@article {pmid40647144,
year = {2025},
author = {Sreenesh, B and Varghese, E and Kubatka, P and Samuel, SM and Büsselberg, D},
title = {Prebiotic Potential of Dietary Polyphenols in Colorectal Cancer Immunomodulation.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647144},
issn = {2304-8158},
support = {NPRP14S-0311-210033//Qatar National Research Fund/ ; },
abstract = {Molecular crosstalk between the gut microbiome and human diet represent a potential therapeutic avenue requiring further investigation as it can be applied to human health management and treatment. Colon cancer, the third leading cause of cancer mortality, is often linked to the gut microbiome. In vitro and in vivo studies and metagenomic research have revealed alterations in gut microbial flora among diseased individuals. The human diet is connected to these changes in microbial inhabitants related to the pathophysiology underlying colorectal cancer (CRC). Polyphenols are well-studied, naturally occurring plant secondary metabolites recognized for their anti-inflammatory and antioxidant properties. The anticancer activities of these compounds are increasingly reported, offering insights into the administration of these natural molecules for managing various types of cancer and developing novel medications from them. Recent investigations have highlighted the prebiotic-like effects of these compounds on gut microbial dysbiosis and their metabolism concerning colorectal cancer, influencing colon cancer by interfering with multiple signaling pathways. This review will focus on the existing literature regarding the prebiotic potential of dietary polyphenols, and further research in this area would be valuable, as the integration of artificial intelligence (AI) and machine learning (ML) can enable analysis of the connections between unique gut microbiome profiles and other dependent factors such as physiological and genetic variables, paving the way for personalized treatment strategies in gut microbiome-based health management and precision medicine.},
}

@article {pmid40647099,
year = {2025},
author = {Krongdang, S and Sawongta, N and Pheepakpraw, J and Ngamsomchat, A and Wangtueai, S and Wongsa, J and Parametthanuwat, T and Charoenphun, N and Chitov, T},
title = {Comprehensive Analysis of Bacterial Communities and Microbiological Quality of Frozen Edible Insects.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647099},
issn = {2304-8158},
support = {Fundamental Fund: Grant no. 31/2567//(i) Burapha University (BUU), (ii) Thailand Science Research and Innovation (TSRI), (iii) National Science Research and Innovation Fund (NSRF) (Fundamental Fund: Grant no. 31/2567), and was partially supported by Chiang Mai University./ ; },
abstract = {Edible insects are gaining traction worldwide; however, the existing data regarding their microbiological quality remain inadequate. This study investigated the bacterial communities and microbiological quality of five types of frozen edible insects commercially available in Thailand. Amplicon sequencing revealed Firmicutes (Bacillota) and Proteobacteria (Pseudomonadota) as the main phyla across all samples; Bacteroidota was predominant in house crickets, Actinobacteriota in silkworms, and Desulfobacterota was exclusively found in house and mole crickets. Culture-based assays showed total viable counts, lactic acid bacteria, yeasts-molds, and spore-formers ranging from 3.41-6.58, 2.52-7.41, 1.83-5.62, to 2.00-4.70 log CFU·g[-1], respectively. In some samples, Enterobacteriaceae and Escherichia coli, key hygiene indicators, reached 5.05 and 2.70 log CFU·g[-1], respectively. Among foodborne pathogens, presumptive Bacillus cereus was found to vary from <1.70 to 3.93 log CFU·g[-1], while Clostridium perfringens and Staphylococcus aureus were under the quantitation limit, and Salmonella was absent. Overall, the results indicate significant variation in microbial diversity and quality among different insect types. The high levels of microbial hygiene indicators and foodborne pathogens in some samples raised food safety concerns and point to the need to develop or implement production guidelines and microbiological criteria for frozen edible insects to ensure food safety.},
}

@article {pmid40647045,
year = {2025},
author = {Zhang, J and Li, Q and Liu, S and Wang, N and Song, Y and Wu, T and Zhang, M},
title = {Lactobacillus rhamnosus LRa05 Alleviates Constipation via Triaxial Modulation of Gut Motility, Microbiota Dynamics, and SCFA Metabolism.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647045},
issn = {2304-8158},
support = {2022YFF1100201//the Key Research and Development Program of China/ ; 24PTLYHZ00020//2024 Tianjin "the Belt and Road" Innovation Platform Project/ ; 24JCQNJC00740//Natural Science Foundation of Tianjin Municipality/ ; },
abstract = {Constipation, a widespread gastrointestinal disorder, imposes significant burdens on healthcare systems the and global health-related quality of life, yet current options remain suboptimal due to limited mechanistic understanding and efficacy limitations. Given the pivotal significance of the interactions between the gut microbiota and the host on governing bowel movement, we employed a multi-modal approach integrating animal experiments, ELISA, histopathology, qRT-PCR, GC-MS, and 16S rRNA metagenomics to evaluate the functional potential of Lactobacillus rhamnosus LRa05 against loperamide-induced constipation in mice. LRa05 treatment markedly alleviated constipation symptoms, as evidenced by reduced first black stool expulsion time, increased fecal moisture, and enhanced intestinal motility. Mechanistic investigations revealed that LRa05 balanced gastrointestinal regulatory peptides. It also downregulated aquaporin (AQP4/AQP8) mRNA levels and activated the SCF/C-Kit signaling pathway. These effects contributed to the restoration of intestinal peristalsis. Furthermore, LRa05 rebalanced gut microbiota composition by enriching beneficial, including Alloprevotella and Lachnospiraceae NK4A136, key SCFA producers. Thus, LRa05 could boost short chain fatty acid (SCFA) production, which is vital for stimulating intestinal motility, improving mucosal function, and relieving constipation. These findings demonstrated that LRa05 could mitigate constipation through a multi-target mechanism: regulating motility-related gene transcription, restructuring the microbial community, balancing gastrointestinal peptides, repairing the colonic mucosa, and promoting SCFAs for fecal hydration. Our study positions LRa05 as a promising probiotic candidate for constipation management.},
}

@article {pmid40646857,
year = {2025},
author = {Zhu, W and Guo, J and Li, X and Li, Y and Song, L and Li, Y and Feng, B and Bao, X and Li, J and Gao, Y and Xu, H},
title = {Effects of Gallic Acid on In Vitro Ruminal Fermentation, Methane Emission, Microbial Composition, and Metabolic Functions.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646857},
issn = {2076-2615},
support = {QN2025134//Science Research Project of Hebei Education Department/ ; HBCT2023180207//Hebei Dairy Cattle Innovation Team of Modern Agro-industry Technology Research System/ ; HBCT2024230205//Hebei Dairy Cattle Innovation Team of Modern Agro-industry Technology Research System/ ; 202202F016//Construction of the Weichang Yidukou Smart and Circular Agriculture and Animal Husbandry Demonstration Zone/ ; C2024204012//Natural Science Foundation of Hebei Province/ ; 6012018//The Top Talent Project of Hebei Province/ ; YJ2021053//Research Special Project for Talent Introduction of Hebei Agricultural University/ ; KY2024003//Research Project Funding for Basic Scientific Research of Universities in Hebei Province/ ; CARS-36-20//CARS-36-20/ ; },
abstract = {The objective of this study was to assess the effects of gallic acid (GA) on nutrient degradability, gas production, rumen fermentation, and the microbial community and its functions using in vitro fermentation methods. An in vitro experiment was conducted to test GA dose levels (0, 5, 10, 20, and 40 mg/g DM) in the cow's diet. Based on the results of nutrient degradability, gas production, and rumen fermentation, the control group (0 mg/g DM, CON) and the GA group (10 mg/g DM, GA) were selected for metagenomic analysis to further explore the microbial community and its functions. The degradability of dry matter and crude protein, as well as total gas production, CH4 production, CH4/total gas, CO2 production, and CO2/total gas, decreased quadratically (p < 0.05) with increasing GA doses, reaching their lowest levels at the 10 mg/g DM dose. Total volatile fatty acid (VFA) (p = 0.004), acetate (p = 0.03), and valerate (p = 0.03) exhibited quadratic decreases, while butyrate (p = 0.0006) showed a quadratic increase with increasing GA doses. The 10 mg/g DM dose group had the lowest levels of total VFA, acetate, and valerate, and the highest butyrate level compared to the other groups. The propionate (p = 0.03) and acetate-to-propionate ratio (p = 0.03) linearly decreased with increasing gallic acid inclusion. At the bacterial species level, GA supplementation significantly affected (p < 0.05) a total of 38 bacterial species. Among these, 29 species, such as Prevotellasp.E15-22, bacteriumP3, and Alistipessp.CAG:435, were less abundant in the GA group, while 9 species, including Aristaeella_lactis and Aristaeella_hokkaidonensis, were significantly more abundant in the GA group. At the archaeal species level, the relative abundances of Methanobrevibacter_thaueri, Methanobrevibacter_boviskoreani, and Methanobrevibactersp.AbM4 were significantly reduced (p < 0.05) by GA supplementation. Amino sugar and nucleotide sugar metabolism, Starch and sucrose metabolism, Glycolysis/Gluconeogenesis, and Pyruvate metabolismwere significantly enriched in the GA group (p < 0.05). Additionally, Alanine, aspartate and glutamate metabolism was also significantly enriched in the GA group (p < 0.05). GA use could potentially be an effective strategy for methane mitigation; however, further research is needed to assess its in vivo effects in dairy cows over a longer period.},
}

@article {pmid40646853,
year = {2025},
author = {Liu, H and Xiao, L and Liu, Z and Deng, Y and Zhu, J and Yang, C and Liu, Q and Tian, D and Cui, X and Peng, J},
title = {Impacts of Captive Domestication and Geographical Divergence on the Gut Microbiome of Endangered Forest Musk Deer.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646853},
issn = {2076-2615},
support = {No. 31470570//The People's Republic of China Wildlife Protection Program of the Central Forestry Reform and Development Fund of the State Forestry Administration, and the National Natural Science Foundation of China/ ; },
abstract = {Forest musk deer (Moschus berezovskii Flerov), a critically endangered ruminant species, faces extinction risks, with captive populations further threatened by prevalent digestive and immune disorders. This study utilized comparative metagenomic sequencing to assess intestinal microbiota structure and functional profiles between wild populations in Chongqing and Hunan and captive individuals. Wild populations exhibited a Pseudomonadota-dominated gut microbiota (significantly more abundant than in captive counterparts), enriched with lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, the captive group demonstrated increased abundances of Bacillota/Bacteroidota, alongside abnormal proliferation of Escherichia and Clostridium. Both alpha and beta diversity analyses confirmed significant compositional divergences among the three groups, with wild populations maintaining higher diversity than captive populations. Notably, while substantial disparities in microbial abundance existed between wild populations (attributed to habitat vegetation differences), core microbial diversity and carbohydrate metabolic functions exhibited convergence. Functional analyses marked divergences in metabolic pathways: Captive microbiota showed enrichment in translation and glycan metabolism pathways, whereas wild populations displayed pronounced enrichment in immune regulation and environmental sensing pathways. These findings establish a theoretical foundation for optimizing wild population conservation strategies and developing science-based captive management protocols.},
}

@article {pmid40646844,
year = {2025},
author = {Kerek, Á and Szabó, Á and Jerzsele, Á},
title = {Amoxicillin Resistance: An In Vivo Study on the Effects of an Approved Formulation on Antibiotic Resistance in Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646844},
issn = {2076-2615},
support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; },
abstract = {Background: Antimicrobial resistance (AMR) is a growing global concern in poultry production, where antibiotic use can disrupt gut microbiota and enrich antimicrobial resistance genes (ARGs). Objectives: This study aimed to assess the in vivo effects of a veterinary-approved amoxicillin formulation on gut microbiome composition and ARG profiles in broiler chickens. Methods: A total of 120 Ross-308 broiler chickens were randomly allocated into 12 experimental groups (n = 10 per group), with three replicates per treatment. Birds received either full-dose (1×), a subtherapeutic quarter-dose (¼×) of amoxicillin, a placebo (starch), or no treatment. Cloacal swabs were collected on days 0, 14, and 28 for shotgun metagenomic sequencing. One-way ANOVA was used to evaluate treatment effects on body weight, with significant differences observed from day 14 onward (p < 0.0001). Results: The ¼× dose caused a more pronounced microbiome shift than the 1× dose, with a marked reduction in Pseudomonadota and increase in Bacillota and Bacteroidota. ARG abundance declined in the ¼× group (from 1386 to 1012). While TEM-type ESBL genes were ubiquitous, CTX-M-1 emerged only after ¼× treatment. Worryingly, 20 types of vancomycin resistance genes were detected across all samples. Plasmid-borne ARGs and mobile genetic elements decreased in the ¼× group. Conclusions: Even subtherapeutic antibiotic exposure significantly reshapes the gut microbiota composition and ARG landscape, highlighting the need for refined risk assessments and microbiome-conscious antimicrobial policies in poultry farming.},
}

@article {pmid40646819,
year = {2025},
author = {Lv, X and Qiao, Z and Chen, C and Hua, J and Zhou, C},
title = {Exploration of Multi-Source Lignocellulose-Degrading Microbial Resources and Bioaugmentation Strategies: Implications for Rumen Efficiency.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646819},
issn = {2076-2615},
support = {DKYJ202303//High-level Talents Introduction Project of Anhui Science and Technology University/ ; 32261143467//Projects of International Cooperation and Exchanges NSFC/ ; 2022YFD1300805//National Key Research and Development Program/ ; },
abstract = {Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive tracts, forest soil, and microbial populations in papermaking processes. The rumen of ruminants harbors a diverse range of microbial species, making it a promising source of lignocellulose-degrading microorganisms. Exploring alternative systems like insect intestines and forest soil is essential for future research. Current studies primarily rely on traditional microbial isolation techniques to identify lignocellulose-degrading strains, underscoring the necessity to transition to utilizing microbial culturomics and genome-editing technologies for discovering and manipulating cellulose-degrading microbes. This review provides an overview of lignocellulose-degrading microbial communities from diverse environments, encompassing bacterial and fungal populations. It also delves into the use of metagenomic, metatranscriptomic, and metaproteomic approaches to pinpoint highly efficient cellulase genes, along with the application of genome-editing tools for engineering lignocellulose-degrading microorganisms. The primary objective of this review is to offer insights for further exploration of potential lignocellulose-degrading microbial resources and high-performance cellulase genes to enhance roughage utilization in ruminant rumen ecosystems.},
}

@article {pmid40646273,
year = {2025},
author = {Mikolas, M and Fauszt, P and Petrilla, A and Nemeth, P and David, P and Szilagyi-Tolnai, E and Szilagyi-Racz, A and Stagel, A and Gal, F and Gal, K and Sohajda, R and Szoke, Z and Hossain, SA and Stundl, L and Biro, S and Remenyik, J and Paholcsek, M},
title = {Analysis of ICU resistome dynamics in patients, staff and environment for the identification of predictive biomarkers of sepsis and early mortality.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25080},
pmid = {40646273},
issn = {2045-2322},
mesh = {Humans ; *Intensive Care Units ; *Sepsis/mortality/microbiology ; Biomarkers/analysis ; Male ; Female ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Aged ; *Drug Resistance, Multiple, Bacterial ; Health Personnel ; Oropharynx/microbiology ; Bacteria/drug effects/genetics ; Microbiota ; Drug Resistance, Bacterial ; },
abstract = {Antimicrobial resistance (AMR) is a global crisis, posing a critical challenge to healthcare systems, particularly in intensive care units (ICUs), where multidrug-resistant organisms (MDROs) threaten patient survival. This study offers a unique, real-world perspective on AMR dynamics by analyzing 96 metagenomic samples from three key sources: oropharyngeal and rectal swabs of deceased ICU patients (both postadmission and antemortem), healthcare workers, and high-touch ICU surfaces. Findings revealed the ICU environment as a major AMR reservoir, with oropharyngeal swabs carrying the highest AMR burden. While healthcare staff facilitated MDRO spread, they were not primary sources. Staff microbiomes' MDRO pattern closely resembled environmental samples. Key AMR species included B. fragilis, E. coli, S. pneumoniae, S. aureus, with P. aeruginosa persisting on high-touch surfaces. Tetracycline resistance was the most prevalent, with common resistances comprising 36.1% of all detected AMR markers. Staff microbial community exhibited higher resistance to macrolides, fluoroquinolones, lincosamides, and cephamycins. A 10-day survival threshold distinguished early (EM) and late mortality (LM) groups. EM patients exhibited unique AMR species in the oropharynx, suggesting respiratory-driven infections, while LM patients showed greater gut-associated resistance. Higher rectal AMR counts correlated with prolonged survival. Notably, four key MDROs (L. monocytogenes, M. tuberculosis, S. haemolyticus, and S. agalactiae) were enriched in sepsis patients, suggesting early risk markers. Fewer new resistances emerged in rectal than oropharyngeal swabs, likely due to antibiotic selection pressure. Vancomycin and levofloxacin, frequently co-administered, exerted stronger selective pressure in the oropharynx, possibly explaining the high MRSA prevalence in patient and environmental samples.},
}

Humans
*Intensive Care Units
*Sepsis/mortality/microbiology
Biomarkers/analysis
Male
Female
Middle Aged
Anti-Bacterial Agents/pharmacology
Aged
*Drug Resistance, Multiple, Bacterial
Health Personnel
Oropharynx/microbiology
Bacteria/drug effects/genetics
Microbiota
Drug Resistance, Bacterial

@article {pmid40645966,
year = {2025},
author = {Kim, S and Park, MS and Kang, I and Cho, JC},
title = {Microbial metagenomes from Lake Soyang, the largest freshwater reservoir in South Korea.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1201},
pmid = {40645966},
issn = {2052-4463},
support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NRF-2022R1C1C2004070//National Research Foundation of Korea (NRF)/ ; },
mesh = {Republic of Korea ; *Lakes/microbiology ; *Metagenome ; *Microbiota ; Metagenomics ; Ecosystem ; Fresh Water/microbiology ; },
abstract = {Lake ecosystems play a fundamental role in the global biogeochemical cycling of essential elements such as carbon, nitrogen, and phosphorus. Microorganisms within these ecosystems mediate key processes that regulate these cycles. Metagenomic analyses provide valuable insights into the taxonomic and functional diversity of microbial communities in various environments, including freshwater habitats. Here, we present a comprehensive metagenomic dataset derived from Lake Soyang, the largest freshwater reservoir in South Korea. A total of 28 metagenomes were generated from water samples collected across two distinct sampling periods: the first set (n = 8) was obtained between April 2014 and January 2015 from two depths (1 m and 50 m) in four different seasons, while the second set (n = 20) was collected between January 2019 and November 2019 from five depths (1, 10, 20, 40, and 90 m) over four seasons. Metagenomic sequencing yielded 9.3-21.8 Gbp per sample. This dataset provides a valuable resource for future studies exploring the ecophysiological characteristics of microbial communities in pelagic freshwater environments.},
}

Republic of Korea
*Lakes/microbiology
*Metagenome
*Microbiota
Metagenomics
Ecosystem
Fresh Water/microbiology

@article {pmid40645948,
year = {2025},
author = {Calayag, AM and Priest, T and Oldenburg, E and Muschiol, J and Popa, O and Wietz, M and Needham, DM},
title = {Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6427},
pmid = {40645948},
issn = {2041-1723},
mesh = {Arctic Regions ; Seasons ; *Seawater/virology/microbiology ; Metagenome ; *Virome/genetics ; Oceans and Seas ; *DNA Viruses/genetics/classification/isolation & purification ; Biodiversity ; Bacteria/virology/genetics ; Host Microbial Interactions ; },
abstract = {Viruses of microbes play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemistry. However, we know little about the diversity, seasonality, and host interactions of viruses in polar waters. Here, we study dsDNA viruses in the Arctic Fram Strait across four years via 47 long-read metagenomes of the cellular size-fraction. Among 5662 vOTUs, 98% and 2% are Caudoviricetes and Megaviricetes, respectively. Viral coverage is, on average, 5-fold higher than cellular coverage, and 8-fold higher in summer. Viral community composition shows annual peaks in similarity and strongly correlates with prokaryotic community composition. Using network analysis, we identify putative virus-host interactions and six ecological modules associated with distinct environmental conditions. The network reveals putative novel cyanophages with time-lagged correlations to their hosts (in late summer) as well as diverse viruses correlated with Flavobacteriaceae, Pelagibacteraceae, and Nitrosopumilaceae. Via global metagenomes, we find that 42% of Fram Strait vOTUs peak in abundance in high latitude regions of both hemispheres, and encode proteins with biochemical signatures of cold adaptation. Our study reveals a rich diversity of polar viruses with pronounced seasonality, providing a foundation for understanding viral regulation and ecosystem impacts in changing polar oceans.},
}

Arctic Regions
Seasons
*Seawater/virology/microbiology
Metagenome
*Virome/genetics
Oceans and Seas
*DNA Viruses/genetics/classification/isolation & purification
Biodiversity
Bacteria/virology/genetics
Host Microbial Interactions

@article {pmid40645526,
year = {2025},
author = {Xu, J and Zhang, Y and Wang, X and Xu, W and Chen, S and Pan, L and Gao, J},
title = {A P2X7 receptor antagonist alleviates PTSD-like behaviors in adolescent rats through gut microbiota modulation and hippocampal transcriptomic remodeling.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {119859},
doi = {10.1016/j.jad.2025.119859},
pmid = {40645526},
issn = {1573-2517},
abstract = {Post-traumatic stress disorder (PTSD) is a debilitating psychiatric disorder that frequently manifests during adolescence, a critical neurodevelopmental period. Although the P2X7 receptor is implicated in the pathophysiology of PTSD, its role in adolescent-onset PTSD, particularly concerning gut microbiota dysbiosis and hippocampal transcriptomic alterations, remains unclear. This study investigated the effects of the P2X7 receptor antagonist Brilliant Blue G (BBG) on PTSD-like behaviors, gut microbiota, and hippocampal transcriptomic profiles in adolescent rats subjected to single prolonged stress and electric foot shock (SPS&S). BBG treatment significantly ameliorated SPS&S-induced fear- and anxiety-like behaviors and spatial working memory deficits. Metagenomic analysis revealed that BBG partially reversed SPS&S-induced gut microbiota dysbiosis, significantly enriching key bacterial taxa (e.g., Bacteroidota) and modulating functional pathways related to immunity and metabolism. Hippocampal transcriptomic analysis demonstrated that BBG normalized a majority of SPS&S-induced differentially expressed genes; these corrected genes were significantly enriched in pathways for extracellular matrix organization, neural differentiation, and PI3K-Akt signaling pathway. Integrated multi-omics correlation analyses revealed significant correlations among key microbial abundances, hippocampal gene expression, and behavioral outcomes, supporting a gut-brain axis mechanism underlying the therapeutic effects of BBG. These findings position the P2X7 receptor as a promising therapeutic target for adolescent PTSD and highlight the crucial role of gut microbiota in modulating stress-related neuropathology via the gut-brain axis.},
}

@article {pmid40645301,
year = {2025},
author = {Melamed, E and Rungratanawanich, W and Liangpunsakul, S and Maki, KA and McCullough, RL and Llorente, C},
title = {Alcohol, Aging, and the Gut Microbiome: Intersections of Immunity, Barrier Dysfunction, and Disease.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2025.07.001},
pmid = {40645301},
issn = {1873-6823},
abstract = {Alcohol consumption exerts complex, dose- and context-dependent effects on human health, particularly by influencing the gut microbiome, intestinal barrier integrity, immune regulation, and aging processes. Genetic variation and advancing age are two major, and often interacting, factors that modify the risk of alcohol-related diseases. Among genetic factors, the prevalent aldehyde dehydrogenase 2 polymorphism (ALDH2*2) compromises acetaldehyde clearance, driving toxic metabolite accumulation, oxidative stress, and increased intestinal permeability that disrupts gut microbial communities, even at low levels of alcohol consumption. Heavy and chronic alcohol use further disrupts gut microbial communities, erodes mucosal integrity, and drives systemic inflammation, contributing to alcohol-associated liver disease (ALD), neuroinflammation, and multi-organ injury. Aging independently worsens these effects by promoting chronic low-grade inflammation and impaired immune responses, heightening susceptibility to alcohol-induced pathology. In specific contexts, such as certain autoimmune diseases, low to moderate alcohol intake may exert immunomodulatory effects and influence the gut microbiome, potentially contributing to reduced inflammation and alterations in microbial composition. This review synthesizes current mechanistic insights into how alcohol, host genetics, the gut microbiome, immune regulatory pathways, and aging intersect to influence disease risk. As global populations age and the burden of alcohol-related health issues rises, there is an urgent need for integrated, systems-level approaches. Future research should prioritize precision-based, gut-targeted strategies aimed at restoring microbial balance, maintaining intestinal barrier integrity, and mitigating alcohol-related harm across the lifespan.},
}

