crucial role in it. Intestinal bacteria affect the development of liver cancer through various pathways. In this study, the gut bacteria of liver cancer patients are analysed in detail by using metagenomic sequencing technology, and some of the bacterial species and metabolic pathways that may affect the development of liver cancer have been identified. Additionally, we identified bacterial factors that may impact key clinical indicators of the tumour. The findings of this study provide a scientific foundation for understanding the mechanisms underlying liver cancer development. This study freshened insights into clinical treatment strategies for liver cancer.

RevDate: 2025-08-25

Wang D, Wang H, Zhang D, et al (2025)

Early diagnosis of streptococcus cristatus in blood culture-negative infective endocarditis by capture-based metagenomic next-generation sequencing: a case report.

Frontiers in cardiovascular medicine, 12:1604687.

BACKGROUND: Infective endocarditis (IE) is a life-threatening infectious cardiac condition characterized by therapeutic complexity and high mortality rates, for which precise pathogen identification is critical to guide accurate treatment. Although this disease is frequently caused by commensal microorganisms of the oral flora, including Streptococcus cristatus (S. cristatus); however, S. cristatus is not a common pathogen associated with IE.

CASE PRESENTATION: A 59-year-old male patient was admitted to our intensive care unit due to chest tightness and shortness of breath persisting for 10 days, with symptoms worsening over the last 6 h, including dyspnea and an inability to lie down. After the patient was admitted to the hospital for comprehensive examinations, a preliminary clinical diagnosis of IE, aortic valve vegetation formation, acute non-ST-segment elevation myocardial infarction, and heart failure was established. The patient had negative preoperative blood culture results and received empiric therapy with moxifloxacin combined with piperacillin-tazobactam for infection control, subsequently undergoing cardiac surgery. Intraoperatively obtained valve vegetations were sent for pathological testing, tissue bacterial culture, and capture-based mNGS (metagenomic next-generation sequencing) testing. The capture-based mNGS results for the vegetation was returned as S. cristatus within 24 h, with 250,119 sequences detected and 54.56% coverage, which facilitated the rapid identification of the pathogenic microorganism of IE in the early stage. The tissue culture result of the vegetation was returned on the 5th day of delivery, confirming the presence of S. cristatus. The patient was successfully discharged after comprehensive treatment and returned to the hospital 3 weeks post-discharge for a follow-up examination, which suggested a good recovery.

CONCLUSIONS: This case highlights a rare instance of S. cristatus endocarditis, which was ultimately confirmed at an early stage through capture-based mNGS performed on valvular vegetation. This suggests that for postoperative patients with persistent infection and blood culture-negative IE, valvular capture-based mNGS serves as a rapid and efficient diagnostic tool to expedite pathogen identification and guide targeted antimicrobial therapy.

RevDate: 2025-08-25

Goh YQ, Cheam G, Yeong M, et al (2025)

Ex vivo study on prebiotic & choline combination to modulate gut bacteria, enhance choline bioavailability, and reduce TMA production.

Microbiome research reports, 4(2):21.

Aim: Choline is a universal methyl group donor, playing an essential role in DNA methylation, signaling pathways, and the transport and metabolism of lipids. The primary source of choline intake is diet, and chronic deficiency has been associated with dementia, cardiovascular disease, and liver disease. Choline bioavailability can be diminished by gut microbes that express choline trimethylamine-lyase (cutC), an enzyme that converts choline into trimethylamine (TMA), a precursor for TMA N-oxide (TMAO), which is associated with an increased risk of cardiovascular diseases. Gut microbiota modulation can be achieved by prebiotics such as galactooligosaccharides, inulin, and fructooligosaccharides. The aim of our study is to use choline with prebiotics to modulate the gut microbiota to enhance choline bioavailability and minimize TMA production. Methods: We employed an ex vivo microcosm system consisting of healthy human stool samples with choline and different prebiotics and measured TMA and choline levels by targeted metabolomics. Shotgun metagenomic profiling was also performed to investigate alternation in gut microbiota composition during choline and prebiotic interventions. Results: Our study showed that choline to TMA conversion is dependent on a choline derivative and supplementing galactooligosaccharides (GOS) reduces this conversion. Choline to TMA conversion was associated with enriched microbiota from the genus Dialister, whereas GOS supplementation led to an increase in Blautia and a reduction in Clostridia populations. Loss of Clostridia also reduced a subset of Clostridium species, Clostridium citroniae, known to encode the cutC gene. The abundance of Dialister enhanced the chorismate biosynthesis pathway, while a reduction in Clostridium supported tryptophan and methionine pathways. Conclusion: This study is the first to identify the combination of choline and GOS supplementation as a potential strategy to modulate gut microbiota and its metabolites in order to improve disease etiology.

RevDate: 2025-08-25

Shen J, Kong J, Xu Y, et al (2025)

Virus in infectious uveitis: bibliometric analysis and a clinical study.

Frontiers in microbiology, 16:1588195.

INTRODUCTION: In recent years, advancements in detection technology have led to increased research interest in viral uveitis.

METHODS: This study conducted a comprehensive analysis, comprising a bibliometric examination of literature on virus and infectious uveitis and a retrospective study focusing on infectious uveitis. The bibliometric analysis aimed to elucidate past and emerging trends in this field over several decades. In the retrospective study, intraocular fluid samples were collected from 73 patients suspected of having infectious uveitis for metagenomic next-generation sequencing (mNGS), with 29 samples also subjected to microbiological culture.

RESULTS: Analysis of the literature revealed a steady rise in annual publications on virus and infectious uveitis from 1990 to 2021, reaching a peak in 2021. The United States emerged as the most prolific contributor, with significant collaborative relationships with other nations. Keywords were clustered into five categories, covering diagnostic criteria, diagnostic tools, clinical manifestations, epidemiology, and etiology of viral uveitis. Interestingly, research focus shifted from predominant viral types and serodiagnosis towards intraocular fluid testing. mNGS demonstrated a notably higher positivity rate (73.97%) compared to culture (3.45%), identifying various pathogens including viruses, bacteria, fungi, Toxoplasma gondii, and Rickettsia felis. Varicella-Zoster Virus, Epstein-Barr Virus, Klebsiella pneumoniae, and Torque Teno Virus were among the most common pathogens detected. Additionally, coexisting microorganisms such as Torque Teno Virus and Epstein-Barr Virus were identified.

CONCLUSION: Viral uveitis has consistently garnered research attention, with future directions likely focusing on virus types and diagnostic tools. Viruses are the main causative microorganisms of infectious uveitis. The high efficacy of mNGS in identifying diverse pathogens from minute volumes of intraocular fluid samples highlights its pivotal role in diagnosing infectious uveitis.

RevDate: 2025-08-25

Zou C, Dai T, Liang Z, et al (2025)

Loquat-tea intercropping enhances rhizosphere microbial diversity and functional profiles in tea soil ecosystems.

Frontiers in microbiology, 16:1651997.

INTRODUCTION: Intercropping systems can significantly influence soil microbial communities, affecting plant health and soil nutrient cycling, which has better economic and ecological benefits than monoculture of tea.

METHODS: This study investigated the impact of loquat-tea intercropping on the microbial community structure and functional gene composition in the rhizosphere soil of tea (Camellia sinensis). Using metagenomic sequencing, we analyzed rhizosphere soils from loquat-tea intercropping (PP_CS), tea monoculture (CS), and loquat monoculture (PP).

RESULTS AND DISCUSSION: A total of 161 phyla, 269 classes, 485 orders, 1,000 families, 3,838 genera, and 27,624 species were annotated across samples. Dominant phyla included Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi. The genera Bradyrhizobium (4.20%) and Trebonia (3.78%) were notably enriched in the intercropping system. The analysis of community differences showed that unclassified_c_acidobacteria was in pp_cs group, demonstrating the highest LDA score (4.4 score). Functional annotation via the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that metabolic pathways were predominant across all treatments, with 36,111,608 reads assigned to metabolism. The comparative analysis at KEGG level 3 revealed that Metabolic pathways 289 constituted the most abundantly annotated functional category across all three groups. Redundancy analysis (RDA) showed strong correlations between key microbial genera (Trebonia, Bradyrhizobium) and soil properties, including organic matter (OM), alkali hydrolyzed nitrogen (AN), available phosphorus (AP), and available potassium (AK). These findings suggest that loquat-tea intercropping promotes microbial diversity and enhances functional potential, improving soil health and nutrient availability in tea cultivation systems.

RevDate: 2025-08-24
CmpDate: 2025-08-24

Zhang L, Wang S, Wong MCS, et al (2025)

The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients.

NPJ biofilms and microbiomes, 11(1):171.

The study aims to tackle the seed and soil microbiome and mechanisms that contribute to the effect of synbiotics in enhancing immunogenicity after SARS-CoV-2 vaccination in elderly and diabetic patients. Among 369 subjects who received 3 months of SIM01, a gut microbiota-derived synbiotic formula of three Bifidobacterium strains (B. adolescentis, B. bididum, and B. longum) or a placebo after the SARS-CoV-2 vaccines (mRNA vaccine BNT162b2 (Pfizer-BioNTech) or the inactivated vaccine Sinovac-CoronaVac), we performed metagenomic sequencing in stool samples of 280 vaccinees collected at baseline and 3-month postvaccination and metabonomic sequencing in 276 vaccinees collected at baseline and 1-month postvaccination. The open niche of autochthonous gut microbiota (lower levels of Bifidobacterium and decreased functional potential for carbohydrate metabolism) was associated with enhancing SIM01-contained species. The enrichment of three bifidobacterial species after 3 months of SIM01 intervention (BABBBL_fc) was positively correlated with the level of neutralizing antibodies to the BNT162b2 vaccine at 6-month postvaccination. The fold change of benzoic acid was positively correlated with BABBBL_fc in the BNT162b2 vaccinees, which was also implicated with SARS-CoV-2 surrogate virus neutralization test (sVNT)% levels at 1-month postvaccination. Importantly, SIM01 strain engraftment assessed by StrainPhlAn (A metagenomic strain-level population genomics tool) was associated with a higher fold change of three bifidobacterial species and could be predicted based on the baseline gut microbiome. Therefore, the resident gut microbiome affected the SIM01 engraftment, which was associated with the immunogenicity of SARS-CoV-2 BNT162b2 vaccines.

RevDate: 2025-08-22

Grant ML, Petri RM, Baecklund TM, et al (2025)

Subspecific variation in gut microbiota of North American bison in a sympatric setting reveals differentially abundant taxa.

Animal microbiome, 7(1):89.

UNLABELLED: Gut microbiomes play critical roles in host-environment interactions, reflecting habitat and foraging niches. North American bison (Bison bison) subspecies—plains bison (B. bison bison) and wood bison (B. bison athabascae)—exhibit limited genetic variation from historic population bottleneck events, potentially undermining their evolutionary potential. Understanding variation in gut microbiota composition between subspecies may shed light on genetic, phenotypic, and ecological divergence relevant to their adaptive capacities. Using 16S rRNA metabarcoding of fecal samples, we characterized the gut microbiota of both subspecies in the sympatric environment of Elk Island National Park, providing insight into potential phylogenetic gut microbiome divergence. Like other ruminants, the gut microbial community of both subspecies consists primarily of the bacterial phyla Firmicutes and Bacteroidetes. Subspecific classification explained no significant differences in alpha diversity (p > 0.05) in the overall dataset, but has a potentially significant effect on beta diversity (p < 0.05, R[2] = 0.04). Gut microbiota divergence between subspecies may be driven by differential abundance of specific taxa and associated functional pathways, likely influenced by dietary preferences, ancestral phenotypes, and historical ranges. Our findings support further investigation into diet-microbiome relationships between subspecies in sympatric environments and metagenomic approaches to explore functional differences in the gut microbiome.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00451-7.

RevDate: 2025-08-24

Suppiah J, Zulkifli MMS, Adiee AH, et al (2025)

Genomic evidence links human dengue cases with undetermined serotypes to sylvatic lineages.

Tropical medicine and health, 53(1):114.

BACKGROUND: Sylvatic dengue viruses, typically maintained in non-human primate and forest mosquito cycles, have rarely been associated with human infections. However, sporadic spillovers have been reported in Southeast Asia, including Malaysia. These events are often under-detected due to the genetic divergence of sylvatic strains from endemic urban dengue viruses. During routine surveillance in Malaysia (2024-2025), a subset of clinically confirmed dengue cases yielded undetectable serotype results by commercial real-time reverse transcription polymerase chain reaction (RT-PCR) assays, prompting investigation into a possible sylvatic origin.

METHODS: We investigated 22 such cases through clinical, serological, molecular, and phylogenetic analyses. NS1 antigen and broad-range RT-PCR confirmed acute dengue infection. Selected samples underwent sequencing and lineage determination.

RESULTS: Most patients presented with severe dengue during early illness (mean day 3), with 95.5% NS1 positivity and predominantly primary infection profiles. Despite serotyping failure, sequencing revealed that eight of nine analyzed samples belonged to sylvatic DENV2, while one represented a divergent DENV3. Comparative amino acid analysis uncovered a unique signature in recent Malaysian sylvatic DENV2 strains, differentiating them from both urban and historical sylvatic lineages. This includes the V270 mutation in the M gene; R844, V884, and I898 in the NS1 gene; T1207 in the NS2A gene; A1597 in the NS3 gene; and D3048 and I3373 in the NS5 gene. Phylogenetic analysis clustered these strains into a distinct Malaysian clade, separate from the African sylvatic lineage.

CONCLUSIONS: This study provides the first genomic evidence of a recent sylvatic DENV2 spillover into humans in Malaysia, likely undetected by standard diagnostics due to genetic divergence. These findings underscore the urgent need to enhance surveillance tools and explore the sylvatic transmission cycle's role in dengue epidemiology.

RevDate: 2025-08-24
CmpDate: 2025-08-24

Tang M, Li C, Ge X, et al (2025)

Honeybee-Gilliamella synergy in carbohydrate metabolism enhances host thermogenesis in cold acclimation.

NPJ biofilms and microbiomes, 11(1):172.

How gut symbionts contribute to host adaptation remains largely elusive. Studying co-diversified honeybees and gut bacteria across climates, we found cold-adapted species (Apis mellifera, A. cerana) exhibit enhanced genomic capacity for glucose, pyruvate, lipid and glucuronate production versus tropical species. Metagenomics revealed Gilliamella as the most enriched gut bacterium in cold-adapted bees. Germ-free honeybees inoculated with the Gilliamella from A. cerana showed increased activity, body temperature and fat storage upon cold exposure. Saccharide metabolomics demonstrated higher hindgut glucose levels in Gilliamella-colonized A. mellifera versus germ-free bees, and in A. cerana versus three sympatric tropical species. Although Gilliamella can hydrolyze β-glucan into glucose, cultural experiments suggest it preferentially degrades glucuronate to pyruvate. In turn, monocolonized bees upregulated hindgut glucose/pyruvate utilization while increasing glucuronate provision, suggesting nutritional complementarity. Gilliamella's transporter genes predominantly target ascorbate (a glucuronate derivative), which is elevated in inoculated hindguts. Accordingly, Gilliamella converts ascorbate to D-xylulose-5P (promoting lipogenesis), while showing reduced growth on glucuronate/ascorbate versus glucose, potentially minimizing glucose competition with hosts. We revealed a highly coordinated host-symbiont metabolic synergy enhancing host energy acquisition for cold adaptation.

