@article {pmid40377870,
year = {2025},
author = {Amen, RA and Hassan, YM and Essmat, RA and Ahmed, RH and Azab, MM and Shehata, NR and Elgazzar, MM and El-Sayed, WM},
title = {Harnessing the Microbiome: CRISPR-Based Gene Editing and Antimicrobial Peptides in Combating Antibiotic Resistance and Cancer.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40377870},
issn = {1867-1314},
abstract = {The growing crisis of antibiotic resistance and the increasing incidence of cancer have prompted the exploration of innovative approaches, such as gene editing and antimicrobial peptides (AMPs). The human microbiome is integral to various aspects of health, disease, and therapeutic development, influencing metabolic pathways, immune function, and pathogen resistance. Recent advances in gene editing technologies, particularly CRISPR (clustered regularly interspaced short palindromic repeats), have opened new avenues for leveraging the microbiome to address complex medical challenges, including combating multidrug-resistant pathogens and cancer. The microbiome plays a crucial role in combating antibiotic resistance by modulating microbial communities, influencing pathogen survival and susceptibility to treatments. This review explores the microbiome's dynamic role in metabolic regulation, its contribution to cancer management, and how AMPs help maintain homeostasis and exhibit emerging anticancer properties, supported by both preclinical findings and clinical evidence. Additionally, CRISPR-based microbiome engineering offers potential to enhance host-microbiome interactions, optimizing therapeutic outcomes. The integration of microbiome metagenomics and proteomics has led to the discovery of novel AMPs with targeted anticancer effects. Innovative strategies, such as engineered probiotics and CRISPR-based microbiome engineering, present exciting prospects for next-generation therapies. Despite these advances, the translation of microbiome-based therapies into clinical settings remains challenging due to ethical, regulatory, and ecological hurdles. This review underscores the transformative potential of microbiome-based interventions, emphasizing the role of personalized medicine in maximizing therapeutic efficacy. Furthermore, we also address critical research gaps, limitations, and future directions, including optimizing AMP stability, delivery, and bioavailability, as well as overcoming the regulatory and ethical challenges in clinical translation.},
}

@article {pmid40377844,
year = {2025},
author = {Paul, B and Pan, P and Bhattacharyya, N},
title = {Investigating the impact of fly ash contamination on soil microbial diversity: a metagenomic study near Kolaghat Thermal Power Plant, India.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40377844},
issn = {1614-7499},
abstract = {Soil metagenomics using whole genome shotgun sequencing (WGS) uncovers microbial diversity and functionality in soils. This study aimed to explore microbial diversity and functional adaptation in soils exposed to fly ash near the Kolaghat Thermal Power Plant, West Bengal, India, using whole genome shotgun sequencing. Understanding how microbial communities respond to such contamination is essential for developing effective bioremediation strategies. Soil samples were collected from the area, designated as BP1 sample selected for detailed metagenomics analysis. The study extracted DNA with a concentration of 46.2 ng/µl, followed by quality checks and profiling to identify microbial communities. Analysis showed that bacterial communities were dominated by Actinobacteria (48.28%) and Proteobacteria (40.80%), while fungi were primarily represented by Ascomycota (89.50%). Among viruses, Negarnaviricota were most prevalent, with the class Insthoviricetes accounting for 94.60%. Diversity analysis indicated that bacterial populations remained stable, fungal diversity fluctuated, and viral diversity increased, reflecting complex ecological interactions. The presence of key genes involved in lipid and carbohydrate metabolism suggests that microbes adapted to contamination by heavy metals and organic pollutants. The dominance of stress-tolerant Proteobacteria and Actinobacteria highlights their potential role in bioremediation. Future research should explore the potential of these microbes, particularly the role of ABC transporters, in improving pollutant degradation.},
}

@article {pmid40377330,
year = {2025},
author = {Thajudeen, J and Venkatachalam, S and Vipindas, PV},
title = {Antibiotic resistome in the glacier forelands of polar regions.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0076225},
doi = {10.1128/aem.00762-25},
pmid = {40377330},
issn = {1098-5336},
abstract = {UNLABELLED: Antibiotic resistance genes (ARGs) pose a significant threat, exacerbated by climate change impacts on polar regions, particularly melting glaciers and permafrost. While ancient antibiotic resistance exists in the environments, the release and dissemination of ARGs remain poorly understood. This study investigated ARG composition and distribution in 43 metagenomes from Arctic and Antarctic glacier forelands. We identified 154 ARGs, predominantly bacitracin resistance, followed by rifamycin, fosfomycin, vancomycin, tetracycline, and beta-lactam resistance genes. Significant correlations were observed between ARGs and mobile genetic elements (MGEs), with 20 ARGs associated with tnpA MGEs. Actinomycetota and Pseudomonadota were the primary ARG-carrying phyla. Metagenome-assembled genomes revealed Mycobacterium sp., Pseudomonas sp., and Tatlockia sp. as major ARG-harboring pathogens in the glacier forelands. Evolutionarily adapted, distinct ancient ARGs were abundant in the polar environments, varying between different geographic regions. The environmental parameters such as pH and total organic carbon significantly influenced the ARG distribution in the Arctic and Antarctic glacier forelands. This study provides crucial baseline data on antimicrobial resistance, highlighting potential risks associated with rapid environmental change in the regions.

IMPORTANCE: Antibiotic resistance poses a significant global health threat, exacerbated by the release of antibiotic resistance genes from melting glaciers and permafrost due to climate change. This study provides crucial baseline data on the composition and distribution of antibiotic resistance genes in these vulnerable polar environments, which is essential for understanding and mitigating the risks associated with their release. The findings have far-reaching implications for global health security and emphasize the need for further research to address this emerging threat.},
}

@article {pmid40377187,
year = {2025},
author = {Veseli, I and Chen, YT and Schechter, MS and Vanni, C and Fogarty, EC and Watson, AR and Jabri, B and Blekhman, R and Willis, AD and Yu, MK and Fernàndez-Guerra, A and Füssel, J and Eren, AM},
title = {Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {40377187},
issn = {2050-084X},
support = {1746045//National Science Foundation Graduate Research Fellowship Program/ ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM128716/NH/NIH HHS/United States ; RC2 DK122394/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Stress, Physiological ; Metagenome ; *Bacteria/metabolism/genetics/classification ; },
abstract = {A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Stress, Physiological
Metagenome
*Bacteria/metabolism/genetics/classification

@article {pmid40376801,
year = {2025},
author = {Prisco, SZ and Blake, M and Kazmirczak, F and Moon, R and Kremer, BP and Hartweck, LM and Kim, M and Vogel, N and Mendelson, JB and Moutsoglou, D and Thenappan, T and Prins, KW},
title = {Lactobacillus Restructures the Micro/Mycobiome to Combat Inflammation-Mediated Right Ventricular Dysfunction in Pulmonary Arterial Hypertension.},
journal = {Circulation. Heart failure},
volume = {},
number = {},
pages = {e012524},
doi = {10.1161/CIRCHEARTFAILURE.124.012524},
pmid = {40376801},
issn = {1941-3297},
abstract = {BACKGROUND: Inflammation suppresses right ventricular (RV) function in pulmonary arterial hypertension (PAH). In particular, we showed GP130 (glycoprotein-130) signaling promotes pathological microtubule remodeling and RV dysfunction in rodent PAH. Emerging data demonstrate the intestinal microbiome regulates systemic inflammation, but the impact of modulating the gut microbiome on the GP130-microtubule axis in RV failure is unknown.

METHODS: Two weeks following monocrotaline injection, rats were administered daily Lactobacillus rhamnosus (4×10[7] colony-forming units) via oral gavage for 10 days. Next-generation metagenomics and internal transcribed spacer 2 sequencing delineated fecal bacterial and fungal compositions. SomaScan proteomics measured levels of 7596 serum proteins. RV immunoblots quantified protein abundances. Light or super resolution confocal microscopy assessed RV, lung, and jejunal morphology. Echocardiography and invasive closed-chest pressure-volume loops evaluated PAH severity and RV function. The relationship between Lactobacillus abundance and RV function was assessed in 65 patients with PAH.

RESULTS: Lactobacillus administration restructured both the intestinal micro- and mycobiome. The alteration in the gut ecosystem improved intestinal health as demonstrated by increased jejunal villus length and glycocalyx thickness and diminished intestinal permeability biomarkers. Serum proteomics revealed Lactobacillus modulated systemic inflammation and decreased circulating GP130 ligands. Lactobacillus-mediated suppression of GP130 signaling blunted pathological microtubule remodeling in RV cardiomyocytes. Microtubule-associated phenotypes, including RV cardiomyocyte and nuclear hypertrophy, transverse tubule integrity, and connexin-43 localization, were all corrected with Lactobacillus. These cellular changes manifested as improved RV function despite no significant alteration in PAH severity. Finally, patients with PAH and detectable fecal Lactobacillus had superior RV function despite similar mean pulmonary arterial pressure and pulmonary vascular resistance as compared with those without detectable Lactobacillus.

CONCLUSIONS: Lactobacillus supplementation restructures the gut micro/mycobiome, restores intestinal health, dampens systemic inflammation, and reduces GP130 ligands and associated RV cardiomyocyte microtubule remodeling. These data identify a novel microbiome-inflammation-microtubule axis that has therapeutic relevance for RV dysfunction.},
}

@article {pmid40376464,
year = {2025},
author = {Shao, X and Yang, C and Chen, Y and Liu, C and Liu, C and Shi, X and Zhou, Y},
title = {Sorghum-peanut intercropping under salt stress mediates rhizosphere microbial community shaping in sorghum by affecting soil sugar metabolism pathways.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589415},
pmid = {40376464},
issn = {1664-302X},
abstract = {Soil salinization is a substantial impediment to agricultural production, and investigating sustainable mitigation measures is essential for addressing food security. We conducted a two-year pot experiment to investigate the shaping mechanism of sorghum rhizosphere microbial community in sorghum-peanut intercropping system under salt stress. The experiment comprised four treatments: sole-cropped sorghum under normal soil conditions (NSS), intercropped sorghum under normal soil conditions (NIS), sole-cropped sorghum under salt-stress conditions (SSS), and intercropped sorghum under salt-stress conditions (SIS). The sorghum rhizosphere soil metabolites were examined using GC-MS, and the rhizosphere microbial community was characterized through metabolome sequencing. We identified 123 metabolites across treatments, with significant differences between normal and salt-stress soil conditions. The major metabolite classes included carbohydrates, alcohols, and acids. Key carbohydrates, including fructose and sucrose, were significantly reduced in the SIS than in SSS, NSS, and NIS treatments. Metabolic pathway analyses revealed that these differences were primarily associated with "Fructose and mannose metabolism," "Starch and sucrose metabolism" and "ABC transporter." Metabolome analyses revealed significant differences in microbial community structure across diverse soil conditions and cropping patterns. At phylum level, Proteobacteria, Gemmatimonadetes, and Verrucomicrobia predominated, with their relative abundance experiencing substantial changes under salt stress. SIS facilitated the enrichment of specific genera (Rhodanobacter), which were associated with soil health and stress tolerance. Additionally, the responses of rare microbial taxa to salt stress and intercropping varied, with specific rare microbial taxa (Rhizopus) exhibiting relative abundance under salt stress. Correlation analysis of metabolites and microbial taxa revealed that certain carbohydrates were significantly positively correlated with specific microbial phyla (Cyanobacteria and Nitrospirae) while demonstrating a significant negative correlation with Planctomycetota and Bacteroidota. These correlations indicate that sorghum intercropped with peanuts can promote the enrichment of microbial taxa under salt stress, thereby enhancing soil metabolic functions and stress tolerance by optimizing the rhizosphere microbial community. This study reveals the mechanism through which sorghum-peanut intercropping under salt stress influences the composition of sorghum's rhizosphere microbial community by modulating soil sugar metabolism pathways. This finding provides a new perspective on sustainable agricultural practices in saline soils and emphasizes the pivotal role of plant-metabolite-microbe interactions in abiotic stress mitigation.},
}

@article {pmid40376462,
year = {2025},
author = {Han, Y and Cao, B and Tang, J and Wang, J},
title = {A comprehensive multi-omics analysis uncovers the associations between gut microbiota and pancreatic cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1592549},
pmid = {40376462},
issn = {1664-302X},
abstract = {Pancreatic cancer is one of the most lethal malignant neoplasms. Pancreatic cancer is related to gut microbiota, but the associations between its treatment and microbial abundance as well as genetic variations remain unclear. In this study, we collected fecal samples from 58 pancreatic cancer patients including 43 pancreatic ductal adenocarcinoma (PDAC) and 15 non-PDAC, and 40 healthy controls, and shotgun metagenomic sequencing and untargeted metabolome analysis were conducted. PDAC patients were divided into five groups according to treatment and tumor location, including treatment-naive (UT), chemotherapy (CT), surgery combined with chemotherapy (SCT), Head, and body/tail (Tail) groups. Multivariate association analysis revealed that both CT and SCT were associated with increased abundance of Lactobacillus gasseri and Streptococcus equinus. The microbial single nucleotide polymorphisms (SNPs) densities of Streptococcus salivarius, Streptococcus vestibularis and Streptococcus thermophilus were positively associated with CT, while Lachnospiraceae bacterium 2_1_58FAA was positively associated with Head group. Compared with Tail group, the Head group showed positive associations with opportunistic pathogens, such as Escherichia coli, Shigella sonnei and Shigella flexneri. We assembled 424 medium-quality non-redundant metagenome-assembled genomes (nrMAGs) and 276 high-quality nrMAGs. In CT group, indole-3-acetic acid, capsaicin, sinigrin, chenodeoxycholic acid, and glycerol-3-phosphate were increased, and the accuracy of the model based on fecal metabolites reached 0.77 in distinguishing healthy controls and patients. This study identifies the associations between pancreatic cancer treatment and gut microbiota as well as its metabolites, reveals bacterial SNPs are related to tumor location, and extends our knowledge of gut microbiota and pancreatic cancer.},
}

@article {pmid40376454,
year = {2025},
author = {Yu, T and Cheng, L and Zhang, Q and Yang, J and Zang, H and Zeng, Z and Yang, Y},
title = {Characterization of antibiotic resistance genes and virulence factors in organic managed tea plantation soils in southwestern China by metagenomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1580450},
pmid = {40376454},
issn = {1664-302X},
abstract = {Sustainable organic management practices have gained significant attentions for its potential health and environmental benefits. However, the spread of antibiotic resistance genes (ARGs) and virulence factors (VFs) in soils, plants, and agricultural products has severely limited the development of organic managements on agriculture. At present, the distribution and assembly of ARGs and VFs in organic managed tea plantation systems remains largely unknown. Here, we used metagenomic analysis to explore soil microbial taxa, ARGs and VFs in 20 years of conventional managed (CM) and organic managed (OM) tea plantation soils. Results showed that total abundance of ARGs in OM was 16.9% (p < 0.001) higher than that in CM, and the increased ARGs were rpoB2, evgS, MuxB, TaeA, and efrA. As for VFs, OM significantly increased the abundance of adherence, stress protein and actin-based motility compared to CM. Moreover, OM increased the relative abundance of soil microbial taxa harboring ARGs and VFs, which were Streptomyces, Pseudomonas, and Terrabacter, compared to CM. Network analysis suggested that OM increased the positive interactions of microbial taxa-ARGs, microbial taxa-VFs and ARGs-VFs compared to CM. Impact of stochastic process on the assembly of soil microbial taxa, ARGs and VFs in OM was stronger than that in CM. Overall, these findings provide a basis for integrating ARGs, VFs and pathogen hosts to assess the ecological and health risks in long-term organic managed soils, and increased efforts need to be done in reducing ARGs, VFs and bacterial pathogens in fertilizers for organic managements on agriculture.},
}

@article {pmid40375904,
year = {2025},
author = {Santarelli, G and Bianco, DM and Capriati, M and Sanguinetti, M and Rendeli, C and De Maio, F},
title = {Bladder Microbiota Snapshots Help to Monitor Urinary Tract Infections in Vulnerable Patients.},
journal = {Mediterranean journal of hematology and infectious diseases},
volume = {17},
number = {1},
pages = {e2025028},
pmid = {40375904},
issn = {2035-3006},
}

@article {pmid40375895,
year = {2025},
author = {Chen, S and Ouyang, T and Wang, K and Hou, X and Zhang, R and Li, M and Zhang, H and He, Q and Li, X and Liu, Z and Wang, X and Huang, B},
title = {Application of metagenomic next-generation sequencing in pathogen detection of lung infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1513603},
pmid = {40375895},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/genetics/isolation & purification/classification ; Adult ; Viruses/genetics/isolation & purification/classification ; Fungi/genetics/isolation & purification/classification ; Sensitivity and Specificity ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; *Lung Diseases/microbiology/diagnosis ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been widely reported to provide crucial information for the diagnosis and treatment of infectious diseases. In this study, we aimed to evaluate mNGS in pathogens diagnosis of lung infections.

METHODS: A total of 188 patients who were suspected of pulmonary infection and received medical treatment at the Second Affiliated Hospital of Nanchang University from August 2022 to December 2023 were enrolled in this study. Conventional microbiological tests (CMTs) and mNGS were employed for pathogens diagnosis.

RESULTS: Statistical results indicated that mNGS were significantly better than CMTs in sensitivity, negative predictive value, and negative likelihood ratio. Remarkably, the positive detection rate of mNGS was significantly higher than that of CMTs (86.17% vs 67.55%, P < 0.01). Through mNGS, we identified 96 pathogens, comprising 59 bacteria, 18 fungi, 15 viruses, and 4 special pathogens. In contrast, CMTs detected 28 species, including 25 bacteria and 3 fungi. The effectiveness rate of antibiotic treatment decisions based on mNGS results was 40.60%. Out of 54 cases with positive treatment impacts, mNGS results contributed to the treatment and improved prognosis of 16 infections caused by atypical pathogens.

CONCLUSION: Our results proved the essential role of mNGS in lung infection diagnosis, enabling early detection and the prompt development of targeted anti-infection therapies. We recommended that the clinical application of mNGS can enhance treatment effectiveness and improve patient prognosis.},
}

Humans
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Middle Aged
Aged
*Bacteria/genetics/isolation & purification/classification
Adult
Viruses/genetics/isolation & purification/classification
Fungi/genetics/isolation & purification/classification
Sensitivity and Specificity
*Respiratory Tract Infections/microbiology/diagnosis
Aged, 80 and over
*Lung Diseases/microbiology/diagnosis

@article {pmid40375193,
year = {2025},
author = {Chen, P and Wei, X and Que, T and Yan, T and Li, S and Zhong, Y and Li, Y and He, M and Liu, W and Hu, Y},
title = {Molecular detection of novel Jingmen tick virus in hard ticks from diverse hosts in Guangxi, southwestern China.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {143},
pmid = {40375193},
issn = {1743-422X},
support = {2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; 2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; 2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; No. Guike AB22035027//Guangxi Key Research and Development Program/ ; 2023YFC2605400//National Natural Science Foundation of China/ ; },
mesh = {Animals ; China ; Phylogeny ; *Ixodidae/virology/classification ; Genome, Viral ; Genetic Variation ; Metagenomics ; Recombination, Genetic ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Ticks are the second most important vectors of arboviruses after mosquitoes, and they also serve as reservoir hosts for some zoonotic diseases. It is essential to understand the prevalence of tick-borne viruses in ticks from different sampling sites and vectors, as this information can facilitate the surveillance and prevention of arboviral infectious diseases.

METHODS: We systematically collected ticks from a variety of animals, including wildlife and domestic livestock, across 18 distinct regions in Guangxi Zhuang Autonomous Region(Guangxi). We then identified the ticks using traditional morphological classification and molecular biology methods to investigate the diversity of ticks in the regionWe also systematically examined the diversity of viruses carried by ticks using comprehensive virological methods based on viral metagenomics. We performed phylogenetic and recombination analyses for the assembled viral sequences.

RESULTS: We collected 1286 Ixodidae from 18 sampling sites in 17 districts of Guangxi. We identified 4 genera and 6 species of Ixodidae. We annotated 2 unclassified viruses and 13 known viral families. We assembled 208 nucleotide sequences and obtained six near full-length sequences of Jingmen tick virus (JMTV). Among these sequences, GXTV-PC4.2 and GXTV-43 were new mutant strains of JMTV. We detected genetic recombination of JMTV in segments 2, 3, and 4 of JMTV.

CONCLUSIONS: Our study uncovers a diverse tick fauna in Guangxi, including 4 genera and 6 species, and a broad virome with 13 viral families and 2 novel viruses. The JMTV, in particular, shows significant genetic diversity and potential for cross-species transmission, marked by new strains and recombination events. These findings underscore the need for vigilant tick-borne disease surveillance in Guangxi.},
}

Animals
China
Phylogeny
*Ixodidae/virology/classification
Genome, Viral
Genetic Variation
Metagenomics
Recombination, Genetic
Sequence Analysis, DNA

@article {pmid40375084,
year = {2025},
author = {Rahman Hera, M and Koslicki, D},
title = {Estimating similarity and distance using FracMinHash.},
journal = {Algorithms for molecular biology : AMB},
volume = {20},
number = {1},
pages = {8},
pmid = {40375084},
issn = {1748-7188},
support = {R01GM146462//National Institutes of Health, United States/ ; R01GM146462//National Institutes of Health, United States/ ; },
abstract = {MOTIVATION: The increasing number and volume of genomic and metagenomic data necessitates scalable and robust computational models for precise analysis. Sketching techniques utilizing k -mers from a biological sample have proven to be useful for large-scale analyses. In recent years, FracMinHash has emerged as a popular sketching technique and has been used in several useful applications. Recent studies on FracMinHash proved unbiased estimators for the containment and Jaccard indices. However, theoretical investigations for other metrics are still lacking.

