@article {pmid41203168,
year = {2025},
author = {Vangah, SJ and Kermani, AA and Vali, H and Noghabi, KA and Zahiri, HS},
title = {Engineering Saccharomyces cerevisiae for the secretion of an acidic, halotolerant, and cold-adapted xylanase derived from the camel rumen metagenome: Enzyme characterization and strain assessment.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148805},
doi = {10.1016/j.ijbiomac.2025.148805},
pmid = {41203168},
issn = {1879-0003},
abstract = {This study reports the development of a recombinant Saccharomyces cerevisiae strain engineered to produce and secrete a novel xylanase (rXylM) derived from the camel rumen metagenome. The recombinant enzyme exhibited optimal activity at 35 °C, pH 5.0, and retained 58 % of its activity even at 5 °C. The enzyme activity was not significantly affected by high sodium chloride (NaCl) concentrations up to 5 M. These properties characterize rXylM as an acidic, halotolerant, and cold-adapted xylanase. The combination of these adaptive traits in a single enzyme offers substantial advantages for industrial applications. Enzyme kinetic analysis was performed at 35 °C and pH 5.0 using beechwood xylan, wheat bran, and high-extraction wheat flour as substrates, yielding specific activities of 1190 U/mg, 1029 U/mg, and 383 U/mg respectively. Scanning electron microscopy (SEM) revealed noticeable morphological alterations indicating substantial degradation of the substrates following treatment with rXylM. The engineered strain, CEN.PK-Xyl, was assessed as a leavening agent for baking applications. Rheological analysis of the dough demonstrated a significant reduction in elasticity and viscous resistance, improving dough handling and kneading properties. Correspondingly, the resulting bread exhibited a significant decrease in hardness, gumminess, and chewiness, indicating an improvement in texture and overall quality. Cytotoxicity evaluation using the MTT assay showed that rXylM did not affect the viability of L929 mouse fibroblast cells under the tested conditions. The favorable biochemical properties and non-toxicity of rXylM, together with the established safety of S. cerevisiae, highlight CEN.PK-Xyl as a promising platform for applications in food, feed, bioprocessing, and fermentation.},
}

@article {pmid41203007,
year = {2025},
author = {Li, H and Wang, X and Zhang, X and Mu, H and Hao, R and Li, Y and Liu, Q and Chi, R and Zhai, D},
title = {Disrupted Microbiome-Metabolome Networks Underlie Gut Barrier and Immune Imbalance in Severe Fever with Thrombocytopenia Syndrome.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105586},
doi = {10.1016/j.micinf.2025.105586},
pmid = {41203007},
issn = {1769-714X},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening tick-borne viral infection with a high mortality rate and limited treatment options. While gastrointestinal symptoms are common, the contribution of gut microbiome disruption to disease progression remains unclear. Previous studies have noted taxonomic shifts in SFTS-associated microbiota, but their functional and metabolic consequences have not been systematically characterized. We conducted an integrated metagenomic and metabolomic analysis of fecal samples from 20 SFTS patients and 20 healthy controls. At the time of admission, patients with SFTS exhibited acute-stage infection, characterized by symptoms such as fever, thrombocytopenia, and gastrointestinal disturbances. Metagenomic sequencing was used to assess the microbial gene content, taxonomic composition, and functional potential. Untargeted metabolomics analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to profile fecal metabolites. The SFTS patients showed a significantly reduced microbial gene richness, alpha diversity, and compositional stability. Short-chain fatty acid (SCFA)-producing genera (e.g., Faecalibacterium and Roseburia) were depleted, while mucin-degrading and opportunistic taxa (e.g., Pseudomonas and Akkermansia) were enriched. Functionally, biosynthetic and homeostatic pathways were suppressed; while stress-adaptive, biofilm-forming, and virulence-associated pathways were elevated. Metabolomic profiling revealed depletion of anti-inflammatory metabolites (e.g., bile acids and curcumin sulfate) and enrichment of proinflammatory compounds (e.g., porphyrins and beta-tyvelose). Multi-omic correlation highlighted strong links between microbial disruption and altered metabolite production. In conclusion, SFTS is associated with significant alterations in the gut microbiome and its metabolic profile, which is characterized by the loss of beneficial microbial taxa and functions, alongside the emergence of virulence factors and stress-related signatures. These findings underscore the role of microbiome dysfunction in SFTS and suggest that microbiota-targeted strategies may offer supportive benefits, particularly in alleviating SFTS-associated gastrointestinal disturbances and secondary microbial imbalance.},
}

@article {pmid41202935,
year = {2025},
author = {Wu, B and Cheng, Y and Gu, J and Yuan, H and Murphy, JD},
title = {Toward sustained and efficient n-caproate production: Insights into magnetite-encapsulated biochar mediated microbial chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133617},
doi = {10.1016/j.biortech.2025.133617},
pmid = {41202935},
issn = {1873-2976},
abstract = {Decarbonization of the chemical sector may be facilitated by microbial chain elongation, through conversion of organic waste into chemical products. Challenges in efficient interspecies electron transfer is a barrier to this technology. Here we introduce a magnetite-encapsulated biochar (Fe@biochar) amendment strategically integrated with chain elongation to facilitate sustained and efficient n-caproate production. This strategy increased n-caproate yields to 13.92 g COD/L, 199 % and 71 % higher than the control (4.66 g COD/L) and biochar (8.13 g COD/L) groups, respectively. Most importantly, Fe@biochar consistently enhanced n-caproate production after recycle, a continuity not observed with biochar. This difference may be attributed to the inhibitory effects of high concentrations of undissociated n-caproic acid (up to 9.06 mM or 2.32 g COD/L) on functional microbes in the biochar group. Microbial community analysis identified Clostridium_sensu_stricto as the key genus involved in n-caproate production. Comparative metagenomic and microbial activity analyses revealed the energy metabolism, where Fe@biochar promoted extracellular iron-based electron transfer, and further accelerated intracellular electron sinks. This is substantiated by a 3.6 fold increase in electron transfer system activity and evaluated relative abundances of key genes encoding acetyl-CoA synthetase (15.0 % increase), cytochrome c biosynthesis (28.7 % increase) and NADH dehydrogenase (48.0 % increase). This study offers a new paradigm for sustained n-caproate production.},
}

@article {pmid41202544,
year = {2025},
author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X},
title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140322},
doi = {10.1016/j.jhazmat.2025.140322},
pmid = {41202544},
issn = {1873-3336},
abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.},
}

@article {pmid41202381,
year = {2025},
author = {Jiang, CH and Zhang, SJ and Li, P and Miao, H and Zhao, YY},
title = {Natural products targeting TGF-β/Smad signaling in renal fibrosis: Multiomics-based novel molecular mechanisms and therapeutic strategies.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157496},
doi = {10.1016/j.phymed.2025.157496},
pmid = {41202381},
issn = {1618-095X},
abstract = {BACKGROUND: Renal diseases including acute kidney injury (AKI) and chronic kidney disease (CKD) have become one of the major global public health challenges. Regardless of the underlying aetiology, renal fibrosis is a common pathological endpoint in the progression of diverse kidney diseases to end-stage renal disease. Increasing studies have highlighted that emerging multi-omics techniques (metagenomics, transcriptomics, proteomics and metabolomics) have been used for elucidating the pathogenesis of kidney disease and underlying molecular mechanism of renal fibrosis. However, few reviews provide a comprehensive and systematic presentation of multi-omics signaling-mediated TGF-β/Smad pathway in both AKI and CKD as well as therapeutic strategies for targeting signaling cascades by natural products.

PURPOSE AND STUDY DESIGN: This review summarizes multi-omics signaling-mediated TGF-β/Smad pathway and therapeutic strategies of natural products by targeting this signaling axis in patients and animal models with kidney disease.

METHODS: All the available information is searched by several electronic database such as Web of Science, Pubmed, ScienceDirect, Splinker, Google Scholar, etc., that covered approximately 1000 publications from 2015 to 2025.

RESULTS: Ample evidence has indicated that transforming growth factor-β (TGF-β)/suppressor of mothers against decapentaplegic (Smad) signaling pathway plays a central role in renal fibrosis. Based on the multi-omics techniques, a variety of novel mediators are identified and affects kidney diseases by regulating TGF-β/Smad pathway. Therefore, targeting TGF-β/Smad pathway is an important and promising antifibrotic therapy. This review summarizes TGF-β/Smad pathway in both AKI and CKD, elaborate on the multidimensional regulatory mechanisms in renal fibrosis by crosstalk between TGF-β/Smad pathway and novel multi-omics signaling-associated mechanisms including microbial dysbiosis, dysregulating non-coding ribonucleic acids including long non-coding RNAs and microRNAs and metabolite disorder and shed light on the latest therapeutic effects of natural products such as terpenoids, anthraquinones, xanthones and flavonoids as well as natural polysaccharides by targeting multi-omics signaling-mediated TGF-β/Smad pathway.

CONCLUSION: This review presents a multiomics-driven therapeutic strategy for the development of effective and precise antifibrotic therapies.},
}

@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
doi = {10.1016/j.neo.2025.101245},
pmid = {41201920},
issn = {1476-5586},
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}

*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology
Animals
*Gastrointestinal Microbiome
Mice
*Tumor Microenvironment/genetics
Humans
*Diet
*Gene Expression Regulation, Neoplastic
Disease Models, Animal
Age Factors
Male
*Aging

@article {pmid41201839,
year = {2025},
author = {da Silva Fong, D and Abrantes, J and Moura, T and Serra-Pereira, B and Xavier, R and Veríssimo, A and Varsani, A and Neves, F},
title = {Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata).},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001541},
pmid = {41201839},
issn = {2057-5858},
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Skates, Fish/virology ; *Papillomaviridae/genetics/isolation & purification/classification ; *Papillomavirus Infections/virology/veterinary ; Sequence Analysis, DNA ; DNA, Viral/genetics ; },
abstract = {Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.},
}

Animals
Phylogeny
Genome, Viral
*Skates, Fish/virology
*Papillomaviridae/genetics/isolation & purification/classification
*Papillomavirus Infections/virology/veterinary
Sequence Analysis, DNA
DNA, Viral/genetics

@article {pmid41201733,
year = {2025},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41201733},
issn = {1439-0973},
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}

@article {pmid41201496,
year = {2025},
author = {Ren, QD and Li, MR and Farag, MA and Qiu, LL and Wang, YA and Liu, D and Liu, HR and Sun, JY and Li, NY and Liu, C},
title = {Pomegranate peel extract alleviates diabetic retinopathy by suppressing the PI3K/AKT/HIF-1α/VEGF pathway and gut microbiota modulation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.10.048},
pmid = {41201496},
issn = {2090-1224},
abstract = {INTRODUCTION: Diabetic retinopathy (DR) is a severe microvascular complication of diabetes mellitus. Pomegranate peel extract (PPE) has shown potential in mitigating various diabetic complications, yet its role in DR remains unexplored.

OBJECTIVE: To investigate the beneficial effects and underlying action mechanisms of PPE in managing DR.

METHODS: PPE was extracted using 50 % ethanol. The effects and underlying mechanisms of PPE on DR were evaluated in streptozotocin (STZ)-induced DR rats and high-glucose-incubated adult retinal pigment epithelial cell line (ARPE-19) cells. Phenotypic parameters, network pharmacology (NP), and gut microbiota metagenomic analysis were employed to elucidate the impact and mechanisms of PPE in DR.

RESULTS: In DR rats, oral administration of PPE significantly mitigated retinal damage. NP analysis indicated potential mechanisms, involving the hypoxia-inducible factor-1/vascular endothelial growth factor (HIF-1/VEGF), phosphoinositide 3-kinase/protein kinase B (PI3K/AKT), and reactive oxygen species (ROS) pathways. PPE suppressed oxidative stress and inhibited the activation of PI3K/AKT/HIF-1α/VEGF pathway in the retina of DR rats and high-glucose-incubated ARPE-19 cells. Moreover, PPE improved gut microbiota dysbiosis in DR rats, particularly increasing Akkermansia muciniphila, which likely contributed to reduced inflammation and oxidative stress.

CONCLUSION: PPE exhibited therapeutic effects in DR by directly alleviating retinal damage via the suppression of oxidative stress and inhibition of PI3K/AKT/HIF-1α/VEGF pathway, as well as indirectly modulating gut microbiota. These findings suggested that PPE may serve as a promising nutraceutical for DR management.},
}

@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration & dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.

METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.

RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 ± 0.76 kg; LDG: -2.40 ± 0.67 kg), body fat percentage (HDG: -1.87 ± 0.69; LDG: -1.49 ± 0.45), cortisol (HDG: -6.79 ± 4.26 μg/dL; LDG: -4.5 ± 4.84 μg/dL), maximum power (HDG: 27.16 ± 9.77 W; LDG: 14.50 ± 9.43 W), maximal oxygen uptake (HDG: 8.78 ± 0.97; LDG: 6.90 ± 1.37), and half-court triangle run times (HDG: -0.48 ± 0.36 s; LDG: -0.25 ± 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 ± 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.

CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}

Humans
Male
*Gastrointestinal Microbiome/drug effects
*Basketball/physiology
*Athletic Performance/physiology
Young Adult
*Dietary Fiber/administration & dosage
Adolescent
*Dietary Supplements
Adult
Body Composition
Athletes
Universities

@article {pmid41200800,
year = {2025},
author = {Quarton, S and Livesey, A and Jeff, C and Hatton, C and Chen, CH and Scott, A and Parekh, D and Thickett, D and McNally, A and Sapey, E},
title = {Metagenomics in the diagnosis of pneumonia: a systematic review.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/23744235.2025.2580954},
pmid = {41200800},
issn = {2374-4243},
abstract = {BACKGROUND: Pneumonia is a major cause of morbidity and mortality, yet causative organisms are rarely identified. Metagenomic next-generation sequencing (mNGS) may improve this, however the impact on outcomes is uncertain and the relative utility in pneumonia subtypes or different clinical samples is unclear.

METHODS: This systematic review compared mNGS with conventional microbiology, assessing pathogen identification, turnaround time and clinical impact. It also reviewed difference related to the pneumonia subtype, or sample used. We searched EMBASE, MEDLINE, Scopus, and the Cochrane Central Register of Controlled Trials (CENTRAL) for studies comparing mNGS with conventional microbiology, in patients with pneumonia. All study types were included (excluding case reports of <10 people). Eligibility assessment and data extraction was performed by two independent reviewers, and risk of bias assessed using the QUADAS-2.

RESULTS: We identified 74 studies including 10,566 people, with all studies having high risk of bias or applicability concerns in at least one domain. Conventional tests identified a pathogen in 43.2% of cases (3559/8229) compared to 78.9% for mNGS (6242/7980). mNGS had faster turnaround times than conventional microbiology (MD -73.6h, CI-111.36 - -35.73 hrs) but meta-analysis was not possible for other outcomes. Most studies did not specify the pneumonia subtype. 92%of studies used exclusively or predominantly bronchoalveolar lavage fluid (BALF), and the utility of other sample types could not be established.

CONCLUSIONS: mNGS may identify possible pathogens with greater frequency than standard techniques although bias in study design limits definite conclusions, and the clinical relevance of this remains unresolved. There is a need for studies assessing clinical outcomes, and the differential impact in pneumonia subtypes and in samples other than BALF.},
}

@article {pmid41200470,
year = {2025},
author = {Maldonado, M and Pita, L and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge, Corticium candelabrum Schmidt, 1862 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {535},
pmid = {41200470},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Corticium candelabrum (sponge; Porifera; Homoscleromorpha; Homosclerophorida; Plakinidae). The genome sequence has a total length of 185.49 megabases. Most of the assembly (99.4%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,198 protein-coding genes. The metagenome of the specimen was also assembled, and 53 binned bacterial genomes were identified, including 44 high-quality MAGs that were typical of high microbial abundance sponge and included, besides the phyla Chloroflexota (class Dehalococcoidia), Acidobacteriota (order Acidomicrobiales), Alpha- and Gammaproteobacteria, also representatives of several candidatus phyla (Candidatus Latescibacterota, Binatota, Poribacteria).},
}

@article {pmid41200317,
year = {2025},
author = {Kazemzadeh, S and Korneeva, O and Shabunin, S and Syromyatnikov, M},
title = {Antibiotic resistance in mastitis-causing bacteria: Exploring antibiotic-resistance genes, underlying mechanisms, and their implications for dairy animal and public health.},
journal = {Open veterinary journal},
volume = {15},
number = {9},
pages = {3980-4006},
pmid = {41200317},
issn = {2218-6050},
mesh = {Animals ; *Mastitis, Bovine/microbiology/drug therapy ; Female ; Cattle ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Public Health ; *Bacteria/drug effects/genetics ; Dairying ; Humans ; Milk/microbiology ; },
abstract = {The development and spread of superbugs, which are bacterial strains resistant to several types of antibiotics, threatening the lives of myriad people and animals worldwide, is one of the most concerning issues facing both global and animal health. Dairy animals are considered to be key reservoirs of antibiotic-resistant bacteria, which are closely correlated with the widespread and inappropriate application of antibiotics in agriculture and veterinary medicine, particularly for mastitis treatment. Although antimicrobial agents are administered in dairy farming for various conditions beyond mastitis, such as respiratory infections and digestive disorders, as well as prophylaxis and growth promotion, the most common reason for antimicrobial use in this industry is mastitis treatment. Since raw milk can be contaminated with opportunistic pathogens carrying antimicrobial resistance genes, these pathogens increase the gene pool from which pathogenic bacteria can acquire resistance traits. Indeed, these resistance genes may be horizontally transferred from livestock to human pathogens through mobile genetic elements through the consumption of raw milk. This phenomenon poses a global health threat, emphasizing the necessity of applying the "One Health" approach in global health and medicine to safeguard animal health and public health. Given the high prevalence and economic impact of mastitis and the evidence supporting mastitis as a major driver of antimicrobial use in dairy farming, this review summarizes recent genomic and metagenomic studies on major mastitis-causing pathogens (Staphylococcus aureus, Escherichia coli, Streptococcus spp., and Pseudomonas spp.) in dairy animals, detailing their primary resistance mechanisms. We highlight advanced surveillance tools, such as metagenomics, whole-genome sequencing, and quantitative polymerase chain reaction, for the rapid detection of resistance genes and mobile elements in the dairy chain.},
}

Animals
*Mastitis, Bovine/microbiology/drug therapy
Female
Cattle
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Public Health
*Bacteria/drug effects/genetics
Dairying
Humans
Milk/microbiology

@article {pmid41199950,
year = {2025},
author = {Sang, Z and Zhang, Y and Kao, E and Zhu, T and Yang, J and Xu, ZZ and Huang, S and Teng, F and Wang, W},
title = {Decoding oral leukoplakia: microbiome dysbiosis and inflammatory dynamics unveiled in a rat model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1613165},
pmid = {41199950},
issn = {1664-302X},
abstract = {INTRODUCTION: Oral leukoplakia (OLK) is an oral precancerous lesion associated with oral microbiome dysbiosis and systemic inflammation. However, the longitudinal changes of the microbiome and its causal relationship with inflammation remain unclear, and traditional sequencing struggles to detect low-biomass samples.

METHODS: A 4-nitroquinoline-1-oxide (4-NQO)-induced rat OLK model was used. The oral microbiome was analyzed via 2bRAD-M sequencing; serum levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were measured. Additionally, functional pathway analysis of the microbiome and its correlation with inflammation were conducted.

RESULTS: In OLK, we observed significant shifts in the oral microbial diversity, marked by elevated abundances of Streptococcus, Glaesserella, and Pseudomonas aeruginosa. Moreover, shifts in the microbiota precede the manifestation of clinical symptoms of OLK. Functional pathway analysis highlighted enrichment in metabolism, quorum sensing, and cancer-associated microRNA pathways. Serum levels of inflammatory markers (TNF-α and IL-6) were significantly elevated in OLK and significantly correlated with specific bacterial taxa.

