@article {pmid40851063,
year = {2025},
author = {Suppiah, J and Zulkifli, MMS and Adiee, AH and Zainudin, NAZ and Dukut Soeharto, ME and Ramli, N and Wan, MK and Sulong, MR and Suli, Z and Mohd Zain, R},
title = {Genomic evidence links human dengue cases with undetermined serotypes to sylvatic lineages.},
journal = {Tropical medicine and health},
volume = {53},
number = {1},
pages = {114},
pmid = {40851063},
issn = {1348-8945},
abstract = {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.},
}

@article {pmid40850953,
year = {2025},
author = {Tang, M and Li, C and Ge, X and Kuang, Y and Qiu, L and Chan, KC and Chen, Z and Guo, L and Zhao, Z and Zhang, B and Liu, S and Zhou, X},
title = {Honeybee-Gilliamella synergy in carbohydrate metabolism enhances host thermogenesis in cold acclimation.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {172},
pmid = {40850953},
issn = {2055-5008},
support = {RDF-23-01-067//Research Development Fund of Xi'an Jiaotong-Liverpool University/ ; 2023YFD2201804//Program of the Ministry of Science and Technology of China/ ; 2023YFD2201804//Program of the Ministry of Science and Technology of China/ ; 32470455//National Natural Science Foundation of China/ ; 2023IOZ0104//program from Institute of Zoology, Chinese Academy of Sciences/ ; No.SYND-2021-30//Program from the Sanya Institute of China Agricultural University/ ; },
mesh = {Animals ; Bees/microbiology/physiology ; *Carbohydrate Metabolism ; Cold Temperature ; *Acclimatization ; *Thermogenesis ; Gastrointestinal Microbiome ; Glucose/metabolism ; Symbiosis ; Metagenomics ; Metabolomics ; Pyruvic Acid/metabolism ; },
abstract = {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.},
}

Animals
Bees/microbiology/physiology
*Carbohydrate Metabolism
Cold Temperature
*Acclimatization
*Thermogenesis
Gastrointestinal Microbiome
Glucose/metabolism
Symbiosis
Metagenomics
Metabolomics
Pyruvic Acid/metabolism

@article {pmid40850684,
year = {2025},
author = {Lei, G and Han, Z and Wang, X and Malacrinò, A and Kang, T and Zhang, D and Zhang, J and Zhang, Z and Wu, H},
title = {Synthetic microbial communities rescues strawberry from soil-borne disease by enhancing soil functional microbial abundance and multifunctionality.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.040},
pmid = {40850684},
issn = {2090-1224},
abstract = {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.},
}

@article {pmid40850647,
year = {2025},
author = {Rieber, H},
title = {Re: 'Diagnostic accuracy of 16S rDNA PCR, Multiplex PCR and Metagenomic Next-Generation Sequencing in Periprosthetic Joint Infections' by Olearo et al.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.08.021},
pmid = {40850647},
issn = {1469-0691},
}

@article {pmid40850580,
year = {2025},
author = {Chalwatzis, L and Cruyssen, CV and Mazzini, I and Morandini, A and Mautner, A and Vielnascher, R and Guebitz, GM and Ribitsch, D},
title = {Depolymerisation of waste- and bio-based polyesters by an activated sludge hydrolase.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133186},
doi = {10.1016/j.biortech.2025.133186},
pmid = {40850580},
issn = {1873-2976},
abstract = {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.},
}

@article {pmid40850300,
year = {2025},
author = {Gupta, S and Chauhan, R and Pandey, S},
title = {Biopriming with halotolerant microbes enhances growth performance, resilience and rhizospheric microbial diversity of Solanum melongena under saline conditions.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt A},
pages = {110400},
doi = {10.1016/j.plaphy.2025.110400},
pmid = {40850300},
issn = {1873-2690},
abstract = {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.},
}

@article {pmid40849730,
year = {2025},
author = {Zhou, SY and Lie, Z and Lei, C and Zhang, Q and Liu, X and Wu, G and Neilson, R and Huang, FY and Chu, G and Meng, Z and Zhu, D and Tissue, DT and Peñuelas, J and Liu, J},
title = {Multi-Scale Evidence for Declining Microbial Carbon Fixation Along Forest Succession Gradients.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf191},
pmid = {40849730},
issn = {1751-7370},
abstract = {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.},
}

@article {pmid40849632,
year = {2025},
author = {Jang, S and Lee, EJ and Park, S and Lim, H and Ahn, B and Huh, Y and Koh, H and Park, YR},
title = {Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {189},
pmid = {40849632},
issn = {2049-2618},
mesh = {Humans ; *Crohn Disease/microbiology/genetics/pathology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Child ; Male ; *Bacteria/classification/genetics/isolation & purification ; Female ; *Ileum/microbiology/pathology ; Prospective Studies ; Adolescent ; Transcriptome ; Gene Expression Profiling ; Metagenome ; Computational Biology/methods ; *Host Microbial Interactions/genetics ; },
abstract = {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.},
}

Humans
*Crohn Disease/microbiology/genetics/pathology
*Gastrointestinal Microbiome/genetics
Case-Control Studies
Child
Male
*Bacteria/classification/genetics/isolation & purification
Female
*Ileum/microbiology/pathology
Prospective Studies
Adolescent
Transcriptome
Gene Expression Profiling
Metagenome
Computational Biology/methods
*Host Microbial Interactions/genetics

@article {pmid40849498,
year = {2025},
author = {Feng, Y and Shi, J and Li, Z and Li, Y and Yang, J and Huang, S and Zheng, J and Han, W and Qiao, Y and Zhang, J and Liu, Q and Yang, Y and Hu, C and Wu, L and Zhang, X and Tang, J and Huang, X and Ma, P},
title = {Discovery of CRISPR-Cas12a clades using a large language model.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7877},
pmid = {40849498},
issn = {2041-1723},
support = {23HC1400700//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; 32161133022//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22177073//National Natural Science Foundation of China (National Science Foundation of China)/ ; 24141901302//Shanghai Science and Technology Development Foundation (Shanghai Science and Technology Development Fund)/ ; },
mesh = {*CRISPR-Cas Systems/genetics ; *CRISPR-Associated Proteins/genetics/metabolism/chemistry/classification ; *Bacterial Proteins/genetics/metabolism/chemistry ; Machine Learning ; *Endodeoxyribonucleases/genetics/metabolism/chemistry ; Polymorphism, Single Nucleotide ; Cryoelectron Microscopy ; Large Language Models ; },
abstract = {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.},
}

*CRISPR-Cas Systems/genetics
*CRISPR-Associated Proteins/genetics/metabolism/chemistry/classification
*Bacterial Proteins/genetics/metabolism/chemistry
Machine Learning
*Endodeoxyribonucleases/genetics/metabolism/chemistry
Polymorphism, Single Nucleotide
Cryoelectron Microscopy
Large Language Models

@article {pmid40849482,
year = {2025},
author = {Zhang, Y and Liao, YT and Liu, F and Li, RW and Wu, VCH},
title = {Impact of diet in shaping gut virome of grain-fed and grass-fed beef cattle revealed by a comparative metagenomic study.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {190},
pmid = {40849482},
issn = {2049-2618},
support = {2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; },
mesh = {Animals ; Cattle ; *Virome/genetics ; Metagenomics/methods ; *Animal Feed/analysis ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Viruses/classification/genetics/isolation & purification ; *Poaceae ; *Diet/veterinary ; *Edible Grain ; },
abstract = {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.},
}

Animals
Cattle
*Virome/genetics
Metagenomics/methods
*Animal Feed/analysis
*Gastrointestinal Microbiome/genetics
Feces/virology
*Viruses/classification/genetics/isolation & purification
*Poaceae
*Diet/veterinary
*Edible Grain

@article {pmid40848995,
year = {2025},
author = {Wang, J and Xue, L and Zhang, M and Shen, P and Zhao, W and Tong, Q and Wu, S and Dai, W and Yang, X and Wang, H},
title = {Colonoscopic fecal microbiota transplantation for Mild-to-Moderate Parkinson's Disease: A randomized controlled trial.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106086},
doi = {10.1016/j.bbi.2025.106086},
pmid = {40848995},
issn = {1090-2139},
abstract = {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.},
}

@article {pmid40848874,
year = {2025},
author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Petersen, AM and Holzknecht, BJ and Westh, H and Rosenberg, J},
title = {A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102675},
doi = {10.1016/j.clinre.2025.102675},
pmid = {40848874},
issn = {2210-741X},
abstract = {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).},
}

@article {pmid40848630,
year = {2025},
author = {Zhang, L and Zhang, Y and Huang, J and Zhou, R and Wu, C},
title = {Temperature-driven functional microbial interactions in soy sauce fermentation: Effects of Zygosaccharomyces rouxii and Wickerhamiella versatilis on flavor enrichment and biogenic amine reduction.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111399},
doi = {10.1016/j.ijfoodmicro.2025.111399},
pmid = {40848630},
issn = {1879-3460},
abstract = {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.},
}

@article {pmid40848515,
year = {2025},
author = {Ni, J and Fu, L and Xiao, J and Li, C and Wu, X and Yuan, Z and Wang, J and Tang, S and Deng, F and Shen, S},
title = {Metagenomic evidence of viral secretion from tick salivary glands to saliva: implications for potential horizontal transmission.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {5},
pages = {102540},
doi = {10.1016/j.ttbdis.2025.102540},
pmid = {40848515},
issn = {1877-9603},
abstract = {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.},
}

@article {pmid40848105,
year = {2025},
author = {Proskynitopoulos, PJ and Woltemate, S and Rhein, M and Böke, I and Molks, J and Schröder, S and Schneider, HU and Bleich, S and Frieling, H and Geffers, R and Glahn, A and Vital, M},
title = {The effect of alcohol withdrawal therapy on gut microbiota in alcohol use disorder and its link to inflammation and craving.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70128},
pmid = {40848105},
issn = {2993-7175},
support = {//Hetzler Foundation for Addiction Research and Prevention/ ; },
abstract = {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.},
}

@article {pmid40848091,
year = {2025},
author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W},
title = {RNA-viromics unveils diverse RNA viral communities in Large-billed crows and Northern Ravens.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {40848091},
issn = {1572-994X},
support = {grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; grant No. 2022-HZ-812//program of science and technology international cooperation project of Qinghai province/ ; },
abstract = {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.},
}

@article {pmid40847462,
year = {2025},
author = {Ma, H and Wang, M and Feng, Y and Zhang, W and Wang, W and Xie, Y and Kong, G and Feng, J and Wang, P and Wang, Q and Huang, X},
title = {Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70105},
pmid = {40847462},
issn = {2211-5463},
support = {GSWSKY2020-50//Gansu Provincial Health Commission, Provincial Health Industry Research Project/ ; 20240050058//Lanzhou University Student Innovation and Entrepreneurship Action Plan Project/ ; CY2023-QN-B17//Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University in 2023/ ; },
abstract = {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.},
}

@article {pmid40847380,
year = {2025},
author = {Wang, X and Liu, J and Chai, B and Wu, T},
title = {Protozoa-driven micro-food webs shaping carbon and nitrogen cycling in reservoir ecosystems.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {109},
pmid = {40847380},
issn = {2524-6372},
support = {YDZJSX2022B001//Shanxi Provincial Central Guidance Special Project/ ; 202304041101020//Science and Technology Cooperation and Exchange Special Project of Shanxi Province/ ; U23A20157//Key Project of the National Natural Science Foundation of China Joint Fund for Regional Innovation and Development/ ; },
abstract = {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.},
}

@article {pmid40847349,
year = {2025},
author = {Li, X and Liu, J},
title = {Molecular diagnostic technology: beyond analytical accuracy.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {382},
pmid = {40847349},
issn = {1466-609X},
mesh = {Humans ; *Molecular Diagnostic Techniques/methods/standards/trends ; Multiplex Polymerase Chain Reaction/methods/standards ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; },
abstract = {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.},
}

Humans
*Molecular Diagnostic Techniques/methods/standards/trends
Multiplex Polymerase Chain Reaction/methods/standards
High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity

@article {pmid40847308,
year = {2025},
author = {Wan, S and Li, M and Li, W and Ren, Y and Wu, Y and Luo, Q and Gong, W},
title = {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.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {129},
pmid = {40847308},
issn = {1475-2891},
support = {82401448//National Natural Science Foundation of China/ ; 2021A1515110799//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20240813145414019//Shenzhen Science and Technology Program/ ; NSZD2024015//Shenzhen Nanshan District Science and Technology Plan Funding Program/ ; },
}

@article {pmid40847279,
year = {2025},
author = {Azmi, MAI and William-Dee, J and Morni, MA and Azhar, NAA and Sabarudin, NA and Jinggong, ER and Zolkapley, S and Baharom, NIM and Haqeem, MD and Sien, VL and Mohamad Azmi, AH and Adrus, M and Tan, CS and Khan, FAA},
title = {Metagenomic insights into host-specific gastroenteritis bacteria in forest rodents of Sarawak, Borneo: implications for one health surveillance of rodent-borne pathogens.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {531},
pmid = {40847279},
issn = {1471-2180},
support = {GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; F07/PGRG/2046/2020//Postgraduate Research Grant, UNIMAS/ ; },
mesh = {Animals ; *Gastroenteritis/microbiology/veterinary ; Borneo/epidemiology ; Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Forests ; *Rodentia/microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; One Health ; Host Specificity ; Phylogeny ; Zoonoses/microbiology ; DNA, Bacterial/genetics ; Disease Reservoirs/microbiology ; *Rodent Diseases/microbiology ; },
abstract = {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.},
}