RevDate: 2025-08-24

Lei G, Han Z, Wang X, et al (2025)

Synthetic microbial communities rescues strawberry from soil-borne disease by enhancing soil functional microbial abundance and multifunctionality.

Journal of advanced research pii:S2090-1232(25)00653-8 [Epub ahead of print].

INTRODUCTION: Synthetic microbial communities (SynCom) contribute to mitigating soil-borne crop diseases while enhancing both crop quality and yield. However, relatively little research has been done on the intricate regulatory mechanisms of SynCom on the suppression of soil-borne diseases.

OBJECTIVES: We aimed to elucidate the dynamic regulatory mechanisms and legacy effects of a SynCom on the composition of soil functional microorganisms, soil multifunctionality and crucial functions, and the suppression of soil-borne diseases.

METHODS: We conducted an extensive series of experiments to assess the effect of a SynCom on the changes in the rhizosphere functional microorganisms and soil functions (e.g., multifunctionality, functionality of C, N, and P cycling) across six successive generations of strawberry in consecutive monoculture soils by employing amplicon metagenomics and transcriptome sequencing.

RESULTS: Our results showed that the SynCom increased the aboveground fresh biomass of strawberry by 31-70.3% and the fruit biomass by 171.39-280.71%, and decreased the Fusarium oxysporum abundance by 17.91-49.51% compared to the consecutive monoculture. The SynCom significantly enhanced the soil C cycling and P cycling function, and soil multifunctionality (SMF). SynCom treatment significantly increased the Shannon diversity index and relative abundances of potentially beneficial bacteria and consumer protistan communities, while exerted a significant inhibitory effect on the Shannon diversity index and relative abundances of fungal pathogen. SEM result showed that SynCom significantly affected SMF by influencing soil nutrients, the abundance and diversity of functional microbial community. Our result also showed that the SynCom established the positive legacy effects on the abundance of rhizosphere soil beneficial bacteria, strawberry biomass and plant disease resistance-associated pathways (phenylpropanoid biosynthesis pathway, alpha-linolenic acid metabolism pathway), and negative effect on the abundance of pathogenic F. oxysporum under the 7th generation of strawberry cropping.

CONCLUSION: Collectively, our study demonstrated the effectiveness of employing SynCom in mitigating soil-borne Fusarium oxysporum diseases by enhancing soil functional microbial abundance and soil multifunctionality.

RevDate: 2025-08-24

Rieber H (2025)

Re: 'Diagnostic accuracy of 16S rDNA PCR, Multiplex PCR and Metagenomic Next-Generation Sequencing in Periprosthetic Joint Infections' by Olearo et al.

RevDate: 2025-08-24

Chalwatzis L, Cruyssen CV, Mazzini I, et al (2025)

Depolymerisation of waste- and bio-based polyesters by an activated sludge hydrolase.

Bioresource technology pii:S0960-8524(25)01153-8 [Epub ahead of print].

This study investigates enzymatic hydrolysis of four novel polyesters (REPolymers) with different structures based on terephthalic acid, ethylene glycol, glutaric acid, and decanediol. These polyesters were synthesized from PET building blocks and bio-based monomers. A hydrolase from Rhizobacter sp. (Rhb), identified from a wastewater treatment sludge metagenome, was used to predict biodegradation and to assess enzymatic recycling potential of the REPolymers. Rhb shows homology to Ideonella sakaiensis PETase but exhibits superior thermostability and activity due to specific amino acids previously identified in PETase engineering. Using mass spectrometry and HPLC-DAD analysis, hydrolysis of REPolymers (5 - 34 kDa) was mechanistically studied. Mono-(2-hydroxyethyl) terephthalic acid (MHET) was the primary product, with longer PET oligomers and aliphatic dimers also detected, indicating endo-wise cleavage of aromatic and aliphatic ester bonds. Consistent degradation patterns showed dimer accumulation across different REPolymers. These findings illuminate how the polyester structure affects enzymatic hydrolysis, supporting the development of novel waste/bio-based polymers and recycling strategies.

RevDate: 2025-08-24

Gupta S, Chauhan R, S Pandey (2025)

Biopriming with halotolerant microbes enhances growth performance, resilience and rhizospheric microbial diversity of Solanum melongena under saline conditions.

Plant physiology and biochemistry : PPB, 229(Pt A):110400 pii:S0981-9428(25)00928-3 [Epub ahead of print].

The study demonstrated the beneficial effects of halotolerant Bacillus licheniformis O1 and Brevibacterium sp. O5 from the Aloe vera rhizosphere on aubergine growth performance in a saline environment (200 mM NaCl). qRT-PCR confirmed the upregulation of IAA biosynthesis genes (trpA and trpB), salt tolerance (kdpA, kdpB, nhaA), osmoprotectants (proA and proB), and antioxidants (sodA, sodB, and HPII) under saline conditions. This supports the intrinsic bacterial resilience of both the strains, which maintains cellular homeostasis under saline conditions (10 % NaCl). The strains exhibited multipartite PGP traits, including phosphate solubilization and the production of IAA, ammonia, siderophores, HCN, ACC deaminase, EPS, and biofilms. Furthermore, seed biopriming with a bacterial consortium synergistically improved the physiological and biochemical responses, including germination rate (87 %), total chlorophyll (by ∼1.10-fold), carotenoids (by∼1.55-fold), proline (by 4.56-fold), total soluble sugar (by 2.76-fold), and vegetative parameters, including shoot and root biomass (by 1.12- and 3.23-fold, respectively) of eggplants under saline stress. They mitigated salt-induced oxidative stress by reducing the H2O2 and O2[.] levels and MDA levels (by > 50 %) in plants, as confirmed by histochemical and quantitative assays. The key mechanisms involved in the enhancement of antioxidant activity (SOD, PPO, POD, APX, and CAT) by 1.71-13.21 times and non-enzymatic activity (phenolic and flavonoid content) by 2.39 and 4.07 times, respectively, in eggplants. The inoculants also improved soil resilience by increasing enzymatic activity (dehydrogenase, urease, amylase, and phosphatase) 0.74- to 12.7-fold under saline stress. Taxonomic analysis revealed that consortium inoculation increased species richness and relative abundance of beneficial bacteria in the eggplant rhizosphere, supporting enhanced soil and plant resilience to salinity stress.

RevDate: 2025-08-24

Zhou SY, Lie Z, Lei C, et al (2025)

Multi-Scale Evidence for Declining Microbial Carbon Fixation Along Forest Succession Gradients.

The ISME journal pii:8240394 [Epub ahead of print].

Although soil carbon accumulates during subtropical forest succession, changes in microbial communities and their carbon fixation capacity remain unclear. Using an integrative approach that combines field experimentation, extensive global metagenomic data, and isotope labelling, we analyzed 84 soil microbiomes from a long-term successional site and 755 global metagenomes to investigate microbial community dynamics and their role in carbon fixation. Based on field data, bacteria, fungi, and protists had synchronous succession with vegetation; however, the relative abundance of carbon fixation genes declined significantly in later successional stages. To further investigate this outcome, we analyzed global data from planted and mature natural forests and found significantly higher carbon fixation potential in planted forests, predominantly driven by Pseudomonadota and Actinomycota members. Field-based 13C labelling results further confirmed a significant decline in microbial CO2 fixation rates with forest succession. These findings underscore the ecological importance of microbial carbon fixation in early forest succession, emphasizing its foundational role in initiating soil carbon accumulation and shaping long-term carbon cycling trajectories.

RevDate: 2025-08-23
CmpDate: 2025-08-24

Jang S, Lee EJ, Park S, et al (2025)

Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.

Microbiome, 13(1):189.

BACKGROUND: Crohn's disease (CD) is a chronic inflammatory bowel disease involving complex relationships between the gut microbiome and host immune system. However, the spatial relationships between tissue-resident bacteria and host cells in CD pathogenesis remain poorly understood. We developed a spatial host-microbiome profiling approach to simultaneously detect host transcriptomics and bacterial species at high taxonomic resolution in pediatric ileal CD tissues.

RESULTS: In this prospective case-control study, we analyzed 14 terminal ileal tissue samples from six pediatric patients with ileal CD and two controls. Spatial host-microbiome sequencing, combined spatial transcriptomics and in-situ polyadenylation, and bulk shotgun metagenome sequencing were performed. We developed a comprehensive bioinformatics pipeline to identify bacterial species and analyze host-microbiome interactions at cellular resolution, resulting in 13,876 analyzed cells. Our approach revealed increased bacterial abundance in CD tissues compared with controls. The extent of bacterial infiltration at diagnosis correlated with disease prognosis and severity of endoscopic findings. We identified 16 potentially beneficial and nine pathogenic microbiome members in ileal CD, including several newly discovered risk-modulating bacterial species. Cell-type-specific host gene expression analysis revealed transcriptome alterations related to bacterial defense mechanisms in the presence of various bacterial species.

CONCLUSIONS: Our spatial host-microbiome profiling approach enables simultaneous species-level identification of bacteria and host transcriptomics. It reveals the intricate interactions between host cells and bacteria, providing cellular-level insights into CD pathogenesis. Our approach offers a powerful tool for investigating host-microbiome interactions in various microbiome-associated diseases to direct new strategies for microbiome-based therapeutics and prognostic markers. Video Abstract.

RevDate: 2025-08-23
CmpDate: 2025-08-23

Feng Y, Shi J, Li Z, et al (2025)

Discovery of CRISPR-Cas12a clades using a large language model.

Nature communications, 16(1):7877.

CRISPR-Cas systems revolutionize life science. Metagenomes contain millions of unknown Cas proteins. Traditional mining relies on protein sequence alignments. In this work, we employ an evolutionary scale language model (ESM) to learn the information beyond sequences. Trained with CRISPR-Cas data, ESM accurately identifies Cas proteins without alignment. Limited experimental data restricts feature prediction, but integrating with machine learning enables trans-cleavage activity prediction of uncharacterized Cas12a. We discover 7 undocumented Cas12a subtypes with unique CRISPR loci. Structural analyses reveal 8 subtypes of Cas1, Cas2, and Cas4. Cas12a subtypes display distinct 3D-folds. CryoEM analyses unveil unique RNA interactions with the uncharacterized Cas12a. These proteins show distinct double-strand and single-strand DNA cleavage preferences and broad PAM recognition. Finally, we establish a specific detection strategy for the oncogene SNP without traditional Cas12a PAM. This study highlights the potential of language models in exploring undocumented Cas protein function via gene cluster classification.

RevDate: 2025-08-23
CmpDate: 2025-08-23

Zhang Y, Liao YT, Liu F, et al (2025)

Impact of diet in shaping gut virome of grain-fed and grass-fed beef cattle revealed by a comparative metagenomic study.

Microbiome, 13(1):190.

BACKGROUND: In the United States beef industry, grain-feeding and grass-feeding are the two most common types of cattle feeding. Different feeding methods are likely to affect gut microbiota compositions and subsequently change microbial adaptation and cattle metabolism. However, there is limited information regarding the impact of diet on cattle gastrointestinal virome. This study examined the composition of fecal virome from grain-fed and grass-fed beef cattle and identified unique virome features to understand the relationship between these two feeding types.

RESULTS: Six grain-fed and six grass-fed Angus beef cattle were weighed, and their fecal samples were collected for further viral metagenomic sequencing. The difference in animal growth revealed a significantly higher post-weaning weight in grain-fed cattle than in grass-fed cattle after day 56. Furthermore, the analysis of the fecal viral population showed that approximately 795 and 1266 predicted viral sequences were obtained in the grain-fed and grass-fed samples, respectively. Among those, 54.3% of the grain-fed and 26.3% of the grass-fed viral sequences were identified as known viruses. The taxonomic classification showed that viruses belonging to the order Caudovirales, mostly bacteriophages, dominated the cattle virome in both sample groups, followed by the order Cremeviriles and Petitvirales. At the family level, 13 and 16 different viral families were detected in the grain and grass-fed groups, respectively. The comparison of virome features from the two groups indicated that the viral population from the kingdom Bamfordvirae had a significantly higher abundance in the grain-fed group than in the grass-fed cattle virome. In contrast, the kingdom Heunggongvirae had a significantly higher abundance in the grass-fed group than in the grain-fed cattle virome. Moreover, the viruses, belonging to the order Caudovirales and the family Podoviridae, had significantly higher abundances in the grass-fed virome than in the grain-fed virome.

CONCLUSIONS: The findings indicate the influence of animal feeds on the changes in gastrointestinal viral compositions and their potential association with cattle weight gain. The current outcome can contribute to further understanding of phage-bacterial interactions and their underlying mechanisms in regulating the animal host's metabolism and feed efficiency. Video Abstract.

RevDate: 2025-08-23

Wang J, Xue L, Zhang M, et al (2025)

Colonoscopic fecal microbiota transplantation for Mild-to-Moderate Parkinson's Disease: A randomized controlled trial.

Brain, behavior, and immunity pii:S0889-1591(25)00321-6 [Epub ahead of print].

OBJECTIVE: Growing evidence supports the efficacy and safety of fecal microbiota transplantation (FMT) in treating Parkinson's disease (PD). Fecal microbiota are commonly transplanted via oral capsules, a nasojejunal tube, or colonoscopy, but freezing often decreases the diversity and viability of transplanted microbiota. This single-center, double-blind, randomized, placebo-controlled trial aims to explore the efficacy and safety of fresh FMT via colonoscopy in dealing with PD.

METHODS: Thirty patients with mild-to-moderate PD (Hoehn-Yahr stage I-III) were randomly assigned into the FMT group (fresh FMT via colonoscopy) and placebo group (saline injection via colonoscopy) in a 1:1 ratio. Motor and non-motor symptoms, constipation, quality of life, cognitive function, emotional state and sleep quality were assessed using relevant scales. Fecal samples were harvested before and at 4, 8 and 12 weeks after treatment for metagenomic and metabolomics analyses.