DISCUSSION: This study demonstrates the utility of 2bRAD-M sequencing in overcoming traditional metagenomic limitations, offering a high-resolution view of microbiome dynamics in low-biomass environments such as the oral mucosa. These findings establish the oral microbiota as candidate early biomarkers for OLK screening and prevention, opening avenues for precision diagnostics and targeted therapies to mitigate cancer risk associated with OLK.},
}

@article {pmid41199948,
year = {2025},
author = {Vasanthrao, R and Nidhin, IK and Taj, Z and Chattopadhyay, I},
title = {Comprehensive whole metagenomics analysis uncovers microbial community and resistome variability across anthropogenically contaminated soils in urban and suburban areas of Tamil Nadu, India.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649872},
pmid = {41199948},
issn = {1664-302X},
abstract = {INTRODUCTION: Environmental contamination by heavy metals and hydrocarbons significantly impacts microbial diversity and soil functionality.

METHODS: This study employs whole-genome metagenome sequencing to analyse microbial compositions, antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRs), and virulence genes (VGs) in soil samples from diverse locations, including gardens, poultry farms, cattle sheds, markets, hospitals, thermal power plants, paper industries, and waste disposal sites.

RESULTS: The findings indicate that heavy metal concentrations (Pb, Cr, Cd, and Cu) and hydrocarbons (heptadecane, triacontane, docosane, and heneicosane) were positively correlated with several microbial phyla with relatively high abundances in these contaminated sites, such as Actinobacteria, Proteobacteria, Basidiomycota, Ascomycota, Euryarchaeota, and Apicomplexa. The prevalence of multidrug resistance genes, including MexD, MexC, MexE, MexF, MexT, CmeB, MdtB, MdtC, and OprN, was significant, facilitating antibiotic resistance primarily via efflux pump mechanisms (42%), followed by antibiotic inactivation (23%) and changes in antibiotic targets (18%). Virulence genes such as espR, regX3, sigA/rpoV, bap, and sugB were significantly prevalent in contaminated locations, indicating microbial pathogenic potential in polluted ecosystems. The functional gene analysis revealed significant metabolic pathways related to protein metabolism, carbohydrates, amino acids and their derivatives, metabolism, and DNA metabolism, highlighting the microbial adaptation processes engaged in pollution degradation and resource utilisation.

DISCUSSION: This study establishes a clear link between environmental pollution, microbial adaptations, and functional resilience, emphasizing the ecological significance of microbial bio-remediation in shaping targeted remediation strategies and long-term ecological recovery. Understanding these microbial interactions is essential for developing targeted remediation techniques and assessing long-term ecological recovery in contaminated regions.},
}

@article {pmid41199944,
year = {2025},
author = {Dai, L and Guo, XR and Chen, XR and Ma, MH and Liu, ZH and Lai, J and Lu, J and Feng, M and Liu, XX and Yang, SH},
title = {A review of the mechanism, diagnosis, and treatment of Naegleria fowleri infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1686695},
pmid = {41199944},
issn = {1664-302X},
abstract = {Naegleria fowleri is a rare pathogen responsible for primary amoebic meningoencephalitis (PAM), a fatal central nervous system infection characterized by rapid clinical progression and an extremely high mortality rate. The existing diagnostic methods are insufficiently sensitive, and therapeutic options are minimal, making early recognition and intervention extremely challenging. This review systematically examines the biological characteristics and pathogenic mechanisms of this pathogen, as well as current diagnostic and treatment strategies, with a particular focus on the groundbreaking applications of emerging technologies such as metagenomic next-generation sequencing (mNGS) in the diagnosis of difficult-to-treat infections. The aim is to provide theoretical support and practical guidance for rapid identification, accurate diagnosis, and timely intervention in clinical practice, serving as a reference for the prevention and treatment of N. fowleri infections.},
}

@article {pmid41199943,
year = {2025},
author = {Zhang, M and Di, H and Wang, S and Ning, Z},
title = {Column experiment reveals high natural attenuation potential for toluene in iron-rich aquifers but significant concomitant secondary Fe pollution risk.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687219},
pmid = {41199943},
issn = {1664-302X},
abstract = {INTRODUCTION: Iron mineral reduction mediated by indigenous microbes represents a crucial natural attenuation mechanism for organic contaminants like toluene in anaerobic aquifers, yet the partitioning of generated Fe(II) species and associated secondary pollution risks remain poorly constrained.

METHODS: This study employed controlled column experiments simulating an iron-rich aquifer (ferrihydrite-amended quartz sand) to track the biogeochemical dynamics of toluene degradation coupled with iron transformation. Over 43 days, we quantified spatiotemporal changes in toluene concentrations, dissolved/solid-phase iron species, and microbial community structure through high-frequency hydrochemical monitoring and metagenomic sequencing.

RESULTS AND DISCUSSION: Results demonstrated that iron-reducing consortia (notably Thiobacillus and Pseudomonas) drove > 99% toluene degradation within 10 cm flow distance, effectively containing plume migration. However, Fe(III) reduction generated Fe(II) predominantly (98%) as immobile solid-phase minerals, with only 1%-2% manifesting as dissolved Fe[2+]. This dissolved fraction accumulated progressively across space and time, exceeding China's groundwater quality threshold (0.3 mg/L) at 90% of monitoring points by experiment termination despite near-complete toluene removal. The study confirms that iron-rich aquifers provide significant natural attenuation capacity for petroleum hydrocarbons but concurrently pose substantial secondary contamination risks through highly mobile Fe[2+] generation. Therefore, it is recommended to include solidphase ferrous iron [Fe(II)] as an indicator in natural attenuation assessments and to take into account biogeochemical by-products such as Fe[2+] in risk assessment efforts.},
}

@article {pmid41199942,
year = {2025},
author = {Zeng, W and Yang, L and Cui, L and Liang, C and Zhu, D and Fang, Y and Zhang, Y and Liu, H},
title = {Virome analysis and detection of ticks and tick-borne viruses in Shanghai, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699705},
pmid = {41199942},
issn = {1664-302X},
abstract = {INTRODUCTION: Ticks are well-known ectoparasites and vectors responsible for transmitting a diverse range of pathogens, including viruses, bacteria, and protozoa, many of which pose substantial risks to public health and livestock. In recent decades, the incidence and diversity of tick-borne diseases have increased globally, with several novel tick-borne viruses (TBVs) being discovered.

METHODS: This study aimed to characterize the virome of ticks collected from various locations in Shanghai, China, using next-generation sequencing (NGS). A total of 2,568 ticks belonging to three dominant species-Haemaphysalis flava, Haemaphysalis longicornis, and Rhipicephalus sanguineus sensu lato-were collected and analyzed through metagenomic sequencing.

RESULTS: The sequencing analysis identified 214 viral contigs classified into 32 viral families, including Chrysoviridae, Phenuiviridae, Partitiviridae, Nairoviridae, Dicistroviridae, Reoviridae, Botourmiaviridae, and Flaviviridae. Several TBVs with potential relevance to human and animal health, such as Cheeloo Jingmen-like virus (CJLV), Songling virus (SGLV), brown dog tick phlebovirus 1 (BDTPV1), brown dog tick phlebovirus 2 (BDTPV2), and Wuhan mosquito virus 1 (WMV1), were detected. Significant differences in virome composition among tick species based on geographical locations were also observed.

DISCUSSION: These findings highlight the influence of environmental factors on viral diversity in ticks and underscore the need for ongoing surveillance of TBVs. Implementation of longitudinal virome monitoring across tick developmental stages in Shanghai will provide critical insights for early warning systems, disease prevention strategies, and public health interventions.},
}

@article {pmid41199613,
year = {2025},
author = {Kagemasa, S and Kuroda, K and Nakai, R and Sato, M and Li, YY and Kubota, K},
title = {Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70231},
doi = {10.1111/1758-2229.70231},
pmid = {41199613},
issn = {1758-2229},
support = {JP18H01564//Japan Society for the Promotion of Science/ ; JP21H01460//Japan Society for the Promotion of Science/ ; JP23H02545//Japan Society for the Promotion of Science/ ; JP23K27236//Japan Society for the Promotion of Science/ ; JP23K19153//Japan Society for the Promotion of Science/ ; JP24H00328//Japan Society for the Promotion of Science/ ; JP21J11654//Japan Society for the Promotion of Science/ ; //Tohou University - AIST matching fund/ ; //MEXT WISE Program for Sustainability in Dynamic Earth (SyDE), Japan/ ; },
mesh = {*Sewage/microbiology ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Wastewater/microbiology ; },
abstract = {Candidatus Saccharimonadia is a class-level lineage of ultrasmall bacteria within the phylum Minisyncoccota (formerly Candidate Phyla Radiation or Ca. Patescibacteria), commonly found in activated sludge processes treating municipal wastewater. In this study, we aimed to elucidate the metabolic potential of Ca. Saccharimonadia by using shotgun metagenomic sequencing combined with a filtration-based size-fractionation approach for activated sludge from five wastewater treatment plants. A total of 65 high-quality metagenomic bins were recovered, belonging to four orders and 19 families of Ca. Saccharimonadia, including previously unreported lineages in activated sludge. These bins had small genomes (approximately 0.46-1.73 Mbp) with limited metabolic capabilities, indicating dependency on other microorganisms. Notably, the order Ca. Saccharimonadales retained a type IV secretion system and effector gene cluster for parasitic interactions with the hosts, suggesting that Ca. Saccharimonadales bacteria may exhibit a parasitic lifestyle. Co-occurrence network analysis showed that members of the order Ca. Saccharimonadales were significantly correlated with multiple lineages, including Actinobacteriota, for which a parasitic relationship has been previously demonstrated. Our results shed light on the potential ecophysiology of the diverse members of Ca. Saccharimonadia, providing a comprehensive understanding of Ca. Saccharimonadia in activated sludge.},
}

*Sewage/microbiology
Phylogeny
Genome, Bacterial
Metagenomics
*Bacteria/metabolism/genetics/classification/isolation & purification
Wastewater/microbiology

@article {pmid41199348,
year = {2025},
author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N},
title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {227},
pmid = {41199348},
issn = {2049-2618},
support = {ANR-11-DPBS-0001//Metagenopolis/ ; },
mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.

RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3 min for taxonomic analysis and 10 min for strain-level analysis against the human microbial gene catalogue when processing 10 M paired reads - operating within a modest 5 GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.

CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.},
}

*Metagenomics/methods
Animals
Mice
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
*Gastrointestinal Microbiome/genetics
*Software
Computational Biology/methods

@article {pmid41198952,
year = {2025},
author = {Makarova, KS and Shmakov, SA and Wolf, YI and Mutz, P and Altae-Tran, H and Beisel, CL and Brouns, SJJ and Charpentier, E and Cheng, D and Doudna, J and Haft, DH and Horvath, P and Moineau, S and Mojica, FJM and Pausch, P and Pinilla-Redondo, R and Shah, SA and Siksnys, V and Terns, MP and Tordoff, J and Venclovas, Č and White, MF and Yakunin, AF and Zhang, F and Garrett, RA and Backofen, R and van der Oost, J and Barrangou, R and Koonin, EV},
title = {An updated evolutionary classification of CRISPR-Cas systems including rare variants.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41198952},
issn = {2058-5276},
support = {Intramural funds//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The known diversity of CRISPR-Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR-Cas systems. The updated CRISPR-Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR-Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR-Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR-Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally.},
}

@article {pmid41198823,
year = {2025},
author = {Navarro Marcos, C and Gutiérrez-Rivas, M and Goiri, I and García-Rodríguez, A and González-Recio, Ó},
title = {The association of the rumen virome with methane emissions in dairy cattle.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1534},
pmid = {41198823},
issn = {2399-3642},
mesh = {Animals ; Cattle ; *Methane/metabolism/biosynthesis ; *Rumen/virology/microbiology/metabolism ; *Virome ; Female ; Viruses/genetics/classification ; Metagenome ; Bacteria/metabolism ; Metagenomics ; },
abstract = {Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.},
}

Animals
Cattle
*Methane/metabolism/biosynthesis
*Rumen/virology/microbiology/metabolism
*Virome
Female
Viruses/genetics/classification
Metagenome
Bacteria/metabolism
Metagenomics

@article {pmid41197746,
year = {2025},
author = {Yu, PF and Jiang, DL and Wang, D and Ma, XG and Jun-Li, and Han, LY and Wang, A and Fu, YB and Jin, X},
title = {Manganese cycle-mediated synchronous bacteria-algae/anammox coupled denitrification system under low-temperature conditions: Performance and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133593},
doi = {10.1016/j.biortech.2025.133593},
pmid = {41197746},
issn = {1873-2976},
abstract = {The treatment of high-nitrogen complex wastewater in an efficient, economical, and environmentally friendly manner has attracted growing attention in recent years. However, slow reaction rates remain a significant obstacle to its broad application. This study investigated the addition of Mn@BC to enhance the low-temperature resistance of an anaerobic ammonia oxidation (anammox) process coupled with denitrification. The results demonstrated that under 17℃ conditions, the average nitrogen removal efficiency increased to 82% with the addition of Mn@BC, representing a 9% improvement compared to the addition of BC alone. Moreover, Mn@BC promoted the secretion of extracellular polymeric substances and diversified the microbial community structure.The incorporation of microalgae created a synergistic microalgal-bacterial system that maintained a phosphorus removal rate of 50% and reduced the reliance on external organic carbon, as confirmed by TOC analysis.The underlying intra- and extracellular metabolic pathways, formed by functional genes including mtrC, nirS/K, and c-Cyts, were elucidated using metagenomic sequencing. Therefore, the development of a high-efficiency nitrogen and phosphorus removal process capable of synchronizing microalgal-bacterial interactions, overcoming low-temperature inhibition, enhancing microbial synergy, and reducing carbon source dependency holds practical application value for treating high-nitrogen and low-temperature wastewater, while also providing theoretical support for constructing microalgal-bacterial synergistic systems to achieve efficient autotrophic nitrogen removal.},
}

@article {pmid41197744,
year = {2025},
author = {Li, Y and Wang, G and Yang, Y and Liu, L and Dang, X and Li, YY and Chen, R},
title = {Operational thresholds and microbial mechanisms in high-solid anaerobic membrane bioreactors treating swine wastewater: from process performance to metabolic pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133596},
doi = {10.1016/j.biortech.2025.133596},
pmid = {41197744},
issn = {1873-2976},
abstract = {This study investigated swine wastewater treatment using a high-solid anaerobic membrane bioreactor (HSAnMBR), focusing on microbial adaptive mechanisms and process stability under stepwise-increased organic loading rates (OLRs: 5-26 g COD/L/d). The HSAnMBR achieved high efficiency at OLRs ≤ 17 g COD/L/d, with COD removal > 96 % and optimal methane yield (0.28 L CH4/g CODremoved). However, OLR elevation to 26 g COD/L/d induced volatile fatty acid (VFA) accumulation (5.57 g/L), causing acute methanogenic inhibition that reduced methane yield efficiency by 39 %. System functionality was rapidly restored within 10 days after OLR reduction to 21 g COD/L/d. Microbial analysis revealed divergent diversity dynamics: bacterial alpha diversity peaked at 14 g COD/L/d before declining, while archaeal diversity increased continuously, enhancing functional redundancy. Sludge acclimation enriched key functional taxa (such as Clostridium_sensu_stricto and hydrogenotrophic methanogens), forming a resilient "metabolic complementarity-functional substitution" network that maintained process stability under VFA stress. Metagenomic evidence confirmed metabolic pathway restructuring, including upregulation of hydrogenotrophic methanogenesis genes (e.g., coenzyme F420 biosynthesis) and a decline in acetoclastic dominance. This work deciphers the microbial mechanisms enabling high-load operation of HSAnMBRs, establishing the foundation for energy-efficient swine wastewater valorization.},
}

@article {pmid41197631,
year = {2025},
author = {Klag, K and Ott, D and Tippetts, TS and Nicolson, RJ and Tatum, SM and Bauer, KM and Stephen-Victor, E and Weis, AM and Bell, R and Weagley, J and Maschek, JA and Vu, DL and Heaver, S and Ley, R and O'Connell, R and Holland, WL and Summers, SA and Stephens, WZ and Round, JL},
title = {Dietary fat disrupts a commensal-host lipid network that promotes metabolic health.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.10.007},
pmid = {41197631},
issn = {1932-7420},
abstract = {The microbiota influences metabolic health; however, few specific microbial molecules and mechanisms have been identified. We isolated a Turicibacter strain from a community of spore-forming bacteria that promotes leanness in mice. Human metagenomic analysis demonstrates reduced Turicibacter abundance in individuals with obesity. Similarly, a high-fat diet reduces Turicibacter colonization, preventing its weight-suppressive effects, which can be overcome with continuous Turicibacter supplementation. Ceramides accumulate during a high-fat diet and promote weight gain. Transcriptomics and lipidomics reveal that the spore-forming community and Turicibacter suppress host ceramides. Turicibacter produces unique lipids, which are reduced during a high-fat diet. These lipids can be transferred to host epithelial cells, reduce ceramide production, and decrease fat uptake. Treatment of animals with purified Turicibacter lipids prevents obesity, demonstrating that bacterial lipids can promote host metabolic health. These data identify a lipid metabolic circuit between bacteria and host that is disrupted by diet and can be targeted therapeutically.},
}

@article {pmid41197619,
year = {2025},
author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM},
title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101218},
doi = {10.1016/j.crmeth.2025.101218},
pmid = {41197619},
issn = {2667-2375},
abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.},
}

@article {pmid41197616,
year = {2025},
author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X},
title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102431},
doi = {10.1016/j.xcrm.2025.102431},
pmid = {41197616},
issn = {2666-3791},
abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.},
}

@article {pmid41197513,
year = {2025},
author = {Luo, J and Hou, C and Wang, Z and Gui, N and Wang, YX and Jiang, X and Mu, Y and Shen, J},
title = {Simultaneous removal of nitrate and ammonia at the sulfur/pyrite-microbe interface: A novel insight of pyrite in wastewater polishing treatment for nitrogen metabolism.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140316},
doi = {10.1016/j.jhazmat.2025.140316},
pmid = {41197513},
issn = {1873-3336},
abstract = {The development of advanced nitrogen removal technologies for municipal wastewater effluents is critical to meeting increasingly stringent discharge standards. We present a sulfur/pyrite-microbe interfacial system that optimizes nitrogen-transformation pathways to achieve simultaneous removal of NO3[-]-N and NH4[+]-N with reduced sulfate production. This overcomes the drawbacks of conventional sulfur autotrophy (poor NH4[+] removal and excessive sulfate production) and stand-alone iron systems (low denitration rate and easy passivation), delivering synchronous ammonia and nitrate elimination in a single step. A comprehensive analysis of the microstructure and composition of the bio-abiotic interface was performed to elucidate the regulatory role of pyrite in electron transfer and substance transformation. The formation of secondary minerals, structural alterations in extracellular proteins, and enhanced activity of redox-active proteins collectively activated both intracellular and extracellular electron transfer channels. Pyrite-induced quorum sensing promoted iron transport and stimulated microbial metabolic functions. Driven by Fe(II)/Fe(III) redox cycling, nitrate-dependent Fe(II) oxidation (NDFO) and Fe(III)-mediated ammonium oxidation (Feammox) reduced sulfate production and suppressed sulfur disproportionation. Metagenomic analysis further confirmed that Feammox, rather than conventional Anammox, served as the dominant pathway for NH4[+]-N conversion. Pilot-scale validation demonstrated robust nitrogen removal (TN > 90 %) and low sulfate production with a treatment cost 40 % lower than conventional carbon-driven systems. This study offers a sustainable, low-carbon alternative for advanced nitrogen polishing and provides mechanistic insights into bio-abiotic interface engineering for wastewater treatment.},
}

