@article {pmid41075379,
year = {2025},
author = {Pichler, I and Krischer, E and Obenhuber, T and Hirsch, B and Reinhold, I and Wiedmer, C and Ziltener, G and Weller, D and Roth, P and Weiss, T and Kufner, V and Bloemberg, GV and Trkola, A and Müller, NJ and Huber, M},
title = {Viral metagenomic sequencing reveals rare pathogens and improves diagnostic accuracy in neuroinflammatory disorders.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117140},
doi = {10.1016/j.diagmicrobio.2025.117140},
pmid = {41075379},
issn = {1879-0070},
abstract = {BACKGROUND: Neuroinflammatory disorders are frequently of unknown aetiology. Unbiased metagenomic next-generation sequencing of cerebrospinal fluid could help bridge the current diagnostic gap by identifying more infectious pathogens inducing central nervous system disorders. This study examined the advantages of adding viral metagenomics to standard testing procedures.

METHODS: Patients presenting with symptoms indicative of a neuroinflammatory disorder were enrolled at a Swiss tertiary care hospital through prospective and retrospective recruitment. Participants were diagnosed with infectious or autoimmune neuroinflammatory disorders based on the results of routine diagnostics and viral metagenomic sequencing.

RESULTS: Of the 70 study participants, 50 were classified as having an infectious disorder. Among these, a total of 37 pathogens were identified in 29 individuals (56 %), including 32 viral, three bacterial, one fungal, and one prion infection. Conventional virus testing and viral metagenomic sequencing produced the same positive and negative results for 13 and 21 cases, respectively. This resulted in an overall percent agreement of 59 %. Disparate viral results were observed in 19 cases. Ten cases were detected only by conventional testing, and nine were detected only by viral metagenomics. Notably, we report the detection of Toscana virus by viral metagenomic sequencing, a relatively rare pathogen in Switzerland that is not routinely screened for, underscoring the advantages of integrating viral metagenomics with conventional testing.

CONCLUSIONS: Viral metagenomic sequencing as a first-line diagnostic tool in combination with conventional methods yields the most comprehensive results to diagnose patients with infectious neuroinflammatory disorders. Its unbiased approach enables the detection of rare or unconsidered viruses.},
}

@article {pmid41075335,
year = {2025},
author = {Ghaffar, A and Liljebjelke, K and Checkley, SL and Farooq, M and Abdul-Careem, MF},
title = {Exploring the indoor airborne microbiome and resistome in layer barns across Alberta, Canada.},
journal = {Research in veterinary science},
volume = {196},
number = {},
pages = {105930},
doi = {10.1016/j.rvsc.2025.105930},
pmid = {41075335},
issn = {1532-2661},
abstract = {The air in poultry barns carries a diverse range of microbial communities including potential opportunistic pathogens, which are important for both animal and human health. Bacteria carrying antimicrobial resistance genes (ARGs) can become airborne within poultry barns and be transmitted to animals and poultry workers, presenting a serious One Health concern. This study was aimed at characterizing the microbiome and resistome of bioaerosols sampled from layer chicken barns across Alberta. In total, 15 barns (9 cage housed and 6 floor housed) were sampled in this study using a microbial air sampler to characterize the microbiome and resistome using a shotgun metagenomic sequencing approach. The most abundant bacterial phyla found in the air of both housing systems for pullets were Bacilliota, Actinomycetota, and Bacteroidota. The respiratory pathogens such as Gallibacterium anatis, Ornithobacterium rhinotracheale, and Pasteurella multocida were relatively more abundant in the air of cage-housed barns, whereas Escherichia coli and Avibacterium paragallinarum were more prevalent in floor-housed barns. In total, 113 unique ARGs subtypes from 19 classes of antimicrobials were identified in this study. ARGs were significantly more abundant in the air of cage-housed barns compared to floor-housed barns. In particular, genes associated with resistance to tetracyclines, lincosamides, and macrolides were more frequently detected in cage-housed environments. Overall, both microbial and resistance gene levels were higher in the bioaerosols of cage-housed barns than in those from floor-housed pullet barns. The study results demonstrate the potential for air as a reservoir of ARGs and highlights microbial differences within cage and floor housing.},
}

@article {pmid41074949,
year = {2025},
author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H},
title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {354},
pmid = {41074949},
issn = {1420-9071},
support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; },
mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; },
abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.},
}

Humans
Adolescent
*Dysbiosis/microbiology
Female
Male
*Mouth/microbiology
*Obesity/microbiology
Microbiota/genetics
Saliva/microbiology
Body Mass Index
Kuwait

@article {pmid41074769,
year = {2025},
author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS},
title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf216},
pmid = {41074769},
issn = {1751-7370},
abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.},
}

@article {pmid41074341,
year = {2025},
author = {Zhang, Z and Wang, Y and Yao, Y and Li, Y and Xu, X and Hou, Q and Hu, X and Mei, X and Guo, Z},
title = {Microbial and flavor dynamics of medium-high temperature Daqu: regional influences and implications for Daqu quality optimization.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117155},
doi = {10.1016/j.foodres.2025.117155},
pmid = {41074341},
issn = {1873-7145},
mesh = {*Taste ; China ; *Hot Temperature ; *Wine/microbiology/analysis ; Odorants/analysis ; *Food Microbiology ; Bacteria/classification/genetics/metabolism ; Metagenomics ; Microbiota ; Fermentation ; Humans ; },
abstract = {Medium-high temperature Daqu (MHTD) plays a crucial role in Chinese strong-flavor Baijiu production, yet its microbial dynamics and the drivers of regional variation remain underexplored. In this study, we investigated the microbial community structure, enzyme activity, and flavor profiles of MHTD from three geographically adjacent regions in China, using metagenomic sequencing, E-sensory analysis, and multivariate statistics. Despite significant regional differences in microbial diversity, community composition, and taste, aroma profiles were relatively consistent. Redundancy analysis revealed that water content and acidity were the primary environmental drivers of microbial and flavor variation. Notably, increased water content was positively correlated with microbial richness, enzyme activity, and flavor complexity. Functional annotation of metagenomic data uncovered key microbial pathways for starch, cellulose, and lignin degradation, as well as for the biosynthesis of pyrazines and guaiacol derivatives. Limosilactobacillus fermentum, the dominant species across all samples, was found to possess the genetic potential to produce both compound classes-representing a novel finding. Fungal species such as Thermoascus sp. and Rasamsonia emersonii appeared to cooperate in guaiacol synthesis, while Acetobacter pasteurianus and A. oryzoeni in MHTD from Chuzhou City contributed to pyrazine production. These findings highlight the microbial and environmental basis of flavor formation in MHTD and offer practical implications for MHTD production. Specifically, moisture regulation during fermentation and selective enrichment of functional strains like L. fermentum and Acetobacter spp. may help optimize flavor development and product consistency.},
}

*Taste
China
*Hot Temperature
*Wine/microbiology/analysis
Odorants/analysis
*Food Microbiology
Bacteria/classification/genetics/metabolism
Metagenomics
Microbiota
Fermentation
Humans

@article {pmid41073968,
year = {2025},
author = {Onohuean, H and Choonara, YE},
title = {Epidemiological distribution of bacterial meningitis infections in South Africa: a systematic review and meta-analysis.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1284},
pmid = {41073968},
issn = {1471-2334},
mesh = {Humans ; South Africa/epidemiology ; *Meningitis, Bacterial/epidemiology/microbiology ; Prevalence ; Child ; Adolescent ; Child, Preschool ; Female ; Male ; Adult ; Infant ; Middle Aged ; Young Adult ; },
abstract = {Scientific evidence from public health findings can enhance the management, treatment, and prevention policies for bacterial meningitis (BM) infections. However, comprehensive epidemiological data on BM prevalence in South Africa is limited. We aimed to assess the prevalence and characteristics of laboratory-confirmed BM cases at the national population level. Using PRISMA standards, we retrieved data from electronic databases and selected reference articles. Out of 115,626 participants, 57,964 (50.13%) were infected with BM, with the highest prevalence (7.67%) in the age group 6-17 years. Our meta-analysis of 19 studies revealed an overall pooled prevalence of 38.01%, 95% confidence interval (CI: 0.26-0.50), with significant heterogeneity (I[2] = 99.86%, Q = 13117.45, p < 0.0001). The Egger test indicated publication bias (z = 3.4977, p = 0.0005). Subgroup analyses showed a higher prevalence in studies with sample sizes over 1000 (60.22%, 95% CI: 0.3899-0.7819, I[2] = 99.92%), over long study years (37.50%, 95% CI: 0.2642-0.5005, I[2] = 99.84%), cross-sectional study design (58.69%, 95%CI: 0.4906-0.6770, I2 = 99.72%), and particularly in Gauteng province (60.42%, 95% CI: 0.4539-0.7371, I[2] = 98.45%). The infectious types included Listeria (83.33%, 95% CI: 0.1936-0.9905, I[2] = 0.00%) and Neisseria (62.64%, 95% CI: 0.6126-0.6400, I[2] = 0.00%). Significant heterogeneity was noted in study design (R[2] = 52.93%, p < 0.0001), sample size (R[2] = 0.00%, p = 0.0117), and province (R[2] = 0.0%, p < 0.0001). These findings underscore a high prevalence of BM infections in South Africa's epidemiological landscape, highlighting the urgent need for targeted surveillance for effective prevention and treatment strategies.},
}

Humans
South Africa/epidemiology
*Meningitis, Bacterial/epidemiology/microbiology
Prevalence
Child
Adolescent
Child, Preschool
Female
Male
Adult
Infant
Middle Aged
Young Adult

@article {pmid41073886,
year = {2025},
author = {Mao, K and Lu, G and Qiu, Q and Zang, Y and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M and Li, Y},
title = {Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {658},
pmid = {41073886},
issn = {1471-2180},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology ; Rumen/microbiology/metabolism ; *Creatine/pharmacology/administration & dosage ; Metabolomics ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Animal Feed/analysis ; *Pyruvic Acid/pharmacology ; Bacteria/genetics/classification/metabolism ; },
abstract = {Transport stress is a critical factor affecting the health and growth performance of beef cattle, potentially leading to oxidative stress, inflammation, and metabolic disorders. Creatine pyruvate (CrPyr), as a potential stress alleviator, has unclear mechanisms of action. We monitored the growth of 17 Simmental calves (control, n = 8; CrPyr, n = 9) over 30 days post-transportation, collecting rumen and blood samples on days 1/4, and 30. This study aims to investigate the effects of CrPyr on the growth performance, rumen microbiome, and metabolome of calves subjected to transport stress. Results showed that CrPyr increased average daily gain and antioxidant capacity, while reducing the level of stress hormones and inflammation. In the 4 days post-transport, CrPyr mainly increases Ruminococcus abundance to boost ruminal nitrogen metabolism, providing substrates for microbial protein synthesis. CrPyr also provides energy for the proliferation of Ruminococcus by regulating ATP synthesis genes (ATPVC) and enriching purine metabolism products. Meanwhile, it strengthens the host's amino acid metabolism, especially aspartate, to enhance antioxidative capacity. By day 30, CrPyr primarily boosts Prevotella abundance to regulate VFA synthesis, supplying host energy. It regulates the ATP synthesis gene ATPF0A and enriches purine metabolism products, supporting Prevotella growth. Increased citric acid and ATP levels further aid host growth. The findings distinctly demonstrate that the mechanisms by which CrPyr alleviates transport stress through the regulation of the rumen microbiome and metabolome, and confirms that its effects are time-dependent. These findings provide a theoretical basis for the development of stress-alleviation strategies based on CrPyr and hold significant implications for enhancing the health and production performance of beef cattle.},
}

Animals
Cattle/growth & development/microbiology
Rumen/microbiology/metabolism
*Creatine/pharmacology/administration & dosage
Metabolomics
Metagenomics
Gastrointestinal Microbiome/drug effects
Metabolome/drug effects
Animal Feed/analysis
*Pyruvic Acid/pharmacology
Bacteria/genetics/classification/metabolism

@article {pmid41073868,
year = {2026},
author = {Leoni, C and Marzano, M and Filomena, E and D'Erchia, AM},
title = {Digital Droplet PCR (ddPCR) for Absolute Quantification of 16S rRNA Copy Number in Metagenomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2969},
number = {},
pages = {235-247},
pmid = {41073868},
issn = {1940-6029},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Polymerase Chain Reaction/methods ; *Gene Dosage ; DNA Copy Number Variations ; Fluorescent Dyes/chemistry ; },
abstract = {Digital Droplet PCR (ddPCR) is a quantitative PCR method that offers high sensitivity and accuracy in measuring the amount of nucleic acid in a sample, without the need of a standard curve. In ddPCR, a single sample is partitioned into up to 20,000 droplets, using the water-oil emulsion technology, and the amplification reaction occurs within each droplet using a fluorescent hydrolysis probe (Taqman) or a DNA-binding fluorescent dye. Following PCR, the emitted signals are individually measured in each droplet. Here, we describe a ddPCR optimized protocol for accurately quantifying the total copy number of the 16S rRNA gene in a metagenomic DNA sample. The protocol utilizes a primer pair, targeting the 16S V5-V6 hypervariable regions, in combination with a double-strand DNA-binding fluorescent dye.},
}

*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Polymerase Chain Reaction/methods
*Gene Dosage
DNA Copy Number Variations
Fluorescent Dyes/chemistry

@article {pmid41073663,
year = {2025},
author = {Yoo, JS and Jung, DJ and Goh, B and Heo, K and Zheng, W and Lee, CC and Seo, JI and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF},
title = {Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41073663},
issn = {2058-5276},
support = {K01-DK102771//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01-AT010268//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01-AI165987//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2021R1A6A3A14044113//National Research Foundation of Korea (NRF)/ ; RS-2024-00411992//National Research Foundation of Korea (NRF)/ ; RS-2024-00348702//National Research Foundation of Korea (NRF)/ ; 2021R1A6A3A14039202//National Research Foundation of Korea (NRF)/ ; RS-2023-00217123//National Research Foundation of Korea (NRF)/ ; 2014R1A3A2030423//National Research Foundation of Korea (NRF)/ ; 2012M3A9C4048780//National Research Foundation of Korea (NRF)/ ; },
abstract = {Gut symbiont Bacteroides fragilis can produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway of B. fragilis and determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution of agcT is restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly in Enterococcus. Analysis of infant gut metagenomes revealed that B. fragilis predominantly accounts for agcT abundance regardless of the cohort, but bgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs from bgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life.},
}

@article {pmid41073345,
year = {2025},
author = {Guo, WB and Wang, TT and Song, ZK and Liu, QY and Sun, JJ},
title = {[One case of occupational pulmonary anthrax].},
journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases},
volume = {43},
number = {9},
pages = {705-707},
doi = {10.3760/cma.j.cn121094-20240719-00326},
pmid = {41073345},
issn = {1001-9391},
mesh = {Humans ; *Anthrax ; Male ; Bacillus anthracis ; *Occupational Diseases ; *Anthracosis ; Adult ; },
abstract = {Pulmonary anthrax is an acute zoonotic infectious disease caused by Bacillus anthracis infecting the human body. Humans can be infected by coming into contact with diseased animals and their products or by consuming diseased animals. According to the different infection routes, it can be classified into cutaneous anthrax, pulmonary anthrax and intestinal anthrax, etc. Among them, cutaneous anthrax is the most common, while case reports of pulmonary anthrax are rare. This article analyzes the clinical data of a case of occupational pulmonary anthrax diagnosed by metagenomic next-generation sequencing (mNGS) and successfully treated, so as to provide a reference for the clinical treatment of pulmonary anthrax.},
}

Humans
*Anthrax
Male
Bacillus anthracis
*Occupational Diseases
*Anthracosis
Adult

@article {pmid41072965,
year = {2025},
author = {Odukwe, C and Abdelrahman, A and Zaidi, AN and Love, B and El-Hamamsy, I and Ghesani, M and Hopkins, KA},
title = {Culture-Negative Transcatheter Pulmonary Valve Endocarditis.},
journal = {JACC. Case reports},
volume = {30},
number = {31},
pages = {105324},
doi = {10.1016/j.jaccas.2025.105324},
pmid = {41072965},
issn = {2666-0849},
abstract = {CLINICAL CONDITION: We present a case of transcatheter pulmonary valve endocarditis in a 38-year-old woman with a history of atrial septal defect, pulmonary stenosis, and bicuspid aortic valve, all previously repaired with mechanical and bioprosthetic valve replacements. Despite negative initial studies, [18]F-fluorodeoxyglucose positron emission tomography-computed tomography revealed septic pulmonary emboli and abnormal uptake at the pulmonary valve. Metagenomic sequencing identified Haemophilus parainfluenzae as the pathogen.

KEY QUESTIONS: What is the differential diagnosis of a cardiac mass in this context? How should imaging and laboratory testing be approached in prosthetic valve endocarditis with negative studies? What surgical factors matter in patients with prior cardiac repairs?

OUTCOME: The patient underwent successful replacement of the pulmonary and aortic valves and completed a course of antibiotics, with full recovery.

TAKE-HOME MESSAGE: Consider bioprosthetic valve endocarditis in patients with persistent fevers and negative cultures. Use advanced diagnostics early when the clinical suspicion is high.},
}

@article {pmid41072853,
year = {2025},
author = {Li, Y and Sun, C and Zhao, T and Ni, Y and Liu, Q and Song, M and Xu, X and Sun, W and Li, Y and Zhou, J and Li, D and Zhang, Q and Feng, C and Shi, J and Cao, M and Huang, B and Su, N and Lu, X and Wang, L and Lei, J and Sang, L and Zhou, W and Cai, X and Wang, J and Wang, Y and Cai, Y and Lu, Y and Zhong, J and Su, X},
title = {Etiology of Initial Treatment Failure in Non-immunosuppressed Adult Patients with Community-acquired Pneumonia.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108110},
doi = {10.1016/j.ijid.2025.108110},
pmid = {41072853},
issn = {1878-3511},
abstract = {OBJECTIVES: Initial treatment failure (ITF) of community-acquired pneumonia (CAP) is a significant clinical problem. The study aimed to explore the etiology of ITF using metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), and to provide optimized management strategies for patients with CAP.

METHODS: From June 2022 to August 2024, we conducted a prospective, multicenter study in 15 hospitals of non-immunosuppressed adult CAP patients with ITF in Jiangsu Province, China. Conventional microbiological tests (CMTs), mNGS, and tNGS were applied to detect microorganisms in bronchoalveolar lavage fluid.

RESULTS: ITF was mainly caused by responsible pathogens not covered by initial treatment (59.0%) despite the high compliance with guideline-recommended regimens. The top 5 responsible pathogens were Chlamydia psittaci (21.5%), Mycoplasma pneumoniae (16.7%), influenza virus (14.6%), SARS-CoV-2 (8.3%), and Pseudomonas aeruginosa (6.3%). The positive pathogen identification rate for mNGS and tNGS was 74.4% and 72.7%, respectively, while for CMTs it was 12.2%. Based on NGS results, treatment was optimized in 53.5% of patients, and 95.8% were improved or cured.

