@article {pmid41138860,
year = {2025},
author = {Mishra, S and Vadakkethil, AA and Iquebal, MA and Jaiswal, S and Kumar, D and Singh, BP and Ajlouni, S and Ranadheera, CS and Chakkaravarthi, S},
title = {Deciphering microbial diversity and predicting metabolic functionalities in fermented pigmented rice water using culture-independent characterization.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107295},
doi = {10.1016/j.mimet.2025.107295},
pmid = {41138860},
issn = {1872-8359},
abstract = {Fermented rice water is gaining importance lately due to its traditional food culture and potential beneficial effects. Flavored fermented rice water (FFRW) produced from pigmented rice varieties, viz., black, brown, and red, is shown to have rich nutritional and functional profiles. However, the microbiota in this spontaneously fermented beverage is scantly known. Hence, this study aimed to explore the total bacterial and fungal diversity using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, respectively, along with the phytochemicals and their metabolites produced/utilized during storage. The bacterial diversity showed significant differences (p < 0.05) in black FFRW while depicting stability for brown- and red-FFRW on the 0th day and 30th day of refrigerated storage. Lactic acid bacteria (LAB) like Weissella were abundantly recorded; similarly, fungal diversity showed dominance of various yeasts. Predictive functional/metabolic pathways suggested 23 pathways of which the predominant were metabolism amino acids like branched-chain amino acids (BCAAs) viz., leucine, valine, and isoleucine, aromatic amino acids such as tryptophan, and metabolites of glycan biosynthesis, polyphenols, lipids, cofactors and vitamins. KEGG pathways revealed a shift in microbial metabolism from amino acid degradation pathways dominating on day 0 to carbohydrate and fatty acid metabolism by day 30. Enzymes like lactate dehydrogenase showed increased abundance by the 30th day, particularly in red and black-FFRW. The untargeted profiling showed that brown FFRW had more polyphenol-related compounds, followed by black and red FFRW. Decrements in the compounds were detected on the 30th day of storage compared to the 0th day. The findings provide insights into the microbial diversity, metabolic potential, and phytochemical composition of FFRW, supporting its potential as a functional beverage.},
}

@article {pmid41138814,
year = {2025},
author = {Matsumoto, A and Yoshimura, Y and Wakabayashi, H and Nagano, F and Shimazu, S and Kido, Y and Shiraishi, A and Hamada, T and Yoneda, K and Maeda, K},
title = {Polypharmacy is associated with altered gut microbiota diversity in older post-stroke inpatients.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.10.015},
pmid = {41138814},
issn = {2405-4577},
abstract = {RATIONALE: Gut microbiota diversity plays a crucial role in various health outcomes, including metabolic regulation and nutritional status. Polypharmacy, common among older adults, has been linked to adverse clinical outcomes, yet its impact on gut microbiota diversity remains poorly understood. This study aimed to investigate the association between polypharmacy and gut microbiota diversity in older post-stroke patients.

METHODS: This cross-sectional study included post-stroke inpatients aged 65 years or older undergoing rehabilitation. Polypharmacy was defined as the prescription of five or more drugs. Metagenomic analysis of DNA from patient fecal samples was conducted, calculating three alpha diversity indices: the Shannon Diversity Index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analysis was used to determine whether polypharmacy was independently associated with the gut microbiota diversity upon admission, adjusting for potential confounders.

RESULTS: A total of 156 patients (mean age 78.4 years; 55.8% male) were analyzed. The median number of medications taken on admission was 6 (4-8), and 69.9% of patients had polypharmacy. Polypharmacy was independently associated with decreased Shannon Diversity Index (β = -0.202, p = 0.019). No statistically significant association was found with Observed OTUs (β = -0.159, p = 0.067) and Faith's PD (β = -0.38, p = 0.111).

CONCLUSIONS: Polypharmacy is associated with qualitative alterations in the gut microbiota of older post-stroke patients, with a potential negative trend in quantitative alterations and phylogenetic classification. The findings underscore the need to consider the impact of polypharmacy on the gut microbiome in stroke management.},
}

@article {pmid41138407,
year = {2025},
author = {Zhao, Q and Zhao, Y and Liu, W and Wang, J and Xie, H and Wu, H and Hu, Z},
title = {Nitrogen-transforming bacteria as key hosts and disseminators of antibiotic resistance genes in constructed wetlands: Metagenomic and metatranscriptomic evidence.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140220},
doi = {10.1016/j.jhazmat.2025.140220},
pmid = {41138407},
issn = {1873-3336},
abstract = {Given global concerns over antibiotic resistance genes (ARGs), constructed wetlands (CWs) have emerged as a cost-effective strategy to remove nitrogen (N) and mitigate ARG-related ecological risks. The occurrence and dissemination of ARGs are mainly driven by microorganisms. Although nitrogen transformation is a key process in CWs, the relationship between nitrogen-transforming bacteria (NTB) and ARG dynamics remains unclear. In this study, metagenomic and metatranscriptomic analyses were employed to comprehensively examine the associations between N transformation and the abundance, hosts, and ecological risks of ARGs in full-scale CWs. NTB, particularly dissimilatory nitrate reducers and bacteria involved in N organic degradation and synthesis, were identified as the primary hosts of ARGs. Furthermore, CWs substantially reduced ARG-related ecological risks, achieving decreases of 79.5 % in ARG expression, 94.9 % in mobile genetic elements, and 88.0 % in antibiotic-resistant pathogens, and identified NTB as key contributors to these risks. Both the decline in NTB abundance and adaptive fitness costs were identified as key mechanisms driving ARG reduction and mitigating ecological risk. This study highlights the critical role of N transformation in shaping ARG dynamics from a microbial perspective, providing a theoretical foundation for engineering practice in the co-control of ARGs and nitrogen removal in CWs.},
}

@article {pmid41138387,
year = {2025},
author = {Ochoa-Bernal, TG and Huber, DH and Espinosa-Solares, T},
title = {The progressive shift in anaerobic digestion communities under extreme propionate levels led to a redundant microbiome capable of producing methane.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127698},
doi = {10.1016/j.jenvman.2025.127698},
pmid = {41138387},
issn = {1095-8630},
abstract = {Propionate accumulation exerts a significant inhibitory effect on anaerobic digestion, which may result in the cessation of methane production. It has been reported that propionate can be degraded solely by a limited group of syntrophic propionate-oxidizing bacteria belonging to the following genera: Syntrophobacter, Smithella, and Pelotomaculum. Chicken litter is a substrate rich in protein and nitrogen, which makes it more susceptible by total ammonia nitrogen toxicity. This study aimed to elucidate the alterations and responses of microbial communities to extreme concentrations of propionate in co-digestion with chicken litter, thereby providing an extensive overview of community composition and functional potential through shotgun metagenomics sequencing. An enrichment process was conducted over 1220 days in co-digestion with chicken litter, utilizing a 10 L digester operating in semi-continuous mode and progressively increasing sodium propionate concentrations to create a selection pressure. The feed had 12 propionate concentration levels, varying from 0 to 24 g L[-1]; chicken litter was kept at 3 %. At the end of the enrichment process, it was surprisingly observed that the well known syntrophic bacteria were not present; instead, bacteria from the Proteiniphilum, Petrimonas, Vibrio, Corynebacterium, Coprobacter, Brachymacterium, Cloacimonas, and Treponema genera were found. Propionate degradation was mainly attributed to Corynebacterium stationis and Corynebacterium casei, through the ackA and pta enzymes. The putative lactate pathway was also detected by the pct enzyme. Methanogenic archaea increased relative abundance, particularly the genera Methanoculleus, Methanospirillum, Methanococcus, and Methanocella, synthesizing methane in several pathways, mainly hydrogenotrophic in the range from 0.189 to 0.320 mL CH4 kgvsadded[-1]. The enrichment using extreme propionate concentrations in co-digestion with chicken litter resulted in a microbial consortium that stabilized propionate degradation and methane production, which can be attributed to an adaptive functional redundancy.},
}

@article {pmid41138382,
year = {2025},
author = {Chen, C and Zhang, L and Tong, C and Ding, B and Li, A and Ji, B},
title = {Intermittent nighttime lighting enhances microalgal-bacterial granular sludge in synthetic wastewater treatment.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127689},
doi = {10.1016/j.jenvman.2025.127689},
pmid = {41138382},
issn = {1095-8630},
abstract = {The microalgal-bacterial granular sludge (MBGS) system is a promising technology due to its low energy demand and high treatment efficiency under illumination. However, its performance declines at night owing to the absence of light, reducing dissolved oxygen and microbial activity. This study proposes and evaluates an intermittent nighttime lighting strategy (12 h-light/3 h-dark/6 h-light/3 h-dark using LEDs) to enhance MBGS performance for treating synthetic wastewater. Supplemental lighting improved removal efficiencies of chemical oxygen demand, ammonia nitrogen, and phosphate by 7.5 %, 27.7 %, and 27.1 %, respectively. Metagenomic analysis revealed an increased genetic potential for pollutant degradation, evidenced by a higher abundance of genes involved in key metabolic pathways (e.g., GLU, ppa). Microbial community structure shifted, with increased abundances of Cyanobacteria and Verrucomicrobia and a decreased abundance of Proteobacteria. Genetic potential analysis suggested enhanced nitrogen assimilation, ATP cycling, and glycogen synthesis, alongside reduced lactate metabolism, indicating a shift toward aerobic pathways. These results demonstrate that intermittent nighttime lighting enables sustainable round-the-clock wastewater treatment.},
}

@article {pmid41138328,
year = {2025},
author = {Bai, X and Bi, J and Li, A and Deng, X and Zhao, Z and Hu, H and Pan, H},
title = {Walnut cake meal improves amino acids, fatty acid composition and flavor of egg yolk via the microbiota-yolk metabolites crosstalk in Jingfen-1 laying hens.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105981},
doi = {10.1016/j.psj.2025.105981},
pmid = {41138328},
issn = {1525-3171},
abstract = {Egg production is important for both human nutrition and its economic contribution. However, regions with a shortage of soybean meal (SM) may not meet the nutritional needs of the laying hen industry. Walnut cake meal (WM), a by-product of walnut processing, can be reused in laying hen production. In this study, we evaluated the feasibility of using WM to reduce the demand for SM in the laying hen industry. A total of 144 47-week laying hens (with similar performance) were randomly assigned to two groups (12 hens in each replicate and six replicates for each group). One group was fed a maize-SM diet (SM group), and the other was fad a maize-WM diet (WM group). The diets of both groups had similar crude protein and ME contents. After replacing SM with WM, the laying rate, egg weight, and feed efficiency did not significantly change (P > 0.05). WM increased (P < 0.05) the polyunsaturated fatty acids content, particularly linoleic acid, as well as umami and essential amino acids, in the eggs. WM diet also enhanced the flavor of eggs by enriching multiple volatile organic compounds that smell of sweet and herb-like foods. In addition, probiotic bacteria such as Cyanobacteriota and Prevotella, were enriched in the cecal microbiota of laying hens fed WM. Moreover, targeted metabolomics revealed the enrichment of butyric acid, 4-methylvaleric acid, isoleucine, and valine in the cecal digesta of laying hens fed with WM. Metagenomic sequencing revealed genes in the cecal microbiota associated with the synthesis of these enriched metabolites. Increased isoleucine and 4-methylvaleric acid in the digestive system contributed to the enrichment of fatty acids and amino acids in the yolks, whereas elevated flavor substances in the yolk could be associated with more amino acids in the intestine of laying hens. In conclusion, WM can reduce the need for soybean meal, improve cecal metabolism and egg quality, and ultimately achieve sustainable agriculture.},
}

@article {pmid41138271,
year = {2025},
author = {Mishra, R and Singh, R and Goel, R and Hasmi, RR and Malik, M and Gaur, PK and Lata, K},
title = {Biologically Active Molecules from Marine Brown Algae: A Review of Their Potential and Applications.},
journal = {Chemistry & biodiversity},
volume = {},
number = {},
pages = {e01813},
doi = {10.1002/cbdv.202501813},
pmid = {41138271},
issn = {1612-1880},
abstract = {The highly bioactive secondary metabolites present in marine flora may prove to be abundant sources for producing innovative pharmaceuticals. Numerous brown algae species are being researched extensively because of their commercial relevance in nutraceuticals and medication discovery. The difficult environments that these creatures live in aid in the synthesis of special and powerful bioactive substances such as fucoidans, polysaccharides, hentriacontane, sterols like fucosterol, 24-ketocholesterol, and so forth. Despite its promising characteristics, additional in vivo studies are needed to validate algae's efficacy in a variety of applications. Effective extraction techniques must also be known to inexpensively isolate these chemicals, permit industrial application, and facilitate large-scale manufacturing. A comprehensive study of the genomes, metagenomics, transcriptomics metagenomics, transcriptomics, and metabolomics of marine algae is also necessary to elaborate on the underlying genetic and metabolic pathways involved in the manufacture of algal chemicals; these topics are covered in detail in this review. Brown algae are a major source of numerous secondary metabolites as evidenced by their phytoconstituents. This review elucidates the bioactive substance found in marine brown algae and their major pharmacological role so as to pave the way for maximum utilization of these underused resources.},
}

@article {pmid41138185,
year = {2025},
author = {Waschina, S and Pagel, J and Seeger, K and Pasderski, E and Rühlemann, M and Froitzheim, S and Künzel, S and Sommer, F and Franzenburg, S and Fortmann, I and Sugihara, F and Faust, K and Marissen, J and Demmert, M and Baines, JF and Göpel, W and Herting, E and Kaleta, C and Rupp, J and Härtel, C},
title = {Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116431},
doi = {10.1016/j.celrep.2025.116431},
pmid = {41138185},
issn = {2211-1247},
abstract = {The effect of multi-strain probiotics containing Bifidobacterium longum (B. longum) on late-onset sepsis (LOS) risk in very-low-birth-weight infants (VLBWIs; birth weight < 1,500 g) remains uncertain. In a single-center study, we analyzed intestinal metagenome and metabolome data in VLBWIs during the period of highest vulnerability of LOS. Using a unit's policy change to routinely administer B. longum subspecies infantis plus Lactobacillus acidophilus as natural experiment, we compared 97 infants (including 38 LOS cases) after change with 78 infants (including 32 LOS cases) before. Probiotic supplementation was associated with more beneficial bacteria and reduced abundance of nosocomial pathobionts, such as Klebsiella spp. Infants in the probiotic group had significantly lower concentrations of B. longum fermentation products prior to sepsis diagnosis than matched non-LOS cases (acetate: padj = 0.0049; lactate: padj = 0.048). Modulation of the gut metabolic milieu is an interesting target for LOS prevention.},
}

@article {pmid41138182,
year = {2025},
author = {Gao, SM and Lan, LY and Yang, L and Chen, T and Fan, PF},
title = {Health-associated key gut microbiota drives the variation in community metabolic interactions in non-human primates.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116477},
doi = {10.1016/j.celrep.2025.116477},
pmid = {41138182},
issn = {2211-1247},
abstract = {Gut microbiota often undergo metabolic cross-feeding and resource competition. However, our understanding of global variations in these interactions and their implications for host health remain elusive. By analyzing a microbial genome catalog from 841 fecal metagenomes across 53 primate species worldwide, we identified key microbiota assigned to two taxa, i.e., Bacillota_A and Pseudomonadota, which well predicted the trade-off of community-level interaction types between metabolic competition and cooperation. Specifically, Bacillota_A species were inherently competitive and amino acid auxotrophic and typically found in anaerobic habitats. In contrast, members of Pseudomonadota were inherently cooperative, siderophore producers, and more abundant in aerobic conditions. Random forest models successfully distinguished unhealthy gut samples from healthy samples through the key competitive and cooperative microbiota, suggesting potential links between community metabolic interactions and host health. Together, this study enhances our mechanistic understanding of microbial interaction dynamism within complex gut ecosystems, offering new targets for understanding host health.},
}

@article {pmid41138002,
year = {2025},
author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M},
title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {178},
pmid = {41138002},
issn = {1572-9699},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.},
}

Humans
*Microbiota
*Mouth/microbiology
Periodontal Diseases/microbiology/therapy
Dental Caries/microbiology/therapy
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid41137523,
year = {2025},
author = {Tegegne, HA and Savidge, TC},
title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2569739},
doi = {10.1080/19490976.2025.2569739},
pmid = {41137523},
issn = {1949-0984},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; },
abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.},
}

Humans
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Precision Medicine/methods

@article {pmid41137517,
year = {2025},
author = {Bayne, J and Charavaryamath, C and Hu, Y and Yousefi, F and Murphy, M and Law, A and Michael, A and Muyyarikkandy, MS and Nibbering, B and Smits, WK and Kuijper, E and Opriessnig, T and Sauer, M and Scaria, J and Sponseller, B and Ramirez, A and Mooyottu, S},
title = {The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2568706},
doi = {10.1080/19490976.2025.2568706},
pmid = {41137517},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Ileum/microbiology/surgery ; *Host Microbial Interactions ; Humans ; Feces/microbiology ; Clostridioides difficile/physiology ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation & purification ; Models, Animal ; Disease Models, Animal ; },
abstract = {Understanding gut-host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and minimal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host-microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust transcriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host-microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.},
}

Animals
*Gastrointestinal Microbiome/physiology
Swine
Ileum/microbiology/surgery
*Host Microbial Interactions
Humans
Feces/microbiology
Clostridioides difficile/physiology
Fecal Microbiota Transplantation
Bacteria/classification/genetics/isolation & purification
Models, Animal
Disease Models, Animal

@article {pmid41137451,
year = {2025},
author = {Liu, Y and Wu, X and Wegner, CE and Ma, K and Xu, G and Cui, Z and Zhang, F and Liesack, W and Peng, J},
title = {Temperature Increase in Paddy Soils Remodels the Relationship Between the Anaerobic Food Web and the Q10 of CH4 Production.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70156},
doi = {10.1111/mec.70156},
pmid = {41137451},
issn = {1365-294X},
support = {2021YFD1900100//National Key Research and Development Program of China/ ; 42277307 and 41977038//National Natural Science Foundation of China/ ; },
abstract = {Rice paddies are a major source of anthropogenic CH4 emissions globally, with the temperature sensitivity (Q10) of CH4 production playing a key role in forecasting emissions under future climate scenarios. However, the mechanistic links among Q10, the soil microbiome and mean annual temperature (MAT) in paddy soils remain poorly understood. To address this gap, we employed quantitative PCR, amplicon sequencing, genome-resolved metagenomics and metatranscriptomics to investigate CH4 production dynamics and the response of the methanogenic food web to warming in low MAT (LMAT, 4°C-9°C) and high MAT (HMAT, 14°C-16°C) soils. Our results indicate that CH4 production exhibits a higher Q10 in LMAT soils, while warming exerts a more pronounced impact on the methanogenic food web in HMAT soils. Notably, we identified negative correlations between the Q10 and the metagenomic abundance of genes encoding glycoside hydrolases, carbohydrate-binding modules, polysaccharide lyases-related carbohydrate-active enzymes (CAZymes), hydrogenotrophic methanogenesis, and the average genome size (AGS) of the microbiome. Conversely, genes encoding auxiliary activity CAZymes and those associated with acetate metabolism and fermentation were positively correlated with Q10. Genes linked to acetoclastic and hydrogenotrophic methanogenesis exhibited lower responsiveness to warming in LMAT soils compared to HMAT soils. Additionally, warming led to a significant reduction in both gene and transcript abundances associated with methylotrophic methanogenesis across both MAT regimes. These findings provide novel insights into the temperature-dependent restructuring of methanogenic pathways and resource utilisation strategies in paddy soils, with important implications for predicting CH4 emissions under climate change.},
}

@article {pmid41137177,
year = {2025},
author = {Correa, F and Luise, D and Palladino, G and Estellé, J and Turroni, S and Scicchitano, D and Babbi, G and Rampelli, S and Candela, M and Martelli, PL and Stefanelli, C and Perez-Calvo, E and Trevisi, P},
title = {Early antimicrobial regimen shapes gut microbiota and health trajectories in pigs: a longitudinal study from weaning to finishing.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {110},
pmid = {41137177},
issn = {2524-4671},
support = {818290//Horizon 2020 Framework Programme/ ; },
}

@article {pmid41137068,
year = {2025},
author = {Asin, ICA and Egana, JMC and Paul, RE and Bautista, MAM},
title = {Virome sequencing and analysis of Aedes aegypti and Aedes albopictus from ecologically different sites in the Philippines.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {426},
pmid = {41137068},
issn = {1756-3305},
mesh = {Animals ; *Aedes/virology ; Philippines ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; *Insect Viruses/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is also affected by land use.

METHODS: Viral metagenomics was used to determine the virome compositions of 260 Ae. aegypti and 75 Ae. albopictus collected from the three study sites in Los Baños, Laguna, Philippines, that differ in topography and land use transformations.

