@article {pmid42135082,
year = {2026},
author = {Saranya, RG and Ramesh Babu, K and Viswanathan, P},
title = {Corrigendum to "Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR" [Life Sci. 393 (2026) 124336].},
journal = {Life sciences},
volume = {},
number = {},
pages = {124457},
doi = {10.1016/j.lfs.2026.124457},
pmid = {42135082},
issn = {1879-0631},
}

@article {pmid42135536,
year = {2026},
author = {Adedire, DE and Onilude, AA and Odeniyi, OA and Nash, O and Semenya, K and Unuofin, JO},
title = {Snapshot reflection of the seasonal resilience and diversity of fungal phylotypes in the tropical Ikogosi spring.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42135536},
issn = {1614-7499},
abstract = {Freshwater ecosystems like rivers, streams, and springs harbour diverse microbial communities, including fungal and bacterial phylotypes. These communities are an important part of the aquatic ecosystem, playing key roles in biogeochemical cycles. However, research on the seasonal differences concerning the fungal diversity of Ikogosi Warm Spring's sediments and water has been lacking. In this pilot study, we aimed to bridge this gap by employing high-throughput DNA sequencing to examine the fungal microbiome of this spring during the wet and dry seasons. Metagenomic DNA was extracted from water and sediment samples from different locations of the spring, and the fungal ITS1 region was sequenced using Illumina HiSeq technology. Sequences were processed with the DADA2 pipeline in R, enabling comprehensive taxonomic and diversity analyses. In addition, the spring's sediment and water physicochemical characteristics were assessed, and the impact of environmental variables on fungal communities was examined using redundancy analysis. Taxonomic analysis revealed that the spring was dominated by Ascomycota and Basidiomycota, irrespective of seasonal differences. In water samples, Ascomycota represented 62.0% (wet season) and 89.0% (dry season), while Basidiomycota accounted for 37.7% and 10.7%, respectively. Sediments exhibited a similar dominance, with Ascomycota comprising 65.1% in both seasons and Basidiomycota contributing 34.8% (wet season) and 33.5% (dry season). Alpha diversity indices indicated that fungal diversity was higher during the dry season than in the wet season, with no significant difference at p < 0.05. Redundancy analysis showed that some physicochemical factors, such as potassium and sulphate ions in water samples, were associated with seasonal patterns. These factors also influenced fungal communities in the spring, such as Cladosporium, Trichosporon, and Meyerozyma.},
}

@article {pmid42135633,
year = {2026},
author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X},
title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05137-x},
pmid = {42135633},
issn = {1471-2180},
support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; },
abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.

RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p < 0.05, |log2FC| ≥ 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+ 52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.

CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.},
}

@article {pmid42136553,
year = {2026},
author = {Yang, L and Chen, X and Jia, A and Liu, Q and Chu, J},
title = {Atypical Streptococcus sinensis infective endocarditis complicated by bacterial meningitis: A case report and literature review.},
journal = {The Journal of international medical research},
volume = {54},
number = {5},
pages = {3000605261447124},
doi = {10.1177/03000605261447124},
pmid = {42136553},
issn = {1473-2300},
mesh = {Humans ; Male ; *Meningitis, Bacterial/microbiology/drug therapy/complications/diagnosis ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Streptococcus/isolation & purification/genetics ; *Endocarditis, Bacterial/microbiology/drug therapy/complications/diagnosis ; *Streptococcal Infections/microbiology/drug therapy/complications/diagnosis ; RNA, Ribosomal, 16S/genetics ; Vancomycin/therapeutic use ; *Endocarditis/microbiology/complications/drug therapy ; Mitral Valve/microbiology ; Ceftriaxone/therapeutic use ; Echocardiography ; },
abstract = {Infective endocarditis caused by Streptococcus sinensis complicated by bacterial meningitis is exceedingly rare. We report a case of a middle-aged man who initially presented with ischemic symptoms in both lower limbs. Echocardiography revealed mitral valvular vegetations, and blood cultures confirmed S. sinensis. During antibiotic therapy, the patient developed somnolence, dysarthria, and left-sided weakness. Metagenomic next-generation sequencing of cerebrospinal fluid detected S. sinensis, thereby confirming infective endocarditis complicated by bacterial meningitis. Given the high surgical risk, combination antimicrobial therapy with vancomycin and ceftriaxone was administered. The patient's consciousness recovered, and inflammatory and cerebrospinal fluid parameters gradually normalized. This case demonstrates that S. sinensis-associated infective endocarditis can occur in patients with immunocompetent status and often involves the mitral valve, with potential intracranial complications. Early identification by blood culture, metagenomic next-generation sequencing, and 16S rRNA sequencing enables precise pathogen diagnosis. Standardized antibiotic therapy and individualized surgical assessment are crucial to optimize outcomes. For patients with neurological complications, multidisciplinary management is essential to improve survival and long-term prognosis.},
}

Humans
Male
*Meningitis, Bacterial/microbiology/drug therapy/complications/diagnosis
Middle Aged
Anti-Bacterial Agents/therapeutic use
*Streptococcus/isolation & purification/genetics
*Endocarditis, Bacterial/microbiology/drug therapy/complications/diagnosis
*Streptococcal Infections/microbiology/drug therapy/complications/diagnosis
RNA, Ribosomal, 16S/genetics
Vancomycin/therapeutic use
*Endocarditis/microbiology/complications/drug therapy
Mitral Valve/microbiology
Ceftriaxone/therapeutic use
Echocardiography

@article {pmid42136736,
year = {2026},
author = {Takahashi, Y and Sada, RM and Matsuo, H and Yamamoto, S and Matsuzaki, S and Okada, A and Sunada, A and Takao, M and Yamamoto, G and Chuang, CK and Liu, CH and Kutsuna, S},
title = {Diagnostic challenges in postoperative pelvic infections associated with Metamycoplasma hominis: a two-case analysis using metagenomic sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1823299},
pmid = {42136736},
issn = {2235-2988},
mesh = {Humans ; Female ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Mycoplasma hominis/genetics/isolation & purification ; Middle Aged ; *Pelvic Infection/diagnosis/microbiology ; *Postoperative Complications/diagnosis/microbiology ; DNA, Bacterial/genetics ; Adult ; *Mycoplasma Infections/diagnosis/microbiology ; },
abstract = {Postoperative gynecological infections may present diagnostic challenges, particularly in the presence of fastidious genital mollicutes and inherently mixed microbial DNA, both of which limit the diagnostic performance of microbiological methods, including Gram staining, conventional culture, 16S rRNA gene PCR followed by Sanger sequencing. This study aimed to illustrate the limitations of conventional microbiological methods in the diagnosis of gynecologic pelvic infections and highlight key considerations for the clinical use of metagenomic next-generation sequencing (mNGS), based on two contrasting cases of postoperative pelvic infections associated with Metamycoplasma hominis (M. hominis). In both cases, neither conventional culture nor 16S rRNA gene PCR/Sanger sequencing identified the causative organism, and shotgun mNGS was subsequently performed. Although the mNGS findings differed markedly between the two cases, M. hominis was considered the most plausible pathogen. These two cases show that the clinical relevance of organisms detected by mNGS should not be judged by read counts alone, particularly in non-sterile specimens or after antibiotic exposure. Even low-abundance reads may represent clinically meaningful pathogens when interpreted within the clinical context. They also highlighted the value of mNGS as a complementary diagnostic tool for gynecological pelvic infections when conventional diagnostic methods are intrinsically limited.},
}

Humans
Female
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
*Mycoplasma hominis/genetics/isolation & purification
Middle Aged
*Pelvic Infection/diagnosis/microbiology
*Postoperative Complications/diagnosis/microbiology
DNA, Bacterial/genetics
Adult
*Mycoplasma Infections/diagnosis/microbiology

@article {pmid42136790,
year = {2026},
author = {Ariyasiri, A and Altaf, A and Mirza, H and Rehman, M},
title = {Genomics for precision surgical source control in anti-microbial resistant infections: A global review with focus on resource-limited settings.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {411AASC},
pages = {S151-S156},
pmid = {42136790},
issn = {1682-024X},
abstract = {BACKGROUND & OBJECTIVE: Antimicrobial resistance (AMR) critically threatens surgical safety, impairing perioperative prophylaxis and complicating infection management. Timely surgical source control is essential but relies on accurate microbiological diagnosis. Conventional culture-based methods are slow and insensitive, often leading to empirical broad-spectrum therapy. This review evaluates the role of advanced genomic diagnostics in enhancing surgical source control for AMR infections, with a focus on challenges and opportunities in low- and middle-income countries (LMICs) like Pakistan.

METHODOLOGY: A narrative review was conducted via a structured search of PubMed, Google Scholar, and ScienceDirect (January 2015-October 2025). Studies involving genomic tools in the management of AMR-related surgical infections were included. Evidence was synthesized thematically, covering genomic platforms, clinical applications, implementation barriers, and LMIC specific perspectives.

RESULTS: Genomic tools, particularly metagenomic next-generation sequencing (mNGS) and rapid multiplex PCR, demonstrate superior sensitivity (80.6-95.45%) and faster turnaround times (e.g., roughly 27 hours for mNGS) compared to culture. They improve pathogen detection in complex infections (e.g., prosthetic joints, necrotizing soft tissue), guide targeted antibiotic therapy, and can reduce broad-spectrum use. However, major implementation barriers exist, including high costs, need for specialized infrastructure and expertise, bioinformatic challenges, and ethical data concerns, which are especially pronounced in LMICs.

CONCLUSION: Genomic diagnostics offer a powerful approach to accelerate and refine surgical source control in the era of AMR. Strategic investments in local capacity, affordable platforms, and integration with antimicrobial stewardship are needed to realize their potential for improving surgical outcomes, particularly in resource-limited settings.},
}

@article {pmid42136862,
year = {2026},
author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M},
title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1805596},
pmid = {42136862},
issn = {2296-858X},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.

OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.

METHODS: Skin samples were collected from 12 AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).

RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p = 0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p = 0.042) and between moderate and severe groups (p = 0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.

CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.},
}

@article {pmid42136870,
year = {2026},
author = {Zhou, Y and Chen, L and Wang, L and Zhao, Z and Tu, J and Chen, H and Wang, S},
title = {Cavitary nodule caused by Emergomyces orientalis in a diabetic patient: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1829356},
pmid = {42136870},
issn = {2296-858X},
abstract = {Emergomyces orientalis is a rare thermally dimorphic fungus belonging to the family Ajellomycetaceae. It exists in the environment as a mold producing conidia, which are inhaled and transform into yeast-like cells at body temperature to cause disseminated infections. While primarily associated with immunocompromised individuals, especially those with HIV. Diagnosis remains challenging due to its morphological similarity to Blastomyces dermatitidis and the frequent failure of routine cultures. Thus, molecular methods such as metagenomic next-generation sequencing (mNGS) have become crucial for early identification. This case report describes a 51-year-old man with type 2 diabetes mellitus presented (T2DM) with a 10-day history of back pain, pharyngeal discomfort, and scant sputum. Chest CT showed multiple bilateral pulmonary nodules, one of which had cavitated. mNGS of a percutaneous lung biopsy confirmed Emergomyces orientalis. Histopathology also supported the diagnosis. The patient was discharged on oral itraconazole after partial symptomatic improvement, with outpatient follow-up arranged. Two months of antifungal therapy resulted in mild reduction of cavitary lesions on follow-up CT.},
}

@article {pmid42137133,
year = {2025},
author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K},
title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {85-96},
pmid = {42137133},
issn = {2008-2258},
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).

METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.

RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.

CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.},
}

@article {pmid42137225,
year = {2026},
author = {Meknas, A and Bessonov, K and Eagle, SHC and Peterson, CL and Robertson, J and Ricker, N and Signorelli, T and Nash, J and Reimer, A},
title = {Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.},
journal = {Access microbiology},
volume = {8},
number = {5},
pages = {},
pmid = {42137225},
issn = {2516-8290},
abstract = {This article presents Sequenoscope: a bioinformatics pipeline for analysing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: filter_ONT for filtering raw reads and creating a FASTQ file with a subset of reads for further analyses, analyze for generating sequencing and read mapping statistics against the provided reference taxon sequences and plot for interactive data summarization, comparison, and visualization between two datasets/test conditions. Here, we demonstrate the ability of the pipeline to analyse ONT adaptive sampling sequence data and provide examples of the outputs users can expect using data we generated. Adaptive sampling was performed on two ZymoBIOMICS Microbial Community DNA Standards, log-distributed (Cat# D6311) and even-distributed (Cat# D6306) formulations, with targeted depletions of Listeria monocytogenes. By comparing the test and control experimental data in FASTQ files from the sequencing runs, Sequenoscope showed that depletion of L. monocytogenes was successful by providing users with parameters to compare such as taxon coverage, read length and types of pore-level decisions made during sequencing. Although Sequenoscope was designed for ONT adaptive sampling data analysis, it supports short-read data from other sequencing platforms such as Illumina, allowing for the direct comparison of any two experimental conditions or cross-platform benchmarking.},
}

@article {pmid42137573,
year = {2026},
author = {Sun, J and Gao, W and Tan, H},
title = {The role of targeted next-generation sequencing and ultrasound in diagnosing fetal cytomegalovirus infection: a case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1734139},
pmid = {42137573},
issn = {2296-2360},
abstract = {BACKGROUND: Cytomegalovirus (CMV) infection is a leading cause of congenital infection and neonatal morbidity. Conventional diagnostic methods, such as polymerase chain reaction (PCR) and amniocentesis, remain important in the diagnosis of congenital CMV infection, although each method has its own limitations in clinical practice.

CASE PRESENTATION: A 31-year-old woman, gravida 3 para 1, presented for routine prenatal evaluation. At 18 weeks of gestation, ultrasound revealed echogenic bowel and fetal ascites. Amniocentesis at 19 weeks showed normal chromosomal results, but targeted next-generation sequencing (tNGS) detected CMV DNA with a high viral load, confirming intrauterine infection.

RESULTS: Despite counseling regarding poor fetal prognosis, the patient chose to continue the pregnancy under close ultrasound surveillance. Progressive hydrops fetalis was observed at 23 weeks, and the pregnancy was terminated at 24 weeks.