Animals
*Gastroenteritis/microbiology/veterinary
Borneo/epidemiology
Feces/microbiology
*Bacteria/genetics/classification/isolation & purification
Forests
*Rodentia/microbiology
Humans
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
One Health
Host Specificity
Phylogeny
Zoonoses/microbiology
DNA, Bacterial/genetics
Disease Reservoirs/microbiology
*Rodent Diseases/microbiology

@article {pmid40847264,
year = {2025},
author = {Shinge, SAU and Zhang, B and Zheng, B and Qiang, Y and Ali, HM and Melchiade, YTV and Zhang, L and Gao, M and Feng, G and Zeng, K and Yang, Y},
title = {Unveiling the Future of Infective Endocarditis Diagnosis: The Transformative Role of Metagenomic Next-Generation Sequencing in Culture-Negative Cases.},
journal = {Journal of epidemiology and global health},
volume = {15},
number = {1},
pages = {108},
pmid = {40847264},
issn = {2210-6014},
support = {GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Endocarditis/diagnosis/microbiology ; },
abstract = {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.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Endocarditis/diagnosis/microbiology

@article {pmid40841623,
year = {2025},
author = {Zhang, Y and Ma, Y and Yue, R and Meng, Y and Jin, Y and Yin, C and Zhou, Q and Shi, R},
title = {Meningitis caused by Aspergillus fumigatus: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1051},
pmid = {40841623},
issn = {1471-2334},
abstract = {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.},
}

@article {pmid40846880,
year = {2025},
author = {Kotrbová, L and Grabicová, K and Švecová, H and Staňová, AV and Petrlíková, M and Grabic, R and Kodešová, R and Chroňáková, A},
title = {The effect of WWTP products amendments on Phaseolus vulgaris rhizosphere and its ability to inactivate clarithromycin.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30950},
pmid = {40846880},
issn = {2045-2322},
support = {QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; 063/2023/P//Grantová agentura Jihočeské univerzity v Českých Budějovicích/ ; },
mesh = {*Rhizosphere ; *Phaseolus/microbiology/drug effects/growth & development ; *Clarithromycin/pharmacology/metabolism ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Wastewater/chemistry ; Phylogeny ; Microbiota/drug effects ; },
abstract = {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.},
}

*Rhizosphere
*Phaseolus/microbiology/drug effects/growth & development
*Clarithromycin/pharmacology/metabolism
Soil Microbiology
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Wastewater/chemistry
Phylogeny
Microbiota/drug effects

@article {pmid40846855,
year = {2025},
author = {Zhang, M and Wang, X and Yao, H and Shen, Y and Teng, Y and Garber, PA and Pan, H and Li, M},
title = {Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {169},
pmid = {40846855},
issn = {2055-5008},
support = {32330015, 31821001//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Diet ; *Colobinae/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; },
abstract = {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.},
}

Animals
*Seasons
*Gastrointestinal Microbiome
*Diet
*Colobinae/microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology

@article {pmid40846661,
year = {2025},
author = {Qin, Q and Zhu, Y and Yang, L and Guo, R and Song, L and Wang, D and Li, W},
title = {Oral microbiome between patients with non-obstructive and obstructive hypertrophic cardiomyopathy.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {40846661},
issn = {2542-5641},
abstract = {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.},
}

@article {pmid40846194,
year = {2025},
author = {Han, Y and Cui, J and Guo, P and Yang, S},
title = {Remediation Effects of Straw Combined with Microbial agents on Cinnamon Soils with Varying Degradation Based on Metagenomics and Untargeted Metabolome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122649},
doi = {10.1016/j.envres.2025.122649},
pmid = {40846194},
issn = {1096-0953},
abstract = {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.},
}

@article {pmid40846080,
year = {2025},
author = {Hshieh, K and Maloney, JG},
title = {Sequencing on the edge: Tools and techniques for sequencing low biomass isolates from unicellular eukaryotic parasites and other challenging samples.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107233},
doi = {10.1016/j.mimet.2025.107233},
pmid = {40846080},
issn = {1872-8359},
abstract = {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.},
}

@article {pmid40845954,
year = {2025},
author = {Moore, CO and Andrews, CV and Lemley, EM and Gonçalves Funnicelli, MI and André, MR and Breitschwerdt, EB and Lashnits, E},
title = {Wildlife fleas and ticks in Wisconsin, USA: unrecognized vectors of bacterial pathogens.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2025.08.004},
pmid = {40845954},
issn = {1879-0135},
abstract = {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.},
}

@article {pmid40845656,
year = {2025},
author = {Xu, X and Zhou, P and Cheng, T and Zhang, Y and Pei, H and Weng, Y and Huang, T and Wu, B and Du, S and Zhuang, J},
title = {Phosphate-modified calamus-based biochar filler enhanced constructed wetland mitigating antibiotic resistance risks: insight from metagenomics.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127080},
doi = {10.1016/j.jenvman.2025.127080},
pmid = {40845656},
issn = {1095-8630},
abstract = {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.},
}

@article {pmid40845638,
year = {2025},
author = {Bai, X and Bi, J and Li, A and Zhu, X and Zhao, Z and Hu, H and Pan, H},
title = {Phylosymbiosis of antibiotic resistance genes in pig feces and potential transmission to piggery workers.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118907},
doi = {10.1016/j.ecoenv.2025.118907},
pmid = {40845638},
issn = {1090-2414},
abstract = {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.},
}

@article {pmid40845582,
year = {2025},
author = {Li, Y and Zhang, C and Meng, Z and You, M and Shi, H},
title = {Microbial dysbiosis induced in Cyprinus carpio by tetrabromobisphenol A exposure: Mediation through gut barrier impairment and oxidative stress.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {56},
number = {},
pages = {101609},
doi = {10.1016/j.cbd.2025.101609},
pmid = {40845582},
issn = {1878-0407},
abstract = {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.},
}

@article {pmid40845163,
year = {2025},
author = {Zhang, T and Jiang, M and Li, H and Gao, Y and Yousuf, S and Yu, K and Yi, X and Wang, J and Yang, L and Liu, YX},
title = {Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf075},
pmid = {40845163},
issn = {2210-3244},
abstract = {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.},
}

@article {pmid40844735,
year = {2025},
author = {Bhatt, P and Rajesh, P and Kukkar, D and Kim, KH},
title = {Metagenomic profiling of gut microbime: associating their role with the advancement of diabetic nephropathy.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {135},
pmid = {40844735},
issn = {1572-9699},
support = {DST/WISE-PhD/LS/2023/73/G//Department of Science and Technology, Ministry of Science and Technology, India/ ; EMDR/SG/13/2023-0756//Indian Council of Medical Research/ ; 2021R1A3B1068304//Ministry of Science, ICT and Future Planning/ ; 2022R1A6C101A779//National Center for Inter-University Research Facilities, Seoul National University/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Diabetic Nephropathies/microbiology ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/complications ; Disease Progression ; },
abstract = {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.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Diabetic Nephropathies/microbiology
*Metagenomics/methods
Diabetes Mellitus, Type 2/microbiology/complications
Disease Progression

@article {pmid40844556,
year = {2025},
author = {Pereira, EL and Pereira, GR and Osório, ML and Terra, JLA and Gayger, JB and Gularte, JS and Demoliner, M and Pereira, VMAG and Filippi, M and de Matos, QS and Tessman, A and Canal, CW and Daudt, C and Silva, FC and Sita, A and Fleck, JS and Weber, MN and Almeida, PR and Spilki, FR and da Silva, MS},
title = {Bovine and ovine deltapapillomavirus coinfection associated with equine sarcoid.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40844556},
issn = {1678-4405},
support = {405786/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 23/2551-0002221-4//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; },
abstract = {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.},
}

@article {pmid40842870,
year = {2025},
author = {Li, H and Zhang, Z and Chen, J and Nair, S and Xiong, T and Zhao, H and He, D and Lee, K and Jiao, N and Zhang, Y},
title = {Fate and carbon sequestration potential of sunken macroalgae in coastal oceans from long-term microbial degradation perspective.},
journal = {National science review},
volume = {12},
number = {8},
pages = {nwaf273},
pmid = {40842870},
issn = {2053-714X},
abstract = {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.},
}

@article {pmid40842835,
year = {2025},
author = {Gou, F and Han, Y and Sun, Y and Ding, W and Jin, S and Liu, Y and Chen, J},
title = {Macrogenomics-based analysis of rumen microbial composition and their metabolic pathways in yaks under different dietary concentrate-to-forage ratios.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1587474},
pmid = {40842835},
issn = {1664-302X},
abstract = {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.},
}

@article {pmid40842029,
year = {2025},
author = {Chen, X and Zhao, H and Jiang, C and Sun, T and Xu, X and You, K},
title = {Human herpes virus-7-related severe encephalitis diagnosed using mNGS in immunocompetent pediatric patients.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {287},
pmid = {40842029},
issn = {1743-422X},
support = {81501292//National Natural Science Foundation of China Youth Fund/ ; 2017M611285//China Postdoctoral Fund Surfacmee Project/ ; 2022JH2/101500053//Basic Research Program of Liaoning Province/ ; },
mesh = {Humans ; Male ; Female ; Child ; Child, Preschool ; *Herpesvirus 7, Human/genetics/isolation & purification ; *Encephalitis, Viral/diagnosis/virology/pathology/drug therapy ; *Roseolovirus Infections/diagnosis/virology/drug therapy/pathology ; Infant ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics/cerebrospinal fluid ; Antiviral Agents/therapeutic use ; Prognosis ; Magnetic Resonance Imaging ; Metagenomics/methods ; Immunocompetence ; Acyclovir/therapeutic use ; Brain/diagnostic imaging/pathology ; Electroencephalography ; },
abstract = {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.},
}

Humans
Male
Female
Child
Child, Preschool
*Herpesvirus 7, Human/genetics/isolation & purification
*Encephalitis, Viral/diagnosis/virology/pathology/drug therapy
*Roseolovirus Infections/diagnosis/virology/drug therapy/pathology
Infant
High-Throughput Nucleotide Sequencing
DNA, Viral/genetics/cerebrospinal fluid
Antiviral Agents/therapeutic use
Prognosis
Magnetic Resonance Imaging
Metagenomics/methods
Immunocompetence
Acyclovir/therapeutic use
Brain/diagnostic imaging/pathology
Electroencephalography

@article {pmid40841920,
year = {2025},
author = {Mo, X and Guo, S and He, D and Cheng, Q and Yang, Y and Wang, H and Ren, Y and Liu, L and Xie, P},
title = {Lactobacillus reuteri DSM 17,938 ameliorates LPS-induced depression-like and anxiety-like behaviors by modulating gut microbiota and brain metabolic function.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {65},
pmid = {40841920},
issn = {1757-4749},
support = {Approval No. CYS23330//Graduated Research Innovation Project Foundation of Chongqing/ ; 82401814//the Natural Science Foundation Project of China/ ; 82201683//the Natural Science Foundation Project of China/ ; CSTB2024NSCQ-MSX0649//the General Program of Chongqing Natural Science Foundation/ ; 2023CCXM003//the Joint Project of Chongqing Municipal Science and Technology Bureau and Chongqing Health Commission/ ; },
abstract = {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.},
}

@article {pmid40841874,
year = {2025},
author = {Dinçer, S and Ülger, Y and Delik, A},
title = {Mucosal microbiota signatures reveal diagnostic insights in chronic liver disease.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {607},
pmid = {40841874},
issn = {1471-230X},
support = {CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; *Intestinal Mucosa/microbiology/pathology ; Female ; Case-Control Studies ; Metagenomics ; *Colon/microbiology/pathology ; Adult ; *Liver Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S ; Aged ; Chronic Disease ; Biopsy ; High-Throughput Nucleotide Sequencing ; Principal Component Analysis ; },
abstract = {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.},
}

Humans
*Gastrointestinal Microbiome/genetics
Male
Middle Aged
*Intestinal Mucosa/microbiology/pathology
Female
Case-Control Studies
Metagenomics
*Colon/microbiology/pathology
Adult
*Liver Diseases/microbiology/diagnosis
Dysbiosis/microbiology
RNA, Ribosomal, 16S
Aged
Chronic Disease
Biopsy
High-Throughput Nucleotide Sequencing
Principal Component Analysis

@article {pmid40841691,
year = {2025},
author = {Yau, PT and Taketani, RG and Bonnin, JM and Stewart, H and Thompson, CMA and Clark, IM and Mauchline, TH and Malone, JG and Ryan, MJ and Jones, S and Holden, N},
title = {Introducing the UK Crop Microbiome Cryobank data resource, AgMicrobiomeBase, with case studies and methods on metabarcoding analyses.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {108},
pmid = {40841691},
issn = {2524-6372},
support = {BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T019492/1, BB/T019484/1, BB/T019700/1, BB/T019808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {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.},
}

@article {pmid40841555,
year = {2025},
author = {Wang, T and Zhang, P and Anantharaman, K and Wang, H and Zhang, H and Zhang, M and Xu, J},
title = {Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7806},
pmid = {40841555},
issn = {2041-1723},
support = {42377469//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001151//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; Microbiota/genetics ; Lakes/microbiology/virology ; *Fresh Water/microbiology/virology ; Ecosystem ; Metagenome ; *Viruses/genetics/classification ; *Bacteria/genetics/virology ; Pesticides ; *Host Microbial Interactions/genetics ; Stress, Physiological ; Climate Change ; },
abstract = {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.},
}

*Metagenomics/methods
Microbiota/genetics
Lakes/microbiology/virology
*Fresh Water/microbiology/virology
Ecosystem
Metagenome
*Viruses/genetics/classification
*Bacteria/genetics/virology
Pesticides
*Host Microbial Interactions/genetics
Stress, Physiological
Climate Change