RESULTS: A total of 30 patients with mild-to-moderate PD were enrolled in the present study, involving 18 males and 12 females with a median age of 68 years, a median age of onset of 63.5 years, and a median disease duration of 3 years. At 12 weeks, scores of the UPDRS Ⅲ (group × time effect, B =  - 8.80 [-13.79, -3.81]), PAC-QOL (group × time effect, B =  - 29.67 [-45.35, -13.98]), UPDRS Ⅱ (group × time effect, B =  - 5.07 [-8.85, -1.28]), NMSS (group × time effect, B =  - 35.60 [-53.59, -17.61]), PDQ-39 (group × time effect, B =  - 17.80 [-28.21, -7.39]), HAMA (group × time effect, B =  - 1.66 [-2.92, -0.40]), and HAMD (group × time effect, B =  - 1.33 [-2.49, -0.16]) were significantly reduced in the FMT group, while CSBM per week (group × time effect, B = 3.03 [1.42, 4.63]) and the Bristol Stool Scale score (group × time effect, B = 1.95 [0.12, 3.79]) significantly increased (all P < 0.05). Significant alterations were seen in the gut microbiota and fecal metabolites in the FMT group. No adverse events were observed during the follow-up period.

CONCLUSION: Fresh FMT via colonoscopy is a safe and well-tolerated procedure for treating mild-to-moderate PD. It effectively alleviates motor and non-motor symptoms, thus facilitating defecation and improving the quality of life. These effects can be maintained for a minimum of 12 weeks and may be attributed to the optimization of gut microbiota and fecal metabolites.

RevDate: 2025-08-23

Fonnes S, Mollerup S, Paulsen SJ, et al (2025)

A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.

Clinics and research in hepatology and gastroenterology pii:S2210-7401(25)00152-4 [Epub ahead of print].

PURPOSE: Diagnosing appendicitis is difficult. An infectious origin has been proposed, therefore signals from the microbiome could be a potential diagnostic measure. The aim was to evaluate the diagnostic potential of the rectal microbiome in patients with suspected appendicitis.

METHODS: We included adult Danish patients with suspected appendicitis undergoing appendectomy in a prospective, observational cohort study. Patients were first grouped as patients with and without appendicitis according to histopathological findings, and second, as having uncomplicated or complicated appendicitis according to the surgical report. Rectal swabs were analysed with shotgun metagenomics. The outcomes were alpha diversity, beta diversity, and differential abundance of bacteria.

RESULTS: Rectal swabs from 220 patients were analysed: 49 patients without appendicitis, 111 patients with uncomplicated and 60 patients with complicated appendicitis, respectively. Across all groups, both the alpha and beta diversity were similar. The relative abundance of bacterial genera and species was also similar across all groups. Thus, the three groups of patients had similar rectal microbiomes.

CONCLUSION: The rectal microbiome in adult patients with suspected appendicitis was similar and does not seem to have the potential to be used to diagnose neither appendicitis nor the severity of appendicitis preoperatively.

TRIAL REGISTRATION: NCT03349814 (clinicaltrials.gov).

RevDate: 2025-08-23

Zhang L, Zhang Y, Huang J, et al (2025)

Temperature-driven functional microbial interactions in soy sauce fermentation: Effects of Zygosaccharomyces rouxii and Wickerhamiella versatilis on flavor enrichment and biogenic amine reduction.

International journal of food microbiology, 442:111399 pii:S0168-1605(25)00344-7 [Epub ahead of print].

This study elucidates the temperature-dependent interactions between halotolerant yeasts and microbial communities during secondary fortified soy sauce fermentation (SFFSS) and their implications for flavor enhancement and safety. A dual-mode fermentation system compared natural temperature fermentation (NTF) and controlled temperature fermentation (CTF, 30 °C), each with and without co-inoculation of Zygosaccharomyces rouxii and Wickerhamiella versatilis (ZC). Multi-omics analyses integrating amplicon sequencing, metagenomics, and metabolomics revealed that CTF control elevated amino acid nitrogen and aroma compounds, while increasing biogenic amines (BA) by 47.88 %. In both NTF and CTF modes, the ZC pattern significantly reduced lactic acid while enhancing succinic acid, umami/sweet free amino acids, and key aroma compounds (e.g., 4-ethylguaiacol, 5-ethyl-4-hydroxy-2-methyl-3(2H)-furanone), alongside enriching functional bacteria (Staphylococcus, Weissella), stabilizing fungal communities, and suppressing Tetragenococcus and Ligilactobacillus pobuzihii. Mechanistically, ZC pattern promoted tricarboxylic acid cycle flux and amino acid metabolism, synergistically enhancing volatile phenolics, esters, and alcohols, and reduced BA by >87 % via dual modulation of decarboxylase inhibition and oxidase activation. Network analyses linked microbial composition shifts to targeted flavor metabolite synthesis, providing a mechanistic framework for microbial community engineering. These findings highlight yeast-mediated, temperature-driven modulation of microbiota-metabolite networks as a viable strategy for producing high-quality, safe soy sauce with optimized flavor complexity.

RevDate: 2025-08-23

Ni J, Fu L, Xiao J, et al (2025)

Metagenomic evidence of viral secretion from tick salivary glands to saliva: implications for potential horizontal transmission.

Ticks and tick-borne diseases, 16(5):102540 pii:S1877-959X(25)00104-9 [Epub ahead of print].

Ticks transmit diverse viral pathogens to hosts during blood-feeding via saliva secretion. This study characterized viral compositions in salivary glands and saliva from adults of four tick species (Ixodes persulcatus, Rhipicephalus microplus, Haemaphysalis longicornis, and Haemaphysalis concinna) collected in China. Meta-transcriptomic analysis revealed distinct viromes across species, with Flaviviridae dominant in R. microplus, Nairoviridae in H. concinna and I. persulcatus, and Phenuiviridae in H. longicornis and I. persulcatus. Among 27 viruses detected in salivary glands, 14 were identified in saliva, indicating horizontal transmission potential. Viruses with higher abundance (transcripts per thousand bases per million, TPM) in salivary glands were more likely to be secreted in saliva. Genomic sequences of eight viruses, including severe fever with thrombocytopenia syndrome virus (SFTSV), tick-borne encephalitis virus (TBEV), Jingmen tick virus (JMTV), Songling virus (SGLV), Wetland virus (WELV), Beiji nairovirus (BJNV), Mukawa virus (MKWV), and Wuhan tick virus 2 (WHTV2), which are associated with human diseases or possess spillover potentials, were fully assembled from salivary glands and confirmed in saliva. Notably, SFTSV in H. longicornis; MKWV, Sichuan tick hepe-like virus, and Jilin luteo-like virus 2 in I. persulcatus; and JMTV in R. microplus showed significantly increased abundance in saliva, indicating an enhanced secretion of these viruses into saliva. Conversely, TBEV, BJNV, and Sara tick phlebovirus in I. persulcatus, SGLV and WELV in H. concinna, and WHTV2 in R. microplus exhibited reduced salivary abundance despite glandular presence. These findings demonstrate differential secretion capabilities of tick-borne viruses (TBVs) from glands to saliva, advancing understanding of horizontal transmission risks for pathogens affecting human health.

RevDate: 2025-08-23

Proskynitopoulos PJ, Woltemate S, Rhein M, et al (2025)

The effect of alcohol withdrawal therapy on gut microbiota in alcohol use disorder and its link to inflammation and craving.

Alcohol, clinical & experimental research [Epub ahead of print].

BACKGROUND: Alcohol use disorder (AUD) is linked to changes in the function and composition of the human gut microbiome (GM). The GM affects inflammation by producing anti-inflammatory molecules such as short-chain fatty acids (SCFA), in particular butyrate, which are linked to appetite regulation, a mechanism involved in alcohol craving. This study investigates changes in GM composition and functional capacity to produce SCFA during alcohol withdrawal and their link to inflammation and craving.

METHODS: Sixty-three patients (mean age 48, SD = 12) with AUD were enrolled. We collected stool (n = 63) and blood (n = 48) during the first 48 h (timepoint A) of withdrawal therapy and between Days 10-14 (timepoint B). Microbiota were analyzed using shotgun metagenomics along with bacterial load determinations. TNF-α, IL-6, IL-8, and IL-10 were measured in plasma.

RESULTS: Bacterial diversity (species richness, Shannon Index) did not change significantly throughout withdrawal, while overall bacterial load increased. Abundances of several taxa changed, and the overall community composition during withdrawal was approaching those of healthy controls; the potential to synthesize butyrate, a key SCFA, increased. However, it remained at lower levels compared with controls. Both diversity parameters correlated with cell concentrations and the butyrate pathway at baseline. The latter was negatively associated with IL-6 at baseline. IL-8 and IL-10 levels decreased significantly during withdrawal, as did craving, which was linked to abundance alterations of six species and IL-8.

CONCLUSIONS: Alcohol withdrawal affected GM composition and increased concentration of the butyrate pathway along with overall bacterial load. Changes in bacterial composition and the butyrate production capacity demonstrate a shift toward healthier microbiota during withdrawal therapy. Changes in some species and IL-8 were linked to alcohol craving, replicating findings of previous studies. Our study adds new findings helping to understand the microbiome-gut-brain axis.

RevDate: 2025-08-23

Dong Y, Fan S, He S, et al (2025)

RNA-viromics unveils diverse RNA viral communities in Large-billed crows and Northern Ravens.

Virus genes [Epub ahead of print].

Birds have historically served as key vectors for viruses causing significant diseases. Corvid birds, often living in close proximity to livestock, poultry, and humans, provide substantial opportunities for cross-species viral transmission. Such transmission can occur through their feces or via ectoparasites (such as ticks, mites, and fleas) on their bodies, thereby releasing viruses into the environment. Despite the development of viral metagenomics, an increasing number of RNA viruses are being characterized across different species. RNA viruses in birds' gut microbial communities remain poorly studied. Here we report an extensive analysis of an RNA virome in fecal samples from Large-billed crows (Corvus macrorhynchos) and Northern Ravens (Corvus corax), both of which are common Corvus species found in the high-altitude forest and grassland regions of the Qinghai-Tibetan Plateau. This study aims to assess the RNA viruses present in the intestines of these corvids and provides the first comprehensive characterization of the diversity of gut-colonizing viruses in these two crow species.

RevDate: 2025-08-23

Ma H, Wang M, Feng Y, et al (2025)

Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach.

FEBS open bio [Epub ahead of print].

Relatively little is known about the microbial variations within the human appendix niche. To overcome this knowledge gap, we employed endoscopic retrograde appendicitis treatment (ERAT) technology to collect microbial samples from the appendix lumen, followed by shotgun metagenomic sequencing on participants with acute appendicitis without antibiotic treatment. Compared to the cecum and terminal ileum, the appendix had a higher abundance at the genus level of Sphingobium, Leptotrichia and Oribacterium, as well as a significant increase in species-level abundance of oral bacteria, including Streptococcus sanguinis, Streptococcus australis, Streptococcus sp. A12, Leptotrichia sp. oral taxon 215, Veillonella dispar, Veillonella infantium and Oribacterium sinus. Pearson correlation analysis showed that bacterial species abundant in the appendix, such as Acinetobacter johnsonii, Sphingobium yanoikuyae and Agrobacterium tumefaciens, had negative correlations with the top five most abundant Gene Ontology (GO) categories (molecular function, biological process and cellular component). Conversely, species underrepresented in the appendix, including Mogibacterium diversum, Streptococcus sanguinis, Megasphaera micronuciformis and Actinomyces graevenitzii, had significant positive correlations with these GO categories. Our results show that ERAT technology can be used to improve sampling and microbiome profiling in the appendix. Furthermore, this in-depth microbial characterization could inform clinicians during antibiotic prescription. However, further large sample size studies are required to validate these results.

RevDate: 2025-08-23

Wang X, Liu J, Chai B, et al (2025)

Protozoa-driven micro-food webs shaping carbon and nitrogen cycling in reservoir ecosystems.

Environmental microbiome, 20(1):109.

Protozoa-driven micro-food webs are pivotal regulators of microbial community structure and carbon-nitrogen cycling. By mediating trophic cascades that regulate bacterial and algal populations, protozoa influence nutrient remineralization and energy flow. Their regulation is crucial for stabilizing biogeochemical processes and preventing harmful algal blooms. However, little is known about the detailed relationship between the traits of micro-food webs and carbon/nitrogen cycling processes. Using metagenomic data, we investigated the complexity and stability of micro-food webs in three distinct zones of the Fenhe Reservoir-the inflow river zone, shallow wetland, and deep-water zone-to assess their impacts on carbon and nitrogen cycling. Our findings revealed distinct spatial patterns in micro-food web complexity and stability, with the highest diversity and interaction density in inflowing river zones and a gradual simplification towards deep-water zones. Functional gene analysis shows significant differences in carbon degradation, fixation pathways, and nitrogen transformation processes, with shallow waters exhibiting strong microbial-mediated nitrification and denitrification, while deep waters rely on anaerobic nitrogen reduction pathways. Partial least squares path modeling (PLS-PM) indicated that protozoan-driven micro-food web structures regulate microbial functional differentiation, thereby influencing carbon and nitrogen cycle. Additionally, environmental parameters such as organic carbon concentration and nitrogen availability significantly shape microbial interactions and biogeochemical transformations. These findings highlight the intricate relationship between microbial community composition, food web stability, and elemental cycling, providing critical insights for reservoir ecosystem management and water quality optimization.

RevDate: 2025-08-23
CmpDate: 2025-08-23

Li X, J Liu (2025)

Molecular diagnostic technology: beyond analytical accuracy.

Critical care (London, England), 29(1):382.

Infectious diseases cause high morbidity and mortality, and early, effective antimicrobial therapy improves outcomes. However, conventional microbiology methods like culture are slow and insensitive. Emerging molecular diagnostics-such as multiplex PCR (mPCR), droplet digital PCR (ddPCR), and metagenomic next-generation sequencing (mNGS)-offer rapid, accurate pathogen identification. Challenges persist in result interpretation (e.g., setting positivity thresholds, low positive predictive value) and clinician trust. While molecular diagnostics excel in sensitivity, their real-world impact on specificity and patient prognosis - clinical accuracy -remains limited. Key hurdles include patient selection, timing, result interpretation, and pathogen relevance. Addressing these gaps is critical for standardizing these technologies and maximizing their clinical benefit.

RevDate: 2025-08-23

Wan S, Li M, Li W, et al (2025)

Development and validation of a multimodal model integrating gut microbiota and metabolite for identifying sarcopenia in patients with MASLD: a study from two centers in China.

Nutrition journal, 24(1):129.

RevDate: 2025-08-23
CmpDate: 2025-08-23

Azmi MAI, William-Dee J, Morni MA, et al (2025)

Metagenomic insights into host-specific gastroenteritis bacteria in forest rodents of Sarawak, Borneo: implications for one health surveillance of rodent-borne pathogens.

BMC microbiology, 25(1):531.