CONCLUSION: This case suggests that combining tNGS with ultrasound may provide complementary diagnostic information in selected cases of suspected fetal infection. In this patient, tNGS supported the identification of CMV in amniotic fluid when conventional genetic testing was unremarkable. However, as this is a single-case report, the broader diagnostic performance and clinical utility of tNGS require further validation in larger studies.},
}

@article {pmid42137610,
year = {2026},
author = {Oguzie, JU and Cummings, DB and Groves, JT and Hagan, AG and Rodriguez, J and Hernandez-Vidal, G and Moreno-Degollado, G and Shittu, I and Marushchak, LV and Nguyen-Tien, T and Trujillo-Vargas, CM and Silva, DB and Li, F and Richeson, JT and Schneider, NE and Gray, GC},
title = {Detection and Genomic Characterization of Novel Respiratory Viruses in US and Mexican Cattle Farms.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {},
pages = {3247802},
pmid = {42137610},
issn = {1865-1682},
mesh = {Animals ; Cattle ; United States/epidemiology ; *Cattle Diseases/virology/epidemiology ; Mexico/epidemiology ; *Respiratory Tract Infections/veterinary/virology/epidemiology ; Farms ; Humans ; Genome, Viral ; *Viruses/isolation & purification/genetics/classification ; *Virus Diseases/veterinary/epidemiology/virology ; },
abstract = {Respiratory virus infections in cattle cause an estimated more than $1 billion in production losses and can threaten human health. During February 2024 to May 2025, we employed a One Health approach to surveil for respiratory viruses among cattle, farm workers, and environmental samples from 11 US and Mexican beef or dairy cattle farms. We studied nasal and ocular swabs from cattle, nasal swabs from cattle workers, bioaerosol samples, and other environmental farm samples using molecular and virological techniques. Among 26 distinct viruses identified in cattle, we detected bovine nidovirus 1, influenza D virus (D/OK-like and D/660-like), bovine coronavirus, bovine rhinitis A and B viruses, bovine respirovirus 3 and bovine respiratory syncytial virus (BRSV); 11 of the 26 detected viruses were non-bovine-associated. Two bovine rhinitis A virus was markedly divergent (provisionally designated BRAV-4). Environmental metagenomics additionally identified influenza D virus, bovine coronavirus, and bovine rhinitis B virus. One human nasal swab tested positive for SARS-CoV-2 (cladeLF.7.3). Our findings reveal the presence of emerging, co-circulating, and environmentally linked pathogens at the human-animal-environment interface, underscoring the constant need for One Health surveillance to safeguard livestock and mitigate zoonotic risk.},
}

Animals
Cattle
United States/epidemiology
*Cattle Diseases/virology/epidemiology
Mexico/epidemiology
*Respiratory Tract Infections/veterinary/virology/epidemiology
Farms
Humans
Genome, Viral
*Viruses/isolation & purification/genetics/classification
*Virus Diseases/veterinary/epidemiology/virology

@article {pmid42137790,
year = {2026},
author = {Qi, J and Zhang, K and Zhan, C and Lu, X and Chen, X and Li, X and Zhang, C and Wang, H and Tu, C and Tong, W and Dai, L and Zeng, D},
title = {Microbial and metabolic crosstalk in the rhizosphere shapes the divergent drought resilience of contrasting rice genotypes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1788826},
pmid = {42137790},
issn = {1664-302X},
abstract = {Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe-metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.},
}

@article {pmid42137793,
year = {2026},
author = {Adeleke, RA and Machailoe, TME and Malemagovha, M and Olanrewaju, OS and Alayande, KA and Obi, LU and Makinde, OM},
title = {Diversity and functional potential of bacterial and fungal endophytes in traditional food wrapping leaves reveal implications for artisanal food safety and quality.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1641069},
pmid = {42137793},
issn = {1664-302X},
abstract = {Plant leaves are widely utilised globally for the packaging and serving of traditionally prepared foods. The microbial communities associated with these wrapping leaves, particularly endophytes, are recognised to potentially influence food quality, safety, and preservation. Specifically, certain endophytes can enhance sensory attributes and nutritional value through fermentative processes, while the presence of harmful microorganisms may lead to spoilage and pose a risk of foodborne illness. This study utilised 16S rRNA, ITS metabarcoding and metagenomic functional analysis (PICRUSt2) to comprehensively investigate the composition and infer the putative functional potential of putative endophytic bacterial and fungal communities present in 53 samples of four different food wrapping leaves. The leaves examined included Thaumatococcus daniellii (n = 10), Alstonia macrophylla (n = 18), Theobroma species (n = 14), and Megaphrynium macrostachyum (n = 11). Distinct microbial community profiles were observed across the different leaf types. Highest bacterial species richness and community variability were detected in A. macrophylla samples, reflected by Principal Coordinates Analysis (PCoA) values (PCoA1 = 43.97%; PCoA2 = 10.68%). Conversely, M. macrostachyum exhibited the greatest fungal species richness and variability (PCoA1 = 20.08%; PCoA2 = 8.72%). Taxonomic analysis identified Proteobacteria as the dominant bacterial phylum and Stenotrophomonas as the dominant bacterial genus. Other notable bacterial taxa included the phyla Bacteroidota and Firmicutes, and genera such as Pseudomonas, Faecalibacterium, and Bacteroides. For fungal communities, Ascomycota was the dominant phylum. Additional fungal taxa included the phylum Basidiomycota and genera Cryptococcus, Candida, and Meyerozyma. A core microbiome analysis revealed that 42 bacterial (notably Stenotrophomonas and Chryseobacterium) and 7 fungal taxa (notably Pleosporaceae and Ascomycota) were shared across all examined wrapping leaves. The identified microbial communities (e.g., Lactobacillus and Geotrichum) encompass taxa with potential beneficial roles, such as enhancing food fermentation and potentially contributing to human gut health upon consumption of the packaged food. However, the detection of potentially pathogenic and toxigenic bacterial taxa highlights a possible public health risk associated with the use of these leaves. Further investigation into the specific functionalities of these associated bacteria and fungi is essential to maximise their beneficial applications while simultaneously mitigating potential health risks posed by harmful strains.},
}

@article {pmid42137803,
year = {2026},
author = {Liu, Y and Chen, C and Gao, J},
title = {Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818141},
pmid = {42137803},
issn = {1664-302X},
abstract = {Microorganisms are intricately interrelated with each other in the gut microecosystem, which influences the colonization and functional roles of probiotics. However, how these interactions dynamically change during host development and whether their topological features influence host phenotypes, such as average daily gain (ADG), remain poorly understood. In this study, we performed metagenome analysis for 2,311 fecal samples collected from a specifically designed eight genetically divergent breed intercrossed mosaic F6 and F7 population, at three developmental ages of 25 days (D25), 120 days (D120), and 240 days (D240) of each individual, covering pre-weaning to market. By constructing their microbiota co-abundance networks, we systematically characterized dynamic changes in beneficial commensal bacteria involved co-abundance networks in the pig gut microbiome across three ages. We elucidated conserved and variable co-abundance features involving these bacteria across developmental stages. We observed that the cross-age stable co-abundance correlations of beneficial commensal bacteria were maintained by a large set of weak correlations. A subset of age-shared co-abundance correlations remained variable across different ages in correlation strength and direction. Topological analysis revealed that beneficial commensal bacteria involved co-abundance networks were highly age-specific. Among the three age stages sampled in this study, the D120 stage represented a critical window for the structural and functional reorganization of gut microbiota. Using metagenomic sequencing data at the D120, we identified two guilds that were significantly associated with ADG from D120 to D240. Guild 1 included short chain fatty acid-producing taxa and was positively associated with ADG, whereas Guild 2 tended to self-utilization of energy and was negatively associated with ADG. We also inferred the ecological interaction mechanisms of ADG-associated microbial communities using genome-scale metabolic models. These findings provided a theoretical basis for stage-specific intervention in the pig gut microbiome using probiotics to improve production traits.},
}

@article {pmid42137806,
year = {2026},
author = {Doughan, GE and Walthart, BK and Schau, CE and Skoland, KJ and Mou, KTY and Brown, JT and Bonnema, JL and Plummer, PJ and Zhang, D and Li, G and Karriker, LA},
title = {Presence of antimicrobial resistance genes in biofilms from swine drinking water pipes before and after treatment with peracetic acid.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1770950},
pmid = {42137806},
issn = {1664-302X},
abstract = {Biofilms can be problematic to swine drinking water systems as they can harbor pathogens, decrease water quality, and may contribute to antimicrobial treatment failure. Water-administered antimicrobials are used for disease treatment in swine populations, yet, little is known about water line ecology and the impact it can have on antimicrobial resistance and stewardship. Water line cleaning and disinfection may aid in removal of water line biofilms, improve swine health, and antimicrobial stewardship. Water line samples were collected pre-treatment (0), 24 h post-treatment with 0.78% CID 2000 Pro (peracetic acid) (1), and 3, 5, 7, 14, 21, 42, 56, and 77-days post-treatment from six wean-to-finish swine farms in Iowa, USA. Biofilm was aseptically extracted from the interior of the water line pipe (n = 119) and submitted for metagenomic analysis to detect antimicrobial resistance genes (ARGs). This study demonstrates high prevalence of ARGs in swine water line biofilms that could confer resistance to both medically important antimicrobials to humans and animals such as aminoglycosides, beta-lactams, fluoroquinolones, colistin, and fosfomycin. From 115 samples, a frequency of 3,904 ARGs were reported, with 184 unique ARGs defined. Four samples contained no ARGs. One hundred and fifty-one integron genes representing three classes were found in 115 of 119 samples, indicating mechanisms of potential spread of multiple drug resistance. ARGs and integron genes combined were significantly lower on average by 10 unique ARGs/ integron genes 24-h post-treatment (1) when compared to pre-treatment (0) counts (p-value = 0.01). The number of unique ARG and integron genes quickly rebounded and were not statistically significant compared to pre-treatment counts on post-treatment dates 3, 5, and 7 (adjusted p-value ≥ 0.05), and by post-treatment date 14, unique ARG and integron genes were significantly higher than pre-treatment (adjusted p-value = 0.012). This study demonstrates that swine water line biofilms can harbor antimicrobial resistance genes which could have potential clinical impacts on pig health and treatment response.},
}

@article {pmid42137815,
year = {2026},
author = {Geng, S and Shi, X and Zhang, Q and Yang, J and Yang, C and Yang, L},
title = {Organic fertilizer enhances microbial functional genes related to nitrogen and phosphorus cycling in rubber tree (Hevea brasiliensis) rhizosphere.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1833968},
pmid = {42137815},
issn = {1664-302X},
abstract = {INTRODUCTION: Nitrogen (N) and phosphorus (P) are the essential nutrient for rubber growth. However, the effect of organic fertilizer application on soil microbial communities and functional genes related to N and P cycling in rubber plantation are unclear.

METHODS: A field trial was established in a rubber plantation with two treatments: organic fertilizer (OF) and an unfertilized control (CK). In this study, we used metagenomics analysis to examine the structural and functional alterations in the microbial community within the rhizospheric soil of rubber when organic fertilizers were applied.

RESULTS: Results showed that compared with the CK treatments, the OF treatment significantly increased soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), alkali-hydrolyzable nitrogen (AN), and available phosphorus (AP) contents. Taxonomic analysis revealed that OF treatment significantly enriched the phyla Pseudomonadota and Myxococcota, and the genera Pseudolabrys and Gaiella. At the functional level, organic fertilization significantly up-regulated key genes associated with N cycling, including organic N metabolism (gltB), N transport (nrtA, nrtB, nrtC), denitrification (norB, nosZ), nitrification (nxrB), and dissimilatory nitrate reduction (napA, napC). Regarding the P cycle, organic fertilization leads to the downregulation of the high-affinity phosphate transporter gene pstS and the concurrent upregulation of genes governing organic P mineralization (phnA, phoN), regulation (phoB), polyphosphate synthesis (ppk1), and polyphosphate degradation (spoT, relA). The variation partitioning analysis (VPA) results indicated that pH, SOM, and nitrogen nutrients (comprising TN and AN) explained 71.52% of the variation in the abundance of nitrogen-cycling functional genes, while pH, SOM, and phosphorus nutrients (comprising TP and AP) explained 64.95% of the variation in the abundance of phosphorus-cycling functional genes.

CONCLUSION: In summary, the application of organic fertilizer reshapes soil microbial communities and enhances the functional potential for nitrogen (N) and phosphorus (P) cycling. Our study provides a mechanistic basis for developing sustainable nutrient management strategies to optimize N and P bioavailability in tropical rubber agroecosystems.},
}

@article {pmid42137872,
year = {2026},
author = {Parrino, J and Sunshine, J and Tripp, K and Shaffer, M and Sughra, U and Procházková, N and Jara, M and Moll, JM and Noble, R and Muir, L and McIntyre, E and Guduk, E and Zachariah, D and Vernochet, C and Frahm, N and Schmidt, AC},
title = {Impact of Bifidobacterium infantis supplementation on growth, health outcomes, and gut microbiome features in underweight infants from Pakistan.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1783141},
pmid = {42137872},
issn = {2296-861X},
abstract = {BACKGROUND: Alterations in the gut microbiome are implicated in infant malnutrition. Bifidobacterium longum subspecies infantis (B. infantis), a commensal common in breastfed infants, has been shown to have reduced abundance in malnourished infants. This trial (NCT05952076) evaluated if B. infantis strain Bi-26 supplementation could improve growth and health outcomes in underweight infants in Pakistan.

METHODS: In this double-blind, randomized, placebo-controlled trial, 40 infants aged 30-120 days (d) with a weight-for-age Z score (WAZ) below -2 received daily oral Bi-26 or placebo for 28d, with follow-up to d90 for safety. The primary endpoint was change in WAZ from baseline to d56. The intended sample size was 396 infants but study was terminated early due to operational delays. Total B. infantis levels microbiome, metabolome, and cytokine profiles were assessed.

RESULTS: Bi-26 supplementation increased fecal B. infantis levels at d28 (p = 0.001) and d56 (p = 0.03) but did not result in significant change in WAZ (p = 0.69) or weight gain (p = 0.56) compared to placebo. Fewer adverse events (AEs) occurred in the Bi-26 group compared to placebo (40% vs. 80% of infants; 17 vs. 49 events). Probiotic engraftment was impacted by presence of baseline endogenous B. infantis, suggesting that Bi-26 complemented rather than outcompeted endogenous strains. Bi-26 altered microbiome composition with transient alterations in function and metabolite abundance that reverted to baseline by d56, without cytokine differences between groups. B. infantis levels and Bifidobacterium-community types were associated with fewer AEs but not changes in WAZ or weight.

DISCUSSION: Bi-26 supplementation had an acceptable safety profile but did not improve growth. The findings of this trial support further evaluation of B. infantis strains in larger studies of underweight infants across diverse LMIC settings. Future trials should determine whether sustained metabolic and functional remodeling can translate into measurable improvements in growth and health outcomes.

CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov/study/NCT05952076, NCT05952076.},
}

@article {pmid42137970,
year = {2026},
author = {Feser, M and Arend, D and Beier, S and Bolger, M and Lübke, NC and Meister, M and Steilen, L and Usadel, B and Scholz, U},
title = {Evolving bioinformatics services - the journey of KPI metrics with Scorpion.},
journal = {Journal of integrative bioinformatics},
volume = {},
number = {},
pages = {},
pmid = {42137970},
issn = {1613-4516},
abstract = {Key Performance Indicators (KPIs) are essential for evaluating project success and establishing control mechanisms to monitor development, performance, and user acceptance of services in joint projects. However, the absence of standardized frameworks and effective monitoring tools, combined with service providers' reluctance due to fears of comparability, has limited their adoption in scientific contexts. To address this gap, we developed Scorpion, a flexible tool for KPI monitoring in project management. Scorpion enables service providers to retain control over their metrics while supporting centralized reporting. It offers both web-based and programmatic access, with features for KPI submission, visualization, and user and service management. Initially created for bioinformatics and biodiversity projects, Scorpion is applicable across diverse domains. It is particularly valuable for initiatives like the German National Research Data Infrastructure (NFDI), where funding agencies require KPI reporting for evaluation. We present the Scorpion framework, highlighting its design principles, features, and potential to improve project management practices. Use cases illustrate how Scorpion enhances KPI monitoring efficiency and accuracy, contributing to better impact evaluation, quality assurance, and informed decision-making in project and service management.},
}

@article {pmid42138445,
year = {2026},
author = {Ndhlovu, K and Salawu-Rotimi, A and Bopape, FL and Mtsweni, PN and Babalola, OO and Hassen, AI},
title = {Elucidating the Functional and Taxonomic Diversity of Soil Microbial Communities From Three Commercial Soybean Farms in South Africa.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70360},
doi = {10.1111/1758-2229.70360},
pmid = {42138445},
issn = {1758-2229},
support = {135456//National Research Foundation (NRF), South Africa/ ; },
mesh = {South Africa ; *Glycine max/growth & development/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Bradyrhizobium/genetics/isolation & purification/classification ; Metagenomics ; Nitrogen Fixation ; Phylogeny ; *Biodiversity ; Farms ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Prior to the introduction of the exotic inoculant strain of Bradyrhizobium, South African soils lacked the rhizobia that nodulate soybean. Five decades of soybean inoculation practice resulted in the establishment of the Bradyrhizobium population in many soybean growing fields. However, there is no record of the magnitude of this establishment and its impact on the taxonomic and functional abundance of other microbes. Here we use a shotgun metagenomics approach to elucidate the taxonomic and functional profiles of the soil microbes from selected commercial soybean farms in South Africa. Metagenomics of the total sequences revealed that Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria and Bacteroitedes are the prevalent phyla which differed in their relative abundance. Bradyrhizobium was the predominant genus at all three locations. Predicted functions detected genes essential for nitrogen metabolism, including nitrogen fixation, which have been unveiled in this study at a higher rate in all locations investigated. This study uncovers the microbial communities associated with soybean soils in South Africa. The study also generated vital information on the establishment of Bradyrhizobium spp. in the soils of soybean farms, providing a clue on whether inoculation of soya beans is always necessary. The findings, however, warrant further field investigations before any recommendations are rendered.},
}

South Africa
*Glycine max/growth & development/microbiology
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Bradyrhizobium/genetics/isolation & purification/classification
Metagenomics
Nitrogen Fixation
Phylogeny
*Biodiversity
Farms
*Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid42138618,
year = {2026},
author = {Ran, L and Mao, Y and He, B and Pan, H and Ma, H},
title = {Wildfire-Altered Soil Water-Extractable Organic Matter Drives Divergent Greenhouse Gas Emissions in Anaerobic Subsurface Soils.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04642},
pmid = {42138618},
issn = {1520-5851},
abstract = {Intensifying global climate change has increased wildfire frequency. Wildfire-altered soil water-extractable organic matter (burned-WEOM) is hydrologically transported to unburned areas, profoundly affecting cross-ecosystem carbon-nitrogen cycling and greenhouse gas (GHG) emissions. Taking soils from unburned subtropical forests as the research object, this study combined anaerobic incubation with high-resolution mass spectrometry and metagenomic sequencing to elucidate the regulatory mechanisms of burned-WEOM on soil GHG emissions under anaerobic conditions. The results showed that burned-WEOM increased CO2 emissions by 17.0%, induced a 164.6% surge in N2O emissions, and simultaneously inhibited CH4 emissions by 52.9%. With unique properties of high unsaturation and strong electron exchange capacity, burned-WEOM not only reshapes soil organic matter composition but also drives differential GHG emissions by enhancing complete carbon fixation pathways and recalcitrant carbon decomposition, increasing the abundance of anaerobic methane oxidation (AMO) genes and methanotrophs, enriching denitrifying microorganisms (especially fungi), and boosting N2O-generating gene activity without altering the reduction pathway. Moreover, WEOM molecular characteristics drive differences in GHG emissions: CH4 is mainly fueled by reduced, unsaturated lipid-like compounds, N2O is associated with nitrogen-rich, complex aromatic compounds, and CO2 has a broader range of source substrates. This study provides insights that may improve mechanistic understanding of postfire GHG dynamics and inform process representations in climate models.},
}

@article {pmid42138754,
year = {2026},
author = {Guimarães, LO and Couto, RDS and Reginato, SL and Mucci, LF and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, E},
title = {Wyeomyia confusa Lispivirus (WcLispV-SP): a novel neotropical mosquito virus in the Lispiviridae family.},
journal = {Archives of virology},
volume = {171},
number = {6},
pages = {},
pmid = {42138754},
issn = {1432-8798},
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Culicidae/virology ; Open Reading Frames ; Brazil ; Viral Proteins/genetics ; RNA, Viral/genetics ; *Mononegavirales/genetics/classification/isolation & purification ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {Metatranscriptomic analysis of Wyeomyia confusa mosquitoes collected in the Atlantic Forest (Pindamonhangaba, São Paulo, Brazil) led to the identification of a previously uncharacterized virus, designated Wyeomyia confusa Lispivirus (WcLispV-SP), classified within the family Lispiviridae, genus Canmovirus. The viral genome consists of a negative-sense single-stranded RNA (ssRNA-) of 12,698 nucleotides, encoding six open reading frames (ORFs): nucleoprotein (N), two hypothetical proteins (HP/1 and HP/2), glycoprotein (G), ORFan protein, and RNA-dependent RNA polymerase (RdRp-L). Phylogenetic analysis supports the classification of WcLispV-SP as a distinct species within the genus Canmovirus. Structural analysis of the RdRp revealed conserved domains and catalytic motifs characteristic of members of the order Mononegavirales, supporting its functional integrity. These findings expand the known diversity of the Lispiviridae family and highlight the utility of metagenomic approaches for the discovery and characterization of RNA viruses associated with Neotropical sylvatic mosquitoes.},
}

Animals
Phylogeny
Genome, Viral
*Culicidae/virology
Open Reading Frames
Brazil
Viral Proteins/genetics
RNA, Viral/genetics
*Mononegavirales/genetics/classification/isolation & purification
RNA-Dependent RNA Polymerase/genetics

@article {pmid42138983,
year = {2026},
author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A},
title = {Urban greenspaces harbour distinct plasmid communities enriched in heavy metal resistance and competitive traits in arid soils.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
doi = {10.1099/mic.0.001705},
pmid = {42138983},
issn = {1465-2080},
mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Metals, Heavy/pharmacology ; Soil/chemistry ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Gene Transfer, Horizontal ; Metagenome ; Microbiota/genetics ; Cities ; Humans ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Plasmids drive horizontal gene transfer, a fundamental mechanism for soil bacterial evolution and antibiotic resistance emergence. In arid regions, the transformation of natural soils into urban greenspaces introduces dramatic environmental changes that influence the adaptive strategies of soil micro-organisms. Additionally, urban greenspaces can act as interfaces of antibiotic resistance spread between environmental and human microbiomes. Here, we inferred plasmids from soil metagenomes of urban greenspaces in Tucson, AZ, USA, and nearby natural arid habitats. We found urban greenspaces to select for plasmids that carried genes that confer competitive advantages, including motility, prokaryotic defence and resistance to heavy metals. Notably, urban greenspace plasmids exhibited reduced diversity (genetic and functional variants), which could in turn constrain their adaptability to rapid environmental changes. These findings underscore the importance of plasmids as agents mediating soil microbial adaptation to human activities.},
}

*Plasmids/genetics
*Soil Microbiology
*Metals, Heavy/pharmacology
Soil/chemistry
*Bacteria/genetics/drug effects/classification/isolation & purification
Gene Transfer, Horizontal
Metagenome
Microbiota/genetics
Cities
Humans
*Drug Resistance, Bacterial/genetics

@article {pmid42139081,
year = {2026},
author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Dietary Niches Drive Microbial Community Assembly, Network Reorganization, and Symbiont Evolution in Freshwater Fish Gut Microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag125},
pmid = {42139081},
issn = {1751-7370},
abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.},
}

@article {pmid42139090,
year = {2026},
author = {Parienti, JJ and Yang, SS and Grinspoon, S},
title = {Selected Industry Highlights From IDWeek 2025.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {82},
number = {Supplement_4},
pages = {S85-S86},
doi = {10.1093/cid/ciag206},
pmid = {42139090},
issn = {1537-6591},
mesh = {Humans ; *HIV Infections/complications/drug therapy ; High-Throughput Nucleotide Sequencing ; },
abstract = {This supplement presents scientific reports from industry-sponsored IDWeek 2025 symposia, highlighting selected advances in infectious diseases and HIV care through clinical case scenarios. One article explores therapeutic approaches to metabolic complications in people with HIV, emphasizing treatment strategies and the clinical reasoning that supports individualized management of excess adiposity. The second examines the clinical integration of metagenomic next-generation sequencing for diagnosing central nervous system infections, outlining both its opportunities and limitations within current diagnostic pathways.},
}

Humans
*HIV Infections/complications/drug therapy
High-Throughput Nucleotide Sequencing

@article {pmid42139092,
year = {2026},
author = {Waldrop, G and Reddy, SP},
title = {Metagenomic Next-generation Sequencing in Central Nervous System Infections: Clinical Strategies, Evidence, and Best Practices.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {82},
number = {Supplement_4},
pages = {S92-S99},
doi = {10.1093/cid/ciag120},
pmid = {42139092},
issn = {1537-6591},
support = {//Delve Bio/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; Immunocompromised Host ; Female ; Middle Aged ; },
abstract = {BACKGROUND: Central nervous system (CNS) infections are diagnostically challenging due to their nonspecific clinical presentations and wide array of potential pathogens. The rising population of immunocompromised patients further complicates this landscape, increasing the prevalence of atypical and opportunistic infections that are often missed by conventional testing.

OBJECTIVE: This article provides guidance on the use and clinical interpretation of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in suspected CNS infections.

DISCUSSION: We highlight the paradigm shift from targeted molecular testing to agnostic mNGS, emphasizing key factors that impact diagnostic utility, including specimen handling, neuroanatomical factors, host inflammatory response, and pathogen kinetics. Using illustrative cases, we demonstrate how these biological and technical variables influence test sensitivity and result adjudication. We further discuss the impact of mNGS on clinical decision-making and current limitations regarding cost and turnaround time.

CONCLUSIONS: Cerebrospinal fluid mNGS is a transformative diagnostic tool, particularly for unusual presentations and in immunocompromised hosts. However, it does not replace clinical judgment and requires careful multidisciplinary interpretation. When integrated thoughtfully with clinical and laboratory data, mNGS can meaningfully reduce the diagnostic gap in CNS infections.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology
Immunocompromised Host
Female
Middle Aged

@article {pmid42139793,
year = {2026},
author = {Jibril, AH and Alencar, ALF and Olsen, JE and Hounmanou, YMG},
title = {Effect of age, severity of diarrhoea, number of pathogens present and blooming of E. coli on metagenomic characteristics of stools from Danish dairy calves with diarrhoea.},
journal = {Veterinary microbiology},
volume = {319},
number = {},
pages = {111070},
doi = {10.1016/j.vetmic.2026.111070},
pmid = {42139793},
issn = {1873-2542},
abstract = {BACKGROUND: Calf diarrhoea causes substantial welfare and economic losses, and it is one of the major drivers of antimicrobial use. This study aimed to characterize the faecal microbiome of diarrhoeic calves, with a specific focus on Escherichia coli, and to assess whether microbial profiles vary with age, diarrhoea severity, and high E. coli abundance in the absence of other detectable enteric pathogens.

METHODS: Stool samples from Danish diary calves (n = 32) below 4 weeks of age were collected from 11 herds and were analysed using direct long-read sequencing (mgt) as well as analyses of a subset of samples by swiping microbiota from faecal samples grown on McConkey agar plates (plate-swipe). Metagenomes were analysed to characterise community structure (Shannon α-diversity; Bray-Curtis PCoA with PERMANOVA) and to assess differential abundance at the species level while adjusting for sample type (mgt/plate swipe), herd, age, number of other pathogens detected by qPCR (rotavirus, coronavirus, Cryptosporidium parvum, Salmonella Dublin, Clostridium perfringens A, B, C, Eimeria and Escherichia coli F5) and recorded as presence/absence and summarised into infection classes (None/Mono/Co-2/Co-3 +). Binning was performed to build metagenome assembled genomes (MAGs) of E. coli.

RESULTS: Microbiome structure was dominated by methodological and contextual factors: sample type (direct metagenomic vs plate swipe) and herd explained far more variation than clinical severity and age. Metagenomic species profiles from plate swabs were comparatively homogeneous and E. coli-rich, whereas direct metagenomes captured higher diversity. Differential abundance identified species enriched with increasing diarrhoea severity and with infection classes, while pathogen-specific contrasts (e.g., C. perfringens A-positive vs negative) revealed discrete sets of bacterial co-occurrences. Classical pathotype markers (virulence-genes) were uncommon among E. coli MAGs.