RESULTS: The virome of Ae. aegypti and Ae. albopictus revealed virus sequences belonging to 12 different taxon groups, dominated by insect-specific viruses (ISVs) such as Phasi Charoen-like phasivirus (PCLV), Humaita Tubiacanga virus (HTV), and Wenzhou sobemo-like virus 4 (WSLV4). Both species were found to share the majority of identified viruses. Moreover, a relatively higher number of viral families were observed in sites that had undergone transformation from agriculture to bare and built-up areas, compared with a forest site.

CONCLUSIONS: The findings of this study underscore the vast diversity of Ae. aegypti and Ae. albopictus viruses from the selected sites in the Philippines generated by viromics. Results also impact the understanding that land use may contribute to virus diversity. The prevalence of ISVs and nondetection of arboviruses in the virome composition of Ae. aegypti and Ae. albopictus were notable, suggesting further examination of the roles of ISVs in arbovirus transmission.},
}

Animals
*Aedes/virology
Philippines
*Virome/genetics
*Mosquito Vectors/virology
Metagenomics
Phylogeny
*Insect Viruses/genetics/classification/isolation & purification

@article {pmid41136898,
year = {2025},
author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S},
title = {Prevalence of oxalotrophy in the human microbiome.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {954},
pmid = {41136898},
issn = {1471-2164},
support = {40B2-0_194701//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert Rüf Stiftung/ ; },
mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.

RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.

CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.},
}

Humans
*Oxalates/metabolism
*Microbiota/genetics
Metagenome
Gene Transfer, Horizontal
*Bacteria/genetics/metabolism

@article {pmid41136619,
year = {2025},
author = {Fujikawa, K and Saito, T and Kawashima, A and Jingushi, K and Motooka, D and Nakai, S and Hagi, T and Momose, K and Yamashita, K and Tanaka, K and Makino, T and Takahashi, T and Kurokawa, Y and Tsujikawa, K and Wada, H and Eguchi, H and Doki, Y},
title = {Bacteria-derived DNA in serum extracellular vesicles as a biomarker for gastric cancer.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {11},
pages = {346},
pmid = {41136619},
issn = {1432-0851},
mesh = {Humans ; *Stomach Neoplasms/blood/microbiology/diagnosis ; *Extracellular Vesicles/genetics/microbiology ; *Biomarkers, Tumor/blood/genetics ; Male ; *DNA, Bacterial/genetics/blood ; Middle Aged ; Female ; RNA, Ribosomal, 16S/genetics ; Prognosis ; Aged ; Adult ; Case-Control Studies ; Tumor Microenvironment/immunology ; },
abstract = {Bacterial flora is present in various parts of the human body, and bacterial 16S rRNA genes have been detected in the bloodstream. Distinct blood microbiomes have been identified in various diseases, including cancer, and are thought to play a role in disease pathogenesis. In this study, we conducted a 16S rRNA metagenomic analysis of serum extracellular vesicles from 89 patients with gastric cancer (GC) and 25 healthy donors. We identified lower levels of Bacteroidetes and Actinobacteria and higher levels of Firmicutes in patients with GC than in healthy donors. By integrating this characteristic bacterial DNA profile, we developed a BAF index, defined as the ratio of Bacteroidetes and Actinobacteria to Firmicutes, which exhibited high sensitivity for detecting GC in both the discovery and validation cohorts, suggesting its potential utility as a screening tool. A high BAF index was significantly associated with an advanced tumor stage and poor prognosis. Moreover, a high BAF index was linked to an immunosuppressive tumor microenvironment, which may contribute to the unfavorable outcomes observed in these patients. These findings indicate that circulating bacterial signatures may serve as promising biomarkers for GC.},
}

Humans
*Stomach Neoplasms/blood/microbiology/diagnosis
*Extracellular Vesicles/genetics/microbiology
*Biomarkers, Tumor/blood/genetics
Male
*DNA, Bacterial/genetics/blood
Middle Aged
Female
RNA, Ribosomal, 16S/genetics
Prognosis
Aged
Adult
Case-Control Studies
Tumor Microenvironment/immunology

@article {pmid41136439,
year = {2025},
author = {Xue, W and Liu, Z and Zhang, Y and Raza, W and Li, Y and Jiang, L and Tao, Y and Qian, J and Alexandre, J and Zhao, FJ and Xu, Y and Sedlazeck, F and Shen, Q and Jiang, G and Wei, Z},
title = {LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9353},
pmid = {41136439},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; Humans ; Cluster Analysis ; Gastrointestinal Microbiome/genetics ; *Software ; Algorithms ; },
abstract = {Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially designed to reconstruct MAGs in natural microbiomes. LorBin deploys a two-stage multiscale adaptive DBSCAN and BIRCH clustering with evaluation decision models using single-copy genes to maximize MAG recovery. LorBin outperforms six competing binners in both simulated and real microbiomes, including oral, gut, and marine samples. LorBin generated 15-189% more high-quality MAGs with high serendipity and identified 2.4-17 times more novel taxa than state-of-the-art binning methods. Together, LorBin is a promising long-read metagenomic binner for accessing species-rich samples containing unknown taxa and is efficient at retrieving more complete genomes from imbalanced natural microbiomes.},
}

*Metagenome/genetics
*Metagenomics/methods
*Microbiota/genetics
Humans
Cluster Analysis
Gastrointestinal Microbiome/genetics
*Software
Algorithms

@article {pmid41136135,
year = {2026},
author = {Du, R and Li, X and Xu, Y and Jing, K and Ao, L and Deng, B and Xu, Q and Song, P and Yu, J},
title = {Metagenomics reveals potential antimicrobial peptides in Chinese baijiu fermentation.},
journal = {Food microbiology},
volume = {134},
number = {},
pages = {104918},
doi = {10.1016/j.fm.2025.104918},
pmid = {41136135},
issn = {1095-9998},
mesh = {Humans ; Fermentation ; Metagenomics ; *Antimicrobial Peptides/pharmacology/chemistry/metabolism ; Bacteria/genetics/drug effects/metabolism/classification/isolation & purification ; Molecular Docking Simulation ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; *Fermented Foods/microbiology ; Escherichia coli/drug effects ; A549 Cells ; China ; Hep G2 Cells ; Food Microbiology ; },
abstract = {Antimicrobial peptides (AMPs) from food fermentation microbiota hold promise for food preservation and as potential antimicrobial agents. However, the biosynthetic potential of AMPs in food fermentations remains largely unclear. Here, using Chinese baijiu fermentation as a model, we provided a workflow for AMP mining by combining metagenomics and machine learning. We recovered 389 metagenome-assembled genomes (MAGs) spanning both bacteria and archaea from 18 fermented samples. In total, 414 AMPs, including 290 novel AMPs, were predicted in 59.38 % of these MAGs using a machine learning model. Correlation network analysis showed that AMP-producing microorganisms potentially mediated negative microbial interactions. We selected ten AMPs for experimental validation, and eight AMPs exhibited antimicrobial activity against five human pathogens and two food spoilage microorganisms. One peptide, AMP_22, showed a broad-spectrum activity (all seven test strains) with high potency (MIC = 3.06-200 μg/mL) and cytotoxicity was not observed below 25 μg/mL using HepG2 and A549 cell lines. We further investigated the antimicrobial mechanism of AMP_22 using Escherichia coli as a model. Treatment with AMP_22 caused severe damage to the bacterial cell membrane, inhibited intracellular protein synthesis, and led to a significant accumulation of reactive oxygen species (ROS). Furthermore, molecular docking analysis indicated that AMP_22 can bind to DNA gyrase and dihydrofolate reductase via hydrogen bonding. This study highlights the potential of food-derived AMPs for application as preservatives and antimicrobial agents.},
}

Humans
Fermentation
Metagenomics
*Antimicrobial Peptides/pharmacology/chemistry/metabolism
Bacteria/genetics/drug effects/metabolism/classification/isolation & purification
Molecular Docking Simulation
Microbial Sensitivity Tests
Anti-Bacterial Agents/pharmacology
*Fermented Foods/microbiology
Escherichia coli/drug effects
A549 Cells
China
Hep G2 Cells
Food Microbiology

@article {pmid41135804,
year = {2025},
author = {Dang, H and Zhang, Y and Zhang, L and Liu, Y},
title = {Transitional role of granular activated carbon for potentially promoting the expression of conductive pili and quorum sensing during anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133544},
doi = {10.1016/j.biortech.2025.133544},
pmid = {41135804},
issn = {1873-2976},
abstract = {Granular activated carbon (GAC) amendment mediated the microorganisms to significantly enhances methane production in anaerobic digestion. To elucidate the underlying microbial mechanisms, a genome-centric metagenomic analysis was conducted on DNA extracted from lab-scale anaerobic digesters treated with GAC. A total of 431 non-redundant metagenome-assembled genomes (MAGs) were recovered. Co-occurrence network analysis demonstrated that methanogens exhibit a distinct preference for associating with syntrophic partners that harboring potential pilA (e-pilA) producing conductive pili. Analysis revealed a potential temporal succession of key enhancement mechanisms: in the less developed community, QS facilitates biofilm formation and granulation, particularly for that of methanogens and MAGs with e-pilA. As the community became more developed, this QS-mediated influence weakens, concurrently e-pilA enrichment signifying established conductive pili connections. These connections optimize interspecies electron transfer for sustained methane yield enhancement. These results realved GAC sequentially promoting biofilm assembly via QS and optimizing electron flux for enhanced AD performance.},
}

@article {pmid41135729,
year = {2025},
author = {Li, M and Wang, H and Chu, H and Wang, Y and Lu, J},
title = {Deciphering Microbial Dynamics in Coastal Ecosystems Under Polycyclic Aromatic Hydrocarbon Stress: Community Assembly, Interaction Networks, and Metabolic Adaptations.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123179},
doi = {10.1016/j.envres.2025.123179},
pmid = {41135729},
issn = {1096-0953},
abstract = {The significant toxicity and carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) have raised increasing concern about their contamination, particularly in coastal regions with intensive human activities and urbanization. However, limited information exists on microbial response mechanisms across varying levels of PAHs contamination. In this study, sediment samples at 18 locations along the Yantai inland river and estuary were collected in October 2024 to examine the partitioning and spatial dispersal of PAHs, while microbial community assembly, interaction networks, and metabolic adaptations were analysed using metagenomics. Results showed that the average ∑PAHs concentration in the estuary (27.95 ± 2.91 ng/g) was significantly lower than that in the river (77.54 ± 43.39 ng/g), with a correspondingly higher ecological risk in the river. High-molecular-weight (HMW) PAHs dominated in both estuary and river sediments due to their high hydrophobicity and stability. Microbial community analysis revealed increased microbial diversity and a higher abundance of PAHs-degrading microbes (e.g., Ruegeria, known for degrading low-molecular-weight PAHs) under higher PAHs contamination. Co-occurrence network and topological analyses demonstrated dual regulatory effects of PAHs stress on microbial interactions, where elevated PAHs contamination intensified interspecies connectivity while simultaneously inducing destabilizing negative covariance patterns that weakened microbial network integrity. Additionally, neutral community model analysis indicated that stochastic processes dominated community assembly, with higher proportions of stochasticity observed in rivers under high PAHs stress. Notably, elevated PAHs concentrations significantly impaired energy metabolism and nitrogen metabolic pathways (p < 0.05), suggesting altered nitrogen biogeochemistry under PAHs contamination. This study advances the understanding of microbial population responses to different PAHs contamination levels in coastal regions.},
}

@article {pmid41135463,
year = {2025},
author = {Zhang, A and Pan, P and Zhou, NY and Li, T},
title = {Synergistic mineralization of the UV filter benzophenone-3 by a cross-feeding consortium from wastewater treatment plants: Insights into novel pathway and bioremediation strategy.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140176},
doi = {10.1016/j.jhazmat.2025.140176},
pmid = {41135463},
issn = {1873-3336},
abstract = {Benzophenone-3 (BP-3), used as an organic UV filter in diverse consumer products including cosmetics, has been frequently detected in wastewater treatment plants (WWTPs) and aquatic environments. BP-3 and its transformation products are regarded as emerging micropollutants due to their low biodegradability. Here, we investigate the synergistic degradation of BP-3 by a bacterial consortium seeded from aerobic sludge WWTPs. BP-3 is found to be initially degraded through a novel pathway involving a C-C bond cleavage step, producing intermediates 3-methoxyphenol (3MOP) and benzoate, two naturally occurring compounds which can be readily degraded in the environment. Metagenome-guided pure culture isolation and pathway analysis reveal that bacterial strains from genera Pigmentiphaga and Brucella synergistically contribute to the BP-3 mineralization. Specifically, the Pigmentiphaga strain degrades BP-3 into benzoate and 3MOP, with the former being utilized by itself and the latter utilized by the Brucella strain. A reconstructed consortium, consisting of two isolated strains from Pigmentiphaga and Brucella, exhibits similar degradation performance to that of the natural consortium, indicating their crucial roles in environmental BP-3 degradation. These findings provide new insights into BP-3 biodegradation at the microbial community level, offering potential strategies for wastewater treatment applications by manipulating synthetic microbial consortia.},
}

@article {pmid41135184,
year = {2025},
author = {Meng, J and Yang, C and Jing, M and Huang, J and Wang, W and Li, X and Zhao, P},
title = {Metagenomic sequencing of bronchoalveolar lavage fluid in pediatric pneumonia: A single-center study in Gansu province.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117153},
doi = {10.1016/j.diagmicrobio.2025.117153},
pmid = {41135184},
issn = {1879-0070},
abstract = {BACKGROUND: Pneumonia is one of the important causes of death in children. Conventional detection methods such as bacterial culture and polymerase chain reaction (PCR) are very limited for the detection of pathogens. Metagenomic next generation sequencing (mNGS) has shown strong coverage in nucleic acid detection, but its research in lower respiratory tract samples of children with pneumonia is still quite limited, especially in northwest China.

AIM: To characterize the pathogenic microbial spectrum in bronchoalveolar lavage fluid (BALF) of pediatric pneumonia patients in Gansu Province, China, using mNGS, and to demonstrate the advantages of mNGS in pediatric pneumonia diagnostics.

METHODS: A total of 128 pediatric pneumonia patients admitted to Gansu Provincial Maternal and Child Health Hospital (Gansu Central Hospital) between March 1, 2023 and February 5, 2025 were enrolled. BALF data, including bacterial culture, Polymerase chain reaction (PCR), and mNGS results, were collected from each patient for comprehensive analysis.

RESULTS: A total of 128 patients were enrolled in this retrospective study. Out of all patients, 68(53 %) were male and the median age was 3 years. A total of 31 patients had underlying diseases. mNGS demonstrated a significantly higher pathogen detection rate compared to conventional testing. Through mNGS analysis, viruses were identified as the predominant pathogenic microorganisms in children with pneumonia, and the most common infection pattern was a combination of viral and bacterial infections. Additionally, mNGS detected three types of difficult-to-culture bacteria, namely Tropheryma whipplei, Legionella pneumophila, and Mycobacterium tuberculosis complex, in the BALF from pediatric pneumonia patients in this study.

CONCLUSIONS: mNGS has shown obvious advantages in the detection of pathogenic microorganisms in children with pneumonia. Its universality helps to identify the pathogen as soon as possible and make up for the shortcomings of conventional testing, which is particularly important for the accurate treatment of patients with unclear infection or no obvious curative effect.},
}

@article {pmid41134432,
year = {2025},
author = {Kumar, A and Kumar, T and Batra, K and Dhania, NK and Jangir, BL and Budania, S and Maan, S},
title = {Detection, isolation, and complete genome sequencing of pigeon torque teno virus in Indian racing pigeons with pock-like lesions.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {41134432},
issn = {1572-994X},
support = {State scheme//LUVAS, Hisar/ ; },
abstract = {This study investigates the potential pathogens associated with joint swelling, yellow exudates, and scab formation near the joints and eyelids in adult white racing pigeons.Pooled samples of scab and swab were collected and subjected to molecular, microbiological, and histopathological analyses. Initial screening focused on the detection of poxvirus using polymerase chain reaction (PCR). Subsequently, next-generation sequencing (metagenomic sequencing) using the Illumina MiSeq platform was performed, followed by virus isolation in embryonated specific pathogen-free chicken eggs and Vero cells, along with histopathological examination.Polymerase chain reaction (PCR) analysis for pigeon pox virus did not produce the expected amplicons, indicating a negative result for this virus. However, metagenomic sequencing identified the complete genome of Pigeon Torque Teno Virus (PTTV), with a genome size of 1574 nucleotides. Comparative sequence analysis revealed a nucleotide sequence similarity of 96.47%-97.7%, with the highest identity to a Canadian PTTV genome previously detected in the Bursa of Fabricius of a dead pigeon. Genome annotation identified two open reading frames (ORFs): encoding replication-associated protein and viral capsid protein. The presence of PTTV was further confirmed through real-time PCR and virus isolation in embryonated SPF chicken eggs and Vero cell cultures.The present study marks the first identification of PTTV in white racing pigeons with joint, ocular, and pock-like lesions. Although pigeon pox virus (PPV) was not detected, the findings suggest that PTTV could be an emerging avian pathogen necessitating further investigation into its pathogenicity, transmission dynamics, and clinical significance in pigeons.},
}

@article {pmid41134295,
year = {2025},
author = {Muralidhar, M and Naseem, MN and Mesa, JRB and Omaleki, L and Turni, C},
title = {Optimization of DNA extraction methods from pig farm wastewater for pathogen detection using metagenomic sequencing.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001532},
pmid = {41134295},
issn = {2057-5858},
mesh = {Animals ; Swine ; *Wastewater/microbiology/virology ; *Metagenomics/methods ; Farms ; DNA, Bacterial/isolation & purification/genetics ; SARS-CoV-2/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Wastewater can be a useful sample to monitor disease outbreaks in the community, as it was demonstrated during the recent Severe acute respiratory syndrome coronavirus 2 pandemic. Due to housing conditions, diseases can rapidly spread within pig herds, resulting in high mortalities and significant economic losses. Monitoring piggery wastewater using Oxford Nanopore Technology's (ONT) sequencing platform combined with metagenomic analysis can provide early disease detection to deploy preventative measures. Nevertheless, obtaining DNA of the required purity and integrity from piggery wastewater is a major challenge. This study aims to identify and optimize the most effective method for obtaining high-quality and quantity DNA, which can be used in downstream applications for pathogen detection. Six DNA extraction protocols were tested on piggery wastewater samples and evaluated based on yield and overall DNA quality. The three best-performing methods, using commercially available kits (QIAGEN QIAamp® PowerFecal® Pro, QIAGEN DNeasy® PowerLyzer® PowerSoil® and Macherey-Nagel NucleoSpin® Soil), were then used to extract DNA from piggery wastewater samples spiked with a mock community composed of known pig pathogens. The extracted DNA samples were then sequenced on the ONT platform, and the effectiveness of the methods was evaluated using kraken2 taxonomic classifier and an in-house database. Results demonstrated that the optimized QIAGEN PowerFecal® Pro protocol was the most suitable and reliable extraction method. Overall, this study highlights the importance of determining the optimal DNA extraction method in effective disease surveillance using a complex environmental sample and takes an important step in making metagenomic disease surveillance a practical reality.},
}

Animals
Swine
*Wastewater/microbiology/virology
*Metagenomics/methods
Farms
DNA, Bacterial/isolation & purification/genetics
SARS-CoV-2/genetics
Sequence Analysis, DNA/methods

@article {pmid41133998,
year = {2025},
author = {Bağci, C and Negri, T and Atienza, EB and Gross, C and Ossowski, S and Ziemert, N},
title = {Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf135},
pmid = {41133998},
issn = {2047-217X},
abstract = {BACKGROUND: Soil ecosystems have long been recognised as hotspots of microbial diversity, but most estimates of their microbial and functional complexity remain speculative despite decades of study, in part because conventional sequencing campaigns lack the depth and contiguity required to recover low-abundance and repetitive genomes. Here, we revisit this question using one of the deepest metagenomic sequencing efforts to date, applying 148 billion base pairs of Nanopore long-read and 122 billion base pairs of Illumina short-read data to a single forest soil sample.

RESULTS: Our hybrid assembly reconstructed 837 metagenome-assembled genomes, including 466 that meet high- and medium-quality standards, nearly all lacking close relatives among cultivated taxa. Rarefaction and k-mer analyses reveal that, even at this depth, we capture only a fraction of the extant diversity: non-parametric models project that more than ten trillion base pairs of sequencing data would be required to approach saturation. These findings offer a quantitative, technology-enabled update to long-standing diversity estimates and demonstrate that conventional metagenomic sequencing efforts likely miss the majority of microbial and biosynthetic potential in soil. We further identify more than 11 000 biosynthetic gene clusters, over 99% of which have no match in current databases, underscoring the breadth of unexplored metabolic capacity.

