@article {pmid40935888,
year = {2025},
author = {Otani, K and Nakatsu, G and Fujimoto, K and Miyaoka, D and Sato, N and Nadatani, Y and Nishida, Y and Maruyama, H and Ominami, M and Fukunaga, S and Hosomi, S and Tanaka, F and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y},
title = {Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40935888},
issn = {1435-5922},
support = {JP22K08040//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Autoimmune gastritis (AIG) is a chronic atrophic gastritis that affects the gastric corpus, leading to achlorhydria, hypergastrinemia, and a precursor of neuroendocrine tumors (NETs). This study aimed to elucidate the underlying mechanisms of gastric NET formation in AIG by analyzing gastric mucosa-associated microbiota and host tissue-derived metabolite profiles.

METHODS: A total of 19 patients diagnosed with AIG and 12 controls uninfected with Helicobacter pylori underwent gastric mucosal biopsies for microbiome analysis using next-generation sequencing with primers targeting the V3-V4 region of the 16S rRNA gene, and metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry.

RESULTS: Microbiome analysis revealed significantly reduced α-diversity indices in patients with AIG when compared with the control group. β-Diversity analysis showed distinct microbial compositions among the control, NET-negative, and NET-positive groups. The NET-positive group exhibited a significantly higher abundance of Proteobacteria and Fusobacteriota, particularly Haemophilus parainfluenzae, Fusobacterium periodonticum, and Fusobacterium nucleatum, whereas Firmicutes, including Streptococcus salivarius and Veillonella atypica, were significantly decreased compared with the NET-negative group. Metabolome analysis revealed a shift away from glycolysis and tricarboxylic acid cycle activity toward alternative metabolic pathways in patients with AIG. Integrated analysis of gastric microbiota signatures (GMS) and tissue metabotypes demonstrated significant associations among GMS, tissue metabotypes, and NET diagnosis.

CONCLUSIONS: These findings highlight marked shifts in gastric mucosa-associated microbiota profiles in patients with AIG who developed gastric NETs. Tissue-specific metabolic alterations may precede mucosal dysbiosis in patients with AIG and promote the development of a microenvironment implicated in NET formation.},
}

@article {pmid40935532,
year = {2025},
author = {Webster, AM and Triumph, Z and Wei, B and Martin, RM and Smith, LE and Wilhelm, SW and Cleckner, LB and Razavi, NR and Boyer, GL},
title = {First report of nodularin production by Nostochopsis sp. in a temperate eutrophic lake.},
journal = {Harmful algae},
volume = {149},
number = {},
pages = {102956},
doi = {10.1016/j.hal.2025.102956},
pmid = {40935532},
issn = {1878-1470},
abstract = {Benthic cyanobacteria are understudied in comparison to their planktonic counterparts. Consequently, our understanding of cyanotoxin production in benthic mats remains limited. We detected nodularin-R (NOD-R) in a population of Nostochopsis from Honeoye Lake (New York, United States). Identification as Nostochopsis was supported by morphological (see section 3.1 for a detailed description) and metagenomic analyses. The first metagenome assembled genome of Nostochopsis was drafted and estimated at 99.28 % complete. Cyanotoxin testing of Nostochopsis biomass showed production of NOD-R but not microcystins, anatoxins, or cylindrospermopsins. The complete nodularin synthetase cluster was confirmed in the Nostochopsis genome. To our knowledge, this is the first report of nodularin production, or any cyanotoxin production, by the benthic cyanobacteria Nostochopsis. This is the fourth genus of cyanobacteria reported to produce nodularins.},
}

@article {pmid40935105,
year = {2025},
author = {Zhao, J and Guo, Z and Tang, L and Lu, X and Li, Y and Yang, K},
title = {Dynamic evolution of antibiotic resistance risk in sewage sludge-amended soil during crop growth: a field-based metagenomic perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122799},
doi = {10.1016/j.envres.2025.122799},
pmid = {40935105},
issn = {1096-0953},
abstract = {Sewage sludge, a ubiquitous by-product of wastewater treatment, accumulates globally. Land application, a prominent waste valorization strategy, inadvertently disseminates the sludge antibiotic resistome into ecosystems, threatening ecological security and public health. Risk assessment of antibiotic resistance (AR) during sludge land application is urgently needed. Herein, we conducted a field study by planting three crops in sludge-amended soil, and monitoring the dynamic evolution of AR risk throughout their growth cycles. Metagenomic sequencing assessed antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factors (VFs), and their co-occurrence. Sludge amendment exerted persistent, yet largely recoverable, impacts on soil microbial community and the resistome. The resulting AR risk evolution was nonlinear and fluctuating, dominated by soil microbial community reconstruction. Given the differences in crop edible parts, growth periods of crops, complex AR risk dynamics, and external factors like weather, we propose a time-sensitive control strategy targeting critical risk windows. This strategy aims to mitigate AR risk under the "One Health" paradigm for sustainable sludge land application.},
}

@article {pmid40935093,
year = {2025},
author = {Marangi, M and Palladino, G and Valzano, F and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M and Arena, F},
title = {Genetic characterization of enteric protozoan microorganisms in newly arrived migrants in Italy and correlation with the gut microbiome layout.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102901},
doi = {10.1016/j.tmaid.2025.102901},
pmid = {40935093},
issn = {1873-0442},
abstract = {The prevalence of the enteric protozoan microorganisms, its genetic characterization as well as its associated gut microbiome has been molecularly and 16S metagenomic characterized in a cohort of newly arrived migrants in Italy from African countries over the period 2022-2024. Out of 199 individuals, 92 (46.2 %) were found to be carrier of protozoan microorganisms with a higher prevalence of Blastocystis sp. (15.5 %), followed by Giardia duodenalis (12.6 %), Dientamoeba fragilis (7.5 %), Cryptosporidium parvum (6.5 %), and Entamoeba histolytica (4 %). Subtypes ST1, ST2 and ST3 were genetically characterized for Blastocystis sp., assemblages A and B for G. duodenalis, subtypes families IIa and IIc for C. parvum and genotype 1 for D. fragilis. High prevalence of Butyrivibrio, Lachnospiraceae UGC 10 and Paraprevotella, were identified in the protozoan non-carrier individual group. This work shed lights on the circulation of enteric protozoan microorganisms in apparently healthy migrants from African countries and the potential relationship with the host-microbiome composition. Moreover, these results give an overview of the importance of microbiological surveys among migrants and asylum seekers arriving to hosting countries in order to evaluate the reliable risk of several microorganisms introduction though migration. Ultimately, further investigation of interplays between the intestinal microbiota and protozoan microorganisms will provide new approaches in the diagnosis and treatment of intestinal infections.},
}

@article {pmid40934662,
year = {2025},
author = {Zhang, J and Zhao, J and Gao, Z and Ding, X and Li, Y and Shi, J and Zhao, D and Shi, L and Bi, X and Miao, Y},
title = {An effective method for enhancing metabolic activity of anammox bacteria: Accelerating heme biosynthesis by glutamate.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127301},
doi = {10.1016/j.jenvman.2025.127301},
pmid = {40934662},
issn = {1095-8630},
abstract = {Enhancing and maintaining anammox bacteria (AnAOB) activity is a major challenge for application of anammox process, which could be achieved by accelerating heme biosynthesis. Heme is crucial for electron transport and redox reaction and its biosynthesis may be promoted by glutamate. To explore the effect of glutamate on AnAOB activity, four parallel anammox systems (named R0, R1, R2, and R3) with different concentrations of glutamate (0, 0.125, 0.25, and 0.5 mM) were set up. The results showed that AnAOB activities and nitrogen removal efficiencies of R1 and R2 were about 58.3 % and 48.8 %, and 80.5 % and 64.1 % higher than that of R0, respectively, whereas excessive glutamate (0.5 mM) deteriorated the system performance. Moreover, heme content, activities of hydrazine synthase and hydrazine dehydrogenase, and sludge particle size in R1 and R2 were significantly higher than R0. Metagenomic sequencing analysis further revealed that the moderate amount of glutamate (0.125 mM, 0.25 mM) could effectively improve AnAOB activity by enhancing heme biosynthesis, accelerating electron transport and energy synthesis, and promoting the aggregation of microorganisms. This study provides an effective method for enhancing AnAOB metabolic activity and clarifies the underlying mechanism.},
}

@article {pmid40934587,
year = {2025},
author = {Wang, F and Xiong, J and Lin, L and Xu, W and Liu, L and Yang, S and Cao, W},
title = {Antibiotic resistance genes link to nitrogen removal potential via co-hosting preference for denitrification genes in a subtropical estuary.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139801},
doi = {10.1016/j.jhazmat.2025.139801},
pmid = {40934587},
issn = {1873-3336},
abstract = {Estuaries are important sinks for antibiotic resistance genes (ARGs) and hotspots of nitrogen cycling. However, the interactions between nitrogen cycling functional genes (NCGs) and ARGs in estuaries remain poorly understood. This study employed metagenomic sequencing to explore potential interactions between nitrogen, ARGs, and microbial-mediated nitrogen cycling processes in estuarine waters. Results showed beta-lactam was the predominant subtype of ARGs (407 species), and sul1 exhibited the highest relative abundance (4.11 %). Nitrogen was the important factor driving spatiotemporal variation of ARGs, promoting their proliferation and dispersal by enhancing microbial growth and reproduction. Network analysis revealed wide and complex correlations between ARGs and NCGs. Nitrate-reducing bacteria were the main hosts of ARGs, and the greatest number of potential hosts were those involved in assimilatory nitrate reduction to ammonium (17.44 %), dissimilatory nitrate reduction to nitrite (16.59 %), and denitrification (15.71 %). Compared with dissimilatory nitrite reduction to ammonium genes, ARGs prefer to form co-hosting relationships with denitrification genes, indicating that ARGs had a stronger effect on the nitrogen removal potential than on the nitrogen retention potential. This study highlights the complex interactions between ARGs and nitrogen cycling processes in subtropical estuaries, and will provide a scientific base for couple management strategies of nitrogen and antibiotic pollution.},
}

@article {pmid40934284,
year = {2025},
author = {Lucas, A and Schäffer, DE and Wickramasinghe, J and Auslander, N},
title = {kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013470},
doi = {10.1371/journal.pcbi.1013470},
pmid = {40934284},
issn = {1553-7358},
abstract = {Shotgun metagenomic sequencing can determine both the taxonomic and functional content of microbiomes. However, functional classification for metagenomic reads remains highly challenging as protein mapping tools require substantial computational resources and yield ambiguous classifications when short reads map to homologous proteins originating from different bacteria. Here we introduce kMermaid for the purpose of uniquely mapping bacterial short reads to taxa-agnostic clusters of homologous proteins, which can then be used for downstream analysis tasks such as read quantification and pathway or global functional analysis. Using a nested hash map containing amino acid k-mer profiles as a model for protein assignment, kMermaid achieves the sensitivity of popular existing protein mapping tools while remaining highly resource efficient. We evaluate kMermaid on simulated data and data from human fecal samples as well as demonstrate the utility of kMermaid for classifying reads originating from new, unseen proteins. kMermaid allows for highly accurate, unambiguous and ultrafast metagenomic read assignment into protein clusters, with a fixed memory usage, and can easily be employed on a typical computer.},
}

@article {pmid40933810,
year = {2025},
author = {Tigrero-Vaca, J and Villavicencio-Vásquez, M and Coronel, J and Cevallos-Cevallos, JM},
title = {Multi-platform metagenomic characterization of the microbial community during spontaneous cacao fermentation.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1630515},
doi = {10.3389/fbioe.2025.1630515},
pmid = {40933810},
issn = {2296-4185},
abstract = {Cacao fermentation is a spontaneous process in which microorganisms play a key role in the development of distinctive chocolate flavors. The microbiota acting during cacao fermentation has been routinely characterized by culture-based techniques and next-generation sequencing using Illumina's platform. However, the potential of in situ sequencing technologies to monitor microbial dynamics during cacao fermentation has not been assessed. In this study, cacao bean samples were collected at 0, 24, 48, 72, and 96 h after the start of the fermentation. Total DNA was extracted, and sequencing libraries were prepared for further sequencing using Illumina's and Nanopore's MinION sequencing platforms. Additionally, microorganisms were isolated using traditional culture-based methods. At the order and family taxonomic levels, Illumina and MinION sequencing revealed similar microbial composition in the samples. However, discrepancies were observed at the genus and species levels. In this sense, Illumina sequencing revealed a predominance of Limosilactobacillus, Levilactobacillus, Lactiplantibacillus, Frauteria, Saccharomyces and Acetobacter, while MinION sequencing showed a prevalence of Escherichia, Salmonella, Liquorilactobacillus, Lentilactobacillus, Acetobacter and Komagataeibacter during fermentation. The three methods were consistent in detecting the major yeast (Saccharomyces cerevisiae), lactic acid bacteria (Lactiplantibacillus plantarum, Leuconostoc pseudomesenteroides, Levilactobacillus brevis, Liquorilactobacillus mali, and Lentilactobacillus hilgardii) and acetic acid bacteria (Acetobacter pasteurianus) species during fermentation. Functional analysis based on a hybrid assembly of Illumina and MinION data revealed the roles of lactic acid bacteria and acetic acid bacteria in the metabolism of carbohydrates, amino acids, and secondary metabolites such as polyphenols and theobromine. This study represents the first report assessing the applicability of MinION sequencing for the characterization of microbial populations during cacao fermentation, demonstrating its potential as a complementary tool to established sequencing platforms.},
}

@article {pmid40933579,
year = {2025},
author = {Lin, B and Zhong, D and Qin, L and Liu, Q and Wu, L and Wang, B and Wang, K and Lu, X and Deng, S and Pan, L},
title = {Application of metagenomics sequencing to diagnose paralytic rabies with stroke-like onset: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1639262},
doi = {10.3389/fmed.2025.1639262},
pmid = {40933579},
issn = {2296-858X},
abstract = {BACKGROUND: Rabies is an acute zoonotic infectious disease caused by infection with a virus of the genus Lyssavirus. We report a case of paralytic rabies with a stroke-like onset, which was diagnosed using metagenomics next-generation sequencing (mNGS).

CASE PRESENTATION: A 58-year-old man was admitted to the hospital with "numbness and weakness in the right upper extremity for 2 days, aggravated for 1 day." Twenty-five days before his admission, the patient was bitten on the back of right hand by an unvaccinated domestic dog, resulting in a penetrating injury, classified as grade III according to the rabies exposure classification method. Following admission, the patient exhibited rapidly progressive stroke symptoms, and on the second day, he suffered a sudden respiratory arrest accompanied by a weakened heartbeat and a decreased heart rate. He was treated with emergency tracheal intubation, cardiopulmonary resuscitation, and dehydration to lower cranial pressure.

RESULTS: The patient's condition deteriorated rapidly after admission. A lumbar puncture was conducted on the morning of the second day of admission, and cerebrospinal fluid (CSF) was sent to Weiyuan Genetic Laboratories (Guangzhou, China) for rabies virus identification. The patient died on the third day of admission. Pathogen capture macro-genomics was performed on CSF using an Illumina NextSeq second-generation sequencer, and nine rabies virus sequences, which shared more than 99% nucleotide homology with the genome sequence of the rabies virus Rabies lyssavirus (NCBI accession no. MN175989.1), were detected. The Q30 ratio of this test was 98.3%.

CONCLUSION: Compared to polymerase chain reaction (PCR) and direct fluorescent antibody (DFA) test, mNGS shortens the diagnostic window and improves sensitivity to low-virus or seronegative manifestations by simultaneously capturing and sequencing the entire pathogen genome. The mNGS technology can effectively aid in the diagnosis of paralytic rabies.},
}

@article {pmid40933366,
year = {2025},
author = {Gutleben, J and Podell, S and Mizell, K and Sweeney, D and Neira, C and Levin, LA and Jensen, PR},
title = {Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.},
journal = {PNAS nexus},
volume = {4},
number = {9},
pages = {pgaf260},
doi = {10.1093/pnasnexus/pgaf260},
pmid = {40933366},
issn = {2752-6542},
abstract = {Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of "anthropogenic" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.},
}

@article {pmid40933132,
year = {2025},
author = {Li, X and Lu, H},
title = {Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626002},
doi = {10.3389/fmicb.2025.1626002},
pmid = {40933132},
issn = {1664-302X},
abstract = {The human gastrointestinal tract (GIT) is inhabited by a heterogeneous and dynamic microbial community that influences host health at multiple levels both metabolically, immunologically and via neurological pathways. Though the gut microbiota-overwhelmingly Bacteroidetes and Firmicutes-has essential functions in nutrient metabolism, immune regulation, and resistance to pathogens, its dysbiosis is likewise associated with pathologies, such as inflammatory bowel disease (IBD), obesity, type 2 diabetes (T2D), and neurodegenerative diseases. While conventional metagenomic techniques laid the groundwork for understanding microbial composition, next-generation enhanced metagenomic techniques permit an unprecedented resolution in exploring the functional and spatial complexity of gut communities. Advanced frameworks such as high-throughput sequencing, bioinformatic and multi-omics technologies are expanding the understanding of microbial gene regulation, metagenomic pathways, and host-microbe communication. Beyond taxonomic profiling, they map niche-specific activities of gut microbiota along a dichotomy of facultative mutualism, evidenced by relations of beneficial symbionts, represented here by Enterobacteriaceae. In this review, we critically consider the latest approaches (e.g., long-read sequencing, single-cell metagenomics and AI-guided annotation) that mitigate biases stemming from DNA extraction, sequencing depth and functional inference.},
}

@article {pmid40933127,
year = {2025},
author = {Akhtar, MF and Wenqiong, C and Umar, M and Changfa, W},
title = {Biochemical properties of lactic acid bacteria for efficient silage production: an update.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1581430},
doi = {10.3389/fmicb.2025.1581430},
pmid = {40933127},
issn = {1664-302X},
abstract = {Ensiling, a microbial-driven process employed for preserving fresh forage in both bio-refineries and animal production, triggers significant biochemical transformations. These changes have spurred the exploration of novel silage additives, with a particular emphasis on the potential of microbial strains that exhibit superior biopreservation capabilities. Lactic acid bacteria (LAB) species have gained widespread recognition for their diverse applications as additives in the fermentation of crops and forage biomasses during ensiling. Nonetheless, recent variations in silage quality might be attributed to a lack of comprehensive information on the gene expression and molecular mechanisms of the microbiota involved in silage production. Contemporary research efforts have been directed toward uncovering nutrient-rich animal feed solutions through enhanced LAB inoculants. This review aims to shed light on the role of LAB inoculants in silage production and the modern biotechnological methods, including metabolomics, proteomics, metagenomics, genomics, transcriptomics, and genetic manipulation. These powerful tools are instrumental in the identification, enhancement, and development of high-performance LAB strains. Additionally, the review outlines emerging trends and prospective developments in LAB advancement for the enhancement of silage, which holds significant promise for breakthroughs in sustainable agriculture and improved animal feed production.},
}

@article {pmid40933007,
year = {2025},
author = {Le, J and Hakimjavadi, H and Parsana, R and Chamala, S and Michail, S},
title = {Fecal Microbiota Transplantation Induces Sustained Gut Microbiome Changes in Pediatric Ulcerative Colitis: A Combined Randomized and Open-Label Study.},
journal = {Gastro hep advances},
volume = {4},
number = {10},
pages = {100741},
doi = {10.1016/j.gastha.2025.100741},
pmid = {40933007},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising tool to modulate the gut microbiome in pediatric ulcerative colitis (UC). We investigated the long-term impact of FMT on the gut microbiome and identified microbial signatures associated with disease severity and clinical outcomes.

METHODS: This study combined a randomized, double-blind trial comparing FMT to autologous placebo with an open-label extension to assess FMT's effects on the gut microbiome in pediatric UC patients over 48 weeks. Stool samples were collected at baseline and postintervention, and clinical response was evaluated using the Pediatric Ulcerative Colitis Activity Index. Shotgun metagenomic sequencing characterized the fecal microbiome's composition and functional potential. Taxon set enrichment analysis identified microbial taxon sets associated with UC and FMT.

RESULTS: FMT induced significant, sustained increases in gut microbial diversity over 48 weeks. Key changes included decreases in Klebsiella oxytoca and increases in Coprobacter fastidiosus post-FMT. Microbial signatures were associated with disease severity, including increased indole producers and decreased mucin degraders in mild UC compared to remission. Patients with clinical improvement post-FMT showed decreased Fusobacterium nucleatum and Veillonella parvula. Klebsiella pneumoniae and Klebsiella variicola decreased after open-label FMT.

CONCLUSION: FMT induces sustained changes in the pediatric UC gut microbiome, with distinct microbial signatures associated with disease severity and clinical outcomes. However, the high autologous placebo response rate underscores the need for further research to elucidate the mechanisms underlying FMT and placebo responses. Our study provides insights into the gut microbiome's role in pediatric UC, laying the foundation for developing personalized microbiome-targeted therapies. ClinicalTrials.gov number, NCT02291523.},
}

@article {pmid40932661,
year = {2025},
author = {Sachdeva, S and Sarethy, IP},
title = {Antibiotic resistance profiling in an ancient Indian sulfur-rich stepwell: a case study of Gandhak-ki-Baoli.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {895},
pmid = {40932661},
issn = {1573-4978},
mesh = {India ; *Sulfur/analysis ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; Metagenome ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, increasingly recognized to emerge not only from clinical and agricultural sources but also from natural and historical environments. Despite their ecological and cultural significance, ancient water bodies such as stepwells remain largely unexplored in the context of environmental resistomes.

METHOD: This study investigates AMR in Gandhak-ki-Baoli, an ancient sulfur-rich stepwell located in Delhi, India. A combined methodological approach involving culture-based microbial isolation and metagenomics sequencing was used to identify bacterial taxa and associated antibiotic resistance genes (ARGs).

RESULTS: The analysis revealed a diverse microbial community harboring ARGs, including those conferring multidrug resistance. Several genes showed evidence of co-selection mechanisms with heavy metals and biocides. The stepwell's unique environmental conditions characterized by stagnant water, low light, variable moisture, and limited nutrients that likely contribute to the persistence and potential horizontal transfer of resistance traits.