@article {pmid40841245,
year = {2025},
author = {Antoniadou, C and Gavriilidis, E and Chatzopoulos, P and Gkouliavera, M and Skendros, P},
title = {Fever and inflammation of unknown origin in the 21st century.},
journal = {European journal of internal medicine},
volume = {},
number = {},
pages = {106443},
doi = {10.1016/j.ejim.2025.106443},
pmid = {40841245},
issn = {1879-0828},
abstract = {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.},
}

@article {pmid40841065,
year = {2025},
author = {Jia, M and Gao, Z and Hu, X and Feng, M and Liu, F and Huang, J and Zhang, R and Li, J and Zhang, G and Wang, Y},
title = {Wetland types shape microbial function related to soil phosphorus cycling based on metagenomics analysis.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {930-943},
doi = {10.1016/j.jes.2025.03.009},
pmid = {40841065},
issn = {1001-0742},
mesh = {*Wetlands ; *Phosphorus/analysis/metabolism ; *Soil Microbiology ; Metagenomics ; Soil/chemistry ; China ; *Environmental Monitoring ; },
abstract = {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.},
}

*Wetlands
*Phosphorus/analysis/metabolism
*Soil Microbiology
Metagenomics
Soil/chemistry
China
*Environmental Monitoring

@article {pmid40841038,
year = {2025},
author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X},
title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {610-620},
doi = {10.1016/j.jes.2025.02.028},
pmid = {40841038},
issn = {1001-0742},
mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {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.},
}

Animals
*Manure
*Drug Resistance, Microbial/genetics
*Snails/microbiology
Humans
Introduced Species
Gastrointestinal Microbiome
Soil Microbiology
Environmental Monitoring
RNA, Ribosomal, 16S
Feces/microbiology

@article {pmid40841030,
year = {2025},
author = {Nie, E and He, P and Zhang, H and Lü, F},
title = {Genome-centric metagenomic analysis unveils the influence of temperature on the microbiome in anaerobic digestion.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {516-526},
doi = {10.1016/j.jes.2024.10.007},
pmid = {40841030},
issn = {1001-0742},
mesh = {Anaerobiosis ; *Microbiota ; Metagenomics ; *Temperature ; *Metagenome ; Archaea/genetics ; Bacteria/genetics ; },
abstract = {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.},
}

Anaerobiosis
*Microbiota
Metagenomics
*Temperature
*Metagenome
Archaea/genetics
Bacteria/genetics

@article {pmid40840611,
year = {2025},
author = {Guo, D and Liu, X and Zhang, Y and Li, Y and Hou, B and Duan, J},
title = {Combining Simulated Immersion and Statistical Analysis to Reveal Microbial Evidence of Corrosion Failure in Fuel Aluminum Alloys.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122511},
doi = {10.1016/j.envres.2025.122511},
pmid = {40840611},
issn = {1096-0953},
abstract = {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.},
}

@article {pmid40840604,
year = {2025},
author = {Tiwari, A and Jaén-Gil, A and Karavaeva, A and Gomiero, A and Ásmundsdóttir, ÁM and Silva, MJ and Salmivirta, E and Tran, TT and Sarekoski, A and Cook, J and Lood, R and Pitkänen, T and Krolicka, A},
title = {Antibiotic resistance genes, antibiotic residues, and microplastics in influent and effluent wastewater from treatment plants in Norway, Iceland, and Finland.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122629},
doi = {10.1016/j.envres.2025.122629},
pmid = {40840604},
issn = {1096-0953},
abstract = {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.},
}

@article {pmid40840441,
year = {2025},
author = {Shi, Q and Kristiansen, K},
title = {Spatial dissimilarity analysis in single-cell transcriptomics.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101141},
doi = {10.1016/j.crmeth.2025.101141},
pmid = {40840441},
issn = {2667-2375},
abstract = {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.},
}

@article {pmid40840439,
year = {2025},
author = {He, X and Gao, Y and Zhang, Y and Yang, Z and Wang, C and Ma, Q and Lei, P and Yu, L and Fan, Y and Liu, R and Wang, W and Zhang, J and Ma, X and Zhu, F},
title = {Distinct Gut Microbial Signatures and Diminished Anti-Inflammatory Effect of Short-Chain Fatty Acids in Schizophrenia With Immune Activation.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf110},
pmid = {40840439},
issn = {1745-1701},
support = {82171505//National Natural Science Foundation of China/ ; 82230044//National Natural Science Foundation of China/ ; 82022023//National Natural Science Foundation of China/ ; 82271572//National Natural Science Foundation of China/ ; },
abstract = {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.},
}

@article {pmid40840192,
year = {2025},
author = {Yang, SB and Lu, ZM and Shen, HJ and Fu, JJ and Yang, Y and Zhang, XJ and Chai, LJ and Wang, ST and Zhang, SY and Shen, CH and Shi, JS and Xu, ZH},
title = {Unraveling Qu-aroma variation between inner and outer layers of medium-temperature Daqu: A multi-omics and sensory approach.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111392},
doi = {10.1016/j.ijfoodmicro.2025.111392},
pmid = {40840192},
issn = {1879-3460},
abstract = {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.},
}

@article {pmid40838886,
year = {2025},
author = {Xie, T and Lin, D and Cai, XD and Ma, LJ and Wang, L and Cai, TG and Ye, YQ and Shen, LQ and Sun, MM and Ye, M and Neilson, R and Zhu, D},
title = {Nano-biochar regulates phage-host interactions, reducing antibiotic resistance genes in vermicomposting systems.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {34},
pages = {e2511986122},
doi = {10.1073/pnas.2511986122},
pmid = {40838886},
issn = {1091-6490},
support = {Grant XDB0750400//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 42307033 and 42222701//the National Natural Science Foundation of China/ ; 2022A-163-G//the Ningbo Yongjiang Talent Project/ ; RESAS//the James Hutton Institute receives financial support from Scottish Government Rural and Environment Science and Analytical Services/ ; },
mesh = {Animals ; *Oligochaeta/virology/microbiology ; *Bacteriophages/physiology/genetics ; *Drug Resistance, Microbial/genetics ; *Composting/methods ; *Host Microbial Interactions ; Bacteria/genetics/virology ; Soil Microbiology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; },
abstract = {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.},
}

Animals
*Oligochaeta/virology/microbiology
*Bacteriophages/physiology/genetics
*Drug Resistance, Microbial/genetics
*Composting/methods
*Host Microbial Interactions
Bacteria/genetics/virology
Soil Microbiology
*Drug Resistance, Bacterial/genetics
Metagenomics

@article {pmid40838858,
year = {2025},
author = {Hashimoto, K and Fukushima, K and Matsumoto, Y and Saito, H and Funauchi, A and Hamada, N and Niitsu, T and Abe, Y and Yamauchi, J and Nitta, T and Motooka, D and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Kumanogoh, A and Nakamura, S and Kida, H},
title = {Molecular epidemiological surveillance for non-tuberculous mycobacterial pulmonary disease: a single-center prospective cohort study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0043625},
doi = {10.1128/spectrum.00436-25},
pmid = {40838858},
issn = {2165-0497},
abstract = {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.},
}

@article {pmid40838847,
year = {2025},
author = {Gao, X and Zheng, Y and Chang, H and Liu, J and Sun, X and Ren, Y and Li, L and Zhao, G and Cheng, Y and Ma, S and Zhao, J and Deng, J and Kang, T and Qiao, Z and Zhao, H and Xie, D and Wang, T and Li, S and Shi, H and Shi, A and Zhang, P},
title = {Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis.},
journal = {Journal of medical virology},
volume = {97},
number = {8},
pages = {e70570},
doi = {10.1002/jmv.70570},
pmid = {40838847},
issn = {1096-9071},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Virome ; *Arthritis, Rheumatoid/diagnosis/virology ; *Metagenomics ; Male ; Female ; Middle Aged ; *Palatine Tonsil/virology ; Adult ; *Viruses/genetics/classification/isolation & purification ; Aged ; Microbiota ; },
abstract = {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.},
}

Humans
*Virome
*Arthritis, Rheumatoid/diagnosis/virology
*Metagenomics
Male
Female
Middle Aged
*Palatine Tonsil/virology
Adult
*Viruses/genetics/classification/isolation & purification
Aged
Microbiota

@article {pmid40838747,
year = {2025},
author = {Acharya, SM and Yang, Y and Enalls, BC and Walian, PJ and Van Houghton, BD and Rosenblum, JS and Cath, TY and Tringe, SG and Chakraborty, R},
title = {Unraveling the ecological success of Iodidimonas in a bioreactor treating oil and gas produced water.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/spectrum.00683-25},
pmid = {40838747},
issn = {2165-0497},
abstract = {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.},
}

@article {pmid40838736,
year = {2025},
author = {Fang, J and Chen, Z and Yu, Z and Shan, S and Hou, Y and Liu, L and Huang, J and Li, B and Guo, J},
title = {Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf187},
pmid = {40838736},
issn = {1751-7370},
abstract = {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.},
}

@article {pmid40837017,
year = {2025},
author = {Li, Q and Zhang, L and Li, R and Tang, J and Lin, B and Qin, C and Jiang, W and An, L and Zhang, F and Shi, X and Yang, S and Yang, Q and Chen, S},
title = {Metagenomics-based analysis of microbial community dynamics and flavor compound correlations during rice-flavor Baijiu brewing.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1638716},
pmid = {40837017},
issn = {2296-4185},
abstract = {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.},
}

@article {pmid40836310,
year = {2025},
author = {Wang, X and Dong, Q and Huang, P and Yang, S and Gao, M and Zhang, C and Zhang, C and Deng, Y and Huang, Z and Ma, B and Jiao, Y and Zhou, Y and Wu, T and Zou, H and Shi, J and Sheng, Y and Wang, Y and Consortium, C and Tang, L and Hu, S and Duan, Y and Sun, W and Chen, W and Zhai, Q and Kong, X and Chen, L},
title = {The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {188},
pmid = {40836310},
issn = {2049-2618},
support = {32270077//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Genome, Viral ; Feces/virology/microbiology ; *Genetic Variation ; *Polymorphism, Single Nucleotide ; *Viruses/genetics/classification/isolation & purification ; China ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {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.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Virome/genetics
Genome, Viral
Feces/virology/microbiology
*Genetic Variation
*Polymorphism, Single Nucleotide
*Viruses/genetics/classification/isolation & purification
China
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing

@article {pmid40836306,
year = {2025},
author = {Gao, H and Li, B and Guo, Z and Zheng, L and Chen, J and Liang, G},
title = {Highly accurate prophage island detection with PIDE.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {254},
pmid = {40836306},
issn = {1474-760X},
mesh = {*Prophages/genetics ; Humans ; *Software ; Genome, Bacterial ; Algorithms ; Metagenome ; *Genomic Islands ; Genome, Viral ; },
abstract = {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 .},
}

*Prophages/genetics
Humans
*Software
Genome, Bacterial
Algorithms
Metagenome
*Genomic Islands
Genome, Viral

@article {pmid40836223,
year = {2025},
author = {Wibberg, D and Bakuła, Z and García-Cunchillos, I and Gawor, J and Gromadka, R and Karnkowska, A and Bielecki, J and Jagielski, T},
title = {Complete mitochondrial genomes of the Prototheca genus: comparative genomics and evolutionary insights.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {766},
pmid = {40836223},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; Phylogeny ; *Genomics/methods ; *Evolution, Molecular ; *Prototheca/genetics/classification ; Base Composition ; },
abstract = {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.},
}

*Genome, Mitochondrial
Phylogeny
*Genomics/methods
*Evolution, Molecular
*Prototheca/genetics/classification
Base Composition

@article {pmid40835852,
year = {2025},
author = {Weber, J and Hillen, M and Seuberlich, T and Fürmann, A and Gurtner, C and Becker, J and Syring, C and Ruiters, MW and Alsaaod, M and Mazurek, L and Schüpbach, G and Steiner, A},
title = {Successful implementation of a risk assessment and mitigation program to control bovine digital dermatitis at the herd-level.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30577},
pmid = {40835852},
issn = {2045-2322},
abstract = {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.},
}

@article {pmid40836093,
year = {2025},
author = {He, G and Wang, W and Chen, G and Xie, Y and Parks, JM and Davin, ME and Hettich, RL and Konstantinidis, KT and Löffler, FE},
title = {A novel bacterial protein family that catalyses nitrous oxide reduction.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40836093},
issn = {1476-4687},
abstract = {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].},
}

@article {pmid40835708,
year = {2025},
author = {Chuchaona, W and Izquierdo-Lara, RW and Schapendonk, CME and Khongwichit, S and Koopmans, MPG and de Graaf, M and Poovorawan, Y},
title = {Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30672},
pmid = {40835708},
issn = {2045-2322},
support = {No. 874735 (VEO)//The European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement/ ; No. 874735 (VEO)//The European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement/ ; No. 874735 (VEO)//The European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement/ ; No. 874735 (VEO)//The European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement/ ; },
mesh = {Humans ; Thailand ; *Gastroenteritis/virology ; *Coinfection/virology ; *Norovirus/genetics/isolation & purification ; Phylogeny ; Genome, Viral ; Metagenomics/methods ; *Caliciviridae Infections/virology ; *Enterovirus Infections/virology ; *Enterovirus A, Human/genetics/isolation & purification ; Male ; Genomics ; },
abstract = {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.},
}

Humans
Thailand
*Gastroenteritis/virology
*Coinfection/virology
*Norovirus/genetics/isolation & purification
Phylogeny
Genome, Viral
Metagenomics/methods
*Caliciviridae Infections/virology
*Enterovirus Infections/virology
*Enterovirus A, Human/genetics/isolation & purification
Male
Genomics

@article {pmid40835198,
year = {2025},
author = {Liu, Q and Wang, M and Xie, JW and Du, YT and Yin, ZG and Cai, JH and Zhao, MH and Jiang, YT and Zhang, HD},
title = {Macrogenome Analysis of Rodents from Heilongjiang Province, China.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107789},
doi = {10.1016/j.actatropica.2025.107789},
pmid = {40835198},
issn = {1873-6254},
abstract = {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.},
}