Rodents are known to act as reservoirs for zoonotic diseases due to their widespread distribution and synanthropic nature. Among these, foodborne pathogens capable of causing gastroenteritis in humans are of particular concern, as rodents can facilitate their transmission through contamination of food sources. Forest-dwelling rodents may harbour bacterial taxa native to their habitat, posing a risk of zoonotic spillover to nearby human settlements. This risk is further heightened by the growing prevalence of ecotourism activities, particularly in tropical countries like Malaysia. In this study, rodent trapping was conducted in selected forested areas adjacent to human settlements across Sarawak. Nanopore sequencing of the full-length 16 S rRNA gene was conducted on faecal DNA from 46 rodent individuals representing seven different species (Maxomys surifer, M. tajuddinii, M. whiteheadi, Niviventer cremoriventer, Rattus tanezumi, R. tiomanicus and Sundamys muelleri). A total of ten bacterial species associated with gastroenteritis were successfully detected. Notable findings in this study include Campylobacter, Salmonella and Shigella species, which are known to cause bacterial gastroenteritis in humans. Also, the presence of certain bacterial taxa in specific rodent genera suggests potential host specificity of foodborne pathogens. This study highlights the potential public health risks caused by rodent-borne bacterial transmission and the importance of monitoring forest rodents as potential reservoirs of zoonotic pathogens.

RevDate: 2025-08-23
CmpDate: 2025-08-23

Shinge SAU, Zhang B, Zheng B, et al (2025)

Unveiling the Future of Infective Endocarditis Diagnosis: The Transformative Role of Metagenomic Next-Generation Sequencing in Culture-Negative Cases.

Journal of epidemiology and global health, 15(1):108.

Culture-negative infective endocarditis (CNE) remains a significant diagnostic challenge in cardiology and infectious disease, often leading to delayed or empirical treatment. Metagenomic next-generation sequencing (mNGS) has emerged as a complementary diagnostic tool capable of identifying fastidious, unexpected, or novel pathogens without prior assumptions. This narrative review synthesizes evidence from 152 studies (2015-2024), evaluating mNGS within existing diagnostic frameworks for culture-negative IE. Compared to conventional diagnostics (blood cultures, PCR, 16 S rRNA sequencing), mNGS demonstrates enhanced detection capabilities for polymicrobial infections and rare pathogens, though methodological heterogeneity across studies precludes definitive performance comparisons. Performance varies substantially based on sample type, sequencing platform, and bioinformatic pipelines. Real-world applications reveal persistent challenges, including cost barriers, interpretive complexities in low-biomass samples, and contamination risks. Integration with host-response biomarkers and AI-driven interpretation platforms shows promise for advancing clinical utility. For mNGS to be effectively integrated into routine CNE care, standardization, regulatory clarity, and equitable implementation will be essential.

RevDate: 2025-08-21

Zhang Y, Ma Y, Yue R, et al (2025)

Meningitis caused by Aspergillus fumigatus: a case report.

BMC infectious diseases, 25(1):1051.

BACKGROUND: Aspergillus fumigatus is a common pathogen that causes intracranial aspergillosis. A. fumigatus intracranial infection mainly occurs in the brain parenchyma. Head CT or MRI examination showed aspergillous abscess, which is extremely rare to caused meningitis alone. We report a case of aspergillosis meningitis with short-term death.

METHOD: We utilized the DNBSEQ™ sequencing platform, which employs DNA nanoballs (DNBs) technology. Briefly, DNBs are arrayed on a patterned flow cell, where DNA polymerase catalyzes the incorporation of fluorescently labeled nucleotides during sequencing-by-synthesis. The emitted fluorescence signals are digitally captured and computationally processed to generate high-accuracy base sequence data.

CASE PRESENTATION: A 51-year-old woman with a medical history of post-hepatitis B cirrhosis, type 2 diabetes mellitus, and thyroid carcinoma presented with acute-onset altered mental status. Physical examination revealed positive meningeal signs. Initial neuroimaging studies, including two serial head CT scans and two MRI examinations, showed no evidence of fungal abscess formation in the brain parenchyma. The diagnosis of A. fumigatus meningitis was confirmed through cerebrospinal fluid (CSF) analysis, including metagenomic next-generation sequencing (mNGS) and galactomannan (GM) testing. Despite prompt initiation of voriconazole therapy, the patient’s condition deteriorated, resulting in death after 10 days of treatment.

CONCLUSION: A. fumigatus meningitis represents a rare but life-threatening infection characterized by diagnostic challenges and alarmingly high mortality rates. Stringent diagnostic vigilance is essential to avoid diagnostic errors in these cases. The PMseq-DR platform, a high-throughput metagenomic sequencing technology for cerebrospinal fluid (CSF) analysis, provides a valuable diagnostic tool for rapid pathogen identification. For patients presenting with meningitis of unknown etiology following conventional diagnostic workup (including microbial culture, galactomannan assay, and 1-3-β-D-glucan testing), comprehensive CSF pathogen analysis becomes critical. In such scenarios, prompt implementation of high-throughput sequencing is recommended to enable accurate diagnosis and timely therapeutic intervention.

RevDate: 2025-08-22
CmpDate: 2025-08-22

Kotrbová L, Grabicová K, Švecová H, et al (2025)

The effect of WWTP products amendments on Phaseolus vulgaris rhizosphere and its ability to inactivate clarithromycin.

Scientific reports, 15(1):30950.

With increasing efforts to reuse wastewater treatment plant (WWTP) products in agriculture, assessing their impact on soil-plant systems is crucial, while the effects of accompanying antibiotic residues on soil microbial communities have not yet been adequately studied. This study focuses on clarithromycin (CLR), highly present in wastewater, and investigates the CLR-degradation potential of plant-associated microorganisms. Phaseolus vulgaris plants were grown in raised beds filled with Haplic Cambisol and amended with or without WWTP products (treated wastewater, biosolid, or composted biosolid), as a source of CLR residues. The rhizosphere microbiomes after biosolid amendments was significantly enriched by Pseudomonadaceae as assessed by 16S rRNA metagenomics and cultures enriched by CLR revealed dominance of Proteobacteria. However, no degradation of CLR by microbial consortia or enrichment cultures was observed, suggesting the multiplication of CLR-resistant bacteria with other resistance mechanisms. Cultivation-based approach combined with antibiotic modulation assays and subsequent LC-MS analysis confirmed the complete CLR removal by seven phylogenetic groups of actinomycetes in vitro. The proportion of isolates indicated that the rhizosphere is a natural reservoir for CLR-inactivating microorganisms; however, the amendment of soils with WWTP products can significantly increase their abundance and diversity.

RevDate: 2025-08-22
CmpDate: 2025-08-22

Zhang M, Wang X, Yao H, et al (2025)

Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.

NPJ biofilms and microbiomes, 11(1):169.

The effects of seasonal fluctuations in food availability on gut microbiome composition, diversity, and function present significant challenges to animals with hard-to-digest diets. Here, we investigate seasonal variation the gut microbiome of wild golden snub-nosed monkeys (Rhinopithecus roxellana), a foregut fermenting primate, using metagenomics and metatranscriptomics data. We reconstructed 578 metagenome-assembled genomes (MAGs), 76.5% of which did not have exact matches in reference databases, highlighting the novelty of their gut microbiota. The gut microbiome of wild golden snub-nosed monkeys exhibited high diversity and enrichment in plant secondary compound metabolism during summer, while in winter it was enriched with enzymes that function in lichen polysaccharide degradation and Lachnospiraceae, which is important for energy balance. Captive monkeys on a consistent diet showed minimal seasonal variation in gut microbiome composition. Habitat changes also affected golden snub-nosed monkey microbiota community assembly and carbon cycling pathways. These findings underscore the gut microbiome's plasticity in meeting host dietary needs under varying environmental conditions.

RevDate: 2025-08-22

Qin Q, Zhu Y, Yang L, et al (2025)

Oral microbiome between patients with non-obstructive and obstructive hypertrophic cardiomyopathy.

Chinese medical journal [Epub ahead of print].

BACKGROUND: The profile and clinical significance of the oral microbiome in patients with non-obstructive hypertrophic cardiomyopathy (noHCM) and obstructive hypertrophic cardiomyopathy (oHCM) remain unexplored. The objective of this study was to evaluate the difference of oral microbiome between noHCM and oHCM patients.

METHODS: This cross-sectional study enrolled 18 noHCM patients and 26 oHCM patients from Fuwai Hospital, Chinese Academy of Medical Sciences between 2020 and 2021. Clinical and periodontal evaluations were conducted, and subgingival plaque samples were collected. Metagenomic sequencing and subsequent microbial composition and functional analyses were performed.

RESULTS: Compared to oHCM patients, those with noHCM had higher systolic blood pressure (138.1 ± 18.8 mmHg vs. 124.2 ± 13.8 mmHg, P = 0.007), a larger body circumference (neck circumference: 39.2 ± 4.0 cm vs. 35.1 ± 3.7 cm, P = 0.001; waist circumference: 99.7 ± 10.5 cm vs. 92.2 ± 10.8 cm, P = 0.027; hip circumference: 102.5 ± 5.6 cm vs. 97.5 ± 9.1 cm, P = 0.030), a greater left ventricular end-diastolic diameter (46.6 ± 4.9 mm vs. 43.1 ± 4.9 mm, P = 0.026), and a lower left ventricular ejection fraction (64.1 ± 5.7 % vs. 68.5 ± 7.8%, P = 0.048). While overall biodiversity and general microbial composition were similar between the noHCM and oHCM groups, ten taxa displayed significant differences at the genus and species levels, with Porphyromonas gingivalis showing the highest abundance and greater enrichment in noHCM (relative abundance: 7.79535 vs. 4.87697, P = 0.043). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis identified ten distinct pathways, with pathways related to energy and amino acid metabolism being enriched in oHCM patients, and those associated with genetic information processing less abundant in the oHCM group. Metabolic potential analysis revealed ten significantly altered metabolites primarily associated with amino sugar and nucleotide sugar metabolism, porphyrin metabolism, pentose and glucuronate interconversion, and lysine degradation.

CONCLUSIONS: The higher abundance of Porphyromonas gingivalis, which is known to impact cardiovascular health, in noHCM patients may partially account for clinical differences between the groups. Pathway enrichment and metabolic potential analyses suggest microbial functional shifts between noHCM and oHCM patients, potentially reflecting inherent metabolic changes in HCM.

RevDate: 2025-08-22

Han Y, Cui J, Guo P, et al (2025)

Remediation Effects of Straw Combined with Microbial agents on Cinnamon Soils with Varying Degradation Based on Metagenomics and Untargeted Metabolome.

Environmental research pii:S0013-9351(25)01901-2 [Epub ahead of print].

Microbial agents show potential for improving soil quality and crop yield. However, in the context of different soil degraded degrees, the effects of straw combined with microbial agents on soil microbial communities and their associated metabolic processes remain insufficiently explored. Here, we conducted pot experiments using cinnamon soils at three degradation levels (highly, moderately, and non-degraded), applying straw alone or straw combined with microbial agents during alfalfa cultivation. In this study, we combined metagenomic sequencing and untargeted metabolomics to study the effects of straw and straw combined with microbial agents on soil quality and plant biomass, and metabolites as well as on the network complexity and stability of soil microbial communities. Our findings showed that both straw and straw-microbial agent combinations enhanced the soil quality and alfalfa yield, as well as on the complexity and stability of bacterial networks in highly degraded soils. Meanwhile, the straw-microbial agent combination significantly altered key metabolic pathways (e.g., steroid hormone biosynthesis, cofactor biosynthesis, and nucleotide metabolism) and differentially regulated metabolites (e.g., amino acids/peptides, organosulfur compounds, and alkaloids) compared to straw alone, with distinct effects observed across degradation levels. Overall, the microbial community and their metabolites shaped by straw and straw combined with microbial agents promoted the remediation of degraded soils, ultimately enhancing soil quality and plant biomass. These findings advance the understanding of straw and microbial agents as a synergistic remediation strategy for modulating soil microbial communities and offer practical insights for soil health restoration.

RevDate: 2025-08-22

Hshieh K, JG Maloney (2025)

Sequencing on the edge: Tools and techniques for sequencing low biomass isolates from unicellular eukaryotic parasites and other challenging samples.

Journal of microbiological methods pii:S0167-7012(25)00149-6 [Epub ahead of print].

Low biomass samples are difficult to study as many sequencing protocols require minimum inputs that exceed the DNA available from unculturable microorganisms, single cells, or environmental samples. This limitation makes the genomes of unicellular eukaryotic parasites difficult to obtain as culture methods are unavailable for many species. This review will highlight and summarize techniques that have been applied to a variety of low biomass samples from unculturable microbes to microbial communities. Because unicellular eukaryotic parasite sequencing shares many of the same challenges as other low biomass sample types including single cell and environmental metagenomic sequencing, studies addressing these types of samples are included in this review. We highlight that method validation and selection can be an important factor influencing experiment outcome and success when sequencing low biomass samples, and suggest that when feasible, method validation should be considered in experimental design. Reviewing the benefits and challenges associated with different techniques for enhancing sequencing success for low biomass samples will be useful for those who work within these fields and can assist in method selection and experimental design for exploring challenging samples.

RevDate: 2025-08-22

Moore CO, Andrews CV, Lemley EM, et al (2025)

Wildlife fleas and ticks in Wisconsin, USA: unrecognized vectors of bacterial pathogens.

International journal for parasitology pii:S0020-7519(25)00138-9 [Epub ahead of print].

Small wildlife species host flea and tick species that can also infest or transmit pathogens to domestic animals and humans, including Anaplasma, Babesia, Bartonella, Borrelia, Ehrlichia, and Rickettsia species. Despite their zoonotic potential, little is known regarding the prevalence, diversity, and epidemiology of these pathogens. Therefore, we aimed to survey the ectoparasites found on Eastern Cottontail Rabbits (rabbits), Eastern Grey Squirrels (squirrels), and Virginia Opossums (opossums) in south-central Wisconsin, and describe the prevalence of select pathogens. Ectoparasites were opportunistically collected from small mammals, then identified to the species level, pooled, washed, and DNA extracted for quantitative PCR (qPCR) to detect Anaplasmataceae, Apicomplexa, Bartonella, hemotropic Mycoplasma, and Rickettsia. To analyze the genomic diversity of uncharacterized Bartonella, three flea pools were subject to metagenomic sequencing. Cediopsylla simplex and Haemaphysalis leporispalustris were the most common ectoparasites on rabbits, while Orchopeas howardi was most common on squirrels and opossums. Bartonella species were detected in C. simplex pools (n = 52), most commonly two distinct Bartonella alsatica-like bacteria (38%; 20/52). Bartonella durdenii, definitively identified by metagenomic sequencing, was detected in 42% (13/31) of O. howardi pools from squirrels. From metagenomic sequencing, B. alsatica-like species displayed a 4.8% dissimilarity rate while B. durdenii displayed a 0.4% dissimilarity rate. Sequencing of one B. alsatica-like flea pool also identified phage-associated genes not found in the B. alsatica genome. Rickettsia felis (n = 1) and opossum-associated hemotropic Mycoplasma sp. (n = 2) were detected in O. howardi from opossums. Rickettsia bellii and Anaplasma sp. were detected in Haemaphysalis leporispalustris from rabbits. These findings reinforce the value of metagenomic sequencing, facilitating the correct identification of B. durdenii and identifying genes not found in the type strain, specifically phage related genes. Due to the known zoonotic potential of B. alsatica, further examination of B. alsatica-like and B. durdenii pathogenicity is warranted.