@article {pmid41197508,
year = {2025},
author = {Wen, M and Deng, C and Lei, J and Yang, X and Li, J and Al-Dhabi, NA and Wen, S and Tang, W and Feng, B and Zhang, P},
title = {Amoxicillin effects on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) in the algal-bacterial biofilm.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140363},
doi = {10.1016/j.jhazmat.2025.140363},
pmid = {41197508},
issn = {1873-3336},
abstract = {The algal-bacterial wastewater treatment process is characterized by its efficiency in water quality purification and bioresource recovery. This study investigated the effects of amoxicillin (AMX) on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) within the algal-bacterial biofilm. AMX significantly suppressed ammonia and phosphorus removal by inhibiting nitrogen and phosphorus assimilation in cyanobacteria. A total of 72 metagenomic assembled genomes carrying cyanophycin biosynthetic genes were identified, with Pantanalinema and Planktothrix being the primary cyanophycin-producing species. AMX concentrations of 0.5 and 1 mg/L suppressed both cyanobacterial growth and cyanophycin synthesis, with the inhibitory effect intensifying as AMX concentration increased. AMX also promoted the proliferation of sul1, OXA-101, VEB-3, and qacEdelta1, while decreased the abundance of OXA-36, erm(F), and tet types. Pseudomonadota and Bacteroidota were the primary hosts for ARGs proliferation and dissemination, with bacA and tetX1 actively spreading within the algal-bacterial biofilm. Cyanobacteria played a negligible role in the propagation of ARGs. This study offers new insights into the spread of ARGs and bioresource recovery in algal-bacterial systems, focusing on both gene and strain levels.},
}

@article {pmid41197330,
year = {2025},
author = {Ke, T and Jiang, T and Li, H and Dong, X and Khoo, HE},
title = {Probiotic-fermented milk alleviates hypertension in preeclampsia rats and is associated with increases in branched fatty acid esters of hydroxy fatty acids.},
journal = {Nutrition research (New York, N.Y.)},
volume = {144},
number = {},
pages = {1-15},
doi = {10.1016/j.nutres.2025.10.004},
pmid = {41197330},
issn = {1879-0739},
abstract = {Branched fatty acid esters of hydroxy fatty acids (FAHFAs), a newly-discovered class of endogenous lipids closely associated with obesity, cardiovascular disease, and aging, are potential drug candidates or targets for the prevention and treatment of related conditions. The antihypertensive potential of probiotic-fermented milk has been recognized, but its relevance to preeclampsia (PE) is unclear. It was hypothesized that probiotic-fermented milk could reduce blood pressure in PE rats and influence the contents of FAHFAs, with FAHFAs potentially playing a critical role in this process. To test this hypothesis, the PE rat model was constructed using L-NAME (125 mg/kg), and probiotic-fermented milk (20 mg/kg) was administered for a total of 21 d. Metagenomic sequencing and LC-MS/MS based metabolomics were used. Probiotic-fermented milk substantially attenuated hypertension in PE rats, with an efficacy comparable to that of labetalol (4 mg/kg). Probiotic-fermented milk significantly increased the contents of specific FAHFAs (e.g., 18:0/20:2, 16:0/18:2) in the gut and serum (P < .05) and FAHFAs was negatively correlated with blood pressure (P < .05). Probiotic-fermented milk regulated the composition of gut microbiota (increasing Lactiplantibacillus and Staphylococcus and decreasing Methanobrevibacter and Limosilactobacillus), and down-regulated purine, glyoxylate/dicarboxylate, and amino metabolism, and the one-carbon pool produced by folate. These metabolic shifts were strongly correlated with the gut microbiota and FAHFAs. These results indicate that probiotic-fermented milk alleviates hypertension in PE rats, potentially mediated by FAHFAs. This study provides foundational evidence for the antihypertensive mechanism of probiotic-fermented milk in preeclampsia and supports the development of novel strategies for its prevention and treatment.},
}

@article {pmid41196658,
year = {2025},
author = {Verna, G and De Santis, S and Islam, BN and Sommella, EM and Licastro, D and Zhang, L and De Almelda Celio, F and Miller, EN and Merciai, F and Caponigro, V and Xin, W and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI196712},
pmid = {41196658},
issn = {1558-8238},
abstract = {Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors. In this report, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a missense mutation in the Muc2 gene. Upon rederivation from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice developed severe colitis and, notably, spontaneous CAC that progressively worsened over time. In contrast, CONV Winnie showed only mild colitis but no tumorigenesis. By comparison, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis and colon tumors, indicating an essential role for the gut microbiome in the development of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of the donor, only FMT from SPF Winnie donors resulted in CAC. Our studies present a relevant model of CAC, providing strong evidence that the microbiome plays a key role in its pathogenesis, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.},
}

@article {pmid41196057,
year = {2025},
author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU},
title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0094425},
doi = {10.1128/spectrum.00944-25},
pmid = {41196057},
issn = {2165-0497},
abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.},
}

@article {pmid41196055,
year = {2025},
author = {Plaza Oñate, F and Quinquis, B and Thirion, F and Gilles, M and Morabito, C and Valeille, K and Martin, R and Guidet, B and Kern, C and Pécastaings, S},
title = {Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173225},
doi = {10.1128/spectrum.01732-25},
pmid = {41196055},
issn = {2165-0497},
abstract = {The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp., whereas the forehead microbiome was dominated by Cutibacterium spp. Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advantages over 16S rRNA metabarcoding for comprehensive skin microbiome research.IMPORTANCEWith growing evidence of the role of microorganisms in maintaining healthy skin, accurately characterizing the skin microbiome remains a significant challenge. In this study, we demonstrate that shotgun sequencing, carried out with adapted wet lab protocols, provides deep insights into the microbiome composition of specific areas, such as the forehead or the armpits. Notably, it enables the characterization of fungi and viruses while offering direct functional insights into microbial communities, providing a clear advantage over 16S ribosomal RNA gene sequencing. Our findings highlight the potential of shotgun metagenomics as a powerful tool for comprehensive skin microbiome analysis. They emphasize the importance of tailored protocols for low-biomass samples, improving the reliability of shotgun sequencing and paving the way for more robust clinical studies focused on the skin microbiome.},
}

@article {pmid41196050,
year = {2025},
author = {Lee, S and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Kim, H-L and Kang, S-H and Kim, H-N},
title = {Metagenome-assembled genomes reveal microbial signatures and metabolic pathways linked to coronary artery disease.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095425},
doi = {10.1128/msystems.00954-25},
pmid = {41196050},
issn = {2379-5077},
abstract = {Gut microbiota has emerged as a critical factor influencing cardiovascular disease (CVD) risk, particularly coronary artery disease (CAD) development. Using fecal metagenomic shotgun sequencing, we investigated gut microbiota signatures associated with CAD and provided strain-resolved insights through metagenome-assembled genome (MAG) reconstruction. We analyzed 14 patients with CAD and 28 propensity score-matched healthy controls. Differential abundance analysis identified 15 CAD-associated bacterial species. Members of the Lachnospiraceae family, previously associated with trimethylamine-N-oxide production, were significantly enriched in patients with CAD. Conversely, short-chain fatty acid-producing bacteria Slackia isoflavoniconvertens and Faecalibacterium prausnitzii were depleted, suggesting a potential contribution to gut-mediated inflammation and metabolic dysregulation. Metabolic pathway analysis revealed significant urea cycle and L-citrulline biosynthesis enrichment in CAD cases, with Alistipes and Coprococcus as key contributors. Among predicted metabolites, inosine, which is implicated in coronary artery relaxation, was elevated in patients with CAD, whereas C18:0e MAG and α-muricholate were depleted. A random forest model achieved a mean AUC of 0.89 for CAD classification, with improved performance when integrating microbial taxa and metabolites. CAD-derived MAGs showed metabolic signatures linked to inflammatory dysbiosis and cardiovascular dysfunction, such as enriched N2 fixation and sulfite reduction. Strain-resolved comparative genomic analysis of MAGs revealed distinctive functional characteristics between CAD-derived and control-derived strains of Akkermansia muciniphila and Megamonas fumiformis. F. prausnitzii MAG from the control group carried non-trimethylamine-producing gene, mtxB, suggesting its potential protective role in CAD pathophysiology. These findings provide insights into gut microbial alterations in CAD and highlight potential targets for microbiome-based therapeutic interventions to reduce CVD risk.IMPORTANCEGut microbiota plays a pivotal role in cardiovascular disease; however, its specific contribution to coronary artery disease (CAD) remains underexplored. This study identified distinct microbial signatures associated with CAD, including the enrichment of pro-inflammatory bacterial taxa and depletion of short-chain fatty acid-producing bacteria, which may contribute to systemic inflammation and metabolic dysregulation. Perturbations in key pathways, such as the urea cycle and glycolysis, suggest metabolic links between the gut microbiota and CAD. Additionally, the metagenome-assembled genome-based analysis revealed strain-resolved functional heterogeneity that shapes host-microbe interactions and may contribute to CAD pathophysiology. These findings provide novel insights into gut dysbiosis in CAD and highlight the potential of microbiome-targeted therapeutic strategies in precision medicine.},
}

@article {pmid41195400,
year = {2025},
author = {Zhili, G and Jie, L and Peihao, Y},
title = {Macro- and metabolome-based characterization between gut microbiota and metabolites in patients with colorectal adenomas.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1628315},
pmid = {41195400},
issn = {1664-302X},
abstract = {OBJECTIVE: The gut microbiota has been recognized as a significant regulator in the development and progression of colorectal adenoma (CRA). However, few studies have investigated the presence and association of resident microbial species and metabolites in patients with CRA. Our aim was to analyze differences in gut microbiome composition and metabolites, as well as to evaluate their diagnostic potential for CRA.

METHODS: We conducted metagenomic and metabolomic analyses on fecal samples from 90 subjects, including 60 patients with CRA (CRA group) and 30 healthy subjects who served as normal controls (NC group). By integrating fecal metagenomic and metabolomic data, we identified gut microbiota-associated metabolites that showed significant abundance changes in CRA patients. Furthermore, we explored whether these metabolites and microbial species could distinguish CRA patients from healthy individuals.

RESULTS: 16S rRNA gene sequencing and untargeted metabolomics analysis revealed microbial changes that distinguished CRA patients from controls. Microbial population analysis showed that the CRA group formed distinct clusters from the controls, with significant β-diversity (PCA and PCoA analyses, p < 0.05). At the phylum level, the dominant taxa in terms of relative abundance included Firmicutes, Ascomycota, Mycobacteria, Actinobacteria, and Clostridia. Differential analysis of the gut flora based on species abundance revealed significant differences in taxonomic composition between healthy individuals and CRA patients. KEGG functional enrichment analysis indicated that the differential flora were primarily involved in metabolic pathways, including metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, amino acid biosynthesis, and cofactor biosynthesis. In this study, three microbial species-Fusobacterium mortiferum, Alistipes, and Bacteroides fragilis-were validated as discriminators between healthy individuals and CRA patients, with Alistipes showing higher classification efficacy. Metabolomic analysis revealed differences in tryptophan metabolism, protein degradation products, amides, and phenolic acid metabolites. KEGG enrichment results indicated that metabolic pathways were the most significantly enriched. Differential metabolites were mainly associated with the biosynthesis of plant secondary metabolites. Procrustes and Venn analyses were performed on functional entries of the two omics datasets, highlighting enriched pathways including Metabolic pathways, Glycerophospholipid metabolism, Sphingolipid metabolism, and Alpha-linolenic acid metabolism. A review of the literature confirmed that the differential flora and metabolites are associated with adenoma growth.

CONCLUSION: In this study, metagenomic and metabolomic analyses were conducted in subjects with CRA. The findings based on fecal metagenomic and metabolomic assays suggest that intestinal microecology is altered in CRA patients, leading to changes in gut cellular structure.},
}

@article {pmid41195399,
year = {2025},
author = {, },
title = {Correction: Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721706},
doi = {10.3389/fmicb.2025.1721706},
pmid = {41195399},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1652229.].},
}

@article {pmid41195309,
year = {2025},
author = {Xu, Z and Li, X and Yuan, X and Sun, C and Zhang, M and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fang, X and Wu, J and Li, Q and Luo, F},
title = {HLA-C⁣ [∗] 0304 Associates With Beneficial Gut Microbiota and Later Onset of Type 1 Diabetes in Pediatric Cohorts.},
journal = {Pediatric diabetes},
volume = {2025},
number = {},
pages = {3013063},
pmid = {41195309},
issn = {1399-5448},
mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; Cross-Sectional Studies ; Adolescent ; Child, Preschool ; Age of Onset ; Cohort Studies ; Infant ; },
abstract = {OBJECTIVE: To investigate whether human leukocyte antigens (HLAs) influence gut microbiota composition and contributes to delayed type 1 diabetes mellitus (T1DM) onset in children.

METHODS: This multicenter cross-sectional study included 106 newly diagnosed pediatric T1DM patients (age <18 years) and 69 healthy controls from nine Chinese cities. Gut microbiota was profiled via whole-metagenome shotgun sequencing, and HLA alleles were genotyped by PCR sequence-based typing. Participants were stratified by HLA-risk scores. Statistical analyses included α/β-diversity metrics, linear discriminant analysis effect size analysis (LEfSe), and Spearman correlation adjusted for confounders.

RESULTS: Principal coordinates analysis (PCoA) exposed discernible disparities in gut microbiota structures within the high-HLA-risk T1DM cohort relative to both high- and low-HLA-risk control groups (R [2] = 0.0562, p=0.003 and R [2] = 0.0343, p=0.003). HLA-C [∗] 0304 carriers exhibited delayed T1DM onset compared to noncarriers (adjusted R [2] = 0.225, p=0.017). High-HLA-risk T1DM patients showed distinct microbiota divergence from controls (R [2] = 0.0562, p=0.003), driven by reduced Lachnospiraceae and Blautia (butyrate producers) in noncarriers. Conversely, HLA-C [∗] 0304-positive T1DM patients had enriched Blautia (p=0.005) and Lachnospiraceae (p=0.039), alongside lower opportunistic pathogens (Citrobacter; p < 0.05). High-HLA-risk patients also displayed lower fasting C-peptide levels than low-risk counterparts (0.19 ± 0.14 vs. 0.26 ± 0.19 µg/mL, p=0.029).

CONCLUSIONS: Our study demonstrates that specific HLA class I subtypes (e.g., C [∗] 0304) may modulate T1DM onset through selective enrichment of beneficial gut microbiota. Elucidating the mechanisms by which HLA variants regulate mucosal immunity and coordinate HLA-microbiota-immune interactions holds significant potential for developing targeted interventions against T1DM pathogenesis.},
}

Humans
*Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology
*Gastrointestinal Microbiome/genetics
Child
Male
Female
Cross-Sectional Studies
Adolescent
Child, Preschool
Age of Onset
Cohort Studies
Infant

@article {pmid41194765,
year = {2025},
author = {Li, J and Zhao, S and Guo, F and Zhang, W and Chen, M and den Haan, R and Xin, F and Jiang, Y and Jiang, M},
title = {Strategies to Improve the Efficiency of Enzymatic Carbon Dioxide Conversion In Vitro.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00760},
pmid = {41194765},
issn = {2161-5063},
abstract = {With the rapid industrial development, massive fossil fuel use has caused excessive carbon dioxide (CO2) emissions, triggering global warming and environmental issues. Thus, CO2 recovery and reuse have become a research focus, among which artificially designed in vitro biocatalytic pathways for converting CO2 into high-value chemicals show promise, with advantages like shorter routes, higher efficiency and lower energy consumption compared to natural pathways. However, challenges remain due to natural enzymes' issues in specificity, affinity, efficiency, stability and oxygen sensitivity. To tackle these problems, extensive research efforts have been undertaken. These include elucidating the mechanisms and catalytic efficiencies of carbon-fixing enzymes from diverse sources, as well as developing and refining novel in vitro carbon fixation pathways. Moreover, significant progress has been made in computer-aided investigations of enzyme structure, function, and engineering optimization, alongside advancements in enzyme immobilization strategies, cofactor regeneration systems, and the development of artificial cofactors. By summarizing the latest research progress in recent years, we can identify the current bottlenecks and challenges in in vitro enzymatic CO2 conversion, propose effective methods to enhance the efficiency of CO2 conversion, and thus promote the development of research in related fields.},
}

@article {pmid41194716,
year = {2025},
author = {Liu, YH and Sheng, SY and Hu, HB and Wang, Y and Zhang, LW and Feng, YF and Feng, YY},
title = {Effects of drought on the thermal adaptation of soil microbial respiration: A review.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {10},
pages = {2965-2977},
doi = {10.13287/j.1001-9332.202510.032},
pmid = {41194716},
issn = {1001-9332},
mesh = {*Droughts ; *Soil Microbiology ; Climate Change ; Soil/chemistry ; *Adaptation, Physiological/physiology ; Ecosystem ; Carbon Cycle ; },
abstract = {Drought induced by global climate change affects the thermal adaptation of soil microbial respiration, which has complex consequences on the carbon (C) cycle. Drought can either enhance C emissions and create a positive feedback loop, or promote C sequestration and generate a negative feedback effect. We reviewed the effects of drought on microbial thermal adaptation, analyzed the underlying mechanisms, and summarized current research findings and related debates. Drought significantly influences microbial thermal adaptation through altering soil aggregate structure, organic carbon molecular composition, and microbial community structure. Due to variations in climatic zones, ecosystem types, and soil conditions, the impacts of drought on microbial thermal adaptation exhibit regional variety and complexity. Future research should focus on experimental designs that simulate natural environments, utilizing diverse organic substrates (e.g., cellulose, oxalic acid and xylan) to generate more accurate data and explore the synergistic effects of drought with other environmental factors (e.g., elevated CO2 concentrations, increased ultraviolet radiation, and nitrogen deposition) to reveal their combined impacts on microbial thermal adaptation. Advanced techniques like metagenomics and DNA-stable isotope probing should be warranted to further reveal the microbial mechanisms involved in the regulation of drought on microbial thermal adaptation.},
}

*Droughts
*Soil Microbiology
Climate Change
Soil/chemistry
*Adaptation, Physiological/physiology
Ecosystem
Carbon Cycle

@article {pmid41194562,
year = {2025},
author = {Martínez-Mercado, MA and Latisnere-Barragán, H and Ramírez-Arenas, PJ and Vázquez-Juárez, R and García-Maldonado, JQ and López-Cortés, A},
title = {Genome-Resolved Approach of Guerrero Negro Hypersaline Microbial Mats Reveals the Metabolic Potential of Key Players in a Stratified Community.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70199},
doi = {10.1111/1462-2920.70199},
pmid = {41194562},
issn = {1462-2920},
support = {CF-2019-848287//Consejo Nacional de Humanidades Ciencia y Tecnología/ ; },
mesh = {*Archaea/genetics/metabolism/classification/isolation & purification ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Genome, Bacterial ; Metagenome ; *Microbiota ; Sulfur/metabolism ; *Geologic Sediments/microbiology ; Salinity ; Genome, Archaeal ; Carbon/metabolism ; Nitrogen/metabolism ; Phylogeny ; },
abstract = {Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H2/CO2, TMA, and H2/CO2-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.},
}

*Archaea/genetics/metabolism/classification/isolation & purification
*Bacteria/metabolism/genetics/classification/isolation & purification
*Genome, Bacterial
Metagenome
*Microbiota
Sulfur/metabolism
*Geologic Sediments/microbiology
Salinity
Genome, Archaeal
Carbon/metabolism
Nitrogen/metabolism
Phylogeny

@article {pmid41194295,
year = {2025},
author = {Breukers, E and Kim, H and Banihashem, F and Andersson, K and Leijon, M and Westin, R and Sjölund, M and Zohari, S},
title = {The first detection of swine orthopneumovirus in a pig farm in Sweden: a case report.},
journal = {Porcine health management},
volume = {11},
number = {1},
pages = {56},
pmid = {41194295},
issn = {2055-5660},
abstract = {BACKGROUND: Respiratory diseases are globally a major challenge in today's pig production. Despite the efforts to manage the disease, the number of pigs affected is still increasing, indicating gaps in the current knowledge. In 2016, a novel pneumovirus, swine orthopneumovirus, was detected in the USA. Since then, the virus has been detected in a few European countries and in South Korea. However, the wider distribution of the virus is still greatly unknown, as well as its clinical relevance.