CONCLUSIONS: Long-read metagenomics revealed insignificant influence of severity of diarrhoea, age below 4 weeks and number of pathogens detected in stool samples on diversity and microbial communities in diarrheic dairy calves. In contrast, large variation was observed between herds. On average, E. coli constituted about half of the microbiota. MAGs generated by binning indicated non-specific blooming of strains without particular virulence genes.},
}

@article {pmid42139982,
year = {2026},
author = {Yuan, M and Dong, S and Luo, J and Li, Y and Li, YA and Wen, W and Zhao, R},
title = {Habitat-driven taxonomic and functional differentiation of microbial communities across water and sediments in a large eutrophic shallow lake deciphered by metagenomics.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128553},
doi = {10.1016/j.micres.2026.128553},
pmid = {42139982},
issn = {1618-0623},
abstract = {Shallow lakes in arid and semi-arid regions are vulnerable to hydrological fluctuations and nutrient loading. However, the composition and functional traits of microbial communities and their roles in mediating internal nutrient cycling across the water column and sediments remain poorly understood. Here, we applied an integrated metagenomic framework to investigate microbial community structure and metabolic potential in Wuliangsuhai Lake, a typical eutrophic shallow lake in the Yellow River Basin. Read-based taxonomic profiling revealed pronounced habitat-driven community differentiation, with significantly higher microbial diversity and evenness in sediments than in water. Both habitats were dominated by Pseudomonadota, while water was enriched in Cyanobacteriota, Actinomycetota, and Bacteroidota, and sediments in Actinomycetota, Thermodesulfobacteriota, and Bacillota. Contig-based functional profiling based on a non-redundant catalog of 9.45 million genes showed clear habitat-specific divergence. Sediments were significantly enriched in pathways associated with complex carbon degradation, reductive nitrogen transformations, and sulfur redox metabolism. Genome-resolved analysis recovered 974 non-redundant metagenome-assembled genomes spanning 54 phyla, including one putative novel lineage. Metabolic reconstruction indicated community-wide dominance of heterotrophic carbon oxidation and fermentation, while methanogenic potential was largely confined to sediments. Nitrogen cycling was biased toward reductive processes, and sulfur cycling showed strong representation of both sulfite oxidation and sulfate/sulfite reduction. Metabolic weight scores further revealed a clear functional division of labor among major microbial lineages, with Pseudomonadota contributing broadly across multiple biogeochemical processes. These results indicate pronounced sediment-water functional differentiation in eutrophic shallow lakes, with sediments primarily supporting metabolic processes related to internal nutrient turnover.},
}

@article {pmid42140024,
year = {2026},
author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L},
title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.},
journal = {International journal of food microbiology},
volume = {457},
number = {},
pages = {111847},
doi = {10.1016/j.ijfoodmicro.2026.111847},
pmid = {42140024},
issn = {1879-3460},
abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.},
}

@article {pmid42140051,
year = {2026},
author = {Missaoui, Y and Venditti, M and Zhang, L and Vaccaric, F and Abelouah, MR and Abouda, S and Gaaieda, S and Puglisi, E and Lucini, L and Minnucci, S and Banni, M},
title = {Microplastic-induced gut dysbiosis and metabolic alterations in juvenile European seabass (Dicentrarchus labrax): A multi-omics approach.},
journal = {Marine pollution bulletin},
volume = {230},
number = {},
pages = {119879},
doi = {10.1016/j.marpolbul.2026.119879},
pmid = {42140051},
issn = {1879-3363},
abstract = {Environmental microplastics (MPs) are increasingly recognized as emerging contaminants with the potential to disrupt intestinal homeostasis in marine organisms. However, most experimental evidence is based on pristine particles rather than environmentally weathered forms. This study investigated the intestinal effects of environmentally derived microplastics (EMPs) in juvenile European seabass (Dicentrarchus labrax) using an integrated multi-omics approach. Fish were exposed for five days to two concentrations of EMPs (0.5 and 1 mg/kg of feed), followed by analyses combining histological, transcriptomic, metabolomic, and metagenomic endpoints. EMP exposure led to significant particle accumulation in gut tissues, predominantly consisting of small polyethylene fragments. Gene expression and immunofluorescence analyses revealed activation of p53 and Caspase-3 mediated apoptosis together with NF-κB and IL-6 driven inflammatory signalling, indicating concurrent oxidative and immune stress. Untargeted metabolomics identified marked alterations in lipid metabolism, redox regulation, and amino acid turnover, consistent with mitochondrial dysfunction and impaired energy homeostasis. Parallel metagenomic profiling revealed subtle but coherent shifts in gut bacterial communities, with enrichment of pollutant-tolerant taxa such as Acidovorax and Halioglobus and reduction of beneficial commensals such as Ligilactobacillus. Multi-omics data integration demonstrated a coordinated restructuring of microbial and metabolic networks underlying host physiological stress. Collectively, these findings highlight the intestine as a primary target of microplastic toxicity and provide mechanistic insight into early biological responses to environmentally realistic microplastic exposure in marine fish.},
}

@article {pmid42140215,
year = {2026},
author = {Hughes, N and Sathiananthamoorthy, S and Sergaki, C},
title = {Antimicrobial resistance surveillance through wastewater: methodological considerations for metagenomic approaches and public health perspectives.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101400},
doi = {10.1016/j.lanmic.2026.101400},
pmid = {42140215},
issn = {2666-5247},
abstract = {Antimicrobial resistance (AMR) is a recognised global threat with substantial predicted impact on lives, agriculture, and the economy. Metagenomic sequencing is being increasingly used for AMR surveillance and detection, given its capacity for community-level AMR profiling with high-level resolution. This technology has seen an explosion of surveillance efforts and data generation; however, the variation between workflows has direct implications on the sequencing results and their interpretation. In this Personal View, we summarise aspects of the sequencing workflow that need to be considered during metagenomic study design, for meaningful and reliable population-based surveillance. We reflect on the vital role of standardisation for capturing the ground truth of AMR and data comparability and reproducibility, and in addition, review the limitations of the various phenotypic and genotypic methods of AMR detection. We further highlight complex mechanisms of resistance to antimicrobials that could hinder our ability to confidently assess the true AMR burden in the environment and those that are often overlooked during surveillance.},
}

@article {pmid42140378,
year = {2026},
author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA},
title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121086},
doi = {10.1016/j.cca.2026.121086},
pmid = {42140378},
issn = {1873-3492},
abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.},
}

@article {pmid42140478,
year = {2026},
author = {Mehne, ZS and Honarjou, E and Kahdouee, MK},
title = {Chronic Infections of the Spine: A Systematic Review of Microbial Etiologies, Diagnostic Approaches, and Treatment Outcomes.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108769},
doi = {10.1016/j.ijid.2026.108769},
pmid = {42140478},
issn = {1878-3511},
abstract = {BACKGROUND: Chronic spinal infections are uncommon but potentially devastating conditions, frequently associated with delayed diagnosis, heterogeneous microbiology, and complex management. Existing evidence remains fragmented, and a comprehensive synthesis of microbial etiologies, diagnostic approaches, and treatment outcomes is needed.

METHODS: A systematic review was conducted in accordance with PRISMA guidelines. PubMed, Scopus, Web of Science, and Embase were searched for studies published between October 2015 and September 2025 involving adult patients with chronic spinal infections. Data were extracted on causative pathogens, diagnostic modalities, medical and surgical interventions, and clinical outcomes. Risk of bias was assessed using standardized methodological criteria.

RESULTS: Fifty-five studies comprising 3,036 patients were included. Mycobacterium tuberculosis was the most frequently identified pathogen, followed by Brucella species and pyogenic bacteria. Metagenomic next-generation sequencing (mNGS) demonstrated the highest diagnostic yield, with reported sensitivities ranging from 82% to 92%, and showed particular utility in detecting mixed or atypical infections. Biomarker-based and RNA-derived assays demonstrated promising performance in differentiating tuberculous spondylitis from other spinal conditions. Surgical interventions, including minimally invasive and combined approaches, were associated with high fusion and neurological recovery rates.

CONCLUSIONS: Chronic spinal infections show marked microbiological heterogeneity. Integrating molecular diagnostics with tailored surgical and antimicrobial strategies may improve diagnostic accuracy and clinical outcomes.},
}

@article {pmid42140665,
year = {2026},
author = {Vollmers, J and Correa Cassal, M and Kaster, AK},
title = {Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280099.124},
pmid = {42140665},
issn = {1549-5469},
abstract = {Since the majority of microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomics and single-cell genome sequencing have individual drawbacks, which can limit the quality as well as completeness of the reconstructed genomes. Current attempts to combine both approaches still use whole genome amplification techniques which are prone to bias. Here, we propose a novel approach for the purpose of genome reconstructions that utilizes the potential of cell sorting for targeted enrichment and depletion of different cell types to create distinct cell fractions with sufficient DNA amounts, circumventing amplification. By distributing sequencing efforts over these fractions as well as the original sample, coassemblies become highly optimized for coabundance variation based binning approaches. "Midi-metagenomics" enables accurate metagenome-assembled genome (MAG) reconstruction from individual sorted samples with higher quality than coassembly and binning of multiple distinct samples and therefore improves analyses of the so-called "microbial dark matter".},
}

@article {pmid42140743,
year = {2026},
author = {Lee, JB and Baek, S and Kim, DK and Kwon, BE and Ahn, JS and Nagasaka, M and Davar, D and Park, H and Kim, H and Im, J and Yang, J and Yang, E and Shin, GH and Choi, S and Kwon, JE and Kim, JM and Kang, SY and Kim, Y and Park, SY and Kim, JH and Oh, HS and Chalita, M and Min, A and Cho, BC},
title = {Phase I trial of CJRB-101 plus pembrolizumab in patients with metastatic non-small cell lung cancer, head and neck squamous cell carcinoma and melanoma.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {5},
pages = {},
doi = {10.1136/jitc-2025-014702},
pmid = {42140743},
issn = {2051-1426},
mesh = {Humans ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Female ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; Aged ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology ; *Melanoma/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Mice ; *Head and Neck Neoplasms/drug therapy/pathology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Animals ; Adult ; },
abstract = {BACKGROUND: Dysbiosis of gut microbiome leads to resistance to immunotherapy in various advanced solid tumors. CJRB-101 is a live biotherapeutic product consisting of a novel strain belonging to the species Leuconostoc mesenteroides. To modulate the tumor microenvironment, CJRB-101 was combined with pembrolizumab.

METHODS: Preclinical efficacy and mechanistic studies were performed using humanized non-small cell lung cancer (NSCLC) patient-derived xenograft (PDX) models. This is a multicenter, first-in-human, two-part, phase I, open-label study of CJRB-101 (1×10[11] or 4×10[11] colony forming unit (CFU)/day) plus pembrolizumab (200 mg every three weeks (Q3W)) in advanced NSCLC, melanoma, and head and neck squamous cell carcinoma in both immune checkpoint inhibitor (ICI)-naive and ICI-refractory settings. The primary endpoint was to assess the dose-limiting toxicities (DLTs), adverse events, and preliminary activity of the combination treatment. Exploratory endpoints included stool metagenomics analysis and pharmacodynamics parameters.

RESULTS: In four PDX models, CJRB-101 with pembrolizumab demonstrated enhanced antitumor efficacy, showing a tumor growth inhibition (TGI) of 77.3% in the CJRB-101 monotherapy group and 61.9% in the combination group, which was significantly improved compared with pembrolizumab alone. A distinct M2-to-M1 repolarization was observed and validated in vitro. Notably, increased activation of cytotoxic T cells was observed, suggesting an immune-mediated antitumor mechanism of CJRB-101. A total of 42 patients were enrolled in the low-dose cohort (one capsule once a day; n=6) and high-dose cohort (two capsules two times a day, n=36). Metastatic NSCLC accounted for 86% (n=36) and 67% (n=28) of the patients were refractory to ICIs. None of the patients experienced DLT. In ICI-naïve NSCLC (n=12) with programmed death-ligand 1 (PD-L1) >50%, the overall response rate (ORR) and disease control rate (DCR) were 58% and 75%, respectively. The ORR was 5% and DCR was 41% in the ICI-refractory NSCLC (n=22) with an ORR of 5% and DCR of 41%. After a median follow-up of 15.6 months and 8.9 months for ICI-naïve and ICI-refractory NSCLC, the median progression-free survival was 9 months (95% CI 5.6 to not reached) and 1.8 months (95% CI 1.6 to 4.3), respectively. CJRB-101 plus pembrolizumab was well-tolerated, and none of the patients experienced grade >3 treatment-related adverse events.

CONCLUSIONS: Early clinical data show encouraging antitumor response of CJRB-101 plus pembrolizumab in ICI-naïve metastatic NSCLC with PD-L1 >50%.

TRIAL REGISTRATION NUMBER: NCT05877430.},
}

Humans
*Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
Female
Male
Middle Aged
*Carcinoma, Non-Small-Cell Lung/drug therapy/pathology
Aged
*Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology
*Melanoma/drug therapy/pathology
*Lung Neoplasms/drug therapy/pathology
Mice
*Head and Neck Neoplasms/drug therapy/pathology
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology
Animals
Adult

@article {pmid42140896,
year = {2026},
author = {Blázquez-Sánchez, P and Gunkel, J and Useini, A and Zlobin, A and Zakary, JD and Schöler, A and Graefe, N and Engelberger, F and Cantanhede, F and Frank, R and Zhao, Z and Zarei, A and Butenschön, E and Matysik, J and Zimmermann, W and Sträter, N and Sonnendecker, C and Künze, G},
title = {Computational engineering of the polyester hydrolase PHL7 for efficient poly(ethylene terephthalate) degradation in biocatalytic recycling processes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42140896},
issn = {2041-1723},
support = {887913//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ScaDS.AI//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
mesh = {*Polyethylene Terephthalates/metabolism/chemistry ; Biocatalysis ; *Protein Engineering/methods ; *Hydrolases/metabolism/genetics/chemistry ; Recycling ; Enzyme Stability ; Biodegradation, Environmental ; Molecular Dynamics Simulation ; Metagenome ; *Bacterial Proteins/metabolism/genetics/chemistry ; },
abstract = {Polyethylene terephthalate (PET) plastic waste causes serious environmental pollution due to insufficient recycling rates. Enzymatic PET depolymerization offers a sustainable recycling strategy, but limited stability and activity of current PET-degrading enzymes restrict practical implementation. Here, we engineer Polyester Hydrolase Leipzig 7 (PHL7), a PET hydrolase from a compost metagenome, to enhance its stability and catalytic performance under recycling-relevant conditions. Using Rosetta PROSS-based computational design combined with rational mutagenesis, we introduce up to 24 mutations, generating variants with melting temperatures of 88-95 °C and over 110-fold higher activity in 0.1 M phosphate buffer compared to the parent enzyme. Benchmarking shows that the best variants (R4M6, R4M9, and R4M10) match or exceed the performance of established engineered PET hydrolases, including ICCG and LCC-A2, and approach that of TurboPETase across multiple conditions. Under high substrate loadings, the PHL7-R4 variants degrade 75-78% of 10% (w/w) PET within 24 h at 65 °C, outperforming ICCG, while an optimized variant R4M10-H185Y achieves up to 84% degradation of 20% (w/w) PET. X-ray structure determination and molecular dynamics simulations reveal key stabilizing and activity enhancing mechanisms. These engineered PHL7 variants represent robust biocatalysts for scalable enzymatic PET recycling.},
}

*Polyethylene Terephthalates/metabolism/chemistry
Biocatalysis
*Protein Engineering/methods
*Hydrolases/metabolism/genetics/chemistry
Recycling
Enzyme Stability
Biodegradation, Environmental
Molecular Dynamics Simulation
Metagenome
*Bacterial Proteins/metabolism/genetics/chemistry