@article {pmid40835141,
year = {2025},
author = {Bu, Q and Jiao, L and Liu, Y and Fan, N and Zhang, H and Xu, J and He, A and Xi, Y},
title = {H2O2-modified shrimp shell biochar enhances the digestion of cow manure to produce caproic acid.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133173},
doi = {10.1016/j.biortech.2025.133173},
pmid = {40835141},
issn = {1873-2976},
abstract = {Nitrogen-doped biochar materials can improve electron transfer efficiency through defects between carbon atoms. In this study, H2O2 was used to treat nitrogen-rich shrimp shell biochar to enhance its oxygen-containing functional group structure and improve the electron transfer efficiency of the anaerobic system by investigating the impact of H2O2 on caproic acid production. The results indicated that the concentration of caproic acid reached 29.7 g COD/L following the addition of 15 g/L of H2O2-modified shrimp shell biochar. These concentrations were 58.8 % and 31.4 % higher than those of the control group and the original biochar group, respectively. Mechanistic analysis revealed that H2O2-modified shrimp shell biochar (HBC) facilitated the enrichment of microorganisms linked to caproic acid production, enhanced interspecific electron transfer, and increased the abundance of enzymes related to reverse β-oxidation and fatty acid biosynthesis pathways. Ultimately, these findings pave the way for the development of more efficient processes to produce caproic acid.},
}

@article {pmid40835139,
year = {2025},
author = {Zhong, Y and He, J and Duan, S and Pan, X and Zou, X and Zhang, J and Su, Q and Ng, HY},
title = {Nitrogen-doped biochar supported magnetite enhances hydrolysis and methanogenesis during anaerobic digestion of waste activated sludge in continuously operated reactors: Metagenomic Approach.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133174},
doi = {10.1016/j.biortech.2025.133174},
pmid = {40835139},
issn = {1873-2976},
abstract = {While conductive materials (CMs) are known to enhance anaerobic digestion (AD), comparative efficacies of carbon- and iron-based CMs during AD of waste activated sludge (WAS) have not been investigated. In this study, a novel hybrid conductive material, namely nitrogen-doped biochar supported magnetite (Fe3O4@N-BC), was synthesized and applied in continuously operated up-flow anaerobic sludge blanket reactors. The addition of Fe3O4@N-BC increased methane production rate by 25 %, higher than that of Fe3O4 (19 %) and biochar (13 %). Chryseobacterium and Methanothrix were enriched as key bacteria and archaea responsible for hydrolysis and direct interspecies electron transfer (DIET) in methanogenesis, respectively. Fe3O4@N-BC enhanced hydrolase activities and the construction of e-pili network for electron transfer. Metagenomic data further revealed that electrons were efficiently transferred for CO2-to-CH4 conversion. The results highlight that Fe3O4@N-BC can improve CH4 production during AD of WAS by simultaneously enhancing hydrolysis and DIET in methanogenesis, thereby demonstrating its applicability in continuous AD reactors.},
}

@article {pmid40835054,
year = {2025},
author = {Wu, Y and Tao, S and Xiao, L and Zhang, J and Tang, Y and Zhang, M and Liu, S and Huang, Y and Liu, Y and Xie, M and Zhao, Z and Lv, Q and Cai, J and Pei, K and Ma, Q and Yin, Y and Dai, M and Wei, M and Chen, Y and Wang, Q},
title = {Gut virome alterations in schizophrenia: identifying viral biomarkers associated with schizophrenia and treatment response.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106080},
doi = {10.1016/j.bbi.2025.106080},
pmid = {40835054},
issn = {1090-2139},
abstract = {BACKGROUND: The gut virome is an important component of the microbiome with potential implications for schizophrenia. However, its role in disease pathology and treatment response remains unclear.

METHODS: We performed metagenomic sequencing on fecal samples from 49 first-episode schizophrenia patients and 49 healthy controls. Viral diversity and taxonomic profiles were compared between groups. Within patients, we assessed associations between viral alpha diversity and symptom severity, as well as between specific viral taxa and treatment outcomes, including short- and long-term PANSS reduction and response trajectories. Response trajectories were identified by clustering patients based on the longitudinal PANSS reduction patterns.

RESULTS: There were no significant differences in alpha diversity between schizophrenia patients and healthy controls. Among patients, higher viral diversity was associated with more severe negative symptoms. Although several viral taxa showed nominal associations with schizophrenia, none remained significant after FDR correction. Regarding treatment outcomes, the abundance of Brigitvirus was negatively associated with the 6-week symptom reduction rate (FDR = 0.012), and two viral species were reduced in the low-response trajectory group.

CONCLUSIONS: Although virome differences between patients with schizophrenia and healthy controls were modest, associations between viral features and both symptom severity and treatment response indicate potential clinical relevance.},
}

@article {pmid40834840,
year = {2025},
author = {Jia, X and Zheng, Y and Li, D and Cai, J and Yang, J and Rao, Q and Ye, X},
title = {Diagnosis of Leishmania donovani infection via bronchoalveolar lavage fluid next-generation sequencing:A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {4},
pages = {117067},
doi = {10.1016/j.diagmicrobio.2025.117067},
pmid = {40834840},
issn = {1879-0070},
abstract = {Visceral leishmaniasis usually presents with fever, weight loss, enlargement of the spleen and liver, and anemia. Its diagnosis relies on etiological examination, typically by detecting Leishmania parasites in smears of bone marrow, splenic, or lymph node aspirates. We report a case of Leishmania infection presenting predominantly as interstitial pneumonia. The patient showed no significant improvement in pulmonary lesions after empirical antibiotic therapy. Targeted next-generation sequencing (tNGS) of bronchoalveolar lavage fluid (BALF) detected Leishmania donovani species complex. The pulmonary lesions gradually resolved following standard treatment with amphotericin B colloidal dispersion. Through a comprehensive review of previous studies, we examined the pulmonary manifestations of visceral leishmaniasis, encompassing both interstitial pneumonia and secondary parasitic lung infections. Based on our findings, we emphasize the need for enhanced clinical recognition of visceral leishmaniasis-related pulmonary complications among healthcare professionals. Furthermore, we addressed the limitations of this case report.},
}

@article {pmid40834737,
year = {2025},
author = {Xu, J and Gao, Y and Sheng, Z and Bi, X and Huang, S and Ng, HY},
title = {Calcium-loaded activated carbon microtubes as a structural framework of aerobic granules: crosslinking networks overcome native framework limitations.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124418},
doi = {10.1016/j.watres.2025.124418},
pmid = {40834737},
issn = {1879-2448},
abstract = {Aerobic granular sludge (AGS) technology is often constrained by slow granulation and structural instability, issues largely attributed to imbalances in filamentous bacteria and extracellular polymeric substances (EPS). In this study, calcium-loaded activated carbon microtubes (ACMTs-Ca) were developed as novel frameworks to enhance AGS formation and stability. The interfacial energy barrier between microorganisms and ACMTs-Ca was reduced by 67.43 % compared to that between microorganisms and conventional sludge. Incorporation of ACMTs-Ca significantly accelerated granulation kinetics, achieving mature granulation (89.36 % granules >200 μm, SVI30 = 48.35 mL·g[-1], SVI30/SVI5 = 99.15 %) within 30 d, in contrast to 140 d required by the control. AGS with ACMTs-Ca as the primary framework exhibited an 80 % enhancement in structural strength relative to the control. The improved structural integrity was attributed to the formation of a calcium-alginate coordination network with β-polysaccharides, thereby reducing dependence on filamentous bacteria for granule stability. Enhanced pollutant removal efficiencies were observed, with AGS-ACMTs-Ca system achieving COD, TN, and TP removal rates of 96 %, 80 %, and 99.48 %, respectively, facilitated by the enrichment of functional genera such as Candidatus_Competibacter, Thauera, and Flavobacterium. Metagenomic analysis revealed increased relative abundance of algE genes (associated with β-polysaccharide synthesis) alongside decreased abundance of genes involved in amino acid biosynthesis pathways. These abundance shifts suggest potential microbial regulation favoring EPS compositional changes toward calcium-stabilized frameworks. This study demonstrates the dual role of ACMTs-Ca in structural reinforcement and microbial niche regulation, offering a sustainable strategy for rapid and robust AGS cultivation.},
}

@article {pmid40834730,
year = {2025},
author = {Páez-Watson, T and Jansens, C and van Loosdrecht, MCM and Roy, S},
title = {Co-substrate utilisation in "Candidatus Accumulibacter" enhances metabolic fitness in dynamic environments.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124401},
doi = {10.1016/j.watres.2025.124401},
pmid = {40834730},
issn = {1879-2448},
abstract = {Optimizing resource use is essential for the survival and fitness of species in microbial communities ubiquitous in natural and engineered ecosystems. These ecosystems are often characterized by the simultaneous presence of multiple substrates such as volatile fatty acids, amino acids and sugars. Yet, the evaluation of metabolic potential for these microbial community members is predominantly based on single substrate utilisation. Metabolic and ecological implications of the interactions of multiple substrates, particularly in environments with changes in redox conditions and substrate availability, remain poorly understood. In this study, we investigate the metabolic interactions resulting from co-substrate utilization in polyphosphate-accumulating organisms within wastewater treatment systems. We combined experimental analysis of highly enriched "Ca. Accumulibacter" mixed cultures with genome-resolved metagenomics and conditional flux balance analysis (cFBA) to quantify the physiological relevance of co-substrate uptake. We observe that anaerobic co-substrate utilisation of acetate and aspartate result in metabolic interactions leading to optimized redox balance, reduced ATP losses and increased biomass yields by up to 8% compared to individual substrate use. Metabolic modelling revealed that these benefits emerge from the network topology, where the interaction of different metabolic routes gives rise to synergistic effects. Extending our analysis to additional substrate pairs, we classify metabolic interactions into three general types: (i) neutral, (ii) one-way synergistic and (iii) reciprocal synergistic. Our findings highlight the importance of metabolic interactions and cellular resource allocation strategies in dynamic microbial ecosystems. This study provides a broader ecological framework for understanding competitive metabolic strategies in environmental organisms. Co-substrate utilization can have direct implications for improving the yield or productivity of bioprocesses.},
}

@article {pmid40834728,
year = {2025},
author = {Bains, A and Dahal, S and Manna, B and Lyte, M and Yang, L and Singhal, N},
title = {L-norepinephrine induces community shift, oxidative stress response, metabolic reprogramming, and virulence potential in wastewater microbiomes.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124353},
doi = {10.1016/j.watres.2025.124353},
pmid = {40834728},
issn = {1879-2448},
abstract = {Neuroendocrine compounds discharged into wastewater systems represent an emerging challenge at the intersection of human physiology and environmental microbiology. l-norepinephrine (L-NE), which has been recognized to potentiate growth of human and animal bacterial pathogens, is discharged in sewage through urine and faeces. While extensive pure culture studies have established l-NE's capacity to modulate bacterial virulence through iron acquisition and quorum sensing pathways, its impact on complex microbial communities, where intricate metabolic networks and interspecies interactions dominate, remains largely unexplored. This knowledge gap is particularly critical as urbanization drives increasing neuroendocrine compound loads in wastewater influents in metropolitan areas. Through parallel treatments of l-NE (1 × 10[-5] M to 1 × 10[-4] M), dextrose, and H2O2 in municipal and agricultural wastewater communities, we uncovered sophisticated metabolic and regulatory mechanisms that challenge the conventional understanding of microbial substrate utilization. Despite containing 10-fold less carbon, l-NE treatments achieved superior growth (10[8] CFU mL[-1]) while maintaining Pseudomonadaceae-dominated communities. Targeted metaproteomics revealed coordinated upregulation of oxidative stress genes (oxyR, soxRS) and antioxidant enzymes, while proteome-constrained metabolic modeling demonstrated distinct pathway modulation in central carbon and nitrogen metabolism. Notably, when compared to dextrose-supplemented controls, representing typical carbon substrate utilization, l-NE treatments showed similar taxonomic profiles without preferential enrichment of known pathogenic families. However, l-NE significantly enhanced autoinducer gene (luxS, qseC) expression, suggesting increased virulence potential through community-level metabolic reprogramming. These findings reveal l-NE as a potent modulator of microbial community dynamics in engineered ecosystems, with important implications for treatment process stability and downstream environmental impacts.},
}

@article {pmid40834570,
year = {2025},
author = {Ansari, SA and Ramteke, A and Sawarkar, R and Kumar, T and Khan, D and Agashe, A and Patil, MP and Singh, L},
title = {"Innovative approaches in microbial community engineering for food waste management: A comprehensive review".},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127000},
doi = {10.1016/j.jenvman.2025.127000},
pmid = {40834570},
issn = {1095-8630},
abstract = {Food waste (FW) is a critical global issue, exacerbating environmental degradation and resource scarcity. Traditional FW management methods are often inefficient and unsustainable. This review highlights advances in microbial community engineering for FW valorization, focusing on synthetic biology, metagenomics, metabolic engineering, and electro-fermentation. Engineered microbial consortia enhance the breakdown of complex organics while producing bioenergy, bioplastics, and organic acids. Metagenomics enables precise metabolic optimizations, and electro-fermentation improves bioconversion yields. These systems outperform conventional methods in reducing greenhouse gases, recovering nutrients, and promoting a circular bioeconomy. Challenges persist, including microbial stability, scalability, and incomplete knowledge of interspecies interactions. Future research should integrate AI and machine learning to design robust synthetic consortia and optimize metabolic pathways. Scaling electrochemical technologies (e.g., microbial electrosynthesis) requires further validation. Standardized biosafety protocols, techno-economic analyses, and supportive policies are essential for industrial adoption. Interdisciplinary collaboration is crucial to address these gaps. In conclusion, microbial engineering offers a sustainable FW management solution, improving biodegradation efficiency and resource recovery. Future efforts must prioritize scalable, stable systems with real-time monitoring and ecological safety. Overcoming these challenges will enable engineered microbes to mitigate environmental impacts, generate renewable energy, and advance a resource-efficient future.},
}