@article {pmid40645053,
year = {2025},
author = {Zhao, M and Xiong, S and Du, T and Xu, X and Li, H and Zhang, L and Xu, Y and Wei, T and Xiong, T and Xie, M},
title = {Elucidating microbial succession dynamics and flavor metabolite formation in korean style spicy cabbage fermentation: Integration of flavoromics, amplicon sequencing, and metagenomics.},
journal = {Food chemistry},
volume = {492},
number = {Pt 2},
pages = {145464},
doi = {10.1016/j.foodchem.2025.145464},
pmid = {40645053},
issn = {1873-7072},
abstract = {Korean style spicy cabbage (KSC) is a prominent fermented vegetable consumed globally. Nevertheless, microbial succession dynamics, interactions, and flavor-core microbiome correlations lack comprehensive understanding. Metabolomics revealed eight taste-active compounds and sixteen aroma-active compounds as key flavor determinants throughout fermentation. Amplicon sequencing elucidated dynamic shifts in bacterial and fungal community structures during KSC fermentation, with subsequent analyses identifying free sugars as the primary drivers of microbial succession. Spearman correlation analysis further identified Psychrobacter, Latilactobacillus, Weissella, Pseudomonas, Rothia, Candida, Vishniacozyma, Kazachstania, and Cutaneotrichosporon as core microbes driving the formation of characteristic flavor metabolites in KSC. Through metagenomic analysis, we reconstructed the metabolic network underlying the formation of characteristic flavor compounds. Our study elucidates microbial diversity dynamics and flavor metabolite formation during KSC fermentation, offering actionable insights for identifying critical fermentation phases and optimizing inoculated starter culture.},
}

@article {pmid40645041,
year = {2025},
author = {Pei, J and Chen, S and Yu, K and Liang, J and Zhang, R and Li, P and Hou, Z and Fu, L and Ma, H},
title = {Microbial regulation of dissolved organic matter revealed by integrated metabolomics and metagenomics in the World's deepest blue hole.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107354},
doi = {10.1016/j.marenvres.2025.107354},
pmid = {40645041},
issn = {1879-0291},
abstract = {Dissolved organic matter (DOM) is central to marine biogeochemical cycles, with its composition and dynamics closely linked to microbial communities. In oxygen-stratified extreme environments, however, the ecological relationships between DOM and microbes remain insufficiently explored. This study explores the dynamics of DOM and microbial communities in the Sansha Yongle Blue Hole, the world's deepest ocean blue hole, using an integrated metabolomics and metagenomics approach. Our findings elucidate significant alterations in microbial communities and DOM composition in response to variations in oxygen concentrations. Specifically, various DOM components, including dissolved organic sulfur (DOS) and dissolved organic nitrogen (DON), along with a spectrum of small molecule metabolites, were affected by microbial metabolic activities. Higher concentrations of DOS in the anoxic layer were positively correlated with increased sulfur metabolism in microbial communities, whereas lower concentrations of DON in the chemocline were associated with the coupling of nitrification and denitrification processes. Additionally, metabolites such as lipids, amino acids, isovalerylcarnitine, and peptides, associated with microbial physiological functions, energy metabolism, and signal transduction processes, varied with oxygen stratification. These findings contribute to a deeper understanding of the intricate relationships between microbial communities and DOM dynamics in extreme marine environments.},
}

@article {pmid40644847,
year = {2025},
author = {Zhang, H and Jiang, H and Yin, J and Wang, T and Zeng, W and Lin, D and Xu, B and Bai, L and Liang, H and Ng, HY},
title = {Biofilm response in potential difference-enhanced membrane-aerated biofilm systems for accelerated antibiotic removal and ARG mitigation.},
journal = {Water research},
volume = {285},
number = {},
pages = {124154},
doi = {10.1016/j.watres.2025.124154},
pmid = {40644847},
issn = {1879-2448},
abstract = {A membrane-aerated bio-cathode configuration was engineered, leveraging counter-diffusion biofilm architecture to physically segregate oxygen from cathode reactions. This design minimized electron diversion to oxygen (a competing terminal electron acceptor), thereby optimizing electron allocation for antibiotic co-metabolism. Further, the biofilms self-regulation and the molecular dynamics (MD) mechanism of antibiotic/antibiotic resistance genes (ARGs) reduction were simultaneously investigated. At 80 V/m potential difference, anode biofilms exhibited enhanced protein secretion (2.31-fold increase versus controls), which mitigated SMX-induced static quenching of tyrosine-like fluorophores by shifting to dynamic quenching mechanisms. Concurrent cathode analyses revealed substantial ARG suppression, with sul1 (-1.25 log2) and sul2 (-1.22 log2) reductions attributed to host genus inactivation (Nitrateductor, Pseudomonas, Methylobacterium abundance undetectable). MD simulations elucidated critical interaction mechanism: Reduced polar solvation energy (ΔGPB=-31.363 kJ/mol) promoting Sul1-encoded protein and SMX interactions strengthened, enhancing resistance sustainability under ARGs reduction. Besides, Flavin mononucleotide activation promoted SMX degradation via Cytochrome P450, likely driving rapid SMX removal under electric fields, with a 1.5-fold SMX removal rate enhancement versus conventional MABR.},
}

@article {pmid40644733,
year = {2025},
author = {Zhou, Y and Wen, C and Zhang, Q and Gu, Z and Lian, L and Xue, K and Xu, T and Lin, Z and Wang, W and Zhu, H},
title = {Characteristics of oral microbiomics with soldiers in the army before and after high-intensity physical training.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106347},
doi = {10.1016/j.archoralbio.2025.106347},
pmid = {40644733},
issn = {1879-1506},
abstract = {OBJECTIVES: This paper aims to investigate the changes in soldiers' oral microbiome and metabolic levels after a month of high-intensity training.

DESIGN: We collected saliva samples from 10 soldiers with good oral health and hygiene habits before and after training. Subsequently, DNA extraction, metagenomic sequencing, and phylogenetic analysis of the oral microbiome were conducted.

RESULTS: 7733 bacterial species from 113 known bacterial phyla and 2017 genera detected in 20 samples. The diversity and richness of saliva microorganisms before and after training were similar (p > 0.05), while beta diversity analysis showed structural differences in microbiota at the phylum and genus levels (p < 0.05). The relative abundance of 27 genera such as Proteobacteria, Neisseria, Morococcus cerebrosus and Eikenella in soldiers' saliva significantly increased after high-intensity training (p < 0.05). Conversely, the relative abundance of 20 genera such as Bacteroidota, Veillonella, Parvimonas micra, Prevotella oris, Peptostreptococcus, and Treponema decreased (p < 0.05). At the metabolic level, training resulted in a relative increase (p < 0.05) in various pathways, including amino acid metabolism, sulfur metabolism, glutathione metabolism, and Tyrosine metabolism. By comparison, after training, carbohydrate metabolism, glycan biosynthesis, metabolism, the HIF-1 signaling pathway, and necroptosis revealed a relative decrease (p < 0.05).

CONCLUSIONS: This paper reveals the changes in the saliva microbiome of soldiers after one month of high-intensity training, in which the relative abundance of biomarkers of periodontal disease, caries, and other oral diseases represented by peptostreptococcus, prevotella oris, treponema, etc., are significantly reduced, suggesting that long-term high-intensity training may have a positive effect on oral health.},
}

@article {pmid40643937,
year = {2025},
author = {Jenkins, MC and Parker, C and Campos, P and Grimm, K and Davies, C and Tucker, MS and Heeder, C and Quist, M and Thompson, P},
title = {Use of Deep Amplicon Sequencing Based on the Cytochrome Oxidase I Gene to Quantify the Relative Percentages of Eimeria spp. Oocysts in Poultry Litter.},
journal = {Avian diseases},
volume = {69},
number = {2},
pages = {177-182},
doi = {10.1637/aviandiseases-D-25-00006},
pmid = {40643937},
issn = {1938-4351},
mesh = {Animals ; *Eimeria/genetics/isolation & purification/classification ; *Chickens ; Oocysts ; *Coccidiosis/veterinary/parasitology ; *Poultry Diseases/parasitology ; *Electron Transport Complex IV/genetics/metabolism ; *High-Throughput Nucleotide Sequencing/veterinary ; *Protozoan Proteins/genetics/metabolism ; Housing, Animal ; },
abstract = {The purpose of this study was to evaluate a deep amplicon sequencing approach for estimating the relative abundances of different Eimeria spp. oocysts in litter from commercial broiler farms that may or may not be experiencing necrotic enteritis (NE) infections. Oligonucleotide primers directed to the mitochondrial cytochrome oxidase I (COI) gene, a sequence that is conserved among all chicken Eimeria spp., were first used to PCR amplify Eimeria acervulina, Eimeria maxima, and Eimeria tenella oocyst DNA. COI amplification was applied to samples containing either a single Eimeria species or an equal mixture of E. acervulina, E. maxima, and E. tenella oocysts. Amplicon sequencing and mapping to the relevant COI sequences in the GenBank database confirmed the expected ∼100% mapping to the appropriate Eimeria sp. and in approximately equal percentages (∼33%) for mixtures of equal numbers of Eimeria spp. oocysts. This approach was then applied to DNA derived from Eimeria oocysts obtained at 0, 2, and 4 wk after chick placement (growout) from a total of 20 individual houses on six different commercial broiler farms. Of the seven Eimeria spp. known to infect chickens, only five were consistently found in litter at each collection time point: E. acervulina, E. maxima, Eimeria mitis, Eimeria praecox, and E. tenella. The relative numbers of E. maxima and non-E. maxima (Eamipt) oocysts in all litter samples as estimated by COI deep amplicon sequencing showed a modest correlation with the respective E. maxima or Eamipt oocyst counts (R ∼ 0.30). The results revealed an interesting phenomenon that supports the role of E. mitis in predisposing chickens to NE. In this study, the percentage of E. mitis as estimated by deep amplicon sequencing at 0, 2, and 4 wk growout showed a strong positive correlation with NE incidence (0 wk, R = 0.57; 2 wk, R = 0.52; 4 wk, R = 0.61). This study provides evidence for the usefulness of a deep amplicon sequencing approach to estimating the relative abundances of different Eimeria oocysts infecting chickens because it allows reactions to take place in a single tube, thus avoiding the time-consuming, labor-intensive, species-specific internal transcribed spacer 1 (ITS1) PCR analyses. More importantly, it allows one to explore relationships between NE incidence and the abundance of minor Eimeria species, which would have been missed by oocyst counting or ITS1 PCR because most Eimeria species are not distinguishable by microscopy, and ITS1 PCR is not quantitative.},
}

Animals
*Eimeria/genetics/isolation & purification/classification
*Chickens
Oocysts
*Coccidiosis/veterinary/parasitology
*Poultry Diseases/parasitology
*Electron Transport Complex IV/genetics/metabolism
*High-Throughput Nucleotide Sequencing/veterinary
*Protozoan Proteins/genetics/metabolism
Housing, Animal

@article {pmid40643235,
year = {2025},
author = {Wang, X and Lv, Y and Zhao, W and Xiao, X and Wang, J},
title = {D-amino acid metabolic versatility as a common adaptive strategy in the Mariana Trench microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0058125},
doi = {10.1128/msystems.00581-25},
pmid = {40643235},
issn = {2379-5077},
abstract = {UNLABELLED: Hadal trenches, the Earth's deepest marine environments, harbor thriving microbial communities that promote the turnover of recalcitrant dissolved organic matter (RDOM) under extreme conditions. However, the effects of microbes on D-amino acid (D-AA) reservoirs, which are important components of deep-sea RDOM, remain largely unknown. To address this knowledge gap, we curated a comprehensive reference database of D-AA functional genes for accurate identification of D-AA metabolic potential from metagenomic data. Using this database, we identified the presence of various D-AA anabolic and catabolic genes that were closely correlated with central carbon metabolism and ammonia oxidation genes throughout the water column and in the sediment of the Mariana Trench. Furthermore, 93.6% of the recovered bacterial and archaeal genomes contained at least one of these D-AA functional genes, substantially expanding our understanding of potential D-AA utilizers. Notably, we discovered that glutamate racemase, an enzyme previously thought to be exclusive to bacteria, is ubiquitously present in ammonia-oxidizing archaea. This finding suggests that D-glutamate could be integrated into hadal carbon and nitrogen cycling by this crucial microbial taxon. Finally, we observed an increase in both D-AA production and degradation potential with water depth, with higher levels in near-bottom seawater than in sediment. These findings suggest that diverse microbial taxa promote increased D-AA turnover in hadal zones, potentially representing a common adaptive response to extreme hadal conditions.

IMPORTANCE: Deep-sea microorganisms play a crucial role in the turnover of RDOM. In this study, we investigated the metabolic potential of D-AAs, which are important constituents of RDOM and are used for indicating the recalcitrance of organic matter. By elucidating the genetic profiles of D-AA metabolism and associated microbial taxa, we observed that D-AA metabolism is a fundamental ecological function that is prevalent in the deepest ocean. Our finding of higher D-AA turnover potentials in deeper environments challenges the conventional view of the constant recalcitrance of D-AAs, suggesting that D-AA turnover may be environmentally dependent. This insight provides a new paradigm for understanding RDOM turnover, with broad implications for marine biogeochemistry.},
}

@article {pmid40643197,
year = {2025},
author = {Xu, T and Wu, X and Zhang, Y and Cai, Y and Zhang, X and Zeng, Q and Luo, J and Wei, J and Chen, T},
title = {L-Tryptophan Produced by Bifidobacterium pseudocatenulatum NCU-08 Delays Aging in SAMP8 Mice by Activating the Sirt1/P53/P21/Rb Signaling Pathway.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70166},
doi = {10.1111/acel.70166},
pmid = {40643197},
issn = {1474-9726},
support = {32201250//National Natural Science Foundation of China/ ; 2024YFA1307103//National Key R&D Program of China/ ; 2024SSY07061//Jiangxi Province Key Laboratory of bioengineering drugs/ ; 20242BAB25464//Jiangxi Provincial Natural Science Foundation/ ; },
abstract = {Gut microbiota delays aging by regulating the immune, metabolic, and neurological functions of the host. However, current research on novel probiotics with antiaging properties significantly lags, impacting their application in clinical treatments. In this study, metagenomics, culturomics, and probiotic property screening were used to identify Bifidobacterium pseudocatenulatum NCU-08 as a potential probiotic with anti-aging properties. In addition, B. pseudocatenulatum NCU-08 effectively improved the behavioral characteristics, significantly reduced the levels of the age-related protein β-galactosidase (β-gal) (BP: M = 0.81 vs. 1.13, p < 0.05), attenuated neuronal damage in the hippocampus, and improved the composition of the gut microbiota of senescence-accelerated mouse tendency-8 (SAMP8) mice. The targeted metabolomics suggested that L-tryptophan (L-Trp) may be a key substance for B. pseudocatenulatum NCU-08 to exert anti-aging effects (BP: M = 14878.6 ng/mL vs. 5464.99 ng/mL, p < 0.01). Mechanistically, using the aging model of SAMP8 mice and HT22 mouse hippocampal neuronal cells, it was found that B. pseudocatenulatum NCU-08 might enter the intestine to regulate L-Trp, and then transport it to the brain. In the brain, L-Trp was metabolized to NAD[+], which activated the Sirt1/P53/P21/Rb signaling pathway, thereby exerting antiaging effects. Interestingly, this antiaging effect was inhibited after the intervention of the Sirt1 inhibitor EX-527. This study is the first to confirm the antiaging properties of NCU-08 isolated from the fecal samples of seven centenarians in Jiangxi Province, providing data support for the future development of probiotic preparations with antiaging effects.},
}

@article {pmid40642988,
year = {2025},
author = {Wang, F and Wu, Y and Ni, J and Xie, Q and Shen, J and Chen, H and Ma, C and Yao, Y and Wang, J and Xu, L and Xiang, Q and Zhao, Y and Chen, Y and Li, L},
title = {Gut microbiota links to histological damage in chronic HBV infection patients and aggravates fibrosis via fecal microbiota transplantation in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0076425},
doi = {10.1128/spectrum.00764-25},
pmid = {40642988},
issn = {2165-0497},
abstract = {Gut microbiota dysbiosis has been observed in HBV-related cirrhosis, but its role in early-stage disease and its correlation with liver pathology remain unclear. Moreover, whether dysbiosis is a cause or consequence of liver cirrhosis is still debated. We recruited 20 treatment-naïve patients with chronic HBV infection, assessing liver injury via biopsy. Fecal metagenomic sequencing was used to analyze the correlation between gut microbiota and liver histology. To explore the causality, fecal samples from an HBV-related cirrhosis patient were transplanted into mice with CCl4-induced liver fibrosis. Patients with significant histological damage exhibited reduced alpha diversity and greater microbial homogeneity. Species such as Eubacterium_sp_CAG_180, Gemmiger_formicilis, and Oscillibacter_sp_ER4 had decreased abundance, while Parabacteroides_distasonis, Bacteroides_dorei, and Bacteroides_finegoldii were enriched. Mice receiving fecal transplants from the cirrhotic patient showed aggravated liver fibrosis, with increased collagen deposition; elevated ALT, AST, and ALP levels; and heightened hepatic inflammatory gene expression. Additionally, abnormal bile acid profiles with elevated unconjugated bile acids (e.g., GCA and CA) were observed. Gut microbiota dysbiosis is closely associated with liver histological damage in chronic HBV infection and may drive fibrosis progression via microbial-bile acid interactions. These findings suggest potential for gut microbiota-based assessment and treatment strategies in chronic hepatitis B.IMPORTANCEThis study elucidates a significant association between gut microbiota dysbiosis and liver histological damage in patients with chronic hepatitis B (HBV), potentially exacerbating fibrosis progression through bile acid interactions. By analyzing patient gut microbiota and conducting fecal transplant experiments in mice, researchers have identified that gut microbiota dysbiosis contributes to hepatic fibrosis during chronic HBV infection. These findings underscore the importance of the gut-liver axis in HBV disease progression, indicating that monitoring or modulating gut bacteria may facilitate early diagnosis or therapeutic interventions. This research bridges the gap in understanding whether microbial alterations drive disease progression or result from it, providing a foundation for developing therapies targeting the microbiome to mitigate liver damage in chronic HBV infections.},
}

@article {pmid40642980,
year = {2025},
author = {Jia, X and Xiong, Y and Xu, Y and Chen, F and Han, P and Qu, J and He, Q and Rao, G},
title = {Machine learning-selected minimal features drive high-accuracy rule-based antibiotic susceptibility predictions for Staphylococcus aureus via metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0055625},
doi = {10.1128/spectrum.00556-25},
pmid = {40642980},
issn = {2165-0497},
abstract = {Antimicrobial resistance (AMR) represents a critical global health challenge, demanding rapid and accurate antimicrobial susceptibility testing (AST) to guide timely treatments. Traditional culture-based AST methods are slow, while existing whole-genome sequencing (WGS)-based models often suffer from overfitting, poor interpretability, and diminished performance on clinical metagenomic data. In this study, we developed an interpretable genotypic AST approach for Staphylococcus aureus using minimal genomic determinants. Analysis of 4,796 S. aureus genomes and AST data for 18 antibiotics revealed one to five key resistance genes per antibiotic, including two previously uncharacterized vancomycin resistance markers. These features enabled highly accurate rule-based predictions, achieving area under the curve (AUC) values ranging from 0.94 to 1.00. The model demonstrated an overall sensitivity of 97.43% and specificity of 99.02%, respectively, with a very major error (VME) rate of 2.57% and a major error (ME) rate of 0.98% for isolate-level testing. Furthermore, after optimization for shallow-depth metagenomic sequencing, the model achieved 81.82% to 100% accuracy in AST predictions for 59 clinical samples, bypassing the need for bacterial isolation and reducing diagnostic time by an average of 39.9 hours. By combining minimal feature selection with strong interpretability and adaptability to metagenomic data, this method offers a practical and transformative solution for rapid and reliable AST in clinical settings.IMPORTANCEAntimicrobial resistance (AMR) in Staphylococcus aureus poses a critical challenge to global health, necessitating rapid and reliable antimicrobial susceptibility testing (AST) for timely treatment decisions. Traditional culture-based AST is slow, while existing whole-genome sequencing (WGS)-based approaches often suffer from overfitting and poor interpretability. This study introduces a rule-based, interpretable genotypic AST model for S. aureus that leverages minimal genomic determinants, achieving over 97% accuracy in isolate-level testing and high accuracy in clinical metagenomic samples. By extracting key resistance features and applying a rule-based approach, our model enables faster AST predictions and enhances hospital surveillance of resistant strain outbreaks. This culture-independent method reduces diagnostic time by nearly 40 hours, providing a scalable and actionable solution for clinical AMR management.},
}

@article {pmid40642907,
year = {2025},
author = {Liu, H and Shi, K and Zhang, Y and Zhang, L and Chen, Y and Shi, Y},
title = {Foliar Application of Nanoselenium: A Novel Strategy to Enhance Tuber Quality, Yield, and Nitrogen Use Efficiency in Potato.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c03576},
pmid = {40642907},
issn = {1520-5118},
abstract = {Excessive nitrogen application reduces nitrogen use efficiency (NUE) and exacerbates environmental risks. Nanoselenium (nano-Se) has been shown to enhance plant nitrogen uptake efficiency. This study investigated nano-Se influences potato (Solanum tuberosum L.) tuber yield, quality, rhizosphere soil enzyme activity, and inorganic nitrogen content under different nitrogen application levels, integrating metabolomic, metagenomic, and soil metabolomic analyses. Results showed that the N2 + Se treatment matched the yield of the N3 + Se treatment but notably boosted vitamin C (Vc), starch content, and NUE. Metabolomic analysis showed that nano-Se promoted the accumulation of d-glucose-1-phosphate (a starch precursor) and amino acids (raw materials for protein) in tubers. Multiomics data indicated that nano-Se recruited beneficial rhizobacteria such as Flavobacterium and Pseudoxanthomonas by exuding l-tyrosine, l-valine, and 4-oxoproline. In addition, It promoted nitrate assimilation genes (narB and nirB) and suppressed nitrification genes (amoA and hao), reducing nitrogen losses.},
}

@article {pmid40641875,
year = {2025},
author = {Yu, F and Jin, J and Jin, X and Ding, X and Lou, Y},
title = {Altered upper respiratory tract microbiota in laryngeal cough attributed to lung yin deficiency and the modulatory effects of Yangyin Qingfei Oral Liquid.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1592294},
pmid = {40641875},
issn = {1664-302X},
abstract = {OBJECTIVE: This study investigates changes in upper respiratory tract microbiota in laryngeal cough patients with lung yin deficiency using high-throughput sequencing of the 16S rDNA gene. It also examines the modulatory effects of Yangyin Qingfei Oral Liquid (YYQFOL).

METHODS: We included 100 laryngeal cough patients and 65 healthy subjects, collecting throat swab samples for microbiota comparison. Patients were randomly assigned to a control group receiving methoxyphenamine capsules and an experimental group receiving YYQFOL and methoxyphenamine for 10 days. We assessed changes in microbiota, symptom scoring, and Leicester Cough Questionnaire (LCQ) results. Each group was divided into responders (R) and non-responders (NR).

RESULTS: Patients with laryngeal cough had significantly lower microbial abundance and diversity than healthy subjects (p < 0.05). After treatment, symptom scores and LCQ results improved significantly (p < 0.05), with responders in the experimental group (ER) showing significantly better improvement than those in the responders in the control group (CR) (p < 0.05). Post-treatment, the experimental group saw a significant reduction in Streptococcus, Haemophilus, and other genera, while Veillonella increased (p < 0.05).

CONCLUSION: Laryngeal cough patients with lung yin deficiency are imbalanced in the upper respiratory tract microbiota. Treatment with methoxyphenamine and YYQFOL improves microbiota composition and alleviates symptoms.},
}

@article {pmid40641865,
year = {2025},
author = {Nyimbo, WJ and Fallah, N and Mutombo, AM and Xu, H and Bin, Q and Makungu, JS and Lin, W},
title = {Exploring the change of coastal saline agroecosystem diversity, composition and predicted function of soil microbial community mediated by soybean and corn intercropping.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1427196},
pmid = {40641865},
issn = {1664-462X},
abstract = {INTRODUCTION: Soil microbial community is the key determinant of coastal agroecosystem soil health. However, the response of soil microbial community and its anticipated functions to soybean and corn intercropping in coastal saline agroecosystems is not well understood.

METHOD: Soybean and corn intercropping was done in Putian city of Fujian province. After harvest, soil total carbon (TC), total phosphorus (TP), total nitrogen (TN), total organic carbon (TOC), soil organic matter (SOM), salinity content and elemental ratios of C: N, C: P and N: P were examined. High-throughput sequencing was performed to investigate the community composition and diversity of rhizospheric bacterial and fungal communities as influenced by monoculture soybean (MS) and corn (MC), first (FP) and second (SP) intercropping pattern. LEfSe cladogram was generated to identify potential microbial markers and metagenome was annotated with the metabolic cycles and pathways in the KEGG database to predict the microbial function. The co-occurrence and RDA analysis assessed the correlation between microbes and soil microbes with soil chemical parameters.

RESULTS AND DISCUSSION: The intercropping patterns FP and SP significantly influenced soil TC, TP, TN, SOM, EC, pH and salinity content. The C: N, C: P, and N: P ratios were influenced by C, N, and P concentrations. Our investigation found that Chao1 was significantly higher in intercropping patterns than in monoculture patterns. Nevertheless, the Shannon index was substantially higher in monoculture than in intercropping patterns FP and SP indicating reduced bacterial and fungi diversity measured by species richness and evenness. The Non-Metric multidimensional scaling (NDMS) diversity showed that all samples were significantly clustered into four major groups, according to the bacteria and fungi communities of origin. Further statistical analysis revealed that cropping patterns strongly affected microbial communities. Furthermore, Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were enriched bacterial phyla in the rhizosphere of MS, MC, FP, and SP. Ascomycota, Mortierellomycota, and Basidiomycota were the most enriched fungi phyla in each intercropping pattern. These phyla were identified as sensitive biomarkers for soil nutrient circulation, ecosystem bioremediation and chemical degradation.