CONCLUSIONS: This is the first study to profile AMR in a historical stepwell, revealing the presence of a complex environmental resistome. The findings suggest that ancient water structures like stepwells can act as hidden reservoirs of AMR. These insights highlight the need to include such environments in future AMR surveillance efforts to better understand the broader ecological landscape of resistance.},
}

India
*Sulfur/analysis
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Metagenomics/methods
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Water Microbiology
Metagenome

@article {pmid40932534,
year = {2025},
author = {Wang, F and Xia, J and Sun, J},
title = {Microbiological diagnostics and their impact on hematology nursing.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40932534},
issn = {1874-9356},
abstract = {Microbiological diagnostics have become a foundational element in hematology nursing, where early and accurate infection detection is vital for immunocompromised patients. This review explores how both traditional techniques, such as microscopy, culture, and antigen detection, and emerging technologies, including polymerase chain reaction (PCR), metagenomic next-generation sequencing (mNGS), and MALDI-TOF mass spectrometry, contribute to clinical decision-making and infection control. These tools not only accelerate pathogen identification and resistance profiling but also support precision medicine approaches tailored to hematologic patient needs. The expanding role of hematology nurses is emphasized, particularly in diagnostic stewardship, specimen collection, result interpretation, and coordination of infection management strategies. Educational interventions have proven effective in reducing contamination rates and improving antimicrobial targeting. Furthermore, novel point-of-care platforms, such as CRISPR-based diagnostics and AI-enhanced digital PCR, are shifting diagnostic capabilities closer to the bedside, redefining nursing workflows and responsibilities. These innovations empower nurses to engage in real-time clinical decisions, monitor therapy responses, and enhance patient education regarding diagnostic procedures and infection risks. However, gaps remain in microbiology-related training and confidence among nurses, highlighting the need for integrated educational curricula and interdisciplinary collaboration. By aligning technological advancements with frontline nursing practice, microbiological diagnostics not only optimize patient outcomes but also elevate the role of nurses as key stakeholders in infection prevention, antimicrobial stewardship, and evidence-based care. This review underscores the urgent need to equip hematology nurses with the skills and tools necessary to adapt to the rapidly evolving diagnostic landscape in order to support safe, timely, and personalized healthcare delivery.},
}

@article {pmid40932289,
year = {2025},
author = {Zhao, Y and Du, L and Song, J and Sun, W and Chen, Y and Yu, X and Huang, H and Huang, G and Huang, E and Wang, N and An, S and Ai, L and Chen, P},
title = {Hierarchical integration of mNGS, PCR, and other conventional methods for precision TB diagnostics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0193125},
doi = {10.1128/spectrum.01931-25},
pmid = {40932289},
issn = {2165-0497},
abstract = {UNLABELLED: This study systematically compared the diagnostic accuracy of seven assays for detecting the Mycobacterium tuberculosis complex, including metagenomic next-generation sequencing (mNGS), droplet digital polymerase chain reaction, real-time quantitative polymerase chain reaction, EasyNAT MTC, GeneXpert MTB/RIF, interferon-gamma release assay (IGRA), and acid‒fast staining (AFS). We try to select appropriate combinations of tuberculosis (TB) detection methods for regions with varying levels of medical resources, based on sensitivity, cost-effectiveness, and operational feasibility. A retrospective analysis was conducted on 141 samples collected from patients with suspected active TB at The First Affiliated Hospital of Sun Yat-sen University between April 2022 and April 2024. Among these samples, there were 100 cases assigned to the case group and 41 cases to the control group, based on the tuberculosis diagnostic criteria. Historical data for Xpert, IGRA, and AFS were collected, and parallel experiments using mNGS, droplet digital PCR (ddPCR), real-time quantitative polymerase chain reaction (RT-qPCR), and EasyNAT were conducted on all samples. Diagnostic performance was evaluated by comparing it with the final clinical diagnoses. Sensitivity, specificity, positive predictive value, negative predictive value, and receiver operating characteristic (ROC) curve analysis were conducted, along with DeLong tests for statistical comparison. Compared with the final clinical diagnosis, mNGS demonstrated the highest sensitivity (100%), followed by IGRA (79.2%), EasyNAT (79.1%), RT-qPCR (78.0%), ddPCR (75.8%), Xpert (75.3%), and AFS (16.7%). The specificity was 100% for both Xpert and AFS, followed by ddPCR (97.6%), RT-qPCR (95.1%), EasyNAT (92.7%), IGRA (72.7%), and mNGS (75.6%). ROC analysis revealed a significantly greater area under the ROC curve for mNGS (0.878) than for ddPCR (0.817, P = 0.031). DeLong tests revealed statistically significant differences in diagnostic performance between mNGS and ddPCR (P < 0.05) and between IGRA and AFS (P < 0.01). mNGS uniquely identified the pathogens involved in co-infection and quantified pathogen-specific sequencing reads. Through a comprehensive evaluation of the diagnostic efficacy, cost-effectiveness, and timeliness of tuberculosis detection methods, we propose corresponding combinations of TB testing approaches for regions with different healthcare resources. For undeveloped regions with limited resources, a combination of AFS +EasyNAT + chest X-ray is recommended. Primary care facilities may additionally employ IGRA + RT-qPCR. Intermediate-level hospitals can incorporate Xpert MTB/RIF for drug resistance testing, while tertiary hospitals or specialized centers should, on the basis of these fundamental tests, utilize mNGS for diagnosis and ddPCR for therapeutic monitoring in patients with complex mixed infections.

IMPORTANCE: This study is the first to comprehensively evaluate the diagnostic efficacy, cost-effectiveness, and timeliness of seven TB detection methods in a single-center cohort. Our findings provide actionable solutions for optimizing TB diagnostics in diverse healthcare ecosystems, aligning with the WHO's End TB Strategy to ensure equitable access to rapid diagnostics.},
}

@article {pmid40931802,
year = {2025},
author = {Gernert, JA and Klein, M and Schöberl, F and Müller, KJ and Schmidbauer, ML and Forbrig, R and Roeber, S and Herms, J and Terpolilli, N and Milakovic Obradovic, M and Graf, A and Dächert, C and Keppler, OT and Münchhoff, M and Dimitriadis, K},
title = {Severe course of tick-borne encephalitis (TBE) in a patient with relapsing multiple sclerosis (MS) treated with ocrelizumab.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585251369425},
doi = {10.1177/13524585251369425},
pmid = {40931802},
issn = {1477-0970},
abstract = {Description of a patient with multiple sclerosis (MS) who underwent immunotherapy with ocrelizumab and suffered a severe course of tick-borne encephalitis (TBE): A 33-year-old man presented with acute cerebellitis with tonsillar herniation. The initial suspected diagnosis of TBE was confirmed after a significant diagnostic delay, likely caused by negative serological testing due to B-cell depletion from ocrelizumab treatment for underlying MS. TBE diagnosis was made using polymerase chain reaction (PCR) and oligo-hybrid capture metagenomic next-generation sequencing (mNGS) of cerebral spinal fluid and brain biopsy samples which yielded a near-full length TBE Virus (TBEV) genome.},
}

@article {pmid40931531,
year = {2025},
author = {Gasparini, J},
title = {Targeted 'infectiosome' for disease ecology: A new tool to answer old questions.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70130},
pmid = {40931531},
issn = {1365-2656},
abstract = {Research Highlight: Bralet, T., Aaziz, R., Tornos, J., Gamble, A., Clessin, A., Lejeune, M., Galon, C., Michelet, L., Lesage, C., Jeanniard du Dot, T., Desoubeaux, G., Guyard, M., Delannoy, S., Moutailler, S., Laroucau, K. and Boulinier, T. (2025). High-throughput microfluidic real-time PCR as a promising tool in disease ecology. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.70088. Disease ecology aims to understand the causes and consequences of the maintenance and transmission of pathogenic infectious agents. A crucial step in studying disease ecology is identifying the 'infectiosome', which I define as all infectious agents circulating among individuals, populations and the community of a given ecosystem. In a recent study, Bralet et al. (2025) propose a new, cheap and adaptable toolkit for determining a targeted 'infectiosome', which appears very useful in disease ecology approaches: high-throughput microfluidic real-time PCR (Htrt PCR). This method is a good alternative to costly metagenomic approaches and consists of running several dozen PCRs from a single tissue sample. This technique enables screening, from a single sample, the presence of dozens of targeted infectious agents: the targeted 'infectiosome', allowing one to answer several questions. For example, Bralet et al. (2025) applied this method to 274 seabirds and 80 mammals samples collected from the Southern Ocean islands and detected pathogenic infectious agents in new locations. The results also show that some species are potential 'reservoirs' of several infectious agents in this ecosystem. This method is really promising and can be easily adapted and used to test different hypotheses in disease ecology at the scales of the population and the community in other ecosystems, such as the urban ecosystem.},
}

@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}

*Metagenome
*Metagenomics/methods
*Databases, Genetic
*Microbiota

@article {pmid40931024,
year = {2025},
author = {Tan, MH and Bangre, O and Rios-Teran, CA and Tiedje, KE and Deed, SL and Zhan, Q and Rasyidi, F and Pascual, M and Ansah, PO and Day, KP},
title = {Metagenomic complexity of high, seasonal transmission of Plasmodium spp. in asymptomatic carriers in Northern Sahelian Ghana.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {386},
pmid = {40931024},
issn = {2730-664X},
support = {R01-AI149779//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01-AI149779//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {BACKGROUND: Mixed-species, mixed-strain plasmodia infections are known to occur in humans in malaria endemic areas. It may be surprising that to date, the extent of this complexity has not been systematically explored in high-burden countries of sub-Saharan Africa, especially in the reservoir of asymptomatic infections in all ages, which sustains transmission.

METHODS: Here we take a metagenomic lens to these infections by sampling variable blood volumes from 188 afebrile residents living in high, seasonal transmission in Northern Sahelian Ghana. We estimated multiplicity of infection for different Plasmodium spp. through genotyping of antigens and microsatellites. We further defined 'metagenomic complexity' as a measure of overall within-host complexity across the combination of species and strains.

RESULTS: We show that prevalence of Plasmodium spp. and inter-/intra-species complexity is significantly higher in larger blood volumes from these individuals. Overall, malaria infections display high levels of metagenomic complexity comprising single-, double-, and triple-species infections with varying levels of intra-species complexity for P. falciparum, P. malariae, P. ovale curtisi, and P. ovale wallikeri. We also report a subset of individuals with highly-complex infections that cannot be explained by age or location. The implications of these findings to malaria epidemiology and control are illustrated by a geographic scaling exercise to district and region levels in northern Ghana.

CONCLUSIONS: Our metagenomic investigation underscores the need to more sensitively measure within-host Plasmodium spp. complexity in asymptomatic carriers of infection. This will optimise strategies for malaria surveillance and control.},
}

@article {pmid40930091,
year = {2025},
author = {Minich, JJ and Allsing, N and Din, MO and Tisza, MJ and Maleta, K and McDonald, D and Hartwick, N and Mamerto, A and Brennan, C and Hansen, L and Shaffer, J and Murray, ER and Duong, T and Knight, R and Stephenson, K and Manary, MJ and Michael, TP},
title = {Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.08.020},
pmid = {40930091},
issn = {1097-4172},
abstract = {The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.},
}

@article {pmid40929977,
year = {2025},
author = {Han, F and Guo, Y and Zhao, C and Zhang, W and Zhang, M and Zhou, W},
title = {Halophilic heterotrophic ammonia assimilation biosystem shows stronger resilience and decreased ARGs abundance under sulfamethoxazole gradient stress compared with halophilic nitrification biosystem.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139749},
doi = {10.1016/j.jhazmat.2025.139749},
pmid = {40929977},
issn = {1873-3336},
abstract = {Differences of niche and nitrogen metabolism between halophilic nitrification (AN) and heterotrophic ammonia assimilation (HAA) biosystems determine microbiome resilience and antibiotic resistance genes (ARGs) transfer under antibiotic stress. However, the underlying mechanism of this difference remains unclear. This study compared the bioresponses and ARGs characteristics of the two biosystems under sulfamethoxazole (SMX) stress. Results revealed that both biosystems maintained above 90 % NH4[+] -N and 95 % SMX removal efficiencies at SMX concentrations below 1 mg/L. However, exposure to 5 mg/L SMX impaired both NH4[+]-N and SMX removal efficiencies. HAA biosystem exhibited stronger robustness and resilience than the AN biosystem under SMX stress. The microbial products synthesis, extracellular protein structure, and extracellular electron transfer in both biosystems displayed distinct responses to SMX. Metagenomic results revealed SMX shock decreased the abundance of ammonia-oxidizing bacteria and ammonia-monooxygenase gene in the AN biosystem, while the rapid turnover of heterotrophic microorganisms and the flexibility of ammonia assimilation genes maintained the HAA function in the HAA biosystem. Furthermore, SMX stress induced ARGs enrichment in the AN biosystem, whereas the abundance and diversity of ARGs in the HAA biosystem decreased under SMX stress. These findings highlighted the potential of novel HAA biosystem for antibiotics degradation and ARGs control.},
}

@article {pmid40929972,
year = {2025},
author = {Liu, K and Wang, X and Li, F and Tao, J and Weng, CH and Hu, Q and Kang, D and Luo, Z and Tang, Z and Liu, N and Qiu, J},
title = {Metagenomic characterization of antibiotic resistance genes and human bacterial pathogens in groundwater from agricultural, landfill, and hazardous waste disposal sites (HWDS) sources: Drivers, risks, and source tracking.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139803},
doi = {10.1016/j.jhazmat.2025.139803},
pmid = {40929972},
issn = {1873-3336},
abstract = {Agricultural sources, landfills, and hazardous waste disposal sites (HWDS) are major hotspots for the spread of groundwater antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, there is a lack of systematic understanding regarding the environmental behavior of groundwater ARGs, the pathogenic risks of HBPs, and the relative contribution mechanisms of different sources, presenting critical scientific challenges for developing targeted groundwater pollution control strategies. To address this, this study collected 26 groundwater metagenomic samples to characterize the composition, influencing factors, and health risks of ARGs and HBPs near key ARG reservoirs, and constructed a source-tracking indicator system. The research identified 16 clinically critical high-risk ARGs (e.g., tetM, sul1) and 14 priority HBPs (e.g., Escherichia coli, Klebsiella pneumoniae) associated with severe human diseases and high transmissibility. Screening ARG source-specific indicators demonstrated high accuracy in predicting contributions from artificially mixed sources (prediction errors < 4 %). Validation with real groundwater samples showed that landfills contributed more significantly to groundwater ARGs pollution than other sources. This study deepens our understanding of antibiotic resistance risks in groundwater near key ARG reservoirs and provides a robust framework for tracing ARGs in complex groundwater environments by integrating microbe-gene-environment interactions across multiple pollution sources.},
}

@article {pmid40929881,
year = {2025},
author = {Liu, Y and Li, K and Xu, J and Shen, W and Li, Y and Ma, J and Wang, T and Liu, J and Li, T and Zhang, X and Tian, W and Tian, J and Wang, H and Zhang, X},
title = {Alpha-linolenic acid ameliorates T2DM via reshaping gut-liver axis and inflammatory GPR120-NF-κB/NLRP3 pathway in mouse and rat models.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {147},
number = {},
pages = {157214},
doi = {10.1016/j.phymed.2025.157214},
pmid = {40929881},
issn = {1618-095X},
abstract = {BACKGROUND: The gut-liver axis, pivotal in managing glucose balance and insulin responsiveness, is central to the development of type 2 diabetes mellitus (T2DM). Research has highlighted the regulatory effects of dietary alpha-linolenic acid (ALA), but it remains unclear how ALA modulates gut microbiota and liver inflammation in T2DM.

PURPOSE: This study aimed to systematically investigate ALA's influence on liver inflammation, intestinal barrier integrity, gut microbial composition, and metabolic homeostasis in T2DM, with a focus on the underlying molecular mechanisms.

STUDY DESIGN: A dual-model approach was employed using both db/db mouse model and the SCZ/NA-induced T2DM rat model to ensure robust species and model validation.

METHODS: Animals received oral ALA supplementation, followed by assessments of glucose tolerance, insulin sensitivity, hepatic histology, and inflammatory markers. Intestinal barrier function, permeability, and systemic LPS levels were evaluated. Mechanistic analysis focused on the GPR120-NF-κB/NLRP3 signaling pathway. Multi-omics profiling including fecal metagenomics, SCFA quantification, and plasma metabolomics were conducted to assess gut microbiota and host metabolic responses.

RESULTS: Our results revealed that ALA therapy significantly mitigated insulin resistance and glucose intolerance in db/db mice. Histopathological analysis revealed a decrease in hepatic steatosis following ALA administration, alongside a reduction in inflammatory markers indicative of T2DM. Importantly, our findings demonstrated that ALA mitigates liver inflammation by inhibiting the NF-κB/NLRP3 pathway, possibly via its interaction with GPR120. Beyond this, augmenting ALA bolstered intestinal integrity, minimized permeability, curbed lipopolysaccharide leakage, and suppressed pro-inflammatory cytokine expression within the intestines. Significantly, an integrated multi-omics investigation, encompassing fecal metagenomic sequencing, SCFA evaluation, and plasma non-targeted metabolomics, disclosed a potent correlation between ALA's hypoglycemic efficacy and the modulation of gut microbial community structure, elevation of SCFA synthesis, and enhancement of metabolic signatures.

CONCLUSION: Our study's initial insights indicated that dietary ALA modulates inflammation and metabolism in T2DM via the gut-liver axis, specifically through the GPR120-NF-κB/NLRP3 pathway. This elucidates ALA's dual function in reshaping the gut microbiota and combating systemic inflammation, positioning it as a potentially efficacious dietary component for managing T2DM.},
}

@article {pmid40929831,
year = {2025},
author = {Liu, F and Yang, B and Han, T and Li, F and Wang, L and Xu, H},
title = {Metagenomic and Micro-CT insights into Fe(III)-modulated extracellular polymeric substances driving anammox granulation and enhancement of nitrogen removal.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127283},
doi = {10.1016/j.jenvman.2025.127283},
pmid = {40929831},
issn = {1095-8630},
abstract = {Multivalent cations are commonly employed to accelerate sludge aggregation and granulation, yet they often compromise intragranular mass transfer and diminish microbial activity. Here, the effect of Fe(III) dosing on granule formation and anammox-driven nitrogen removal over a 110-day continuous operation was investigated. Fe(III) supplementation enhanced interactions with extracellular polymeric substances (EPS), transforming flocculent biomass into highly porous granules and yielding a 67.9 % increase in specific anammox activity (SAA). During the first 30 days of Fe(III) dosing, the Zeta potential shifted from -12.0 to -9.3 mV and EPS content surged from 32.8 mg/g VSS to 49.0 mg/g VSS, accelerating primary floc aggregation. Subsequently, the protein-to-polysaccharide ratio of EPS escalated from 1.7 to 5.3, reflecting a transition from a carbohydrate-rich, hydrophilic gel to a protein-dominated, hydrophobic network that facilitated granulation. Micro-computed tomography revealed that smaller (1.5 mm) granules exhibited dense architectures, whereas larger (2.5 mm) granules developed internal cavities as a result of mass transfer limitations, approaching structural fragmentation. Metagenomic analysis showed that Fe(III) upregulated pathways for hydrophobic amino acids (e.g., isoleucine, leucine, valine) synthesis and downregulated polysaccharide biosynthesis, thereby increasing EPS hydrophobicity and promoting granulation. The observed SAA enhancement was linked to Fe(III)-dependent activation of iron-containing enzymes (e.g., hzs ABC), cytochrome c maturation, and Fe-S cluster assembly. Concurrently, the relative abundance of Ca. Kuenenia rose from 14.1 % during aggregation to 18.6 % after sludge granulation. This work elucidates the mechanism of Fe(III)-EPS-mediated granulation and offers a sustainable strategy to reconcile structural integrity with metabolic efficiency in metal-driven anammox wastewater treatment processes.},
}

@article {pmid40929513,
year = {2025},
author = {Bhaya, D and Birzu, G and Rocha, EPC},
title = {Horizontal Gene Transfer and Recombination in Cyanobacteriota.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-100420},
pmid = {40929513},
issn = {1545-3251},
abstract = {Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.},
}

@article {pmid40929468,
year = {2025},
author = {Xiang, Y and Man, X and Zhang, H and Chen, M and Yang, R},
title = {Nitrogen removal efficiency and pathways of the simultaneous nitrification and denitrification process under ultra-low oxygen conditions.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/09593330.2025.2556497},
pmid = {40929468},
issn = {1479-487X},
abstract = {To explore strategies for further reducing aeration energy consumption in the simultaneous nitrification and denitrification (SND) process, an SND reactor was constructed to treat low carbon-to-nitrogen (C/N) ratio domestic wastewater under ultra-low dissolved oxygen (DO) conditions (DO < 0.05 mg·L[-][1]). The effects of hydraulic retention time (HRT) and C/N ratio on nitrogen removal performance were systematically evaluated, and batch experiments were conducted to determine nitrification and denitrification rates. Under influent condition of 50.0 mg·L[-][1] ammonia and a C/N ratio of 2.2, the reactor maintained stable ultra-low DO levels, achieved effluent ammonia concentrations below 5.0 mg·L[-][1], and attained optimal SND efficiencies exceeding 80.0%. Although a shortened HRT destabilised performance, increasing the C/N ratio successfully restored nitrogen removal stability. Nitrification and denitrification rates ranged from 4.20-30.89 mg·L[-][1]·h[-][1] and 1.57-21.92 mg·L[-][1]·h[-][1], respectively, under C/N ratios from 2.2-8.0. High-throughput sequencing and metagenomic analysis revealed that heterotrophic nitrification and aerobic denitrification dominated nitrogen transformation, with microorganisms utilising low-energy nap and nirK enzymes to adapt to the ultra-low DO environment. These findings provide novel insights into energy-efficient nitrogen removal pathways under ultra-low oxygen conditions.},
}

@article {pmid40929372,
year = {2025},
author = {Huereca, A and Allen, CCG and McMullin, RT and Simon, A and Belosokhov, A and Spribille, T},
title = {Evidence for extensive diversity in the pollen-parasitic genus Retiarius in western North America, including two new species associated with lichens.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-27},
doi = {10.1080/00275514.2025.2513197},
pmid = {40929372},
issn = {1557-2536},
abstract = {Understanding the diversity of microscopic hyphomycetes is an ongoing effort, and many species remain undescribed. While studying lichen organismal composition in western Canada, metagenomic data revealed the presence of an unknown species of Retiarius (Orbiliaceae, Ascomycota), a genus of pollen-parasitic fungus with no previous records in the region. We developed genus-specific primers to amplify Retiarius DNA in lichen and adjacent substrate extractions, successfully detecting multiple lineages of Retiarius across a wide geographic range within North America. We proceeded to screen accumulations of pollen on the undersurface of lichen thalli to isolate any pollen-associated fungi. Using dilution series and PCR for identification, we isolated two specifically distinct strains of Retiarius with morphology unlike any described member of the genus. Inclusion of DNA from these strains in a multilocus phylogeny using the internal transcribed spacer regions ITS1-5.8S-ITS2 (ITS), partial nuc 28S rDNA (28S), and nuc small subunit (18S) confirmed their evolutionarily distinct position in the genus. We describe these two species here as Retiarius canadensis and R. crescentus. The former possesses trinacrium-shaped conidia, similar to those of R. bovicornutus and R. revayae but morphometrically different, and the latter is distinguished by its canoe-shaped conidia, a morphological character heretofore unknown from Retiarius.},
}

@article {pmid40929115,
year = {2025},
author = {Gonzalez, FL and Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE},
title = {Genomic characterization of novel bat kobuviruses in Madagascar: Implications for viral evolution and zoonotic risk.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331736},
doi = {10.1371/journal.pone.0331736},
pmid = {40929115},
issn = {1932-6203},
mesh = {*Chiroptera/virology ; Animals ; Madagascar ; Phylogeny ; *Zoonoses/virology ; *Genome, Viral ; *Evolution, Molecular ; *Viral Zoonoses/virology ; Humans ; Genomics ; High-Throughput Nucleotide Sequencing ; *Picornaviridae Infections/virology/veterinary/epidemiology ; },
abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, lyssaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g., SARS-related coronaviruses), a handful of prior reports catalog kobuvirus carriage in bats and posit the role of bats as progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing a significant public health threat. Here, we report detection of kobuvirus RNA in Malagasy fruit bats (Eidolon dupreanum) and undertake phylogenetic characterization of Malagasy kobuvirus sequences, which nest within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species transmission, further characterization of this clade is critical for accurate evaluation of future zoonotic threats.},
}

*Chiroptera/virology
Animals
Madagascar
Phylogeny
*Zoonoses/virology
*Genome, Viral
*Evolution, Molecular
*Viral Zoonoses/virology
Humans
Genomics
High-Throughput Nucleotide Sequencing
*Picornaviridae Infections/virology/veterinary/epidemiology