@article {pmid42140961,
year = {2026},
author = {Li, CW and Liao, HX and Callaway, RM and Su, ZY and Zou, JK and Liu, A and Wu, YR and Fang, YQ and Peng, SL and Chen, BM},
title = {Divergence among species with "good competitor" and "good cultivator" strategies promotes asymmetric facilitation among co-invaders.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73076-2},
pmid = {42140961},
issn = {2041-1723},
support = {32471739//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023A1515010669//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; },
abstract = {Facilitative interactions among co-invaders may lead to invasional meltdown, accelerating non-native species accumulation and exacerbating ecological impacts over time. However, it remains unclear why certain non-native combinations promote facilitation while others do not, and may even constrain invasions. To address this question, we examine six invasive species in the Asteraceae family along two strategic dimensions: competitiveness and capacity to cultivate invader-promoting microbial communities. We then create experimental combinations to mix "good competitors" and "good cultivators" to varying degrees to form a "strategic divergence" gradient. We hypothesize greater strategic divergences generate more intense facilitations, whereas similar strategies generate inhibitions. Strategic divergence correlates with facilitation, but interactions are asymmetric: strong competitive suppressors of natives benefit from co-invasions with weaker competitors that cultivate favorable microbial environments but the performance of the latter are generally suppressed by the strong competitors. Metagenomic sequencing further indicates that good cultivators may promote facilitation by repelling pathogens (Ascomycota) and deterring microbes that might be exclusively beneficial for natives (Proteobacteria, Firmicutes, and Planctomycetota). Our results provide empirical evidence for the importance of strategic divergence among invasive species and offer a mechanistic basis for predicting which combinations of co-invading species might generate facilitation and which might result in inhibition.},
}

@article {pmid41915167,
year = {2026},
author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E},
title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41915167},
issn = {1432-184X},
abstract = {UNLABELLED: Microbiome studies reveal the taxonomic and functional composition of microbial communities inhabiting many diverse environments. Comprehensive microbiome repositories, such as MGnify, organize data into studies, each consisting of multiple sequencing runs or assemblies and accompanying metadata. This structure enables integrative, large-scale, cross-study analyses, leading to broader insights across ecosystems, hosts, and experimental contexts. Despite extensive microbiome research, methods for defining similarity between studies and validating those similarity metrics, remain insufficiently established, especially for large-scale analyses. To address this, we evaluate whether taxonomic and functional similarities from MGnify can serve as reliable indicators of study relatedness between study pairs, testing multiple metrics against conceptual relatedness (e.g., shared environments, goals, or methods). To scale validation, we introduce a framework that applies a Large Language Model (LLM) to study descriptions, categorizing study pairs by relatedness. Our results show that functional similarity correlates more strongly with LLM-inferred study relatedness than taxonomic similarity, highlighting both the promise and limitations of current metrics. Via the above, we demonstrate the value of combining microbial profiles with LLM-driven semantic reasoning to navigate the expanding landscape of metagenomic research.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02730-5.},
}

@article {pmid41917256,
year = {2026},
author = {Shen, Z and Liu, Y and Liu, Y and Zhang, P and Li, Y and Li, Z and Qi, H},
title = {Clinical characteristics and mixed infection patterns of ocular surface infection with Epstein-Barr virus.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {16},
number = {1},
pages = {},
pmid = {41917256},
issn = {1869-5760},
abstract = {PURPOSE: To analyze the clinical features of ocular surface diseases caused by Epstein-Barr virus (EBV) infection.

METHODS: A retrospective case series study was conducted. Data from 48 patients (54 eyes) with EBV infection who visited Peking University Third Hospital between January 2023 and October 2025 were collected. Patient demographics and baseline information were recorded. Ophthalmic slit-lamp examination, ocular surface (conjunctiva/cornea) scrapings, bacterial culture of ocular secretions, real-time fluorescence quantitative PCR detection, EBV-specific antibody testing, and metagenomic next-generation sequencing (mNGS) were performed.

RESULTS: Among patients infected with EBV on the ocular surface, the majority were middle-aged individuals in the 31–40 age group. The primary risk factors for onset were keeping pets (10/48), followed by colds (6/48); among those keeping pets, parrots were the most common (5/9). The main clinical manifestations were foreign body sensation (37/54) and yellow discharge (34/54). Common signs included mixed conjunctival hyperemia (31/54), follicles on the lower eyelid conjunctiva (17/54), papillae on the upper eyelid conjunctiva (8/54), and punctate epithelial defects on the cornea (17/54). In most ocular surface scrapings, small round lymphocytes were observed alongside a small number of reactive lymphocytes (44/54), which could simultaneously present with a large number of neutrophils (36/54). There was a significant difference between the presence of yellow discharge and the type of conjunctival hyperemia [Formula: see text]. However, no statistically significant correlation was found between the presence of yellow discharge and the presence of neutrophils in the scraping results [Formula: see text]. Significant differences were found in EBV viral loads among different groups of combined symptoms [Formula: see text] and among different follicle groups [Formula: see text]. No statistically significant correlation was found between the lymphocyte count in the scraping and the EBV viral load in the affected eye [Formula: see text].

CONCLUSION: EBV infection of the ocular surface is prone to concurrent infections; therefore, a detailed medical history inquiry is crucial. Ocular surface tissue scraping examination can rapidly identify viral infection-related inflammatory characteristics and rule out bacterial/fungal infections, providing effective supportive auxiliary diagnostic evidence for viral ocular surface infection, and precise diagnosis of EBV infection needs to be achieved in combination with molecular biological and serological tests.},
}

@article {pmid42014454,
year = {2026},
author = {Muller, E and Bamberger, T and Borenstein, E},
title = {Navigating multi-omic integration methods for human microbiome research.},
journal = {Nature microbiology},
volume = {11},
number = {5},
pages = {1153-1167},
pmid = {42014454},
issn = {2058-5276},
support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 2266/25//Israel Science Foundation (ISF)/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Host Microbial Interactions ; *Metagenomics/methods ; Multiomics ; },
abstract = {Multi-omic studies in human microbiome research hold great potential for advancing our understanding of host-microbiome interactions. However, despite the growing availability of multi-omic datasets, analysing such data remains a major conceptual, analytical and computational challenge. Introduction of new multi-omic integration methods to address these challenges further complicates researchers' efforts to navigate this expanding field. In this Review, we outline the landscape of multi-omic integration methods in the context of human microbiome research. In contrast to previous reviews, we specifically emphasize the different biological questions addressed by various integration approaches, including questions related to interactions between different molecular layers, molecular shifts that occur in disease, subgrouping of patients based on molecular profiles, and identification of biological mechanisms that underlie such associations. Our aim is to provide a timely, convenient and comprehensive resource for the microbiome research community, allowing researchers to identify the multi-omic integration approach that is best suited to their data and objectives.},
}

Humans
*Microbiota/genetics
*Computational Biology/methods
Host Microbial Interactions
*Metagenomics/methods
Multiomics

@article {pmid42128850,
year = {2026},
author = {Fujii, N and Nakajima, M and Narihiro, T and Kuroda, K and Kindaichi, T},
title = {Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota.},
journal = {Microbes and environments},
volume = {41},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25084},
pmid = {42128850},
issn = {1347-4405},
mesh = {*Bacteria/classification/genetics/isolation & purification/metabolism ; Phylogeny ; Ecosystem ; Genome, Bacterial ; },
abstract = {The phylum Minisyncoccota (formerly known as "Candidatus Patescibacteria"/candidate phyla radiation [CPR] and designated under SeqCode as Patescibacteriota) represents one of the major bacterial phyla; however, its physiological and ecological characteristics remain unclear. This review summarizes relevant studies on currently available isolate and genomic/metagenomic data, outlining the phylogenetic placement, metabolic features, host interactions, and unique genetic code usage of Minisyncoccota. Minisyncoccota play complementary and interdependent roles within microbial communities, while being restricted by incomplete metabolic capabilities that prevent independent survival. Studies on Minisyncoccota offer important insights into the diversity and evolution of uncultivated bacteria, as well as the hidden interaction networks that shape microbial ecosystems.},
}

*Bacteria/classification/genetics/isolation & purification/metabolism
Phylogeny
Ecosystem
Genome, Bacterial

@article {pmid42129189,
year = {2026},
author = {Lacruz-Pleguezuelos, B and Pérez-Cuervo, A and Coleto-Checa, D and Bazán, GX and Romero-Tapiador, S and Freixer, G and Fernández-Cabezas, J and Aguilar-Aguilar, E and Martín-Segura, A and Cárdenas-Roig, N and Carrasco-Guijarro, L and Fernández, LP and Espinosa-Salinas, I and Ramírez de Molina, A and Morales, A and Tolosana, R and Ortega-Garcia, J and Pancaldi, V and Marcos-Zambrano, LJ and Carrillo de Santa Pau, E},
title = {Network topology of the gut microbiome associates with metabolic health in obesity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42129189},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; *Obesity/microbiology/metabolism ; Middle Aged ; Cross-Sectional Studies ; Adult ; Feces/microbiology ; Metagenomics ; *Obesity, Metabolically Benign/microbiology/metabolism ; Dysbiosis/microbiology ; Phenotype ; },
abstract = {Obesity is a heterogeneous condition comprising a continuum of phenotypes with various metabolic and inflammatory profiles. Metabolically healthy obesity (MHO) identifies individuals with obesity but a relatively preserved metabolic state, although little is known about the gut microbiome features underlying this phenotype. Here, we analyzed gut microbial network structures of 931 individuals living with metabolically healthy non-obesity (MHNO), MHO, metabolically unhealthy non-obesity (MUNO), and metabolically unhealthy obesity (MUO), performing cross-sectional analyses on feces shotgun metagenomics data. Individuals with MHNO and MHO harbor more robust and functionally cohesive microbial networks, while communities from MUO and MUNO phenotypes exhibit a potentially dysbiotic state with reduced connectivity. A nutritional intervention cohort showed an improvement in network connectivity in parallel with metabolic improvements. Our findings show differences in microbial connectivity and association patterns across metabolic and obesity phenotypes, shedding light on how distinct microbial network structures may associate with host metabolic health and disease.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Male
Female
*Obesity/microbiology/metabolism
Middle Aged
Cross-Sectional Studies
Adult
Feces/microbiology
Metagenomics
*Obesity, Metabolically Benign/microbiology/metabolism
Dysbiosis/microbiology
Phenotype

@article {pmid42129350,
year = {2026},
author = {Parkin, K and Christophersen, CT and Verhasselt, V and Palmer, DJ and Cooper, MN and Prescott, SL and Silva, D and Martino, D},
title = {Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01626-2},
pmid = {42129350},
issn = {2730-664X},
abstract = {BACKGROUND: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.

OBJECTIVE: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.

DESIGN: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n = 197) received either de-chlorinated drinking water via benchtop filtration (treatment, n = 99), or regular chlorinated water (control, n = 98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.

RESULTS: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p = 0.84), richness (-4.25, 95% CI; -14.85 to 6.35, p = 0.43) or Shannon Index (-0.14, 95% CI; -0.32 to 0.04, p = 0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p < 0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.

CONCLUSION: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.

TRIAL REGISTRATION: ACTRN12619000458134; https://www.anzctr.org.au.},
}

@article {pmid42129659,
year = {2026},
author = {Chen, J and Li, X and Deng, Z and Ying, Y and Lu, M},
title = {Clinical characteristics of sporadic acute Q fever diagnosed by metagenomic next-generation sequencing: a retrospective analysis and literature review in China.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13477-2},
pmid = {42129659},
issn = {1471-2334},
support = {MISP-102684//MSD Investigator Initiated Studies Program Review Committee/ ; 2022YFC2303203-01//National Key Research and Development Program of China/ ; Z-2017-24-2202//Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; },
abstract = {BACKGROUND: Acute Q fever manifests sporadically in mainland China, where its clinical spectrum and optimal diagnostic strategies remain under-recognized. This study aimed to delineate the clinical phenotype and antimicrobial prescribing patterns of sporadic acute Q fever diagnosed via metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective, single-center cohort study of adult patients with sporadic acute Q fever. A comprehensive literature review of all published sporadic cases across China was subsequently performed to delineate the national clinical spectrum of sporadic Q fever.

RESULTS: The cohort comprised 22 male patients (mean age 36.7±13.5 years). All patients presented with high-grade pyrexia (>39°C) accompanied by a characteristic symptom constellation of headache, fatigue, myalgia, and hepatic involvement (100%, mean ALT 122.2±56.9 U/L). Pneumonia was observed in 2 patients (2/22, 9.1%). A distinct dissociation was observed between markedly elevated C-reactive protein (mean 67.4 ± 33.6 mg/L) and normal leukocyte counts. A pooled analysis of 94 published cases and 22 consecutive patients from our center yielded 116 confirmed Q fever cases (male-to-female ratio 11.9:1, the proportion of hepatitis and pneumonia:87.9% and 24.1%) The median interval from symptom onset to pathogen confirmation was 7.8 ± 2.8 days. mNGS yielded a diagnosis in 77.5 % of 116 patients, the remaining 22.5 % were identified by PCR and antibody testing.

CONCLUSION: Acute Q fever in China predominantly affects young males, presenting as a systemic febrile illness with a distinctive hepatic phenotype (elevated liver enzymes) rather than prominent pneumonia. The clinical triad of high fever, influenza-like symptoms (headache/myalgia), and "WBC-CRP dissociation" (normal white cell count with elevated CRP) serves as a potential clinical indicator. Empiric doxycycline should be initiated promptly in suspected cases. mNGS is a valuable tool for definitive diagnosis, particularly when empiric therapy fails or in severe/complicated cases.},
}

@article {pmid42129710,
year = {2026},
author = {Wang, Z and Tang, J and Yang, K and Cui, Z and Li, Z},
title = {Diagnostic challenges and lessons learned of Guillain-Barré syndrome mimicking central nervous system infection - a case report.},
journal = {BMC neurology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12883-026-04942-1},
pmid = {42129710},
issn = {1471-2377},
abstract = {BACKGROUND: Guillain-Barré syndrome (GBS) is an immune-mediated disorder affecting the peripheral nervous system, often triggered by infections, vaccinations, trauma, or surgery. Typically, it presents as progressive, symmetric limb weakness with hyporeflexia. However, some GBS subtypes can present atypically with symptoms like headache, facial palsy, and confusion. These symptoms overlap significantly with central nervous system (CNS) infections, often causing diagnostic delays.

CASE PRESENTATION: A 57-year-old man was admitted with cough, sputum, and shortness of breath, having received a rabies vaccination a month earlier. He developed headache, dysphagia, progressive muscle weakness, and impaired consciousness, requiring Intensive Care Unit (ICU) transfer, endotracheal intubation, and mechanical ventilation. The initial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) detected Pseudomonas aeruginosa (sequence count: 6094), combined with fever and a series of clinical symptoms before transfer to the ICU, CNS infection was considered. Treatment with piperacillin-tazobactam, meropenem, and ciprofloxacin yielded no improvement. Albumino-cytological dissociation in the CSF led to a neurology consultation for suspected GBS, and intravenous immunoglobulin (IVIg) therapy began. Negative CSF bacterial cultures and mNGS, along with positive anti-GT1a IgM ganglioside antibodies and electromyogram(EMG) result indicating nerve damage, confirmed the GBS diagnosis. After five days of IVIg, the patient was weaned from mechanical ventilation and showed significant neurological recovery.