CONCLUSION: This study increases our understanding of soybean and corn intercropping in coastal saline agroecosystems microbiomes.},
}

@article {pmid40641180,
year = {2025},
author = {Echeveste Medrano, MJ and Su, G and Blattner, LA and Leão, P and Sánchez-Andrea, I and Jetten, MSM and Welte, CU and Zopfi, J},
title = {Methanotrophic Flexibility of 'Ca. Methanoperedens' and Its Interactions With Sulphate-Reducing Bacteria in the Sediment of Meromictic Lake Cadagno.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70133},
pmid = {40641180},
issn = {1462-2920},
support = {024.002.002//Dutch Research Council (NWO), Gravitation Grant SIAM/ ; VI.Vidi.223.012//NWO-VIDI Talent Grant/ ; 854088/ERC_/European Research Council/International ; },
mesh = {*Lakes/microbiology ; *Methane/metabolism ; *Geologic Sediments/microbiology ; Oxidation-Reduction ; Sulfates/metabolism ; Deltaproteobacteria/genetics/metabolism ; Phylogeny ; *Sulfur-Reducing Bacteria/metabolism/genetics ; *Microbial Interactions ; Metagenomics ; Electron Transport ; },
abstract = {The greenhouse gas methane is an important contributor to global warming, with freshwater sediments representing important potential methane sources. Anaerobic methane-oxidising archaea mitigate methane release into the atmosphere by coupling the oxidation of methane to the reduction of extracellular electron acceptors or through interspecies electron transfer with microbial partners. Understanding their metabolic flexibility and microbial interactions is crucial to assess their role in global methane cycling. Here, we investigated anoxic sediments of the meromictic freshwater Lake Cadagno (Switzerland), where 'Ca. Methanoperedens' co-occur with a specific sulphate-reducing bacterium, with metagenomics and long-term incubations. Incubations were performed with different electron acceptors, revealing that manganese oxides supported highest CH4 oxidation potential but enriched for 'Ca. Methanoperedens' phylotypes that were hardly present in the inoculum. Combining data from the inoculum and incubations, we obtained five 'Ca. Methanoperedens' genomes, each harbouring different extracellular electron transfer pathways. In a reconstructed Desulfobacterota QYQD01 genome, we observed large multi-heme cytochromes, type IV pili, and a putative loss of hydrogenases, suggesting facultative syntrophic interactions with 'Ca. Methanoperedens'. This research deepens our understanding of the metabolic flexibility and potential interspecific interactions of 'Ca. Methanoperedens' in freshwater lakes.},
}

*Lakes/microbiology
*Methane/metabolism
*Geologic Sediments/microbiology
Oxidation-Reduction
Sulfates/metabolism
Deltaproteobacteria/genetics/metabolism
Phylogeny
*Sulfur-Reducing Bacteria/metabolism/genetics
*Microbial Interactions
Metagenomics
Electron Transport

@article {pmid40640914,
year = {2025},
author = {Zhao, J and Kui, L and Huang, J and Deng, J and Liu, L and Zhu, C and Shi, Y and Li, C and Xiao, Y and Yu, J and Li, Q and Yang, B and Leng, B and Chan, H},
title = {Bifidobacterium animalis subsp. Lactis BX-BC08 modulates gut microbiota and secretes alpha-Ketoglutaric acid to alleviate MC903-induced atopic dermatitis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {768},
pmid = {40640914},
issn = {1479-5876},
support = {SL2024A04J01394//Guangzhou Municipal Science and Technology Bureau Young Doctor "Qihang" Program/ ; },
mesh = {Animals ; *Dermatitis, Atopic/microbiology/chemically induced/drug therapy ; *Gastrointestinal Microbiome ; *Bifidobacterium animalis/physiology/metabolism ; *Ketoglutaric Acids/metabolism ; Mice ; Disease Models, Animal ; Female ; Probiotics ; Mice, Inbred BALB C ; },
abstract = {OBJECTIVE: Bifidobacterium is known to be depleted in patients with atopic dermatitis (AD). This study aims to investigate the potential prophylactic effects of Bifidobacterium animalis subsp. lactis BX-BC08 (B. lactis BX-BC08) in a murine model of AD.

DESIGN: The immunosuppressive and anti-inflammatory effects of BX-BC08 were evaluated in a MC903-induced AD mouse model. Gut microbiota composition was analyzed by metagenomic sequencing, while high-performance liquid chromatography-mass spectrometry (HPLC-MS) was employed to identify anti-inflammatory molecules produced by B. lactis BX-BC08.

RESULTS: BX-BC08 significantly attenuated pro-inflammatory responses, scaling and swelling in the MC903-induced AD like murine model compared to controls. Fecal microbial profiling revealed an enrichment of probiotics and a reduction of pro-inflammatory bacteria in BX-BC08 treated mice. Metabolic analysis of BX-BC08 bacteria culture supernatant and treated mice identified a significant enrichment of alpha-Ketoglutaric acid (AKG). Functional validation in the murine AD model demonstrated that AKG strongly suppressed T helper 2 (Th2)-driven pro-inflammatory responses.

CONCLUSION: BX-BC08 mitigates AD-like inflammation by producing the anti-inflammatory metabolite AKG. BX-BC08 could serve as a novel prophylactic agent for AD prevention.},
}

Animals
*Dermatitis, Atopic/microbiology/chemically induced/drug therapy
*Gastrointestinal Microbiome
*Bifidobacterium animalis/physiology/metabolism
*Ketoglutaric Acids/metabolism
Mice
Disease Models, Animal
Female
Probiotics
Mice, Inbred BALB C

@article {pmid40640502,
year = {2025},
author = {Liu, L and Firrman, JA and Narrowe, AB and Mahalak, KK and Lemons, JMS and Marzorati, M and Duysburgh, C and Rotsaert, C and Van de Wiele, T},
title = {Structural and functional characterization of a porcine intestinal microbial ecosystem developed in vitro.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24821},
pmid = {40640502},
issn = {2045-2322},
support = {8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; EOS-Homistasis project//FWO-FNR/ ; GOA-Microbes4Immunity//UGent-BOF/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; *Bacteria/genetics/classification ; Metagenomics/methods ; Metabolomics ; *Intestines/microbiology ; Ecosystem ; },
abstract = {The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.},
}

Animals
Swine
*Gastrointestinal Microbiome
Metagenome
Feces/microbiology
*Bacteria/genetics/classification
Metagenomics/methods
Metabolomics
*Intestines/microbiology
Ecosystem

@article {pmid40640272,
year = {2025},
author = {Xie, Y and Xiang, JY and Long, L and Ma, Y and Xing, Z and Wang, L and Shao, C and Liu, N and Li, F},
title = {Impact of different treatment methods and timings on soil microbial communities with transgenic maize straw return.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24820},
pmid = {40640272},
issn = {2045-2322},
support = {20230508091RC//Jilin Provincial Scientific and Technological Development Program/ ; 20230508091RC//Jilin Provincial Scientific and Technological Development Program/ ; },
mesh = {*Zea mays/genetics ; *Soil Microbiology ; *Plants, Genetically Modified ; *Microbiota ; Soil/chemistry ; Agriculture/methods ; Crops, Agricultural ; Metagenomics/methods ; },
abstract = {Understanding the impact of genetically modified (GM) crop straw return on soil ecosystems is crucial as GM crops become more prevalent. This study assesses the effects of straw mulching and deep tillage on soil microbial communities from GM and non-GM maize, highlighting potential ecological impacts. Shotgun metagenomic sequencing was utilized to analyze the microbial community structure and functional genes in soil samples collected at different times (30, 180, and 270 days) after straw mulching and deep tillage treatments. The study included insect-resistant transgenic maize varieties 2A-7 and CM8101 and their non-transgenic counterparts B73 and Zheng58. Different treatment methods significantly affect soil microbial alpha-diversity and beta-diversity, with deep tillage resulting in higher alpha-diversity compared to mulching, and the 180-day mark exhibiting the highest alpha-diversity across all sampling times. Early straw treatment prompted a rapid microbial response to nutrient availability, with notable changes in diversity and function over time. Straw treatments notably altered soil microbial functions, especially in carbon cycling and nutrient metabolism. Interestingly, the microbial effects of GM versus non-GM maize straw were similar, suggesting crop residue type under consistent soil management practices might not significantly alter microbial community structures. The methods and timing of straw treatments have a significant impact on soil microbial communities, surpassing the differences between GM and non-GM straw. These findings highlight the importance of straw management practices for sustainable agricultural ecosystem management.},
}

*Zea mays/genetics
*Soil Microbiology
*Plants, Genetically Modified
*Microbiota
Soil/chemistry
Agriculture/methods
Crops, Agricultural
Metagenomics/methods

@article {pmid40639969,
year = {2025},
author = {Shi, C and Wang, C and He, J and Zhang, M and Huang, W},
title = {Epichloë Endophytes Potentially Facilitate Host Plant Recruitment of Rhizosphere Microbiota Carrying Beneficial Traits.},
journal = {Physiologia plantarum},
volume = {177},
number = {4},
pages = {e70397},
doi = {10.1111/ppl.70397},
pmid = {40639969},
issn = {1399-3054},
support = {31760704//National Natural Science Foundation of China/ ; 2022D01A79//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 23XJTRZW07//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; },
mesh = {*Rhizosphere ; *Endophytes/physiology ; Plant Roots/microbiology ; *Epichloe/physiology ; *Microbiota/physiology ; Soil Microbiology ; Symbiosis ; },
abstract = {Plant-microbe symbiotic relationships drive ecosystem evolution. This study employed metabolomics and metagenomic technologies to investigate the effects of the aboveground-restricted endophytic fungus Epichloë guerinii in the host plant Melica transsilvanica on the rhizosphere microbial community structure and functional traits. Our results revealed that the presence of E. guerinii significantly increased the secretion of organic acids, amino acids, and sugar alcohols from the host root system. These exudates correlated strongly with abundant, plant growth-promoting rhizosphere microorganisms like Pseudomonas, Bradyrhizobium, and Nitrospira. Functional genes that were significantly enriched in the host rhizosphere microbiota were predominantly associated with biofilm formation and organic acid metabolic pathways. Co-enrichment analyses of rhizosphere soil metabolites and genes highlighted pathways such as flagellar assembly and carbon/nitrogen/sulfur metabolism. Notably, the abundance of key genes governing the flagellar motor MotA protein in the host rhizosphere, as well as those involved in the reductive tricarboxylic acid (rTCA) cycle, nitrification, and thiosulfate oxidation, were significantly elevated. This study demonstrates that E. guerinii positively regulates rhizosphere microbial community functions by reprogramming the composition of host root exudates. These findings deepen the mechanistic understanding of Epichloë-plant-rhizosphere microbe interactions.},
}

*Rhizosphere
*Endophytes/physiology
Plant Roots/microbiology
*Epichloe/physiology
*Microbiota/physiology
Soil Microbiology
Symbiosis

@article {pmid40639658,
year = {2025},
author = {Ravelo, AD and Salfer, IJ and Caixeta, LS},
title = {GRADUATE STUDENT LITERATURE REVIEW: Contemporary perspectives and the use of omics techniques to improve our understanding of hyperketonemia in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26542},
pmid = {40639658},
issn = {1525-3198},
abstract = {Hyperketonemia (HYK) is a metabolic disorder defined by increased ketone concentrations, particularly β-hydroxybutyrate (BHB). It is linked to increased disease risk and reduced milk production in dairy cows due to energy deficits during early lactation. Recently, omics approaches such as genomics, transcriptomics, proteomics, and metabolomics have been used to better understand mechanisms associated to HYK. These studies have helped characterize pathways associated to energy metabolism, lipid mobilization, insulin resistance, and immune response, with associated genes identified in several genome regions, including Bos taurus autosome 6. Omics studies have identified biomarkers, such as methanol, C16, and phosphatidylcholine acyl-alkyl C30:2, which have been associated with or predictive of HYK, with elevated levels detectable up to 4 weeks before calving. Limitations of omics studies include the small sample sizes of controlled study designs, standardizing sampling timelines, and translating the large amounts of data generated into practical applications. While global changes in other body fluids have been well-characterized, research focused on the role of the rumen fluid metagenome and metabolome is much more limited. Changes in rumen metabolites and microbes are important to consider in relation to HYK, as associated shifts in dry matter intake and diet can alter rumen function and subsequent nutrient metabolism and absorption. Shifts in microbial communities, such as Ruminococcaceae, and altered metabolite profiles, including increased butyrate in HYK cows, may offer insights to guide on farm decisions, such as dietary interventions or feed additive use. Overall, although HYK in dairy cows is a topic that has been extensively studied, improved understanding of its etiology and advances in 'big data' technologies have created continued opportunities to further understand HYK and the factors associated with it. Thus, the focus of this review is to provide an overview of omics methods and how they have been used to further describe HYK as well as explore new associations of omics methods and rumen parameters with HYK.},
}

@article {pmid40639330,
year = {2025},
author = {Liu, K and Wang, Y},
title = {Metatranscriptomics catches gut microbes in the act.},
journal = {Cell host & microbe},
volume = {33},
number = {7},
pages = {1040-1042},
doi = {10.1016/j.chom.2025.06.004},
pmid = {40639330},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Humans ; *Transcriptome ; *Bacteria/genetics ; *Metagenome ; Animals ; Circadian Rhythm ; *Gastrointestinal Tract/microbiology ; },
abstract = {In this issue of Cell Host & Microbe, Flores Ramos et al.[1] employ metatranscriptomics to uncover diurnal microbial functional shifts in the gut microbiome driven by time-restricted feeding. Their work highlights the value of metatranscriptomics over metagenomics in capturing real-time microbial activity and guiding therapeutic bacterial engineering.},
}

*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Humans
*Transcriptome
*Bacteria/genetics
*Metagenome
Animals
Circadian Rhythm
*Gastrointestinal Tract/microbiology

@article {pmid40638549,
year = {2025},
author = {Dasgupta, S},
title = {Unraveling the Microbiome-Asthma Axis: Metagenomic Insights from Airway and Gut Microbial Communities.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1177/15578100251358958},
pmid = {40638549},
issn = {1557-8100},
abstract = {Asthma is a heterogeneous respiratory disease with complex pathogenesis involving immune dysregulation, environmental triggers, and increasingly recognized to have contributions from the human microbiome. Emerging evidence from longitudinal birth cohorts and multi-omics studies reveals that early-life microbial colonization patterns in both the gastrointestinal and respiratory tracts play a crucial role in shaping immune trajectories and influencing asthma susceptibility. This expert review highlights the findings from pivotal studies that associate dysbiosis in the gut and airway microbiota with asthma development and its diverse phenotypic manifestations. Reduced abundance of immunomodulatory genera such as Bifidobacterium, Faecalibacterium, and Lachnospira in the gut has been consistently associated with increased asthma risk. In the airways, increased colonization by potentially pathogenic taxa, including Moraxella, Haemophilus, and Streptococcus, correlates with viral respiratory infections and persistent wheezing. Microbiome diversity patterns also differ between asthma phenotypes: eosinophilic asthma typically features a community profile closer to healthy individuals, while neutrophilic asthma is marked by enrichment of pro-inflammatory bacterial species. Moreover, protective genera such as Dolosigranulum and Corynebacterium in the upper airways are associated with lower risk of asthma and reduced respiratory infections. Elucidating these microbiome-mediated mechanisms holds promise for the development of targeted microbiota-based strategies for asthma prevention and phenotype-specific therapeutic interventions. The present review unpacks these localized microbial patterns and their mechanistic implications for asthma development, severity, and endotypic variation. Finally, unraveling the microbiome-asthma axis from airway and gut microbial communities also has implications for new ways of thinking personalized medicine in the future.},
}

@article {pmid40638514,
year = {2025},
author = {David, EDS and Komninakis, SV and Fonseca, EDC and Soledade, ACDS and Santos, KCD and Souto, RNP},
title = {The application of metagenomics in the detection of arboviruses in mosquitoes (Diptera: Culicidade): a systematic review.},
journal = {Revista do Instituto de Medicina Tropical de Sao Paulo},
volume = {67},
number = {},
pages = {e46},
pmid = {40638514},
issn = {1678-9946},
mesh = {Animals ; *Metagenomics/methods ; *Arboviruses/genetics/isolation & purification ; *Culicidae/virology ; *Mosquito Vectors/virology ; },
abstract = {Advances in deforestation and climate change directly cause changes in habits and the distribution of Culicidae across the globe, especially mosquitoes of medical importance and the main vectors of arboviruses. The viral metagenomics technique can be an important tool in characterizing viral diversity in mosquitoes. Thus, this study aimed to identify evidence of the effectiveness of the viral metagenomics technique in detecting arboviruses in mosquitoes. This is a systematic review based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 protocol. The research was carried out using five electronic databases: LILACS, PubMed, SciELO, Scopus, and Web of Science, and included studies published in health and interdisciplinary fields, as well as complementary research on Google Scholar. Studies that used the viral metagenomics approach for the genomic evaluation of arboviruses found in mosquito samples were included; the results demonstrated the presence of viral diversity and the identification of the genome of probable pathogenic viruses. The protocol was registered on the International Prospective Register of Systematic Reviews (PROSPERO) platform under the number CRD42024484713. Thus, 249 studies were identified via searches on electronic databases. According to the inclusion/exclusion criteria, only 23 studies met the objectives for the systematic review. In all studies, genomic sequencing was applied to detect viruses, mainly those related to insect-specific viruses (ISV) and arboviruses known to infect humans and animals, belonging to various viral families. Despite the challenges reagrdingthe absence of reference sequences in genomic databases, the effectiveness of the metagenomics technique in characterizing the mosquito virome is clear from the studies, which broadens the understanding of viral diversity.},
}

Animals
*Metagenomics/methods
*Arboviruses/genetics/isolation & purification
*Culicidae/virology
*Mosquito Vectors/virology

@article {pmid40637872,
year = {2025},
author = {Dimattia, LM and Saglam, N and Saunders, R and Shain, DH},
title = {An ice inhabiting bdelloid rotifer from North America.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {30},
pmid = {40637872},
issn = {1433-4909},
mesh = {Animals ; *Rotifera/genetics/physiology/classification ; North America ; Ice Cover ; Ice ; Phylogeny ; },
abstract = {Bdelloid rotifers are major components of zooplankton worldwide and have been reported in glacier ice in both Northern and Southern Hemispheres. Curiously, no reports of psychrophilic bdelloids have surfaced in North America despite exhaustive surveys of other ice-dwelling invertebrates, e.g., glacier ice worms. This distribution gap may be partially explained by a predator-prey relationship between these two animals, but the current study suggests that ice worms and bdelloids can co-inhabit at least some glacial ecosystems over geological time. Here we report the first ice-inhabiting bdelloid rotifer from North America, collected from the northern aspect of Mt. Deception, WA, USA. Nuclear and mitochondrial genotyping identified sister-species relationships within a clade of Nordic ice-dwelling bdelloids, and close evolutionary relationships with Antarctic/New Zealand specimens. Intrapopulation genetic divergences suggest that bdelloids arrived in North America near the onset of the Pleistocene (2.58 myr BP), but their circumpolar dispersal capabilities and robustness (e.g., freeze-thaw tolerance, ability to propagate at elevated temperatures and under extreme laboratory conditions) cannot rule out multiple transoceanic dispersal events throughout the Quaternary.},
}

Animals
*Rotifera/genetics/physiology/classification
North America
Ice Cover
Ice
Phylogeny

@article {pmid40637797,
year = {2025},
author = {Giani, NM and Lim, SJ and Anderson, LC and Paterson, AT and Engel, AS and Campbell, BJ},
title = {Variation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf074},
pmid = {40637797},
issn = {1574-6941},
abstract = {Lucinid bivalves harbor environmentally acquired endosymbionts within the class Gammaproteobacteria and genus Candidatus Thiodiazotropha. Despite recent studies focused on lucinid endosymbiont genomic and functional diversity, processes influencing species diversity have been understudied. From the analysis of 333 metagenome-assembled genomes (MAGs) from 40 host species across eight waterbodies and 77 distinct locations, 272 were high quality MAGs of Ca. Thiodiazotropha endosymbionts that represented 11 genomospecies. Of those, two new genomospecies from lucinids collected from The Bahamas and Florida (USA) were identified, Ca. Thiodiazotropha fisheri and Ca. Thiodiazotropha grosi. Metabolic specialization was evident, such as potential adaptations to diverse carbon sources based on detection of C1 metabolic genes in eight genomospecies. Genes associated with defense, symbiosis/pathogenesis, and horizontal gene transfer (HGT) were also distinct across genomospecies. For instance, Ca. T. taylori exhibited lower abundances of HGT-associated genes compared to other genomospecies, particularly Ca. T. endolucinida, Ca. T. lotti, and Ca. T. weberae. HGT-associated genes were linked to previously unreported retron-type reverse transcriptases, dsDNA phages, and phage resistance. Collectively, the pangenome highlights how lucinid endosymbiont diversity has been shaped by geographic and host-specific interactions linked to gene loss and HGT through time.},
}

@article {pmid40637448,
year = {2025},
author = {Tian, S and Xiao, Y and Dong, C},
title = {Psittacosis Combined With Central Nervous System Infection and Acute Cerebral Infarction: A Case Report Based on Metagenomic Next-Generation Sequencing.},
journal = {The neurologist},
volume = {},
number = {},
pages = {},
doi = {10.1097/NRL.0000000000000636},
pmid = {40637448},
issn = {2331-2637},
abstract = {INTRODUCTION: The diagnosis of psittacosis is still challenging due to the high risk of underdiagnosis and misdiagnosis. Here, we reported our diagnostic experience with psittacosis in combination with central nervous system (CNS) infection and acute cerebral infarction (CI).

CASE REPORT: A 62-year-old gentleman presented to our department due to episodic vertigo for 4 hours. Pulmonary CT scan revealed high-density shadows in the right upper lobe, and brain MRI initially excluded new CI lesions. Seven days later, the patient began to show fever, with the highest temperature of 39.3°C. Pulmonary CT scan showed pneumonia. Cerebral MR was performed as the patient showed loss of consciousness and convulsion, which indicated pontine infarction. The patient was eventually transferred to the ICU due to severe pneumonia complicated by type I respiratory failure and acute respiratory distress syndrome (ARDS). Metagenomic next-generation sequencing (mNGS) confirmed psittacosis, and then the patient was treated with a regimen of piperacillin-tazobactam, moxifloxacin, and minocycline. However, the patient continued to have a fever and exhibited irritability after withdrawal of sedative medication, thereby, CNS infection was suspected. Upon cerebrospinal fluid collection following lumbar puncture, mNGS sequencing indicated Candida albicans infection. MR revealed progression of infarction featured by increased lesions in the right cerebellum, right pons, right fronto-parietal-temporal-occipital, and right corona radiata.