RevDate: 2025-08-22

Xu X, Zhou P, Cheng T, et al (2025)

Phosphate-modified calamus-based biochar filler enhanced constructed wetland mitigating antibiotic resistance risks: insight from metagenomics.

Journal of environmental management, 393:127080 pii:S0301-4797(25)03056-7 [Epub ahead of print].

In this study, an innovative phosphate-modified calamus-biochar (PBC) filler with high antibiotic adsorption capacity was developed to enhance constructed wetlands (CWs) wastewater treatment. Results showed that the erythromycin (ERY) and sulfamethoxazole (SMX) removal efficiency of PBC-CW was 86.5 % and 84.0 %, which was 2-fold higher than those of the blank group. Metagenomic analysis found that the ERY and SMX would significantly promote the increase in abundance of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and virulence factor genes (VFGs). Compared to blank group, the abundances of ARGs, MGEs and VFGs were reduced by 67.2 %, 33.3 % and 11.1 % in PBC-CW. Among them, the abundance of sulfonamide and MLS, which were key genes to resistance to SMX and ERY, respectively, were reduced by 71.8 % and 63.1 % in PBC-CW. Moreover, these persistent ARG subtypes, detected simultaneously in all the samples, reduced the total abundance by 44.8 %. In addition, microbial community analysis found that the sum abundance of Arenimonas, Chryseobacterium and Hydrogenophaga, which were suggested as potential antibiotic-resistant bacteria (ARB) via correlation analysis, were significantly decreased from 1.54 % in blank group to 0.23 % in PBC group. Moreover, Chryseobacterium and Hydrogenophaga were positively correlated with VFGs, they could be pathogens with resistance genes. Therefore, PBC-CW could effectively reduce the abundance of ARGs and pathogenic microorganisms, thereby improving water security.

RevDate: 2025-08-22

Bai X, Bi J, Li A, et al (2025)

Phylosymbiosis of antibiotic resistance genes in pig feces and potential transmission to piggery workers.

Ecotoxicology and environmental safety, 303:118907 pii:S0147-6513(25)01252-7 [Epub ahead of print].

Animal feces are recognized as reservoirs of antibiotic resistance genes (ARGs) that threaten public health and environmental safety. However, it remains unclear whether livestock breeds affect ARGs in feces and how they are transferred from animals to workers. Here, an approach integrated with metagenomics and whole-genome resequencing was used to study Saba (SB) and Large White (LW) pigs on the same pig farm. Higher abundance of both gut bacterial and viral communities and lower abundance of tetracycline and aminoglycoside resistance genes were observed in SB pigs. Gut bacterial communities control the shape of the antibiotic resistome in pig feces. The co-occurrence network showed a close association between ARGs, mobile genetic elements, and gut microbiota in SB pigs. By integrating whole-genome resequencing, an apparent phylosymbiosis was revealed in the antibiotic resistome in pig feces. The structural equation model revealed that host phylogeny primarily directly controlled the antibiotic resistome in pig feces, with additional indirect effects mediated by gut bacterial communities. The flow of ARGs, including pig feces, sludge, flies, and worker feces, between pig farms was further investigated. The findings revealed a direct contribution of pig feces to the ARGs in worker feces, while flies played only a minor role in the transfer of ARGs to pig workers. These findings are essential for developing effective measures to combat antimicrobial resistance in pigs and potential threats to public health.

RevDate: 2025-08-22

Li Y, Zhang C, Meng Z, et al (2025)

Microbial dysbiosis induced in Cyprinus carpio by tetrabromobisphenol A exposure: Mediation through gut barrier impairment and oxidative stress.

Comparative biochemistry and physiology. Part D, Genomics & proteomics, 56:101609 pii:S1744-117X(25)00198-4 [Epub ahead of print].

The frequent detection of Tetrabromobisphenol A (TBBPA) in environmental media has elicited considerable scientific concern. The ecotoxicological impacts of TBBPA on intestinal health in the common carp (Cyprinus carpio) were systematically investigated through integrated histopathological, biochemical, and metagenomic analyses. Fish were exposed to environmentally relevant TBBPA concentrations (0, 0.005, 0.05, and 0.5 mg/L) for a 14-day duration. Dose-dependent intestinal damage was induced by TBBPA exposure, manifested as villus fusion and atrophy, oxidative stress (diminished SOD/CAT activities and elevated MDA levels), and downregulated expression of tight junction proteins (ZO-1, Claudin-3, Occludin). This collectively compromised barrier integrity and triggered pro-inflammatory cytokine upregulation of TNF-α alongside anti-inflammatory IL-10 suppression. Significant intestinal microbial dysbiosis was detected via 16S rRNA sequencing. Alpha diversity indices were reduced at low concentrations (0.005 mg/L) of TBBPA but elevated at higher concentrations (0.05-0.5 mg/L). TBBPA exposure induced gut microbiota perturbations, characterized by depletion of beneficial taxa (Cetobacterium) and enrichment of opportunistic pathogens (Legionella and Thermomonas). Functional prediction analyses indicated that these microbial alterations may influence carbohydrate metabolism, and vitamin biosynthesis within the intestinal tract of common carp. Collectively, these findings demonstrated that TBBPA disrupted intestinal health via synergistic mechanisms involving oxidative stress, histopathological damage, and microbiota-mediated dysregulation. This investigation addresses a critical knowledge gap regarding the impacts of TBBPA on fish gut microbiota, while providing provided a reference for assessing the potential ecological risks of TBBPA in the environment.

RevDate: 2025-08-22

Zhang T, Jiang M, Li H, et al (2025)

Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.

Genomics, proteomics & bioinformatics pii:8239969 [Epub ahead of print].

In recent years, the field of shotgun metagenomics has witnessed remarkable advancements, primarily driven by the development and refinement of next-generation sequencing technologies, particularly long-read sequencing platforms such as Nanopore and PacBio. These platforms have significantly improved the ability to analyze microbial communities directly from environmental samples, providing valuable information on their composition, function, and dynamics without the need for pure cultivation. These technologies enhance metagenomic data assembly, annotation, and analysis by addressing longer reads, higher error rates, and complex data. In this review, we provide a comprehensive overview of the historical development of long-read metagenomics, highlighting significant landmarks and advancements. We also explore the diverse applications of long-read metagenomics, emphasizing its impact across various fields. Additionally, we summarize the essential computational resources, including software, databases, and packages, developed to enhance the efficiency and accuracy of metagenomic analysis. Finally, we provide a practical guide for the installation and use of notable software available on GitHub (https://github.com/zhangtianyuan666/LongMetagenome). Overall, this review assists the metagenomics community in exploring microbial life in unprecedented depth by providing a roadmap for successful resource utilization and emphasizing possibilities for innovation.

RevDate: 2025-08-22
CmpDate: 2025-08-22

Bhatt P, Rajesh P, Kukkar D, et al (2025)

Metagenomic profiling of gut microbime: associating their role with the advancement of diabetic nephropathy.

Antonie van Leeuwenhoek, 118(9):135.

Emerging evidence suggests that alterations in the gut microbiome should play a critical role in the development and progression of type 2 diabetes and its complication such as diabetic nephropathy (DN). Nevertheless, a considerable gap remains in our understanding of the interconnection between DN pathogenesis and gut microbiota arrangement. In this context, this review highlights recent research on the connection between the intestinal microbiota and DN risk, with a particular focus on the role of microbial metabolites in disease development. It also highlights recent advancements in metagenomic analyses of gut microbial communities and their potential contribution to the progression of DN. Further, it describes the challenges associated with the metagenomics-based analysis of intestinal microbiota and the advancement of therapeutics for DN. An exploration of the surveyed literature reveals the lack of any definitive correlation between gut microbiota and DN transition, even when assessed in view of widespread geographical and ethnic diversity. Future research in this domain should be conducted to address various issues like increasing the number of participants, intake patient diversity, logistical difficulties, and racial disparities. A critical assessment of these parameters will help improve our understanding of the potential contribution of gut microbiota to the DN progression.

RevDate: 2025-08-22

Pereira EL, Pereira GR, Osório ML, et al (2025)

Bovine and ovine deltapapillomavirus coinfection associated with equine sarcoid.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] [Epub ahead of print].

Papillomaviruses (PV) are significant agents capable of inducing simple, multiple, and/or proliferative lesions in the dermis and epidermis of animals, known as cutaneous papillomatosis. These lesions can be benign or malignant and have been identified in various hosts, including mammals, birds, reptiles, and fish. PVs are strictly species- and tissue-specific, although some established and unusual cases of cross-infection, such as BPV in equine sarcoids, have been reported. Sarcoids are horses' most common skin tumors, which can be locally aggressive and cause significant clinical signs. It is recurrently associated with Bos taurus papillomavirus (BPV) and, more recently, Ovis aries papillomavirus (OaPV). Interestingly, OaPV2s, initially identified in sheep, have been detected in other species, such as horses, cattle, and pigs. Therefore, the present study aimed to detect and sequence PVs in an equine sarcoid through rolling circle amplification followed by high-throughput sequencing (RCA-HTS) on the Illumina MiSeq platform. Sequencing yielded 387,923 reads and 17 contigs classified as Deltapapillomavirus genus. A complete BPV1 genome, with 99% coverage, was sequenced, and partial E1 and L1 genes of OaPV2 were detected. Histopathological analysis revealed fibroblastic sarcoid, which has been associated with BPV1 and OaPVs. Our results agree with recent BPV and OaPV2 association observations in sarcoid lesions in equine and swine. This broad host range of OaPVs deserves attention, as it may indicate potential interspecies transmission that is not yet fully understood, especially in coinfections, which could influence viral dynamics, transmission patterns, and disease outcomes. Until now, only OaPV1, 3, and 4 had been detected in equine sarcoids; thus, this is the first detection of OaPV2 in an equine sarcoid. In conclusion, OaPV2 should be considered a potential etiological agent of sarcoids, particularly in association with BPV1.

RevDate: 2025-08-22

Li H, Zhang Z, Chen J, et al (2025)

Fate and carbon sequestration potential of sunken macroalgae in coastal oceans from long-term microbial degradation perspective.

National science review, 12(8):nwaf273.

Although deep-sea macroalgae sinking as a carbon sequestration strategy remains controversial, natural sinking of massive macroalgae frequently occurs in coastal oceans. In the Yellow Sea, millions of tons of the macroalga Ulva prolifera sink to the seafloor annually following green tides, yet their ultimate fate and carbon sequestration potential remain poorly understood. Microbial communities play a crucial role in decomposing organic matter and determining the fate of sunken macroalgae. Our 2-year simulated microbial degradation of U. prolifera revealed that approximately 38% of the carbon in sunken macroalgal biomass was ultimately sequestered in various forms. Of this retained carbon, 10% was transformed into dissolved inorganic bicarbonate ions, enhancing seawater alkalinity and contributing to inorganic carbon storage. Meanwhile, 28% was transformed into recalcitrant dissolved/particulate organic carbon and algal detritus, consisting of degradation-resistant compounds rich in humic-like substances, polycyclic aromatic hydrocarbons and highly aromatic compounds. Metagenomic analysis showed that these transformations were driven by a coordinated microbial succession from r-strategists to K-strategists, mediated by a microbial carbon pump and a 'microbially driven alkalinity pump'. Our findings suggest that large-scale sinking of U. prolifera holds substantial potential for long-term ocean carbon sequestration, contributing to stable carbon pools in both organic and inorganic forms.

RevDate: 2025-08-22

Gou F, Han Y, Sun Y, et al (2025)

Macrogenomics-based analysis of rumen microbial composition and their metabolic pathways in yaks under different dietary concentrate-to-forage ratios.

Frontiers in microbiology, 16:1587474.

This study aimed to investigate the regulatory mechanisms underlying feed efficiency (FE) in yaks by analyzing the composition of rumen microorganisms and their major metabolic pathways using metagenomic analysis under different dietary concentrate-to-forage ratios. A total of 40 Qinghai Plateau yaks (8-9 months old) with similar body weights (68.725 ± 18.973 kg) were randomly assigned to four treatment groups (n = 10per group). The experimental groups were fed diets with concentrate-to-forage ratios of 80:20 (C80), 65:35 (C65), 50:50 (C50), and 35:65 (C35), respectively. The study included a 15-day pre-feeding period followed by a 105-day experimental feeding period. The results indicated that the total weight gain in the C65 group was significantly higher than in the C50 and C35 groups by 29.91 and 28.97%, respectively (p < 0.05). Additionally, the rumen pH in the C80 group was significantly higher than in the C65, C50, and C35 groups (p < 0.05). Metagenomic analysis revealed significant differences (p < 0.05) in bacterial and archaeal community compositions across groups. Bacteroidota, Bacillota, Prevotella, Bacteroides, and Ruminococcus were identified as the dominant bacterial taxa at the phylum and genus levels. Functional analysis of rumen microbial metabolism showed that in the C35 group, pathways related to starch and sucrose metabolism, as well as fructose and mannose metabolism, were significantly different from those in other groups. The C35 group exhibited higher activity in functional pathways related to starch and sucrose metabolism, fructose and mannose metabolism, cellulose degradation, and methanolysis. In contrast, the C80 group showed greater activity in cellulose degradation and methane metabolism. Notably, the C65 group exhibited the highest activity in sugar metabolism pathways (ko00500), facilitating starch and soluble sugar degradation and the rapid conversion of pyruvic acid into acetic acid and propionate. This enhanced energy utilization efficiency, suggesting a superior capacity for sugar metabolism. In conclusion, the dietary composition of the C65 group demonstrated the most favorable effects on growth performance, rumen fermentation optimization, and microbial balance maintenance.

RevDate: 2025-08-22
CmpDate: 2025-08-22

Chen X, Zhao H, Jiang C, et al (2025)

Human herpes virus-7-related severe encephalitis diagnosed using mNGS in immunocompetent pediatric patients.

Virology journal, 22(1):287.

BACKGROUND: This study sought to describe the clinical characteristics, examination results, and prognoses of immunocompetent children with human herpes virus 7 (HHV-7)-related severe encephalitis.

METHODS: Twelve immunocompetent children with severe HHV-7-related encephalitis were included, all of whom had HHV-7 DNA ( +) detected in the cerebrospinal fluid via metagenomic next-generation sequencing (mNGS) and were followed up for > 6 months.