@article {pmid40928986,
year = {2025},
author = {Miao, Q and Qu, L and Jiang, J and Liu, Q and Zhao, W and Tan, L and Li, J and Cao, W and Wang, B and Xia, X},
title = {Identification and Molecular Characterization of Two Novel Picorna-Like Viruses in Armigeres subalbatus Mosquitoes in Yunnan, China.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1177/15303667251372308},
pmid = {40928986},
issn = {1557-7759},
abstract = {Background: Mosquitoes harbor diverse insect-specific viruses (ISVs) frequently overlooked in arbovirus surveillance. Comprehensive characterization of ISVs is crucial for understanding their impact on host ecology and potential roles in arbovirus transmission. Methods: Using metagenomic sequencing on Armigeres subalbatus from Yunnan, China, we identified two novel picorna-like viruses, assembled their genomes, and conducted phylogenetic analysis. Detection was confirmed via RT-PCR and Sanger sequencing. Results: Both viruses are closely related to Hubei picorna-like virus 59, previously reported in spiders but unconfirmed. This work provides the first genomic evidence of this lineage in mosquitoes. Conclusion: This study characterizes two novel ISVs, expanding known picorna-like virus diversity and offering insights into cross-species virus evolution and arbovirus ecology.},
}

@article {pmid40928296,
year = {2025},
author = {Martinez, A and Ruth, N and Hatch, A and Chain, P and Shakya, M},
title = {Aerosol biome of a cafeteria and medical facility in Los Alamos, New Mexico, USA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0076625},
doi = {10.1128/mra.00766-25},
pmid = {40928296},
issn = {2576-098X},
abstract = {Aerosol sampling with next-generation sequencing was used to characterize microbial communities in a cafeteria and medical facility waiting room in Los Alamos, New Mexico, USA. We detected sequences from human, bacteria, archaea, fungi, other eukaryotes, and viruses, providing insights into the diversity of the aerosol microbiome.},
}

@article {pmid40928292,
year = {2025},
author = {Fujii, C and Vernon, S and Félix, M-A and Wang, D},
title = {Orsay virus variants isolated from wild Caenorhabditis elegans nematodes, France.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0055025},
doi = {10.1128/mra.00550-25},
pmid = {40928292},
issn = {2576-098X},
abstract = {Four new variants of Orsay virus were identified from wild isolates of Caenorhabditis elegans nematodes collected from decaying plant matter in France. Near-complete genomes of the viruses were determined by metagenomic sequencing. The four genomes share 96.1-98.9% nucleotide identity with the reference Orsay virus sequence JUv1580.},
}

@article {pmid40928236,
year = {2025},
author = {Liu, D and Hu, J and Zhang, D and Ren, S and Zhao, L and Gao, H and Hu, S and Xu, S and Liang, G},
title = {Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0084025},
doi = {10.1128/msystems.00840-25},
pmid = {40928236},
issn = {2379-5077},
abstract = {Human-associated metagenomic data often contain human nucleic acid information, which can affect the accuracy of microbial classification or raise ethical concerns. These reads are typically removed through alignment to the human genome using various metagenomic mapping tools or human reference genomes, followed by filtration before metagenomic analysis. In this study, we conducted a comprehensive analysis to identify the optimal combination of alignment software and human reference genomes using benchmarking data. Our findings show that the combination of bwa-mem and the telomere-to-telomere human genome (CHM13-T2T) is the most effective in removing human reads in simulated data. We also analyzed CHM13-T2T-derived sequences in RefSeq to understand how CHM13-T2T reduces false positive results. Finally, we assessed clinical samples and found that CHM13-T2T effectively reduces host-derived contamination, particularly in low microbial biomass samples. This study provides a thorough overview of the application of CHM13-T2T in metagenomic analysis and highlights its significance in improving microbial classification accuracy.IMPORTANCEHuman gene sequences account for a large proportion of metagenomic sequences. To gain accurate and precise microbiome information, effective host-derived contamination removal methods are required. Both the alignment algorithm and the reference genome could influence the effectiveness of this process. The telomere-to-telomere human genome (CHM13-T2T) is a state-of-the-art human genome with 216 Mbp of additional new sequences compared with the commonly used GRCh38.p14. Our findings show the optimal dehosting effect of CHM13-T2T combined with the bwa-mem software in metagenomic analysis. We also investigate the reasons for the superiority of CHM13-T2T. Our study provides insights into optimal strategies for host sequence removal from metagenomic data. A standard reference is proposed for future metagenomic analysis, which can improve the accuracy of microbial identification.},
}

@article {pmid40928232,
year = {2025},
author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS},
title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0103925},
doi = {10.1128/msystems.01039-25},
pmid = {40928232},
issn = {2379-5077},
abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.},
}

@article {pmid40928220,
year = {2025},
author = {Dong, L and Yang, J and Wu, H and Sun, Y and Liu, J and Yuan, H and Wang, M and Dai, Y and Teng, F and Jing, G and Yang, F},
title = {Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0004425},
doi = {10.1128/msystems.00044-25},
pmid = {40928220},
issn = {2379-5077},
abstract = {Development of dental caries is a dynamic process; yet, there is limited knowledge on microbial differences at various stages of caries at higher resolution. To investigate the shifting microbiome profiles across different caries stages, 30 children were enrolled in this study, including 15 caries-active patients and 15 caries-free individuals. Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health (CH; n = 15). For caries-active individuals, plaque samples were collected from non-cavitated surfaces (defined as relative health [RH], n = 15), enamel caries (EC; n = 15), and dentin caries samples (DC; n = 15). All the above samples were sequenced through the 2bRAD sequencing platform to reveal the microbial community structures in each group. We identified significant differences in microbial community structures from different caries stages. First, the CH group showed the highest species richness (P < 0.05), and then followed by the RH and EC groups with lower richness, and the lowest richness was found in the DC group, yet no significant difference was found among the last three groups (P > 0.05). Second, the microbial structure exhibited the greatest difference between CH and DC groups, followed by the distance between RH/EC and DC groups, and the smallest difference was found between RH and EC groups. Third, specific species were found with a significant difference during the different caries stages. Therefore, we developed a diagnostic model using deep learning methods based on neural networks to diagnose different caries stages with an AUC of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.IMPORTANCEThe diagnosis and treatment of dental caries are crucial for human oral health. Previous studies have focused on the microbial differences between caries and healthy teeth, but there was not enough knowledge on the microbial differences at different stages of dental caries. Our findings could provide a high-resolution understanding of the microbial divergencies among different stages of dental caries and thus build microbial-based diagnostic models for differentiating dental caries status using deep learning methods with an accuracy of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.},
}

@article {pmid40928217,
year = {2025},
author = {Russell, JN and Kos, D and Yacoub, E and Sies, AN and Warr, B and Jelinski, M and Ruzzini, A and Cameron, ADS},
title = {Enhanced metagenomic surveillance for bovine respiratory disease pathogens and antimicrobial resistance by hybridization capture sequencing.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0097725},
doi = {10.1128/aem.00977-25},
pmid = {40928217},
issn = {1098-5336},
abstract = {UNLABELLED: Bovine respiratory disease (BRD) is the primary disease of cattle and is responsible for most of the antibiotic use in the beef industry, both for metaphylaxis and treatment. Infection prevention and targeted treatments would benefit from detecting and identifying bacterial pathogens and, ideally, assessing antibiotic sensitivity. Here, we report success refining targeted metagenomics by hybridization capture sequencing (CapSeq) to detect and genotype bacterial pathogens and genes for antibiotic resistance in BRD. We developed a novel multi-locus sequence typing (MLST) strategy to both enhance assay sensitivity and provide epidemiological data compatible with traditional typing assays. Phylogenetically informed panel design by ProbeTools coupled with hybridization capture enabled the sequencing of novel genotypes and elucidated coinfection by distinct strains of Mycoplasmopsis bovis. CapSeq was orders of magnitude more sensitive than classical metagenomics at a scale compatible with low-throughput DNA sequencing capacity in diagnostic laboratories. Iterative design and testing of longer typing loci confirmed improvements in locus detection through a strategy applicable to future target selection. CapSeq detected bacterial pathogens that evaded detection by traditional metagenomics, and it demonstrated greater range and sensitivity for antibiotic resistance gene detection.

IMPORTANCE: Shotgun metagenomic sequencing for infectious disease diagnostics and surveillance benefits from simultaneous detection of multiple pathogens in a sample. Adding a hybridization probe capture step to the metagenomics workflow enriches targeted loci to improve the sensitivity of pathogen detection without compromising the ability to detect pathogen variants. Our custom probe panel enables multi-locus sequence typing of bovine respiratory disease agents as well as capture of antibiotic resistance genes, which improves the sensitivity of metagenomic testing and provides genotyping data compatible with traditional assays. This study demonstrates the utility of new design principles for probe panels; it also demonstrates how targeted metagenomics provides important new insights into co-infections and is equally useful for surveillance of environmental reservoirs of disease agents.},
}

@article {pmid40928095,
year = {2025},
author = {Darwiche, L and Goff, JL},
title = {Beyond tellurite: the multifunctional roles of genes annotated as tellurium resistance determinants in bacteria.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/1040841X.2025.2555936},
pmid = {40928095},
issn = {1549-7828},
abstract = {The metalloid tellurium (Te) is toxic to bacteria; however, the element is also extremely rare. Thus, most bacteria will never encounter Te in their environment. Nonetheless significant research has been performed on bacterial Te resistance because of the medical applications of the element. The so-called "tellurium resistance (Te[R]) genes" were first described on plasmids isolated from clinically relevant Enterobacteriaceae. With time, it has become apparent that, given the rarity of Te on the planet, these genes may have functions beyond tellurium resistance. Nonetheless, the description of these genes as "tellurium resistance genes" has persisted. In this review, we first examine the history and discovery of the Te[R] genes. We then performed an analysis of 184,000 high-quality, prokaryotic (meta)genomes, which revealed that terZABCDF, telA, and tehAB are relatively common in genome annotations and that they are frequently described as "tellurium resistance genes". We synthesized the literature to describe the functions of these ubiquitous genes beyond tellurium resistance. These genes have functions in diverse cellular processes including phage resistance, antibiotic resistance, virulence, oxidative stress resistance, cell cycle regulation, metal resistance, and metalation of exoenzymes. Considering this analysis, we propose that it is time to appreciate the multifunctional nature of the "tellurium resistance genes".},
}

@article {pmid40927879,
year = {2025},
author = {Wang, X and Wang, J and Chen, J and Bezemer, TM and Song, Z and Wanek, W and Liu, G and Zhang, C},
title = {Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70096},
doi = {10.1111/mec.70096},
pmid = {40927879},
issn = {1365-294X},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; },
abstract = {Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.},
}

@article {pmid40927726,
year = {2025},
author = {Eiman, L and Moazzam, K and Anjum, S and Kausar, H and Sharif, EAM and Ibrahim, WN},
title = {Gut dysbiosis in cancer immunotherapy: microbiota-mediated resistance and emerging treatments.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1575452},
pmid = {40927726},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; *Drug Resistance, Neoplasm ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Tumor Microenvironment/immunology ; },
abstract = {Cancer is a multifaceted disease driven by a complex interplay of genetic predisposition, environmental factors and lifestyle habits. With the accelerating pace of cancer research, the gut microbiome has emerged as a critical modulator of human health and immunity. Disruption in the gut microbial populations and diversity, known as dysbiosis, has been linked with the development of chronic inflammation, oncogenesis, angiogenesis and metastasis. This review discusses the microbial species associated with various types of cancer and the pathways involved in their tumorigenic effect including mechanisms like inflammatory cytokine response, immune modulation, genotoxicity and modification of the tumor microenvironment. Diagnostic tools such as metagenomics, metabolomics, and the use of dysbiosis indexes help in the detection of gut bacterial imbalances, enabling early detection of cancer and potential intervention. Gut dysbiosis diminishes the efficacy of cancer treatments including immunotherapies, and creates immunotherapy resistance by altering drug metabolism and driving immunometabolic reprogramming, allowing tumor cells to evade immune attack. Immunometabolic reprogramming through gut microbiota modulation provides a new avenue to be explored that can restore anti-tumor immunity and reverse resistance to cancer treatments. This review also highlights the use of fecal microbiota transplantation and probiotics to mitigate chances of dysbiosis-related cancer progression. Through a comprehensive assessment of the role of gut microbiota in cancer, this review underscores the need for the use of gut microbial biomarkers for cancer detection and microbiome-targeting strategies to individualize cancer treatment.},
}

Humans
*Dysbiosis/immunology/therapy
*Gastrointestinal Microbiome/immunology
*Neoplasms/therapy/immunology/microbiology
*Immunotherapy/methods
Animals
*Drug Resistance, Neoplasm
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Tumor Microenvironment/immunology

@article {pmid40927460,
year = {2025},
author = {Feng, Y and Chang, Q and Zhou, H and Zhang, W and Xie, L and Deng, X and Chen, T and Liu, W},
title = {Effects of gut microbiota on cognitive impairment in Parkinson's disease: a comprehensive Mendelian randomization and case-control study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620449},
pmid = {40927460},
issn = {1664-302X},
abstract = {BACKGROUND: Increasing evidence suggests a potential role of the gut microbiota in Parkinson's disease (PD). However, the relationship between the gut microbiome (GM) and PD dementia (PDD) remains debated, with their causal effects and underlying mechanisms not yet fully understood.

METHODS: Utilizing data from large-scale genome-wide association studies (GWASs), this study applied bidirectional and mediating Mendelian randomization (MR) to investigate the causal relationship and underlying mechanisms between the GM and PDD. In our analysis, inverse-variance weighting (IVW) was used as the primary method. Clinical validation was performed using metagenomic sequencing and bioinformatic analysis. The relationships between the GM and PDD were visualized using receiver operating characteristic (ROC) curves, confusion matrices, and correlation analyses.

RESULTS: Our study revealed a significant causal impact of five GM genera, 10 metabolites, two metabolite ratios, and 22 immune cells on PDD. Notably, the maltose to sucrose ratio was identified as a mediator of the positive causal effect of Subdoligranulum on PDD, with a mediation value of 13.2%. The clinical samples confirmed the efficacy of Subdoligranulum sp. in distinguishing patients with PDD from normal controls (area under the curve (AUC) = 0.80, 95% CI: 0.674-0.924). In addition, correlation analysis revealed a potential negative association between Subdoligranulum abundance and the Mini-Mental State Examination (MMSE) scores (r = -0.316, p = 0.006). Finally, bioinformatic analysis suggested that Subdoligranulum may influence PDD risk through the regulation of starch and sucrose metabolism pathways.

CONCLUSION: Our study confirms the potential role of Subdoligranulum in PDD progression, potentially mediated through starch and sucrose metabolism. These findings highlight the importance of the gut-brain axis in PDD and may provide insights into targeted interventions for PDD.},
}

@article {pmid40927458,
year = {2025},
author = {Li, Y and Duan, Y and Zhang, J and Petropoulos, E and Zhao, J and Wu, F and Wang, L and Chen, Y and Wang, X},
title = {Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595810},
pmid = {40927458},
issn = {1664-302X},
abstract = {While soil microorganisms underpin terrestrial ecosystem functioning, how their functional potential adapts across environmental gradients remains poorly understood, particularly for ubiquitous taxa. Employing a comprehensive metagenomic approach across China's six major terrestrial ecosystems (41 topsoil samples, 0-20 cm depth), we reveal a counterintuitive pattern: oligotrophic environments (deserts, karst) harbor microbiomes with significantly greater metabolic pathway diversity (KEGG) compared to resource-rich ecosystems. We provide a systematic catalog of key functional genes governing biogeochemical cycles in these soils, identifying: 6 core CAZyme genes essential for soil organic carbon (SOC) decomposition and biosynthesis; 62 nitrogen (N)-cycling genes (KOs) across seven critical enzymatic clusters; 15 sulfur (S)-cycling genes (KOs) within three key enzymatic clusters. These functional gene abundances exhibit distinct, geography-driven clustering patterns, strongly correlated with eight environmental drivers (latitude, NDVI, pH, EC, SOC, TN, C:N ratio, and MAP). This work provides a predictive framework and actionable genetic targets (e.g., specific CAZyme, N/S cycling genes) for potentially manipulating soil microbiomes to enhance ecosystem resilience and biogeochemical functions under stress.},
}

@article {pmid40926888,
year = {2025},
author = {Chen, WY and Lan, YC and Chen, JW and Wu, JH},
title = {Genomic personalities of Dehalococcoides subspecies and Dehalogenimonas illuminate complete trichloroethene dechlorination in high-salt conditions.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf101},
pmid = {40926888},
issn = {2730-6151},
abstract = {Global salinization increasingly threatens ecosystem integrity and the regulation of biogeochemical cycles. Our study reveals novel insights into the microbial contributions to the organohalide decomposition in saline environments, demonstrating the unprecedented ability of organohalide-respiring bacteria Dehalococcoides and Dehalogenimonas to completely dechlorinate trichloroethene to non-toxic ethene under hypersaline conditions (up to 31.3 g/L) in long-term operations. Using gradient salinity reactors and metagenomic analyses, we identified the evolved genomic features associated with high-salt tolerance. The Cornell subgroup of Dehalococcoides and Dehalogenimonas exhibit significantly lower average protein isoelectric points and retain the ribosomal protein L33p gene, unlike the Victoria and Pinellas subgroups. Dehalococcoides shows subspecies-level genomic divergence and unique codon usage biases. Intriguingly, the L33p gene is found in diverse bacterial phyla from saline environments, suggesting it may provide a growth advantage under salt stress. These genomic traits, hypothesized to enhance salt tolerance and dechlorination efficiency under salt stress, correlate with performance at elevated salinity. Our findings advance the understanding of microbial salt adaptation mechanisms and support the development of bioremediation strategies tailored for saline environments.},
}

@article {pmid40926875,
year = {2025},
author = {Zhao, J and Ye, J},
title = {Diagnostic Challenges of Six-Pathogen Detected by mNGS in an Immunocompromised ICU Patient with Severe Community-Acquired Pneumonia-Induced Sepsis: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4659-4665},
pmid = {40926875},
issn = {1178-6973},
abstract = {INTRODUCTION: Severe community-acquired pneumonia (SCAP) in immunocompromised patients is often caused by rare atypical pathogens, which are difficult to detect using conventional microbiological tests (CMTs) and can progress to sepsis in severe cases. Metagenomic next-generation sequencing (mNGS), an emerging pathogen detection technique, enables rapid identification of mixed infections and provides valuable guidance for clinical treatment decisions. SCAP-induced sepsis caused by a six-pathogen co-infection has not been previously reported, but interpretation remains a challenge.

CASE PRESENTATION: This report describes a case of SCAP-induced sepsis detected six pathogens by mNGS in a patient with IgA nephropathy who developed immunosuppression following long-term treatment with rituximab and corticosteroids. Bronchoalveolar lavage fluid (BALF) mNGS detected six pathogens, including Pneumocystis jirovecii, Klebsiella pneumoniae, Primate bocaparvovirus 1, Cytomegalovirus, Elizabethkingia anophelis, and Candida albicans. The patient was admitted to the intensive care unit (ICU) and received a combination of meropenem, trimethoprim-sulfamethoxazole, ganciclovir, piperacillin-tazobactam, and caspofungin. Following appropriate treatment, the patient recovered and was successfully discharged.

CONCLUSION: mNGS offers significant advantages for the diagnosis and identification of mixed infections in immunocompromised patients with SCAP-induced sepsis. It enables clinicians to initiate timely and targeted antimicrobial therapy, which facilitates early recovery, reduces the overuse of broad-spectrum antibiotics, and ultimately improves patient prognosis. Nevertheless, its interpretation requires caution, as distinguishing true pathogens from colonizers or contaminants still relies on clinical correlation and complementary diagnostic methods.},
}

@article {pmid40926846,
year = {2025},
author = {Prihambodo, TR and Mulianda, R and Wulandari, W and Anggrahini, S and Qomariyah, N and Ella, A and Winarti, E and Yusriani, Y and Suyatno, S and Firison, J and Fitra, D and Harahap, AE and Sari, DAP and Hidayat, T and Jayanegara, A},
title = {Scopus-based bibliometric analysis of research trends in silage feed and its impact on rumen fermentation in ruminants.},
journal = {Veterinary world},
volume = {18},
number = {7},
pages = {1972-1990},
pmid = {40926846},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Silage plays a pivotal role in ruminant nutrition, significantly influencing rumen fermentation, animal productivity, and environmental sustainability. Despite extensive research on silage and fermentation, a comprehensive synthesis of global trends and collaborations in this domain has not been systematically explored. This study aimed to conduct a bibliometric analysis of global research on silage feed and its effects on rumen fermentation in ruminants. It sought to identify publication trends, leading contributors, research themes, and international collaboration networks, thereby informing future directions in ruminant nutrition research.

MATERIALS AND METHODS: A total of 1,007 documents published between 1961 and 2024 were retrieved from the Scopus database using targeted keywords. Bibliometric and network analyses were performed using VOSviewer, Bibliometrix (R package), and Microsoft Excel. Inclusion criteria were limited to peer-reviewed English-language articles focused on silage feed and rumen fermentation in ruminants. Data cleaning and preprocessing involved harmonization of author names, keywords, and institutional affiliations.

RESULTS: Publication output has increased significantly since 2010, with China, the United States, and Canada emerging as the top contributors. Major research themes include silage quality, microbial fermentation, methane mitigation, and feed efficiency. Core journals identified include Journal of Dairy Science and Journal of Animal Science. Leading institutions such as China Agricultural University and the University of Florida demonstrated high productivity and citation impact. Keyword analysis highlighted emerging trends, including microbiome, methanogenesis, and sustainability. Collaboration network analysis revealed strong regional clusters, with North America and Europe forming central hubs, while Asia and South America showed growing but less integrated networks.