THEORETICAL CONTRIBUTIONS: In this paper, we present a theoretical framework for estimating similarity/distance metrics by using FracMinHash sketches, when the metric is expressible in a certain form. We establish conditions under which such an estimation is sound and recommend a minimum scale factor s for accurate results. Experimental evidence supports our theoretical findings.

PRACTICAL CONTRIBUTIONS: We also present frac-kmc, a fast and efficient FracMinHash sketch generator program. frac-kmc is the fastest known FracMinHash sketch generator, delivering accurate and precise results for cosine similarity estimation on real data. frac-kmc is also the first parallel tool for this task, allowing for speeding up sketch generation using multiple CPU cores - an option lacking in existing serialized tools. We show that by computing FracMinHash sketches using frac-kmc, we can estimate pairwise similarity speedily and accurately on real data. frac-kmc is freely available here: https://github.com/KoslickiLab/frac-kmc/.},
}

@article {pmid40374064,
year = {2025},
author = {Wang, J and Zhou, Y and Zhang, T and Zhang, Y and Lian, Q},
title = {Pre-treatment of excess sludge with sulfide-containing wastewater for composite electron donor formation to enhance denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132673},
doi = {10.1016/j.biortech.2025.132673},
pmid = {40374064},
issn = {1873-2976},
abstract = {Utilizing the fermentation liquor of excess sludge (ES) for the denitrification process represents an effective strategy for the valorization of ES and achieving environmentally friendly denitrification. However, ES fermentation technologies require significant energy or chemical product inputs. The present study proposes a novel method utilizing sulfide-containing wastewater to pretreat ES for generating dissolved organic matter (DOM), with sulfides and DOM collectively forming a composite electron donor (S-ES-DOM). The introduction of S-ES-DOM enables the establishment of integrated autotrophic and heterotrophic denitrification (IAHD) process, achieving 100 % denitrification efficiency. Molecular analysis identified an increase in biodegradable components within S-ES-DOM, which were effectively utilized during the IAHD process. The functional genes associated with nitrate-sulfide-organic carbon metabolism and electron transfer exhibited upregulation. The mixotrophic microbial community enables flexible adoption of multiple metabolic pathways. This strategy simultaneously achieves low-cost ES valorization and low-carbon nitrate/sulfide removal through integrated nitrogen-sulfur-carbon metabolism.},
}

@article {pmid40373994,
year = {2025},
author = {Pereira, S and Rubina, M and Roga, A and Selga, T and Skinderskis, E and Gudrā, D and Kalniņa, I and Vonda, K and Fridmanis, D and Muter, O},
title = {Evaluation of functional capacity and plastic-degrading potential of Bacillus spp. and other bacteria derived from the Getliņi landfill (Latvia).},
journal = {Environmental research},
volume = {},
number = {},
pages = {121849},
doi = {10.1016/j.envres.2025.121849},
pmid = {40373994},
issn = {1096-0953},
abstract = {The mechanisms of plastic biodegradation by microorganisms remain poorly understood because of high variability in environmental conditions. This study aimed to isolate, identify, and characterise bacteria with plastic-degrading potential derived from the Getliņi EKO landfill (Riga, Latvia). Among the bacteria selected, Bacillus was the predominant genus identified, whereas Pseudomonas dominated the metagenome. Comparative testing revealed the highest non-specific esterase activity in cultures of B. licheniformis and B. altitudinis. Following a 6-week batch experiment, a newly developed bacterial consortium biologically reduced the weight of untreated low-density polyethylene (LDPE), polyethylene terephthalate (PET), and high-density polyethylene (HDPE) by 19.44%, 5.99%, and 2.58%, respectively. Thermally pre-treated PET and acid pre-treated HDPE resulted in greater weight losses than their respective untreated forms. Scanning electron microscopy primarily showed single cells and microcolonies attached to the granule surfaces. Microbial respiration and fluorescein diacetate hydrolysis tests suggested that the granules had a stimulating effect on the metabolic activity of planktonic cells. Cultures with untreated LDPE and PET exhibited the highest ecotoxicity for Thamnocephalus platyurus, reducing ingestion activity by 60.39% and 71.25% of the control, respectively. In conclusion, the Getliņi EKO landfill appears to be a promising sampling source for bacteria capable of biodegrading fossil-based polymers. Further refinement of methods for the isolation and evaluation of plastic degraders will provide new insights into the potential of microbial resources for plastic degradation.},
}

@article {pmid40373900,
year = {2025},
author = {Yin, CY and Sadiq, H and Liao, WH and Wang, HN and Fu, Z and Yu, WG and Han, F},
title = {Identification and functional characterization of two novel hyaluronate lyases BxHly33 and BiHly33, from the human gut microbiome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {144153},
doi = {10.1016/j.ijbiomac.2025.144153},
pmid = {40373900},
issn = {1879-0003},
abstract = {Hyaluronic acid (HA) is a key glycosaminoglycan in the extracellular matrix, essential for cellular signaling, hydration, and tissue homeostasis. This study identified two novel polysaccharide lyase family 33 (PL33) hyaluronate lyases, BxHly33 and BiHly33, from the human gut microbiome using metagenomic screening. These enzymes demonstrated high specificity and stability in degrading HA, with optimal activity at pH 6.6-7.6 and temperatures of 35-40 °C. Furthermore, structural and biochemical analyses revealed their catalytic mechanisms, highlighting key residues responsible for their function. Notably, specific alanine substitutions significantly enhanced their enzymatic activity. BxHly33 and BiHly33 present promising alternatives to conventional hyaluronidases, which are often costly and immunogenic, for drug delivery and tissue engineering applications. This study will provide novel insights into exploring their therapeutic potential in HA degradation therapies.},
}

@article {pmid40373514,
year = {2025},
author = {Tong, X and Zhang, X and Fu, J and He, R},
title = {Mechanisms on nitrogen amendment stimulating methane oxidation in landfill cover soils.},
journal = {Waste management (New York, N.Y.)},
volume = {203},
number = {},
pages = {114893},
doi = {10.1016/j.wasman.2025.114893},
pmid = {40373514},
issn = {1879-2456},
abstract = {Landfill cover soil plays a pivotal role in mitigating CH4 input to the atmosphere. However, the community and activity of methane-oxidizing bacteria (MOB), and their responses to nutrient amendment remain insufficiently understood in landfill cover soils. In this study, the influencing mechanisms of nitrogen amendment on MOB activity, and their functional microorganisms and genes were investigated in landfill cover soils. An exogenous ammonium and nitrate addition could enhance CH4 oxidation activity of 13.9-34.1 times in the landfill cover soil. The NH4[+]-N addition of 800 mg kg[-1] could cause a maximum nitrite accumulation of 41.2 mg kg[-1] in the landfill cover soils and inhibit CH4 oxidation. Nitrogen was mainly deposited in the landfill cover soil in the form of organic nitrogen, with a slight loss of 1.47-3.21 % in the treatments amended with ammonium and nitrate at each stage. A high CH4 oxidation could increase the secretion of CH4-derived carbon and improve the organic matter of soil. Compared with ammonium, the nitrate addition had a greater stimulating effect on microbial and MOB growth. Type I MOB predominated in the soils amended with ammonium and nitrate, whereas type II MOB dominated in the nitrogen-deficient soils. Metagenomic analysis showed that the genes related to nitrogen fixation (nifDKH) were more abundant in the nitrogen-deficient soil than the others. These findings suggest that an appropriate ammonium and nitrate addition could induce carbon and nitrogen accumulation, and stimulate microbial metabolism such as CH4 oxidation and element cycles in the landfill cover soils to mitigate CH4 emission.},
}

@article {pmid40373448,
year = {2025},
author = {Liu, H and Fan, Y and Su, E and Liu, S and Ming, Y and Huang, Z and Yu, H and Liu, F and Wang, C and Yu, X and Niu, M and Wu, K and Yang, Y and He, Z and Zhang, T and Yan, Q},
title = {Mariculture increases microbially-driven carbon metabolism and sequestration in coastal ecosystems.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125756},
doi = {10.1016/j.jenvman.2025.125756},
pmid = {40373448},
issn = {1095-8630},
abstract = {Mariculture has expanded significantly in recent decades due to rising seafood demand and its contribution to ocean carbon sequestration. While the mechanisms of carbon sequestration in mariculture are well-established, the roles of microorganisms in sedimentary carbon sequestration have rarely been explored. How microorganisms mediate organic carbon metabolism and their effects on coastal carbon pools remain unclear. Here we tested the carbon fraction and contents, as well as extracellular hydrolase activities in macroalgae culture area, fish or abalone culture area, and control area without mariculture. We profiled microbial community composition and carbon metabolism characteristics in sediments through 16S rRNA gene amplicon sequencing and metagenomics. Our findings revealed that macroalgae culture areas exhibited a significantly greater potential for carbon sequestration than the control area, the concentration of TOC in seawater and the contents of SOC, DOC, and ROC in sediments were significantly (p < 0.05) increased by 18.93 %, 6.98 %, 33.98 %, and 18.30 % respectively. These results can be attributed to decreased activities of extracellular hydrolase and a lower abundance of carbon-degrading genes. Moreover, metabolic profiling identified taxa from families such as Alteromonadaceae, Pseudomonadaceae, Rhodobacteraceae, Enterobacteriaceae, and Flavobacteriaceae, which are highly metabolically flexible in utilizing a wide range of organic and inorganic energy sources, playing crucial roles in carbon formation. Their respiratory metabolism, such as sulfate reduction, thiosulfate oxidation, and denitrification as well as secondary metabolism products could also affect the formation and persistence of sedimentary carbon pools. Specifically, increased total nitrogen (TN) and nitrate-nitrogen (NO3[-]) could potentially enhance microbial degradation of organic carbon, decreasing carbon stock within coastal sediments. This study enhanced our understanding of microbial regulation of the organic carbon pool in the mariculture ecosystem.},
}

@article {pmid40373419,
year = {2025},
author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS},
title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.},
journal = {Meat science},
volume = {226},
number = {},
pages = {109848},
doi = {10.1016/j.meatsci.2025.109848},
pmid = {40373419},
issn = {1873-4138},
abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.},
}

@article {pmid40373403,
year = {2025},
author = {Zhao, F and Wu, S and Shen, X and Huang, Y and Zhang, B and Luo, Z and Wu, D and Shen, L and Cao, S and Wang, Y and Zhang, J and Yu, S},
title = {Metagenomic analysis reveals the diversity, transmission and potential ecological risks of yak nasal bacteria-carried antibiotic resistance genes in the Sichuan region of Qinghai-Tibet plateau.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138476},
doi = {10.1016/j.jhazmat.2025.138476},
pmid = {40373403},
issn = {1873-3336},
abstract = {The Qinghai-Tibet Plateau (QTP) and yaks play respectively vital roles in global and plateau ecosystems. Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants. However, few studies have investigated the abundance and diversity of ARGs and mobile genetic elements (MGEs) in the yak upper respiratory tract and their surrounding pastures. Moreover, the possible pathways for ARG transmission within these ecosystems have not yet been elucidated. Therefore, we investigated the ARG profiles, MGE profiles, and ARG-carrying host bacteria in yaks and their pasture collected from Ganzi and Aba region in Sichuan Province. Metagenomic analyses showed that 22 ARG types and 5 MGEs types were identified in 18 samples. Multidrug resistance gene (mexT) and bacitracin resistance gene (bacA) was identiffed as hotspots, which may compromise medical treatment options. Co-occurrence network analysis revealed that 12 bacterial genera may be potential hosts at the genus level. The enrich of ARGs and MGEs diversity were observed in QTP (Sichuan province) pasture ecosystems which demands evidence-based interventions to mitigate ARGs transmission risks.},
}

@article {pmid40373385,
year = {2025},
author = {Xu, Z and Pei, Y and Wang, H and Li, X},
title = {Comparative analysis of gut microbiota-mediated bile acid profiles in Bufo gargarizans and Rana chensinensis tadpoles.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {55},
number = {},
pages = {101530},
doi = {10.1016/j.cbd.2025.101530},
pmid = {40373385},
issn = {1878-0407},
abstract = {Bile acids (BAs) are cholesterol derivatives synthesized by the liver, exhibit variation between different species. Researchers have long appreciated that microbiota play the roles in the biotransformation of BAs. However, relatively few studies have been reported on microbial-mediated production and transformation of BAs in amphibians. Our focus here is principally on difference of intestinal microbial diversity and BAs profiles between two common amphibians, Bufo gargarizans (B. gargarizans) and Rana chensinensis (R. chensinensis) tadpoles, through intestinal targeted BAs metabolomics and fecal metagenomic sequencing. The results demonstrated that B. gargarizans possessed higher levels of total BAs and higher ratio of unconjugated / conjugated BAs. In addition, the relative abundance of microbiota with bile salt hydrolase (BSH) activity in B. gargarizans was significantly higher than that of R. chensinensis, which may facilitate the conversion of conjugated to unconjugated BAs. Meanwhile the higher prevalence of bile-acid-induced (BAI) gene encoding microbiota in R. chensinensis may promote the synthesis of deoxycholic acid (DCA). Furthermore, discrepancies in virulence factors (VFs) and energy metabolism were observed between the two species, which may be linked to differences in the microbiota. This study revealed substantial differences in intestinal microbes and BAs across amphibian species, emphasizing the significant impact of intestinal microbes on BAs metabolism.},
}

@article {pmid40373374,
year = {2025},
author = {Li, Y and Bhatt, P and Xagoraraki, I},
title = {In-depth comparison of untargeted and targeted sequencing for detecting virus diversity in wastewater.},
journal = {Water research},
volume = {283},
number = {},
pages = {123803},
doi = {10.1016/j.watres.2025.123803},
pmid = {40373374},
issn = {1879-2448},
abstract = {Sequencing approaches may enable monitoring of a broad range of viruses in wastewater, including potential emerging and non-reportable human viruses. Considering the fact that metagenomic sequencing may be non-specific for low-abundance human viruses, integration of viral amplification and enrichment strategies are proposed to enhance the accurate detection of a broad range of human viruses in municipal wastewater. In this study, we focused on the in-depth comparison analysis of three untargeted amplification methods (Multiple Displace Amplification [MDA], Reverse Transcription - MDA [RT-MDA], and a PCR-based random amplification [PCR-based]) and one targeted method (Twist Comprehensive Viral Research Panel [TWIST]) for detecting virus diversity in wastewater. In addition, we included the comparisons of two extraction kits (Qiagen QIAamp VIRAL RNA Mini Kit and ZymoBIOMICSTM DNA/RNA Minipre Kit) and four virus identification tools (Diamond blast, Kraken2, VirSorter2 and geNomad) for a systematic study. Performances of Qiagen and Zymo extraction kits in recovering viruses and human viruses in wastewater were comparable. By the three untargeted methods we detected 12,808 contigs with lengths longer than 10,000 bp. No contig longer than 10,000 bp was detected by the targeted method. Presence of human viruses were analyzed further by comparing the viral contigs against a custom Swiss-Prot human virus database. There were 45 viruses that are potentially associated with human health found in wastewater, 8 of them were unique to the targeted method and 7 of them were unique to the three untargeted methods. Four enteric viruses Mamastrovirus, Norovirus, Rotavirus and Sapovirus were detected with high abundance in samples prepared with the targeted method. Dimensional scaling analysis demonstrated the divergent virus and human virus communities from the untargeted and targeted methods. Patterns of virus and human virus populations identified by Kraken2 and geNomad were similar. Presence of selected viruses (SARS-CoV-2 [N1&N2], SC2, RSV, Norovirus GI and GII) were confirmed with ddPCR. This work indicates integration of untargeted and targeted sequencing methods, and complementary ddPCR can ensure the accurate detection of known and novel viruses using wastewater surveillance.},
}

@article {pmid40372916,
year = {2025},
author = {Ramar, M and Wiscovitch-Russo, R and Yano, N and Singh, H and Lamere, E and Short, M and Gonzalez-Juarbe, N and Fedulov, AV},
title = {Live bacteria in gut microbiome dictate asthma onset triggered by environmental particles via modulation of DNA methylation in dendritic cells.},
journal = {Cell reports},
volume = {44},
number = {5},
pages = {115684},
doi = {10.1016/j.celrep.2025.115684},
pmid = {40372916},
issn = {2211-1247},
abstract = {Despite broad knowledge of the pathogenesis, our understanding of the origin of allergy and asthma remains poor, preventing etiotropic treatments. The gut microbiome is seen to be altered in asthmatics; however, proof of causality of the microbiome alterations is lacking. We report on gut microbiome transplantation (GMT) from mice predisposed to asthma by maternal exposure to pro-allergy environmental particles into naive recipients. This GMT confers asthma predisposition, and the effect is abrogated by gamma sterilization of the transplant material or by co-administration of antibacterials, indicating that viable bacteria are mediating the effect. Metagenomics identifies key changes in the "pro-asthma" microbiome, and metabolomics links the identified species to altered production of butyrate known to act on immune cells and epigenetic mechanisms. We further show that transplant recipients develop DNA methylation alterations in dendritic cells. Finally, dendritic cells with an altered methylome present allergen to T cells, and this effect is abrogated by an epigenetically acting drug in vitro.},
}

@article {pmid40372723,
year = {2025},
author = {Al-Najim, A and Hauns, S and Tran, VD and Backofen, R and Alkhnbashi, OS},
title = {HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40372723},
issn = {2047-217X},
support = {2168/23//Deutsche Forschungsgemeinschaft/ ; 2168/25-1//Deutsche Forschungsgemeinschaft/ ; //University of Freiburg/ ; },
mesh = {*Deep Learning ; *Metagenomics/methods ; *Bacteriophages/genetics ; Genome, Viral ; *DNA, Viral/genetics ; Metagenome ; *Computational Biology/methods ; *Sequence Analysis, DNA/methods ; Humans ; *Software ; },
abstract = {BACKGROUND: Bacteriophages are among the most abundant organisms on Earth, significantly impacting ecosystems and human society. The identification of viral sequences, especially novel ones, from mixed metagenomes is a critical first step in analyzing the viral components of host samples. This plays a key role in many downstream tasks. However, this is a challenging task due to their rapid evolution rate. The identification process typically involves two steps: distinguishing viral sequences from the host and identifying if they come from novel viral genomes. Traditional metagenomic techniques that rely on sequence similarity with known entities often fall short, especially when dealing with short or novel genomes. Meanwhile, deep learning has demonstrated its efficacy across various domains, including the bioinformatics field.

RESULTS: We have developed HVSeeker-a host/virus seeker method-based on deep learning to distinguish between bacterial and phage sequences. HVSeeker consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. In addition to the robust architecture of HVSeeker, three distinct preprocessing methods were introduced to enhance the learning process: padding, contigs assembly, and sliding window. This method has shown promising results on sequences with various lengths, ranging from 200 to 1,500 base pairs. Tested on both NCBI and IMGVR databases, HVSeeker outperformed several methods from the literature such as Seeker, Rnn-VirSeeker, DeepVirFinder, and PPR-Meta. Moreover, when compared with other methods on benchmark datasets, HVSeeker has shown better performance, establishing its effectiveness in identifying unknown phage genomes.

CONCLUSIONS: These results demonstrate the exceptional structure of HVSeeker, which encompasses both the preprocessing methods and the model design. The advancements provided by HVSeeker are significant for identifying viral genomes and developing new therapeutic approaches, such as phage therapy. Therefore, HVSeeker serves as an essential tool in prokaryotic and phage taxonomy, offering a crucial first step toward analyzing the host-viral component of samples by identifying the host and viral sequences in mixed metagenomes.},
}

*Deep Learning
*Metagenomics/methods
*Bacteriophages/genetics
Genome, Viral
*DNA, Viral/genetics
Metagenome
*Computational Biology/methods
*Sequence Analysis, DNA/methods
Humans
*Software

@article {pmid40372371,
year = {2025},
author = {Li, X and He, N and Wang, H and Wu, Z and Wang, M and Liang, H and Xiao, L and Yang, Z and Li, C and Xu, P and Dai, T and Li, S and Zou, Y},
title = {Therapeutic effect of Faecalibacterium longum CM04-06 on DSS-induced ulcerative colitis in mice.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf119},
pmid = {40372371},
issn = {1365-2672},
abstract = {AIMS: This study explores the impact of Faecalibacterium longum CM04-06 on inflammatory bowel disease (IBD) by regulating gut microbiota in mice.