CONCLUSION: We reported a case report of psittacosis combined with CNS infection based on the mNGS sequencing, along with acute CI based on conventional imaging technique.},
}

@article {pmid40637407,
year = {2025},
author = {Chin, HS and Ravi Varadharajulu, N and Teo, KC and Cheong, PCH and Tang, S-L},
title = {Key findings from 15 years of Mangrovibacter research: a generalist bacterium beyond endophytes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0247924},
doi = {10.1128/aem.02479-24},
pmid = {40637407},
issn = {1098-5336},
abstract = {Since the discovery of Mangrovibacter plantisponsor in 2010, research on Mangrovibacters (MGBs) has stagnated. Although laboratories worldwide have isolated various MGB strains and deposited their 16S rDNA sequences in the NCBI database, a limited understanding of MGBs has resulted in only a few publications from these collections. Recent advancements in metagenomic technology have revealed the presence of MGBs in a broader range of habitats. Most microbiomes exhibit low MGB abundance (typically <1%). Even in environments with higher prevalence, such as salt-tolerant aerobic granular sludge (75%), the gut of superworms fed with polyurethane (22%), or fermented foods like mandai (16%), the functional roles of MGBs remain unclear. Through meticulous curation of publications and data from MicrobeAtlas and AMIBASE, MGBs can be classified as free living, endophytic, or zoonotic. Recent evidence suggests their presence in food sources and potential interactions with humans. Current studies confirm the coexistence of MGBs with humans. This review underscores the phenotypic features and genomic foundations of MGBs, highlighting attributes such as endophytic behavior, diverse metabolite utilization, tolerance to salinity and pH, metal homeostasis, biofilm formation, and bioremediation potential. Insights are derived from the analysis of four MGB genomes deposited in NCBI since 2014, along with three newly reported genomes in 2024. Experimental and genetic evidence suggests that MGBs act as "generalist microbes" capable of thriving in diverse nutrient sources and harsh environments. This review elucidates prospective research trajectories and highlights numerous potential commercial applications of MGBs, emphasizing the need for further investigation into their roles and benefits.},
}

@article {pmid40637245,
year = {2025},
author = {Adak, S and Chase, AB and Skrip, AE and Moore, BS and Lukowski, AL},
title = {Metagenomic Identification of Brominated Indole Biosynthetic Machinery from Cyanobacteria.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c00492},
pmid = {40637245},
issn = {1520-6025},
abstract = {Halogenated indole natural products have been isolated from a variety of organisms, including plants, marine algae, marine invertebrates, and bacteria. Aquatic cyanobacteria, in particular, are rich producers of brominated indoles, but their cognate biosynthetic enzymes have only been successfully linked in a limited number of natural products, such as the eagle-killing toxin aetokthonotoxin (AETX). The biosynthetic pathway for AETX involves five enzymes, two of which were previously undescribed due to incomplete annotations as hypothetical proteins. Our recent elucidation of AETX biosynthesis established functions of the two previously unknown proteins as enzymes responsible for tryptophan halogenation (AetF) and nitrile synthesis (AetD). Given their sequence novelty, we queried metagenomic data sets for these two enzymes and identified two new cyanobacterial haloindole biosynthetic gene clusters (BGCs) from marine sediment in Moorea, French Polynesia, and soil-derived samples in Maunawili Falls, Hawaii. We characterized the recovered BGCs by biochemically validating a new AetF homologue that exclusively halogenates free indole, rather than tryptophan as observed in AETX biosynthesis, and a new AetD homologue that harbors distinct substrate preferences, expanding the scope of nitrile biosynthesis. Additional characterization of core and accessory enzymes within these AETX-like BGCs highlights the breadth and diversity of haloindole biosynthetic machinery in cyanobacteria.},
}

@article {pmid40636508,
year = {2025},
author = {Li, L and Kong, W and Sun, J and Jiang, Y and Li, T and Xia, Z and Zhou, J and Fang, Z and Chen, L and Feng, S and Song, H and Xiao, H and Zhang, B and Fang, B and Peng, H and Gao, L},
title = {MGV-seq: a sensitive and culture-independent method for detecting microbial genetic variation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1603255},
pmid = {40636508},
issn = {1664-302X},
abstract = {BACKGROUND: Precise detection of microbial genetic variation (MGV) at the strain level is essential for reliable disease diagnosis, pathogen surveillance, and reproducible research. Current methods, however, are constrained by limited sensitivity, specificity, and dependence on culturing. To address these challenges, we developed MGV-Seq, an innovative culture-independent approach that integrates multiplex PCR, high-throughput sequencing, and bioinformatics to analyze multiple dispersed nucleotide polymorphism (MNP) markers, enabling high-resolution strain differentiation.

METHODS: Using Xanthomonas oryzae as a model organism, we designed 213 MNP markers derived from 458 genome assemblies. Method validation encompassed reproducibility, accuracy, sensitivity (detection limit), and specificity using laboratory-adapted strains, artificial DNA mixtures, and uncultured rice leaf samples. Performance was benchmarked against whole-genome sequencing (WGS) and LoFreq variant calling.

RESULTS: MGV-Seq achieved 100% reproducibility and accuracy in major allele detection, with sensitivity down to 0.1% (n = 12 strains) for low-abundance variants and significantly higher specificity than LoFreq. Analysis to 40 X. oryzae strains revealed widespread heterogeneity (90% of strains) and misidentification (e.g., HN-P5 as Xoc). Homonymous strains exhibited significant genetic and phenotypic divergence, attributed to contamination rather than mutation. MGV-Seq successfully identified dominant strains and low-frequency variants in rice leaf samples and authenticated single-colony strains with 100% major allele similarity.

CONCLUSION: MGV-Seq establishes a robust, high-throughput solution for strain identification, microevolution monitoring, and authentication, overcoming limitations of culture-dependent and metagenomics-based methods. Its applicability extends to other microorganisms, offering potential for clinical, agricultural, and forensic diagnostics.},
}

@article {pmid40636504,
year = {2025},
author = {Li, L and Liu, Z and Qin, J and Xiong, G and Yang, C and Cai, F and Huang, J},
title = {Constructing inflammatory bowel disease diagnostic models based on k-mer and machine learning.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1578005},
pmid = {40636504},
issn = {1664-302X},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is linked to significant alterations in gut microbiota. Conventional diagnostic approaches frequently rely on invasive procedures, contributing to patient discomfort; hence, non-invasive diagnostic models present a valuable clinical alternative.

METHODS: Metagenomic and amplicon sequencing data were collected from fecal samples of patients with IBD and healthy individuals across diverse geographic regions. Diagnostic models were developed using Logistic Regression (LR), Support Vector Machine (SVM), Naïve Bayes (NB), and Feedforward Neural Network (FFNN), complemented by an ensemble model via a voting mechanism. Five-fold cross-validation facilitated the differentiation between normal controls (NC) and IBD, as well as between CD and UC.

RESULTS: K-mer-based methods leveraging metagenomic sequencing data demonstrated robust diagnostic performance, yielding ROC AUCs of 0.966 for IBD vs. NC and 0.955 for CD vs. UC. Similarly, models based on amplicon sequencing achieved ROC AUCs of 0.831 for IBD vs. NC and 0.903 for CD vs. UC. In comparison, k-mer-based approaches outperformed traditional microbiota-based models, which produced lower ROC AUCs of 0.868 for IBD vs. NC and 0.810 for CD vs. UC. Across all machine learning frameworks, the FFNN consistently attained the highest ROC AUC, underscoring its superior diagnostic performance.

CONCLUSION: The integration of k-mer-based feature extraction with machine learning offers a non-invasive, highly accurate approach for IBD diagnosis, surpassing traditional microbiota-based models. This method holds considerable potential for clinical use, offering an effective alternative to invasive diagnostics and enhancing patient comfort.},
}

@article {pmid40636496,
year = {2025},
author = {Ding, Z and Xu, Y and Wang, Y and Liu, M and Zhu, P and Cui, K and Yang, C and Xu, C and Feng, T and Liu, Q},
title = {Host-driven remodeling of rumen microbiota supports lactation metabolism in buffalo.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1617388},
pmid = {40636496},
issn = {1664-302X},
abstract = {INTRODUCTION: Rumen microbiota and host metabolites play a key role in regulating ruminant production performance and physiological adaptation. However, the interplay between host physiological status and rumen microbial-metabolite dynamics across lactation stages in buffaloes remains unclear.

METHODS: This study employed a multi-omics approach, integrating metagenomic and serum metabolomic analyses, to investigate microbial remodeling and metabolic adaptations in buffaloes during lactation and dry periods.

RESULTS: Metagenomic analysis revealed increased abundances of Anaerovibrio, Succiniclasticum, and Methanobrevibacter_A during lactation, associated with lipid hydrolysis, propionate production, and methanogenesis, respectively. Glycoside hydrolase families GH2, GH3, GH5, and GH13 were enriched, indicating elevated carbohydrate degradation potential. In contrast, Butyrivibrio, Fibrobacter, and Eubacterium_Q were predominant during the dry period, contributing to fiber degradation and butyrate synthesis. Functional pathways related to niacin metabolism, bicarbonate reabsorption, and neuroactive ligand-receptor interaction were significantly upregulated during lactation. Metabolomic profiling identified lactation-enriched metabolites such as indole-3-methylacetate, D-maltose, and gluconic acid, correlating with immune and metabolic indicators (e.g., IgA, glucose, LDL). Conversely, dry period metabolites such as 1-methylhistidine and 5-hydroxyindoleacetic acid indicated physiological shifts toward tissue repair and stress mitigation.

DISCUSSION: The integrative analysis revealed that host physiological demands during lactation coordinate rumen microbial restructuring to enhance triglyceride degradation, fatty acid biosynthesis, and energy mobilization, thereby supporting milk production. These findings provide novel insights into the host-driven microbiome-metabolite axis underlying lactation in buffaloes.},
}

@article {pmid40636495,
year = {2025},
author = {Chen, F and Cheng, M and Rong, D and Wang, Y and Liang, R and Irfan, M and Kang, Y and Cao, Y},
title = {Metagenomic insights into the microbial communities and functional traits of hot springs in Guizhou Province, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615879},
pmid = {40636495},
issn = {1664-302X},
abstract = {INTRODUCTION: Hot springs were previously believed to be uninhabitable due to their hostile nature. However, recent studies have determined that hot springs not only have a rich microbiota but are also involved in various biogeochemical processes and possess unique characteristics that can be utilized for several biotechnological applications. This study aimed to determine the bacterial taxonomic diversity and functional profiles of 11 hot springs in the Guizhou Province, China.

METHODS: Illumina high-throughput sequencing was used to sequence the V3-V4 region of the 16S rRNA gene from microorganisms in samples collected from these hot springs. Software such as Mothur, the SILVA ribosomal RNA database, and Quantitative Insights into Microbial Ecology (QIIME) were utilized for taxonomic and operational taxonomic unit (OTU) analysis, while PICRUST2 was employed for functional predictions.

RESULTS: Guizhou Baili Rhododendron Hot Spring No.1 (BLDJA) had the highest diversity in terms of species richness, while Jianhe Hot Spring (YAS) had the lowest diversity. At the phylum level, the highest reported phyla included Pseudomonadota, Bacillota, Nitrospirota, Bacteroidota, and Actinomycetota, where Pseudomonadota had the highest abundance (92.094%) in Jianhe Hot Spring (YAS) and the lowest (41.238%) in Guizhou Baili Rhododendron Hot Spring No. 2 (BLDJB). Bacillota has the highest abundance (39.178%) in Guizhou Baili Rhododendron Hot Spring No. 2 (BLDJB) and the lowest (0.547%) in Jiutian Hot Spring (SNJT). The highest predicted functions were observed for amino acid metabolism, followed by carbohydrates. Predicted pathways for secondary metabolite and vitamin synthesis, along with stress-adaptation genes, underscore the biotechnological value of these habitats.

DISCUSSION: This study presents a preliminary survey of 11 hot springs in Guizhou Province, providing important insights into the origin and evolution of microorganisms. Furthermore, studying these microorganisms is crucial for understanding the adaptive mechanisms of life under extreme conditions, such as high temperatures, and for exploring the potential biotechnological applications of these microbes. An in-depth approach combining functional metagenomics and next-generation culturomics is required to fully understand the microbial flora and its potential biotechnological applications.},
}

@article {pmid40636492,
year = {2025},
author = {van Essen, RRT and Kaur, J and Li, T and Mann, RC and Sawbridge, TI},
title = {The diversity, dynamics, and culturability of bacterial and fungal communities present in warm-season pasture grass seeds.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1621463},
pmid = {40636492},
issn = {1664-302X},
abstract = {A rapidly changing climate has resulted in increasing challenges for farmers. This has led to an increase in demand for beneficial microbes to help fight these challenges faced by farmers, improving crop production under harsh conditions. Increasing temperatures caused by the changing climate will also affect the dairy industry in temperate climates around the world. This has resulted in an increasing importance of warm-season pasture grasses to fill the feed gaps left by the affected temperate grasses. In this study, we assessed the microbial communities present in commercially available warm-season pasture grass seeds. We utilised amplicon metagenomics to profile and compare the bacterial and fungal communities of seeds from three different genera of warm-season pasture grasses. Microbial isolations have also been performed to assess the culturability of the seed microbiome. Significant differences in drivers of bacterial and fungal communities within warm-season pasture grass seeds were observed. In addition, most of the bacteria present in high abundance were found to be culturable, while a relatively lower percentage of abundant fungi were culturable. Analysis of the bacterial communities showed considerable variation between different distributors, possibly driven by differing seed processing methods. This variation indicates that the bacterial communities could be manipulated by providing different bacteria to the seed to promote plant growth under different conditions. In contrast, the fungal communities were more strongly driven by the genetics of the respective host genera. This suggests that differences in fungal strain levels could be exploited for modification of fungal microbiome effects.},
}

@article {pmid40636491,
year = {2025},
author = {Hu, R and Liu, Y and Wen, M and Zhou, N and Wang, J},
title = {Crop rotation complexity affects soil properties shaping antibiotic resistance gene types and resistance mechanisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1603518},
pmid = {40636491},
issn = {1664-302X},
abstract = {Crop rotation enhances agricultural productivity and soil fertility but may also contribute to the accumulation of antibiotic resistance genes (ARGs). However, the changes in soil ARGs and their associated resistance mechanisms under different crop rotation regimes are not well understood. In this study, we employed metagenomics to comprehensively investigate soil ARGs under different crop rotation regimes and complexity. Our findings revealed that soil properties varied significantly with crop rotation regime and complexity. Specifically, soil pH and the total carbon/nitrogen ratio (C/N) were the highest in bare land (BL) and gradually decreased in the order non-rotation, simple rotation, and complex rotation systems. The composition of soil ARGs exhibited significant differentiation by crop rotation complexity. Furthermore, differential gene analysis identified four specific types of ARGs-glycopeptide, multidrug, fluoroquinolone, and macrolide-lincosamide-streptogramin B (MLSB)-and two resistance mechanisms-cellular protection and efflux pump. Notably, soil microbial biomass carbon, soil microbial biomass nitrogen, and soil organic carbon are significantly correlated with ARGs in complex crop rotation systems, whereas soil pH and C/N ratio show significant associations in BL. The C/N ratio was identified as the most relevant determinant for glycopeptide, multidrug, fluoroquinolone, and MLSB resistance genes. Overall, these findings elucidate key factors associated with ARGs under long-term crop rotation, thereby providing valuable insights into the influence of crop rotation regimes on soil ARGs and enhancing soil fertility by improving soil properties.},
}

@article {pmid40636480,
year = {2025},
author = {Yu, J and Chen, J and Huang, T and Gu, X},
title = {Infection Leading to Breast Abscess Formation in Pregnancy: A Case Report.},
journal = {International medical case reports journal},
volume = {18},
number = {},
pages = {791-809},
pmid = {40636480},
issn = {1179-142X},
abstract = {INTRODUCTION: Breast abscess, the most severe complication of mastitis, occurs when an infection spreads through the nipple into the breast tissue, contaminating the milk ducts and forming a purulent cavity. Nonetheless, this condition is less common in pregnant women. Staphylococcus aureus is the predominant causative agent in lactating women; however, Prevotella bivia-associated breast abscesses during pregnancy remain clinically rare, with limited documented cases.

CASE PRESENTATION: A 26-year-old Chinese woman with G1P0 singleton at 33 weeks of pregnancy presented with right breast pain and lumps without obvious triggers, accompanied by enlarged right axillary lymph nodes and a large amount of pus with a peculiar odor in the right breast. After breast ultrasonography, cytological puncture smear, pus culture, and metagenomic next-generation sequencing, the patient was confirmed to have gestational mastitis with P. bivia infection. Given that the patient had a high-risk pregnancy, the use of antibiotics sensitive to Prevotella, such as metronidazole, might affect the intrauterine fetus, and infection with this bacterium could increase the risk of placental abruption and intrauterine fetal distress. Based on the obstetrician's and pediatrician's recommendations, the patient opted for a cesarean section at 37 weeks to facilitate the delivery of a healthy neonate weighing 3110 g (Apgar scores of 10 at 1 min and 5 min) in the left anterior sacral position and was advised to opt for lactation-suppressing medication and postpartum antibiotics.

CONCLUSION: This case highlights the importance of close monitoring of pus characteristics (eg, color, odor, and volume) in pregnancy-associated breast abscesses to expedite the diagnosis of infectious mastitis and pathogen identification. Treatment with small incision drainage and targeted antibiotics during pregnancy significantly improved the outcomes. Postpartum breast milk return and combined antibiotic therapy further contributed to the resolution of inflammation.},
}

@article {pmid40636004,
year = {2025},
author = {Xiao, J and Gao, P and Lai, K and Binbin, Y and Wang, S and Zhao, Y and Wan, X and Lyu, C and Kang, C and Guo, L and Zhang, Y},
title = {Mechanistic insights from metagenomics into the early-stage quality improvement of licorice under partial replacement of chemical by organic fertilizers.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1613771},
pmid = {40636004},
issn = {1664-462X},
abstract = {Substituting chemical fertilizers with organic alternatives has gained increasing attention for its potential to enhance crop yield, quality, and soil health. In the early stages of licorice cultivation, the short-term effects of organic fertilization on microbial community dynamics, soil properties, and bioactive compound accumulation remain insufficiently understood. A metagenomic approach was applied to analyze microbial compositions in both bulk and rhizosphere soils under different fertilization treatments. Results showed that organic fertilization significantly increased licorice yield and the accumulation of bioactive compounds compared to chemical fertilization. Full organic substitution improved soil nutrient content, organic matter, and carbon levels while reducing enzyme activities such as urease and protease. Additionally, organic fertilization promoted bacterial diversity, with notable increases in Actinobacteria and fungal taxa such as Ascomycota and Basidiomycota. Correlations between soil microbial communities, enzyme activity, and secondary metabolite synthesis-particularly glycyrrhizic acid-were observed. These findings suggest that organic fertilization fosters microbial diversity and soil health, ultimately benefiting licorice production and quality in the early stages of cultivation while contributing to sustainable agricultural practices.},
}

@article {pmid40635073,
year = {2025},
author = {Zhao, GH and Zhou, BB and Cao, ZH and Xiao, T and Li, YN and Zhu, WJ and Sun, H and Xie, HH and Xie, XM and Zhang, JM and Wang, Q and Zhang, X and Xie, JJ and Dong, HJ and Xu, C and Yin, K},
title = {The development and excretion of Toxoplasma gondii oocyst manipulate the gut microbiota in its definitive host.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {273},
pmid = {40635073},
issn = {1756-3305},
support = {202401050157//The Health Science and Technology Development Program of Shandong Province/ ; 202401050156//The Health Science and Technology Development Program of Shandong Province/ ; 202201050466//The Health Science and Technology Development Program of Shandong Province/ ; ZR2023QH253//The Natural Science Foundation of Shandong Province/ ; ZR2022MH197//The Natural Science Foundation of Shandong Province/ ; tsqn202103186//The Taishan Scholars Project of Shandong Province/ ; 202407//Joint Innovation Team for Clinical & Basic Research/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Toxoplasma/growth & development/physiology ; Cats ; *Oocysts/growth & development/physiology ; *Toxoplasmosis, Animal/parasitology/microbiology ; Bacteria/genetics/classification ; Metagenomics ; Feces/parasitology ; Host-Parasite Interactions ; },
abstract = {BACKGROUND: Oocysts serve as the primary source of Toxoplasma infection. Therefore, understanding oocyst development and exploring effective strategies to prevent oocyst excretion are crucial for controlling toxoplasmosis.

METHODS: In this study, shotgun metagenomics was employed to characterize the functional and compositional changes in the gut microbiota of cats during oocyst development. The Spearman correlation test was utilized to analyze the correlation between differential Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and carbohydrate-active enzymes (CAZymes) in key bacteria regulating oocyst excretion.

RESULTS: The results revealed that group A (sexual initiation stage) displayed a lower number of functional genes, which were restored to normal levels in group B (oocyst excretion stage), compared with group C (Toxoplasma-uninfected samples). The abundance of 39 KEGG pathways, 106 CAZymes, and 98 virulence factors (VFs) varied significantly among the three groups. The atrazine degradation pathway, associated with sexual development, was upregulated in group B. CAZymes involved in restoring the intestinal mucosal barrier and VFs related to iron metabolism, antibiotic resistance, and suppression of host immunity were enriched in group B. Sexual initiation and oocyst excretion resulted in reduced gut bacterial diversity and microbiota dysbiosis. Probiotics and bacteria related to linoleic acid (LA) uptake were dominant in both group A and group B. Bacteroides stercoris was the most significantly upregulated bacterium and could influence the expression of carbohydrate-binding modules (CBMs) and glycoside hydrolases (GHs) in group B.

CONCLUSIONS: During the oocyst development/excretion stage, the function and composition of the cat gut microbiota changed significantly. In addition, Bacteroides stercoris may play a crucial role in oocyst excretion by regulating key candidates of CBMs and GHs. Our findings lay the foundation for investigating the regulatory mechanisms of oocyst excretion.},
}

*Gastrointestinal Microbiome
Animals
*Toxoplasma/growth & development/physiology
Cats
*Oocysts/growth & development/physiology
*Toxoplasmosis, Animal/parasitology/microbiology
Bacteria/genetics/classification
Metagenomics
Feces/parasitology
Host-Parasite Interactions

@article {pmid40635072,
year = {2025},
author = {Sheybani, F and Haddad, M},
title = {Diagnostic criteria for Epstein-barr virus-associated encephalitis: a comment on Liu et al.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {232},
pmid = {40635072},
issn = {1743-422X},
mesh = {Humans ; *Epstein-Barr Virus Infections/diagnosis/virology ; *Herpesvirus 4, Human/isolation & purification/genetics ; *Encephalitis, Viral/diagnosis/virology ; DNA, Viral/cerebrospinal fluid ; Retrospective Studies ; Viral Load ; },
abstract = {BACKGROUND: We read with great interest the article by Liu et al., titled "Clinical features and risk factors for Epstein-Barr virus-associated encephalitis: a retrospective cohort study." The study provides valuable insights into the clinical spectrum and risk factors associated with EBV-related encephalitis.

MAIN BODY: While Epstein-Barr virus (EBV) is frequently detected in cerebrospinal fluid (CSF) during CNS infections, its role as a primary pathogen remains uncertain, especially in immunocompromised patients. We commend the authors for their efforts but seek clarification on the diagnostic criteria used to attribute causality to EBV. Specifically, we question whether the diagnosis relied solely on the detection of EBV DNA in the CSF or whether supporting parameters, such as viral load, CSF/serum ratios, or intrathecal antibody synthesis, were considered. The distinction between causative and incidental EBV detection is clinically significant and remains a challenge in neuroinfectious disease practice.

CONCLUSION: Further elaboration on how EBV-associated encephalitis was defined in the study would enhance its clinical relevance and aid practitioners encountering similar diagnostic complexities.},
}

Humans
*Epstein-Barr Virus Infections/diagnosis/virology
*Herpesvirus 4, Human/isolation & purification/genetics
*Encephalitis, Viral/diagnosis/virology
DNA, Viral/cerebrospinal fluid
Retrospective Studies
Viral Load

@article {pmid40634364,
year = {2025},
author = {Ben, H and Wang, X and Yang, P and Li, L and Liu, P and Gao, Y and Wang, Y and Liu, Y and Huang, C and Chen, D},
title = {Metagenomic analysis uncovers novel hepadnaviruses and nackednaviruses.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24699},
pmid = {40634364},
issn = {2045-2322},
support = {YNKTQN2021020//Beijing YouAn Hospital Youth Innovation Foundation/ ; 2022-ZZ-039//Beijing Postdoctoral Research Foundation/ ; Z171100001117119//Beijing Nova Program/ ; 82073676//National Natural Science Foundation of China/ ; 82073676//National Natural Science Foundation of China/ ; 82073676//National Natural Science Foundation of China/ ; 82073676//National Natural Science Foundation of China/ ; 82073676//National Natural Science Foundation of China/ ; 82073676//National Natural Science Foundation of China/ ; 82073676//National Natural Science Foundation of China/ ; KZ202010025037//Key Programs of Beijing Municipal Education Commission of China/ ; KZ202010025037//Key Programs of Beijing Municipal Education Commission of China/ ; KZ202010025037//Key Programs of Beijing Municipal Education Commission of China/ ; KZ202010025037//Key Programs of Beijing Municipal Education Commission of China/ ; KZ202010025037//Key Programs of Beijing Municipal Education Commission of China/ ; KZ202010025037//Key Programs of Beijing Municipal Education Commission of China/ ; KZ202010025037//Key Programs of Beijing Municipal Education Commission of China/ ; BJYAYY-YN2022-19//Scientific Research Project of Beijing YouAn Hospital/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Hepadnaviridae/genetics/classification/isolation & purification ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Virus Replication ; },
abstract = {The rapid expansion of next-generation sequencing (NGS) databases over the past decade has significantly advanced the identification of novel viruses across a wide range of host species. The Serratus platform and the NCBI Sequence Read Archive (SRA) database were utilized to reassess and analyze publicly available NGS datasets, aiming to identify novel hepadnaviruses and nackednaviruses. Our analysis uncovered multiple complete genomes of previously unrecognized hepadnaviruses and nackednaviruses, including those putatively infecting animals such as hamsters and buffaloes. Additionally, we identified the presence and distribution of various hepadnaviruses and nackednaviruses in African cichlid fishes. In vitro assays employing replication-competent plasmids derived from the identified rice rat and frog hepadnaviruses demonstrated their capacity to support viral replication. The identification of these novel hepadnavirus and nackednavirus species provides valuable insights into the origin and evolutionary history of hepadnaviruses. Moreover, these findings open new avenues for investigating potential animal models to study hepadnavirus replication and infection.},
}

Animals
*Metagenomics/methods
*Hepadnaviridae/genetics/classification/isolation & purification
Genome, Viral
Phylogeny
High-Throughput Nucleotide Sequencing
Virus Replication

@article {pmid40634275,
year = {2025},
author = {Özçam, M and Lin, DL and Gupta, CL and Li, A and Gomez, JC and Wheatley, LM and Baloh, CH and Sanda, S and Jones, SM and Lynch, SV},
title = {Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6330},
pmid = {40634275},
issn = {2041-1723},
support = {AI128482//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI148104//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UM1AI160040//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI089473//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/immunology/physiology ; *Bile Acids and Salts/metabolism ; *Peanut Hypersensitivity/therapy/immunology/microbiology ; Feces/microbiology/chemistry ; *Arachis/immunology ; *Amino Acids/metabolism ; Male ; Administration, Oral ; Female ; Child ; *Desensitization, Immunologic/methods ; Double-Blind Method ; Child, Preschool ; Treatment Failure ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Antigens, Plant/immunology ; },
abstract = {Peanut Oral Immunotherapy (POIT) holds promise for remission of peanut allergy, though treatment is protracted and successful in only a subset of patients. Because the gut microbiome has been linked to food allergy, we sought to identify fecal predictors of POIT efficacy and mechanistic insights into treatment response. Here, we conducted a secondary analysis of the IMPACT randomized, double-blind, placebo-controlled POIT trial (NCT01867671), using longitudinal fecal samples from 90 children, and performed 16S rRNA sequencing, shotgun metagenomics, and untargeted metabolomics. Integrated multi-omics analyses revealed a relationship between gut microbiome metabolic capacity and treatment outcomes. Five fecal bile acids present prior to treatment initiation predicted POIT efficacy (AUC 0.71). Treatment failure was associated with a specific bile acid profile, enhanced amino acid utilization, and higher copy number of the ptpA gene encoding a bacterial hydrolase that cleaves tripeptides containing proline residues - a feature of immunogenic peanut Ara h 2 proteins. In vitro, peanut-supplemented fecal cultures of children for whom POIT failed to induce remission evidenced reduced Ara h 2 concentrations. Thus, distal gut microbiome metabolism appears to contribute to POIT failure.},
}

Humans
*Gastrointestinal Microbiome/genetics/immunology/physiology
*Bile Acids and Salts/metabolism
*Peanut Hypersensitivity/therapy/immunology/microbiology
Feces/microbiology/chemistry
*Arachis/immunology
*Amino Acids/metabolism
Male
Administration, Oral
Female
Child
*Desensitization, Immunologic/methods
Double-Blind Method
Child, Preschool
Treatment Failure
RNA, Ribosomal, 16S/genetics
Metagenomics
Antigens, Plant/immunology

@article {pmid40634121,
year = {2025},
author = {Oates, A and Brown, ST and Everett, CC and Game, F and Nixon, JE and Sloan, T and Lister, MM and Backhouse, M and Lipsky, BA and Russell, D and Collier, H and Dennett, J and Gilberts, R and Nelson, EA},
title = {Concordance of molecular microbiology and conventional culture techniques for infected diabetic foot ulcer management.},
journal = {Diabetic medicine : a journal of the British Diabetic Association},
volume = {},
number = {},
pages = {e70089},
doi = {10.1111/dme.70089},
pmid = {40634121},
issn = {1464-5491},
support = {//Health Technology Assessment Programme/ ; },
abstract = {AIM: The management of infected diabetic foot ulcers (DFUs) requires balancing the need for timely interventions against the desire for targeted antibiotic therapy, which relies on laboratory results. This study aimed to evaluate concordance between molecular and conventional culture and sensitivity (C&S) methods in identifying bacteria from infected DFUs.