CONCLUSIONS: Taken together, our results emphasise both the power and the present limitations of metagenomics in resolving natural microbial complexity, and they provide a new baseline for evaluating future advances in microbial genome recovery, taxonomic classification, and natural product discovery.},
}

@article {pmid41133101,
year = {2025},
author = {Li, Q and Zhou, D and Cao, L and Li, Y and Li, J and Ye, J and Chen, H and Zhao, J and Cao, S and Peng, Z},
title = {Profiling the composition of resistome and bacteriome in the upper respiratory tract of domestic cats with respiratory signs in China.},
journal = {Microbiome research reports},
volume = {4},
number = {3},
pages = {27},
pmid = {41133101},
issn = {2771-5965},
abstract = {Aim: Domestic cats, among the most popular pets globally, may harbor antimicrobial resistance genes (ARGs) and zoonotic pathogens that impact human health. This study aims to investigate the resistome and bacteriome composition in the upper respiratory tract of domestic cats with respiratory signs in China. Methods: We performed metagenomic sequencing on 1,454 oropharyngeal-nasal swabs from cats with respiratory signs across diverse living conditions in 22 Chinese provinces. Resistome and bacteriome profiles were analyzed using these sequencing data. Results: We characterized the resistome and bacteriome in the upper respiratory tract of cats, identifying a wide range of ARGs - including those conferring resistance to last-resort antibiotics {e.g., carbapenems (bla NDM, bla OXA-244, bla VIM-13, bla VIM-33), colistin (mcr), and high-level tigecycline [MIC ≥ 4 µg/mL; tet(X3), tet(X4), tet(X5), tet(X6)]}.
Additionally, we detected numerous bacterial species of public health concerns, including the six leading antimicrobial resistance-associated pathogens (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa) and other high-burden pathogens linked to global morbidity, mortality, and therapeutic challenges. Conclusion: The findings highlight the potential zoonotic risks posed by cats. Including monitoring of this companion species within the One Health approach to address public health concerns is necessary.},
}

@article {pmid41132634,
year = {2025},
author = {Liu, Y and Xia, F and Cai, W and Zhang, Y and Zhu, J and Shen, Z and Li, J and Yang, Q and Qu, Q and Chen, J},
title = {Blinatumomab Along With Combined Antifungal Agents for Refractory Adult Acute Lymphoblastic Leukemia With Invasive Aspergillosis: A Case Report.},
journal = {Clinical case reports},
volume = {13},
number = {10},
pages = {e71342},
pmid = {41132634},
issn = {2050-0904},
abstract = {There is an increased risk of invasive aspergillosis (IA) during the induction of acute lymphoblastic leukemia (ALL) because of the use of cytoreductive chemotherapy and high-dose steroids. This case demonstrates the utility of metagenomic next-generation sequencing and repeat sampling in clarifying complex infections and highlights blinatumomab as an effective antileukemic option when conventional chemotherapy is limited by active infection. Together, these strategies enabled the successful management of refractory ALL in a patient with pulmonary IA and fungal DNAemia.},
}

@article {pmid41132583,
year = {2025},
author = {Zou, Z and Lei, D and Wang, X and Yin, Y and Li, H and Di, X and Li, X},
title = {Crocin Ameliorates Cognitive Impairment and Pathological Changes in Alzheimer's Disease Model Mice by Regulating Gut Microbiota.},
journal = {Food science & nutrition},
volume = {13},
number = {10},
pages = {e71117},
pmid = {41132583},
issn = {2048-7177},
abstract = {Alzheimer's disease (AD), a primary cause of dementia, places a significant strain on both patients and society due to the absence of effective treatments. Recent research suggests that the gut microbiota may play a role in the development of AD. Crocin, a compound derived from traditional medicine, has demonstrated potential in alleviating neurological disorders and influencing gut microbiota, yet its specific mechanisms in AD remain unclear. In this study, we administered Crocin or saline to 5xFAD mice and wild-type controls. We discovered that Crocin treatment led to notable improvements in cognitive function, as measured by the Morris water maze test, reduced beta-amyloid (Aβ) accumulation, and decreased neuroinflammation, as indicated by reduced microglial and astrocyte activation. Metagenomic sequencing revealed a significant increase in the gut microbiota diversity, specifically the abundance of Firmicutes, Verrucomicrobiota, and Akkermansia. Additionally, Crocin enhanced intestinal barrier function by upregulating tight junction proteins and Secretory immunoglobulin A, while improving the structure of the jejunal mucosa. These results suggest that Crocin may alleviate cognitive deficits and neuropathological changes in 5xFAD mice, possibly through modulation of the gut microbiota and strengthening the gut barrier, presenting it as a promising therapeutic approach for AD.},
}

@article {pmid41132557,
year = {2025},
author = {Chen, J and Luo, Y and Hao, Y and Wang, Q and Wang, Q},
title = {Structural and functional characterization of gut microbiota in dyslipidemic patients from high-altitude Tibetan pastoral areas.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1676238},
pmid = {41132557},
issn = {2296-861X},
abstract = {INTRODUCTION: Approximately 49.3% of individuals living at high altitudes suffer from dyslipidemia. Emerging evidence indicates that gut microbiota can regulate lipid metabolism and cholesterol homeostasis, but the composition and function of gut microbiota in dyslipidemic patients from Tibetan pastoral regions remain unclear.

METHODS: To address this, we enrolled a cohort consisting of 22 dyslipidemic patients and 33 healthy controls (HCs) from the Gannan Tibetan pastoral region (average altitude: 3,600 m). Phenotypic data, blood, and fecal samples were collected from all the participants for a metagenome-wide association study based on shotgun metagenomic sequencing.

RESULTS: Compared with HCs, dyslipidemic patients showed a significant reduction in gut microbial diversity. Specifically, the abundance of beneficial species-including Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium bifidum, and Parabacteroides distasonis-was significantly decreased, while opportunistic pathogens such as Veillonella parvula, V. tobetsuensis, Streptococcus oralis, and Streptococcus mitis were notably enriched. Functional prediction revealed that pathways involved in glycolysis, starch degradation, and biosynthesis of L-methionine, L-arginine, L-lysine, L-citrulline, and L-threonine were significantly downregulated in dyslipidemic patients, whereas pathways for the biosynthesis of lipopolysaccharides, fatty acids, polyamines, and (Kdo)₂-lipid A were enriched. Correlation analysis showed that the enriched taxa in dyslipidemic patients were significantly positively associated with total cholesterol (TC), total triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C). In contrast, the enriched functional pathways were significantly negatively correlated with TC but positively correlated with high-density lipoprotein cholesterol (HDL-C).

DISCUSSION: These findings clarify the alterations in gut microbiota composition and function in plateau-dwelling dyslipidemic populations and their associations with blood lipid levels, suggesting potential microbial biomarkers for hyperlipidemia in plateau environments.},
}

@article {pmid41132537,
year = {2025},
author = {Liu, X and Wang, L and Huang, B and Jiao, Y and Guan, Y and Nuli, R},
title = {Barnesiella intestinihominis improves gut microbiota disruption and intestinal barrier integrity in mice with impaired glucose regulation.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1635579},
pmid = {41132537},
issn = {1663-9812},
abstract = {INTRODUCTION: Impaired glucose regulation (IGR) is a prediabetic state closely associated with gut microbiota dysbiosis. Our previous metagenomic analysis identified a significant deficiency of Barnesiella intestinihominis (B. intestinihominis) in IGR patients (p < 0.01). The present study was therefore designed to investigate the therapeutic potential of B. intestinihominis supplementation in a high-fat diet (HFD)-induced IGR mouse model and to explore its potential mechanisms of action.

METHODS: A mouse model of IGR was established by HFD. The treatment group received a daily supplementation of live B. intestinihominis (1×10[8] CFU) for 5 weeks. Gut microbiota composition was analyzed. Colonic expression levels of tight junction proteins (ZO-1 and occludin) and cytokines (IL-10, TNF-α, IL-6) were measured. In vitro experiments using Caco-2 human intestinal epithelial cells were conducted to assess the direct effects of B. intestinihominis. B. intestinihominis fermentation broth, heat-inactivated bacterial solution, and bacterial solution were co-cultured with Caco-2 cells. Cell viability was assessed using the CCK-8 assay, and the expression levels of tight junction proteins were evaluated. Trans-epithelial electrical resistance (TEER) and alkaline phosphatase activity were also assessed in the Caco-2 model.

RESULTS: Daily supplementation with B.intestinihominis significantly attenuated HFD-induced hyperglycemia in mice. It also modulated the gut microbiota, evidenced by an increased abundance of beneficial Ligilactobacillus and a reduction in pathogenic Lachnoclostridium. Furthermore, B. intestinihominis administration upregulated the expression of colonic tight junction proteins (ZO-1 and occludin) and the anti-inflammatory cytokine IL-10, while simultaneously inhibiting the pro-inflammatory mediators TNF-α and IL-6. In vitro, the fermentation broth of B.intestinihominis (10%) increased Caco-2 cell viability, and heat-inactivated bacteria (1×10[7] CFU) enhanced ZO-1 expression. However, neither treatment significantly affected trans-epithelial electrical resistance (TEER) nor alkaline phosphatase activity in Caco-2 cells.

DISCUSSION: These findings suggest that intestinal probiotics B. intestinihominis may ameliorate IGR by modulating the gut microbiota, enhancing intestinal barrier integrity, and attenuating inflammation, thus supporting their potential as a therapeutic intervention for metabolic disorders.},
}

@article {pmid41132377,
year = {2025},
author = {Han, Z and Jia, L and Zhu, R and Fu, H and Lin, C and Huang, H and Deng, L and Zhang, J and Zhao, L},
title = {The genetic and proliferation characterization analysis of novel coxsackievirus A12 in Beijing, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1665461},
pmid = {41132377},
issn = {1664-302X},
abstract = {INTRODUCTION: Coxsackievirus A12 (CVA12) is a serotype of Enterovirus A. Its evolutionary and molecular characteristics remain poorly understood.

METHODS: The metagenomic Next-Generation Sequencing (mNGS) strategy were used to investigate the viral diversity. The viral isolation, proliferation assays, phylogenetic relationships and recombination events were analyzed.

RESULTS: In this study, nine clinical specimens collected in Beijing, China, during March 2010 to October 2019 were identified as CVA12 positive, among which five were confirmed by mNGS. Then five CVA12 strains were isolated, and the proliferation assays demonstrated the preferential replication of CVA12 in rhabdomyosarcoma (RD) cells, with rapid intracellular replication before being released extracellularly, over Hep-2 cells. Transcriptomic profiling of infected RD cells revealed that the significant up-regulated genes were involved in inflammatory responses and transcriptional regulation (e.g., JUN, FOS), suggesting robust host immune activation. Phylogenetic analysis identified that four strains were clustered into genogroup E, indicating a lineage undergoing active transmission in Beijing, China, the other one into genogroups B. Recombination analysis revealed that strain s7275 exhibited recombination with CVA5 (strain 3,490, GenBank access number OK334538) at the breakpoint position 3,373-6,634, while the others showed recombination with EV-A71 (strain EV71/P1034/2013/China, GenBank access number KP289419) at breakpoint position 3,370-6,645.

DISCUSSION: These findings underscored the genetic diversity and recombination dynamics which provided insights into the evolutionary implications of CVA12, and its proliferation features in RD cells of CVA12. Further research is needed to elucidate the functional mechanisms of CVA12 infection and its role for disease.},
}

@article {pmid41132089,
year = {2025},
author = {Zhao, Y and Wang, H and Lin, W and Wang, H and Cao, LL},
title = {Gut microbiota and bile acids changes in MASLD mice model with hepatic PLD1 knockout.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2025183},
pmid = {41132089},
issn = {1745-7270},
abstract = {Hepatocyte phospholipase D1 (PLD1) knockout alleviates metabolic dysfunction-associated steatotic liver disease (MASLD) in mice, but the underlying mechanism is largely unknown. In this study, the mice were divided into four groups: Con (wild-type mice with normal control diet), HFHC (wild-type mice with high-fat diet), Con_KO (hepatocyte PLD1-knockout mice with normal control diet), and HFHC_KO (hepatocyte PLD1-knockout mice with high-fat diet). Intestinal contents of mice are analyzed via metagenomics and metabolomics, and the liver bile acids are assessed by mass spectrometry imaging. The results show that at the phylum level the abundance of Bacillota in the intestines of MASLD model mice is significantly increased, whereas that of Bacteroidota significantly is decreased. However, after the deletion of hepatocyte PLD1, Pseudomonadota and Candidatus Bathyarchaeota are significantly decreased in the MASLD model mice. At the species level, compared with that in the Con group, the abundance of Faecalibaculum rodentium is significantly increased in the HFHC group, whereas hepatocyte PLD1 knockout causes the abundances of Desulfovibrionaceae bacterium LT0009 and Lachnospiraceae bacterium 10-1 to be significantly decreased. In terms of intestinal bile acids, the levels of two bile acids (hyodeoxycholic acid and glycolithocholic acid) differ between the HFHC_KO group and the HFHC group. Association analysis shows that Faecalibaculum co-occurs with DCA, βMCA, ΩMCA and αMCA, while probiotic Bacteroides uniformis is significantly correlated with UDCA, 12-KetoLCA, and 7-KetoLCA. Finally, mass spectrometry imaging reveals that the TCA and TDCA contents in the liver are significantly decreased after PLD1 knockout in hepatocytes. These findings demonstrate that hepatocyte PLD1 knockout alters the gut microbiota and bile acids profiles, suggesting that PLD1 deficiency may modulate MASLD progression by changing intestinal microbiota-bile acid homeostasis.},
}

@article {pmid41131686,
year = {2025},
author = {Ramchandar, N and Farnaes, L and Coufal, N},
title = {Host Transcriptomic Analysis of Operative Samples From Children With Suspected Osteoarticular Infections.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004969},
pmid = {41131686},
issn = {1532-0987},
}

@article {pmid41131658,
year = {2025},
author = {Li, Z and Luo, W and Xie, H and Mo, C and Qin, B and Zhao, Y and Chen, X and Zhang, S and Zhao, Y and Wang, M and Yang, Y and Cai, J and Wang, B and Liu, X and Shi, Y},
title = {Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {214},
pmid = {41131658},
issn = {2049-2618},
mesh = {*Oryza/virology/microbiology ; *Rhizosphere ; *Reoviridae/physiology/pathogenicity ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Metagenomics/methods ; *Plant Diseases/virology/microbiology ; Metabolomics/methods ; },
abstract = {BACKGROUND: Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus in the Reoviridae family, has caused severe yield losses in rice due to its rapid transmission. However, its specific effects on rhizosphere microbiota and the dynamics of microbial community changes have not been fully elucidated.

RESULTS: By leveraging metabolomics with amplicon and metagenomics, this study provided a comprehensive understanding of the effect of SRBSDV infection on the rhizosphere microbial community and their functions. The results revealed that SRBSDV invasion led to significant changes in rhizosphere metabolites and microbial assembly processes. Specifically, the estimated overdispersion of cations sharply decreased following viral infection, while anion levels decreased markedly during early infection and then increased rapidly after 15 days. Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance but also showed strong involvement in the microbial assembly processes. These key microbes were closely linked to specific metabolites and organized into two distinct network modules. Both modules predominantly recruited beneficial microbes, but one module also actively excluded potentially harmful taxa (e.g., Salmonella), which could disrupt community stability. Further experiments with exogenous metabolites confirmed the vital role of quercetin in attracting beneficial microbes while repelling harmful ones.

CONCLUSION: The findings indicate that arboviruses can strongly influence the belowground rhizosphere microbial assembly processes by modulating metabolite profiles to selectively recruit or exclude key microbial species. These taxa, in turn, play fundamental roles in rhizosphere functions. These insights lay the groundwork for strategies to enhance rice immunity against viral infections by managing the rhizosphere microbial community. Video Abstract.},
}

*Oryza/virology/microbiology
*Rhizosphere
*Reoviridae/physiology/pathogenicity
Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
Metagenomics/methods
*Plant Diseases/virology/microbiology
Metabolomics/methods

@article {pmid41131656,
year = {2025},
author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S},
title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {215},
pmid = {41131656},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
mesh = {Animals ; Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; Animal Feed/analysis ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Gastrointestinal Microbiome ; *Inflammation ; *Goat Diseases/microbiology/metabolism ; Diet ; Female ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Fermentation ; Metagenome ; },
abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.

RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the β diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.

CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.},
}

Animals
Goats/microbiology
*Rumen/microbiology/metabolism
*Acidosis/veterinary/microbiology/metabolism
Animal Feed/analysis
*Tryptophan/metabolism
*Indoleacetic Acids/metabolism
*Gastrointestinal Microbiome
*Inflammation
*Goat Diseases/microbiology/metabolism
Diet
Female
Metagenomics
Bacteria/classification/genetics/metabolism/isolation & purification
Fermentation
Metagenome

@article {pmid41131583,
year = {2025},
author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y},
title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1162},
pmid = {41131583},
issn = {1479-5876},
support = {No. CCCF-QF-2022B04-4//the China Crohn's & Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; },
abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.

METHODS: A cohort of treatment-naïve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.

RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p = 0.02) compared to HC, which was restored after EEN treatment at remission status (p < 0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r = 0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-α, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).

CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.},
}

Humans
*Gastrointestinal Microbiome
Animals
Male
*Bile Acids and Salts/metabolism
*Inflammatory Bowel Diseases/microbiology
*Ruminococcus/physiology
*Intestinal Mucosa/pathology/microbiology
Child
Colitis/pathology/microbiology
Mice
Female
Mice, Inbred C57BL
Crohn Disease/microbiology
Adolescent

@article {pmid41131579,
year = {2025},
author = {Niemann, J and Huang, Y and Lanigan, LT and Willingham Grijalba, AL and Dunn, RR and Sikora, M and Schroeder, H},
title = {ParaRef: a decontaminated reference database for parasite detection in ancient and modern metagenomic datasets.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {365},
pmid = {41131579},
issn = {1474-760X},
support = {101045643//HORIZON EUROPE European Research Council/ ; },
mesh = {*Metagenomics/methods ; *Parasites/genetics ; *Databases, Genetic ; DNA Contamination ; Animals ; Humans ; },
abstract = {Shotgun metagenomics holds great potential for identifying parasite DNA in biological samples, but its effectiveness is limited by widespread contamination in publicly available reference genomes, which hinders accurate detection. In this study, we systematically quantify and remove contamination from 831 published endoparasite genomes to create ParaRef, a curated reference database for species-level parasite detection. We show that decontamination significantly reduces false detection rates and improves overall detection accuracy. Our study highlights the pervasive issue of contamination in public databases and offers a resource that will enhance the reliability of parasite detection using metagenomics.},
}

*Metagenomics/methods
*Parasites/genetics
*Databases, Genetic
DNA Contamination
Animals
Humans

@article {pmid41131543,
year = {2025},
author = {Lin, P and Xu, Y and Sun, Z and Li, J and Ban, Y and Zhang, M and Wang, Y and Zhang, C},
title = {Investigating the relationship between intestinal microbiota and Th1/Th2/Th17 imbalance in subclinical hypothyroidism during the first half of pregnancy: a multi-omics approach.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {83},
pmid = {41131543},
issn = {1757-4749},
abstract = {BACKGROUND: Gestational subclinical hypothyroidism (SCH), marked by elevated Thyroid-stimulating hormone (TSH) with normal free thyroxine (FT4), links to adverse perinatal outcomes. During early pregnancy (< 20 weeks), maternal thyroid hormones are crucial for fetal neurodevelopment, with deficiencies risking irreversible deficits. SCH pregnancies show gut microbiota alterations and metabolic dysregulation. Emerging evidence suggests these changes may drive Th(helper T cells)1/Th2/Th17 immune imbalance, though mechanisms remain unclear. This study combines metagenomics and lipidomics to investigate gut microbiota-Th1/Th2/Th17 interactions in patients with SCH in the first 20 weeks during pregnancy.

METHODS: This study included 20 pregnant women with SCH (SCH group) in the first half of pregnancy (≤ 20 gestational weeks) and 20 normal pregnant women (CON group) in the same period. Collect fecal and blood samples from both groups. Metagenomic sequencing was used to determine the differences in the composition of the intestinal microbiota between the two groups, and non-targeted lipidomics was used to compare the lipid differences between the two groups. Flow cytometry was used to assess Th1, Th2 and Th17 cells in peripheral blood, and a cell microbead array was used to determine cytokine levels.

RESULTS: (1) Metagenomic sequencing showed an increased abundance of Faecalibacterium prausnitzii and a decreased abundance of Bacteroides uniformis in the SCH group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant enrichment in lipid and polysaccharide biosynthesis and mucopolysaccharide biodegradation pathways in the SCH group. (2) Lipidomics identified 692 different lipids, with Triglyceride (TG) being the most significant. KEGG pathway analysis revealed that TG was mainly concentrated in the Th1, Th2, and Th17 cell differentiation pathways. (3) Additionally, serological indicators of the two groups showed that TSH, Interleukin (IL)-2,IL-10, Tumor necrosis factor (TNF)-α, TG, Th1, and Th17 in the SCH group were higher than those in the CON group, while Th2 was significantly lower (P < 0.05).