METHODS AND RESULTS: We reanalyzed the distribution of the CM04-06 genome in the metagenome of the IBD cohort and observed a significantly higher abundance of CM04-06 in healthy individuals compared to patients with UC or CD. The prophylactic administration of CM04-06 was evaluated for its effects on intestinal microbial diversity and community composition after a two-week trial in mice. The intestinal microbiota was characterized using metagenomic sequencing of fecal samples on the DNBSEQ platform. CM04-06 treatment resulted in a significant reduction in the Disease Activity Index (DAI) and histological scores, as well as a decrease in the levels of pro-inflammatory cytokines, including IL-1β, IL-6, and TNF-α, in both the colon and serum of DSS-induced mice. Furthermore, supplementation with CM04-06 significantly reduced the levels of pro-inflammatory cytokines in both the colon and serum. Additionally, CM04-06 enhanced the integrity of the intestinal epithelial barrier by increasing the expression of tight junction proteins and mucin. Moreover, we observed greater abundances of Faecalibaculum rodentium, Alistipes onderdonkii, Alistipes shahii, and Bifidobacterium animalis after CM04-06 treatment.

CONCLUSIONS: CM04-06 prevents and alleviates intestinal inflammation by modulating the composition of the microbiota community, increasing the abundance of beneficial probiotics, and suppressing pro-inflammatory cytokine levels.},
}

@article {pmid40372056,
year = {2025},
author = {Kok, CR and Thissen, JB and Cerroni, M and Tribble, DR and Cancio, A and Tran, S and Schofield, C and Colombo, RE and Troth, T and Joya, C and Lalani, T and Be, NA},
title = {Field expedient stool collection methods for gut microbiome analysis in deployed military environments.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081824},
doi = {10.1128/msphere.00818-24},
pmid = {40372056},
issn = {2379-5042},
abstract = {Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.},
}

@article {pmid40371968,
year = {2025},
author = {Jansen, D and Deleu, S and Caenepeel, C and Marcelis, T and Simsek, C and Falony, G and Machiels, K and Sabino, J and Raes, J and Vermeire, S and Matthijnssens, J},
title = {Virome drift in ulcerative colitis patients: faecal microbiota transplantation results in minimal phage engraftment dominated by microviruses.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2499575},
doi = {10.1080/19490976.2025.2499575},
pmid = {40371968},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Colitis, Ulcerative/therapy/virology/microbiology ; *Virome ; Male ; Female ; Feces/virology ; Adult ; Gastrointestinal Microbiome ; Middle Aged ; *Bacteriophages/genetics/isolation & purification/classification ; Young Adult ; },
abstract = {Ulcerative colitis (UC) is an inflammatory bowel disease characterized by recurrent colonic inflammation. Standard treatments focus on controlling inflammation but remain ineffective for one-third of patients. This underscores the need for alternative approaches, such as fecal microbiota transplantation (FMT), which transfers healthy donor microbiota to patients. The role of viruses in this process, however, remains underexplored. To address this, we analyzed the gut virome using metagenomic sequencing of enriched viral particles from 320 longitudinal fecal samples of 44 patients enrolled in the RESTORE-UC FMT trial. Patients were treated with FMTs from healthy donors (allogenic, treatment) or themselves (autologous, control). We found that colonic inflammation, both its presence and location, had a greater impact on the gut virome than FMT itself. In autologous FMT patients, the virome was unstable and showed rapid divergence over time, a phenomenon we termed virome drift. In allogenic FMT patients, the virome temporarily shifted toward the healthy donor, lasting up to 5 weeks and primarily driven by microviruses. Notably, two distinct virome configurations were identified and linked to either healthy donors or patients. In conclusion, inflammation strongly affects the gut virome in UC patients, which may lead to instability and obstruct the engraftment of allogeneic FMT.},
}

Humans
*Fecal Microbiota Transplantation
*Colitis, Ulcerative/therapy/virology/microbiology
*Virome
Male
Female
Feces/virology
Adult
Gastrointestinal Microbiome
Middle Aged
*Bacteriophages/genetics/isolation & purification/classification
Young Adult

@article {pmid40371337,
year = {2025},
author = {Lehner, MD and Ulsemer, P and Christochowitz, S},
title = {Menthacarin, a proprietary combination of peppermint and caraway oil, alters cultured human fecal microbiota composition, resulting in increased SCFA production.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1569052},
pmid = {40371337},
issn = {1663-9812},
abstract = {BACKGROUND: Disruptions in the gut microbiota metabolism may contribute to the pathophysiology of gut-brain interaction disorders, and correction of intestinal dysbiosis is considered a promising therapeutic approach. Menthacarin, a proprietary fixed combination of Mentha x piperita L. and Carum carvi L. essential oils, is used clinically for the treatment of functional dyspepsia and irritable bowel syndrome. Rodent model data indicate that treatment effects of Menthacarin on visceral hypersensitivity could be mediated via the normalization of gut dysbiosis. However, the impact of Menthacarin on human bacterial gut microbiota has not yet been studied.

AIM: The aim of the present study was to assess whether Menthacarin affects the composition and metabolic activity of human fecal microbiota.

METHODS: Fecal slurry samples from 10 healthy volunteers were cultivated for 36 h under anoxic conditions with and without Menthacarin. Relative bacterial abundance at the phylum and genus levels was evaluated using 16S rRNA metagenomic analysis. Short-chain fatty acids (SCFAs) in the supernatants were measured using the LC-MS technology.

RESULTS: Menthacarin induced robust changes in microbial composition at both the phylum and genus levels among the 10 donor microbiomes. The relative abundance of Firmicutes (+13.6 ± 8.6%) and Actinobacteria (+54.9 ± 47.6%) significantly increased, whereas that of Bacteroidetes (-27.7% ± 21.9%) and Proteobacteria (-25.7% ± 12.3%) significantly decreased in the presence of Menthacarin. At the genus level, the most notable changes were significant increases in Bifidobacterium (+105.1 ± 78.4%) and several SCFA-producing genera accompanied by a significant decrease in genera containing members involved in pro-inflammatory processes. In addition, Menthacarin significantly increased the levels of several SCFAs, namely, propionate, butyrate, isobutyrate, valerate, and isovalerate.

CONCLUSION: Menthacarin alters the microbiota composition and enhances SCFA production in human microbiota samples under in vitro conditions. These effects may contribute to the clinical benefits observed with Menthacarin treatment.},
}

@article {pmid40371178,
year = {2025},
author = {Lanclos, VC and Feng, X and Cheng, C and Yang, M and Hider, CJ and Coelho, JT and Kojima, CY and Barnes, SJ and Cleveland, CS and Xie, M and Zhao, Y and Luo, H and Thrash, JC},
title = {New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf068},
pmid = {40371178},
issn = {2730-6151},
abstract = {The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Candidatus Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007[T] (= ATCC TSD-433[T] = NCMA B160[T]).},
}

@article {pmid40370734,
year = {2025},
author = {Yu, F and Guo, Y and Li, Y and Gai, W and Zhang, Q and Li, P and Xu, R and Zhang, L and Zheng, Y and Zhang, X},
title = {Liver abscess and septic shock due to Clostridium perfringens infection: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1575454},
pmid = {40370734},
issn = {2296-858X},
abstract = {Clostridium perfringens causes liver abscesses with a low incidence, rapid progression, and high mortality. Within a few days or even within 24 h, patients may progress from a liver abscess to sepsis, multi-organ failure, and potentially death. Diagnosing Clostridium perfringens infection by routine microbiological testing (CMT) is often challenging. Here, we present a patient with negative blood cultures who was ultimately diagnosed with a liver abscess due to Clostridium perfringens infection, confirmed by metagenomic next-generation sequencing (mNGS). The patient initially presented with fever only, and his blood cultures were negative. Subsequently, the patient's condition progressed rapidly, and he developed signs of septic shock. Immediately after admission to the ICU, he received combined anti-infective therapy with meropenem and tigecycline, as well as urgent ultrasound-guided puncture and drainage. Blood mNGS identified Clostridium perfringens and a variety of anaerobic bacteria, confirming that the pathogen had been covered by empirical antibiotics. Continued anti-infective therapy and drainage improved the patient's symptoms, and he was eventually discharged from the hospital. Clinicians should be highly suspicious of liver abscesses with negative blood cultures. The use of mNGS to identify the pathogen, appropriate antibiotics, and abscess aspiration and drainage are key to patient survival.},
}

@article {pmid40370716,
year = {2025},
author = {Yang, Z and Zhou, S and Yang, Z and Liu, P and Chen, S and Zhu, W},
title = {Metagenomic next-generation sequencing enabled diagnosis of Aspergillus spondylitis in an immunocompetent patient: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1575363},
pmid = {40370716},
issn = {2296-858X},
abstract = {BACKGROUND: Aspergillus fumigatus spondylitis is a rare fungal spondylitis that often occurs in immunocompromised patients. This article reports a case of Aspergillus spondylitis with specific image signs, which is rarely reported in an immunocompetent patient.

CASE PRESENTATION: This is a case of L3-4 segmental Aspergillus spondylitis diagnosed. The diagnosis was confirmed by intraoperative metagenomic next-generation sequencing (mNGS) testing of the diseased tissue. The patient was treated with voriconazole and underwent surgical debridement and internal fixation with pedicle screws.

CONCLUSION: The diagnosis of Aspergillus spondylitis is often delayed or missed. Doctors should consider Aspergillus spondylitis in the differential diagnosis of unexplained low back pain so that appropriate treatment can be administered to prevent spinal cord injury and disability. Aspergillus spondylitis usually results in endplate inflammatory response line on fluid or enhancement sequences and a diffuse low signal in the diseased vertebral body on T2-weighted imaging (T2WI). It also results in large paraspinal abscesses, which requires further research to better differentiate between Aspergillus spondylitis and tuberculous spondylitis. Prompt diagnosis and treatment can improve the patient's prognosis.},
}

@article {pmid40370098,
year = {2025},
author = {Wang, N and Wu, M and Gu, W and Dai, C and Shao, Z and Subbalakshmi, KP},
title = {MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
pmid = {40370098},
issn = {1477-4054},
support = {JUSRP123035//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Computational Biology/methods ; Algorithms ; },
abstract = {More and more recent studies highlight the crucial role of the human microbiome in maintaining health, while modern advancements in metagenomic sequencing technologies have been accumulating data that are associated with human diseases. Although metagenomic data offer rich, multifaceted information, including taxonomic and functional abundance profiles, their full potential remains underutilized, as most approaches rely only on one type of information to discover and understand their related correlations with respect to disease occurrences. To address this limitation, we propose a multistage fusion tabular transformer architecture (MSFT-Transformer), aiming to effectively integrate various types of high-dimensional tabular information extracted from metagenomic data. Its multistage fusion strategy consists of three modules: a fusion-aware feature extraction module in the early stage to improve the extracted information from inputs, an alignment-enhanced fusion module in the mid stage to enforce the retainment of desired information in cross-modal learning, and an integrated feature decision layer in the late stage to incorporate desired cross-modal information. We conduct extensive experiments to evaluate the performance of MSFT-Transformer over state-of-the-art models on five standard datasets. Our results indicate that MSFT-Transformer provides stable performance gains with reduced computational costs. An ablation study illustrates the contributions of all three models compared with a reference multistage fusion transformer without these novel strategies. The result analysis implies the significant potential of the proposed model in future disease prediction with metagenomic data.},
}

*Metagenomics/methods
Humans
*Metagenome
*Computational Biology/methods
Algorithms

@article {pmid40369676,
year = {2025},
author = {Zhang, Y and Liu, H and Jing, H},
title = {Community differences and potential function along the particle size spectrum of microbes in the twilight zone.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {121},
pmid = {40369676},
issn = {2049-2618},
support = {424QN341//the Hainan Provincial Natural Science Foundation of China/ ; JRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; 2023YFC2812804//the National Key R&D Program of China/ ; 183446KYSB20210002//the International Partnership Program of Chinese Academy of Sciences for Big Science/ ; },
mesh = {Particle Size ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seawater/microbiology/chemistry ; *Microbiota/genetics ; Metagenomics/methods ; Carbon/metabolism ; Metagenome ; },
abstract = {BACKGROUND: The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.

RESULTS: Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.

CONCLUSION: Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.},
}

Particle Size
*Bacteria/classification/genetics/metabolism/isolation & purification
*Seawater/microbiology/chemistry
*Microbiota/genetics
Metagenomics/methods
Carbon/metabolism
Metagenome

@article {pmid40369669,
year = {2025},
author = {Purse, C and Parker, A and James, SA and Baker, DJ and Moss, CJ and Evans, R and Durham, J and Funnell, SGP and Carding, SR},
title = {Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {47},
pmid = {40369669},
issn = {2524-4671},
support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1//BBSRC/ ; },
abstract = {BACKGROUND: Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.

RESULTS: Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20 years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.

CONCLUSIONS: We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.},
}

@article {pmid40368959,
year = {2025},
author = {Song, XL and Wang, ZJ and Yin, XW and Sun, YL and Jang, DJ and Hong, SK},
title = {The impact of nitrogen deposition on nitrogen metabolism in ryegrass lawn with different soil nutrient levels.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16755},
pmid = {40368959},
issn = {2045-2322},
mesh = {*Nitrogen/metabolism ; *Lolium/metabolism ; *Soil/chemistry ; Soil Microbiology ; Nitrogen Fixation ; Nitrification ; *Nutrients/metabolism ; Denitrification ; Nitrogen Cycle ; Microbiota ; Nitrates/metabolism ; },
abstract = {Nitrogen deposition is a crucial factor in global change, which is widespread across various regions globally. It has drawn extensive attention due to its direct modification of soil nitrogen retention and nitrogen species distribution, thereby influencing nitrogen metabolism across entire ecosystems. Previous studies on its influence on nitrogen metabolism have not reached a consensus. In an urban ryegrass lawn mesocosm experiment, we set two levels of nitrogen deposition and soil nutrients respectively, aiming to study the impacts of these factors on the N-cycling process through metagenomic analysis. The results demonstrated nitrogen deposition increased nitrification, nitrogen fixation, denitrification, and dissimilatory nitrate reduction, but decreased assimilatory nitrate reduction in the nitrogen metabolism process by changing soil nitrogen availability and the abundance of N-cycling functional genes in the soil microbial community. The soil nutrient levels exhibited effects opposite to those of nitrogen deposition, negatively impacting nitrification, denitrification, and nitrogen fixation in the nitrogen metabolism process. This work further elucidates the impacts of nitrogen deposition on the ecological functions of the ryegrass lawn with different soil nutrient levels, and predicts the potential impacts of intensified nitrogen deposition on these ecological functions. It provides valuable theoretical support for understanding and evaluating complex ecological interactions.},
}

*Nitrogen/metabolism
*Lolium/metabolism
*Soil/chemistry
Soil Microbiology
Nitrogen Fixation
Nitrification
*Nutrients/metabolism
Denitrification
Nitrogen Cycle
Microbiota
Nitrates/metabolism

@article {pmid40368955,
year = {2025},
author = {Krishnavajhala, A and Gingras, MC and Urquieta, E and Chao, H and Bandaranaike, D and Chen, Y and Bhamidipati, S and Korchina, V and Griffin, SM and Masternak, MM and Moreno, H and Mohammed, J and Murugan, M and Posey, JE and Wu, JH and Muzny, D and Gibbs, RA and Doddapaneni, H},
title = {The GENESTAR manual for biospecimen collection biobanking and omics data generation from commercial space missions.},
journal = {NPJ microgravity},
volume = {11},
number = {1},
pages = {16},
pmid = {40368955},
issn = {2373-8065},
abstract = {The surge in commercial and civilian spaceflight enables the systematic and longitudinal, large-scale biospecimen collection to understand the prospective effects of space travel on human health. The Genomics and Space Medicine (Space Omics) project at BCM-HGSC involves a comprehensive biospecimen collection plan from commercial/private space flight participants. The manuscript addresses the critical gaps in the biospecimen collection process including details of the informed consent process, a provision for subjects to obtain custom CLIA-WGS reports, a data dictionary and a LIMS enabled biobank. The manuscript also discusses the biospecimens collection, processing methodologies and nucleic acid suitability for Omics data generation. Results from Axiom-2 mission where, 339 biospecimens were collected using 'Genomic Evaluation of Space Travel and Research (GENESTAR)' manual, at two different sites, showed that 98% of the blood samples and 91.6% of the non-blood samples passed the QC requirements for Omics assays, underscoring the reliability and effectiveness of the GENESTAR manual.},
}

@article {pmid40368948,
year = {2025},
author = {Serivichyaswat, PT and Scholte, T and Wilms, T and Stranddorf, L and van der Valk, T},
title = {Metagenomic biodiversity assessment within an offshore wind farm.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16786},
pmid = {40368948},
issn = {2045-2322},
mesh = {*Biodiversity ; *Metagenomics/methods ; North Sea ; Animals ; *Wind ; Seawater ; *DNA, Environmental/genetics/analysis ; Ecosystem ; *Metagenome ; Denmark ; },
abstract = {Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.},
}

*Biodiversity
*Metagenomics/methods
North Sea
Animals
*Wind
Seawater
*DNA, Environmental/genetics/analysis
Ecosystem
*Metagenome
Denmark

@article {pmid40368316,
year = {2025},
author = {Wang, P and He, D and Zhao, J and Xiao, Z and Tan, J and Ma, J and Zheng, M},
title = {Transition from Anammox to Feammox metabolic modes: Regulation strategies for nitrite in Anammox enrichment cultures.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132674},
doi = {10.1016/j.biortech.2025.132674},
pmid = {40368316},
issn = {1873-2976},
abstract = {This studyachievedthe metabolic transition from anaerobic ammonium oxidation (Anammox) to Fe(III)-mediated ammonium oxidation (Feammox)usingiron-carbon micro-electrolytic spheres as a slow-release iron sourcethrougha stepwise reductionin influent NO2[-]-N concentration. The results demonstrated that sustained Feammox activitywas governed bynitrate-dependent ferrous oxidation (NDFO) metabolismcombined withoxygen-regulated Fe(III) regeneration,resulting ina peak total nitrogen removal efficiency of 91.6 %at40 mg/L NO2[-]-N.Whileexclusive NH4[+]-N feeding inhibited Feammox activity,this suppression was reversible upon NO2[-]-N supplementation. Intriguingly, Anammox activityremained robustdespite decreasing NO2[-]-N levelsand showedsignificant positive correlation with Feammox activity,suggesting shared metabolic modules. Metagenomic profilingfurther identifiedCa. Brocadia as the core functional genus driving NH4[+]-N oxidation,highlighting its niche adaptationin iron-mediated systems.These mechanistic insights establish a framework fordesigning energy-efficient nitrogen removal processesleveraging iron-redox cycling.},
}

@article {pmid40368259,
year = {2025},
author = {Wu, S and Zhang, N and Wan, Q},
title = {Disulfide bonds enhance thermal stability and thumb region drives activity of the glycoside hydrolase 11 xylanase rMxyl[cd].},
journal = {Journal of structural biology},
volume = {},
number = {},
pages = {108209},
doi = {10.1016/j.jsb.2025.108209},
pmid = {40368259},
issn = {1095-8657},
abstract = {Thermostable enzymes have significant advantages in industries, yet uncovering novel candidates with superior properties remains a scientific pursuit. This study identified rMxyl[cd], a glycoside hydrolase 11 family thermophilic xylanase from compost-soil metagenome, which exhibited a high specific activity of 5954 U·mg[-1] at pH 5.5 and 80°C. rMxyl[cd] was crystallized and diffracted to 1.5 Å resolution. Compared to the mesophilic xylanase Xyn II, rMxyl[cd] exhibits a more compact architecture. Notably, B-factor analysis reveals a uniquely flexible thumb region, hinting at its critical role in the enzyme's catalytic mechanism. rMxyl[cd] contains two disulfide bonds in the thumb and the N-terminal regions. Breaking these disulfide bonds by mutagenesis has dramatically decreased activities and thermostability. Conversely, introducing an extra disulfide bond at the N-terminal region of its α-helix extended its half-life for more than five folds at 80°C. Our studies firmly establish that the disulfide bonds are essential for its high thermal stability and the flexibility of the thumb region is crucial for its activity. Comparing the rMxyl[cd] crystal structure with the AlphaFold2-predicted model shows overall similarity, but the crystal structure offers higher local accuracy, especially in key functional regions. These findings not only deepen our understanding of the structure-function relationship of thermophilic xylanases but also inform a rational design of industrial enzymes.},
}

@article {pmid40368038,
year = {2025},
author = {Silvester, R and Perry, WB and Webster, G and Rushton, L and Baldwin, A and Pass, DA and Byrnes, NA and Farkas, K and Heginbothom, M and Craine, N and Cross, G and Kille, P and Kasprzyk-Hordern, B and Weightman, AJ and Jones, DL},
title = {Metagenomic profiling of hospital wastewater: A comprehensive national scale analysis of antimicrobial resistance genes and opportunistic pathogens.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106503},
doi = {10.1016/j.jinf.2025.106503},
pmid = {40368038},
issn = {1532-2742},
abstract = {BACKGROUND: Healthcare settings are recognised as potential hotspots for the emergence and spread of antimicrobial resistance (AMR).

METHOD: Metagenomic sequencing was conducted on a national scale using wastewater from hospitals across Wales to screen for antimicrobial resistance genes (ARGs) and opportunistic pathogens.