RESULTS: The cohort comprised 75% males, with a median age of 4.5 years; all patients presented with fever and altered consciousness and required PICU admission for severe neurological symptoms. Two patients developed encephalitis sequelae and epilepsy. Abnormal electroencephalography and brain magnetic resonance imaging findings were observed in 90.9% (10/11) and 72.7% (8/11) of the patients, respectively. Five patients required ventilator support due to central respiratory failure (four invasive and one noninvasive). One patient underwent plasma exchange, while another received continuous renal replacement therapy. All patients were treated with acyclovir and immunomodulatory therapy. Four patients had poor prognoses, including one 9-year-old male who died and one 9-year-old female who was diagnosed with febrile infection-related epilepsy syndrome and remained in a coma with a Modified Rankin Scale score of 5 at the 6-month follow-up.

CONCLUSIONS: Older immunocompetent children with severe HHV-7-related encephalitis have poor prognosis and low survival rates, both of which may be improved via empiric acyclovir administration combined with immunosuppressive therapy.

RevDate: 2025-08-22

Mo X, Guo S, He D, et al (2025)

Lactobacillus reuteri DSM 17,938 ameliorates LPS-induced depression-like and anxiety-like behaviors by modulating gut microbiota and brain metabolic function.

Gut pathogens, 17(1):65.

BACKGROUND: Lactobacillus reuteri DSM 17,938 exhibits antidepressant and anxiolytic potential. The purpose of this study is to validate the effects of L. reuteri DSM 17,938 and preliminarily explore its underlying antidepressant and anxiolytic mechanisms, thereby providing a general direction for researching the targets of its antidepressant and anxiolytic effects.

METHODS: The depressive mouse model induced by lipopolysaccharide (LPS) was intervened with L. reuteri DSM 17,938 (5 × 10[9] cfu/ml), and behavioral experiments were conducted to evaluate the therapeutic effects of the probiotic on depression. Moreover, the antidepressant and anxiolytic mechanism of probiotics was investigated through fecal metagenomics and fecal non-targeted metabolomics, as well as non-targeted metabolomics of the hippocampus and prefrontal cortex.

RESULTS: In the behavioral experiments, L. reuteri DSM 17,938 significantly reversed the phenomena of reduced total moving distance, decreased center zone stay time and increased peripheral zone stay time in the open field test of LPS-induced depressed mice, and significantly reduced the immobility time of mice in the forced swimming test. L. reuteri DSM 17,938 restored gut microbial richness and ameliorated intestinal metabolic pathways in a depression mouse model, with lipopolysaccharide biosynthesis and ATP-binding cassette transporter (ABC) transporter metabolic pathways being significantly enriched. Untargeted metabolomics of the hippocampus and prefrontal cortex revealed that LPS intervention primarily induced dysregulation of amino acid metabolism-related pathways in these brain regions. In contrast, L. reuteri DSM 17,938 administration restored neural homeostasis, as evidenced by KEGG functional enrichment analysis identifying activated amino acid metabolism and unsaturated fatty acid metabolism pathways.

CONCLUSION: These findings collectively suggest that L. reuteri DSM 17,938 exerts antidepressant and anxiolytic effects by modulating gut microbiota composition to improve intestinal metabolism and subsequently rectifying amino acid and unsaturated fatty acid metabolic pathways in the hippocampus and prefrontal cortex. This study elucidate the gut-brain axis mechanisms underlying its antidepressant and anxiolytic effect and highlight its potential as a novel probiotic-based strategy for mood disorders.

RevDate: 2025-08-22
CmpDate: 2025-08-22

Dinçer S, Ülger Y, A Delik (2025)

Mucosal microbiota signatures reveal diagnostic insights in chronic liver disease.

BMC gastroenterology, 25(1):607.

PURPOSE: Chronic liver disease (CLD) and complications of cirrhosis are responsible for the deaths of approximately two million people per year worldwide. Abnormal intestinal permeability in the intestinal-liver axis and development of intestinal dysbiosis increase disease progression contributing to chronic systemic inflammation in CLD patients. The intestinal microbiota acts as a bioreactor for autonomous metabolic and immunological functions in regulating the host's response to external stimuli in the intestinal microbiota. The study aimed to analyze the gut microbiota profile from colonic mucosal biopsy materials in CLD patients using a metagenomic application.

MATERIALS AND METHODS: CLD and control groups were formed based on predefined inclusion and exclusion criteria from the study. In the metagenomic study, colonic mucosal biopsy material was studied from a total of 40 individuals, 20 with CLD and 20 healthy controls. We analyzed gut microbiota by 16 S rRNA metagenomic next-generation sequencing (NGS) method from colonic mucosal biopsy samples in CLD and healthy individuals. Metagenomic results were analyzed by Principal Component Analysis (PCA).

RESULTS: Significant differences were observed between the CLD and control groups across multiple taxonomic levels. At the phylum level, Proteobacteria were significantly enriched in CLD patients, while Firmicutes predominated in controls. Class-level analysis showed increased Gammaproteobacteria in CLD, the former associated with inflammatory pathways. At the order level, Enterobacterales were significantly higher in CLD (OR: 1.89, p = 0.04), whereas Clostridiales were more abundant in controls. Family-level comparisons revealed elevated Enterobacteriaceae in CLD, while Ruminococcaceae and Veillonellaceae were relatively preserved in controls. At the genus level, Prevotella and Streptococcus were increased in controls. Alpha diversity indices (Shannon, Chao1) were significantly lower in the CLD group (p < 0.001), indicating reduced microbial richness. Beta diversity analysis (PCoA, Bray-Curtis) showed distinct clustering between groups, supporting compositional divergence. Integration of metagenomic findings with biochemical markers (e.g.

, GGT: OR 0.79, p = 0.03) further underscored group-specific microbial signatures.

CONCLUSION: We observed a significant compositional shift in the gut microbiota of patients with CLD. Notably, pro-inflammatory taxa were increased and a decrease in beneficial bacterial groups involved in maintaining microbial homeostasis. Diversity analyses indicated a reduction in microbial richness in the CLD group. These findings may aid in identifying CLD-specific microbial signatures. Furthermore, integrating metagenomic data with biochemical parameters may contribute to improved diagnostic strategies.

RevDate: 2025-08-21

Yau PT, Taketani RG, Bonnin JM, et al (2025)

Introducing the UK Crop Microbiome Cryobank data resource, AgMicrobiomeBase, with case studies and methods on metabarcoding analyses.

Environmental microbiome, 20(1):108.

BACKGROUND: Here, we describe AgMicrobiomeBase as an output of the UK Crop Microbiome Cryobank (UKCMCB) project, including details of the underlying meta-barcode sequence-based methods and three microbiome analysis case studies. The UKCMCB links genomic datasets and associated soil metadata with a cryobank collection of samples, for six economically significant crops: fava bean (Vicia faba), oil seed rape (Brassica napus), spring barley (Hordeum vulgare), spring oats (Avena sativa), spring wheat (Triticum aestivum) and sugar beet (Beta vulgaris). The crops were grown in nine agricultural soils from the UK, representing three major soil texture classes. The UKCMCB is a scalable sequence-based data catalogue linked to a cryo-preserved sample collection.

RESULTS: The focus of this paper is the amplicon sequencing, associated bioinformatics workflows, and development of the project data catalogue. Short-read amplicon sequencing (16 S rRNA gene and ITS region) was implemented to describe the rhizosphere and bulk soil communities, for the multiple crop-soil combinations. Three case studies illustrate how different biological questions in phytobiome research can be addressed using this data resource. The three case studies illustrate how to (1) determine the impact of soil texture and location on microbiome composition, (2) determine a core microbiome for a single crop across different soil types, and (3) analyse a single genus, Fusarium within a single crop microbiome. The UKCMCB data catalogue AgMicroBiomeBase (https://agmicrobiomebase.org/data) links the sequence-based data with soil metadata and to cryopreserved samples.

CONCLUSIONS: The UKCMCB provides baseline data and resources to enable researchers to assess the impact of soil type, location and crop type variables on crop soil microbiomes. The resource can be used to address biological questions and cross-study comparisons. Development of the UKCMCB will continue with the addition of metagenome and bacterial isolate genomic sequence data and has the potential to integrate additional data types including microbial phenotypes and synthetic microbial communities.

RevDate: 2025-08-21
CmpDate: 2025-08-21

Wang T, Zhang P, Anantharaman K, et al (2025)

Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.

Nature communications, 16(1):7806.

Virus-host interactions are vital to microbiome ecology and evolution, yet their responses to environmental stressors under global change remain poorly understood. We perform a 10-month outdoor mesocosm experiment simulating multi-trophic freshwater shallow lake ecosystems. Using a fully factorial design comprising eight treatments with six replicates each, we assess the individual and combined effects of climate warming, nutrient loading, and pesticide loading on DNA viral communities and their interactions with microbial hosts. Metagenomic sequencing recovers 12,359 viral OTUs and 1628 unique prokaryotic metagenome-assembled genomes. Our analysis shows that combined nutrient and pesticide loading causes significant disruption by synergistically reducing viral alpha diversity while altering beta diversity and predator-prey linkages. Stressors lead to the simplification of virus-bacteria cross-kingdom networks, with nutrient-pesticide combinations exerting the strongest influence, although warming impacts diminish in the presence of pesticides. Stressor-driven changes also affect the abundance and composition of viral auxiliary metabolic genes, leading to complex shifts in virus-mediated metabolic pathways under multiple stress conditions. These findings underscore the importance of understanding the regulatory role of viruses on microbial communities to effectively address the challenges posed by global change.

RevDate: 2025-08-21

Antoniadou C, Gavriilidis E, Chatzopoulos P, et al (2025)

Fever and inflammation of unknown origin in the 21st century.

European journal of internal medicine pii:S0953-6205(25)00321-8 [Epub ahead of print].

Fever and inflammation of unknown origin (FUO/IUO) remain challenging clinical syndromes today, in which the internists play a central role in orchestrating the diagnostic process and interpreting key findings. FUO and IUO share similar diagnostic evaluations and overlapping etiologies, although the relative frequencies of their causes may differ. The established five-category classification includes infectious diseases (INF), non-infectious inflammatory diseases (NIID), malignancies (MAL), miscellaneous (MISC) and undiagnosed illnesses (UI). The relative distribution of these categories varies depending on the FUO diagnostic criteria applied, as well as geographical region and socioeconomic factors. Although infectious diseases were historically the predominant cause of FUO, in recent years there has been a shift toward UI and NIID, especially in high-income settings. IUO is typically associated with a lower likelihood of infections compared to FUO, while the most common causes are mainly NIID. Meticulous medical history and clinical examination, aimed at identifying potential diagnostic clues (PDCs), remain pivotal to FUO/IUO diagnostics. Modern technologies such as PET/CT and next-generation sequencing (NGS) have advanced the diagnostic workup of FUO/IUO. However, they should be employed selectively, guided by PDCs, and with consideration of their limitations and cost-effectiveness. Emerging techniques, including metagenomic NGS and cytokine-based assays (e.g. IL-1β/DNA complex detection), show promising results in distinguishing sterile from infectious inflammation. Despite advancements in diagnostics and considering that UI now represent a leading cause of FUO in the European region, there remains an urgent need to deepen our understanding of underlying disease mechanisms and to develop novel, pathophysiology-based diagnostic tools.

RevDate: 2025-08-21
CmpDate: 2025-08-21

Jia M, Gao Z, Hu X, et al (2025)

Wetland types shape microbial function related to soil phosphorus cycling based on metagenomics analysis.

Journal of environmental sciences (China), 158:930-943.

Limitations regarding phosphorus (P) are widespread in ecosystems. Understanding the impacts of the wetland types on microbially mediated soil P availability and cycling is essential for the effective management of wetlands. In this study, the Beidagang wetland, Baodi paddy field, and Dahuangpu wetland in Tianjin, China were chosen as representatives of the coastal wetland (B), constructed wetland (R), and swampy wetland (W), respectively. Sequential P extraction and metagenomics approaches were adopted to explore the soil P fraction and microbially regulated P cycle. Proteobacteria were the predominant microbes-related soil P cycle. IMPA, gph, rsbU_P, ugpQ, and glpK genes were dominant in organic P (Po) mineralization, while gcd, ppa, and ppx genes were dominant in inorganic P (Pi) solubilization. The salinity, NO3[-]-N concentration, the ratio of total carbon to total nitrogen (TC/TN), total carbon (TC), and the ratio of soil organic carbon to total P (SOC/TP) were the co-drivers of microbially mediated P cycle processes. Microbial network complexity-relate P cycle was the lowest in the coastal wetland. Salinity and NO3[-]-N exhibited a significant negative relation to the abundance of most genes-relate Pi solubilization and a remarkable positive correlation with the abundance of many genes-relate Po mineralization. These findings demonstrated that Po mineralization tended to occur in habitats with high salinity and nutrient imbalances, whereas the dissolution of Pi was prone to occur in low-salinity environments with relatively balanced soil nutrients. This study improves understanding of how salinity and soil nutrients jointly shape microbial-regulated soil P cycle in different types of wetlands.

RevDate: 2025-08-21
CmpDate: 2025-08-21

Tang Z, Zhang Y, Shangguan H, et al (2025)

Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.

Journal of environmental sciences (China), 158:610-620.

The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.

RevDate: 2025-08-21
CmpDate: 2025-08-21

Nie E, He P, Zhang H, et al (2025)

Genome-centric metagenomic analysis unveils the influence of temperature on the microbiome in anaerobic digestion.

Journal of environmental sciences (China), 158:516-526.

Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion. However, the specific microbial communities and their functions across a wide temperature range still remain elusive. This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35, 44, 53, 55, and 65 °C. A total of 84 metagenome assembled genomes (MAGs) were assembled, with over 65 % of these MAGs corresponding to novel bacterial and archaeal species (including Firmicutes, Chloroflexota, Bacteroidia and Methanobacteriota), greatly enhancing our current comprehension anaerobic digestion process. Notably, functional annotation identified that 44_bin.2 (Methanothrix_A sp. 001602645) harbors enzymes associated with hydrogenotrophic metabolism. Additionally, this microorganism exhibited diverse metabolic capabilities at 44 °C, a temperature commonly employed in industrial practice yet less explored in bench studies. Consequently, it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature, as opposed to the conventional mesophilic range. The microorganism exhibited a variety of metabolic capabilities at 44 °C, a temperature frequently employed in industrial applications but underexplored in laboratory investigations. The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.

RevDate: 2025-08-21

Guo D, Liu X, Zhang Y, et al (2025)

Combining Simulated Immersion and Statistical Analysis to Reveal Microbial Evidence of Corrosion Failure in Fuel Aluminum Alloys.

Environmental research pii:S0013-9351(25)01763-3 [Epub ahead of print].