CONCLUSION: In the first half of pregnancy, patients with SCH may experience intestinal microbiota disorder, characterized by increased levels of Faecalibacterium prausnitzii and decreased levels of Bacteroides uniformis, at the same time, it was accompanied by an increase in TG synthesis and a Th1/Th2/Th17 imbalance, these factors may be involved in the occurrence of SCH during pregnancy.},
}

@article {pmid41131518,
year = {2025},
author = {Zhang, Y and Zhang, Q and Wang, L and Hu, Y},
title = {The value of second-generation gene sequencing in lung cancer immunotherapy with concurrent infections.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {1636},
pmid = {41131518},
issn = {1471-2407},
support = {023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; 023YZ09//Medical and Health Talent Training Program/ ; },
}

@article {pmid41052877,
year = {2025},
author = {Tran, LN and Castellano, D and Gutenkunst, RN},
title = {Interpreting Supervised Machine Learning Inferences in Population Genomics Using Haplotype Matrix Permutations.},
journal = {Molecular biology and evolution},
volume = {42},
number = {10},
pages = {},
pmid = {41052877},
issn = {1537-1719},
support = {R01GM127348/GM/NIGMS NIH HHS/United States ; R35GM149235/GM/NIGMS NIH HHS/United States ; },
mesh = {*Haplotypes ; *Supervised Machine Learning ; *Genetics, Population/methods ; *Metagenomics/methods ; Linkage Disequilibrium ; Gene Frequency ; Humans ; Neural Networks, Computer ; },
abstract = {Supervised machine learning methods, such as convolutional neural networks (CNNs), that use haplotype matrices as input data have become powerful tools for population genomics inference. However, these methods often lack interpretability, making it difficult to understand which population genetics features drive their predictions-a critical limitation for method development and biological interpretation. Here, we introduce a systematic permutation approach that progressively disrupts population genetics features within input test haplotype matrices, including linkage disequilibrium, haplotype structure, and allele frequencies. By measuring performance degradation after each permutation, the importance of each feature can be assessed. We applied our approach to three published CNNs for positive selection and demographic history inference. We found that the positive selection inference CNN ImaGene critically depends on haplotype structure and linkage disequilibrium patterns, while the demographic inference CNN relies primarily on allele frequency information. Surprisingly, another positive selection inference CNN, disc-pg-gan, achieved high accuracy using only simple allele count information, suggesting its training regime may not adequately challenge the model to learn complex population genetic signatures. Our approach provides a straightforward, model-agnostic, and biologically-motivated framework for interpreting any haplotype matrix-based method, offering insights that can guide both method development and application in population genomics.},
}

*Haplotypes
*Supervised Machine Learning
*Genetics, Population/methods
*Metagenomics/methods
Linkage Disequilibrium
Gene Frequency
Humans
Neural Networks, Computer

@article {pmid40755398,
year = {2025},
author = {Johnson, BJ and Graham, MC and Panahi, E and Vieira, CJSP and Nath, NS and Mason, P and Gleadhill, J and Thomas, D and Onn, MB and Shivas, MA and Shearman, D and Darbro, JM and Devine, GJ},
title = {An All-in-One Metabarcoding Approach to Mosquito and Arbovirus Xenosurveillance.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70022},
doi = {10.1111/1755-0998.70022},
pmid = {40755398},
issn = {1755-0998},
support = {//Mosquito and Arbovirus Research Committee Inc./ ; },
mesh = {Animals ; *Arboviruses/genetics/isolation & purification/classification ; *Culicidae/virology/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; *Mosquito Vectors/virology/classification ; High-Throughput Nucleotide Sequencing ; *Biosurveillance/methods ; *Metagenomics/methods ; Vertebrates/virology/classification ; Arbovirus Infections ; },
abstract = {Next-generation sequencing (NGS) has the potential to transform mosquito-borne disease surveillance but remains under-utilised. This study introduces a comprehensive multi-loci metabarcoding-based MX (molecular xenomonitoring) approach to mosquito and arbovirus surveillance, enabling parallel identification of mosquito vectors, circulating arboviruses, and vertebrate hosts from bulk mosquito collections. The feasibility of this approach was demonstrated through its application to a large set (n = 110) of bulk field collections. This set was complemented by a number (n = 28) of single-species mosquito pools that had previously been screened for viruses using quantitative reverse transcription PCR (RT-qPCR) and metatranscriptomics. Universal alphavirus and flavivirus primer sets were used to screen for arboviruses in the resulting metabarcoding library. Viral amplicons were then indexed and combined with mosquito-specific (ITS2), universal invertebrate (COI), and vertebrate (Cyt b) barcode amplicons prior to sequencing. This approach confirmed the presence of all previously identified mosquito species, as well as those commonly misidentified morphologically, and enabled a degree of quantification regarding their relative physical abundance in each collection. Additionally, the developed approach identified a diverse vertebrate host community (18 species), demonstrating its potential for defining host preferences and, in tandem with the viral screens and associated vector data, understanding disease transmission pathways. Importantly, metabarcoding detected a diversity of regionally prevalent arboviruses and insect-specific viruses, with all three viral diagnostics demonstrating a similar sensitivity and specificity in detecting Ross River virus and Barmah Forest virus, Australia's most common arboviruses. In summary, multi-loci metabarcoding is an affordable and efficient MX tool that enables complete mosquito-borne disease surveillance.},
}

Animals
*Arboviruses/genetics/isolation & purification/classification
*Culicidae/virology/classification/genetics
*DNA Barcoding, Taxonomic/methods
*Mosquito Vectors/virology/classification
High-Throughput Nucleotide Sequencing
*Biosurveillance/methods
*Metagenomics/methods
Vertebrates/virology/classification
Arbovirus Infections

@article {pmid40755083,
year = {2025},
author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H},
title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70023},
doi = {10.1111/1755-0998.70023},
pmid = {40755083},
issn = {1755-0998},
support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; },
mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; },
abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).},
}

*DNA, Environmental/genetics
*DNA Barcoding, Taxonomic/methods
*Computational Biology/methods
*Genetic Variation
*Metagenomics/methods
*Software
Sequence Analysis, DNA/methods

@article {pmid41131465,
year = {2025},
author = {Hamdene, I and Bez, C and Bertani, I and López-Menchero, JR and Yahyaoui, A and Venturi, V and Sadfi-Zouaoui, N},
title = {Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {683},
pmid = {41131465},
issn = {1471-2180},
abstract = {In the arid regions of southern Tunisia, soil and irrigation water salinity represent major challenges to agricultural sustainability. Despite the increasing interest in plant-associated microbes, the role of endophytic bacteria in conferring salt tolerance remains largely unexplored in this context. To address this gap, twenty-two halophytic plants and their associated soils were sampled from five distinct sites across the Kebili and Gabes governorates. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter, Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas, and Streptomyces formed the common core microbiome. Functional predictions of endophytic bacteria in halophytes highlighted multiple KEGG functional pathways, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic bacteria.},
}

@article {pmid41131367,
year = {2025},
author = {Welsh, C and Cabotaje, PR and Marcelino, VR and Watts, TD and Kountz, DJ and Jespersen, M and Gould, JA and Doan, NQ and Lingford, JP and Koralegedara, T and Solari, J and D'Adamo, GL and Huang, P and Bong, N and Gulliver, EL and Young, RB and Land, H and Walter, K and Cann, I and Pereira, GV and Martens, EC and Wolf, PG and Ridlon, JM and Gaskins, HR and Giles, EM and Lyras, D and Lappan, R and Berggren, G and Forster, SC and Greening, C},
title = {A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41131367},
issn = {2058-5276},
support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE220100965//Department of Education and Training | Australian Research Council (ARC)/ ; FL210100258//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; NNF21OC0066716//Novo Nordisk/ ; "STEM" 48574-1//Energimyndigheten (Swedish Energy Agency)/ ; },
abstract = {Disruption of hydrogen (H2) cycling in the gut is linked to gastrointestinal disorders, infections and cancers. However, the mechanisms and microorganisms controlling H2 production in the gut remain unresolved. Here we show that gut H2 production is primarily driven by the microbial group B [FeFe]-hydrogenase. Metagenomics and metatranscriptomics of stool and tissue biopsy samples show that hydrogenase-encoding genes are widely present and transcribed in gut bacteria. Assessment of 19 taxonomically diverse gut isolates revealed that the group B [FeFe]-hydrogenases produce large amounts of H2 gas and support fermentative growth of Bacteroidetes and Firmicutes. Further biochemical and spectroscopic characterization of purified enzymes show that they are catalytically active, bind a di-iron active site and reoxidize ferredoxin derived from the pyruvate:ferredoxin oxidoreductase reaction. Group B hydrogenase-encoding genes are significantly depleted in favour of other fermentative hydrogenases in patients with Crohn's disease. Finally, metabolically flexible respiratory bacteria may be the dominant hydrogenotrophs in the gut, rather than acetogens, methanogens and sulfate reducers. These results uncover the enzymes and microorganisms controlling H2 cycling in the healthy human gut.},
}

@article {pmid41131151,
year = {2025},
author = {Buffington, JD and Kuo, HC and Hu, K and Chang, YC and Javanmardi, K and Voigt, B and Li, YR and Little, ME and Devanathan, SK and Xhemalçe, B and Gray, RS and Finkelstein, IJ},
title = {Discovery and engineering of retrons for precise genome editing.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41131151},
issn = {1546-1696},
support = {F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; F-1808//Welch Foundation/ ; },
abstract = {Retrons can produce multicopy single-stranded DNA in cells through self-primed reverse transcription. However, their potential for inserting genetic cargos in eukaryotes remains largely unexplored. Here we report the discovery and engineering of highly efficient retron-based gene editors for mammalian cells and vertebrates. Through bioinformatic analysis of metagenomic data and functional screening, we identify retron reverse transcriptases that are highly active in mammalian cells. Rational design further improves the editing efficiency to levels comparable with conventional single-stranded oligodeoxynucleotide donors but from a genetically encoded cassette. Retron editors exhibit robust activity with Cas12a nuclease and Cas9 nickase, expanding the genomic target scope and bypassing the need for a DNA double-stranded break. Using a rationally engineered retron editor, we incorporate a split GFP epitope tag for live-cell imaging. Lastly, we develop an all-RNA delivery strategy to enable DNA-free gene editing in cells and vertebrate embryos. This work establishes retron editors as a versatile and efficient tool for precise gene editing.},
}

@article {pmid41131078,
year = {2025},
author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B},
title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37098},
pmid = {41131078},
issn = {2045-2322},
support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; },
mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention & control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; },
abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.},
}

*Bacillus/physiology
*Glycine max/microbiology/metabolism/immunology
*Plant Roots/microbiology/metabolism
*Botrytis/pathogenicity
*Microbiota
*Plant Diseases/microbiology/prevention & control
Rhizosphere
*Disease Resistance
Soil Microbiology

@article {pmid41130610,
year = {2025},
author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K},
title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.},
journal = {BMJ open respiratory research},
volume = {12},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003456},
pmid = {41130610},
issn = {2052-4439},
mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; },
abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.

METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.

RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.

CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.

PROSPERO REGISTRATION NUMBER: CRD42023436934.},
}

Humans
*Trachea/microbiology
*Microbiota
*Bronchoalveolar Lavage Fluid/microbiology
*Bronchoalveolar Lavage/methods
*Specimen Handling/methods

@article {pmid41130504,
year = {2025},
author = {Song, Y and Zhang, J and Shen, X and Yang, L and Jia, Y and Song, F and Huang, Y and Han, B and Zhang, N and Ma, G},
title = {Study on the association between microplastic exposure and gut microbiota based on metagenomics: A pilot study on 66 young college students in China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122995},
doi = {10.1016/j.envres.2025.122995},
pmid = {41130504},
issn = {1096-0953},
abstract = {OBJECTIVE: This study aimed to evaluate the types and mass concentrations of microplastics found in the stools of young college students. The underlying connections between microplastic exposure and gut microbiota were revealed.

METHODS: The study involved 66 participants, from whom stool samples were collected. Pyrolysis gas chromatography/mass spectrometry(Py-GCMS) was used to identify the types and mass concentrations of microplastics. Metagenomic sequencing was performed on the gut microbiota using high-throughput sequencing and metagenomic analysis techniques. Participants were divided into low group (LG) and high group (HG) based on the median mass concentration of microplastics in their stools. The differences in microbial diversity and species with significant differences between the two groups were analyzed. Spearman's correlation analysis was conducted to assess the associations between microbial characteristics and gene functions.

RESULTS: The detection rate of microplastics in the stool samples was 98.5%, with a median mass concentration of 54.7 μg/g. Significant differences were observed in gut microbiota between the two groups in terms of alpha and beta diversities. The relative abundance of Segatella copri was higher in the LG, while the relative abundance of Escherichia coli was higher in the HG. Compared with the LG, the gut microbiota in the HG exhibited an increase in the relative abundance of harmful bacteria, such as Dialister invisus, Clostridium fessum, and Evtepia gabavorous. The ADONIS analysis revealed that PS microplastics had a significant impact on the structure of the gut microbiota. However, no significant differences were observed among the metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes database between the two groups at either level I or II.

CONCLUSION: Participants with higher mass concentrations of microplastics in their stools exhibited an increase in the abundance of harmful intestinal bacteria. PS microplastics had the most profound impact on the gut microbiota structure.},
}

@article {pmid41130083,
year = {2025},
author = {Tripathy, B and Singh, S and Behera, ID and Mishra, S and Das, AP},
title = {Metagenomic profiling of diversified marine microbiome across microplastic-contaminated niches of Bay of Bengal, India.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118872},
doi = {10.1016/j.marpolbul.2025.118872},
pmid = {41130083},
issn = {1879-3363},
abstract = {Diverse microorganisms in the marine sediment share a significant section of the global marine ecosystem and play a dominant role in marine biogeochemistry. The present study is the first to report an evaluation of shotgun metagenomic sequencing of microplastic-contaminated marine water and sediment samples from the coastal shores of the Bay of Bengal, India, across a stretch of 25 km, which houses a plethora of ubiquitous and uncultured microbial biodiversity coexisting with multitudinous human interventions. Illumina Nova sequencing 6000 suggested the presence of 88,539 scaffolds of data containing 132,568 identified genes of marine microorganisms. Taxonomic identification with the assistance of curated global databases ensued in the presence of Proteobacteria (53.12 %), Bacteroidetes (7.13 %), Actinobacteria (5.87 %), and miscellaneous (33.86 %) in abundance. Azonexus hydrophillus, Mycobacteroides abscessus, and Acidaminobacter hydrogenoformans were identified in profusion from the sequenced samples of the study area. The adaptation, sustenance, and survivability in the presence of plastic pollutants confirm the presence of microplastic-degrading enzymes in the microorganisms. The functional annotations revealed 54.32 % and 58.34 % similarities in genes with KEGG and COG databases, revealing the heavy presence of inorganic and amino acid transport channels. Further metabolic profiling of the identified novel microorganisms will assist in engineering the enhancement of microbial enzymes, such as cutinases, lipases, and esterases, leading to microplastic degradation activity. The present research work signifies the analysis and documentation of native microbiota of the marine shores of the Bay of Bengal and their interactive potentialities with microplastic-contaminated anthropogenic environments.},
}

@article {pmid41130000,
year = {2025},
author = {Jin, G and Wang, M and Wang, X and Yuan, S and Peng, A and Chen, Z},
title = {Effects of sub-inhibitory antibiotic exposure on elemental cycling genes in an aquatic microbial community.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140201},
doi = {10.1016/j.jhazmat.2025.140201},
pmid = {41130000},
issn = {1873-3336},
abstract = {Understanding how low concentrations of antibiotics influence biogeochemical cycling mediated by aquatic microbes is essential for assessing the ecological risks of antibiotic pollution. Here we examined the responses of carbon, nitrogen, and sulfur cycling genes in an aquatic microbial community to trimethoprim, lincomycin, and their combined exposure across seven sub-inhibitory concentrations spanning three orders of magnitude. We found that while the diversity of elemental cycling genes remained largely unchanged, the abundance of associated metabolic pathways declined significantly under high antibiotic levels,particularly after seven days of exposure to 10 mg/L lincomycin or ≥ 1 mg/L trimethoprim-lincomycin combinations. Some elemental cycling genes increased in abundance under elevated antibiotic exposure, accompanied by concentration-dependent enrichment of antibiotic resistance genes (ARGs). Metagenomic assembly further revealed that enriched ARGs and cycling genes co-localized on the same contigs. In addition, antibiotic exposure reshaped the topological structure of molecular ecological networks among cycling genes, indicating altered microbial interactions and ecological processes. Together, these findings show that antibiotics not only enrich resistance determinants but also modulate the abundance of carbon, nitrogen, and sulfur cycling genes, underscoring the complex impacts of anthropogenic antibiotic pollution on microbially mediated biogeochemical cycles.},
}

@article {pmid41129998,
year = {2025},
author = {Hu, K and Wang, Z and Xu, Q and Chu, Y and Qian, Y and Zhang, X and Li, W and Han, Y and Wang, B and Zhang, H},
title = {Metagenomic insights into the effects of ecological water replenishment on resistome and pathogens in urban wetland.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140117},
doi = {10.1016/j.jhazmat.2025.140117},
pmid = {41129998},
issn = {1873-3336},
abstract = {Urban wetland restoration increasingly relies on water replenishment, yet its impacts on resistome dissemination remain critically understudied. Here, we performed a comprehensive metagenomic survey of water and sediment from the Xixi National Wetland Park to investigate how water diversion from the surrounding Qiantang River affects the distribution and composition of antibiotic-resistant genes (ARGs), mobile genetic elements (MGEs), virulence factors (VFs), and pathogens. Among the detected ARGs, multidrug, macrolide-lincosamide-streptogramin, and bacitracin resistance genes were predominant. MGEs such as tnpA, IS91, and istA, and VFs involved in adherence and immune modulation were also abundant. Pathogens including Fusobacterium varium and Leptospira noguchii were frequently observed. RDA and MRM analysis revealed certain antibiotics emerged as influent factors of resistome composition. Notably, the vast majority of resistome types were shared between the wetland park and the external riverine environment, with a decline in resistome richness as distance from the water diversion source increased. This phenomenon indicates that river-to-wetland water diversion acts as a conduit, facilitating the broad dissemination of resistome components and pathogens into the wetland, while the wetland's self-purification capacity also plays a role. Nevertheless, a small subset of ARGs and MGEs was significantly enriched within the wetland interior. Collectively, these results highlight the ecological risks of water replenishment in urban wetlands and underscores the need for mitigation strategies, such as source-water pretreatment and wetland sediment remediation.},
}

@article {pmid41129997,
year = {2025},
author = {Lu, W and Sun, S and Wang, Q and Wang, Z and Lu, YZ and Guo, J and Zhao, HP and Lai, CY},
title = {Acesulfame degradation within a methane-fed biofilm: a novel and efficient biodegradation route.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140152},
doi = {10.1016/j.jhazmat.2025.140152},
pmid = {41129997},
issn = {1873-3336},
abstract = {Acesulfame (ACE), a persistent organic pollutant, is frequently detected across diverse aquatic environments, yet its environmental remediation remains challenging due to the inherently slow biodegradation. Here, we unveil a highly efficient ACE removal strategy using a methane-fed biofilm, achieving a degradation rate of 59.6 mg ACE/g VSS/h. Comprehensive analyses of transformation products (TPs) and toxicity profiles revealed that the biofilm mediated important and effective biodegradation pathways, promoting deep ACE degradation. Microbial community analysis, methane interruption experiments and pure culture studies implicated aerobic methanotrophs Methylococcus sp. and Methylomonas sp. as key players in ACE degradation. Metagenomic and metatranscriptomic analyses demonstrated that these methanotrophs exhibited high expression levels of particulate methane monooxygenase (pMMO) and cytochrome P450 monooxygenase (CYP450) genes within the biofilm community. Enzyme inhibition assays, combined with TP profiling, suggested that pMMO and CYP450 initiated the degradation of ACE. Scavenging experiments further suggested that hydroxyl radicals (•OH) generated through the catalytic activity of pMMO and CYP450 are crucial mediators in the ACE hydroxylation pathway. These findings provide the first evidence of ACE degradation in a methane-fed biofilm system, offering a promising and sustainable approach for the removal of recalcitrant organic contaminants from wastewater.},
}

@article {pmid41128819,
year = {2025},
author = {Zhao, Y and Chen, J and Zhu, S and Xu, Y and Zhu, J and Yang, J and Zhou, W and Yang, Y and Lin, M and Chen, Q and Xia, M and Chen, Y and Liu, Y},
title = {Olsenella scatoligenes-derived Skatole Promotes Smooth Muscle Cell Proliferation and Migration to Aggravate Atherosclerosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf238},
pmid = {41128819},
issn = {1751-7370},
abstract = {Coronary artery disease remains the leading cause of mortality and morbidity globally. The gut microbiota has been implicated in the development of coronary artery disease through unclear mechanisms. Here, we demonstrate that the abundance and inter-species interactions of Olsenella scatoligenes are 4.7-fold and 1.6-fold higher in patients with coronary artery disease, respectively, and positively associated with disease severity. Furthermore, integrative metagenomic and metabolomic analyses identify skatole as the key microbial effector mediating the pro-atherogenic effect of Olsenella scatoligenes. Consistently, supplementation with Olsenella scatoligenes or skatole results in 1.26- and 1.23-fold increases in aortic plaque area, respectively, by promoting vascular smooth muscle cell proliferation and migration to the intima. Mechanistically, Olsenella scatoligenes -derived skatole facilitates nuclear translocation of the aryl hydrocarbon receptor, and enhances its binding to the promoter region of calponin 1. Silencing either aryl hydrocarbon receptor or calponin 1 attenuates approximately 40% of the vascular smooth muscle cell proliferation and migration induced by skatole. Collectively, our study identifies increased skatole production as the principal microbial effector linking Olsenella scatoligenes to aggravated atherosclerosis through activation of aryl hydrocarbon receptor -calponin 1 axis and underscores the therapeutic potential of targeting skatole production for the management of coronary artery disease.},
}

@article {pmid41128801,
year = {2025},
author = {Blomström, AL and Hansen, S and Riihimäki, M},
title = {Identification and whole-genome characterization of a novel equine papillomavirus.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {41128801},
issn = {1572-994X},
support = {H-20-47-555//The Swedish-Norwegian Foundation for Equine Research/ ; },
abstract = {Papillomaviruses (PVs) are small, non-enveloped viruses with double-stranded circular DNA genomes that infect a wide range of hosts, including mammals, birds, reptiles, and fish. While human papillomaviruses are extensively studied, recent advancements in high-throughput sequencing techniques have increased the detection and genetic characterization of PVs from various animal species. Here, we describe the identification and whole-genome characterization of a divergent equine papillomavirus (EcPV) detected through a viral metagenomic investigation of a horse in Denmark exhibiting neurological signs. Using Nanopore sequencing and Sanger sequencing, we assembled a complete viral genome of 7767 nucleotides. Phylogenetic analysis, based on concatenated E1, E2, L2, and L1 gene sequences, showed that the identified virus clustered within the same clade as EcPV3 (genus Dyoiotapapillomavirus) and EcPV6 (genus Dyorhopapillomavirus) but was situated on a distinct separate branch. Comparative genome analysis revealed approximately 52% nucleotide sequence similarity to EcPV3 and EcPV6, which share 66% similarity with each other. The L1 gene, commonly used for papillomavirus classification, exhibited a sequence identity to EcPV3 (58.4%) and EcPV6 (60.0%). The other viral genes displayed a 39-62% identity to the respective genes from EcPV3 and 6 further supporting the divergence of this newly identified PV. The combination of the phylogenetic analysis and the genetic divergence suggests that this newly identified papillomavirus may constitute a novel species or genus within the Papillomaviridae family. Our findings expand the known diversity of equine papillomaviruses and contribute valuable insights into their evolutionary relationships.},
}

@article {pmid41128541,
year = {2025},
author = {Liu, C and He, Y and Zhang, H and Zhang, D and Ai, C and Tang, X and Yang, Q and Yu, Z and Tan, S and Friman, V-P and Liao, H and Zhou, S},
title = {Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095625},
doi = {10.1128/msystems.00956-25},
pmid = {41128541},
issn = {2379-5077},
abstract = {UNLABELLED: Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management.