@article {pmid40834509,
year = {2025},
author = {Poshvina, DV and Balkin, AS and Dilbaryan, DS and Vasilchenko, AS},
title = {Unravelling the response of the soil microbiome to macrolactin A: A metagenomic study.},
journal = {Chemosphere},
volume = {387},
number = {},
pages = {144645},
doi = {10.1016/j.chemosphere.2025.144645},
pmid = {40834509},
issn = {1879-1298},
abstract = {The development of environmentally sustainable biopreparations for crop protection requires comprehensive assessment of their microbiome impacts. This study investigates how macrolactin A (McA)-a polyketide antibiotic produced by plant-beneficial Bacillus velezensis-shapes soil microbial communities and antibiotic resistance gene (ARG) profiles under various agricultural scenarios. Using high-throughput metagenomics and network analysis, we compared untreated soils with those exposed to two McA concentrations: a high dose (10 mg/kg soil, representing potential point-source accumulation) and a low dose (1 mg/kg, mimicking natural rhizosphere levels). While overall ARG α- and β-diversity remained stable, we observed significant taxonomic restructuring, with Pseudomonadota increasing by 1.36-2.15 % and Actinomycetota declining by 1.14-1.74 % across treatments. Resistome analysis showed dose-dependent ARG selection: control soils favored target alteration mechanism, whereas McA promoted efflux, inactivation, and protection mechanisms. Network analysis demonstrated disruption of complex ARG-host associations, as control-dominant genera belonging to Actinomycetota (Conexibacter, Baekduia, and Capillimicrobium) maintaining 16-21 ARGs per genome decreased, while genera belonging to Pseudomonadota (Bradyrhizobium, Mesorhizobium, Paraburkholderia, and Piscinibacter) with streamlined resistomes (1-2 ARGs) became prevalent. Functional gene profiling (COGs) and annotation of MAGs revealed dose-dependent restructuring: low-dose McA enriched chemotaxis systems and broad-spectrum efflux pumps, facilitating motile escape and energy-efficient resistance, whereas high-dose exposure selected for secondary metabolite synthesis, metal transporters, and cell wall remodeling genes, indicating defensive countermeasures. These findings demonstrate McA's biphasic selection: low doses favor avoidance strategies (efflux/motility), while high doses enforce biosynthetic defenses and structural resilience. The results support the hypothesis that narrow-spectrum antibiotics act as ecosystem engineers through metabolic trade-offs, highlighting the need to evaluate resistome restructuring in biocontrol agent risk assessments.},
}

@article {pmid40833948,
year = {2025},
author = {Kanyerezi, S and Guerfali, FZ and Anzaku, AA and Babaleye, OA and Calvert-Joshua, T and Nguinkal, JA and Amoo, OP and Atri, C and Khan, W and Saleh, I and Nisar, MI and Kasambula, AS and Morapedi, K and Mboowa, G},
title = {Correction: Wastewater metagenomics in Africa: Opportunities and challenges.},
journal = {PLOS global public health},
volume = {5},
number = {8},
pages = {e0005097},
doi = {10.1371/journal.pgph.0005097},
pmid = {40833948},
issn = {2767-3375},
abstract = {[This corrects the article DOI: 10.1371/journal.pgph.0004044.].},
}

@article {pmid40833852,
year = {2025},
author = {Vander Donck, L and Victor, M and Van Beeck, W and Van Rillaer, T and Dillen, J and Ahannach, S and Wittouck, S and Allonsius, CN and Lebeer, S},
title = {Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.},
journal = {Cell reports},
volume = {44},
number = {9},
pages = {116171},
doi = {10.1016/j.celrep.2025.116171},
pmid = {40833852},
issn = {2211-1247},
abstract = {The human vagina is a unique microbiome, typically predominated by Lactobacillus species in healthy women. However, we currently lack an understanding of why lactobacilli predominate in this environment and how these bacteria interact, aspects that are crucial for developing microbiome-based therapeutics. In this study, we used cost-efficient synthetic communities (SynComs) to investigate the stability and dynamics of Lactobacillus-predominated vaginal communities from healthy women independent of host influence. Reproducible communities of Lactobacillus crispatus co-occurring with Limosilactobacillus species and Lactobacillus jensenii were established in top-down experiments. Co-occurrence was verified with compositional correlation patterns in metagenome sequencing data and reproduced through a bottom-up approach. This co-occurrence pattern was independent of strain selection, host factors, and inoculation ratio. Genome-scale metabolic models predicted potential cross-feeding involving amino acids (e.g., L-arginine, L-lysine, and γ-aminobutyric acid [GABA]) and vitamins as mechanisms mediating their co-occurrence. This study provides a framework for developing reproducible synthetic vaginal Lactobacillus communities and informs future microbiome-based therapies.},
}

@article {pmid40833800,
year = {2025},
author = {Kaspersen, HP and Estensmo, EL and Slettemeås, JS and Haverkamp, THA and Sjurseth, SK and Granstad, S and Sekse, C and Frederiksen, RF and Urdahl, AM},
title = {Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001466},
pmid = {40833800},
issn = {2057-5858},
mesh = {Animals ; *Monensin/pharmacology ; *Turkeys/microbiology ; *Bifidobacterium/drug effects/genetics/classification/isolation & purification ; Poultry Diseases/prevention & control/microbiology ; Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; Norway ; Female ; Male ; Coccidiosis/veterinary/prevention & control ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; *Coccidiostats/pharmacology ; },
abstract = {Intestinal tissue damage caused by coccidiosis is an important predisposing factor for necrotic enteritis in turkeys, and both diseases are common health issues in turkey production. In Norway, the in-feed ionophore coccidiostat monensin has been used as a preventive measure to combat coccidiosis since the late 1980s. In 2022, however, preventive use of monensin was phased out, which led to an undesired increase in antibiotic treatments among turkey flocks, largely due to necrotic enteritis. The aim of this study was to investigate the overall effects of the preventive monensin use and antibiotic treatment on the turkey caecal microbiota. A total of 102 flock samples from the Norwegian turkey population were included, and metagenomic datasets were generated through shotgun sequencing. All datasets were processed with the Taxprofiler pipeline, followed by diversity, redundancy and differential abundance analyses in R. A significant decrease in alpha and beta diversity was observed for the caecal samples from turkeys exposed to monensin, compared with the non-exposed. An increased abundance of Bifidobacterium spp. was observed in the samples from monensin-exposed turkeys, including Bifidobacterium pullorum, Bifidobacterium longum, Bifidobacterium pseudolongum, Bifidobacterium pseudocatenulatum and Bifidobacterium animalis. Additionally, a decrease in Megamonas and Megasphaera species was detected in these samples. Further, species within the Clostridium genus were higher in abundance among the samples from female turkeys compared with male turkeys. The results indicate that the use of monensin seems to decrease the overall diversity and promote the abundance of Bifidobacterium spp. in the caecum of turkeys, while decreasing the abundance of Megamonas and Megasphaera species. The use of monensin may be beneficial for the gut microbiota due to an increase in favourable Bifidobacterium spp. In contrast, treatment with phenoxymethylpenicillin (penicillin V) early in the turkey life cycle does not seem to cause long-term changes in the caecal microbiota composition. However, further studies are needed to investigate the effects of a decreased abundance of Bifidobacterium spp. and increased gut microbiota diversity in turkeys in the absence of monensin use.},
}

Animals
*Monensin/pharmacology
*Turkeys/microbiology
*Bifidobacterium/drug effects/genetics/classification/isolation & purification
Poultry Diseases/prevention & control/microbiology
Cecum/microbiology
*Gastrointestinal Microbiome/drug effects
Norway
Female
Male
Coccidiosis/veterinary/prevention & control
Metagenomics
Anti-Bacterial Agents/pharmacology
*Coccidiostats/pharmacology

@article {pmid40833797,
year = {2025},
author = {O'Ferrall, AM and Juhász, A and Jones, S and Makaula, P and Namacha, G and Ame, S and Oguttu, D and Foo, A and Kayuni, SA and LaCourse, EJ and Musaya, J and Stothard, JR and Roberts, AP},
title = {Freshwater snail faecal metagenomes reveal environmental reservoirs of antimicrobial resistance genes across two continents.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001480},
pmid = {40833797},
issn = {2057-5858},
mesh = {Animals ; *Feces/microbiology ; *Metagenome ; *Snails/microbiology ; Fresh Water/microbiology ; Anti-Bacterial Agents/pharmacology ; Uganda ; Tanzania ; United Kingdom ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Bacterial Proteins/genetics ; Bacteria/genetics ; },
abstract = {The transfer of antimicrobial resistance genes (ARGs) from environmental microbes to pathogens is a critical but underexplored One Health driver of antimicrobial resistance. Here, we evaluate freshwater snails, which are geographically widespread aquatic invertebrates, as environmental reservoirs of ARGs. We collected faeces from eight gastropod genera at 15 freshwater locations across Malawi, Uganda, Zanzibar and the UK and conducted the first freshwater snail faecal metagenomic study. We detected putative ARGs predicted to confer resistance to 13 antibiotic classes, including carbapenems. All ARGs that could be assembled into metagenome-assembled genomes (MAGs) were found within Proteobacteria, which dominated the faecal microbiomes and were strongly associated with the total ARG load. In Malawi, we linked bla OXA-181 (bla OXA-48-like), a previously mobilized carbapenemase gene, to Shewanella xiamenensis, the gene's known progenitor. We detected another bla OXA-48-like gene by read mapping from a sample in the UK. We identified mobile colistin resistance (mcr)-like genes at 11 of 15 locations, with two mcr-7-like genes being found in an Aeromonas jandaei MAG in Uganda. Our findings highlight freshwater snail faeces as a One Health-relevant environmental reservoir of clinically important ARGs.},
}

Animals
*Feces/microbiology
*Metagenome
*Snails/microbiology
Fresh Water/microbiology
Anti-Bacterial Agents/pharmacology
Uganda
Tanzania
United Kingdom
*Drug Resistance, Bacterial/genetics
Metagenomics
Bacterial Proteins/genetics
Bacteria/genetics

@article {pmid40833630,
year = {2025},
author = {Sampasivam, Y and Razman, KK and Mazlan, NSM and Azizan, KA and Ahlawat, YK and Othman, R},
title = {Towards Sustainable Agarwood Production: Integrating Microbial Interactions, Anatomical Changes, and Metabolite Biosynthesis.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jimb/kuaf025},
pmid = {40833630},
issn = {1476-5535},
abstract = {Agarwood is a highly valuable non-timber forest product mainly derived from the Aquilaria genus, widely traded in the perfumery, religious items, and traditional medicine industries. Naturally, agarwood forms within the xylem as part of the tree's defense mechanism against environmental stressors and microbial infection. The escalating demand for agarwood has led to the overexploitation of Aquilaria species, with some now classified as critically endangered. Despite advancements in artificial induction methods for sustainable agarwood supply, the intricate links between physiological and molecular mechanisms governing its formation remain poorly understood. This review addresses these knowledge gaps by examining the interplay between morphological changes in xylem structure during tylose formation and molecular alterations, particularly the biosynthesis of 2-(2-phenylethyl)chromones (PECs), key compounds in agarwood. Additionally, it integrates findings from multi-omics approaches including genomics, transcriptomics, proteomics, and metagenomics to reveal how secondary metabolite biosynthesis, including PECs and terpenes, is regulated across various Aquilaria species, regions, and induction techniques. The role of microbial communities, particularly endophytes such as Fusarium, in regulating agarwood formation is also discussed, emphasizing their involvement in both natural and artificial induction strategies. Furthermore, this review explores the role of reactive oxygen species (ROS) in mediating morphological and biochemical defense responses, alongside the functions of transcription factors (TFs), protein kinases, and signaling molecules in balancing defense and growth. However, the crosstalk between key genes such as chalcone synthases, MAPK, cytochromes, NADPH oxidases, TFs, and miRNAs require further study to fully understand the complex defense mechanisms in Aquilaria trees. Overall, this review aims to bridge the current knowledge gaps by linking morphological and biochemical changes in agarwood formation, particularly PEC biosynthesis, while proposing metabolite engineering using microbial hosts as a promising tool for sustainable and technology-driven agarwood production.},
}

@article {pmid40833501,
year = {2025},
author = {Annamalai, A and Sasikumar, R},
title = {Enzymatic valorization of fishery by-products: harnessing cold-adapted marine proteases for sustainable production of bioactive peptides.},
journal = {Archives of microbiology},
volume = {207},
number = {9},
pages = {232},
pmid = {40833501},
issn = {1432-072X},
mesh = {*Peptide Hydrolases/metabolism/chemistry ; Cold Temperature ; Animals ; *Peptides/metabolism/chemistry ; Fisheries ; Fishes ; Aquatic Organisms/enzymology ; Aquaculture ; },
abstract = {The rapid expansion of aquaculture and fish processing industries has resulted in the annual generation of approximately 99 million tons of fishery byproducts, including heads, bones, skin, viscera, and fish scales. These residual biomasses are typically underutilized despite their richness in proteins, lipids, collagen, and other bioactive compounds. Recent advancements in enzymatic valorization, particularly through the application of cold-adapted marine proteases, have offered eco-efficient solutions for converting these byproducts into high-value bioactive peptides and nutraceutical ingredients. Cold-adapted proteases function efficiently at low temperatures, preserving thermolabile compounds, reducing energy input, and minimizing undesirable reactions. This review critically examines the biochemical composition of fishery by-products and explores the distinctive structural and catalytic properties of cold-adapted proteases. We highlight novel strategies for their discovery using metagenomics, bioinformatics and AI-assisted enzyme engineering. Process optimization aspects, including the use of membrane bioreactors, immobilization supports, and downstream purification techniques, are discussed, with an emphasis on improving the yield, stability, and scalability. The bioactivities of the derived peptides, such as antioxidant, ACE-inhibitory, antimicrobial, and anti-inflammatory effects, are summarized alongside their emerging functional roles in metabolic regulation and in wound healing. This article presents case studies, economic assessments, and regulatory considerations to evaluate the commercial viability of cold-adapted biocatalysis in the circular blue bioeconomy. Finally, technical limitations, such as enzyme deactivation, recovery, and cost-performance ratios, are critically analyzed, and future directions for sustainable marine biorefinery development are discussed.},
}