Microbial contamination has caused engineering problems such as fuel deterioration, corrosion of maritime aviation aluminium alloys, and fuel tank leakage. By integrating metagenomic analysis of a fuel corrosion biofilm and microbial cultivation techniques, we selected ten types of microbial resources that might affect the deteriorated corrosion of aluminium alloys in aviation fuel for corrosion immersion simulation experiments. Through multidimensional analysis of corrosive microorganisms, medium environment, and material surfaces, the qualitative and quantitative microbial evidence for the failure of aluminium alloy in aviation fuel tanks was presented. The statistical analysis results indicated that anaerobic microorganisms exhibited a higher corrosiveness towards the 2024 T3 aluminium alloy than aerobic microorganisms. The corrosion extent of microorganisms was significantly influenced by the types of microorganisms present, as evidenced by the presence of potential corrosion-inhibiting microorganisms within the biofilm. In mixed microbial contamination, aerobic microorganisms accelerated fuel degradation and rust formation. In contrast, anaerobic microorganisms, particularly co-culture systems of Desulfovibrio bizertensis and Methanosarcine barkeri accelerated the pitting of aluminium alloy. The galvanic electrochemical effect was considered to be an important indicator for characterizing the corrosion of aluminium materials in fuel-water systems.

RevDate: 2025-08-21

Tiwari A, Jaén-Gil A, Karavaeva A, et al (2025)

Antibiotic resistance genes, antibiotic residues, and microplastics in influent and effluent wastewater from treatment plants in Norway, Iceland, and Finland.

Environmental research pii:S0013-9351(25)01881-X [Epub ahead of print].

Monitoring antimicrobial resistance genes (ARGs) in wastewater influents (pre-treatment) and effluents (post-treatment) provides insights into community-level circulation, potential amplification during treatment, and risks associated with gene release into surface waters. Pollutants such as antibiotic residues and microplastics (MPs) may influence ARG dynamics, highlighting the need to assess their dynamics across wastewater environments. In this study, we analyzed ARGs and bacterial communities using Oxford Nanopore (ONP) metagenomics and qPCR in wastewater samples from Mekjarvik (Norway), Reykjavik (Iceland), and Mariehamn (Åland, Finland). Antibiotic residues were quantified via High-Performance Liquid Chromatography (HPLC), and MPs were characterized using Micro-Fourier Transform Infrared Spectroscopy (μ-FTIR) in Mekjarvik and Reykjavik. Metagenomic analysis identified 193 unique ARGs, with the highest average (±SD) in Reykjavik (66.3 ± 4.1), followed by Mekjarvik (61.3 ± 14.1) and Mariehamn (18.0 ± 2.2). ONP sequencing revealed that many ARGs were plasmid-associated, co-occurring with metal stress genes. Common plasmids were Col440I, IncQ2, and ColRNAI. Mercury-related genes dominated metal stress genes (64.9%), followed by multimetal (23.7%) and copper (6.4%). Of 45 antibiotics screened, only sulfamethoxazole and sulfapyridine were consistently detected. Polyethylene (∼60%) was the dominant MP type; Reykjavik influent had the highest MP load (8200 MPs/m[3]). While treatment reduced ARGs, antibiotic residues, and larger MPs, it was less effective against fine particles and key ARGs, including carbapenemase- and ESBL-associated genes. Clinically relevant ARGs and potential pathogens (e.g., Acinetobacter baumannii, Pseudomonas aeruginosa) persisted in effluents, highlighting risks to downstream ecosystems. These findings underscore the need for regular monitoring of both influents and effluents to assess treatment performance and safeguard environmental health.

RevDate: 2025-08-21

Shi Q, K Kristiansen (2025)

Spatial dissimilarity analysis in single-cell transcriptomics.

Cell reports methods pii:S2667-2375(25)00177-8 [Epub ahead of print].

We develop the spatial dissimilarity method to uncover complex bivariate relationships in single-cell and spatial transcriptomics data, addressing challenges such as alternative splicing and allele-specific gene expression. Applying this method to detect alternative splicing in neurons demonstrates improved accuracy and sensitivity compared to existing tools, notably identifying neuron subtypes. In tumor cells, spatial dissimilarity analysis reveals somatic variants that emerge during tumor progression, validated through whole-exome sequencing. These findings highlight how allele-specific genetic variants contribute to the subclone architecture of cancer cells, offering insights into cellular heterogeneity. Applied on a human cell atlas, we uncover numerous cases of allele-specific expression of genes in normal cells. We provide a software package for spatial dissimilarity analysis to enable enhanced understanding of cellular complexity and gene expression dynamics under homeostatic conditions and during states of transitions.

RevDate: 2025-08-21

He X, Gao Y, Zhang Y, et al (2025)

Distinct Gut Microbial Signatures and Diminished Anti-Inflammatory Effect of Short-Chain Fatty Acids in Schizophrenia With Immune Activation.

Schizophrenia bulletin pii:8239456 [Epub ahead of print].

BACKGROUND AND HYPOTHESIS: A subset of patients with schizophrenia (SCZ) exhibit subclinical immune activation. However, the gut microbial features of this subgroup and their interplay with the immune function remain poorly understood. This study aimed to identify the gut microbiome signature of immune-activated SCZ and elucidate the role of short-chain fatty acids (SCFAs) in the gut-immune crosstalk.

STUDY DESIGN: In this study, 297 patients with SCZ and 301 healthy controls (HCs) were assessed for 4 serum immune mediators. Immune-activated subgroups were classified based on these biomarkers. Fecal metagenomic sequencing, SCFA metabolomics, and in vitro peripheral blood mononuclear cells (PBMCs) stimulation experiments were performed to analyze the microbial composition, SCFA levels, and immune responses.

STUDY RESULTS: We found that 46.5% of the patients with SCZ exhibited elevated immune activation biomarker levels, which displayed unique bacterial signatures. Microbiome-based machine learning classifiers demonstrated robustness in SCZ and immune activation classification. Notably, microbial species abundance, functional metagenomics, and SCFA levels have confirmed an elevated capacity for SCFA production in patients with immune activation. Furthermore, in vitro PBMC stimulation experiments revealed a diminished anti-inflammatory effect of SCFAs in immune-activated patients when exposed to lipopolysaccharide-induced inflammation.

CONCLUSIONS: This study delineates the gut microbiome and SCFA metabolic profiles of immune-activated SCZ patients, revealing an association between gut microbiota dysbiosis, enhanced SCFA production capacity, and diminished anti-inflammatory effect of SCFA. These findings provide new insights into the underlying mechanisms and potential targeted treatments for SCZ patients with immune activation.

RevDate: 2025-08-21

Yang SB, Lu ZM, Shen HJ, et al (2025)

Unraveling Qu-aroma variation between inner and outer layers of medium-temperature Daqu: A multi-omics and sensory approach.

International journal of food microbiology, 442:111392 pii:S0168-1605(25)00337-X [Epub ahead of print].

Solid-state fermentation heterogeneity causes microenvironmental differences, shaping diverse microbial communities and metabolite compositions. Here, we aimed to investigate the variations in Qu-aroma between the inner (I-) and outer (O-) layers of medium-temperature Daqu (MT-Daqu) starter, and to analyze the differences in microbial communities as well as the associated metabolic pathways related to Qu-aroma volatile organic compounds (VOCs). Firstly, quantitative descriptive analysis revealed that the I-layer exhibited intensified rancid-roasted notes, whereas the O-layer showed stronger grain and woody notes. Secondly, a total of 225 VOCs were identified from 88 inner and outer layer samples using HS-SPME-GC-MS, among which 43 differential VOCs were confirmed between the layers (VIP > 1, P < 0.05, and Fold change ≥1.5 or ≤0.67). Thin film (TF)-SPME-GC-O/MS revealed 52 and 47 odors with corresponding VOCs in the I- and O-layers, respectively. Subsequently, cross-referencing metagenomic and metabolic databases revealed that 37 aroma-active VOCs were functionally linked to six metabolic modules within the MT-Daqu microbial metabolic network. Finally, integrated metagenomic and amplicon sequencing identified potential functional microorganisms associated with specific metabolic modules. Five genera, including Kroppenstedtia and Thermomyces, were identified as characteristic of the I-layer, while 22 genera, such as Lactobacillus and Saccharomycopsis, were characteristic of the O-layer. Notably, Kroppenstedtia, Thermomyces, Lactobacillus, Saccharomycopsis, and Weissella were ubiquitously associated with all six metabolic modules across both layers of MT-Daqu. This study delivers a perspective for clarifying the spatial heterogeneity of Qu-aroma and its microbial drivers.

RevDate: 2025-08-21
CmpDate: 2025-08-21

Xie T, Lin D, Cai XD, et al (2025)

Nano-biochar regulates phage-host interactions, reducing antibiotic resistance genes in vermicomposting systems.

Proceedings of the National Academy of Sciences of the United States of America, 122(34):e2511986122.

Biochar amendment reshapes microbial community dynamics in vermicomposting, but the mechanism of how phages respond to this anthropogenic intervention and regulate the dissemination of antibiotic resistance genes (ARGs) remains unclear. In this study, we used metagenomics, viromics, and laboratory validation to explore how nano-biochar affects phage-host interactions and ARGs dissemination in vermicomposting. Our results revealed distinct niche-specific phage life strategies. In vermicompost, lytic phages dominated and used a "kill-the-winner" strategy to suppress antibiotic-resistant bacteria (ARB). In contrast, lysogenic phages prevailed in the earthworm gut, adopting a "piggyback-the-winner" strategy that promoted ARGs transduction through mutualistic host interactions. Nano-biochar induced the conversion of lysogenic to lytic phages in the earthworm gut, while concurrently reducing the abundance of lysogenic phages and their encoded auxiliary metabolic genes carried by ARB. This shift disrupted phage-host mutualism and inhibited ARGs transmission via a "phage shunting" mechanism. In vitro validation with batch culture experiments further confirmed that lysogenic phages increased transduction of ARGs in the earthworm gut, while nano-biochar reduced the spread of ARGs by enhancing lysis infectivity. Our study constructs a mechanistic framework linking nano-biochar induced shifts in phage lifestyles that suppress ARG spread, offering insights into phage-host coadaptation and resistance mitigation strategies in organic waste treatment ecosystems.

RevDate: 2025-08-21

Hashimoto K, Fukushima K, Matsumoto Y, et al (2025)

Molecular epidemiological surveillance for non-tuberculous mycobacterial pulmonary disease: a single-center prospective cohort study.

Microbiology spectrum [Epub ahead of print].

UNLABELLED: Bacterial species cultured from sputum change during treatment or observation for non-tuberculous mycobacterial pulmonary disease; however, strain-level changes remain unrecognized. Variable number tandem repeat typing is a standard technique for strain identification; nonetheless, its labor-intensive and time-consuming nature limits routine clinical use. Therefore, we aimed to elucidate species-subspecies and strain dynamics in non-tuberculous mycobacteria and develop a simple sequence-based strain-level determination method. We performed a single-center prospective cohort study of 112 patients with non-tuberculous mycobacterial pulmonary disease. Whole-genome sequencing was performed on two sputum samples collected at enrollment and at the end of follow-up, followed by variable number tandem repeat (VNTR) typing. We also developed a simple long-read sequencing-based digital VNTR (dVNTR) typing method and evaluated its efficacy. Our results demonstrate that core genome multi-locus sequencing typing revealed species/subspecies changes in 13 patients (11.6%); VNTR typing detected strain changes in 16 patients (14.3%) without species/subspecies changes. Overall, pathogen shifts occurred in 29 patients (shift [+] group, 25.9%), whereas 83 had no detectable pathogen shift (shift [-] group, 74.1%). Interestingly, macrolide and amikacin susceptibility changed in both groups, but resistance remained higher in shift (-) patients. dVNTR results aligned with those of conventional VNTR typing. In conclusion, since susceptibility factors remain unclear, routine species/subspecies identification and molecular typing, such as VNTR, are optimal for patient care. Core genome multi-locus sequencing typing with a dVNTR identified pathogen shifts, innovating non-tuberculous mycobacterial pulmonary disease management.Clinical TrialsThis study is registered with UMIN as UMIN 000056067.

IMPORTANCE: Pulmonary non-tuberculous mycobacterial disease is a chronic infection in which the causative pathogens may change at the species, subspecies, or strain level over time. Accurate tracking of these changes is essential for optimizing treatment; however, conventional clinical practice lacks efficient methods for monitoring such dynamics. Our study revealed pathogen changes in approximately one-quarter of patients over 1.5 years, prompting the development of a novel surveillance system that integrates next-generation sequencing for both species-subspecies identification and strain-level molecular epidemiology. This innovation enables real-time monitoring of pathogen dynamics, allowing clinicians to promptly adjust treatment strategies and improve patient care through more informed decision-making.

RevDate: 2025-08-21
CmpDate: 2025-08-21

Gao X, Zheng Y, Chang H, et al (2025)

Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis.

Journal of medical virology, 97(8):e70570.

Rheumatoid arthritis (RA) is a chronic autoimmune disease whose exact pathogenesis remains unclear, despite links to genetics, environmental factors, and microbial dysbiosis. Recent studies have highlighted the role of the microbiome in RA, yet the contribution of the tonsil virome remains unexplored. This study aims to investigate whether changes in the tonsil virome are associated with RA progression and assess its diagnostic potential. Using metagenomic data from 32 RA patients and 30 healthy controls (HCs), we identified 45 782 viral operational taxonomic units (vOTUs), with 14 341 classified as core vOTUs. RA patients exhibited significantly reduced virome richness and diversity, whereas Siphoviridae and Microviridae dominated both groups. Statistical analysis identified 235 RA-associated viral markers, including 13 enriched in RA and 222 in HCs. RA-enriched markers were primarily bacteriophages infecting Streptococcaceae, whereas HCs displayed more diverse viral-host interactions. Random forest models demonstrated strong discriminatory power of viral markers in distinguishing RA patients from HCs, achieving an AUC of 0.960, outperforming bacterial markers. Correlation analyses further linked viral markers to immune cell subsets, suggesting that tonsil virome alterations may influence immune dysregulation in RA. This study reveals significant changes in the tonsil virome of RA patients, highlighting its potential as a diagnostic tool and offering new insights into RA pathogenesis. These findings pave the way for future research into the virome's role in autoimmune diseases and therapeutic development.

RevDate: 2025-08-21

Acharya SM, Yang Y, Enalls BC, et al (2025)

Unraveling the ecological success of Iodidimonas in a bioreactor treating oil and gas produced water.

Microbiology spectrum [Epub ahead of print].