CONCLUSIONS: Atypical pathogens and viruses not covered by empirical treatment regimens were the main causes of ITF. mNGS and tNGS outperformed CMTs in identifying responsible pathogens and could optimize the treatment of patients with ITF.},
}

@article {pmid41072822,
year = {2025},
author = {Chen, Z and Zhang, J and Lin, L and Sun, Y and Li, XY and Li, B},
title = {Enhanced fermentation for lactic acid production from food waste via hydrothermal pretreatment: performance evaluation and metagenomic analysis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133456},
doi = {10.1016/j.biortech.2025.133456},
pmid = {41072822},
issn = {1873-2976},
abstract = {Mixed-culture lactic acid fermentation of food waste (FW) commonly requests low pH conditions. However, this can pose the challenge of insufficient substrate hydrolysis. To address this, we investigated hydrothermal pretreatment coupled with centrifugal supernatant recovery as a technical strategy to enhance the FW hydrolysis and lactic acid production. The study characterized the supernatant substrate after the pretreatment at different temperatures (80-140 °C), focusing on organic solubilization, supernatant-solid separation for organic recovery, grease removal, and subsequently evaluated lactic acid production in 8-day batch fermentation. The results showed that hydrothermal pretreatment significantly boosted FW hydrolysis, improved organic recovery in the supernatant, and enhanced lactic acid yields. Optimal lactic acid production (12.4 g/L) representing a 68 % increase over the control without hydrothermal pretreatment, was achieved at 120 °C, despite the maximum hydrolysis occurring at 140 °C. Metagenomic sequencing further revealed that the pretreated substrate fostered the development of a lactic acid bacteria-dominated microbial community at low pH, notably enriched with Lactobacillus amylolyticus and Lactobacillus delbrueckii, along with functional genes associated with lactic acid production. Crucially, the absence of genes related to propionate and butyrate pathways in the dominant bacteria would explain the reduced byproduct spectrum and enhanced fermentation stability. These findings indicate that hydrothermal pretreatment improves both the quantity and quality of FW supernatant substrate, promoting a lactic acid bacteria-dominated community that drives favorable metabolic pathways under low pH conditions for more efficient and stable lactic acid production.},
}

@article {pmid41072348,
year = {2025},
author = {Tang, Y and Khan, E and Gu, AZ and Tsang, DCW},
title = {Graphitic biochar-anammox achieved by multi-heme-based extracellular electron transfer.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124704},
doi = {10.1016/j.watres.2025.124704},
pmid = {41072348},
issn = {1879-2448},
abstract = {The anammox process decarbonizes nitrogen removal by avoiding greenhouse gas emissions and organic carbon demand, yet its reliance on nitrification and denitrification undermines these advantages. To address this, we developed a biochar-assisted anammox system that leverages graphitic defects as redox-active sites to enable interspecies, multi-heme extracellular electron transfer (EET). Biochar produced at 800 °C for 4 h (BC800-4 h) exhibited the greatest graphitic defect density and the highest electron accepting capacity, uniquely exceeding the daily stoichiometric electron demand for complete ammonium oxidation in the present study. Metagenomic and in vitro assays revealed that BC800-4 h promoted hydroxylamine-dependent ammonium oxidation by anaerobic ammonia-oxidizing bacteria (AnAOB) via EET. A cooperative microbial network was identified: AnAOB in suspension supplied heme precursors, while ammonia-oxidizing and denitrifying bacteria colonizing the biochar facilitated heme assembly and transport. This partitioning enabled direct electron transfer to biochar, achieving 62 % nitrogen removal without exogenous nitrite and reducing N2O emissions by 28 %. The pore-size-dependent reduction in graphitic defects suggests that large molecular-weight biological channels (>10 kDa) are essential for electron transfer between anammox consortia and biochar. Our findings indicate an opportunity to develop a biochar-anammox reactor-with suspended AnAOB and a fixed-bed biochar biofilm-to exploit this synergy for efficient and low-emission nitrogen removal.},
}

@article {pmid41072344,
year = {2025},
author = {Yu, K and Xia, J and Zhu, D and He, B and Yu, Z and Zhu, DZ and Yao, Z},
title = {Public risk of sewage sediments in different functional areas - deciphered by metagenome assembly.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124691},
doi = {10.1016/j.watres.2025.124691},
pmid = {41072344},
issn = {1879-2448},
abstract = {Understanding public risk of sewage sediments, particularly those risks related to methane, sulfide emission and bio-risk, is critical for ensuring citizen safety. However, the underlying microbial mechanisms causing these risks remain unclear. This study employed metagenomic assembly to analyze methane/sulfur cycling pathways and bio-risks in sewage sediments from three typical functional areas: commercial, multifunctional, and residential. Results demonstrated that the sewage sediments in the multifunctional area exhibited the highest potential public risk levels, characterized by intensified methane/sulfur metabolic activity and increased abundance of mobile gene elements (MGEs) and high-risk antibiotic resistance genes (ARGs). In addition, the co-occurrence network complexity of ARGs, MGEs and pathogens were higher in the multifunctional sewage sediments. Intriguingly, we found genus Thiobacillus which participated in sulfur cycling, as the host of high risk ARGs, significantly enriched in the multifunctional area, also distributed in sewer systems around the world. Additionally, total organic carbon (TOC) emerged as key driver of sediment public risks. These findings highlight variations in sewage sediment public risks across different functional areas, providing a foundation for targeted risk mitigation strategies.},
}

@article {pmid41072198,
year = {2025},
author = {Jamtsho, K and Lund, MA and Blake, D and Van Etten, E},
title = {Contrasting effects of impervious cover on riparian plant and soil bacterial communities in a rapidly urbanising Himalayan city.},
journal = {The Science of the total environment},
volume = {1003},
number = {},
pages = {180681},
doi = {10.1016/j.scitotenv.2025.180681},
pmid = {41072198},
issn = {1879-1026},
abstract = {Rapid urbanisation-particularly the expansion of impervious surfaces-is reshaping riparian landscapes worldwide. These areas are frequently targeted for development due to their favourable topography, abundant water resources, and aesthetic appeal. However, the impact of increasing impervious cover on soil bacterial communities in biodiverse urban riparian zones remains poorly understood, especially in developing countries, raising concerns about potential declines in essential ecosystem functions. In this study, we investigated the effects of impervious cover, quantified as the Percentage of Total Impervious Area (PTIA), on the taxonomic and functional diversity of riparian soil bacteria in Thimphu City, Bhutan. Using plot-based taxonomic profiling and metagenomic analysis across a PTIA gradient, we tested the hypothesis that bacterial diversity and functional pathways would decline beyond 40 % PTIA, mirroring patterns observed in riparian plant communities. Contrary to our hypothesis, plots with PTIA exceeding 40 % exhibited greater bacterial richness and functional diversity. These findings suggest opposing responses to impervious cover, with belowground microbial communities increasing in diversity while aboveground plant diversity declines. A significantly lower carbon-to‑nitrogen ratio in urban plots-likely driven by nutrient enrichment-emerged as the primary factor promoting bacterial diversity in high PTIA areas. This enrichment appeared to favour copiotrophic bacteria, enhancing both diversity and functional capacity. Our results suggest that bacterial communities may be effective bioindicators of riparian ecosystem health than plant communities. Incorporating microbial metrics into urban riparian management and monitoring could therefore provide valuable insights for sustaining ecosystem functions in rapidly urbanising regions.},
}

@article {pmid41072177,
year = {2025},
author = {Uribarri, A and Henriquez, L and Beguiristain, I and Rodriguez, I and Alfaro, M and Sancho, I and Portillo, ME},
title = {Toward a clinical algorithm for the detection of periprosthetic joint infections using targeted NGS.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117133},
doi = {10.1016/j.diagmicrobio.2025.117133},
pmid = {41072177},
issn = {1879-0070},
abstract = {OBJECTIVES: Periprosthetic joint infection (PJI) represents a severe surgical complication, and despite advances have been made in PJI diagnosis, many cases remain microbiologically negative. In this context, metagenomic Next-Generation Sequencing (mNGS) emerged as a promising diagnostic tool for PJI. This study aimed to establish objective, widely-usable methodology and criteria for diagnosing PJI based on sequence analysis.

METHODS: We retrospectively analyzed sonication fluid samples from 34 patients who underwent surgical treatment for PJI in 2022. A 16S rRNA-based targeted NGS (tNGS) approach was carried out amplifying 16S rRNA gene for 25 and 35 cycles. Sequencing was performed on the Illumina MiSeq platform and data was processed using nf-core/ampliseq.

RESULTS: A significantly higher number of classifiable reads was observed in PJI cases (p < 0.0001). A negative control database was created using negative tNGS controls and samples from patients classified as aseptic failure. The database was then employed to establish three tNGS diagnostic criteria. The diagnostic efficacy of tNGS employing these criteria was assessed through receiver operating characteristic (ROC) curve analysis, which revealed optimal results after 25 cycles of 16S rRNA amplification (AUC = 0.924, p < 0.0001). An optimal cut-off of >12 % was calculated, obtaining a sensitivity of 100 % (95 % CI 75.3 %-100 %) and a specificity of 90.5 % (95 % CI 69.9 %-98.8 %). In both of our culture-negative PJI cases potential pathogens were detected: Listeria and Cutibacterium.

CONCLUSIONS: To the best of our knowledge, this is one of the few studies that attempts to establish standardized criteria and diagnostic cut-offs for the analysis of PJI tNGS data. We believe that these results could serve as a valuable reference for future PJI metagenomics diagnostic studies.},
}

@article {pmid41071829,
year = {2025},
author = {Akanbi, DO and Abaye, BB and Averhoff, F and Berg, MG and Orf, GS and Lawan, KM and Beckett, GA and Omotoso, AB and Mata, M and Cloherty, GA and Chabuka, L and de Oliveira, T and Mac-Fisi, KW and Walter, A and Mark, II and Edeki, G and Sinayoko, A and Nasrullah, M and Justina, BI and Balogun, MS},
title = {Detection of dengue, malaria, and additional causes of acute febrile illness: The need for expanded testing, Bayelsa State, Nigeria.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {10},
pages = {e0013060},
doi = {10.1371/journal.pntd.0013060},
pmid = {41071829},
issn = {1935-2735},
abstract = {Dengue virus (DENV) infection has not been previously reported from Bayelsa State, Nigeria. We aimed to determine the prevalence of dengue virus (DENV) infection, malaria, and coinfection, and other pathogens among febrile patients in the capital city, Yenagoa.We conducted a cross-sectional study among persons aged ≥1 year who presented with acute febrile illnesses (AFI) at four hospitals in Bayelsa State during 20 May - 15 June 2022. Blood samples from 443 participants were tested for DENV seromarkers (NS1, IgM, IgG), using serology and RT-PCR, and malaria was diagnosed by thick smear microscopy. Sociodemographic and risk factor data were collected using electronic questionnaires administered via smart phones/tablets and analyzed using univariate and multivariate methods. Metagenomic libraries were prepared and enriched by viral target capture and sequenced by NGS. The seroprevalence of acute DENV infection was 14.5% (n = 64) while the prevalence of malaria was 42.4% (n = 188); 6.5% (n = 29) of participants were coinfected with acute DENV infection and malaria. An additional 17.6% (n = 78) of participants had markers for past DENV infection. Rural/suburban residence and age ≥ 31 years were significantly correlated with having any dengue seromarker. Residence in a larger household (≥5 persons), and borehole water-use were predictors for malaria fever. RT-PCR results revealed multiple DENV serotypes, with serotype 3 dominant. Sequencing of unknown AFI cases revealed numerous viral causes such as adenovirus, EBV, and hepatitis A, as well as additional dengue and malarial infections missed by conventional testing. Of interest were Coxsackievirus A5 (hand, foot and mouth disease; HFMD) which has been diversifying locally for years in Nigeria and an mPox clade IIb (lineage A.2.3) strain that emerged in Nigeria during the 2022 global outbreak. The results of this study provide the first documentation of human DENV infection in Bayelsa State, Nigeria and suggests that dengue is an emerging and important cause of febrile illness in this area. Our findings support the need for routine testing to identify DENV among patients who present with acute febrile disease. Metagenomic NGS results highlight the benefits of unbiased surveillance to identify circulating and emerging pathogens.},
}

@article {pmid41070991,
year = {2025},
author = {Brennan, C and Shaffer, JP and Belda-Ferre, P and Mohanty, I and Weng, Y and Cantrell, K and Ackermann, G and Allaband, C and Bryant, M and Farmer, S and González, A and McDonald, D and Martino, C and Meehan, MJ and Rahman, G and Salido, RA and Schwartz, T and Song, SJ and Tribelhorn, C and Tubb, HM and Dorrestein, PC and Knight, R},
title = {Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191225},
doi = {10.1128/spectrum.01912-25},
pmid = {41070991},
issn = {2165-0497},
abstract = {UNLABELLED: An essential aspect of population-based research is collecting samples outside of a clinical setting. This is crucial because microbial populations are highly dynamic, varying significantly across hosts, environments, and time points, a variability that clinical sample collection alone cannot fully capture. At-home sample collection enables the inclusion of a larger and more diverse group of participants, accounting for differences in ethnicity, age, and other factors. However, managing large studies is challenging due to the complexities involved in sample acquisition, processing, and analysis. Building on our previous work demonstrating the effectiveness of single 1 mL barcoded, racked Matrix Tubes in reducing sample processing time and well-to-well contamination for paired DNA and metabolite extraction, we further validate this method against a previously benchmarked plate-based approach using the same extraction reagents. This validation focuses on samples from the built environment, human skin, human saliva, and feces from mice and humans. Importantly, we explore the impact of using a mix of bead sizes during bead-beating for cell lysis, demonstrating that it enhances taxonomic recovery compared to a single bead size. Finally, we assess the potential of 95% isopropanol for room-temperature sample preservation. Our results show that isopropanol performs comparably to 95% ethanol in many cases, suggesting it is viable as an alternative when ethanol is unavailable. Beyond minimizing contamination, halving processing time, eliminating human error during sample plating, and streamlining metadata curation, the Matrix tube approach produces metabolomic, 16S, and shotgun metagenomic data consistent with the Plate-based Method for both high- and low-biomass samples.

IMPORTANCE: Numerous studies have linked the microbiome to human and environmental health, yet many fundamental questions remain unanswered. Large-scale studies with robust statistical power are required to identify important covariates against a background of confounding factors. Cross-contamination, limited throughput, and human error have been identified as major setbacks when processing large numbers of samples. We present a streamlined method for sample accession and extraction of metabolites and DNA for both high- and low-biomass samples. This approach, previously shown to significantly reduce cross-contamination, employs an automation-friendly, single barcoded tube per sample. Additionally, we demonstrate that 95% isopropanol serves as an effective ambient-temperature storage solution for many sample types, providing an alternative in regions where ethanol is unavailable or restricted. This method has significant implications for the field, enabling large-scale studies to generate accurate insights with greater efficiency and expanded accessibility in situations in which ethanol is more costly or otherwise not available.},
}

@article {pmid41070134,
year = {2025},
author = {Li, Q and Liu, F and Zhong, J and Fang, X and Zhang, X and Xiong, H and Li, G and Chen, H},
title = {Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656016},
pmid = {41070134},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) is strongly associated with alterations in the gut microbiome. While numerous studies have examined this association, most focus on genus- or species-level taxonomic classifications, overlooking functional heterogeneity at the strain level.

METHODS: We integrated 1,123 metagenomic samples from seven global CRC cohorts to conduct multi-level metagenome-wide association studies (MWAS). Fecal microbial load (FML) correction was applied to mitigate technical confounding. We evaluated the performance of taxonomic models at various resolutions strain, species, and genus levels in classifying CRC status both within and across cohorts.

RESULTS: Strain-level analysis revealed conspecific strains with divergent associations to CRC. For instance, distinct strains of Bacteroides thetaiotaomicron exhibited both protective and risk-increasing effects across different cohorts. Genomic functional annotation suggested potential mechanistic bases for these opposing roles. Correction for FML reduced confounding and significantly improved the performance of within-cohort and cross-cohort CRC classification models. Interestingly, genus- and species-level models demonstrated superior predictive robustness compared to strain-level models, likely due to higher microbial abundance and greater cross-population conservation at these taxonomic ranks.

CONCLUSION: Our study underscores the biological relevance of strain level analysis in elucidating functional diversity within the microbiome. However, higher taxonomic levels provide more robust and clinically translatable diagnostic markers for CRC. Integrating FML correction with multi-level taxonomic profiling enhances both mechanistic insight into microbiom CRC interactions and the generalizability of diagnostic models across diverse populations.},
}

@article {pmid41070121,
year = {2025},
author = {Long, C and Fu, X and Wu, Q and Wang, S and Zhou, X and Mao, J and Guo, L and Shi, W and Yang, H and Yang, T and Du, Y and Yue, J and Wu, D and Liu, H},
title = {Poncirus trifoliata vs. Citrus junos rootstocks: reshaping lemon rhizosphere microecology through microbial and metabolic reprogramming.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1650631},
pmid = {41070121},
issn = {1664-302X},
abstract = {INTRODUCTION: Trifoliate orange (Poncirus trifoliataL. Raf) and "Ziyang Xiangcheng" (Citrus junos Sieb. ex Tanaka) are the predominant rootstocks for lemon production in China, exhibiting distinct adaptations to soil pH and differential impacts on plant resilience. As pivotal mediators of scion-soil interactions, rootstocks have emerged as key research targets for their regulatory potential in rhizosphere microbial communities and metabolites.

METHODS: Pot-cultured systems were established with lemon (Citrus × limon "Eureka") saplings grafted onto trifoliate orange (PTL) and "Ziyang Xiangcheng" (CJL) rootstocks. Integrated metagenomic and GC-MS metabolomic approaches were employed to analyze rhizosphere microbial communities and metabolites.

RESULTS: The results demonstrated no significant difference in rhizospheric microbial α-diversity (richness) between PTL and CJL, although PTL exhibited higher evenness. β-Diversity and LEfSe analysis revealed significant structural divergence in communities. A total of 15 differentially enriched genera across three phyla were identified, among which Pseudomonas, Cupriavidus, and Burkholderia in CJL, along with Sphingobium in PTL, exhibited strong effects. Random forest modeling identified 15 key differential metabolites, with 4 significantly upregulated in CJL and 11 in PTL. Microbial-metabolite correlation and GSEA analysis uncovered 10 core pathways involving genetic information processing, energy metabolism, environmental adaptation, and disease resistance mechanisms. Soil analysis showed CJL significantly surpassed PTL in organic matter content, catalase activity and plant height, whereas PTL exhibited superior cellulase, sucrase and urease activities. Mechanistically, PTL appears to recruit Pseudomonas mediterranea via 1-Monostearin secretion to activate glycerolipid metabolism, enhancing drought tolerance. Its caffeate and salicyl alcohol-β-glucoside secretions potentially mobilize Sphingobium and Ensifer adhaerens to regulate amino sugar metabolism, promoting carbon sequestration and root defense. Conversely, CJL likely employs L-alanine exudation to recruit Pseudomonas putida, triggering exopolysaccharide biosynthesis through arginine-proline metabolism as a key tolerance mechanism (such as drought tolerance and alkali tolerance).

DISCUSSION: The findings elucidate rootstock-specific modulation of rhizosphere microecosystems, highlighting distinct microbial-metabolite interactions and tolerance mechanisms. These results provide theoretical support for precision rootstock selection and microbiome engineering to advance sustainable citrus production.},
}

@article {pmid41070117,
year = {2025},
author = {He, C and Yang, S and Dong, S and Wang, S and Zhang, P and Yang, Y and Xu, D and Yang, R and Zeng, B and Hu, Y and Zhang, Q},
title = {Fermentation-driven microbial and metabolic shifts in filler tobacco leaves of different grades.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1651289},
pmid = {41070117},
issn = {1664-302X},
abstract = {INTRODUCTION: Filler tobacco leaves (FTLs) serve as the primary raw material for cigar production, and notable differences in physicochemical properties and fermentation responsiveness exist across different grades. However, the underlying mechanisms governing microbial and metabolic evolution during FTL fermentation remain poorly understood. This study systematically investigated the microbial community structures and metabolomic profiles of FTLs of varying grades before and after fermentation using metagenomic sequencing and untargeted metabolomics.

RESULTS: Metagenomic analysis revealed marked differences in microbial composition among FTL grades at the onset of fermentation. The fermentation process further facilitated the enrichment of functional genera such as Bacillus, Escherichia, and Alternaria, while low-grade FTLs exhibited excessive accumulation of Corynebacterium, potentially contributing to off-flavors and undesirable odors. Untargeted metabolomics identified numerous significantly differential metabolites after fermentation, primarily enriched in pathways related to amino acid biosynthesis, sugar metabolism, and carotenoid biosynthesis. Principal component analysis and hierarchical clustering indicated partial continuity in metabolomic profiles within the same grade before and after fermentation. Correlation analysis further revealed strong positive associations between several dominant genera and flavor-related metabolites.

CONCLUSION: This study demonstrates that FTLs of different grades exhibit distinct patterns of microbial succession and metabolic remodeling during fermentation. The initial leaf grade plays a pivotal role in shaping microbial communities and metabolite accumulation. These findings offer mechanistic insights into the fermentation process of FTLs and provide theoretical and practical guidance for optimizing raw material grading and fermentation management in the cigar industry.},
}

@article {pmid41070051,
year = {2025},
author = {Zhang, Y and Chen, A and Yang, C and Guan, L and Wang, C},
title = {Metagenomic next-generation sequencing assists in diagnosing Pneumocystis Jirovecii pneumonia in non-HIV patients: a case report.},
journal = {Respiratory medicine case reports},
volume = {58},
number = {},
pages = {102289},
pmid = {41070051},
issn = {2213-0071},
abstract = {BACKGROUND: Pneumocystis jirovecii Pneumonia (PJP) is a pulmonary opportunistic fungal infection with an incompletely elucidated pathogenesis. In recent years, non-human immunodeficiency virus (HIV) -infected PJP patients have exhibited rapid progression, poor prognosis, and a greater mortality rate compared to their HIV equivalents, necessitating timely detection and management, which are both critical and problematic.

CASE REPORT: We report a young patient admitted with diabetic ketoacidosis characterized by rapidly progressing acute respiratory failure with negative pathogen blood cultures, serum antibodies and polymerase chain reaction results, and a normal CD4[+] lymphocyte count. Anti-HIV antibody were negative. A computed tomography scan of the chest revealed patchy opacities in both lower lungs, a nonspecific manifestation. However, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected high Pneumocystis jiroveci sequence counts and a markedly elevated 1,3-β-D-glucan test titer. Following the diagnosis of non-HIV-infected PJP, the patient was discharged after 13 days with a positive outcome, attained through systematic management involving Trimethoprim-sulfamethoxazole anti-infective medication and stringent glycemic control.