CASE PRESENTATION: This report describes the first detection of swine orthopneumovirus in a Swedish pig herd. The virus was detected as the result of an investigation conducted between September 2023 to June 2024, where all clinical samples (n = 682) sent to the Swedish Veterinary Agency for diagnostic purposes from 112 Swedish pig farms exhibiting clinical signs of respiratory disease were screened for the presence of swine orthopneumovirus. The virus was detected in one piglet producing farm that had a respiratory disease outbreak in autumn 2023, which presented with cough and nasal discharge. In November 2023, 11 nasal swabs were collected, of which 9 were PCR-positive for swine orthopneumovirus. In addition, each sample was also PCR-positive for Mesomycoplasma hyorhinis and Pasteurella multocida, and 2 samples were PCR-positive for Actinobacillus pleuropneumoniae, indicating a polymicrobial respiratory infection.

CONCLUSIONS: This report emphasises the importance of ongoing efforts to identify emerging pathogens and determine their clinical significance. Therefore, further research is needed to assess the distribution and potential clinical relevance of swine orthopneumovirus.},
}

@article {pmid41194257,
year = {2025},
author = {Parsons, C and Fournier, GP},
title = {Horizontal transfer of matrix metalloproteinase genes links early animal and microbial evolution.},
journal = {Biology direct},
volume = {20},
number = {1},
pages = {107},
pmid = {41194257},
issn = {1745-6150},
support = {EAR-1615426//National Science Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; *Bacteria/genetics/enzymology ; Phylogeny ; *Matrix Metalloproteinases/genetics ; *Evolution, Molecular ; Archaea/genetics/enzymology ; *Biological Evolution ; Metagenome ; },
abstract = {BACKGROUND: The early evolution of animals is characterized by the emergence of complex tissues, organs, and integument, made possible in part by the diversification of groups of structural proteins. The abundance of this new kind of organic material in the environment would have provided novel nutrient opportunities for microbes, as part of the beginnings of animal-microbial coevolution. Indeed, a diverse ensemble of extant microbial groups appear to possess the enzymatic ability to cleave collagen, the most abundant animal-specific protein, through the use of matrix metalloproteinases (MMPs). In animals, MMPs serve to reshape the extracellular matrix in the course of development, but their prevalence in the microbial world has been largely overlooked.

RESULTS: MMPs have extensive diversity in Bacteria, Eumetazoa, and Streptophyta. We show that in marine metagenomes, MMP abundance is highly correlated with chitinase abundance, implying that even microbial MMPs are associated with animal-derived substrates. Reconstructing the phylogeny of MMP proteins reveals a history of rapid diversification, as well as multiple interkingdom and interdomain horizontal gene transfers. Included among these is a transfer to the ancestral lineage of the archaeal family Methanosarcinaceae, constraining this group to postdate the evolution of collagen, and therefore animal diversification.

CONCLUSIONS: MMPs have an unusual genetic history, marked by multiple instances of gene transfer between bacteria and multicellular eukaryotes, a smoking gun for some of the earliest coevolution between prokaryotes and metazoans. By calculating an end-Permian divergence of Methanosarcina, we demonstrate that the phylogenies of substrate-specific enzymes can provide valuable older-bound age calibrations for improving molecular clock age estimates across the Tree of Life.},
}

*Gene Transfer, Horizontal
Animals
*Bacteria/genetics/enzymology
Phylogeny
*Matrix Metalloproteinases/genetics
*Evolution, Molecular
Archaea/genetics/enzymology
*Biological Evolution
Metagenome

@article {pmid41194238,
year = {2025},
author = {Ellis, VA and Theodosopoulos, A and Sharma, I and Bardil, A and Stjernman, M and Hellgren, O},
title = {Simultaneous population genomics of hosts and their parasites with selective whole genome amplification.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {448},
pmid = {41194238},
issn = {1756-3305},
support = {NIH/NIGMS P20 GM103446, S10 OD028725/GF/NIH HHS/United States ; DEL00854, NE1943, NE2443//USDA Hatch/ ; VR 2021-03663//Swedish Research Council/ ; },
mesh = {Animals ; *Haemosporida/genetics ; *Host-Parasite Interactions/genetics ; *Protozoan Infections, Animal/parasitology ; *Bird Diseases/parasitology ; *Genome, Protozoan ; DNA, Protozoan/genetics ; Genomics ; *Passeriformes/parasitology/genetics ; Metagenomics/methods ; },
abstract = {BACKGROUND: Generating parasite genomes is challenging when little of the DNA in infected host tissue is from the parasite. We used selective whole genome amplification (SWGA) to generate genomic data from wildlife samples of the avian haemosporidian Haemoproteus majoris (lineage PARUS1) and its host, the blue tit (Cyanistes caeruleus).

METHODS: We used SWGA to amplify the parasite DNA in nine avian blood samples collected between 1996 and 2021, and subsequently performed short-read sequencing and bioinformatically separated the host and parasite reads in each sample.

RESULTS: SWGA increased the percentage of parasite reads significantly. Sequencing to a depth of about 56 million reads (forward and reverse) per sample resulted on average (± standard error [SE]) in 11.3X ± 1.85 for the host genome and 1.17X ± 0.446 mean depth of coverage for the host and parasite, respectively, after SWGA. Furthermore, about 74% of the host genome (genome size approx. 1.2 Gb) and 33% of the parasite genome (approx. 23.9 Mb) had at least 1X coverage on average; two samples had 1X coverage of approximately 60% of the parasite genome. Parasite sequencing success was positively correlated with parasitemia. When comparing the parasite sequences in the four best samples, we identified 9895 sites (minimum 5X coverage) that varied among the infections. When filtering the full dataset to at least six samples per variant, we identified 14,512,339 and 7068 sites that varied among samples in the host and parasite populations, respectively, revealing variation among samples and years.

CONCLUSIONS: SWGA facilitates dual host-parasite population genomics in this system and will greatly expand our understanding of host-parasite interactions over space and time.},
}

Animals
*Haemosporida/genetics
*Host-Parasite Interactions/genetics
*Protozoan Infections, Animal/parasitology
*Bird Diseases/parasitology
*Genome, Protozoan
DNA, Protozoan/genetics
Genomics
*Passeriformes/parasitology/genetics
Metagenomics/methods

@article {pmid41194219,
year = {2025},
author = {Liu, Y and Yu, M and Chen, X and Ran, L and Zhang, XH},
title = {Diversity, metabolic potential and global distribution of the anaerobic fermentative bacteria Phylum Candidatus Cloacimonadota.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {136},
pmid = {41194219},
issn = {2524-6372},
support = {32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3, LSKJ202203201 and LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; },
abstract = {BACKGROUND: The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.

RESULTS: In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and α-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.

CONCLUSION: This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.},
}

@article {pmid41194006,
year = {2025},
author = {Ivanova, A and Buzova, V},
title = {A novel enzymatic approach for a targeted fungal growth inhibition.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {719},
pmid = {41194006},
issn = {1471-2180},
support = {03-ZP23-087//SkyLab AG/ ; 03-ZP23-087//SkyLab AG/ ; },
abstract = {BACKGROUND: Dandruff represents a complex, multifactorial disorder characterized by impaired barrier function, altered lipid composition, and microbial imbalance. The principal pathogenic mechanism, however, involves excessive colonization by Malassezia species, notably M. furfur, M. restricta and M. globosa, on the scalp. Standard antifungal options often lead to undesirable effects, including itching and irritation, and may negatively impact the scalp microbiome. This study evaluates combination of chitinase and chitosanase, targeting fungal cell wall chitin and chitosan, as a promising targeted approach for scalp Malassezia spp.

METHODS: The in vitro antifungal activities of chitinase (100 U/g) and chitosanase (200 U/g) were evaluated against Malassezia furfur, Malassezia restricta, and Malassezia globosa at concentrations ranging from 0.125% to 5% w/w. Their efficacy was compared to that of conventional antifungal agents, including climbazole, piroctone olamine, selenium sulfide, zinc pyrithione, and propanediol caprylate. Cytotoxicity was assessed using fibroblast cell lines via MTT assay and fluorescence microscopy. A clinical study (n = 18) evaluated the impact of a solution containing 0.25% chitinase and 0.25% chitosanase on scalp M. furfur and M. restricta DNA and RNA levels using quantitative PCR (qPCR). A metagenomic analysis was conducted to assess the impact of enzymatic treatment on bacterial composition and diversity.

RESULTS: Individually, 0.25% chitinase and 0.25% chitosanase inhibited Malassezia spp. growth by 23.85% and 26.15%, respectively (p < 0.05). When combined at 0.25%, they achieved 98.38% inhibition (p < 0.05), with complete suppression observed at 0.5%. In a clinical study, a 3-hour scalp treatment with a solution containing 0.25% chitinase and 0.25% chitosanase followed by quantitative PCR of post-treatment samples demonstrated significant reductions in DNA and RNA levels of M. furfur and M. restricta. DNA content decreased 2.4- and 1.9-fold, and RNA levels declined 2.4- and 4.6-fold, respectively. Cytotoxicity was detected only at concentrations ≥ 7.6%, well above the effective antifungal doses. The metagenomic analysis demonstrated that a three-hour scalp treatment with chitinase - chitosanase solution increased alpha diversity (Chao1 index) and doubled the number of identifiable operational taxonomic units (OTUs).

CONCLUSIONS: The chitinase-chitosanase combination offers a promising targeted approach for scalp Malassezia spp. control without broad antimicrobial effects.},
}

@article {pmid41193697,
year = {2025},
author = {Chica Cardenas, LA and Leonard, MM and Baldridge, MT and Handley, SA},
title = {Gut virome dynamics: from commensal to critical player in health and disease.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {41193697},
issn = {1759-5053},
abstract = {The gut virome is a complex ecosystem characterized by the interplay of diverse viral entities, predominantly bacteriophages and eukaryotic viruses. The gut virome has a critical role in human health by shaping microbial community profiles, modulating host immunity and influencing metabolic processes. Different viral metagenomics approaches have revealed the remarkable diversity of the gut virome, showing individual-specific patterns that evolve over time and adapt dynamically to environmental factors. Perturbations in this community are increasingly associated with chronic immune and inflammatory conditions, metabolic disorders and neurological conditions, highlighting its potential as a diagnostic biomarker and therapeutic target. The early-life gut virome is particularly influential in establishing lifelong health trajectories through its interactions with diet, immune pathways and others, thereby contributing to inflammatory and metabolic regulation. This Review synthesizes current knowledge of gut virome composition, dynamics and functional relevance, critically evaluating evidence distinguishing causal from correlative roles in disease pathogenesis. The interactions of the virome with other microbiome components and host immunity are examined, and emerging translational applications, including phage therapy and biomarker development, are discussed. Integrating these insights while acknowledging methodological challenges provides a comprehensive framework for understanding the complex roles of the gut virome in health and disease.},
}

@article {pmid41193636,
year = {2025},
author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and , and Probst, AJ},
title = {Author Correction: A roadmap for equitable reuse of public microbiome data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-025-02212-3},
pmid = {41193636},
issn = {2058-5276},
}

@article {pmid41193635,
year = {2025},
author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R},
title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41193635},
issn = {2058-5276},
support = {991222//Simons Foundation/ ; },
abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.},
}

@article {pmid41192565,
year = {2025},
author = {Tóth, GE and Petersen, M and Chevenet, F and Sikora, M and Tomazatos, A and Bialonski, A and Baum, H and Horváth, B and Siriyasatien, P and Heitmann, A and Jansen, S and Offergeld, R and Lachmann, R and Schmidt, M and Schmidt-Chanasit, J and Cadar, D},
title = {Blood donors as sentinels for genomic surveillance of West Nile virus in Germany using a sensitive amplicon-based sequencing approach.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106647},
doi = {10.1016/j.jinf.2025.106647},
pmid = {41192565},
issn = {1532-2742},
abstract = {BACKGROUND: West Nile virus (WNV) has emerged as a public health concern in Germany since its first detection in 2018, with evidence of expanding geographic spread. Genomic surveillance is critical for tracking viral evolution, identifying introductions, and monitoring local transmission. However, genome recovery from low-viremia samples such as those obtained through blood donor screening remains technically challenging.

AIM: To develop and validate a sensitive amplicon-based sequencing protocol optimized for WNV lineage 2 and apply it to low-titer samples to support genomic surveillance in Germany.

METHODS: A novel primer scheme was designed for WNV lineage 2 and applied to 43 nucleic acid testing (NAT)-positive blood donor samples collected between 2020 and 2024. Amplicon-based sequencing performance was benchmarked against metagenomic next-generation sequencing (mNGS). Recovered genomes were subjected to phylogenomic analysis to assess viral diversity and transmission dynamics.

RESULTS: The amplicon protocol enabled genome recovery (>70% coverage) from samples with viral loads as low as ~10¹ RNA copies/µL, outperforming metagenomic NGS (mNGS). Of the 43 samples, 30 yielded complete or near-complete genomes. Six distinct WNV subclades (2A-2F), including German strains, were identified, indicating multiple introductions into Germany from Central Europe. Subclade 2F emerged as the dominant and widely distributed group. Berlin, Brandenburg, Saxony, and Saxony-Anhalt were identified as persistent transmission hubs.

CONCLUSION: This study highlights blood donors as valuable sentinels for WNV genomic surveillance. The validated amplicon-based sequencing approach enables sensitive, scalable genome recovery from low-viremia samples, and when integrated with routine blood donor screening, provides a robust framework for early detection, transmission dynamics, and public health preparedness.},
}

@article {pmid41192489,
year = {2025},
author = {Meng, F and Wang, L and Xu, J and Li, X and Hao, J},
title = {Enhanced electron transfer mediated by surface functional groups of targetedly modified sludge-based biochar for sustainable microbial chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133600},
doi = {10.1016/j.biortech.2025.133600},
pmid = {41192489},
issn = {1873-2976},
abstract = {While unmodified sludge-based biochar (SBBC) exhibits limited electron transfer capacity in chain elongation (CE), its surface functional groups are recognized as critical factor influencing direct interspecies electron transfer (DIET). This study employed three modification methods, i.e., H2O2, HNO3, and anthraquinone sulfonate (AQS), to explore the effects of modified SBBC on CE process. Results indicated that the AQS-modified SBBC (SBBC-AQS) exhibited optimal electron transfer properties and electrochemical activity. Thus, SBBC-AQS greatly promoted DIET-mediated CE, leading to 62% higher caproate production compared to no biochar. Further recycling experiments confirmed the reusability of SBBC-AQS, along with the biofilm formation. Lastly, metagenomic analysis revealed that modified SBBC improved the abundance of CE bacteria such as Clostridium kluyveri, and introduced electron-transferring bacteria such as Petrimonas, so as to reinforce ethanol oxidation and medium-chain fatty acids production. This study offers novel insights into the sustainable material and microbes synergistic regulation to achieve an efficient CE system.},
}

@article {pmid41192488,
year = {2025},
author = {Chen, W and Yang, Y and Chang, S and Zhang, K and Xu, T and Li, J and Liang, X and Xu, Y and Nghiem, LD and Johir, MAH and Wei, Y},
title = {Microbial necromass analogues reshape composting humification pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133583},
doi = {10.1016/j.biortech.2025.133583},
pmid = {41192488},
issn = {1873-2976},
abstract = {Microbial necromass is increasingly recognized as a key driver of soil carbon stabilization, yet its mechanistic role in compost humification remains elusive. Here, by integrating metagenomics, quantitative necromass tracing, and partial least squares structural equation modeling (PLS-SEM), the regulatory effects of two microbial necromass analogues-N-acetyl-d-glucosamine (GlcNAc) and chitin-on pig manure composting were systematically investigated. Both analogues significantly altered the physicochemical properties, microbial community composition, and necromass dynamics during composting. Chitin addition markedly enhanced early microbial biomass and bacterial diversity but inhibited humic acid (HA) formation, while promoting fulvic acid (FA) accumulation and resulting in humic substances (HS) with lower molecular complexity. In contrast, GlcNAc selectively stimulated bacterial proliferation during the maturation phase, reduced both bacterial and fungal diversity, and led to increased FA content, accompanied by reduced HS molecular complexity. Metagenomic and PLS-SEM analyses revealed that both analogues fundamentally reprogrammed humification metabolic pathways: chitin suppressed genes involved in complex precursor metabolism, whereas GlcNAc narrowed the functional repertoire and shifted humification toward simpler pathways. These analogue-driven microbial metabolic shifts decoupled necromass accumulation from stable HA formation and favored the accumulation of simpler humic fractions. This study provides the first mechanistic evidence that targeted regulation of necromass transformation can precisely optimize humification efficiency and molecular characteristics, laying a theoretical foundation for improved organic waste utilization and process control in composting.},
}

@article {pmid41192424,
year = {2025},
author = {Li, P and Sun, J and Geng, Y and Jiang, Y and Li, YZ and Zhang, Z},
title = {Assessment of enzyme diversity in the fermented food microbiome.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101430},
doi = {10.1016/j.cels.2025.101430},
pmid = {41192424},
issn = {2405-4720},
abstract = {Microbial bioactivity is essential for the flavor, appearance, quality, and safety of fermented foods. However, the diversity and distribution of enzymatic resources in fermentation remain poorly understood. This study explored 10,202 metagenome-assembled genomes from global fermented foods using machine learning, identifying over 5 million enzyme sequences grouped into 98,693 homologous clusters, representing over 3,000 enzyme types. Functional analysis revealed that 84.4% of these clusters were unannotated in current databases, with high novelty in terpenoid and polyketide metabolism enzymes. Peptide hydrolases exhibited broad environmental adaptability based on predicted optimal temperatures and pH, and niche breadth calculations indicated 31.3% of enzyme clusters displayed food-type specificity. Additionally, we developed a machine learning model to classify fermented food sources by enzyme clusters, highlighting key enzymes differentiating habitats. Our findings emphasize the untapped potential of fermented food environments for enzyme resource exploration, offering valuable insights into microbial functions for future food research. A record of this paper's transparent peer review process is included in the supplemental information.},
}

@article {pmid41192191,
year = {2025},
author = {Zhou, G and Wang, YS and Zhang, GF and Zhang, SY and Wen, X and Cui, ZB and Shi, QS and Xie, XB},
title = {Gut microbiota composition and antibiotic resistance ontology landscape in Micropterus salmoides: Insights from metagenomic and metabolomic analyses.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {57},
number = {},
pages = {101666},
doi = {10.1016/j.cbd.2025.101666},
pmid = {41192191},
issn = {1878-0407},
abstract = {Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.},
}

@article {pmid41192179,
year = {2025},
author = {Wu, GG and Jin, JA and Han, NN and Guo, WL and Fan, NS and Jin, RC},
title = {Multiomic insights into the regulatory mechanism of anammox consortia: Interspecies cooperation, degradation and self-adaptation to plasticizer stress.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140319},
doi = {10.1016/j.jhazmat.2025.140319},
pmid = {41192179},
issn = {1873-3336},
abstract = {Phthalates are prevalent in wastewater treatment systems and pose a potential threat to microbial communities. In this study, it was found that the nitrogen removal efficiency of anaerobic ammonium oxidation (anammox) process remained at 92.5 ± 2.4 % after the long-term exposure to di-(2-ethylhexyl) phthalate (DEHP). Although the relative abundance of Candidatus Kuenenia decreased by 5.5 %, that of other denitrifying functional bacteria increased to maintain the system stability. The adaptation of anammox consortia to DEHP mainly depended on microbial cooperation and molecular regulation. Combined with metagenomic and metatranscriptomic analyses, Bacillus subtilis functioned as the DEHP-degrading species and exhibited a collaborative relationship with other degrading microorganisms. The expression levels of carbon metabolism, two-component system and quorum sensing related genes were significantly (p < 0.05) upregulated by 0.4-6.6 folds. The structural equation model further proved that biodegradation was the main contributor to mitigating DEHP inhibition. Notably, Ca. Kuenenia and transposons were the host of most antibiotic resistance genes (ARGs) and the main mobile genes elements, respectively. DEHP also triggered oxidative stress and resistance dissemination in anammox consortia. These findings provide molecular insights into the microbial regulatory mechanism in responding to plasticizer stress and drive the expansion of anammox process application.},
}

@article {pmid41192168,
year = {2025},
author = {Skalny, AV and Korobeinikova, TV and Morozova, G and Menshikova, IV and Gritsenko, VA and Zhang, F and Mak, DV and Guo, X and Sotnikova, TI and Aschner, M and Tinkov, AA},
title = {Serum trace element and mineral levels and fecal microbiota in relation to cartilage damage in rheumatoid arthritis patients.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {92},
number = {},
pages = {127787},
doi = {10.1016/j.jtemb.2025.127787},
pmid = {41192168},
issn = {1878-3252},
abstract = {UNLABELLED: The objective of the present study was to evaluate serum trace element and mineral levels as well as taxonomic characteristics of gut microbiota and their association with cartilage damage in patients with rheumatoid arthritis (RA).