IMPORTANCE: Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.},
}

@article {pmid41128412,
year = {2025},
author = {Peng, L and Song, H and Shi, H and Wu, L and Ma, Y and Fan, X and Wu, M and Duan, L and Li, Z and Yuan, H},
title = {Oral Multi-Enzymatic Manganese-Carbon Dots Alleviate Sepsis-Associated Lung Injury via the Gut-Lung Axis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c10625},
pmid = {41128412},
issn = {1936-086X},
abstract = {Sepsis-induced pulmonary injury represents a life-threatening global health challenge due to poorly defined pathological mechanisms. The gut-lung axis has been proven to be widely involved in sepsis-induced lung injury, yet effective interventions targeting gut microbiota homeostasis remain unknown. Single-cell sequencing revealed increased alveolar apoptosis and impaired macrophage efferocytosis during sepsis pathogenesis. Thus, we designed oral manganese-doped carbon dots (Mn-CDs) to alleviate septic lung injury by remodeling gut microbiota homeostasis and targeting the gut-lung axis. Biochemical characterization demonstrated Mn-CDs possess multienzyme mimetic activities (SOD-, CAT-, POD-, GPx-like) and potent ROS scavenging capacity. In murine sepsis models, Mn-CDs significantly improved systemic indices and were associated with macrophage anti-inflammatory states with enhanced efferocytosis, as evidenced by transcriptomic profiling. Integrated metagenomic/metabolomic analyses identified Mn-CDs-mediated enrichment of g_Clostridium and g_Bacteroides, concomitant with elevated indole-3-propionic acid (IPA) production. Subsequent in vitro studies demonstrate that IPA likely binds primarily to the aryl hydrocarbon receptor (AHR), promoting both efferocytosis and anti-inflammatory polarization in macrophages, thereby mitigating septic lung injury. Notably, the fecal microbiota transplantation (FMT) from Mn-CDs-treated mice not only alleviated systemic symptoms but also effectively promoted efferocytic polarization of pulmonary macrophages in septic mice. Depletion of the gut microbiota resulted in a significant loss of the protective efficacy of Mn-CDs in a murine model of septic lung injury. Collectively, the gut-lung axis mediated by microbiota-derived IPA and macrophage efferocytosis contributes to the remediation of septic lung injury, highlighting the potential of Mn-CDs in microbiome-directed critical care.},
}

@article {pmid41127841,
year = {2025},
author = {Turner, Z and Drabovich, AP},
title = {Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {10},
pages = {1139-1153},
pmid = {41127841},
issn = {2833-8278},
abstract = {Detection and monitoring of pathogens is a central aspect of maintaining public health. Rare and neglected zoonotic viruses have the potential to evolve and expand exponentially, leading to unforeseen outbreaks, epidemics, and pandemics. The emerging multiomics and meta-omics techniques and workflows, such as proteogenomics and meta-genomics, offer the potential for the detection of harmful pathogens, as well as opportunities for the discovery of previously unknown bacterial, parasitic, or viral pathogens. Multiomics and meta-omics workflows provide molecular information for tracking pathogens and understanding the effectiveness of spread mitigation strategies. In addition to environmental monitoring, multiomics and meta-omics approaches have the potential for clinical applications and in-depth characterization of novel pathogens. In this review, we discuss recent applications of multiomics and meta-omics techniques, their advantages over traditional methods, and their potential implementations in biomedical research, environmental studies, and healthcare. We critically assess the benefits and challenges of multiomics and meta-omics studies and discuss their future perspectives.},
}

@article {pmid41127630,
year = {2025},
author = {Kamau, M and Ergunay, K and Bourke, BP and Mutura, J and Lebunge, R and Ochieng, G and Gathii, K and Waitumbi, J and Mutai, B and Hassell, J and von Fricken, ME and Zimmerman, D and Murray, S and Jiang, L and Liao, HM and Grieco, JP and McDermott, EG and Achee, NL and Linton, YM},
title = {Potential spillover investigated by metagenome sequencing in Laikipia, Kenya reveals tick-borne pathogens and a novel bunyavirus.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101226},
pmid = {41127630},
issn = {2352-7714},
abstract = {Tick-borne infections continue to present a global public health threat, and require a One Health approach for successful mitigation. We conducted cross-sectional tick screening utilizing an agnostic metagenomic screening strategy based on nanopore sequencing (NS), in an area spanning a range of habitats with intensified human-livestock-wildlife interactions in central Kenya. We further used targeted amplification by polymerase chain reaction (PCR) and sequence independent single primer amplification (SISPA) for confirmation and genome characterization, as necessary. We initially screened 44 ticks across pooled and individual samples belonging to seven species. Tick-associated bacteria-including spotted fever Rickettsia (13.3 %) and Coxiella-like endosymbionts, Francisella turcica and Francisella opportunistica, and tick-associated Borrelia-were detected in 86.6 % of samples. Viruses were detected in 93.3 % of samples, where Jingmen tick virus (JMTV) was observed as the most prevalent virus, detectable in 80 % of samples. A follow-up specific PCR confirmed JMTV virus detection in 75 %, associated with viral read abundance in NS. A complete JMTV genome was assembled from an Amblyomma sparsum tick, that displayed conserved motifs of putative structural and replication proteins. Maximum likelihood analyses placed the virus genome within a distinct clade in the proposed East African-Asian JMTV lineage. We further investigated a virus contig generated during the initial screening, with limited identities to Volzhskoe tick virus (VSTV). Subsequent NS and targeted PCR screening in an additional collection of 650 ticks from 11 species revealed a JMTV prevalence of 12.3 % in Amblyomma, Hyalomma and Rhipicephalus species. Follow-up NS and SISPA generated viral genomic segments, encoding a putative replicase and glycoprotein precursor. Pairwise comparisons and phylogeny indicated a novel virus-herein named as the Mpala tick virus-which is related to but distinct from VSTV and placed among unclassified members of Bunyaviricetes. In conclusion, our approach provides an effective strategy to detect a wide range of tick-borne bacteria and viruses, facilitating identification of opportunistic or endosymbiotic bacteria as well as novel viruses.},
}

@article {pmid41126918,
year = {2025},
author = {Li, W and Zhou, D and Ji, Y and Tian, H and Meng, N and Li, J and Guo, N and He, X and Dao, M and Jin, X},
title = {Exploring the molecular intersection for hypertension, hyperlipidemia and their comorbid conditions through multi-omics approaches.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1593688},
pmid = {41126918},
issn = {2297-055X},
abstract = {BACKGROUND: Hypertension and hyperlipidemia are interconnected conditions that heighten cardiovascular risk, yet their intricate multi-scale molecular signatures remain inadequately mapped. This study aimed to conduct an integrated multi-omics investigation to unravel the key pathways and biomarkers underlying hypertension, hyperlipidemia, and both conditions.

METHODS: Metabolomic analysis was performed on serum samples and metagenomic analysis on fecal samples collected from individuals with hypertension (n = 16), hyperlipidemia (n = 19), or both conditions concurrently (n = 20). In addition, 20 healthy individuals were recruited as controls.

RESULTS: Metabolomics uncovered altered levels of sphingolipids, phosphatidylcholines, glycylprolines, and nucleic acid metabolites, which may be associated with changes in vascular tone, lipid and protein homeostasis, and thyroid signaling. Metagenomics showed depletion in the abundance of the Fibrobacteres phylum. Altered abundances of Escherichia coli and Bacteroides vulgatus were also observed, which were correlated with deviations in lipid and carbohydrate metabolism. Sphingomyelin d18:1/16:0 and sphingomyelin d18:1/24:1(15Z) were the key metabolites that were identified as potential diagnostic biomarkers across conditions. Microbial taxa such as Enterococcus cecorum, Lachnospiraceae bacterium, Prevotella histicola, and Flavobacterium discriminated these diseases. Pathway analysis revealed glycoxylate, amino acid, purine, and sphingolipid metabolism alterations intersecting hypertension and hyperlipidemia.

CONCLUSIONS: This multi-omics landscape of comorbid disease pathways and biomarkers lays the foundation for precision diagnosis and treatment of prevalent cardiovascular conditions.},
}

@article {pmid41126179,
year = {2025},
author = {Heuberger, M and Wehrkamp, CM and Pfammatter, A and Poretti, M and Graf, JP and Herger, A and Isaksson, J and Schlagenhauf, E and Honegger, R and Wicker, T and Sotiropoulos, AG},
title = {A reference metagenome sequence of the lichen Cladonia rangiformis.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {319},
pmid = {41126179},
issn = {1741-7007},
support = {310030_212428//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Lichens/genetics/microbiology ; *Metagenome ; Symbiosis/genetics ; *Genome, Fungal ; *Ascomycota/genetics ; Chlorophyta/genetics ; },
abstract = {BACKGROUND: Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners, and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis, aiming to illuminate the genomic complexity and evolutionary interactions within lichen symbioses.

RESULTS: Using long-read sequences from an entire symbiotic complex, plus short-read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises ~ 22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. Analysis of gene content in fungus, algae, and bacteria identified 22 distinct biosynthetic gene cluster categories for known secondary metabolites.

CONCLUSIONS: Our findings revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria. This study provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.},
}

*Lichens/genetics/microbiology
*Metagenome
Symbiosis/genetics
*Genome, Fungal
*Ascomycota/genetics
Chlorophyta/genetics

@article {pmid41125958,
year = {2025},
author = {Fan, Y and Ni, M and Aggarwala, V and Mead, EA and Ksiezarek, M and Cao, L and Kamm, MA and Borody, TJ and Paramsothy, S and Kaakoush, NO and Grinspan, A and Faith, JJ and Fang, G},
title = {Long-read metagenomics for strain tracking after faecal microbiota transplant.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41125958},
issn = {2058-5276},
support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; },
abstract = {Accurate tracking of bacterial strains that stably engraft in faecal microbiota transplant (FMT) recipients is critical for understanding the determinants of strain engraftment, evaluating correlations with clinical outcomes and guiding the development of therapeutic consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. Here we describe LongTrack, a method that uses long-read metagenomic assemblies for FMT strain tracking. LongTrack shows higher precision and specificity than short-read approaches, especially when multiple strains co-exist in the same sample. We uncovered 648 engrafted strains across six FMT cases involving patients with recurrent Clostridioides difficile infection and inflammatory bowel disease. Furthermore, long reads enabled assessment of the genomic and epigenomic stability of engrafted strains at the 5-year follow-up timepoint, revealing structural variations that may be associated with strain adaptation in a new host environment. Our findings support the use of long-read metagenomics to track microbial strains and their adaptations.},
}

@article {pmid41125530,
year = {2025},
author = {Wang, X and Zhang, P and Suo, JS and Li, QJ and Wang, LZ and Zhang, Y and Wang, ZL},
title = {Clinical and microbiological insights into endogenous endophthalmitis: A ten-year study highlighting mNGS efficacy.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2025.10.002},
pmid = {41125530},
issn = {1995-9133},
abstract = {BACKGROUND: Endophthalmitis is an ophthalmic emergency. In recent years, the incidence of endogenous endophthalmitis (EE) has increased. This study aims to elucidate the clinical characteristics and risk factors associated with the visual prognosis of EE.

METHODS: This study included 111 patients (121 eyes) diagnosed with EE who received intraocular and systemic treatment at Huashan Hospital, Fudan University, between January 2014 to December 2023. We conducted a comprehensive review of the demographic and clinical characteristics of the cohort and analyzed the risk factors linked to poor visual prognosis.

RESULTS: A total of 111 patients (121 eyes) were included in this study, of whom 101 eyes (83.5 %) had identifiable pathogenic microorganisms, with Klebsiella pneumoniae (KP) was the most common pathogen. Compared to conventional culture methods (sensitivity 47.6 %), metagenomic next-generation sequencing (mNGS) demonstrated significantly higher sensitivity (97.6 %) in vitreous samples. Outcome analysis indicated that mNGS played a critical role in guiding clinical antibiotic adjustments, and patients receiving targeted therapy showed significant visual improvement (P = 0.002), with stable systemic recovery. Furthermore, vitreous surgery had a positive effect on visual prognosis (P < 0.001). Regression analysis revealed that poor initial visual acuity (VA) (OR: 20.622, 95 % CI: 3.894-109.2) and KP infection (OR: 3.398, 95 % CI: 1.096-10.538) were independent risk factors for poor final VA.

CONCLUSION: Our findings identify KP as the most common causative pathogen of EE. Infections caused by KP and poor initial VA are significant risk factors for poor visual outcomes. Looking ahead, mNGS holds promise as a crucial tool for the clinical diagnosis of EE.},
}

@article {pmid41124971,
year = {2025},
author = {Gao, Y and Liu, Z and Sun, Y and Wang, J and Wu, X and Lu, X and Zhen, G},
title = {Mitigating perfluorooctanoic acid inhibition in electrochemically-assisted spiral upflow anaerobic membrane reactor for wastewater treatment: EPS interaction-desorption dynamics and metabolic pathway reconstruction.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124761},
doi = {10.1016/j.watres.2025.124761},
pmid = {41124971},
issn = {1879-2448},
abstract = {The widespread occurrence of perfluorooctanoic acid (PFOA) in industrial wastewater poses a major challenge to anaerobic treatment systems due to its chemical stability and persistence. Here, an electrochemical spiral upflow anaerobic membrane reactor (EC-SU-AnMBR) was developed by integrating a Ru-Ir/Ti-mesh-wrapped hollow-fiber membrane anode and a spiral Ti-mesh cathode to facilitate PFOA desorption and detoxification. PFOA readily accumulated in tightly bound extracellular polymeric substances (EPS) under open-circuit mode via hydrophobic interactions and electrostatic adsorption, disrupting anaerobic granular sludge (AnGS) structure and impairing microbial functionality. Electrochemical regulation (closed-circuit) effectively alleviated PFOA inhibition, achieving COD removal of 80.7 % (vs. 66.7 %) and a 1.5-fold higher CH4 recovery (227.7 vs. 140.8 mL/g COD/d). Electric field-migration and bioanode-membrane interception/oxidation together weakened PFOA-AnGS binding capability by altering EPS structural stability and interaction-desorption dynamics, decreasing PFOA retention rate in the bioreactor from initial 60.4 % to 2.1 % (p < 0.01) and reinforcing sludge regranulation. Further analysis demonstrated that the bioelectrocatalysis upregulated the relative abundance of functional genes involved in glucose metabolism (pfk, por, and ackA) and methanogenesis (fwd, mtr, and mcr) by selectively enriching hydrolytic/acidogenic bacteria and syntrophic-methanogenic consortia (Smithellaceae, Kosmotogaceae, and Methanotrichaceae) at both bioelectrodes. This study proposes a promising EC-SU-AnMBR system for the sustainable treatment of PFOA-contaminated wastewater and elucidates the metagenome-informed metabolic adaptation mechanisms under PFOA stress.},
}

@article {pmid41124778,
year = {2025},
author = {Ohlsson, C and Li, L and Horkeby, K and Lawenius, L and Colldén, H and Sjögren, K and Baldanzi, G and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Grahnemo, L},
title = {The circulating dihydrotestosterone/testosterone ratio is increased by gut microbial 5α-reductase activity in females.},
journal = {EBioMedicine},
volume = {121},
number = {},
pages = {105978},
doi = {10.1016/j.ebiom.2025.105978},
pmid = {41124778},
issn = {2352-3964},
abstract = {BACKGROUND: Dihydrotestosterone (DHT), the most potent ligand to the androgen receptor, is synthesised from testosterone (T) by 5α-reductase type 1 and 2. While type 1 is expressed in several non-reproductive tissues in both sexes, men also express high levels of the high-affinity type 2 isoform in reproductive tissues; yet women have a higher circulating DHT to T (DHT/T) ratio than men. We hypothesised that the high DHT/T ratio in women is caused by high gut microbiota (GM) 5α-reductase activity or altered β-glucuronidase-induced androgen reabsorption from the gut.

METHODS: We used a large cross-sectional subsample of the Swedish CArdioPulmonary bioImage Study (2897 women and 4338 men, 50-65 years of age) with GM composition and functionality determined by metagenome sequencing and circulating androgens determined by liquid chromatography-tandem mass spectrometry.

FINDINGS: We confirmed that women had higher (+194%) circulating DHT/T ratio than men. The relative abundance of microbial genes for 5α-reductase type 1 (P = 3 × 10[-4]), but not β-glucuronidase, was positively associated with the DHT/T ratio in women. In women, the GM relative abundances of Odoribacter splanchnicus and Parabacteroides distasonis were positively associated with the relative abundance of microbial genes for 5α-reductase type 1 (P < 2 × 10[-149]) and the circulating DHT/T ratio (O. splanchnicus P = 3 × 10[-6]; P. distasonis P = 5 × 10[-5]). In mechanistic studies, we observed very high DHT/T ratio in intestinal content of female conventionally-raised but not germ-free mice. In female mice, the DHT/T ratio was 86.9% higher in serum from the portal vein than in inferior vena cava (P = 0.007).

INTERPRETATION: These findings demonstrate that the circulating DHT/T ratio is increased by GM 5α-reductase activity in females. We propose that the GM acts as an endocrine organ influencing the androgenic status in females.