CONCLUSION: Insufficient glucose management may be an important susceptibility factor for immunocompetent persons with non-HIV-infected PJP patients. MNGS serves as an effective method for rapid diagnosis and medication adjustment when signs, symptoms, and imaging findings of PJP are nonspecific.},
}

@article {pmid41069861,
year = {2025},
author = {George, C and Dharan, HM and Drescher, L and Lee, J and Qi, Y and Wang, Y and Chang, Y and Teo, SLM and Wainwright, BJ and Yung, C and Lauro, FM and Hazen, TC and Pointing, SB},
title = {Tropical intertidal microbiome response to the 2024 Marine Honour oil spill.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100623},
pmid = {41069861},
issn = {2666-4984},
abstract = {Marine fuel oil (MFO) spills in tropical coastal environments are under-characterized despite increasing risk from maritime activities. Microbial and geochemical responses to the June 2024 Marine Honour MFO spill on Singapore's intertidal sediments were analyzed in real time over 185 days. Using metagenomics and hydrocarbon profiling, microbial community shifts and hydrocarbon degradation were quantified across visibly oiled (high-impact) and clean (low-impact) sites. Microbiomes at all sites adapted rapidly to the spill through increased diversity and abundance of genes encoding alkane and aromatic compound degradation, detoxification, and biosurfactant production. The dominant hydrocarbon-degrading bacteria differed markedly from those reported in other crude oil spills and in regions with different climates. Oil deposition intensity strongly influenced microbial succession and hydrocarbon-degrading gene profiles, and this reflected early toxicity constraints in heavily oiled areas. The persistence of hydrocarbon degradation genes beyond hydrocarbon detection in sediments suggested long-term functional priming may occur. The study provides novel genome-resolved insight into the microbial response to MFO pollution, advances understanding of marine environmental biodegradation, and provides urgently needed baseline data for oil spill response strategies in Southeast Asia and beyond.},
}

@article {pmid41069710,
year = {2025},
author = {Burakova, I and Smirnova, Y and Gryaznova, M and Morozova, P and Kotarev, V and Lyadova, L and Ivanova, N and Denisenko, L and Syromyatnikov, M},
title = {Effect of interferon on broilers' fecal microbiome composition.},
journal = {Journal of advanced veterinary and animal research},
volume = {12},
number = {2},
pages = {487-496},
pmid = {41069710},
issn = {2311-7710},
abstract = {OBJECTIVE: The purpose of our study was to investigate the effect of chicken interferon on the intestinal microbiota of broiler chickens.

MATERIALS AND METHODS: The study used next-generation sequencing on the Ion Torrent pragmatic general multicast platform to target the V3 16S ribosomal ribonucleic acid hypervariable region gene, allowing us to analyze in detail changes in the composition of the broiler chicken microbiome.

RESULTS: Forty-one bacterial genera were identified in the studied groups of broilers. The highest abundance in both groups was observed for Lactobacillus, which was 31.08% ± 6.52 in the control group and 36.08% ± 7.25 in the interferon group. There was no clustering between the microbiome communities of the groups studied. We found a decrease or complete absence of Escherichia-Shigella, Eubacterium fissicatena group, Lachnospiraceae CHKCI001, and Pediococcus in the interferon-treated broiler group compared to the control group and an increase in the number of genera Ruminococcaceae CAG-352 and Turicibacter in the interferon group.

CONCLUSION: A decrease in E.-Shigella may indicate normalization of the intestinal microbiota of broilers, and it can also be concluded that the introduction of interferon helps to suppress opportunistic bacteria. In the interferon group, a sharp increase in the number of Turicibacter was observed. Representatives of this genus are among the most common members in the intestines of broilers.},
}

@article {pmid41069707,
year = {2025},
author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A},
title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf157},
pmid = {41069707},
issn = {2730-6151},
abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.},
}

@article {pmid41069598,
year = {2025},
author = {Wang, Z and Lin, X and Wu, J and Su, C and Luo, Y and Yu, G},
title = {Radix Pseudostellaria polysaccharides alleviate sepsis-induced liver injury by modulating the gut microbiota via the TLR4/NF-κB pathway.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1658147},
pmid = {41069598},
issn = {1663-9812},
abstract = {BACKGROUND: Sepsis-induced liver injury (SLI) is a life-threatening complication with limited therapeutic options. Radix Pseudostellariae polysaccharides (RPPS), a component of traditional Chinese medicine, exert immunomodulatory, anti-inflammatory, and antioxidant properties. Herein, we investigated the therapeutic effects and mechanisms of RPPS on SLI.

METHODS: A murine sepsis model was established using cecal ligation and puncture. Mice were pretreated with RPPS or saline for 14 days. Subsequently, multi-omics integration-including metagenomics, proteomics, and network pharmacology-was employed to elucidate the mechanisms of RPPS. Liver injury was assessed via serum biomarkers, histopathology, and transmission electron microscopy, while intestinal barrier integrity was evaluated through histopathological analysis. Gut microbiota composition and functional pathways were examined using metagenomic sequencing. Furthermore, Kyoto Encyclopedia of Genes and Genomes enrichment analyses of gut microbiota, liver proteomics, and network pharmacology data were integrated to predict key target pathways, which were experimentally validated in mice.

RESULTS: RPPS pretreatment significantly improved survival, reduced liver injury markers, attenuated hepatic necrosis and inflammation, and restored intestinal barrier integrity. RPPS also modulated the gut microbiota by enriching beneficial taxa and suppressing pathogens. Multi-omics integration identified the toll-like receptor 4 (TLR4)/nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway as the core mechanism, and experimental validation confirmed that RPPS inhibited TLR4 membrane expression, MyD88/IKKα/β activation, NF-κB p65 phosphorylation, and nuclear translocation. In conclusion, RPPS alleviates SLI by protecting the intestinal barrier, modulating gut microbiota, and suppressing the TLR4/NF-κB signaling pathway.

CONCLUSION: This study provides a scientific foundation for RPPS as a potential therapeutic candidate in sepsis treatment.},
}

@article {pmid41069450,
year = {2025},
author = {Chen, W and Yang, P and Hu, J and Liu, X and Jiang, C and Wu, H and Wang, Y and Yan, Q and Lu, S and Xiong, J and Huang, X and Pan, Y and He, F and Chen, Q and Hu, S and Chen, M and Xiong, C},
title = {Echoes in the Deep: Revealing Influenza A Viruses' Persistence and Microbial Associations in Aquatic Ecosystems.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {5586400},
pmid = {41069450},
issn = {1865-1682},
mesh = {*Influenza A virus/isolation & purification/genetics/classification ; China/epidemiology ; Animals ; *Seawater/virology/microbiology ; Phylogeny ; Lakes/virology ; Ecosystem ; Humans ; *Water Microbiology ; Fresh Water/virology ; },
abstract = {BACKGROUND: Influenza A viruses (IAVs) are significant pathogens with complex transmission dynamics in aquatic ecosystems, yet their persistence, evolutionary relationships, and associations with environmental microorganisms remain poorly understood. This study aimed to elucidate the phylogenetic characteristics and ecological associations of IAV in freshwater and seawater ecosystems in Eastern China to inform public health strategies.

METHODS: Water samples were collected from three freshwater lakes and a coastal seawater site. Viral particles were concentrated, and nucleic acids were extracted for metatranscriptomic and metagenomic sequencing. Phylogenetic analyses, population dynamics assessments, and microbial association networks were constructed using bioinformatic tools. Statistical tests, including Tajima's D and Fu and Li's tests, were applied to evaluate evolutionary trends.

RESULTS: IAV fragments in seawater showed high homology with recent human H3N2 strains from North America (2021-2024), while freshwater-derived fragments aligned with historical avian strains from Asia. Microbial association networks revealed significant associations between IAV and environmental bacteria (e.g., Brevundimonas aurantiaca) and fungi (e.g., Thamnidium), implying potential ecological associations that may underpin viral persistence. Freshwater environments with higher abundances of Uroviricota exhibited more frequent IAV detection. PERMANOVA confirmed distinct overall microbial community compositions in IAV-positive versus IAV-negative samples across both freshwater and seawater ecosystems (p < 0.05).

CONCLUSION: Aquatic ecosystems, particularly freshwater habitats, may serve as reservoirs for IAV persistence and evolution, driven by complex microbial associations. Regional disparities in viral strain origins highlight the role of migratory waterfowl and environmental transmission routes. Integrated surveillance of aquatic IAV dynamics is critical to anticipate zoonotic risks and mitigate future outbreaks.},
}

*Influenza A virus/isolation & purification/genetics/classification
China/epidemiology
Animals
*Seawater/virology/microbiology
Phylogeny
Lakes/virology
Ecosystem
Humans
*Water Microbiology
Fresh Water/virology

@article {pmid41069107,
year = {2025},
author = {Ozel, B and Agirman, B and Simsek, O and Erten, H},
title = {Effects of Backslopping on Yeast Diversity and the Volatile Profile of Tarhana.},
journal = {Yeast (Chichester, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/yea.70003},
pmid = {41069107},
issn = {1097-0061},
support = {//Cukurova University Academic Research Projects Unit (Project no: FDK-2017-7769)./ ; },
abstract = {The primary challenge in tarhana production is the occurrence of spontaneous fermentation, which leads to non-standardized products. Thus, we investigated the effects of backslopping, a traditional method for inoculating fermented foods, on the yeast and volatile aroma compound diversity of tarhana dough. Backslopping fermentations were conducted at different temperatures (25°C and 30°C), pHs (3.70 and 4.00), and inoculation rates (5%, 10%, and 15%). The results revealed that the fermentation temperature and pH significantly influenced the diversity of yeast species and the volatile compound profile of the tarhana dough. However, despite some variations in the PCR-DGGE profiles, the metagenomic analysis revealed that the inoculation rate had minimal effect on yeast diversity, with species diversity remaining relatively constant over the cycles. Kazachstania humilis, Kazachstania bulderi, and Pichia kluyveri were the most prevalent yeast species across all experimental conditions. Pichia membranifaciens was exclusively detected in doughs fermented at 25°C and pH 4.00, whereas Saccharomyces cerevisiae was observed only in doughs fermented at 30°C. Tarhana doughs had a wide range of volatile compounds, the most abundant of which were terpenes and terpenoids, followed by esters, alcohols, aldehydes, and phenols. Doughs fermented at 25°C and pH 3.70 were differentiated from other groups, particularly for their content of esters (e.g., ethyl acetate, ethyl lactate, ethyl decanoate, and ethyl octanoate) and alcohols (e.g., ethyl alcohol, isobutyl alcohol, benzyl alcohol). This study highlights the direct influence of backslopping on yeast diversity and its indirect impact on the aroma profile of tarhana dough, providing insights into the optimization of fermentation conditions for improved product standardization.},
}

@article {pmid41069041,
year = {2025},
author = {Koketsu, A and Fukase, S and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Kumada, K and Li, B and Shimada, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Bacterial Involvement in Oral Squamous Cell Carcinoma and Potentially Malignant Oral Disorders.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70115},
pmid = {41069041},
issn = {1601-0825},
abstract = {OBJECTIVE: To clarify the relationship between oral squamous cell carcinoma (OSCC), potentially malignant oral disease (OPMD), and bacterial flora using metagenomic analysis.

METHODS: This cross-sectional observational study included 50 patients in the control group and 77 patients with OPMDs, 41 with early OSCCs, and 20 with advanced OSCCs. Patient saliva samples were subjected to high-throughput sequencing of 16S rRNA gene amplicons to evaluate the composition and diversity of the oral microbiome.

RESULTS: No significant differences were observed in patient backgrounds, other than sex. Patients with advanced OSCCs had greater oral bacterial diversity than those with early OSCC or OPMD. The advanced OSCC group formed a distinct cluster separate from the other groups. Sixteen and 275 species were identified at the phylum and genus levels, respectively. Compared with the control group, Actinomycetia and Streptococcus were significantly elevated in the early OSCC and OPMD groups. Peptostreptococcus and Fusobacterium were significantly higher in the advanced OSCC group than in the control, OPMD, and early OSCC groups.

CONCLUSIONS: The composition and diversity of oral microbiota may be associated with OPMD development and progression to OSCC. Consequently, the salivary microbiome may serve as a biomarker for oral cancer and help predict cancer progression.},
}

@article {pmid41068938,
year = {2025},
author = {Xu, J and Chen, X and Ren, J and Xu, J and Zhang, L and Yan, F and Liu, T and Zhang, G and Huws, SA and Yao, J and Wu, S},
title = {Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {345},
pmid = {41068938},
issn = {1474-760X},
support = {32272829//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; },
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; *Gastrointestinal Microbiome ; Epithelium/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Female ; *Goat Diseases/microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance.

RESULTS: Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis, promoting rumen epithelial VFAs absorption and reducing ruminal inflammation.

CONCLUSIONS: This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.},
}

Animals
*Goats/microbiology
*Rumen/microbiology/metabolism
*Acidosis/veterinary/microbiology/metabolism
*Gastrointestinal Microbiome
Epithelium/metabolism/microbiology
Fatty Acids, Volatile/metabolism
Female
*Goat Diseases/microbiology
Hydrogen-Ion Concentration
*Microbiota
Transcriptome
Multiomics

@article {pmid41068590,
year = {2025},
author = {Chen, Y and Miao, Q and Bao, R and Qu, H and Shen, J and Li, N and Luan, S and Yin, X and Pan, J and Hu, B},
title = {Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {653},
pmid = {41068590},
issn = {1471-2180},
support = {2023ZSLC24//Zhongshan Hospital/ ; },
mesh = {Humans ; Male ; *Microbiota ; Female ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; *Lung/microbiology ; Prognosis ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Adult ; },
abstract = {BACKGROUND: The incidence of nontuberculous mycobacterial pulmonary disease (PNTM) is rising, but the available treatments have limitations. Currently, the understanding of the ecology of the airway microbiota in PNTM is limited, especially regarding community structure, dynamics, and their relationship with clinical outcomes.

METHODS: We used metagenomic sequencing to characterize the lung microbiota in bronchoalveolar lavage fluid (BALF). We evaluated the prognosis of patients with PNTM through respiratory specimen cultures and chest CT scans.

RESULTS: PNTM exhibit distinct airway microbiota characteristics compared to controls, however, no significant differences were observed in NTM species. A Dirichlet multinomial mixture model was used to identify two distinct community types (pneumotypes) and investigate their association with host immunity and prognosis. At the 13-month median follow-up, pneumotype 1 (including Mycobacterium, opportunistic pathogens, and anaerobes) presented a lower probability of sustained culture conversion (hazard ratio = 0.29; 95% confidence interval = 0.12-0.73; P = 0.009) than pneumotype 2, indicating a worse prognosis. Based on microbial community abundance and interactions, Ralstonia (NetMoss score = 1.0; log2FoldChange = 3.6) and Dolosigranulum (NetMoss score = 0.6; log2FoldChange = 1.4) emerged as prominent taxa associated with the shift from pneumotype 1 to pneumotype 2, which correlated with differences in clinical outcomes.

CONCLUSION: Our research indicates that distinct baseline microbial characteristics in PNTM patients are associated with prognosis. Furthermore, we identified candidate microbes driving changes in the PNTM microbial community state, serving as potential therapeutic targets.},
}

Humans
Male
*Microbiota
Female
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
*Lung/microbiology
Prognosis
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Nontuberculous Mycobacteria/genetics/isolation & purification/classification
Bacteria/classification/genetics/isolation & purification
Metagenomics
Adult

@article {pmid41068306,
year = {2025},
author = {Shin, AS and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Dong, A and Xu, H and Gao, X},
title = {Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35375},
pmid = {41068306},
issn = {2045-2322},
support = {K23DK122015/DK/NIDDK NIH HHS/United States ; R03DK132446/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Adult ; Middle Aged ; Bile Acids and Salts/metabolism ; Constipation/microbiology ; Metagenome ; Diarrhea/microbiology ; Bacteria/classification/genetics/metabolism ; },
abstract = {Short chain fatty acids (SCFA) are key microbial metabolites that modulate intestinal homeostasis and may influence irritable bowel syndrome (IBS) pathophysiology. We aimed to assess microbial features associated with SCFA and determine if features varied across IBS subtypes and endophenotypes. We analyzed stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across groups. We further compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption (BAM). Microbe-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that could underlie subtype-specific microbially-mediated mechanisms. The greatest number of microbe-SCFA associations were observed in IBS-D. Several SCFA-producing species demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM. Keystone taxa responsible for SCFA production differ by IBS subtype and traits. IBS microbiomes appear exhibit reduced functional redundancy. Differences in substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS.},
}

Humans
*Irritable Bowel Syndrome/microbiology/metabolism
Female
*Gastrointestinal Microbiome
Male
*Fatty Acids, Volatile/metabolism
Feces/microbiology/chemistry
Adult
Middle Aged
Bile Acids and Salts/metabolism
Constipation/microbiology
Metagenome
Diarrhea/microbiology
Bacteria/classification/genetics/metabolism

@article {pmid40704526,
year = {2025},
author = {Capps, B and Chadwick, R and Joly, Y and Lajaunie, C and Hauptmannova, I and Mackenzie, S and Mulvihill, JJ and Mumford, E and Rasmussen, SA and Sanghavi, K and Thaldar, DW and Yeates, J and Quinzin, MC and Lederman, Z},
title = {The Ecological Genome Project and the Promises of Ecogenomics for Society: Realising a Shared Vision as One Health.},
journal = {Bioethics},
volume = {39},
number = {9},
pages = {788-795},
doi = {10.1111/bioe.70020},
pmid = {40704526},
issn = {1467-8519},
mesh = {Humans ; *One Health/ethics ; *Genomics/ethics ; *Ecology/ethics ; *Metagenomics/ethics ; *Ecosystem ; },
abstract = {This paper develops a vision for The Ecological Genome Project: an aspirational, global endeavour to connect human genomic sciences with the ethos of ecological sciences. The Project's goal is to strengthen interdisciplinary networks that relate to diverse initiatives using genomic technologies, with respect to shared ethical frameworks and governance structures. To this end, this paper proposes a practical definition of ecogenomics to align various methodologies and values in a single environmental field using principles used to safeguard all forms of life in their habitats. We achieve this by using a One Health approach as a pretext for disparate disciplines to collaborate and also a lens to view the Ethical, Legal and Social Implications (ELSI) inherent in ecological systems.},
}

Humans
*One Health/ethics
*Genomics/ethics
*Ecology/ethics
*Metagenomics/ethics
*Ecosystem

@article {pmid41068233,
year = {2025},
author = {Giovannini, N and Limena, A and Ercolino, C and Renteria, SCU and Strati, F and Giuffrè, MR and Maragno, P and Carbone, IF and Facciotti, F and Ceriotti, F and Ferrazzi, E and Lattuada, D},
title = {Nasopharyngeal and oral microbiota profiling in SARS-CoV-2 infected pregnant women.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35306},
pmid = {41068233},
issn = {2045-2322},
mesh = {Humans ; Female ; Pregnancy ; *COVID-19/microbiology/virology ; *Nasopharynx/microbiology ; Adult ; *Microbiota ; *Mouth/microbiology ; SARS-CoV-2/isolation & purification ; *Pregnancy Complications, Infectious/microbiology/virology ; },
abstract = {Variations have been found in the upper respiratory tract microbiota in SARS-CoV-2 positive patients compared to healthy subjects, with different dominant species and diversity indexes detected, including a decrease in biodiversity and an increased abundance of bacterial pathogens. Moreover, these discrepancies were observed in patients with both mild and severe symptoms. Notably, the inflammatory state appears to be significantly influenced by the characteristics of the indigenous microbiota. This is particularly interesting in pregnant patients, as pregnancy involves an adaptive adjustment of the microbiota due to hormonal changes aimed at providing immune protection. The relationship between the microbiota of pregnant women and SARS-CoV-2 has not been deeply explored so far. The purpose of the present study is to investigate the relationship between SARS-CoV-2, nasopharyngeal and oral microbiota, and pregnancy. To our knowledge this is the first simultaneous investigation on both nasopharyngeal and oral microbiota in SARS-Cov-2 infected pregnant women. In this study, the nasopharyngeal and oral microbiota were analysed in 43 women in their third trimester of pregnancy enrolled from April 2020 to February 2021. The differential abundance of taxa was tested and alpha and beta diversity were evaluated. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. In both the nasopharyngeal and oral microbiota of the SARS-CoV-2 infected pregnant women, we found a variation in taxa, represented by an enrichment of pathobionts, which increased particularly with the severity of symptoms. Specifically, a significant reduction in microbial biodiversity has been identified within the nasopharyngeal microbiota of SARS-CoV-2 positive women. Furthermore, enrichment in pathobionts was noted in both asymptomatic and symptomatic women, with these changes being more pronounced in the nasopharyngeal microbiota compared to the oral one. The nasopharyngeal microbiota of asymptomatic and symptomatic SARS-CoV-2 infected women showed an enrichment of pathogens and pathobionts such as Corynebacterium, Fusobacterium, Neisseria, Streptococcus, Haemophilus, Mycobacterium and Porphyromonas compared with the control group. The oral microbiota showed an enrichment of pathobionts such as Neisseria, Fusobacterium and Streptococcus. A random forest classifier applied to metagenomic data from nasopharyngeal and oral swabs showed that the nasopharyngeal microbiota is the best sampling site to predict the patients' SARS-CoV-2 infection status. Gulbenkiania, Burkholderia and Actinomyces, all taxa significantly enriched in the control group compared to SARS-CoV-2 infected women, were the most important features selected by the classifier. Finally, correlations between the nasopharyngeal and oral microbiota and clinical parameters of pregnant women, particularly BMI and procalcitonin, were observed. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. We found a variation in taxa, represented by the enrichment of pathobionts in both the nasopharyngeal and oral microbiota of SARS-CoV-2 infected pregnant women, particularly increased in symptomatic individuals. The nasopharyngeal microbiota appears to be a better predictor of SARS-CoV-2 infection and its severity than the oral microbiota.},
}