MATERIALS AND METHODS: Serum trace element and mineral levels in 41 healthy controls and 41 RA patients were assessed using inductively-coupled plasma mass-spectrometry. Taxonomic characteristics of fecal microbiota were assessed using 16S metagenomic sequencing. RA patients were characterized by increased cartilage oligomeric matrix protein (COMP) and complement component 3 (C3) levels, indicative of cartilage damage and inflammation.

RESULTS: Serum Ca, Fe, Se, and Zn levels in RA patients were lower, whereas circulating Cr, Cu, and Mo concentrations exceeded the respective control values. 16S metagenomic sequencing of fecal samples revealed lower relative abundance of Firmicutes and Actinomycetota with a reduction in Firmicutes-to-Bacteroidetes ratio in RA patients. At the class level, the relative abundance of Bacilli, Coriobacteria, and Clostridia in RA patients was lower, whereas that of Bacteroidia and Negativicutes was higher compared to the control group. Tight negative association between serum Zn levels and the abundance of Bacteroidetes and Bacteroidia was observed, whereas correlation between Zn and Firmicutes-to-Bacteroidetes ratio was positive. Multiple linear regression analysis demonstrated that serum COMP level was inversely associated with serum Fe and Se levels, as well as relative abundance of Bacilli and Clostridia, being positively associated with serum Ca and C3 levels.

CONCLUSION: These novel findings demonstrate a multilateral relationship between trace element metabolism, gut microbiota, and cartilage damage in RA.},
}

@article {pmid41192067,
year = {2025},
author = {Świderek, K and Arafet, K and de Sousa Batista, V and Grajales-Hernández, D and López-Gallego, F and Moliner, V},
title = {Insights into the Catalytic Activity of a Metagenome-Derived Urethanase.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c13147},
pmid = {41192067},
issn = {1520-5126},
abstract = {The discovery of urethanases shows an opportunity to access the biotechnological recycling of polyurethane-based plastics (PURs), widely used in the manufacture of everyday materials. However, the mechanistic understanding of these enzymes remains under debate. In this work, we report a QM/MM-based mechanistic study of the metagenome-derived urethanase UMG-SP2 catalyzing the degradation of a urethane-like model compound, 4-nitrophenyl benzylcarbamate (pNC). A high-quality structural model generated with AlphaFold2, prior to the availability of the crystal structure, accurately captured the Ser-Ser-Lys catalytic triad characteristic of amidase signature enzymes. Highly accurate constant-pH nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) simulations provided the full titration curve of active site Lys, explaining the need for alkaline media for the enzyme to be active. The generation of the free energy landscape, obtained by means of free energy perturbation methods with the M06-2X DFT functional describing the QM region of the full system, reveals an esterase-like three-step mechanism of UMG-SP2, i.e., acylation, hydrolysis, and decarboxylation, with all steps being kinetically feasible. Our computational results show very good agreement with experimental kinetic data, with a calculated free energy barrier of 21.2 kcal·mol[-1] for the rate-determining step compared to 22.9 kcal·mol[-1] derived from the experimentally measured turnover frequency (TOF). The present results also open the door for the final decarboxylation occurring in the solution after the release of the product of the hydrolysis step or within the active site. These findings provide an atomistic insight into the urethanase function and establish a robust framework for the future design of biocatalysts targeting polyurethane degradation.},
}

@article {pmid41192043,
year = {2025},
author = {Kumar, A and Xu, C and Dakal, TC},
title = {Microbiome based precision medicine through integrated multiomics and machine learning.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128384},
doi = {10.1016/j.micres.2025.128384},
pmid = {41192043},
issn = {1618-0623},
abstract = {Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m[OMICS]) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m[OMICS] approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m[OMICS] and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.},
}

@article {pmid41192026,
year = {2025},
author = {Chen, Y and Kong, X and Mao, X and Fan, X and Yuan, J},
title = {Unlocking methanogenesis at 45°C: Synergistic roles of Zero-Valent iron and magnetite in Restoring cellulose anaerobic digestion.},
journal = {Waste management (New York, N.Y.)},
volume = {210},
number = {},
pages = {115225},
doi = {10.1016/j.wasman.2025.115225},
pmid = {41192026},
issn = {1879-2456},
abstract = {Anaerobic digestion (AD) operated at transitional temperature is a promising technology for treating de-oiled food waste (FW). However, under such conditions, the metabolic activity of methanogens will be significantly negatively affected compared to conventional mesophilic or thermophilic conditions, which limits its practical application. In this study, the AD of cellulose at 45 °C were investigated, and the synergistic effects of zero-valent iron (ZVI) and magnetite (Fe3O4) on enhancing methanogenesis were explored. The results indicated that the combination of ZVI and Fe3O4 played a crucial role in promoting cellulose methanogenesis during AD at 45 °C. Specifically, the methane yield reached 300.1 mL/g VS, representing a 58 % increase compared to the control group. Further analysis revealed that ZVI + Fe3O4 enhanced the levels of coenzyme F420 and acetate kinase. Firmicutes and Methanosarcina were the dominant microbial groups involved in normal methanogenesis at 45 °C, and a positive correlation between these two groups was observed. Metagenomic sequencing further demonstrated that the combination of ZVI and Fe3O4 synergistically increased the abundance of genes associated with both acetate cleavage and CO2 reduction methanogenic pathways. The dominant pathways achieved a dynamic equilibrium, functioning according to the available substrates at different stages within the reactor. Life Cycle Assessment (LCA) results indicated that coupling ZVI and Fe3O4 could effectively reduce carbon emissions and fossil resource depletion. The study provided theoretical evidence for the application of AD in treating cellulose-based substrates at transitional temperatures.},
}

@article {pmid41191113,
year = {2025},
author = {Cheng, J and Yang, F and Zhang, L and Zhao, J and Zhang, X and Qiao, H and Yan, Z and Luo, Y and Dai, Y},
title = {Genomic Analysis, Metabolite Characterization, and Wheat Seedling Growth Promotion of Variovorax Endophyticus sp. nov., A Novel Endophyte from Wheat Root Tissue.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {2},
pmid = {41191113},
issn = {1432-0991},
support = {41877042//National Natural Science Foundation of China/ ; 2023YB007//Hebei Normal University of Science and Technology/ ; 2022JDTD0027//Science and Technology Department of Sichuan Province/ ; },
mesh = {*Triticum/microbiology/growth & development ; *Plant Roots/microbiology/growth & development ; *Endophytes/genetics/isolation & purification/classification/metabolism ; Phylogeny ; *Comamonadaceae/genetics/isolation & purification/classification/metabolism/physiology ; RNA, Ribosomal, 16S/genetics ; *Seedlings/growth & development/microbiology ; Base Composition ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Genome, Bacterial ; Bacterial Typing Techniques ; Genomics ; },
abstract = {A bacterial strain CY25R-8[T] (= CGMCC 1.16908[T] = KACC 21250[T]) was isolated from the root tissues of wheat. It is aerobic, motile (with a single flagellum), Gram-negative, rod-shaped and yellow, and capable of growing at 10-40 ℃, pH 3.0-10.0 and NaCl 0.0-5.0%; its major fatty acids were C16:0, C17:0 cyclo, summed feature 8 and 3; its genomic DNA G + C content was 69.5%. Its respiratory quinone was ubiquinone-8 and major polar lipids were phosphatidylethanolamine, phosphatidylglycerol diphospatidylglycerol and unidentified aminophospholipid. Strain CY25R-8[T] exhibited the highest 16S rRNA gene sequence similarity (99.0%-99.6%) with the type strains of several Variovorax species. However, the dDDH and ANI values between strain CY25R-8[T] with these type strains were 28.6%-29.5% and 84.65%-86.0%, respectively. These values indicated that strain CY25R-8[T] represents a novel species of the genus Variovorax. The name Variovorax endophyticus sp. nov. is proposed. Furthermore, genomic comparisons with uncharacterized isolates and uncultured strains (metagenome-assembled genomes) revealed no close relatives of CY25R-8[T], suggesting this species is novel and potentially aquatic. Through LC-MS, NMR, and MS data, 25 metabolites were identified in strain CY25R-8[T], with cyclo (L-Phe-L-Ser), cyclo (L-Phe-D-4-OH-Pro), H-DPro-β[3]-Glu-NH2 1-ααβ and pGlu-His-Pro-OH being the major compounds. Notably, strain CY25R-8[T] is the first reported natural producer of H-DPro-β[3]-Glu-NH2 1-ααβ. As an endophyte of wheat, strain CY25R-8[T] also demonstrated the ability to enhance wheat seedling growth by promoting main root elongation in vivo. These findings suggest that V. endophyticus CY25R-8[T] has potential applications in biotechnology and agriculture.},
}

*Triticum/microbiology/growth & development
*Plant Roots/microbiology/growth & development
*Endophytes/genetics/isolation & purification/classification/metabolism
Phylogeny
*Comamonadaceae/genetics/isolation & purification/classification/metabolism/physiology
RNA, Ribosomal, 16S/genetics
*Seedlings/growth & development/microbiology
Base Composition
Fatty Acids/chemistry/analysis
DNA, Bacterial/genetics
Genome, Bacterial
Bacterial Typing Techniques
Genomics

@article {pmid41190884,
year = {2025},
author = {van Scheijen, S and Neerincx, AH and Weersink, EJM and Altenburg, J and Majoor, C and van Muijlwijk-Koezen, JE and Maitland-van der Zee, AH and Abdel-Aziz, MI and , },
title = {Metagenomics approach to predict antibiotic resistance genes in sputum samples of adult people with cystic fibrosis: a pilot study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0229924},
doi = {10.1128/spectrum.02299-24},
pmid = {41190884},
issn = {2165-0497},
abstract = {UNLABELLED: Lung infections in people with cystic fibrosis (CF) cause lung damage, which is the leading factor in the morbidity and mortality of CF. Prescription of antibiotics to treat these infections is essential to maintain a higher quality of life and increase life expectancy. Determination of antibiotic susceptibility (ABS) is done by culture-dependent, phenotypic methods. These procedures take several days, while timely intervention is key. The analysis of antibiotic resistance genes by use of shotgun metagenomics might offer a time-sensitive alternative. Twenty people with CF with a homozygous Phe508del mutation provided 68 sputum samples during different visits over a period of roughly a year. After shotgun sequencing, the samples were analyzed using the deep learning tool deepARG. These results were compared with the results from routine ABS testing. The performance was determined by area under the curve-receiver operating characteristics (AUCROC) and sensitivity. Significant results were obtained for the following antibiotic classes: aminoglycoside (AUCROC = 0.81 [95% CI: 0.67-0.95, sensitivity = 73%]), cephalosporin (AUCROC = 0.70 [95% CI: 0.54-0.86, sensitivity = 95%]), and fluoroquinolone (AUCROC = 0.73 [95% CI: 0.56-0.89, sensitivity = 88%]). For other antibiotic classes, results were not significant. Using antibiotic class-specific cut-offs for positive reads of ARGs, a metagenomics approach potentially offers a culture-independent and more time-efficient manner to predict ABS for commonly prescribed antibiotic classes for sputum samples of adult people with CF. The use of metagenomics and artificial intelligence in clinical care will add to more personalized care for people with CF as well as better antibiotic stewardship.

IMPORTANCE: Damage induced by lung infections in people with cystic fibrosis (CF) is the leading factor to the mortality and morbidity of CF. To treat bacterial infections, people with CF are prescribed antibiotics. Routine antibiotic susceptibility (ABS) testing relies on culture-dependent, phenotypic techniques. These take several days up to more than a week, while timely intervention is key. To bridge this time gap, physicians in CF care use patient history of ABS data to start antibiotics, with risk of resistance to it. This pilot study explores a time saving alternative: the possibility to predict antibiotic resistance genes using shotgun metagenomics and artificial intelligence. By quicker prediction of ABS, people with CF can receive more adequate care, which results in the possible prevention of chronic infections and contributes to antibiotic stewardship.},
}

@article {pmid41190675,
year = {2025},
author = {McHugh, O and Ayilaran, E and Jung, Y},
title = {Maple sap microbial communities and tubing sanitation: dominance of Pseudomonas species.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0069325},
doi = {10.1128/mra.00693-25},
pmid = {41190675},
issn = {2576-098X},
abstract = {Shotgun metagenomic data from maple (Acer saccharum) sap collected via 3/16-inch tubing (new, unsanitized, or sanitized with 400 ppm calcium hypochlorite) during weeks 1 and 5 revealed 317 species. Applying a 5% relative abundance cutoff, 20 dominant species were identified. Pseudomonas_E proteolytica and/or Pseudomonas_E lurida were abundant across conditions.},
}

@article {pmid41190646,
year = {2025},
author = {Brown, KM and Beall, BFN and Bullerjahn, GS and Finlay, JC and Glavina Del Rio, T and Small, GE and Sterner, RW and McKay, RM},
title = {Depth-resolved paired metagenomes and metatranscriptomes from the Lake Erie 'dead zone'.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0101325},
doi = {10.1128/mra.01013-25},
pmid = {41190646},
issn = {2576-098X},
abstract = {Metagenomes and metatranscriptomes were generated from the surface mixed layer and hypolimnion at a NOAA-Great Lakes Environmental Research Laboratory Real-Time Coastal Observation Network (ReCON) site in Lake Erie's central basin during the onset of hypolimnetic hypoxia. Here, we describe the sequencing of the samples, metagenome assembly, and binning of microbial taxa.},
}

@article {pmid41190270,
year = {2025},
author = {Li, W and Li, X and Cheng, J and Liu, J and Liu, J and Wang, Y and Yuan, W and Ren, E},
title = {Lung microbiota of raccoon dogs (Nyctereutes procyonoides) using high-throughput sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1677761},
pmid = {41190270},
issn = {1664-302X},
abstract = {Pneumonia frequently causes mass mortality in raccoon dogs, resulting in significant economic loss. Additionally, raccoon dogs carry various zoonotic pathogens. This study systematically assessed pulmonary pathogens in raccoon dogs and their potential public health implications utilizing 2bRAD microbiome sequencing (2bRAD-M) and viral metagenomics. We analyzed 30 lung tissue samples for microbial composition. Sequencing revealed Pseudomonadota, Ascomycota, and Actinobacteria as dominant phyla and Acinetobacter, Escherichia, and Klebsiella as predominant genera. The most abundant species were Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae. In total, 158 species across 84 genera were identified, including 49 potentially zoonotic species. Viral metagenomics revealed Peduoviridae, Rountreeviridae, and Parvoviridae as dominant families, with Valbvirus ValB1MD2, Andhravirus andhra, and Amdoparvovirus carnivoran3 comprising over 80% of the viral composition. These findings highlight the pathogenic complexity of raccoon dog pneumonia and its zoonotic risks, providing crucial insights for disease control and public health management.},
}

@article {pmid41190207,
year = {2025},
author = {You, Y and Liu, X and Wang, L and Khalid, M and Wang, X and Jiang, L and Wang, F and Pang, Z and Peng, Y and Zhao, X},
title = {Integrated metagenomic and soil chemical analyses revealed shifts of microbial nutrient cycling with poplar plantation age.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1513281},
pmid = {41190207},
issn = {1664-462X},
abstract = {INTRODUCTION: Poplar (Populus spp.) is widely recognized as an ideal model system for studying plant-microbial interactions due to its rapid growth, genetic tractability, and ecological importance in afforestation programs. Leveraging these advantages, we investigated how poplar cultivation reshapes soil microbial communities and their nutrient cycling functions. Although plant roots are known to profoundly influence microbial community structure and functionality, comprehensive studies systematically linking poplar-induced microbiome shifts to nutrient cycling remain limited.

METHODS: Here, we employed an integrative approach combining metagenomic sequencing with soil nutrient analyses to assess poplar-induced changes in microbial community and metabolic activities at the root-soil interface.

RESULTS: Our analyses revealed three major findings: (1) poplar cultivation significantly altered the composition of microbial communities-including bacteria, fungi, and archaea-and reduced the complexity of microbial interaction networks, as revealed by co-occurrence analysis; (2) poplar cultivation enhanced microbial genetic potential related to degradation pathways for starch, lignin, and aromatic compounds, as well as carbon (C) fixation, while suppressing cellulose/hemicellulose decomposition; and (3) soil nutrient cycling processes involving nitrogen (N), phosphorus (P), and sulfur (S) were reprogrammed through changes in both gene abundance (e.g., nifH, pqqC, aprA) and nutrient availability (e.g., NO3-, P). Moreover, specific microbial taxa showed strong correlations with these functional shifts, i.e., Bacteroidota correlated with P metabolism in roots/soil, Actinobacteria and Firmicutes with organic C turnover, and Gemmatimonadetes and Nitrospirae with nitrate cycling dynamics.

DISCUSSION: By integrating poplar's roles as both a model species and a driver of ecological change, this study elucidates how afforestation shapes soil ecosystems through complex plant-microbe-environment interactions. These findings provide critical insights for sustainable land management strategies.},
}

@article {pmid41190090,
year = {2025},
author = {Watkinson, JI},
title = {Habitat Disturbance Promotes Shifts in the Abundance of Major Fungal Phyla in the Roots of a Native Orchid, Tipularia discolor.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {6},
number = {6},
pages = {e70096},
pmid = {41190090},
issn = {2575-6265},
abstract = {Orchids are a widely distributed group of flowering plants with important roles in ecosystems around the globe. However, many species are in decline due, in part, to human-driven changes in their habitat. It is well established that orchids are reliant on specific groups of mycorrhizal fungi for growth and reproduction and that these fungi can vary across the range in which an orchid species resides. Recent studies have shown that the orchid fungal mycobiome (mycobiome) includes a diverse array of non-mycorrhizal endophytic fungi that may also contribute to growth and resilience and that can vary across a particular orchid's range. The communities of mycorrhizal and non-mycorrhizal species that make up the orchid mycobiome may be altered by habitat disturbance, which could affect the ability of these plant species to thrive in different environments. Here a metagenomic approach is used to provide a snapshot of the root mycobiome of Tipularia discolor in habitats defined as disturbed or undisturbed. While amplicon sequence variant (ASV) richness and evenness were similar, the structure of the mycobiome differed between the two sites. Orchids growing in disturbed locations were associated with a greater abundance of Basidiomycota and Glomeromycota, while orchids in undisturbed habitats were associated with Ascomycota and Mucoromycota. The overall abundance of mycorrhizal families was similar across the two habitats. The data indicate that habitat disturbance induces a change in the composition of the fungal mycobiome of T. discolor , suggesting that the community of root fungi could be key to the ability of orchids to successfully adapt to different environments.},
}

@article {pmid41189926,
year = {2025},
author = {Chen, X and Qin, H and Song, Y and Lian, Y and Long, Q},
title = {Metagenomics next-generation sequencing for diagnosis of invasive fungal diseases in patients with hematological diseases.},
journal = {IJID regions},
volume = {17},
number = {},
pages = {100780},
pmid = {41189926},
issn = {2772-7076},
abstract = {OBJECTIVES: To investigate the clinical characteristics and risk factors of invasive fungal disease (IFD) in patients with hematological disorders.

METHODS: From January 2023 to January 2025, 67 patients with blood diseases hospitalized at the Hematology Department who were suspected of infection with IFD underwent metagenomic next-generation sequencing (mNGS) and fungal pathogen detection. Their clinical characteristics and laboratory examinations were retrospectively analyzed.