FUNDING: See Acknowledgements.},
}

@article {pmid41124743,
year = {2025},
author = {Chu, S and Chen, Y and Xu, Z and Zhou, J and Li, K and Zhang, Q and Qian, M and Han, J and Qu, D},
title = {Metagenomic analysis of bacterial fitness and plasmids carrying blaTEM-1 and virulence genes before and after cleaning and disinfection in pig slaughterhouses.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140168},
doi = {10.1016/j.jhazmat.2025.140168},
pmid = {41124743},
issn = {1873-3336},
abstract = {The identification of antibiotic resistance genes (ARGs), virulence genes, and pathogens in animal slaughterhouses poses a major threat to human health. However, limited data is available about the contamination and dissemination of ARGs in commercial pig slaughterhouses before and after disinfectant application. In this study, we used metagenomics and plasmid profiling to analys ethe effect of quaternary-ammonium-based cleaning and disinfection (C&D) on the microbiota, antibiotic resistance genes (ARGs), and virulence genes (VFs) in a pig slaughterhouse. According to results C&D effectively reduced the total microbial population and abundance of ARGs. However, the prevalence of disinfectant-resistant bacteria, particularly Escherichia coli, increased dramatically from 5.9 % to 14.9 %. Additionally, the clinically significant β-lactamase gene blaTEM-1 remained intact throughout C&D process. The persistence of blaTEM-1 is primarily facilitated by low-fitness-cost IncR-type plasmids (pTZ17 and pSB24), which are characterised by their simplified structures that have no effect on bacterialgrowth or motility and exhibit stability in the absence of antibiotics. On the other hand, the high-virulence IncFIB plasmid (pYA21) harbors numerous ARGs and VFs. Despite their low survival rate after C&D, the remaining bacteria may pose an even greater risk. The results suggest that current disinfection protocols may unintentionally promote the persistence and dissemination of resistance plasmids with potential fitness or economic advantages. Our findings highlight the need of integrating plasmid ecology and virulence profiling into standard surveillance practices, which will enhance disinfection strategies and help to mitigate the spread of antimicrobial resistance.},
}

@article {pmid41124226,
year = {2025},
author = {Barcytė, D and Žihala, D and Eliáš, M},
title = {Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles.},
journal = {PLoS genetics},
volume = {21},
number = {10},
pages = {e1011901},
doi = {10.1371/journal.pgen.1011901},
pmid = {41124226},
issn = {1553-7404},
abstract = {Mitochondria and plastids of various lineages exhibit genetic code alterations. However, the knowledge of the diversity and occurrence, mechanistic underpinnings, and evolutionary origins of codon reassignments in organelles remains incomplete. To address this gap, we focused on organelles of the neglected green algal class Pedinophyceae, as well as pedinophyte-derived secondary plastids of green-coloured dinoflagellates (peDinoflagellates). We isolated and characterized a novel pedinophyte, herein formally described as Oistococcus okinawensis gen. et sp. nov., and phenotypically documented the previously sequenced but morphologically uncharacterized strain YPF-701, herein described as Akinorimonas japonica gen. et sp. nov. Based on phylogenetic analyses, both new taxa were classified into the expanded family Resultomonadaceae. We sequenced the organellar genomes of O. okinawensis, and utilizing existing raw (meta)genomic data we assembled organellar genome sequences from other previously unexplored pedinophyte lineages. Bioinformatic analyses of the expanded set of pedinophyte organellar genomes painted a complex picture of their genetic code landscape. Concerning mitochondria, the stop-to-Trp reassignment of the UGA codon turned out to have evolved multiple times in pedinophytes, and the Arg-to-Ala reassignment of AGA/AGG codons was shown to be apomorphic for the whole order Marsupiomonadales. The latter has additionally converted UUA and UUG into termination codons, relying on specific mutations in the mtRF1a protein. All pedinophyte mitochondria seem to decode AUA as methionine rather than the standard isoleucine, and an analogous reassignment seems to be evolving also in plastids of two separate pedinophyte lineages. Finally, apart from the previously reported Ile-to-Met AUA reassignment, peDinoflagellate plastids have switched the meaning of the AGA/AGG codons from arginine to another amino acid (most likely alanine), and have modified their pRF2 protein to mediate translation termination at UUA/UCA codons. Pedinophyte(-derived) organelles present a broad spectrum of codon reassignments and provide important insights into the emergence and mechanisms of non-standard codon translation.},
}

@article {pmid41123794,
year = {2025},
author = {Xiong, L and Liu, X and Zhang, L and Chen, W and Mo, Q and Sun, C},
title = {Q fever sternum osteomyelitis in a patient with history of cardiovascular surgery: A case report from China.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41123794},
issn = {1435-4373},
abstract = {This article reports a rare case of sternal osteomyelitis caused by Coxiella burnetii. The patient, a 59-year-old male with a history of aortic dissection and hypertension, had undergone ascending aorta replacement and aortic valvuloplasty. He was admitted in May 2022 due to a chest mass that had been enlarging since its discovery in October 2021. Despite antibiotic treatment, the symptoms did not improve, and he experienced recurrent low-grade fevers. Upon admission, CT imaging revealed multiple mediastinal lymph node enlargements and a cystic shadow anterior to the sternum handle. The infection was confirmed as Coxiella burnetii through surgical debridement and metagenomic next-generation sequencing (mNGS). The treatment was subsequently changed to doxycycline and hydroxychloroquine. Positron emission computed tomography with 18 F-fluorodeoxyglucose ([18 F] FDG PET/CT) imaging showed that the infection was localized to the sternum, excluding vascular and implant infections. The patient completed an 18-month course of antibiotics, leading to controlled infection and normalized renal function. This case highlights the complexities of diagnosing and managing Q fever osteomyelitis in patients post-cardiovascular surgery, demonstrating the crucial roles of mNGS and [18 F] FDG PET/CT in rapid diagnosis and effective treatment. These findings provide valuable insights and guidance for managing similar cases in the future.},
}

@article {pmid41123363,
year = {2025},
author = {Yue, Z and Zhang, J and Xu, W and Peng, L and Liu, T and Sheng, S and Tao, Y and Zeng, L and Zhao, Z and Alberoni, D and Baffoni, L and Zhang, Q and Liu, B and Li, Q and Zhang, J and Zou, Y},
title = {CNPS.cycle: streamlining shotgun metagenomic data analysis for biogeochemical cycles.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0102125},
doi = {10.1128/msystems.01021-25},
pmid = {41123363},
issn = {2379-5077},
abstract = {UNLABELLED: Shotgun metagenomic data analysis for investigating biogeochemical cycles in the environment remains challenging, primarily due to the steep learning curve, intensive time investment, and high computational demands, all of which pose significant barriers for many researchers. We present a new R package called "CNPS.cycle," designed to streamline the interpretation of shotgun metagenomic data related to biogeochemical processes, complete with visually informative outputs. This comprehensive package comprises four distinct analysis modules, focused on carbon, nitrogen, phosphorus, and sulfur cycling. Users can easily utilize the package by uploading annotation result files derived from shotgun metagenomic data, specifically those based on the Kyoto Encyclopedia of Genes and Genomes and the NCBI non-redundant protein sequence database. The package then automates essential steps, including data preprocessing, curation, and differential analysis of biogeochemical cycle-related genes; analysis of microorganisms possessing biogeochemical cycle-related genes at the contig level; β-diversity analysis; and, finally, data visualization. The outcome is a comprehensive analysis revealing differentially abundant genes and functionally significant microbial entities associated with the carbon, nitrogen, phosphorus, and sulfur cycles, presented in the form of tables and high-quality images. This tool will provide profound insights into the relationship between soil microorganisms and elemental chemical cycles, thereby advancing our comprehension of soil ecosystems. For accessibility, the CNPS.cycle package is available on GitHub (https://github.com/yuezhengfu/CNPS.cycle), where detailed instructions on its usage can be found in the project's GitHub page (https://github.com/yuezhengfu/CNPS.cycle/wiki).

IMPORTANCE: The "CNPS.cycle" R package offers significant environmental implications by simplifying the analysis of shotgun metagenomic data related to biogeochemical cycles. Its automated workflow identifies key genes and microbes involved in carbon, nitrogen, phosphorus, and sulfur cycling, enhancing our understanding of microbial contributions to ecosystem functions. This tool enables researchers to explore microbial-mediated nutrient cycling more efficiently, supporting informed decisions in environmental management and climate change mitigation. By providing accessible, high-quality outputs, "CNPS.cycle" facilitates data-driven insights into the interplay between microbes and global biogeochemical processes.},
}

@article {pmid41123352,
year = {2025},
author = {Akinsola, OA and Dahunsi, SO and Odekanle, EL},
title = {Metagenomic study of food waste anaerobic digestion.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0208725},
doi = {10.1128/spectrum.02087-25},
pmid = {41123352},
issn = {2165-0497},
abstract = {This study explores anaerobic digestion of food waste to understand the microbial community dynamics and metabolic pathways that drive the conversion of organic waste into biogas. Sampling was done at multiple time points during those 4 weeks (weekly) to capture microbial succession/changes over time. The microbial profile was evaluated using QIIME2 and BV-BRC, while functional annotation tools (PICRUSt2) were used to identify dominant pathways. The results reveal a temporal shift in microbial communities, with fermentative bacteria, such as Lactobacillus and Clostridia, dominating the early stages of digestion, followed by methanogenic archaea like Methanomicrobia in the later stages. Pathway analysis showed that fermentation, aromatic compound degradation, and methanogenesis were the primary metabolic processes, with methanogenesis becoming more prominent by week 3 (FW3_S162_R1). The study highlights the critical role of microbial community adaptation in maximizing methane production and offers new insights into optimizing anaerobic digestion for more efficient food waste biogas generation. By combining metagenomic and metabolomic approaches, this research provides a comprehensive understanding of the microbial and metabolic factors that shape the anaerobic digestion process, contributing to the development of sustainable waste management practices.IMPORTANCEThis study employs a metagenomic approach to elucidate the intricate microbial communities and metabolic processes involved in the anaerobic digestion of food waste. It highlights microbial interactions that influence biogas production, offering insights for optimizing waste-to-energy conversion. Understanding these dynamics is key to improving digestion efficiency, reducing environmental impacts, and advancing sustainable waste management and circular economy strategies. The findings provide a valuable foundation for future innovations addressing global waste and energy challenges.},
}

@article {pmid41122951,
year = {2025},
author = {Vilonen, L and Thompson, A and Adams, B and Ayres, E and Franco, ALC and Wall, DH},
title = {Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70062},
doi = {10.1111/1755-0998.70062},
pmid = {41122951},
issn = {1755-0998},
support = {//U.S. National Science Foundation/ ; },
abstract = {Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under-characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long-term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom-built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large-scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America.},
}

@article {pmid41122237,
year = {2025},
author = {Terra Machado, D and Bernardes Brustolini, OJ and Dos Santos Corrêa, E and Ribeiro Vasconcelos, AT},
title = {Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20232},
pmid = {41122237},
issn = {2167-8359},
mesh = {*Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Spores, Bacterial/genetics ; Animals ; Humans ; *Firmicutes/genetics/physiology ; Cattle ; Feces/microbiology ; Metagenome ; Swine ; Phylogeny ; Ensemble Learning ; },
abstract = {Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In addition, SHapley Additive exPlanations (SHAP) analysis indicated 16 consensus genes consistently contributing to predictions (namely lytH, cotP, spoIIIAG, spoIIR, spoVAD, gerC, yabP, yqfD, gerD, spoVAA, gpr, ytaF, gdh, ypeB, spoVID, and ymfJ), bringing biologically meaningful features across sporulation stages. By combining gene annotation with interpretable machine learning, SpoMAG provides a reproducible and accessible framework to infer sporulation potential in uncultured microbial taxa. This tool enhances targeted investigations into microbial survival strategies and supports research in microbiome ecology, probiotic discovery, food safety, and public health surveillance. SpoMAG is freely available as an R package and expands current capabilities for functional inference in metagenomic datasets.},
}

*Gastrointestinal Microbiome/genetics
*Machine Learning
*Spores, Bacterial/genetics
Animals
Humans
*Firmicutes/genetics/physiology
Cattle
Feces/microbiology
Metagenome
Swine
Phylogeny
Ensemble Learning

@article {pmid41121668,
year = {2025},
author = {Enagbonma, BJ and Modise, DM and Babalola, OO},
title = {Effects of Legume‒Cereal Rotation on Sorghum Rhizosphere Microbial Community Structure and Nitrogen-Cycling Functions.},
journal = {MicrobiologyOpen},
volume = {14},
number = {5},
pages = {e70085},
doi = {10.1002/mbo3.70085},
pmid = {41121668},
issn = {2045-8827},
support = {//This study was supported by the ICGEB Research Project (CRP/ZAF22-03) awarded to O.O.B./ ; },
mesh = {*Sorghum/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fabaceae/growth & development/microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil/chemistry ; Zea mays/microbiology/growth & development ; *Edible Grain/growth & development/microbiology ; Agriculture/methods ; },
abstract = {Legumes form mutualistic interactions with specific soil microbiomes that fix atmospheric nitrogen and improve soil fertility. However, legume-based rotations influence on soil microorganisms and their correlations with soil physicochemical parameters during subsequent crop development are not yet clear. We examined the shifts in microbial community structure and nitrogen genes via shotgun sequencing across cowpea-sorghum, soybean-sorghum, maize-sorghum rotations, and sorghum without precrops. Precropping in rotation significantly affected N-NO3, clay, and silt, and caused a shift in the rhizosphere microbiome. Actinomycetota was the most predominant bacteria across all the cropping systems, followed by Pseudomonadota, whose composition differed across the cropping systems. Legume in rotation increased the relative abundance of Streptomyces and reduced the relative abundances of Pyxidicoccus, Microbacterium, and Microvirga. Nocardioides and Solirubrobacter predominated in the soil after the maize crops. Shannon index, non-metric multidimensional scaling, and permutational multivariate analysis of variance revealed that crop rotation caused significant differences in both the alpha and beta diversity of the microbial community and the nitrogen-cycling functional genes. The relative abundances of amoC, narH, gltB, glnA, ureC, napA, and napA significantly increased in legume monocrops in rotation. The relative abundances of glnA, gltB, narZ, and narH increased in the soil after maize cropping, whereas sorghum without precrops significantly increased the relative abundances of glnA, narZ, and ureC. Several soil physicochemical parameters drive microbial communities. *S, Na, N-NH4, N-NH3, and P were the most significant environmental variables regulating microbiome and nitrogen-cycling genes by crop rotation. This study supports sustainable agricultural practices and promotes sorghum development through rhizosphere microbiome optimization.},
}

*Sorghum/microbiology/growth & development
*Rhizosphere
*Soil Microbiology
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Fabaceae/growth & development/microbiology
Nitrogen/metabolism
*Nitrogen Cycle
Soil/chemistry
Zea mays/microbiology/growth & development
*Edible Grain/growth & development/microbiology
Agriculture/methods

@article {pmid41121143,
year = {2025},
author = {Zhou, H and Li, X and Mao, Y and Chen, Q and Zhu, D and Liu, C and Yao, Y and Yao, Y and Yu, Y and Feng, Y},
title = {Strain-level characterization of bacterial pathogens using metagenomic sequencing for patients with pneumonia.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1149},
pmid = {41121143},
issn = {1479-5876},
support = {82072241//National Natural Science Foundation of China/ ; 82272338//National Natural Science Foundation of China/ ; 2022YFC2504502//Key R&D Plan of the Ministry of Science and Technology of China/ ; 2023C03068//Research and Development Program of Zhejiang Province/ ; 2024C03187//Research and Development Program of Zhejiang Province/ ; },
mesh = {Humans ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Acinetobacter baumannii/genetics/pathogenicity ; *Pneumonia/microbiology ; Klebsiella pneumoniae/genetics/pathogenicity ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/genetics/pathogenicity ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has emerged as an indispensable diagnostic tool for infectious diseases. The disparity in virulence and antimicrobial resistance among strains of the same species requires mNGS to reach strain-level resolution.

METHODS: To compare the subtyping performance between mNGS and culture, thirty bronchoalveolar lavage fluid (BALF) or blood specimens positive by culture were sequenced using the Illumina NextSeq platform, while whole genome sequencing (WGS) was conducted on the corresponding cultured colonies. Additionally, thirty BALF specimens underwent both mNGS and Oxford nanopore technology (ONT)-based metagenomic third-generation sequencing (mTGS) to compare the subtyping efficacy of the two platforms. To characterize the strain-level composition of pneumonia pathogen Acinetobacter baumannii and Klebsiella pneumoniae, 185 BALF specimens from three hospitals were analyzed by mNGS.

RESULTS: WGS of the cultured colonies yielded identical subtyping results to mNGS at the level of clonal complex (CC). Although mNGS and mTGS predicted largely consistent primary CCs, mTGS demonstrated less accuracy and precision in CC identification. Co-infections at the CC level were detected in 5.40% of A. baumannii-positive and 19.55% of K. pneumoniae-positive BALF specimens. CC composition differed markedly according to bacterial load and between primary and secondary CCs in co-infection specimens. Antimicrobial resistance profiles remained constant for patients with single-infection but varied for those with co-infection. Spatial and temporal consistency of CC composition was observed within individual patients.

CONCLUSIONS: The heterogeneity in virulence and antimicrobial resistance among CCs, together with the prevalence of strain-level co-infections, highlights the need to extend pathogen identification to the strain level. Under current technical conditions, mNGS is a more suitable subtyping tool compared to culture and mTGS.},
}

Humans
*Metagenomics/methods
Bronchoalveolar Lavage Fluid/microbiology
High-Throughput Nucleotide Sequencing
Acinetobacter baumannii/genetics/pathogenicity
*Pneumonia/microbiology
Klebsiella pneumoniae/genetics/pathogenicity
Male
Female
Middle Aged
Aged
*Bacteria/genetics/pathogenicity
Whole Genome Sequencing

@article {pmid41121093,
year = {2025},
author = {Jia, Y and He, M and Wang, F and Zhan, Y and Deng, Q and Shen, J and Wang, X and Ran, Q and Huang, W and Ling, Y and Wen, S},
title = {Indole-3-lactic acid protects the gut vascular barrier following intestinal ischemia injury through AhR/Nrf2/STAT3 mediated claudin 2 downregulation.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {447},
pmid = {41121093},
issn = {1478-811X},
support = {82302457//National Natural Science Foundation of China/ ; 82372187//National Natural Science Foundation of China/ ; 82272223//National Natural Science Foundation of China/ ; 23qnpy134//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *NF-E2-Related Factor 2/metabolism ; Mice ; *Reperfusion Injury/metabolism/pathology/drug therapy ; *Down-Regulation/drug effects ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Male ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; Tryptophan ; *Intestines/pathology/blood supply/drug effects ; *Protective Agents/pharmacology ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND & AIMS: Dysfunction of the intestinal epithelial barrier (IEB) and gut vascular barrier (GVB) contributes to the development of intestinal ischemia/reperfusion (IR) injury. Tryptophan (TRP), an essential amino acid, plays a crucial role in maintaining intestinal homeostasis, yet its regulatory effects on the GVB following IR remain unexplored. We aimed to better define the role of TRP in intestinal IR in vivo and in vitro.

METHODS: Mice underwent intestinal ischemia/reperfusion (IR) and were fed control, TRP-recommended (TRP-r), or TRP-sufficient (TRP-s) diets. Fecal metagenomic sequencing analyzed microbial composition, and targeted metabolomics quantified tryptophan and its metabolites in intestinal and serum samples. ILA's effects on barrier integrity were assessed via tight junction protein expression and FITC-dextran permeability assays. RNA sequencing of intestinal endothelial cells elucidated mechanisms by which ILA modulated GVB function. The STAT3-claudin 2 relationship was validated in vitro by ChIP-qPCR.

RESULTS: TRP supplementation significantly reshaped the gut microbiota, mitigated tissue damage and enhanced the integrity of both the IEB and GVB. Indole-3-lactic acid (ILA), a key tryptophan metabolite, was identified as an important factor in preserving GVB function. Mechanistically, our results show that the aryl hydrocarbon receptor (AhR)/Nrf2/signal transducer and activator of transcription 3 (STAT3) pathway is essential for ILA-mediated improvement of GVB integrity and downregulation of the pore-forming protein claudin 2.