Humans
Female
Pregnancy
*COVID-19/microbiology/virology
*Nasopharynx/microbiology
Adult
*Microbiota
*Mouth/microbiology
SARS-CoV-2/isolation & purification
*Pregnancy Complications, Infectious/microbiology/virology

@article {pmid41068119,
year = {2025},
author = {Liu, S and Feng, B and Zhang, Z and Miao, J and Lai, X and Zhao, W and Xie, Q and Ye, X and Cao, C and Yu, P and Sun, J and Guo, J and Wang, Z and Wang, Q and Zhang, Z and Pan, Y},
title = {UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {196},
pmid = {41068119},
issn = {2055-5008},
support = {LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 32272832//National Natural Science Foundation of China/ ; 32272832//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Metagenome ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Metagenomics ; },
abstract = {The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.},
}

Animals
*Gastrointestinal Microbiome/genetics
Swine/microbiology
*Bacteria/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Metagenome
*Genome, Bacterial
Interspersed Repetitive Sequences
Phylogeny
Metagenomics

@article {pmid41068096,
year = {2025},
author = {Wu, Y and Ji, G and Han, D and Zhang, Y and Zhu, X and Li, H and Li, M and Gao, Y and Xie, R and Xu, M and Lu, L and Deng, Z and Wei, Q and Qin, H and Bi, D},
title = {Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {197},
pmid = {41068096},
issn = {2055-5008},
support = {82072634//National Natural Science Foundation of China/ ; 82072236//National Natural Science Foundation of China/ ; SHDC2020CR2069B//Shanghai Municipal Hospital Development Center/ ; ZJ2022-ZD-005//Major Projects of Special Development Funds in Zhangjiang National Independent Innovation Demonstration Zone, Shanghai/ ; },
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Fusobacterium/genetics/classification/isolation & purification/pathogenicity ; Feces/microbiology ; *Fusobacterium Infections/microbiology ; Male ; Female ; Fusobacterium nucleatum/genetics ; Real-Time Polymerase Chain Reaction ; Middle Aged ; Aged ; Metagenomics ; },
abstract = {Non-nucleatum Fusobacterium may play a nonnegligible role in colorectal cancer (CRC) and certain Fusobacterium lineages (namely, L1 and L5) have shown specific associations with CRC. We aim to clarify the complex connections between Fusobacterium and CRC. We found that the widely adopted quantitative PCR (qPCR) method could overestimate F. nucleatum abundance and, in fact, reflect L1 levels in clinical samples. A lineage-specific qPCR assay targeting L1/L5 was developed and validated using mock and clinical samples. Its application in independent cohorts confirmed that L1 was overabundant in CRC, whereas L5 correlated with lymphovascular invasion. Importantly, faecal L1 abundance was more predictive of CRC than F. nucleatum, supported also by cross-population metagenomic data. CRC-associated virulence and colonisation genes were found in various L1 species other than F. nucleatum. Our results highlight the clinical importance of L1/L5 in CRC with high-diversity Fusobacterium contexts and suggest that non-nucleatum Fusobacterium may also contribute to CRC.},
}

*Colorectal Neoplasms/microbiology
Humans
*Fusobacterium/genetics/classification/isolation & purification/pathogenicity
Feces/microbiology
*Fusobacterium Infections/microbiology
Male
Female
Fusobacterium nucleatum/genetics
Real-Time Polymerase Chain Reaction
Middle Aged
Aged
Metagenomics

@article {pmid41067450,
year = {2025},
author = {Liu, N and Zhang, Y and Zhang, Y and Yang, Y and Long, H and Huang, A and Zeng, Y and Xie, Z},
title = {Quorum sensing mediates spatiotemporal microbial community dynamics and nitrogen metabolism in biofloc-based Litopenaeus vannamei aquaculture systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133459},
doi = {10.1016/j.biortech.2025.133459},
pmid = {41067450},
issn = {1873-2976},
abstract = {Biofloc technology (BFT) enables sustainable aquaculture by leveraging microbial communities to enhance water quality and nutrient cycling. However, the role of quorum sensing (QS) in regulating microbial dynamics and metabolic functions within BFT systems remains poorly understood. This study examined how QS spatiotemporally regulates microbial succession and nutrient metabolism in a biofloc-based Litopenaeus vannamei aquaculture system over 82 days culture. Ammonia and nitrite concentrations shifted through four phases: initial (IP), rising (RP), declining (DP), and stabilization (SP). Notably, nitrite levels decreased rapidly from 1.21 mg/L to 0.03 mg/L during DP. Metagenomic analysis revealed Pseudomonadota, Actinomycetota, and Bacteroidota as the consistently dominant phyla, while dominant genera shifted over time. QS pathways displayed temporal heterogeneity: acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) predominated during IP, whereas aromatic hydrocarbon kinases (AHKs) and cyclic dimeric guanosine monophosphate (c-di-GMP) were more enriched during SP. KEGG analysis indicated that nitrogen metabolism genes were more abundant in bioflocs than in the water. Genes associated with dissimilatory nitrate reduction and denitrification were significantly more abundant than those involved in other nitrogen metabolic processes (p < 0.05). Furthermore, QS signaling coordinated the complex interaction networks among 30 dominant bacterial genera (e.g., Amaricoccus and Ruegeria) involved in carbon, nitrogen, and sulfur metabolism, which is crucial for maintaining the stability and functionality of the biofloc system. This study elucidates the mechanisms through which microbial signaling orchestrates efficient nitrogen removal and sustains system stability, thereby providing a foundation for developing targeted bioaugmentation strategies to enhance sustainable aquaculture practices.},
}

@article {pmid41067299,
year = {2025},
author = {Feng, Y and Yuan, Q and Kang, Y and Zheng, M and Li, Z},
title = {Deciphering the mobility, pathogenic hosts, and co-selection of antibiotic resistance genes in untreated wastewater from three different hospitals.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105840},
doi = {10.1016/j.meegid.2025.105840},
pmid = {41067299},
issn = {1567-7257},
abstract = {OBJECTIVE: Antibiotic resistance genes (ARGs) in hospital wastewater pose significant environmental and public health risks, yet the co-selection mechanisms involving metal/biocide resistance genes (MRGs/BRGs) and the role of mobile genetic elements (MGEs) remain poorly characterized. This study aimed to comprehensively assess the abundance, mobility, pathogenic hosts, and co-selection patterns of ARGs, MRGs, and BRGs in untreated wastewater from three types of hospitals.

METHODS: Untreated wastewater samples from nine sources across three hospital types (general, traditional Chinese medicine, and dental) were analyzed using metagenomic sequencing and assembly. ARGs, MRGs, and BRGs were identified via the SARG and BacMet databases. ARG hosts, mobility, and MGE co-occurrence were analyzed using PlasFlow and MOB-suite, with risk levels evaluated alongside pathogenic bacteria databases.

RESULTS: A total of 1911 ARGs (222 subtypes), 1662 MRGs (167 subtypes), and 916 BRGs (139 subtypes) were detected. Tetracycline, multidrug, and β-lactam resistance genes were predominant, with 46.43 % of ARGs being plasmid-associated. Key pathogens including Klebsiella pneumoniae and Enterococcus spp. harbored high-risk ARGs such as KPC-2 and NDM-1. Notably, 76.2 % of ARGs in traditional Chinese medicine hospital wastewater were classified as high-risk. Significant co-occurrence of ARGs with MGEs (e.g., DDE recombinases) and MRGs/BRGs was observed, underscoring the role of horizontal gene transfer and co-selection.

CONCLUSION: Untreated hospital wastewater represents a significant reservoir of ARGs, with risks exacerbated by pathogenic hosts, MGE-mediated HGT, and metal/biocide co-selection. These findings underscore the urgent need for optimized wastewater treatment strategies to curb the spread of antibiotic resistance and inform future intervention efforts.},
}

@article {pmid41067045,
year = {2025},
author = {Li, LH and Pabst, M and van Loosdrecht, MCM and Pronk, M},
title = {Distinct roles of granules and flocs in aerobic granular sludge processes.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124671},
doi = {10.1016/j.watres.2025.124671},
pmid = {41067045},
issn = {1879-2448},
abstract = {Aerobic Granular Sludge (AGS) is an innovative and efficient biotechnology for wastewater treatment that has been successfully applied on full-scale worldwide. Full-scale municipal AGS systems typically contain both granular sludge (granules) and flocculent sludge (flocs). Studies on the different roles of granules and flocs remain limited. In this study, a laboratory-scale AGS reactor fed with complex synthetic wastewater was operated to simulate full-scale AGS systems and to study the different functional roles of granules and flocs. The laboratory reactor achieved a coexistence of granules and flocs with a floc mass fraction of 17 %. The activities of different size fractions were evaluated using batch experiments and compared for carbon, nitrogen, and phosphorus removal: flocs (FL; <0.2 mm), small granules (SG; 0.2∼1.0 mm), medium granules (MG; 1.0∼2.0 mm), and large granules (LG; >2.0 mm). During feeding, large granules and medium granules exhibited more substrate uptake than small granules and flocs due to preferential substrate access. For aerobic conversion, flocs and small granules showed higher biomass-specific nitrification rates, while medium granules and large granules showed higher phosphorus uptake and denitrification capacity. Furthermore, large granules and medium granules showed stronger mass transfer limitation of oxygen, which limits their nitrification capability. Microbial community analysis using metagenomics and metaproteomics was performed across size fractions, and distinct communities in granules and flocs were shown. Granules showed a high abundance of Candidatus Accumulibacter (polyphosphate-accumulating organisms, PAOs) and Candidatus Competibacter (glycogen-accumulating organisms, GAOs). Flocs showed a high abundance of Nitrosomonas (ammonium-oxidizing bacteria, AOB) and Tetrasphaera (fermentative PAOs) and a low abundance of Ca. Accumulibacter. The distribution of microbial activities and microbial community over sludge size fractions in the laboratory reactor is similar to full-scale AGS systems, indicating that this laboratory setup can simulate full-scale systems and can be used for future research. Overall, this study highlights the importance of maintaining a good balance between different granule sizes and flocs to optimize nutrient removal.},
}

@article {pmid41067043,
year = {2025},
author = {Xu, D and Liu, T and Fan, J and Chen, W and Li, Y and Zhang, M and Zheng, P and Guo, J},
title = {Mechanical resistance of higher EPS contents in larger granules restricts anammox bacterial growth.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124705},
doi = {10.1016/j.watres.2025.124705},
pmid = {41067043},
issn = {1879-2448},
abstract = {Extracellular polymeric substances (EPS) are core granular components, playing critical roles in its structural stability. However, little is known about the effect of EPS on bacterial growth due to physical and mechanical resistances posed by EPS matrix. Herein, anaerobic ammonium oxidation (anammox) granules with different sizes and EPS contents were collected from a full-scale plant. Using [13]C isotope labelling and qPCR assays, we confirmed that larger granules with higher EPS content exhibited the higher maximum nitrogen removal activity but much lower bacterial growth yield, resulting in a significantly lower maximum specific growth rate (-26.8%), compared to smaller granules. Metagenomic sequencing revealed that anammox species were identical in different granules, and actual EPS production yields were similar in 15-day incubation, ruling out the possibility that more energy was diverted to produce additional EPS in larger granules. Interestingly, the EPS mechanical strength was significantly greater in large granules, which reduced cell membrane fluidity and severely deformed bacterial cells. These mechanical constraints imposed by the dense EPS matrix limited anammox bacterial proliferation and reduced their growth yield. Using low-intensity ultrasound to loosen EPS structure improved the growth yield of anammox bacteria in large granules, while also enhancing nitrogen removal activity. These together contributed to a substantial increase in bacterial growth rate (+153.3%). The findings highlight that physical and mechanical resistance imposed by EPS plays a previously overlooked role in bacterial growth, and provide the basis for promoting anammox bacterial proliferation within granules.},
}

@article {pmid41066987,
year = {2025},
author = {Zhang, C and Zhang, Y and Diao, G and Hou, N and Zhao, X and Li, D},
title = {Decoding pyrene-induced reactive oxygen species production in the rhizosphere and their role in biodegradation: The repair mechanism of symbiotic driving by Fe(II) and microorganisms.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140073},
doi = {10.1016/j.jhazmat.2025.140073},
pmid = {41066987},
issn = {1873-3336},
abstract = {Reactive oxygen species (ROS) are considered key drivers of biogeochemical processes. However, there is limited research on the factors influencing ROS generation in the rhizosphere due to polycyclic aromatic hydrocarbon (PAHs) pollution during plant-microbe joint remediation, as well as their role in biodegradation. This study demonstrated that exposure to pyrene at a concentration of 100 mg/kg significantly enhanced the release of hydrogen peroxide (H2O2), hydroxyl radicals (•OH), and superoxide anions (O2•[-]) in the rhizosphere of ryegrass during root development. The concentrations of these reactive oxygen species were 1.5-7.8 times higher than those in the control group. Additionally, the Fe(II) concentration increased by 37.5 ± 3.2 %, and the pyrene degradation rate reached 26.8 ± 1.4 %. These results indicate that pyrene serves as a major factor stimulating ROS generation in ryegrass. Among these processes, Fe(II) catalyzes the production of •OH, which directly attacks the benzene ring structure of pyrene. High-throughput analysis further revealed that ROS enhanced the diversity, cohesion, and robustness of the rhizosphere microbial community structure. Furthermore, Pseudomonas, Marmoricola, Nocardioides and Dietzia were identified as core microbial genera involved in pyrene degradation and ecological restoration. Metagenomics analysis suggests that rhizosphere microorganisms respond to ROS-induced oxidative stress by enhancing ATP synthesis, which provides energy for antioxidant-related protein production and damage repair, thereby accelerating pyrene degradation. These results elucidate the ROS-mediated driving mechanism behind microbial pyrene degradation in plant-microbe combined remediation systems, thereby providing a theoretical basis for optimizing bioremediation strategies for organically contaminated soils.},
}

@article {pmid41066873,
year = {2025},
author = {Hou, J and Liu, M and Li, Y and Li, L and Yao, Y and Xu, H and An, Y},
title = {Seed-borne and environmental transmission mechanisms drive diverse heavy metal-resistant plant growth-promoting bacteria (PGPB) in rice.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109840},
doi = {10.1016/j.envint.2025.109840},
pmid = {41066873},
issn = {1873-6750},
abstract = {Heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in mitigating heavy metal stress and reducing heavy metal accumulation in plants. However, the origins and transmission mechanisms of PGPB and their associated heavy metal resistance genes (MRGs) in plants remain unclear. To fill this knowledge gap, we collected rice and related environmental samples from heavy metal-contaminated paddy fields. The microbial DNA was recovered from these rice and environmental samples and then analyzed using shotgun metagenomics at the metagenome-assembled genomes (MAGs) level. As a result, 805 MRG-PGPB combinations were detected in rice tissues and related environments under heavy metal contamination conditions. Core MRG-PGPB combinations shared across seed-rice (42.46%) and environment-rice (13.34%) interfaces collectively constituted 55.80% of the detected combinations, demonstrating that environmental translocation and seed-borne vertical transmission jointly drive over half of MRG-PGPB colonization in rice systems. Subsequent source-tracking analysis indicated that PGPBs present in rice primarily originated from seeds, with a substantial proportion also attributed to translocation within rice tissues. Phylogenetic analysis of dominant MRGs further demonstrated the seed-borne vertical transmission of MRGs-PGPB, while simultaneously elucidating that MRGs harbored by PGPB in rice could also be acquired via horizontal gene transfer (HGT) from environmental or seed-borne MRG-PGPB, particularly from atmospheric microbes such as Methylophilus and Serratia. These findings provide valuable insights into harnessing PGPB to enhance rice resilience against heavy metal contamination, thereby contributing to improved food security and sustainable agricultural practices.},
}

@article {pmid41066697,
year = {2025},
author = {Li, Y and Gao, Y and Liu, X and Mao, Y and Wang, M and Qin, Y and Zhang, C and Chen, Q and Ning, K and Wang, Z and Han, M},
title = {Quantifying antibiotic resistome risks across environmental niches: the L-ARRAP for long-read metagenomic profiling.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
doi = {10.1093/bib/bbaf535},
pmid = {41066697},
issn = {1477-4054},
support = {82300645//National Natural Science Foundation of China/ ; 41877409//National Natural Science Foundation of China/ ; U23A2059//National Natural Science Foundation of China/ ; 2408085Y039//Outstanding Youth Program of Anhui Provincial Natural Science Foundation/ ; YQZD202406//Key Project for cultivating outstanding young teachers of Higher Education in Anhui Province/ ; tsqn202312094//Taishan Scholars Program of Shandong Province/ ; 2023KJ034//Shandong Provincial Higher Education Institution Youth Innovation Teams/ ; XJ201916//Grants for Scientific Research of BSKY/ ; 2022zhyx-B15//Anhui Medical University, Research Fund of Anhui Institute of translational medicine/ ; },
mesh = {Humans ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Metagenome ; Risk Assessment ; Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Feces/microbiology ; },
abstract = {The global dissemination of antibiotic resistance genes (ARGs) represents a critical challenge to One Health. Existing ARG risk assessment tools (e.g. MetaCompare, ARRI) are constrained by short-read sequencing data, limiting their utility for long-read platforms. To address this gap, we developed the Long-read based Antibiotic Resistome Risk Assessment Pipeline (L-ARRAP), which calculates the Long-read based Antibiotic Resistome Risk Index (L-ARRI) to quantify antibiotic resistome risks. Building upon our previous ARRI framework, L-ARRAP leverages long-read sequencing advantages to concurrently identify ARGs, mobile genetic elements, and human bacterial pathogens, integrating their interactions for risk scoring. Our results showed that L-ARRAP was not only able to accurately identify ARGs and evaluate the antibiotic resistance risk scores in samples of hospital wastewater (HWW), Chaohu lake, and human fecal samples, but also significantly distinguish the ARG risk in HWW samples between before and after disinfection groups, demonstrating the performance of L-ARRAP. Furthermore, L-ARRAP scores exhibited strong concordance with those generated by our laboratory-adapted MetaCompare variant (L-MetaCompare), corroborating its methodological reliability. Overall, to our knowledge, L-ARRAP is the first assessment pipeline of antibiotic resistome for long sequencing reads and has a great potential for monitoring the risk of ARGs in various environmental niches.},
}

Humans
*Metagenomics/methods
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Metagenome
Risk Assessment
Wastewater/microbiology
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
Feces/microbiology

@article {pmid41066275,
year = {2025},
author = {Mutafcilar Velioglu, E and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, S},
title = {Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.},
journal = {Journal of medical microbiology},
volume = {74},
number = {10},
pages = {},
doi = {10.1099/jmm.0.002065},
pmid = {41066275},
issn = {1473-5644},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Periodontitis/therapy/microbiology ; Middle Aged ; Adult ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; },
abstract = {Introduction. Intestinal dysbiosis is associated with systemic health, and approaches targeting the microbiome can influence the host. Oral and intestinal microbiota are interrelated; therefore, we aimed to determine whether non-surgical periodontal treatment (NSPT) affects systemic health through its impact on the intestinal microbiota.Hypothesis/Gap Statement. Although the association between oral and gut microbiota has been suggested, there is limited evidence regarding how periodontal therapy may influence intestinal microbial composition. We hypothesized that NSPT in patients with periodontitis would lead to favourable changes in the gut microbiome, which may parallel improvements in clinical periodontal parameters.Aim. This study aimed to investigate the effect of NSPT on both oral and intestinal microbiota and to evaluate whether changes in gut microbial composition correlate with periodontal clinical outcomes.Methodology. Five systemically healthy individuals with grade C periodontitis and five systemically and periodontally healthy individuals were included. Saliva and stool samples were collected at baseline and 1 month after NSPT. DNA extractions were performed and subjected to 16S ribosomal RNA gene sequencing on the Illumina Novaseq at the V3-V4 hypervariable regions.Results. Grade C periodontitis patients displayed distinct oral and gut microbiomes compared to healthy individuals. NSPT resulted in a reduction in the diversity of both saliva and stool samples in healthy individuals (P>0.05). Salivary Fusobacteriota levels (P<0.05) and the gut Firmicutes/Bacteroides ratio decreased after NSPT. Moreover, changes in gut microbiota significantly correlated with improvements in periodontal probing depth and clinical attachment level in periodontitis patients.Conclusion. The improvement in clinical periodontal parameters after NSPT correlates with a positive shift in the gut microbiome towards health. Although the number of participants was limited, these findings support a strong relationship between periodontal and gut status. Further studies with larger cohorts and long-term follow-up are required to confirm these results.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
*Periodontitis/therapy/microbiology
Middle Aged
Adult
Saliva/microbiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology

@article {pmid41066239,
year = {2025},
author = {Cook, RA and Ponsero, AJ and Telatin, A and Yang, Y and Liang, Z and Wang, F and Chen, R and Wang, Z and Adriaenssens, EM and Clokie, MRJ and Millard, AD and Brightling, CE},
title = {Bacteriophage diversity declines with COPD severity in the respiratory microbiome.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116413},
doi = {10.1016/j.celrep.2025.116413},
pmid = {41066239},
issn = {2211-1247},
abstract = {Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterized the lung DNA virome by re-analyzing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. While viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Comparing all COPD patients to controls, phages infecting anaerobic oral bacteria showed disproportionately lower abundance-Porphyromonas phages were 40-fold less abundant, despite only 4-fold lower bacterial abundance-while pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonized patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognized feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.},
}

@article {pmid41066109,
year = {2025},
author = {Zhou, T and Delgado-Baquerizo, M and Ren, C and He, N and Zhou, Z and He, Y},
title = {Soil microbial life history strategies covary with ecosystem multifunctionality across aridity gradients.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2511071122},
doi = {10.1073/pnas.2511071122},
pmid = {41066109},
issn = {1091-6490},
support = {202206600027//China Scholarship Council (CSC)/ ; 32522067//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Ecosystem ; *Desert Climate ; Soil/chemistry ; },
abstract = {Aridity thresholds shape ecosystem functions worldwide. Despite the importance of soil microbiomes in engineering ecosystem processes, the specific strategies employed by soil microbiomes to support ecosystem multifunctionality (EMF) across aridity gradients remain virtually unknown. Here, we investigated 474 soil samples across a continental-scale aridity gradient and identified an aridity threshold beyond which plot-level EMF declines sharply. Microbial habitat and decomposition functions were among the last to respond to aridity, with thresholds occurring under more arid conditions compared to plant productivity and soil fertility. Combining metagenomic sequencing with physiological assays to characterize microbial life history strategies of high yield (Y), resource acquisition (A), and stress tolerance (S), we introduce a microbial trait-based framework to mechanistically link community-level microbial life history strategies to EMF. Our results reveal that microbial Y-strategy is positively correlated with EMF across aridity gradients, A-strategy exhibits a negative association with EMF across aridity gradients, and S-strategy is negatively correlated with EMF in arid ecosystems. Collectively, this study offers empirical evidence and insights into how aridification interacts with soil microbiomes in shaping EMF, highlighting the pivotal role of microbial life history strategies in understanding the mechanisms behind EMF variation in an increasingly arid world.},
}

*Soil Microbiology
*Microbiota/physiology
*Ecosystem
*Desert Climate
Soil/chemistry

@article {pmid41065113,
year = {2025},
author = {Palacios, N and Gordon, S and Wang, T and Burk, R and Qi, Q and Huttenhower, C and Gonzalez, HM and Knight, R and De Carli, C and Daviglus, M and Lamar, M and Telavera, G and Tarraf, W and Kosciolek, T and Cai, J and Kaplan, RC},
title = {Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877251376911},
doi = {10.1177/13872877251376911},
pmid = {41065113},
issn = {1875-8908},
abstract = {BackgroundThere is limited work on the association between the gut microbiome and Alzheimer's disease and related dementia (AD/ADRD) in Latinos.ObjectiveWe examined, within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) cohort, the association between gut microbiome and cognitive function.MethodsWe analyzed the fecal metagenomes of 2471 HCHS/SOL participants to identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition.ResultsEubacterium species (E. siraeum and E. eligens), and C phoceensis, among other species were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition.ConclusionsIn a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.},
}

@article {pmid41064842,
year = {2025},
author = {Kuswandi, W and Budiman, C and Khaerunnisa, I and Sumantri, C},
title = {Rearing system and immune status influence the small intestinal microbiota of IPB-D3 chickens: A full-length 16S rRNA metagenomic approach.},
journal = {Veterinary world},
volume = {18},
number = {8},
pages = {2206-2221},
pmid = {41064842},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The small intestinal microbiota plays a pivotal role in poultry digestion and immune function. Rearing systems can influence their composition, thereby affecting the overall health and performance of the birds. This study aimed to investigate how rearing systems (intensive [IN] vs. free-range [FR]) and immune status, reflected by leukocyte profiles, influence the small intestinal microbiome of IPB-D3 chickens, a genetically improved Indonesian local breed.

MATERIALS AND METHODS: Ninety IPB-D3 chickens were reared for 12 weeks under either IN or FR systems. Hematological profiling was conducted to assess health status, with leukocyte counts used to stratify birds. Microbiota samples from the small intestine were analyzed using full-length 16S ribosomal RNA (V1-V9) sequencing on the Oxford Nanopore platform. Taxonomic identification was performed using the SILVA database. Statistical comparisons were made using t-tests, and microbial diversity was assessed through alpha and beta diversity metrics.

RESULTS: While most hematological parameters did not differ significantly between rearing systems, total leukocyte counts were higher in intensively reared chickens (p = 0.002). FR chickens exhibited significantly greater microbial diversity (p < 0.05) across multiple alpha diversity indices. A total of 1,294 unique species were identified in FR birds versus 720 in the IN group, with 1,761 shared species. Leukocyte level further influenced microbial profiles; chickens with high leukocyte (HL) counts were dominated by Ligilactobacillus aviarius, whereas low-leukocyte chickens had a higher abundance of Bacteroides caecigallinarum. Gallibacterium anatis, a potential pathogen, dominated in IN systems with elevated leukocytes.

CONCLUSION: This study demonstrates that both the rearing environment and immune status substantially influence small intestinal microbial composition in IPB-D3 chickens. FR systems promoted richer, more beneficial microbial communities, while IN systems, especially with HL levels, were associated with opportunistic pathogens. Leukocyte profiling may serve as a non-invasive biomarker for gut health, supporting future development of precision poultry management strategies and immune-responsive probiotics.},
}

@article {pmid41064771,
year = {2025},
author = {Giraldo-Badillo, I and Pineda-Vélez, E and Carbonell-Medina, BA and Ardila, CM},
title = {Microbiological and Pharmacological Aspects Involved in Dentin-Pulp Complex Regeneration: A Scoping Review.},
journal = {Journal of clinical and experimental dentistry},
volume = {17},
number = {9},
pages = {e1149-e1158},
pmid = {41064771},
issn = {1989-5488},
abstract = {BACKGROUND: The regeneration of the dentin-pulp complex represents a pivotal challenge in endodontics, requiring a delicate balance between microbial eradication and tissue repair. This scoping review, conducted in accordance with PRISMA-ScR guidelines, synthesizes current evidence on microbiological and pharmacological factors influencing regenerative outcomes.

MATERIAL AND METHODS: A systematic search of PubMed, Scopus, Web of Science, and Cochrane Library identified 242 studies, with 15 meeting inclusion criteria after screening.

RESULTS: The review highlights the dominance of anaerobic biofilm-forming pathogens (Enterococcus faecalis, Porphyromonas gingivalis) in periapical lesions, their virulence mechanisms (e.g., proteolytic enzymes, immune evasion), and the rising threat of antibiotic resistance driven by β-lactamases and efflux pumps. Pharmacologically, while triple/double antibiotic pastes promote dentin thickening, their cytotoxicity at high concentrations and disruption of commensal microbiota underscore the need for optimized dosing. Emerging alternatives-such as antimicrobial peptides, calcium hypochlorite, and immunomodulatory biomolecules-demonstrate superior biocompatibility and dual action against pathogens while supporting stem cell viability.

CONCLUSIONS: Future directions emphasize microbiome-targeted therapies, advanced biomaterials, and personalized approaches leveraging metagenomics. This review underscores the imperative to integrate selective antimicrobial strategies with regenerative biology to advance endodontic outcomes. Key words:Dentin-pulp regeneration, endodontic infections, biofilm, antimicrobial resistance, regenerative endodontics.},
}

@article {pmid41064045,
year = {2025},
author = {Zhao, S and Wang, F and Song, L and Zhu, S and Liu, S and Zhao, K and Liu, R and Li, YY},
title = {Interspecies electron transfer as one of key drivers of methanogenic consortia succession within quorum sensing regulation.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf165},
pmid = {41064045},
issn = {2730-6151},
abstract = {Robust interspecies interactions are essential for efficient methanogenesis in anaerobic digestion. This study investigated the impact of quorum sensing (QS) enhancement on the succession of methanogenic communities during anaerobic digestion. The QS stimulation via exogenous N-acyl-homoserine lactones enhanced methane production by 18.8%-22.1%. Moreover, QS shaped microbial community succession toward a more deterministic assembly, selectively enriching key syntrophs (Pelotomaculum, Smithella), and methanogens (Methanobacterium, Methanothrix). Metagenomic analysis revealed that QS induced genes related to transcription, transport, and cofactor biosynthesis instead of directly regulating carbon metabolism. In this context, interspecies electron transfer emerges as a critical factor regulating interspecies interactions under QS regulation. Specifically, QS enhancement boosted redox mediator secretion, and the concentration of 2-amino-3-carboxy-1,4-naphthoquinone and phenazine increased by 7.8- and 4.8-fold, respectively. QS enhancement also induced higher abundance of c-type cytochromes. Moreover, the higher electron transfer coefficients were detected with 40.2%-89.9% increase. Further, QS also enhanced relative abundance of genes involved in Complex I/III and ferredoxin-dependent hydrogenases, promoting electron flow from syntrophs to methanogens. These effects induced higher relative abundance of genes associated with syntrophic propionate/butyrate oxidation and hydrogenotrophic/acetotrophic methanogenesis. Collectively, given that the similar regulation pathway is widely distributed in anaerobes, these findings identify QS as a critical ecological signal that drives functional microbial succession.},
}

@article {pmid41063294,
year = {2025},
author = {Sun, S and Wang, H and Han, B and Wu, H and Wang, Y and Xu, T},
title = {Combined effects of low temperature, hyperosmolarity and seawater-conditioned pathogens on open fracture healing in a rat model simulating circumpolar environments.},
journal = {Journal of orthopaedic surgery and research},
volume = {20},
number = {1},
pages = {875},
pmid = {41063294},
issn = {1749-799X},
mesh = {Animals ; Rats, Sprague-Dawley ; Male ; *Seawater/microbiology/adverse effects ; Rats ; *Fracture Healing/physiology ; *Cold Temperature/adverse effects ; *Fractures, Open/microbiology/diagnostic imaging ; Disease Models, Animal ; *Femoral Fractures/microbiology/diagnostic imaging ; },
abstract = {OBJECTIVE: To investigate the factors influencing the healing of open fractures in circumpolar latitude region seawater immersion conditions.

MATERIALS AND METHODS: A femoral fracture model was established in ninety 6-to-8-week-old male Sprague-Dawley rats, randomly assigned to five groups (n = 18 per group): (1) fracture only, (2) fracture with circumpolar seawater immersion, (3) fracture with low-temperature isotonic solution immersion, (4) fracture with aseptic circumpolar seawater immersion, and (5) fracture with low-temperature aseptic circumpolar seawater immersion. Fractures were confirmed postoperatively by radiographs on days 7, 21, and 42. Micro-CT and H&E staining were performed on day 42 to assess bone healing. Bacterial cultures from internal fixation devices were analyzed on day 3. Blood samples were collected on days 3, 7, and 14 to assess leukocyte and neutrophil counts, and serum ALP and VEGF levels were measured on days 7, 14, and 21. Pathogenic microorganisms in the seawater were identified by metagenomic analysis. Fracture healing and callus formation rates were compared using the Log-rank test.

RESULTS: X-ray, micro-CT, and histological analyses revealed significantly impaired fracture healing in the group exposed to circumpolar seawater immersion compared to the fracture-only group (P < 0.05). Bacterial colony counts on internal fixation devices were highest in the circumpolar seawater group (P < 0.05). Leukocyte and neutrophil levels were significantly elevated in this group on days 3 and 7 (P < 0.05), with no significant differences observed on day 14 (P > 0.05). Serum ALP and VEGF levels were significantly reduced on days 7, 14, and 21 (P < 0.05), although ALP levels on day 21 showed no significant difference (P > 0.05). Log-rank analysis indicated that the bone union and callus maturation rates were significantly lower in the circumpolar seawater group compared to the other four groups. Metagenomic analysis identified Flavobacterium, Rhodobacter, and Bacteroides as the dominant pathogens in circumpolar seawater.

CONCLUSIONS: This study demonstrates that hyperosmolarity, low temperature, and exposure to opportunistic pathogens under circumpolar seawater conditions collectively delay open fracture healing. Among these factors, opportunistic pathogens exert the most significant impact, highlighting microbial contamination as the primary barrier to bone regeneration in such environments and providing direction for future therapeutic strategies.

CLINICAL TRIAL NUMBER: not applicable.},
}

Animals
Rats, Sprague-Dawley
Male
*Seawater/microbiology/adverse effects
Rats
*Fracture Healing/physiology
*Cold Temperature/adverse effects
*Fractures, Open/microbiology/diagnostic imaging
Disease Models, Animal
*Femoral Fractures/microbiology/diagnostic imaging

@article {pmid41062579,
year = {2025},
author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J},
title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35107},
pmid = {41062579},
issn = {2045-2322},
support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; },
mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Microbiota ; },
abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.},
}

China
*Museums
*Air Microbiology
*Bacteria/genetics/classification/isolation & purification/drug effects
Microbiota

@article {pmid41062543,
year = {2025},
author = {Prast-Nielsen, S and Granström, AL and Kiasat, A and Ahlström, G and Edfeldt, G and Rautiainen, S and Boulund, F and Andersson, FO and Lindberg, J and Schuppe-Koistinen, I and Gustafsson, UO and Engstrand, L},
title = {Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35039},
pmid = {41062543},
issn = {2045-2322},
mesh = {Humans ; *Bile Acids and Salts/blood ; *Gastrointestinal Microbiome ; *Crohn Disease/blood/microbiology ; *Colitis, Ulcerative/blood/microbiology ; Female ; Male ; Adult ; Biomarkers/blood ; Middle Aged ; *Inflammation/blood ; Case-Control Studies ; Feces/microbiology ; },
abstract = {Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.},
}

Humans
*Bile Acids and Salts/blood
*Gastrointestinal Microbiome
*Crohn Disease/blood/microbiology
*Colitis, Ulcerative/blood/microbiology
Female
Male
Adult
Biomarkers/blood
Middle Aged
*Inflammation/blood
Case-Control Studies
Feces/microbiology

@article {pmid41062510,
year = {2025},
author = {Feng, S and Zhang, B and Wang, H and Xiong, Y and Tian, A and Yuan, X and Pan, C and Guo, X},
title = {Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8934},
pmid = {41062510},
issn = {2041-1723},
support = {R15LM013460//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; },
mesh = {*Deep Learning ; *Proteomics/methods ; *Peptides/analysis ; Humans ; Gastrointestinal Microbiome ; Neural Networks, Computer ; Databases, Protein ; Metagenome ; },
abstract = {Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning-based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS[2]Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine.},
}

*Deep Learning
*Proteomics/methods
*Peptides/analysis
Humans
Gastrointestinal Microbiome
Neural Networks, Computer
Databases, Protein
Metagenome

@article {pmid41062486,
year = {2025},
author = {Tu, Z and Sun, H and Wang, T and Liu, Y and Xu, Y and Peng, P and Qin, S and Tu, C and He, B},
title = {Node role of wild boars in virus circulation among wildlife and domestic animals.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8938},
pmid = {41062486},
issn = {2041-1723},
mesh = {Animals ; *Sus scrofa/virology ; *Animals, Wild/virology ; Swine/virology ; *Animals, Domestic/virology ; China/epidemiology ; Disease Reservoirs/virology ; Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation & purification ; *Swine Diseases/virology ; Zoonoses/virology ; Phylogeny ; },
abstract = {Wild boars are considered pest animals in most of their distribution ranges, but their role as virus reservoirs has long been overlooked, with the circulation dynamics of their viruses rarely investigated. Here we prepared a data set, that is, BrCN-Virome, of 9281 viral metagenomes by pan-viromic analyses of 2535 organ and 274 blood samples from 466 healthy and 50 dead wild boars across 127 locations in 26 provincial regions of China. Compared to domestic pigs, BrCN-Virome shows different viromic composition, with a great expansion in the DNA virus diversity. Some wild boar viruses are traced to humans, domestic animals, wildlife, and arthropods, with several evidently or potentially related to epizootics or zoonoses. Pig pathogens spread widely in wild boars and are responsible for a substantial portion of wild boar mortality, with occurrences of co-infection with multiple African swine fever viruses. These results indicate that wild boars are a node animal connecting different animal taxa in the virus circulation network, and that their viruses not only pose a major threat to the pig industry but also challenge wildlife conservation and public health, highlighting the need for routine surveillance of wild boar viruses and active control of the wild boar population.},
}

Animals
*Sus scrofa/virology
*Animals, Wild/virology
Swine/virology
*Animals, Domestic/virology
China/epidemiology
Disease Reservoirs/virology
Virome/genetics
Humans
*Viruses/genetics/classification/isolation & purification
*Swine Diseases/virology
Zoonoses/virology
Phylogeny

@article {pmid41062001,
year = {2025},
author = {Ghaffar, T and Valeriani, F and Romano Spica, V},
title = {The Sex Related Differences in Health and Disease: A Systematic Review of Sex-Specific Gut Microbiota and Possible Implications for Microbial Pathogenesis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108094},
doi = {10.1016/j.micpath.2025.108094},
pmid = {41062001},
issn = {1096-1208},
abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.

METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.

RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.

CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.},
}

@article {pmid41061960,
year = {2025},
author = {Wang, H and Sheng, J and Zhang, Y and Lan, H and Lu, X and Li, X and Zhao, X},
title = {Detection of zoonotic Coxiella burnetii causing chronic Q fever endocarditis in a Chinese geriatric patient by mNGS.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.09.015},
pmid = {41061960},
issn = {2213-7173},
abstract = {OBJECTIVES: Q (query) fever, caused by Coxiella burnetii, is often linked to negative bacterial cultures. Infective endocarditis with negative cultures is difficult to diagnose and treat. Our case demonstrates that metagenomic next-generation sequencing (mNGS) can provide a rapid and accurate method for pathogenetic diagnosis in infectious diseases.

CASE PRESENTATION: We reported a case of infective endocarditis with negative blood cultures in a male patient with a history of sheep farming and previous aortic valve replacement (AVT) and atrial septal defect atrial septal defect (ASD) repair. Blood tests showed positive serum immunofluorescent antibodies to rickettsia, while mNGS of perivalvular abscess tissue suggested C. burnetii. Doxycycline 0.1 g q12h and hydroxychloroquine 0.2 g q12h were used for postoperative antibiotic treatment. The genome of the C. burnetii C2245173Z was assembled on the Illumina platform, and no known antibiotic resistance genes were detected. Phylogenetic analysis of C. burnetii genomes shows a genetic relationship between animal-derived strains and human-derived strains.