RESULTS: A cohort of 67 patients was enrolled in the study, among which 32 cases were diagnosed with IFD through mNGS and etiological culture, while no fungal pathogens were detected in the remaining 35 cases. The diagnostic yield of mNGS for fungal infection detection (47.76%) demonstrated superior sensitivity compared to conventional pathogenic microbial culture (14.93%), β-D-glucan assay (11.94%), and galactomannan assay (2.99%). Within the IFD cohort, Candida species constituted the most prevalent etiology (46.88%, n = 15), followed by Aspergillus (18.75%, n = 6), Penumocystis (12.5%, n = 4), and Rhizomucor (12.5%, n = 4), with other fungal species accounting for the remaining cases (9.37%, n = 3). Multivariate logistic regression analysis revealed six independent risk factors associated with IFD in patients with hematological disorders: cluster of differentiation 4+ T cell count <400 cells/µL (odds ratio [OR] = 9.45, P = 8.9×10[-5]), elevated C-reactive protein (OR = 3.18, P = 0.027), elevated interleukin (IL)-6 (OR = 5.75, P = 0.001), elevated IL-10 (OR = 3.31, P = 0.033), hypoproteinemia (OR = 42.17, P = 0.013), and neutropenia lasting for more than 10 days (OR = 4.11, P = 0.015).

CONCLUSIONS: mNGS has high sensitivity in detecting IFD in patients with hematological diseases. Cluster of differentiation 4+ cell count below 400/uL, increased level of C-reactive protein, IL-6, and IL-10, hypoproteinemia, and neutropenia lasting for more than 10 days are independent risk factors for IFD in patients with hematological diseases.},
}

@article {pmid41189709,
year = {2025},
author = {Chen, Y and Zhang, R and Wen, J and Zhao, J and Zhang, J},
title = {Metagenomic analysis of blood microbiota alterations: insights into HIV progression and immune restoration.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1619059},
pmid = {41189709},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/immunology/drug therapy/microbiology/blood/virology ; Metagenomics ; Male ; Female ; Adult ; *Microbiota ; Middle Aged ; Disease Progression ; Viral Load ; *Bacteria/classification/genetics/isolation & purification ; *Immune Reconstitution ; *Blood/microbiology ; CD4-CD8 Ratio ; },
abstract = {INTRODUCTION: Emerging evidence suggests that the blood microbiome may influence the progression of HIV infection and immune restoration. This study aims to comprehensively characterize blood microbiota alterations associated with HIV infection and antiretroviral therapy (ART), and to evaluate their potential as microbial indicators for assessing infection status and immune restoration.

METHODS: We recruited 91 participants, including 31 treatment-naïve HIV-infected individuals, 30 ART-treated individuals with undetectable viral loads, and 30 healthy controls. Blood samples were collected for metagenomic sequencing and immunological profiling.

RESULTS: HIV infection profoundly disrupted blood microbiota diversity and composition, with a marked reduction in α-diversity and enrichment of opportunistic pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, alongside depletion of beneficial taxa like Bifidobacterium longum. ART partially restored microbial diversity but did not fully reestablish a healthy microbiota. Correlation analysis revealed that Acinetobacter pittii, Xanthomonas campestris and Diaphorobacter nitroreducens were significantly associated with viral load, suggesting their potential role in HIV progression. Additionally, after ART, Acinetobacter junii and Pseudomonas putida were significantly correlated with the CD4/CD8 ratio, indicating their potential role in immune restoration.

DISCUSSION: These findings provide new insights into the interactions between blood microbiota and HIV progression. The identified blood microbiota may serve as potential indicators for evaluating HIV infection status and treatment efficacy, offering a basis for microbial-based diagnostic and therapeutic strategies.},
}

Humans
*HIV Infections/immunology/drug therapy/microbiology/blood/virology
Metagenomics
Male
Female
Adult
*Microbiota
Middle Aged
Disease Progression
Viral Load
*Bacteria/classification/genetics/isolation & purification
*Immune Reconstitution
*Blood/microbiology
CD4-CD8 Ratio

@article {pmid41189593,
year = {2025},
author = {Huang, Y and Wei, X and Huang, X and Peng, C and Lin, B and Ren, X and He, G and Zhang, X and Jiang, C and Huang, L and Gu, S},
title = {Pneumocystis jirovecii associated with Lung Virome in patients with severe pneumonia.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113710},
pmid = {41189593},
issn = {2589-0042},
abstract = {Pneumocystis jirovecii (P. jirovecii) threatens immunocompromised patients, yet its role in the lung microbiome remains unclear. We performed metagenomic sequencing on bronchoalveolar lavage fluid from two retrospective cohorts: a multicenter study of 1,737 patients with pneumonia and a validation cohort of 72 intubated ICU patients. Participants were categorized into P. jirovecii infection, colonization, or negative groups based on qPCR and clinical characteristics. Our analysis revealed minimal bacterial differences but significant viral and fungal variations. Notably, negative patients with P. jirovecii exhibited the lowest viral diversity. Even after adjusting for potential confounders, including immunosuppression and disease severity, P. jirovecii status remained most strongly associated with virome alterations. Furthermore, in cytomegalovirus-positive individuals, P. jirovecii positivity was significantly associated with higher 28-day mortality. These findings suggest that P. jirovecii colonization represents a distinct intermediate state in the lung microbial ecosystem between infection and negative, shedding light on its potential role in pneumonia pathogenesis and outcomes.},
}

@article {pmid41189414,
year = {2025},
author = {Zheng, Z and Zhao, L and Liu, Y and Wang, W and Zheng, K and Chen, X and Zhang, S and Sun, Y and Ma, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M and Gao, C and Sun, L and Liang, Y},
title = {Identification and Genomic Analysis of a New Viral Species With Low Similarity to Existing Viruses.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70201},
doi = {10.1111/1462-2920.70201},
pmid = {41189414},
issn = {1462-2920},
support = {LSKJ202203201//Laoshan Laboratory/ ; 42120104006//National Natural Science Foundation of China/ ; 42176111//National Natural Science Foundation of China/ ; 42306111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions/ ; 2025M770867//China Postdoctoral Science Foundation/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 201812002//Fundamental Research Funds for the Central Universities/ ; 202072001//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Genome, Viral ; Metagenomics ; *Bacteriophages/genetics/isolation & purification/classification ; Phylogeny ; *Pseudoalteromonas/virology ; Genomics ; *Viruses/genetics/classification/isolation & purification ; },
abstract = {Viruses are among the most abundant and diverse biological entities on Earth. Over the past decades, metagenomic sequencing has revealed thousands of viral genomes. However, viral isolation methods remain indispensable for discovering viruses that are missed by metagenomic sequencing due to limitations like low abundance (1, 2). Here, a novel phage, vB_PshM_Y4, which infects Pseudoalteromonas shioyasakiensis, an economically important, opportunistic marine pathogen was isolated. A comparison of vB_PshM_Y4 with over 15 million viral genomes, including both cultivated and uncultivated viruses in the NCBI and IMG/VR v4 datasets, found no closely related genome. This study provides evidence that traditional isolation methods can detect viruses that cannot be identified through metagenomic sequencing. In addition, a comparison of virus isolates deposited in the NCBI database with uncultured viruses in the IMG/VR viral database shows that approximately only half of the isolates can be detected using metagenomic approaches. Notably, viruses that are not able to be detected by metagenomic sequencing often exhibit low abundance and possess unique genomes. These results suggest that traditional viral isolation methods remain important for obtaining rare, low-abundance viruses and underscore the significance of traditional experimental methods in the era of metagenomes.},
}

*Genome, Viral
Metagenomics
*Bacteriophages/genetics/isolation & purification/classification
Phylogeny
*Pseudoalteromonas/virology
Genomics
*Viruses/genetics/classification/isolation & purification

@article {pmid41189006,
year = {2025},
author = {Popall, RM and Roland, A and Davidson, S and Combet-Blanc, Y and Price, RE and Quéméneur, M and Postec, A and Erauso, G},
title = {Cultivating microbial communities from the serpentinite-hosted Prony Bay hydrothermal field on different carbon sources in hydrogen-fed bioreactors.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {135},
pmid = {41189006},
issn = {2524-6372},
support = {19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; 19-CE02-0020-02//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: The primary source of carbon is one of the most fundamental questions regarding the development of microbial communities in serpentinite-hosted systems. The hydration of ultramafic rock to serpentinites releases large amounts of hydrogen and creates hyperalkaline conditions that deplete the environment of dissolved inorganic carbon. Metagenomic studies suggest that serpentinite-hosted microbial communities depend on the local redissolution of bicarbonate and on small organic molecules produced by abiotic reactions associated with serpentinization.

METHODS: To verify these bioinformatic predictions, microbial consortia collected from the Prony Bay hydrothermal field were enriched under anoxic conditions in hydrogen-fed bioreactors using bicarbonate, formate, acetate, or glycine as the sole carbon source.

CONCLUSIONS: With the exception of glycine, the chosen carbon substrates allowed the growth of microbial consortia characterized by significant enrichment of individual taxa. Surprisingly, these taxa were dominated by microbial genera characterized as aerobic rather than anaerobic as expected. Our results indicate the presence of both autotrophic and heterotrophic taxa that may function as foundation species in serpentinite-hosted shallow subsurface ecosystems. We propose that an intricate feedback loop between these autotrophic and heterotrophic foundation species facilitates ecosystem establishment. Bicarbonate-fixing Meiothermus and Hydrogenophaga, as well as formate-fixing Meiothermus, Thioalkalimicrobium, and possibly a novel genotype of Roseibaca might produce organic compounds for heterotrophs at the first trophic level. In addition, the base of the trophic network may include heterotrophic Roseibaca, Acetoanaerobium, and Meiothermus species producing CO2 from acetate for a more diverse community of autotrophs. The cultivated archaeal community is expected to recycle CH4 and CO2 between Methanomicrobiales and Methanosarcinales with putative Woesearchaeales symbionts.},
}

@article {pmid41188784,
year = {2025},
author = {Luo, H and Wu, P and Yang, H and Zhang, B and Zheng, M and Kuang, W and Li, W and Li, X and Zhang, X and Huang, J and Fan, Q and He, S},
title = {Clinical analysis of Pneumocystis jirovecii pneumonia in children with malignant disease.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {906},
pmid = {41188784},
issn = {1471-2431},
mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/complications ; Male ; Female ; Retrospective Studies ; Child ; Child, Preschool ; *Pneumocystis carinii/isolation & purification ; Adolescent ; *Neoplasms/drug therapy/complications ; Glucocorticoids/therapeutic use/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Antifungal Agents/therapeutic use ; Immunocompromised Host ; Tomography, X-Ray Computed ; },
abstract = {OBJECTIVE: To characterize Pneumocystis jirovecii pneumonia (PJP) in pediatric malignancy patients receiving chemotherapy or glucocorticoids, and provide guidance for timely diagnosis and effective treatment.

METHODS: A retrospective analysis of clinical features, laboratory findings, radiological characteristics, treatment approaches, and outcomes in pediatric malignancy patients who developed PJP.

RESULTS: Ten patients (1:1 male-to-female ratio; median age 6.50 years, range 2.83-14.58 years) were followed for a median of 14 months (range 6-53 months). Eight developed PJP during chemotherapy and two post-completion. Nine received glucocorticoids in their chemotherapy regimen. PJP prophylaxis was either absent (n = 4) or discontinued > 1 month prior (n = 5). Clinical presentations included fever, dyspnea, and wheezing, often without significant cough. Laboratory findings showed elevated (1,3)-β-D-glucan(BDG)in 7 cases. Chest CT typically revealed bilateral diffuse patchy infiltrates, ground-glass opacities, and nodular shadows. All cases had a positive metagenomic next-generation sequencing (mNGS) or targeted next-generation sequencing (tNGS) result for P. jirovecii from sputum or bronchoalveolar lavage fluid (BALF) samples.Treatment included Trimethoprim-sulfamethoxazole(TMP/SMZ) with/without caspofungin and adjunctive corticosteroids. Eight patients required PICU admission (median stay 7.5 days, range 0-45 days) for respiratory support. Nine patients survived PJP, with one PJP-related death and one death from underlying disease.

CONCLUSION: High clinical suspicion for PJP is warranted in pediatric malignancy patients presenting with fever, dyspnea, elevated BDG, and characteristic imaging findings, particularly in those with inadequate prophylaxis. Early pathogen detection and treatment initiation are crucial. While TMP/SMZ remains first-line therapy, combination with caspofungin may improve outcomes. Short-term adjunctive corticosteroids may benefit moderate to severe cases.},
}

Humans
*Pneumonia, Pneumocystis/diagnosis/drug therapy/complications
Male
Female
Retrospective Studies
Child
Child, Preschool
*Pneumocystis carinii/isolation & purification
Adolescent
*Neoplasms/drug therapy/complications
Glucocorticoids/therapeutic use/adverse effects
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use
Antifungal Agents/therapeutic use
Immunocompromised Host
Tomography, X-Ray Computed

@article {pmid41184794,
year = {2025},
author = {Chen, J and Chen, C and Xie, Y and Xu, G and Lin, M and Gong, X and Zhang, X and Chen, X and Chen, J and Zhang, L and He, G},
title = {Clinical value of quantitative PCR in diagnosis of suspected mycobacterial pulmonary infections.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1476},
pmid = {41184794},
issn = {1471-2334},
abstract = {BACKGROUND: Due to the difficulty in clinically distinguishing pulmonary infections caused by Mycobacterium tuberculosis (MTB) and Non-tuberculous mycobacteria (NTM), the study utilizes quantitative PCR (qPCR) technology to simultaneously detect MTB, Mycobacterium abscessus complex (MABC), Mycobacterium avium complex (MAC), and Mycobacterium kansasii(M. kansasii),to explore its clinical value in diagnosing of patients suspected mycobacterial pulmonary infections.

METHODS: A retrospective analysis was conducted on a cohort of 102 patients suspected of mycobacterial pulmonary infections. Samples of sputum and bronchoalveolar lavage fluid were extracted for testing with acid-fast staining (AFS), qPCR, and metagenomic next-generation sequencing (mNGS). Assess the diagnostic performance of AFS, qPCR, and mNGS for four types of mycobacteria based on comprehensive pulmonary tuberculosis (PTB) CRS composite criteria, non-tuberculous mycobacteria (NTM) diagnostic and treatment guidelines, as well as clinical observations.

RESULTS: The sensitivity, specificity, positive predictive value, negative predictive value, and AUC of qPCR for mycobacteria (MTB, MABC, MAC) were 90.00% (76.33–97.20), 100.00% (94.22–100.00), 100.00% (99.90–100.00), 93.93% (85.95–97.51), and 0.950 (0.888–0.983), respectively. For mNGS, the corresponding estimates were 87.50% (73.19–95.81), 96.77% (88.82–99.60), 94.59%(81.66–98.56),92.30% (84.07–96.46), and 0.921(0.851–0.965), respectively. The research showed that the sensitivity and specificity of qPCR and mNGS method for detecting mycobacteria are higher than AFS; and there was no statistical difference in the diagnostic performance for mycobacteria between qPCR and mNGS, but qPCR was superior to mNGS in specific values.

CONCLUSION: Compared with AFS, qPCR has higher sensitivity and specificity but statistical significance needs to be assessed with larger sample sizes for mycobacteria identification. In this regard, qPCR and mNGS demonstrate exhibit similar performance. However, qPCR is less expensive and more convenient for pathogen detection, which make it a promising lower-cost alternative diagnostic method for patients suspected of mycobacterial pulmonary infections in resource-limited settings.},
}

@article {pmid41188680,
year = {2025},
author = {Falk, NW and Smith, H and Papudeshi, B and Martin, B and Qian, G and Gerson, AR and Prasad, A and Harmer, SL and Dinsdale, EA},
title = {Metagenomics reveals water, biofilm, and sediment microbial communities exhibit distinct responses and functions in neutral and metalliferous drainage (NMD).},
journal = {Environmental geochemistry and health},
volume = {47},
number = {12},
pages = {547},
pmid = {41188680},
issn = {1573-2983},
support = {CRC TiME project 3.10 and Teck Resources Limited//CRCTiME/ ; },
abstract = {Neutral and metalliferous drainage (NMD) poses an environmental risk for both operating and legacy mine sites. Near-neutral pH distinguishes NMD from more acidic conditions of acid and metalliferous drainage (AMD), however NMD contains elevated levels of metals that necessitate strict management. Microbial communities are key indicators of ecological conditions and play important roles in NMD biogeochemical cycling, often exhibiting distinct dynamics compared to AMD. Shotgun sequencing and metagenome assembled genomes (MAGs) were used to characterize microbial diversity and functional potential across water, biofilm, and sediment microbiomes along a flow path at a historical lead-zinc mine in Western Australia. Zn levels peaked upstream and declined downstream, corresponding to shifts in microbial diversity. In water microbiomes, a Polynucleobacter MAG became dominant where Zn concentrations dropped below known toxicity thresholds. The genomic traits of Polynucleobacter, including a streamlined genome, Zn- (LpxC) and heat-responsive membrane genes, and enriched lipid metabolism pathways, enabled survival under metal and nutrient stress. Photosynthetic biofilms, dominated by cyanobacteria such as Synechococcaceae and Leptolyngbyaceae, played a central role in ecosystem function. These biofilms contained genes for photosynthesis, metal transport, and motility, and likely contributed organic carbon and sulfur intermediates that supported heterotrophs like Polynucleobacter and Sediminibacterium. Coordinated microbial sulfur metabolism across habitats was evident, with sulfur oxidation occurring in water and biofilms and sulfate reduction localized to sediment, evidenced with ZnS mineral phases associated with increased DsrMKJOP gene abundance. These findings are vital for mine closure and land reclamation, offering knowledge on key microbial adaption and syntrophy in NMD systems.},
}

@article {pmid41188618,
year = {2025},
author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S},
title = {Enhanced biodegradation of ibuprofen using bacterial consortia isolated from landfill leachate.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1295},
pmid = {41188618},
issn = {1573-2959},
support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST), New Delhi, India, under the PURSE grant/ ; },
mesh = {*Ibuprofen/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Microbial Consortia ; *Bacteria/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis ; RNA, Ribosomal, 16S ; },
abstract = {The widespread use of non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen, has led to a persistent occurrence across various environmental matrices, raising concern regarding potential human health and ecological impacts. The potentially detrimental risks of ibuprofen exposure highlight the need for exploring effective and cost-efficient remediation techniques. The microbial degradation of ibuprofen represents a significant technological and economical approach. The present study investigates the biodegradation of ibuprofen using two distinct microbial consortia (MC I and MC II) isolated from landfill leachate using Postgate media and acclimated with ibuprofen. Batch mode experiments were conducted to assess the removal of 500 mg/L ibuprofen in the presence and absence of a carbon source (glucose and acetate). MC I and MC II achieved complete removal of ibuprofen within 78 h and 60 h, respectively, under substrate-free conditions. When supplemented with glucose, the removal time was reduced to 54 h for MC I and 36 h for MC II, whereas acetate addition resulted in removal extended to 60 h and 48 h, respectively. The metagenomics analysis (16S rRNA sequencing) of microbial consortia revealed Firmicutes (Bacillota), Actinobacteria (Actinomycetota), Proteobacteria, Bacteroidetes, and Thermotogae as the dominant phyla and GC-MS analysis confirmed the presence of significant metabolites (endpoint of the bioassay) in the biodegradation of ibuprofen, i.e., 2-hydroxy ibuprofen, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol. The findings of the study highlight the potential of microbial consortia for efficient ibuprofen biodegradation and provide insights into their metabolic pathway.},
}

*Ibuprofen/metabolism/analysis
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism/analysis
*Microbial Consortia
*Bacteria/metabolism
*Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis
RNA, Ribosomal, 16S