CONCLUSION: Research on silage and rumen fermentation has evolved from foundational studies to interdisciplinary approaches integrating microbiology, environmental science, and precision agriculture. The field is rapidly expanding, with increasing emphasis on reducing methane emissions and enhancing livestock performance through improved silage practices. However, global collaboration remains fragmented, particularly in underrepresented regions. Future research should focus on metagenomics, smart technologies (e.g., Artificial Intelligence and Internet of Things), and policy-driven strategies to optimize feed systems and support sustainable livestock production.},
}

@article {pmid40926709,
year = {2025},
author = {Zhao, R and He, G and Zhou, D and Li, X and Kuyper, TW and Zhang, F and Zhang, J},
title = {Arbuscular mycorrhizal fungi enhance nitrate ammonification in hyphosphere soil.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70561},
pmid = {40926709},
issn = {1469-8137},
support = {U23A2054//National Natural Science Foundation of China/ ; 42377128//National Natural Science Foundation of China/ ; 201913043//China Scholarship Council/ ; 201906350223//China Scholarship Council/ ; },
abstract = {Microbial nitrate ammonification is a crucial process to retain nitrogen (N) in soils, thereby reducing N loss. Nitrate ammonification has been studied in enrichment and axenic bacterial cultures but so far has been merely ignored in environmental studies. In particular, the capability of arbuscular mycorrhizal fungi (AMF) to regulate nitrate ammonification has not yet been explored. Here, nitrate ion ([15]NO3 [-]) was used to trace N transformations in hyphosphere and bulk soils. Metagenomic analysis was conducted, and cross-kingdom interactions between AMF and an isolated nirBD-carrying Paenibacillus sp. strain DP01 from hyphosphere soil were investigated. AMF hyphae significantly increased ammonium ion (NH4 [+]) concentration and [15]NH4 [+] derived from [15]NO3 [-] in hyphosphere soil, which were 1.42 and 5.01 times as high as those in bulk soil. Metagenomic analysis showed that the nirB gene involved in nitrite reduction to ammonium was prevalent in hyphosphere and bulk soils. Hyphal exudates enhanced ammonification efficiency and biofilm formation of the nitrite-ammonifying strain DP01. Additionally, accelerated oxygen depletion was detected on hyphal surface. This study demonstrates a novel interaction in which AMF significantly enhanced nitrate ammonification in the hyphosphere. Given the widespread presence of nitrate-ammonifying microbes in soils, this newly described interkingdom interaction offers guidance for agricultural practices aimed at increasing N efficiency and environmental sustainability.},
}

@article {pmid40926344,
year = {2025},
author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P},
title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70190},
doi = {10.1111/1758-2229.70190},
pmid = {40926344},
issn = {1758-2229},
support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; },
mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation & purification ; Plant Leaves/parasitology ; },
abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.},
}

*Solanum lycopersicum/microbiology/parasitology/immunology
Animals
*Microbiota
*Soil Microbiology
*Diptera/physiology
Ecuador
Plant Roots/microbiology/parasitology
Introduced Species
Bacteria/classification/genetics/isolation & purification
Plant Leaves/parasitology

@article {pmid40925458,
year = {2025},
author = {Zhao, Z and Gao, B and Henawy, AR and Ur Rehman, K and Ho, JWK and Xue, Y and Wu, J and Jiménez, N and Subirats, J and Zheng, L and Huang, F and Yu, C and Zhang, J and Cai, M},
title = {Effects of chicken manure-derived black soldier fly organic fertilizer on soil carbon and nitrogen cycling: insights from metagenomic and microbial network analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122775},
doi = {10.1016/j.envres.2025.122775},
pmid = {40925458},
issn = {1096-0953},
abstract = {Black soldier fly (BSF) organic fertilizer is known to enhance soil fertility and promote plant growth. However, its effects on soil carbon (C) and nitrogen (N) cycling remains unclear. In this study, we established a BSF chicken manure bioconversion system to produce BSF organic fertilizer and investigate its impacts on soil C and N cycling, as well as microbial ecological networks through metagenomic analysis. Compared to the control, BSF organic fertilizer significantly increased soil organic matter by 16.1% (p < 0.05) and total potassium by 11.0% (p < 0.05). Metagenomic sequencing revealed that BSF organic fertilizer significantly enhanced soil C and N cycling. For instance, the abundance of carbon fixation genes such as Calvin-Benson-Bassham (CBB) cycle genes pyc, pycA, and pycB increased by 35.7% (p < 0.01), 107.1% (p < 0.001), and 14.6% (p < 0.05), respectively. In nitrogen cycling, denitrification genes nirB, nirK, and nirS increased by 181.5 % (p < 0.001), 102.7% (p < 0.001), and 25.9% (p < 0.05), respectively. Furthermore, soils amended with BSF organic fertilizer displayed a 9.9% higher proportion of positive microbial interactions, particularly enhancing synergistic associations between bacteria and fungi, suggesting improved microbial community stability. Importantly, bacteria and fungi were interdependent in regulating C and N cycling processes, together orchestrating soil ecosystem functions. Overall, BSF organic fertilizers effectively promoted soil C and N cycling and maintained the stability of microbial communities. These findings provide valuable insights for the rational selection of fertilizers and the optimization of fertilization management practices, thereby contributing to the sustainable development of agricultural production.},
}

@article {pmid40779866,
year = {2025},
author = {Lin, XQ and Li, ZL and Chen, XQ and Wang, L and Yu, L and Wang, AJ},
title = {Microbial synergistic metabolic mechanism of enhanced tetrabromobisphenol A removal by bio-electrochemical system coupled constructed wetland.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139382},
doi = {10.1016/j.jhazmat.2025.139382},
pmid = {40779866},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Bioreactors/microbiology/statistics & numerical data ; Desulfovibrio/metabolism ; Geobacter/metabolism ; Metagenome ; *Microbiota ; Nitrates/metabolism ; *Polybrominated Biphenyls/metabolism ; *Water Pollutants, Chemical/metabolism ; *Water Purification/methods/statistics & numerical data ; Wetlands ; Electrochemical Techniques ; },
abstract = {The widespread existence of tetrabromobisphenol A (TBBPA) in the aquatic environment requires efficient treatment technology. The feasibility and related molecular mechanisms for the simultaneous deep removal of nitrate and TBBPA in a bio-electrochemical system coupled with a constructed wetland (BES-CW) are unclear. This study fabricated the BES-CW to achieve simultaneously deep removal of nitrate and TBBPA. TBBPA majorly went through reductive debromination, hydrolytic debromination, ring-cleavage, and oxidation in the open and closed circuits of BES-CW. Electricity activated key genes encoded in oxidoreductase (pflA, pflX) and oxygenase (dmpB, pobA) from electroactive bacteria (Geobacter and Desulfovibrio), accelerating TBBPA metabolites' oxidation and mineralization. Nitrate enriched the Acinetobacter and stimulated genes encoded in hydrolytic dehalogenase, inducing TBBPA hydrolytic debromination and further mineralization. Electricity and nitrate synergistically enhance TBBPA degradation and mineralization, guiding the advanced treatment of emerging pollutants in the aquatic environment.},
}

Biodegradation, Environmental
*Bioreactors/microbiology/statistics & numerical data
Desulfovibrio/metabolism
Geobacter/metabolism
Metagenome
*Microbiota
Nitrates/metabolism
*Polybrominated Biphenyls/metabolism
*Water Pollutants, Chemical/metabolism
*Water Purification/methods/statistics & numerical data
Wetlands
Electrochemical Techniques

@article {pmid40925130,
year = {2025},
author = {Sahu, KK and Yadav, K and Pradhan, M and Sharma, M and Dubey, A and Sucheta, and Kirubakaran, JJ},
title = {Pharmacological insights into gut microbiota modulation in systemic lupus erythematosus: Mechanisms, treatment strategies, and clinical implications.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {392},
number = {9},
pages = {103659},
doi = {10.1016/j.jpet.2025.103659},
pmid = {40925130},
issn = {1521-0103},
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by widespread inflammation and immune system dysregulation. Recent research suggests that the gut microbiota may play a role in the development of SLE by modulating immune system responses, affecting cytokine production, and altering the activity of T and B cells lymphocytes. As a result, there is a growing interest in microbiota-targeted therapies, including probiotics, dietary changes, and fecal microbiota transplantation. These methods may help restore the balance of microbes and reduce disease activity, but there are still a number of problems to solve. For example, microbiota composition varies greatly from person to person, and it is not clear how dysbiosis causes disease onset. There are also safety concerns about fecal microbiota transplantation. Experimental and clinical studies have started to shed light on the complicated ways in which microbial communities and immune function affect each other in SLE. These studies provide useful information, but their results are often inconsistent. As research continues, integrative methods like metagenomics and metabolomics may help find microbial signatures linked to disease, helping create more accurate and personalized treatments. The gut microbiome is a promising yet still developing area of research that could help us learn more about autoimmune diseases and their treatment, such as SLE. SIGNIFICANCE STATEMENT: Grasping the complex interplay between gut microbiota and systemic lupus erythematosus (SLE) has provided an avenue for therapeutic intervention. This study emphasizes the importance of gut dysbiosis in immune dysregulation, with connections between microbial translocation, molecular mimicry, and inflammatory pathways as contributing factors to the progression of SLE. This work sets the stage for novel and targeted approaches to treating SLE and improving patient outcomes by investigating microbiota-centric treatment options, such as probiotics, dietary interventions, and fecal microbiota transplantation.},
}

@article {pmid40925069,
year = {2025},
author = {Ji, Y and Gu, J and Xiao, S and Zhao, M and Xu, J and Lin, J and Cui, J and Zhao, W},
title = {Prognostic value of Nanopore sequencing-based metagenomics next-generation sequencing in clinical infectious cases: A retrospective observational study.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {1},
pages = {117092},
doi = {10.1016/j.diagmicrobio.2025.117092},
pmid = {40925069},
issn = {1879-0070},
abstract = {OBJECTIVES: This study aimed to evaluate the prognostic value of metagenomic next-generation sequencing(mNGS) using Nanopore sequencing technology (NST) versus traditional culture methods in infectious disease cases.

METHODS: We conducted a retrospective, single-center observational study comparing clinical outcomes between patients and specimen types in NST group and those in culture-based control group. Cox Proportional Hazards regression and Kaplan-Meier survival analysis were conducted to evaluate the association between diagnostic strategy and 28-day mortality. To minimize bias, Propensity Score Matching (PSM) and robust multivariate Cox regression analysis were employed to control for confounding factors. Diagnostic accuracy was quantified by calculating sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).

RESULTS: The NST-based diagnosis was independently associated with a significantly reduced 28-day mortality rate, as indicated by the robust multivariate Cox regression analysis. (HR = 0.29, 95 %CI:0.09-0.91, p = 0.033). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of NST in detecting bacterium were 0.93,0.54, 0.5and 0.94, respectively. Additionally, the NST group was associated with higher Antibiotic De-escalation Rate (ADE) and reduced Duration of Therapy (DOT), with p values of 0.0238 and 0.008, respectively.

CONCLUSION: NST-based mNGS demonstrated superior performance in diagnosing bacterial infections compared to traditional culture methods. The NST group and positive pathogen detection were associated with a reduced 28-day mortality rate. Additionally, higher APACHE II scores upon admission were identified as independent predictors of worse prognosis, highlighting the importance of early severity assessment in patient outcomes.},
}

@article {pmid40924942,
year = {2025},
author = {Hooper, C and Tidy, AM and Jessop, R and Bateman, KS and Green, MJ and Ross, SH and Ward, GM and Hazelgrove, R and Hunt, JE and Parker, M and Bass, D},
title = {Genomic and morphological characterization of a novel iridovirus, bivalve iridovirus 1 (BiIV1), infecting the common cockle (Cerastoderma edule).},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001494},
pmid = {40924942},
issn = {2057-5858},
mesh = {Animals ; *Iridovirus/genetics/classification/isolation & purification/ultrastructure ; Phylogeny ; *Cardiidae/virology ; *Genome, Viral ; Base Composition ; Open Reading Frames ; Genomics ; },
abstract = {High rates of mortality of the common cockle, Cerastoderma edule, have occurred in the Wash Estuary, UK, since 2008. A previous study linked the mortalities to a novel genotype of Marteilia cocosarum, with a strong correlation between cockle moribundity and the presence of M. cocosarum. Here, we characterize a novel iridovirus, identified by chance during metagenomic sequencing of a gradient purification of Marteilia cells, with the presence also correlated to cockle moribundity. The novel 179,695 bp iridovirus, bivalve iridovirus 1 (BiIV1), encodes 193 predicted ORFs and has a G+C content of 41 mol%. BiIV1 clusters together with other aquatic invertebrate iridoviruses in phylogenetic analyses and has a similar genome size to other invertebrate iridoviruses. Comparative analysis revealed that BiIV1 has lost three genes that were previously thought to be common amongst all iridoviruses but has also gained genes, potentially from horizontal transfer from its bivalve mollusc host(s). Electron microscopy showed 158 nm icosahedral virions present in the haemocytes of cockles, typical of those observed in host tissues infected with viruses of the family Iridoviridae. Prevalence of BiIV1 in moribund cockles was higher than that in apparently healthy cockles at most sites in the Wash Estuary, with up to 100% PCR prevalence in moribund cockles. Our findings provide the first genome for a bivalve-infecting iridovirus and identify a second bivalve-associated iridovirus in publicly available genomic datasets, adding to the knowledge of invertebrate iridovirus genomics and diversity.},
}

Animals
*Iridovirus/genetics/classification/isolation & purification/ultrastructure
Phylogeny
*Cardiidae/virology
*Genome, Viral
Base Composition
Open Reading Frames
Genomics

@article {pmid40924621,
year = {2025},
author = {Liu, L and Hu, L and Kuzyakov, Y and Rillig, MC and Duan, G and Wei, G and Chen, C},
title = {Microbial Physiological Adaptation to Biodegradable Microplastics Drives the Transformation and Reactivity of Dissolved Organic Matter in Soil.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09633},
pmid = {40924621},
issn = {1520-5851},
abstract = {The turnover of dissolved organic matter (DOM) in soil regulated by biodegradable microplastics (MPs) has garnered much attention due to its profound impact on the storage and stability of soil organic matter. However, the transformation and reactivity of plant-derived and microbially derived DOM by microorganisms adapted to biodegradable MPs, and the involved microbial physiological processes, remain nearly unknown. Here, we added virgin and aged polylactic acid (PLA) and polyhydroxyalkanoate (PHA) to agricultural soils and incubated for 56 days. Using stable isotope techniques, reactomics, and metagenomics, we found that the addition of both virgin and aged PLA induced hydroxylation, demethylation, and dehydrogenation of lignin-derived DOM, resulting in a 3-fold increase in their oxidation degree. PLA activated the enzymatic pathway for lignin-derived DOM decomposition and downregulated genes involved in bacterial anabolism, such as those related to protein, amino sugar, and peptidoglycan biosynthesis. In contrast, PHA increased the content of microbially derived DOM compounds such as proteins and amino sugars by 2.1-fold relative to the control with peptide chain elongation. PHA resulted in the degradation of lignin-derived DOM into pyruvate and acetyl-CoA, accelerated bacterial ATP synthesis, the de novo biosynthesis of proteins and peptidoglycan, and cell renewal and death, thereby increasing PHA- and soil organic matter-derived microbial necromass carbon. Our study provides new insights into the impact of biodegradable MPs on soil DOM transformation and underscores the importance of the microbial physiological processes involved.},
}

@article {pmid40924014,
year = {2025},
author = {Wei, Y and Chen, Y and Zhao, T and Zhang, X and Wang, N and Shen, L and Liang, Y and Ye, S and He, H},
title = {Treatment of non-sterile biogas slurry from a pig farm using microalgae isolated from the activated sludge of sewage plants.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0068825},
doi = {10.1128/spectrum.00688-25},
pmid = {40924014},
issn = {2165-0497},
abstract = {UNLABELLED: Microalgae treatment is regarded as a green and environmentally acceptable method of treating pig farm biogas slurry (BS). Numerous studies have been conducted on the use of microalgae to treat sterilized BS. Nevertheless, in large-scale application settings, this method will undoubtedly result in high costs and low efficiency. In this study, microalgae were isolated from activated sludge, and their capacity to treat non-sterile BS with high ammonium nitrogen levels was investigated, along with examining alterations in microbial composition within BS. The results showed that both Chlorella sp. HH01 and Chlorella sp. HS02 treatments effectively removed ammonia nitrogen and phosphorus from BS. They also showed some removal capabilities for chemical oxygen demand, heavy metals, and antibiotics. Algal treatment significantly reduced the number of species, richness, variety, and pathogens within the microorganisms of BS, according to the results of metagenomic research. Meanwhile, algal treatment demonstrated a significant removal effect on certain antibiotic resistance genes, while increasing the abundance of some others. This study provides a comprehensive exploration of microalgae-mediated mitigation effects on antibiotic resistance genes in BS.

IMPORTANCE: Numerous studies have been conducted on the use of microalgae to treat sterile biogas slurry (BS). However, in large-scale applications, this approach undoubtedly results in high costs and inefficiencies. Therefore, it is crucial to identify microalgae capable of growing in non-sterilized and undiluted BS while effectively treating major pollutants. The findings of this study reveal that microalgae isolated and purified from activated sludge in sewage treatment plants can withstand crude BS containing high concentrations of ammonia nitrogen and effectively remove ammonia nitrogen and total phosphorus. Additionally, they exhibit some removal capabilities for chemical oxygen demand, heavy metals, pathogens, antibiotics, and certain antibiotic resistance genes.},
}

@article {pmid40923736,
year = {2025},
author = {Zhang, X and He, Q and Mao, G and Liang, M},
title = {Diagnosis of Pulmonary Actinomycosis Caused by Actinomyces graevenitzii: a Case Series of Three Patients.},
journal = {Clinical laboratory},
volume = {71},
number = {9},
pages = {},
doi = {10.7754/Clin.Lab.2025.250254},
pmid = {40923736},
issn = {1433-6510},
mesh = {Humans ; *Actinomycosis/diagnosis/microbiology/drug therapy ; *Actinomyces/isolation & purification/genetics ; Male ; Middle Aged ; Female ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid/microbiology ; *Lung Diseases/microbiology/diagnosis ; Aged ; Adult ; Lung/microbiology ; },
abstract = {BACKGROUND: Actinomyces graevenitzii is a relatively uncommon Actinomyces species, which is an oral species and predominantly recovered from respiratory locations [1,2]. It is a gram-positive anaerobic bacteria or microaerobic filamentation bacteria, which can induce pyogenic and granulomatous inflammation characterized by swelling and concomitant pus, sinus formation, and the formation of yellow sulfur granules. All tissues and organs can be infected; the most common type involves the neck and face (55%), followed by the abdominal and pelvic cavities (20%). Chest involvement is the third most common type (15%), affecting the lung parenchyma, central airway, pleura, mediastinum, and chest wall [3-5]. Diagnosis of actinomycosis mainly relies on sputum, pus or biopsy specimens to find actinomycetes. Metagenomics next-generation sequencing (mNGS) in recent years has been increasingly valued and recognized for its application in infectious diseases. It provides a more efficient and accurate means for the pathological diagnosis of respiratory infections, updating the diagnostic strategy for lower respiratory tract infections [6].

METHODS: This study systematically summarized the clinical characteristics of Actinomyces graevenitzii infection by analyzing three cases of this pathogen. Bronchoalveolar lavage fluid (BAL) samples were collected for bacterial culture and mNGS. The isolated strains were routinely identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

RESULTS: Microbiological analysis demonstrated Actinomyces graevenitzii growth in all three bronchoalveolar la-vage (BAL) cultures. Metagenomic next-generation sequencing (mNGS) results showed concordant detection of A. graevenitzii in two cases, while unexpectedly identifying Tropheryma whipplei as the predominant pathogen in the remaining case.

CONCLUSIONS: Actinomycosis infections often present with subtle and nonspecific clinical manifestations, making them difficult to distinguish from pulmonary tuberculosis, fungal infections, and lung malignancies through imaging studies alone, frequently resulting in misdiagnosis or delayed diagnosis. Early and accurate diagnosis can be achieved through timely analysis of BAL fluid using advanced diagnostic techniques, including MALDI-TOF/MS for bacterial identification and mNGS, facilitating prompt and appropriate treatment.},
}

Humans
*Actinomycosis/diagnosis/microbiology/drug therapy
*Actinomyces/isolation & purification/genetics
Male
Middle Aged
Female
High-Throughput Nucleotide Sequencing
Bronchoalveolar Lavage Fluid/microbiology
*Lung Diseases/microbiology/diagnosis
Aged
Adult
Lung/microbiology

@article {pmid40923351,
year = {2025},
author = {Stensvold, CR},
title = {Aspects of Genetic Diversity, Host Specificity and Public Health Significance of Single-Celled Intestinal Parasites Commonly Observed in Humans and Mostly Referred to as 'Non-Pathogenic'.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {9},
pages = {e70036},
doi = {10.1111/apm.70036},
pmid = {40923351},
issn = {1600-0463},
mesh = {Humans ; *Intestinal Diseases, Parasitic/parasitology ; *Genetic Variation ; *Host Specificity ; *Public Health ; Blastocystis/genetics ; Animals ; },
abstract = {Clinical microbiology involves the detection and differentiation of primarily bacteria, viruses, parasites and fungi in patients with infections. Billions of people may be colonised by one or more species of common luminal intestinal parasitic protists (CLIPPs) that are often detected in clinical microbiology laboratories; still, our knowledge on these organisms' impact on global health is very limited. The genera Blastocystis, Dientamoeba, Entamoeba, Endolimax and Iodamoeba comprise CLIPPs species, the life cycles of which, as opposed to single-celled pathogenic intestinal parasites (e.g., microsporidia and sporozoa), do probably not include gut-invasive stages that could result in pathological processes and thereby disease (except for Entamoeba histolytica). All five genera are parasites in the sense that they use a host to complete their life cycle; still, by many specialists, these are considered to be of limited clinical relevance and could possibly be referred to as 'eukaryotic endobionts' or even 'endosymbionts', in case they would have health-protective effects. The articles included in this thesis exemplify the work and the data that support the view that it might be more relevant to study these genera in a public health and gut ecology context than in a clinical microbiology context. Essential to investigating the impact of intestinal parasites on health and disease are accurate diagnostic tools, including DNA-based technology such as PCR and sequencing, plus accurate reference databases. Small subunit (SSU) ribosomal RNA (rRNA) genes consistently present in both pro- and eukaryotic organisms are today avidly used as taxonomic markers. DNA-based methods have been developed for genetic characterisation of microorganisms and provided data on species/subtypes/genotypes, etc. Metagenomics and metabarcoding (the use of low-specific PCR coupled with next-generation sequencing) can provide information on co-infection/co-colonisation with other organisms and enable screening for genetic diversity, even in complex matrices. By developing and implementing sensitive and specific DNA-based diagnostic tools and typing assays primarily based on the SSU rRNA gene, we have increased insight into the diversity, distribution and significance of CLIPPs. With these tools, we have shown that the genera Blastocystis and Dientamoeba are far more common than previously thought. Only 10-15 years ago, hypotheses on their distribution typically relied on data generated by traditional parasitological diagnostic methods, such as light microscopy. Hence, we have shown that most older children in Nigeria host Blastocystis, and that most children in day-care institutions in Denmark, if not all, get colonised by Dientamoeba at some point. Single-celled non-pathogenic intestinal parasites can be hosted by patients with diarrhoea and functional or inflammatory bowel diseases. However, emerging data appear to suggest that CLIPPs are generally more common in gut-healthy individuals than in patients with gastrointestinal symptoms. The research we have carried out on associations between CLIPPs and gut bacteria suggests that colonisation with these parasites is seen primarily in individuals with a healthy 'gut flora' (eubiosis). This observation should prompt future research projects focusing on the use of CLIPPs as biomarkers, and it should be investigated to which extent manipulation with CLIPPs could lead to changes in the gut flora and thereby be used as probiotics. In the event that it makes sense to speak of 'infection' by CLIPPs, we still lack tools to differentiate between colonisation and infection. We have known for decades that morphologically similar parasites can differ in terms of clinical impact and be genetically distinct, a feature that we refer to as 'cryptic genetic diversity'. One example is E. histolytica, which cannot be differentiated from Entamoeba dispar by cyst morphological features. However, whereas E. histolytica can be invasive and give rise to amoebic dysentery and amoebiasis, E. dispar is by most specialists considered non-invasive and generally non-pathogenic. This insight led us to investigate genetic diversity among other species of Entamoeba as well as other CLIPPs genera. If we could demonstrate similar-or higher-degrees of diversity within Blastocystis, Dientamoeba, Endolimax and Iodamoeba, these differences might be key to explaining differences in parasite phenotype and thereby differences in the ability of the parasites to cause symptoms. Despite the disclosure of striking genetic diversity among some CLIPPs, we have found little support for such theories; however, more studies are needed. As for Dientamoeba, we have observed a more or less clonal expansion of one of the two genotypes known to exist, and this genotype appears to have global predominance. In contrast, extensive genetic diversity is observed between and within subtypes of Blastocystis: to date, more than 30 species, the so-called subtypes, have been acknowledged. We, and many others, have sought to identify whether one or more of these subtypes could be linked to the development of intestinal symptoms, but there is little evidence to support this hypothesis. We know that Subtypes 1-4 reflect about 95% of Blastocystis colonisation in humans, and we have shown that individuals with zoonotic subtypes (e.g., ST6, ST7 and ST8) might typically experience symptoms. We have disclosed astonishing genetic variation among other CLIPPs, which has led to the recognition of Iodamoeba bütschlii, Endolimax nana, Entamoeba coli and Entamoeba hartmanni as species complexes, where each species should be regarded as a complex of species (referred to as 'subtypes' or 'ribosomal lineages') with overlapping morphology. And where E. histolytica and E. dispar differ by only 1%-2% diversity across the SSU rRNA gene, we have observed up to at least 10% and 30% genetic difference among ribosomal lineages within E. coli and I. bütschlii, respectively, challenging species concepts currently applied. Our research has resulted in the recognition of three ribosomal lineages within both E. coli and E. hartmanni, as well as two ribosomal lineages of E. nana and I. bütschlii. Moreover, we have discovered a new lineage of Entamoeba moshkovskii. Molecular characterisation of intestinal parasites collected from different host species (humans, non-human primates, other mammals, birds, etc.) can help identify opportunity for transmission between human and non-human hosts. We have shown that pigs can host a few species/lineages that can readily colonise humans, such as Entamoeba hartmanni and I. bütschlii. Many other species of larger mammals are common hosts of Blastocystis and Entamoeba. However, for the two latter genera, the species/genetic variants observed in non-human hosts are typically different from those observed in humans, which could indicate that many species of CLIPPs have adapted to their respective hosts over a long period, resulting in relatively high host specificity. For Blastocystis, we have shown that even though a given subtype may be found in more than one host species, it is possible to demonstrate cryptic host specificity at allele level. For instance, even though both human and non-human primates can be colonised by ST3, host species-specific strains of ST3 circulate within these two host populations. With regards to E. coli, it is possible that ST1 has adapted to human hosts, while E. coli ST2 has adapted to a broader host range, including non-human primates and rodents. It has become clear that CLIPPs are common colonisers of the human background population, and even though we cannot disprove the existence of infection by any of these, it should be reasonable to consider clinical and medical intervention redundant in most cases. Perhaps it might even be so that one should try not to eradicate these organisms from the gut when first established. However, more studies are warranted to elucidate the significance of the pronounced genetic diversity observed in some CLIPPs with regards to transmission patterns and clinical significance. Future research in CLIPPs should also include studies that can elucidate those factors that favour colonisation with CLIPPs and what role CLIPPs have in host-gut ecology, metabolism and overall health condition. Finally, as human and non-human hosts share these parasitic genera, and as some protozoa possibly contribute to overall gut function in ruminants, it would be interesting to study these in domesticated and wild animals to learn more about the role of these parasites in health and disease, including investigations into whether some CLIPPs might be endosymbionts.},
}