RESULTS: The total abundance and diversity of ARGs varied significantly across the hospitals. Genes conferring resistance to aminoglycosides, beta-lactams, and Macrolide-Lincosamide-Streptogramin-class antibiotics were predominant, with distinct resistome patterns emerging spatially. OXA-type beta-lactamases were the dominant ARG types. Spatial variability was observed in the distribution of the "big five" carbapenemases (KPC, IMP, VIM, NDM, OXA-48-like) and mcr genes, as well as WHO-listed fungal priority pathogens and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli (ESKAPEE) pathogens. Furthermore, antibiotic concentrations in the effluents often exceeded risk quotients, posing a substantial risk for AMR emergence.

CONCLUSIONS: Overall, the study highlights the effectiveness of combining wastewater-based epidemiology with metagenomics to gain critical insights into the distinct resistome and microbiome profiles in hospital settings. Tailored strategies are essential to mitigate the spread of antibiotics, clinically relevant ARGs and pathogens in these settings. This study underscores the necessity of implementing pre-treatment processes for hospital effluents before release into community sewers and environmental waters to curb the spread of these micro-pollutants.

AVAILABILITY OF DATA: The data will be made available upon request.},
}

@article {pmid40367945,
year = {2025},
author = {Antonaru, LA and Rad-Menéndez, C and Mbedi, S and Sparmann, S and Pope, M and Oliver, T and Wu, S and Green, DH and Gugger, M and Nürnberg, DJ},
title = {Evolution of far-red light photoacclimation in cyanobacteria.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.04.038},
pmid = {40367945},
issn = {1879-0445},
abstract = {Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of ∼20 genes and involves the synthesis of red-shifted chlorophylls d and f, together with paralogs of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups, but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to help clarify this issue: sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 51 new gene clusters. These data enable high-resolution phylogenetics and-by relying on multiple gene trees, together with gene arrangement conservation-support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and we hypothesize that the process was associated with the formation of microbial mats and stromatolites in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing features that have been maintained for billions of years. Overall, far-red-light-driven oxygenic photosynthesis may have played a significant role in Earth's early history.},
}

@article {pmid40367908,
year = {2025},
author = {Yuan, L and Chen, Y and Xie, M and Wang, J and Zheng, J and Zhou, J and Li, B and Zhang, D and Han, D},
title = {Utility of clinical metagenomics in complex infections: Cryptococcal meningitis complicated by Nocardia brain abscess.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {1},
pages = {116895},
doi = {10.1016/j.diagmicrobio.2025.116895},
pmid = {40367908},
issn = {1879-0070},
abstract = {Nocardia farcinica brain abscess (BA) is a rare yet life-threatening infection of the central nervous system (CNS) that predominantly affects immunocompromised patients. Its nonspecific symptoms often lead to delayed diagnosis and poor outcomes. Early diagnosis and precise treatment are essential to improve the prognosis of patients. We report the rare case of a 75-year-old man with IgG4-related disease undergoing long-term methylprednisolone therapy who presented with a N. farcinica brain abscess. The patient initially presented with cryptococcal meningitis but exhibited persistent symptoms despite standard antifungal treatment. Follow-up neuroimaging revealed new intracranial abscess formations. Metagenomic next-generation sequencing (mNGS) of brain tissue and cerebrospinal fluid (CSF) identified abundant N. farcinica-specific sequences, confirming a concurrent Nocardia brain abscess complicating the cryptococcal infection. The patient's condition gradually improved with timely antibiotic treatment and is currently in recovery. This case underscores the heightened risk of sequential opportunistic infections in immunocompromised individuals and exemplifies the clinical value of mNGS in detecting rare infectious diseases. We further conducted a systematic review of patients with Nocardia central nervous system infections confirmed by mNGS, analyzing their clinical presentations, laboratory parameters, therapeutic regimens, and prognostic outcomes. In summary, our study demonstrates that mNGS offers significant diagnostic advantages compared to conventional microbiological methods for uncommon infections. These findings provide clinically actionable, evidence-based guidance for the diagnosis and management of Nocardia brain abscesses.},
}

@article {pmid40367885,
year = {2025},
author = {Mo, S and Wu, X and Kashif, M and Zeng, S and Sang, Y and Meng, C and He, S and Jiang, C},
title = {Effects of Spartina alterniflora invasion on carbon fixation and sulfate reduction in a subtropical marine mangrove ecosystem.},
journal = {Marine pollution bulletin},
volume = {217},
number = {},
pages = {118128},
doi = {10.1016/j.marpolbul.2025.118128},
pmid = {40367885},
issn = {1879-3363},
abstract = {Mangrove sediments host diverse microbial communities that are crucial for carbon fixation, but their functions and pathways in subtropical ecosystems-particularly under Spartina alterniflora invasion and across varying sediment depths-remain unclear. This study employed metagenomic and qPCR analyses to explore microbial carbon fixation in Rhizophora stylosa, S. alterniflora, and bare beach habitats. Environmental factors like Cd, sulfide, pH, and salinity significantly influenced carbon fixation and sulfate reduction. Specifically, the invasion increased the abundance of key carbon fixation genes, including aclA/B, cbbL, and korA, which are involved in the Calvin-Benson-Bassham (CBB) and Arnon-Buchanan (rTCA) cycles, respectively. This shift in gene abundance was accompanied by elevated Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity (0.47-21.82 nmol CO2 g[-1] soil min[-1]), suggesting a potential increase in microbial CO2 fixation rates in S. alterniflora-invaded sediments. Sediment depth also affected the distribution of carbon fixation genes and carbon-metabolizing microbes. Desulfobacterota were identified as major contributors to carbon fixation via both the rTCA and CBB cycles. Moreover, a strong correlation was observed between carbon fixation and sulfate reduction. These findings reveal how S. alterniflora invasion impacts carbon fixation and enhance our understanding of the mangrove ecosystems' role in climate change regulation.},
}

@article {pmid40367854,
year = {2025},
author = {Ahmad, W and Coffman, L and Ray, R and Woldesenbet, S and Singh, G and Khan, AL},
title = {Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.},
journal = {The Science of the total environment},
volume = {982},
number = {},
pages = {179554},
doi = {10.1016/j.scitotenv.2025.179554},
pmid = {40367854},
issn = {1879-1026},
abstract = {Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.},
}

@article {pmid40367785,
year = {2025},
author = {Wang, Y and Huang, S and He, J and Feng, Z and Wu, W and Guo, C and He, J},
title = {Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138594},
doi = {10.1016/j.jhazmat.2025.138594},
pmid = {40367785},
issn = {1873-3336},
abstract = {Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.},
}

@article {pmid40367670,
year = {2025},
author = {Yu, S and Cao, T and Xu, Z and Zhou, H and Li, Q},
title = {Metagenomic next-generation sequencing (mNGS) identified Clostridium perfringens infection presenting as acute hemolysis after surgery.},
journal = {Journal of infection and public health},
volume = {18},
number = {8},
pages = {102798},
doi = {10.1016/j.jiph.2025.102798},
pmid = {40367670},
issn = {1876-035X},
abstract = {Clostridium perfringens (C. perfringens) septicaemia is a rare, but rapidly fatal infection, characterized by massive hemolysis. In numerous documented instances, the patient was not diagnosed in time due to the absence of typical clinical features. In order to enhance diagnostic accuracy, metagenomic next-generation sequencing (mNGS) has been adopted as a novel approach to pathogen identification. CASE PRESENTATION: A 67-year-old male who had undergone transcatheter arterial chemoembolization (TACE) surgery four days earlier presented with severe anemia, and laboratory investigations disclosed intravascular hemolysis. Swift and accurate identification was imperative, resulting in the confirmation of mNGS analysis, his medical history, clinical symptoms, physical signs, additional tests, and C. perfringens as the causative pathogen of hemolysis. After successful treatment with effective antibiotics, the patient recovered and was discharged from the hospital after 19 days. CONCLUSIONS: mNGS achieves expedited diagnostic turnaround time through rapid pathogen identification, significantly surpassing conventional culture methods. This may enable the diagnosis of atypical cases of C. perfringens infection, which can cause rapid systemic shock, renal failure, intravascular hemolysis, and even death.},
}

@article {pmid40367615,
year = {2025},
author = {Guo, Y and Cheng, S and Fang, H and Geng, J and Shi, F and Wang, H and Chen, L and Pu, H and Liu, B and Zhou, Y},
title = {Water regime alters microbial mechanisms of N2O emission in metal-contaminated paddy soils.},
journal = {Ecotoxicology and environmental safety},
volume = {298},
number = {},
pages = {118304},
doi = {10.1016/j.ecoenv.2025.118304},
pmid = {40367615},
issn = {1090-2414},
abstract = {Microorganisms are essential for soil nitrous oxide (N2O) emissions through participating in key nitrogen (N)-related processes. However, the effect of water regimes on the interactions between N2O emissions and microbial processes in metal-contaminated soils is unclear. Here, we conducted a soil microcosm experiment with two water management strategies (non-flooding and flooding) and six metal addition treatments including low (2 and 200 mg kg[-1]) and high (10 and 1000 mg kg[-1]) levels of individual and combined Cd and Cu. The effects of high levels of individual Cd and Cu contamination on soil N2O emissions varied depending on water regimes, showing antagonistic effects under non-flooding conditions and synergistic effects under flooding conditions. High levels of co-contamination significantly inhibited nitrification under both water regimes, primarily due to reduced abundance of Nitrosospira. In contrast, this co-contamination decreased the abundance of Ramlibacter, thereby inhibiting denitrification and dissimilatory nitrate reduction to ammonium (DNRA) under flooding conditions. The inhibition of these key microorganisms and their mediated N-cycle processes reduced soil N2O emissions under both water regimes. This reduction was greater under flooding conditions because more N-related processes were inhibited. Metagenomic binning further indicated that Nitrosospira carried nitrifying genes, while Ramlibacter contained genes involved in denitrification, assimilatory nitrate reduction to ammonium (ANRA), and DNRA. These findings implied that both microorganisms had potential to produce N2O. Overall, water management strategies and metal contamination altered the microbial processes of N2O emissions, highlighting the importance of appropriate water management in mitigating greenhouse gas emissions from metal-contaminated paddy soils in southern China.},
}

@article {pmid40367351,
year = {2025},
author = {Heo, H and Nguyen-Dinh, T and Jung, MY and Greening, C and Yoon, S},
title = {Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf092},
pmid = {40367351},
issn = {1751-7370},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is a key process used by diverse microorganisms in the global nitrogen cycle. For long, DNRA has been considered primarily as an organotrophic reaction, despite evidence that oxidation of inorganic electron donors also supports DNRA. Evidence of DNRA coupling with molecular hydrogen (H2) oxidation has been reported for several microbial isolates; however, the underlying physiology of the microbial process remains understudied. In this study, we report the isolation of two Campylobacterotastrains, Aliarcobacter butzlerihDNRA1 and Sulfurospirillumsp. hDNRA2, which grow using H2as the sole electron donor for DNRA, and physiological insights gained from a close examination of hydrogenotrophic DNRA in these isolates. In both batch and continuous cultures, DNRA sensu stricto(i.e. NO3-reduction that includes stoichiometric NO2--to-NH4+reduction) was strictly dependent on the presence of H2and exhibited stoichiometric coupling with H2oxidation, indicating that electrons required for NO2-reduction were unequivocally derived from H2. Successful chemostat incubation further demonstrated that hydrogenotrophic DNRA is viable under NO3-limiting, H2-excess conditions. Genomic and transcriptomic analyses identified group 1b [NiFe]-hydrogenase and cytochrome c552nitrite reductase as the key enzymes catalyzing hydrogenotrophic DNRA. Additionally, metagenomic surveys revealed that bacteria capable of hydrogenotrophic DNRA are taxonomically diverse and abundant in various ecosystems, particularly in the vicinity of deep-sea hydrothermal vents. These findings, integrating physiological, genomic, and transcriptomic analyses, clarify that H2can solely serve as a growth-supporting electron donor for DNRA and suggest potential significance of this microbial process in nitrogen- and hydrogen-related environmental biogeochemical cycles.},
}

@article {pmid40366862,
year = {2025},
author = {Wang, L and Chen, X and Pollock, NR and Villafuerte Gálvez, JA and Alonso, CD and Wang, D and Daugherty, K and Xu, H and Yao, J and Chen, Y and Kelly, CP and Cao, Y},
title = {Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2505269},
doi = {10.1080/19490976.2025.2505269},
pmid = {40366862},
issn = {1949-0984},
abstract = {Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.},
}

@article {pmid40366770,
year = {2025},
author = {Baba, Y and Tsuge, D and Aoki, R},
title = {Enhancement of carbohydrate metabolism by probiotic and prebiotic intake promotes short-chain fatty acid production in the gut microbiome: A randomized, double-blind, placebo-controlled crossover trial.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbaf071},
pmid = {40366770},
issn = {1347-6947},
abstract = {Short-chain fatty acids (SCFAs) are thought to be a key factor in the health benefits of prebiotics and probiotics. This study investigated the effect of Bifidobacterium animalis subsp. lactis GCL2505 and inulin (BL+IN) on fecal SCFAs and gut microbial composition and function. A placebo-controlled, randomized, double-blind, crossover study was conducted with 120 participants. Two weeks of BL+IN intake significantly increased acetate, propionate, and butyrate concentrations and Bifidobacterium abundance compared to placebo. Functional analysis of the gut metagenome showed enrichment of genes associated with carbohydrate and amino acid metabolism, suggesting an enhanced capacity for SCFA production. A responder was defined as a participant with increased fecal SCFAs after BL+IN consumption. Responder metagenomes exhibited greater enrichment of genes involved in SCFA production and carbohydrate metabolism. In conclusion, short-term BL+IN ingestion may benefit healthy adults by increasing fecal SCFAs through influencing the composition and functional activation of SCFA-associated pathways in the gut microbiome.},
}

@article {pmid40366182,
year = {2025},
author = {Martin Říhová, J and Vodička, R and Hypša, V},
title = {An obligate symbiont of Haematomyzus elephantis with a strongly reduced genome resembles symbiotic bacteria in sucking lice.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0022025},
doi = {10.1128/aem.00220-25},
pmid = {40366182},
issn = {1098-5336},
abstract = {The parvorder Rhynchophthirina with a single genus Haematomyzus is a small group of ectoparasites of unclear phylogenetic position, related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated that Haematomyzus harbors a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the smallest known genomes are found in the symbionts associated with sucking lice, which feed exclusively on mammal blood, compared to the generally larger genomes of the symbionts inhabiting chewing lice, which feed on skin derivatives. In this study, we investigate the genome characteristics of the symbiont associated with Haematomyzus elephantis. We sequenced and assembled the H. elephantis metagenome, extracted a genome draft of its symbiotic bacterium, and showed that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice and also with Wigglesworthia glossinidia, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, the H. elephantis symbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.IMPORTANCERhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, i.e., mammals' blood vs vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role is not known. In this study, we assemble the genome of symbiotic bacterium from Haematomyzus elephantis (Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other sucking louse symbionts, it retains essential pathways for the synthesis of several B vitamins.},
}

@article {pmid40366158,
year = {2025},
author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB},
title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174924},
doi = {10.1128/msystems.01749-24},
pmid = {40366158},
issn = {2379-5077},
abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.

IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.},
}

@article {pmid40366141,
year = {2025},
author = {Li, J and Zheng, K and Ding, W and Lu, L and Liang, Y and Xiong, Y and Wei, Z and Gao, C and Su, Y and Wang, Z and Chen, X and Bao, Z and Hu, X and McMinn, A and Wang, M},
title = {Healthy and moribund Zhikong scallops (Chlamys farreri) developed different viral communities during a mass mortality event.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0034225},
doi = {10.1128/msystems.00342-25},
pmid = {40366141},
issn = {2379-5077},
abstract = {UNLABELLED: Viral assemblages of scallops are still relatively unknown. Here, metagenomic analysis was used to study virus communities in the gut of scallops to establish the first scallop virome data set (SVD); this contains 7,447 viral operational taxonomic units. Protein-sharing networks and phylogenetic analyses demonstrated the high diversity and novelty of the SVD, which is very different from viromes from other habitats. Potentially pathogenic viruses are prevalent in the gut of scallops. In particular, the novel smacoviruses were identified, indicating that scallops may be a potential hotspot for this viral group. Inference of virus-host associations found extensive interactions between viruses and major prokaryotic lineages. Intriguingly, moribund scallops showed a higher diversity of auxiliary metabolic genes (AMGs) related to amino acid metabolism and cofactor and vitamin genes, while healthy scallops had fewer AMGs, with those present focusing on secondary metabolite biosynthesis and carbohydrate metabolism. These findings provide the first landscape of scallop gut viruses based on metagenomes and highlight the potential roles of diverse and unique gut viruses for the health of filter-feeding bivalves.

IMPORTANCE: This study uses metagenome sequencing to establish the first scallop virome database. The study reveals previously unknown diversity of scallop-associated viruses and provides insights into links between disease status and viral diversity and genome content. The study will interest many aquatic virologists and could have important implications in managing marine resources.},
}

@article {pmid40366139,
year = {2025},
author = {Crouch, AL and Severance, BM and Creary, S and Hood, D and Bailey, M and Mejias, A and Ramilo, O and Gillespie, M and Ebelt, S and Sheehan, V and Kopp, BT and Anderson, MZ},
title = {Altered nasal and oral microbiomes define pediatric sickle cell disease.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0013725},
doi = {10.1128/msphere.00137-25},
pmid = {40366139},
issn = {2379-5042},
abstract = {UNLABELLED: Sickle cell disease (SCD) is a chronic blood disorder that disrupts multiple organ systems and can lead to severe morbidity. Persistent and acute symptoms caused by immune system dysregulation in individuals with SCD could contribute to disease either directly or indirectly via dysbiosis of commensal microbes and increased susceptibility to infection. Here, we explored the nasal and oral microbiomes of children with SCD (cwSCD) to uncover potential dysbiotic associations with the blood disorder. Microbiota collected from nasal and oral swabs of 40 cwSCD were compared to eight healthy siblings using shotgun metagenomic sequencing. Commensal taxa were present at similar levels in the nasal and oral microbiome of both groups. However, the nasal microbiomes of cwSCD contained a higher prevalence of Pseudomonadota species, including pathobionts such as Yersinia enterocolitica and Klebsiella pneumoniae. Furthermore, the oral microbiome of cwSCD displayed lower α-diversity and fewer commensal and pathobiont species compared to the healthy siblings. Thus, subtle but notable shifts seem to exist in the nasal and oral microbiomes of cwSCD, suggesting an interaction between SCD and the microbiome that may influence health outcomes.

IMPORTANCE: The oral and nasal cavities are susceptible to environmental exposures including pathogenic microbes. In individuals with systemic disorders, antibiotic exposure, changes to the immune system, or changes to organ function could influence the composition of the microbes at these sites and the overall health of individuals. Children with sickle cell disease (SCD) commonly experience respiratory infections, such as pneumonia or sinusitis, and may have increased susceptibility to infection because of disrupted microbiota at these body sites. We found that children with SCD (cwSCD) had more pathobiont bacteria in the nasal cavity and reduced bacterial diversity in the oral cavity compared to their healthy siblings. Defining when, why, and how these changes occur in cwSCD could help identify specific microbial signatures associated with susceptibility to infection or adverse outcomes, providing insights into personalized treatment strategies and preventive measures.},
}

@article {pmid40366134,
year = {2025},
author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X},
title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/msystems.00375-25},
pmid = {40366134},
issn = {2379-5077},
abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.},
}

@article {pmid40366096,
year = {2025},
author = {Ragupathy, V and Kelley, K and Hewlett, I},
title = {Near-complete torque teno virus (TTV) genome identified in a blood donor infected with hepatitis B virus (HBV).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0117824},
doi = {10.1128/mra.01178-24},
pmid = {40366096},
issn = {2576-098X},
abstract = {We have identified a near full-length torque teno virus (TTV) genome sequence in plasma from a blood donor infected with hepatitis B virus. The consensus sequence of TTV was extracted from Nanopore metagenomic sequencing. The identified TTV open reading frame 1 is 3,062 nucleotides (nt) long and shares 90%-100% identity with other human TTVs.},
}

@article {pmid40365535,
year = {2025},
author = {Li, M and Chen, J and Zhang, L and Chen, X and Zhou, J and Liu, F and Zhou, X and Xiao, J and Yang, K and Qi, L and Han, X and Liu, T and Zhao, H and Zhou, Z and Chen, X and Sun, L},
title = {Clinicopathological characteristics and diagnostic performance of metagenomic pathogen detection technology in mycobacterial infections among HIV patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1584189},
pmid = {40365535},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; *HIV Infections/complications ; Adult ; Middle Aged ; Mycobacterium tuberculosis/isolation & purification/genetics ; *Metagenomics/methods ; Sputum/microbiology ; *Mycobacterium Infections/diagnosis/microbiology/pathology ; Sensitivity and Specificity ; *Molecular Diagnostic Techniques/methods ; Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Biopsy ; },
abstract = {BACKGROUND: Mycobacterial infections represent a major cause of morbidity and mortality in HIV-infected individuals. This study evaluated diagnostic techniques for mycobacterial identification and compared clinicopathological features between HIV-positive and HIV-negative patients.