*Peptide Hydrolases/metabolism/chemistry
Cold Temperature
Animals
*Peptides/metabolism/chemistry
Fisheries
Fishes
Aquatic Organisms/enzymology
Aquaculture

@article {pmid40833454,
year = {2025},
author = {Fong, GY and Chan, KG and Goh, WL and Yap, ML},
title = {Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {134},
pmid = {40833454},
issn = {1572-9699},
support = {IPSR/RMC/UTARRF/2022-C1/Y01//Universiti Tunku Abdul Rahman/ ; },
mesh = {Animals ; *Columbidae/microbiology/virology ; *Feces/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Metagenomics ; Viruses/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification/drug effects ; Metagenome ; Malaysia ; *Microbiota ; Biodiversity ; Phylogeny ; *Drug Resistance, Microbial/genetics ; },
abstract = {Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.},
}

Animals
*Columbidae/microbiology/virology
*Feces/microbiology/virology
*Bacteria/genetics/classification/isolation & purification/drug effects
Metagenomics
Viruses/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification/drug effects
Metagenome
Malaysia
*Microbiota
Biodiversity
Phylogeny
*Drug Resistance, Microbial/genetics

@article {pmid40833093,
year = {2025},
author = {Lai, Z-L and Su, Y-D and Lin, H-H and Wang, S-Y and Lin, Y and Liang, S and Chen, W-C and Hsueh, P-R},
title = {Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0311924},
doi = {10.1128/spectrum.03119-24},
pmid = {40833093},
issn = {2165-0497},
abstract = {UNLABELLED: The widespread adoption of metagenomic next-generation sequencing has revolutionized microbial detection, yet contaminating DNA in laboratory reagents poses significant challenges for result interpretation. This study investigated microbial contamination profiles across four commercial DNA extraction reagent brands (M, Q, R, and Z) and assessed batch-to-batch variability. Extraction blanks were generated using molecular-grade water or ZymoBIOMICS Spike-in Control I as input materials. Analysis revealed distinct background microbiota profiles between brands, with some containing common pathogenic species that could affect clinical interpretation. Notably, background contamination patterns varied significantly between different lots of the same brand, highlighting the need for lot-specific microbiota profiling. Site-specific environmental contaminants were identified through analysis of 30 control samples from a single study site. Additionally, comparison of blood samples from healthy individuals with control samples suggested no evidence of a consistent blood microbiome, suggesting that "extraction blanks" may serve as negative controls in clinical metagenomic testing of sterile liquid biopsy samples. These findings emphasize the importance of including negative controls in every run and underscore the need for manufacturers to provide comprehensive background microbiota data for each reagent lot to optimize clinical interpretation and minimize false-positive results.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection and microbiome studies, but contamination from DNA extraction reagents remains a critical challenge. This study highlights the significant variability in background microbiota profiles across reagent brands and manufacturing lots, emphasizing the need for manufacturers to provide detailed contamination profiles. Our findings underscore the importance of implementing extraction blanks as standard controls and incorporating bioinformatics tools to account for background noise. These measures are essential to enhance the reliability of mNGS results and prevent diagnostic errors, particularly in clinical settings where contamination could mask or mimic pathogen signals. Additionally, our confirmation that healthy blood lacks a consistent microbiome helps streamline control selection in clinical testing protocols, potentially reducing costs and complexity in clinical mNGS workflows.},
}

@article {pmid40832979,
year = {2025},
author = {Zhou, W and Fan, Y and Zhang, X and Liu, M and Jiang, S and Shang, E and Duan, J},
title = {Amelioration of Guishao Yigong Decoction on Colorectal Cancer Through the Integration of 16S rRNA Sequencing and Fecal Metabolomics.},
journal = {Biomedical chromatography : BMC},
volume = {39},
number = {10},
pages = {e70198},
doi = {10.1002/bmc.70198},
pmid = {40832979},
issn = {1099-0801},
support = {ZDXM-3-9//Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization/ ; },
mesh = {Animals ; *Colorectal Neoplasms/metabolism/drug therapy/microbiology ; *Feces/chemistry/microbiology ; *Drugs, Chinese Herbal/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; Mice ; Metabolomics/methods ; *Metabolome/drug effects ; Male ; },
abstract = {Guishao Yigong Decoction (GYD), a classical formula, has been used to treat colorectal cancer (CRC) in clinical practices. However, its mechanism is still unclear. Increasing evidence suggests that the gut microbiota may serve as a potential target for treating CRC. Therefore, this study aims to elucidate the amelioration and potential mechanism of GYD on CRC by comprehensively analyzing the metagenome of gut microbiota and fecal metabolome. The results indicated that GYD significantly reduced the number and size of adenomas in the mouse colon, decreased spleen index, alleviated mouse emaciation and rectal bleeding, and protected the colonic barrier. 16S rRNA gene sequencing analysis revealed that GYD could markedly improve the dysbiosis of gut microbiota in CRC mice, increasing the abundance of beneficial bacteria and decreasing the abundance of pathogenic bacteria. Furthermore, the disordered fecal metabolic profiling of CRC mice was notably reversed by GYD. Following GYD administration, metabolites such as thiamine pyrophosphate, 3-methylpentanoic acid, and propanoic acid significantly increased, whereas 2-hydroxy-2-methylpropanoic acid, levodopa, and stearic acid remarkably decreased. Correlation analysis further indicated a close relationship between differential gut microbiota and metabolites. In conclusion, the amelioration of GYD on CRC might involve the regulation of gut microbiota and its metabolism.},
}

Animals
*Colorectal Neoplasms/metabolism/drug therapy/microbiology
*Feces/chemistry/microbiology
*Drugs, Chinese Herbal/pharmacology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/drug effects
Mice
Metabolomics/methods
*Metabolome/drug effects
Male

@article {pmid40832781,
year = {2025},
author = {Tian, Y and Xu, Q and Wu, Z and Wang, H and Hu, X and He, N and Li, H and Liu, B and Zhong, Y and Zhang, H and Wang, M and Xiao, L and Li, S and Zou, Y},
title = {Ameliorating Effect of Bifidobacterium breve CM02-09T on High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease in Mice.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {16},
pages = {e70957},
doi = {10.1096/fj.202501250RR},
pmid = {40832781},
issn = {1530-6860},
support = {32100009//National Natural Science Foundation of China-Guangdong Joint Fund/ ; },
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/etiology/microbiology/metabolism/pathology/therapy ; *Diet, High-Fat/adverse effects ; Male ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Mice ; *Bifidobacterium breve/physiology ; *Gastrointestinal Microbiome ; Liver/metabolism/pathology ; },
abstract = {Evidences have demonstrated that the regulation of gut microbiota by probiotics can be utilized to prevent nonalcoholic fatty liver disease (NAFLD); Bifidobacterium was widely used as a potential therapeutic alternative for metabolic diseases. In this study, the probiotic functions of Bifidobacterium breve CM02-09T and its effects on NAFLD were investigated through genome annotation and high-fat diet (HFD)-induced mouse model. The genome of B. breve CM02-09T consists of a single circular chromosome of 2 372 890 bp. Eighteen male C57BL/6J mice were fed a normal chow diet (NCD), a high-fat diet, and a high-fat diet (HFD) with B. breve CM02-09T separately for 12 weeks. Histopathology, lipid content, biochemical markers in the liver and blood, and metagenomics were assessed and compared. Our results indicate that supplementation with B. breve CM02-09T alleviated liver damage, reduced fat accumulation in the liver and epididymal adipose tissue, decreased TNF-α concentration, and improved NAFLD activity scores. Metagenomic analysis revealed that administration of B. breve CM02-09T promoted a decreased Firmicutes/Bacteroidetes ratio (F/B), an increase in beneficial bacteria, and enhanced lipid metabolism functions. Correlation analysis between the differential species and NAFLD-related indicators suggested that the anti-NAFLD effect of B. breve CM02-09T is related to the gut microbiota. Therefore, B. breve CM02-09T attenuates NAFLD by modulating the gut microbiota and could be used as an alternative therapeutic strategy.},
}

Animals
*Non-alcoholic Fatty Liver Disease/etiology/microbiology/metabolism/pathology/therapy
*Diet, High-Fat/adverse effects
Male
*Probiotics/pharmacology
Mice, Inbred C57BL
Mice
*Bifidobacterium breve/physiology
*Gastrointestinal Microbiome
Liver/metabolism/pathology

@article {pmid40832572,
year = {2025},
author = {Zhang, S and Wu, J and Wang, D and Song, J and Li, Y and Yin, C and Sun, C and Ding, S and Liu, T and Kou, Z},
title = {The First Imported Case of Zika Virus Infection - Shandong Province, China, 2025.},
journal = {China CDC weekly},
volume = {7},
number = {30},
pages = {1004-1008},
pmid = {40832572},
issn = {2096-7071},
abstract = {Zika virus (ZIKV) is transmitted primarily through mosquito vectors, including Aedes albopictus and Aedes aegypti, both of which are distributed across multiple provinces in China. Approximately 80% of ZIKV infections remain asymptomatic, while symptomatic cases typically manifest as mild, self-limiting illnesses lacking pathognomonic features. Common clinical presentations include maculopapular rash, low-grade fever, conjunctivitis, arthralgia, and myalgia.

WHAT IS ADDED BY THIS REPORT?: The clinical manifestations of ZIKV infection are nonspecific and may closely mimic other febrile illnesses, complicating differential diagnosis. This study documents the first laboratory-confirmed ZIKV infection case in Shandong Province. The patient exhibited fever accompanied by extensive subcutaneous petechiae, predominantly distributed across the chest and upper extremities.

This investigation provides a comprehensive epidemiological analysis and phylogenetic characterization of a ZIKV infection case imported from Thailand. In accordance with China's Border Health and Quarantine Law, international port cities must strengthen surveillance and diagnostic testing for imported infectious diseases. For cases presenting with unclear diagnoses, healthcare providers should prioritize obtaining detailed 30-day travel histories to evaluate potential exposure risks of imported infectious diseases.},
}

@article {pmid40832300,
year = {2025},
author = {Horvath, ERB and Winter, JM},
title = {SeqForge: A scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.12.669971},
pmid = {40832300},
issn = {2692-8205},
abstract = {BACKGROUND: The rapid increase in publicly available microbial and metagenomic data has created a growing demand for tools that can efficiently perform custom large-scale comparative searches and functional annotation. While BLAST+ remains the standard for sequence similarity searches, population-level studies often require custom scripting and manual curation of results, which can present barriers for many researchers.

RESULTS: We developed SeqForge, a scalable, modular command-line toolkit that streamlines alignment-based searches and motif mining across large genomic datasets. SeqForge automates BLAST+ database creation and querying, integrates amino acid motif discovery, enables sequence and contig extraction, and curates results into structured, easily parsed formats. The platform supports diverse input formats, parallelized execution for high-performance computing environments, and built-in visualization tools. Benchmarking demonstrates that SeqForge achieves near-linear runtime scaling for computationally intensive modules while maintaining modest memory usage.

CONCLUSIONS: SeqForge lowers the computational barrier for large-scale meta/genomic exploration, enabling researchers to perform population-scale BLAST searches, motif detection, and sequence curation without custom scripting. The toolkit is freely available and platform-independent, making it suitable for both personal workstations and high-performance computing environments.},
}

@article {pmid40832205,
year = {2025},
author = {Fan, Y and Ni, M and Aggarwala, V and Mead, EA and Ksiezarek, M and Cao, L and Kamm, MA and Borody, T and Paramsothy, S and Kaakoush, NO and Grinspan, A and Faith, JJ and Fang, G},
title = {Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.30.615906},
pmid = {40832205},
issn = {2692-8205},
abstract = {Fecal microbiota transplantation (FMT) has revolutionized the treatment of recurrent Clostridioides difficile infection (rCDI) and is being evaluated across other diseases. Accurate tracking of bacterial strains that stably engraft in recipients is critical for understanding the determinants of strain engraftment, evaluating their correlation with clinical outcomes, and guiding the development of therapeutic bacterial consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. In this study, we described a novel framework, LongTrack, which uses long-read metagenomic assemblies and rigorous informatics tailored for FMT strain tracking. We highlighted LongTrack advantage over short-read approaches especially when multiple strains co-exist in the same sample. We showed LongTrack uncovered hundreds of engrafted strains across six FMT cases of rCDI and inflammatory bowel disease patients. Furthermore, long reads also allowed us to assess the genomic and epigenomic stability of engrafted strains during the 5-year follow-ups, revealing structural variations that may be associated with strain adaptation in a new host environment. Combined, our study advocates the use of long-read metagenomics and LongTrack to enhance strain tracking in future FMT studies, paving the way for the development of more effective defined biotherapeutic as an alternative to FMT.},
}

@article {pmid40832181,
year = {2025},
author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H},
title = {A prevalent huge phage clade in human and animal gut microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.10.669567},
pmid = {40832181},
issn = {2692-8205},
abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (Jumbo gut) phages with genomes of 360-402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38-57% identity, suggesting horizontal acquisition from other phages. Over 1,500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.},
}

@article {pmid40831761,
year = {2025},
author = {Nikaein, H and Sharifi-Zarchi, A},
title = {Multi-metric locality sensitive hashing enhances alignment accuracy of bisulfite sequencing reads: BisHash.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf144},
pmid = {40831761},
issn = {2635-0041},
abstract = {MOTIVATION: Locality-Sensitive Hashing (LSH) is a widely used algorithm for estimating similarity between large datasets in bioinformatics, with applications in genome assembly, sequence alignment, and metagenomics. However, traditional single-metric LSH approaches often lead to inefficiencies, particularly when handling biological data where regions may have diverse evolutionary histories or structural properties. This limitation can reduce accuracy in sequence alignment, variant calling, and functional analysis.