CONCLUSIONS: The application of mNGS could provide a rapid and accurate assay in clinical diagnosis and play a decisive role in the pathogenetic diagnosis of some infectious diseases. Doxycycline plus hydroxychloroquine remains an effective treatment for chronic Q fever endocarditis. In addition, phylogenetic tree analysis indicates that C. burnetii infection may pose a potential risk to humans working with livestock.},
}

@article {pmid41061540,
year = {2025},
author = {Zhang, L and Gao, X and Li, G and Xu, Z and Luo, W},
title = {Metagenomic insights to effective elimination of resistomes in food waste composting by lime addition.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140065},
doi = {10.1016/j.jhazmat.2025.140065},
pmid = {41061540},
issn = {1873-3336},
abstract = {Food waste contains abundant resistomes, including antibiotic and heavy metal resistance genes (ARGs and MRGs), which pose risks to the environment and human health. Composting can be used for food waste treatment, but it fails to effectively eliminate these resistomes. Thus, this study investigated the performance of lime to regulate the dynamics and mobility of ARGs and MRGs in food waste composting by metagenomics. Genome-resolved analysis was further conducted to identify the ARGs and MRGs hosts and their horizontal gene transfer (HGT) events. Results showed that lime addition at 1 % (wet weight) could significantly promote temperature and pH increase to sterilize hosts, particularly pathogen bacteria (e.g. Acinetobacter johnsonii and Enterobacter cloacae), thus reducing the abundance of resistomes by more than 57.1 %. This sterilization notably reduced the number of mobile ARGs and MRGs driven by mobile genetic elements (MGEs). The contribution of MGEs located on chromosomal sequences to horizontally transfer ARGs and MRGs was significantly higher than that on mobilizable plasmids. Further analysis indicated that the reduced resistomes by lime was mainly attributed to effective sterilization of hosts rather than decreased HGT diversity. Thus, this study provides valuable insights into use lime as a low-cost control of resistomes in waste recycling.},
}

@article {pmid41061488,
year = {2025},
author = {Yang, M and Huang, Y and Liu, J and Wang, G and Mei, Y and Ge, L and Du, Q and Li, H and Zhao, N},
title = {Characterisation of microbial succession and exploration of the stability maintenance strategy of phage community on microbes in radish paocai.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111479},
doi = {10.1016/j.ijfoodmicro.2025.111479},
pmid = {41061488},
issn = {1879-3460},
abstract = {Previous research focused on the safety control of phages in food. In recent years, numerous phages have been extensively characterised in fermented foods, where they change along with fermentation process but do not compromise product quality. However, the potential roles of phages in fermented foods remain unclear. Microbial steady state is critical for maintaining normal radish paocai fermentation. To explore stability maintenance strategies for phages, their structure and interactions with microbes were investigated across two microbial structural systems during fermentation. Microbial counts showed the absence of fungi in the non-steady-state environment (NE), whereas high fungal levels (6.78 ± 0.09 log colony-forming units/mL) were detected in the steady-state environment (SE). Metagenomic analysis revealed that microbial structure remained stable in SE but changed markedly in NE. Pediococcus ethanolidurans and Lactococcus lactis were the species that differed significantly between SE and NE. Microbial succession exhibited a significant association with physicochemical environments in NE (P < 0.05), whereas microbial abundance fluctuations were unaffected by physicochemical stress in SE. Caudoviricetes was identified as the dominant viral class. Cluster analysis showed that NE systems displayed high variability with dramatic shifts across multiple viral genera (Clusters 3-6). In NE, 25 lytic and 226 lysogenic phages were identified, while 3 lytic and 29 lysogenic phages were found in SE. Phage host prediction indicated preferential targeting of harmful bacteria (e.g., Escherichia) in NE, contrasted with phage predation on fermentation-associated lactic acid bacteria in SE. Genomic analysis indicated that Lactiplantibacillus abundance and its corresponding phages remained stable in SE but increased sharply in NE on day 3. Lactiplantibacillus phages isolated from NE and SE displayed strict host specificity at the strain level and exhibited potent lytic activity across different fermented food matrices. This study advances our understanding of steady-state maintenance mechanisms in vegetable fermentation systems and offers new insight for cross-system phage applications.},
}

@article {pmid41060906,
year = {2025},
author = {Sawyer, FM and Stossi, F and Nachman, E and Britton, RA and Bolt, MJ and Mancini, MA and Estes, MK and Blutt, SE},
title = {A pipeline for rapid, high-throughput imaging and quantitative analysis of human intestinal organoids.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332418},
doi = {10.1371/journal.pone.0332418},
pmid = {41060906},
issn = {1932-6203},
mesh = {Humans ; *Organoids/cytology/metabolism ; *Intestinal Mucosa/cytology ; *High-Throughput Screening Assays/methods ; Microscopy, Confocal/methods ; Image Processing, Computer-Assisted/methods ; *Intestines/cytology ; Cell Proliferation ; },
abstract = {Human intestinal organoids (HIOs) are a model system for studying human intestinal epithelium. Utilizing HIOs for high-throughput studies remains inefficient, as analyzing their cellular composition and responses to varying experimental conditions requires extensive time and labor. We describe a 96-well plate-based automated pipeline for rapidly imaging and quantifying fluorescent labeling in HIOs using a high-throughput confocal microscope and image analysis software. The pipeline was leveraged to quantify varying levels of cell proliferation among donor HIO lines in response to microbial products. Cytoplasmic fluorescence via antibody labeling was also quantified with the pipeline, enabling measurement of the prevalence of specific cell types in HIOs. This platform offers a novel approach to efficiently and rapidly image and quantify fluorescent staining and immunolabeling in HIOs and has many potential applications, including drug screening, toxicity testing, intestinal barrier integrity and transport studies, microbiome and host-pathogen interaction studies, and lineage tracking.},
}

Humans
*Organoids/cytology/metabolism
*Intestinal Mucosa/cytology
*High-Throughput Screening Assays/methods
Microscopy, Confocal/methods
Image Processing, Computer-Assisted/methods
*Intestines/cytology
Cell Proliferation

@article {pmid41060725,
year = {2025},
author = {Liu, Y and Tang, J and Wang, Y and Cui, F and Yang, Y},
title = {Intracranial infection caused by Mycoplasma hominis after neurosurgical operation: an easily overlooked but serious condition.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {9},
pages = {1425-1431},
doi = {10.3855/jidc.20729},
pmid = {41060725},
issn = {1972-2680},
mesh = {Humans ; Male ; *Mycoplasma hominis/isolation & purification/genetics ; *Mycoplasma Infections/diagnosis/drug therapy/microbiology ; Aged ; Anti-Bacterial Agents/therapeutic use ; *Neurosurgical Procedures/adverse effects ; *Postoperative Complications/microbiology/diagnosis/drug therapy ; },
abstract = {INTRODUCTION: Mycoplasma hominis (M. hominis) is a commensal that mainly colonizes in the microflora of the genitourinary tracts and is associated with urogenital tract infections. There are reports of central nervous system (CNS) infections in neonates caused by M. hominis. Nevertheless, M. hominis CNS infections in non-neonatal patients are extremely rare. Herein, we have reported a case of a man who suffered from intracranial infection secondary to M. hominis after neurosurgical operation. Additionally, we reviewed the relevant published literature to raise awareness on such infections and highlight the importance of proper treatments.

CASE PRESENTATION: A 68-year-old man underwent emergence craniotomy for intracerebellar hemorrhage. He presented with a moderate fever unresponsive to piperacillin-tazobactam on the seventh day after the surgery. His body temperature continued to increase, and he presented with signs of CNS infection. The antimicrobial therapy was switched to meropenem and vancomycin. No obvious reduction in the body temperature was observed. The cerebrospinal fluid (CSF) obtained previously revealed tiny point colonies which were morphologically consistent with M. hominis and subsequently confirmed by metagenomic next-generation sequencing (mNGS). Thus, M. hominis induced intracranial infection was diagnosed, and a combination therapy with moxifloxacin and minocycline was implemented. Fortunately, the patient's body temperature decreased to normal range after effective antibiotic therapy.

CONCLUSIONS: Based on the lesson of our case and a thorough review of published literature, the possibility of M. hominis induced CNS infections after neurosurgical intervention should not be ignored, especially when there is no response to standard antimicrobial therapy.},
}

Humans
Male
*Mycoplasma hominis/isolation & purification/genetics
*Mycoplasma Infections/diagnosis/drug therapy/microbiology
Aged
Anti-Bacterial Agents/therapeutic use
*Neurosurgical Procedures/adverse effects
*Postoperative Complications/microbiology/diagnosis/drug therapy

@article {pmid41060484,
year = {2025},
author = {Khan, MF},
title = {Enhancing stability of enzymes for industrial applications: molecular insights and emerging approaches.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {362},
pmid = {41060484},
issn = {1573-0972},
support = {82930-NP//University College Dublin/ ; },
mesh = {Enzyme Stability ; *Enzymes/chemistry/metabolism/genetics ; Protein Engineering/methods ; Hydrogen-Ion Concentration ; Biocatalysis ; Biotechnology ; },
abstract = {The growing demand for robust biocatalysts in industrial bioprocesses has intensified the pursuit of enzymes capable of functioning under extreme physicochemical conditions. This work critically examines the molecular determinants of enzyme stability, including thermostability, pH tolerance, halotolerance, resistance to solvents and oxidative stress, mechanical resilience to shear and pressure, and storage stability. These traits are essential for sustained catalytic performance in sectors such as bioenergy, pharmaceuticals, food, textiles, and environmental remediation. Recent advances in structure-guided engineering, molecular dynamics, and mutational profiling have enabled rational strategies to enhance enzyme resilience. By adopting a multi-parametric lens, this study bridges specific molecular adaptations with industrial challenges, offering a systems-level framework often lacking in single-condition analyses. It also explores emerging frontiers, including AI-assisted enzyme design, metagenomic discovery from extremophiles, and synthetic reconstruction of adaptive pathways, paving the way for next-generation biocatalysts optimised for scalability, performance, and sustainability. The novelty of this work lies in its integrative approach combining molecular insight, environmental origin, and computational tools to guide the development of industrially robust enzymes.},
}

Enzyme Stability
*Enzymes/chemistry/metabolism/genetics
Protein Engineering/methods
Hydrogen-Ion Concentration
Biocatalysis
Biotechnology

@article {pmid41060313,
year = {2025},
author = {Hays, MD and Fuchsman, CA},
title = {SAR11 ecotypes across ocean basins change with depth due to changes in light and oxygen.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf221},
pmid = {41060313},
issn = {1751-7370},
abstract = {SAR11 bacteria are ubiquitous and abundant heterotrophs that are important mediators of marine biogeochemical cycles. Within the SAR11 clade smaller ecotypes inhabit different ecological niches. Using metagenomic read placement onto a phylogenetic tree of RNA polymerase (rpoB), we were able to determine the distribution of different ecotypes both geographically and by depth. Our method avoids biases from the absence of quality sequenced genomes for deep SAR11 ecotypes. Depth profiles that range from the surface to the bathypelagic were analyzed at 30 stations in 6 ocean basins. In the euphotic zone, changes in the dominant primary producer from eukaryotic algae to cyanobacteria, did not cause the abundance of SAR11 to shift between stations. However, specific SAR11 ecotypes did correlate with eukaryotic phytoplankton (1a.3 and 1a.4) or picocyanobacteria (1b.2, 1b.4, and IIaB). In the lower euphotic and mesopelagic zones, group IIb.x was overwhelmingly the dominant species but group 1c was also present, and we found several new deep sub-ecotypes of 1b. The shift between the surface SAR11 community, dominated by 1a and surface 1b sub-ecotypes, and the mesopelagic ecotype groups, corresponded to the maximum decrease in the light-dependent proteorhodopsin/rpoB ratio, indicating that many deep ecotypes did not possess proteorhodopsin. This ecotype switch repeatedly corresponded to the maximum in Low Light I Prochlorococcus, leading to the hypothesis that changes in light motivates the ecotype switch. Environmentally abiotic factors like light and temperature appear to be determining factors in the SAR11 ecotype distribution throughout the global oceans.},
}

@article {pmid41060304,
year = {2025},
author = {Bueno de Mesquita, CP and Olm, MR and Bissett, A and Fierer, N},
title = {High strain-level diversity of Bradyrhizobium across Australian soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf222},
pmid = {41060304},
issn = {1751-7370},
abstract = {Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so abundant and prevalent across a wide range of soil types and environmental conditions. Here we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium, a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. Although members of the genus Bradyrhizobium were detected in >80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.},
}

@article {pmid41059692,
year = {2025},
author = {Bedi de Silva, A and Polson, SW and Schvarcz, CR and Steward, GF and Edwards, KF},
title = {Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258324},
doi = {10.1128/spectrum.02583-24},
pmid = {41059692},
issn = {2165-0497},
abstract = {Viruses that infect phytoplankton are an integral part of marine ecosystems, but the vast majority of viral diversity remains uncultivated. Here, we introduce four near-complete genomic assemblies of viruses that infect the widespread marine picoeukaryote Micromonas commoda, doubling the number of reported genomes of Micromonas dsDNA viruses. All host and virus isolates were obtained from tropical waters of the North Pacific, a first for viruses infecting green algae in the order Mamiellales. Genome length of the new isolates ranges from 205 to 212 kb, and phylogenetic analysis shows that all four are members of the genus Prasinovirus. Three of the viruses form a clade that is adjacent to previously sequenced Micromonas viruses, while the fourth virus is relatively divergent from previously sequenced prasinoviruses. We identified 61 putative genes not previously found in prasinovirus isolates, including a phosphate transporter and a potential apoptosis inhibitor novel to marine viruses. Forty-eight genes in the new viruses are also found in host genome(s) and may have been acquired through horizontal gene transfer. By analyzing the coding sequences of all published prasinoviruses, we found that ~25% of prasinovirus gene content is significantly correlated with host genus identity (i.e., Micromonas, Ostreococcus, or Bathycoccus), and the functions of these genes suggest that much of the viral life cycle is differentially adapted to the three host genera. Mapping of metagenomic reads from global survey data indicates that one of the new isolates, McV-SA1, is relatively common in multiple ocean basins.IMPORTANCEThe genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.},
}

@article {pmid41059690,
year = {2025},
author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A},
title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0129125},
doi = {10.1128/spectrum.01291-25},
pmid = {41059690},
issn = {2165-0497},
abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.},
}

@article {pmid41059063,
year = {2025},
author = {Hu, J and Cyle, KT and Yuan, W and Shi, W},
title = {Metagenomic evidence clarifies the texture-dependent cascading effects of organic degradation on soil hypoxia and N2O emission.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670657},
pmid = {41059063},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil pore-scale aeration is a crucial yet often overlooked factor influencing the effectiveness of nitrous oxide (N2O) emission mitigation strategies. Our previous work revealed a hundred-fold variation in N2O emissions among soils under apparently aerobic conditions and texture-dependent mitigation effects of biochar-manure co-compost (BM) compared to manure compost (M).

METHODS: We analyzed soils of three textures-clay loam (CL), silt loam (SL), and sand (SA)-amended with BM or M. Metagenomic sequencing was used to profile microbial community composition and functional genes, with a focus on aeration-sensitive taxa and pathways.

RESULTS: We demonstrate that these changes of N2O emissions are aligned with variations in aeration-sensitive microbes and genes. SA, with the highest N2O emissions, was most abundant in obligate and facultative anaerobes and denitrification-related genes, while CL, with the lowest emissions, had more genes related to fermentation and dissimilatory nitrate reduction. Compared to M, BM in CL favored genes for microbial processes requiring a more reducing environment, likely because biochar-induced finer pores, exacerbating oxygen diffusion limitations. This severe oxygen restriction in CL after BM addition was substantiated by greater reductions in CO2 efflux and C-cycling genes than in the other soils.

DISCUSSION: Our findings suggest that hypoxic pore abundance and the severity of pore anaerobiosis imparted by degradation of organic amendments varied with soil texture and are the overriding factors of soil greenhouse gas (GHG) emissions. Metagenomic traits provide a sensitive tool for detecting pore-scale environmental shifts, improving our mechanistic understanding of soil-dependent GHG emissions following organic amendments.},
}

@article {pmid41059058,
year = {2025},
author = {Wang, Y and Bai, Z and Liu, Y and Wang, Y and Xu, J and Lai, Z},
title = {Influence of the gut microbiota on the pharmacokinetics of tacrolimus in liver transplant recipients: insights from microbiome analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1616985},
pmid = {41059058},
issn = {1664-302X},
abstract = {INTRODUCTION: Tacrolimus is crucial for immunosuppression after liver transplantation, but its pharmacokinetics vary markedly among individuals. Emerging evidence suggests that the gut microbiota may influence its metabolism, although the underlying mechanisms remain unclear.

METHODS: This study analyzed the fecal microbiota from 38 postliver transplant patients and 31 healthy controls via 16S rDNA amplicon and shotgun metagenomic sequencing. Patients were stratified into three groups on the basis of oral tacrolimus dosage and blood concentration: LDLBC (low dose, low blood concentration), LDHBC (low dose, high blood concentration), and SDLBC (standard dose, low blood concentration).

RESULTS: Posttransplant patients presented significantly reduced gut microbial diversity. Specific bacterial taxa, including Enterococcus raffinosus, Intestinibacter bartlettii, and Bacteroides fragilis, were enriched in patients with lower tacrolimus blood concentrations. In contrast, Phascolarctobacterium faecium and Streptococcus salivarius were associated with increased drug levels. Functional analysis revealed differences between patient subgroups in ATP-binding cassette (ABC) transporters and drug efflux pumps, suggesting a potential microbial influence on tacrolimus absorption and metabolism. Additionally, antibiotic resistance genes were more abundant in patients with lower tacrolimus blood concentrations, particularly in the Escherichia coli-enriched groups.

DISCUSSION: These findings underscore the influence of the gut microbiota on tacrolimus pharmacokinetics and support the potential of microbial composition as a biomarker for optimizing immunosuppressive therapy.},
}

@article {pmid41059040,
year = {2025},
author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q},
title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1637352},
pmid = {41059040},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; },
abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.

METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by α-diversity, β-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.

RESULTS: Overall, no significant differences in viral and bacterial α- or β-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.

CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.},
}

Humans
*Respiratory Tract Infections/virology/microbiology/complications
*Metagenomics
Male
Middle Aged
Female
Bacteria/classification/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
*Virome
Bronchoalveolar Lavage Fluid/virology/microbiology
Microbiota
Aged
*Respiratory Insufficiency/virology/microbiology
Adult

@article {pmid41059035,
year = {2025},
author = {Huang, Y and Zhang, M and Tian, Y and Lan, X and Jin, W and Bai, Y and Zang, Q and Chen, M and Su, Z and Zhang, W and Aishan, G and Geng, M and Xie, J and Tong, P},
title = {A novel broad-spectrum lytic phage vB_EcoM_P3322: isolation, characterization, and therapeutic potential against avian pathogenic Escherichia coli.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1645263},
pmid = {41059035},
issn = {2235-2988},
mesh = {Animals ; *Escherichia coli/virology/pathogenicity ; *Escherichia coli Infections/therapy/veterinary/microbiology ; *Myoviridae/isolation & purification/classification/ultrastructure/genetics/physiology ; Host Specificity ; *Phage Therapy/methods ; Wastewater/virology ; *Coliphages/isolation & purification/classification/ultrastructure/physiology/genetics ; Columbidae/microbiology ; Genome, Viral ; Phylogeny ; Poultry Diseases/therapy/microbiology ; Hydrogen-Ion Concentration ; },
abstract = {INTRODUCTION: The widespread misuse of antibiotics has accelerated the emergence of multidrug-resistant bacterial strains, presenting a major threat to global public health. Bacteriophages (phages), owing to their host-specific lytic activity and self-replicating nature, have emerged as promising alternatives or adjuncts to conventional antibiotic therapies.

METHODS: In this study, a lytic phage targeting avian pathogenic Escherichia coli (APEC) was isolated from farm wastewater. The phage's morphological characteristics, host range, optimal multiplicity of infection (MOI), one-step growth curve, pH stability, thermal stability, chloroform sensitivity, and in vitro antibacterial activity were determined. Subsequently, the therapeutic efficacy of the phage was evaluated in a pigeon model.

RESULTS: In this study, we isolated and characterized a lytic phage, designated vB_EcoM_P3322, from farm wastewater targeting APEC. Transmission electron microscopy classified vB_EcoM_P3322 within the Myoviridae family. The phage exhibited broad lytic activity against five Escherichia coliserotypes (O8:H10, O15:H18, O51:H20, O149:H20, and O166:H6). Optimal biological parameters included a multiplicity of infection (MOI) of 1, a latent period of 10 minutes, an 80-minute burst period, and a burst size of 252 PFUs/cell. vB_EcoM_P3322 maintained stable lytic activity across a pH range of 5-9 and temperatures from 4°C to 50°C, although it was sensitive to chloroform. In vitro, the phage effectively suppressed bacterial growth within 6 hours at MOIs of 0.1, 1, and 10. Whole-genome sequencing revealed a 151,674 bp double-stranded DNA genome encoding 279 predicted open reading frames. No virulence factors, toxin genes, antibiotic resistance genes, or lysogeny-related elements were identified, affirming its safety for therapeutic application. Phylogenetic analysis indicated 98.44% nucleotide identity (97% coverage) with phage vB_EcoM_Ro121c4YLVW (GenBank: NC_052654), suggesting a close evolutionary relationship. In a pigeon infection model, vB_EcoM_P3322 treatment significantly improved survival and reduced histopathological damage in the liver and spleen. Metagenomic analysis of duodenal contents revealed a marked reduction (P < 0.01) in E. coli abundance in the treatment group, indicating selective pathogen clearance and modulation of gut microbiota.

