@article {pmid40064809,
year = {2025},
author = {Ouarabi, L and Taminiau, B and Daube, G and Barache, N and Bendali, F and Drider, D and Lucau-Danila, A},
title = {Insights into fungal diversity and dynamics of vaginal mycobiota.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40064809},
issn = {1678-4405},
support = {Alibiotech CPER/FEDER 2016-2021//Région Hauts-de-France/ ; },
abstract = {Although less studied than its bacterial counterpart, the fungal component of the vaginal microbiota plays a critical role in maintaining vaginal homeostasis. Most research on the composition of the vaginal mycobiota has focused on pathological conditions, with relatively few studies involving healthy women. To gain comprehensive insights into the vaginal mycobiota of Algerian women in two different age groups, we performed a targeted metagenomic analysis using ITS2 region sequencing data from 14 vaginal samples collected from healthy women in reproductive and postmenopausal stages. A single dominant fungal species per individual was observed in both young and postmenopausal women, with differences in fungal community composition between the two groups being related to hormone levels. Our results show that Candida and Saccharomyces were the dominant genera in both young and postmenopausal women. Notably, the postmenopausal group had twice as many species, along with the presence of uncommon taxa such as Dipodascus and Fusarium, indicating greater taxonomic diversity. These findings suggest that menopause is associated with increased microbial variability, likely due to hormonal changes that disrupt the vaginal environment. This study paves the way for more extensive analyses involving diverse age groups and ethnic backgrounds.},
}

@article {pmid40064789,
year = {2025},
author = {Wang, H and Ma, H and Yan, H and Pei, Z and Zhao, J and Zhang, H and Zhang, Z and Lu, W},
title = {Study on the Effect of Bifidobacterium adolescentis CCFM1066 on Exercise Performance, Gut Microbiota, and Its Metabolites in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40064789},
issn = {1867-1314},
support = {32172212, 32394052//National Natural Science Foundation of China/ ; 2022YFF1100403//National Key Research and Development Program of China/ ; WMCC202403//Cohort and Clinical Research Program of Wuxi Medical Center, Nanjing Medical University/ ; },
abstract = {Prolonged high-intensity exercise consumes significant energy, leading to fatigue and decreased performance. This study explores the effects of Bifidobacterium adolescentis CCFM1066 on exercise performance, gut microbiota, and its metabolites in mice. The results of the mouse experiments showed the mice which were intervened by Bifidobacterium adolescentis CCFM1066 have a significant increase in exercise performance, including forceful swimming time, fatigue baton turning time, and forelimb grip strength. Through metagenomic sequencing and differential metabolites, analysis indicated that the intervention of CCFM1066 increased Lachnospiraceae bacterium, Parabacteroides goldsteinii, Bacteroides xylanisolvens, and Bifidobacterium adolescentis and altered the key metabolic pathways including protein digestion and absorption and biosynthesis of amino acids. Supplementation with CCFM1066 modulates the production of short-chain fatty acids (SCFAs) and fatty acid amides (FAAs) by gut microbiota, decreasing levels of lactic acid (LA), blood urea nitrogen (BUN), lactate dehydrogenase (LDH), and creatine kinase (CK) while increasing muscle and hepatic glycogen content, thus reducing central nervous system fatigue and thereby improving exercise endurance and performance. These findings provide new insights into nutritional interventions for sports performance.},
}

@article {pmid40064739,
year = {2025},
author = {Thakur, SS and González, SS and Suravajhala, P and Jain, SK and Yadav, S and Narayan, KS and Esack, E and Kuzyakov, Y and Ratnasari, A},
title = {Metagenomic insights of microbial functions under conventional and conservation agriculture.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {3},
pages = {100},
pmid = {40064739},
issn = {1573-0972},
support = {Grant ID: 3203/SKMCCC/EPCO/2021//Environmental Planning & Coordination Organisation (EPCO), Ministry of Environment, Government of Madhya Pradesh, India/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Agriculture ; *Archaea/genetics/classification ; *Soil/chemistry ; Metagenome ; Phylogeny ; Biodiversity ; Carbon/metabolism ; Nitrogen/metabolism ; },
abstract = {Agricultural practices such as conventional (CN) and conservation agriculture (CA) influence the composition and structure of soil microorganisms. We used short reads and genome-resolved metagenomic-based dual sequencing approaches to create a profile of bacterial and archaeal communities in hyperthermic Typic Haplustepts soil after seven years of CA and CN. The most differences in the physico-chemical and biological properties of soil were higher pH, organics carbon, available nitrogen and microbial biomass contents, activities of dehydrogenase, β-glucosidase, and arylsulfatase, found in CA soil. The dominant bacterial taxa under both management types were Pseudomonadota (46-48%), Acidobacteriota (12-13%), Planctomycetota (8-10%), Bacteroidota (7-8%), and Actinomycetota (6-7%). Nitrososphaerota (1.1-1.5%) was the predominant archaeal phyla in CA and CN soils. The alpha diversity was 1.5 times higher in CA compared to CN soils. Fourteen high-quality (HQ) metagenomic-assembled genomes (MAGs) were recovered from both groups. Four HQ metagenome-assembled genomes (MAGs) from the Pseudomonadota phylum were exclusively recovered from the CA soil. The dominance of this phylum in the CA soil might be correlated with its nutrient richness, as certain classes of Pseudomonadota, such as Alpha, Beta-, Gamma-, and Deltaproteobacteria, are known to be copiotrophic. Copiotrophic organisms thrive in nutrient-rich environments, which could explain their prevalence in the CA soil. CAZyme gene analysis showed that Glycoside Hydrolases (GH) and GlycosylTransferases (GT) classes are dominant in the CA group, possibly due to higher substrate availability from the application of crop residues, which provide a rich source of complex carbohydrates. Several biogeochemical gene families related to C1 compounds, hydrogen, oxygen, and sulfur metabolism were enriched in CA soils, suggesting these practices may contribute to a soil environment with increased organic matter content, microbial diversity, and nutrient availability. Overall, CA practices seemed to improve soil health by supporting soil microbial communities abundance.},
}

*Soil Microbiology
*Bacteria/genetics/classification/isolation & purification
*Metagenomics
*Agriculture
*Archaea/genetics/classification
*Soil/chemistry
Metagenome
Phylogeny
Biodiversity
Carbon/metabolism
Nitrogen/metabolism

@article {pmid40064231,
year = {2025},
author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y},
title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126028},
doi = {10.1016/j.envpol.2025.126028},
pmid = {40064231},
issn = {1873-6424},
abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.},
}

@article {pmid40064141,
year = {2025},
author = {She, Y and Wu, L and Qi, X and Sun, S and Li, Z},
title = {Aging behaviors intensify the impacts of microplastics on nitrate bioreduction-driven nitrogen cycling in freshwater sediments.},
journal = {Water research},
volume = {279},
number = {},
pages = {123448},
doi = {10.1016/j.watres.2025.123448},
pmid = {40064141},
issn = {1879-2448},
abstract = {Microplastics (MPs) inevitably undergo aging processes in natural environments; however, how aging behaviors influence the interactions between MPs exposures and nitrate bioreduction in freshwater sediments remains poorly understood. Here, we explored the distinct impacts of virgin and aged MPs (polystyrene (PS) and polylactic acid (PLA)) on nitrate bioreduction processes in lake sediments through a long-term microcosm experiment utilizing the [15]N isotope tracing technique and molecular analysis. Compared to virgin MPs, aged PLA significantly increased the rates of denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) (p < 0.05), facilitating sediment nitrogen loss, while aged PS only significantly improved the rates of DNRA by 272-297 % and contributed to nitrogen retention in sediments. Metagenomic sequencing demonstrated that a more significant enrichment of functional genes responsible for nitrate bioreduction pathways occurred with aged MPs exposures than with virgin MPs. By combining analyses of MPs aging traits and the key drivers of nitrate bioreduction, we revealed that aging behaviors directly regulated sediment nutrient status (e.g., DOC/NOx[-] ratio) and microbiological properties (from genes to bacteria), thereby further determining the activity of nitrate bioreduction. This work provides new insights into the impacts of aged MPs on sediment nitrate reduction and highlights the role of MPs aging in future assessments of long-term MPs pollution in freshwater ecosystems.},
}

@article {pmid40063888,
year = {2025},
author = {Saraphol, B and Hinthong, W and Chienwichai, P and Pumipuntu, N and Reamtong, O and Srisook, T and Premsuriya, J},
title = {Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0319461},
pmid = {40063888},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *Feces/microbiology ; *Metabolome ; Female ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; },
abstract = {Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥ 3, n = 16) and thin (BCS < 3, n = 16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.},
}

Animals
Cattle
*Feces/microbiology
*Metabolome
Female
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome

@article {pmid40063675,
year = {2025},
author = {Chavarria, X and Park, HS and Oh, S and Kang, D and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001365},
pmid = {40063675},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Supervised Machine Learning ; *Diabetes Mellitus, Type 1/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; Support Vector Machine ; Aged ; Algorithms ; },
abstract = {Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Diabetes Mellitus, Type 2/microbiology
*RNA, Ribosomal, 16S/genetics
*Supervised Machine Learning
*Diabetes Mellitus, Type 1/microbiology
*Metagenomics/methods
Male
Female
Middle Aged
Adult
Bacteria/genetics/classification/isolation & purification
Metagenome
Support Vector Machine
Aged
Algorithms

@article {pmid40063348,
year = {2025},
author = {Koul, M and Kaushik, S and Singh, K and Sharma, D},
title = {VITALdb: to select the best viroinformatics tools for a desired virus or application.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf084},
pmid = {40063348},
issn = {1477-4054},
support = {BT/2014-15/Plan/P-955//MHRD/ ; R.11013/51/2021-GIA/HR//DHR/ ; },
mesh = {Humans ; *Computational Biology/methods ; Antiviral Agents/therapeutic use ; COVID-19/virology/epidemiology ; SARS-CoV-2/genetics ; Viruses/genetics/classification ; Virus Diseases/virology ; Algorithms ; Software ; },
abstract = {The recent pandemics of viral diseases, COVID-19/mpox (humans) and lumpy skin disease (cattle), have kept us glued to viral research. These pandemics along with the recent human metapneumovirus outbreak have exposed the urgency for early diagnosis of viral infections, vaccine development, and discovery of novel antiviral drugs and therapeutics. To support this, there is an armamentarium of virus-specific computational tools that are currently available. VITALdb (VIroinformatics Tools and ALgorithms database) is a resource of ~360 viroinformatics tools encompassing all major viruses (SARS-CoV-2, influenza virus, human immunodeficiency virus, papillomavirus, herpes simplex virus, hepatitis virus, dengue virus, Ebola virus, Zika virus, etc.) and several diverse applications [structural and functional annotation, antiviral peptides development, subspecies characterization, recognition of viral recombination, inhibitors identification, phylogenetic analysis, virus-host prediction, viral metagenomics, detection of mutation(s), primer designing, etc.]. Resources, tools, and other utilities mentioned in this article will not only facilitate further developments in the realm of viroinformatics but also provide tremendous fillip to translate fundamental knowledge into applied research. Most importantly, VITALdb is an inevitable tool for selecting the best tool(s) to carry out a desired task and hence will prove to be a vital database (VITALdb) for the scientific community. Database URL: https://compbio.iitr.ac.in/vitaldb.},
}

Humans
*Computational Biology/methods
Antiviral Agents/therapeutic use
COVID-19/virology/epidemiology
SARS-CoV-2/genetics
Viruses/genetics/classification
Virus Diseases/virology
Algorithms
Software

@article {pmid40062866,
year = {2025},
author = {Ingle, DJ and Walsh, CJ and Samuel, GR and Wick, RR and Davidovich, N and Fiocchi, E and Judd, LM and Elliman, J and Owens, L and Stinear, TP and Basso, A and Pretto, T and Newton, HJ},
title = {The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0100224},
doi = {10.1128/msphere.01002-24},
pmid = {40062866},
issn = {2379-5042},
abstract = {The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever, Coxiella burnetii, represents the best-characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here, we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the species previously referred to as Candidatus Coxiella cheraxi represents a novel genus within this family, herein denoted Candidatus Paracoxiella cheracis. Interestingly, we demonstrate that Candidatus P. cheracis encodes a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen. In silico analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologs of several important C. burnetii effectors, including a homolog of CpeB that was demonstrated to be a Dot/Icm substrate in C. burnetii.IMPORTANCEUsing long-read sequencing technology, we have uncovered the full genome sequence of Candidatus Paracoxiella cheracis, a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insights into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. Candidatus P. cheracis also represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. Candidatus P. cheracis possesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology-manipulating effector proteins.},
}

@article {pmid40062856,
year = {2025},
author = {Kralj, JG and Servetas, SL and Forry, SP and Hunter, ME and Dootz, JN and Jackson, SA},
title = {Analytical assessment of metagenomic workflows for pathogen detection with NIST RM 8376 and two sample matrices.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0280624},
doi = {10.1128/spectrum.02806-24},
pmid = {40062856},
issn = {2165-0497},
abstract = {We assessed the analytical performance of metagenomic workflows using NIST Reference Material (RM) 8376 DNA from bacterial pathogens spiked into two simulated clinical samples: cerebrospinal fluid (CSF) and stool. Sequencing and taxonomic classification were used to generate signals for each sample and taxa of interest and to estimate the limit of detection (LOD), the linearity of response, and linear dynamic range. We found that the LODs for taxa spiked into CSF ranged from approximately 100 to 300 copy/mL, with a linearity of 0.96 to 0.99. For stool, the LODs ranged from 10 to 221 kcopy/mL, with a linearity of 0.99 to 1.01. Furthermore, discriminating different E. coli strains proved to be workflow-dependent as only one classifier:database combination of the three tested showed the ability to differentiate the two pathogenic and commensal strains. Surprisingly, when we compared the linear response of the same taxa in the two different sample types, we found those functions to be the same, despite large differences in LODs. This suggests that the "agnostic diagnostic" theory for metagenomics (i.e., any organism can be identified because DNA is the measurand) may apply to different target organisms and different sample types. Because we are using RMs, we were able to generate quantitative analytical performance metrics for each workflow and sample set, enabling relatively rapid workflow screening before employing clinical samples. This makes these RMs a useful tool that will generate data needed to support the translation of metagenomics into regulated use.IMPORTANCEAssessing the analytical performance of metagenomic workflows, especially when developing clinical diagnostics, is foundational for ensuring that the measurements underlying a diagnosis are supported by rigorous characterization. To facilitate the translation of metagenomics into clinical practice, workflows must be tested using control samples designed to probe the analytical limitations (e.g., limit of detection). Spike-ins allow developers to generate fit-for-purpose control samples for initial workflow assessments and inform decisions about further development. However, clinical sample types include a wide range of compositions and concentrations, each presenting different detection challenges. In this work, we demonstrate how spike-ins elucidate workflow performance in two highly dissimilar sample types (stool and CSF), and we provide evidence that detection of individual organisms is unaffected by background sample composition, making detection sample-agnostic within a workflow. These demonstrations and performance insights will facilitate the translation of the technology to the clinic.},
}

@article {pmid40062854,
year = {2025},
author = {Zhang, F and Luan, J and Suo, L and Wang, H and Zhao, Y and Sun, T and Ni, Y and Cao, H and Zou, X and Liu, B},
title = {Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0263924},
doi = {10.1128/spectrum.02639-24},
pmid = {40062854},
issn = {2165-0497},
abstract = {UNLABELLED: Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as Faecalibacterium, Ruminococcus, and Eubacterium, as well as species like Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and Prevotella copri were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.

IMPORTANCE: This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.},
}

@article {pmid40062772,
year = {2025},
author = {Connolly, JP and Kelly, L},
title = {The physical biogeography of Fusobacterium nucleatum in health and disease.},
journal = {mBio},
volume = {},
number = {},
pages = {e0298924},
doi = {10.1128/mbio.02989-24},
pmid = {40062772},
issn = {2150-7511},
abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.

IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.},
}

@article {pmid40062294,
year = {2025},
author = {Kuzudisli, C and Bakir-Gungor, B and Qaqish, B and Yousef, M},
title = {RCE-IFE: recursive cluster elimination with intra-cluster feature elimination.},
journal = {PeerJ. Computer science},
volume = {11},
number = {},
pages = {e2528},
pmid = {40062294},
issn = {2376-5992},
abstract = {The computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a significant challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniques that seek to detect strong correlations among features and identify irrelevant features. In this work, we propose the Recursive Cluster Elimination with Intra-Cluster Feature Elimination (RCE-IFE) method that utilizes feature grouping and iterates grouping and elimination steps in a supervised context. We assess dimensionality reduction and discriminatory capabilities of RCE-IFE on various high-dimensional datasets from different biological domains. For a set of gene expression, microRNA (miRNA) expression, and methylation datasets, the performance of RCE-IFE is comparatively evaluated with RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE. On average, RCE-IFE attains an area under the curve (AUC) of 0.85 among tested expression datasets with the fewest features and the shortest running time, while RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE achieve similar AUCs of 0.84 and 0.83, respectively. RCE-IFE and SVM-RCE yield AUCs of 0.79 and 0.68, respectively when averaged over seven different metagenomics datasets, with RCE-IFE significantly reducing feature subsets. Furthermore, RCE-IFE surpasses several state-of-the-art FS methods, such as Minimum Redundancy Maximum Relevance (MRMR), Fast Correlation-Based Filter (FCBF), Information Gain (IG), Conditional Mutual Information Maximization (CMIM), SelectKBest (SKB), and eXtreme Gradient Boosting (XGBoost), obtaining an average AUC of 0.76 on five gene expression datasets. Compared with a similar tool, Multi-stage, RCE-IFE gives a similar average accuracy rate of 89.27% using fewer features on four cancer-related datasets. The comparability of RCE-IFE is also verified with other biological domain knowledge-based Grouping-Scoring-Modeling (G-S-M) tools, including mirGediNET, 3Mint, and miRcorrNet. Additionally, the biological relevance of the selected features by RCE-IFE is evaluated. The proposed method also exhibits high consistency in terms of the selected features across multiple runs. Our experimental findings imply that RCE-IFE provides robust classifier performance and significantly reduces feature size while maintaining feature relevance and consistency.},
}

@article {pmid40061332,
year = {2025},
author = {Moore, CM and Secor, EA and Fairbanks-Mahnke, A and Everman, JL and Elhawary, JR and Witonsky, JI and Pruesse, E and Chang, CH and Contreras, MG and Eng, C and Canales, K and Rosado, T and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Lopez, N and Valentin, AM and Medina, V and Montanez-Lopez, CA and Morin, A and Nieves, NA and Oh, SS and Otero, RA and Colon, R and Rodriguez, L and Sajuthi, SP and Salazar, S and Serrano, G and Morales, EV and Vazquez, G and Morales, NV and Williams, BJM and Zhang, P and Sheppard, D and Rodriguez Santana, JR and Seibold, MA},
title = {Independent and interactive effects of viral species on risk for lower respiratory tract illnesses in early life.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.25.25322678},
pmid = {40061332},
abstract = {IMPORTANCE: All children experience upper respiratory tract illnesses (URI) caused by viral infections. However, some of these illnesses progress to the lower airways. Although studies have found infection with certain viral species are more likely to trigger lower respiratory illnesses (LRIs), a comprehensive analysis of viruses underlying early-life LRIs is lacking.