METHODS: We analyzed 88 tissue samples (with 41 matched blood and 28 sputum samples) using histopathology (HE and acid-fast staining), bacterial culture, MTB-PCR (sputum/biopsy), PCR-reverse dot blot hybridization (RDBH), and metagenomic pathogen detection technology (MetaPath™). Logistic regression analyses were performed to identify factors affecting detection rates.

RESULTS: Mycobacterial infection was detected in 95.5% (84/88) of patients. Among HIV-positive patients (n=63), 46% (29/63) had Mycobacterium tuberculosis (MTB) infections, and 44% (28/63) had non-tuberculous mycobacteria (NTM) infections, significantly higher than the 20% (5/25) NTM rate in HIV-negative patients. Univariate analysis identified HIV-positive status (p=0.009), lymph node involvement (p=0.020), and positive MetaPath™ results (p=0.002) as significant predictors of detection, while multivariate analysis confirmed these as independent factors (p=0.036; p=0.042; p=0.006). Lymph nodes were the most common infection site in HIV-positive patients (42.9%, 27/63), while lung tissue predominated in HIV-negative patients (48%, 12/25). MetaPath™ demonstrated superior sensitivity and specificity for detecting both MTB and NTM. Biopsy samples provided higher diagnostic accuracy than sputum or blood for lung and lymph node infections, but not for brain. In HIV-positive patients, NTM infections showed significantly more granuloma formation (p=0.032) and foam cells (p=0.005), but less necrosis (p=0.0005) compared to MTB infections. No significant differences were observed in HIV-negative patients.

CONCLUSIONS: MetaPath™ is a highly effective diagnostic tool for mycobacterial infections, particularly in tissue biopsies. HIV-positive status, lymph node involvement, and MetaPath™ positivity independently predict mycobacterial detection. HIV-positive patients exhibit distinct clinicopathological features, emphasizing the need for tailored diagnostic and therapeutic approaches based on immune status.},
}

Humans
Male
Female
*HIV Infections/complications
Adult
Middle Aged
Mycobacterium tuberculosis/isolation & purification/genetics
*Metagenomics/methods
Sputum/microbiology
*Mycobacterium Infections/diagnosis/microbiology/pathology
Sensitivity and Specificity
*Molecular Diagnostic Techniques/methods
Mycobacterium Infections, Nontuberculous/diagnosis/microbiology
Biopsy

@article {pmid40365473,
year = {2025},
author = {Pu, T and Tan, Y and Zhao, Y and Zhao, Z and Zhang, N and Li, C and Song, Y},
title = {Effect of Seasonal Variations on Soil Microbial, Extracellular Enzymes, and Ecological Stoichiometry in Tea Plantations.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71362},
pmid = {40365473},
issn = {2045-7758},
abstract = {Tea plantations are important agricultural ecosystems in karst areas, yet the seasonal dynamics of soil microbial communities, functional genes, and extracellular enzyme activities (EEA) under different management practices remain poorly understood. This study investigated organic (HY), pollution-free (TS), and conventional (XY) tea plantations in Weng'an County, Southwest China, during the spring (April) and autumn (August) tea seasons via metagenomics and stoichiometric analyses. Seasonal variations significantly altered the soil physicochemical properties (e.g., SOC, TN, and TP) and EEA (p < 0.05), with higher C-acquiring enzyme activity in autumn and elevated soil C:N:P ratios in spring. The soil extracellular enzyme stoichiometry (EES C:N:P) deviated from the theoretical 1:1:1 ratio, indicating that microbial metabolism was constrained by soil resource availability rather than homeostasis. Phosphorus limitation (vector angle > 45°) persisted across seasons, contradicting initial hypotheses, with acid phosphatase (ACP) activity and EES C:P identified as critical drivers. Random forest (RF) and structural equation modeling (SEM) revealed that the spring season had stronger impacts on microbial communities and functional genes, with the soil TN, C:N, NAG, ACP, and EES C:P ratios as key predictors. Compared with conventional practices, organic management enhances microbial diversity and functional redundancy, buffering seasonal fluctuations. These findings highlight the interplay between seasonal climatic shifts and agricultural practices regulating soil nutrient cycling and microbial adaptation. Strategic interventions-such as spring carbon supplementation, autumn organic phosphorus fertilization, and intercropping-are proposed to optimize microbial resilience and ecosystem stability in fragile karst tea plantations. This study provides novel insights into soil ecological stoichiometry and microbial metabolic strategies, offering a reference for the sustainable management of agroecosystems in karst areas.},
}

@article {pmid40365061,
year = {2025},
author = {Liu, L and Wang, Z and Luo, C and Deng, Y and Wu, W and Jin, Y and Wang, Y and Huang, H and Wei, Z and Zhu, Y and He, X and Guo, L},
title = {Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1571684},
pmid = {40365061},
issn = {1664-302X},
abstract = {BACKGROUND: Root rot disease is a major threat to the sustainable production of Panax notoginseng. Tetramycin has a broad-spectrum fungicidal efficacy, low toxicity, and high efficiency, However, the prevention and control of root rot disease of P. notoginseng and the specific mechanism of action are still unclear.

METHODS: In this paper, a combination of indoor and pot experiments was used to assess the effectiveness of tetramycin at alleviating root rot disease challenges encountered by P. notoginseng. Amplicon sequencing, metagenomic analysis with microbial verification were used to investigate the microecological mechanisms underlying tetramycin's ability to reduce soil biological barriers.

RESULTS: We found that tetramycin significantly inhibited mycelial growth and spore germination of pathogenic fungi. Tetramycin, T2 (1000×) and T3 (500×), applied to continuous cropping soil, increased the seedling survival rates of P. notoginseng. Additionally, tetramycin reduced fungal α-diversity and shifted the fungal community assembly from deterministic to stochastic process. The microbial functions influenced by tetramycin were primarily associated with antibiotic synthesis and siderophore synthesis. Antibiotic efflux and inactivation have also been identified as the main resistance mechanisms. Microbial verification results showed that the artificially assembled tetramycin-regulated microbial community could indeed alleviate the occurrence of diseases. Furthermore, the cross-kingdom synthetic community assembled by the three key strains (Pseudomonas aeruginosa, Variovorax boronicumulans, and Cladosporium cycadicola) significantly improved the control of root rot disease and promoted plant growth.

DISCUSSION: This study provides novel insights into developing efficient biological control strategies and elucidates the role and mechanism of tetramycin in modulating soil microflora assembly to strengthen host disease resistance.},
}

@article {pmid40364394,
year = {2025},
author = {Cao, K and Shi, P and Xu, X and Wang, J},
title = {Self-Inhibition Effects of Litter-Mediated Plant-Phyllosphere Feedback on Seedling Growth in Invasive and Native Congeneric Species.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/plants14091355},
pmid = {40364394},
issn = {2223-7747},
abstract = {Plant-phyllosphere feedback (PPF) is an ecological process in which phyllosphere microbiota, originating from plant litter, are transmitted via aerosols and subsequently influence the growth of conspecific or heterospecific plants. However, the cross-species generality of this mechanism and its role in invasive plant success remain to be fully elucidated. This study systematically examined PPF effects using three invasive/native congeneric plant pairs from distinct families (Phytolaccaceae, Asteraceae, and Amaranthaceae) in Jiangxi Province, China. Key findings include the following: (1) Wide conspecific negative feedback across families, with four of six species exhibiting 6.2-12.7% biomass reduction under their own litter treatments (p < 0.05). (2) Comparable feedback intensity between invasive and native species, as indicated by average pairwise indices (invasive I = -0.05 vs. native I = -0.04; p = 0.15). Notably, the invasive species Phytolacca americana uniquely showed a positive biomass response (+7.1%), though underlying mechanisms (phytochemical or microbial) were not investigated. (3) Lack of correlation between PPF strength and plant functional traits or phylogenetic distance, as indicated by Mantel tests (p > 0.8), in contrast to the trait/phylogeny associations commonly observed in soil feedback systems. This study provided the first evidence of PPF universality across multiple plant families-previously documented only within Asteraceae-and highlights the potential microbial-mediated advantages in plant invasions. Future research should integrate spatiotemporal metagenomic and metabolomic approaches to decipher the dynamic pathogen/microbe networks and their phytochemical interactions.},
}

@article {pmid40363788,
year = {2025},
author = {Zhou, L and Li, J and Ding, C and Zhou, Y and Xiao, Z},
title = {Mechanistic Advances in Hypoglycemic Effects of Natural Polysaccharides: Multi-Target Regulation of Glycometabolism and Gut Microbiota Crosstalk.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {9},
pages = {},
doi = {10.3390/molecules30091980},
pmid = {40363788},
issn = {1420-3049},
support = {2024JJ8163//Hunan Natural Science Foundation/ ; C2023005//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 201923//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 2022ZYYGN06//2022 Annual Natural Drug Resources and Function Development Fund Project/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polysaccharides/pharmacology/chemistry/therapeutic use ; Animals ; *Hypoglycemic Agents/pharmacology/chemistry/therapeutic use ; Signal Transduction/drug effects ; Insulin Resistance ; Glucose/metabolism ; },
abstract = {Natural polysaccharides (NPs), as a class of bioactive macromolecules with multitarget synergistic regulatory potential, exhibit significant advantages in diabetes intervention. This review systematically summarizes the core hypoglycemic mechanisms of NPs, covering structure-activity relationships, integration of the gut microbiota-metabolism-immunity axis, and regulation of key signaling pathways. Studies demonstrate that the molecular weight, branch complexity, and chemical modifications of NPs mediate their hypoglycemic activity by influencing bioavailability and target specificity. NPs improve glucose metabolism through multiple pathways: activating insulin signaling, improving insulin resistance (IR), enhancing glycogen synthesis, inhibiting gluconeogenesis, and regulating gut microbiota homeostasis. Additionally, NPs protect pancreatic β-cell function via the nuclear factor E2-related factor 2 (Nrf2)/Antioxidant Response Element (ARE) antioxidant pathway and Toll-like receptor 4 (TLR4)/nuclear factor-κB (NF-κB) anti-inflammatory pathway. Clinical application of NPs still requires overcoming challenges such as resolving complex structure-activity relationships and dynamically integrating cross-organ signaling. Future research should focus on integrating multi-omics technologies (e.g., metagenomics, metabolomics) and organoid models to decipher the cross-organ synergistic action networks of NPs, and promote their translation from basic research to clinical applications.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Polysaccharides/pharmacology/chemistry/therapeutic use
Animals
*Hypoglycemic Agents/pharmacology/chemistry/therapeutic use
Signal Transduction/drug effects
Insulin Resistance
Glucose/metabolism

@article {pmid40362493,
year = {2025},
author = {Žukienė, G and Narutytė, R and Rudaitis, V},
title = {Association Between Vaginal Microbiota and Cervical Dysplasia Due to Persistent Human Papillomavirus Infection: A Systematic Review of Evidence from Shotgun Metagenomic Sequencing Studies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094258},
pmid = {40362493},
issn = {1422-0067},
mesh = {Humans ; Female ; *Papillomavirus Infections/complications/microbiology/virology ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Metagenomics/methods ; *Uterine Cervical Dysplasia/microbiology/virology/etiology ; Papillomaviridae ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The role of vaginal dysbiosis in the progression of human papilloma virus (HPV) associated cervical lesions has gained attention in recent years. While many studies use 16S rRNA gene sequencing for microbiota analysis, shotgun metagenomic sequencing offers higher taxonomic resolution and insights into microbial gene functions and pathways. This systematic review evaluates the relationship between compositional and functional changes in the vaginal microbiome during HPV infection and cervical lesion progression. A literature search was performed according to PRISMA guidelines in PubMed, Web of Science, Scopus, and ScienceDirect databases. Seven studies utilizing metagenomic sequencing in patients with HPV infection or HPV-associated cervical lesions were included. Progression from HPV infection to cervical lesions and cancer was associated with a reduction in Lactobacillus species (particularly Lactobacillus crispatus) and an enrichment of anaerobic and pathogenic species, especially Gardnerella vaginalis. Heterogeneous enriched metabolic pathways were also identified, indicating functional shifts during lesion progression. As most studies were conducted in Asia, further research in diverse regions is needed to improve the generalizability of findings. Future studies employing metagenomic sequencing may help identify biomarkers for early pre-cancerous lesions and clarify the role of vaginal microbiota in persistent HPV infection and cervical dysplasia.},
}

Humans
Female
*Papillomavirus Infections/complications/microbiology/virology
*Vagina/microbiology/virology
*Microbiota/genetics
Metagenomics/methods
*Uterine Cervical Dysplasia/microbiology/virology/etiology
Papillomaviridae
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40362462,
year = {2025},
author = {Chakraborty, N and Holmes-Hampton, G and Rusling, M and Kumar, VP and Hoke, A and Lawrence, AB and Gautam, A and Ghosh, SP and Hammamieh, R},
title = {Delayed Impact of Ionizing Radiation Depends on Sex: Integrative Metagenomics and Metabolomics Analysis of Rodent Colon Content.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094227},
pmid = {40362462},
issn = {1422-0067},
support = {xxxxx//AFRRI/ ; },
mesh = {Animals ; Male ; Female ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *Radiation, Ionizing ; *Colon/radiation effects/metabolism/microbiology ; *Gastrointestinal Microbiome/radiation effects ; Sex Factors ; Whole-Body Irradiation/adverse effects ; Mice, Inbred C57BL ; },
abstract = {There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host's colon could meet this knowledge gap since the microbes play major roles in a host's response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.},
}

Animals
Male
Female
Mice
*Metabolomics/methods
*Metagenomics/methods
*Radiation, Ionizing
*Colon/radiation effects/metabolism/microbiology
*Gastrointestinal Microbiome/radiation effects
Sex Factors
Whole-Body Irradiation/adverse effects
Mice, Inbred C57BL

@article {pmid40362406,
year = {2025},
author = {Krivonos, DV and Fedorov, DE and Konanov, DN and Vvedensky, AV and Sonets, IV and Korneenko, EV and Speranskaya, AS and Ilina, EN},
title = {Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094168},
pmid = {40362406},
issn = {1422-0067},
support = {24-15-00419//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Fungi/genetics/classification ; *Nanopore Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Algorithms ; Metagenome ; *Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; *Software ; },
abstract = {The Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data. The tools used for nanopore amplicon sequencing data analysis often provide only taxonomy annotation without OTU sequence assembly. Conversely, tools that facilitate OTU assembly are constrained in their analysis to long reads, such as the V1-V9 regions of 16S rRNA for bacterial community studies or the full-length ITS cluster (ITS1-5.8S-ITS2) for fungal community studies. In other cases, researchers propose their own solutions without dedicated tools. In this paper, we present Pike, a novel tool for analyzing Oxford Nanopore amplicon sequencing data. Pike allows analysis without amplicon size limitations and allows de novo assembly of OTU sequences. In our research, we created mock communities of fungi and bacteria, which we then used to demonstrate the efficiency of our algorithm. Furthermore, we validated the algorithm using externally available data. We also compared our approach with similar ones to show its applicability.},
}

*Metagenomics/methods
Fungi/genetics/classification
*Nanopore Sequencing/methods
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Algorithms
Metagenome
*Nanopores
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
*Software

@article {pmid40361215,
year = {2025},
author = {Ma, Y and Jiang, J and Yang, Z and Li, Y and Bai, H and Liu, Z and Zhang, S and Zhi, Z and Yang, Q},
title = {Changes of gastric microflora and metabolites in patients with chronic atrophic gastritis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {537},
pmid = {40361215},
issn = {1479-5876},
support = {No.21377724D//Hebei Provincial Department of Science and Technology/ ; No. 18//National Administration of Traditional Chinese Medicine Science and Technology/ ; 246W7701D//Provincial Science and Technology Plan of Hebei Province/ ; },
mesh = {Humans ; *Gastritis, Atrophic/microbiology/metabolism ; Chronic Disease ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Metabolome ; *Stomach/microbiology ; Metabolomics ; *Microbiota ; Bacteria/genetics/metabolism ; Adult ; Aged ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is related to the body's microbial and metabolic systems. Combined studies of microbiome and metabolomics can clarify the mechanisms of disease occurrence and progression. We used 16S rRNA sequencing, metagenomics sequencing and metabolomics sequencing to depict the landscapes of bacterium and metabolites, construct correlation networks of different bacterium and metabolites describe potential pathogenic mechanisms of chronic atrophic gastritis.

METHODS: The gastric juices of 30 non-atrophic gastritis (NAG) patients and 30 CAG patients were collected. Gastric microflora was analyzed by 16S rRNA sequencing and metagenomics sequencing. Gastric metabolites were analyzed by LC-MS analysis. Different bioinformatics methods were used to analyze the data of microbiome and metabolome, and to analyze the relationship between them.

RESULTS: In atrophic gastritis, bacteria diversity decreased. The genera with a mean decrease in Gini greater than 1.5 included peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides. KEGG pathway included renal cell carcinoma, proximal tubule bicarbonate reclamation, citrate cycle and aldosterone synthesis and secretion with significant enrichment of differential metabolites. Peptostreptococcus, fusobacterium, prevotella and sphingomonas were in pivot positions of the correlation network of differential metabolites and differential bacterium. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism were enriched in chronic atrophic gastritis based on the metagenomic sequencing data.

CONCLUSION: Peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides were the essential features that distinguish atrophic gastritis from non-atrophic gastritis, and caused disease by altering various metabolic pathways. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism may be related to the occurrence and progression of CAG.},
}

Humans
*Gastritis, Atrophic/microbiology/metabolism
Chronic Disease
Middle Aged
Female
Male
RNA, Ribosomal, 16S/genetics
Metabolome
*Stomach/microbiology
Metabolomics
*Microbiota
Bacteria/genetics/metabolism
Adult
Aged
*Gastrointestinal Microbiome

@article {pmid40360994,
year = {2025},
author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W},
title = {The gut-liver axis plays a limited role in mediating the liver's heat susceptibility of Chinese giant salamander.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {475},
pmid = {40360994},
issn = {1471-2164},
support = {31900327//National Natural Science Foundation of China/ ; 2023NSFSC1153//Natural Science Foundation of Sichuan Province of China/ ; },
mesh = {Animals ; *Liver/metabolism ; *Gastrointestinal Microbiome ; *Caudata/physiology/genetics/microbiology ; Heat-Shock Response ; Transcriptome ; Gene Expression Profiling ; Energy Metabolism ; Larva ; },
abstract = {The Chinese giant salamander (CGS, Andrias davidianus), a flagship amphibian species, is highly vulnerable to high temperatures, posing a significant threat under future climate change. Previous research linked this susceptibility to liver energy deficiency, accompanied by shifts in gut microbiota and reduced food conversion rates, raising questions about the role of the gut-liver axis in mediating heat sensitivity. This study investigated the responses of Chinese giant salamander larvae to a temperature gradient (10-30 °C), assessing physiological changes alongside histological, gut metagenomic, and tissue transcriptomic analyses. Temperatures above 20 °C led to mortality, which resulted in delayed growth. Histological and transcriptomic data revealed metabolic exhaustion and liver fibrosis in heat-stressed salamanders, underscoring the liver's critical role in heat sensitivity. While heat stress altered the gut microbiota's community structure, their functional profiles, especially in nutrient absorption and transformation, remained stable. Both gut and liver showed temperature-dependent transcriptional changes, sharing some common variations in actins, heat shock proteins, and genes related to transcription and translation. However, their energy metabolism exhibited opposite trends: it was downregulated in the liver but upregulated in the gut, with the gut showing increased activity in the pentose phosphate pathway and oxidative phosphorylation, potentially countering metabolic exhaustion. Our findings reveal that the liver of the larvae exhibits greater thermal sensitivity than the gut, and the gut-liver axis plays a limited role in mediating thermal intolerance. This study enhances mechanistic understanding of CGS heat susceptibility, providing a foundation for targeted conservation strategies in the face of climate change.},
}

Animals
*Liver/metabolism
*Gastrointestinal Microbiome
*Caudata/physiology/genetics/microbiology
Heat-Shock Response
Transcriptome
Gene Expression Profiling
Energy Metabolism
Larva

@article {pmid40360555,
year = {2025},
author = {Baek, JW and Lim, S and Park, N and Song, B and Kirtipal, N and Nielsen, J and Mardinoglu, A and Shoaie, S and Kim, JI and Son, JW and Koh, A and Lee, S},
title = {Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {78},
pmid = {40360555},
issn = {2055-5008},
support = {2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial ; Metagenome ; *Microbiota/drug effects ; Microbial Sensitivity Tests ; Metagenomics ; },
abstract = {In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/genetics/classification/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
*Drug Resistance, Bacterial
Metagenome
*Microbiota/drug effects
Microbial Sensitivity Tests
Metagenomics