CONCLUSION: The significant clinical overlap between GBS and CNS infections poses a major diagnostic and therapeutic challenge. This case highlights the importance of thorough history-taking, comprehensive neurological assessment, careful interpretation of lab results, and early neurologist involvement to minimize diagnostic delays in GBS and prevent subsequent treatment delays.},
}

@article {pmid42129938,
year = {2026},
author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z},
title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02426-5},
pmid = {42129938},
issn = {2049-2618},
support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.

RESULTS: No significant difference was observed in the ruminal microbial α-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.

CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.},
}

@article {pmid42130304,
year = {2026},
author = {Preston, S and Jones, J and Huggett, MJ and Adam, AAS and White, NE and Tan, KC and Richards, Z},
title = {Comparing Microbial Communities of Diseased and Healthy Isopora palifera Corals and Adjacent Waters at the Cocos (Keeling) Islands.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70324},
pmid = {42130304},
issn = {1462-2920},
support = {LP160101508//Australian Research Council/ ; },
mesh = {*Anthozoa/microbiology/growth & development ; Animals ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Seawater/microbiology ; Islands ; Coral Reefs ; },
abstract = {Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood. Microorganisms are integral to coral health, but the role of bacterial communities in GAs remains unclear. We investigated an outbreak of GAs in Isopora palifera at the Cocos (Keeling) Islands using 16S rRNA amplicon sequencing to compare bacterial communities of GA-affected and asymptomatic corals, surrounding water and potential pollution sources. Significant differences in bacterial beta diversity were observed across sites, with an interaction between location and coral health status. Coral and water samples hosted distinct microbial communities, but there was no evidence linking GA-affected corals to local pollution. Moreover, no consistent bacterial taxa were associated with disease, suggesting that resident microbes may not be primary drivers of GAs. However, our study does not account for transient microbes that may have initiated GAs. Our findings challenge assumptions of single-agent causality and microbial compositional homogeneity in coral diseases. This study advances understanding of microbial dynamics in coral disease ecology and underscores the importance of early-stage investigation and functional metagenomics to identify viral, fungal and microbial functional shifts in disease emergence. Studying outbreaks in minimally impacted systems offers valuable baselines for disentangling natural disease processes.},
}

*Anthozoa/microbiology/growth & development
Animals
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
*Microbiota
*Seawater/microbiology
Islands
Coral Reefs

@article {pmid42130363,
year = {2026},
author = {DU, WQ and Liu, LJ and Zhang, L and Tang, YF and Liu, LQ and Li, XF and Xiao, YY},
title = {[A case of Bartonella henselae meningitis characterized by bone marrow hemophagocytosis].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {28},
number = {5},
pages = {618-623},
pmid = {42130363},
issn = {1008-8830},
mesh = {Humans ; Male ; Adolescent ; *Bartonella henselae ; *Cat-Scratch Disease/complications ; *Lymphohistiocytosis, Hemophagocytic/etiology ; *Bone Marrow/pathology ; *Meningitis, Bacterial ; },
abstract = {A 13-year-old boy with Bartonella henselae meningitis is reported. He presented with recurrent fever with no history of cat scratches and no lymphadenopathy. Cerebrospinal fluid analysis showed an elevated white blood cell count, and Bartonella henselae infection was confirmed by metagenomic next-generation sequencing. Bone marrow examination revealed hemophagocytosis predominantly involving nucleated erythrocytes; to our knowledge, this bone marrow morphological abnormality is the first reported worldwide in association with Bartonella henselae infection. Transient bilateral hip pain occurred during the illness and was considered infection-related joint involvement. The patient improved with treatment and had no neurological sequelae. This case expands the spectrum of clinical and bone marrow manifestations of Bartonella henselae infection and warrants vigilance for possible central nervous system and bone marrow involvement in cases of fever of infectious etiology presenting without typical lymphadenopathy.},
}

Humans
Male
Adolescent
*Bartonella henselae
*Cat-Scratch Disease/complications
*Lymphohistiocytosis, Hemophagocytic/etiology
*Bone Marrow/pathology
*Meningitis, Bacterial

@article {pmid42130962,
year = {2026},
author = {Tomar, SS and Khairnar, K},
title = {Disruption in the Host-Phage Dynamics and Altered Microbial Diversity in the Upper Respiratory Tract of SARS-CoV-2-Infected Individuals.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {7},
number = {1},
pages = {9-20},
pmid = {42130962},
issn = {2641-6549},
abstract = {BACKGROUND: The upper respiratory tract (URT) is an important site for the predisposition and multiplication of the SARS-CoV-2 virus. Therefore, URT is a critical site for investigating the changes in the microbiome caused by the SARS-CoV-2 infection. This study aims to compare phageome diversity and investigate the correlation of the phageome profiles with the sample type (SARS-CoV-2 or control) to determine the nature of phage-host interactions in the human URT microbiome and to assess the effect of SARS-CoV-2 viral load on host and phage abundance.

MATERIALS AND METHODS: In this study, we have used the whole-genome shotgun metagenomic approach to investigate URT swab samples (n = 96) collected from SARS-CoV-2-positive individuals (n = 48) (nonhospitalized but symptomatic) and healthy controls (n = 48) belonging to five districts of central India.

RESULTS: The results revealed distinct phageome profiles among the groups; Detrevirus dominated the composition in the control samples, while Maxrubnervirus was dominant in SARS-CoV-2 samples. Microbial diversity analysis showed significantly higher richness in the SARS-CoV-2 group compared to controls for both bacteria (Chao1: 886.00 vs. 351.00, p < 0.0001) and phages (Chao1: 39.00 vs. 16.00, p = 0.0002). Bacterial diversity (Simpson index) was lower in the SARS-CoV-2 group (0.88 vs. 0.93, p = 0.0024), whereas phage diversity was higher in the SARS-CoV-2 group (0.86 vs. 0.79, p = 0.0384). Viral load, as reflected by cycle threshold (Ct) values, significantly influenced both bacteria (H = 6.69, p = 0.035) and phage (H = 8.97, p = 0.011) abundances. Host-phage interaction networks appeared disrupted in SARS-CoV-2 samples, with a weaker logistic model fit (R [2] = 0.7425) than controls (R [2] = 0.9265).

CONCLUSION: SARS-CoV-2 infection alters URT microbiome composition, increasing microbial diversity but disrupting host-phage dynamics. SARS-CoV-2 Viral load correlates with the shifts in microbial abundance, indicating infection-driven shifts in microbiome stability compared to healthy controls.},
}

@article {pmid42131203,
year = {2026},
author = {Zahra, M and Ouf, A and Azzazy, HME and Moustafa, A},
title = {Metagenomic profiling of gut microbiome signatures across liver disease stages and HCV-related hepatocellular carcinoma in Egyptian patients.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1758563},
pmid = {42131203},
issn = {1664-302X},
abstract = {INTRODUCTION: Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study examines the gut microbiome's role in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt.

METHODS: Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients.

RESULTS: Healthy and treated HCV patients exhibited distinct microbial profiles characterized by an abundance of beneficial bacteria, Faecalibacterium and Bifidobacterium (p < 0.05), associated with anti-inflammatory short-chain fatty acid production. Conversely, liver disease and HCC patients displayed increased pathogenic bacteria, Escherichia (p < 0.05), and genes linked to inflammation and oncogenesis, including lipopolysaccharide biosynthesis.

DISCUSSION: These findings suggest a dominance of Faecalibacterium in healthy Egyptians, likely attributable to traditional dietary patterns, and cytochrome P450 genes as potential HCC biomarkers, possibly connected to aflatoxin exposure. Treated HCV patients showed significant microbiome recovery, reflecting effective antiviral therapy. These findings emphasize that Egypt-specific factors, such as persistent resistance genes post-HCV due to antibiotic use and the prominence of bile acid metabolism genes, are influenced by high HCV prevalence and environmental exposures like aflatoxins. Taken together, the results highlight the need for region-specific microbiome research priorities in Egypt and underscore how local dietary, clinical, and environmental factors may shape future objectives in understanding liver disease pathogenesis and prevention.},
}

@article {pmid42131208,
year = {2026},
author = {Hembram, DB and Panda, SP and Das, BK and Soren, D and Singh, NR},
title = {Microbial elicitors to metabolic reprogramming: an integrative model of plant-microbe interactions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1816468},
pmid = {42131208},
issn = {1664-302X},
abstract = {Plant growth, soil health, and crop productivity with nutritional quality can be significantly enhanced by employing microbial consortia that incorporate diverse microorganisms with complementary functions. Plants produce various types of secondary metabolites such as terpenoids, alkaloids, phenolics, essential oils, and other metabolites through various cellular mechanisms, which are often stimulated by microbial interactions. These metabolites exert beneficial effects on plants and perform multiple roles in agriculture, contributing significantly to growth and economy. This review summarizes microbial consortia-mediated enhancement of plant health and their intricate interactions with host plants. Beneficial microbes of a consortium trigger complex signaling cascades leading to a dynamic regulatory strategy through which plants enhance their secondary metabolite synthesis. Secondary messengers and hormonal cross-talk further integrate the signal to transcription factors, which play a central role in activating or repressing the key genes of the metabolic pathways. Thus, the interplay of microbial signal, secondary messengers, hormonal cross-talk, and key metabolite genes forms the basis of plant secondary metabolite biosynthesis. In addition, recent advances in systems microbiology, including metagenomics, metatranscriptomics, and metabolomics, have enabled a holistic understanding of microbial community dynamics and their collective role in regulating secondary metabolism.},
}

@article {pmid42131214,
year = {2026},
author = {Sudianto, E and Shlafstein, MD and Durieu, B and Harmel, M and Cornet, L and Saw, JH},
title = {Taxonomic description of cyanobacteria from extreme habitats through genome-based classification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1824103},
pmid = {42131214},
issn = {1664-302X},
abstract = {INTRODUCTION: Cyanobacteria form a morphologically and phylogenetically diverse group of oxygenic phototrophic bacteria inhabiting a wide range of environments, including extreme habitats such as hot springs and volcanic steam vents. Many lineages, particularly those from these extreme environments, remain uncultured and are known only from metagenome-assembled genomes (MAGs), limiting their integration into formal taxonomy.

METHODS: Analysis of 46 steam vent associated samples from Hawai'i using 16S rRNA amplicon sequencing revealed that cyanobacteria dominate these communities. Gloeobacter kilaueensis dominated pit-like environments with low-light conditions, while Leptolyngbyaceae and other families are more dominant in structured soil and wall communities. We further reconstructed 38 high-quality cyanobacterial MAGs and incorporated them into a phylogenomic analysis comprising 343 cyanobacterial genomes, followed by genome-based comparisons against 9,026 reference genomes.

RESULTS: This revealed eight novel species and one novel genus spanning five orders: Chroococcidiopsidales, Leptolyngbyales, Nostocales, Oculatellales, and Oscillatoriales. Following SeqCode guidelines, we provide the first formal taxonomic descriptions of cyanobacterial MAGs and propose guidelines for integrating genome-based and cultivated material.

CONCLUSION: These findings highlight Hawaiian steam vents as hotspots of previously uncharacterized cyanobacterial diversity and underscore the importance of genome-based nomenclature.},
}

@article {pmid42131265,
year = {2026},
author = {Cheng, J and Ni, J and Zhao, Y and Jiang, L and Huang, Y and Zhang, Y and Yan, P and Long, Z and Fu, H and Jiang, X},
title = {The clinical utility of metagenomic next-generation sequencing in the management of fever in patients with hematological disorders.},
journal = {Nagoya journal of medical science},
volume = {88},
number = {1},
pages = {84-98},
pmid = {42131265},
issn = {2186-3326},
mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Adult ; *Metagenomics/methods ; Aged ; *Hematologic Neoplasms/complications/microbiology ; *Fever/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Patients with hematological malignancies frequently present with severe and intricate infections that pose life-threatening risks. Conventional pathogen detection methods offer limited clinical insights and therapeutic guidance. This retrospective study evaluated the clinical application of metagenomic next-generation sequencing (mNGS) in hematologic patients who remained febrile despite prolonged antibiotic therapy, which means unresponsive to antibiotic therapy. This retrospective analysis included 204 patients with hematologic malignancies, undergoing conventional pathogen detection and peripheral blood mNGS. The cohort was stratified into neutropenia and non-neutropenia groups to compare the diagnostic and therapeutic implications of mNGS versus conventional microbiological tests (CMT). Among the 204 patients with mNGS, the overall positive detection rate was significantly higher than that of CMT (68.1% vs 30.9%, P<0.001). In both the neutropenia and non-neutropenia group, mNGS demonstrated a higher positivity rate for bacteria than for CMT (bacteria, 36.4% vs 15.6%, P<0.01). mNGS proved notably advantageous for bloodstream infections with clinically relevant drug-resistant strains, particularly in the neutropenia cohort (26.4% vs 12.5%, P<0.001). Using a composite reference standard, mNGS manifested sensitivity and specificity rates of 78.4% and 61.9%, respectively. Patients in the neutropenia group derived superior clinical benefit from mNGS, including higher diagnostic accuracy and treatment efficacy (diagnosis, 56.4% vs 40.6%, P=0.036; treatment, 49.3% vs 31.3%, P = 0.016). Additionally, the 30-days mortality rate was notably higher among mNGS-positive patients who tested compared to those who tested negative (17.3% vs 1.5%, P<0.001). mNGS demonstrated clinical relevance in patients with hematologic malignancy who received prolonged antibiotic treatment and holds promise in predicting patient survival prognosis.},
}

Humans
Male
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Adult
*Metagenomics/methods
Aged
*Hematologic Neoplasms/complications/microbiology
*Fever/microbiology/drug therapy/diagnosis
Anti-Bacterial Agents/therapeutic use

@article {pmid42131305,
year = {2026},
author = {Toto, F and Cardile, S and Scanu, M and Marzano, V and Petito, V and Masi, L and Puca, P and Giorgio, V and Alterio, T and Diamanti, A and De Angelis, P and Lopetuso, LR and Scaldaferri, F and Putignani, L and Del Chierico, F},
title = {Ecological patterns of the gut mycobiome and microbiome in ulcerative colitis across life stages.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1769892},
pmid = {42131305},
issn = {2235-2988},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/immunology ; *Mycobiome ; *Gastrointestinal Microbiome ; Adult ; Child ; Male ; Female ; *Fungi/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Young Adult ; Adolescent ; Dysbiosis/microbiology ; Metagenome ; Child, Preschool ; Age Factors ; Aged ; Feces/microbiology ; },
abstract = {INTRODUCTION: Age-related variations in the gut microbial communities may influence immune regulation and inflammatory processes in inflammatory bowel diseases (IBD). However, distinguishing age effects from differences in clinical characteristics remains challenging.