OBJECTIVE: Determine the incidence of URIs, mild and severe LRIs (mLRI, sLRI) during the first 2 years of life and the association between viral respiratory pathogens and odds of LRIs versus URIs in Puerto Rican children, a population at high risk for respiratory disease.

Healthy mother-infant pairs were enrolled in the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes birth cohort, in Caguas, Puerto Rico. Infants (n=2,061) were surveilled for respiratory illnesses during the first two years of life (March 2020 to April 2024). Nasal swabs from a subset of 1,363 illnesses from 774 participants were screened for 21 pathogens.

EXPOSURES: Infection with respiratory pathogens.

MAIN OUTCOMES AND MEASURES: URI, mLRI, and sLRI in the first two years of life.

RESULTS: RSV infections occurred in 23% of sLRIs and were associated with dramatically increased odds of sLRI vs URI (OR=9.28; 95% CI, 5.43-15.85). Metapneumovirus, parainfluenza, and non-SARS-CoV-2 coronavirus infections also increased odds of sLRIs. SARS-CoV-2 was associated with lower risk of sLRIs vs. URIs (OR=0.33; 95% CI, 0.16-0.68). Though rhinovirus (43%) and bocavirus (16.1%) were commonly detected in sLRIs, neither was associated with increased sLRI risk. Infection with multiple viral species (i.e. co-infection) occurred in one-third of sLRIs and was associated with 2.92-fold greater odds of sLRI (95% CI, 2.05-4.16) compared to single viral species infections. Rhinovirus-bocavirus was the most common co-infection (32.4%), and interaction between these viral infections was associated with increased sLRI risk (OR=2.21; 95% CI, 1.20-4.09) relative to illnesses that were negative for rhinovirus and bocavirus.

CONCLUSIONS AND RELEVANCE: A diversity of viral pathogens drive early-life sLRIs. Some viral pathogens (e.g. RSV and metapneumovirus) have intrinsic propensity to cause sLRIs, whereas many sLRIs are caused by viruses whose lower airway pathogenicity is dependent on other factors, including co-infection.

KEY POINTS: Question: How do common respiratory viruses differ in their prevalence and risk of causing severe lower respiratory illnesses (LRIs) during early childhood?Findings: RSV, metapneumovirus, and parainfluenza are independent risk factors for early childhood severe LRIs. While rhinovirus and bocavirus infections alone do not increase the risk of severe LRIs, these two viruses significantly elevate risk when they occur as co-infections.Meaning: Our findings highlight significant variability in viruses that drive severe early-life LRIs. Some viral species appear to inherently predispose individuals to lower airway disease, while for others, the development of disease likely depends on co-infections and/or host susceptibility.},
}

@article {pmid40060957,
year = {2025},
author = {Zhao, JH and Li, WJ and Jiao, J and Wang, MX and Zhang, XM and Yin, JY and Hu, WZ and Song, Q and Liu, J},
title = {Treatment of a rare and severe infection of central nervous system by Angiostrongylus cantonensis: A case report.},
journal = {World journal of radiology},
volume = {17},
number = {2},
pages = {105059},
pmid = {40060957},
issn = {1949-8470},
abstract = {BACKGROUND: Angiostrongylus cantonensis-induced acute parasitic infection is a rare food-borne disease in clinical practice. Lack of its specific laboratory markers and subsequent difficulty in detecting pathogens cause high misdiagnosis and missed diagnosis rates.

CASE SUMMARY: A 20-year-old male developed persistent neck and back pain after consuming raw snail meat, followed by urinary retention and low fever. After admission, the patient was misdiagnosed as viral infection and Mycobacterium tuberculosis in central nervous system. After detection of Angiostrongylus cantonensis in blood and cerebrospinal fluid by metagenomics next generation sequencing, albendazole was administered with ceftriaxone and methylprednisolone treatment simultaneously. With effective antiparasitic treatment, the patient weaned from mechanical ventilation successfully and transferred out of intensive care unit for hyperbaric oxygen and rehabilitation treatment.

CONCLUSION: This case highlights the diagnostic challenges of Angiostrongylus cantonensis infection and the importance of advanced sequencing techniques in identifying rare pathogens.},
}

@article {pmid40060808,
year = {2025},
author = {Gao, B and Shi, X and Zhao, M and Ren, F and Xu, W and Gao, N and Shan, J and Shen, W},
title = {Mixture Effects of Polystyrene Microplastics on the Gut Microbiota in C57BL/6 Mice.},
journal = {ACS omega},
volume = {10},
number = {8},
pages = {7597-7608},
pmid = {40060808},
issn = {2470-1343},
abstract = {Microplastics are plastic particles with sizes of less than 5 mm. The ubiquity of microplastics in the environment has raised serious public health concerns. Microplastics could disturb the composition of the gut microbiota due to both chemical composition and physical interactions, which might further influence the metabolism and immune function of the host. However, most of the exposure studies chose microplastics of specific sizes. In the natural environment, living organisms are exposed to a mixture of microplastics of various sizes. In this study, male C57BL/6 mice were exposed to polystyrene (PS) microplastics with different sizes, including microplastics with diameters of 0.05-0.1 μm (PS0.1 group, 100 ppb), 9-10 μm (PS10 group, 100 ppb), and microplastic mixtures of both 0.05-0.1 and 9-10 μm (PSMix group) at a total concentration of 100 ppb (50 ppb for each size). Mixture effects of microplastics were investigated on the composition of bacteria and fungi as well as functional metagenome and microbial genes encoding antibiotic resistance and virulence factors. We found that some bacteria, fungi, and microbial metabolic pathways were only altered in the PSMix group, not in the PS0.1 or PS10 group, suggesting the toxic effects of the microplastic mixture on the composition of fungi and bacteria, and the functional metagenome is different from the effects of microplastics at specific sizes. Meanwhile, altered genes encoding antibiotic resistance and virulence factors in the PSMix group were shared with the PS0.1 and PS10 groups, possibly due to functional redundancy. Our findings help improve the understanding of the toxic effects of the microplastic mixture on the gut microbiome.},
}

@article {pmid40060671,
year = {2025},
author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A},
title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.28.640732},
pmid = {40060671},
issn = {2692-8205},
abstract = {UNLABELLED: Despite effective HIV suppression, neuroinflammation and neurocognitive issues are prevalent in people with HIV (PWH) yet poorly understood. HIV infection alters the human virome, and virome perturbations have been linked to neurocognitive issues in people without HIV. Once thought to be sterile, the cerebrospinal fluid (CSF) hosts a recently discovered virome, presenting an unexplored avenue for understanding brain and mental health in PWH. This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA/RNA viruses. Taxonomic composition (reads and contigs), α and β diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV infection, markers of neuroinflammation and neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of viral groups and blood-brain barrier permeability were also performed. Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. Alpha diversity was lower in PWH versus CWH, although p>0.05. At β diversity analysis, HIV status explained 3.3% of the variation in viral composition (p=0.016). Contigs retained 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100β (p=0.002) and β-Amyloid 1-42 fragment (βA-42, p=0.026), while higher RA of nhEV with poorer cognitive performance (p=0.022). Conversely, higher RA of hEV correlated with better cognition (p=0.003) and lower βA-42 (p=0.012). Sensitivity analyses in virome-positive samples only confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, βA-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and nhEV-enriched CSF (models'p<0.05). This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.

AUTHOR SUMMARY: HIV can affect brain health and mental well-being, even in people on successful antiretroviral therapy. The reasons behind this are still unclear. HIV also influences the communities of microbes and viruses living in the human body, and recent research suggests that the human virome, the collection of all viruses within the body, may play a role in cognitive functions, mood, and brain health. For a long time, scientists believed that the cerebrospinal fluid (CSF), which surrounds the brain, was sterile, while robust evidence has shown that the CSF hosts its own unique virome. Via advanced genetic sequencing (shotgun metagenomics), we analyzed the CSF virome in people with and without HIV looking for possible links to neuroinflammation, cognitive performance, and depression. We found that while HIV infection does affect the composition of CSF viral communities, there were no remarkable differences in the CSF virome of individuals with and without HIV. Most viral sequences appeared to come outside the brain. A higher abundance of non-human viral sequences, such as viruses of bacteria, plants, fungi, and animals, was associated with neuroinflammation and poorer cognitive performance. On the other hand, a higher abundance of human viruses correlated with better cognitive function and healthier signature of neuromarkers. These findings provide new insights into the presence and characteristics of the human CSF virome and how it might influence brain health. They also suggest new potential mechanisms of HIV-associated neuropathology.},
}

@article {pmid40060627,
year = {2025},
author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ},
title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.28.640651},
pmid = {40060627},
issn = {2692-8205},
abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defense systems. Using functional metagenomic selections, we identified new examples of these systems from human fecal, human oral, and grassland soil microbiomes. Our antiphage selections in Escherichia coli revealed over 200 putative defenses from 14 diverse bacterial phyla, highlighting the broad phylogenetic interoperability of these systems. Many defense systems were unrecognizable based on sequence or predicted structure, so could only be identified via functional assays. In mechanistic studies, we show that some defense systems encode nucleases that only degrade covalently modified phage DNA, but which accommodate diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of previously unknown defense systems with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed among non-model bacteria.},
}

@article {pmid40060500,
year = {2025},
author = {Depuydt, L and Ahmed, OY and Fostier, J and Langmead, B and Gagie, T},
title = {Run-length compressed metagenomic read classification with SMEM-finding and tagging.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.25.640119},
pmid = {40060500},
issn = {2692-8205},
abstract = {Metagenomic read classification is a fundamental task in computational biology, yet it remains challenging due to the scale, diversity, and complexity of sequencing datasets. We propose a novel, lossless, run-length compressed index that enables efficient multi-class metagenomic classification in O (r) space, based on the move structure. Our method identifies all super-maximal exact matches (SMEMs) of length at least L between a read and the reference dataset and associates each SMEM with one class identifier using a sampled tag array. A consensus algorithm then compacts these SMEMs with their class identifier into a single classification per read. We are the first to perform run-length compressed read classification based on full SMEMs instead of semi-SMEMs. We evaluate our approach on both long and short reads in two conceptually distinct datasets: a large bacterial pan-genome with few metagenomic classes and a smaller 16S rRNA gene database spanning thousands of genera or classes. Our method consistently outperforms SPUMONI 2 in accuracy and runtime, with only a modest memory overhead. Compared to Cliffy, we demonstrate better memory efficiency while achieving superior accuracy on the simpler dataset and comparable performance on the more complex one. Overall, our implementation carefully balances accuracy, runtime, and memory usage, offering a versatile solution for metagenomic classification across diverse datasets. The open-source C++11 implementation is available at https://github.com/biointec/tagger under the AGPL-3.0 license.},
}

@article {pmid40060387,
year = {2025},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.03.592475},
pmid = {40060387},
issn = {2692-8205},
abstract = {Decline in ovarian function with age not only affects fertility but is also linked to a higher risk of age-related diseases in women (e.g . osteoporosis, dementia). Intriguingly, earlier menopause is linked to shorter lifespan; however, the underlying molecular mechanisms of ovarian aging are not well understood. Recent evidence suggests the gut microbiota may influence ovarian health. In this study, we characterized ovarian aging associated microbial profiles in mice and investigated the effect of the gut microbiome from young and estropausal female mice on ovarian health through fecal microbiota transplantation. We demonstrate that the ovarian transcriptome can be broadly remodeled after heterochronic microbiota transplantation, with a reduction in inflammation-related gene expression and trends consistent with transcriptional rejuvenation. Consistently, these mice exhibited enhanced ovarian health and increased fertility. Using metagenomics-based causal mediation analyses and serum untargeted metabolomics, we identified candidate microbial species and metabolites that may contribute to the observed effects of fecal microbiota transplantation. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}

@article {pmid40060187,
year = {2025},
author = {Cao, J and Ma, Y and Fu, J and Wang, Z and Zhao, Y and Zhong, N and Zhao, P},
title = {Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome.},
journal = {aBIOTECH},
volume = {6},
number = {1},
pages = {33-49},
pmid = {40060187},
issn = {2662-1738},
abstract = {UNLABELLED: Potato common scab (CS) is a worldwide disease, caused by Streptomyces spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, Bacillus atrophaeus DX-9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX-9 on CS. These studies revealed that DX-9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX-9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as Bradyrhizobium, Agrobacterium, and Nitrobacter, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX-9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8-dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of Bacillus atrophaeus DX-9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00199-3.},
}

@article {pmid40060112,
year = {2024},
author = {Wei, B and Xu, Q and Kong, J and Su, X and Chen, K and Wang, H},
title = {Metagenomics-based study of rhizospheric microorganisms of Poa alpigena L. in Qinghai Lake, Ganzi River Plateau.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1518637},
pmid = {40060112},
issn = {1664-462X},
abstract = {INTRODUCTION: Poa alpigena Lindm., a dominant forage grass on the Tibetan Plateau, plays a critical role in livestock production and grassland restoration. This study investigates the rhizospheric and non-rhizospheric soil microorganisms of Poa alpigena L. in the Ganzi River area of the Qinghai Lake basin using metagenomic sequencing to understand their diversity and potential ecological functions.

METHODS: Soil samples were collected from rhizospheric and non-rhizospheric areas of Poa alpigena L. using the S-type five-point sampling method. DNA was extracted, and metagenomic sequencing was performed using the BGISEQ-500 platform. Alpha and Beta diversity analyses were conducted, and LEfSe analysis was used to identify differentially abundant microbial taxa and metabolic pathways.

RESULTS: A total of 5,681 microbial species across 1,606 genera, 521 families, 61 phyla, and 246 orders were identified. Non-rhizospheric soils exhibited higher species richness than rhizospheric soils. Proteobacteria was the most abundant phylum in both soil types. Rhizospheric soils showed significant enrichment in pathways related to antibiotic biosynthesis, carbon metabolism, and methane metabolism, while non-rhizospheric soils were enriched in quorum sensing and drug-metabolizing pathways.

DISCUSSION: The findings highlight the selective influence of Poa alpigena L. on soil microbial communities and their potential role in mitigating methane emissions. The study provides a foundation for understanding the ecological functions of soil microorganisms in alpine meadows and supports sustainable grassland management practices.},
}

@article {pmid40059905,
year = {2025},
author = {Su, Z and Gu, AZ and Wen, D and Li, F and Huang, B and Mu, Q and Chen, L},
title = {Rapid identification of antibiotic resistance gene hosts by prescreening ARG-like reads.},
journal = {Environmental science and ecotechnology},
volume = {23},
number = {},
pages = {100502},
pmid = {40059905},
issn = {2666-4984},
abstract = {Effective risk assessment and control of environmental antibiotic resistance depend on comprehensive information about antibiotic resistance genes (ARGs) and their microbial hosts. Advances in sequencing technologies and bioinformatics have enabled the identification of ARG hosts using metagenome-assembled contigs and genomes. However, these approaches often suffer from information loss and require extensive computational resources. Here we introduce a bioinformatic strategy that identifies ARG hosts by prescreening ARG-like reads (ALRs) directly from total metagenomic datasets. This ALR-based method offers several advantages: (1) it enables the detection of low-abundance ARG hosts with higher accuracy in complex environments; (2) it establishes a direct relationship between the abundance of ARGs and their hosts; and (3) it reduces computation time by approximately 44-96% compared to strategies relying on assembled contigs and genomes. We applied our ALR-based strategy alongside two traditional methods to investigate a typical human-impacted environment. The results were consistent across all methods, revealing that ARGs are predominantly carried by Gammaproteobacteria and Bacilli, and their distribution patterns may indicate the impact of wastewater discharge on coastal resistome. Our strategy provides rapid and accurate identification of antibiotic-resistant bacteria, offering valuable insights for the high-throughput surveillance of environmental antibiotic resistance. This study further expands our knowledge of ARG-related risk management in future.},
}

@article {pmid40059755,
year = {2025},
author = {Munk, P and Brinch, C and Aarestrup, FM},
title = {Resistance genes are not like chemical pollutants and surveillance of them should reflect that.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1080/17460913.2025.2476880},
pmid = {40059755},
issn = {1746-0921},
}

@article {pmid40059174,
year = {2025},
author = {Jin, X and Cheng, AG and Chanin, RB and Yu, FB and Dimas, A and Jasper, M and Weakley, A and Yan, J and Bhatt, AS and Pollard, KS},
title = {Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {71},
pmid = {40059174},
issn = {2049-2618},
support = {1563159//National Science Foundation/ ; HL160862/HL/NHLBI NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Bacterial Adhesion/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Animals ; Metagenome ; Mice ; Promoter Regions, Genetic ; Intestines/microbiology ; },
abstract = {BACKGROUND: Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.

RESULTS: Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.