@article {pmid40360028,
year = {2025},
author = {Fang, B and Liu, YF and Wei, HX and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Enhancing methanogenesis from long-chain fatty acids (LCFA) and enrichment of novel bacteria with resuscitation-promoting factors.},
journal = {Bioresource technology},
volume = {432},
number = {},
pages = {132663},
doi = {10.1016/j.biortech.2025.132663},
pmid = {40360028},
issn = {1873-2976},
abstract = {Long-chain fatty acids (LCFA) are important intermediate metabolites in lipid hydrolysis during anaerobic digestion for biogas production. High LCFA loads inhibit microbial activity by toxicity, impairing the coupling of β-oxidation and methanogenesis, thus reducing LCFA degradation efficiency. This study employed and tested seven stimulants, including the resuscitation-promoting factors (Rpf and YeaZ), the quorum-sensing molecules (cAMP, and AHLs), the chemical stimulants (pyruvate), the growth promoter (fumarate), and yeast extract + peptone (YP) for enhancement of methanogenic degradation of LCFA. The results indicate that the chemical stimulants and resuscitation-promoting factors enhanced maximum methane-production rate 1.58 to 2.20 fold versus the NS, reducing the lag phase by 1.46-9.76 days. Analysis of the microbial community composition revealed that the quorum sensing factors only increased species richness, while Rpf, YeaZ fumarate, and YP stimulated the growth of core members of the communities. Metagenomic analysis detected three previously unreported LCFA-degrading bacterial taxa, Marinisomatota, Thermoanaerobaculaceae and Pelomonas. Particularly, Rpf and YeaZ significantly enriched LCFA-degrading bacteria such as Syntrophomonadaceae, Leptospiraceae, and Marine Group B within the core species, while YeaZ also stimulated methanogenic bacteria, possibly due to resuscitating dormant microbes from unfavorable conditions. Syntrophic interactions between LCFA degraders and non-degraders, rather than methanogen abundance, govern methanogenic LCFA degradation. These results demonstrate that the use of stimulants is an effective approach to enhance LCFA degradation and provide a new pathway for energy recovery.},
}

@article {pmid40359864,
year = {2025},
author = {Fan, M and Li, H and Liu, C and Du, L and Xu, Y and Chen, Y},
title = {Insights into the molecular mechanism on high salt tolerance of electroactive microorganisms collaborated by biochar supported cerium dioxide.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125679},
doi = {10.1016/j.jenvman.2025.125679},
pmid = {40359864},
issn = {1095-8630},
abstract = {Electroactive microorganisms are a promising approach for treating high-salinity organic wastewater, however, they are highly susceptible to salt stress, which can compromise their metabolic activity. In this paper, biochar supported nano-cerium dioxide catalyst (BC-CeO2) was prepared to strengthen electroactive microorganisms in high salt environment. It was found that BC-CeO2 significantly improved the bioelectrochemical and metabolic activity of microorganisms in high salt environment (600 mM NaCl) compared with the Control. At the initial stage of the reaction, the maximum power density of microbial fuel cells (MFCs) reached 343.21 mW/m[2], and the degradation efficiency of norfloxacin (NOR) was 64.8 %, which was 1.7 times that of the Control. The analysis of microbial antioxidant properties demonstrated that BC-CeO2 could significantly increase the activities of superoxide dismutase (SOD) and catalase (CAT), effectively enhancing the ability of microorganisms to scavenge reactive oxygen species produced by salt stress. Metagenomic analysis revealed that the abundance of KEGG pathways conducive to microbial growth and metabolism under BC-CeO2 was relatively high, such as biosynthesis of amino acids (ko01230), microbial metabolism in diverse environments (ko01120) and so on. The enrichment of salt tolerant genes further illustrated the strengthening effect of BC-CeO2 on microbial adaptation to high salt environment, including genes related to NADH ubiquinone oxidoreductase, Na[+]/H[+] antiporter, intracellular small molecule compatible substance synthesis and transport related enzyme system and K[+] transporter related genes. Furthermore, the activity changes of Na[+]/K[+]-ATPase, which regulates cell permeability, in different environments also confirmed this point. This paper provides an effective strategy for enhancing the treatment of high-salt organic wastewater by electroactive microorganisms.},
}

@article {pmid40359746,
year = {2025},
author = {Bansal, M and Santhiya, D and Sharma, JG},
title = {Simulated dump yard microbes drive significant biodegradation of polypropylene and polyvinyl chloride microplastics.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138545},
doi = {10.1016/j.jhazmat.2025.138545},
pmid = {40359746},
issn = {1873-3336},
abstract = {Bacterial culture isolates were used to demonstrate the breakdown of polypropylene (PPs) and polyvinyl chloride (PVCs) microplastics for the first time. Using metagenomics and phylogenetic analysis, bacterial isolates were discovered from a simulated dump yard. PPs and PVCs were broken down using bacterial isolates found to be Acinetobacter baumannii and mixed culture species with a Bacillus sp. dominance. After 50 days of activity, the dry weight of microplastics decreased by 33.3 % (PPs) and 27.1 % (PVCs) due to the breakdown process aided by Acinetobacter baumannii. Weight reductions of 20.3 % for PPs and 18.2 % for PVCs have been observed in mixed bacterial cultures, respectively. Microplastics' thermal stability and transition properties changed, according to experiments like DTG NMR, Raman, and WCA. FTIR analysis captured the structural changes in PPs and PVCs. SEM, TEM, and cell hydrophobicity tests showed that microplastics were biodegrading. GC-MS identified the released byproducts, which included carboxylic acids, alkanes, esters, and aromatic chemicals. Based on these findings, it can be concluded that bacterial isolates are effective in degrading PPs and PVCs and may help create sustainable methods of handling plastic trash.},
}

@article {pmid40359745,
year = {2025},
author = {Yang, T and Gong, X and Xu, A and Wang, B and Huang, Z and Wang, C and Gao, D},
title = {Integrated evaluation for advanced removal of nitrate using novel solid carbon biochar/corncob/PHBV composite: Insight into electron transfer and metabolic pathways.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138549},
doi = {10.1016/j.jhazmat.2025.138549},
pmid = {40359745},
issn = {1873-3336},
abstract = {This study developed a novel Biochar/Corncob/PHBV (BCP) composite material, integrating the electron transfer capability of biochar, the cost-effectiveness of corncob, and the sustained carbon release performance of PHBV. The BCP system achieved a maximum nitrate removal efficiency of 97.3 %, significantly outperforming the single PHBV system (91.05 %), while effectively reducing nitrous oxide and other greenhouse gas emissions. It also demonstrated stable carbon release and enhanced electron transfer capabilities, contributing to a more sustainable denitrification process. The physical and chemical characterization of BCP confirmed that its superior performance is attributed to the uniformly distributed functional groups (e.g., CO and -COOH) on the surface and its porous structure, which facilitated electron transfer and microbial adhesion. Metagenomic and microbial analyses further revealed that BCP enriched functional genera such as Cellulomonas and Chryseobacterium and significantly increased the abundance of key functional genes related to nitrate reduction (e.g., NaR and NiR), enhancing organic matter decomposition and microbial nitrogen transformation. Beyond improving nitrate removal efficiency compared to PHBV, the BCP material offers practical engineering value by addressing carbon source limitations in long-term wastewater treatment applications. Its enhanced electron transfer and microbial enrichment suggest strong potential for application in constructed wetlands, biofilters, and other decentralized wastewater treatment systems. The study demonstrates that the BCP composite is not only a viable alternative to traditional PHBV but also a cost-effective and environmentally friendly material with broad applicability in nitrogen pollution control.},
}

@article {pmid40359589,
year = {2025},
author = {Silva, MKP and Nicoleti, VYU and Rodrigues, BDPP and Araujo, ASF and Ellwanger, JH and de Almeida, JM and Lemos, LN},
title = {Exploring deep learning in phage discovery and characterization.},
journal = {Virology},
volume = {609},
number = {},
pages = {110559},
doi = {10.1016/j.virol.2025.110559},
pmid = {40359589},
issn = {1096-0341},
abstract = {Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.},
}

@article {pmid40359177,
year = {2025},
author = {, },
title = {Editorial Note: Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324350},
doi = {10.1371/journal.pone.0324350},
pmid = {40359177},
issn = {1932-6203},
}

@article {pmid40359062,
year = {2025},
author = {Jules, E and Decker, C and Bixler, BJ and Ahmed, A and Zhou, ZC and Arora, I and Tafesse, H and Dakanay, H and Bombin, A and Wang, E and Ingersoll, J and Bifulco, K and Frediani, JK and Parsons, R and Sullivan, J and Greenleaf, M and Waggoner, JJ and Martin, GS and Lam, WA and Piantadosi, A},
title = {Respiratory Virus Detection and Sequencing from SARS-CoV-2-Negative Rapid Antigen Tests.},
journal = {Emerging infectious diseases},
volume = {31},
number = {13},
pages = {39-44},
doi = {10.3201/eid3113.241191},
pmid = {40359062},
issn = {1080-6059},
mesh = {Humans ; *SARS-CoV-2/genetics ; Genome, Viral ; COVID-19/diagnosis/virology ; *Respiratory Tract Infections/virology/diagnosis ; Phylogeny ; Antigens, Viral ; *Viruses/genetics/isolation & purification/classification ; },
abstract = {Genomic epidemiology offers insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 rapid antigen tests to identify a wide range of respiratory viruses and generate full genome sequences. This process offers a streamlined mechanism for broad respiratory virus genomic surveillance.},
}

Humans
*SARS-CoV-2/genetics
Genome, Viral
COVID-19/diagnosis/virology
*Respiratory Tract Infections/virology/diagnosis
Phylogeny
Antigens, Viral
*Viruses/genetics/isolation & purification/classification

@article {pmid40358997,
year = {2025},
author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and , and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R},
title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e64894},
doi = {10.2196/64894},
pmid = {40358997},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; },
abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.

OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote français" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.

METHODS: "Le French Gut - Le microbiote français" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Système National des Données de Santé). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.

RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.

CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.

DERR1-10.2196/64894.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
France
*Life Style
Feces/microbiology
*Diet
Adult
Prospective Studies
*Health Status
Female
Male
Metagenomics/methods

@article {pmid40358144,
year = {2025},
author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW},
title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0091324},
doi = {10.1128/msphere.00913-24},
pmid = {40358144},
issn = {2379-5042},
abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.},
}

@article {pmid40357419,
year = {2025},
author = {Liu, H and Xu, T and Fu, H and Dai, B and Xie, Y},
title = {Application of Metagenomic Next-Generation Sequencing in HIV-Infected Patients with Bloodstream Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2389-2399},
pmid = {40357419},
issn = {1178-6973},
abstract = {BACKGROUND: Bloodstream infections (BSI) are common complications in HIV-infected patients and are prone to septic shock and death. This study aimed to analyze the application of blood metagenomic next-generation sequencing (mNGS) in HIV-infected patients with BSI.

METHODS: Fifty-four HIV-infected patients with suspected BSI were hospitalized at the First Affiliated Hospital of the Zhejiang University School of Medicine between August 2020 and June 2023. Blood mNGS and blood culture (BC) results were retrospectively reviewed and compared to the application value of BSI.

RESULTS: The mNGS was more sensitive for detecting pathogens (82.4% versus 35.3%; P < 0.05), and when combining blood mNGS with culture results, the sensitivity increased to 88.2%. The detection rate of mNGS for blood-mixed infection was significantly higher than that of BC (P < 0.05). Among the positive results for fungi and bacteria detected by mNGS, 13.5% of the pathogenic microorganisms were consistent with the results of BC.

CONCLUSION: The mNGS combined with BC can improve pathogen detection sensitivity and the comprehensive identification of pathogenic microorganisms in HIV-infected patients with BSI.},
}

@article {pmid40357399,
year = {2025},
author = {Xing, ZC and Guo, HZ and Zhen, P and Ao, T and Hu, M},
title = {Clinical application of metagenomic next-generation sequencing in etiologic diagnosis of severe pneumonia in adults.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1561468},
pmid = {40357399},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Aged ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; COVID-19/diagnosis/virology ; Risk Factors ; *Pneumonia/diagnosis/microbiology/mortality ; Aged, 80 and over ; Bacteria/genetics/isolation & purification/classification ; SARS-CoV-2/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology/virology ; },
abstract = {OBJECTIVE: To analyze the clinical characteristics and risk factors for death of severe pneumonia (SP) in adults and explore the application value of metagenomic next-generation sequencing in the detection of pathogens.

METHODS: A total of 132 adult patients with SP admitted from May 2021 to October 2023 were selected. Data on gender, age, smoking, underlying diseases, laboratory tests and prognosis were collected. BALF samples were sent for mNGS, smear-stained microscopy and culture. Meanwhile, conventional methods were used for pathogen detection of blood, urine and throat swab specimens. The detection efficiencies of different methods were compared and the associated pathogen profiles were analyzed.

RESULTS: Among the 132 patients, there were 92 males and 40 females, with a total of 52 deaths. Age≥65 years, heart failure, renal insufficiency, positive of COVID-19, use of vasoactive drugs, use of mechanical ventilation and use of CRRT were statistically different between the survivors and non-survivors. Heart failure (OR=4.751) and use of mechanical ventilation (OR=11.914) were risk factors of SP mortality. The bacteria detected were mainly Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa. The fungi detected were mainly Candida and Aspergillus. The viruses detected were mainly COVID-19 and influenza virus. The positive rate of mNGS was higher than conventional methods in both bacteria, fungus and virus (82.58% vs 63.64%, 50.76% vs 37.88% and 67.42% vs 37.88%, respectively) (P<0.05). The sensitivity and accuracy of mNGS in bacterial detection were significantly higher than traditional methods (P<0.05). Compared to culture, mNGS detected more Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae and Escherichia coli, and had a significant advantage in the detection of Mycobacterium tuberculosis complex, Nontuberculous mycobacterial, Legionella pneumophila, Chlamydia psittaci, Pneumocystis jirovecii and Aspergillus. Moreover, mNGS can better indicate mixed infections of bacteria, viruses, or fungi.

CONCLUSION: Elderly people with chronic diseases were the main group of severe pneumonia in adults. The pathogenic microorganisms that caused SP are complex, and mixed infection is common. mNGS enhanced the effectiveness of pathogen detection, makes up for the shortcomings of conventional methods, especially in identifying unexpected pathogens, and provides a new means for early targeted anti-infection treatment.},
}

Humans
Male
Female
Aged
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Adult
COVID-19/diagnosis/virology
Risk Factors
*Pneumonia/diagnosis/microbiology/mortality
Aged, 80 and over
Bacteria/genetics/isolation & purification/classification
SARS-CoV-2/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology/virology

@article {pmid40357303,
year = {2025},
author = {Fu, C and Sun, Y and Chen, C},
title = {First reported Tannerella forsythia infection in a patient with extensive bronchiectasis: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1571506},
pmid = {40357303},
issn = {2296-858X},
abstract = {Tannerella forsythia infection was common in oral diseases but less reported in lung diseases. This report presents a patient with bronchiectasis who was infected by Tannerella forsythia and subsequently hospitalized with symptoms including fever, progressive cough, sputum production, and shortness of breath. A chest computed tomography (CT) scan revealed multiple bilateral pulmonary bronchiectasis with signs of infection. Metagenomic next-generation sequencing (mNGS) of the bronchoalveolar lavage fluid primarily detected Tannerella forsythia. Treatment with Piperacillin-tazobactam and ornidazole resulted in a favorable outcome. This case first reported a patient with extensive bronchiectasis infected by Tannerella forsythia and provided an effective treatment.},
}

@article {pmid40357282,
year = {2025},
author = {Wu, A and Gai, W and Guo, Y and Zhou, C and Xu, Y and Zhang, X and Wang, H},
title = {Clinical features of Talaromyces marneffei infection and colonization in HIV-negative patients: the role of mNGS in diagnosis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1579522},
pmid = {40357282},
issn = {2296-858X},
abstract = {BACKGROUND: Talaromycosis, caused by Talaromyces marneffei (T. marneffei), has become more common in HIV-negative and immunocompetent patients. The fungus colonizes the body through dormant spores, causing opportunistic infections. Early diagnosis is challenging. This study aims to analyze the clinical features, diagnosis, treatment, and prognosis of T. marneffei infections.

METHODS: Patients diagnosed with T. marneffei infection or colonization at the People's Hospital of Ningbo University between August 2022 and July 2024 were included. Demographic characteristics, clinical data, diagnostic approaches, and treatment outcomes were analyzed.

RESULTS: Seven patients were diagnosed with T. marneffei infection, and three with colonization. Productive cough and fever were the predominant symptoms in all patients. Nodules, cavitary lesions, and pleural effusions on chest imaging were observed exclusively in infected patients. The positivity rates for metagenomic next-generation sequencing (mNGS) and conventional microbiological testing were 100 and 10%, respectively. Of the seven infected patients, three had a single infection with T. marneffei, and four had co-infection with T. marneffei and Mycobacterium avium complex. All patients were treated with monotherapy or combination therapy using voriconazole. All but one recovered.

CONCLUSION: Early diagnosis and combination therapy are critical for T. marneffei infection. mNGS complements traditional methods, facilitating accurate diagnosis and guiding targeted treatment.},
}

@article {pmid40356662,
year = {2025},
author = {Vallejo-Espín, D and Galarza-Mayorga, J and Lalaleo, L and Calero-Cáceres, W},
title = {Beyond clinical genomics: addressing critical gaps in One Health AMR surveillance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1596720},
pmid = {40356662},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) poses an escalating global threat that demands comprehensive surveillance approaches beyond traditional clinical contexts. Although next-generation sequencing (NGS), particularly whole-genome sequencing (WGS), has revolutionized AMR surveillance, current implementation predominantly targets clinical isolates, largely neglecting critical environmental and animal reservoirs. Consequently, significant gaps persist in our understanding of AMR dynamics across diverse ecosystems. This Perspective emphasizes the urgent need to adopt an integrated genomic framework, combining isolate-based WGS with shotgun metagenomics within a cohesive One Health strategy. Such an integrated approach would significantly enhance the detection, tracking, and containment of resistance determinants, facilitating proactive rather than reactive AMR management. Achieving this vision requires global standardization of sequencing methods, harmonization of bioinformatics pipelines, and strengthened cross-sectoral collaboration to ensure timely interventions against AMR threats worldwide.},
}

@article {pmid40356641,
year = {2025},
author = {Xing, Y and Xie, Y and Wang, X},
title = {Enhancing soil health through balanced fertilization: a pathway to sustainable agriculture and food security.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1536524},
pmid = {40356641},
issn = {1664-302X},
abstract = {Sustainable soil health management is pivotal for advancing agricultural productivity and ensuring global food security. This review comprehensively evaluates the effects of mineral-organic fertilizer ratios on soil microbial communities, enzymatic dynamics, functional gene abundance, and holistic soil health. By integrating bioinformatics, enzyme activity assays, and metagenomic analyses, we demonstrate that balanced fertilization significantly enhances microbial diversity, community stability, and functional resilience against environmental stressors. Specifically, the synergistic application of mineral and organic fertilizers elevates β-glucosidase and urease activities, accelerating organic matter decomposition and nutrient cycling while modulating microbial taxa critical for nutrient transformation and pathogen suppression. Notably, replacing 20-40% of mineral fertilizers with organic alternatives mitigates environmental risks such as greenhouse gas emissions and nutrient leaching while sustaining crop yields. This dual approach improves soil structure, boosts water and nutrient retention capacity, and increases microbial biomass by 20-30%, fostering long-term soil fertility. Field trials reveal yield increases of 25-40% in crops like rice and maize under combined fertilization, alongside enhanced soil organic carbon (110.6%) and nitrogen content (59.2%). The findings underscore the necessity of adopting region-specific, balanced fertilization strategies to optimize ecological sustainability and agricultural productivity. Future research should prioritize refining fertilization frameworks through interdisciplinary approaches, addressing soil-crop-climate interactions, and scaling these practices to diverse agroecosystems. By aligning agricultural policies with ecological principles, stakeholders can safeguard soil health-a cornerstone of environmental sustainability and human wellbeing-while securing resilient food systems for future generations.},
}

@article {pmid40356191,
year = {2025},
author = {Charalambous, H and Brown, C and Vogazianos, P and Katsaounou, K and Nikolaou, E and Stylianou, I and Papageorgiou, E and Vraxnos, D and Aristodimou, A and Chi, J and Costeas, P and Shammas, C and Apidianakis, Y and Antoniades, A},
title = {Dysbiosis in the Gut Microbiome of Pembrolizumab-Treated Non-Small Lung Cancer Patients Compared to Healthy Controls Characterized Through Opportunistic Sampling.},
journal = {Thoracic cancer},
volume = {16},
number = {9},
pages = {e70075},
pmid = {40356191},
issn = {1759-7714},
support = {//Investigator-Initiated Studies Program of Merck Sharp & Dohme Corp/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology/pathology ; Male ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/microbiology ; Female ; *Lung Neoplasms/drug therapy/pathology/microbiology ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology/adverse effects ; Middle Aged ; Aged ; Prospective Studies ; Case-Control Studies ; *Antineoplastic Agents, Immunological/therapeutic use ; },
abstract = {BACKGROUND: The gut microbiome influences the host immune system, cancer development and progression, as well as the response to immunotherapy during cancer treatment. Here, we analyse the composition of the gut bacteriome in metastatic Non-Small Cell Lung Cancer (NSCLC) patients receiving Pembrolizumab immunotherapy within a prospective maintenance trial through opportunistic sampling during treatment.