METHODS: We investigated life-stage-associated patterns of the gut microbiome and mycobiome while accounting for clinical heterogeneity between paediatric and adult ulcerative colitis (UC) populations. We analysed 73 targeted metagenomes of bacteria and 69 targeted metagenomes of fungi from 26 paediatric and 47 adult patients with UC. Microbial diversity metrics and multivariate analyses were applied to evaluate community variation, and mucosal immune markers were assessed by ELISA. Clinical variables, including disease activity, duration, and treatment exposure, were considered when interpreting age-related microbial differences.

RESULTS: Fungal communities exhibited higher richness in adults and formed distinct age-related clusters in beta-diversity analyses, whereas bacterial composition remained largely comparable across age groups. Children were enriched in inflammation-associated fungi (Saccharomycetes, Aureobasidium, Cladosporium) and depleted in taxa commonly linked to gut health (Clavispora, Vishniacozyma, Betamyces). Stratification by life stage identified young adults as displaying the most pronounced dysbiosis, characterised by Basidiomycota/Ascomycota and Firmicutes/Bacteroidota ratios, and reduced Faecalibacterium prausnitzii abundance. Age-associated immune patterns were observed, with lysozyme levels increasing across life stages, correlating with sIgA, and positively associating with F. prausnitzii, although declining with increasing disease severity.

DISCUSSION: Age-related variation was more evident in fungal than bacterial communities, suggesting that host developmental and immunological factors contribute to mycobiome configuration beyond clinical imbalance alone. Together, these findings indicate that life stage is linked to ecological variation of the gut mycobiome and mucosal immune responses in UC, while bacterial communities appear primarily shaped by disease-related factors. The transition from childhood to adulthood may represent a critical window of host-fungal interaction relevant for age-tailored microbiome-based strategies.},
}

Humans
*Colitis, Ulcerative/microbiology/immunology
*Mycobiome
*Gastrointestinal Microbiome
Adult
Child
Male
Female
*Fungi/classification/genetics/isolation & purification
Bacteria/classification/genetics/isolation & purification
Middle Aged
Young Adult
Adolescent
Dysbiosis/microbiology
Metagenome
Child, Preschool
Age Factors
Aged
Feces/microbiology

@article {pmid42131468,
year = {2026},
author = {Mazibuko, X and Mtimka, S and Ngobese, LM and Mafuna, T and Simelane, MB and Yakobi, SH and Gumede, X and Pooe, OJ},
title = {Metagenomic Profiling of Taxonomic and Functional Diversity in Soil Microbial Communities at Buffelsdraai Landfill, South Africa: Implications for Bioremediation.},
journal = {Bioinformatics and biology insights},
volume = {20},
number = {},
pages = {11779322251413418},
pmid = {42131468},
issn = {1177-9322},
abstract = {Soil microbial communities in landfills play a crucial in waste degradation and pollution mitigation, yet their diversity and functionality in many regions remain underexplored. This study used shotgun metagenomic sequencing to characterise microbial communities in soil samples from the Buffelsdraai landfill waste site (samples: XM-AA, XM-BB, XM-CC, XM-DD). We identified dominant taxa, namely, Actinobacteria, Acidobacteria, and Bacteroidetes, and evaluated their taxonomic diversity and metabolic potential. Diversity indices revealed high richness in XM-AA (Shannon: 4.188), suggesting the potential of a strong waste-processing capacity, while XM-BB showed reduced diversity (Shannon: 1.453), likely due to contaminant stress (eg, nickel, cobalt). XM-CC and XM-DD exhibited moderate diversity (Shannon: 2.671-2.942) with Actinobacteria dominance (99%), suggesting adaptation to landfill conditions. Functional profiling via Kyoto Encyclopaedia of Genes and Genomes pathways highlighted carbohydrate and lipid metabolism, alongside xenobiotic biodegradation, pointing to potential for organic waste and pollutant breakdown. Physicochemical analyses detected elevated sodium (22 640 mg/kg in cell 1) and trace metals (eg, Ni: 0.1469 mg/kg), influencing microbial composition. These results emphasise microbial diversity's role in landfill soil functionality and position Actinobacteria as a bioremediation target for degrading leachate organics and immobilising metals. This study provides a baseline profile of microbial taxonomic and functional responses to landfill-associated environmental stressors in South Africa. The findings highlight the ecological roles of landfill microbial communities and their potential relevance for future bioremediation research.},
}

@article {pmid42131611,
year = {2026},
author = {Zhai, X and Pan, H and Zheng, J},
title = {Spinal infection caused by Coxiella burnetii and surgical treatments: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1785109},
pmid = {42131611},
issn = {2296-858X},
abstract = {Q fever is a rare global zoonosis caused by Coxiella burnetii, with bone and joint involvement being an uncommon manifestation that poses significant diagnostic challenges. This article reports a case of persistent focal spinal infection caused by C. burnetii in an elderly female without a clear epidemiological exposure history, who was initially misdiagnosed with vertebral compression fractures. The diagnosis was confirmed by third-generation nanopore-based metagenomic next-generation sequencing (mNGS), which detected 12,170 reads of C. burnetii with a relative abundance of 98.27%. The patient was initially treated with oral doxycycline (0.1 g q12h) and rifampin capsules (0.45 g daily) for 4 weeks, resulting in decreased inflammatory markers and reduced paravertebral abscess size. After clinical stabilization, surgical intervention (posterior approach T12-L1 vertebral lesion resection, intervertebral bone graft fusion, and pedicle screw rod fixation) was performed under general anaesthesia. Postoperative follow-up for 3 months showed a significant improvement in the patient's low back pain [visual analogue scale (VAS) score from 6 preoperatively to 1 at 3 months] and functional status [Oswestry Disability Index (ODI) from 65% preoperatively to 10% at 3 months], with normalized inflammatory markers and a reduced C. burnetii IgG antibody titre (from 1:256 to 1:128). Serological follow-up revealed persistent negative IgM antibodies throughout the treatment course. This case highlights the diagnostic value of third-generation mNGS for rare spinal infections caused by C. burnetii and the efficacy of a multimodal treatment approach combining targeted antimicrobial therapy and surgical intervention. The rationale for antibiotic selection and surgical management is discussed, along with the limitations of the present case and clinical insights for managing similar cases.},
}

@article {pmid42132311,
year = {2026},
author = {Tulloch, RL and Rojahn, J and Neaves, LE and Trujillo-González, A and Holleley, CE and Hahn, EE},
title = {Evaluating the Molecular Potential and Interpretability of DNA in Historical Spirit Collection Media.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70153},
doi = {10.1111/1755-0998.70153},
pmid = {42132311},
issn = {1755-0998},
support = {//Centre for Biodiversity Analysis/ ; },
mesh = {*DNA/isolation & purification/genetics ; *Specimen Handling/methods ; Animals ; Metagenomics/methods ; DNA Barcoding, Taxonomic/methods ; Museums ; *Preservation, Biological/methods ; },
abstract = {Advancements in historical genomics increasingly leverage museum collections to study past ecosystems, species interactions and biodiversity. Formalin-fixed, ethanol-preserved specimens, once thought inaccessible to molecular analyses due to DNA degradation, are emerging as valuable genomic resources. If recoverable and reliably attributable, DNA within preservation media could provide a non-destructive alternative to conventional tissue sampling, with the potential to expand molecular access to valuable or irreplaceable specimens. We tested whether preservation media contains recoverable DNA suitable for taxonomic inference. We coupled passive adsorption and active filtration of specimen media with hot alkaline lysis DNA extraction followed by metabarcoding and shotgun metagenomics. DNA was recoverable across samples, including 41 of 61 (~67%) targets in a composite sample. However, detections were dominated by non-target taxa, indicating that preservation media retain a layered mixture of specimen-derived DNA and broader collection-level background. Detection success tracked with preservation chemistry (near-neutral pH and low residual formaldehyde) rather than specimen age. Method choice influenced detections: active filtration increased target detections but admitted more background; passive capture was sparser but more selective; shotgun sequencing retrieved broader vertebrate signals, including reptiles, but was heavily enriched for non-targets. Because both target and non-target taxa were often abundant, read-abundance cut-offs were unreliable for attribution. Spirit-media DNA is therefore best interpreted as a collection-level signal and a screening tool to identify jars with molecular potential (e.g., taxa of conservation or biosecurity interest), rather than as a definitive non-destructive proxy for specimen identity. Prioritising chemically favourable jars and implementing rigorous contamination controls should improve signal interpretability and help unlock the value of preservation media for historical genomics.},
}

*DNA/isolation & purification/genetics
*Specimen Handling/methods
Animals
Metagenomics/methods
DNA Barcoding, Taxonomic/methods
Museums
*Preservation, Biological/methods

@article {pmid42132424,
year = {2026},
author = {Bae, J and Takemura, M},
title = {Refining a giant virus lineage: a novel order unifying Mamonoviridae and "Manesviridae," unveiled by the discovery of furtivovirus.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0203125},
doi = {10.1128/jvi.02031-25},
pmid = {42132424},
issn = {1098-5514},
abstract = {UNLABELLED: The evolutionary origins and taxonomic framework of giant viruses related to the family Mamonoviridae and its relative group, including clandestinovirus, remain unclassified due to gaps in genome size and host range between these two groups. This study aimed to address this gap by integrating our newly isolated virus with publicly available metagenome-assembled genomes (MAGs) to construct a more robust phylogenetic framework. Here, we report the isolation and characterization of a new giant virus, furtivovirus, using the unicellular amoeba Vermamoeba vermiformis as a host. Furtivovirus has a genome of approximately 560 kbp and shares key features with its closest relative, clandestinovirus. Ultrastructural analysis revealed a unique host-nucleus-dependent replication strategy characterized by the breakdown of the nuclear membrane and the packaging of nascent virions directly within the nucleoplasm, distinguishing it from canonical cytoplasmic virion factories. Comprehensive phylogenetic and comparative genomic analyses of shared orthologous groups and nucleocytovirus marker proteins revealed that furtivovirus, clandestinovirus, ushikuvirus, and usurpativirus form a distinct monophyletic clade, for which we propose a new family, "Manesviridae." Further analysis using amino acid-based similarity metrics of Nucleocytoviricota viral genomes, including established MAGs, demonstrated that this new family is robustly placed as a sister group to the family Mamonoviridae. This study elucidated the evolutionary relationships between viruses with large and small genomes that possess similar virion sizes within this lineage. Based on this cumulative evidence, we propose the establishment of a new order to unify these two families, thereby expanding their diversity and clarifying the evolutionary history of this branch within Nucleocytoviricota.

IMPORTANCE: Giant viruses challenge our traditional understanding of viral evolution, raising the question of how a single related group can diverge to infect different hosts while evolving into vastly different genome sizes and replication strategies. The family Mamonoviridae and its relatives epitomize this evolutionary divergence: one group possesses massive genomes, whereas the other has genomes that are less than half their size. The discovery of furtivovirus and its unique nucleoplasm-dependent replication cycle provides a critical biological context for this genomic disparity. Through deep comparative genomic analysis, we demonstrated that these seemingly disparate lineages share a cohesive evolutionary origin that is distinct from other established orders. This finding highlights the complexity of genome evolution, demonstrating that giant viruses can expand their overall genome size to adapt to uncertain environments while reducing their core essential genes, thereby providing new insights into the evolutionary pressures that shape the diversity of the virosphere.},
}

@article {pmid42132850,
year = {2026},
author = {Bright, K and Dienes, B and van Dongen, B and Strashnov, I and Han, X and Aeppli, M},
title = {Emerging investigator series: metagenomic insights into microbial controls of carbon cycling in alpine soils.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5em01047k},
pmid = {42132850},
issn = {2050-7895},
abstract = {Alpine riparian zones span topographic gradients from wet soils on the plain near streams to drier soils on adjacent slopes. These differences in soil moisture are generally associated with shifts in the soil redox state from anoxic on the plain to oxic on the slope. In anoxic plain soils, soil organic carbon (SOC) may accumulate due to thermodynamic constraints on microbial activity. Here, we used shotgun metagenomics to examine how microbial diversity and functional potential vary across differing redox conditions on plain and slope soils in two catchments in the Swiss Alps. We complemented these analyses with soil physicochemical characteristics and information on the chemical composition of organic matter. Plain soils had higher SOC stocks and higher relative abundance of phenol compounds relative to slope soils, consistent with SOC preservation and preferential mineralisation of easily degradable organic compounds under anoxic conditions. Microbial communities in plain soils further exhibited greater taxonomic and functional diversity, including increased potential for anaerobic respiration pathways. Genes for nitrate, iron, and sulfate reduction were linked to the Chloroflexota, Acidobacteria, and Desulfobacterota phyla, respectively. Based on NMDS correlations, electron accepting capacity, calcium content, and pH shaped microbial community composition. Slope soils, by contrast, supported less diverse microbial communities, determined mainly by electron donating capacity and clay content. Our work demonstrates how soil redox conditions and microbial functional potential shape carbon cycling across landscape positions in alpine riparian zones. This mechanistic understanding is critical to anticipate changes in carbon cycling in alpine ecosystems in a changing climate.},
}

@article {pmid42132937,
year = {2026},
author = {Enuh, BM and Myers, KS and Bott, C and Klaus, S and McCullough, K and McIntosh, L and Beach, N and Young, M and Donohue, TJ and Noguera, DR},
title = {Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Hamptons Road Sanitation District (HRSD) with high and low dissolved oxygen conditions.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0149225},
doi = {10.1128/mra.01492-25},
pmid = {42132937},
issn = {2576-098X},
abstract = {Aeration is a major cost at biological nutrient removal (BNR) plants. We report on microbial communities in a pilot-scale BNR system before and after a dissolved oxygen transition from 2.5 to 0.2 mg/L implemented over 18 months. Four PacBio metagenomes and 316 metagenome-assembled genomes are announced.},
}