Humans
*Intestinal Diseases, Parasitic/parasitology
*Genetic Variation
*Host Specificity
*Public Health
Blastocystis/genetics
Animals

@article {pmid40923293,
year = {2025},
author = {Lauritsen, JG and Carøe, C and Gaun, N and Martin-Bideguren, G and Leonard, A and Eisenhofer, R and Odriozola, I and Gilbert, MTP and Aizpurua, O and Alberdi, A and Pietroni, C},
title = {Robust, Open-Source and Automation-Friendly DNA Extraction Protocol for Hologenomic Research.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70042},
doi = {10.1111/1755-0998.70042},
pmid = {40923293},
issn = {1755-0998},
support = {CF20-0460//Carlsbergfondet/ ; DNRF143//Danmarks Grundforskningsfond/ ; //The Danish Dairy Association and the Danish Agriculture and Food Sector Dairy/ ; },
abstract = {Global efforts to standardise methodologies benefit greatly from open-source procedures that enable the generation of comparable data. Here, we present a modular, high-throughput nucleic acid extraction protocol standardised within the Earth Hologenome Initiative to generate both genomic and microbial metagenomic data from faecal samples of vertebrates. The procedure enables the purification of either RNA and DNA in separate fractions (DREX1) or as total nucleic acids (DREX2). We demonstrate their effectiveness across faecal samples from amphibians, reptiles and mammals, with reduced performance observed on bird guano. Despite some variation in laboratory performance metrics, both DREX1 and DREX2 yielded highly similar microbial community profiles, as well as comparable depth and breadth of host genome coverages. Benchmarking against a commercial kit widely used in microbiome research showed comparable recovery of host genomic data and microbial community complexity. Our open-source method offers a robust, cost-effective, scalable and automation-friendly nucleic acid extraction procedure to generate high-quality hologenomic data across vertebrate taxa. The method enhances research comparability and reproducibility by providing standardised, high-throughput, open-access protocols with fully transparent reagents. It is designed to integrate automatised pipelines, and its modular structure also supports continuous development and improvement.},
}

@article {pmid40923121,
year = {2025},
author = {Li, Z and Zhao, K and Liu, H and Liu, J and Chen, X and Hu, W and Wen, E and Zhang, K and Chen, L},
title = {Construction of Predictive Machine Learning Model of Glioma-Associated Gut Microbiota.},
journal = {Brain and behavior},
volume = {15},
number = {9},
pages = {e70843},
doi = {10.1002/brb3.70843},
pmid = {40923121},
issn = {2162-3279},
support = {W2024SNKT13//the Research on Neurological Diseases and Nutritional Health at the Capacity Building and Continuing Education Center of the National Health Commission of China/ ; 82172680//the National Natural Science Foundation of China/ ; 82303586//the National Natural Science Foundation of China/ ; 82373220//the National Natural Science Foundation of China/ ; 82473264//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/physiology/genetics ; *Glioma/microbiology/diagnosis ; *Brain Neoplasms/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiota plays a crucial role in the development of glioma. With the evolution of artificial intelligence technology, applying AI to analyze the vast amount of data from the gut microbiome indicates the potential that artificial intelligence and computational biology hold in transforming medical diagnostics and personalized medicine.

METHODS: We conducted metagenomic sequencing on stool samples from 42 patients diagnosed with glioma after operation and 30 non-intracranial tumor patients and developed a Gradient Boosting Machine (GBM) machine learning model to predict the glioma patients based on the gut microbiome data.

RESULTS: The AUC-ROC for the GBM model was 0.79, indicating a good level of discriminative ability.

CONCLUSIONS: This method's efficacy in discriminating between glioma cells and normal controls underscores the potential of machine learning models in leveraging large datasets for clinical insights.},
}

Humans
*Machine Learning
*Gastrointestinal Microbiome/physiology/genetics
*Glioma/microbiology/diagnosis
*Brain Neoplasms/microbiology/diagnosis
Male
Female
Middle Aged
Adult
Feces/microbiology

@article {pmid40922296,
year = {2025},
author = {Li, J and He, J and Yin, Y and Liu, Y},
title = {Timely diagnosis of atypical Japanese spotted fever: A case report.},
journal = {Medicine},
volume = {104},
number = {36},
pages = {e44345},
doi = {10.1097/MD.0000000000044345},
pmid = {40922296},
issn = {1536-5964},
mesh = {Humans ; Female ; Middle Aged ; *Spotted Fever Group Rickettsiosis/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Doxycycline/therapeutic use ; Rickettsia/isolation & purification/genetics ; },
abstract = {RATIONALE: Japanese spotted fever (JSF) is a rare tick-borne disease caused by Rickettsia japonica. Atypical manifestations and a lack of standardized diagnostic assays often result in delayed diagnosis and treatment, potentially leading to life-threatening complications.

PATIENT CONCERNS: A 57-year-old immunocompetent female from a region with no previously reported JSF cases presented with acute-onset high-grade fever (39.5°C), a generalized maculopapular rash, and systemic symptoms after participating in agricultural activities. The patient denied having any history of tick exposure and presented without eschar, leading to the initial misdiagnosis of respiratory infection.

DIAGNOSES: Metagenomic sequencing (MetaCAP) technology enabled a definitive diagnosis by identifying Rickettsia japonica-specific DNA sequences in the patient's blood. The genomic results completely aligned with the clinical presentation.

INTERVENTIONS: The patient was treated with doxycycline, which achieved rapid clinical resolution.

OUTCOMES: The patient achieved full recovery with only residual lower-limb hyperpigmentation at the month follow-up, without disease recurrence.

LESSONS: This case demonstrates the diagnostic value of metagenomic testing for fevers of unknown origin. JSF should be a key consideration for agricultural and forestry workers presenting with compatible symptoms, even in nonendemic areas without documented insect bites. The optimal diagnostic approach combines clinical evaluation with advanced molecular testing to ensure the accurate identification and proper management of tropical febrile illnesses.},
}

Humans
Female
Middle Aged
*Spotted Fever Group Rickettsiosis/diagnosis/drug therapy
Anti-Bacterial Agents/therapeutic use
Doxycycline/therapeutic use
Rickettsia/isolation & purification/genetics

@article {pmid40922266,
year = {2025},
author = {Liu, Y and Yue, Y and Dong, C and Wang, Z},
title = {Isolated spinal osteomyelitis caused by Nocardia farcinica in an immunocompetent patient: A case report and literature review.},
journal = {Medicine},
volume = {104},
number = {36},
pages = {e42797},
doi = {10.1097/MD.0000000000042797},
pmid = {40922266},
issn = {1536-5964},
mesh = {Humans ; Female ; *Osteomyelitis/microbiology/drug therapy/diagnosis/diagnostic imaging ; *Nocardia Infections/drug therapy/diagnosis/microbiology ; *Nocardia/isolation & purification ; Child ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Magnetic Resonance Imaging/methods ; Immunocompetence ; Tomography, X-Ray Computed ; *Spinal Diseases/microbiology/drug therapy ; },
abstract = {RATIONALE: Nocardia spp. are opportunistic pathogens that invade the human body via respiratory inhalation or direct skin wounds. Spinal nocardial osteomyelitis is a rare disease with only a few cases reported to date. To the best of our knowledge, this is the second case of spinal osteomyelitis caused by Nocardia farcinica.

A 12-year-old immunocompetent girl was diagnosed with spinal osteomyelitis. The causative agent has been confirmed as N farcinica by metagenomic next-generation sequencing analysis of vertebral biopsy tissue in December 2022. It was noteworthy that the onset of the disease in this patient was insidious and the symptoms were atypical, which differed from previously reported cases.

INTERVENTIONS: Trimethoprim/sulfamethoxazole was given first, showing good clinical effects. To clarify the changes in the patient's condition, we performed magnetic resonance imaging (MRI) and computed tomography examinations on the patient in August 2023.

OUTCOMES: After 2 months of medication, the patient's clinical symptoms completely disappeared. The results of the latest computed tomography and MRI scans showed the formation of hardened bone in the area of the L2 vertebral body bone erosion, and MRI showed a significant reduction in the abnormal signal range of the L2 vertebral body, which was considered cured.

LESSONS: This study suggests that N farcinica, a rare pathogen, can present with atypical symptoms and can easily be misdiagnosed in immunocompromised patients. Its diagnosis relies on advanced testing techniques, and determining the nature of the pathogen is of great significance for a clear diagnosis. Moreover, early, sufficient, and comprehensive treatment with sulfonamide antibiotics or combination therapy usually results in a good prognosis.},
}

Humans
Female
*Osteomyelitis/microbiology/drug therapy/diagnosis/diagnostic imaging
*Nocardia Infections/drug therapy/diagnosis/microbiology
*Nocardia/isolation & purification
Child
Anti-Bacterial Agents/therapeutic use
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use
Magnetic Resonance Imaging/methods
Immunocompetence
Tomography, X-Ray Computed
*Spinal Diseases/microbiology/drug therapy

@article {pmid40922265,
year = {2025},
author = {Zhao, C and Li, H and Guo, L and Jia, M and Liu, J},
title = {Diagnosis of Cytomegalovirus infection in a very low birth weight infant using metagenomic next-generation sequencing: A case report.},
journal = {Medicine},
volume = {104},
number = {36},
pages = {e44264},
doi = {10.1097/MD.0000000000044264},
pmid = {40922265},
issn = {1536-5964},
mesh = {Humans ; Infant, Newborn ; Antiviral Agents/therapeutic use ; *Cytomegalovirus/genetics/isolation & purification ; *Cytomegalovirus Infections/diagnosis/drug therapy/virology ; Ganciclovir/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; *Infant, Very Low Birth Weight ; *Metagenomics/methods ; },
abstract = {RATIONALE: Cytomegalovirus (CMV) is a DNA virus from the herpesvirus family that is widespread among humans. Very low birth weight infants (VLBWI) are particularly susceptible to postnatal CMV infection due to their compromised immune systems. The clinical manifestations of postnatal CMV infection are often nonspecific, which complicates early detection and may lead to multi-organ dysfunction and long-term sequelae.

PATIENT CONCERNS: A VLBWI developed unexplained persistent fever during hospitalization. Conventional diagnostic methods, including routine microbiological tests, failed to identify the causative pathogen.

DIAGNOSES: Metagenomic next-generation sequencing (mNGS) was performed and successfully identified CMV as the etiologic agent. Traditional diagnostic approaches were insufficient, but mNGS provided a comprehensive analysis of microbial nucleic acids, leading to a definitive diagnosis.

INTERVENTIONS: The patient received antiviral treatment with ganciclovir following the identification of CMV by mNGS.

OUTCOMES: After antiviral therapy, the fever resolved, and no long-term sequelae were observed during follow-up.

LESSONS: This case demonstrates the efficacy of mNGS as a powerful diagnostic tool for identifying the causes of unexplained infections in VLBWI. Compared with conventional methods, mNGS offers significant advantages, particularly in detecting a wide range of pathogens simultaneously. The successful diagnosis and treatment in this case underscore its clinical utility in managing complex neonatal infectious diseases.},
}

Humans
Infant, Newborn
Antiviral Agents/therapeutic use
*Cytomegalovirus/genetics/isolation & purification
*Cytomegalovirus Infections/diagnosis/drug therapy/virology
Ganciclovir/therapeutic use
*High-Throughput Nucleotide Sequencing/methods
*Infant, Very Low Birth Weight
*Metagenomics/methods

@article {pmid40922218,
year = {2025},
author = {Di Gianvito, P and Englezos, V and Ferrocino, I and Cocolin, L and Rantsiou, K},
title = {Survey of a grapevine microbiome through functional metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {117000},
doi = {10.1016/j.foodres.2025.117000},
pmid = {40922218},
issn = {1873-7145},
mesh = {*Vitis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Rhizosphere ; Fruit/microbiology ; Plant Leaves/microbiology ; },
abstract = {Microorganisms colonizing grapevines possess diverse functional capabilities that influence the health, growth, productivity and, consequently, wine quality. In this study, spatial and temporal dynamics of the microbiome of Vitis vinifera cv. Barbera grapevine were determined by shotgun sequencing. Bacterial and fungal populations and functions were monitored in samples of rhizosphere, leaves, and grapes, collected at different stages from fruit development to harvest in a conventionally managed vineyard. A compartmental specificity of diverse species was observed within both bacterial and fungal communities. A core microbiome was also identified. LEfSe analysis revealed significantly discriminant taxa associated with each plant compartment, but not according to the sampling time. KEGG genes associated with carbohydrate metabolism were the most abundant in all samples, followed by genes related to amino acid metabolism, respectively involved in carbon and nitrogen metabolic pathways. Interestingly, differences were observed in the functions of rhizosphere and phyllosphere communities with additional differences observed between functions of bacterial and fungal communities. Pathways involved in critical functions like nutrient acquisition, stress resistance, metabolic flexibility, and interaction with the grapevine, were detected within the microbiome. The findings of this study unravel ecological and functional characteristics of the Barbera microbiome. This fundamental understanding is a prerequisite for the development of tailored strategies to protect vineyards and promote sustainability in grapevine production.},
}

*Vitis/microbiology
*Metagenomics/methods
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification
Rhizosphere
Fruit/microbiology
Plant Leaves/microbiology

@article {pmid40922213,
year = {2025},
author = {Zhang, Z and Guo, Z and Cao, L and Hou, Q and Liu, Z and Zhong, J and Liu, N and Mei, X and Wang, Y},
title = {Dissecting the microbial, physicochemical, and flavor dynamics of core and peel layers in Houhuo Daqu: Insights into quality regulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {116992},
doi = {10.1016/j.foodres.2025.116992},
pmid = {40922213},
issn = {1873-7145},
mesh = {*Taste ; *Fruit/microbiology/chemistry ; Odorants/analysis ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; Humans ; Amino Acids/analysis ; Metagenomics ; },
abstract = {Houhuo Daqu (HHD) exhibits significant heterogeneity between its core and peel layers, yet their differences remain underexplored. This study integrates metagenomic sequencing and electronic sensory technologies to compare the physicochemical properties, microbial communities, and flavor profiles of HHD's core and peel. Results reveal distinct microbial communities and diversity between the layers. Both are dominated by bacteria (>90 % relative abundance). The core shows significantly higher relative abundance of Bacillus licheniformis, Bacillus haynesii, and Bacillus paralicheniformis, while the peel has elevated levels of Streptomyces sp. NHF165, Pantoea agglomerans, and Lactiplantibacillus plantarum. Bacillus licheniformis is linked to acetic acid biosynthesis. Flavor analysis indicates both layers are rich in pyrazines, contributing to HHD's distinctive aroma. Enzyme activities differed markedly between the core and peel. Structural equation modeling, regression, and ENVFIT analyses show that amino acid nitrogen directly influences enzymatic activity and indirectly affects it by shaping microbial community and diversity. Additionally, amino acid nitrogen significantly impacts HHD's taste and aroma, modulated by starch and ash content. These findings highlight amino acid nitrogen as a key factor for controlling HHD quality in future production.},
}

*Taste
*Fruit/microbiology/chemistry
Odorants/analysis
*Food Microbiology
*Microbiota
Bacteria/classification/genetics
Humans
Amino Acids/analysis
Metagenomics

@article {pmid40922169,
year = {2025},
author = {Li, X and Liao, B and Wang, X and Dong, W and Li, J and Hu, Y and Li, Y and Peng, N and Zhao, S},
title = {Non-Saccharomyces yeasts enhance yield and flavor in industrial xiaoqu light-flavor baijiu production.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {117040},
doi = {10.1016/j.foodres.2025.117040},
pmid = {40922169},
issn = {1873-7145},
mesh = {Fermentation ; *Pichia/metabolism/growth & development ; *Taste ; Saccharomyces cerevisiae/metabolism/growth & development ; *Flavoring Agents/metabolism ; Food Microbiology ; Rhizopus/metabolism/growth & development ; *Alcoholic Beverages/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Wine/microbiology/analysis ; Butylene Glycols ; },
abstract = {This study investigated the effects of adding Saccharomycopsis fibuligera (SF) and Pichia kudriavzevii (PK) on microbial communities and flavor substances in industrial xiaoqu light-flavor baijiu production. The result showed that the highest acidity was found in the control group (CK: Saccharomyces cerevisiae and Rhizopus) at the end of fermentation. SF and PK promoted the growth of Rhizopus while decreasing the abundance of S. cerevisiae during the saccharification stage. Metagenomic sequencing showed that S. cerevisiae and Lactobacillus helveticus were the dominant fungus and bacterium during the late stage of fermentation, and the fungal community tended to be stable before the bacterial community. Notably, the temperature change rate in zaopei (fermented grains) of PK was faster than that in CK and SF, whereas the synthesis of flavor substances was later than that in CK and SF. Moreover, the liquor yield of SF and PK increased by 4.08 % and 4.26 %, respectively. Flavor substance analysis of the base liquor demonstrated that both SF and PK elevated ethyl acetate content and decreased ethyl lactate. Meanwhile, β-phenethyl alcohol, 2,3-butanediol, isoamyl alcohol, and isobutanol contents were increased in SF, and 2,3-butanediol, isoamyl alcohol, and methanol contents were lowest in PK. These findings demonstrate the potential of non-Saccharomyces yeasts for flavor and yield optimization in baijiu production.},
}

Fermentation
*Pichia/metabolism/growth & development
*Taste
Saccharomyces cerevisiae/metabolism/growth & development
*Flavoring Agents/metabolism
Food Microbiology
Rhizopus/metabolism/growth & development
*Alcoholic Beverages/microbiology/analysis
Volatile Organic Compounds/analysis
*Wine/microbiology/analysis
Butylene Glycols

@article {pmid40922105,
year = {2025},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Plastic-Microbial BioRemediation DB: A Curated Database for Multi-Omics Applications.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70178},
doi = {10.1111/1758-2229.70178},
pmid = {40922105},
issn = {1758-2229},
mesh = {Biodegradation, Environmental ; *Plastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; Soil Microbiology ; Metagenome ; Genomics ; Multiomics ; },
abstract = {Plastic pollution is a major environmental challenge, with millions of tonnes produced annually and accumulating in ecosystems, causing long-term harm. Conventional disposal methods, such as landfilling and incineration, are often inadequate, emphasising the need for sustainable solutions like bioremediation. However, the bacterial biodiversity involved in plastic biodegradation remains poorly understood. To address this gap, we present the Plastic-Microbial BioRemediation (Plastic-MBR) database, a curated multi-omics resource that integrates publicly available genetic and enzymatic data related to putative plastic-degrading microorganisms. This database supports in silico analyses of metagenomic data from plastic-contaminated environments and comparative genomics, aiming to identify microbial taxa with potential plastic-degrading functions. We validated the functionality of the Plastic-MBR database by applying it to metagenomic datasets from plastic-contaminated soil and river water, successfully identifying numerous putative plastic-degrading genes across diverse microbial taxa. These results support the use of the Plastic-MBR database as a tool to identify candidate bacteria for future experimental validation, strain isolation, and functional studies, ultimately contributing to a deeper understanding of microbial potential in plastic bioremediation. While this study focuses on database development and computational validation, future studies will be essential to confirm and translate these genomic predictions into effective bioremediation strategies.},
}

Biodegradation, Environmental
*Plastics/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenomics
Soil Microbiology
Metagenome
Genomics
Multiomics

@article {pmid40921745,
year = {2025},
author = {Zhang, X and Li, Y and Qin, Y and Liao, Z and Deng, C and Chen, Y and Li, Y and Qian, H and He, Y and Chen, S and Shi, G and Liu, Y},
title = {Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren's disease.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40921745},
issn = {2058-5276},
support = {82471833//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82101841//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82171779//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82371802//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023J06055//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; 2022XMSLCYX01//Xiamen Municipal Bureau of Science and Technology (Xiamen Science and Technology Bureau)/ ; },
abstract = {Viral infections are implicated in the pathogenesis of autoimmune diseases, including Sjögren's disease (SjD), but the mechanisms linking viral antigens to disease development remain poorly understood. To address this, we conducted shotgun metagenomic sequencing of saliva samples from 35 patients with SjD and 25 healthy controls. The salivary virome of the patients with SjD, particularly those with high disease activity, had an expansion of Siphoviridae bacteriophages and increased eukaryotic viral sequences, including Vientovirus. This virus was associated with lacrimal gland dysfunction and elevated anti-SSA/Ro52 autoantibody levels. Alignment analysis and cross-blocking assay identified molecular mimicry between the Vientovirus capsid protein and the autoantigen SSA/Ro52. Mice immunized with a Vientovirus capsid peptide developed anti-SSA/Ro52 antibodies and showed immunological features resembling those of patients with SjD. These findings highlight distinct virome profiles in SjD and provide mechanistic evidence supporting the role of Vientovirus in triggering autoimmunity through molecular mimicry.},
}

@article {pmid40921287,
year = {2025},
author = {Akel, R and Zaki, AI and Kerekes, É and Kacsir, I and Kiss, GA and Freytag, C and Szoták, E and Boros-Pál, D and Janka, EA and Kardos, G and Bai, P and Somsák, L and Kun, S and Sipos, A and Bokor, É},
title = {Platinum-group metal half-sandwich complexes with C-glucopyranosyl 1,2,3-triazoles and isoxazoles as ligands: synthesis and evaluation as antineoplastic and antimicrobial agents.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107259},
doi = {10.1016/j.ejps.2025.107259},
pmid = {40921287},
issn = {1879-0720},
abstract = {Half-sandwich complexes of platinum-group metals are a widely studied subgroup of organometallic compounds with promising anticancer and antimicrobial properties. Recently, we have published a set of polyhapto arene/arenyl Ru(II), Os(II), Ir(III) and Rh(III) complexes with hetaryl-substituted 1-N-glucopyranosyl-1,2,3-triazole and C-glycopyranosyl-1,3,4- and -1,2,4-oxadiazole-type N,N-bidentate ligands, several of which exhibited (sub)micromolar antineoplastic and bacteriostatic potencies. The structure-activity relationships of these series indicated that the nature of the azole ring and its way of connection to the pyranoid sugar unit played crucial roles in the biological activity of such complexes. In order to further study the influence of the five-membered heteroaromatic moiety, in this work we have synthesised new complexes with O-protected 4-C-(β-D-glucopyranosyl)-1-(pyridin-2-yl)-1,2,3-triazoles and 5-C-(β-D-glucopyranosyl)-3-(pyridin-2-yl)-isoxazoles as N,N-chelating ligands of η[6]-p-cym-Ru(II)/Os(II) and η[5]-Cp*-Ir(III)/Rh(III) complexes and have studied their cytostatic and antibacterial properties. All but the Rh(III)-derived complexes exerted cytostasis on a plethora of neoplasia cell models. The Ru(II)- and Os(II)-based complexes had the best IC50 values. The isoxazole-containing compounds outperformed the triazole-containing ones in terms of their cytostatic properties with submicromolar IC50 values. A subset of the complexes with Ru(II) and Ir(III) ions had bacteriostatic properties with low micromolar MIC values.},
}

@article {pmid40920777,
year = {2025},
author = {Nendl, A and Raju, SC and Braadland, PR and Nordborg, A and Bratseth, V and Broch, K and Jørgensen, SF and Aukrust, P and Kristiansen, K and Hov, JR and Trøseid, M and Awoyemi, A},
title = {Circulating metabolites in patients with chronic heart failure are not related to gut leakage or gut dysbiosis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331692},
doi = {10.1371/journal.pone.0331692},
pmid = {40920777},
issn = {1932-6203},
mesh = {Humans ; *Dysbiosis/blood/microbiology/metabolism ; *Heart Failure/blood/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Feces/microbiology ; Chronic Disease ; Case-Control Studies ; Metabolomics ; Metabolome ; },
abstract = {BACKGROUND: The gut microbiota produces numerous metabolites that can enter the circulation and exert effects outside the gut. Several studies have reported altered gut microbiota composition and circulating metabolites in patients with chronic heart failure (HF) compared to healthy controls. Limited data is available on the interplay between dysbiotic features of the gut microbiota and altered circulating metabolites in HF patients. We aimed to examine differences in circulating metabolites between people with and without chronic HF, and their association with gut microbiota dysbiosis and cardiac function.