METHODS: This study was conducted alongside CODIFI2, a Phase III randomised controlled trial comparing tissue sampling with wound swabbing. It assessed C&S and metagenomic 16S rRNA gene sequencing (M16S) in DFUs with suspected mild or moderate infections using both tissue and swab samples.

RESULTS: In 145 participants, C&S identified 248 microorganisms across 25 genera including eight anaerobic genera. M16S identified a greater number and diversity of microorganisms, detecting 455 across 40 genera, including 173 anaerobes from 15 distinct genera. No bacterial growth was reported in 25.5% (95% CI: 18.0%-32.3%) of C&S samples, whereas M16S identified at least one organism in all samples. While the observed agreement between methods was high (75%), Cohen's Kappa revealed low concordance overall, except for Pseudomonas spp. and Streptococcus spp. (Kappa ≥ 0.5).

CONCLUSIONS: M16S detected a broader microbial spectrum, including fastidious anaerobes, but its low concordance with C&S and lack of antibiotic sensitivity data, challenge its suitability as a replacement for C&S in mild or moderate DFU infections. It may offer advantages in infections where increased sensitivity is beneficial, particularly where extended culture approaches are recommended to detect fastidious or low-abundance organisms. For mild to moderate DFU infections, our findings support continued reliance on conventional C&S testing.},
}

@article {pmid40633697,
year = {2025},
author = {Tan, J and Wang, Z and Luo, M and Fang, L and Hou, J and Song, S and García Meza, JV and Xia, L},
title = {Microbial-mediated carbon acquisition drives phosphorus turnover within soil initial development in oligotrophic tailing sites.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132946},
doi = {10.1016/j.biortech.2025.132946},
pmid = {40633697},
issn = {1873-2976},
abstract = {Metabolic strategies of indigenous functional microorganisms drive initial nutrient accumulation in oligotrophic environment. However, their specific roles in carbon-phosphorus interactions remain poorly understood. Here, phosphate tailings were investigated across different aging stages through controlled inoculation experiments with native phosphate-solubilizing bacteria (PSB) and microalgae. Results revealed that initial soil development was constrained by severe stoichiometric imbalance between microbial phosphorus demand and resource supply. Co-inoculation reduced insoluble inorganic phosphorus by 10.0 %-17.5 % while increasing organic carbon accumulation by 87.7 %-212.9 %. Metagenomic revealed this was primarily attributed to the carbon-fixing and organic phosphorus mineralization pathways. Enzymatic stoichiometry showed that microbial carbon acquisition (through both carbon fixation and fresh organic matter input) alleviated phosphorus limitation (R[2] = 0.54, p < 0.01), reducing carbon:phosphorus imbalance by 51.8 %-98.6 %. Structural equation modeling (SEM) confirmed carbon acquisition precedes phosphorus turnover. This study demonstrate that targeted regulation of carbon availability overcomes nutrient constraints in oligotrophic tailings, enabling sustainable soil development from tailings.},
}

@article {pmid40633655,
year = {2025},
author = {Parab, AS and Ghose, M and Manohar, CS},
title = {Antibiotic-resistant bacteria in marine productive zones of the eastern Arabian Sea: Implications for human and environmental health.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {383},
number = {},
pages = {126793},
doi = {10.1016/j.envpol.2025.126793},
pmid = {40633655},
issn = {1873-6424},
abstract = {The increasing threat of antibiotic resistance is a major global concern affecting human and environmental health. Marine environments, though underexplored, are emerging as significant reservoirs for antibiotic resistance genes (ARGs). This study provides genome-resolved shotgun metagenomic insights into the seasonal and spatial dynamics of ARGs in the chlorophyll maximum zones of the eastern Arabian Sea, focusing on bacterial communities from coastal (30 m) and offshore (600 m) depths. Using a shotgun metagenomic approach, 31 potential ARGs were identified across both non-monsoon and monsoon seasons, with higher abundance observed in offshore stations during the non-monsoon season. Multidrug resistance genes such as blaEFM-1, catB2 and mexK, conferring resistance to carbapenems, chloramphenicol and multiple antibiotics, were prevalent in taxa like Staphylococcus sp., Qipengyuania sp. and Alcanivorax sp. Clinically relevant taxa, including Pseudomonas sp. and Staphylococcus sp., harbored ARGs, which may raise concerns regarding potential seafood-mediated ARG transmission. The significant enrichment and co-localization of mobile genetic elements (MGEs) with ARGs suggest enhanced horizontal gene transfer among native marine bacteria in the offshore environments. However, the limited distribution of ARGs and the absence of associated MGEs during the monsoon season may result from dilution caused by freshwater influx. Comparative functional analysis revealed stress-related functional enrichment in ARG-carrying metagenomic assembled genomes, suggesting environmental stress may enhance the spread of ARGs within offshore microbial communities. These findings challenge the coastal-centric view of marine antibiotic resistance by identifying offshore waters as underrecognized ARG reservoirs. Establishing a genomic baseline for One Health ARG surveillance, this study underscores the urgent need to integrate offshore regions into global monitoring frameworks to protect marine ecosystems and safeguard public health.},
}

@article {pmid40633493,
year = {2025},
author = {Sibinga, NA and Werner, E and Tegtmeier, D and De Smet, J},
title = {Animal board invited review: The need for, and the path towards, a functional understanding of the farmed insect microbiome.},
journal = {Animal : an international journal of animal bioscience},
volume = {19},
number = {8},
pages = {101575},
doi = {10.1016/j.animal.2025.101575},
pmid = {40633493},
issn = {1751-732X},
abstract = {The rapid growth of research on industrially produced insect species over the past two decades has coincided with breakthroughs in the speed and affordability of DNA sequencing. This has allowed researchers to rapidly generate data on the microbial communities associated with farmed insects, especially the gut-residing bacteria of the two cornerstone production species: black soldier fly (BSF, Hermetia illucens) and yellow mealworm (Tenebrio molitor). A picture of the most prevalent and abundant microbes associated with these species has rapidly come into focus. Specific microbial functions have been suggested under extreme or challenging rearing settings, but less is known about the contributions of the microbiome to insect rearing under realistic production conditions. There is limited understanding of how microbial communities of farmed insects arise, are maintained, and change in response to stimuli. Likewise for seemingly basic questions: what functions do insect-associated microbes perform for the host? Which (if any) taxa are essential for healthy insects? This is not intended as a criticism of existing research; indeed, these questions turn out not to be simple. Answering them requires targeted research approaches testing specific hypotheses about farmed insect microbiome function. This review aims to recalibrate the state of knowledge by critically assessing common and emerging strategies to study these microbiomes and existing knowledge gaps about the functional role of the microbiome for BSF and mealworm. Overall, it is clear that microbes are an intrinsic part of the ecology of these two farmed insects. Reciprocal interactions between microbes and insects are extensive, though microbiome community composition depends to a large extent on environmental conditions. To date, it remains unclear how taxonomical shifts correspond to functional shifts and to what extent such changes impact insect physiology. For example, when mealworms are fed plastics, their microbiomes undergo significant changes in microbial composition. These changes are presumed to increase the ability of mealworms and their microbiota to degrade plastic, but this change in function is hard to conclusively demonstrate with current tools. Furthermore, analysis of the literature shows that taxonomically disparate microbial communities may provide similar functional benefits, e.g. lignocellulose breakdown in BSF larvae. This review therefore aims to critically assess the state of the art with regard to functional analysis of the farmed insect microbiome and how available experimental methods can be best applied to identify links between microbial functions and insect physiology and improve the efficiency and sustainability of the farmed insect industry.},
}

@article {pmid40633350,
year = {2025},
author = {Huang, C and Wang, T and Chen, W and Wang, J and Cui, M and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Xu, L and Fang, H},
title = {Sheep and rapeseed cake manure promote antibiotic resistome in agricultural soil.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139157},
doi = {10.1016/j.jhazmat.2025.139157},
pmid = {40633350},
issn = {1873-3336},
abstract = {The application of manure in agriculture caused the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil environments. However, the co-occurrence pattern and host diversity of ARGs and MGEs in soils amended with animal and green manures remains unclear. In this study, metagenomic assembly and binning techniques were employed to comprehensively explore the effects of sheep manure and green manure on soil microbiome, antibiotic resistomes, and ARG hosts. Both rapeseed cake manure and sheep manure increased the abundance and diversity of ARGs, with sheep manure particularly enhancing the abundance of ARGs conferring resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB). Mobile genetic elements (MGEs), such as plasmids, transposases, and integrases, preferentially enhanced the potential mobility of some ARGs subtypes (i.e. sul2, aadA, qacH, and folp), facilitating the spread of ARGs. Additionally, sheep manure reshaped the bacterial community structure and composition as well as ARG hosts, some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant. It is concluded that rapeseed cake manure and sheep manure increased the co-occurrence of ARGs and MGEs, enriched the potential ARG hosts, and promoted the dissemination of ARGs in agricultural soils.},
}

@article {pmid40633189,
year = {2025},
author = {Wu, Y and Fan, Y and Tao, Y and Guo, Q and Pang, S and Yang, W and Zhang, X},
title = {Seasonal dynamics and risk assessment of antibiotic resistome in straw-retained agroecosystems.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118630},
doi = {10.1016/j.ecoenv.2025.118630},
pmid = {40633189},
issn = {1090-2414},
abstract = {Straw retention (SR) is an essential management practice of sustainable agriculture. However, the seasonal dynamics on the antibiotic resistome and associated ecological risks in seasonally frozen agroecosystems remain unclear. Here, we conducted a multi-site field study in the Sanjiang Plain, a seasonally frozen agricultural region of Northeast China, combining time-series soil sampling with metagenomic sequencing to reveal antibiotic resistome dynamics. SR elevated relative abundance of antibiotic resistance genes (ARGs) across all seasons and induced significant seasonal variations in richness. ARG richness peaked during freezing season favoring the dominance of low-risk ARGs. The soil C/N ratio emerged as the primary driver shaping the relative abundance and diversity of antibiotic resistome, with 23 core low-risk ARGs accounting for 73 % of the observed abundance increase, whereas high-risk ARGs constituted merely 0.44 % of the total resistome abundance. Straw retention also reduced interactions among high-risk ARGs with ecological risk remaining stable, demonstrating decoupling between resistome abundance and environmental risk. Structural equation modeling revealed straw retention exerting both direct effects (0.45) and indirect regulation (-0.16) via modulating nutrient content. Our findings evaluated the antibiotic resistance risks of straw retention with the enrichment of low-risk ARGs and suppression of interactions among high-risk ARGs, promoting its safe adoption in agroecosystems. Overall, this study provides a comprehensive antibiotic risk assessment framework, demonstrating straw retention as a beneficial strategy that enhances soil fertility with practically manageable resistance risks in agroecosystems.},
}

@article {pmid40631858,
year = {2025},
author = {Qu, S and Gu, Y and Hou, X and Wei, M and Wang, M and Su, Y and Miao, Y and Yang, J and Sun, Y and Zeng, Z},
title = {Dual associations of gut and oral microbial networks with kidney transplantation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0025225},
doi = {10.1128/msystems.00252-25},
pmid = {40631858},
issn = {2379-5077},
abstract = {UNLABELLED: Gut and oral microbiomes play an essential role in the occurrence and development of kidney disease, but their changes after kidney transplantation in patients with end-stage renal disease and their relationships with host health remain unclear. Through shotgun metagenomic sequencing of fecal and saliva samples, we found that for both gut and oral microbiome, the initial loss of species diversity after kidney transplantation led to a reduction in network nodes and interactions, but strengthened the connections among the remaining species, which started to get a recovery approximately 7-14 days later. Different network modules tended to exhibit unique functions and showed different responses to transplantation. These network changes were significantly correlated with clinical indicators, especially with estimated glomerular filtration rate, suggesting that microbial networks contributed to regulating kidney function and host health from dual dimensions. Our study provides novel insights into associating microbiomes with patient recovery after kidney transplantation and offers new diagnostic strategies.

IMPORTANCE: Understanding the dynamics of gut and oral microbiomes after kidney transplantation is crucial for improving post-transplant outcomes and managing potential complications. Through shotgun metagenomic sequencing of fecal and saliva samples from patients following kidney transplantation, our study emphasizes that, in addition to focusing on the various microbial species themselves, the topological properties of gut and oral microbial networks are also critically important for kidney function. We aim to explore the relationship between host health and the oral and gut microbiomes following kidney transplantation from an ecological perspective and extend to other diseases to advance the study of the microbiome and its clinical impact.},
}

@article {pmid40631381,
year = {2025},
author = {Huang, X and Gao, X and Fan, Y and Wang, D and Chen, X and Qi, X and Yang, Z and Wang, YE and Meng, J and Zou, G and Liu, Z and Li, X},
title = {Moderate altitude exposure impacts extensive host-microbiota multi-kingdom connectivity with serum metabolome and fasting blood glucose.},
journal = {Virulence},
volume = {},
number = {},
pages = {2530660},
doi = {10.1080/21505594.2025.2530660},
pmid = {40631381},
issn = {2150-5608},
abstract = {The contributions and interactions of multi-kingdom microbiota (i.e. bacteriome, mycobiome, archaeaome, and phageome) with serum metabolome and host phenome in healthy individuals under moderate altitude exposure remain unclear. We applied shotgun metagenomic sequencing in faeces and targeted metabolomics technology in serum to explore how the human gut multi-kingdom microorganisms influence the serum metabolome and phenome in healthy Chinese individuals following moderate altitude exposure. The results indicated that individuals with moderate altitude exposure exhibited more substantial alterations in gut bacteriome and phageome compared to those in mycobiome and archaeaome. Both intra-kingdom and inter-kingdom correlations at baseline were denser than those following moderate altitude exposure. Bacteriophages-host interactions analysis revealed symbiosis between bacteriophages and Bacteroidetes, Proteobacteria, and short-chain fatty acids (SCFAs) producers. Furthermore, bacteriophage Shirahamavirus PTm1 (odds ratio (OR) = 3.82; 95% confidence interval (CI): 1.20-12.16), archaeon Crenarchaeota (OR = 3.70; 95% CI: 1.35-10.14) and bacterium Bacteroidetes (OR = 3.69; 95% CI: 1.34-10.15) showed a positive association with lowered fasting blood glucose (FBG) benefits, while bacteriophage Candidatus Nitrosopelagicus brevis (OR = 0.30; 95% CI: 0.10-0.89) and butyric acid (OR = 0.07; 95% CI: 0.01-0.37) exhibited a negative association with lowered FBG benefits. These findings suggest that targeting gut multi-kingdom microorganisms could serve as an alternative therapeutic approach to mitigate dysglycemia and its associated metabolic disorders.},
}

@article {pmid40631226,
year = {2025},
author = {Berk Şapcı, AO and Mirarab, S},
title = {A k -mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.20.633730},
pmid = {40631226},
issn = {2692-8205},
abstract = {Comparing each sequencing read in a sample to large databases of known genomes has become a fundamental tool with wide-ranging applications, including metagenomics. These comparisons can be based on read-to-genome alignment, which is relatively slow, especially if done with the high sensitivity needed to characterize queries without a close representation in the reference dataset. A more scalable alternative is assigning taxonomic labels to reads using signatures such as k-mer presence/absence. A third approach is placing reads on a reference phylogeny, which can provide a far more detailed view of the read than a single label. How-ever, phylogenetic placement is currently only possible at scale for marker genes, constituting a small fraction of the genome. No current method is able to place all reads originating from anywhere in the genome on an ultra-large reference phylogeny. In this paper, we introduce krepp, an alignment-free k-mer-based method that enables placing reads from anywhere on the genome on an ultra-large reference phylogeny by first computing a distance from each read to every reference genome. To compute these distances and placements, krepp uses a host of algorithmic techniques, including locality-sensitive hashing to allow inexact k-mer matches, k-mer coloring graphs to map k-mers to reference genomes, maximum likelihood distance estimation, and likelihood ratio test for placement. Our experiments show that krepp is extremely scalable, improving on alignment by up to roughly 10×, computes very accurate distances that approximate those using alignments, and produces highly accurate placements. When used in the metagenomics context, the precise phylogenetic identifications provided by krepp improve our ability to compare and differentiate samples from different environments.},
}

@article {pmid40631147,
year = {2025},
author = {Real, MVF and Vitousek, MN and Sheehan, MJ and Moeller, AH},
title = {The mouse gut microbiota responds to predator odor and predicts host behavior.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.01.662568},
pmid = {40631147},
issn = {2692-8205},
abstract = {In mammals, chronic stressors can alter gut microbial communities in ways that mediate host stress responses. However, the effects of acute stressors on the gut microbiota, and how these interact with host stress responses, are less well understood. Here, we show that acute exposure of wild-derived mice (Mus musculus domesticus) to predator odor altered the composition of the gut microbiota, which in turn predicted host behavior. We experimentally tested the individual and combined effects of brief (15-minute) exposure to synthetic fox fecal odor and prolonged (4-week) social isolation-a well-established chronic stress paradigm. Leveraging behavioral assays, transcriptomics of visceral adipose tissue, and analyses of 3,500 metagenome-assembled genomes (MAGs) generated from our data, we found significant effects of predator odor on host behavior, gene expression, and gut microbiota. Gut microbial communities and host gene expression profiles responded more strongly to brief predator-odor exposure than to prolonged social isolation. The relative abundances of predator odor-responsive bacterial species-including members of the Muribaculaceae and Lachnospiraceae-measured a week after a single predator-odor exposure were associated with host phenotypes assessed the following week, namely grooming and social behaviors and the expression of genes involved in anti-microbial defense, even after accounting for the effects of the stressors. Using random forest classifiers, we found that variation in gut-microbiota composition significantly predicted variation in behavior within treatment groups. These results indicate interactions between the gut microbiota and the responses of wild-derived mice to the threat of predation, and ecologically relevant acute stressor.},
}

@article {pmid40630933,
year = {2025},
author = {Takács, B and Jaksa, G and Qorri, E and Gyuris, Z and Pintér, L and Haracska, L},
title = {Advancing metagenomic classification with NABAS+: a novel alignment-based approach.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {3},
pages = {lqaf092},
pmid = {40630933},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; Algorithms ; *Software ; *Sequence Alignment/methods ; *Metagenome ; Microbiota/genetics ; },
abstract = {Microbiome research has expanded rapidly in the last decade due to advances in sequencing technology, resulting in larger and more complex data. This has also led to the development of a plethora of metagenomic classifiers applying different algorithmic principles to classify microorganisms. However, accurate metagenomic classification remains challenging due to false positives and the need for dataset-specific tuning, limiting the comparability of distinct studies and clinical use. In this study, we demonstrate the discrepancy between current, commonly used classifiers and propose a novel classifier, NABAS+ (Novel Alignment-based Biome Analyzing Software+). NABAS+ uses BWA (Burrows-Wheeler aligner) alignment with strict RefSeq curation to ensure one reliable genome per species and filters for genomes with only high-quality reads for precise species-level identification from Illumina shotgun data. The performance of our algorithm and three commonly used classifiers was evaluated on in silico datasets modelling human gastrooral communities, as well as on deeply sequenced microbial community standards. Additionally, we illustrated the usefulness of NABAS+ in detecting pathogens in real-world clinical data. Our results show that NABAS+, due to its extensive alignment process, is superior in accuracy and sensitivity compared to leading microbiome classifiers, particularly in reducing false positives in deep-sequenced microbial samples, making it suitable for clinical diagnosis.},
}

Humans
*Metagenomics/methods
Algorithms
*Software
*Sequence Alignment/methods
*Metagenome
Microbiota/genetics

@article {pmid40630755,
year = {2025},
author = {Bergauer, K and Suffridge, CP and Wittmers, F and Sudek, S and Giovannoni, SJ and Worden, AZ},
title = {Dark ocean archaeal and bacterial chemoautotrophs drive vitamin B1 production in oxygen minimum zones.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf077},
pmid = {40630755},
issn = {2730-6151},
abstract = {Vitamin B1 (thiamine) is essential for all cells, yet many marine microbes cannot synthesize B1 de novo. Dissolved thiamine and its related chemical congeners (TRCs) concentrations are not well characterized beyond the surface ocean, where they are typically low. Here, we observed unexpected enrichment of TRCs in regions of low dissolved oxygen levels (9.4 < O2 < 12.5 μmol kg[-1]) across vertical profiles in Monterey Bay and Pacific waters 145 km offshore (Station 67-70). TRC concentrations ranged from fM to pM, with 1.1 to 4.5 fold increases from near-surface waters to the mesopelagic Oxygen Minimum Zone (OMZ). Notably, at 67-70, dissolved B1 increased 3.5-fold within the mesopelagic OMZ. Paired metagenomic analysis suggests that chemoautotrophic ammonia-oxidizing Archaea (AOA) and Thioglobaceae, alongside nitrite-oxidizing Nitrospina, are important B1 producers in OMZs. Metagenome-assembled genomes indicate that Nitrospina may alternate between B1 biosynthesis and energy-preserving salvage pathways in synergy with co-occurring AOA. Re-analysis of metatranscriptomic reads from a previous study established Thioglobaceae can be dominant expressors of key de novo B1 biosynthesis genes in Monterey Bay. These findings suggest that deep ocean chemoautotrophs are B1 prototrophs in OMZs, analogous to photoautotrophs in the epipelagic ocean, and provide the foundation for B1 trafficking.},
}

@article {pmid40630748,
year = {2025},
author = {Bilal, H and Li, X and Lv, QL and Qiu, H and Qiu, YA and Xu, B},
title = {Invasive Mucormycosis in a Chronic Lymphocytic Leukemia Patient on Zanubrutinib: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3281-3287},
pmid = {40630748},
issn = {1178-6973},
abstract = {BACKGROUND: Invasive mucormycosis is a severe fungal infection that predominantly affects immunocompromised and diabetic patients. This case study highlights the importance of early diagnosis and pathogen-specific antifungal therapy in managing invasive mucormycosis among high-risk patients.