CONCLUSIONS: Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/genetics/classification/isolation & purification
*Bacterial Adhesion/genetics
*Metagenomics/methods
Computational Biology/methods
Animals
Metagenome
Mice
Promoter Regions, Genetic
Intestines/microbiology

@article {pmid40058902,
year = {2025},
author = {Revelo-Romo, DM and Hurtado Gutiérrez, NH and Hidalgo Troya, A and Amaya-Gómez, CV and Flórez-Martínez, DH and Overmann, J and Villegas Torres, MF and González Barrios, AF},
title = {Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality.},
journal = {Food research international (Ottawa, Ont.)},
volume = {206},
number = {},
pages = {116035},
doi = {10.1016/j.foodres.2025.116035},
pmid = {40058902},
issn = {1873-7145},
mesh = {*Fermentation ; *Coffee/microbiology ; *Coffea/microbiology/chemistry/metabolism ; Microbiota ; Metagenomics/methods ; Seeds/microbiology/metabolism ; Food Handling/methods ; },
abstract = {The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.},
}

*Fermentation
*Coffee/microbiology
*Coffea/microbiology/chemistry/metabolism
Microbiota
Metagenomics/methods
Seeds/microbiology/metabolism
Food Handling/methods

@article {pmid40058900,
year = {2025},
author = {Wang, X and Li, Q and Li, W and Cai, G and Wu, D and Xie, G and Lu, J},
title = {Metagenomics unveils the roles of microbes in the metabolic network of purine formation during Huangjiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {206},
number = {},
pages = {116031},
doi = {10.1016/j.foodres.2025.116031},
pmid = {40058900},
issn = {1873-7145},
mesh = {*Fermentation ; *Purines/metabolism ; *Metagenomics ; Metabolic Networks and Pathways ; Bacteria/metabolism/genetics/classification ; Microbiota/physiology ; Fermented Foods/microbiology ; },
abstract = {Purine is a major factor contributing to the development of hyperuricemia and gout, and it is found in large quantities in Huangjiu as free bases. Purine production in Huangjiu is strongly associated with microbial metabolism. However, to the best of our knowledge the microorganisms responsible for and the mechanisms of purine formation during Huangjiu fermentation are yet to be evaluated. Herein, changes in purine levels during Huangjiu fermentation were analyzed. Further, the microbes responsible for purine production were identified and their gene abundance was studied. Results revealed that adenine, guanine, hypoxanthine, and xanthine are produced during Huangjiu fermentation. The total purines content on day 0 (27.99 mg/L) was found to be considerably lower than that produced on day 24 (122.15 mg/L) during Huangjiu fermentation. Metagenomics showed that the composition of the microbial community fluctuates sharply during five fermentation periods of Huangjiu, with the microbial community richness and diversity being the most prominent on day 3. At the genus level, Klebsiella, Lactobacillus, Staphylococcus, Saccharopolyspora, and Saccharomyces were abundant during Huangjiu fermentation and were involved in purine metabolism. Relationships between the dominant microorganisms and key enzyme genes of the purine pathways were also established based on the Kyoto Encyclopedia of Genes and Genomes database. Correlation analysis showed that Lactobacillus and Saccharomyces were the main genera involved in purine formation. Saccharomyces cerevisiae, Lactobacillus paralimentarius, and Lactiplantibacillus plantarum were involved in purine formation during Huangjiu fermentation. Overall, this study improves our understanding of the purine formation mechanism during Huangjiu fermentation and provides valuable insights into the regulation of purine formation by microorganisms.},
}

*Fermentation
*Purines/metabolism
*Metagenomics
Metabolic Networks and Pathways
Bacteria/metabolism/genetics/classification
Microbiota/physiology
Fermented Foods/microbiology

@article {pmid40058503,
year = {2025},
author = {Chang, Z and Deng, J and Zhang, J and Wu, H and Wu, Y and Bin, L and Li, D and Liu, J and Yu, R and Lin, H and An, L and Sun, B},
title = {Rapid and Accurate Diagnosis of Urinary Tract Infections Using Targeted Next-Generation Sequencing: A Multicenter Comparative Study with Metagenomic Sequencing and Traditional Culture Methods.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106459},
doi = {10.1016/j.jinf.2025.106459},
pmid = {40058503},
issn = {1532-2742},
abstract = {BACKGROUND: Urinary tract infections (UTIs) rank among the most prevalent bacterial infections globally. Traditional urine culture methods have significant limitations in detection time and sensitivity, prompting the need to evaluate targeted next-generation sequencing (tNGS) as a potential diagnostic tool.

METHODS: The study included a discovery cohort of 400 suspected UTI patients (202 analyzed) and a validation cohort of 200 patients (110 analyzed). The study assessed detection time, concordance rates, ability to identify polymicrobial infections, and antibiotic resistance genes (ARGs). Both clear and turbid urine samples were evaluated across different clinical settings.

RESULTS: In the discovery cohort, tNGS demonstrated 96.5% concordance with culture-positive samples, while showing superior specificity in culture-negative specimens (53.1% vs 28.1% for mNGS). Detection time for tNGS (12.89h) was notably shorter than mNGS (17.38h) and traditional culture (61.48h). tNGS exhibited remarkable capability in identifying polymicrobial infections (55.4% of samples), significantly outperforming both mNGS (27.7%) and traditional culture methods, which failed to detect any co-infections. The method showed particular strength in detecting fastidious organisms like Ureaplasma parvum and fungal species such as Candida tropicalis. For antibiotic resistance prediction, tNGS detected more ARGs (52.67% vs 41.22% for mNGS) and achieved 100% sensitivity for vancomycin and methicillin resistance in Gram-positive pathogens. The validation cohort confirmed tNGS's robust performance, maintaining high concordance rates for both culture-positive (90.00%) and culture-negative samples (55.00%), demonstrating consistent reliability across different clinical settings CONCLUSIONS: tNGS demonstrates advantages in rapid and accurate UTI diagnosis, particularly in detecting polymicrobial infections and analyzing antibiotic resistance genes. It shows promise as an effective complementary tool for UTI diagnostics.},
}

@article {pmid40058443,
year = {2025},
author = {Zhou, Y and Li, MY and Li, CY and Sheng, YJ and Ye, QT and Chen, RY and Zhou, KY and Zhang, Y and Shen, LF and Shou, D},
title = {Effective mechanism of polysaccharides from Erxian herbal pair in promoting bone repair in traumatic osteomyelitis by activating osteoblast GPR41 and inhibiting the MEK/ERK/MAPK signalling axis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {141858},
doi = {10.1016/j.ijbiomac.2025.141858},
pmid = {40058443},
issn = {1879-0003},
abstract = {Polysaccharides are the key components of natural products; however, their effects on bone repair haven't been fully evaluated. This study aimed to assess the efficacy and mechanism of polysaccharides in promoting bone repair. The Erxian herb pair polysaccharide (EHP) was isolated and purified using water extraction (1:20 (w/v); 100 ± 2 °C; 5 h) and alcohol precipitation (80 ± 2 %). A traumatic osteomyelitis (TO) rat model was established using lipopolysaccharide (LPS). The gut microbiota was analysed through intestinal flora and metagenomic sequencing. The results revealed that the yields of crude polysaccharide and purified polysaccharide EHP were 3.73 ± 0.34 % and 0.48 ± 0.06 %, respectively. The total sugar content of EHP was 83.53 ± 0.16 %. The EHP, with a molecular weight of 31.964 kDa, was primarily composed of mannose, rhamnose, glucose, galactose, and arabinose. In vivo experiments demonstrated that EHP intervention (300 mg/kg/day) significantly augmented bone density and enhanced the activity of alkaline phosphatase (ALP) (P < 0.01). EHP upregulated the abundance of probiotics and increased the production of butyric acid (P < 0.05). In vitro experiments revealed that butyric acid (500-1000 μM) enhanced osteoblast activity and inhibited the expression of mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK) (P < 0.01). These findings indicate that polysaccharides may represent a promising therapeutic agent for bone-healing.},
}

@article {pmid40058279,
year = {2025},
author = {Chen, H and Zeng, Z and Lal, R and Wu, J and Chen, J and Li, M and Cao, L and Liu, X and Zhang, R and Gong, C},
title = {Acetic acid production from corn straw via enzymatic degradation using putative acetyl esterase from the metagenome assembled genome.},
journal = {Enzyme and microbial technology},
volume = {187},
number = {},
pages = {110619},
doi = {10.1016/j.enzmictec.2025.110619},
pmid = {40058279},
issn = {1879-0909},
abstract = {Acetic acid production from corn straw by enzyme catalysis shows its application value in food industry. In this study, a gene encoding for a putative acetyl esterase derived from Sphingobacterium soilsilvae Em02 was discovered in metagenome assembled genome. The gene was expressed in Escherichia coli BL21 to obtain enzyme with a molecular mass of 38.8 kDa. P-Nitrophenyl acetate was used as a substrate to determine the enzyme activity. The enzyme demonstrated optimal activity under conditions of 40 °C and a neutral pH of 7.0. Under optimal conditions, 17.58 mg of acetic acid was obtained using the enzyme from 50 mg corn straw pretreated with amylase. The acetyl esterase derived from Sphingobacterium soilsilvae Em02, demonstrates significant potential for biotechnological applications, particularly in biomass degradation.},
}

@article {pmid40058278,
year = {2025},
author = {Neri, LCM and Guðmundsson, H and Meurrens, G and Robert, A and Fridjonsson, OH and Hreggvidsson, GO and Adalsteinsson, BT},
title = {Identification and characterization of endo-xylanases from families GH10 and GH11 sourced from marine thermal environments.},
journal = {Enzyme and microbial technology},
volume = {187},
number = {},
pages = {110592},
doi = {10.1016/j.enzmictec.2025.110592},
pmid = {40058278},
issn = {1879-0909},
abstract = {Seaweed biomass is an underutilized resource that is rich in polysaccharides, including xylan. Seaweed polysaccharides could be used as a feedstock in industrial microbiology and and for production of prebiotic oligosaccharides and rare monosaccharides - processes that would benefit from the availability of robust enzymes that break down the seaweed polysaccharides. The present study aimed to identify genes encoding endo-xylanases in bacterial genomes and metagenomes sourced from marine thermal environments, and to characterize the respective enzymes. Twelve endo-xylanases were studied which displayed 59 % median maximal sequence similarity to characterized GH10 or GH11 enzymes. Overall, most of the enzymes functioned optimally at high temperatures, in the presence of salt, and at circumneutral pH. Eight enzymes functioned optimally at temperatures of 50°C or higher, and in the most extreme cases at 85°C to 95°C. Six enzymes retained activity after three-hour incubation at 60°C or higher. Ten enzymes displayed improved catalytic function in the presence of salt, and several retained high catalytic function at 10 % NaCl concentration. All the enzymes hydrolyzed xylan from diverse sources, including crude biomass. The study contributes to an increased understanding of the structural diversity of xylanases; it expands the availability of thermostable xylanases of marine origin; and contributes to increased valorization of seaweed biomass.},
}

@article {pmid40058228,
year = {2025},
author = {Tromas, N and Simon, DF and Fortin, N and Hernández-Zamora, M and Pereira, A and Mazza, A and Pacheco, SM and Levesque, MJ and Martínez-Jerónimo, L and Antuna-González, P and Munoz, G and Shapiro, BJ and Sauvé, S and Martínez-Jerónimo, F},
title = {Metagenomic insights into cyanotoxin dynamics in a Mexican subtropical lake.},
journal = {Chemosphere},
volume = {376},
number = {},
pages = {144285},
doi = {10.1016/j.chemosphere.2025.144285},
pmid = {40058228},
issn = {1879-1298},
abstract = {Valle de Bravo is a vital water supply for part of the metropolitan area of the Valle de Mexico megacity, providing 30% of Mexico City's water demand. This water body has experienced an acceleration in its trophic status, going from oligotrophic to eutrophic in just a few years. This temperate lake (at a tropical latitude) is in a persistent bloom dominated by a variety of co-occurring cyanobacteria, many of which have toxigenic potential based on microscopic identification, that makes it difficult or even impractical to identify the cyanotoxin producers. To unravel this complexity and directly identify the toxigenic genera, we showed that integrating classical approaches with metagenomic is required. We first characterized, from genes to metagenomes assembled genomes, the toxigenic Cyanobacteria. We found that Microcystis was the most dominant cyanobacterial genus and the sole carrier of the mcy operon, making it the only microcystin producer. We then quantified twenty-one different cyanopeptides, including twelve microcystin congeners using a high-performance liquid chromatography-high-resolution. Nine microcystins (MCs) and the emerging cyanotoxin anabaenopeptin-A and -B were found at varying concentrations throughout the year, with MC-LA being the most common and abundant. Our findings, constrained by our sampling strategy, indicate that conventional cyanotoxin biomarkers (e.g., toxin mcy genes) were not consistently reliable indicators of cyanotoxin concentrations in this freshwater system. In this study, we followed the dynamics of the cyanobacterial community and the associated cyanopeptides with unprecedented resolution. Our results have implications for better management of toxic blooms in this freshwater system, which supplies drinking water to more than 7 million people in the megalopolis of Valle de México.},
}

@article {pmid40058051,
year = {2025},
author = {Castellano-Hinojosa, A and Gallardo-Altamirano, MJ and Pozo, C and González-Martínez, A and González-López, J and Marshall, IPG},
title = {Salinity levels influence treatment performance and the activity of electroactive microorganisms in a microbial fuel cell system for wastewater treatment.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124858},
doi = {10.1016/j.jenvman.2025.124858},
pmid = {40058051},
issn = {1095-8630},
abstract = {There is growing interest in developing effective treatment technologies to mitigate the environmental impact of saline wastewater while also potentially recovering valuable resources from it. However, it remains largely unknown how different salinity levels impact treatment performance, energy generation, and the diversity and composition of electroactive microorganisms in MFCs treating real effluents such as urban wastewater. This study explores the impact of three salinity levels (3.5, 7, and 15 g/L NaCl) on current production, organic removal rates, and bacterial community dynamics in a continuous-flow microbial fuel cell (MFC) fed with urban wastewater. Using metagenomics and metatranscriptomics, we explored variations in the abundance and expression of extracellular electron transfer (EET) genes and those involved in other general metabolisms. We found that low salinity (3.5 g/L NaCl) enhanced both current production and organic removal efficiency compared to higher salinity levels. This improvement was linked to an increased abundance and activity of electroactive microorganisms, particularly taxa within the Ignavibacteria class, which possess genes coding for outer membrane cytochromes and porin cytochromes. Additionally, salinity influenced general metabolic genes and microbial community composition, with higher salinity levels limiting bacterial growth and diversity. This research provides valuable insights into the interplay between salinity stress and microbial adaptation, contributing to the optimization of MFC technologies for enhanced environmental and bioengineering applications.},
}

@article {pmid40057978,
year = {2025},
author = {Jeevannavar, A and Florenza, J and Divne, AM and Tamminen, M and Bertilsson, S},
title = {Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf046},
pmid = {40057978},
issn = {1751-7370},
abstract = {Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.},
}

@article {pmid40057571,
year = {2025},
author = {Adams, SE and Cawley, AK and Arnold, D and Hoptroff, MJ and Slomka, V and Matheson, JR and Marriott, RE and Gemmell, MR and Marsh, PD},
title = {A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8136},
pmid = {40057571},
issn = {2045-2322},
mesh = {Humans ; *Toothpastes/pharmacology/therapeutic use ; *Dental Plaque/microbiology ; Male ; Female ; Adult ; *Microbiota/drug effects ; Double-Blind Method ; Middle Aged ; Zinc Compounds/pharmacology/therapeutic use/administration & dosage ; Young Adult ; Bacteria/classification/drug effects/genetics/isolation & purification ; },
abstract = {The oral microbiome is a diverse community of microbes residing on all oral surfaces. A balanced oral microbiome is associated with good oral health, and disruption can result in imbalance associated with diseases including gingivitis and dental caries. It is important, therefore, to understand how daily use of oral hygiene products impacts the microbiome. Composition and activity of dental plaque microbiome from 115 participants was analysed after brushing with one of two toothpastes, one containing zinc citrate trihydrate and the other a control toothpaste, in a parallel design. Each participant brushed twice daily for 6-weeks, with samples collected at baseline, 2 and 6-weeks. Metataxonomic analysis demonstrated changes in bacterial communities with use of the zinc toothpaste compared to the control product at community and species level. Increases at the species level were observed for taxa from the genus Veillonella with decrease in a taxon from the genus Fusobacterium for the zinc toothpaste. Analysis of microbiome function based on predicted metagenomic and metatranscriptomic analysis show that use of the zinc toothpaste is associated with an in-vivo reduction in glycolysis, consistent with the mode of action of zinc and, increases in processes linked to gum-health (lysine biosynthesis), and to whole-body health (nitrate reduction). Our findings provide the first understanding of the beneficial modulation of microbiome composition and function by zinc-containing toothpaste in-vivo for oral care benefits.},
}

Humans
*Toothpastes/pharmacology/therapeutic use
*Dental Plaque/microbiology
Male
Female
Adult
*Microbiota/drug effects
Double-Blind Method
Middle Aged
Zinc Compounds/pharmacology/therapeutic use/administration & dosage
Young Adult
Bacteria/classification/drug effects/genetics/isolation & purification

@article {pmid40057258,
year = {2025},
author = {Ragone, P and Parodi, C and Tomasini, N and Ramos, F and Uncos, A and Brandán, CP},
title = {The interplay between Trypanosoma cruzi and the microbiome of Triatoma infestans: Implications for the host's immune response.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107577},
doi = {10.1016/j.actatropica.2025.107577},
pmid = {40057258},
issn = {1873-6254},
abstract = {The infection dynamics of Trypanosoma cruzi is shaped by the parasite's genetics and interactions with host and vector factors. While most studies in the area use axenic parasite cultures devoid of insect fecal components, this study is focused on the immune response and the parasite loads generated after the interaction of T. cruzi with feces from Triatoma infestans in a murine model. First, using metagenomics, we analyzed the microbiota of infected and uninfected feces. Illumina sequencing of the 16S rRNA gene (V3-V4 region) revealed a predominance of the genus Arsenophonus in infected feces and of Enterococcus in uninfected ones. C57BL/6J mice inoculated with T. cruzi infected feces, displayed distinct immune responses compared to those inoculated with culture-derived metacyclic trypomastigotes alone, with lower levels of pro-inflammatory cytokines (IFN-ɣ, TNF-α) and higher amounts of IL-10, suggesting a regulatory response. Besides, total anti-T. cruzi IgG levels remained similar among groups, but IgG1 and IgG2c were reduced in the T. cruzi infected feces group, indicating a balanced Th1/Th2 response. Notably, mice inoculated with T. cruzi infected feces demonstrated significantly reduced blood and muscle parasite loads, potentially limiting inflammation and parasite dissemination. These findings highlight the possible role of vector fecal microbiota in shaping immune responses and influencing disease outcomes during natural T. cruzi infections.},
}