METHODS: We collected plasma, serum, and stool samples from 123 adult patients with stable chronic HF and left ventricular ejection fraction (LVEF) ≤40%, and healthy controls (plasma: n = 51, stool samples: n = 69). Metabolomic and lipidomic profiling of plasma was performed using liquid chromatography with tandem mass spectrometry. Principal component analysis was used to explore differences in circulating profiles. Over-representation analysis was performed to identify pathways in which relevant metabolites were involved. Stool samples were sequenced using shotgun metagenomics. We calculated a dysbiosis index based on differential abundances of microbial taxa in patients vs. controls.

RESULTS: After adjusting for age, sex, and sampling location, we identified 67 enriched metabolites and 24 enriched lipids, and 115 depleted metabolites and 6 depleted lipids in HF patients compared to healthy controls. LVEF, N-terminal pro B-type natriuretic peptide, gut leakage markers, dysbiosis index, and fiber intake were not significantly related to any of the differentially abundant metabolites or lipids. Pathways related to energy metabolism differed most between HF patients and controls, however medication adjustment abolished all differences in circulating profiles.

CONCLUSIONS: Patients with chronic HF had distinct metabolomic and lipidomic profiles and energy metabolism differed significantly compared to healthy controls before adjusting for medication use. However, the alterations were not related to gut dysbiosis, gut leakage markers, cardiac function, or fiber intake.},
}

Humans
*Dysbiosis/blood/microbiology/metabolism
*Heart Failure/blood/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Middle Aged
Aged
Feces/microbiology
Chronic Disease
Case-Control Studies
Metabolomics
Metabolome

@article {pmid40920735,
year = {2025},
author = {Mumcu, H and Zaugg, J and Keles, I and Kayrav, A and Balci, N and Nelson, DR and Hugenholtz, P and Gillam, EMJ and Gul Karaguler, N},
title = {Exploring extreme environments in Türkiye for novel P450s through metagenomic analysis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330523},
doi = {10.1371/journal.pone.0330523},
pmid = {40920735},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; *Cytochrome P-450 Enzyme System/genetics/metabolism/classification ; Phylogeny ; *Extreme Environments ; *Metagenome ; },
abstract = {Cytochrome P450 enzymes (P450s), particularly those of microbial origin, are highly versatile biocatalysts capable of catalyzing a broad range of regio- and stere-oselective reactions. P450s derived from extremophiles are of particular interest due to their potential tolerance to high temperature, salinity, and acidity. This study aimed to identify and classify novel microbial P450 enzymes from extreme environments across Türkiye, including hydrothermal springs, hypersaline lakes, and an acid-mine drainage site. The focus of this study was on classifying the sequence diversity of P450 enzymes in these sites. To that end, shotgun metagenomic analysis of six sites, using de novo binning, phylogenetic analysis, and functional gene annotation, was used to discover 311 putative P450 sequences, assigned to 87 families and 158 subfamilies, including 8 novel families and 49 new subfamilies. Of these, 237 were in 138 metagenomic bins, including 45 high-quality metagenome-assembled genomes. The distribution of P450 families varied across sites, reflecting distinct environmental conditions and microbial community compositions. These findings highlight the untapped potential of Türkiye's extreme habitats as a source of novel biocatalysts. Beyond their industrial relevance, extremophile-derived P450s may also play key roles in enabling microbial adaptation to harsh environmental conditions, through their involvement in stress-responsive metabolic pathways and structurally resilient enzyme forms. This work provides a foundation for future studies into both their biotechnological applications and ecological functions.},
}

*Metagenomics/methods
*Cytochrome P-450 Enzyme System/genetics/metabolism/classification
Phylogeny
*Extreme Environments
*Metagenome

@article {pmid40920725,
year = {2025},
author = {Deng, S and Wu, Y and Hu, P and Lin, J and Yao, J and Wang, B},
title = {Detection of pathogens and epidemiological characteristics of community-acquired pneumonia in children using metagenomic next-generation sequencing.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {8},
pages = {1189-1195},
doi = {10.3855/jidc.20668},
pmid = {40920725},
issn = {1972-2680},
mesh = {Humans ; *Community-Acquired Infections/epidemiology/microbiology/virology ; Child, Preschool ; Infant ; Child ; Male ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Infant, Newborn ; *Pneumonia/epidemiology/microbiology ; Seasons ; Adolescent ; Sputum/microbiology/virology ; *Bacteria/isolation & purification/classification/genetics ; Fungi/isolation & purification/genetics/classification ; Community-Acquired Pneumonia ; },
abstract = {INTRODUCTION: Community-acquired pneumonia (CAP) is a common respiratory disease in children and a significant factor in child mortality.

METHODOLOGY: We aimed to investigate metagenomic next-generation sequencing (mNGS) technology to explore pathogens and epidemiological characteristics of pediatric CAP. We retrospectively analyzed mNGS detection and microbiological culture results of bronchoalveolar lavage fluid (BALF) and sputum samples from children with CAP.

RESULTS: Mycoplasma pneumoniae was the predominant pathogen. Bacteria/fungi detection rates using mNGS in sputum and BALF were higher than those using microbiological culture (p < 0.05). Cytomegalovirus was the predominant pathogen in children aged 0-1; Mycoplasma pneumoniae was the predominant pathogen in those over 1. Haemophilus influenzae, Mycoplasma pneumoniae, human bocavirus 1, and Streptococcus pneumoniae were the predominant pathogens in spring, summer, autumn, and winter, respectively.

CONCLUSIONS: mNGS is superior to traditional microbiological culture for pediatric CAP potential pathogen detection. CAP pathogenic infection characteristics at different ages and seasons detected by mNGS will benefit clinical practitioners in the prevention and treatment of pediatric CAP in their local/regional areas.},
}

Humans
*Community-Acquired Infections/epidemiology/microbiology/virology
Child, Preschool
Infant
Child
Male
Retrospective Studies
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Female
Bronchoalveolar Lavage Fluid/microbiology/virology
Infant, Newborn
*Pneumonia/epidemiology/microbiology
Seasons
Adolescent
Sputum/microbiology/virology
*Bacteria/isolation & purification/classification/genetics
Fungi/isolation & purification/genetics/classification
Community-Acquired Pneumonia

@article {pmid40920721,
year = {2025},
author = {Wang, SK and Zhang, XT and Liu, YE and Wang, MT},
title = {Metagenomic next-generation sequencing for diagnosis of severe pneumonia caused by Nocardia otitidiscaviarum.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {8},
pages = {1269-1275},
doi = {10.3855/jidc.20869},
pmid = {40920721},
issn = {1972-2680},
mesh = {Humans ; Female ; Aged ; *Nocardia/genetics/isolation & purification/classification ; *Nocardia Infections/diagnosis/drug therapy/microbiology ; *High-Throughput Nucleotide Sequencing ; *Pneumonia, Bacterial/diagnosis/microbiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Metagenomics/methods ; Tomography, X-Ray Computed ; Community-Acquired Infections/diagnosis/microbiology/drug therapy ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; },
abstract = {INTRODUCTION: Nocardia spp. are Gram-positive, aerobic actinomycetes, which can cause pulmonary, primary cutaneous, and lymphocutaneous infections. However, severe pneumonia caused by Nocardia otitidiscaviarum has rare reported.

PATIENT CONCERNS: In this case report, a 73-year-old female presented with a 7-day history of fever, cough, followed by a 1-day history of dyspnea. Both lungs showed patchy shadows on a chest CT scan. Bronchoalveolar lavage and mNGS were performed for the rapid diagnosis of the Nocardia otitidiscaviarum induced infection.

DIAGNOSIS: Community-acquired pneumonia was diagnosed following clinical assessment, including characteristic physical examination findings, abnormal laboratory results, and consolidations observed on CT imaging. And the evidence of pathogen was supplied by mNGS.

INTERVENTIONS: The anti-infection therapy regimen was: trimethoprim-sulfamethoxazole (1.44 g q6h) for 3 months according to the detection of the Nocardia otitidiscaviarum.

OUTCOMES: After 3 months of follow-up, the patient has a good outcome and chest CT suggested that the inflammation in the lungs had been almost absorbed.

CONCLUSIONS: Rapid pathogen identification is pivotal for enhancing clinical outcomes and survival in severe pneumonia patients. This case report presents an exceptional case of severe pneumonia caused by Nocardia otitidiscaviarum and the uncommon potential occurrence of human-to-human transmission. mNGS could help avoid misdiagnosis and mistreatment in clinical practice.},
}

Humans
Female
Aged
*Nocardia/genetics/isolation & purification/classification
*Nocardia Infections/diagnosis/drug therapy/microbiology
*High-Throughput Nucleotide Sequencing
*Pneumonia, Bacterial/diagnosis/microbiology/drug therapy
Anti-Bacterial Agents/therapeutic use
*Metagenomics/methods
Tomography, X-Ray Computed
Community-Acquired Infections/diagnosis/microbiology/drug therapy
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use

@article {pmid40920635,
year = {2025},
author = {Xie, P and Shen, J and Yang, Y and Wang, X and Liu, W and Cao, H and Zheng, Y and Wu, C and Mao, G and Chen, L and He, J and Zheng, W and Yang, Z and Zhang, X and Jiang, X and Yang, X and Fang, K and Zhang, Z and Xue, X and Chen, X and Wang, C and Liu, X and Liu, L and Yao, X and Jing, N and Xie, W and Liu, J and Cao, H and Luo, Z and Fang, X and Lin, C},
title = {Digital reconstruction of full embryos during early mouse organogenesis.},
journal = {Cell},
volume = {188},
number = {17},
pages = {4754-4772.e18},
doi = {10.1016/j.cell.2025.05.035},
pmid = {40920635},
issn = {1097-4172},
mesh = {Animals ; *Organogenesis/genetics ; Mice ; *Embryo, Mammalian/metabolism ; Gene Expression Regulation, Developmental ; Mesoderm/metabolism ; Embryonic Development ; Signal Transduction ; Transcriptome ; Endoderm/metabolism ; Female ; Heart/embryology ; },
abstract = {Early organogenesis is a crucial stage in embryonic development, characterized by extensive cell fate specification to initiate organ formation but also by a high susceptibility to developmental defects. Here, we profiled 285 serial sections from six E7.5-E8.0 embryos to generate full spatiotemporal transcriptome and signal maps during early organogenesis at single-cell resolution. By developing SEU-3D, we reconstructed digital embryos, enabling investigation of regionalized gene expression in the native spatial context. We established a space-informed gene-cell co-embedding approach, systematically characterized the spatial atlas of endoderm and mesoderm derivatives, and elucidated signaling networks across germ layers and cell types. Furthermore, we characterized a primordium determination zone (PDZ) formed along the anterior embryonic-extraembryonic interface at E7.75, and it revealed that the coordinated signaling communications contribute to the formation of cardiac primordium. Collectively, the high-resolution "digital embryo" provides significant insights into early organogenesis and a unique spatial platform for studying development and diseases.},
}

Animals
*Organogenesis/genetics
Mice
*Embryo, Mammalian/metabolism
Gene Expression Regulation, Developmental
Mesoderm/metabolism
Embryonic Development
Signal Transduction
Transcriptome
Endoderm/metabolism
Female
Heart/embryology

@article {pmid40920605,
year = {2025},
author = {Yu, L and Jia, R and Liu, S and Li, S and Shen, Y and Rensing, C and Zhou, S},
title = {Rice Root Iron Plaque as a Mediator to Stimulate Methanotrophic Nitrogen Fixation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11221},
pmid = {40920605},
issn = {1520-5851},
abstract = {Iron plaque (IP) on rice root surfaces has been extensively documented as a natural barrier that effectively reduces contaminant bioavailability and accumulation. However, its regulatory mechanisms in rhizospheric methane oxidation and biological nitrogen fixation (BNF) remain elusive. This study reveals a previously unrecognized function of IP: mediating methanotrophic nitrogen fixation through coupled aerobic methane oxidation and IP reduction (Fe-MOX). Using a hydroponic coculture system integrating methane-oxidizing bacteria and rice seedlings, we demonstrated that IP enhanced microbial methane oxidation by 46.8% and significantly stimulated BNF rate by 33.6%, with methane-derived carbon accounting for 89.1% of the BNF energy source. Notably, dissolved iron removal did not diminish the BNF enhancement, excluding mediation by soluble iron species. Intriguingly, ferrihydrite supplementation at equivalent iron concentrations failed to replicate the BNF stimulation observed with IP, suggesting the indispensability of root-associated iron redox cycling. Mechanistic analyses identified that Methylosinus/Methylocystis species mediated Fe(III) reduction, synergistically collaborating with specific rhizobial strains to execute Fe-MOX-dependent BNF. These findings uncover a previously overlooked yet pronounced contribution of IP to BNF, providing novel insights for developing dual-strategy approaches to mitigate methane emissions and reduce nitrogen fertilizer dependency in paddy ecosystems.},
}

@article {pmid40920330,
year = {2025},
author = {Allos, H and John, TM and Stewart, AG},
title = {Microbial cell-free DNA for diagnosis of bacterial and fungal infection in the immunocompromised host - what do we know?.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
pmid = {40920330},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Plasma metagenomic next-generation sequencing (mNGS) enables detection of microbial cell-free deoxyribonucleic acid (mcfDNA) in blood without the need for culture or organism-specific primers. Here, we review clinical performance, methodological variability, and real-world application of plasma mNGS for infectious disease diagnosis in immunocompromised hosts (ICHs).

RECENT FINDINGS: Plasma mNGS has rapidly gained attention as a novel diagnostic tool for infections in ICHs, offering broad-range pathogen detection from a noninvasive blood sample. A growing number of observational studies have assessed its diagnostic yield, clinical impact, and potential to reduce invasive procedures or time to diagnosis. However, results remain variable, with significant differences in study design, patient populations, and adjudication methods. While some studies report meaningful added value, others highlight challenges related to clinical interpretation, limited standardization, and uncertain cost-effectiveness. Moreover, although mNGS offers a wide organismal scope, its sensitivity is influenced by pathogen type, immune status, and technical limitations - particularly in fungal infections and low-burden diseases. Overall, mNGS has yet to find a clearly defined role in routine diagnostic workflows.

SUMMARY: Understanding the current evidence, limitations, and variability surrounding plasma mNGS is essential to guide its appropriate clinical use and to inform future integration into diagnostic pathways for ICHs.},
}

@article {pmid40919923,
year = {2025},
author = {Francis, JD and Yanaç, K and Uyaguari-Diaz, MI},
title = {Seasonal patterns of viromes in urban aquatic environments of Manitoba.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0040824},
doi = {10.1128/aem.00408-24},
pmid = {40919923},
issn = {1098-5336},
abstract = {UNLABELLED: Although wastewater treatment plants harbor many pathogens, traditional methods that monitor the microbial quality of surface water and wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. We used metagenomics and quantitative PCR to assess the taxonomy, functional profiling, and seasonal patterns of DNA and RNA viruses, including the virome distribution in aquatic environments receiving wastewater discharges. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba, along the Red and Assiniboine rivers during the Spring, Summer, and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration. The taxonomy of classified DNA was primarily bacteriophages such as Autographiviridae, Kyanoviridae, and Peduoviridae, which were abundant to a lesser extent. Phage-related functionalities such as portal proteins and bacteriophage T4 major head proteins accounted for approximately 20%-40% of aquatic samples across seasons, which may possibly correspond to the DNA phages that were previously identified. RNA viruses went unclassified in the study; however, similar to DNA viruses, many were found to be non-enveloped or "naked viruses" such as Partiviridae, Picobirnaviridae, Tombusviridae, and Picornaviridae, which accounted for 3%-30% of RNA viruses in the study locations across season. Interestingly, aquatic samples were revealed to maintain an abundance of RNA phage-related functionalities such as long tail fiber protein and putative tail proteins, which accounted for approximately 2%-5% of aquatic samples during the Fall of 2021.

IMPORTANCE: Municipal wastewater effluents discharged into the Red and Assiniboine rivers of Winnipeg, Manitoba, rely on traditional methods that monitor the microbial quality of effluents and receiving surface waters focus solely on the detection of coliforms, which are not necessarily good indicators of viruses or other pathogens. There is also a lack of current wastewater system effluent regulations at the federal and provincial level. Furthermore, previous literature has shown that when viral DNA and RNA sequences are blasted against current genomic databases, approximately 50% of the viral reads are classified as unknown. The significance of our research in characterizing the virome distribution in aquatic environments addresses a knowledge gap in the current effluent guidelines and a need for regulatory practices. In the long run, fecal indicator bacteria, combined with the detection of enteric viruses, may complement assessment of water quality in effluents discharged into rivers.},
}

@article {pmid40919801,
year = {2025},
author = {Chamonara, K and Uddin, MS and Masum, MHU},
title = {16S rRNA metagenome analysis of gut bacteriome of Rohu (Labeo rohita) from Halda River and Kaptai Lake, Bangladesh.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0059025},
doi = {10.1128/mra.00590-25},
pmid = {40919801},
issn = {2576-098X},
abstract = {This research evaluated the gut microbiota of Rohu fish from the Halda River and Kaptai Lake in Bangladesh by 16S rRNA sequencing. Distinct microbial profiles were identified, with Halda samples concentrated in pathogens and Kaptai samples abundant in probiotics.},
}

@article {pmid40919785,
year = {2025},
author = {Zou, Y-y and Yu, B-j and He, C and Ding, L and Xu, X and Wan, J-h and Lei, Y-p and Huang, X and Xiong, H-f and He, W-h and Luo, L-y and Xia, L and Lv, N-h and Zhu, Y},
title = {Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0129925},
doi = {10.1128/spectrum.01299-25},
pmid = {40919785},
issn = {2165-0497},
abstract = {UNLABELLED: Severe acute pancreatitis (SAP) is characterized by systemic inflammation and intestinal barrier dysfunction and is often associated with gut microbiota dysbiosis. Rifaximin, a gut-specific non-absorbable antibiotic, is known to modulate the gut microbiota. Here, we investigated rifaximin's effects and mechanisms in SAP using murine models and a single-center, open-label, randomized controlled trial (Chinese Clinical Trial Registry: ChiCTR2100049794). In mice, rifaximin attenuated pancreatic injury and systemic inflammation and altered gut microbiota composition by decreasing mucin-degrading genera such as Akkermansia (P < 0.05). These protective effects persisted in antibiotic-treated and germ-free mice, suggesting mechanisms not solely dependent on gut microbiota modulation. In patients with predicted SAP (n = 60), rifaximin significantly reduced systemic inflammation compared with controls. WBC decreased from a median of 11.50 × 10[9]/L (IQR 8.76-15.68) to 8.49 × 10[9]/L (6.93-10.20; P = 0.04) and TNF-α from 15.05 pg/mL (12.73-19.75) to 11.00 pg/mL (8.74-15.40; P = 0.009). However, the incidence of culture-confirmed infection did not differ between the rifaximin and control groups (13.3% vs. 13.3%; RR, 1.00; 95% CI, 0.28-3.63). Adverse events were comparable between groups. Metagenomic analyses revealed suppression of mucin-degrading bacteria (e.g., Akkermansia, Bacteroides fragilis, and Hungatella hathewayi) (P < 0.05) and reductions in mucin-degrading carbohydrate-active enzymes, including sialidases and fucosidases. In conclusion, among patients with predicted SAP, rifaximin did not reduce culture-confirmed infectious complications within 90 days after randomization compared with standard care, despite significant improvements in systemic inflammatory markers and selected fecal microbiome features. Larger randomized controlled trials are warranted to validate these findings.

IMPORTANCE: Although rifaximin has been used to target gut-derived inflammation in other contexts, its role in SAP remains largely unexplored. In this study, rifaximin treatment was associated with reduced pancreatic injury and systemic inflammation in both murine models and patients with predicted SAP. Treatment also led to changes in gut microbial composition, notably a decrease in mucin-degrading taxa. Importantly, similar protective effects were also observed in antibiotic-treated and germ-free mice, indicating that rifaximin may act via microbiota-dependent and host-directed pathways. These findings offer novel insights into the gut-pancreas axis and suggest that rifaximin holds therapeutic potential by modulating gut microbial composition and host inflammatory responses in SAP.},
}

@article {pmid40919775,
year = {2025},
author = {Liu, J and Yu, L and Ma, X and Wang, Q and Jin, X and Peng, S and Fu, L},
title = {Clinical Characteristics, Radiological, and Outcomes of Mucormycosis: A 14-Year Retrospective Study From Southern China.},
journal = {Mycoses},
volume = {68},
number = {9},
pages = {e70110},
doi = {10.1111/myc.70110},
pmid = {40919775},
issn = {1439-0507},
support = {//National Natural Science Foundation of China/ ; //Natural Science Foundation of Hunan Province/ ; },
mesh = {Humans ; *Mucormycosis/epidemiology/diagnostic imaging/drug therapy/diagnosis/microbiology/pathology ; Retrospective Studies ; Male ; Female ; China/epidemiology ; Middle Aged ; Adult ; Aged ; Antifungal Agents/therapeutic use ; Tomography, X-Ray Computed ; Treatment Outcome ; Tertiary Care Centers ; Comorbidity ; Amphotericin B/therapeutic use ; Young Adult ; },
abstract = {BACKGROUND: Mucormycosis is a rare, rapidly progressive fungal infection with a high mortality rate. However, clinical data of mucormycosis patients, especially those related to adverse outcomes in China, remain limited.