UNLABELLED: Iodidimonas sp., a bacterium found in bioreactors treating oil and gas produced water as well as iodide-rich brines, has garnered attention for its unique ability to oxidize iodine. However, little is known about the metabolic capabilities that enable Iodidimonas sp. to thrive in certain unique ecological niches. In this study, we isolated, characterized, and sequenced three strains belonging to the Iodidimonas genus from the sludge of a membrane bioreactor used for produced water treatment. We investigated the genomic features of these isolates and compared them with the four publicly available isolate genomes from this genus, as well as a metagenome-assembled genome from the source bioreactor. Our Iodidimonas isolates had several genes associated with mitigating salinity, heavy metal, and organic compound stress, which likely help these bacteria to survive in produced water. Phenotyping tests revealed that while the isolates could utilize a wide variety of simple carbon substrates, they failed to degrade aliphatic or aromatic hydrocarbons, consistent with the lack of genes associated with common hydrocarbon degradation pathways in their genomes. We hypothesize that these microbes may lead a scavenging lifestyle in the bioreactor and similar iodide-rich brines.

IMPORTANCE: Occupying a niche habitat and having few representative isolates, the genus Iodidimonas is a relatively understudied alphaproteobacterial group. Its ability to corrode pipes in iodine production facilities has economic implications, and its ability to generate potentially carcinogenic iodinated organic compounds during treatment of oil and gas produced water may cause environmental and health concerns with the recycling of treated water. Therefore, detailed characterization of the metabolic potential of the Iodidimonas isolates in this study both sheds light on their adaptation to the environmental conditions they inhabit and has environmental and economic significance.

RevDate: 2025-08-21

Fang J, Chen Z, Yu Z, et al (2025)

Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils.

The ISME journal pii:8239162 [Epub ahead of print].

The environmental dissemination of antibiotic resistance genes (ARGs), particularly in manure-amended soils, poses a growing threat to public health due to the potential transfer of ARGs to humans and animals. Effective strategies are urgently needed to mitigate ARG spread in agricultural settings. Biochar, an eco-friendly soil amendment, shows promise for pollution control, yet its role in suppressing ARG horizontal gene transfer remains unclear. Here, metagenomic analysis showed that manure application significantly increased the relative abundance of ARGs in soil microbiota, whereas biochar amendment reduced it. To determine whether biochar suppresses ARG dissemination by inhibiting horizontal transfer, we established a soil microcosm. Manure application increased the conjugative transfer ratio by 3-fold, whereas biochar effectively suppressed this transfer reducing it to levels observed in unamended soils. Cell sorting and 16S rRNA gene amplicon sequencing demonstrated that biochar treatment reduced the diversity of transconjugant pools at both phylum and genus level. Transconjugants were primarily affiliated with Pseudomonadota, Bacillota, and Actinomycetota, with Massilia, Delftia, and Ammoniphilus being the most abundant genera in biochar treatment soil. Mechanistic investigations revealed that biochar-mediated inhibition of ARG transfer was linked to reduced ATP energy supply, decreased reactive oxygen species production, and lower cell membrane permeability, and diminished bioavailability of heavy metals and antibiotics. Additionally, biochar altered soil enzyme activity and microbial community structure, further limiting ARG dissemination. The findings provide insights into biochar-induced mitigation of ARG spread in manure-amended soils and highlight its potential as an effective strategy for controlling environmental ARG transmission.

RevDate: 2025-08-21

Li Q, Zhang L, Li R, et al (2025)

Metagenomics-based analysis of microbial community dynamics and flavor compound correlations during rice-flavor Baijiu brewing.

Frontiers in bioengineering and biotechnology, 13:1638716.

This study aimed to explore the microbial contribution to flavor compound production by analysing the succession patterns and metabolic functional characteristics of microbial communities during Jiuqu preparation, saccharification, and fermentation processes of rice-flavor Baijiu (RFB). The physicochemical parameters during RFB fermentation were systematically monitored, and the volatile flavor profile was characterized using headspace solid-phase microextraction gas chromatography‒mass spectrometry (HS-SPME-GC-MS). Concurrently, metagenomic sequencing was employed to elucidate the microbial community structure and its temporal dynamics throughout the fermentation process. The results of the physicochemical parameters revealed that the reducing sugar content peaked at the end of saccharification and subsequently decreased throughout fermentation, whereas the total acid and total ester contents progressively increased, reaching maximum levels at the fermentation endpoint and maintaining stability. HS-SPME-GC-MS analysis revealed 84 volatile flavor compounds including phenylethanol, ethanol, dimethyl ether, isopentyl alcohol, and acetic acid. Notably, compounds such as L-ethyl lactate, diethyl succinate, and isobutanol were initially synthesized during saccharification and subsequently accumulated during fermentation, emerging as major flavor constituents. Ascomycota and Mucoromycota dominated the fungal community (average relative abundance >1%), whereas Firmicutes and Proteobacteria prevailed among the bacterial phyla. Six genera, Lichtheimia, Kluyveromyces, Lacticaseibacillus, Lactobacillus, Limosilactobacillus, and Schleiferilactobacillus were identified as primary contributors to flavor production during fermentation. Functional analysis revealed that microbial metabolism in fermented mash primarily involved amino acid and carbohydrate metabolism, with glycoside hydrolases (GHs) and glycosyl transferases (GTs) serving as key carbohydrate-active enzymes. This study could improve the comprehensive understanding of the brewing mechanism of RFB and provide a theoretical basis for the development and utilization of microbial resources in the fermented grains and the improvement of RFB quality.

RevDate: 2025-08-21
CmpDate: 2025-08-21

Wang X, Dong Q, Huang P, et al (2025)

The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.

Microbiome, 13(1):188.

BACKGROUND: Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities.

RESULTS: Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral operational taxonomic units (vOTUs), nearly 90% of which are likely absent from current databases. Analysis of single-nucleotide variations (SNVs) in 233 globally prevalent vOTUs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. Video Abstract CONCLUSIONS: Our analysis underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.

RevDate: 2025-08-21
CmpDate: 2025-08-21

Gao H, Li B, Guo Z, et al (2025)

Highly accurate prophage island detection with PIDE.

Genome biology, 26(1):254.

As important mobile elements in prokaryotes, prophages shape the genomic context of their hosts and regulate the structure of bacterial populations. However, it is challenging to precisely identify prophages through computational methods. Here, we introduce PIDE for identifying prophages from bacterial genomes or metagenome-assembled genomes. PIDE integrates a pre-trained protein language model and gene density clustering algorithm to distinguish prophages. Benchmarking with induced prophage sequencing datasets demonstrates that PIDE pinpoints prophages with precise boundaries. Applying PIDE to 4744 human gut representative genomes reveals 24,467 prophages with widespread functional capacity. PIDE is available at https://github.com/chyghy/PIDE , with model training code at https://zenodo.org/records/16457629 .

RevDate: 2025-08-21
CmpDate: 2025-08-21

Wibberg D, Bakuła Z, García-Cunchillos I, et al (2025)

Complete mitochondrial genomes of the Prototheca genus: comparative genomics and evolutionary insights.

BMC genomics, 26(1):766.

BACKGROUND: Prototheca (Chlorophyta: Trebouxiophyceae) is a genus of non-photosynthetic microalgae that causes increasingly frequent infections in both humans and animals, collectively referred to as protothecosis The genetic landscape of the Prototheca algae has remained largely uncharted until recent advances in sequencing and genomics. In this study, a combination of Illumina and Oxford Nanopore technologies was employed for sequencing of 18 mitochondrial genomes, representing all currently recognized Prototheca species.

RESULTS: The genomes differed in terms of size and GC content, ranging from 38 kbp to 68 kbp and from 25 to 30%, respectively. The gene content and gene order within the mitochondrial DNA exhibited specific characteristics. The gene content was conserved but showed variable number of hypothetical proteins and a clustering tendency for nad genes. Noteworthy, most genes were located on the clockwise strand, with type I introns, containing long open reading frames encoding homing endonucleases, suggesting a mechanism for intron mobility and genome plasticity. Comparative genomic analyses and phylogenetic classification across the 21 core genes showed a close relationship between the mitochondrial genomes, as evidenced by average nucleotide identity (ANI) and average amino acid identity (AAI), supportive for the current cytb gene-based taxonomy. The phylogenetic tree constructed from concatenated alignments of the core genes confirmed the presence of three distinct Prototheca clades, indicating the polyphyletic nature of the genus.

CONCLUSIONS: In conclusion, this work provides another important step toward elucidating the genetics of Prototheca algae, serving as a framework for future studies on the phylogeny and evolution of these peculiar microorganisms.

RevDate: 2025-08-20

Weber J, Hillen M, Seuberlich T, et al (2025)

Successful implementation of a risk assessment and mitigation program to control bovine digital dermatitis at the herd-level.

Scientific reports, 15(1):30577.

UNLABELLED: This nonrandomized clinical intervention study was designed as a prospective, multicenter group comparison to evaluate the efficacy of a risk assessment and mitigation program to control bovine digital dermatitis (BDD). The program was implemented over a 1-year period on 9 intervention (INT) farms and 10 control (CTR) farms. Mainstays of the program derived from results of a previous BDD risk factor analysis. All farms were visited monthly to assess within-herd BDD prevalences to perform risk assessments and to treat BDD lesions with salicylic acid paste. Bulk milk samples were collected every 4 months. Diagnosis of BDD was based on visual inspection (clinical scoring) of the feet. Risk-associated management practices were identified on each farm, and management changes expected to prevent further introduction or spread of BDD within INT farms were suggested and agreed upon with farmers of the INT farms. Lesional biopsies were taken from a subset of cows of the INT group before and 2 months after treatment for histopathological and molecular biological examination to confirm histological and bacteriological cure in addition to clinical cure. The initial BDD prevalences for the INT and CTR farms averaged 39.8% (IQR 16.2) and 41.0% (IQR 12.4) for overall BDD lesions, 25.9% (IQR 10.8) and 26.2% (IQR 14.5) for active BDD lesions, and 22.1% (IQR 6.9) and 23.7% (IQR 22.3) for chronic BDD lesions, respectively. After 1 year of implementation, overall BDD prevalences were reduced to 14.1% (IQR 8.2) on INT farms but remained at 41.6% (IQR 10.8) on CTR farms. A significant decline in bulk milk anti-Treponema antibodies over the 1-year period was found in INT as compared to CTR farms. Considering the results of the histopathological examination, of 16S metagenomic sequencing and of the Fluorescence in situ hybridization as indicators for healing, 6/7 (85.7%) selected lesions were cured 2 months post completion of treatment. The results of this study show that the described BDD control measures can markedly reduce the within-herd prevalence of BDD. The proposed procedure might provide the basis for a nationwide BDD mitigation program that could be of importance also beyond national borders.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-12093-5.

RevDate: 2025-08-20

He G, Wang W, Chen G, et al (2025)

A novel bacterial protein family that catalyses nitrous oxide reduction.

Nature [Epub ahead of print].

Nitrous oxide (N2O), a driver of global warming and climate change, has reached unprecedented concentrations in Earth's atmosphere[1]. Current N2O sources outpace N2O sinks, emphasizing the need for comprehensive understanding of processes that consume N2O. Microbes that express the enzyme N2O reductase (N2OR) convert N2O to climate change-neutral dinitrogen (N2). Known N2ORs belong to the canonical clade I and clade II NosZ reductases and are considered key enzymes for N2O reduction[2-4]. Here we report a previously unrecognized protein family with a role in N2O reduction, clade III lactonase-type N2OR (L-N2OR), which diverges in sequence from canonical NosZ but conserves three-dimensional protein structural features. Integrated physiological, metagenomic, proteomic and structural modelling studies demonstrate that L-N2ORs catalyse N2O reduction. L-N2OR genes occur in several phyla, predominantly in uncultured taxa with broad geographic distribution. Our findings expand the known diversity of N2ORs and implicate previously unrecognized taxa (for example, Nitrospinota) in N2O consumption. The expansion of N2OR diversity and the identification of a novel type of catalyst for N2O reduction advances the understanding of N2O sinks, has implications for greenhouse gas emission and climate change modelling, and expands opportunities for innovative biotechnologies aimed at curbing N2O emissions[5,6].

RevDate: 2025-08-20
CmpDate: 2025-08-20

Chuchaona W, Izquierdo-Lara RW, Schapendonk CME, et al (2025)

Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand.

Scientific reports, 15(1):30672.

Acute gastroenteritis (AGE) remains a significant global health concern, with noroviruses among the most prevalent viral pathogens. However, other enteric viruses also contribute substantially to the public health burden. This study provides the first molecular characterization of a co-infection involving a rarely reported enterovirus A76 (EV-A76) and a norovirus GI.6[P11] in a patient from Thailand. Metagenomic sequencing successfully identified complete viral genomes, revealing unique genetic variations. Phylogenetic analysis demonstrated that the EV-A76 strain shares high nucleotide similarity with a recently reported strain from Nepal, distinguishing it from previously identified recombinant strains. The amino acid sequence alignment of the complete EV-A76 genome revealed several distinctive amino acid substitutions compared to the most closely related strains. Notably, variations in the VP1 C-terminus and VP2 EF loop, known for high variability, were observed. These regions, crucial for epitope formation, are particularly susceptible to high-frequency mutations. This study reports the first documented co-infection of EV-A76 and norovirus GI.6[P11] in a single sample, identified through metagenomic sequencing in an AGE case in Thailand in 2023. The observed genetic variations highlight the necessity for ongoing monitoring of viral diversity to strengthen genomic surveillance and inform prevention strategies, especially for emerging pathogens with significant public health implications.

RevDate: 2025-08-20

Liu Q, Wang M, Xie JW, et al (2025)

Macrogenome Analysis of Rodents from Heilongjiang Province, China.

Acta tropica pii:S0001-706X(25)00260-8 [Epub ahead of print].

Rodents are carriers and hosts of numerous zoonotic pathogens, analysing the diversity of viruses and bacteria carried by rodents is important for predicting and reducing the risk of future outbreaks of zoonotic diseases. Heilongjiang is a border province in China with rich ecological resources. In this study, we characterized the zoonotic microbiota (viruses and bacteria) in wild rodents. Sixty-seven rodents representing two species (20 Apodemus peninsulae; 47 Myodes rufocanus) were collected in Hengdaohezi Town, Heilongjiang Province, China. Metagenomic sequencing was employed to characterize pathogen carriage in these reservoirs. The sequencing results showed that the annotated viruses covered 21 viral families, including family Arenaviridae and family Hantaviridae. The annotated bacteria cover 1051 bacterial genera, including genus Salmonella and genus Yersinia. Results of de novo assembly of extracted viral sequences using Megahit showed that 154 contigs were assembled from these two hosts, and 110 of these contigs were mapped to 19 viruses from eight families, including Rat arterivirus1, Amur virus and Lassa mammarenavirus, these results can provide a certain reference for the monitoring and control of rodents in Heilongjiang Province.

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ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin and even a collection of poetry — Chicago Poems by Carl Sandburg.

Timelines

ESP now offers a large collection of user-selected side-by-side timelines (e.g., all science vs. all other categories, or arts and culture vs. world history), designed to provide a comparative context for appreciating world events.

Biographies

Biographical information about many key scientists (e.g., Walter Sutton).

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 28 JUL 2024 )