@article {pmid41188566,
year = {2025},
author = {Kondratov, IG and Ogarkov, OB and Sinkov, VV and Suzdalnitsky, AE and Koshcheyev, ME and Orlova, EA and Belkova, NL and Zhdanova, SN and Rychkova, LV and Kolesnikova, LI},
title = {Prediction of Metabolic Profile and Virulence Factors of Facultative-Anaerobic Bacteria from Tuberculous Necrosis Foci Based on Whole-Genome Sequencing Data.},
journal = {Bulletin of experimental biology and medicine},
volume = {},
number = {},
pages = {},
pmid = {41188566},
issn = {1573-8221},
abstract = {Metagenomics of bacterial communities in tuberculosis caseous necrotic mass indicates the predominance of facultative anaerobes. Nine strains isolated from the tuberculosis necrosis were identified to species and whole-genome sequencing was performed: Staphylococcus hominis (3 strains), S. epidermidis (3 strains), Corynebacterium ureicelerivorans (2 strains), and C. kefirresidentii (1 strain). Prediction of metabolic pathways and virulence factors showed that Corynebacterium and Staphylococcus possess gene sets that are absent in Mycobacterium tuberculosis: lipases and proteases for the degradation of caseous necrosis, glutamate and polysaccharide capsules, ureases capable of increasing pH of the caseum; and Fe(III) uptake systems. The isolated species can form a bacterial consortium with M. tuberculosis at the early (Corynebacterium) and later (Staphylococcus) stages of necrotization of the tuberculosis focus in the lungs.},
}

@article {pmid41188334,
year = {2025},
author = {Kang, R and Yu, Z and Kim, H and Seo, J and Kim, M and Park, T},
title = {Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38587},
pmid = {41188334},
issn = {2045-2322},
mesh = {*Rumen/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Species Specificity ; Metagenomics/methods ; *Bacteria/classification/genetics ; },
abstract = {Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases-SILVA, Greengenes2 (GG2), RDP, NCBI RefSeq, and GTDB-against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results indicated that providing taxonomic weights partially increased classification counts and fully classified ratios, although the extent of improvement varied across databases. A reduction in error rates was also observed compared to the unweighted taxonomy classifier (P < 0.05). While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.},
}

*Rumen/microbiology
Animals
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Species Specificity
Metagenomics/methods
*Bacteria/classification/genetics

@article {pmid41188324,
year = {2025},
author = {Kwak, MS and Cha, JM and Kim, CW and Won, KY and Hwang, CI},
title = {Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38611},
pmid = {41188324},
issn = {2045-2322},
support = {NRF- 2022R1A2C100309913//National Research Foundation of Korea/ ; 2022//Medical Science Research Institute grant, Kyung Hee University Hospital at Gangdong/ ; R37CA249007/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/microbiology ; *Lymphatic Metastasis/genetics ; DNA Methylation ; Male ; Female ; *Biomarkers, Tumor/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling ; Multiomics ; },
abstract = {Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.A total of 30 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient. In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving "MULTI CANCER INVASIVENESS" in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.},
}

Humans
*Colorectal Neoplasms/genetics/pathology/microbiology
*Lymphatic Metastasis/genetics
DNA Methylation
Male
Female
*Biomarkers, Tumor/genetics
Middle Aged
*Gastrointestinal Microbiome
Aged
Transcriptome
Gene Expression Regulation, Neoplastic
Gene Expression Profiling
Multiomics

@article {pmid41188219,
year = {2025},
author = {Ndiaye, M and Bonilla-Rosso, G and Mazel, F and Engel, P},
title = {Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9738},
pmid = {41188219},
issn = {2041-1723},
mesh = {Animals ; *Bacteriophages/genetics/classification/physiology ; *Gastrointestinal Microbiome/genetics ; Bees/microbiology/virology ; *Bacteria/genetics/classification/virology ; Biodiversity ; Metagenomics ; Metagenome ; },
abstract = {Bacteriophages (phages) play a crucial role in shaping bacterial communities. Documenting the relationship between phage and bacterial diversity in natural systems is fundamental to understand eco-evolutionary dynamics that shape community composition, such as host specificity, emergence of phage resistance and phage-driven microbial diversification. However, our current understanding of this relationship is still limited, particularly in animal-associated microbiomes. Here, we analyze paired bacterial and viral metagenomics data from the gut microbiota of 49 individual honeybees and reconstruct the phage-bacteria interaction network by leveraging CRISPR spacer matches and genome homology. The resulting interaction network displays a highly modular structure with nested phage-bacteria interactions within each module. Viral and bacterial alpha and beta diversity are correlated, particularly at the bacterial strain level and when considering the interaction network. Overall, our results suggest that the most relevant approach to study phage-bacteria diversity patterns should rely on strain-level resolution and the explicit use of the interaction network. This may explain why previous studies have obtained mixed results when testing for phage-bacteria diversity correlations. Finally, we call for further studies building up on these correlation patterns to probe the underlying mechanisms by considering both bottom-up and top-down regulatory mechanisms in microbiome assembly.},
}

Animals
*Bacteriophages/genetics/classification/physiology
*Gastrointestinal Microbiome/genetics
Bees/microbiology/virology
*Bacteria/genetics/classification/virology
Biodiversity
Metagenomics
Metagenome

@article {pmid41187758,
year = {2025},
author = {Yilmaz, B and Baertschi, I and Meier, KHU and Le Gac, C and Jordi, SBU and Black, C and Li, J and Lindholm, AK and , and König, B and Sauer, U and Stelling, J and Macpherson, AJ},
title = {A global survey of taxa-metabolic associations across mouse microbiome communities.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.010},
pmid = {41187758},
issn = {1934-6069},
abstract = {Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.},
}

@article {pmid41187361,
year = {2025},
author = {Zhang, T and Xia, Q and Wang, Y and Sun, Y and Pan, D and Cao, J and Zhou, C},
title = {The molecular mechanism of Rhodotorula mucilaginosa on the accumulation of γ-glutamyl peptides and taste development of dry-cured ham: the insights of metagenomics and metabolomics.},
journal = {International journal of food microbiology},
volume = {445},
number = {},
pages = {111511},
doi = {10.1016/j.ijfoodmicro.2025.111511},
pmid = {41187361},
issn = {1879-3460},
abstract = {To explore the mechanism of Rhodotorula mucilaginosa on the accumulation of γ-glutamyl peptides and taste development in Jinhua ham, the influences of R. mucilaginosa on fungal community structure, functional enzyme gene expression, key enzyme activities, γ-glutamyl peptides accumulation and taste attributes were investigated during the dry-ripening. In comparison with Pichia kudriavzevii XS-5 (PK), Rhodotorula mucilaginosa XZY63-3 (RX) and no inoculation (CK), the inoculation with Rhodotorula mucilaginosa EIODSF019 (RE) showed the highest overall acceptance and richness. Metagenomics revealed that RE inoculation inhibited Aspergillus abundance, and the profile of Rhodotorula reached 45.94 % at genus level. The treatment of RE increased the gene abundance of amino acid metabolism pathways; the expression levels of γ-glutamyl transpeptidase gene in RE were increased by 83.27 % compared with CK, and the activities of γ-glutamyl transpeptidase increased from 214 U/g proteins of CK to 567 U/g proteins of RE. LC-MS/MS analysis revealed the total contents of γ-glutamyl peptides increased from 136.40 μg/g of CK to 518.18 μg/g of RE. Partial least squares regression and correlation analysis indicated that γ-Glu-Cys and γ-Glu-Gln were mainly responsible for the improvement of overall acceptance and richness of Jinhua ham with RE inoculation.},
}

@article {pmid41187181,
year = {2025},
author = {Xu, P and Huang, Z},
title = {Omadacycline treatment of severe Chlamydia psittaci pneumonia with septic shock diagnosed via metagenomic next-generation sequencing.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {10},
pages = {1570-1576},
doi = {10.3855/jidc.21299},
pmid = {41187181},
issn = {1972-2680},
mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation & purification/drug effects ; High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use ; *Psittacosis/drug therapy/diagnosis/microbiology ; *Shock, Septic/drug therapy/diagnosis/microbiology ; *Tetracyclines/therapeutic use ; Metagenomics ; Male ; Treatment Outcome ; Doxycycline/therapeutic use ; },
abstract = {INTRODUCTION: Parrot fever, caused by Chlamydia psittaci, is a zoonotic disease typically treated with tetracyclines. Omadacycline, a novel aminomethyl tetracycline, has limited reports on its efficacy in severe Chlamydia psittaci pneumonia in the literature.

CASE PRESENTATION: We present a case of a patient with severe Chlamydia psittaci pneumonia showing symptoms of chills, high fever, shock, hepatic and renal insufficiency, and acute respiratory failure with copious yellow watery sputum. Chlamydia psittaci was confirmed by metagenomic next-generation sequencing (mNGS). Despite initial treatment with moxifloxacin and doxycycline, the patient did not improve and was subsequently discharged after receiving omadacycline.

CONCLUSIONS: Our findings highlight the potential of mNGS for rapid diagnosis of Chlamydia psittaci pneumonia and suggest omadacycline as a potential therapeutic option for severe cases that do not respond to conventional treatment.},
}

Humans
*Chlamydophila psittaci/genetics/isolation & purification/drug effects
High-Throughput Nucleotide Sequencing
*Anti-Bacterial Agents/therapeutic use
*Psittacosis/drug therapy/diagnosis/microbiology
*Shock, Septic/drug therapy/diagnosis/microbiology
*Tetracyclines/therapeutic use
Metagenomics
Male
Treatment Outcome
Doxycycline/therapeutic use

@article {pmid41187070,
year = {2025},
author = {De Vivo, G and Pelletier, E and Feuda, R and D'Aniello, S},
title = {An Ocean of Opsins.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
doi = {10.1093/gbe/evaf189},
pmid = {41187070},
issn = {1759-6653},
support = {//Stazione Zoologica Anton Dohrn/ ; UF160226//Royal Society University Research Fellowship/ ; URF/R/221011//Royal Society University Research Fellowship/ ; RGF\R1\181012//Royal Society/ ; RGP009/2023//Human Frontier Science Program/ ; },
mesh = {*Opsins/genetics ; Animals ; Phylogeny ; *Evolution, Molecular ; Oceans and Seas ; Vertebrates/genetics ; },
abstract = {In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.},
}

*Opsins/genetics
Animals
Phylogeny
*Evolution, Molecular
Oceans and Seas
Vertebrates/genetics

@article {pmid41186403,
year = {2025},
author = {Lugli, GA and Argentini, C and Tarracchini, C and Longhi, G and Mancabelli, L and Bianchi, MG and Taurino, G and Amaretti, A and Candeliere, F and Bussolati, O and Milani, C and Turroni, F and Ventura, M},
title = {Host interactions of Lactococcus lactis and Streptococcus thermophilus support their adaptation to the human gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0154725},
doi = {10.1128/aem.01547-25},
pmid = {41186403},
issn = {1098-5336},
abstract = {UNLABELLED: Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production.

IMPORTANCE: The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.},
}

@article {pmid41186329,
year = {2025},
author = {Liu, Y and Liu, X and Hu, Y and Gao, F and Yu, W and Cheng, F},
title = {Evaluating untargeted metabolomics pipelines for sports nutrition research: a review.},
journal = {Analytical methods : advancing methods and applications},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5ay01484k},
pmid = {41186329},
issn = {1759-9679},
abstract = {Untargeted metabolomics has emerged as a transformative approach in sports nutrition research, offering an unbiased means to characterize the complex biochemical responses to exercise, training, and dietary interventions. Unlike targeted assays restricted to predefined metabolites, untargeted strategies capture broad metabolic perturbations across lipid, carbohydrate, amino acid, and nucleotide pathways, enabling the discovery of novel biomarkers and unanticipated physiological mechanisms. This review critically evaluates the design and application of untargeted metabolomic pipelines in the context of exercise and nutrition science, from pre-analytical sample handling and analytical platforms such as NMR, LC-MS, and GC-MS, to data processing using tools like XCMS, MZmine, and MS-DIAL, and subsequent statistical and bioinformatic interpretation. Key applications include delineating acute metabolic shocks induced by endurance exercise, identifying athlete-specific metabolic phenotypes shaped by chronic training, and assessing the impact of nutritional interventions such as fruit intake, amino acid supplementation, or polyphenol-rich foods on exercise recovery and oxidative stress. The integration of metabolomics with other omics, particularly microbiome metagenomics and lipidomics, highlights the potential for systems-level insights into host-microbe-diet interactions. Nonetheless, significant challenges remain, including the reproducibility of findings, difficulties in metabolite identification, and the translational gap between large datasets and actionable nutritional strategies. By synthesizing current strengths, limitations, and controversies, this review emphasizes that the future of sports metabolomics lies in methodological standardization, multi-omics integration, and validation of candidate biomarkers in independent cohorts. Collectively, these efforts position untargeted metabolomics as a cornerstone for advancing precision nutrition and personalized performance monitoring in athletes.},
}

@article {pmid41186225,
year = {2025},
author = {Chuang, H-Y and Chen, W-Y and Chen, S-H and Shao, Y-H and Wu, J-H},
title = {Metagenome-assembled genome sequence of Candidatus Loosdrechtia sp. KJ reconstructed from an alkaline anammox reactor.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0102425},
doi = {10.1128/mra.01024-25},
pmid = {41186225},
issn = {2576-098X},
abstract = {Candidatus Loosdrechtia sp. KJ is an anaerobic ammonium-oxidizing bacterium enriched from a bioreactor operated under alkaline conditions (pH 9.2 ± 0.4). We report its 3.39 Mb draft genome, containing 3,065 predicted coding sequences, 47 tRNA genes, and a single rrn operon.},
}

@article {pmid41186205,
year = {2025},
author = {Li, Z and Zhang, X and Peng, L and Fang, Y and Liu, H and Zhou, Y and Wang, J and Lu, W},
title = {Response of Bovine Uterine Microbiota to Staphylococcus aureus Infection.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {94},
number = {5},
pages = {e70178},
doi = {10.1111/aji.70178},
pmid = {41186205},
issn = {1600-0897},
support = {U20A2053//National Natural Science Foundation of China/ ; 2024BBF01007//Key R&D Program of Ningxia Hui Autonomous Region/ ; CARS-37//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; Female ; Cattle ; *Staphylococcus aureus/physiology ; *Staphylococcal Infections/microbiology/immunology/veterinary ; *Microbiota ; *Uterus/microbiology/immunology ; *Endometritis/microbiology/immunology/veterinary ; *Cattle Diseases/microbiology/immunology ; },
abstract = {BACKGROUND: Endometritis is a highly prevalent reproductive disorder in cows, causing serious adverse effects on reproductive performance, which brings huge economic losses to the livestock industry. Staphylococcus aureus is detected in a high proportion of endometritis pathogens (alone or in combinations of infections). Uterine microbial composition plays an important role in endometritis.

OBJECT AND METHOD: In order to determine the role of S. aureus in endometritis, we established an endometritis model using this bacterium and utilized metagenomics to detect the structure and function of the bovine uterine microbiota.

RESULTS: We found that S. aureus infection significantly increased the relative abundance of bacteria such as Escherichia coli, Trueperella pyogenes, and Streptococcus spp., while reducing the relative abundance of Akkermansia and Prevotella bacteria. The functions of microorganisms in the uterus are mainly manifested in metabolic levels, including carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism processes. The number of genes continues to increase with the duration of S. aureus infection, which disrupts the balance that maintains the bovine uterine flora.

CONCLUSION: This study provides a descriptive analysis of changes in the uterine microbiota of cows infected with S. aureus, which contributes to a new understanding of uncultured or unidentified pathogenic bacteria.},
}

Animals
Female
Cattle
*Staphylococcus aureus/physiology
*Staphylococcal Infections/microbiology/immunology/veterinary
*Microbiota
*Uterus/microbiology/immunology
*Endometritis/microbiology/immunology/veterinary
*Cattle Diseases/microbiology/immunology

@article {pmid41186087,
year = {2025},
author = {Bortoletto, E and Rosani, U},
title = {Domoic Acid Risk and the Potential of Meta-Omics for Environmental Surveillance.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70593},
doi = {10.1111/gcb.70593},
pmid = {41186087},
issn = {1365-2486},
support = {101186013//HORIZON EUROPE European Innovation Council/ ; },
}

@article {pmid41185941,
year = {2025},
author = {Al-Husseini, A and Komijani, M and Sabah, R},
title = {Impact of Dust Storms on Airborne Bacteria, Heavy Metals, and Inflammatory Markers in Asthmatic Patients.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70109},
doi = {10.1002/mbo3.70109},
pmid = {41185941},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Asthma/blood/microbiology ; *Metals, Heavy/analysis ; *Bacteria/classification/isolation & purification/genetics ; Iraq ; *Dust/analysis ; Female ; Male ; Biomarkers/blood ; Adult ; *Air Microbiology ; Cytokines/blood ; Metagenomics ; Middle Aged ; Young Adult ; Adolescent ; Child ; },
abstract = {Asthma, a chronic bronchial disorder prevalent in children/adolescents, is exacerbated under environmental conditions like dust storms. The current study investigated heavy metal levels, airborne bacteria, and serum IL-4/IL-8 in asthmatics during before/after dust storms in Iraq's Al-Anbar, Baghdad, and Kirkuk provinces. Airborne heavy metals were quantified by ICP-MS, serum cytokines by ELISA, and bacterial communities via metagenomics. Statistical analysis was performed using GraphPad Prism (p < 0.05 significant). ICP-MS revealed considerably elevated post-storm concentrations of As, Ag, B, Ba, Co, Hg, Mg, Mn, Ni, Sn, S, Ti, and V. Asthmatic subjects presented with considerably elevated IL-4 and IL-8 post-storm (p < 0.05) compared to controls (p > 0.05). Metagenomics revealed storm-induced bacterial alterations: Al-Anbar contained elevated Burkholderiaceae, Methylophilaceae, and Rhodobacteraceae; Kirkuk contained elevated Ilumatobacteraceae, Microbacteriaceae, Burkholderiaceae, and Rhodobacteraceae. Baghdad's most prevalent species included Rhodocyclaceae (50%), Burkholderiaceae (17%), and Arcobacteraceae (4.5%). Al-Anbar was significantly richer in microbes (Chao1) and more diverse (Shannon) than other regions following the dust storm (p < 0.0001). These findings indicate that dust storms raise heavy metals, alter airborne bacteria, and increase inflammatory cytokines in asthma sufferers, and these emphasize their role in exacerbating asthma in Iraq.},
}

Humans
*Asthma/blood/microbiology
*Metals, Heavy/analysis
*Bacteria/classification/isolation & purification/genetics
Iraq
*Dust/analysis
Female
Male
Biomarkers/blood
Adult
*Air Microbiology
Cytokines/blood
Metagenomics
Middle Aged
Young Adult
Adolescent
Child

@article {pmid41185633,
year = {2025},
author = {Villarreal, CX and Chan, DD},
title = {Multiomic Integration Reveals Taxonomic Shifts Correlate to Serum Cytokines in an Antibiotics Model of Gut Microbiome Disruption.},
journal = {Cellular and molecular bioengineering},
volume = {18},
number = {5},
pages = {369-385},
pmid = {41185633},
issn = {1865-5025},
abstract = {PURPOSE: The gut microbiome interacts with many systems throughout the human body. Microbiome disruption reduces bone tissue mechanics but paradoxically slows osteoarthritis progression. The microbiome also mediates inflammatory and immune responses, including serum cytokines. Towards our long-term goal of studying how the gut microbiome interacts with synovial joint health and disease, we examined how antibiotics-induced changes to microbial taxa abundance associated to serum cytokine levels.

METHODS: Mice (n = 5 + ) were provided ad libitum access to water containing antibiotics (1 g/L neomycin, 1 g/L ampicillin, or 1 g/L ampicillin with 0.5 g/L neomycin) or control water from 5- to 16-weeks old, corresponding in skeletal development to ~ 10 to ~ 25 years in humans. At humane euthanasia, we collected cecum contents for 16S metagenomics and blood for serum cytokine quantification for comparison to control and among antibiotic groups. We used dimensional reduction techniques, multiomic integration, and correlation to discriminate antibiotic groups and identify specific relationships between high-abundance taxa and serum cytokines.