@article {pmid40057163,
year = {2025},
author = {Leonard, AFC and Higgins, SL and Hui, M and Gaze, WH},
title = {Investigating landscape-scale variables impacting human exposure to antibiotic resistant bacteria using a targeted metagenome approach.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126015},
doi = {10.1016/j.envpol.2025.126015},
pmid = {40057163},
issn = {1873-6424},
abstract = {Research has shown that exposure to coastal waters containing antibiotic resistant bacteria (ARB) is associated with higher likelihood of gut colonisation by ARB. The aim was to identify landscape-scale processes contributing to the spread of ARB in Hong Kong's coastal waters and to estimate the scale of bathers' exposure to ARB. Twelve recreational water locations were sampled in 2017 for Escherichia coli. A targeted metagenomic approach was used to quantify the abundance and diversity of antibiotic resistance genes (ARGs) harboured by viable E. coli. Data on environmental variables related to ARB distribution in the environment were modelled to identify processes driving the abundance and diversity of ARG-bearing E. coli in coastal waters. These data were combined with data about Hong Kong residents' use of blue space to quantify human exposure to E. coli borne ARG. Several meteorological variables, like rainfall and temperature, were associated with E. coli-borne ARG profiles. Yet when rigorous statistical methods were applied, these relationships were not significant. Meropenem-resistant bacteria were also isolated from samples, most of which were taken from western beaches. Additionally, there was some evidence of elevated abundances of several ARGs, including blaCTX-M, in western beaches. The average E. coli harboured 6.09 ARGs. Over 1.16 million exposure events occurred in 2017 that involved ingestion of E. coli harbouring at least one ARG. This study used robust methods to quantify and explain the abundance and diversity of ARB in Hong Kong's coastal waters. We detected elevated levels of several E. coli-borne ARGs and meropenem-resistant pathogens at western beaches, indicating an influence of the Pearl River on Hong Kong's water quality. Despite updates to wastewater treatment in Hong Kong, recreational use of natural surface waters remains a significant risk of exposure to ARB capable of human gut colonisation.},
}

@article {pmid40056814,
year = {2025},
author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M},
title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.},
journal = {Chemosphere},
volume = {376},
number = {},
pages = {144296},
doi = {10.1016/j.chemosphere.2025.144296},
pmid = {40056814},
issn = {1879-1298},
abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.},
}

@article {pmid40056517,
year = {2025},
author = {Choonut, A and Wongfaed, N and Wongthong, L and Poolpol, A and Chaikitkaew, S and Sittijunda, S and Reungsang, A},
title = {Microbial degradation of polypropylene microplastics and concomitant polyhydroxybutyrate production: An integrated bioremediation approach with metagenomic insights.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137806},
doi = {10.1016/j.jhazmat.2025.137806},
pmid = {40056517},
issn = {1873-3336},
abstract = {The persistence of plastics, particularly polypropylene (PP), and their conversion into microplastics (MPs), specifically PP-MPs, have emerged as serious ecological threats to soil and aquatic environments. In the present study, we aimed to isolate a microbial consortium capable of degrading PP-MPs. The results revealed that three microbial consortia (CPP-KKU1, CPP-KKU2, and CPP-KKU3) exhibited the ability to degrade PP-MPs, achieving weight losses ranging from 11.6 ± 0.2 % to 17.8 ± 0.5 % after 30 days. Fourier transform infrared (FTIR) spectroscopy analysis confirmed the degradation through oxidation, as evidenced by the presence of new functional groups (-OH and -C=O). In particular, CPP-KKU3 showed the highest degradation efficiency, with scanning electron microscopy (SEM) analysis revealing surface cracking after treatment. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis identified various intermediate compounds, including heterocyclic aromatic compounds, phenyl groups, methylthio derivatives, and ethoxycarbonyl derivatives, indicating complex biochemical processes that were likely mediated by microbial enzymes. Furthermore, polyhydroxybutyrate (PHB) production by these consortia was also investigated. The result showed that both CPP-KKU2 and CPP-KKU3 successfully produced PHB, with CPP-KKU3 demonstrating superior performance in terms of PP-MP degradation and PHB production. Metagenomic analysis of CPP-KKU3 revealed abundant carbohydrate-active enzymes (CAZymes), particularly glycosyl transferases and glycoside hydrolases, which are associated with MP digestion. This study presents a promising bioremediation approach that addresses plastic waste degradation and sustainable bioplastic production, offering a potential solution for environmental plastic pollution.},
}

@article {pmid40056474,
year = {2025},
author = {Wang, H and Zhong, Y and Yang, Q and Li, J and Li, D and Wu, J and Yang, S and Liu, J and Deng, Y and Song, J and Peng, P},
title = {Coupling of sulfate reduction and dissolved organic carbon degradation accelerated by microplastics in blue carbon ecosystems.},
journal = {Water research},
volume = {279},
number = {},
pages = {123414},
doi = {10.1016/j.watres.2025.123414},
pmid = {40056474},
issn = {1879-2448},
abstract = {Microplastics have increasingly accumulated in sulfate- and organic matter-rich mangrove ecosystems, yet their effects on microbially mediated carbon and sulfur cycling in sediments remains poorly understood. In this study, we performed a 70-day anaerobic microcosm experiment to examine the effects of polylactic acid (PLA) microplastics with different sizes on sulfate reduction and dissolved organic carbon (DOC) degradation in mangrove sediments. Our results demonstrated that millimeter-scale PLA (mm-PLA) more effectively enhanced sulfate reduction, sulfur isotope fractionation, reduced sulfide production, and carbon dioxide (CO2) emission compared to micrometer-scale PLA (m-PLA). These results suggested that mm-PLA had a more pronounced impact on the carbon and sulfur cycles. Integrated 16S rRNA gene amplicon sequencing and metagenomic analyses revealed that mm-PLA preferentially enriched key functional microorganisms, including acetate-producing bacteria (e.g., Acetobacteroides), completely oxidizing sulfate-reducing bacteria (e.g., Desulfobacter), and incompletely oxidizing sulfate-reducing bacteria (e.g., Desulfobulbus). These microorganisms exhibited higher abundances and greater genetic potential for carbon metabolism and sulfate reduction under mm-PLA treatment. Their relative abundances showed positive correlations with sulfate reduction rates, sulfur isotope fractionation, and CO2 emission, identifying them as crucial drivers of coupled carbon-sulfur cycling. Furthermore, the synergistic interactions among Acetobacteroides, Desulfobacter, and Desulfobulbus facilitated the oxidation of sediment-derived DOC, highlighting significant implications for carbon sequestration in blue carbon ecosystems.},
}

@article {pmid40056186,
year = {2025},
author = {Chen, XX and Ju, Q and Qiu, D and Zhou, Y and Wang, Y and Zhang, XX and Li, JG and Wang, M and Chang, N and Xu, XR and Zhang, YB and Zhao, T and Wang, K and Zhang, Y and Zhang, J},
title = {Microbial dysbiosis with tryptophan metabolites alteration in lower respiratory tract is associated with clinical responses to anti-PD-1 immunotherapy in advanced non-small cell lung cancer.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {4},
pages = {140},
pmid = {40056186},
issn = {1432-0851},
support = {82103446//National Natural Science Foundation of China/ ; 82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//China Association for Science and Technology/ ; 2021LC2115//Fourth Military Medical University/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy ; *Tryptophan/metabolism ; *Lung Neoplasms/immunology/drug therapy/therapy/metabolism ; *Dysbiosis/immunology ; Female ; Male ; Middle Aged ; Aged ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Microbiota/drug effects/immunology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism ; Respiratory System/immunology/metabolism/microbiology ; Adult ; },
abstract = {Lower respiratory tract microbiome constitutes a unique immune microenvironment for advanced non-small cell lung cancer as one of dominant localized microbial components. However, there exists little knowledge on the associations between this regional microbiome and clinical responses to anti-PD-1 immunotherapy from clinical perspectives. Here, we equivalently collected bronchoalveolar lavage fluids from 56 advanced NSCLC participants treated with none (untreated, n = 28) or anti-PD-1 immunotherapy (treated, n = 28), which was further divided into responder (n = 17) and non-responder (n = 11) subgroups according to clinical responses, aiming to compare their microbial discrepancy by performing metagenomic sequencing and targeted metabolic alterations by tryptophan sequencing. Correspondingly, microbial diversities transformed significantly after receiving immunotherapeutic agents, where Gammaproteobacteria and Campylobacter enriched, but Escherichia, Streptococcus, Chlamydia, and Staphylococcus reduced at the genus level, differences of which failed to be achieved among subgroups with various clinical responses (responder or non-responder; LDA > 2, P < 0.05[*]). And the relative abundance of Staphylococcus and Streptomyces was escalated in response subgroup to anti-PD-1 immunotherapy by microbial compositional analysis (as relative abundance ≥ 3%, P < 0.05[*]), no significance of which was achieved among treated and untreated groups. In addition, relative abundances of bacterial tryptophan metabolites and its derivatives were also higher in the responder subgroup, distinctively being associated with divergent genera (VIP > 1, P < 0.05[*]). Our study revealed predictive performance of lower respiratory tract microbiome to antitumoral immunotherapy and further suggested that anti-PD-1 immunotherapy may alter lower respiratory tract microbiome composition and interact with its tryptophan metabolites to regulate therapeutic efficacy in advanced NSCLC, performing as potential biomarkers to prognosis and interventional strategies.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy
*Tryptophan/metabolism
*Lung Neoplasms/immunology/drug therapy/therapy/metabolism
*Dysbiosis/immunology
Female
Male
Middle Aged
Aged
*Immunotherapy/methods
*Immune Checkpoint Inhibitors/therapeutic use
Microbiota/drug effects/immunology
Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism
Respiratory System/immunology/metabolism/microbiology
Adult

@article {pmid40055840,
year = {2025},
author = {Rannon, E and Shaashua, S and Burstein, D},
title = {DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {67},
pmid = {40055840},
issn = {2049-2618},
mesh = {*Machine Learning ; *Metagenomics/methods ; Humans ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Computational Biology/methods ; Metagenome ; },
abstract = {BACKGROUND: Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infections and limiting the benefits of antibiotics. Therefore, early detection of antimicrobial resistance genes (ARGs), especially in pathogens, is crucial for human health. Most computational methods for ARG detection rely on homology to a predefined gene database and therefore are limited in their ability to discover novel genes.

RESULTS: We introduce DRAMMA, a machine learning method for predicting new ARGs with no sequence similarity to known ARGs or any annotated gene. DRAMMA utilizes various features, including protein properties, genomic context, and evolutionary patterns. The model demonstrated robust predictive performance both in cross-validation and an external validation set annotated by an empirical ARG database. Analyses of the high-ranking model-generated candidates revealed a significant enrichment of candidates within the Bacteroidetes/Chlorobi and Betaproteobacteria taxonomic groups.

CONCLUSIONS: DRAMMA enables rapid ARG identification for global-scale genomic and metagenomic samples, thus holding promise for the discovery of novel ARGs that lack sequence similarity to any known resistance genes. Further, our model has the potential to facilitate early detection of specific ARGs, potentially influencing the selection of antibiotics administered to patients. Video Abstract.},
}

*Machine Learning
*Metagenomics/methods
Humans
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects/classification
Computational Biology/methods
Metagenome

@article {pmid40055835,
year = {2025},
author = {Yin, CF and Pan, P and Li, T and Song, X and Xu, Y and Zhou, NY},
title = {The universal accumulation of p-aminophenol during the microbial degradation of analgesic and antipyretic acetaminophen in WWTPs: a novel metagenomic perspective.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {68},
pmid = {40055835},
issn = {2049-2618},
support = {32400079//the National Natural Science Foundation of China/ ; 2024YFA0919000//the National Key R&D Program of China/ ; 2024YFA0919000//the National Key R&D Program of China/ ; },
mesh = {*Acetaminophen/metabolism ; *Metagenomics ; *Biodegradation, Environmental ; *Aminophenols/metabolism ; *Antipyretics ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; China ; Bacteria/genetics/classification/metabolism/isolation & purification ; Humans ; Microbiota ; Analgesics ; Metagenome ; },
abstract = {BACKGROUND: Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 pandemic. Its high-water solubility leads to its pervasive presence in wastewater treatment plants (WWTPs), posing substantial risks to the environment and human health. Biological treatment is one of the promising approaches to remove such pollutants. Although previous studies have isolated acetaminophen-degrading pure cultures and proposed catabolic pathways, the interactions between microbiotas and acetaminophen, the distribution feature of acetaminophen degradation genes, and the gene-driven fate of acetaminophen in the real-world environment remain largely unexplored.

RESULTS: Among the water samples from 20 WWTPs across China, acetaminophen was detected from 19 samples at concentrations ranging from 0.06 to 29.20 nM. However, p-aminophenol, a more toxic metabolite, was detected in all samples at significantly higher concentrations (23.93 to 108.68 nM), indicating the presence of a catabolic bottleneck in WWTPs. Metagenomic analysis from both the above 20 samples and global datasets revealed a consistently higher abundance of initial acetaminophen amidases compared to downstream enzymes, potentially having explained the reason for the bottleneck. Meanwhile, a close correlation between initial amidases and Actinomycetota revealed by genome-based taxonomy suggests a species-dependent degradation pattern. Additionally, a distinct amidase ApaA was characterized by newly isolated Rhodococcus sp. NyZ502 (Actinomycetota), represents a predominant category of amidase in WWTPs. Significant phylogenetic and structural diversity observed among putative amidases suggest versatile acetaminophen hydrolysis potential in WWTPs.

CONCLUSIONS: This study enhances our understanding of acetaminophen's environmental fate and highlights the possible occurrence of ecological risks driven by imbalanced genes in the process of acetaminophen degradation in global WWTPs. Video Abstract.},
}

*Acetaminophen/metabolism
*Metagenomics
*Biodegradation, Environmental
*Aminophenols/metabolism
*Antipyretics
Wastewater/microbiology
Water Pollutants, Chemical/metabolism
China
Bacteria/genetics/classification/metabolism/isolation & purification
Humans
Microbiota
Analgesics
Metagenome

@article {pmid40055808,
year = {2025},
author = {Avershina, E and Qureshi, AI and Winther-Larsen, HC and Rounge, TB},
title = {Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {66},
pmid = {40055808},
issn = {2049-2618},
support = {2022067//Helse Sør-Øst RHF/ ; },
mesh = {*Software ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification ; *Metagenomics/methods ; Computational Biology/methods ; Ascomycota/genetics/classification/isolation & purification ; Basidiomycota/genetics/isolation & purification/classification ; Databases, Genetic ; },
abstract = {BACKGROUND: The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.

RESULTS: We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.

CONCLUSION: Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.},
}

*Software
*Gastrointestinal Microbiome/genetics
*Metagenome
Humans
*Mycobiome
*Fungi/genetics/classification/isolation & purification
*Metagenomics/methods
Computational Biology/methods
Ascomycota/genetics/classification/isolation & purification
Basidiomycota/genetics/isolation & purification/classification
Databases, Genetic

@article {pmid40054447,
year = {2025},
author = {Xiao, X and Zhao, W and Song, Z and Qi, Q and Wang, B and Zhu, J and Lin, J and Wang, J and Hu, A and Huang, S and Wang, Y and Chen, J and Fang, C and Ji, Q and Zhang, N and Meng, L and Wei, X and Chen, C and Cai, S and Chen, S and Ding, K and Li, D and Liu, S and Song, T and Tian, L and Zhang, H and Zhang, Y and Xu, S and Chen, J and Chen, H and Cen, Q and Jiang, F and Hu, G and Tang, C and Guo, W and Wang, X and Zhan, L and Fan, J and Wang, J and Zhou, C and Li, L and Lv, Z and Hu, Y and Lin, X and Mai, G and Luo, L and Yang, T and Wang, W and Kristiansen, K and Chen, L and Yang, H and Ni, M and Gu, Y and Mu, F and Yang, Y and Zhou, J and Wang, J and Zhang, WJ and Han, M and Xu, X and Liu, S},
title = {Microbial ecosystems and ecological driving forces in the deepest ocean sediments.},
journal = {Cell},
volume = {188},
number = {5},
pages = {1363-1377.e9},
doi = {10.1016/j.cell.2024.12.036},
pmid = {40054447},
issn = {1097-4172},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Oceans and Seas ; *RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.},
}

*Geologic Sediments/microbiology/chemistry
*Oceans and Seas
*RNA, Ribosomal, 16S/genetics
*Ecosystem
Phylogeny
Bacteria/genetics/classification/metabolism
Microbiota/genetics
Metagenome
Metagenomics

@article {pmid40054445,
year = {2025},
author = {Turjeman, S and Rozera, T and Elinav, E and Ianiro, G and Koren, O},
title = {From big data and experimental models to clinical trials: Iterative strategies in microbiome research.},
journal = {Cell},
volume = {188},
number = {5},
pages = {1178-1197},
doi = {10.1016/j.cell.2025.01.038},
pmid = {40054445},
issn = {1097-4172},
mesh = {*Microbiota ; Humans ; *Big Data ; Animals ; Clinical Trials as Topic ; Metagenomics/methods ; Metabolomics/methods ; },
abstract = {Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even "meta-cohort" analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches-such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics-provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream in vitro and in vivo research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.},
}

*Microbiota
Humans
*Big Data
Animals
Clinical Trials as Topic
Metagenomics/methods
Metabolomics/methods

@article {pmid40054329,
year = {2025},
author = {Saticioglu, IB and Ajmi, N and Coskuner-Weber, O and Alpsoy, S and Ay, H and Aydin, F and Abay, S and Karakaya, E and Kayman, T and Dalyan, C and Koca, FD and Tasci, G and Yarim, D and Morick, D and Yibar, A and Erdogan, S and Altun, S and Duman, M},
title = {Three new Microbacterium species isolated from the Marmara Sea mucilage event: Microbacterium istanbulense sp. nov., Microbacterium bandirmense sp. nov., Microbacterium marmarense sp. nov.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {3},
pages = {126600},
doi = {10.1016/j.syapm.2025.126600},
pmid = {40054329},
issn = {1618-0984},
abstract = {Three bacterial strains, Mu-43[T], Mu-80[T], and Mu-86[T], were isolated from the 2021 and 2022 mucilage event in the Marmara Sea and were taxonomically characterized. 16S rRNA gene sequence analysis confirmed that these strains belong to the genus Microbacterium. A polyphasic approach involving genomic and phenotypic analysis was employed to determine their taxonomic positions. A polyphasic approach integrating genomic and phenotypic analyses established their taxonomic positions. M. istanbulense Mu-43[T] showed 99.0 % 16S rRNA similarity to M. bandirmense Mu-80[T], with digital DNA-DNA hybridization (dDDH) and average nucleotide identity using BLAST (ANIb) values of 22.3 % and 78.3 %, respectively. M. bandirmense Mu-80[T] exhibited 99.2 % similarity to M. esteraromaticum DSM 8609[T], with dDDH and ANIb values of 23.6 % and 80 %. M. marmarense Mu-86[T] showed 97.4 % similarity to M. arthrosphaerae JCM 30492[T], with dDDH and ANIb values of 20.1 % and 74.2 %. Metagenomic analysis highlighted their ecological relevance, with relative abundances of 1.43 %, 1.15 %, and 0.95 %, respectively. Further genomic analysis identified biosynthetic gene clusters associated with secondary metabolite production, including non-ribosomal peptide synthetases and terpenoid biosynthesis pathways, suggesting potential antimicrobial activity. Additionally, antibiotic resistance genes, such as ABC efflux pumps and Erm23S_rRNA methyltransferase, indicate adaptation to environmental stress. These findings indicate that these species contribute to nutrient cycling and organic matter decomposition in mucilage-affected environments. Based on genomic and phenotypic data, these strains are proposed as novel species: M. istanbulense sp. nov. Mu-43[T] (LMG 33297[T] = DSM 117065[T]), M. bandirmense sp. nov. Mu-80[T] (LMG 33295[T] = DSM 117210[T]), and M. marmarense sp. nov. Mu-86[T] (LMG 33293[T] = DSM 117066[T]).},
}

@article {pmid40054170,
year = {2025},
author = {Aalam, J and Ahmad Shah, SN and Parveen, R},
title = {An extensive review on infectious disease diagnosis using machine learning techniques and next generation sequencing: State-of-the-art and perspectives.},
journal = {Computers in biology and medicine},
volume = {189},
number = {},
pages = {109962},
doi = {10.1016/j.compbiomed.2025.109962},
pmid = {40054170},
issn = {1879-0534},
abstract = {UNLABELLED: Infectious diseases, including tuberculosis (TB), HIV/AIDS, and emerging pathogens like COVID-19 pose severe global health challenges due to their rapid spread and significant morbidity and mortality rates. Next-generation sequencing (NGS) and machine learning (ML) have emerged as transformative technologies for enhancing disease diagnosis and management.