RESULTS: We propose Multi-Metric Locality-Sensitive Hashing (M2LSH), an extension of LSH that integrates multiple similarity metrics for more accurate analysis of complex biological data. By capturing diverse sequence and structural features, M2LSH improves performance in heterogeneous and evolutionarily diverse regions. Building on this, we introduce Multi-Metric MinHash (M3Hash), enhancing sequence alignment and similarity detection. As a proof of concept, we present BisHash, which applies M2LSH to bisulfite sequencing, a key method in DNA methylation analysis. Although not fully optimized, BisHash demonstrates superior accuracy, particularly in challenging scenarios like cancer studies where traditional approaches often fail. Our results highlight the potential of M2LSH and M3Hash to advance bioinformatics research.

The source code for BisHash and the test procedures for benchmarking aligners using simulated data are publicly accessible at https://github.com/hnikaein/bisHash.},
}

@article {pmid40830754,
year = {2025},
author = {Li, Q and Fan, X and Wang, K and Wu, X and Li, J and An, Y and Wei, P and Shi, W and Shan, Y and Chen, S and Zhao, G},
title = {Subdural empyema caused by Aggregatibacter segnis: a rare case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1042},
pmid = {40830754},
issn = {1471-2334},
support = {Z221100007422016//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; 82030037//National Natural Science Foundation of China/ ; 2023XACX0005//Science and Technology Innovation Program of Xiongan New Area/ ; ZLRK202319//Beijing Hospitals Authority Clinical medicine Development of special funding support/ ; 11000023T000002036286//Translational and Application Project of Brain-inspired and Network Neuroscience on Brain Disorders, Beijing Municipal Health Commission/ ; 2021ZD0201801//STI2030-Major Projects/ ; },
mesh = {Humans ; Female ; Middle Aged ; *Empyema, Subdural/microbiology/diagnosis/drug therapy/surgery/diagnostic imaging ; Anti-Bacterial Agents/therapeutic use ; *Pasteurellaceae Infections/microbiology/diagnosis/drug therapy ; *Pasteurellaceae/isolation & purification/genetics ; Magnetic Resonance Imaging ; Tomography, X-Ray Computed ; },
abstract = {BACKGROUND: Aggregatibacter species are Gram-negative bacteria typically recognized as oral saprophytes in humans, with invasive infections uncommon in immunocompetent individuals. To the best our knowledge, this is the first reported case of subdural empyema attributed to Aggregatibacter segnis (A. segnis).

CASE PRESENTATION: A 50-year-old female was transferred to our hospital from a local facility due to headache, fever, and left-sided limb numbness. Initially suspected of subdural hematoma and viral encephalitis, she did not respond well to prior treatment. Cerebral computed tomography and magnetic resonance imaging revealed a subdural lesion in the frontal-temporal region and sinusitis. Virus-related tests, smear, and culture of cerebrospinal fluid (CSF) were negative. Craniotomy was performed to evacuate the subdual empyema, and A. segnis was detected in the culture of pus. The discrepancy between metagenomic next-generation sequencing (mNGS) and culture highlights diagnostic challenges in this pretreated patient. Antibiotic treatment was guided by culture results and mNGS. Clinical symptoms resolved gradually following surgery and administration of antibiotics.

CONCLUSIONS: This rare case suggested that A. segnis should be considered in the diagnosis of subdural empyema. Multimodal diagnostics, prompt neurosurgical management, and individualized antimicrobial stewardship are crucial in managing rare central nervous system infections.},
}

Humans
Female
Middle Aged
*Empyema, Subdural/microbiology/diagnosis/drug therapy/surgery/diagnostic imaging
Anti-Bacterial Agents/therapeutic use
*Pasteurellaceae Infections/microbiology/diagnosis/drug therapy
*Pasteurellaceae/isolation & purification/genetics
Magnetic Resonance Imaging
Tomography, X-Ray Computed

@article {pmid40830751,
year = {2025},
author = {Ahmad, AA and Fletcher, K and Hesford, N and Glendinning, L},
title = {Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {520},
pmid = {40830751},
issn = {1471-2180},
support = {BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Fundraising from the private sector//The Game and Wildlife Conservation Trust/ ; Fundraising from the private sector//The Game and Wildlife Conservation Trust/ ; Chancellor's Fellowship//University of Edinburgh/ ; },
}

@article {pmid40830497,
year = {2025},
author = {Marialva, EF and Martins-Campos, KM and de Almeida, VR and Ríos-Velasquez, CM and Tempone, AJ and Pessoa, FAC and Traub-Cseko, YM},
title = {Investigation of bacterial microbiota variability in two allopatric populations of Nyssomyia umbratilis, susceptible and nonsusceptible to Leishmania (Viannia) guyanensis infection in the Amazon region.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {354},
pmid = {40830497},
issn = {1756-3305},
mesh = {Animals ; *Psychodidae/microbiology/parasitology ; Brazil ; Female ; *Leishmania guyanensis/physiology ; *Insect Vectors/microbiology/parasitology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Humans ; },
abstract = {BACKGROUND: Sand flies of the species Nyssomyia umbratilis (Diptera: Psychodidae: Phlebotominae) are vectors of the parasite Leishmania (Viannia) guyanensis, one of the etiological agents of cutaneous leishmaniasis in the Amazon region. In addition, Ny. umbratilis is a cryptic species, with populations showing differences in their ability to transmit the parasite. For instance, populations of Ny. umbratilis from the Manacapuru municipality (MAN), located on the south bank of the Negro river, in the Amazonas state of Brazil, shows refractoriness to Leishmania infection, while populations from Rio Preto da Eva municipality (RPE), located on the north bank of the Negro river, are susceptible to infection. This lack of vectorial capacity may be caused by several factors, including the intestinal bacterial microbiota of sand flies.

METHODS: In this work, we carried out a metagenomic study of the intestinal microbiota of Ny. umbratilis populations from MAN and RPE. Ny. umbratilis females were collected in forested areas, sand fly midguts were dissected, DNA was extracted, and the 16 S rRNA gene sequenced to identify the bacterial composition of the microbiota.

RESULTS: In total, 16 phyla, 33 classes, 49 orders, 93 families, and 112 genera of bacteria were identified. The phylum Proteobacteria was the most frequent (85.9%) in both localities, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes with, 9.9%, 4.9%, and 4.4%, respectively. In MAN, 84 genera were identified and 79 in RPE, with MAN having a greater richness compared with RPE. Among these, the genera Rickettsia, Prevotella, Porphyromonas, Peptostreptococcus, and Caulobacter were the most prevalent in MAN, and the genera Rickettsia, Prevotella, Cryocola, Porphyromonas, and Caulobacter were the most prevalent in RPE.

CONCLUSIONS: Bacterial microbiota from MAN insects presents a greater diversity in relation to the RPE insects. Some of the identified bacteria have the potential to be used in alternative transmission control approaches as the development of transgenic vectors, and also, bacteria found exclusively in MAN sand flies may be candidates for a future transmission control approach to combat leishmaniasis in the Amazon region.},
}

Animals
*Psychodidae/microbiology/parasitology
Brazil
Female
*Leishmania guyanensis/physiology
*Insect Vectors/microbiology/parasitology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Microbiota
Humans

@article {pmid40829558,
year = {2025},
author = {Huang, WC and Spang, A},
title = {DPANN archaea.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R791-R794},
doi = {10.1016/j.cub.2025.06.038},
pmid = {40829558},
issn = {1879-0445},
mesh = {*Archaea/genetics/physiology/classification/metabolism ; *Symbiosis ; Phylogeny ; *Genome, Archaeal ; Biological Evolution ; },
abstract = {Archaea are one of the two primary domains of life alongside Bacteria. Extant archaea play an important role in global nutrient cycles and comprise members that were crucial for the evolution of life on Earth including the origin of eukaryotic cells through a symbiotic integration of an archaeal and bacterial partner. Despite their importance in ecology and evolution, our knowledge of archaeal diversity and function remains limited in part because it has proven challenging to cultivate archaea in the laboratory. Over the last two decades, the use of novel cultivation-independent approaches such as metagenomics has not only led to the discovery of a vast diversity of previously unknown archaeal lineages but also provided a window into their genomic content, allowing researchers to make predictions about metabolic functions and lifestyles. For example, by combining genomics approaches with phylogenetic analyses (that is, the reconstruction of species trees) researchers have uncovered several phylum-level lineages of putative genome-reduced archaea referred to as the 'DPANN' archaea, whose members were shown to have limited metabolic capabilities, indicating their dependency on symbiotic partners. These findings are consistent with observations from cultivation-based studies that have succeeded in enriching some of these small-cell symbionts in co-cultures with their hosts. Although they were initially discovered in extreme environments, DPANN archaea have now been shown to be widespread across a variety of environments and may thus play an important role in not only host evolution but also ecology. Herein, we aim to highlight DPANN archaea by providing an overview of their diversity, genomic and metabolic features, unique cell biology and interactions, and evolutionary origins. We also underscore several fascinating topics that remain underexplored.},
}

*Archaea/genetics/physiology/classification/metabolism
*Symbiosis
Phylogeny
*Genome, Archaeal
Biological Evolution

@article {pmid40829433,
year = {2025},
author = {Chen, W and He, Y and Xiang, Y and Xie, L},
title = {Porous filter balls alternating internal structure of aerobic composting to drive rapid stabilization and efficient metabolic collaboration.},
journal = {Waste management (New York, N.Y.)},
volume = {206},
number = {},
pages = {115082},
doi = {10.1016/j.wasman.2025.115082},
pmid = {40829433},
issn = {1879-2456},
abstract = {Co-composting of food waste and agricultural residues offers a promising biotechnological solution for organic solid waste management, where oxygen availability critically governs efficiency. This study evaluated the impact of polypropylene-based porous filter balls (PFB) on composting performance. The results demonstrated that PFB addition elevated peak temperature by 10.1 % and reduced oxygen content by 11.2-55.3 % compared to the control (CK), indicating enhanced oxygen utilization through construction of transport channels. Meanwhile, PFB treatment accelerated organic matter and crude fiber degradation, shortening maturation time by 14 days while improving end-product quality. Three-dimensional excitation emission matrix analysis confirmed enhanced humification, and physical characterization revealed a more porous structure with greater soil amendment potential. Microbial analysis showed that PFB addition enriched organic-degrading taxa (e.g., Aeribacillus) and strengthened metabolic cooperation. Metagenomic analysis further revealed upregulation of key pathways including dissimilatory nitrate reduction to ammonium, glycolysis, fatty acid metabolism, tricarboxylic acid cycle and aromatic amino acid biosynthesis, collectively improving nitrogen retention, degradation efficiency and humification. This study establishes PFB treatment as an effective oxygen-management strategy for enhancing composting efficiency and product quality.},
}

@article {pmid40829401,
year = {2025},
author = {Zhang, J and Chen, J and Wang, C and Wang, P and Feng, B and Gao, H and Chen, D},
title = {Nitrate input enriched the antibiotic resistance genes in lake sediments by shaping co-host community and promoting horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139580},
doi = {10.1016/j.jhazmat.2025.139580},
pmid = {40829401},
issn = {1873-3336},
abstract = {The impact of various non-antibiotic factors on antibiotic resistance has garnered widespread attention. However, there has been little investigation into whether the coexistence of nutrients with antibiotic resistance genes (ARGs) in aquatic ecosystems contributes to the increasing abundance of ARGs. We employed a microcosm experiment and metagenomic analysis to investigate the impact of nitrate on ARG profiles in lake sediments. Our results revealed that increased nitrate input correspondingly elevated the abundance of sediment ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and nitrate reduction genes (NRGs). Among the metagenome-assembled genomes (MAGs) harboring ARGs found by binning analysis, nitrate inputs increased the abundance of 78.4 % ARG-carried MAGs, especially in genera Nitrosomonas and Sulfuriomonas. All MAGs carrying ARGs simultaneously encoded NRGs, suggesting that ARG-NRG co-hosts are important factors for ARG proliferation. Co-localization and Pearson's correlation analyses suggested that nitrate input most likely accelerated the acquisition of ARGs by particular bacterial taxa via horizontal gene transfer (HGT). Genes involved in HGT, including those related to reactive oxygen species production, membrane permeability, ATP synthesis, and pili synthesis, were also upregulated by nitrate input, thus potentially enhancing ARG transfer. Based on the partial least squares path modeling analysis, abundances of genes involved in HGT (r = 0.43) and ARG-NRG co-hosts (r = 0.41) had the highest direct positive impact on the ARG abundance. Our study suggests the increased nitrate levels may drive the dissemination of antibiotic resistance, consequently affecting human health.},
}