DISCUSSION: In summary, vB_EcoM_P3322 displays broad-spectrum lytic activity, robust environmental stability, potent antibacterial efficacy both in vitro and in vivo, and a safe genomic profile. These attributes support its potential as a novel biocontrol agent for managing APEC infections in poultry farming.},
}

Animals
*Escherichia coli/virology/pathogenicity
*Escherichia coli Infections/therapy/veterinary/microbiology
*Myoviridae/isolation & purification/classification/ultrastructure/genetics/physiology
Host Specificity
*Phage Therapy/methods
Wastewater/virology
*Coliphages/isolation & purification/classification/ultrastructure/physiology/genetics
Columbidae/microbiology
Genome, Viral
Phylogeny
Poultry Diseases/therapy/microbiology
Hydrogen-Ion Concentration

@article {pmid41058886,
year = {2025},
author = {Liu, Y and Li, L and Yang, L and Yang, Y and An, H and Li, D and Wang, X},
title = {Clinical Features and Treatment Strategies of Q Fever Spinal Infection: A Pooled Analysis of 39 Cases and Narrative Review of the Literature.},
journal = {Open forum infectious diseases},
volume = {12},
number = {10},
pages = {ofaf584},
pmid = {41058886},
issn = {2328-8957},
abstract = {BACKGROUND: The incidence of spinal infections is increasing; However, pathogen identification remains challenging. Although Q fever spinal infection is reported infrequently, its accrual incidence is likely underestimated. The causative agent, Coxiella burnetii, cannot be routinely cultured. Consequently, physicians often misdiagnose Q fever spinal infection as spinal tuberculosis, leading to severe patient harm. Thus, improving clinicians' awareness of the clinical characteristics of Q fever spinal infection is urgently needed.

METHODS: We present a case of Q fever spinal infection and conducted literature searches in PubMed and the Chinese core journals of the Wanfang Database using keywords including "Q fever," "Coxiella burnetii," "spinal infection," "osteomyelitis," "spondylodiscitis," and "psoas abscess." Additional reports were identified through cross-referencing, with a cutoff date of 6 November 2024. Cases were included if patient age, sex, and baseline medical history were documented. Clinical data were retrospectively analyzed, and clinical features were compared between the aneurysm-associated group and the isolated spinal infection group. Fisher's exact probability test was used to evaluate the incidence difference.

RESULTS: A total of 39 adult patients were enrolled (mean age: 67.82 ± 10.51 years, male: 34,87.2%), Eleven cases reported potential pathogen exposure. Thirty-three cases presented with early-onset of lower back pain, and 13 developed fever during the disease course. Thirty-four cases involved the lumbar spine, exhibiting continuous lesions of 1-3 vertebral bodies, with imaging features of vertebral osteomyelitis, discitis, paravertebral soft-tissue swelling, and/or adjacent aneurysmal changes. Among 21 cases with routine blood tests, 2 showed elevated leukocyte counts, 5 had mild anemia, and the remainder were normal. Serological testing was performed in 34 cases, with 29 testing positive on the first time; PCR testing was conducted in 25 cases, with 23 cases detecting positive specimens; and rapid diagnosis confirmed in all 3 cases via metagenomic next-generation sequencing (mNGS). Inflammatory reactions were identified in all 21 biopsied cases, with inflammatory granulomas reported in 7 and explicitly excluded in 4. There were 24 cases complicated with aneurysm and 15 cases with isolated spinal infection. A significant difference in CRP elevation rate was observed between the two groups (14/15, 93.33% vs 4/8, 50.00%, P = .033). Early local lesion debridement combined with doxycycline-based multidrug therapy showed favorable outcomes. Serological monitoring demonstrated low sensitivity for assessing therapeutic efficacy.

CONCLUSIONS: This study systematically summarizes the clinical characteristics of Q fever spinal infection and, for the first time, reports features associated with its distinct clinical subtypes. Q fever should be considered in case of chronic spinal infections-especially those complicated with vascular lesions. Based on clinical history evaluation, rapid diagnosis may be achieved through mNGS of specimens from local lesions. Combined with early initiation of doxycycline-based regimens, timely debridement of necrotic tissues and purulent material may improve treatment outcomes. Further investigations are needed to identify reliable biomarkers for monitoring therapeutic efficacy and to establish optimal treatment strategies for subtypes of Q fever spinal infection.},
}

@article {pmid41058622,
year = {2025},
author = {Cai, ZZ and Zeng, DM and Lei, LW and Xiao, S},
title = {Rotavirus gastroenteritis complicating meningitis caused by Bacteroides uniformis detected using mNGS: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1601953},
pmid = {41058622},
issn = {2296-858X},
abstract = {This case report describes a rare instance of pediatric meningitis caused by Bacteroides uniformis (B. uniformis) following rotavirus gastroenteritis in a 1-year-4-month-old boy, diagnosed using metagenomics next-generation sequencing (mNGS). Bacterial meningitis (BM) is a life-threatening disease in children, particularly those under 5 years old, and early identification of the pathogen is crucial for reducing mortality and improving prognosis. B. uniformis, a Gram-negative, non-spore-forming, obligate anaerobic bacillus and common gut commensal, is rarely implicated in human infections, particularly pediatric meningitis. The child presented with vomiting, diarrhea, convulsions, and syncope, and was initially treated for meningitis and rotavirus gastroenteritis. Despite negative bacterial cultures, mNGS identified B. uniformis in the cerebrospinal fluid (CSF). Treatment was switched from ceftriaxone to meropenem (0.45 g, IV every 8 h) based on its good blood-brain barrier penetration and likely susceptibility of B. uniformis. The child's condition improved significantly, with follow-up lumbar puncture showing normal CSF parameters and no detectable pathogens. The case suggests that rare anaerobic meningitis may occur against the backdrop of rotavirus gastroenteritis and underscores the importance of using mNGS for accurate pathogen detection in bacterial meningitis, as well as the need for early initiation of appropriate antimicrobial therapy.},
}

@article {pmid41058503,
year = {2025},
author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA},
title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {231},
pages = {20250183},
doi = {10.1098/rsif.2025.0183},
pmid = {41058503},
issn = {1742-5662},
support = {//Agencia Estatal de Investigación/ ; },
mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; },
abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.},
}

*Models, Biological
*Ecosystem
Bayes Theorem
*Microbiota
Humans

@article {pmid41058431,
year = {2025},
author = {Jiménez-Arroyo, C and Molinero, N and Del Campo, R and Delgado, S and Moreno-Arribas, MV},
title = {Human gut microbiome study through metagenomics: Recent advances and challenges for clinical implementation.},
journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eimce.2025.09.011},
pmid = {41058431},
issn = {2529-993X},
abstract = {Metagenomics has decisively advanced the study of the gut microbiome, enabling a better understanding of its importance for human health. Metataxonomics, based on the sequencing of the 16S rRNA gene, provides taxonomic profiles of prokaryotes, while shotgun metagenomics allows a comprehensive characterization of all DNA present in a sample. With adequate sequencing depth, the latter increases taxonomic resolution to the strain level and provides detailed information on the functional potential of the microbiota. However, the lack of standardization in sample collection and processing, sequencing technologies, and data management limits the comparability of results and their implementation in clinical laboratories. This review offers a practical and updated framework on metagenomic methodologies, data analysis, and the application of artificial intelligence tools, highlighting advances and best practices to facilitate the integration of functional microbiome analysis into clinical practice and to overcome current challenges.},
}

@article {pmid41057946,
year = {2025},
author = {Ren, Y and Wu, YH and Chen, J and Luo, ZH and Xu, XW},
title = {New insights into the evolution and metabolism of the bacterial phylum Candidatus Acidulodesulfobacteriota through metagenomics.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {127},
pmid = {41057946},
issn = {2524-6372},
support = {42376133//National Natural Science Foundation of China/ ; 2021YFF0501303//National Key R&D Program of China/ ; },
abstract = {Candidatus Acidulodesulfobacterales, a formerly proposed bacterial order within the Deltaproteobacteria lineage, represents an ecologically significant group in sulfur-rich environments. Their diversity and functional potential in artificial acid mine drainage (AMD) ecosystems have been well studied; however, their distribution and ecological role in marine hydrothermal sulfides remain poorly understood. Here we integrated publicly available metagenome-assembled genomes (MAGs) with a newly reconstructed MAG from hydrothermal sulfides to perform comprehensive phylogenetic, metabolic, and host-virus interaction analyses. Phylogenomic and 16S rRNA gene analyses indicated that this lineage represents a distinct phylum-level clade, leading us to propose the designation Ca. Acidulodesulfobacteriota. Metabolic reconstructions indicated a versatile lifestyle, encompassing pathways for carbon fixation, nitrogen fixation, sulfur metabolism, iron oxidation, and hydrogen oxidation. Notably, the concatenated DsrAB protein phylogeny and the mixed enzyme types involved in Dsr-dependent dissimilatory sulfur metabolism suggest that Ca. Acidulodesulfobacteriota may represent a transitional lineage in the evolutionary shift from reductive to oxidative Dsr metabolism. Viral auxiliary metabolic genes (AMGs) associated with this phylum were predicted to modulate host metabolic pathways, including folate biosynthesis and sulfur metabolism, highlighting intricate host-virus interactions. These findings advance our understanding of the evolution, metabolic potential, and ecological roles of Ca. Acidulodesulfobacteriota in biogeochemical cycling.},
}

@article {pmid41057624,
year = {2025},
author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y},
title = {Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.},
journal = {NPJ digital medicine},
volume = {8},
number = {1},
pages = {599},
pmid = {41057624},
issn = {2398-6352},
support = {2023YFC2308300//Key Technologies Research and Development Program/ ; 82472371//National Natural Science Foundation of China/ ; },
abstract = {Recent advances in unbiased metagenomic next-generation sequencing (mNGS) enable simultaneous examination of microbial and host genetic material. We developed a multimodal machine learning-based diagnostic approach to differentiate lung cancer and pulmonary infections by analyzing 402 bronchoalveolar lavage fluid (BALF) mNGS datasets, including lung cancer (n = 123), bacterial infections (n = 114), fungal infections (n = 79), and pulmonary tuberculosis (n = 86). The training cohort revealed differences in microbial profiles, bacteriophage abundance, host gene and transposable element expression, immune cell composition, and tumor fraction derived from copy number variation (CNV). The integrated model (Model VI) achieved an AUC of 0.937 (95% CI, 0.910-0.964) in the training cohort and 0.847 (95% CI, 0.776-0.918) in the test cohort. A rule-in/rule-out strategy further improved accuracy in differentiating lung cancer from tuberculosis (accuracy = 0.896), fungal (accuracy = 0.915), and bacterial (accuracy = 0.907) infections. These findings highlight the potential of mNGS-based multimodal analysis as a cost-effective tool for early and accurate differential diagnosis.},
}

@article {pmid40631202,
year = {2025},
author = {Palmer, SN and Mishra, A and Gan, S and Liu, D and Koh, AY and Zhan, X},
title = {Identifying Optimal Machine Learning Approaches for Human Gut Microbiome (Shotgun Metagenomics) and Metabolomics Integration with Stable Feature Selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.21.660858},
pmid = {40631202},
issn = {2692-8205},
support = {U01 AI169298/AI/NIAID NIH HHS/United States ; T32 AI005284/AI/NIAID NIH HHS/United States ; R01 GM126479/GM/NIGMS NIH HHS/United States ; R56 HG011035/HG/NHGRI NIH HHS/United States ; P01 AI179406/AI/NIAID NIH HHS/United States ; R01 HG011035/HG/NHGRI NIH HHS/United States ; },
abstract = {UNLABELLED: Microbiome research has been limited by methodological inconsistencies. Taxonomy-based profiling presents challenges such as data sparsity, variable taxonomic resolution, and the reliance on DNA-based profiling, which provides limited functional insight. Multi-omics integration has emerged as a promising approach to link microbiome composition with function. However, the lack of standardized methodologies and inconsistencies in machine learning strategies has hindered reproducibility. Additionally, while machine learning can be used to identify key microbial and metabolic features, the stability of feature selection across models and data types remains underexplored, despite its importance for downstream experimental validation and biomarker discovery. Here, we systematically compare Elastic Net, Random Forest, and XGBoost across five multi-omics integration strategies: Concatenation, Averaged Stacking, Weighted Non-negative Least Squares (NNLS), Lasso Stacking, and Partial Least Squares (PLS), as well as individual omics models. We evaluate performance across 588 binary and 735 continuous models using human gut microbiome-derived metabolomics and taxonomic data derived from metagenomics shotgun sequencing data. Additionally, we assess the impact of feature reduction on model performance and feature selection stability. Among the approaches tested, Random Forest combined with NNLS yielded the highest overall performance across diverse datasets. Tree-based methods also demonstrated consistent feature selection across data types and dimensionalities. These results demonstrate how integration strategies, algorithm selection, data dimensionality, and response type impact both predictive performance and the stability of selected features in multi-omics microbiome modeling.

KEY POINTS: A total of 1,323 models were developed to comprehensively evaluate prediction performance and the robustness of feature selection for human gut microbiome (metabolomics and taxonomy from metagenomics shotgun sequencing) datasets. These models included three widely used machine learning algorithms - Elastic Net, Random Forest and XGBoost - applied across five integration strategies and single-omics approaches on datasets with binary and continuous outcomes.For continuous outcomes, Random Forest combined with NNLS integration achieved the highest performance and maintained strong predictive performance across full-dimensional and feature-reduced datasets.For binary outcomes, Random Forest consistently performed well regardless of the integration strategy. Notably, single-omics models, especially those using metabolomics data, outperformed integrative approaches.Tree-based models demonstrated greater consistency in feature selection across different dimensionalities and integration strategies.},
}

@article {pmid39764050,
year = {2025},
author = {Nasr, E and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, K and Ferrari, E and Griffin, TJ and Gruening, B and Hiltemann, S and Hyde, CJ and Jagtap, P and Mehta, S and Métris, KL and Momin, S and Nelson, TM and Oba, A and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, A and Van Heusden, P and Vohra, M and , and Zierep, P and Batut, B},
title = {Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.23.629682},
pmid = {39764050},
issn = {2692-8205},
support = {U24 AI183870/AI/NIAID NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; },
abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyze it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab: a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbial science. The Microbiology Galaxy Lab enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org, .eu, .org.au, .fr).},
}

@article {pmid41059288,
year = {2023},
author = {Cameron, ES and Blaxter, ML and Finn, RD},
title = {plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets.},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {475},
pmid = {41059288},
issn = {2398-502X},
abstract = {The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes.},
}

@article {pmid41056780,
year = {2025},
author = {Chang, X and Ma, Y and Zhang, J and Wang, T and Li, H and Wang, L},
title = {Size-specific effects of polyethylene microplastics (100-10,000 nm) on the soil resistome and pathogens revealed via metagenomics and machine learning.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127517},
doi = {10.1016/j.jenvman.2025.127517},
pmid = {41056780},
issn = {1095-8630},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are widespread, persistent environmental contaminants. However, the influence of MP particle size on ARGs dissemination and soil ecosystem health remains unclear. Herein, polyethylene MPs of three sizes (100, 1,000, and 10,000 nm) were incubated in ARG-contaminated soils for 45 days to evaluate their effects on soil physicochemical properties, microbial communities, ARGs, mobile genetic elements (MGEs), and pathogen abundance. MP exposure significantly increased soil water (up to 4.07-fold), total nitrogen (up to 50.34 %), and ammonium nitrogen (up to 38.54 %) contents. Conversely, soil organic carbon content decreased with increasing MP size. MPs markedly reduced the activities of key enzymes, including alkaline phosphatase (by 87.65 %), sucrase (by 10.96 %), and urease (by 54.17 %). Microbial α-diversity increased; however, the abundance of potentially pathogenic Pseudomonadota increased by up to 41.88 %, whereas that of beneficial Actinobacteria and Chloroflexi declined. MPs promoted the expression of 44 ARGs and 15 MGEs, with smaller MPs exhibiting stronger enrichment. They also increased the expression of virulence factors and the abundance of human- and plant-associated pathogens. Random forest modeling revealed that smaller MPs primarily drove these changes by altering soil physicochemical properties and microbial dynamics. Collectively, these findings demonstrate that MPs, especially smaller particles, simultaneously alter soil chemistry, suppress enzyme activities, reshape microbial communities, and enhance ARGs expression and pathogen proliferation, underscoring their significant ecological and human health risks in agricultural soils.},
}

@article {pmid41056245,
year = {2025},
author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N},
title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333676},
doi = {10.1371/journal.pone.0333676},
pmid = {41056245},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; },
abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.},
}

Humans
Male
Female
*Dysbiosis/microbiology
*Ischemic Attack, Transient/microbiology
*Microbiota/genetics
Middle Aged
Case-Control Studies
Aged
*Ischemic Stroke/microbiology
RNA, Ribosomal, 16S/genetics
Prospective Studies
Saliva/microbiology
Bacteria/genetics/classification
*Mouth/microbiology

@article {pmid41056240,
year = {2025},
author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS},
title = {Dysglycemia and the airway microbiome in cystic fibrosis.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331847},
doi = {10.1371/journal.pone.0331847},
pmid = {41056240},
issn = {1932-6203},
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; },
abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).

METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.

RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p = 0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p = 0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p = 0.056 and 1.11 [0.58, 1.64] unadjusted p= < .001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p = 0.001 for each 10% increase in virome score).

CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.},
}

Humans
*Cystic Fibrosis/microbiology/complications
*Microbiota
Male
Female
Adult
Sputum/microbiology
*Diabetes Mellitus/microbiology/etiology
Glucose Tolerance Test
Young Adult
Lung/microbiology
Respiratory Function Tests
Pseudomonas aeruginosa

@article {pmid41055380,
year = {2025},
author = {Du, J-Y and Zhang, Z-J and Tan, L and Yang, J-Y and Yang, R-N and Chen, Y-L and Tan, G-F and Li, J and Li, W-J and Yang, L and Cai, J and Shen, D-L and Zhu, H-R and Fan, Z-X and Yuan, M-L and Zhang, W},
title = {Gut microbiota dysbiosis and metabolic perturbations of bile/glyceric acids in major depressive disorder with IBS comorbidity.},
journal = {mBio},
volume = {},
number = {},
pages = {e0244725},
doi = {10.1128/mbio.02447-25},
pmid = {41055380},
issn = {2150-7511},
abstract = {Major depressive disorder (MDD) and irritable bowel syndrome (IBS) exhibit high comorbidity, yet their shared pathophysiology remains unclear. Previous studies have primarily focused on the psychological health in the IBS population, without considering psychiatric diagnoses or stratifying different psychological states, potentially leading to biased findings. This study employed multi-omics approaches to characterize gut microbiota and serum metabolites in 120 MDD patients (47 with IBS and 73 without IBS) and 70 healthy controls (HCs). MDD with IBS patients showed significantly higher depression (Hamilton depression scale [HAMD-17]) and anxiety (Hamilton anxiety scale [HAMA-14]) scores than MDD-only patients (P < 0.05). Metagenomic sequencing of fecal samples revealed increased alpha diversity (Chao1/Shannon indices) and Firmicutes dominance in both MDD groups vs HC, while Actinobacteria enrichment specifically marked MDD with IBS. Functionally, MDD with IBS uniquely activated D-amino acid/glycerolipid metabolism pathways (Kyoto Encyclopedia of Genes and Genomes). Serum metabolomics identified comorbid-specific perturbations: downregulation of bile acids (CDCA, GCDCA, GCDCA-3S) and upregulation of glyceric acid/glutaconic acid. Our study also found that Eggerthella lenta and Clostridium scindens are differentially abundant bacteria that are involved in bile acid metabolism, and that microbial genes (e.g., K03738) are associated with glyceric acid production. These findings implicate gut microbiota-driven bile acid/glyceric acid dysregulation in MDD with IBS comorbidity, supporting the gut-brain axis as a therapeutic target for probiotics or microbiota transplantation.IMPORTANCEMajor depressive disorder (MDD) exhibits a high comorbidity rate with irritable bowel syndrome (IBS). Our study, conducted on 120 MDD patients (47 of whom were comorbid with IBS) and a control group of 70 individuals, revealed that MDD-IBS comorbid patients demonstrated significantly higher depression/anxiety scores. Multi-omics analysis indicated substantial alterations in the gut microbiota (e.g., Firmicutes, Actinobacteria) and serum metabolites (e.g., bile acids, glyceric acid) among MDD-IBS patients, which were associated with specific metabolic pathways. Therefore, the new aspect of this study was the inclusion of patients with MDD but without IBS symptoms, which provided a deeper understanding of the intestinal microbiota dysregulation associated with comorbid IBS and MDD. These findings suggest that there may be involvement of the gut-brain axis, providing new research directions for potential therapeutic targets.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2100041598.},
}

@article {pmid41055333,
year = {2025},
author = {Sharma, S and Narahari, HP and Raman, K},
title = {Harnessing machine learning for metagenomic data analysis: trends and applications.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0164224},
doi = {10.1128/msystems.01642-24},
pmid = {41055333},
issn = {2379-5077},
abstract = {Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.},
}

@article {pmid41054501,
year = {2025},
author = {Wang, W and Mo, Q and Ding, X and Pan, J},
title = {Metagenomic Next-Generation Sequencing Reveals Tannerella forsythia in Lung Abscesses: A Retrospective Case Series Linking Smoking, Oral Health, and Diagnostic Challenges.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5193-5205},
pmid = {41054501},
issn = {1178-6973},
abstract = {PURPOSE: Tannerella forsythia (T. forsythia) is a Gram-negative anaerobic bacterium commonly found in the oral cavity of patients with periodontitis, but lung abscesses caused by this pathogen are extremely rare in the literature. This study aimed to characterize the clinical features, diagnostic challenges, and treatment outcomes of T. forsythia-associated lung abscesses through four case analyses.