CASE DESCRIPTION: A 47-year-old male with chronic lymphocytic leukemia (Rai stage IV) on zanubrutinib and with uncontrolled diabetes was admitted to Jiangxi Cancer Hospital on November 7, 2021. Imaging revealed pulmonary infection and splenic infarction, while laboratory findings suggested disseminated intravascular coagulation. Despite empirical broad-spectrum antibiotics, his condition worsened, necessitating an emergency splenectomy. Postoperatively, fluconazole was added to his antimicrobial regimen, but he developed respiratory failure, liver and renal dysfunction, and persistent hyperglycemia. A bronchial alveolar lavage sample was sent for metagenomic next-generation sequencing (mNGS) to identify the pathogen. Despite intensive care, he deteriorated rapidly, developing myocardial injury, metabolic acidosis, and multiorgan failure, leading to death on November 13, 2021. mNGS results, received after the patient's death, identified Rhizomucor pusillus as the primary pathogen, with co-infection by Enterococcus faecium and Human betaherpesvirus 7.

CONCLUSION: This study presents a case of rapidly progressive mucormycosis co-infected with bacterial and viral pathogens, highlighting the importance of early intervention and accurate diagnosis. Delayed identification of the fungal pathogen significantly hindered timely antifungal intervention, underscoring the importance of appropriate empirical therapies in hematological patients treated with zanubrutinib. Future research should focus on antifungal stewardship and epidemiological surveillance studies to improve early detection and guide targeted empirical treatment for high-risk populations.},
}

@article {pmid40630483,
year = {2025},
author = {Gao, Y and Lin, YJ and Zhang, WL and Ni, JM and Han, SG and Bao, L},
title = {A case-control study on Chlamydia psittaci pneumonia and legionella pneumonia.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1591963},
pmid = {40630483},
issn = {2296-858X},
abstract = {PURPOSE: Atypical pathogens (Chlamydia psittaci and Legionella) are often detected by metagenomic next-generation sequencing (mNGS). However, the two atypical pneumonias are difficult to distinguish. The aim of this study was to retrospectively analyze the two types of atypical pneumonia and use statistics to find points of differentiation for early diagnosis and timely treatment.

METHODS: This retrospective study included all confirmed cases of two types of atypical pneumonia in our institution. The data collected and analyzed included epidemiological, clinical, laboratory, and radiological features.

RESULTS: The study included 84 patients, 63 with Chlamydia psittaci (C. psittaci) pneumonia, 21 with Legionella pneumonia. (1) Up to 61.9% of patients with C. psittaci pneumonia and Legionella pneumonia had high fevers. More than 90% of patients with Legionella pneumonia had a cough score ≥ 3. Legionella pneumonia patients experienced more severe coughing, chest tightness and shortness of breath symptoms than C. psittaci pneumonia patients (both, p < 0.01). (2) Consolidation, bronchial insufflation, ground-glass opacities, and pleural effusion are the most common chest CT signs of C. psittaci pneumonia and Legionella pneumonia. Legionella pneumonia was more likely to cause ground-glass opacities in the upper left lobe than C. psittaci pneumonia (p = 0.05). There was no statistical difference in other CT findings. (3) C. psittaci pneumonia and Legionella pneumonia were identified by leukocytes, lymphocytes ratio, NLR, blood glucose, cough, chest tightness and shortness of breath. They had AUC' s of 0.810, 0.709, 0.728, 0.724, 0.795, 0.675, and respective 95% CI' s of 0.716-0.907, 0.60 5-0.832, 0. 566-0.838, 0.604-0.831, 0.696-0.869, 0.574-0.784; all statistically significant (all P < 0.05; < 0.001, 0.003, 0.008, 0.006, < 0.001, 0.017, respectively). (4) 69.8%, 80.9% of each patients took two or more antibiotics simultaneously before diagnosis, but the difference was not statistically significant (p = 0.32). Some patients received more than four antibiotics, most commonly Legionella pneumonia (23.8%) (p = 0.01).

CONCLUSION: Clinicians should consider atypical pneumonia, particularly C. psittaci and Legionella pneumonia, when patients present with high fever and chest CT scans showing consolidation accompanied by bronchial insufflation, ground-glass opacities, and pleural effusion. Initially, clinicians can differentiate between the two types of pneumonia based on symptoms (e.g., cough severity, chest tightness and shortness of breath), imaging features (e.g., GGO in the left upper lobe), and laboratory markers (e.g., glucose, leukocytes, NLR, and lymphopenia). This allows for the optimization of antibiotic choices and the reduction of unnecessary multidrug combinations, which can improve prognosis and reduce the risk of drug resistance.},
}

@article {pmid40630297,
year = {2025},
author = {Hellman, T and Yeo, LF and Palmu, J and Havulinna, A and Jousilahti, P and Laitinen, V and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Gut Microbiome as a Risk Factor for Future CKD.},
journal = {Kidney international reports},
volume = {10},
number = {6},
pages = {1673-1682},
pmid = {40630297},
issn = {2468-0249},
abstract = {INTRODUCTION: Gut microbiome has been linked with chronic kidney disease (CKD) in several small cross-sectional studies. However, the relationship between baseline gut microbiome and long-term incident CKD remains unknown.

METHODS: We performed fecal sampling and measured serum creatinine (SCR) (N = 6699) and urine albumin-to-creatinine ratio (UACR) (N = 797) in a population-based cohort examined in the year 2002. We assessed the multivariable-adjusted associations of gut metagenome with baseline SCR, baseline UACR, and register-based incident CKD.

RESULTS: The mean age of the participants was 49.5 ± 12.9 years and 45.8% were men. During a median follow-up of 18.6 years, 108 participants developed incident CKD. In prospective analyses, increased baseline gut microbiome alpha diversity was associated with lower risk of incident CKD (hazard ratio per 1 SD: 0.84; 95% confidence interval [CI]: 0.71-0.99; P = 0.04). Gut microbial beta diversity and taxa were not related to incident CKD (P ≥ 0.09 for all). In cross-sectional analyses, alpha diversity (beta per 1 SD: 1.28; 95% CI: 0.64-1.98; P < 0.001) and beta diversity (P = 0.002; R[2] = 0.12%) were associated with SCR, whereas no associations were observed for UACR. In total, 43 significant species-level associations with SCR were observed and 16 negative associations (37.2%) for species belonging to the Lachnospiraceae family.

CONCLUSION: Our results suggest that decreased gut microbial diversity may be related to risk of future CKD and that a potential link between the Lachnospiraceae family and desirable kidney health exists. Our results extend previous cross-sectional studies and help to establish the basis for examining gut microbiome as a CKD risk factor.},
}

@article {pmid40630181,
year = {2025},
author = {Yang, J and Qiang, Z and Zhang, D and Hao, H and Wei, J and Maira, HS and Wang, W and Nie, Z},
title = {Shotgun metagenomics analysis of gut microbiota of three indigenous fish species from the Kizil River, Xinjiang.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1617701},
pmid = {40630181},
issn = {1664-302X},
abstract = {This study investigates the gut microbiota composition and functional adaptations in three indigenous fish species from the Kizil River, Xinjiang: Schizothorax biddulphi (SB), Diptychus maculatus (DM), and Triplophysa yarkandensis (TY), recognizing their ecological significance and the need for conservation insights. Shotgun metagenomics was employed to profile the gut microbiota and functional potential. Taxonomic and functional annotations were analyzed, including identification of dominant taxa, biomarkers (LEfSe), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for metabolic functions, and Carbohydrate-Active enZymes (CAZy) database annotations. Environmental parameters (crude oil pollution, nitrogen levels, pathogen presence) were assessed, and dietary shifts during overwintering were characterized. Distinct gut microbiota profiles were identified: Proteobacteria, Acinetobacter, and Pseudomonas were dominant overall. Species-specific biomarkers were Micromonospora (DM); Proteobacteria, Firmicutes, Aeromonas, and Bacillus (SB); and Mucoromycota, Vibrio, and Alcanivorax (TY). DM and SB exhibited significantly higher Firmicutes/Bacteroidetes ratios and enhanced nutrient utilization capabilities compared to TY. Key functional pathways included enriched fructose/mannose metabolism (SB) and oxidative phosphorylation (DM). CAZy analysis revealed high CE3 abundance across species, with GT6/GT10 (SB) and PL22 (TY) serving as unique enzymatic biomarkers. Dietary shifts during overwintering occurred: DM and TY transitioned towards herbivory, while SB retained carnivorous tendencies despite increased plant consumption. All species showed reduced immunity, with DM and SB particularly vulnerable to Acinetobacter-related infections. Environmental analysis revealed crude oil pollution, elevated nitrogen levels, and contamination with A. baumannii. TY demonstrated notable salinity adaptability but heightened sensitivity to pollution. Host phylogeny exerted a strong influence on microbiota composition and metabolic functions. The results demonstrate host-specific microbial adaptation driven by phylogeny. The distinct functional profiles (nutrient utilization, key metabolic pathways like fructose/mannose metabolism and oxidative phosphorylation, CAZy enzymes) reflect ecological niche specialization. The observed dietary shifts and reduced winter immunity, compounded by environmental stressors (crude oil, nitrogen, A. baumannii), highlight critical vulnerabilities, especially for DM and SB. TY's salinity adaptation is counterbalanced by pollution sensitivity. This study provides essential insights for developing targeted conservation strategies and sustainable aquaculture practices for these indigenous species within their natural habitat, emphasizing the need for pollution mitigation.},
}

@article {pmid40629814,
year = {2025},
author = {Wu, X and Han, X and Zhu, L and Pi, N and Li, Y and Xiang, R},
title = {A Novel Metallo-β-Lactamase AMM-1 From Alteromonas mangrovi Reveals a Cryptic Environmental Reservoir of Carbapenem Resistance.},
journal = {Microbial biotechnology},
volume = {18},
number = {7},
pages = {e70191},
pmid = {40629814},
issn = {1751-7915},
support = {CSTB2022TIAD-KPX0115//Chongqing Municipal Special Fund for Technological Innovation and Application Development/ ; CSTB2024TIAD-CYKJCXX0035//Chongqing Municipal Special Fund for Technological Innovation and Application Development/ ; CSTB2024TIAD-GPX0010//Chongqing Municipal Special Fund for Technological Innovation and Application Development/ ; 32000088//National Natural Science Foundation of China/ ; 32060024//National Natural Science Foundation of China/ ; CQHJ-NBKY-2024-003//Environmental Monitoring Research and Development Fund/ ; },
mesh = {*beta-Lactamases/genetics/metabolism/chemistry ; *Carbapenems/pharmacology ; Phylogeny ; *Alteromonas/genetics/enzymology/drug effects ; Escherichia coli/genetics ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactam Resistance ; Microbial Sensitivity Tests ; Metagenome ; Models, Molecular ; },
abstract = {Carbapenem resistance driven by metallo-β-lactamases (MBLs) poses a formidable global challenge as these enzymes can degrade a wide range of β-lactam antibiotics, including last-line carbapenems. Despite extensive documentation of MBL-producing pathogens, their evolutionary origins and ecological reservoirs are still poorly understood. Here, we report the discovery and in-depth characterisation of AMM-1, a previously unrecognised B1.2 MBL identified within a metagenome-assembled genome of Alteromonas mangrovi obtained from the Yangtze River Estuary. Comparative sequence analyses and phylogenetics reveal that AMM-1 clusters closely with clinically significant MBLs, underscoring its potential impact to human health. Structural modelling confirms the presence of a conserved di-zinc binding site critical for β-lactam hydrolysis, while heterologous expression in Escherichia coli (E. coli) demonstrates a marked increase in resistance against multiple β-lactam classes, including carbapenems. Phylogenetic depth analysis and ancestral reconstruction delineate AMM-1's distinct evolutionary path, placing it deeper than IMP-1 and SPM-1 but shallower than NDM-1. Flexibility simulations reveal unique active-site loop dynamics (L3 and L10), with reduced mobility in key regions that shape substrate binding stability and spectrum. Notably, AMM-1 is stably located on the host chromosome without flanking mobile genetic elements, suggesting that it may have persisted as a vertically inherited trait rather than a recently acquired component of a mobile resistome. These findings highlight the capacity of environmental microbes to serve as long-standing, cryptic reservoirs of potent resistance determinants, emphasising the need for integrated environmental surveillance and preemptive stewardship strategies. By unveiling the molecular and functional properties of AMM-1, this work provides critical insights into how resistance elements can reside, evolve and potentially mobilise within natural habitats, ultimately informing efforts to predict and mitigate the future emergence of carbapenem-resistant bacterial pathogens.},
}

*beta-Lactamases/genetics/metabolism/chemistry
*Carbapenems/pharmacology
Phylogeny
*Alteromonas/genetics/enzymology/drug effects
Escherichia coli/genetics
*Anti-Bacterial Agents/pharmacology
*beta-Lactam Resistance
Microbial Sensitivity Tests
Metagenome
Models, Molecular

@article {pmid40629644,
year = {2025},
author = {He, H and Shen, D},
title = {A case of psittacosis chlamydia pneumonia in patients with anti-infection drugs analysis and pharmaceutical care.},
journal = {Medicine},
volume = {104},
number = {27},
pages = {e41187},
pmid = {40629644},
issn = {1536-5964},
mesh = {Humans ; Middle Aged ; Female ; *Psittacosis/drug therapy/diagnosis ; *Azithromycin/therapeutic use/administration & dosage ; *Chlamydophila psittaci/isolation & purification ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; *Pneumonia, Bacterial/drug therapy ; },
abstract = {RATIONALE: Psittacosis pneumonia, caused by Chlamydia psittaci, is an underdiagnosed zoonotic infection. This case aims to demonstrate the efficacy of azithromycin as an alternative therapy and highlight the value of clinical pharmacists in managing drug-resistant infections.

PATIENT CONCERNS: A 56-year-old female poultry farmer presented with persistent high fever (38.5-39.0°C), chills, body aches, and fatigue for 2 weeks. Initial outpatient treatment with unspecified oral medication provided no relief.

DIAGNOSES: Metagenomic next-generation sequencing of bronchoalveolar lavage fluid confirmed C psittaci and rhinovirus co-infection, explaining treatment failure with empirical piperacillin-tazobactam for presumed bacterial pneumonia.

INTERVENTIONS: After pathogen identification, intravenous azithromycin monotherapy (4.5 g total dose) was initiated. Clinical pharmacists collaborated on regimen design, monitored for QTc prolongation/electrolyte imbalances, and ensured safety during the 12-day course.

OUTCOMES: Fever resolved within 48 hours; all symptoms improved by day 6. Follow-up computed tomography showed significant resolution of lung consolidation. The patient was discharged on day 11 with oral azithromycin continuation.

LESSONS: Azithromycin is effective as second-line therapy for severe psittacosis when tetracyclines are inaccessible. Metagenomic next-generation sequencing enables rapid diagnosis of atypical pathogens, while pharmacist-led pharmaceutical care optimizes antimicrobial selection and safety monitoring, particularly for cardiotoxic drugs.},
}

Humans
Middle Aged
Female
*Psittacosis/drug therapy/diagnosis
*Azithromycin/therapeutic use/administration & dosage
*Chlamydophila psittaci/isolation & purification
*Anti-Bacterial Agents/therapeutic use/administration & dosage
*Pneumonia, Bacterial/drug therapy

@article {pmid40629427,
year = {2025},
author = {Bell, AG and Vaughan, ER and Kasprzyk-Hordern, B and Cable, J and Temperton, B and Tyler, CR},
title = {Impacts of environmentally relevant concentrations of antibiotic cocktails on the skin microbiome of Eurasian carp (Cyprinus carpio).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {73},
pmid = {40629427},
issn = {2524-4671},
support = {NE/R011524/1//Natural Environment Research Council/ ; NE/R011524/1//Natural Environment Research Council/ ; CGR/SD6387//NERC Environmental Bioinformatics Centre/ ; },
abstract = {BACKGROUND: The skin surfaces of fish harbour diverse assemblages of microbes (microbiomes) that play critical roles in host health and disruption of these microbiomes can lead to disease conditions. Antibiotics, widely used in medicine for human and animal health treatments, are increasingly found in waterways and this is a growing concern due to their potential to alter the balance of microbial ecosystems and drive antimicrobial resistance (AMR). The effects of antibiotics on skin microbiomes in fish, however, have been little explored. This study examines how exposure to environmental levels of antibiotics affects the skin microbiomes of Eurasian carp (Cyprinus carpio).

RESULTS: A 2-week exposure of Eurasian carp to cocktails of five antibiotics (ciprofloxacin, clarithromycin, sulfamethoxazole, trimethoprim, and tetracycline) at concentrations found in the environment resulted in significant skin bacterial community compositional shifts. Applying 16S rRNA amplicon sequencing, we found enrichment of the genus Arcicella (Proteobacteria) and depletion of Sphaerotilus (Bacteroidetes) with limited recovery even after maintaining the fish for a further two weeks in clean (antibiotic-free) water. In the low-antibiotic concentration exposure group, the tank water microbiome assemblages resembled those of the fish skin suggesting similar responses to the antibiotic treatments. Metagenomic analysis observed no increase in antibiotic resistance genes or changes in metabolic pathway abundance, possibly due to the relatively short duration of antibiotic exposure.

CONCLUSION: This study highlights that even low-level exposure to chemical mixtures can alter fish skin microbiome compositions, with limited recovery observed after cessation of exposure. These findings warrant further assessments of the long-term effects and functional consequences of these altered microbiomes on fish health, particularly in environments increasingly affected by anthropogenic chemical pollution.},
}

@article {pmid40629292,
year = {2025},
author = {Ying, L and Yuhao, W and Yafang, H and Jiao, L and Lina, D and Qinze, S and Chenghai, Y and Shaoxiong, Z and Yuexi, G and Mingwang, S and Zelin, C and Chuangchuang, W and Zihan, G and Xin, L and Lu, M and Lei, Z},
title = {Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {423},
pmid = {40629292},
issn = {1471-2180},
support = {82103868//National Natural Science Foundation of China/ ; 8191101420//National Natural Science Foundation of China/ ; 20220301//Young Talent Fund of Association for Science and Technology in Shaanxi/ ; 2023BSHTBZZ03//Shaanxi Province Postdoctoral Research Project/ ; 2023P098//Shaanxi Provincial Social Science Project/ ; 3111500001//Outstanding Young Scholars Funding/ ; xtr022019003//Xi'an Jiaotong University Basic Research and Profession Grant/ ; YX6J004//Xi'an Jiaotong University Young Talent Support Grant/ ; },
}

@article {pmid40629022,
year = {2025},
author = {Teo, JJY and Ho, EXP and Ng, AHQ and How, SHC and Chng, KR and Ateş, YC and Fau'di, MT and Aung, KT and Nagarajan, N},
title = {Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {63},
pmid = {40629022},
issn = {2731-8745},
abstract = {The distribution of microorganisms in built environments with high human traffic, such as food centres, can potentially have a significant impact on public health, particularly in the context of increasing worldwide incidence of food and fomite-related outbreaks. In many major Asian cities, public food centres are central to daily food consumption, yet there is a lack of baseline knowledge about their environmental microbiomes. We performed a city-wide metagenomic survey of food-centre microbiomes in Singapore, covering 16 centres and 240 samples, to map the abundances of microbial (bacteria, archaea, fungi, viruses) and non-microbial DNA across two timepoints. Food-centre microbiomes were found to be enriched in food-related DNA signatures compared to other environments, such as hospitals and offices, with specific food-microbe associations (e.g., Enterobacteriaceae and fish) and food DNA providing a partial explanation for the microbial profiles observed (44% of variation explained). Machine learning analysis identified a small set of microbial species (n = 22) that serve as highly accurate (>80%) location-specific signatures for various food centres, some of which persist even after 3 years. Profiling of antibiotic resistance genes (ARGs) and pathogens identified a surprising enrichment of ARGs in food centres relative to other non-healthcare environments (>2.5×), and an order of magnitude enrichment of key pathogenic species (e.g., Klebsiella pneumoniae, Enterobacter spp) even compared to hospital environments. These results highlight the contribution of diverse biotic and abiotic factors in shaping the unique microbiome profiles of different food-centre environments, and the potential for using metagenomic surveillance to understand the risk for infections and antibiotic resistance gene transmission.},
}

@article {pmid40628728,
year = {2025},
author = {Arp, G and Jiang, AK and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, MR and Li, Y and Hall, B and Jiang, X},
title = {Identification of gut bacteria reductases that biotransform steroid hormones.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6285},
pmid = {40628728},
issn = {2041-1723},
mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; Phylogeny ; Male ; Female ; *Oxidoreductases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification ; *Steroids/metabolism ; Biotransformation ; Pregnenolone/metabolism ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {The metabolism of steroid hormones by the gut microbiome is increasingly recognized as a key factor in human health; however, the specific enzymes mediating these transformations remain largely unidentified. In this study, we identify Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, we show that 5β-reductase evolved to specialize in converting both natural and synthetic 3-ketosteroid hormones into their 5β-reduced derivatives, while Δ[6]-3-ketosteroid reductase adapted to produce Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the conversion of pregnenolone, a 3β-hydroxy-5-ene and steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations and enriched in females compared to males. These findings lay the groundwork for mechanistic investigations into how microbial steroid metabolism modulates host hormonal physiology.},
}

*Gastrointestinal Microbiome/physiology/genetics
Humans
Phylogeny
Male
Female
*Oxidoreductases/metabolism/genetics
*Bacteria/enzymology/genetics/classification
*Steroids/metabolism
Biotransformation
Pregnenolone/metabolism
*Bacterial Proteins/metabolism/genetics

@article {pmid40627884,
year = {2025},
author = {Zheng, Y and Chen, P and Wang, E and Ren, Y and Wu, X and Wei, Q and Dong, R and Guo, J},
title = {Metabolic pathway modulation for enhanced acetic acid production in acidogenic fermentation of food waste via gas self-circulation.},
journal = {Bioresource technology},
volume = {435},
number = {},
pages = {132945},
doi = {10.1016/j.biortech.2025.132945},
pmid = {40627884},
issn = {1873-2976},
abstract = {The volatile fatty acids (VFAs) produced through acidogenic fermentation of food waste can be applied as an external carbon source for denitrification in wastewater treatment. However, variations in the concentration and composition of VFAs significantly limit denitrification performance. In this study, a novel gas self-circulation strategy was investigated to enhance acetic acid production. The results indicated that gas self-circulation increased the acetic acid yield by 23.11 %, from 6.88 to 8.47 g/L. Metagenomic analyses revealed that the system reduced reliance on conventional acetogenic bacteria and significantly enriched homoacetogens. The upregulation of genes related to glycolysis and pyruvate metabolism explained the overall improvement in acidogenic metabolism. The increased abundance of key enzyme genes associated with the Wood-Ljungdahl and the acetyl coenzyme A pathways enhanced the metabolic flux toward acetate synthesis. This study presents a novel approach for enhancing selective acetic acid production and investigates the corresponding mechanistic responses.},
}

@article {pmid40627495,
year = {2025},
author = {Onohuean, H and Ogunmola, T and Adesiyan, A and Oluwamayowa Samuel, A and Oni, E and Okechukwu Paul Chima, U},
title = {Updates on cancer vaccines in brain cancer: Advances in neuroblastoma, delivery systems, and emerging technologies.},
journal = {Human vaccines & immunotherapeutics},
volume = {21},
number = {1},
pages = {2526964},
doi = {10.1080/21645515.2025.2526964},
pmid = {40627495},
issn = {2164-554X},
mesh = {Humans ; *Brain Neoplasms/therapy/immunology ; *Neuroblastoma/therapy/immunology ; *Cancer Vaccines/administration & dosage/immunology/therapeutic use ; Blood-Brain Barrier/metabolism ; *Drug Delivery Systems/methods ; Nanoparticles/administration & dosage ; COVID-19 Vaccines ; Child ; Immunotherapy/methods ; SARS-CoV-2/immunology ; COVID-19/prevention & control ; },
abstract = {Neuroblastoma stands as a major concern in pediatric oncology because it develops from neural crest cells as a neuroendocrine cancer. Nanoparticle-based vaccine delivery approaches the therapeutic activity of immune cells only toward tumor cells without inflicting damage to healthy tissues like those sustained by chemotherapy and radiation therapy. Neuroblastoma treatment faces two major barriers: penetrating the blood-brain barrier (BBB) and using nanoparticle technology. The promising developments for neuroblastoma treatment emerge from mRNA COVID-19 vaccine research and brain cancer vaccine clinical trials especially through phase I autologous dendritic cell vaccine studies. Future research needs to develop optimized nanoparticles which can trigger the release of mRNA or peptides based on tumor-specific pH and enzyme signals. The BBB can be opened temporarily through ultrasound and receptor-mediated transport approaches, which enhance vaccine delivery to brain tissues. New immunotherapeutic approaches for pediatric malignancies emerge from these recent findings to yield future success.},
}

Humans
*Brain Neoplasms/therapy/immunology
*Neuroblastoma/therapy/immunology
*Cancer Vaccines/administration & dosage/immunology/therapeutic use
Blood-Brain Barrier/metabolism
*Drug Delivery Systems/methods
Nanoparticles/administration & dosage
COVID-19 Vaccines
Child
Immunotherapy/methods
SARS-CoV-2/immunology
COVID-19/prevention & control

@article {pmid40626932,
year = {2025},
author = {Talwar, C and Guria, A and Hoffman, K and Biest, S and Jimenez, P and Kommagani, R},
title = {A role for gut mycobiome and altered fungal-bacterial interactions in women with endometriosis.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioaf148},
pmid = {40626932},
issn = {1529-7268},
abstract = {Endometriosis is a gynecological pathology prevalent in reproductive age women in which the inner uterine wall (endometrium) grows outside as ectopic lesions. The inflammation resulting from these growing implants closely associates with disease severity, causing chronic pain and infertility. Emerging studies have found altered bacterial communities in endometriosis and a causal role for gut bacteria in endometriosis. However, the role of the gut mycobiome i.e., the fungal component of the microbiome in endometriosis is a current knowledge gap that needs to be addressed. In this study, utilizing the stool samples from women with endometriosis, we found that the gut fungal communities are altered in women with endometriosis. By integrating the bacterial microbiota and studying the co-occurring relationships between fungi and bacteria, we identify the altered fungal-bacterial community interactions in endometriosis. In addition, we studied the microbial interactions with the host and identified the bacterial taxa as 'microbiome-associated host genetic variants' in endometriosis. By determining their interactions with fungi, we highlight the fungal taxa as underlying regulators of the disease. Experimentally, we demonstrate that the progression of endometriosis in mice is significantly impeded by the depletion of fungi, revealing a role for the gut mycobiome in endometriosis. Our results highlight the positive- and negative- co-abundance relationships shared between bacteria-fungi, bacteria-bacteria and microbes-host in the disease pathogenesis. These findings promise to stimulate future experimental research on the bacterial-fungal interactions that must be contemplated when designing microbiome-based therapeutic strategies using antifungal agents.},
}

@article {pmid40626910,
year = {2025},
author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S},
title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf142},
pmid = {40626910},
issn = {1751-7370},
abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.},
}

@article {pmid40626735,
year = {2025},
author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA},
title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174424},
doi = {10.1128/msystems.01744-24},
pmid = {40626735},
issn = {2379-5077},
abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.

IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.},
}

@article {pmid40625833,
year = {2025},
author = {Zhou, M and Sun, S and Chen, L and Xu, H and Liu, L and Lv, J and Zhang, J and Xiong, X},
title = {The impact of bronchoalveolar lavage fluid metagenomics next-generation sequencing on the diagnosis and management of patients with suspected pulmonary infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1521641},
pmid = {40625833},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Metagenomics/methods ; Male ; Female ; Retrospective Studies ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; *Pneumonia/diagnosis/microbiology/drug therapy ; Aged, 80 and over ; },
abstract = {OBJECTIVES: This study aimed to enhance the comprehension of the practical utility of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in the clinical management of patients with suspected pneumonia.

METHODS: We retrospectively analyzed 296 individuals who underwent BALF mNGS and conventional microbial tests (CMTs) for suspected pneumonia. We compared the clinical characteristics between patients with pulmonary infection (PI) and those without pulmonary infection (NPI). The detection rate of mNGS and CMTs in different groups of patients were compared. The Sankey diagram was used to present the results of the influence of mNGS on diagnosis and treatment.

RESULTS: Comparison between PI and NPI showed that individuals with fever, concurrent malignant tumors, consolidation or ground-glass opacity on chest CT(Computed tomography) images, and elevated inflammatory markers on blood tests were more likely to develop lung infections. Analysis of the rate of positive detection between CMTs and mNGS in various subgroups revealed that mNGS had a significantly higher positive detection rate in patients with pulmonary infections (87.95% vs. 71.06%, p<0.001), in immunocompetent patients (86.91% vs. 68.08%, p<0.001), and in patients with malignant tumors (92.31% vs. 69.23%, p=0.035). Furthermore, mNGS helped initiate appropriate antibiotic treatment and confirmed the effectiveness of empirical treatment. Compared to immunocompetent patients, BALF mNGS in immunocompromised individuals with suspected lung infections yielded higher rates of accurate diagnosis (62.86% vs. 42.79%, p = 0.027) and more effective treatment (71.43% vs. 58.56%, p = 0.148).

CONCLUSIONS: BALF mNGS identified a greater variety of pathogens than CMTs. Immunocompromised patients with suspected pneumonia may benefit more from BALF mNGS.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology
*Metagenomics/methods
Male
Female
Retrospective Studies
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Aged
Adult
*Pneumonia/diagnosis/microbiology/drug therapy
Aged, 80 and over

@article {pmid40625831,
year = {2025},
author = {Han, Y and Ding, PH},
title = {Advancing periodontitis microbiome research: integrating design, analysis, and technology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616250},
pmid = {40625831},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; Biofilms/growth & development ; Gingiva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.},
}

Humans
*Periodontitis/microbiology
*Microbiota
Biofilms/growth & development
Gingiva/microbiology
Bacteria/genetics/classification

@article {pmid40625179,
year = {2025},
author = {Zhang, Y and Zong, J and Liu, Y and Zhou, K and Shi, H and Yin, WB and Liu, L and Chen, Y},
title = {Progress on targeted discovery of microbial natural products based on the predictions of both structure and activity.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5np00008d},
pmid = {40625179},
issn = {1460-4752},
abstract = {Covering: up to 2025Microbial natural products (NPs) with diverse structures and fascinating activities are a fertile source of drug discovery. Genomic and metagenomic data have revealed that there are abundant valuable resources to be explored. With the advancement in technology, methods for discovering NPs from microorganisms are undergoing notable changes. In this highlight article, we summarized different NP discovery methods into activity-guided and structure-guided categories, emphasizing the characteristics of target compounds and providing typical examples of NPs. We primarily focused on recently developed representative methods that can simultaneously predict the structure and activity features of target compounds as well as the discovery trends of NPs reflected by these cutting-edge methods.},
}

@article {pmid40624949,
year = {2025},
author = {Wu, M and Zhang, T and Han, S and Huan, S and Jiang, Y and Wang, Y and Cai, Z and Zhou, J},
title = {Structure and Function Features of Abundant and Rare Prokaryotic Communities Along Nearshore to Offshore Transitions.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70144},
doi = {10.1111/1462-2920.70144},
pmid = {40624949},
issn = {1462-2920},
support = {42476137//National Natural Science Foundation of China/ ; KCXFZ20230731093402005//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; SGDX20220530111204028//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; RCJC20200714114433069//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; ZDSYS20230626091459009//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; 2023KCXTD052//Innovation Team Project for Guangdong's Universities/ ; 2025A1515010643//Natural Science Foundation of Guangdong Province/ ; 2025A1515010519//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Biodiversity ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Microbiota ; Metagenome ; Metagenomics ; *Archaea/genetics/classification/isolation & purification ; },
abstract = {Abundant and rare taxa are crucial members of the marine microbial community. However, their biodiversity, assembly mechanisms, functional characteristics and ecological response strategies remain poorly understood. In this study, 16S rRNA and metagenomic sequencing were carried out to reveal the structural and functional features of abundant and rare taxa across the transition from nearshore to offshore. The results showed that the biodiversity of both abundant and rare taxa decreased with increasing distance from shore, with rare taxa exhibiting relatively higher diversity indices than abundant ones. Neutral model analysis revealed that the assembly process gradually changed from deterministic to stochastic from nearshore to offshore among abundant taxa. In contrast, among rare taxa, a stochastic process dominated nearshore, whereas a deterministic process was predominant in the offshore environment. Meanwhile, the proportion of variance that could be explained by environmental factors was relatively higher among abundant communities than among rare ones. A co-occurrence network analysis indicated that rare communities displayed greater complexity and a higher degree of modularity than abundant communities. Functionally, abundant communities tended to favour an r-strategy, whereas rare communities leaned towards a K-strategy. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns along coastal-to-open water transitions.},
}

Biodiversity
*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Phylogeny
*Microbiota
Metagenome
Metagenomics
*Archaea/genetics/classification/isolation & purification

@article {pmid40624695,
year = {2025},
author = {Li, Q and Huang, J and Zhou, Y and Wu, Q and Zhou, J and He, F and He, L and Shi, Y and Guo, C and Dai, J},
title = {Virome profiling of Aedes albopictus across urban ecosystems in Guangdong reveals sex-specific diversity.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {264},
pmid = {40624695},
issn = {1756-3305},
support = {2024HK037//Scientific Research Project of General Administration of Customs/ ; 2024M760629//China Postdoctoral Science Foundation/ ; 2022YFC2302700//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Aedes/virology ; *Virome/genetics ; Female ; Male ; China ; *Mosquito Vectors/virology ; Phylogeny ; Ecosystem ; Metagenomics ; Cities ; Sex Factors ; Arboviruses/genetics/isolation & purification ; },
abstract = {BACKGROUND: Aedes albopictus mosquitoes are key vectors for arboviruses such as Dengue virus, Zika virus, and Chikungunya virus, posing significant global public health risks. Guangdong Province, a densely populated subtropical region in southern China, has experienced recurrent outbreaks of mosquito-borne diseases. However, sex- and geography-specific virome profiles of Aedes albopictus populations in this area remain uncharacterized, limiting the development of targeted surveillance strategies and precise risk assessment.

METHODS: We performed a metagenomic analysis of 1269 adult Aedes albopictus collected from five cities across Guangdong Province during autumn 2021. Mosquito pools underwent viral particle enrichment followed by DNA and RNA sequencing. Bioinformatic analyses were employed to characterize viral communities, evaluate alpha/beta diversity, and conduct phylogenetic reconstruction.

RESULTS: A comparative analysis of virome profiles in male and female Aedes albopictus across five regions of Guangdong Province (Chaozhou, Guangzhou, Shaoguan, Shenzhen, Zhanjiang) revealed significant viral distribution patterns influenced by both sex and geographic location. Female mosquitoes predominantly hosted vertebrate-associated arboviruses, including Flavivirus, consistent with their blood-feeding behavior. RNA virome composition showed significant sex-specific clustering (permutational multivariate analysis of variance, PERMANOVA, P = 0.008), with coastal cities (Shenzhen, Zhanjiang) being dominated by RNA viruses, whereas inland areas (Shaoguan) exhibited a predominance of DNA viruses. DNA virome profiles displayed divergence between sexes but marked regional variation. Guangzhou emerged as an outlier, exhibiting exceptional bacteriophage diversity distinct from other regions. Phylogenetic analysis identified zoonotic pathogens with signatures of cross-species transmission and region-specific evolutionary adaptation. These findings highlight the interplay between mosquito ecology, geographic factors, and viral evolution in shaping virome diversity.

CONCLUSIONS: This study presents the inaugural comparative analysis of DNA/RNA viromes in Aedes albopictus populations across Guangdong Province, revealing distinct sex-specific and geographic patterns in viral composition. The identification of vertebrate-associated viruses in female mosquitoes reinforces their epidemiological significance as arboviral vectors, while male-specific environmental viral signatures suggest potential pathways for ecological spillover. Coastal-inland and urban-rural disparities in viral communities emphasize the need for regionally tailored surveillance. These findings provide essential baseline virome data for forecasting emerging arboviral threats and informing strategies to mitigate zoonotic spillover in subtropical urban ecosystems.},
}

Animals
*Aedes/virology
*Virome/genetics
Female
Male
China
*Mosquito Vectors/virology
Phylogeny
Ecosystem
Metagenomics
Cities
Sex Factors
Arboviruses/genetics/isolation & purification

@article {pmid40624638,
year = {2025},
author = {Yan, X and Lin, X and Wu, J and Zheng, L and Liu, Y and Wu, F and Lin, Y and Lu, Y and Huang, C and Shen, B and Liu, H and Huang, R and Hou, F and Zhou, Q and Song, M and Liu, K and Zhu, F and Li, S and Lin, Y and Wang, W and Li, P and Liao, W and Zhi, F},
title = {Mitigation of chemotherapy-induced gut dysbiosis and diarrhea by supplementation with heat-killed Bacteroides fragilis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {408},
pmid = {40624638},
issn = {1741-7015},
support = {Y20190159//Study on the Mechanism of FUT7 regulating CD15s+eTreg cells in the Pathogenesis of Ulcerative Colitis/ ; NO.2024B03J1282//Key Technology Project in Guangzhou/ ; NO. 201809010014//Innovation Leading Team Project in Guangzhou/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Diarrhea/chemically induced/microbiology/therapy ; Mice ; *Bacteroides fragilis ; Mice, Inbred C57BL ; *Probiotics/therapeutic use ; Mice, Inbred BALB C ; *Antineoplastic Agents/adverse effects ; Middle Aged ; Fluorouracil/adverse effects ; Feces/microbiology ; Female ; Aged ; },
abstract = {BACKGROUND: The role of gut microbial dysbiosis in chemotherapy-induced diarrhea (CID) pathogenesis remains unclear in humans. This study investigates gut microbiota alterations in CID patients and evaluates the therapeutic potential of probiotic supplementation.

METHODS: To establish a paired cohort for longitudinal comparison and minimize confounding factors in assessing CID-related microbiota changes, strict inclusion/exclusion criteria were applied to gastrointestinal cancer patients. Fecal samples from eligible participants underwent shotgun metagenomic sequencing to comprehensively profile the gut microbiome composition and function. To evaluate probiotic efficacy and mechanisms, we utilized 6-8-week-old male BALB/c and C57BL/6 mice in established 5-FU- or CPT-11-induced CID models. Probiotic efficacy was assessed using primary (diarrhea severity) and secondary endpoints (body weight change, intestinal permeability). Mechanistic studies were conducted in murine models, complemented by IEC-6 cells and intestinal organoid experiments to elucidate microbiota-host interactions.

RESULTS: Analysis of paired fecal samples (pre- and post-chemotherapy) from 30 gastrointestinal cancer patients (n = 60) revealed chemotherapy-induced reduction of Bacteroides fragilis (B. f) via metagenomics sequencing, with baseline B. f relative abundance negatively correlating with CID severity (r =  - 0.93, p = 3.1e - 12). Building on these clinical observations, in 5-FU/CPT-11-induced CID murine models, oral gavage of heat-killed B. f (hk-B. f) outperformed live bacteria in diarrhea alleviation. Mechanistically, B. f-derived succinate exacerbated diarrhea, while its capsular polysaccharide (PSA) ameliorated mice diarrhea. This discovery explains the discrepant therapeutic effect between hk-B. f and live B. f. Fluorescence tracing confirmed hk-B. f transiently localized to the upper gastrointestinal tract without extraintestinal colonization. hk-B. f preserved epithelial integrity, mitochondrial function, and intestinal organoid development (higher budding count and larger organoid surface area). Moreover, hk-B. f upregulated the expression of BCL2 and downregulated the expression of BAX. Shifting the balance between BCL2 and BAX alleviates intestinal epithelial apoptosis. Caspase-3 inhibition or BCL2 silencing abrogated hk-B. f's anti-apoptotic effects in IEC-6 cells.

CONCLUSIONS: Pathological process of CID can be partially explained by compositional alterations in the gut microbiota. Supplementation with hk-B. f reduces 5-FU-stimulated epithelial injury through mitochondrial apoptotic pathway in CID murine models. These preclinical findings suggest hk-B. f merits further investigation as a potential strategy for improving CID, pending clinical validation.},
}

Animals
*Dysbiosis/chemically induced/therapy/microbiology
Male
*Gastrointestinal Microbiome/drug effects
Humans
*Diarrhea/chemically induced/microbiology/therapy
Mice
*Bacteroides fragilis
Mice, Inbred C57BL
*Probiotics/therapeutic use
Mice, Inbred BALB C
*Antineoplastic Agents/adverse effects
Middle Aged
Fluorouracil/adverse effects
Feces/microbiology
Female
Aged

@article {pmid40624612,
year = {2025},
author = {De, T and Ma, T and Wang, W and An, X and Liu, D and Yin, H and Wang, Q and Zhao, T and Wang, H},
title = {Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated Blautia species and bile acid metabolic pathways.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {506},
pmid = {40624612},
issn = {1471-230X},
support = {XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/metabolism ; *Bile Acids and Salts/metabolism ; Male ; Middle Aged ; Female ; Metabolic Networks and Pathways ; *Dysbiosis/microbiology ; *Clostridiales/genetics/isolation & purification ; Aged ; Case-Control Studies ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) represents a significant global health concern. The gut and bile microbiota, which can influence the gut-liver axis and disease progression, have not been thoroughly characterized in CCA patients.

METHODS: We selected two clinical centers at our hospital and collected stool samples from CCA patients and healthy controls (HC). These samples underwent whole-genome metagenomic shotgun sequencing, followed by analysis using both marker gene-based and assembly-based methods. Additionally, KEGG pathway enrichment was performed using the cholangiocarcinoma (CHOL) RNA-seq samples.

RESULTS: Our results revealed distinct dysbiosis of the gut microbiota in our regional CCA patients. The results revealed greater heterogeneity in the gut microbiome of CCA patients compared to HC samples. We found Blautia species to be significantly less abundant in CCA samples, and can distinguish CCA patients from HC. Blautia can also play a role in influencing the modification of secondary bile acids. Additionally, down-regulation of arachidonic acid and linoleic acid metabolism was observed in the tumor tissues of CHOL patients. In summary, the results revealed significant heterogeneity difference in the gut microbiome of CCA patients compared to HC samples, and detected the specifically decreased Blautia species in CCA patients, suggesting that Blautia may influence bile acid metabolic pathways. Further investigation is warranted to explore Blautia as a potential biomarker for CCA.},
}

Humans
*Cholangiocarcinoma/microbiology/metabolism
*Gastrointestinal Microbiome
*Bile Duct Neoplasms/microbiology/metabolism
*Bile Acids and Salts/metabolism
Male
Middle Aged
Female
Metabolic Networks and Pathways
*Dysbiosis/microbiology
*Clostridiales/genetics/isolation & purification
Aged
Case-Control Studies
Adult
Feces/microbiology

@article {pmid40624564,
year = {2025},
author = {Zhu, J and Jiang, MZ and Chen, X and Li, M and Wang, YL and Liu, C and Liu, SJ and Chen, WH},
title = {Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {161},
pmid = {40624564},
issn = {2049-2618},
support = {2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/isolation & purification/genetics/growth & development/metabolism ; *Microbial Interactions ; Coculture Techniques ; Metagenome ; Healthy Volunteers ; Feces/microbiology ; China ; },
abstract = {BACKGROUND: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

METHODS: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

RESULTS: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

CONCLUSIONS: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bacteria/classification/isolation & purification/genetics/growth & development/metabolism
*Microbial Interactions
Coculture Techniques
Metagenome
Healthy Volunteers
Feces/microbiology
China

@article {pmid40624535,
year = {2025},
author = {Zhao, Y and Niu, X and Zhang, Y and Zhao, L and Zhang, L and He, J and Zhang, Q and Mao, Y and Wang, F and Zhao, X and Wang, R},
title = {Impact of supplementing Limosilactobacillus fermentum MN-LF23 on the eradication of Helicobacter pylori with 14-day standard quadruple therapy: a randomized, double-blind, placebo-controlled trial.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {106},
pmid = {40624535},
issn = {1475-2891},
support = {2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; Male ; Female ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/therapy ; Double-Blind Method ; Middle Aged ; Adult ; *Limosilactobacillus fermentum ; Drug Therapy, Combination ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome ; Dietary Supplements ; Dyspepsia ; },
abstract = {BACKGROUND: The effect of probiotics on Helicobacter pylori (Hp) infection demonstrates considerable heterogeneity. This study aims to elucidate the role of Limosilactobacillus fermentum MN-LF23 (MN-LF23) in Hp-infected populations.

METHODS: A total of 94 adult patients with confirmed Hp infection were enrolled in this study and randomly allocated to the placebo or MN-LF23 group. Patients initially received either placebo or probiotics along with standard quadruple therapy for 2 weeks, followed by continued administration of either placebo or probiotics for an additional 4 weeks. The eradication of Hp, serum levels of inflammatory factors, and alterations in gastrointestinal symptoms were assessed at weeks 0, 2, and 6, while fecal samples were collected for metagenomic sequencing.

RESULTS: The results showed no significant difference (P = 1) in the eradication rate between the placebo group (85.11%) and the probiotic group (82.98%). Following treatment, the incidence of constipation, dyspepsia, and Gastrointestinal Symptom Rating Scale (GSRS) scores in the probiotic group were markedly lower (P < 0.05) compared to those observed in the placebo group. Throughout the treatment process, there were no significant differences in TNF-α and IL-1β levels between the two groups. Compared to the placebo group, the probiotic group exhibited a significant increase in beneficial bacteria such as Limosilactobacillus fermentum, Lactiplantibacillus plantarum, Bifidobacterium longum, Coprococcus caltus, and Clostridium butyricum.

CONCLUSION: MN-LF23 supplementation did not improve the eradication rate of standard quadruple therapy. However, it significantly reduced the overall GSRS score, improved digestive and constipation symptoms, and promoted the proliferation of beneficial bacteria in the intestine.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
Male
Female
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology/therapy
Double-Blind Method
Middle Aged
Adult
*Limosilactobacillus fermentum
Drug Therapy, Combination
Anti-Bacterial Agents/therapeutic use/administration & dosage
Feces/microbiology
Treatment Outcome
Gastrointestinal Microbiome
Dietary Supplements
Dyspepsia

@article {pmid40624250,
year = {2025},
author = {Fukuda, T and Takagaki, M and Kaimori, J and Motooka, D and Nakamura, S and Kawabata, S and Nakamura, H and Ozaki, T and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Isaka, Y and Kishima, H},
title = {Differences in gut microbiome between autosomal dominant polycystic kidney disease with and without intracranial aneurysms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24204},
pmid = {40624250},
issn = {2045-2322},
support = {22K09282//Japan Society for the Promotion of Science/ ; 21K09072//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Polycystic Kidney, Autosomal Dominant/microbiology/complications ; *Gastrointestinal Microbiome ; *Intracranial Aneurysm/microbiology/complications ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Aged ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by cyst formation in the kidneys, and is associated with an elevated risk of intracranial aneurysms (IAs). Although a family history is a recognized risk factor for IAs in patients with ADPKD, emerging research suggests that gut microbiome composition may influence IA development. We investigated the relationship between the gut microbiome and the development of IA in patients with ADPKD. We recruited patients with ADPKD with (IA group) and without (non-IA group) IA from Osaka University between October 2021 and December 2023. Fecal samples were analyzed using 16S rRNA sequencing. Data were processed using the QIIME 2 pipeline to determine microbial diversity and composition. We included 60 patients: 26 in the IA and 34 in the non-IA groups. There were significant differences in microbial beta diversity between the groups. The IA group had higher abundances of Eubacterium siraeum group, Oscillibacter, Fournierella, Negativibacillus, Colidextribacter, and Adlercreutzia. The non-IA group had higher abundances of Bifidobacterium, Megamonas, Acidaminococcus, Megasphaera, and Merdibacter. There was a significant association between the gut microbiome composition and the presence of IAs in patients with ADPKD. Specific bacterial taxa were differentially abundant between patients with ADPKD with and without IAs, suggesting a potential role of the gut microbiome in the pathogenesis of IAs in this genetically predisposed population.},
}

Humans
*Polycystic Kidney, Autosomal Dominant/microbiology/complications
*Gastrointestinal Microbiome
*Intracranial Aneurysm/microbiology/complications
Female
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
Adult
Feces/microbiology
Aged
Bacteria/genetics/classification/isolation & purification

@article {pmid40624247,
year = {2025},
author = {Lin, YT and Sayols-Baixeras, S and Baldanzi, G and Dekkers, KF and Hammar, U and Nguyen, D and Nielsen, N and Eklund, AC and Varotsis, G and Holm, JB and Nielsen, HB and Lind, L and Bergström, G and Smith, JG and Engström, G and Ärnlöv, J and Sundström, J and Orho-Melander, M and Fall, T},
title = {The association between the gut microbiome and 24-h blood pressure measurements in the SCAPIS study.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {276},
pmid = {40624247},
issn = {2730-664X},
support = {ERC-STG-2018-801965, ERC-CoG-2014-649021, ERC-STG-2015-679242//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 2019-01471; 2018-02784; 2018-02837; 2021-03291//Vetenskapsrådet (Swedish Research Council)/ ; 2023-0687; 20200711 (M.O-M.); 20180343, 20210357; 20200173; 20190526//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; NNF20OC0063886//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; LUDC-IRC 15-0067//Stiftelsen för Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; },
abstract = {BACKGROUND: There is mounting evidence supporting the role of the microbiota in hypertension from experimental studies and population-based studies. We aimed to investigate the relationship between specific characteristics of the gut microbiome and 24-h ambulatory blood pressure measurements.

METHODS: The association of gut microbial species and microbial functions, determined by shotgun metagenomic sequencing of fecal samples, with 24-h ambulatory blood pressure measurements in 3695 participants and office blood pressure was assessed in multivariable-adjusted models in 2770 participants without antihypertensive medication from the Swedish CArdioPulmonary bioImage Study.

RESULTS: Gut microbiome alpha diversity was negatively associated with diastolic blood pressure variability. Additionally, four microbial species were associated with at least one of the 24-h blood pressure traits. Streptococcus sp001556435 was associated with higher systolic blood pressure, Intestinimonas massiliensis and Dysosmobacter sp001916835 with lower systolic blood pressure, Dysosmobacter sp001916835 with lower diastolic blood pressure, and ER4 sp900317525 with lower systolic blood pressure variability. Moreover, office blood pressure data from a subsample without ambulatory blood pressure measurements replicated the association of Intestinimonas massiliensis with systolic blood pressure and Dysosmobacter sp001916835 with diastolic blood pressure. Species associated with 24-h blood pressure were linked to a similar pattern of metabolites.