OBJECTIVE: To enhance understanding of the clinical characteristics of different infection site mucormycosis and identify the factors associated with adverse outcomes.

METHODS: A 14-year retrospective study was conducted at a tertiary care hospital in China. Patients were categorised based on the site of infection and clinical outcomes.

RESULTS: From 2010 to 2024, 32 cases of mucormycosis were identified. Among these, pulmonary mucormycosis (PM) was the most common infection site, followed by disseminated mucormycosis. All patients had underlying comorbidities, predominantly chronic lung disease (37.5%) and diabetes mellitus (34.3%). All received pharmacological treatment, most commonly amphotericin B; 15.6% of patients additionally underwent surgical intervention. Chest CT findings in PM cases most frequently revealed bilateral involvement (68.8%) and cavitation (43.8%). Diagnosis was primarily based on metagenomic next-generation sequencing (mNGS, n = 14) and histopathological examination (n = 11). Adverse outcomes were observed in 46.9% of patients and were significantly associated with corticosteroid or immunosuppressant use, COVID-19 co-infection, disseminated disease, thrombocytopenia, hypoalbuminemia, elevated aspartate aminotransferase (AST), increased incidence of complications, and ICU admission (all p < 0.05).

CONCLUSION: Pulmonary mucormycosis was the predominant subtype in this cohort and was frequently associated with chronic lung disease and diabetes. The high incidence of adverse outcomes highlights the necessity for early diagnosis, prompt antifungal therapy, and aggressive management of complications to improve patient survival.},
}

Humans
*Mucormycosis/epidemiology/diagnostic imaging/drug therapy/diagnosis/microbiology/pathology
Retrospective Studies
Male
Female
China/epidemiology
Middle Aged
Adult
Aged
Antifungal Agents/therapeutic use
Tomography, X-Ray Computed
Treatment Outcome
Tertiary Care Centers
Comorbidity
Amphotericin B/therapeutic use
Young Adult

@article {pmid40919702,
year = {2025},
author = {Zhang, L and Tian, Y and Li, L and Zhan, W and Sun, H and Ren, N and Tang, Z and Ngo, HH},
title = {Movement Mechanisms Harness Lévy Flight for Energy-Efficient Wastewater Treatment in Microalgae-Bacteria Systems.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04676},
doi = {10.1002/advs.202504676},
pmid = {40919702},
issn = {2198-3844},
support = {52341001//National Natural Science Foundation of China/ ; 2022M710953//Postdoctoral Research Foundation of China/ ; 2022ZX02C16//Heilongjiang Key R&D Programme/ ; ES202424//The Open Project of State Key Laboratory of Urban Water Resources and Environment/ ; },
abstract = {Microalgae-bacteria symbiosis system is significant for sustainable and low-carbon wastewater treatment, with self-aggregation being key to its stable operation and effective pollutant removal. Cellular motility is the main driving force behind self-aggregation, crucial for symbiosis stability, but the characteristics and patterns involved still remain largely unexplored. Here, cellular movement dynamics into the microalgae-activated sludge model (ASM3) is incorporated, enabling synchronized simulation of metabolic activities and movement behaviors through physical and biochemical interactions in bioreactor systems. These findings indicate that microalgae induce bacterial movement towards Lévy flights, thereby increasing the bacterial encounter rate by 12.20%, augmenting signaling molecule concentration and biomass by 20.0% and 27.3%, respectively, which in turn strengthens the bacteria self-aggregation effect. Through practical reactor operations with metagenomic analysis, the efficacy of this model in elucidating self-aggregation is further corroborated, improving system stability and pollutant removal efficiency. An optimized microalgae-bacteria system reduces energy costs associated with cellular aggregation processes, economizing on the cost of chemotaxis-related proteins. This study not only elucidate the unique role of Lévy flight in self-aggregation, enhancing the understanding of microalgae-bacteria symbiosis, but also establish response mechanisms between motility patterns and operation dynamics. This allows for targeted regulation across various biosystems, ensuring cost-effective wastewater treatment and proactive prediction.},
}

@article {pmid40919477,
year = {2025},
author = {Xiang, S and Li, J and Chen, Z and Cheng, R and Wang, L and Yu, L and Wei, G and Guan, X and Briggs, BR and King, G and Jiang, H and Shao, Z},
title = {Ecological diversity and metabolic strategies of widespread Marinisomatota in global oceans.},
journal = {Marine life science & technology},
volume = {7},
number = {3},
pages = {523-536},
pmid = {40919477},
issn = {2662-1746},
abstract = {UNLABELLED: Marinisomatota (formerly recognized as Marinimicrobia, Marine Group A, and SAR406) are ubiquitous and abundant in marine environments, traditionally characterized as heterotrophic microorganisms. However, certain members of Marinisomatota have demonstrated the capacity to harness light for carbon dioxide fixation and the synthesis of organic compounds, thriving in the translucent zone or transitioning between the translucent and aphotic layers. The metabolic strategies driving the shift in trophic behaviors, and the factors influencing these transitions, remain largely unexplored. In this study, we investigate the metabolic strategies, ecological distribution, and dietary patterns of Marinisomatota through the analysis of metagenomic and metatranscriptomic data sourced from the global open oceans. A total of 1,588 Marinisomatota genomes were retrieved, representing one class, two orders, 14 families, 31 genera, and 67 species. These organisms are predominantly found in low-latitude marine regions, with relative abundances ranging from 0.18 to 36.21%. Among the 14 families, S15-B10, TCS55, UBA1611, UBA2128, and UBA8226 exhibit potential for light-dependent processes associated with Crassulacean acid metabolism (M00169). Three distinct metabolic strategies were identified within Marinisomatota: MS0 (photoautotrophic potential), MS1 (heterotrophic with a pronounced glycolytic pathway), and MS2 (heterotrophic without glycolysis). The emergence of these metabolic strategies may be a response to nutrient limitations within the ocean. This study reveals the potential for mixotrophic strategies in Marinisomatota, underscoring the critical interplay between life history traits and metabolic strategies in the evolution of novel nutritional groups.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00293-x.},
}

@article {pmid40919468,
year = {2025},
author = {Liu, S and Chen, Q and Qiu, X and Li, W and Tang, K},
title = {Metagenomic analysis reveals genetic coupling between TonB-dependent transporters and extracellular enzymes in coastal bacterial communities.},
journal = {Marine life science & technology},
volume = {7},
number = {3},
pages = {478-491},
pmid = {40919468},
issn = {2662-1746},
abstract = {UNLABELLED: Marine heterotrophic prokaryotes initially release extracellular enzymes to cleave large organic molecules and then take up ambient substrates via transporters. Given the direct influence of extracellular enzymes on nutrient availability, understanding their diversity and dynamics is crucial in comprehending microbial interactions and organic matter cycling in aquatic ecosystems. In this study, metagenomics was employed to investigate the functional diversity and dynamics of extracellular enzymes and transporters in coastal waters over a 22-day period. The metagenome-derived gene pool of organic matter-degrading secretory enzymes and transporters was primarily contributed by three major bacterial classes. Bacteroidota were the primary contributors to the gene pool of secretory carbohydrate-active enzymes (CAZymes), whereas Gammaproteobacteria contribute more to secretory peptidases and TonB-dependent transporters (TBDTs), and Alphaproteobacteria to ATP-binding cassette (ABC) transporters. The distinct substrate targets of the enzymes and transporters combined with the unique dynamics of these taxa across depth layers suggest that organic matter degradation and uptake machinery played a role in ecological niche partitioning. At the community level, the abundance of TBDT genes was more positively correlated with extracellular enzymes than ABC transporters. To further explore taxon-specific differences, we reconstructed 163 bacterial and archaeal metagenome-assembled genomes (MAGs). Correlation patterns at the MAG level varied across taxa: Bacteroidota MAGs exhibited significant positive correlations between TBDTs and extracellular enzymes, whereas Gammaproteobacteria and Alphaproteobacteria MAGs showed weak or no significant correlations. These results suggest the diversity of ecological strategies among marine heterotrophic bacteria and highlight a potential coregulation or functional linkage between extracellular enzymes and TBDTs in the metabolism of marine heterotrophic prokaryotes. Our study advances the understanding of the microbial adaptations driving carbon and nutrient cycling.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00314-9.},
}

@article {pmid40919007,
year = {2025},
author = {Wei, L and Yu, Y and Wang, S and Dong, G and Niu, Y},
title = {Comparison of the Diagnostic Performance of Culture, Histopathology, and mNGS for Periprosthetic Joint Infection Using Periprosthetic Tissue Samples: A Prospective Clinical Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4647-4657},
pmid = {40919007},
issn = {1178-6973},
abstract = {BACKGROUND: This study evaluated the applicability of histopathology, culture, and Metagenomic next-generation sequencing (mNGS) in diagnosing periprosthetic joint infection (PJI).

METHODS: In this prospective trial, 215 consecutive patients with suspected knee PJI were enrolled. Tissue specimens were aseptically collected and processed for histopathological analysis, culture, and mNGS. PJI diagnosis was primarily based on the 2011 MSIS criteria, with reference to the 2018 ICM criteria for improved diagnostic accuracy. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR), and negative likelihood ratio (NLR) of each diagnostic method were calculated.

RESULTS: Among 58 patients included in the final analysis, 38 were diagnosed with PJI and 20 without PJI. The mNGS assay demonstrated a sensitivity of 63.2% (95% CI: 53.6-77.7%), specificity of 80.0% (75.7-90.1%), PPV of 85.7% (76.4-95.3%), NPV of 53.3% (44.6-61.2%), PLR of 1.84 (1.22-2.77), and NLR of 0.27 (0.10-0.40). Culture showed higher specificity at 95.0% (84.6-99.8%) and PPV at 96.5% (88.7-99.7%), with sensitivity of 68.4% (58.2-78.9%). Histopathology exhibited 52.6% sensitivity and perfect specificity (100%). The most commonly detected pathogens by both culture and mNGS were Staphylococcus aureus and coagulase-negative Staphylococci, which are frequently implicated in PJI.

CONCLUSION: mNGS shows promise as a complementary tool for diagnosing PJI, especially in culture-negative or atypical cases. However, it did not outperform conventional methods in accuracy. Its limitations-including a high false-positive rate, interpretive challenges, and lack of susceptibility data-warrant cautious use. Further large-scale studies are needed to define its role in clinical decision-making.},
}

@article {pmid40919002,
year = {2025},
author = {Yang, L and Zhang, Z and Liang, Q and Zhang, H and Wang, Y and Zhuo, C},
title = {Severe Acute Bacterial Skin and Skin Structure Infection Following Fish Spine Injury: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4633-4645},
pmid = {40919002},
issn = {1178-6973},
abstract = {This study presents a rare case of severe acute bacterial skin and soft tissue infection (ABSSSI) following freshwater fish spike injury in a 73-year-old man. Within 24 hours of sustaining the wound, the patient developed septic shock and progressive necrotizing fasciitis. Despite early administration of broad-spectrum antibiotics and intensive care, his condition deteriorated, necessitating below-the-elbow amputation on hospital day four. Metagenomic next-generation sequencing (mNGS) identified Aeromonas veronii as the causative agent. Although the patient showed temporary improvement postoperatively, he later developed hospital-acquired pneumonia and succumbed to complications two months later. This case highlights the potential severity of ABSSSIs caused by aquatic pathogens, particularly in immunocompromised individuals. mNGS provides a comprehensive pathogen snapshot within hours of sample receipt, enabling timely refinement of empiric regimens prior to antimicrobial susceptibility testing availability. Early surgical intervention is essential to control infections and improve clinical outcomes.},
}

@article {pmid40918894,
year = {2025},
author = {Apuy Rodríguez, F and Chacón Quirós, M and Alvarado Fernández, ML and Alvarado Mora, ML and Vanegas Navarro, P},
title = {Microbiome of the Ocular Surface: Resident or Transient Ecosystem?.},
journal = {Cureus},
volume = {17},
number = {8},
pages = {e89487},
pmid = {40918894},
issn = {2168-8184},
abstract = {The ocular surface microbiome (OSM) is a low-density, low-diversity microbial ecosystem influenced by host and environmental factors, including age, hygiene, contact lens use, and systemic disease. Unlike other mucosal sites, the eye lacks a well-defined core microbiome, and its microbial composition varies significantly between individuals. Advances in metagenomics have revealed that commensals such as Corynebacterium and Staphylococcus may contribute to immune regulation and homeostasis. Dysbiosis has been linked to ocular surface disorders, such as dry eye disease (DED), allergic conjunctivitis (AC), and contact lens-related inflammation, with shifts in microbial abundance and diversity. Continued research is needed to define resident versus transient species and to develop microbiome-based diagnostics and therapies.},
}

@article {pmid40918253,
year = {2025},
author = {McMahon, S and Franklin, S and Galloway-Peña, J},
title = {Utilization of machine learning to predict antibiotic resistant event outcomes in acute myeloid leukemia patients undergoing induction chemotherapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629422},
pmid = {40918253},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Leukemia, Myeloid, Acute/drug therapy/microbiology/complications ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Male ; Female ; Middle Aged ; *Induction Chemotherapy/adverse effects ; Bacteria/drug effects/genetics/classification ; Aged ; Adult ; Feces/microbiology ; Metagenomics ; *Drug Resistance, Bacterial ; },
abstract = {INTRODUCTION: Acute myeloid leukemia (AML) patients are highly susceptible to infection. Moreover, prophylactic and empirical antibiotic treatment during chemotherapy disrupts the gut microbiome, raising the risk for antibiotic-resistant (AR) opportunistic pathogens. There is limited data on risk factors for AR infections or colonization events in treated cancer patients, and no predictive models exist. This study aims to combine metagenomic and antibiotic administration data to develop a model predicting AR event outcomes.

METHODS: Baseline stool microbiome, antibiotic administration, resistome, and clinical metadata from 95 patients were utilized to build a Random Forest model to predict AR infection and colonization events by serious AR threats. Additionally, sparse canonical correlation analysis assessed correlations between microbiome and resistome data, while Spearman correlation networks identified direct associations with AR event outcomes and secondary variables.

RESULTS: AR-events were identified in 14 of the 95 included patients, with 8 developing AR infections and 9 identified as AR colonized. A Random Forest model predicted AR event outcomes (AUC = 0.73), identifying bacterial taxa and antibiotic resistance gene (ARG) classes as key variables of importance. Methanobrevibacter smithii, Clostridium leptum, and Bacteroides dorei were identified as key taxa associated with reduced risk of AR events, suggesting the potential roles of commensals in maintaining gut microbial resilience during chemotherapy. ARG classes, particularly those conferring resistance to lincosamides, macrolides, and streptogramins, were negatively associated with AR events.

CONCLUSION: These results underscore the value of integrating microbiome and resistome features to reveal potential protective mechanisms and improve risk prediction for AR outcomes in vulnerable patients.},
}

Humans
*Machine Learning
*Leukemia, Myeloid, Acute/drug therapy/microbiology/complications
*Anti-Bacterial Agents/therapeutic use/pharmacology
Gastrointestinal Microbiome/drug effects
Male
Female
Middle Aged
*Induction Chemotherapy/adverse effects
Bacteria/drug effects/genetics/classification
Aged
Adult
Feces/microbiology
Metagenomics
*Drug Resistance, Bacterial

@article {pmid40918207,
year = {2025},
author = {He, X and Zhang, R and Dong, J and Zhen, W and Zhu, L and Ren, J and Ma, X and Wang, F and Zhang, S and Xu, K and Qiu, F and Su, Q and He, J and Zhou, W and Wu, G},
title = {A metagenomic approach for microbial risk assessment and source attribution in high-risk ports of entry environments.},
journal = {Biosafety and health},
volume = {7},
number = {4},
pages = {228-237},
pmid = {40918207},
issn = {2590-0536},
abstract = {The epidemiological characteristics of emerging infectious disease outbreaks in recent years have underscored the critical importance of controlling imported infectious diseases. In this study, we implemented dynamic tracking of microbial invasions by monitoring environmental microbes at the customs and ports. From July to September 2024, a total of 126 environmental samples were collected from three ports of entry in Shenzhen, China. Metagenomic analysis detected 55 non-viral microbial communities and 12 viral taxa. Among these, 26.8 % of the bacteria, 100 % of the fungi, 71.4 % of the protists, and none of the archaea exhibited potential pathogenic properties. Viruses were the most prevalent, including bacteriophages (100 %), unclassified viruses (96.8 %), giant viruses (27.8 %), fungal viruses (4.8 %), and vertebrate viruses (1.6 %). No statistical differences were observed in viral distribution across areas (χ[2] = 18.70, P = 0.541), sites (χ[2] = 14.02, P = 0.597), or ports of entry (χ[2] = 10.27, P = 0.247). However, viral distribution varied significantly across three sampling months (χ[2] = 21.06, P = 0.002), with a higher proportion of giant viruses detected in July. Thirty-nine and forty microorganisms were identified across the six areas and five sites, respectively, with relatively few area/site-specific microorganisms. Four distinct disinfection level zones were categorized: relatively safe zone, less safe zone, general disinfection zone and key disinfection zone. Two strains of viruses with potential pathogenicity were identified: pigeon circovirus and Influenza A virus (H4N2). This study established a metagenomics-based surveillance framework for microbial risk assessment in high-risk port environments and proposed a four-tier disinfection strategy to prioritize high-contact zones. Our findings highlighted environmental metagenomics as a critical complement to traveler screening and provided early warning signals for the prevention and control of imported infectious diseases.},
}

@article {pmid40917822,
year = {2025},
author = {Li, Q and Jian, L and Zhao, Q},
title = {Improved Etiological Diagnosis of Nonresolving or Slowly Resolving Pneumonia Through Combined Endobronchial Ultrasound-Guided Biopsy and Metagenomic Sequencing.},
journal = {Canadian respiratory journal},
volume = {2025},
number = {},
pages = {7651699},
pmid = {40917822},
issn = {1916-7245},
mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; *Pneumonia/diagnosis/microbiology/etiology ; Metagenomics/methods ; Bronchoscopy/methods ; Image-Guided Biopsy/methods ; Adult ; High-Throughput Nucleotide Sequencing ; Pneumonia, Bacterial/diagnosis ; },
abstract = {Background: Nonresolving or slowly resolving pneumonia (NRP) poses a diagnostic challenge because infectious and noninfectious etiologies often mimic community-acquired pneumonia on imaging. Endobronchial ultrasound-guided transbronchial lung biopsy (EBUS-TBLB) improves tissue acquisition for peripheral lesions, whereas metagenomic next-generation sequencing (mNGS) offers culture-independent pathogen detection. Whether their combination enhances etiological clarification of NRP remains uncertain. Methods: A total of 109 consecutive adults with NRP unresponsive to standard antimicrobial therapy were randomized to EBUS-TBLB alone (n = 66) or EBUS-TBLB + mNGS (n = 43). Baseline characteristics, diagnostic yield, and procedure-related complications were recorded. Diagnostic positivity, sensitivity for infectious agents, and safety profiles were compared using χ [2] or Fisher's exact tests, with p < 0.05 considered significant. Results: Overall diagnostic yield increased from 50.0% with EBUS-TBLB to 72.1% with the combined approach (χ [2] = 4.37, p < 0.05). mNGS significantly improved detection of bacterial/fungal pneumonia (0% vs. 13.9%; p < 0.05) and pulmonary tuberculosis (0% vs. 20.9%; p < 0.05). Malignancy remained the predominant diagnosis (57.8% of all cases); yields for most tumor subtypes were comparable between groups. Complication rates did not differ between the two groups: minor bleeding (19.7% vs. 23.3%), hypoxia (50.0% vs. 48.8%), pneumothorax (4.5% vs. 0%), and delayed recovery (4.5% vs. 7.0%) (p > 0.05). No severe adverse events occurred. Conclusions: EBUS-TBLB + mNGS represents a paradigm shift in the diagnosis of complex respiratory cases, integrating imaging with advanced genomics to enhance precision medicine. In practice, early implementation of the EBUS-TBLB + mNGS diagnostic protocol in patients with NRP can help exclude malignancy or confirm an infectious etiology.},
}

Humans
Male
Female
Middle Aged
Aged
*Pneumonia/diagnosis/microbiology/etiology
Metagenomics/methods
Bronchoscopy/methods
Image-Guided Biopsy/methods
Adult
High-Throughput Nucleotide Sequencing
Pneumonia, Bacterial/diagnosis

@article {pmid40916941,
year = {2025},
author = {Blecksmith, SE and Kalanetra, KM and Weng, CY and Suarez, C and Sitepu, IR and Tang, Y and Ehlers Cheang, S and Jiang, S and Cernioglo, K and Damian-Medina, K and Smilowitz, JT and Lebrilla, CB and Mills, DA and Lemay, DG},
title = {Fecal microbiomes from healthy adult consumers of fruits and vegetables exhibit fiber- and donor-specific fermentation: "5 a day" is not enough.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00947b},
pmid = {40916941},
issn = {2042-650X},
abstract = {To determine the fermentation capacity of gut microbiomes with diverse plant carbohydrate active enzyme (CAZyme) repertoires, we collected fecal samples from 18 healthy adults who reported consuming at least 5 different fruits and vegetables daily and conducted shotgun metagenome analysis. Five fecal samples with the most diverse CAZymes were then fermented in vitro with 7 different fibers selected for their unique monosaccharide profiles-banana, kale,13-bean soup, flax, coconut flour, MS Prebiotic (resistant starch) and Sunfiber (guar gum)-for 72 hours. Samples were collected at 4 timepoints for 16S sequencing, and pH, SCFAs, and monosaccharide measurements. The largest changes in pH, microbial diversity, monosaccharides, and short chain fatty acids (SCFAs) occurred in the first 24 hours of fermentation. SCFA production was highest with flax and lowest with coconut flour. Fermentation patterns ranged from little change to primary degradation (liberated monosaccharides) to robust production of SCFAs. Abundance of Bifidobacteriaceae, Butyricicoccaceae, and Ruminococcaceae correlated with the highest fermentation, Clostridiaceae, Enterococcaceae, and Eggerthellaceae with the lowest. Samples from three of the participants were more responsive than the other two. The donor-specific and fiber-specific responses seen in our study indicate that dietary guidance to consume 5 servings of fruits and vegetables per day may not be enough to ensure that our gut microbiota is capable of unlocking all of fiber's benefits.},
}

@article {pmid40916294,
year = {2025},
author = {Wang, W and Wu, H and Sun, J and Zhai, C and Song, J and Chen, D and Yang, G and Dai, Y and Wang, S and Kong, F},
title = {Enhanced removal of Cr (VI) in constructed wetland with Fe-Ni-LDH-modified crayfish shell biochar: Performance, removal pathways and synergy mechanisms of substrate-microorganism.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139724},
doi = {10.1016/j.jhazmat.2025.139724},
pmid = {40916294},
issn = {1873-3336},
abstract = {In this study, Fe-Ni-layered double hydroxide modified crayfish shell biochar substrate (Fe-Ni-LDH@CSBC) was successfully prepared and introduced into constructed wetland (CW) to research the Cr(VI) removal mechanism through substrate adsorption and microbial action. Adsorption experiments demonstrated the equilibrium adsorption capacities of Fe-Ni-LDH@CSBC for Cr(VI) could reach 1058.48 (C0=10 mg/L) and 1394.59 mg/kg (C0=20 mg/L), respectively. The CW with Fe-Ni-LDH@CSBC showed higher removal efficiencies of COD, TN, TP, and Cr(VI), which respectively reached 72.9 %, 66.8 %, 79.6 %, and 99.3 % with influent Cr(VI) concentration of 50 mg/L. The Fe-Ni-LDH@CSBC stimulated the secretion of extracellular polymeric substances (EPS) (570.6 mg/g VSS), conducive to absorbing Cr(VI) and also delaying or preventing Cr(VI) from entering microorganisms. The increased reduction of Cr(VI) by Fe-Ni-LDH@CSBC was due to its role in enhancing extracellular electron transfer (EET) through boosting cytochrome c, ETSA and NADH levels. Metagenomic sequencing showed that Fe-Ni-LDH@CSBC increased the abundances of resistant microorganisms (Mycobacterium, Mycolicibacterium, and Hyphomicrobium) in CW, and the relative abundance of key functional genes from Cr(VI) reductase (chrR, GST, czcD, zitB, and merR), electron transfer genes (mtrC, fbpC, insB, and afuC) and transport proteins genes (rhtC, pcoB, bpeT, pecM, chrA, and exbB). This research presented an effective method to enhance the removal of Cr(VI) from electroplating wastewater using CW with Fe-Ni-LDH@CSBC.},
}

@article {pmid40915974,
year = {2025},
author = {Ribeiro, MC and Colombo, APV and de Oliveira, AM and Lourenço, TGB and Honório, HM and de Freitas, EC and Messora, MR and Furlaneto, FAC},
title = {The Interplay Between Lifestyle and Oral/Faecal Microbial Profiles Among Periodontal Disease Patients: A Cross-Sectional Study.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70029},
pmid = {40915974},
issn = {1600-051X},
abstract = {AIM: To characterise periodontal and faecal microbiomes of individuals with periodontal health (PH) and diseases, and evaluate associations with periodontal, sociodemographic, anthropometric, nutritional and lifestyle factors.