OBJECTIVE: This review aims to explore integrating ML techniques with NGS for diagnosing infectious diseases, highlighting their effectiveness and identifying existing challenges.

METHODS: A comprehensive literature review spanning the past decade was conducted using reputable databases, including IEEE Xplore, PubMed, Scopus, SpringerLink, and Science Direct. Research papers, articles, and conference proceedings meeting stringent quality criteria were analysed to assess the performance of ML algorithms applied to NGS and metagenomic NGS (mNGS) data.

RESULTS: The findings reveal that ML algorithms, such as deep neural networks (DNNs), support vector machines (SVM), and K-nearest neighbours (KNN), achieve high accuracy rates, often exceeding 95 %, in diagnosing infectious diseases. Deep learning methods excel in genomic and metagenomic data analysis, while traditional algorithms like Gaussian mixture models (GMM) also demonstrate robust classification capabilities. Challenges include reliance on single data types and difficulty distinguishing closely related pathogens.

CONCLUSION: The integration of ML and NGS significantly advances infectious disease diagnosis, offering rapid and precise detection capabilities. Addressing current limitations can further enhance the effectiveness of these technologies, ultimately improving global public health outcomes.},
}

@article {pmid40056781,
year = {2025},
author = {Chen, H and Li, J and Wu, Y and Li, Y and Zheng, S and Wu, Y and Xuan, R and Wu, L and Miao, J and Wang, Y and Tan, H and Zhou, J and Huang, J and Yan, X},
title = {Structural characteristics of intestinal microbiota of domestic ducks with different body sizes.},
journal = {Poultry science},
volume = {104},
number = {4},
pages = {104930},
doi = {10.1016/j.psj.2025.104930},
pmid = {40056781},
issn = {1525-3171},
abstract = {Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.},
}

@article {pmid40056745,
year = {2025},
author = {Zhu, S and Mao, H and Yang, X and Zhao, W and Sheng, L and Sun, S and Du, X},
title = {Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance.},
journal = {Ecotoxicology and environmental safety},
volume = {292},
number = {},
pages = {117956},
doi = {10.1016/j.ecoenv.2025.117956},
pmid = {40056745},
issn = {1090-2414},
abstract = {This study investigates the impact of heavy metal contamination in lead-zinc tailings on plant and soil microbial communities, focusing on the resilience mechanisms of rhizosphere microorganisms in these extreme environments. Utilizing metagenomic techniques, we identified a significant association between Coriaria nepalensis Wall. rhizosphere microbial communities and metal(loid) resistance genes. Our results reveal a notable diversity and abundance of bacteria within the rhizosphere of tailings, primarily consisting of Proteobacteria, Actinobacteria, and Chloroflexi. The presence of metal-resistant bacterial taxa, including Afipia, Bradyrhizobium, Sphingomonas, and Miltoncostaea, indicates specific evolutionary adaptations to metal-rich, nutrient-deficient environments. Elevated expression of resistance genes such as znuD, zntA, pbrB, and pbrT underscores the microorganisms' ability to endure these harsh conditions. These resistance genes are crucial for maintaining biodiversity, ecosystem stability, and adaptability. Our findings enhance the understanding of interactions between heavy metal contamination, microbial community structure, and resistance gene dynamics in lead-zinc tailings. Additionally, this research provides a theoretical and practical foundation for employing plant-microbial synergies in the in-situ remediation of contaminated sites.},
}

@article {pmid40056594,
year = {2025},
author = {Zhang, H and Zhang, Y and Li, L and Huang, S and Ma, W and Xu, B and Ng, HY and Kim, DH and Kang, S and Shi, X},
title = {An innovative high-rate biofilm-based process: Biopolymer production and recovery from wastewater organic pollutants.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124800},
doi = {10.1016/j.jenvman.2025.124800},
pmid = {40056594},
issn = {1095-8630},
abstract = {In this study, a novel high-rate moving bed biofilm reactor (MBBR) was constructed to enhance wastewater COD bio-conversion and biopolymer recovery with a hydraulic retention time (HRT) of 1.0 h and an organic loading rate (OLR) of 4.8 kg COD·m[-3]·d[-1]. A superior specific COD reduction rate of 4.1 kg COD·m[-3]·d[-1] was obtained. The settleability analyses showed that within a settling time of 30 min, a low effluent suspended solids (SS) concentration (40.6 mg/L) with a high biomass recovery rate (83.3%) was achieved. From the recovered biomass, a remarkably higher alginate-like exopolymer (ALE) yield (274.2-385.1 mg/g VSS) was extracted as compared with seeding sludge (148.3 mg/g VSS). In addition, high protein/polysaccharide ratios of 8.5-12.4 were revealed owing to the short HRT condition. Moreover, key functional genes involving classic ALE synthesis were fully detected in such mixed-cultured bioprocess through metagenomic sequencing. Overall, this study offers a proof of concept that bio-refinery of organics into value-added biopolymers could provide a promising direction for the transformation of wastewater treatment plants from energy/resource-consuming factories to resource-recovery factories.},
}

@article {pmid40056581,
year = {2025},
author = {Wu, Y and Xu, L and He, F and Song, X and Ding, J and Ma, J},
title = {Effects of micro-magnetite on anaerobic co-digestion of waste activated sludge and slaughterhouse waste: Microbial community and metabolism analyses.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124896},
doi = {10.1016/j.jenvman.2025.124896},
pmid = {40056581},
issn = {1095-8630},
abstract = {Micro-magnetite has been widely applied to improve anaerobic digestion (AD) performance, while comprehensive investigation of microbial community succession, metabolic pathway and magnetite fate remains unclear. In the current study, the effects of micro-magnetite (Fe3O4) on anaerobic co-digestion (AcD) of waste activated sludge and slaughterhouse waste were investigated. Experimental results indicated that the cumulative methane production was significantly increased from 484.6 mL/g VS to 524.4 mL/g VS with 0.8 g/L Fe3O4 addition. Recycled magnetite remained the initial physicochemical properties, including morphology, particle size and crystal structure, as evidenced by various characterization methods. Microbial community analysis indicated that magnetite addition enriched syntrophic bacteria (Armatimonadota, Syntrophomonas and Petrimonas) and methanogens (Methanosarcina). Metagenomic sequencing analysis demonstrated that hydrolysis and acidogenesis metabolic pathways were reinforced by magnetite addition. Meanwhile, the magnetite stimulated the direct interspecies electron transfer via enriching syntrophic microbes (Syntrophomonas and Methanosarcina) and conductive pili functional genes (pilA, mshA and mshC), finally achieving higher cumulative methane yield. This study provided in-depth investigation of the methane production facilitated by micro-magnetite addition and the magnetite fate during the AcD process.},
}

@article {pmid40056523,
year = {2025},
author = {Zhang, Q and Fan, Y and Qian, X and Zhang, Y},
title = {Unraveling the role of microplastics in antibiotic resistance: Insights from long-read metagenomics on ARG mobility and host dynamics.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137804},
doi = {10.1016/j.jhazmat.2025.137804},
pmid = {40056523},
issn = {1873-3336},
abstract = {As two emerging pollutants, microplastics (MPs) potentially serve as vectors for antibiotic resistance genes (ARGs) in aquatic environments, but the mechanisms driving ARG enrichment remain unclear. This study used long-read metagenomics to investigate ARG mobility and hosts dynamics within the biofilms of MPs and rocks in different water environments. We identified distinct enrichment patterns for microbial communities and ARGs, highlighting the significant role of horizontal gene transfer in ARG enrichment. Specifically, plasmid-encoded ARGs varied significantly among MP biofilms, rock biofilms, and water samples, while chromosome-encoded ARGs remained consistent across these environments, emphasizing the impact of plasmids on ARG enrichment. Despite this, 55.1 % of ARGs were on chromosomes, indicating that host organisms also play a crucial role. The related mechanisms driving ARG enrichment included enhanced cell adhesion, increased transmembrane transporter activity, and responses to environmental stressors, which led to an increased presence of plasmid-encoded ARGs on MP biofilms, facilitating more frequent horizontal gene transfer. Additionally, the diversity of hosts on MPs was notably lower compared to the water column, with specific bacteria, including Herbaspirillu, Limnohabitans, Polaromonas, Variovorax, Rubrivivax, and Thauera significantly driving ARG enrichment. This study highlights key mechanisms and bacterial taxa involved in ARG dynamics on MPs.},
}

@article {pmid40056518,
year = {2025},
author = {Zhu, Y and Li, R and Yan, S and Li, Y and Xie, S},
title = {Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137870},
doi = {10.1016/j.jhazmat.2025.137870},
pmid = {40056518},
issn = {1873-3336},
abstract = {Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.},
}

@article {pmid40054748,
year = {2025},
author = {Wine, E},
title = {Metagenome-informed metaproteomics: a new frontier in gut host-microbe-diet analysis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.02.024},
pmid = {40054748},
issn = {1528-0012},
}

@article {pmid40054424,
year = {2025},
author = {Ding, C and Sun, J},
title = {The potential contribution of microbial communities to carbon fixation and nitrogen cycle in the Eastern Indian Ocean.},
journal = {Marine environmental research},
volume = {207},
number = {},
pages = {107056},
doi = {10.1016/j.marenvres.2025.107056},
pmid = {40054424},
issn = {1879-0291},
abstract = {This study investigated the diversity and metabolic potential of microbial communities in the Eastern Indian Ocean (EIO) through 16S rDNA gene sequencing and metagenomics analyses. Water samples were collected from the surface waters (5 m depth) and 150 m depth layer in the EIO between March 20th and June 6th, 2019. This study reveals microbial-driven biogeochemical dynamics in the oligotrophic Eastern Indian Ocean, where vertically stratified communities (Cyanobacteria/Proteobacteria-dominated surface vs. diversified Proteobacteria at 150 m) and latitudinal diversity gradients reflect nutrient limitations. Metagenomics identified four carbon fixation strategies: the Calvin cycle dominated epipelagic CO2 assimilation, while the 3-hydroxypropionate bicycle showed elevated surface activity, alongside reductive citrate and Wood-Ljungdahl pathways involving novel Actinobacteria. Nitrogen cycling exhibited spatial heterogeneity: nifH-dominated nitrogen fixation in the surface waters, prevalent narGHI nitrate reduction, and divergent nirS/nirK/nosZ distributions tied to nutrient gradients. Proteobacteria and Actinobacteria were key nitrogen fixers, with novel Actinobacteriota diazotrophs expanding known diversity. Elevated nosZ abundance in the Bay of Bengal underscored regional nitrous oxide consumption hotspots. These findings underscore microbial mediation of carbon-nitrogen fluxes in oligotrophic systems, providing genomic insights into ecosystem responses to climate-driven ocean changes.},
}

@article {pmid40054356,
year = {2025},
author = {Yu, Y and Wu, J and Tang, Z and Wan, S and Hu, J and Li, B and Wang, J and Li, F},
title = {Unveiling the nitrogen metabolism mechanism for nitrogen retention in compost via in-situ ammonia recycling strategy.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124863},
doi = {10.1016/j.jenvman.2025.124863},
pmid = {40054356},
issn = {1095-8630},
abstract = {A large amount of ammonia volatilization in compost causes environmental pollution and reduces the quality of compost. Ammonia recycling composting strategy (ARCS) is new strategy for reducing ammonia volatilization by absorbing with backfilling ammonia into the compost. This study revealed the mechanism of ARCS on ammonia volatilization and nitrogen retention during chicken manure composting. The results showed that the adsorption layer containing wood vinegar had an obvious inhibition effect on ammonia volatilization. Compared to CK, ARCS treatment could reduce ammonia emissions and nitrogen loss by 20.65% and 39.6% with T3 (12d), respectively. Different adsorption time would affect the occurrence of various nitrogen components in the adsorption layer, especially the change of inorganic nitrogen content. Metagenomic analysis showed that ARCS treatment resulted in significant changes in bacterial communities, and different backfilling times had significant effects on nitrogen metabolism pathways in compost. Glutamate dehydrogenase and glutamate synthase were the key nitrogen metabolism processes during composting, which played an important role in ammonia volatilization and nitrogen retention. The suitable backfilling time (12d) promoted the acceleration of ammonia nitrogen metabolism in the early stage of composting and enhanced the ammonia assimilation and dissimilatory nitrate reduction function in the maturation stage to achieve nitrogen retention. This study provided valuable insights into the effects of in-situ ammonia absorption and backfilling on nitrogen metabolism pathways during composting.},
}

@article {pmid40054196,
year = {2025},
author = {Wang, S and Li, T and Yuan, X and Yu, J and Luan, Z and Guo, Z and Yu, Y and Liu, C and Duan, C},
title = {Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb-Zn mining wastelands.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137818},
doi = {10.1016/j.jhazmat.2025.137818},
pmid = {40054196},
issn = {1873-3336},
abstract = {The biotic and abiotic mechanisms that drive important biogeochemical processes (carbon, nitrogen, phosphorus and metals dynamics) in metal mine revegetation remains elusive. Metagenomic sequencing was used to explored vegetation, soil properties, microbial communities, functional genes and their impacts on soil processes during vegetation restoration in a typical Pb-Zn mine. The results showed a clear niche differentiation between bacteria, fungi and archaea. Compared to bacteria and fungi, the archaea richness were more tightly coupled with natural restoration changes. The relative abundances of CAZyme-related, denitrification-related and metal resistance genes reduced, while nitrification, urease, inorganic phosphorus solubilisation, phosphorus transport, and phosphorus regulation -related genes increased. Redundancy analysis, hierarchical partitioning analysis, relative-importance analysis and partial least squares path modelling, indicated that archaea diversity, primarily influenced by available lead, directly impacts carbon dynamics. Functional genes, significantly affected by available cadmium, directly alter nitrogen dynamics. Additionally, pH affects phosphorus dynamics through changes in bacterial diversity, while metal dynamics are directly influenced by vegetation. These insights elucidate natural restoration mechanisms in mine and highlight the importance of archaea in soil processes.},
}

@article {pmid40053579,
year = {2025},
author = {Wöhlbrand, L and Dörries, M and Siani, R and Medrano-Soto, A and Schnaars, V and Schumacher, J and Hilbers, C and Thies, D and Kube, M and Reinhardt, R and Schloter, M and Saier, MH and Winklhofer, M and Rabus, R},
title = {Key role of Desulfobacteraceae in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks.},
journal = {Science advances},
volume = {11},
number = {10},
pages = {eads5631},
pmid = {40053579},
issn = {2375-2548},
support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; },
mesh = {*Geologic Sediments/microbiology ; *Deltaproteobacteria/metabolism/genetics ; *Carbon Cycle ; Sulfur/metabolism ; Gene Regulatory Networks ; Phylogeny ; Metagenome ; Carbon/metabolism ; Proteome/metabolism ; Oxidation-Reduction ; Metabolic Networks and Pathways ; },
abstract = {Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol Corg year[-1]. This remarkable activity is largely attributable to the deltaproteobacterial family Desulfobacteraceae of complete oxidizers (to CO2), which our biogeography focused meta-analysis verified as cosmopolitan. However, the catabolic/regulatory networks underlying this ecophysiological feat at the thermodynamic limit are essentially unknown. Integrating cultivation-based (80 conditions) proteogenomics of six representative Desulfobacteraceae spp., we identify molecular commonalities explaining the family's environmental relevance and success. Desulfobacteraceae genomes are specifically enriched in substrate uptake, degradation capacities, and regulatory functions including fine-tuned sulfate uptake. Conserved gene arrangements and shared regulatory patterns translate into strikingly similar (sub-)proteome profiles. From 319 proteins, we constructed a meta-network for catabolizing 35 substrates. Therefrom, we defined a Desulfobacteraceae characteristic gene subset, which we found prevalent in metagenomes of organic-rich, marine sediments. These genes are promising targets to advance our mechanistic understanding of Desulfobacteraceae-driven biogeochemical processes in marine sediments and beyond.},
}

*Geologic Sediments/microbiology
*Deltaproteobacteria/metabolism/genetics
*Carbon Cycle
Sulfur/metabolism
Gene Regulatory Networks
Phylogeny
Metagenome
Carbon/metabolism
Proteome/metabolism
Oxidation-Reduction
Metabolic Networks and Pathways

@article {pmid40053318,
year = {2025},
author = {Nihalani, R and Zola, J and Aluru, S},
title = {Disambiguating a Soft Metagenomic Clustering.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0825},
pmid = {40053318},
issn = {1557-8666},
abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.},
}

@article {pmid40053297,
year = {2025},
author = {Scholand, KK and Schaefer, L and Govindarajan, G and Yu, Z and Galletti, JG and de Paiva, CS},
title = {Aged regulatory T cells fail to control autoimmune lacrimal gland pathogenic CD4[+] T cells.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {40053297},
issn = {2509-2723},
support = {R01EY030447/EY/NEI NIH HHS/United States ; EY-002520/EY/NEI NIH HHS/United States ; EY021725/EY/NEI NIH HHS/United States ; EY007001/EY/NEI NIH HHS/United States ; R01EY035333/EY/NEI NIH HHS/United States ; P30CA125123/CA/NCI NIH HHS/United States ; CPRIT-RP180672//CPRIT/ ; CA125123//National Institutes of Health (US)/ ; RR024574//National Institutes of Health (US)/ ; 221859/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; PICT 2020-00138//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT 2021-00109//Agencia Nacional de Promoción Científica y Tecnológica/ ; },
abstract = {CD25KO mice are a model of Sjögren disease. CD25KO mice have severe inflammation and infiltrating lymphocytes to the lacrimal glands (LG). Whether the pathogenicity of CD25KO CD4[+] T cells can be controlled in vivo by Tregs is unknown. Eight-week-old B6 and CD25KO mice LGs were submitted for RNA bulk sequencing. A total of 3481 genes were differentially expressed in CD25KO LG compared to B6. Tear washing analysis identified CD25KO mice had elevated protein levels of TNF, IFN-γ, and CCL5 and decreased protein levels of IL-12p40 and VEGF-A. Co-adoptive transfer of CD25KO CD4[+] T cells with either young or aged B6 Tregs was performed in RAG1KO mice. Recipients of CD25KO CD4[+] T cells alone had higher LG inflammation than naive mice. However, in recipients of young B6 Tregs plus CD25KO CD4[+] T cells, LGs had significantly reduced inflammation. Recipients of CD25KO CD4[+] T cells with aged B6 Tregs had more inflamed LGs than young Tregs, suggesting aged Tregs have less suppressive capacity in vivo. Altogether, CD25KO mice have phenotypic and genetic changes resulting in increased inflammation and severe lymphocytic infiltration in the LGs. However, this autoimmunity can be controlled by the addition of young, but not aged, Tregs, suggesting that aging Tregs have dysfunctional suppression.},
}

@article {pmid40052570,
year = {2025},
author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L},
title = {Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn's Disease.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf039},
pmid = {40052570},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS: A total of 1,175 fecal metagenomic sequencing samples, predominantly from three cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1,357 KO genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1,256 insertions/deletions (InDels), and 3,567 single nucleotide variants, with a considerable portion of these variants occurred in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an AUC of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC=0.996) and five other microbiome-associated pediatric cohorts.

CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of the non-invasive diagnostic tools and targeted therapies.},
}

@article {pmid40052474,
year = {2025},
author = {Bamigbade, GB and Abdin, M and Subhash, A and Arachchi, MP and Ullah, N and Gan, RY and Ali, A and Kamal-Eldin, A and Ayyash, M},
title = {Plant polysaccharide-capped nanoparticles: A sustainable approach to modulate gut microbiota and advance functional food applications.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {2},
pages = {e70156},
doi = {10.1111/1541-4337.70156},
pmid = {40052474},
issn = {1541-4337},
support = {//United Arab Emirates University/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Nanoparticles/chemistry ; *Polysaccharides/chemistry ; *Functional Food ; Humans ; Plants/chemistry ; },
abstract = {Plant-derived polysaccharides have emerged as sustainable biopolymers for fabricating nanoparticles (polysaccharide-based nanomaterials [PS-NPs]), presenting unique opportunities to enhance food functionality and human health. PS-NPs exhibit exceptional biocompatibility, biodegradability, and structural versatility, enabling their integration into functional foods to positively influence gut microbiota. This review explores the mechanisms of PS-NPs interaction with gut microbiota, highlighting their ability to promote beneficial microbial populations, such as Lactobacilli and Bifidobacteria, and stimulate the production of short-chain fatty acids. Key synthesis and stabilization methods of PS-NPs are discussed, focusing on their role in improving bioavailability, stability, and gastrointestinal delivery of bioactive compounds in food systems. The potential of PS-NPs to address challenges in food science, including enhancing nutrient absorption, mitigating intestinal dysbiosis, and supporting sustainable food production through innovative nanotechnology, is critically evaluated. Barriers such as enzymatic degradation and physicochemical stability are analyzed, alongside strategies to optimize their functionality within complex food matrices. The integration of PS-NPs in food systems offers a novel approach to modulate gut microbiota, improve intestinal health, and drive the development of next-generation functional foods. Future research should focus on bridging knowledge gaps in metagenomic and metabolomic profiling of PS-NPs, optimizing their design for diverse applications, and advancing their role in sustainable and health-promoting food innovations.},
}

*Gastrointestinal Microbiome/drug effects
*Nanoparticles/chemistry
*Polysaccharides/chemistry
*Functional Food
Humans
Plants/chemistry

@article {pmid40052450,
year = {2025},
author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S},
title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2474730},
doi = {10.1080/07853890.2025.2474730},
pmid = {40052450},
issn = {1365-2060},
mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation & purification ; Overweight/microbiology/complications ; },
abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.

METHODS: A total of 103 PLWHIV were followed for 48 weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238 dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.

RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48 weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.

CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48 weeks of ART.},
}

Humans
Male
*HIV Infections/complications/microbiology
Female
*Gastrointestinal Microbiome
Middle Aged
Adult
*Akkermansia
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
Prospective Studies
Feces/microbiology
Metagenomics/methods
Hyperlipidemias/microbiology
Metabolic Diseases/microbiology/epidemiology
Verrucomicrobia/isolation & purification
Overweight/microbiology/complications

@article {pmid40052378,
year = {2025},
author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H},
title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf055},
pmid = {40052378},
issn = {1365-2672},
abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.

METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied > 50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.

CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.},
}

@article {pmid40052334,
year = {2025},
author = {Lu, Y and Dong, Y and Zhang, M and Mao, L},
title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14095},
doi = {10.1111/1755-0998.14095},
pmid = {40052334},
issn = {1755-0998},
support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; },
abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.},
}

@article {pmid40052063,
year = {2025},
author = {Zheng, H and Peng, P and Wang, S and Zhang, B and Yang, L and Wang, Y and Li, L and Pang, G},
title = {Microbiological Diagnostic Performance and Clinical Effect of Metagenomic Next-Generation Sequencing for the Detection of Immunocompromised Patients With Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1223-1236},
pmid = {40052063},
issn = {1178-6973},
abstract = {OBJECTIVE: Community-acquired pneumonia (CAP) presents a significant public health concern, necessitating timely and precise diagnosis. Metagenomic next-generation sequencing (mNGS) has shown promise as a powerful tool for pathogen identification in infectious diseases. This study aimed to evaluate the diagnostic efficacy and clinical applicability of mNGS for immunocompromised patients with CAP compared to the culture method.

METHODS: This study included 168 patients. We used both mNGS and conventional culture methods to identify the pathogen spectrum and evaluate diagnostic performance. Treatment regimens and clinical outcomes were meticulously documented.

RESULTS: The sensitivity of mNGS was greater than that of the culture method across all samples (79.05% vs 16.03%; p < 0.001). mNGS identified pathogens missed by culture in 59.52% of patients and detected polymicrobial infections that were not detected by culture in 47.62% of patients. Streptococcus pneumoniae, Candida albicans, and Human herpesvirus 4 at classification level emerged as the predominant pathogens identified in CAP patients through mNGS. When examining the mNGS results between groups, the proportions of immunocompromised patients with bacterial (p < 0.001), fungal (p < 0.001), viral (p < 0.05), and mixed infections (p < 0.001) were all significantly higher than those in immunocompetent patients. Treatment adjustments guided by mNGS were observed in 73.21% of patients. Specifically, a beneficial clinical effect was observed in 50.60% (85/168) of patients, treatment confirmation in 22.62% (38/168) of patients, and no clinical benefit in 26.80% (45/168) of patients based on mNGS-guided antibiotic treatment adjustments.

CONCLUSION: These findings highlight the diagnostic performance of mNGS for identifying pathogens, particularly in immunocompromised patients vulnerable to infections, offering valuable insights for clinical decision-making.},
}

@article {pmid40051621,
year = {2025},
author = {Chen, Y and Liang, S and Lu, Y and Zhou, X and Zheng, R and Chen, Y},
title = {Case Report: First report of Legionella micdadei pneumonia and organizing pneumonia in a patient with myelodysplastic and Sweet syndromes.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1510948},
pmid = {40051621},
issn = {1664-3224},
mesh = {Humans ; *Myelodysplastic Syndromes/complications ; *Sweet Syndrome/diagnosis/drug therapy ; Male ; Legionella ; Pneumonia, Bacterial/diagnosis/drug therapy/microbiology/immunology ; Immunocompromised Host ; Legionellosis/diagnosis/drug therapy/microbiology ; Aged ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Glucocorticoids/therapeutic use ; Female ; Legionnaires' Disease/diagnosis/drug therapy/complications/immunology ; Organizing Pneumonia ; },
abstract = {The immunocompromised population is susceptible to Legionella pneumonia. The diagnosis and treatment of Legionella pneumonia in immunocompromised individuals are challenging clinical endeavors. Previous studies have identified Legionella pneumonia as a potential cause of organizing pneumonia (OP), however, the association between Legionella pneumonia and OP has not received enough clinical attention. We retrospectively evaluated a case involving Legionella micdadei infection and OP in a patient with myelodysplastic syndrome and concurrent Sweet syndrome. The diagnosis of Legionella micdadei pneumonia was confirmed through various methods: metagenomic next generation sequencing (mNGS), Giemsa-staining and fluorescence in situ hybridization of lung tissue, as well as serum immunofluorescence antibody testing. Histopathological analysis of lung tissue revealed OP. The patient was successfully treated with a combination of antibiotics and low-dose glucocorticoids. In immunocompromised individuals, mNGS was capable of detection non-Legionella pneumophila serogroup 1. The pathological examination is important for identifying secondary OP and provides the evidence for treatment with glucocorticoids.},
}

Humans
*Myelodysplastic Syndromes/complications
*Sweet Syndrome/diagnosis/drug therapy
Male
Legionella
Pneumonia, Bacterial/diagnosis/drug therapy/microbiology/immunology
Immunocompromised Host
Legionellosis/diagnosis/drug therapy/microbiology
Aged
Middle Aged
Anti-Bacterial Agents/therapeutic use
Glucocorticoids/therapeutic use
Female
Legionnaires' Disease/diagnosis/drug therapy/complications/immunology
Organizing Pneumonia

@article {pmid40051412,
year = {2025},
author = {Houttu, V and Boulund, U and Troelstra, M and Csader, S and Stols-Gonçalves, D and Mak, AL and Dijk, AV and Bouts, J and Winkelmeijer, M and Verdoes, X and van den Berg-Faay, S and Lek, D and Ronteltap, T and de Haan, F and Jorstad, H and Männistö, V and Savonen, K and Pentikäinen, H and Hanhineva, K and Babu, AF and Panagiotou, G and van Delden, O and Verheij, J and Doukas, M and Nederveen, A and Schwab, U and Grefhorst, A and Nieuwdorp, M and Holleboom, AG},
title = {Deep phenotyping of patients with MASLD upon high-intensity interval training.},
journal = {JHEP reports : innovation in hepatology},
volume = {7},
number = {3},
pages = {101289},
pmid = {40051412},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: Exercise is a key component of lifestyle management in patients with metabolic dysfunction-associated steatotic liver disease (MASLD), but neither its therapeutic effect on the active stage of the disease, that is metabolic dysfunction-associated steatohepatitis (MASH) nor the mediating mechanisms have been characterized. Therefore, we performed multi-omic phenotyping of patients with MASLD-MASH on an exercise program.

METHODS: Fifteen patients with MASLD conducted high-intensity interval training (HIIT) combined with home-based training for 12 weeks. MASLD was evaluated using histology, transient elastography, and multiparametric magnetic resonance imaging (MRI) before and after the intervention. Change in maximal oxygen consumption (VO2max) and MRI-determined liver fat were compared with a control group of patients with MASLD (n = 22). RNA sequencing was performed on liver, muscle, and fat biopsies of patients in the exercise group. Stool was analyzed by shotgun metagenomics and untargeted metabolomics was performed on plasma, urine, adipose, and stool.

RESULTS: HIIT increased VO2max by 10.1% and improved mitochondrial metabolism in skeletal muscle, indicating improved cardiorespiratory fitness and adherence. VO2max increased significantly in the exercise group compared with controls. Histologically, no reduction in steatosis, MASH, or liver fibrosis was observed; however, transient elastography tended to improve. MRI-determined liver fat did not change in the exercise group compared with controls. HIIT induced changes in mRNA expression of genes related to beiging of adipose tissue and fibrogenesis in liver. In addition, specific gut microbial taxa and metabolites changed.

CONCLUSIONS: HIIT increased cardiorespiratory fitness and induced beneficial gene expression changes in muscle, adipose tissue, and liver, but without translation into histological improvement of MASLD. Longer exercise intervention trials are warranted to validate or refute current recommendations for exercise as a cornerstone treatment for MASLD-MASH.

IMPACT AND IMPLICATIONS: Despite exercise being considered as a key component of lifestyle management for steatotic liver disease, neither the clinical effects nor the mechanisms involved are completely understood. We show that a high-intensity interval training (HIIT) program in 15 patients with metabolic dysfunction-associated steatotic liver disease (MASLD) improved cardiorespiratory fitness, compared with 22 control patients with MASLD who did not participate in an exercise program, however, it did not improve MASLD. HIIT induced a positive effect on fat tissue and muscle metabolism which was accompanied with changes in certain gut bacteria and metabolites in blood and urine. These findings improve our understanding of the effects of exercise on the whole-body metabolism in relation to steatotic liver disease. As such, this study provides a basis for future exercise interventions in patients with MASLD, required to thoroughly test current guideline advice for exercise as a cornerstone treatment for MASLD of all stages.

CLINICAL TRIAL REGISTRY: Dutch Trial Register (registration number NL7932).},
}

@article {pmid40050994,
year = {2025},
author = {Talat, A and Bashir, Y and Khalil, N and Brown, CL and Gupta, D and Khan, AU},
title = {Antimicrobial resistance transmission in the environmental settings through traditional and UV-enabled advanced wastewater treatment plants: a metagenomic insight.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {27},
pmid = {40050994},
issn = {2524-6372},
support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {BACKGROUND: Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.

RESULTS: The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, blaOXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (blaNDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.

CONCLUSIONS: Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.},
}

@article {pmid40050500,
year = {2025},
author = {Dave, M and Tattar, R},
title = {Antimicrobial resistance genes in the oral microbiome.},
journal = {Evidence-based dentistry},
volume = {},
number = {},
pages = {},
pmid = {40050500},
issn = {1476-5446},
abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .

DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.

DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.

STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.

DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.

RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n = 10) or NGS metagenomics (n = 5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.

CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.},
}

@article {pmid39726137,
year = {2025},
author = {Schwesig, K and Zizka, V and Scherber, C and Hölzel, N},
title = {Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14060},
doi = {10.1111/1755-0998.14060},
pmid = {39726137},
issn = {1755-0998},
support = {01UT2101C//Bundesministerium für Bildung und Forschung/ ; 01UT2101B//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Biodiversity ; Animals ; *Amphibians/genetics/classification ; *Ponds ; Germany ; *DNA Barcoding, Taxonomic/methods ; *Lakes ; Odonata/genetics/classification ; Metagenomics/methods ; DNA, Environmental/genetics ; Aquatic Organisms/genetics/classification ; },
abstract = {Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to achieve the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on N = 56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed through exuviae. In total, both methods detected 8 out of 11 amphibian species, while the remaining three species were detected by eDNA only. We did not find differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining 19 species were detected by exuviae only. Species numbers per plot were higher for exuviae and only 30% of species were detected with metabarcoding. The species identified by eDNA were those with high abundance, and their detection probabilities were similar to transect walks. The results for amphibians show equal suitability and high complementarity of the compared methods. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, eDNA metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.},
}

*Biodiversity
Animals
*Amphibians/genetics/classification
*Ponds
Germany
*DNA Barcoding, Taxonomic/methods
*Lakes
Odonata/genetics/classification
Metagenomics/methods
DNA, Environmental/genetics
Aquatic Organisms/genetics/classification

@article {pmid40050382,
year = {2025},
author = {Liu, C and Wang, H and Wang, Z and Liang, L and Li, Y and Liu, D and Lu, Q},
title = {Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7910},
pmid = {40050382},
issn = {2045-2322},
support = {32230071//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Coleoptera/microbiology/genetics ; Metagenome ; Bacteria/genetics/classification/metabolism ; Microbiota ; Symbiosis ; Weevils/microbiology/genetics ; Phylogeny ; },
abstract = {Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.},
}

Animals
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Coleoptera/microbiology/genetics
Metagenome
Bacteria/genetics/classification/metabolism
Microbiota
Symbiosis
Weevils/microbiology/genetics
Phylogeny

@article {pmid40050078,
year = {2025},
author = {Zheng, YJ and Hou, JY and Zhong, J and Ye, XW},
title = {[A case of COVID-19-associated pulmonary aspergillosis combined with COVID-19-associated pulmonary mucormycosis].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {3},
pages = {267-271},
doi = {10.3760/cma.j.cn112147-20240809-00476},
pmid = {40050078},
issn = {1001-0939},
support = {82460015//National Natural Science Foundation of China/ ; 2019PT320003//Special Fund for Basic Scientific Research Operations of the Chinese Academy of Medical Sciences/ ; },
mesh = {Humans ; *Mucormycosis/diagnosis/complications ; *COVID-19/complications ; *Pulmonary Aspergillosis/complications/diagnosis ; Male ; Tomography, X-Ray Computed ; SARS-CoV-2/isolation & purification ; Lung Diseases, Fungal/diagnosis/complications ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/pathology/diagnostic imaging/microbiology ; Antifungal Agents/therapeutic use ; },
abstract = {COVID-19-associated invasive fungal infections are fungal infections that develop during COVID-19, including pulmonary aspergillosis (CAPA) and pulmonary mucormycosis (CAPM). This report presents a case of a patient with recurrent COVID-19 infections who showed pulmonary cavities and pleural effusion on chest CT. A mixed diagnosis of CAPA and CAPM was confirmed by histopathological analysis of bronchoalveolar lavage fluid and metagenomic next-generation sequencing. This study highlights the importance of suspecting CAPA and CAPM in diabetic COVID-19 patients with unexplained radiological findings that cannot be attributed to common infections or pulmonary tumors. Prompt and thorough diagnostic investigations, including histopathology, microbiology, and molecular techniques, are essential for accurate diagnosis. Early and effective antifungal treatment can significantly improve patient outcomes.},
}

Humans
*Mucormycosis/diagnosis/complications
*COVID-19/complications
*Pulmonary Aspergillosis/complications/diagnosis
Male
Tomography, X-Ray Computed
SARS-CoV-2/isolation & purification
Lung Diseases, Fungal/diagnosis/complications
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Lung/pathology/diagnostic imaging/microbiology
Antifungal Agents/therapeutic use