RESULTS: Antibiotic treatment significantly lowered diversity, altered phylum relative abundance, and resulted in significant association with specific taxa. Dimensional reduction techniques and multiomic integration revealed distinct antibiotic-associated clusters based on genera relative abundance and cytokine serum concentration. Cytokines IL-6, MIP-1B, and IL-10 significantly contributed to antibiotic discrimination, significantly different among antibiotic treatments, and had significant correlations with specific taxa.

CONCLUSIONS: Antibiotic treatment resulted in heterogenous response in gut microbiome and serum cytokines, allowing significant microbe-cytokine links to emerge. The relationships identified here will enable further investigation of the gut microbiome's role in modifying joint health and disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12195-025-00861-2.},
}

@article {pmid41185359,
year = {2025},
author = {Cao, R and Zhou, Q and Ma, Y and Yan, X and Li, A and Du, H and Xu, Y},
title = {Multimodal integration: Mechanisms of temperature dynamics and quality formation critical period in Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117622},
doi = {10.1016/j.foodres.2025.117622},
pmid = {41185359},
issn = {1873-7145},
mesh = {*Fermentation ; Machine Learning ; Metagenomics ; *Temperature ; Microbiota ; Hot Temperature ; Quality Control ; *Food Microbiology ; },
abstract = {The quality of medium-high temperature Daqu, the core starter for strong-aroma Baijiu, is regulated by the synergistic mechanisms of temperature, physicochemical properties, and microbial activity. In this study, we aimed to integrate dynamic monitoring of indicators, metagenomic analysis, and machine learning modeling to establish a multimodal approach. The systematic analysis of the differential contributions of spatiotemporal factors to Daqu fermentation temperature highlighted the dynamic changes in physicochemical and microbial processes during Daqu fermentation, as well as the critical period for quality control. The influence of temporal factors on Daqu temperature was significantly higher than that of spatial heterogeneity. Additionally, the temperature difference generated by the interaction of dual pathways between environmental changes and microbial metabolic heat production could regulate the Daqu fermentation through a heat-flow positive feedback mechanism. By combining temperatural and physicochemical data, machine learning models identified and validated the early fermentation stage (S2-S3) as the critical period for Daqu quality formation. Consequently, the quality control of Daqu can be effectively predicted and guided through monitoring the temperature in the early stage of fermentation. Metagenomic analysis revealed the two-phase characteristics of medium-high temperature Daqu fermentation: the core microbiota construction was completed in the S1-S3 stages, and the microbiota function then entered a stable period in the S4-S6 stages. This explains the dynamic change regularity of Daqu quality critical period formative from a microscopic perspective.},
}

*Fermentation
Machine Learning
Metagenomics
*Temperature
Microbiota
Hot Temperature
Quality Control
*Food Microbiology

@article {pmid41185305,
year = {2025},
author = {Ying, H and Yang, J and Yu, L and Wei, J and Sheng, Q and Yuan, Y and Yue, T},
title = {Metagenomics and GC-IMSanalyses reveal microbial community differences and flavor characteristics among three types of Feng flavor Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117551},
doi = {10.1016/j.foodres.2025.117551},
pmid = {41185305},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; *Taste ; Fermentation ; *Microbiota ; Fungi/classification/genetics/metabolism ; *Alcoholic Beverages/microbiology/analysis ; China ; Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Flavoring Agents ; },
abstract = {Feng flavor Baijiu is one of the four famous Baijiu in China, and its quality and flavor are closely related to the microbial flora. Daqu is a saccharifying agent and starter for the production of Feng flavor Baijiu. Different styles of Daqu (Hong-Xin Daqu, Huai-Rang Daqu, Qing-Cha Daqu) reflect different microbial community structures and functions. Understanding the relationship between the microbial characteristics of Daqu and flavor is challenging yet vital for improving Baijiu fermentation. This study used metagenomics combined with GC-IMS to systematically analyze the microbial characteristics and flavor features of three different styles of Feng flavor Daqu. The bacteria mainly include Bacillus, Lactococcus, Lactobacillus and Leuconostoc. Fungi mainly include Aspergillus, Rhizopus, Saccharomyces, Paecilomyces and Rasamsonia. Actinobacteria mainly included Saccharopolyspora and Streptomyces. The community structure and function of microorganisms in different styles of Daqu exhibited strong functional complementarity. The results indicated that the content of esters and alkenes in Qing-Cha Daqu was higher, mainly related to carbon metabolism and amino acid metabolism, and generated aromatic compounds through esterification reactions. While there were more aldehydes, ketones, and esters in Huai-Rang Daqu, mainly participating in enzymatic reactions and biosynthesis of cofactors, generating precursor substances for various aroma compounds. Moreover, the content of ethyl acetate and alkenes in Hong-Xin Daqu was higher, mainly participating in the glycolysis and tricarboxylic acid cycle, generating various alcohols and organic acids. This study revealed the complementary roles of the three styles of Daqu in Feng flavor Baijiu fermentation, providing valuable insights for product enhancement.},
}

*Metagenomics/methods
*Taste
Fermentation
*Microbiota
Fungi/classification/genetics/metabolism
*Alcoholic Beverages/microbiology/analysis
China
Bacteria/classification/genetics/metabolism
*Food Microbiology
Gas Chromatography-Mass Spectrometry
Flavoring Agents

@article {pmid41185132,
year = {2025},
author = {Lonsing, A and Martens, GA and Resteu, A and Kizina, J and Wilkie, I and Bahr, A and Harder, J},
title = {Anaerobic Limonene Metabolism in a Methanogenic Enrichment Involves a Glycine Radical Enzyme.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70192},
doi = {10.1111/1462-2920.70192},
pmid = {41185132},
issn = {1462-2920},
support = {//Max Planck Society/ ; },
mesh = {*Limonene/metabolism ; *Methane/metabolism ; Anaerobiosis ; *Bacteria/genetics/metabolism/enzymology/classification ; *Archaea/genetics/metabolism/enzymology/classification ; *Terpenes/metabolism ; Metagenome ; *Glycine/metabolism ; *Cyclohexenes/metabolism ; Phylogeny ; Metagenomics ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Limonene is a natural monoterpene omnipresent in human environments. It enters wastewater and is also metabolised in methanogenic digesters. A stable limonene-degrading methanogenic enrichment culture was investigated by metagenomic, metatranscriptomic and metaproteomic data sets to characterise the microbial community and identify the limonene degradation pathway. Thirty-two metagenome-assembled genomes revealed a complex community of bacteria and methanogenic archaea dominated by Candidatus Velamenicoccus archaeovorus as the top predator, contributing two-thirds of the reads in the metagenome. The presence of several fermenting bacteria (Anaerolineaceae, Aminidesulfovibrio, Smithellaceae, Lentimicrobium) indicated the recycling of necromass in a microbial loop. Only one hydrocarbon-activating enzyme system was expressed, a member of the alkyl- and arylsuccinate synthase family which is a glycine radical enzyme that adds fumarate to hydrocarbons. The limonenylsuccinate synthase gene encodes a modified substrate binding pocket with two smaller amino acids, suggesting an adaptation for the larger structure of limonene. The limonenylsuccinate synthase operon and a ring cleavage operon, as well as genes for the final syntrophic fermentation to acetate, hydrogen and formate were encoded in a Syntrophobacteraceae genome. Almost all genes for this degradation pathway were highly transcribed and expressed, demonstrating a catalytic role for glycine radical enzymes in methanogenic systems degrading limonene.},
}

*Limonene/metabolism
*Methane/metabolism
Anaerobiosis
*Bacteria/genetics/metabolism/enzymology/classification
*Archaea/genetics/metabolism/enzymology/classification
*Terpenes/metabolism
Metagenome
*Glycine/metabolism
*Cyclohexenes/metabolism
Phylogeny
Metagenomics
Bacterial Proteins/metabolism/genetics

@article {pmid41185061,
year = {2025},
author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , },
title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {225},
pmid = {41185061},
issn = {2049-2618},
support = {OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; },
mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation & purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; },
abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.

METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.

RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.

CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.},
}

Animals
Humans
*Campylobacter/classification/genetics/isolation & purification
Infant
*Campylobacter Infections/microbiology/epidemiology/veterinary
Ethiopia/epidemiology
*Livestock/microbiology
Rural Population
Longitudinal Studies
Female
Male
Chickens/microbiology
Feces/microbiology
Metagenomics/methods
Gastrointestinal Microbiome
Adult
Cluster Analysis
Family
Child, Preschool

@article {pmid41183495,
year = {2025},
author = {Hu, CY and Dai, CY and Anh, PNT and Tsai, HY and Chen, YC},
title = {Tetragenococcus halophilus A003 altered microbiota and repressed the accumulation of biogenic amines in the fermentation of fish Sauce.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf128},
pmid = {41183495},
issn = {1472-765X},
abstract = {Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/L) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.},
}

@article {pmid41183487,
year = {2025},
author = {Xu, Q and He, N and Tian, Y and Wu, Z and Wang, H and Liu, B and Yang, Z and Zhang, H and Luo, Q and Zhong, Y and Xiao, L and Li, S and Zou, Y},
title = {Lactobacillus gasseri TF08-1 ameliorate high-fat diet induced Nonalcoholic fatty liver disease and regulates gut microbiota in mice.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf271},
pmid = {41183487},
issn = {1365-2672},
abstract = {AIMS: This study aimed to investigate the therapeutic potential of Lactobacillus gasseri TF08-1, a gut bacterium isolated from healthy adolescents, in alleviating high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD). This followed our discovery of lipid metabolism-related genes in its complete genome.

METHODS AND RESULTS: The high-precision complete genome map of L. gasseri TF08-1 was constructed for the first time, revealing enriched lipid metabolism pathways, including bile salt hydrolase activity and short-chain fatty acid (SCFA) production. After supplementing Lactobacillus gasseri TF08-1 for 8 weeks in mice fed with a high-fat diet, the serum triglyceride (TG) level decreased by 41.95%, the hepatic total cholesterol (TC) level decreased by 35.09%, and the TNF-α level decreased by 42.91%. Meanwhile the NAS score decreased by 3.66 points. The treatment significantly reduced hepatic lipid accumulation, lowered pro-inflammatory cytokines, and improved steatosis scores. Metagenomic analyses showed L. gasseri TF08-1 restored gut microbiota balance, significantly increasing the abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Phocaeicola vulgatus, while also enriching fatty acid degradation pathways.

CONCLUSIONS: L. gasseri TF08-1 demonstrates probiotic efficacy against NAFLD through dual mechanisms: direct metabolic modulation and gut microbiota restoration. The lipid metabolism capacity encoded by its genome likely contributes to therapeutic effects.},
}

@article {pmid41183417,
year = {2025},
author = {Liu, S and Xiang, Y and Liu, P and Deng, J and He, J and Chen, H and Liao, S and Lu, Y and Zhang, Z and Xu, J and Zhang, Z},
title = {Application of metagenomic next-generation sequencing in the precise and rapid diagnosis of spinal infections.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117165},
doi = {10.1016/j.diagmicrobio.2025.117165},
pmid = {41183417},
issn = {1879-0070},
abstract = {OBJECTIVE: To evaluate the comparative diagnostic efficacy of metagenomic next-generation sequencing (mNGS) versus conventional microbiological culture in spinal infections.

METHODS: A retrospective analysis was conducted in a cohort of 80 patients with suspected spinal infections who underwent concurrent testing via metagenomic next-generation sequencing (mNGS), microbial culture, and histopathological examination. Diagnostic performance of mNGS and microbial culture was compared using a composite clinical reference standard (definitive diagnosis integrating histopathology, clinical history, and laboratory findings) as the diagnostic gold standard.

RESULTS: Pathogens were detected in 64 cases (80 %) by mNGS, compared to 34 cases (42.5 %) via conventional microbial culture, demonstrating a statistically significant difference in detection rates (P < 0.001). Using clinical diagnosis (histopathology combined with medical history and laboratory findings) as the gold standard, mNGS exhibited superior sensitivity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) in tissue specimens. Conversely, microbial culture showed higher specificity. In pus specimens, mNGS maintained advantages in sensitivity, accuracy, and PPV, while culture demonstrated higher specificity and NPV.

CONCLUSION: Compared to conventional microbial culture, mNGS demonstrates superior diagnostic performance in spinal infections, with significantly higher pathogen detection rates and enhanced sensitivity, accuracy PPV and NPV. mNGS exhibits significant advantages over culture in identifying both common pathogens and fastidious organisms, while also demonstrating robust fungal detection capabilities. Additionally, in tissue specimens, mNGS demonstrates relatively pronounced advantages compared to conventional microbial culture. For purulent specimen testing, comprehensive sensitivity and specificity in diagnosis can be achieved through a combined strategy of mNGS and microbial culture.},
}

@article {pmid41183305,
year = {2025},
author = {Yang, R and Ma, J and Abebe, H and Tu, Y},
title = {Divergent Responses of Soil Microbiome Structure and Function to Salinity and Depth Gradients.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08498},
pmid = {41183305},
issn = {1520-5118},
abstract = {Soil salinization profoundly threatens agricultural ecosystems by disrupting soil microbial communities and functions, yet the interplay of salinity and depth on microbiome structure and function is unclear. In the present experiment, soils from two depths (0-20 and 20-40 cm) across a low (LS), medium (MS), and high (HS) salinity gradient were collected. The results indicated that the soil electrical conductivity, available sodium, and available potassium were significantly elevated in HS soil. 16S rRNA gene sequencing identified three key microorganisms associated with soil salinity, including Sphingomonas, Bradyrhizobium, and Chloracidobacterium. Metagenomic analysis indicated that the abundances of carbon and nitrogen cycle genes such as amyA, xylA, nifH, nirK, narG and amoA were significantly upregulated in LS soils. In conclusion, the experiment systematically elucidated the intricate restructuring of soil microbiome responses across distinct salinity gradients and depths, providing new theoretical support for the remediation of soil salinization.},
}

@article {pmid41183096,
year = {2025},
author = {Lv, JX and Pei, YY and Yang, C and Liu, X and Ju, MJ and Holmes, EC and Chen, YM and Zhu, TY and Zhang, YZ},
title = {Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.},
journal = {PLoS pathogens},
volume = {21},
number = {11},
pages = {e1013667},
doi = {10.1371/journal.ppat.1013667},
pmid = {41183096},
issn = {1553-7374},
abstract = {Although pneumonia is a common lung disease with a high morbidity and mortality, aside from well-known pathogens little is known about why, which and how many microorganisms are associated with the disease, particularly in immunocompromised individuals. We enrolled 32 kidney transplant cases with severe pneumonia admitted to Shanghai Zhongshan Hospital between 2019 and 2025, and performed both metagenomic and metatranscriptomic sequencing on the bronchoalveolar lavage fluid (BALF) and blood samples from each case. Comprehensive analyses of immune cells and cytokines, as well as BALF and blood metatranscriptomes, revealed that both adaptive and innate immunity inside and outside of their lungs were severely suppressed. Notably, a high diversity of unusual microorganisms were present in BALF samples, including bacteria and DNA viruses that are rare or absent in healthy individuals, as well as RNA viruses and fungi. Of these, 17 bacteria, 46 DNA viruses, eight RNA viruses and two fungi, which were at high abundance, were considered to be responsible for the lung infections. Remarkably, the majority of these patients experienced co-infections of multiple bacteria, DNA and RNA viruses and fungi, reaching 32 virus species in one individual. In sum, these data indicate that the prosperity or overgrowth of accidental, opportunistic and rare microorganisms within the lungs of these kidney transplant patients substantially altered their lung microbiota, with multiple co-infections further exacerbating the severity of pneumonia.},
}

@article {pmid41182689,
year = {2025},
author = {de Kroon, RR and van Wesemael, AJ and van Kaam, AH and Savelkoul, PHM and Boon, M and Budding, AE and Niemarkt, HJ and de Meij, TGJ},
title = {A Novel Untargeted Molecular Detection Technique for Rapid Fecal Microbiota Profiling in Very Preterm Infants: Optimization, Genus-Level Comparison, and Application.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {21},
pages = {e71207},
doi = {10.1096/fj.202502006RR},
pmid = {41182689},
issn = {1530-6860},
mesh = {Humans ; *Feces/microbiology ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Intensive Care Units, Neonatal ; *Bacteria/genetics/classification ; },
abstract = {Gut microbiota profiling shows potential for improving care in the neonatal intensive care unit (NICU). However, common techniques, including 16S rRNA gene and metagenomic sequencing, have limited bedside applicability. The IS-pro microbiota assay provides species-level abundances within 5 h. We aimed to optimize the taxa annotation for preterm infants (phase 1), compare its findings to 16S sequencing on the genus level (phase 2), and apply the assay in a preterm cohort (phase 3). 1445 fecal samples from 479 preterm infants (24-30 weeks gestation) across 10 NICUs were analyzed with IS-pro. For phase 1 (optimization), IS-pro amplicons of 32 fecal samples were additionally analyzed with nanopore sequencing to expand the IS-pro matching database. For phase 2 (comparison), 41 samples were compared to 16S sequencing. In phase 3 (application), the optimized IS-pro assay was applied to the total cohort. Following phase 1, a mean relative abundance of 82.5% was successfully annotated. In phase 2, IS-pro showed high concordance with 16S sequencing, with a strong positive correlation between the two techniques (Pearson's correlation coefficient: 0.77, SD 0.24). In phase 3, IS-pro analysis of the full cohort revealed Staphylococcus, Klebsiella, Enterococcus, Escherichia-Shigella, and Streptococcus as the predominant genera in the first 4 weeks of life. Our findings demonstrate that the IS-pro microbiota assay effectively detects and quantifies key bacterial taxa in fecal samples of preterm infants, with outcomes highly concordant with 16S sequencing. Unlike traditional techniques, IS-pro is a rapid tool, illustrating its potential for clinical practice. Future studies should explore its applications in the NICU.},
}

Humans
*Feces/microbiology
Infant, Newborn
RNA, Ribosomal, 16S/genetics
*Infant, Premature
*Gastrointestinal Microbiome/genetics
Female
Male
Intensive Care Units, Neonatal
*Bacteria/genetics/classification

@article {pmid41182549,
year = {2025},
author = {Dandare, SU and Dabai, IA and Kumaresan, D and Allen, CCR},
title = {A Novel Salicylaldehyde Dehydrogenase from Alpine Soil Metagenome Reveals a Unique Catalytic Mechanism.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41182549},
issn = {1559-0291},
support = {NGCA-2014-78//Commonwealth Scholarship Commission/ ; },
abstract = {Metagenomic approaches have revolutionised the discovery of novel enzymes with ecological and biotechnological significance from different environments. Here, we report the comprehensive characterisation of a novel salicylaldehyde dehydrogenase (SALDAP) obtained from an alpine soil metagenome. Phylogenetic analysis revealed that SALDAP is the first experimentally characterised Alphaproteobacterial SALD, forming a distinct evolutionary clade among known bacterial enzymes. The recombinant enzyme exhibited strict specificity for NAD[+] and exceptional catalytic efficiency toward aromatic aldehydes, with benzaldehyde as the preferred substrate. Kinetic analyses showed catalytic efficiencies exceeding 10[6] M[-1] s[-1] for aromatics, whereas aliphatics were oxidised with much lower efficiency, consistent with ecological specialisation for aromatic catabolism in alpine soils enriched in lignin-derived compounds. SALDAP was most active under mildly alkaline conditions (optimum pH 8.0) and tolerated a range of chemical environments, though high concentrations of certain metals and solvents were inhibitory. Differential scanning fluorimetry demonstrated that the enzyme was stabilised by ligand binding, with maximal thermal stability observed when both substrate and cofactor were present. Structural alignment with Pseudomonas NahF and docking analyses revealed that SALDAP employs a distinctive catalytic configuration involving ASN-137, ARG-145, GLU-238, and CYS-272, highlighting a non-canonical role for ASN-137 in substrate binding and stabilisation. Based on these findings, we propose a mechanistic model for SALDAP that expands the catalytic diversity of the aldehyde dehydrogenase superfamily. This study establishes a new paradigm for aromatic aldehyde oxidation, underscores the ecological significance of SALDAP in alpine soil microbiomes, and provides a foundation for engineering novel biocatalysts for bioremediation and synthetic biology applications.},
}