CONCLUSIONS: In this large cross-sectional analysis, gut microbiome alpha diversity negatively associates with diastolic blood pressure variability, and four gut microbial species associate with 24-h blood pressure traits.},
}

@article {pmid40624236,
year = {2025},
author = {Wu, D and Niu, J and Hu, J and Wang, H and Kuang, H},
title = {Metabolomics combined with metagenomics analysis reveals the potential mechanism of Zhejiang psyllium polysaccharides against hyperuricemia in rats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24180},
pmid = {40624236},
issn = {2045-2322},
mesh = {Animals ; *Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology ; *Metagenomics/methods ; *Metabolomics/methods ; Rats ; Uric Acid/blood ; Gastrointestinal Microbiome/drug effects ; Male ; *Psyllium/pharmacology/chemistry ; *Polysaccharides/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Kidney/pathology/drug effects/metabolism ; Blood Urea Nitrogen ; Creatinine/blood ; },
abstract = {This study aimed to assess the anti-hyperuricemia efficacy of Zhejiang psyllium polysaccharides (ZPP) in rats and to explore its underlying mechanism. Hyperuricemia was induced by intragastric administration of potassium oxonate, hypoxanthine, and adenine. The serum levels of uric acid (UA), creatinine (Cr), and blood urea nitrogen (BUN) were measured, and kidney pathology was examined. Serum metabolomics was employed to monitor metabolic alterations following ZPP intervention. Metagenomic analysis was conducted to investigate the impact of ZPP on the intestinal flora of hyperuricemia rats. The results showed that ZPP could significantly reduce the serum UA level in hyperuricemia rats and exhibited a certain renal protective effect. The metabolomics results indicated that ZPP regulates uric acid levels in rats with hyperuricemia and ameliorates renal pathological changes by modulating biomarkers associated with purine metabolism, amino acid metabolism, and lipid metabolism. Metagenomic research also found that ZPP could increase the relative abundance of uric acid metabolism-related probiotics, such as Limosilactobacillus reuteri and Lactobacillus murinus, thereby improving intestinal flora imbalance in rats with hyperuricemia.},
}

Animals
*Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology
*Metagenomics/methods
*Metabolomics/methods
Rats
Uric Acid/blood
Gastrointestinal Microbiome/drug effects
Male
*Psyllium/pharmacology/chemistry
*Polysaccharides/pharmacology/therapeutic use
Rats, Sprague-Dawley
Kidney/pathology/drug effects/metabolism
Blood Urea Nitrogen
Creatinine/blood

@article {pmid40624115,
year = {2025},
author = {Liu, L and Wei, L and Mou, FX and Zhang, W and Wang, RF and Wang, Q and Wang, F},
title = {Oral microbiome dysbiosis in women with a history of pregnancy loss: a metagenomic cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24242},
pmid = {40624115},
issn = {2045-2322},
support = {Grant No. YJS-BD-19//the Special Fund for Doctoral Student Training of The Second Hospital of Lanzhou University in 2019/ ; Grant No. 071100107//The Science Foundation of Lanzhou University/ ; },
mesh = {Humans ; Female ; *Dysbiosis/microbiology ; Pregnancy ; Adult ; Cross-Sectional Studies ; Metagenomics/methods ; *Microbiota/genetics ; *Abortion, Spontaneous/microbiology ; Mouth Mucosa/microbiology ; Metagenome ; *Mouth/microbiology ; Young Adult ; },
abstract = {Pregnancy loss is a prevalent condition among women of reproductive age, significantly affecting fertility and psychological well-being. Despite advances in understanding the etiology of pregnancy loss, the role of the oral microbiome-its composition and metabolic activity-in influencing pregnancy outcomes remains underexplored. Previous studies have suggested that imbalances in the microbiota may contribute to adverse health outcomes, but few have investigated its association with pregnancy loss specifically. A total of 182 women of childbearing age were recruited for this study and divided into two groups: those with a history of pregnancy loss (n = 70) and a control group with no history of adverse pregnancy outcomes (n = 112). Clinical data and buccal mucosa samples were collected for metagenomic analysis. The inclusion of participants was based on their reproductive history, with particular attention to selecting women with at least one confirmed pregnancy loss and those with at least one successful live birth to serve as controls. The oral microbiota of women in the pregnancy loss group exhibited significantly lower richness and diversity compared to the control group (p < 0.05). Notably, specific genera such as Faecalibacterium, Roseburia, and Bacteroides were positively correlated with pregnancy loss, whereas Pseudomonas and Leptotrichia were correlated with it. These findings suggest a potential microbial dysbiosis associated with pregnancy loss. Our study identifies significant oral microbiota dysbiosis in women with pregnancy loss, characterized by reduced diversity and altered metabolic pathways. These findings underscore the potential role of oral microbial imbalance in adverse pregnancy outcomes. While our cross-sectional design and sample heterogeneity limit causal inference, they highlight the need for longitudinal cohorts and mechanistic studies. Future research integrating multi-niche microbiome profiling (e.g., gut and vaginal microbiota) is essential to unravel systemic interactions and advance targeted interventions for reproductive health.},
}

Humans
Female
*Dysbiosis/microbiology
Pregnancy
Adult
Cross-Sectional Studies
Metagenomics/methods
*Microbiota/genetics
*Abortion, Spontaneous/microbiology
Mouth Mucosa/microbiology
Metagenome
*Mouth/microbiology
Young Adult

@article {pmid40624015,
year = {2025},
author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M},
title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {130},
pmid = {40624015},
issn = {2055-5008},
support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; },
abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
*Respiratory Tract Infections/microbiology/diagnosis
Oropharynx/microbiology
*Respiratory System/microbiology

@article {pmid40623822,
year = {2025},
author = {Kwok, WC and Pates, K and Shah, A and Jackson, L and Frost, F},
title = {Antimicrobial resistance in chronic lung infection: the road to resistance.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thorax-2024-222396},
pmid = {40623822},
issn = {1468-3296},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health crisis and is particularly relevant to people living with chronic lung diseases such as bronchiectasis, cystic fibrosis and chronic obstructive pulmonary disease. These conditions frequently involve acute and chronic bacterial infections, requiring increased antibiotic usage and risk of AMR. Understanding the dynamics of AMR and emerging diagnostic and therapeutic strategies is crucial for optimising patient outcomes in this setting.

AIMS: This review explores the interplay between AMR and chronic bacterial lung infections, examining current understanding of pathogen epidemiology, diagnostic strategies, clinical implications of resistance and the impact of treatments. Future directions in research and therapeutic innovation are also outlined.

NARRATIVE: Key pathogens in chronic lung infections, such as Pseudomonas aeruginosa, Haemophilus influenzae, Staphylococcus aureus and Moraxella catarrhalis, exhibit diverse resistance mechanisms and AMR is linked to increased disease severity, exacerbation frequency and mortality, particularly with multidrug-resistant strains. Long-term antibiotic therapies, such as macrolides and inhaled agents, improve clinical outcomes but may drive resistance, necessitating ongoing efforts to understand how they can best be employed. Traditional diagnostic methods, such as culture-based antimicrobial susceptibility testing, often fail to capture the complexity of polymicrobial infections and resistomes. Although advanced techniques like next-generation sequencing and metagenomics are able to identify clinically relevant resistotypes, their development toward clinical utility is still in progress.

CONCLUSIONS: AMR in chronic lung infections represents a dynamic and multifaceted challenge. Novel antibiotics, precision medicine approaches and alternative therapies such as bacteriophages show promise but require further validation. Improved stewardship and individualised treatment strategies are critical for mitigating AMR and enhancing patient outcomes. Collaborative efforts among researchers, clinicians and policy-makers are vital to advancing care and combating this global threat.},
}

@article {pmid40623508,
year = {2025},
author = {Yang, X and Huang, J and Zeng, Z and Sun, S and Wang, J and Wang, Z},
title = {Integrated multi-omics analysis reveals the effect of glucose selenol improves rat immunity.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110023},
doi = {10.1016/j.jnutbio.2025.110023},
pmid = {40623508},
issn = {1873-4847},
abstract = {This study aimed to investigate the effects of glucose selenol (SeGlu) on the immune function of rats, with a particular focus on the spleen. Rats were randomly divided into CK (deionized water, oral), Se0.15 group (0.15 mg/L SeGlu, oral), and Se0.4 group (0.4 mg/L SeGlu, oral) for 30 days continuously. 0.15 mg/L SeGlu significantly increased the serum antioxidant levels and the levels of IgM and IgG. The Se0.4 group upregulated the inflammatory factor levels of IL-2 and IL-6, and both concentrations significantly reduced the serum TNF-α level. Transcriptome analysis indicated that the supplementation of SeGlu could affect three types of proteins: peptidases, tumor necrosis factor receptors, and transmembrane transport proteins. KEGG enrichment discovered pathway annotations directly or indirectly related to the immune process, especially phagosomes, natural killer cell-mediated cytotoxicity, and nod-like receptor signaling pathways. We identified 59 SeGlu target differentially expressed genes and 8 (NEG) and 20 (POS) co-expressed differentially expressed metabolites. Immunoglobulin-related DEGs were concentrated in the transcription factor family V-set, and were identified on chromosome 6. In addition, metagenome sequencing showed that SeGlu treatment increased abundance of Roseburia, Ruminococcus, Eubacterium, Coprobacillus, and Intestinimonas at the genus level. Spearman correlation analysis results showed that the modulatory effects of SeGlu on D-proline were related to the regulation of Roseburia, Clostridium, Eubacterium Coprobacillus, Butyricimonas, and Muribaculum. Overall, the analyses of rat physiology, transcriptome, metabolome, and metagenome offer new insights into Se on rat immunity. SeGlu provides beneficial immune protection and is a promising organic selenium enrichment additive.},
}

@article {pmid40622975,
year = {2025},
author = {Kabir, KMA and Sigera, C and Maduranga, S and Weeratunga, P and Rajapakse, S and Fernando, D and Lloyd, AR and Bull, RA and Rodrigo, C},
title = {Chikungunya masquerading as dengue infection in Sri Lanka uncovered by metagenomics.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326995},
pmid = {40622975},
issn = {1932-6203},
mesh = {Humans ; *Dengue/diagnosis/virology ; Sri Lanka ; *Chikungunya Fever/diagnosis/virology ; *Chikungunya virus/genetics ; Female ; Male ; *Metagenomics/methods ; Adult ; Middle Aged ; Phylogeny ; Dengue Virus/genetics ; Prospective Studies ; Diagnosis, Differential ; Young Adult ; High-Throughput Nucleotide Sequencing ; Adolescent ; },
abstract = {INTRODUCTION: Dengue is a significant threat to human health in South and Southeast Asia where patients are treated without diagnostic confirmation during outbreaks. This approach, though cost-effective may miss important infections especially those caused by other arboviruses (e.g., Zika, Chikungunya and West Nile virus). This study aimed to diagnose missed infections mimicking dengue by using metagenomic next generation sequencing (mNGS).

Total nucleic acid (DNA and RNA) was extracted and subjected to mNGS from acute infection plasma of 60 patients from a prospective cohort study in Sri Lanka in which patients with clinically suspected dengue fever were recruited but were later confirmed as dengue-negative by NS1 antigen testing and by dengue-specific reverse transcription and polymerase chain reaction (RT-PCR) analysis. mNGS data revealed missed chikungunya and dengue infections in five patients each, and a possible bacterial infection by Klebsiella pneumoniae in another patient. It was not possible to differentiate chikungunya infections from dengue infections based on clinical features or routine non-diagnostic laboratory tests conducted in early infection (e.g., full blood count, C-reactive protein level). Phylogenetic analysis showed that the chikungunya sequences from this study were closely related to those sequenced from Maldives, Malaysia, India and Singapore between 2015-2019.

CONCLUSIONS: Chikungunya infection may masquerade as dengue especially in low- and middle-income countries where dengue is treated based on clinical suspicion only - without confirmatory testing. As both infections are likely prevalent worldwide, but the complications and natural history of chikungunya and dengue infections are quite different, the addition of cheap and accessible diagnostics for both infections should be pursued in endemic countries.},
}

Humans
*Dengue/diagnosis/virology
Sri Lanka
*Chikungunya Fever/diagnosis/virology
*Chikungunya virus/genetics
Female
Male
*Metagenomics/methods
Adult
Middle Aged
Phylogeny
Dengue Virus/genetics
Prospective Studies
Diagnosis, Differential
Young Adult
High-Throughput Nucleotide Sequencing
Adolescent

@article {pmid40622965,
year = {2025},
author = {Adigoun, RFR and Durand, A and Aholoukpè, HNS and Tchokponhoué, DA and Achigan-Dako, EG and Bokonon-Ganta, AH and Benizri, E},
title = {Plant tissue type and mineral contents shape endophytic bacterial communities in the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] in Benin.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327715},
pmid = {40622965},
issn = {1932-6203},
mesh = {*Endophytes/genetics/classification ; Plant Leaves/microbiology/metabolism ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Benin ; *Bacteria/genetics/classification/isolation & purification ; *Minerals/metabolism/analysis ; Phylogeny ; },
abstract = {Diverse endophytic bacteria inhabit distinct tissues of a given species and are essential for plant growth and resilience to various stresses. Little information is available on bacterial endophytes associated with Synsepalum dulcificum, an opportunity fruit crop with high economic and medicinal values. Using Illumina sequencing of the bacterial 16S rRNA gene, the diversity and structure of the endophytic bacterial community in the roots and leaves of S. dulcificum were determined, considering 29 accessions from three distinct phenotypes located either in home gardens or on farms in Benin. 2,468 Operational Taxonomic Units (OTUs) were recorded in the leaf and root endosphere of S. dulcificum, affiliated with 20 bacterial phyla, 49 classes, 125 orders, 217 families and 365 genera. Actinomycetota, Pseudomonadota and Chloroflexota were the most abundant phyla in the roots. In comparison, Pseudomonadota stood out as almost the unique phylum in the leaves, suggesting a significant decrease in diversity from roots to leaves. Significant correlations (p < 0.05) were observed between the relative abundance of the endophytic bacterial taxa and the mineral contents in the leaves, roots, and soil. While bacterial communities depended highly on accession, plant phenotype and habitat discriminated them in roots and leaves, respectively. Metagenome function prediction indicated that S. dulcificum harbors bacteria with the potential to metabolize carbohydrates and amino acids, as well as synthesize secondary metabolites and antimicrobial compounds beneficial for plant growth and adaptation to environmental stresses. These findings open room for exploiting endophytic diversity to enhance the growth and sustainable production of S. dulcificum.},
}

*Endophytes/genetics/classification
Plant Leaves/microbiology/metabolism
Plant Roots/microbiology
RNA, Ribosomal, 16S/genetics
Benin
*Bacteria/genetics/classification/isolation & purification
*Minerals/metabolism/analysis
Phylogeny

@article {pmid40622630,
year = {2025},
author = {Yuan, R and Jin, X and Liu, X and Hao, K and Shi, Y and Yang, Z and Zhang, L and Chen, J and Guo, C and Wu, Y and Tang, J and Zhao, Z},
title = {Increased pathogens and reduced intestinal immune genes associated with fish diseases during the winter-spring transition.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40622630},
issn = {1618-1905},
support = {cx[23]1007//the Jiangsu Agricultural Science and Technology Independent Innovation fund/ ; },
abstract = {Global climate change has posed significant challenges to the aquaculture industry, leading to the emergence of novel diseases. A recently emerging disease, termed the overwintering syndrome, has been reported in freshwater fish aquaculture systems in China during the winter-spring transition. This syndrome is characterized by weight loss, decreased activity levels, and mass mortality. Currently, little is known about cause of the emerging disease. In this study, the gut microbiota of healthy and diseased channel catfish (Ictalurus punctatus) were analyzed using metagenomic sequencing. Diseased fish exhibited a notable reduction in bacterial diversity compared to healthy controls, while the viral richness was significantly higher. Additionally, random forest models based on gut microbiota composition revealed high accuracy in distinguishing between diseased and healthy fish. Several gut microbiota biomarkers with potential diagnostic value were identified, primarily consisting of rare taxa (relative abundance < 5%), except for Alphaproteobacteira, Siphoviridae and Podoviridae. Furthermore, an increase in the prevalence and abundance of pathogens was observed in the intestines of diseased fish compared to healthy counterparts. Notably, Vibrio cholerae and Dickeya dadantii were enriched in the intestines of fish exhibiting the overwintering syndrome. Concurrently, genes involved in the synthesis of innate immune factors was markedly diminished in the gut microbiota of diseased fish, along with a reduction in the microbial hosts of these genes. Collectively, these findings elucidate the enrichment of pathogens and the attenuation of innate immunity in fish with the overwintering syndrome, correlating with alterations in the gut microbiota.},
}

@article {pmid40622282,
year = {2025},
author = {Ni, Z and Zhou, Y and Chang, M and Xia, T and Zhou, W and Gao, Y},
title = {High-Altitude Impacts on Gut Microbiota: Accelerated Aging and the Urgency for Targeted Health Interventions.},
journal = {High altitude medicine & biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ham.2025.0016},
pmid = {40622282},
issn = {1557-8682},
abstract = {The human gut microbiota is integral to the aging process, and its composition is notably influenced by the unique environmental pressures of high-altitude plateaus, characterized by hypobaric and hypoxic conditions. This study explores the correlation between physiological aging and gut microbiota among high-altitude plateau inhabitants, an essential aspect of health preservation in such regions. We conducted a metagenomic analysis of fecal samples from 105 individuals who migrated to high-altitude areas before the age of 20. Our results demonstrate that advancing age and prolonged high-altitude living significantly modify the gut microbiota, evidenced by reduced diversity and an elevated Firmicutes to Bacteroidetes (F/B) ratio in older subjects. Notably, the abundance of the anti-aging bacterium Akkermansia muciniphila (A. muciniphila) inversely correlates with age, showing a significant decline post the age of 25. A comparative analysis of 2,007 individuals from lower altitudes revealed a similar negative correlation between A. muciniphila and age, with a decline evident from age 38. These findings indicate that the high-altitude plateau environment may accelerate the decline of A. muciniphila by 10 years, underscoring the need for targeted health strategies for high-altitude populations.},
}

@article {pmid40622149,
year = {2025},
author = {Chen, Z and Xun, L and Xia, Y and Gong, X},
title = {Overlooked role of heterotrophic prokaryotes in sulfur oxidation makes the sediment of the Bohai Sea a sufficient sink of hydrogen sulfide.},
journal = {mBio},
volume = {},
number = {},
pages = {e0172225},
doi = {10.1128/mbio.01722-25},
pmid = {40622149},
issn = {2150-7511},
abstract = {Marine sediments are the active sites for the biogeochemical cycling of sulfur. Sulfate is used as a major terminal electron acceptor for the anaerobic oxidation of organic compounds in deep sediments, and the produced sulfide is normally oxidized back to sulfate in upper sediments. However, it is unclear which microorganisms, metabolic pathways, and enzymes are mainly involved in oxidation. Here, we used metagenomics, metatranscriptomics, and the testing of sulfide, thiosulfate, and sulfite oxidation in sediment samples to figure out how sulfide is oxidized in the Bohai Sea sediments. Surprisingly, sulfur oxidation is widespread in the microbial community (>67.1%) of mostly heterotrophic prokaryotes across 44 phyla, dominated by Proteobacteria. Known chemolithotrophic sulfur oxidizers were absent. The prevalent sulfur-oxidizing pathway was sulfide to zerovalent sulfur, sulfite, and then sulfate. Thiosulfate is not a major metabolic intermediate. Genes encoding sulfide oxidation (sqr and fccAB), zerovalent sulfur oxidation (pdo, rdsrAB, and shdr), and sulfite oxidation (aprAB/sat) were abundant and upregulated after adding NaHS. Thiosulfate, which is formed between the reaction of zerovalent sulfur and sulfite, was only slowly oxidized, which was consistent with the lack of key genes encoding for direct oxidation of thiosulfate to sulfate. The findings indicate how sulfur is oxidized in the Bohai Sea sediments. The common participation in sulfur oxidation by most heterotrophic prokaryotes results in the effective oxidation of sulfide in the surface sediment, blocking the release of hydrogen sulfide into the water column.IMPORTANCESulfur cycling is tightly interwoven with other crucial element cycles, including carbon, nitrogen, and iron in marine sediments. Sulfate is the most abundant electron acceptor in marine sediments, and sulfate reduction generates a large amount of sulfide. The majority of sulfide is oxidized to sulfate via abiotic or biological transformations, mainly by sulfur oxidizers with different redox states. However, autotrophic sulfur oxidizers, considered key players for sulfur oxidation, are in low abundance in the sediment, limiting our understanding of the pivotal biogeochemical process. This study shows the prevalent distribution of sulfur oxidation among the microbial community and emphasizes the importance of heterotrophic sulfur oxidation in sediments. It evidences the importance of previously overlooked key enzymes for elemental sulfur oxidation and supports that thiosulfate is not the major intermediate during sulfur oxidation. Understanding these key processes is crucial for elucidating biogeochemical processes in marine sediments.},
}

@article {pmid40621974,
year = {2025},
author = {Chen, J and Aherfi, S and Steichen, P and Rios, G and Waldmann, R and Barbry, P},
title = {[Molecular epidemiology of viruses sequenced from wastewater].},
journal = {Medecine sciences : M/S},
volume = {41},
number = {6-7},
pages = {585-592},
doi = {10.1051/medsci/2025083},
pmid = {40621974},
issn = {1958-5381},
mesh = {*Wastewater/virology ; Humans ; *SARS-CoV-2/genetics/isolation & purification ; COVID-19/epidemiology/virology ; *Molecular Epidemiology/methods ; *Viruses/genetics/isolation & purification ; Metagenomics/methods ; Pandemics ; Genome, Viral ; },
abstract = {Virus surveillance using metagenomic analysis of sequences from wastewater appears to be a promising epidemiological tool for monitoring the spread of viruses in large populations. Its use during the COVID-19 pandemic enabled the monitoring of SARS-CoV-2 circulation without requiring the collection of multiple individual samples. This approach allows both symptomatic and asymptomatic infections to be monitored in a highly cost-effective way. Initially based on PCR detection, the introduction of nucleic acid sequencing has improved this tool by providing more detailed metagenomic information. Experience with COVID-19 pandemics suggests that this epidemiological tool should now be extended to other viruses detectable in wastewater. This review discusses the different methods used, highlighting the challenges of a rapid deployment on an international scale to better understand the global circulation of viral pathogens.},
}

*Wastewater/virology
Humans
*SARS-CoV-2/genetics/isolation & purification
COVID-19/epidemiology/virology
*Molecular Epidemiology/methods
*Viruses/genetics/isolation & purification
Metagenomics/methods
Pandemics
Genome, Viral

@article {pmid40621956,
year = {2025},
author = {Huang, X and Yang, L and Zhou, S and Zhong, L and Xu, G and Bi, M and Yang, X and Su, X and Rillig, MC},
title = {Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70329},
doi = {10.1111/gcb.70329},
pmid = {40621956},
issn = {1365-2486},
support = {42021005//National Natural Science Foundation of China/ ; U23A20145//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo Municipal Science and Technology Innovative Research Team/ ; ANSO-PA-2023-18//Alliance of International Science Organizations/ ; },
mesh = {*Biofilms/growth & development ; *Plastics ; *Nitrogen Cycle ; *Estuaries ; Transcriptome ; Nitrogen/metabolism ; Ecosystem ; Seawater/microbiology ; Bacteria/metabolism/genetics ; Gene Expression Profiling ; Metagenome ; },
abstract = {Biofilms represent a ubiquitous microbial lifestyle that facilitates colonization, symbiosis, and nutrient cycling, shaping environmental chemical transformations. In the Anthropocene, the proliferation of artificial surfaces, particularly plastics, has introduced novel and artificial ecological niches for microbial colonization. However, the biogeochemical potential of biofilms on these emerging artificial substrates remains largely unknown. Here, using [15]N tracing, amplicon, metagenome, and metatranscriptomic sequencing, we explore nitrogen (N) potential biogeochemistry across artificial and natural biofilms as well as the bulk seawater. Our results reveal that plastic biofilms exhibit enhanced N transformation potential, including elevated nitrification (2~45-fold), denitrification (5~44-fold), and N2O production (3~13-fold) rates, compared to natural biofilms and ambient seawater. This functional shift corresponds to distinct microbial community structures, driven by active N-cycling taxa and metabolic pathway reconfigurations on plastic surfaces. We also observe that carbohydrate metabolism pathways, such as glycolysis and the pentose phosphate pathway, were highly expressed in plastic biofilms, with transcriptional levels of glk (encoding glucokinase) and PGK (encoding phosphoglycerate kinase) increased by 6- and 2-fold, respectively. Our findings depict the role of plastic biofilms as active participants in estuarine N cycling and underscore the broader implications of plastic pollution on ecosystem biogeochemistry.},
}

*Biofilms/growth & development
*Plastics
*Nitrogen Cycle
*Estuaries
Transcriptome
Nitrogen/metabolism
Ecosystem
Seawater/microbiology
Bacteria/metabolism/genetics
Gene Expression Profiling
Metagenome