CONCLUSIONS: Our findings highlight the dual role of ILA in reinforcing both IEB and GVB functions and shed light on the molecular mechanisms underlying ILA's GVB-protective effects. This study implicates that ILA or other AhR-activating metabolites may serve as promising pharmacological agents for alleviating IR-induced intestinal damage.},
}

Animals
*Receptors, Aryl Hydrocarbon/metabolism
*NF-E2-Related Factor 2/metabolism
Mice
*Reperfusion Injury/metabolism/pathology/drug therapy
*Down-Regulation/drug effects
*STAT3 Transcription Factor/metabolism
*Indoles/pharmacology
*Intestinal Mucosa/metabolism/drug effects/pathology
Male
Mice, Inbred C57BL
Gastrointestinal Microbiome/drug effects
*Basic Helix-Loop-Helix Transcription Factors/metabolism
Tryptophan
*Intestines/pathology/blood supply/drug effects
*Protective Agents/pharmacology
Signal Transduction/drug effects

@article {pmid41120531,
year = {2025},
author = {Brito, B and DeMaere, M and Lean, I and Hazelton, M and O'Rourke, BA and Holmes, EC and House, JK and Rowe, S and Myers, GSA and Roy Chowdhury, P},
title = {Leveraging metatranscriptomics for the characterisation of bovine blood viromes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36670},
pmid = {41120531},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Virome/genetics ; *Transcriptome ; *Cattle Diseases/virology/blood/genetics ; Kenya ; *Viruses/genetics/classification ; Gene Expression Profiling ; },
abstract = {Understanding the diversity of the bovine virome is essential for assessing their potential impact on cattle health and transmission risks. Viruses present in the blood comprise both those that establish persistent infections in blood cells and those present during transient viremia. Farm management practices, such as the reuse of syringes for treatments, vaccinations, and supplements, may inadvertently contribute to the spread of blood-borne pathogens, emphasizing the need for improved biosecurity measures. Herein, we used a metatranscriptomic approach to analyse 20 bovine blood transcriptomes from dairy cows in New South Wales, Australia, along with 577 publicly available blood transcriptomes from studies in Australia and Kenya. Our analysis identified several viruses that are known to infect blood cells, transmitted either by direct contact or by vectors, including bovine viral diarrhea virus, bovine gammaherpesvirus 6, hepacivirus, foamy virus, ephemeroviruses and a new species of a coltivirus. Our findings highlight the complexity of the bovine blood virome and underscore the importance of sustained surveillance to identify emerging pathogens and assess their potential role in cattle health. This study provides a framework for integrating transcriptomic data into disease monitoring efforts, ultimately contributing to improved cattle management and biosecurity practices.},
}

Animals
Cattle
*Virome/genetics
*Transcriptome
*Cattle Diseases/virology/blood/genetics
Kenya
*Viruses/genetics/classification
Gene Expression Profiling

@article {pmid41120014,
year = {2025},
author = {Zhang, L and Zhang, Y and Li, YY and Dou, Q and Peng, Y},
title = {Sequential oxygen intervention drives novel AOB-DGAOs interaction network enabling advanced nitrogen removal in simultaneous partial nitrification and endogenous denitrification (SPNED) process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133529},
doi = {10.1016/j.biortech.2025.133529},
pmid = {41120014},
issn = {1873-2976},
abstract = {The simultaneous partial nitrification and endogenous denitrification (SPNED) process, driven by ammonia-oxidizing bacteria (AOB) and denitrifying glycogen-accumulating organisms (DGAOs), shows significant potential for low-carbon wastewater treatment. However, rapid startup and efficiency are challenged by persistent nitrite-oxidizing bacteria (NOB) proliferation under low NH4[+]-N conditions and dissolved oxygen depletion of intracellular polyhydroxyalkanoates (PHA) in DGAOs. Here, a sequential oxygen intervention strategy is innovatively proposed: DGAOs population dominance was first established through anaerobic/anoxic mode, followed by a mid-position aerobic phase to construct a DGAOs-dominated AOB-DGAOs interaction network. SPNED startup was achieved within 46 days with > 99 % nitrogen removal efficiency. Co-occurrence networks and metagenomics revealed functional bacterial cooperation enabling carbon-efficient nitrogen removal. Results demonstrated that enriched DGAOs (abundance increased from 9.22 % to 28.25 %) preferentially consumed NO2[-]-N over oxygen under microaerobic conditions, starving NOB and creating a low-competition niche for AOB. Consequently, AOB abundance surged 22.69-fold within 16 days. Correspondingly, AOB-generated low-electron-demand NO2[-]-N reduced endogenous electron (NADH from PHA degradation) requirements for DGAOs denitrification. Furthermore, Candidatus Contendobacter (NO2[-]-N → NO) and Candidatus Competibacter (NO → N2) within DGAOs potentially executed stepwise denitrification, avoiding NADH loss through intra-community substrate competition. Coupled with subsequent oxygen intervention, activation of β-oxidation (151.4 % up-regulation in key enzyme) and TCA cycle (96.0 % increase in α-ketoglutarate dehydrogenase) in DGAOs boosted intracellular NADH levels 1.76-fold. This NADH-rich environment enhanced DGAOs functionality and sustained enrichment, stabilizing the AOB-DGAOs network for advanced nitrogen removal. This study proposes a previously underappreciated NOB-inhibition function of DGAOs, offering a novel strategy for efficient endogenous carbon utilization, advanced nitrogen removal, and operational stability.},
}

@article {pmid41118772,
year = {2025},
author = {Jacoby, C and Scorza, K and Ecker, L and Nol Bernardino, P and Little, AS and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH},
title = {Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.09.014},
pmid = {41118772},
issn = {1934-6069},
abstract = {Steroid hormone metabolism by the gut microbiome affects host physiology, however, the underlying microbial pathways remain incompletely understood. Here, we isolate a gut bacterial species, which we designate Clostridium steroidoreducens, that reduces cortisol and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-Δ[1]-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-a frontline Crohn's disease therapy. OsrB is a 3-oxo-Δ[4]-steroid reductase that converts steroid hormones to 5β-dihydrosteroid intermediates, which OsrC subsequently reduces to 3β,5β-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in metagenomes of Crohn's disease patients. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.},
}

@article {pmid41118252,
year = {2025},
author = {Qi, X and Li, Y and Zhu, Y and Shen, R and Xie, Z},
title = {Rebuilding the gut ecosystem: Emerging strategies targeting the microbiota in antibiotic-associated diarrhea.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02690},
pmid = {41118252},
issn = {1588-2640},
abstract = {Antibiotic-associated diarrhea (AAD) is a prevalent iatrogenic complication of antibiotic therapy, primarily triggered by dysbiosis and loss of intestinal homeostasis. The traditional interventions, such as empirical probiotic use, have shown a modest and a heterogeneous efficacy. This review integrates the current mechanistic understanding of AAD through the lens of the microbiota-mucosal-immune axis and provides a comprehensive overview of emerging therapeutic strategies. By integrating evidence from metagenomics, metabolomics, and immunology, we highlight next-generation approaches, including rationally engineered probiotics, standardized fecal microbiota transplantation (FMT), and synthetic-biology-derived interventions. Recent progress in multi-omics technologies and machine learning has enabled patient-stratified modulation of the gut microbiota, moving beyond empirical supplementation toward precision ecological reprogramming. These advanced therapies demonstrate superior outcomes in restoring microbial diversity, strengthening epithelial barrier function, and re-establishing immunological homeostasis. Ultimately, the management of AAD requires a systems-biology strategy that leverages real-time microbiome analytics for targeted, accurate, and sustainable restoration of gut health.},
}

@article {pmid41117817,
year = {2025},
author = {Gogoi, R and Bora, SS and Gogoi, B and Naorem, RS and Barooah, M},
title = {Insights into the microbial diversity and functionalities of potential hydrocarbon-degrading bioremediation agents in oil spill sludge of Assam, India.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {325},
pmid = {41117817},
issn = {1432-072X},
mesh = {India ; Biodegradation, Environmental ; *Hydrocarbons/metabolism ; *Petroleum Pollution/analysis ; *Sewage/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Surface-Active Agents/metabolism ; RNA, Ribosomal, 16S/genetics ; Petroleum/metabolism ; Phylogeny ; Biodiversity ; },
abstract = {Oil spill contamination poses a significant threat to environmental and ecological health, particularly in crude oil-rich regions such as Assam, a north-eastern state of India. This study explores the microbial diversity and functional potential of hydrocarbon-degrading bacteria in crude oil-contaminated sludge. Sludge samples were collected from three contaminated sites in Assam and analyzed for microbial diversity by culture dependent and independent (using 16 S rRNA amplicon sequencing) approaches. Metagenomic analysis revealed a diverse microbial community, with Proteobacteria and Planctomycetes dominating the metagenomes. Seven bacterial isolates, including Diaphorobacter nitroreducens, Lysinibacillus capsici, and Pseudomonas otitidis, were isolated and identified as potential hydrocarbon degraders. The isolates were screened and evaluated for biosurfactant production, hydrocarbon adhesion, and key enzymatic activities involved in degradation. These isolates exhibited significant biosurfactant-producing abilities, with Diaphorobacter nitroreducens MBRG1 showing the highest emulsification index (79%) and strong adherence to hydrocarbons. The enzymatic activities of alkane hydroxylase and alcohol dehydrogenase confirmed the metabolic capabilities of the isolates in hydrocarbon degradation. Optimal growth conditions for biosurfactant production were determined to be pH 7, 30 °C, 2% sucrose as the carbon source, and 3% yeast extract as the nitrogen source. The study highlights the potential of these indigenous bacterial isolates in bioremediation strategies to mitigate oil contamination. Future studies should focus on large-scale bioreactor studies, field trials, and strain improvement of these bacteria to enhance their degradation efficiency and adaptability to varied environmental conditions.},
}

India
Biodegradation, Environmental
*Hydrocarbons/metabolism
*Petroleum Pollution/analysis
*Sewage/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Surface-Active Agents/metabolism
RNA, Ribosomal, 16S/genetics
Petroleum/metabolism
Phylogeny
Biodiversity

@article {pmid41117699,
year = {2025},
author = {Xie, H and Zhang, X and Liu, X},
title = {The Co-Metabolic Bioremediation of Benzo[a]pyrene Contaminated Soil by Achromobacter xylosoxidans B-2 and Its Effect on Indigenous Microbial Community.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.24576},
pmid = {41117699},
issn = {1522-7278},
support = {2023YFC3709000//National Key Research and Development Program of China/ ; 2018YFC1800600//National Key Research and Development Program of China/ ; 21677093//National Natural Science Foundation of China/ ; 21806100//National Natural Science Foundation of China/ ; },
abstract = {Benzo[a]pyrene (BaP) is a persistent polycyclic aromatic hydrocarbon (PAH) that poses significant environmental and health risks. Co-metabolic bioremediation, which uses additional carbon sources to enhance microbial degradation, offers a promising approach for BaP removal. This study investigated the effects of different co-metabolic carbon sources on the growth of Achromobacter xylosoxidans B-2 and its efficiency in degrading BaP in both mineral salt medium (MSM) and BaP-contaminated soil. The addition of supplementary carbon sources, particularly starch and salicylic acid, significantly enhanced strain B-2 growth and BaP removal in MSM (p < 0.05), with the highest degradation rate reaching 46.35% in the starch-supplemented group. In soil, salicylic acid and starch also markedly improved BaP degradation, achieving 47.99% and 23.53% removal (both p < 0.01) after 30 days, respectively, compared to only 9.78% in the BaP-only group. Metagenomic analysis revealed that co-substrate amendments significantly altered soil microbiota, enriching PAH-degrading genera such as Achromobacter, especially the introduced A. xylosoxidans. This enrichment was accompanied by reduced overall microbial diversity, indicating strong selective pressure from the amendments. Functional gene profiling based on metagenomic data indicated an increased abundance of key PAH-degrading enzymes, including dioxygenases and dehydrogenases, in response to co-substrate addition. Redundancy analysis further indicated that environmental factors such as pH, organic matter, and phosphorus were significantly correlated with microbial community composition and BaP degradation efficiency. These findings demonstrate that co-metabolism not only enhances BaP removal but also drives functional and ecological changes in soil microbiota, providing mechanistic insight and practical guidance for improved bioremediation strategies.},
}

@article {pmid41117680,
year = {2025},
author = {Karakayalı, EM and Tuğlu, Mİ},
title = {The contribution of probiotics to combined cellular therapy in skin wound healing in diabetic rats.},
journal = {Ulusal travma ve acil cerrahi dergisi = Turkish journal of trauma & emergency surgery : TJTES},
volume = {31},
number = {10},
pages = {925-936},
doi = {10.14744/tjtes.2025.37711},
pmid = {41117680},
issn = {1307-7945},
mesh = {Animals ; *Probiotics/therapeutic use/pharmacology ; *Wound Healing/drug effects ; Rats ; *Diabetes Mellitus, Experimental/complications ; Male ; Skin/injuries ; *Cell- and Tissue-Based Therapy/methods ; },
abstract = {BACKGROUND: Diabetes-related wound care is still a major issue due to chronic and non-healing ulcers that are prone to infection and ultimately amputation. In recent years, cellular therapy (CT) products such as mesenchymal stem cells (MSC), platelet-rich plasma (PRP), and stromal vascular fraction (SVF) have been widely used. A combined cellular therapy (CCT) has not yet been tested as a triple combination, although its use alone and in dual combinations has been investigated. Probiotics (PB) accelerate healing by altering the intestinal microbiota. This study aims to examine the role of PB in enhancing the effects of CCT on diabetic wound healing.

METHODS: A 1×1 cm2 full-thickness cutaneous wound was created after administering 40 mg/kg streptozotocin intraperitoneally (STZ i.p.) to induce a diabetic (DB) animal model. Animals were divided into four groups: DB, DB+PB, DB+CCT, and DB+CCT+PB, each with six adult Albino rats. The wound edges were treated with a total of 300 µL of solution, consisting of 30 µL each of 100 µL 1×106 MSC, 100 µL SVF, and 100 µL PRP as CCT. PB was administered orally at a dose of approximately 200 mg daily. Histochemical analyses were performed using hematoxylin and eosin (HE) and Masson's trichrome (MT). Immunohistochemical analyses were conducted for endothelial nitric oxide synthase (eNOS), Caspase-3, interleukin-10 (IL-10), vascular endothelial growth factor (VEGF), and Collagen I. The intestinal microbiome was examined through metagenomic analyses of taxonomic structure.

RESULTS: Combined cellular therapy provided more effective and faster healing in DB animals. It was discovered that PB further accelerated this process, leading to greater improvement. CCT was observed to reverse high eNOS, Caspase-3, and IL-10 expression, as well as low VEGF and Collagen I levels. Moreover, PB therapy significantly enhanced the positive effects of CCT. CCT in combination with PB significantly improved wound healing by preventing oxidative stress, apoptosis, and inflammation, while promoting vascularization and collagen organization.

CONCLUSION: Probiotic support was considered important for diabetic wound healing and was suggested to improve patients' quality of life.},
}

Animals
*Probiotics/therapeutic use/pharmacology
*Wound Healing/drug effects
Rats
*Diabetes Mellitus, Experimental/complications
Male
Skin/injuries
*Cell- and Tissue-Based Therapy/methods

@article {pmid41117333,
year = {2025},
author = {Naureckas Li, C and Jordan, N and Haymond, S and Koscinski, D and Jhaveri, R},
title = {Direct cost savings associated with reduction in plasma metagenomic sequencing.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1017/ice.2025.10329},
pmid = {41117333},
issn = {1559-6834},
abstract = {Following recognition that our hospital had higher use of plasma metagenomic next-generation sequencing than our peers, we implemented a process for approval by infectious diseases before test collection. This intervention is calculated to result in a direct cost savings of $79,505-$84,057/year, driven mainly by reduced laboratory costs.},
}

@article {pmid41115930,
year = {2025},
author = {Fitzjerrells, RL and Meza, LA and Yadav, M and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Cho, TA and Brown, G and Ganesan, SM and Mangalam, AK},
title = {Multiple sclerosis patients exhibit oral dysbiosis with decreased early colonizers and lower hypotaurine level.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {199},
pmid = {41115930},
issn = {2055-5008},
support = {F31DE033564/DE/NIDCR NIH HHS/United States ; T90DE023520/DE/NIDCR NIH HHS/United States ; R03DE030527/DE/NIDCR NIH HHS/United States ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; 1RO1AI137075//National Institute of Allergy and Infectious Diseases/ ; 1I01CX002212//U.S. Department of Veterans Affairs/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Taurine/analogs & derivatives/analysis/metabolism ; Middle Aged ; Metagenomics ; *Mouth/microbiology ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; Metabolomics ; *Bacteria/classification/genetics/isolation & purification ; Microbiota ; Fusobacterium nucleatum/isolation & purification ; Metabolome ; *Multiple Sclerosis/microbiology ; Actinomyces/isolation & purification ; Porphyromonas gingivalis/isolation & purification ; },
abstract = {Although gut microbiome dysbiosis is implicated in the pathobiology of multiple sclerosis (MS), the role of the oral microbiome (OM), the second largest microbiome, remains poorly understood. Additionally, while the salivary metabolome has been linked to other neurodegenerative diseases; its role in people with Relapsing-Remitting MS (pwRRMS), the most prevalent form of MS, is unknown. Combining shotgun metagenomics with untargeted metabolomics, we identified a reduced abundance of several early colonizing species including Streptococcus and Actinomyces in pwRRMS and an enrichment of bacteria with pathogenic potential including Fusobacterium nucleatum, Porphyromonas gingivalis, and several Prevotella species. pwRRMS had an altered metabolite profile including a decreased hypotaurine compared to healthy controls. Thus we report altered oral microbiome and metabolome in pwRRMS which might contribute to MS pathobiology. These findings offer potential microbiome-metabolome based diagnostic biomarkers for MS and pave the way for novel therapeutic interventions to improve disease management and patient outcomes.},
}

Humans
*Dysbiosis/microbiology
Female
Male
Adult
*Taurine/analogs & derivatives/analysis/metabolism
Middle Aged
Metagenomics
*Mouth/microbiology
*Multiple Sclerosis, Relapsing-Remitting/microbiology
Metabolomics
*Bacteria/classification/genetics/isolation & purification
Microbiota
Fusobacterium nucleatum/isolation & purification
Metabolome
*Multiple Sclerosis/microbiology
Actinomyces/isolation & purification
Porphyromonas gingivalis/isolation & purification

@article {pmid41115834,
year = {2025},
author = {Facey, FSB and Maharjan, R and Dinh, H and Buchanan, JS and Connal, LA and Tay, AP and Paulsen, IT and Cain, AK},
title = {Characterising the Multiple-Plastic Degrading Strain of Bacillus subtilis GM_03 From the Galleria mellonella Microbiome.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70216},
doi = {10.1111/1758-2229.70216},
pmid = {41115834},
issn = {1758-2229},
support = {W911NF2320155//US Department of Defense/ ; FT220100152//Australian Research Council Future Fellowship/ ; 20235185//FSBF was supported by Macquarie University Research Excellence Scholarship Programme/ ; },
mesh = {Animals ; *Bacillus subtilis/metabolism/genetics/isolation & purification/classification ; Larva/microbiology ; *Moths/microbiology ; Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Polyethylene/metabolism ; Polyurethanes/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Plastic waste is a mounting global problem with over 400 million tons of plastic produced annually and over 50% ending up in landfill after its intended use. Two types of plastics are particularly problematic and are difficult to recycle: low-density polyethylene (LDPE) and polyurethane (PU). Fortuitously, nature may offer a potential solution; Galleria mellonella larvae can digest various plastics, including LDPE, which is believed to be driven by microbes in their gut microbiome. Although some studies have examined their gut microbiota on a metagenomic level, little is known about their ability to degrade plastics. Here, we isolated six bacterial strains from G. mellonella larvae feeding on LDPE. One of them, identified as Bacillus subtilis GM_03, has the capacity to break down commercial PU (Impranil), in addition to LDPE. This bacterium encodes a suite of genes required for plastic degradation. Directed evolution was used to enhance this strain's plastic degrading rate by over six-fold. Sequencing of the evolved culture revealed four genes, srfAB, fadD, appA and citS, associated with this increased PU degradation rate. This is the first time that B. subtilis isolated from G. mellonella larvae has been shown to be capable of degrading multiple types of plastics.},
}

Animals
*Bacillus subtilis/metabolism/genetics/isolation & purification/classification
Larva/microbiology
*Moths/microbiology
Biodegradation, Environmental
*Plastics/metabolism
*Microbiota
Polyethylene/metabolism
Polyurethanes/metabolism
Phylogeny
Bacterial Proteins/genetics/metabolism
Gastrointestinal Microbiome

@article {pmid41115830,
year = {2025},
author = {Yang, F and Xu, W and Zhu, L and Tian, X and Duan, Y and Xu, Y and Huang, Q and Zhao, F},
title = {Multiple Roles of Extracellular Vesicles in Promoting Microbial-Driven Manganese Reduction.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05310},
pmid = {41115830},
issn = {1520-5851},
abstract = {Microbial-driven manganese (Mn) reduction influences the geochemical cycling of Mn and the environmental fate of various organic and inorganic substances. Extracellular vesicles (EVs) are known to impact microbial metabolic activities, but their specific role in Mn reduction remains arcane. Here, we explored the potential involvement of environmental EVs in this process through metagenomic analysis and validated their function using representative functional strains. There are 8.05 and 12.89% of EVs originating from electroactive microorganisms in soil and wastewater, respectively. The addition of EVs increases the birnessite reduction rate of Shewanella oneidensis MR-1 from 2.31 μmol/(L·h) to 20.86 μmol/(L·h). Microbial physiological assays and in situ electrochemical analyses revealed that EVs enhanced cellular metabolism, promoted biofilm formation, and facilitated extracellular electron transfer (EET). The presence of diverse redox enzymes and metabolites in EVs contributed to more efficient substrate utilization and energy conservation, which promoted biomass accumulation and increased substrate consumption by 45.33%. The inner and outer membrane c-type cytochromes, along with flavins contained in the EVs, are essential for promoting microbial EET. These findings highlight the multifaceted role of EVs in microbial-driven Mn reduction, which might also participate in other element cycles in the same way.},
}

@article {pmid41114585,
year = {2025},
author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T},
title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0042925},
doi = {10.1128/msphere.00429-25},
pmid = {41114585},
issn = {2379-5042},
abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.},
}

@article {pmid41114582,
year = {2025},
author = {Zhang, Z and Wang, Z and Teng, P and Yu, T and Zhang, Y},
title = {Oxygen-tolerant nitrogen fixation in a marine alga-colonizing Planctomycetota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131625},
doi = {10.1128/aem.01316-25},
pmid = {41114582},
issn = {1098-5336},
abstract = {UNLABELLED: The microbiomes colonizing macroalgal surfaces orchestrate nutrient fluxes and symbiotic interactions within the algal environment. Among these communities, Planctomycetota are often dominant taxa. Although nitrogenase (nif) gene clusters have been identified in Planctomycetota isolates and metagenome-assembled genomes, functional validation of nitrogen fixation in pure culture has remained elusive. Moreover, the mechanisms enabling these bacteria to overcome oxygen sensitivity and fix nitrogen in algal-associated oxic niches remain unexplored. Here, we isolated Crateriforma sp. HD03, a Planctomycetota strain from the surface of Saccharina japonica (kelp), and provided the first experimental evidence of nitrogen-fixing activity in pure-cultured Planctomycetota. Strain HD03 harbors a complete nifHDKBEN gene cluster and exhibits a remarkable nitrogen fixation rate of 14.2 ± 1.5 nmol C2H4/(10[7] cells)/h under aerobic conditions. Genomic and physiological analysis reveals a suite of adaptations that likely mitigate oxygen stress, including genes associated with biofilm formation, hopanoid lipid synthesis, FeSII protein, hydrogenase, and bacterial microcompartments. Notably, while strain HD03 demonstrates oxygen-tolerant nitrogen fixation in pure culture, co-culture experiments with kelp under a photoperiod revealed that nifH (nitrogenase reductase gene) expression peaks during the low-oxygen dark phase, indicating that HD03 utilizes diurnal rhythms to temporally separate nitrogen fixation from photosynthetic oxygen production. A genomic survey of 142 Planctomycetota strains from NCBI GenBank database and HD03 identified two distinct clades harboring complete nifHDK gene clusters, suggesting a nitrogen-fixing potential across the phylum. By bridging the gap between genomic potential and functional validation, this study establishes Planctomycetota as important but underappreciated contributors to marine nitrogen input.