PATIENTS AND METHODS: We retrospectively reviewed four patients treated between April 2023 and May 2024 with lung abscesses confirmed by chest computed tomography (CT) and T. forsythia detection via metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Conventional cultures were performed but yielded negative results. Clinical data, including demographics, symptoms, imaging findings, and treatment regimens, were analyzed.

RESULTS: All patients had oral diseases, and 75% were long-term smokers. The primary clinical manifestations were nonspecific respiratory symptoms, including cough, fever, chest pain, and hemoptysis. Chest CT revealed consolidation and cavitation in the upper lobes of the lungs. T. forsythia was successfully detected by mNGS of BALF, while conventional cultures failed to identify pathogens in all cases. All patients received combination antibiotic therapy based on metronidazole and piperacillin-tazobactam, with some cases requiring additional antibiotics. Following treatment, significant clinical improvement was observed, and follow-up imaging demonstrated gradual resolution of the lesions.

CONCLUSION: This study is limited by its small sample size and the lack of confirmatory tests, which warrant validation in larger prospective cohorts. Our findings highlight the advantages of mNGS in detecting fastidious pathogens (such as the anaerobic bacterium T. forsythia), providing new insights for the diagnosis of similar infections in the future. Additionally, the results identify smoking and poor oral health as common features that may be associated with the development of T. forsythia-associated lung abscesses.},
}

@article {pmid41053880,
year = {2025},
author = {Shittu, OE and Enagbonma, BJ and Babalola, OO},
title = {Deciphering the influence of fertilization systems on the Allium ampeloprasum rhizosphere microbial diversity and community structure through a shotgun metagenomics profiling approach.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {126},
pmid = {41053880},
issn = {2524-6372},
support = {CRP/ZAF22-03)//ICGEB, Italy/ ; NRF//South African National Research Foundation/ ; },
abstract = {BACKGROUND: Chemical fertilizer application in agriculture over the years has been a vital instrument to boost agricultural yields and soil fertility, but has threatened the diversity of the rhizosphere microbiomes in the soil. However, knowledge about the impacts of biofertilizers (BF) as well as chemical fertilizers (CF) on Allium ampeloprasum rhizosphere's microbiomes is still limited. Hence, this study investigated the metagenomic profiling of A. ampeloprasum rhizosphere under different fertilization systems and in bulk soils, to obtain a depiction of their associated microbial diversity and community structure, which will inform best agricultural practices.

METHOD: The entire DNA sample was mined from soil samples taken from an independent uncultivated bulk soil and the rhizosphere of A. ampeloprasum treated with chemical and biofertilizer and subjected to shotgun metagenomics sequencing.

RESULTS: The taxonomic analysis of our metagenome unveiled that while all soil samples exhibited similar core microbial phyla, Bacteroidota and Verrucomicrobiota were exclusive to the biofertilizer (G2) plot. Actinobacteria and Pseudomonadota (Proteobacteria) were predominant in the biofertilizer plot (G2), chemical fertilizer (G1), and bulk soil (G3) plots, respectively. Genera such as Dyadobacter, Verrucomicrobium, Streptomyces, and Haliangium were exclusively detected in the biofertilizer plot (G2). Alpha diversity analysis showed that G2 harboured the most diverse microbial community, followed by G3, with the lowest diversity found in the G1 plot, highlighting the importance of biofertilizer in increasing microbial diversity. The observed differences in the microbial diversity and community structure are highly linked to the nature of fertilizer applied and the distinct physicochemical parameters of the three plots. However, redundancy analysis subsequently highlighted total nitrogen and carbon as the key environmental influencers impacting the microbial community structure and composition.

CONCLUSION: This study underscores the potential of biofertilizers in boosting the rhizosphere microbial diversity, improving soil health, and offer a sustainable alternative to chemical fertilizers, thereby supporting long-term agricultural sustainability and resilience in food production systems.},
}

@article {pmid41053318,
year = {2025},
author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC},
title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34702},
pmid = {41053318},
issn = {2045-2322},
support = {W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; },
mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; },
abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.},
}

Humans
*Skin/radiation effects/microbiology/metabolism
Animals
Mice
Microbiota/radiation effects
Bioengineering
Cell Proliferation/radiation effects
Dose-Response Relationship, Radiation

@article {pmid41052982,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y},
title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {383},
pmid = {41052982},
issn = {2158-3188},
support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
*Hippocampus/metabolism/pathology/immunology
Mice
Pregnancy
Fecal Microbiota Transplantation
*Depression/microbiology/metabolism
*Dysbiosis/microbiology/complications
Humans
Lipopolysaccharides/blood
Germ-Free Life
*Neuroinflammatory Diseases/metabolism/microbiology
Microglia
*Pregnancy Complications/microbiology
Disease Models, Animal
Behavior, Animal
Interleukin-6/metabolism
Tumor Necrosis Factor-alpha/metabolism

@article {pmid41052966,
year = {2025},
author = {Tang, W and Hexter, C and Dai, R and Fortin, SG and Tracey, JC and Intrator, N and Kunes, MA and Wan, XS and Jayakumar, A and Shi, D and Ward, BB},
title = {Substrate Effect on the Contribution of Ammonium and Urea to Marine Nitrification and Nitrous Oxide Production.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70187},
doi = {10.1111/1462-2920.70187},
pmid = {41052966},
issn = {1462-2920},
support = {OCE-1946516//National Science Foundation/ ; 675459//Simons Foundation/ ; //University of South Florida/ ; },
mesh = {*Nitrification ; *Nitrous Oxide/metabolism ; *Urea/metabolism ; *Archaea/metabolism/genetics ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; Ammonia/metabolism ; Nitrites/metabolism ; },
abstract = {Nitrification (microbial oxidation of ammonia to nitrite and nitrate) controls nitrogen speciation and is the main source of nitrous oxide (N2O) in the ocean. It was recently shown that the most abundant marine ammonia oxidizers, the ammonia-oxidising archaea (AOA), are also capable of oxidising urea, providing a previously ignored source of nitrite. Here, we show that the relative magnitude of urea and ammonia oxidation rates, and the relative rates of N2O production from the two substrates, is correlated with the ratio of the substrate concentrations. By examining all reported measurements of urea and ammonium concentrations and the paired urea and ammonia oxidation rates, we show that this relationship likely holds across the global ocean. Examination of newly acquired and previously published metagenomic data shows that the fraction of AOA with the genetic capability for urea oxidation increases with the urea:ammonium ratio, rather than depending on the urea or ammonium concentration alone. These results corroborate the correlation between substrate ratios and oxidation rate ratios, and extend it to N2O production. This may help explain the distribution of nitrification rates and N2O production in the ocean.},
}

*Nitrification
*Nitrous Oxide/metabolism
*Urea/metabolism
*Archaea/metabolism/genetics
*Ammonium Compounds/metabolism
Oxidation-Reduction
*Seawater/microbiology/chemistry
Ammonia/metabolism
Nitrites/metabolism

@article {pmid41052412,
year = {2025},
author = {Dias, ME and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Kich, JD and Dorn, M and Siqueira, FM},
title = {Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2566429},
pmid = {41052412},
issn = {1479-487X},
abstract = {The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.},
}

@article {pmid41052332,
year = {2025},
author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C},
title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2514823122},
doi = {10.1073/pnas.2514823122},
pmid = {41052332},
issn = {1091-6490},
support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; },
abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.},
}

Animals
*Methane/metabolism/biosynthesis
*Fermentation/drug effects
*Rumen/microbiology/metabolism
Cattle
*Gastrointestinal Microbiome/drug effects
*Propanols/pharmacology
Animal Feed
*Ruminants/microbiology/metabolism
Microbiota/drug effects
Fatty Acids, Volatile/metabolism

@article {pmid41052251,
year = {2025},
author = {Qin, Z and Yang, Z and Zhang, Y and Qi, L and Peng, Y and Deng, S and Wang, Y},
title = {Biotin Limitation Attenuates Streptococcus mutans Cariogenicity by Disrupting Metabolic Flux and Virulence Pathways.},
journal = {Caries research},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000548822},
pmid = {41052251},
issn = {1421-976X},
abstract = {INTRODUCTION: Our previous metagenomic analysis revealed higher frequencies of biotin-related genes (i.e., bioY, bioM, bccP) in caries-active children, indicating a potential role of biotin in caries pathogenesis. This study investigated a biotin limitation strategy against the primary cariogenic bacterium Streptococcus mutans (S. mutans), including its effects on cariogenic phenotypes, gene expression, and metabolomics.

METHODS: S. mutans UA159 was cultured in biotin-free medium supplemented with different biotin concentrations. The cariogenic phenotypes of the strain, including growth kinetics, biofilm formation, exopolysaccharide (EPS) production, lactate synthesis, acid/oxidative tolerance, and membrane fluidity, were measured and compared across biotin concentrations. Biofilm architecture was visualized via confocal laser-scanning microscopy (CLSM) and scanning electron microscopy (SEM). Quantitative real-time polymerase chain reaction (RT-qPCR) was employed to analyze the expression of genes associated with virulence and biotin metabolism. Metabolomic analysis was performed to characterize metabolic perturbations induced by biotin limitation in S. mutans.

RESULTS: Under biotin limitation, S. mutans exhibited significantly reduced cariogenic phenotypes, accompanied by cell elongation and reduced membrane fluidity. At the molecular level, biotin limitation suppressed the expression of key virulence-associated genes and induced a compensatory upregulation of genes involved in biotin uptake and biotin-dependent carboxylases. Metabolomic analysis under biotin-limited conditions in S. mutans revealed perturbed pathways in central carbon metabolism and nucleotide metabolism.

CONCLUSION: Biotin limitation significantly reduced the cariogenic potential of S. mutans by disrupting metabolic flux and virulence gene expression, highlighting biotin uptake and metabolism as potential targets for anti-caries therapies.},
}

@article {pmid41051042,
year = {2025},
author = {Nancy, and Lakhawat, SS and Kumar, R and Sharma, PK},
title = {Cloning, Expression, Purification, and Characterization of Superoxide Dismutase from the Soil Metagenome.},
journal = {Protein and peptide letters},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298665415743250926072254},
pmid = {41051042},
issn = {1875-5305},
abstract = {INTRODUCTION: Superoxide Dismutases (SODs) are enzymes that catalyze the conversion of toxic free radicals generated during stress conditions into nontoxic forms. Thus, the enzyme superoxide dismutase contributes to the adaptation and survival of microorganisms across a variety of environmental conditions, making it an indispensable enzyme during the response to stress. In this study, we embarked upon investigating and characterizing a Superoxide Dismutase (SOD) from DNA extracted directly from garden soil, where the average temperature ranges from 4°C- 45°C.

MATERIALS AND METHODS: Metagenomic DNA was extracted by employing a kit. The gene was amplified using PCR. The amplified PCR product was gel eluted and ligated into the pGEMT-easy vector and subcloned into an expression vector. The protein was purified using Ni-NTA chromatography and characterized using biophysical, biochemical, and computational approaches.

RESULTS: The recombinant SOD was expressed and purified; the purified protein exhibited activity and stability over a broad pH and temperature range, with optimal activity observed at 40°C and pH 8, respectively. The enzyme remains completely stable at 40°C for 3 h. However, in contrast, it loses 50% of its activity when incubated at 50°C and 60°C for 3 h. The biophysical investigation revealed stable confirmation of the secondary structure of the protein, as evident from circular dichroism and intrinsic Tryptophan (Trp) fluorescence studies. In silico sequence and structural analysis revealed a close similarity of the SOD reported in this study to the Mn SOD of multi- Bacillus species. Molecular simulation dynamics experiments revealed the all-over conformational stability of protein structures at varying pH, indicating broad pH functioning of the enzyme.

DISCUSSION: The study provides a comprehensive analysis of the structure and function of a superoxide dismutase enzyme derived from a soil metagenome. A Mn2+ binding site identified in the study offers an opportunity to further facilitate engineering and design of mutant SOD.

CONCLUSION: The enzyme exhibits distinct attributes that hold significant industrial relevance. Owing to the wide functionality of SOD at different pH and temperature, it can be tailored for its potential industrial applications, which include its therapeutic potential, thus opening new avenues for enhanced antioxidant therapies and novel biocatalyst designing.},
}

@article {pmid41050906,
year = {2025},
author = {Wiese, M and Klaassens, ES and Hatt, V and Kreikamp, A and Baak, ML and Heerikhuisen, M and Van Der Vossen, JMBM},
title = {Demonstration of phage inhibitory action against Clostridium perfringens LMG 11264 within a complex chicken cecal microbiota in vitro.},
journal = {Frontiers in antibiotics},
volume = {4},
number = {},
pages = {1599939},
pmid = {41050906},
issn = {2813-2467},
abstract = {INTRODUCTION: Clostridium perfringens strains may cause foodborne illness, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry, C. perfringens infection may cause necrotic enteritis, and infections are associated with high mortality rates partially due to antibiotic resistance, which hampers efficient treatment. In-vitro screening approaches of alternative treatment options, for instance, specific phages, represent a promising strategy for the selection of novel interventions to combat infections.

MATERIAL AND METHODS: In this study, we explored the application of a C. perfringens strain LMG 11264-specific phage #7 introduced at 10[4] pfu/mL to inhibit the growth of C. perfringens at 10[6] cfu/mL compared to two antibiotics (amoxicillin at 10 µg/mL and clindamycin at 10 µg/mL) within complex chicken cecal microbiota in vitro. Samples for gDNA isolation, qPCR, and metagenome sequencing were taken at the beginning and after 24 and 48 h of incubation.

RESULTS: The C. perfringens strain LMG 11264 proliferated within the untreated complex microbiota and reached levels of approximately 10[8] and 10[9] genome equivalents per mL after 24 and 48 h of incubation, respectively. The phage intervention with phage #7 inhibited the growth of C. perfringens LMG 11264 significantly; the inhibitory effects were similar to those exerted by the antibiotic intervention with amoxicillin and stronger than the inhibitory effects with clindamycin. In the absence of the C. perfringens challenge, we found a significant effect of amoxicillin (p = 0.040) or clindamycin (p = 0.000017) compared to the untreated control after 24 h of incubation, and the phage addition did not affect the alpha diversity expressed as Chao index significantly (p = 1). In addition, the endogenous C. perfringens in the chicken microbiota appeared insensitive to phage #7. The phage titer of phage #7 only increased in the presence of the inoculated C. perfringens strain LMG 11264. In conclusion, the i-screen model can be implemented to test the efficacy and specificity of phage therapy in vitro.},
}

@article {pmid41050878,
year = {2025},
author = {Chetty, C and Mafunda, N and Happel, AU and Khan, A and Cooley Demidkina, B and Yende-Zuma, N and Saidi, Y and Mahabeer Polliah, A and Lewis, L and Osman, F and Radebe, P and Passmore, JS and Kwon, D and Ravel, J and Ngcapu, S and Liebenberg, L and Symul, L and Holmes, S and Mitchell, CM and Potloane, D},
title = {Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101554},
pmid = {41050878},
issn = {2451-8654},
abstract = {BACKGROUND: Globally, approximately 30 % of women have bacterial vaginosis (BV). Antibiotic treatment is frequently followed by recurrence, likely due to lack of colonization with beneficial lactobacilli.

METHODS: This is a Phase 1, randomized, placebo-controlled trial of vaginal live biotherapeutic products (LBP) after antibiotic treatment for BV to establish Lactobacillus colonization. The LBP are vaginal tablets containing 6 L. crispatus strains (LC106) or 15 L. crispatus strains (LC115), at 2 x 10[9] colony forming units (CFU) per dose. Participants with BV in the United States and South Africa will receive seven days of oral metronidazole twice daily and will be randomized 1:1:1:1:1 to: seven days placebo; seven days LC106; three days LC106/four days placebo; seven days LC106 starting day 3 of the metronidazole course; or seven days LC115. Safety will be assessed by the number and percentage of ≥ Grade 2 related adverse events during or after product use. The primary outcome is LBP colonization defined as relative abundance ≥5 % of any LBP strain or ≥10 % of a combination of LBP strains by metagenomic sequencing any time in the 5 weeks after randomization. A generalized linear model will measure the association between treatment group and colonization, adjusting for site.

CONCLUSIONS: This study seeks to establish proof of concept for a multi-strain LBP to promote vaginal L. crispatus colonization in two geographically distinct populations.

TRIAL REGISTRATION: South African National Clinical Trials Registry (SANCTR DOH-27-102023-8342; October 27, 2023) and ClinicalTrials.gov (NCT06135974; November 11, 2023).

PROTOCOL VERSION: 2.0 dated October 03, 2023.},
}

@article {pmid41050761,
year = {2025},
author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X},
title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1631960},
pmid = {41050761},
issn = {2235-2988},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation & purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; },
abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.},
}

Humans
*Mucormycosis/diagnosis/microbiology/drug therapy
*Mucorales/genetics/isolation & purification/classification
Male
Female
Middle Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Aged
Adult
ROC Curve
Antifungal Agents/therapeutic use
Microbiota

@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/metabolism/therapy/microbiology
Animals
Immunotherapy
*Microbiota/immunology
Fatty Acids, Volatile/metabolism

@article {pmid41050203,
year = {2026},
author = {Wang, Q and Shan, S and Sun, Q and Zhao, X and Yuan, C and Mou, Y and Wang, J and Yan, C and Wang, Q and Rui, Q and Li, C},
title = {The coupling effect of Penicillium baileys W2 in the Aspergillus flavus inhibition and peanut growth promotion.},
journal = {Synthetic and systems biotechnology},
volume = {11},
number = {},
pages = {127-140},
pmid = {41050203},
issn = {2405-805X},
abstract = {Aspergillus flavus is a significant plant pathogen, and peanut crops are particularly vulnerable to aflatoxin contamination. This vulnerability underscores the need for more effective control methods. In this study, the strain Penicillium baileys W2 was isolated from the rhizosphere soils of healthy peanut seedlings. The fermentation extract exhibited concentration-dependent inhibition of pathogenic A. flavus growth, with a minimum inhibitory concentration (MIC) of 55 % and a minimum fungicidal concentration (MFC) of 60 %. Physiological data and transcriptome analysis demonstrated that the W2 fermentation supernatant inhibited A. flavus growth by disrupting membrane permeability. Metabolomics analysis identified active compounds, including propylparaben, taxifolin, and phloretin, which exhibited significant antagonistic effects against A. flavus. Additionally, we evaluated the impact of the W2 fermentation broth on peanut growth promotion and on rhizosphere microbial community structure using metagenomic sequencing. The reduction of harmful soil microorganisms contributed to the maintenance of soil health, whereas the increased abundance of beneficial microorganisms enhanced peanut seedling growth by facilitating soil nutrient cycling. These findings indicate that the development and application of P. baileys strain W2 or its fermentation extract aligns with sustainable agricultural principles and offers a promising biological control approach.},
}

@article {pmid41049781,
year = {2025},
author = {Wang, B and He, T and Cheng, Y and Chen, H and Hu, Y and Liu, Y and Wang, F and Chen, L},
title = {Targeted enhancement strategies for Sojae Semen Praeparatum: Impact of Aspergillus oryzae and Bacillus subtilis on microbial communities, flavor substances, and functional components.},
journal = {Food chemistry: X},
volume = {30},
number = {},
pages = {102931},
pmid = {41049781},
issn = {2590-1575},
abstract = {Sojae Semen Praeparatum (SSP), a traditional Chinese fermented soybean product, was optimized through novel single/double enhancement fermentation using Aspergillus oryzae and Bacillus subtilis. Enhanced fermentation significantly increases the production of flavor amino acids. Using headspace solid-phase extraction microextraction gas chromatography-mass spectrometry (HS-SPEM-GC-MS) technology, 51 critical flavor substances were identified, confirming that enhanced fermentation improves the flavor profile of SSP. Isoflavone quantification revealed that enhancement strategies promoted isoflavone conversion. Enzyme inhibition and antioxidant activities were superior in the double enhancement fermentation group. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis demonstrated a significant increase in SSP's enrichment in the flavone and flavonol biosynthesis pathway. Screening identified 19 key flavonoid components strongly correlated with bioactivity, and enhancement fermentation notably enhancing their accumulation. Metagenomic sequencing revealed 14 key differential microorganisms, essential to flavor development and activity enhancement in SSP. This study offers valuable insights for optimizing fermentation processes to enhance product quality.},
}