@article {pmid40829219,
year = {2025},
author = {Jing, J and Wang, T and Guo, X and Huang, P and Li, C and Qu, Y},
title = {Continuous exogenous bioaugmented remediation of petroleum-contaminated soil: Ecological effects, microbial communities, and mechanisms.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127007},
doi = {10.1016/j.jenvman.2025.127007},
pmid = {40829219},
issn = {1095-8630},
abstract = {The exogenous bioaugmentation technique is a widely employed strategy for remediating petroleum-contaminated soil. However, sustaining exogenous functional bacteria over extended periods in complex petroleum-contaminated environments is challenging, leading to reduced efficacy, and the interaction mechanisms with indigenous microorganisms remain poorly understood. This study utilized the previously developed petroleum-degrading bacterial agent ECT in a continuous bioaugmentation (C-Bio) approach for soil remediation. The outcomes were compared with those from a disposable bioaugmentation (D-Bio) and a control group (CG). After a 200-day remediation period, the C-Bio approach achieved a simulated petroleum degradation rate of 99.42 %. Concurrently, assessments of soil physicochemical properties, enzyme activities, and plant growth demonstrated that C-Bio resulted in favorable ecological restoration. Metagenomic analysis confirmed the successful colonization of the three exogenous bacteria in the C-Bio system. Network analysis revealed that this approach facilitated the directional succession of soil microbial communities, with the newly dominant indigenous bacteria forming cooperative or symbiotic relationships with the exogenous strains. Together, they synergistically degrade alkanes via terminal oxidation pathways and aromatic hydrocarbons through salicylic acid and phthalic acid pathways, leading to effective remediation of petroleum-contaminated soil. This study offers theoretical insights and empirical evidence supporting the development of continuous bioaugmentation processes for the remediation of petroleum-contaminated soils.},
}

@article {pmid40828642,
year = {2025},
author = {Davies, RG and Wood, LA and Hengist, A and O'Donovan, C and Barton, W and Crispie, F and Walhin, JP and Valdivia-Garcia, MA and Garcia-Perez, I and Frost, G and O'Sullivan, O and Cotter, PD and Gonzalez, JT and Betts, JA and Koumanov, F and Thompson, D},
title = {Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP287424},
pmid = {40828642},
issn = {1469-7793},
support = {MR/P002927/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Metabolic health improvements in response to exercise and energy restriction may be mediated by the gut microbiome, yet causal evidence in humans remains limited. We used a 3-week exercise and energy restriction intervention to examine changes to the gut microbiome in otherwise healthy sedentary men and postmenopausal women with overweight/obesity. Intervention participants (n = 18) reduced habitual energy intake by 5000 kcal/week and expended 2000 kcal/week in addition to habitual physical activity through treadmill walking at 70% V̇O2Peak. Control participants (n = 12) maintained their usual lifestyle. Participants underwent dual-energy X-ray absorptiometry (DEXA), and samples of faeces, fasted venous blood, subcutaneous adipose tissue and skeletal muscle were collected. Faecal DNA was sequenced and profiled using shotgun metagenomics, Kraken2/Bracken and Human Microbiome Project Unified Metabolic Analysis Network 2 (HUMAnN2). The intervention significantly reduced body mass (mean Δ ± SD: -2.6 ± 1.5 kg), fat mass (-1.5 ± 1.3 kg), fasted insulin (-23.5 ± 38.1 pmol/l), leptin (-10.6 ± 7.3 ng/ml) and total cholesterol (-0.70 ± 0.42 mmol/l) concentrations, and also improved insulin sensitivity (HOMA2%S (homeostatic model of assessment)). Despite these significant metabolic changes the gut microbiome was unchanged in terms of α and β diversity and relative abundance. Thus, despite clinically meaningful improvements in body composition and metabolic health, we found no evidence for changes to the gut microbiome. In conclusion early metabolic changes with weight loss in humans are unlikely to be mediated by changes to the gut microbiome. KEY POINTS: Changes to the gut microbiome could contribute to metabolic improvements associated with weight loss in humans, but there have been limited attempts to address this question using robust randomised controlled trials (RCTs). We used a parallel-group RCT to examine whether a 3-week combined energy intake restriction and vigorous-intensity exercise intervention in people with overweight and obesity was temporally associated with changes to gut microbiome taxonomic composition and functional potential, short-chain fatty acid concentrations and expression of genes related to host-microbiome interactions in skeletal muscle and subcutaneous adipose tissue. We found that the human gut microbiome remains unchanged in the face of an intensive energy intake restriction and vigorous exercise intervention that significantly improved body composition and metabolic health in people with overweight/obesity. These findings indicate that early metabolic changes with weight loss in humans are unlikely to be mediated by changes to the gut microbiome.},
}

@article {pmid40828272,
year = {2025},
author = {Guiglielmoni, N},
title = {De novo Genome Assembly Using Long Reads and Chromosome Conformation Capture.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {1-27},
pmid = {40828272},
issn = {1940-6029},
abstract = {The field of genome assembly merely exists as long as sequencers are not able to yield chromosome-level error-less sequencing reads for all species. It consists in reconstituting the original genome sequence from sequencing reads, with a final number of fragments matching the expected number of chromosomes. This process has been facilitated by the availability of longer and more accurate reads. At the incipit of genome assembly, Sanger sequencing reads Sanger et al (Proc Natl Acad Sci 74(12)spiepr A3B2 twbch ":":spiepr A3B2 twbch5463-5467, 1977) were already used to yield initial assemblies of different species, including the first human genome assembly International Human Genome Sequencing Consortium (Nature 409(6822):860-921, 2001). The higher throughput of second-generation sequencing, often called next-generation sequencing, democratized assemblies for a wider variety of species but brought assembly difficulties as the large datasets of short reads required long computational time, large memory resources, and yielded highly fragmented assemblies, with fragment numbers far over the expected number of chromosomes Metzker (Nat Rev Genet 11(1):31-46, 2010). Third-generation sequencing introduced long reads through the technologies of Oxford Nanopore Deamer et al(Nat Biotechnol 34(5):518-524, 2016) and Pacific BioSciences (PacBio) Eid et al (Science 323(5910):133-138, 2009). Long reads can reach several tens of kilobase, and up to hundreds of thousands of base pairs; although these reads initially had a low accuracy, recent developments to decrease the error rate below 1% Sereika et al (Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. bioRxiv, 2021); Wenger et al (Nat Biotechnol 37(October):1155-1162, 2019) have additionally reduced the complexity of genome assembly.Chromosome-level assemblies have become a standard in genome assembly publications: they can be used for synteny analysis, finding chromosomal rearrangements, they have more complete gene sets, a better resolution of repetitive content, and fewer contaminants. The availability of long reads and Hi-C and the decreasing cost of sequencing have brought about many high-quality insect genome assemblies, with currently 6,194 assemblies published on GenBank (accessed on 20.11.2024). Some remarkable efforts have been put toward Lepidoptera genomes, for which 188 chromosome-level assemblies were generated by the Darwin Tree of Life Wright et al (Nat Ecol Evol 8(4):777-790, 2024). At a smaller scale, a highly contiguous assembly was obtained for the ant Camponotus pennsylvanicus using Nanopore reads with a budget of only 1000$.Traditionally, genome assemblies are collapsed, meaning that sets of homologous chromosomes are represented by a single consensus sequence Guiglielmoni et al (BMC Bioinf 22(1):303, 2021). This approach is most adequate for low-heterozygosity genomes, and variants are documented a posteriori. Along the advent of high-accuracy long reads, phased assemblies, in which all haplotypes are included, are becoming more common.The assembly process typically involves multiple steps to tackle the challenges posed by the characteristics of the genome: ploidy, heterozygosity, repetitiveness… Reads may need to be preprocessed to remove adapters, select the longest and/or most accurate reads, or correct them to further improve accuracy. The most essential part lies, of course, in the assembly step. Reads are overlapped to build an assembly graph, and ad hoc algorithms are applied to find a path giving the most faithful representation of the genome. Assemblers yield a set of contiguous sequences or contigs. The output should then be evaluated to decide whether the assembly has reached the highest contiguity, completeness, and correctness, and if not, which steps should be performed subsequently to increase quality.},
}

@article {pmid40828164,
year = {2025},
author = {Pang, J and Wong, JCC and Wulandari, SM and Tay, M and Karlsson, EA and Oktaria, V and Nisar, I and Alam, M and Murni, IK and Amir, A and Ishtiaq, F and Tong, Z and Kitajima, M and Nolan, M and Mak, ST and Maurer-Stroh, S and Smith, GJ and de Alwis, R and Boucher, YF and Ng, LC and Pronyk, PM},
title = {Wastewater surveillance for early pathogen detection in Asia.},
journal = {International journal of environmental health research},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/09603123.2025.2544736},
pmid = {40828164},
issn = {1369-1619},
abstract = {Wastewater surveillance (WS) has emerged as an important population-based surveillance tool for early pathogen detection to inform timely public health action. Despite global guidance to initiate WS programming in Asia, the priorities and needs in Asia remain poorly understood. To address this gap, we conducted a cross-sectional assessment of WS efforts in Asia. An institutional survey recorded 89 separate projects among 45 institutions in 19 countries in Asia. Financing for WS was equally split between domestic and external resources. Most projects were research-oriented, with one-fifth embedded within national surveillance systems. Influents from urban wastewater treatment plants were the most common sampling sources identified, with either monthly or weekly sampling frequencies. Most efforts were single-pathogen focused, with SARS-CoV-2, antimicrobial resistance (AMR) bacteria, enterovirus, influenza and poliovirus being the top five pathogens assessed. Despite challenges including limited funding and government support, there has been substantial recent progress on the adoption of WS across Asia. Opportunities to enhance sustainability and scale will depend upon efforts to document public health use cases, support national planning and budgeting, develop tailored protocols and regional guidance, and advance innovative multi-pathogen approaches that leverage innovations including pathogen genomics to advance cost-efficient WS systems for public health impact.},
}

@article {pmid40827925,
year = {2025},
author = {Caffrey, EB and Olm, MR and Kothe, CI and Wastyk, HC and Evans, JD and Sonnenburg, JL},
title = {MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0014125},
doi = {10.1128/msystems.00141-25},
pmid = {40827925},
issn = {2379-5077},
abstract = {Fermented foods, which contain a diversity of microbes and microbial metabolites, have been used for millennia to increase food security, flavor, and nutritional content; more recently, they have been recognized as potential mediators of human health. Metagenomics is a powerful approach to characterize microbes in fermented foods, providing high taxonomic resolution and functional insights. Here, we introduce the Microbial Food DataBase, a metagenomics-based approach designed for the identification of fermentation-associated microbes. Using this primary database of metagenome-assembled genomes and relevant deposited genomes of prokaryotes, eukaryotes, and common food-relevant substrates, we investigated 89 fermented food samples. We present a streamlined high-confidence characterization of microbial diversity in fermented food, identifying previously undiscovered genomes and facilitating strain-level tracking across food environments. The easy and robust functionality of the workflow has significant implications for advancing food safety, promoting desired microbial communities, and increasing sustainability in food production.IMPORTANCEFermented foods have microbial communities that influence food safety, flavor, and human health. Microbial Food DataBase (MiFoDB), an alignment-based sequencing workflow and database, addresses the limitations of existing tools by enabling strain-level resolution, identifying novel genomes, and providing functional insights into microbial communities. Applying MiFoDB to fermented food samples, we demonstrate its ability to uncover novel species, track microbial strains across substrates, and integrate functional annotations. Additionally, the outlined workflow is highly customizable and can be used to generate alignment-based databases for other microbial ecosystems. This work highlights the importance of fermentation-specific workflows for studying microbial food ecosystems, advancing food safety, sustainability, and innovation in fermented food research.},
}

@article {pmid40827884,
year = {2025},
author = {Liu, H and Sun, J and Si, J and Liao, Y and Bai, J and Li, X and Wang, L and Cai, K and Ni, W and Zhou, P and Hu, S},
title = {Unexplored diversity and potential functions of extra-chromosomal elements.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0017525},
doi = {10.1128/msystems.00175-25},
pmid = {40827884},
issn = {2379-5077},
abstract = {In addition to the main chromosome, approximately 10% bacterial genomes have one or more large secondary replicons, including a unique type of replicon known as "chromid," which has plasmid-type replication and partition systems but carries core genes. Their nucleotide composition of chromids is very similar to that of their related chromosomes. However, the distribution, characteristics, functions, and origins of these chromids remain unclear. In this study, we established a workflow to identify chromids from complete bacterial genomes and screened 36,322 complete bacterial genomes, resulting in the identification of 1,104 bacterial genomes with chromids as secondary replicons. These chromid-carrying bacteria belong to eight phyla and 73 genera, exhibiting diversity and a wide global distribution. We analyzed the characteristics of chromids and found that their average size is larger than that of "megaplasmids" and that multi-chromid bacteria exist. Furthermore, chromids encode genes related to bacterial respiratory chain enzyme complexes and antiviral systems, expanding bacterial metabolic capabilities and enhancing their antiviral defenses. In addition, we developed an automated identification program, Chromid-Finder, for identifying chromid sequences in metagenomic data, which has demonstrated outstanding performance. To demonstrate its application, we analyzed 92,143 metagenome-assembled genomes (MAGs) from the human gut microbiome. We found that the distribution of chromid-carrying bacteria in the human gut is closely associated with host age, health status, and geographic location. Species with chromids exhibit unique functional capabilities, showing good separation at the phylum level.IMPORTANCEIn this study, we have developed a workflow to identify chromids from complete bacterial genomes. We utilized this workflow to search for chromids in the latest NCBI RefSeq databases, to map the distribution of bacteria carrying chromids, to identify the characteristics of bacterial chromids, to discuss their origins, and to investigate their roles in bacterial life. To address the growing volume of metagenomic data, we developed a high-performance automated identification program, Chromid-Finder, designed to identify chromids and their corresponding bacterial main chromosomes within extensive metagenomic data sets. Using this tool, we analyzed 92,143 metagenome-assembled genomes (MAGs) from the human gut microbiome.},
}