IMPORTANCE: Planctomycetota are abundant colonizers of macroalgal surfaces, yet their role in nitrogen fixation has remained unresolved despite genomic evidence of nitrogenase (nif) genes. Until now, no functional validation of nitrogen fixation in pure-cultured Planctomycetota has been reported. Here, we isolated Crateriforma sp. HD03 from kelp and for the first time demonstrated its ability to fix nitrogen in pure culture, confirming this key metabolic potential in marine Planctomycetota. Strain HD03 overcomes oxygen stress through a combination of biofilm formation and diurnal regulation of nifH expression, allowing nitrogen fixation under aerobic conditions to cope with the algal environment's oxic nature. Furthermore, genomic surveys revealed nitrogen fixation gene clusters across multiple Planctomycetota clades, suggesting widespread nitrogen-fixing capability in this phylum. Collectively, these findings identify Planctomycetota as important nitrogen providers in the ocean.},
}

@article {pmid41114530,
year = {2025},
author = {Xiao, Y and Zhang, X and Shao, B and Wu, Z and Li, X and Yi, D and Li, T and Yang, T and Zhu, J and Huang, T and Deng, Y and Qiu, T and Yang, G and Sun, X and Wang, N},
title = {Hydroxytyrosol Improves Metabolic Dysfunction-Associated Fatty Liver Disease Dependent on the Modulation of Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c07003},
pmid = {41114530},
issn = {1520-5118},
abstract = {The global threat of metabolic dysfunction-associated fatty liver disease (MAFLD) is significant, but effective measures are still lacking. To explore the potential impact of hydroxytyrosol (HT), a plant polyphenol, in the metabolic outcomes of MAFLD and the mediating role of the gut microbiota, we performed an 8-week randomized placebo-controlled clinical trial in MAFLD patients and collected fecal bacteria for metagenomics analysis and targeted metabolomics. In this population-based trial, we have revealed that HT mitigates liver injury and steatosis in patients with MAFLD, as well as systemic glucolipid metabolism disorder. Through analysis of the differences in bacterial taxon and functional profiles, as well as correlation analysis between species and metabolic indicators, it was found that Fusicatenibacter saccharivorans (F. saccharivorans), the microbial species with the greatest difference after HT intervention, was also the most significantly correlated with metabolic parameters of MAFLD and showed a significant positive correlation with the content of fecal butanoic acid. Butanoic acid was further associated with MAFLD-related metabolic indexes. To confirm the potential causal relationship between alterations in gut microbiota induced by HT intervention and improved MAFLD metabolic phenotypes, fecal microbiota transplantation (FMT) was conducted using a model of pseudogerm-free mice. We have further demonstrated that the fecal microbiota from donors of MAFLD patients receiving HT supplementation can ameliorate liver and systemic phenotypes in western-diet-induced MAFLD mice, interpreting the robust action of gut microbiota remodeled by HT in improving MAFLD. Consequently, HT supplementation may represent a tactic for improving MAFLD by modulating the composition and functionality of the gut microbiota.},
}

@article {pmid41114048,
year = {2025},
author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD},
title = {Duration of Hospitalization is Associated with the Gut Microbiome in Patients Undergoing Hematopoietic Stem Cell Transplantation: Early Results from a Randomized Trial of Home Versus Hospital Transplantation.},
journal = {OBM transplantation},
volume = {9},
number = {3},
pages = {},
pmid = {41114048},
issn = {2577-5820},
abstract = {Home-based hematopoietic stem cell transplantation (HCT) is an innovative care model with growing interest, but its impact on the gut microbiome remains unexplored in a randomized setting. We present interim results from the first randomized controlled trials (RCT) evaluating the effect of HCT location-home versus hospital-on gut microbial diversity and antimicrobial resistance (AMR) gene carriage. We hypothesize that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower AMR gene abundance compared to those undergoing standard hospital HCT. We analyzed stool samples from the first 28 patients enrolled in ongoing Phase II RCTs comparing home (n = 16) and hospital (n = 12) HCT at Duke University using shotgun metagenomic sequencing to compare taxa and AMR gene composition between groups. We also performed a secondary analysis comparing patients who received transplants at outpatient infusion clinics versus inpatient standard HCT to evaluate the influence of hospitalization duration. In the primary RCT analysis, taxonomic and AMR gene α- and β-diversity were comparable between home and hospital groups, reflecting similar durations of hospitalization despite group allocation. In contrast, secondary analyses demonstrated that patients transplanted in outpatient infusion clinics who experienced significantly reduced hospitalization had higher gut taxonomic α-diversity and differential β-diversity, although AMR gene diversity remained unchanged. In summary, randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups. This RCT represents a novel investigation into how care setting influences the gut microbiome during HCT. Our findings suggest that hospital duration, rather than randomization allocation alone, is the primary driver of microbial disruption. These results underscore the potential for reducing hospital duration to mitigate microbiome injury, thereby informing future interventions to reduce infection risk and improve patient outcomes.},
}

@article {pmid41114028,
year = {2025},
author = {Huang, H and Tong, Y and Hu, X and Liao, FK and Chen, R},
title = {The application value and challenges of metagenomic next-generation sequencing in the diagnosis of periprosthetic joint infection after arthroplasty.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1686503},
pmid = {41114028},
issn = {2296-858X},
abstract = {Metagenomic next-generation sequencing (mNGS) demonstrates high sensitivity, rapid diagnostic capabilities, and the potential to identify complex pathogens in periprosthetic joint infection (PJI) following arthroplasty, particularly when conventional culture methods are limited. mNGS enables the detection of polymicrobial infections and rare/fastidious pathogens, along with the ability to predict antimicrobial resistance (AMR) genes; however, the concordance between genotypic predictions and phenotypic resistance profiles requires further validation. In clinical practice, mNGS overcomes biofilm-related diagnostic barriers, facilitating early targeted antibiotic therapy and potentially reducing unnecessary revision surgeries, thereby lowering overall healthcare costs and improving patient outcomes. Nevertheless, its widespread adoption is hindered by high costs, lack of standardization, and risks of false-positive/false-negative results. Future research priorities include optimizing sample processing protocols, host DNA depletion, establishing diagnostic thresholds, and validating mNGS through integration with conventional methods. This review synthesizes recent advances in the diagnostic accuracy and clinical utility of mNGS for PJI, aiming to provide evidence-based insights for therapeutic decision-making and enhance the prevention and management of PJI.},
}

@article {pmid41114012,
year = {2025},
author = {Wang, H and Li, J and Huang, W},
title = {Case Report: Fever of unknown origin with hemophagocytic lymphohistiocytosis and intestinal hemorrhage-a successfully treated case of severe visceral leishmaniasis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1663551},
pmid = {41114012},
issn = {2296-858X},
abstract = {In recent years, some cases of severe visceral leishmaniasis (VL) in immunocompetent adults have gradually been reported. Hemophagocytic lymphohistiocytosis (HLH) and intestinal hemorrhage are two rare complications in patients with VL. Without treatment, the mortality rate of such patients is extremely high. We report a case of a 31-year-old immunocompetent male who initially presented with fever of unknown origin (FUO), later developed HLH and experienced multiple episodes of life-threatening intestinal hemorrhage. The diagnosis of visceral leishmaniasis was confirmed through metagenomic next-generation sequencing (mNGS). The patient was successfully treated with amphotericin B deoxycholate (AmB-D) and supportive care. During the two-year follow-up period, no new complications were found. This case highlights the value of mNGS in the diagnosis of complex infectious diseases and emphasizes the clinical significance of the multidisciplinary collaborative model for patients with VL and complex complications. It can provide a reference for the early diagnosis and comprehensive treatment of severe VL.},
}

@article {pmid41114005,
year = {2025},
author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM},
title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf164},
pmid = {41114005},
issn = {2730-6151},
abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.},
}

@article {pmid41113669,
year = {2025},
author = {Onohuean, H and Naik Bukke, SP and Thalluri, C and Abass, KS and Choonara, YE},
title = {Exosome engineering for targeted therapy of brain-infecting pathogens: molecular tools, delivery platforms, and translational advances.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1655471},
pmid = {41113669},
issn = {2673-3129},
abstract = {Central nervous system (CNS) infections caused by pathogens such as HIV, Herpes simplex virus, Cryptococcus neoformans, and Toxoplasma gondii remain among the most difficult to treat due to the physiological barrier posed by the blood-brain barrier (BBB), pathogen latency, and systemic toxicity associated with conventional therapies. Exosome-based delivery systems are becoming a game-changing platform that can solve these therapeutic problems using their natural biocompatibility, minimal immunogenicity, and capacity to cross the BBB. This review current developments in exosome engineering that aim to make brain-targeted therapy for neuroinfectious illnesses more selective and effective. Much focus is on new molecular methods like pathogen-specific ligand display, aptamer conjugation, lipid modification, and click-chemistry-based surface functionalisation. These methods make it possible to target diseased areas of the brain precisely. Exosomes can also carry therapeutic payloads, such as anti-viral and antifungal drugs, gene editing tools like CRISPR/Cas9 and siRNA, and more. This makes them helpful in changing pathogens' persistence and the host's immunological responses. The paper tackle problems with translation, such as biodistribution, immunogenicity, GMP production, and regulatory issues. Future possibilities like synthetic exosomes, combinatory medicines, and delivery design that uses AI. The combination of nanotechnology, molecular biology, and infectious disease therapies shows that exosome engineering offers a new way to meet the clinical needs that are not satisfied in treating CNS infections.},
}

@article {pmid41113648,
year = {2025},
author = {Dong, L and Du, Y and Qiu, F and Zhang, M and Wang, X and Zhu, X and Yao, Y and Li, J and Ji, X and Zhu, X},
title = {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 = {1652229},
pmid = {41113648},
issn = {1664-302X},
abstract = {INTRODUCTION AND METHODS: Sea turtles have been proposed as health indicators of marine ecosystems for their characteristic of longevity and migratory, but they are facing serious threats due to various factors. The microbial communities within animals play an important role in health and disease. Our study aims to explore a thorough evaluation of the sea turtle microbiome by examining the oral, nasal, and cloacal microbial communities of three species: green turtles, hawksbills, and loggerheads, through metagenomic sequencing.

RESULTS: Utilizing approximately 705.81 GB of metagenomic sequencing data from 63 samples collected from different turtle species and tissue regions, we created a nonredundant sea turtle microbial gene catalog (STMGC) containing 10,733,232 unique genes through the de-redundancy of open reading frames (ORFs). Our findings revealed that the sea turtle microbiomes were primarily composed of Pseudomonadota (formerly Proteobacteria) and Bacteroidota (formerly Bacteroidetes). The tissue region was a key factor affecting the variability in the sea turtle microbiome, with green turtles showing notable differences among the three turtle species. Pseudomonadota was significantly more abundant in oral samples, while Bacteroidota was more prevalent in nasal samples. Campylobacterota was identified as significantly more abundant in cloacal samples. Importantly, we discovered 389 genera and 1,445 species of potential pathogens within the sea turtle microbiome, indicating potential pathogenic risks that warrant further investigation alongside culturomics. Additionally, our study highlighted significant functional differences among the three turtles and tissue regions. It is worth noting that among the three sea turtles, antibiotic resistance genes are more prevalent in hawksbills, while virulence genes are more abundant in loggerheads. Moreover, within the three tissue regions, antibiotic resistance genes are higher in oral samples, while virulence genes are more extensive in cloacal samples.

CONCLUSION: The findings in our study demonstrate that the microbial composition and function in these sea turtles exhibit both species-specific and region-specific variations. The implications of these associations and the underlying mechanisms not only provide valuable insights for future studies on the microbial communities of turtles, but also lay the foundation for further research on the health interrelationships among sea turtles, marine and terrestrial animals, humans and the environment, and for defining "One Health" factors.},
}

@article {pmid41113647,
year = {2025},
author = {Meng, Y and Xu, Y and Hu, D and Pan, Q and Weng, L and Huang, W and Zhao, J and Lan, W and Shi, Q and Yu, Y and Jiang, Y},
title = {Evaluating the effects of hospital wastewater treatment on bacterial composition and antimicrobial resistome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620677},
pmid = {41113647},
issn = {1664-302X},
abstract = {Hospital wastewater treatment systems (HWTS) are crucial in reducing the spread of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacterial pathogens in hospital wastewater. This study aims to evaluate the impact of HWTS on the changes of bacterial composition and the relative abundance of ARGs. We collected wastewater samples from influent and effluent in a university hospital, and performed metagenomic sequencing. The results showed that HWTS altered the bacterial composition, with a decrease in the proportion of Gammaproteobacteria. However, phylogenetic analysis of metagenome-assembled genomes showed that Mycobacterium and Zoogloea from influent and effluent had a close relationship. A total of 140 non-redundant ARGs were identified based on open reading fragments analysis, with beta-lactam and aminoglycoside resistance genes being the most prevalent. The relative abundance of ARGs generally decreased after wastewater treatment (p < 0.0001), with 70.0% of genes that conferring resistance to "last-resort" antibiotics being undetectable in the effluent. However, the relative abundance of quaternary ammonium compounds resistance genes increased in the effluent. We identified that 66.4% of ARGs were located on plasmids, and 17.9% of ARGs were adjacent to mobile gene elements (MGEs), suggesting their potential for mobility. Subsequent analysis showed that ARGs originating from plasmids and adjacent to MGEs were negatively associated with their relative abundance reduction. In conclusion, this study provides a comprehensive evaluation of the impact of HWTS on composition of bacteria and the relative abundance of ARGs, highlighting the importance of effective wastewater treatment in combating the spread of antimicrobial resistance.},
}

@article {pmid41113646,
year = {2025},
author = {Chen, X and Wu, J and Fan, D and Zhang, P and Li, Y and Cao, Y and Cao, M},
title = {Gut viral metagenomics identifies viral signatures and their role in depression.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1573851},
pmid = {41113646},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome has been implicated in the onset and progression of depression. Yet, the role of the gut virome in depression remains unexplored, and a diagnostic model has not been satisfactorily constructed.

METHODS: Herein, we analysed the gut virome profiles of 29 patients with depression and 33 healthy controls using bulk metagenome sequencing.

RESULTS: A total of 45 differentially abundant viral taxa were identified, among which four, s_Stenotrophomonas_virus_Pokken, g_Pokkenvirus, s_Dickeya_virus_AD1, and g_Alexandravirus, demonstrated strong diagnostic potential (AUCs > 0.8). These four viruses also exhibited strong correlations, suggesting they may constitute a synergistic ecological cluster. Function annotation revealed seven metabolic pathways with significant differences, including alanine, aspartate, and glutamate metabolism, branched-chain amino acid (BCAA) biosynthesis, and energy metabolism in patients with depression.

CONCLUSION: This study identified four distinct viral signatures for depression and proposes novel viral biomarkers for the diagnosis of depression, offering a robust diagnostic approach and new insights into the pathological mechanisms of depression.},
}

@article {pmid41113645,
year = {2025},
author = {Durán-González, E and Ramírez-Tejero, JA and Pérez-Sánchez, M and Morales-Torres, C and Gómez-Morano, R and Díaz-López, C and Martínez-Lara, A and Cotán, D},
title = {Fibromyalgia diagnosis from a multi-omics approach: a gut feeling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641185},
pmid = {41113645},
issn = {1664-302X},
abstract = {BACKGROUND: Fibromyalgia is a complex disorder whose main symptoms are chronic widespread pain and fatigue and affects between 0.2 and 6.6% of the world population. Nowadays, there are no molecular biomarkers that could facilitate diagnosis. The latest efforts by researchers have focused on studying problems at the level of central nervous system sensitivity, inflammation, and oxidative disorders.

METHODS: A total of 892 women were initially enrolled in the study. For individuals who met the inclusion criteria, a plasma proteome analysis was conducted using blood samples. Briefly, blood was collected, centrifuged, and analyzed by liquid nano-chromatography coupled to tandem mass spectrometry. After the raw data analysis, proteins with statistically significant differential abundance and a fold change over 1.2 (20% increase in fibromyalgia compared with control samples) or under 0.8 (20% decrease in fibromyalgia compared with control samples) in fibromyalgia were selected. For fecal metagenome analysis, fecal samples were collected and processed for DNA extraction. Amplicon sequencing of V3-V4 regions from the 16S ribosomal RNA gene was performed using the Illumina MiSeq platform. The statistical analysis was conducted using R v4.3.2 base packages.

RESULTS: After applying exclusion criteria, 242 women (199 patients and 43 age- and environmentally paired controls) provided plasma and feces samples, as well as properly filled health questionnaires. A total of 30 proteins and 19 taxa were differentially expressed in fibromyalgia patients, and their integration into an algorithm allows for discrimination between cases and controls. The multi-omic approach for biomarker discovery in this study proposes a multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation.

CONCLUSIONS: Plasma and fecal multi-omics analysis suggest an intricate and multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation in FM patients, with glyceraldehyde-3-phosphate dehydrogenase and Streptococcus salivarius as leading actors.

TRIAL REGISTRATION: NCT05921409.},
}

@article {pmid41113638,
year = {2025},
author = {Verma, D and Zhang, Z and Liu, J},
title = {Editorial: Tobacco disease and biological control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1694523},
pmid = {41113638},
issn = {1664-302X},
}

@article {pmid41113400,
year = {2025},
author = {Ning, H and Feng, R and Wu, H and Sun, C},
title = {[Innovative Practices of Precision Nutrition in Obesity Intervention: From Theory to Application].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {56},
number = {4},
pages = {893-899},
pmid = {41113400},
issn = {1672-173X},
mesh = {Humans ; *Obesity/prevention & control ; *Precision Medicine/methods ; Metabolomics ; Genomics ; Diet ; },
abstract = {Obesity has emerged as a critical global public health challenge, with an urgent need for effective prevention and control strategies. Traditional nutritional intervention approaches often overlook individual variability and dietary complexity, which limits their effectiveness in achieving precision-based prevention and control. In this context, nutritional intervention strategies are gradually shifting from population-based models to individualized precision nutrition models, which integrate and analyze multidimensional data to open new pathways for obesity prevention and control. The theoretical framework of precision nutrition is based on the recognition that individual heterogeneity in biological mechanisms underlies individual variations in nutritional needs. The research approaches in precision nutrition include genomics, epigenetics, metagenomics, metabolomics, and integrated multi-omics analyses. In terms of application, precision nutrition combines advanced external dietary exposure assessment tools-such as Internet-based dietary assessment systems and AI-driven image recognition-with omics-derived internal biomarkers to enable accurate quantification of dietary intake. Principles such as holistic dietary integrity, full coverage of dietary restrictions, optimized cooking methods, and chrononutrition are emphasized in intervention strategies. Future efforts in precision nutrition should focus on overcoming technical challenges, including thorough integration of multi-omics data and the development of intelligent decision-making systems. The goal is to move beyond generalized, "one-size-fits-all" model toward tailored, precision-based intervention. Precision nutrition will provide essential scientific and technological support for the Healthy China 2030 initiative and help usher in a new era of scientific and individualized obesity prevention and control.},
}

Humans
*Obesity/prevention & control
*Precision Medicine/methods
Metabolomics
Genomics
Diet