MATERIALS AND METHODS: Dental biofilm and faecal samples from individuals (n = 24/group) with PH, gingivitis (GG) and periodontitis (PE) were sequenced (16S rRNA). Anthropometric data and questionnaires on demographics, lifestyle, diet and intestinal habits were collected. Data were statistically analysed (p < 0.05).

RESULTS: GG and PE groups showed higher age, BMI, waist/abdominal circumferences and trans-fat intake and lower selenium and vitamin E intake compared to PH. Individuals with PE had higher hip circumference and lower income, education and intake of iron as well as vitamins A and B9. PE microbiomes (oral and faecal) showed distinct compositions, with the highest number of unique oral species. Faecal richness was lower in PE and GG compared to PH. Specific microbial taxa correlated with periodontal status and host factors.

CONCLUSION: Periodontal and faecal microbiomes vary across periodontal conditions. Discriminant analysis classified 77% of individuals by periodontal status, with key markers for PE including older age, poor dietary quality and distinct microbial oral and faecal signatures. These findings highlight the role of clinical, dietary and microbial factors in periodontal disease profiling.},
}

@article {pmid40671648,
year = {2025},
author = {Maiello, G and Lippert, MR and Neave, EF and Hanson, EA and Palumbi, SR and Mariani, S},
title = {Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70010},
pmid = {40671648},
issn = {1755-0998},
support = {//The Pew Charitable Trusts under the Lenfest Ocean Program/ ; //The Gordon and Betty Moore Foundation/ ; //Oceankind Labs/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Kelp ; Ecosystem ; California ; Animals ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Biota ; },
abstract = {The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterising marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including 'traditional' surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we 'captured' 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (Humqaq). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.},
}

*DNA Barcoding, Taxonomic/methods
*Kelp
Ecosystem
California
Animals
*Biodiversity
*Aquatic Organisms/classification/genetics
*DNA, Environmental/genetics
*Metagenomics/methods
*Biota

@article {pmid40464364,
year = {2025},
author = {Rousseau, C and Henry, N and Rousvoal, S and Tanguy, G and Legeay, E and Leblanc, C and Dittami, SM},
title = {A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14129},
pmid = {40464364},
issn = {1755-0998},
support = {AAPG2020//Agence Nationale de la Recherche/ ; ANR-20-CE43-0013//Agence Nationale de la Recherche/ ; },
mesh = {*Seaweed/microbiology/genetics ; *DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; *Plastids/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; DNA Primers/genetics ; Fungi/genetics/classification ; },
abstract = {Short-read metabarcoding analysis is the gold standard for accessing partial 16S and ITS genes with high read quality. With the advent of long-read sequencing, the amplification of full-length target genes is possible, but with low read accuracy. Moreover, 16S rRNA gene amplification in seaweed results in a large proportion of plastid reads, which are directly or indirectly derived from cyanobacteria. Primers designed not to amplify plastid sequences are available for short-read sequencing, while Oxford Nanopore Technology (ONT) offers adaptive sampling, a unique way to remove reads in real time. In this study, we compare three options to address the issue of plastid reads: deleting plastid reads with adaptive sampling, using optimised primers with Illumina MiSeq technology, and sequencing large numbers of reads with Illumina NovaSeq technology with universal primers. We show that adaptive sampling using the default settings of the MinKNOW software was ineffective for plastid depletion. NovaSeq sequencing with universal primers stood out with its deep coverage, low error rate, and ability to include both eukaryotes and bacteria in the same sequencing run, but it had limitations regarding the identification of fungi. The ONT sequencing helped us explore the fungal diversity and allowed for the retrieval of taxonomic information for genera poorly represented in the sequence databases. We also demonstrated with a mock community that the SAMBA workflow provided more accurate taxonomic assignment at the bacterial genus level than the IDTAXA and KRAKEN2 pipelines, but many false positives were generated at the species level.},
}

*Seaweed/microbiology/genetics
*DNA Barcoding, Taxonomic/methods
High-Throughput Nucleotide Sequencing/methods
*Plastids/genetics
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics
*Metagenomics/methods
Sequence Analysis, DNA/methods
DNA Primers/genetics
Fungi/genetics/classification

@article {pmid40459094,
year = {2025},
author = {Dahl, MB and Brachmann, S and Söllinger, A and Schnell, M and Ahlers, L and Wutkowska, M and Hoff, KJ and Nath, N and Groß, V and Wang, H and Weil, M and Piecha, M and Schaffer, M and Jensen, C and Kuss, AW and Gall, C and Wimmer, E and Pribasnig, T and Tveit, AT and Sigurdsson, BD and Schleper, C and Richter, A and Urich, T},
title = {Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques-Cross-Validation and Perspectives.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14130},
pmid = {40459094},
issn = {1755-0998},
support = {21-17322M//The Czech Science Foundation/ ; BO 5559/1-1//Deutsche Forschungsgemeinschaft/ ; INST 292/146-1 FUGB//Deutsche Forschungsgemeinschaft/ ; UR198/7-1//Deutsche Forschungsgemeinschaft/ ; 813114//HORIZON EUROPE European Innovation Council/ ; //Research Council of Norway/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gene Expression Profiling/methods ; *Bacteria/genetics/classification ; Transcriptome ; Soil/chemistry ; },
abstract = {Linking meta-omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAEstd). RNA reads originating from NAEstd were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray-Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between-sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT-PCR experiments, NAEstd and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAEstd and MBC extracts. We discuss how simultaneous changes in community size and the soils nucleic acid retention strength might hamper accurate biomass estimation. Adding NAEstd has the potential to shed important light on nucleic acid retention in the substance matrix (e.g., soil) during extraction.},
}

*Soil Microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Gene Expression Profiling/methods
*Bacteria/genetics/classification
Transcriptome
Soil/chemistry

@article {pmid40375355,
year = {2025},
author = {Shaffer, MR and Andruszkiewicz Allan, E and Van Cise, AM and Parsons, KM and Shelton, AO and Kelly, RP},
title = {Observation Bias in Metabarcoding.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14119},
pmid = {40375355},
issn = {1755-0998},
support = {N00014-22-1-2719//Office of Naval Research/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Polymerase Chain Reaction/methods ; *Fishes/genetics/classification ; *Metagenomics/methods ; DNA Primers/genetics ; Cetacea/genetics/classification ; },
abstract = {DNA metabarcoding is subject to observation bias associated with PCR and sequencing, which can result in observed read proportions differing from actual species proportions in the DNA extract. Here, we amplify and sequence a mock community of known composition containing marine fishes and cetaceans using four different primer sets and a variety of PCR conditions. We first compare metabarcoding observations to two different sets of expected species proportions based on total genomic DNA and on target mitochondrial template DNA. We find that calibrating observed read proportions based on template DNA concentration is most appropriate as it isolates PCR amplification bias; calibration with total genomic DNA results in bias that can be attributed to both PCR amplification bias and differing ratios of template to total genomic DNA. We then model the remaining amplification bias and find that approximately 60% can be explained by inherent species-specific DNA characteristics. These include primer-template mismatches, amplicon fragment length, and GC content, which vary somewhat across Taq polymerases. Finally, we investigate how different PCR protocols influence community composition regardless of expected proportions and find that changing protocols most strongly influence the amplification of templates with primer mismatches. Our findings suggest that using primer-template pairs without mismatches and targeting a narrow taxonomic group can yield more repeatable and accurate estimates of species' true, underlying DNA template proportions. These findings identify key factors that should be considered when designing studies that aim to apply metabarcoding data quantitatively.},
}

*DNA Barcoding, Taxonomic/methods
Animals
Polymerase Chain Reaction/methods
*Fishes/genetics/classification
*Metagenomics/methods
DNA Primers/genetics
Cetacea/genetics/classification

@article {pmid40243260,
year = {2025},
author = {Bayer, PE and Bennett, A and Nester, G and Corrigan, S and Raes, EJ and Cooper, M and Ayad, ME and McVey, P and Kardailsky, A and Pearce, J and Fraser, MW and Goncalves, P and Burnell, S and Rauschert, S},
title = {A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14107},
pmid = {40243260},
issn = {1755-0998},
support = {//Minderoo Foundation/ ; },
mesh = {Animals ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; *DNA, Environmental/genetics ; Computational Biology/methods ; Australia ; *Metagenomics/methods ; Biodiversity ; RNA, Ribosomal/genetics ; },
abstract = {Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.},
}

Animals
*Vertebrates/classification/genetics
*Aquatic Organisms/classification/genetics
*DNA Barcoding, Taxonomic/methods
RNA, Ribosomal, 16S/genetics
*DNA, Environmental/genetics
Computational Biology/methods
Australia
*Metagenomics/methods
Biodiversity
RNA, Ribosomal/genetics

@article {pmid40915677,
year = {2025},
author = {Costa, FF and Lustosa, BPR and Perico, CP and Belmonte-Lopes, R and Carvalho, JLVR and Razzolini, EL and Santos, GDD and Lima, BJFS and Souza-Motta, CM and Raittz, RT and Song, Y and Selbmann, L and de Hoog, GS and Meis, J and Vicente, VA},
title = {In silico search reveals the association of lichens with black yeast-like fungi in the order Chaetothyriales.},
journal = {Fungal biology},
volume = {129},
number = {6},
pages = {101618},
doi = {10.1016/j.funbio.2025.101618},
pmid = {40915677},
issn = {1878-6146},
mesh = {*Lichens/microbiology/classification ; *Ascomycota/genetics/classification/isolation & purification/physiology ; Metagenomics ; Symbiosis ; Phylogeny ; Computer Simulation ; Metagenome ; },
abstract = {Lichens exemplify a unique symbiotic relationship between fungi and algae or cyanobacteria, where fungi (mycobionts) provide structural support, while algae or cyanobacteria (photobionts) provide nutrients. Recent discoveries in the order Chaetothyriales have led to the description of several lichenicolous species, underscoring an intricate relationship of some black yeast-like fungi with lichens. The present study aims to investigate public metagenomic data of lichens available in the SRA database, covering a total of 2888 samples. The analysis incorporated 122 molecular marker sequences (barcodes and padlock probes) previously documented in the literature for species classified within Chaetothyriales. Additionally, 11 novel barcodes for species recently identified in lichens of the genera Cladophialophora and Paracladophialophora are described. The selected metagenomes were then compared with molecular marker sequences using local BLASTn (v2.6.0+), considering only alignments with a coverage cut-off and 100 % identity (perfect match). Reads from each sample were retrieved from the SRA as a multifasta file and analyzed with the SWeeP method for vector-based, alignment-free sequence analysis. The analysis identified fungi that are known as environmental inhabitants and, occasionally, opportunistic pathogens of vertebrates, including species in the genera Cladophialophora, Cyphellophora, and Exophiala. These species were distributed across 11 BioProjects from various locations around the world. The findings of this study corroborate extant knowledge concerning fungal colonization in diverse extremophilic environments, including deserts, tundra, and rocky surfaces.},
}

*Lichens/microbiology/classification
*Ascomycota/genetics/classification/isolation & purification/physiology
Metagenomics
Symbiosis
Phylogeny
Computer Simulation
Metagenome

@article {pmid40915583,
year = {2025},
author = {Zhang, Y and Wang, B and Hassan, M and Zhang, X},
title = {Biochar-calcium alginate composite immobilizing Pseudomonas sp. H6 for phosphate and ammonium recovery: Multi-omics insights and practical application evaluation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133274},
doi = {10.1016/j.biortech.2025.133274},
pmid = {40915583},
issn = {1873-2976},
abstract = {Water eutrophication has emerged as a pervasive ecological challenge worldwide. To realize the resource utilization of waste and nutrients, a novel rape straw-derived biochar-calcium alginate composite (M-CA-RBC) immobilized Pseudomonas sp. H6 was synthesized to simultaneously remove phosphate (PO4[3-]) and ammonium (NH4[+]) from distillery wastewater. The removal performance of PO4[3-] and NH4[+] by M-CA-RBC were investigated. The removal mechanisms were explored by using different adsorption models combined with microbial degradation kinetics, analysis of dissolved organic matter components, electrochemical analysis, metagenomics, and metabolomics. The resource application potential of M-CA-RBC was evaluated. The results showed that M-CA-RBC had good removal performance for PO4[3-] (17.81 mg/g) and NH4[+] (25.78 mg/g). Surface precipitation, electrostatic attraction, Poly-P accumulation, microbial-induced calcium precipitation, and microbial assimilation were the main removal mechanisms of PO4[3-] by M-CA-RBC. The removal mechanisms of NH4[+] were micropore filling, ion exchange, electrostatic attraction, and heterotrophic nitrification-aerobic denitrification (HN-AD). M-CA-RBC had a good application potential in the practical distillery wastewater, with removal rates of PO4[3-] and NH4[+] reaching 88% and 65%, respectively. After adsorption saturation, M-CA-RBC exhibited good stability, which could be used as a slow-release fertilizer to promote the growth of mung beans. This study provides practical significance for the efficient removal and recovery of nitrogen and phosphorus in wastewater.},
}

@article {pmid40915551,
year = {2025},
author = {Akel, R and Kacsir, I and Kerekes, É and Freytag, C and Szoták, E and Boros-Pál, D and Janka, EA and Bényei, A and Kardos, G and Bokor, É and Somsák, L and Bai, P and Sipos, A and Kun, S},
title = {Platinum-group metal half-sandwich complexes of sugar-isoxazol(in)e conjugates - synthesis and evaluation of their antineoplastic and antimicrobial activities.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107260},
doi = {10.1016/j.ejps.2025.107260},
pmid = {40915551},
issn = {1879-0720},
abstract = {Platinum-group metal half-sandwich complexes are considered to be potential replacements of the clinically widely used platins which have several side effects and tend to cause resistance to develop. In our previous works, we used a range of 2-pyridyl-substituted N- and C-glycosyl heterocycles as N,N-chelating ligands to prepare ruthenium(II), osmium(II), iridium(III) and rhodium(III) polyhapto arene/arenyl half-sandwich complexes. Some of these complexes, particularly with the C-glucopyranosyl isoxazole derived ligand in its O-perbenzoylated form, exhibited greater anticancer efficiency than cisplatin and had minimal or negligible effects on non-transformed fibroblasts. Additionally, these cytostatic compounds exhibited micromolar antibacterial activity against multiresistant Gram-positive bacteria. In the present work, novel modes of conjugation between the sugar and the isoxazole moieties have been studied. Specifically, glycosylidene-spiro-isoxazoline and polyhydroxyalkylisoxazole scaffolds were synthesised and utilised in complex formation reactions. The spiro-isoxazolines were obtained in 1,3-dipolar cycloadditions of exo-glycals and nitrile oxides generated from pyridine-2-carbaldoximes. Ring opening of the spiro-isoxazolines under basic or transition-metal-mediated conditions produced polyhydroxyalkylisoxazoles. These compounds were then transformed into their O-peracetylated, O-perbenzoylated and O-unprotected variants, which were used for complex formation with the above-mentioned platinum-group metal ions. The complexes induced cytostasis in cellular models of ovarian cancer and pancreatic adenocarcinoma; the best compounds had submicromolar IC50 values (0.4-0.5 µM). A subset of the cytostatic complexes retained their activity on cisplatin resistant ovarian cancer cells. Furthermore, a reasonable therapeutic index was detected when complexes were assessed on primary human fibroblasts pointing towards a potential applicability of the complexes. Unexpectedly, none of the complexes induced bacteriostasis in Gram-positive bacteria as Staphylococcus aureus or Enterococcus species.},
}

@article {pmid40915262,
year = {2025},
author = {Liu, S and Feng, K and Zhang, D and Liu, Y and Wang, J and Lu, B and Xing, D},
title = {Self-regulating adaptability of biofilm microbiomes enhances manganese and ammonia removal in microbial electrochemical filters under dioxane exposure.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139776},
doi = {10.1016/j.jhazmat.2025.139776},
pmid = {40915262},
issn = {1873-3336},
abstract = {Understanding the stability and assemblage of biofilm microbiomes under oligotrophic conditions is critical for improving groundwater bioremediation. In this study, a novel microbial electrochemical filter (MEF) was developed to explore the impact of weak electrical stimulation on functional adaptability of biofilms under oligotrophic and 1,4-dioxane exposure conditions. Under 20 mg/L 1,4-dioxane stress, the MEF achieved 94.72 % manganese removal and 27.27 % ammonia nitrogen removal, while the conventional biofilter exhibited 88.76 % manganese removal with negligible ammonia nitrogen removal. Metagenomics analyses revealed that dominant populations in the MEF included Nitrospira, Bradyrhizobium, and Nitrosomonas, with relative abundance of 6.23 -10.78 %, 5.81 -6.15 %, and 1.62 -5.58 %, respectively. Weak electrical stimulation enriched the manganese oxidation-associated genes cotA, mnxG, and mcoA, whose total relative abundances being 6.3 times that of the conventional biofilter before dioxane exposure and 2.0 times after exposure. Genes encoding ammonia monooxygenase (amoABC), hydroxylamine dehydrogenase (hao) increased by 2.4- and 1.9-fold, respectively, compared to the conventional biofilter. Additionally, genes involved in the reductive tricarboxylic acid cycle and nitrogen fixation were twice as abundant in the MEF than in the conventional biofilter, suggesting enhanced nutrients availability for heterotrophic bacteria during start-up. These findings demonstrated that weak electrical stimulation effectively regulated biofilm microbiomes and enhance pollutant removal in MEF under oligotrophic conditions.},
}

@article {pmid40915207,
year = {2025},
author = {Zhang, M and Xu, Y and Wang, S and Su, W and Zhang, Y and Xu, H and Li, L and Wang, M and Zhang, J and Yang, Z},
title = {Resistomic features and novel genetic element identified in hospital wastewater with short- and long-read metagenomics.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118991},
doi = {10.1016/j.ecoenv.2025.118991},
pmid = {40915207},
issn = {1090-2414},
abstract = {The global spread of antimicrobial resistance (AMR) poses a serious threat to public health, with hospital wastewater treatment plants (WWTPs) recognized as a key hotspot for resistant pathogens and antibiotic resistance genes (ARGs). This study employed advanced hybrid sequencing platforms to provide a comprehensive resistomic analysis of a Qingdao WWTP in China, revealing previously uncovered AMR transmission risks. We identified 175 ARG subtypes conferring resistance to 38 antimicrobials, including the last-resort antibiotics, highlighting the extensive and concerning resistance reservoir within this environment. Multidrug resistance genes predominated, followed by ARGs targeting aminoglycoside, β-lactam, tetracycline, glycopeptide, and macrolide classes, reflecting clinically relevant resistance patterns. Co-occurrence analysis revealed ARGs were strongly associated with mobile genetic elements, especially for ARGs targeting sulfonamide, glycopeptide, macrolide, tetracycline, aminoglycoside, and β-lactam classes, providing concrete evidence of their high dissemination potential. A striking 85 % of 131 metagenome-assembled genomes (MAGs) carried ARGs, demonstrating prevalent resistance in the wastewater microbiome. Furthermore, the identification of several rarely studied genomic islands (GIs), including those conferring resistance to antibiotics and heavy metals, and notably, the novel variant GIAS409 carrying transposases and heavy metal resistance operons, reveals a significant and previously neglected mechanism for co-selection and dissemination. This study significantly advances our understanding of AMR dynamics in hospital WWTPs, demonstrating that current treatment approaches (42 % ARG removal) have limited efficacy and that WWTP may serve as potential hotspots for multidrug resistance development. Collectively, these findings emphasize the urgent need for improved wastewater management to safeguard public health.},
}

@article {pmid40915146,
year = {2025},
author = {Leonard, SR and Mammel, MK and Brassill, N and Champ, C and Lacher, DW and Saber, B and Kase, JA and Kataoka, A and Bell, RL and Brown, EW and Rock, CM and Musser, SM},
title = {Air microbiomes reveal presence of Shiga toxin-producing Escherichia coli in airborne cattle pen soil adjacent to large feedlot.},
journal = {The Science of the total environment},
volume = {1000},
number = {},
pages = {180375},
doi = {10.1016/j.scitotenv.2025.180375},
pmid = {40915146},
issn = {1879-1026},
abstract = {Cattle are a reservoir for the zoonotic human foodborne pathogen Shiga toxin-producing Escherichia coli (STEC), the causative agent of many disease outbreaks associated with contaminated fresh leafy greens. Concentrated animal feeding operations (CAFOs) housing cattle generate fugitive dust, however the potential risk of STEC movement by means of the aerosolized dust is not well known. In this investigation, we used metagenome sequencing of air samples collected in an agricultural setting to investigate airborne transfer of STEC from a large CAFO to the surrounding area. Shiga toxin genes and other E. coli virulence genes were observed in air metagenomes, and their presence was positively correlated with abundance of cattle mitochondrial DNA (mtDNA). Air bacterial community composition differed based on STEC presence, and source tracking utilizing the air metagenomes indicated that cattle feedlot soil contributed to the air bacterial communities. Moreover, a novel biomarker for cattle pen soil, Corynebacterium maris, was identified that correlated with both E. coli virulence gene presence and cattle mtDNA abundance. Overall, our results demonstrate a definitive link between aerosolized cattle feedlot dust and airborne STEC transfer to adjacent and nearby agricultural fields. This work highlights the importance of including the potential for airborne transmission of pathogens in risk assessments for contamination by human foodborne pathogens of fresh produce grown in proximity to CAFOs.},
}