METHODS: The gut microbiome profiles of NSCLC patients were obtained from stool samples collected during Pembrolizumab treatment and analysed with 16S rRNA metagenomics sequencing. Patient profiles were compared to a group of healthy individuals of matching ethnic group, age, sex, BMI and comorbidities.

RESULTS: A significant decrease in the treated patients was observed in two prominent bacterial families of the phylum Firmicutes, Lachnospiraceae and Ruminoccocaceae, which comprised 31.6% and 21.8% of the bacteriome in the healthy group but only 10.9% and 14.2% in the treated patient group, respectively. Species within the Lachnospiraceae and Ruminococcaceae families are known to break down undigested carbohydrates generating short chain fatty acids (SCFA), such as butyrate, acetate and propionate as their major fermentation end-products, which have been implicated in modifying host immune responses. In addition, a significant increase of the Bacteroidacaeae family (Bacteroidetes phylum) was observed from 10.7% in the healthy group to 23.3% in the treated patient group. Moreover, and in agreement with previous studies, a decrease in the Firmicutes to Bacteroidetes ratio in the metastatic NSCLC Pembrolizumab-treated patients was observed.

CONCLUSION: The observed differences indicate dysbiosis and a compromised intestinal health status in the metastatic NSCLC Pembrolizumab-treated patients. This data could inform future studies of immunotherapy treatment responses and modulation of the gut microbiome to minimise dysbiosis prior or concurrent to treatment.

TRIAL REGISTRATION: SWIPE Trial (NCT02705820).},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/chemically induced/microbiology/pathology
Male
*Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/microbiology
Female
*Lung Neoplasms/drug therapy/pathology/microbiology
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology/adverse effects
Middle Aged
Aged
Prospective Studies
Case-Control Studies
*Antineoplastic Agents, Immunological/therapeutic use

@article {pmid40356165,
year = {2025},
author = {Park, C and Park, J and Chang, D and Kim, S},
title = {Development of reference-based model for improved analysis of bacterial community.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116380},
doi = {10.1016/j.foodres.2025.116380},
pmid = {40356165},
issn = {1873-7145},
mesh = {RNA, Ribosomal, 16S/genetics ; *Probiotics ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Polymerase Chain Reaction/methods ; },
abstract = {Probiotic bacteria play a vital role in maintaining gut microbial homeostasis and are widely used in various commercial products. Although 16S rRNA amplicon-based next-generation sequencing (NGS) is commonly used to analyze probiotic products, biases can arise from various 16S rRNA amplification regions, sequencing platforms, and library kits. In this study, a reference-based bias correction model was developed to correct sequencing biases. The model was validated using eight mock communities and 12 commercial products, which were analyzed across multiple NGS platforms and various 16S rRNA regions. Specific primer-probe assays were developed for accurate bacterial quantification, and their specificity was validated and used in conjunction with droplet digital PCR (ddPCR) to establish initial bacterial ratios within communities. Analysis of the mock communities revealed platform- and region-specific biases, with specific species consistently over- or under-represented. Similarly, commercial product analyses have shown biased outcomes owing to varying sequencing protocols. The correction model, based on PCR efficiencies from the reference communities, successfully corrected biased ratios across different amplification regions and platforms to achieve results that closely matched the proportions predicted by ddPCR. The model effectively corrected the biases arising from the different polymerases. Notably, partial references containing approximately 40 % of the species achieved correction results that were comparable to those of the complete references. This approach demonstrates the potential for improving microbiome analysis accuracy within predictable ranges, and could serve as a model for addressing sequencing bias in metagenomic research.},
}

RNA, Ribosomal, 16S/genetics
*Probiotics
High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/genetics
DNA, Bacterial/genetics
Polymerase Chain Reaction/methods

@article {pmid40356145,
year = {2025},
author = {Wang, S and Zheng, C and Bu, C and Guo, D and Zhang, C and Xie, Q and Pan, J and Sun, J and Chen, W and Jiang, S and Zhai, Q},
title = {Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116488},
doi = {10.1016/j.foodres.2025.116488},
pmid = {40356145},
issn = {1873-7145},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant Formula/chemistry ; Infant ; Feces/microbiology ; *Metagenomics/methods ; Milk, Human/chemistry ; Female ; Male ; Breast Feeding ; *Palmitates/pharmacology ; Infant, Newborn ; Phylogeny ; },
abstract = {The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
*Infant Formula/chemistry
Infant
Feces/microbiology
*Metagenomics/methods
Milk, Human/chemistry
Female
Male
Breast Feeding
*Palmitates/pharmacology
Infant, Newborn
Phylogeny

@article {pmid40356136,
year = {2025},
author = {Luo, Y and Tang, R and Huang, Y},
title = {Differences in structure, antioxidant capacity and gut microbiota modulation of red raspberry pectic polysaccharides extracted by different methods.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116474},
doi = {10.1016/j.foodres.2025.116474},
pmid = {40356136},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Rubus/chemistry ; *Antioxidants/pharmacology/chemistry ; *Pectins/chemistry/pharmacology ; Prebiotics/analysis ; *Polysaccharides/chemistry/pharmacology ; *Fruit/chemistry ; Humans ; *Plant Extracts/chemistry/pharmacology ; },
abstract = {Red raspberries are associated with various health benefits, with pectic polysaccharides as their primary component and potential key contributor to these effects. This study aimed to evaluate the antioxidant and prebiotic potential of four red raspberry pectic polysaccharides (RP)-EN-RP (enzyme-assisted extraction), AC-RP (acid-assisted extraction), AL-RP (alkali-assisted extraction), and US-RP (ultrasound-assisted extraction)-and to elucidate the relationship between their structure and function. AC-RP and US-RP contained higher proportions of homogalacturonan (HG) at 50.92 % and 53.10 %, respectively, while EN-RP and AL-RP exhibited higher proportions of rhamnogalacturonan-I (RG-I) at 63.89 % and 43.37 %, respectively. All four polysaccharides demonstrated significant antioxidant and prebiotic properties. AL-RP exhibited the strongest DPPH radical scavenging activity, while US-RP showed the highest hydroxyl radical scavenging ability. These pectic polysaccharides were highly fermentable, significantly modulating gut microbiota composition and promoting the production of propionic acid, particularly EN-RP and AL-RP. Compared to the blank group, RP intervention significantly enriched Bacteroides, Phocaeicola, Bifidobacterium, Limosilactobacillus, and Paraprevotella. Carbohydrate-active enzyme genes in metagenomes revealed that glycoside hydrolases played a vital role in the degradation and utilization of red raspberry polysaccharides. Furthermore, correlation analysis indicated that a higher RG-I proportion and an elevated Rha/GalA ratio enhanced the abundance of certain beneficial microbial species and increased propionic acid production. These findings advance the understanding of the structure-function relationship of natural pectic polysaccharides and highlight their potential for tailoring gut microbiota and promoting health through precise dietary interventions.},
}

*Gastrointestinal Microbiome/drug effects
*Rubus/chemistry
*Antioxidants/pharmacology/chemistry
*Pectins/chemistry/pharmacology
Prebiotics/analysis
*Polysaccharides/chemistry/pharmacology
*Fruit/chemistry
Humans
*Plant Extracts/chemistry/pharmacology

@article {pmid40355758,
year = {2025},
author = {Saeedi Saravi, SS and Pugin, B and Constancias, F and Shabanian, K and Spalinger, M and Thomas, A and Le Gludic, S and Shabanian, T and Karsai, G and Colucci, M and Menni, C and Attaye, I and Zhang, X and Allemann, MS and Lee, P and Visconti, A and Falchi, M and Alimonti, A and Ruschitzka, F and Paneni, F and Beer, JH},
title = {Gut microbiota-dependent increase in phenylacetic acid induces endothelial cell senescence during aging.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {40355758},
issn = {2662-8465},
support = {#310030_21A053//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #CRSK-3_229134//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #21A053//Novartis Stiftung für Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; },
abstract = {Endothelial cell senescence is a key driver of cardiovascular aging, yet little is known about the mechanisms by which it is induced in vivo. Here we show that the gut bacterial metabolite phenylacetic acid (PAA) and its byproduct, phenylacetylglutamine (PAGln), are elevated in aged humans and mice. Metagenomic analyses reveal an age-related increase in PAA-producing microbial pathways, positively linked to the bacterium Clostridium sp. ASF356 (Clos). We demonstrate that colonization of young mice with Clos increases blood PAA levels and induces endothelial senescence and angiogenic incompetence. Mechanistically, we find that PAA triggers senescence through mitochondrial H2O2 production, exacerbating the senescence-associated secretory phenotype. By contrast, we demonstrate that fecal acetate levels are reduced with age, compromising its function as a Sirt1-dependent senomorphic, regulating proinflammatory secretion and redox homeostasis. These findings define PAA as a mediator of gut-vascular crosstalk in aging and identify sodium acetate as a potential microbiome-based senotherapy to promote healthy aging.},
}

@article {pmid40355744,
year = {2025},
author = {Schreiber, S and Waetzig, GH and López-Agudelo, VA and Geisler, C and Schlicht, K and Franzenburg, S and di Giuseppe, R and Pape, D and Bahmer, T and Krawczak, M and Kokott, E and Penninger, JM and Harzer, O and Kramer, J and von Schrenck, T and Sommer, F and Zacharias, HU and , and Millet Pascual-Leone, B and Forslund, SK and Heyckendorf, J and Aden, K and Hollweck, R and Laudes, M and Rosenstiel, P},
title = {Nicotinamide modulates gut microbial metabolic potential and accelerates recovery in mild-to-moderate COVID-19.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {40355744},
issn = {2522-5812},
support = {EXC 2167: CD-1, CD-2, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: RTF-VI//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; miTARGET (RU5042)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SO1141/10-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB1470, SFB1449//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; miTARGET (RU5042)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: CD-1, CD-2, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: CD-2, RTF-VI, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med CKDNapp 01ZX1912A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; K126408//Christian-Albrechts-Universität zu Kiel (Christian-Albrechts-University Kiel)/ ; },
abstract = {Cellular NAD[+] depletion, altered tryptophan metabolism and gut microbiome dysbiosis are associated with disease progression and unfavourable clinical outcomes in COVID-19. Here, we show that supplementing tryptophan metabolism with nicotinamide alleviates COVID-19 symptoms. We evaluate a 4-week intervention with a novel nicotinamide formulation (1,000 mg) in a prospective, double-blind, randomized, placebo-controlled trial in 900 symptomatic outpatients with PCR-proven COVID-19. In the primary analysis population of participants at risk for severe COVID-19, 57.6% of those receiving nicotinamide and 42.6% receiving placebo recover from their performance drop at week 2 (P = 0.004). Nicotinamide is also beneficial for returning to normal activities (P = 0.009). Effects on gut metagenomic signatures parallel clinical efficacy, suggesting that nicotinamide influences COVID-19-associated faecal microbiome changes. After 6 months, responders to nicotinamide in acute COVID-19 show fewer post-COVID symptoms than placebo responders (P = 0.010). No relevant safety signals are observed. Overall, our results show that nicotinamide leads to faster recovery of physical performance and modulates COVID-19-associated faecal microbiome changes.},
}

@article {pmid40355385,
year = {2025},
author = {Wang, L and Chen, Y and Wang, Q and Wang, F},
title = {Microbial imbalances linked to early pregnancy loss: a comparative analysis of vaginal microbiota.},
journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians},
volume = {38},
number = {1},
pages = {2496787},
doi = {10.1080/14767058.2025.2496787},
pmid = {40355385},
issn = {1476-4954},
mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology ; Case-Control Studies ; *Abortion, Spontaneous/microbiology ; Adult ; *Microbiota ; Young Adult ; },
abstract = {OBJECTIVE: To explore the role and related functions of vaginal microbiota in early pregnancy loss.

METHODS: This study was a case-control study with a comparison group (reference group). We recruited 178 women, including 73 who had experienced at least one early clinical pregnancy loss and 105 patients with one live birth and no history of pregnancy loss. Data on demographics, disease history, menstrual and reproductive history was collected. The case group patients were sampled immediately upon presenting with pregnancy loss at their first visit. The reference group patients underwent samples when they chose to participate voluntarily. All vaginal discharge was performed DNA Preparation and Metagenomics Sequencing. DNA extraction was performed using the phenol/trichloromethane method and the DNA fragments were then size-selected to 300-700 bp using magnetic beads. The selected fragments were repaired and ligated with indexed adaptors. The captured DNA was amplified again by PCR and circularized to create a single-stranded circular (ssCir) library. The ssCir library was subsequently amplified through rolling circle amplification (RCA) to produce DNA nanoballs (DNBs). The DNBs were then loaded onto a flow cell and sequenced using the DNBSEQ Platform. Nonparametric tests, including Kruskal-Wallis and Wilcoxon tests, were employed. Relative abundance between groups was compared, and differential species selection was performed using the LEfSe software with linear discriminant analysis.

RESULTS: 1. PCoA analysis based on Bray-Curtis distances at the species level revealed a difference between the groups (p = 0.011). At the genus level, α-diversity, assessed using the Shannon, Simpson, and Inverse Simpson indices, indicated higher bacterial richness and diversity in the control group (Shannon: mean 0.554 vs. 0.383, p = 0.0044; Simpson: mean 0.254 vs. 0.179, p = 0.0043; Inverse Simpson: mean 1.636 vs. 1.414, p = 0.0043); At the genus level, 107 microbial genera were identified, 18 of which displayed statistically significant differences. At the species level, 23 microbial species showed significant differences between the two groups. 2. We analyzed the differences in the most abundant phyla, genera, and species, with a particular focus on the top 20 most abundant genera and species. Firmicutes and Proteobacteria were significantly more prevalent among patients with pregnancy loss (PL). Among the top 20 most abundant genera, Streptococcus and Porphyromonas were significantly more abundant in patients with PL, whereas Bifidobacterium was significantly more prevalent in the reference group. Among the 20 most abundant species, Lactobacillus crispatus was significantly more prevalent in patients with PL, whereas common in the control group. 3. Principal Coordinates Analysis (PCoA) of Bray-Curtis distances, highlight their distinct clustering patterns, suggesting a notable difference between the metabolic pathways of the two groups. Key pathways with a negative correlation to PL include those related to amino acid biosynthesis, lipid metabolism, and nucleotide biosynthesis.

CONCLUSION: Our study highlights the association between vaginal microbiota dysbiosis and EPL, identifying specific microbial taxa that may contribute to pregnancy loss. These findings underscore the importance of the vaginal microbiome in reproductive health and open up new avenues for research into microbiome-based diagnostics and therapies. By integrating microbial, immune, and environmental data, future research has the potential to uncover the mechanisms underlying EPL and develop targeted interventions to improve pregnancy outcomes.},
}

Humans
Female
Pregnancy
*Vagina/microbiology
Case-Control Studies
*Abortion, Spontaneous/microbiology
Adult
*Microbiota
Young Adult

@article {pmid40355358,
year = {2025},
author = {Zhang, WL and Zu, YL and Huang, ZH and Li, Z and Gui, RR and Wang, J and Wang, XJ and Wang, HL and Fan, XX and Song, YP and Fang, BJ and Zhou, J},
title = {[BK virus nephropathy after allogeneic hematopoietic stem cell transplantation: a case report and literature review].},
journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi},
volume = {46},
number = {3},
pages = {273-275},
doi = {10.3760/cma.j.121090-20240810-00298},
pmid = {40355358},
issn = {0253-2727},
mesh = {Humans ; Male ; *Hematopoietic Stem Cell Transplantation/adverse effects ; BK Virus ; Young Adult ; *Polyomavirus Infections ; *Kidney Diseases/virology/etiology ; *Tumor Virus Infections ; Transplantation, Homologous ; },
abstract = {A 20-year-old male patient with T-lymphoblastic lymphoma/leukemia received 9/10 human leukocyte antigen-compatible unrelated peripheral blood stem cell transplantation. He was transplanted with 5.91×10(8) mononuclear cells/kg and 2.88×10(6) CD34(+) cells/kg, and neutrophil engraftment was obtained at +11 days and platelet engraftment at +9 days. After transplantation, he presented with repeatedly increased serum creatinine levels, BK virus (BKV) -associated hemorrhagic cystitis, and BKV viremia. BK virus nephropathy was diagnosed based on renal biopsy and metagenomic next-generation sequencing. After adjusting the immunosuppressant, intravenous immunoglobulin, and donor lymphocyte infusion treatment, the patient's renal function deteriorated progressively, and he eventually died of multiple organ failure at +289 days.},
}

Humans
Male
*Hematopoietic Stem Cell Transplantation/adverse effects
BK Virus
Young Adult
*Polyomavirus Infections
*Kidney Diseases/virology/etiology
*Tumor Virus Infections
Transplantation, Homologous

@article {pmid40354774,
year = {2025},
author = {Hu, T and He, S and Gao, Z and Feng, L and Jiang, J and Zhao, Q and Wei, L},
title = {Micro-mechanism of rhamnolipid promoting acid production during anaerobic digestion: protein structures, metagenomics and molecular dynamics simulations.},
journal = {Water research},
volume = {283},
number = {},
pages = {123795},
doi = {10.1016/j.watres.2025.123795},
pmid = {40354774},
issn = {1879-2448},
abstract = {The addition of rhamnolipid (RL) is a promising strategy to enhance volatile fatty acids (VFAs) production in anaerobic digestion (AD) systems. However, the microscopic mechanisms underlying this enhancement remain poorly understood. This study investigates the micro-mechanisms by which RL promotes VFAs production, integrating protein structural analysis, metagenomics, and molecular dynamics simulations. Experimental results revealed that adding RL at 0.08 g/g TS significantly increased VFAs production to 11,441.8 mg COD/L. Protein structural analysis revealed disruption of amide I-related C = O groups and amide II-related CN and NH bonds, indicating the release or structural alteration of sludge proteins. Metagenomic analysis indicated an increase in the abundance of microbial communities and related genes, suggesting that RL enhanced the activity of acid-producing microorganisms and related metabolic pathways. Furthermore, molecular docking and molecular dynamics simulations indicated that RL spontaneously aggregated and absorbed acetate kinase (AK), altering its conformation and reducing structural compactness, which made acetyl phosphate (AcP) more accessible to the binding site of AK. RL reduced the energy barrier associated with the polar solvation interactions, increasing the contributions of key residues (LYS176 and GLU234) to the binding free energy, which enhanced the binding affinity of AK-AcP complex. This study provides a comprehensive molecular basis for how RL promotes VFAs production in AD, offering a promising strategy for optimizing acid production.},
}

@article {pmid40354675,
year = {2025},
author = {Zhi, N and Chang, X and Zha, L and Zhang, K and Wang, J and Gui, S},
title = {Platycodonis radix polysaccharides suppress progression of high-fat-induced obesity through modulation of intestinal microbiota and metabolites.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156653},
doi = {10.1016/j.phymed.2025.156653},
pmid = {40354675},
issn = {1618-095X},
abstract = {BACKGROUND: Obesity is a prevalent chronic condition worldwide, posing a significant risk to public health. Polysaccharides derived from Platycodonis Radix (PR) have been identified as the primary bioactive compounds in combating obesity, although the underlying molecular mechanisms remain inadequately understood.

PURPOSE: The purpose of the research is to analyze the potential anti-obesity influnces within PR polysaccharides (PG: PG1 and PG2) by analyzing their impact on gut microbiota (GM) composition, SCFA and BA metabolism, and the regulation of associated gene and protein expression.

STUDY DESIGN AND METHODS: In this research, 7-week-old male C57BL/6 mice were assigned to a HFD or a control chow diet for 90 days to evaluate the therapeutic effects of PG intervention. Metagenomic analysis was performed to assess GM alterations, while GC-MS and LC-MS were used to quantify SCFA and BA concentrations in cecal contents, respectively. Furthermore, the effects of PG on SCFA- and BA-associated metabolic pathways were examined through qRT-PCR and WB.

RESULTS: PG1 demonstrated superior efficacy compared to PG2 in reducing HFD-induced obesity and associated metabolic disturbances. High-dose PG1 treatment effectively inhibited weight gain, dyslipidemia, inflammation, liver damage, and fat deposition caused by the HFD. Additionally, PG1 treatment primarily promoted the abundance of SCFA-producing bacteria, enhanced the expression of GPR41 and GPR43 genes, significantly elevated levels of GLP-1 and PYY, and improved circulating leptin and adiponectin levels. The intervention with PG1 notably enhanced the relative abundances of bacteria involved in the production of secondary BAs, such as Lachnospiraceae_NK4A136 and Eubacterium coprostanoligenes. This augmentation facilitated the transformation of primary BAs into secondary forms, diminished the relative expression of intestinal FXR and FGF15, and reduced FGFR4 levels. Consequently, this led to an upregulation of hepatic CYP7A1, accelerating liver cholesterol metabolism and the synthesis of new BAs.