@article {pmid40049907,
year = {2025},
author = {Jia, Z and Li, C and Zhang, S and Tang, Y and Ma, S and Liu, X and Zhang, J},
title = {Microbial inoculants modify the functions of soil microbes to optimize plant growth at abandoned mine sites.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {678-690},
doi = {10.1016/j.jes.2024.10.002},
pmid = {40049907},
issn = {1001-0742},
mesh = {*Soil Microbiology ; *Mining ; *Plant Development ; *Soil/chemistry ; Phosphorus/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; Nitrogen/metabolism ; Microbiota ; Bacillus thuringiensis ; },
abstract = {Mining activities have caused significant land degradation globally, emphasizing the need for effective restoration. Microbial inoculants offer a promising solution for sustainable remediation by enhancing soil nutrients, enzyme activities, and microbial communities to support plant growth. However, the mechanisms by which inoculants influence soil microbes and their relationship with plant growth require further investigation. Metagenomic sequencing was employed for this study, based on a one-year greenhouse experiment, to elucidate the effects of Bacillus thuringiensis NL-11 on the microbial functions of abandoned mine soils. Our findings revealed that the application of microbial inoculants significantly enhanced the soil total carbon (TC), total sulfur (TS), organic carbon (SOC), available phosphorus (AP), ammonium (NH4[+]), urease, arylsulfatase, phosphatase, β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG). Moreover, this led to substantial improvements in plant height, as well as aboveground and belowground biomass. Microbial inoculants impacted functional gene structures without altering diversity. The normalized abundance of genes related to the degradation of carbon and nitrogen, methane metabolism, and nitrogen fixation were observed to increase, as well as the functional genes related to phosphorus cycling. Significant correlations were found between nutrient cycling gene abundance and plant biomass. Partial Least Squares Path Model analysis showed that microbial inoculants not only directly influenced plant biomass but also indirectly affected the plant biomass through C cycle modifications. This study highlights the role of microbial inoculants in promoting plant growth and soil restoration by improving soil properties and enhancing normalized abundance of nutrient cycling gene, making them essential for the recovery of abandoned mine sites.},
}

*Soil Microbiology
*Mining
*Plant Development
*Soil/chemistry
Phosphorus/metabolism
Carbon/metabolism
Biodegradation, Environmental
Nitrogen/metabolism
Microbiota
Bacillus thuringiensis

@article {pmid40049896,
year = {2025},
author = {Yu, Q and Hu, X and Qian, Y and Wang, Y and Shi, C and Qi, R and Heděnec, P and Nan, Z and Li, H},
title = {Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {550-562},
doi = {10.1016/j.jes.2024.08.026},
pmid = {40049896},
issn = {1001-0742},
mesh = {*Bacteria/metabolism/classification/genetics ; *Viruses ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Nitrogen/analysis ; Carbon/metabolism ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Nutrients/analysis ; },
abstract = {The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.},
}

*Bacteria/metabolism/classification/genetics
*Viruses
Phosphorus/analysis
RNA, Ribosomal, 16S/genetics
Nitrogen/analysis
Carbon/metabolism
Water Microbiology
Water Pollutants, Chemical/analysis
Nutrients/analysis

@article {pmid40049874,
year = {2025},
author = {Yao, W and Chang, R and Chen, K and Yang, C and Lu, Y and Wang, S and Dong, K and Huang, B and Jin, R},
title = {Performance and mechanism of enhanced phosphorus release and volatile fatty acid production from Fe-P sludge via co-fermenting with agricultural wastes.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {290-299},
doi = {10.1016/j.jes.2024.07.019},
pmid = {40049874},
issn = {1001-0742},
mesh = {*Phosphorus/metabolism ; *Fatty Acids, Volatile/metabolism ; *Sewage ; *Fermentation ; *Agriculture/methods ; *Waste Disposal, Fluid/methods ; Iron/metabolism ; },
abstract = {Anaerobic fermentation is an efficient method to extract phosphorus from excess sludge, thereby facilitating its recovery and mitigating the phosphorus resource shortage. However, the prevalent metal-bound phosphorus species within sludge was difficult to release into the fermentation liquor. To address this, this study evaluated the enhanced phosphorus release performance from sludge containing iron-phosphorus compounds (Fe-P) via co-fermenting it with agriculture wastes. Specifically, protein-rich feather (Feather Group) and polysaccharide-rich tea residue (Tea Group) was respectively dosed into batch-scale fermentation jar. Results showed that the Feather Group exhibited significantly higher levels of released soluble phosphorus (2.1 folds) and volatile fatty acids (41.4 folds) compared to the Control Group, with concentrations reaching up to 280 mg/L and 9366 mg chemical oxygen demand /L, respectively. The activities of α-glucosidase, neutral protease and acetate kinase in the Feather group were increased by 11.1 %, 92.3 % and 37.6 %, respectively, compared with the Control group. Methanogen abundance decreased while hydrolytic acid-producing bacteria and iron-reducing bacteria increased significantly after supplying agricultural wastes. Metagenomic analysis demonstrated a significant increase in genes related to acetic acid synthesis. Mechanism elucidation suggested that increased iron-reducing bacteria abundance promoted Fe[3+] reduction into Fe[2+], thus enhancing phosphorus release from Fe-P compounds. This work may provide valuable information for developing effective strategy to extract phosphorus resource from complex environmental wastes.},
}

*Phosphorus/metabolism
*Fatty Acids, Volatile/metabolism
*Sewage
*Fermentation
*Agriculture/methods
*Waste Disposal, Fluid/methods
Iron/metabolism

@article {pmid40049354,
year = {2025},
author = {Sun, RZ and Pan, Y and Wang, J and Gao, T and Yu, HQ and Wang, J},
title = {Metabolic and Ecological Responses of Denitrifying Consortia to Different Carbon Source Strategies Under Fluctuating C/N Conditions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121292},
doi = {10.1016/j.envres.2025.121292},
pmid = {40049354},
issn = {1096-0953},
abstract = {Frequent fluctuations in the carbon-to-nitrogen (C/N) ratio of urban wastewater influent can undermine denitrification performance, posing challenges for stable nitrogen removal. Although supplying additional carbon sources is a recognized strategy to mitigate these issues, the underlying microbial interactions and metabolic reconfigurations triggered by changing C/N ratios remain incompletely understood. Here, we employed methanol, glycerol, sodium acetate, and glucose in long-term denitrification reactors and integrated denitrification kinetics, 16S rRNA gene amplicon sequencing, metagenomic binning, and metabolic modeling to elucidate how these systems respond to a declining C/N ratio. Our results show that lower C/N ratios diminished denitrification efficiency in all treatments, with each carbon source eliciting distinct shifts in microbial assemblages. Fluctuations in the C/N ratio determine the extent of directional selection of microbial communities based on carbon source metabolism and induce significant changes in non-dominant microorganisms. Throughout the process, the synthesis potential of PHA is closely linked to the system's ability to withstand fluctuations. Notably, metabolic modeling indicated that heightened tricarboxylic acid (TCA) cycle activity in the methanol- and glucose-fed communities was associated with suboptimal nitrogen removal. These findings offer novel insights into the metabolic and ecological mechanisms governing carbon source-driven denitrification under fluctuating C/N conditions, providing a valuable framework for optimizing nitrogen removal in urban wastewater treatment systems.},
}

@article {pmid40049094,
year = {2025},
author = {Yu, C and He, Q and Nie, WB and Zhang, T and Wu, H and Yang, Y and Fu, S and Tan, X and Chen, Y},
title = {Effluent organic matter facilitates anaerobic methane oxidation coupled with nitrous oxide reduction in river sediments.},
journal = {Water research},
volume = {278},
number = {},
pages = {123415},
doi = {10.1016/j.watres.2025.123415},
pmid = {40049094},
issn = {1879-2448},
abstract = {Effluent organic matter (EfOM) from wastewater treatment plants (WWTPs) contains humic-like substances that function as electron shuttles, thereby facilitating microbially-mediated redox reactions. However, the mechanisms governing the coupled processes of anaerobic oxidation of methane (CH4) (AOM) and nitrous oxide (N2O) reduction in river sediments, which receive WWTPs effluents, remain poorly understood. In this study, an incubation experiment with anoxic river sediments was conducted to assess the impacts of EfOM on AOM and nitrous oxide reduction using different effluent dilution ratios. The results showed that EfOM significantly enhanced both processes. Specifically, the AOM rate increased from 8.1 to 14.3 μg gdw[-1] d[-1], while the N2O reduction rate increased from 29.2 to 56.5 μg gdw[-1] d[-1]. The results of batch tests demonstrated that AOM process enhanced N2O reduction in the presence of EfOM, highlighting the critical role of EfOM in linking these processes. Nitrate-dependent anaerobic methane oxidation (n-DAMO) archaea and denitrifying bacteria dominated the sediment incubated with EfOM. Metagenomic and metatranscriptomic analyses revealed that the denitrifying bacteria exclusively reduce N2O, confirming the role of EfOM in facilitating electron transfer between n-DAMO archaea and N2O reducers. This indicates that effluent discharge could be a potential factor driving the concurrent sinks of methane and nitrous oxide, offering a perspective for investigating the impacts of WWTPs effluent on greenhouse gas sinks in freshwater ecosystems.},
}

@article {pmid40048953,
year = {2025},
author = {Tamai, S and Okuno, M and Ogura, Y and Suzuki, Y},
title = {Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {970},
number = {},
pages = {178989},
doi = {10.1016/j.scitotenv.2025.178989},
pmid = {40048953},
issn = {1879-1026},
abstract = {Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.},
}

@article {pmid40048849,
year = {2025},
author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK},
title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.},
journal = {EBioMedicine},
volume = {114},
number = {},
pages = {105630},
doi = {10.1016/j.ebiom.2025.105630},
pmid = {40048849},
issn = {2352-3964},
abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.

METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.

FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E. coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.

INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.

FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Tromsø Research Foundation, Norway.},
}

@article {pmid40048707,
year = {2025},
author = {Hernández-Verdin, I and Kirasic, E and Mokhtari, K and Barillot, N and Rincón de la Rosa, L and Sourdeau, E and Abada, Y and Le Tarff-Tavernier, M and Nichelli, L and Rozenblum, L and Kas, A and Mathon, B and Choquet, S and Houillier, C and Hoang-Xuan, K and Alentorn, A},
title = {Gut microbiome modulates the outcome in primary central nervous system lymphoma patients undergoing chemotherapy: an ancillary study from the BLOCAGE trial.},
journal = {Neuro-oncology},
volume = {},
number = {},
pages = {},
doi = {10.1093/neuonc/noaf059},
pmid = {40048707},
issn = {1523-5866},
abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) treatment relies on a high-dose methotrexate based chemotherapy (HD-MTX-based CT) regimen; however, whether there is a specific microbiota composition association with treatment response and clinical outcomes remains incompletely understood.

METHODS: We conducted a prospective study of PCNSL patients, included in the clinical trial NCT02313389 and the ancillary study NCT04253496 from 2020 to 2023, where patients were treated with first line HD-MTX-based polychemotherapy without a consolidation treatment. Stool (n=52), cerebrospinal fluid (CSF, n=52), and plasma samples (n=35) were collected before and/or after therapy initiation to perform metagenomic, flow cytometry, and metabolomic analyses. Plasma metabolomic data of 90 patients also included in the BLOCAGE clinical trial was subsequently used as a validation cohort.

RESULTS: Unsupervised clustering of microbial data identified two distinct gut microbial communities, differing in Parabacteroides distasonis abundance, which correlated with progression-free survival and overall survival in both uni- and multivariate analyses. Higher P. distasonis levels were linked to increased plasma betaine/valine metabolites and enhanced CD8 T cell infiltration in the CSF, suggesting a connection between gut microbiota and immune regulation. Stratifying the validation cohort by betaine/valine content confirmed these clinical associations.

CONCLUSIONS: Our findings suggest that gut microbiome communities modulate clinical outcomes in PCNSL patients undergoing standard treatment. Moreover, after future validation in external cohorts, the quantification of Parabacteroides distasonis could potentially provide a basis for patient stratification and guide personalized therapeutic strategies in the near future.},
}

@article {pmid40047424,
year = {2025},
author = {Li, N and Li, M and Zhang, H and Bai, Z and Fei, Z and Dong, Y and Zhang, X and Xiao, P and Sun, X and Zhou, D},
title = {Effects of post-adulthood environmental hygiene improvement on gut microbiota and immune tolerance in mice.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0247724},
doi = {10.1128/aem.02477-24},
pmid = {40047424},
issn = {1098-5336},
abstract = {UNLABELLED: Changes in diet, cleanliness, stress, and exercise patterns may contribute to the disappearance of various gut microbes in humans who relocate to developed countries from developing countries. To explore the impact of environmental cleanliness on the gut microbiota, adult mice housed in a general animal room were divided into three groups. The control group was subjected to an unchanged living environment, SPF mice were moved to a specific pathogen-free (SPF) animal room with higher environmental cleanliness, and SPFL (specific pathogen-free specific with a fecal leakage grid) mice were moved to the SPF animal room and reared in cages with the function of preventing mice from eating feces as much as possible. Metagenome sequencing results showed that the gut microbial diversity decreased after the environmental change, accompanied by a substantial loss in gut microbiota, including genera known to have protective effects against allergies and those involved in short-chain fatty acid production. Additionally, the abundance of functional genes involved in short-chain fatty acid metabolism, amino acid synthesis, vitamin metabolism, flagellar assembly, and bacterial chemotaxis decreased. The environmental hygiene improvement also resulted in significant increases in total serum IgE, IL-4, IL-5, and IL-13 levels in mice with artificially induced chronic inflammatory dermatosis. Compared with SPF mice, preventing mice from eating feces as much as possible decreased the gut microbial diversity but did not markedly change functional gene expression or total serum cytokine levels.

IMPORTANCE: Research has indicated that the human gut microbial diversity gradually decreases, while the prevalence of allergic diseases increases after movement from developing countries to developed countries. A healthy gut microbiota is necessary for proper human immune function. Movement from undeveloped to developed regions is often accompanied by an increase in environmental cleanliness. However, whether changes in environmental cleanliness are an important factor contributing to the decreased gut microbial diversity and increased prevalence of allergic diseases has not been reported. This study demonstrates the impact of increased environmental cleanliness on gut microbiota and susceptibility to allergic diseases and contributes to a better understanding of the increased incidence rate of various chronic diseases.},
}

@article {pmid40047330,
year = {2025},
author = {Gong, S and Li, M and Gao, J and Huang, S and Song, W and Sun, L},
title = {Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites.},
journal = {Journal of food science},
volume = {90},
number = {3},
pages = {e70106},
doi = {10.1111/1750-3841.70106},
pmid = {40047330},
issn = {1750-3841},
support = {42106111//National Natural Science Foundation of China/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; NYJG202303//Fund of Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2023KJ241//Program for Scientific Research Innovation Team of Young Scholar in Colleges and Universities of Shandong Province/ ; R20076//Doctoral Startup Project of Guangdong Ocean University funded by W.S/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis/chemically induced ; *Dextran Sulfate ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism ; Intestines/microbiology/drug effects ; },
abstract = {Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colitis/chemically induced
*Dextran Sulfate
Mice
Male
Disease Models, Animal
Mice, Inbred C57BL
Colon/metabolism/microbiology/drug effects
Cytokines/metabolism
Intestines/microbiology/drug effects

@article {pmid40047235,
year = {2025},
author = {Garg, RK},
title = {Tuberculosis of the central nervous system: current concepts in diagnosis and treatment.},
journal = {Current opinion in neurology},
volume = {},
number = {},
pages = {},
pmid = {40047235},
issn = {1473-6551},
abstract = {PURPOSE OF REVIEW: The outcome of central nervous system (CNS) tuberculosis has shown little improvement over several decades, with diagnosis remaining unconfirmed in nearly half of the cases. This review highlights current insights and advancements in the diagnosis and treatment of CNS tuberculosis.

RECENT FINDINGS: Miliary pulmonary tuberculosis is often linked to CNS tuberculosis and is associated with a worse prognosis. Complications, such as, optochiasmatic arachnoiditis, strokes, and transverse myelitis severely affect prognosis and quality of life. Nearly half of tuberculous meningitis patients exhibited impaired cognition. Diagnosing CNS tuberculosis is challenging because of the low accuracy of standard tests. Advanced techniques like metagenomic and nanopore sequencing enhance detection but are hindered by high costs and limited access. Treatment outcomes remain suboptimal but approaches such as higher drug doses, novel medications, and host-directed therapies are being explored. Drug-resistant tuberculous meningitis is increasingly recognized, posing significant challenges to both diagnosis and treatment. Artificial intelligence (AI) enhances care by enabling early diagnosis, disease monitoring, and personalized treatments, improving outcomes.

SUMMARY: CNS tuberculosis diagnosis faces challenges due to limited sensitivity and delayed results of available tests. Treatments remain suboptimal, with multidrug-resistant cases posing high mortality risks. AI aids in early diagnosis and personalized care.},
}

@article {pmid40046986,
year = {2025},
author = {Zhang, D and Deng, M and Li, F and Shen, R},
title = {A Report of Primary Pyogenic Ventriculitis Caused by Streptococcus Constellatus Diagnosed by Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1209-1214},
pmid = {40046986},
issn = {1178-6973},
abstract = {BACKGROUND: Primary ventriculitis is a rare but serious brain infection characterized by inflammation of the ependyma and purulence within the ventricular system. Due to the challenges in early diagnosis and the potential for suboptimal treatment, this condition carries a significant risk of complications such as recurrence, hydrocephalus, and death. Metagenomic next-generation sequencing (mNGS) enables the rapid and broad-spectrum identification of pathogens, facilitating timely and precise diagnosis.

CASE REPORT: This study presents the first reported case of primary ventriculitis caused by Streptococcus constellatus. An 81-year-old female patient with hydrocephalus and clinical signs of central nervous system infection was diagnosed with primary ventriculitis based on brain magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) analysis using mNGS. The patient underwent external ventricular drainage (EVD) and received a five-week course of ceftriaxone and linezolid. Following timely and targeted therapy, she demonstrated significant clinical improvement and was discharged without residual symptoms.

CONCLUSION: Key insights from this case include: 1) mNGS is an invaluable tool for the early and accurate diagnosis of primary ventriculitis; 2) MRI is indispensable for identifying characteristic radiological features of the condition; 3) prompt initiation and completion of appropriate antibiotic regimens significantly improve clinical outcomes.},
}

@article {pmid40046887,
year = {2025},
author = {Kim, M and Damronglerd, P and Molina Garcia, S and Yetmar, ZA and Razi, S and Ranganath, N and Mahmood, M and Abu Saleh, OM},
title = {Illuminating the Challenges and Diagnostic Utility of Plasma Microbial Cell-Free DNA Sequencing in Suspected Infective Endocarditis: A Retrospective Observational Cohort Study.},
journal = {Open forum infectious diseases},
volume = {12},
number = {3},
pages = {ofaf099},
pmid = {40046887},
issn = {2328-8957},
abstract = {BACKGROUND: Infective endocarditis (IE) is a life-threatening infection often challenging to diagnose, particularly in culture-negative cases. Plasma microbial cell-free DNA (mcfDNA) sequencing has shown potential for detecting pathogens in IE. However, its clinical utility, diagnostic impact, and limitations remain debated. This study evaluates its use in diagnosing and managing IE in a tertiary care setting.

METHODS: This single-center retrospective cohort study included adult patients (≥18 years) who underwent mcfDNA sequencing via the Karius test for suspected IE at Mayo Clinic Rochester between December 2019 and February 2024. Diagnostic classification followed the 2023 Duke-International Society of Cardiovascular Infectious Diseases criteria. Data on demographics, clinical features, routine microbiologic workup, and mcfDNA sequencing results were collected. Statistical analysis was conducted to evaluate diagnostic utility and treatment impact.

RESULTS: Among 141 patients, 66 had a diagnosis of IE, with mcfDNA sequencing identifying pathogens in 60.6% of them, compared with 39.4% with routine workup. mcfDNA sequencing was the sole microbiologic test with positive results in 33.3% of patients, leading to antimicrobial adjustments in 50.0% of that group. Clinically insignificant mcfDNA sequence detection occurred in 28.6% of patients without a diagnosis of IE.

CONCLUSIONS: mcfDNA sequencing is a valuable adjunctive tool for diagnosing culture-negative IE and guiding antimicrobial therapy when clinical suspicion is high. However, its utility depends on appropriate clinical context, highlighting the need for careful test interpretation and further prospective studies to assess patient-centered outcomes and cost-effectiveness.},
}

@article {pmid40046856,
year = {2025},
author = {Tan, L and He, Z and Liang, Y and Wang, K and Chen, X},
title = {Correlation analysis between the severity of respiratory syncytial virus pneumonia and the expression levels of inflammatory cytokines in bronchoalveolar lavage fluid among infants and young children.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1482029},
pmid = {40046856},
issn = {2296-2360},
abstract = {PURPOSE: RSV is the primary cause of lower respiratory tract infections in infants and young children. Current study aims to investigate the correlation between the severity of respiratory syncytial virus pneumonia (RSVP) in infants and young children and the number of RSV infection sequences as well as the levels of cytokines in bronchoalveolar lavage fluid (BALF).

METHODS: Metagenomics next-generation sequencing (mNGS) and enzyme-linked immunosorbent assay (ELISA) were used to detect the number of RSV infection sequences and the levels of related inflammatory cytokines in BALF samples. Comparisons between groups and Logistic regression analysis were performed to examine the differences in RSV infection sequences and inflammatory cytokine levels between the sRSVP and nsRSVP groups. Spearman's correlation coefficient was used to analyze the correlations among PCIS, RSV infection sequences, and inflammatory cytokines. Finally, ROC curve analysis was conducted to assess the diagnostic performance of inflammatory cytokines as biomarkers in determining the severity of RSVP.

RESULTS: A total of 49 infants and young children diagnosed with RSV infection were enrolled and divided into severe RSVP (sRSVP) and non-severe RSVP (nsRSVP) groups based on the pediatric critical illness score (PCIS) scale. The levels of Interleukin (IL)-6, IL-8, IL-10, tumor necrosis factor α (TNF-α), IL-17A, and monocyte chemotactic protein 1 (MCP-1) as well as the number of RSV sequences in BALF were significantly higher in the sRSVP group than in the nsRSVP group. Additionally, elevated levels of IL-6, IL-10, TNF-α, IL-17A, and the number of RSV sequences were identified as risk factors for the severity of RSVP. Spearman's correlation analysis revealed significant negative correlations between the levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1 in BALF with PCIS, and significant positive correlations with the number of RSV sequences. Furthermore, a significant negative correlation was observed between RSV sequence count and PCIS. ROC curve analysis showed that the levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1, as well as their combined diagnostic approach, exhibited high diagnostic performance in determining the severity of RSVP.

CONCLUSION: The levels of inflammatory cytokines and RSV sequences in BALF are significantly correlated with the severity of RSVP in infants and young children. The levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1 can serve as potential biomarkers for diagnosing the severity of RSVP.},
}

@article {pmid40046438,
year = {2025},
author = {Lin, K and Lin, W and Guo, Z and Chen, C and Chen, L and Cai, X},
title = {Plasma exosomal miRNA expression and gut microbiota dysbiosis are associated with cognitive impairment in Alzheimer's disease.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1545690},
pmid = {40046438},
issn = {1662-4548},
abstract = {INTRODUCTION: The gut microbiota composition and the expression profiles of microRNAs (miRNAs) in the brain tissue, cerebrospinal fluid, and blood of patients with Alzheimer's disease (AD) differ significantly from those with normal cognition function. The study aimed to initially explore the relationship between plasma exosomal microRNAs, gut microbiota, and cognitive impairment, providing insights into the pathogenesis and treatment of AD.

METHODS: The study enrolled 8 participants with AD and 8 participants with normal cognition. The Mini-Mental State Examination (MMSE) was utilized to evaluate cognitive function. High-throughput sequencing was used to identify differentially expressed miRNAs in plasma exosomes, while metagenomic sequencing was employed to detect differences in the abundance of gut microbiota. Furthermore, the associations among them were analyzed.

RESULTS: Four exosomal miRNAs and 14 microbiota taxa, which exhibited differential expression and abundance, respectively, in comparison between AD group and normal cognition group, were identified to be significantly associated with MMSE scores. Notably, the abundance of potential probiotics, including Faecalibacterium prausnitzii, Roseburia intestinalis and Roseburia inulinivorans, which was decreased in AD patients, exhibited positive correlations with specific exosomal miRNAs: Roseburia intestinalis correlated with miR-3120-3p and miR-6529-5p; Roseburia inulinivorans correlated with miR-3120-3p, miR-6529-5p and miR-124-3p; Faecalibacterium prausnitzii correlated with miR-3120-3p.

DISCUSSION: The study revealed a close association among gut microbiota, plasma exosomal miRNAs, and cognitive impairment in AD, and suggested that specific components of gut microbiota and exosomal miRNAs may serve as potential biomarkers and therapeutic targets for AD on the microbiota-gut-brain axis.},
}

@article {pmid40046298,
year = {2025},
author = {Sun, W and Li, M and Zhu, X},
title = {Bordetella pertussis bacteremia in infants co-infected with cytomegalovirus and respiratory syncytial virus.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1544935},
pmid = {40046298},
issn = {1664-302X},
abstract = {INTRODUCTION: Hematogenous infections caused by Bordetella pertussis are rare. This study aimed to increase clinicians' knowledge of B. pertussis bacteremia.

METHODS: We described a case of an infant with B. pertussis bacteremia, searched and reviewed for B. pertussis bacteremia-related literatures published in the PubMed database between 1946 to 2022.

RESULTS: A 3-month-old male infant was admitted to the hospital with a respiratory tract infection. Respiratory pathogen testing indicated the presence of B. pertussis, cytomegalovirus, and respiratory syncytial viruses. Blood metagenomic next-generation sequencing (mNGS) confirmed B. pertussis bacteremia. After 32 days of anti-infective treatment and supportive therapy, the patient's condition improved, and he was discharged. The literature review found that B. pertussis bacteremia is rare, often with fever as the first symptom, and is most common in individuals with underlying diseases or prolonged immunosuppressive therapy.

DISCUSSION: In infants lacking specific protective antibodies against B. pertussis, B. pertussis bacteremia should be considered when bacteremia-associated clinical manifestations are present and the causative organism remains undetected. Timely refinement of mNGS can help clarify the diagnosis.},
}

@article {pmid40046038,
year = {2025},
author = {Bird, E and Pickens, V and Molik, D and Silver, K and Nayduch, D},
title = {BALROG-MON: a high-throughput pipeline for Bacterial AntimicrobiaL Resistance annOtation of Genomes-Metagenomic Oxford Nanopore.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40046038},
issn = {2578-9430},
abstract = {BALROG-MON is a Nextflow pipeline for automated analysis of metagenomic long-read data to detect pathogens, annotate antimicrobial resistance genes (ARGs), link ARGs to specific pathogens, predict ARG origin (e.g., plasmid, chromosomal) and optionally perform steps like community analysis. With both assembly-based and assembly-free workflows, BALROG-MON is applicable to a wide range of sample types with low or high coverage, varying complexities and origins. Optional genome binning provides a comprehensive overview of ARGs within the dataset. BALROG-MON additionally presents results in summarized reports, overall serving as a flexible analysis tool for exploring diverse metagenomic samples for pathogens and antibiotic resistance.},
}

@article {pmid40045326,
year = {2025},
author = {Zhang, R and Yu, J and Shang, X and Wang, Z and Li, H and Cao, B},
title = {Heterogeneity in clinical patterns of adult lung abscess patients: an 8-year retrospective study in a tertiary hospital.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {101},
pmid = {40045326},
issn = {1471-2466},
support = {NO. 82030002/H0102//National Natural Science Foundation of China/ ; NO.20220484049//Beijing Nova Program of Science and Technology under grant/ ; No. ZRJY2021-QM09//National High Level Hospital Clinical Research Funding, the Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; },
mesh = {Humans ; *Lung Abscess/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; China/epidemiology ; *Tertiary Care Centers ; Aged ; *Tomography, X-Ray Computed ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Hospital Mortality ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: The widespread use of broad-spectrum antibiotics has led to changes in both the microbiological and clinical characteristics of lung abscesses. It is necessary to re-evaluate the bacterial spectrum associated with these infections. As a novel method for pathogen detection, metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical practice. There is limited research evaluating the use of mNGS in patients with lung abscesses.

METHODS: A retrospective analysis was conducted on patients with lung abscess who were hospitalized between July 2015 and July 2023 at a teaching hospital in China. Patients who underwent both computerized tomography (CT) imaging and conventional pathogen testing were included in the study. The efficacy of pathogen detection using conventional methods was compared with that of mNGS. Additionally, the clinical and radiological features were analyzed to provide a comprehensive understanding of the disease patterns.

RESULTS: A total of 782 patients with lung abscess were included in the study and hematogenous abscess accounting for 7.16% (56/782) of cases. The overall hospital mortality rate was 1.53%. The mean age of the patients with lung abscess was 60 years, with a male predominance (80.2%). A significant proportion of patients had comorbid conditions, including diabetes (29.7%) and cardiovascular disease (18.2%). Lung abscesses were predominantly located in the right lung, and pleural effusion was more commonly observed in the deceased group. The detection rate of pathogen via conventional test was lower at 41.8% (327/782). Among patients with positive mNGS results, only 51.9% had pathogens identified through conventional testing methods. Klebsiella pneumoniae was the most frequently detected pathogen by conventional culture, while mNGS identified was Parvimonas micra. Infections caused solely by anaerobic bacteria or facultative anaerobes were associated with shorter hospital stays. Patient infected with Gram-negative bacilli (GNB) had a higher proportion of liver abscesses (11.8%).

CONCLUSION: Compared to conventional testing methods, mNGS demonstrates superior performance in detecting anaerobic and facultative anaerobic bacteria. The low detection rate of conventional tests may result in an underestimation of the clinical significance of anaerobic bacteria infections. In patients with lung abscess caused by GNB, hematogenous dissemination, liver abscess and diabetes were more commonly observed and these patients tended to have longer hospital stays.},
}

Humans
*Lung Abscess/microbiology
Male
Retrospective Studies
Female
Middle Aged
China/epidemiology
*Tertiary Care Centers
Aged
*Tomography, X-Ray Computed
Adult
High-Throughput Nucleotide Sequencing
Metagenomics
Hospital Mortality
Anti-Bacterial Agents/therapeutic use

@article {pmid40045185,
year = {2025},
author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL},
title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {120},
pmid = {40045185},
issn = {1471-2180},
support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; },
mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; },
abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS: We observed that the water column microbiome significantly varied by season (R[2] = 0.59, P = 0.003). Temperature (R[2] = 0.27, P = 0.004), dissolved organic matter (R[2] = 0.13, P = 0.004), and dissolved oxygen (R[2] = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.},
}

California
*Sulfur/metabolism
*Microbiota
*Lakes/microbiology
*Seawater/microbiology/chemistry
*Bacteria/classification/genetics/metabolism/isolation & purification
*Seasons
Phylogeny
RNA, Ribosomal, 16S/genetics
Ecosystem
Biodiversity

@article {pmid40045177,
year = {2025},
author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S},
title = {Gut Microbiome in Colorectal Cancer: Metagenomics from Bench to Bedside.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkaf026},
pmid = {40045177},
issn = {2515-5091},
abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approaches.},
}

@article {pmid40044917,
year = {2025},
author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A},
title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.},
journal = {Mycorrhiza},
volume = {35},
number = {2},
pages = {17},
pmid = {40044917},
issn = {1432-1890},
support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; },
mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.},
}

*Mycorrhizae/physiology
*Vitis/microbiology
*Soil Microbiology
*Soil/chemistry
Czech Republic
Plant Roots/microbiology
Mycobiome
Basidiomycota/genetics/physiology
Rhizosphere
Phosphorus/metabolism/analysis

@article {pmid40044690,
year = {2025},
author = {Zheng, K and Sun, J and Liang, Y and Kong, L and Paez-Espino, D and Mcminn, A and Wang, M},
title = {VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2226},
pmid = {40044690},
issn = {2041-1723},
support = {41976117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; *DNA Viruses/genetics/classification ; *DNA, Viral/genetics ; Software ; Phylogeny ; Genome, Viral/genetics ; Metagenomics/methods ; Virome/genetics ; Computational Biology/methods ; },
abstract = {The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at https://github.com/DrKaiyangZheng/VITAP .},
}

*RNA, Viral/genetics
*RNA Viruses/genetics/classification/isolation & purification
*DNA Viruses/genetics/classification
*DNA, Viral/genetics
Software
Phylogeny
Genome, Viral/genetics
Metagenomics/methods
Virome/genetics
Computational Biology/methods

@article {pmid40044673,
year = {2025},
author = {Wood, JR and Zhou, C and Cole, TL and Coleman, M and Anderson, DP and Lyver, PO and Tan, S and Xiang, X and Long, X and Luo, S and Lou, M and Southon, JR and Li, Q and Zhang, G},
title = {Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1798},
pmid = {40044673},
issn = {2041-1723},
mesh = {Animals ; Antarctic Regions ; *Spheniscidae/genetics ; *DNA, Mitochondrial/genetics ; *Geologic Sediments ; Phylogeny ; Seals, Earless ; Metagenome ; Ecosystem ; Diet ; },
abstract = {We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.},
}

Animals
Antarctic Regions
*Spheniscidae/genetics
*DNA, Mitochondrial/genetics
*Geologic Sediments
Phylogeny
Seals, Earless
Metagenome
Ecosystem
Diet

@article {pmid40043990,
year = {2025},
author = {Lou, D and Xiao, S and Cui, J and Duan, J and Duan, H and Cao, Y and Wang, D and Zhou, B and Tan, J},
title = {Discovery and characterization of the first hyperthermophilic 3-quinuclidinone reductase from hot-spring metagenomes.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {141706},
doi = {10.1016/j.ijbiomac.2025.141706},
pmid = {40043990},
issn = {1879-0003},
abstract = {Extremozymes play an essential part in the biosynthesis of pharmaceuticals (intermediates). In this study, a mixed assembly was performed for five metagenomes from hot springs. Via a series of procedures, including homology analysis, heterologous expression, and catalytic property characterization, the first hyperthermophilic 3-quinuclidinone reductase (SbQR) was successfully identified. The SbQR exhibits an optimal temperature of ≥95 °C and demonstrates remarkable thermal stability, with over 80 % of its activity retained following a 48-hour incubation at 50 °C. At particular concentrations, Mg[2+], Na[+], and Mn[2+] can substantially enhance the enzymatic activity. However, no significant influence of K[+] on the activity of SbQR was detected within the concentration range of 0-400 mM. Employing AlphaFold2, the three-dimensional structure of SbQR was predicted, which presents the typical traits of the Rossmann fold and is classified as a member of the short-chain dehydrogenases/reductases (SDR) superfamily. Molecular dynamics simulations were carried out and the results showed that when the temperature was increased to 390 K, the flexibility of residues 90-104 and the C-terminal increased significantly. This increase might lead to the destruction of the three-dimensional structure of the enzyme. In conclusion, this study identified the first hyperthermophilic 3-quinuclidinone reductase, providing a potential biocatalyst for the biopreparation of (R)-3-quinuclidinol.},
}

@article {pmid40043973,
year = {2025},
author = {Liu, N and Dai, S and Fan, X and Li, B and Chen, M and Gong, P and Chen, X},
title = {In vitro fermentation of Auricularia auricula polysaccharides and their regulation of human gut microbiota and metabolism.},
journal = {International journal of biological macromolecules},
volume = {306},
number = {Pt 4},
pages = {141714},
doi = {10.1016/j.ijbiomac.2025.141714},
pmid = {40043973},
issn = {1879-0003},
abstract = {Auricularia auricula is abundant in polysaccharides that received increasing attention due to their variety biological activities and prebiotic potential. In order to explore the role of A. auricula polysaccharides (AAP) in regulating human gut microbiota and metabolic health, this study employed metagenomic and metabolomic analyses to examine the impact of AAP on the gut microbiota via in vitro fecal fermentation experiments. After in vitro fermentation, the data indicated that gut microbiota utilized AAP to produce rich short-chain fatty acids (SCFAs) including acetic acid, propionic acid, butyric acid and modulate gut microbiota structure, such as increasing the proportion of Bacteroidetes to Firmicutes, elevating the abundance of beneficial bacteria, including Bacteroides, especially the Parabacteroides, and inhibiting the abundance of harmful bacteria such as Bilophila, Morganella, and Escherichia-Shigella. Furthermore, the metabolomic analysis indicated that AAP utilization by gut microbes substantially alters the metabolic profile, in which 26 potential biological biomarkers were found and affects tryptophan, bile acids, purines, and butyric acid pathways to promote host health. In conclusion, this research indicated that AAP has a prebiotic potential, which can regulate the gut microbiota and promote host health. Moreover, this study provided scientific evidence for using AAP as a functional food with prebiotic effect.},
}

@article {pmid40043931,
year = {2025},
author = {Li, HQ and Wang, WL and Shen, YJ and Su, JQ},
title = {Mangrove Plastisphere as a Hotspot for High-Risk Antibiotic Resistance Genes and Pathogens.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121282},
doi = {10.1016/j.envres.2025.121282},
pmid = {40043931},
issn = {1096-0953},
abstract = {Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.},
}