CONCLUSION: Supplementation with PG1 protects mice from obesity induced by an HFD. The observed protective effects of PG1 appear to be primarily mediated through the activation of the GM-SCFA-GPR pathway and the inhibition of the GM-BA-FXR-FGF15 signaling pathway.},
}

@article {pmid40354439,
year = {2025},
author = {Llarena, AK and Haverkamp, THA and Gulliksen, WS and Herstad, K and Holst-Jensen, A and Skjerve, E and Rannem, L and Rodriguez-Campos, S and Øines, Ø},
title = {DNA extraction protocols for animal fecal material on blood spot cards.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0313808},
doi = {10.1371/journal.pone.0313808},
pmid = {40354439},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology/chemistry ; Dogs ; Cattle ; Metagenomics/methods ; Horses ; Swine ; Sheep ; *DNA/isolation & purification ; *DNA, Bacterial/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Collecting fecal samples using dry preservatives is an attractive option in large epidemiological studies as they are easy to use, cheap and independent of cold chain logistics. Here, we test four DNA extraction methods with the aim of identifying an efficient procedure to extract high-quality DNA from fecal material of canine, sheep, equine, bovine, and pig collected on dry blood spot cards, with the goal of generating good quality shotgun metagenomics datasets. Further, the suitability of Illumina shotgun metagenomic sequencing at 20 million paired-end (PE) read depth per sample was assessed on its ability to successfully characterize the taxonomic and functional aspects of the resulting fecal microbiome.

METHODS: DNA was extracted from pig feces and mock communities collected on blood spot cards using four DNA extraction methods; two different methods of the QIAsymphony® PowerFecal® Pro DNA Kit, the ZymoBIOMICS™ DNA Miniprep Kit, and the MagNA Pure 96 DNA and Viral NA Small Volume Kit. Possible extraction bias was controlled by amplicon sequencing of mock communities. Fecal samples from canine, sheep, equine, bovine, and pig were thereafter subjected to the best performing DNA extraction method and shotgun metagenomic sequencing to determine sequencing efforts for functional and taxonomic analysis.

RESULTS: The four DNA extraction methods demonstrated similar community composition in the sequenced bacterial mock community. The QIAsymphony® PowerFecal® Pro DNA Kit was identified as the DNA extraction method of choice, and the resulting DNA was subjected to shotgun metagenomic sequencing with 20million PE reads. We found that higher number of reads increased the richness of observed genera between 100,000 and 5 million reads, after which higher sequencing effort did not increase the richness of the metagenomes. As for functional analysis, the number of low abundance functions in the metagenomes of the animals' feces increased with sequencing depth above 20 million PE reads.

CONCLUSION: Our experiments identified several methods suitable for extracting DNA from feces collected on blood spot cards. The QIAGEN's Blood and Tissue kit on the QiaSymphony platform fulfilled the criteria of high yield, quality, and unbiased DNA, while maintaining high throughput for shotgun metagenomic sequencing. A sequencing depth of 20 million PE reads proved adequate for taxonomic estimations and identifying common functional pathways. Detecting rarer traits, however, requires more sequencing effort.},
}

Animals
*Feces/microbiology/chemistry
Dogs
Cattle
Metagenomics/methods
Horses
Swine
Sheep
*DNA/isolation & purification
*DNA, Bacterial/isolation & purification/genetics
High-Throughput Nucleotide Sequencing

@article {pmid40353658,
year = {2025},
author = {Laso-Pérez, R and Rivas-Santisteban, J and Fernandez-Gonzalez, N and Mundy, CJ and Tamames, J and Pedrós-Alió, C},
title = {Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation.},
journal = {mBio},
volume = {},
number = {},
pages = {e0074925},
doi = {10.1128/mbio.00749-25},
pmid = {40353658},
issn = {2150-7511},
abstract = {In the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Bloom dynamics are affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community using omics approaches during a phytoplankton bloom focusing on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of metagenomic abundance in early spring, when Nitrososphaeria archaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amo, nirK). The resulting nitrite was presumably further oxidized to nitrate by a Nitrospinota bacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyll a indicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidota, Alphaproteobacteria, Gammaproteobacteria). These bacteria showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter reduced their relative abundance and the expression of their catabolic genes. Based on our functional analysis, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups seem to specialize in different nitrogen sources.IMPORTANCEThe Arctic is one of the environments most affected by anthropogenic climate change. It is expected that the rise in temperature and change in ice cover will impact the marine microbial communities and the associated biogeochemical cycles. In this regard, nitrogen is the main nutrient limiting Arctic phytoplankton blooms. In this study, we combine genetic and expression data to study the nitrogen cycle at the community level over a time series covering from March to July. Our results indicate the importance of different taxa (from archaea to bacteria) and processes (from chemolithoautotrophy to incorporation of different nitrogen sources) in the cycling of nitrogen during this period. This study provides a baseline for future research that should include additional methodologies like biogeochemical analysis to fully understand the changes occurring on these communities due to global change.},
}

@article {pmid40352947,
year = {2025},
author = {Zhong, QL and Xiong, JQ},
title = {A Globally Distributed Cyanobacterial Nitroreductase Capable of Conferring Biodegradation of Chloramphenicol.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0692},
pmid = {40352947},
issn = {2639-5274},
abstract = {Cyanobacteria play pivotal roles in global biogeochemical cycles and aquatic ecosystems due to their widespread distribution and significant contributions to primary production. Yet, the interactions between cyanobacteria and antibiotics remain unclear. This study revealed that Synechocystis sp., a cyanobacterial species, removed 94.27% of 0.1 mg l[-1] chloramphenicol (CAP) through enzyme-mediated degradation. While cytochrome P450 enzymes (CYP450s) were found unnecessary for CAP removal, a gene encoding cyanobacterial nitroreductase was significantly up-regulated (7.85-fold) under CAP exposure. The purified nitroreductase exhibited strong binding affinity to CAP (K d = 2.9 nM) and a Michaelis constant (K m) of 104.0 μM. By engineering a bacterial strain with nitroreductase, 94.43% of 0.1 mg l[-1] CAP was removed within 2 h. Metagenomic and metatranscriptomic analyses showed that nitroreductase genes and transcripts are globally distributed across diverse microbial phyla. These findings uncover a novel enzyme for CAP degradation and advance sustainable biotechnologies to mitigate antibiotic pollution, addressing critical environmental challenges in aquaculture and other industries globally.},
}

@article {pmid40351504,
year = {2025},
author = {Wilkhoo, HS and Islam, AW and Wilkhoo, HS and Hussain, S and Singh, B and Kadam, SR},
title = {Clinical Insights and Advancements in Human Metapneumovirus Management and Prognosis.},
journal = {Discoveries (Craiova, Romania)},
volume = {13},
number = {1},
pages = {e204},
pmid = {40351504},
issn = {2359-7232},
abstract = {Human metapneumovirus is a respiratory pathogen that infects children, the elderly, and immunocompromised individuals. Despite its global prevalence, underdiagnosis persists because of clinical overlap with other respiratory viruses. The current approach is mostly supportive, with oxygen therapy and hydration being crucial interventions. Ribavirin contains antiviral properties but has little clinical application. Vaccine development is moving forward, with prospects including live-attenuated, subunit-based, and virus-like particle vaccines. Molecular diagnostics, such as RT-PCR and metagenomic sequencing, have increased detection rates, which aids epidemiological monitoring. Monoclonal antibodies targeting the fusion (F) protein are being studied for passive immunity, while immunomodulatory treatments such as corticosteroids and intravenous immunoglobulins may help treat severe cases. Emerging treatments include fusion inhibitors and pan-pneumovirus vaccinations that protect against HMPV and RSV. Future research should concentrate on optimizing antiviral methods, increasing vaccination trials, and improving surveillance to detect outbreaks. A multidisciplinary approach that combines virology, immunology, and epidemiology is required to reduce HMPV's effect and improve patient outcomes. This review serves as a comprehensive literature about HMPV which provides all the crucial clinical perspectives and the latest advancements in management, antivirals, patient prognosis as well and diagnostic modalities.},
}

@article {pmid40351315,
year = {2025},
author = {Li, S and Sun, Y and Cao, S and Guo, T and Tong, X and Zhang, Z and Sun, J and Yang, Y and Wang, Q and Li, D and Min, L},
title = {Asparagopsis taxiformis mitigates ruminant methane emissions via microbial modulation and inhibition of methyl-coenzyme M reductase.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1586456},
pmid = {40351315},
issn = {1664-302X},
abstract = {INTRODUCTION: Asparagopsis taxiformis (A. taxiformis) has shown great potential to mitigate methane (CH4) emissions in recent years. This study aims to evaluate the impact of A. taxiformis on methane emissions and to fill the knowledge gap regarding its mechanisms of action in affecting CH4 metabolism and rumen fermentation.

METHODS: The experimental design consisted of a control group (CON) and test groups supplemented with 2% (Low), 5% (Mid), and 10% (High) of dried and freeze-dried treatment A. taxiformis, respectively, for 48 h of in vitro rumen fermentation. The optimal combination strategy for mitigating CH4 emissions was confirmed by analyzing nutrient degradation, CH4 production and rumen fermentation parameters, and the mechanism of action was analyzed by metagenomic and metabolomic approaches.

RESULTS AND DISCUSSION: The results showed that freeze-dried treatment had better potential to mitigate CH4 emissions than dried treatment, and supplementation of freeze-dried treatments at Low, Mid, and High groups significantly reduced CH4 production by 32.44%, 98.53%, and 99.33%, respectively. However, the High group exhibited a huge negative impact on rumen fermentation. Therefore, subsequent analyses focused on the Low and Mid groups to explore the underlying mechanisms. Metagenomics analyses showed that supplementation of freeze-dried treatment with the Mid-level supplementation significantly increased the relative abundance of propionate-producing bacteria such as Prevotella, Ruminobacter, and Succinivibrio, while inhibited acetate-producing bacteria such as Ruminococcus, altered the pattern of volatile fatty acid (VFA) synthesis in the rumen, and reduced H2 availability for methanogenesis and promoted propionate production, indirectly alleviating CH4 production. Moreover, by suppressing the relative abundance of Methanobrevibacter, CH4 production in the rumen was directly suppressed. Furthermore, KEGG pathway analysis showed that A. taxiformis significantly inhibited the abundance of K00399, methyl-coenzyme M reductase alpha subunit, which directly inhibited CH4 synthesis. Metabolomics analysis of A. taxiformis supplementation significantly enriched ketoglutarate, malate, isocitrate, and melatonin, which may have reduced the release of rumen fermented H2, thereby mitigating CH4 emissions. In summary, freeze-dried treatment A. taxiformis at the 5% supplementation level achieved the optimal balance between CH4 mitigation and rumen fermentation efficiency.},
}

@article {pmid40350519,
year = {2025},
author = {Schultz, J and Jamil, T and Sengupta, P and Sivabalan, SKM and Rawat, A and Patel, N and Krishnamurthi, S and Alam, I and Singh, NK and Raman, K and Rosado, AS and Venkateswaran, K},
title = {Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {117},
pmid = {40350519},
issn = {2049-2618},
support = {BAS/1/1096-01-01//KAUST Baseline Grant/ ; PPR-ROSES-2006//National Aeronautical and Space Administration/ ; },
mesh = {*Spacecraft ; United States National Aeronautics and Space Administration ; *Bacteria/genetics/isolation & purification/classification ; United States ; Biofilms/growth & development ; Space Flight ; *Extremophiles/genetics/isolation & purification/classification ; *Genome, Bacterial ; Humans ; Microbiota/genetics ; Genomics ; Metagenome ; Phylogeny ; },
abstract = {BACKGROUND: Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. Maintaining the biological cleanliness of NASA's mission-associated cleanrooms, where spacecraft are assembled and tested, is critical for planetary protection. Even with stringent controls such as regulated airflow, temperature management, and rigorous cleaning, resilient microorganisms can persist in these environments, posing potential risks for space missions.

RESULTS: During the Phoenix spacecraft mission, genomes of 215 bacterial isolates were sequenced and based on overall genome-related indices, 53 strains belonging to 26 novel species were recognized. Metagenome mapping indicated less than 0.1% of the reads associated with novel species, suggesting their rarity. Genes responsible for biofilm formation, such as BolA (COG0271) and CvpA (COG1286), were predominantly found in proteobacterial members but were absent in other non-spore-forming and spore-forming species. YqgA (COG1811) was detected in most spore-forming members but was absent in Paenibacillus and non-spore-forming species. Cell fate regulators, COG1774 (YaaT), COG3679 (YlbF, YheA/YmcA), and COG4550 (YmcA, YheA/YmcA), controlling sporulation, competence, and biofilm development processes, were observed in all spore-formers but were missing in non-spore-forming species. COG analyses further revealed resistance-conferring proteins in all spore-formers (n = 13 species) and eight actinobacterial species, responsible for enhanced membrane transport and signaling under radiation (COG3253), transcription regulation under radiation stress (COG1108), and DNA repair and stress responses (COG2318). Additional functional analysis revealed that Agrococcus phoenicis, Microbacterium canaveralium, and Microbacterium jpeli contained biosynthetic gene clusters (BGCs) for ε-poly-L-lysine, beneficial in food preservation and biomedical applications. Two novel Sphingomonas species exhibited for zeaxanthin, an antioxidant beneficial for eye health. Paenibacillus canaveralius harbored genes for bacillibactin, crucial for iron acquisition. Georgenia phoenicis had BGCs for alkylresorcinols, compounds with antimicrobial and anticancer properties used in food preservation and pharmaceuticals.

CONCLUSION: Despite stringent decontamination and controlled environmental conditions, cleanrooms harbor unique bacterial species that form biofilms, resist various stressors, and produce valuable biotechnological compounds. The reduced microbial competition in these environments enhances the discovery of novel microbial diversity, contributing to the mitigation of microbial contamination and fostering biotechnological innovation. Video Abstract.},
}

*Spacecraft
United States National Aeronautics and Space Administration
*Bacteria/genetics/isolation & purification/classification
United States
Biofilms/growth & development
Space Flight
*Extremophiles/genetics/isolation & purification/classification
*Genome, Bacterial
Humans
Microbiota/genetics
Genomics
Metagenome
Phylogeny

@article {pmid40350492,
year = {2025},
author = {Ding, Y and Ke, J and Hong, T and Zhang, A and Wu, X and Jiang, X and Shao, S and Gong, M and Zhao, S and Shen, L and Chen, S},
title = {Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {287},
pmid = {40350492},
issn = {1471-2180},
support = {STEP 2024QZKK02010//Supported by the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2208085MC39//Natural Science Foundation of Anhui Province, China/ ; },
mesh = {China ; *Lakes/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Archaea/classification/genetics/isolation & purification ; Phylogeny ; DNA, Archaeal/genetics ; Salinity ; *Biodiversity ; Alkalies/analysis ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; Sodium Chloride ; Sequence Analysis, DNA ; Bacteria/classification/genetics ; },
abstract = {Halophilic microorganisms abound in numerous hypersaline environments, such as salt lakes, salt mines, solar salterns, and salted seafood. In the northwest of Dingbian county (Shaanxi province, China), there exists a belt of hypersaline habitats extending from the west to the north consisting of saline-alkali soil and salt lakes. Theoretically, such a hypersaline environment has a high probability of containing abundant halophilic archaea communities. Nevertheless, there is nearly no systematic research on halophilic archaea in this area. Here, we employed a combination of culture-dependent and culture-independent methods to analyze the collected samples. The high-throughput sequencing results of the archaeal 16S rRNA gene indicated that the richness of halophilic archaea in saline-alkali soils was significantly higher than that in salt lakes. In saline-alkali soils, the Natronomonas genus of archaea was more predominant compared to other genera, while in salt lakes, the Halonotius, Halorubrum, and Haloarcula genera of archaea had relatively higher abundances. However, the dominant families of halophilic archaea in both environments were mainly Haloferacaceae (30.96-72%), Halomicrobiaceae (17-53.19%) and Nanosalinaceae (1-19.08%). Based on the outcomes of pure culture experiments, a total of 26 genera and 98 strains were identified. Among the identified halophilic microorganisms, the predominant species were Halorubrum and Fodinibius, accounting for 33.67% and 13.27%, respectively. The remainder were mostly low-abundance groups within the community, and 22 potential novel taxa were discovered. Additionally, metagenomic technology was employed in our research. The analysis results demonstrated that the microorganisms in this area possess metabolic pathways capable of degrading various pollutants such as atrazine, methane, and dioxins, suggesting that some microorganisms in this area play a positive role in environmental remediation. This study roughly reveals the diversity composition and dominant species of halophilic archaea in these hypersaline environments and provides a scientific basis for the possible ecological functions of microorganisms in this area during long-term survival. It also offers scientific evidence for the development and utilization of halophilic microbial resources and ecological protection.},
}

China
*Lakes/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Soil Microbiology
*Archaea/classification/genetics/isolation & purification
Phylogeny
DNA, Archaeal/genetics
Salinity
*Biodiversity
Alkalies/analysis
Soil/chemistry
High-Throughput Nucleotide Sequencing
Sodium Chloride
Sequence Analysis, DNA
Bacteria/classification/genetics

@article {pmid40350460,
year = {2025},
author = {Zhang, X and Zhong, R and Wu, J and Tan, Z and Jiao, J},
title = {Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {118},
pmid = {40350460},
issn = {2049-2618},
support = {32372829, 31972992//National Natural Science Foundation of China/ ; 2023JJ10047//Hunan Provincial Natural Science Foundation of China/ ; 2022RC1158//The Science and Technology innovation Program of Hunan Province/ ; 2023382//Youth Innovation Promotion Association CAS/ ; },
mesh = {Animals ; *Goats/microbiology ; *Dietary Fiber/metabolism ; *Gastrointestinal Microbiome ; Rumen/microbiology/metabolism ; Animal Feed/analysis ; Metagenomics/methods ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fibrobacter/metabolism/genetics/isolation & purification ; Ruminococcus/metabolism/genetics/isolation & purification ; Diet/veterinary ; Cecum/microbiology/metabolism ; Cellulose/metabolism ; Fatty Acids, Volatile/metabolism ; Polysaccharides/metabolism ; *Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: Dietary fiber is crucial to animal productivity and health, and its dynamic utilization process is shaped by the gastrointestinal microorganisms in ruminants. However, we lack a holistic understanding of the metabolic interactions and mediators of intestinal microbes under different fiber component interventions compared with that of their rumen counterparts. Here, we applied nutritional, amplicon, metagenomic, and metabolomic approaches to compare characteristic microbiome and metabolic strategies using goat models with fast-fermentation fiber (FF) and slow-fermentation fiber (SF) dietary interventions from a whole gastrointestinal perspective.

RESULTS: The SF diet selected fibrolytic bacteria Fibrobacter and Ruminococcus spp. and enriched for genes encoding for xylosidase, endoglucanase, and galactosidase in the rumen and cecum to enhance cellulose and hemicellulose utilization, which might be mediated by the enhanced microbial ATP production and cobalamin biosynthesis potentials in the rumen. The FF diet favors pectin-degrading bacteria Prevotella spp. and enriched for genes encoding for pectases (PL1, GH28, and CE8) to improve animal growth. Subsequent SCFA patterns and metabolic pathways unveiled the favor of acetate production in the rumen and butyrate production in the cecum for SF goats. Metagenomic binning verified this distinct selection of gastrointestinal microorganisms and metabolic pathways of different fiber types (fiber content and polysaccharide chemistry).

CONCLUSIONS: These findings provide novel insights into the key metabolic pathways and distinctive mechanisms through which dietary fiber types benefit the host animals from the whole gastrointestinal perspective. Video Abstract.},
}

Animals
*Goats/microbiology
*Dietary Fiber/metabolism
*Gastrointestinal Microbiome
Rumen/microbiology/metabolism
Animal Feed/analysis
Metagenomics/methods
Fermentation
*Bacteria/classification/genetics/metabolism/isolation & purification
Fibrobacter/metabolism/genetics/isolation & purification
Ruminococcus/metabolism/genetics/isolation & purification
Diet/veterinary
Cecum/microbiology/metabolism
Cellulose/metabolism
Fatty Acids, Volatile/metabolism
Polysaccharides/metabolism
*Gastrointestinal Tract/microbiology

@article {pmid40350266,
year = {2025},
author = {Ohyama, Y and Miura, T and Furukawa, M and Shimamura, M and Asami, Y and Yamazoe, A and Uchino, Y and Kawasaki, H},
title = {A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME24076},
pmid = {40350266},
issn = {1347-4405},
mesh = {Chromatography, High Pressure Liquid/methods ; *Bacteria/genetics/isolation & purification/classification ; Humans ; *Microbiota/genetics ; *Genome, Bacterial ; Metagenomics/methods ; Reproducibility of Results ; },
abstract = {Improving the reliability of a metagenomic sequencing ana-lysis requires the use of control samples, known as mock communities. Therefore, mock communities must be prepared with high accuracy and reproducibility, which is particularly challenging for cellular mock communities. In the present study, we prepared a cellular mock community consisting of bacterial strains representative of the human and surrounding environmental microbiomes to demonstrate the suitability of a HPLC-based method that measures the genome number of cells. This method proved to be more accurate and reproducible for preparing cellular mock communities than traditional cell counting-based enumeration methods.},
}

Chromatography, High Pressure Liquid/methods
*Bacteria/genetics/isolation & purification/classification
Humans
*Microbiota/genetics
*Genome, Bacterial
Metagenomics/methods
Reproducibility of Results