@article {pmid42132952,
year = {2026},
author = {Özel, Ş and Lauritano, D},
title = {Oral mucosal microbiome alterations in recurrent aphthous stomatitis: a systematic review of 16 S rRNA gene sequencing studies.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42132952},
issn = {1573-4978},
mesh = {Humans ; *Stomatitis, Aphthous/microbiology/genetics ; *Mouth Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Dysbiosis/microbiology ; Case-Control Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; Recurrence ; },
abstract = {Recurrent aphthous stomatitis (RAS) is a prevalent inflammatory disorder of the oral mucosa characterized by recurrent painful ulcerations in otherwise healthy individuals. This systematic review aimed to evaluate alterations in the oral mucosal microbiome of patients with RAS based on studies using 16 S rRNA sequencing. A systematic search of PubMed, Scopus, and Web of Science was conducted on April 14, 2026. Eligible studies included human case-control investigations evaluating oral mucosal swab samples from patients with clinically diagnosed RAS and healthy controls using 16 S rRNA sequencing. Studies based solely on saliva, culture methods, PCR-only analyses, or lacking controls were excluded. Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies was used for the evaluation of selected articles. Six studies met the inclusion criteria. Considerable heterogeneity was observed in alpha and beta diversity outcomes. Most studies reported reduced microbial richness in RAS lesions, whereas others found increased or unchanged diversity. Ulcerated sites frequently demonstrated reduced abundance of health-associated taxa such as Streptococcus and Firmicutes, with increased levels of Proteobacteria and inflammation-associated genera including Neisseria, Haemophilus, Prevotella, and Fusobacterium. Microbial alterations were most pronounced at active ulcer sites, while non-ulcerated or healed mucosa more closely resembled healthy controls. Current evidence suggests that RAS is associated with localized, site-specific microbial dysbiosis rather than generalized oral microbiome disruption. However, methodological heterogeneity and small sample sizes limit definitive conclusions. Future standardized longitudinal studies integrating functional metagenomics are warranted to clarify the role of the microbiome in RAS pathogenesis.},
}

Humans
*Stomatitis, Aphthous/microbiology/genetics
*Mouth Mucosa/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Dysbiosis/microbiology
Case-Control Studies
Saliva/microbiology
Bacteria/genetics/classification
Recurrence

@article {pmid42133155,
year = {2026},
author = {Zhang, Q and He, G and Guo, Z and He, Y and Xiong, J and He, T and Lee, SL},
title = {Comparative metagenomic and metabolomic characterization of conventionally and nitrogen-only fertilized maize soils and a forest-derived fermentation-enriched microbial community.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42133155},
issn = {1573-0972},
support = {42367039, 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//National Key Research and Development Program of China/ ; Z2024417//Guizhou Provincial Science and Technology Department/ ; Liu Jin Xiang [2024] No. 44, 202406670023//Overseas Study Program for Young Key Teachers/ ; },
mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Zea mays/growth & development/microbiology ; Forests ; Fermentation ; Soil/chemistry ; *Metagenomics/methods ; *Fertilizers ; *Metabolomics/methods ; China ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Agriculture ; Carbon/metabolism ; },
abstract = {Long-term nitrogen-only fertilization can alter soil physicochemical properties and microbial community structure in maize fields. In this study, nitrogen-only fertilized soil (S) and conventionally fertilized soil (B) were collected from a four-year maize field trial in Anshun City, Guizhou Province, China. Meanwhile, a forest-derived microbial enrichment system (T) was prepared through fermentation using forest soil, rice bran, and molasses. Metagenomic sequencing and untargeted metabolomics were used to compare microbial, functional gene, and metabolite differences between S and B soils within the agricultural field system, and to describe the microbial community composition, functional gene profiles, and metabolite features of T as an independent reference system. The results showed that Pseudomonadota accounted for 44.33% of the microbial community in T, compared with 20.63% in S and 22.31% in B. Carbon and nitrogen metabolism-related genes, including ackA, gltB, and ureC, showed higher relative abundances in T than in S. Pathway-level annotation indicated higher representation of genes or modules related to glycolysis and nitrogen metabolism in T. Metabolomic profiling revealed distinct metabolite patterns in T, including differences in amino acids, carbohydrates, and metabolites annotated to phenylpropanoid-related pathways. Candidatus Rokubacteria also showed high relative abundance among nitrogen-metabolism-associated taxa in T. Overall, this study provides descriptive multi-omics evidence of the microbial composition, functional gene profiles, and metabolite features of a forest-derived fermentation-enriched microbial community. Because T was an artificially enriched system and was not introduced into agricultural soil, these results should be interpreted as baseline data for future controlled validation rather than direct evidence of soil remediation or functional compensation.},
}

*Nitrogen/metabolism
*Soil Microbiology
*Zea mays/growth & development/microbiology
Forests
Fermentation
Soil/chemistry
*Metagenomics/methods
*Fertilizers
*Metabolomics/methods
China
*Microbiota/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
Agriculture
Carbon/metabolism

@article {pmid42133463,
year = {2026},
author = {Che, J and Du, J and Piao, Y and Dong, Y and Zhang, L and Su, D and Zhang, C and Zhao, Y and Du, W and Che, N},
title = {Fungal Species Identification in FFPE Tissues: A Comparative Evaluation of Droplet Digital PCR, ITS Sequencing, and Metagenomic Next-Generation Sequencing.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myag049},
pmid = {42133463},
issn = {1460-2709},
abstract = {Accurate histological diagnosis of fungal infections is challenging due to morphological similarities among fungi, which can affect treatment outcomes. This study evaluated the performance of droplet digital PCR (ddPCR), internal transcribed spacer (ITS) sequencing, and metagenomic next-generation sequencing (mNGS) using 111 formalin-fixed, paraffin-embedded tissue samples with histologically confirmed fungal infections. All three methods showed comparable detection rates for filamentous fungi (84.2%-94.7%; p = 0.2). For yeast-like fungi, however, mNGS demonstrated significantly higher detection (66.7%) than ddPCR (46.3%) and ITS sequencing (35.2%) (p < 0.01). mNGS also achieved superior genus- and species-level identification (81.1% for both) compared to ddPCR (65.8% and 64.9%) and ITS sequencing (61.3% and 50.5%) (p < 0.01). Additionally, mNGS identified two unusual fungi (Scedosporium apiospermum and Schizophyllum commune) previously misdiagnosed as Aspergillus. These findings support the integration of mNGS into clinical diagnostic workflows for the accurate identification of yeast-like and rare fungal pathogens, thereby enabling targeted antifungal therapy.},
}

@article {pmid42133477,
year = {2026},
author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW},
title = {Gut Species Porphyromonas asaccharolytica and Bacteroides fragilis Are Associated with Whole Body Fat Percentage.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag117},
pmid = {42133477},
issn = {1365-2672},
abstract = {AIMS: Obesity is linked to various adverse health effects, with body fat percentage being a key indicator of these risks. While the gut microbiota (GM) plays important roles in obesity, the specific species involved remain poorly understood. We aimed to identify gut species that may influence obesity in a cohort of US men.

METHODS AND RESULTS: We conducted a comprehensive integrative analysis using metagenomics and whole-genome sequencing data in the US cohort. MaAsLin2 was used to identify associations between GM and whole body fat percentage (PFAT). Mendelian randomization (MR) was applied to investigate potential directional relationships between GM species and PFAT, as well as possible interactions between microbial species. Porphyromonas asaccharolytica (P.asaccharolytica) was negatively associated (β=-0.181, P=0.005) with PFAT, while Bacteroides fragilis (B.fragilis) was positively associated (β=0.239, P=0.001); these associations were validated in an independent Chinese cohort. MR analysis suggested that P.asaccharolytica may influence PFAT in part through its potential effect on B. fragilis abundance.

CONCLUSION: Gut species P.asaccharolytica and B.fragilis are associated with host body fat percentage and may influence obesity individually or collaboratively. The observed associations provide evidence consistent with a potential directional relationship between these species and human adiposity.},
}

@article {pmid42133579,
year = {2026},
author = {Lai, X and Gao, Q and Wu, L},
title = {A 56-Year-Old Male Farmer From China With Severe Fever With Thrombocytopenia Syndrome and Pulmonary Aspergillosis: A Case Report and Review of Literature.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e951798},
doi = {10.12659/AJCR.951798},
pmid = {42133579},
issn = {1941-5923},
mesh = {Humans ; Male ; Middle Aged ; *Severe Fever with Thrombocytopenia Syndrome/diagnosis/complications ; China ; *Pulmonary Aspergillosis/diagnosis/complications ; Farmers ; COVID-19 ; Coinfection ; Aspergillus fumigatus/isolation & purification ; Antifungal Agents/therapeutic use ; },
abstract = {BACKGROUND Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne infectious disease caused by the Dabie bandavirus (commonly known as SFTS virus, or SFTSV). SFTSV-induced immunosuppression during infection renders patients highly susceptible to invasive pulmonary aspergillosis. SFTS-associated pulmonary aspergillosis (SAPA) presents major therapeutic challenges and is linked to drastically worsened outcomes, including high mortality. This report aims to highlight the diagnostic and therapeutic challenges of SAPA and emphasize the value of early diagnosis using metagenomic next-generation sequencing (mNGS). CASE REPORT We report a case of a previously healthy 56-year-old male farmer admitted with SFTS. On hospital day 3, when only mild cough had begun, mNGS of both blood and sputum concurrently detected Aspergillus fumigatus alongside SFTSV. This very early, pre-radiographic diagnosis prompted immediate targeted therapy with voriconazole and favipiravir. Despite this, imaging showed progressive pulmonary infiltrates with cavitation. The clinical course was further complicated by severe acute respiratory syndrome coronavirus 2 co-infection, but the patient recovered with intensive care and was discharged on day 24. A review of 13 literature-reported SAPA cases revealed a mortality rate of 30.77% (4/13). CONCLUSIONS SAPA is a severe, rapidly progressive complication of SFTS with high mortality, typically emerging 1-2 weeks after onset. This case highlights the importance of early diagnosis using rapid methods such as mNGS and the need for timely antifungal intervention to improve patient outcomes. Early antifungal therapy in high-risk patients is crucial.},
}

Humans
Male
Middle Aged
*Severe Fever with Thrombocytopenia Syndrome/diagnosis/complications
China
*Pulmonary Aspergillosis/diagnosis/complications
Farmers
COVID-19
Coinfection
Aspergillus fumigatus/isolation & purification
Antifungal Agents/therapeutic use

@article {pmid42134120,
year = {2026},
author = {Liang, W and Nong, Q and Huang, H and Huang, J and Shao, J and Wang, M and Hong, P and Liu, S and Zhou, C and Zhong, S},
title = {Correlation analysis between microbial diversity in mixed-fermented shrimp juice and the synthesis pathways of characteristic flavor compounds.},
journal = {Food chemistry},
volume = {518},
number = {},
pages = {149574},
doi = {10.1016/j.foodchem.2026.149574},
pmid = {42134120},
issn = {1873-7072},
abstract = {This study elucidated flavor formation in fermented shrimp juice using metagenomics and correlation analyses. The amino acid nitrogen content peaked at 0.54 g/100 mL on the 30th day, surpassing that of traditional fish sauce. Phenolic compounds, including guaiacol and phenylacetaldehyde, were identified as key flavor contributors. The microbial community gradually developed into a stable microbiota dominated by nine genera, including Aspergillus, Lactiplantibacillus, and Meyerozyma. Metagenomic analysis demonstrated that this core microbiome governed critical metabolic pathways for carbohydrate, amino acid, and lipid metabolisms, collectively driving the efficient flavor development in the fermented product.},
}

@article {pmid42134135,
year = {2026},
author = {Huang, Z and Wang, J and Yang, C and Lv, Z and Wang, R},
title = {Integrated transcriptomics and metagenomics analyze the dynamic correlations between cecal mucosal tissue and cecal microbiota in Liangshan Yanying chickens during early postnatal development.},
journal = {Poultry science},
volume = {105},
number = {8},
pages = {106904},
doi = {10.1016/j.psj.2026.106904},
pmid = {42134135},
issn = {1525-3171},
abstract = {Liangshan Yanying chicken, a precious indigenous Chinese breed listed in the Catalog of Livestock and Poultry Genetic Resources in China, is an economic pillar in Liangshan Yi ethnic area and critical for poverty alleviation-to-rural revitalization transition. It has excellent phenotypic traits, high nutritional value, unique flavor, and strong adaptability to 380-4500 m altitudes. However, the co-evolutionary mechanism between its cecal mucosal tissue and gut microbiota (key to intestinal homeostasis and productivity) remains unclear. We systematically investigated their dynamic crosstalk in 1-, 14-, and 28-day-old chickens (n = 10/group) using transcriptomics, metagenomics, bioinformatics, and qPCR. Cecal length increased from 3.77 cm (1 d) to 8.98 cm (28 d), with higher growth rate at 14-28 d. We identified 67 DEGs (34 upregulated immune-related, 33 downregulated development-related) and 16 dynamically changed microbial taxa. Host-microbiota crosstalk was mediated by 52 shared KEGG pathways, with 10 core genes and 13 functional taxa maintaining homeostasis via PI3K-Akt pathway. This study first reveals a "gut microbial homeostasis" model for cecal dynamic homeostasis, providing insights for local poultry intestinal health and breeding.},
}

@article {pmid42134217,
year = {2026},
author = {Hua, Y and Xue, Y and Li, Z and Zhang, Y and Liu, Q and Liu, L and Tang, J},
title = {Effect of microplastics on arsenic transport in shallow groundwater of coastal transition zones.},
journal = {Water research},
volume = {301},
number = {},
pages = {126097},
doi = {10.1016/j.watres.2026.126097},
pmid = {42134217},
issn = {1879-2448},
abstract = {Coastal transition zones (CTZs) are dynamic zones where seawater intrusion and freshwater discharge interact. Arsenic (As) is a common contaminant in these zones, however its co-transport with increasing abundance microplastics (MPs) remains unclear. In this study, saturated column experiments combined with Hydrus-1D modeling were used to investigate the co-transport of As with polystyrene (PS), polyethylene (PE), and polylactic acid (PLA). Increasing salinity inhibited As transport in the absence of MPs. Under the same salinity, MPs generally increased As breakthrough, following the order PS > PE > PLA. With salinity increased, PS maintained a slight promoting effect on As breakthrough, whereas PE and PLA exhibited reduced breakthrough under high-salinity conditions. Co-transport was most pronounced at an As:MP ratio of 1:2, although PLA showed a non-linear response and lower As mobility at 1:1. Simulated seawater intrusion indicated that ionic-strength fluctuations produced distinct release peaks. MPs further enhanced non-equilibrium As release during flushing. Metagenomic sequencing of samples from the 21-day experiment indicated that MPs altered the microbial communities and increased the relative abundance of several As-related genes (such as AS3MT and arsC), particularly in the PS treatment. These findings clarify the effects of MPs on As transport and support risk assessment for coastal groundwater systems.},
}

@article {pmid42134269,
year = {2026},
author = {Jiang, J and Liu, R and Shen, Y and Yin, Z and Li, Y},
title = {Mechanistic insights into antimony immobilization by sulfur-metabolizing microorganisms under alternating oxic-anoxic conditions.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142328},
doi = {10.1016/j.jhazmat.2026.142328},
pmid = {42134269},
issn = {1873-3336},
abstract = {Antimony (Sb), as a toxic heavy metal(loid) element, poses potential risks to the environment and human health. The migration and transformation of Sb in the environment are closely linked to the macronutrient sulfur. However, under alternating oxic-anoxic conditions, the roles of sulfur and sulfur-metabolizing microorganisms in Sb mobility remain unclear. This study systematically investigated the role of exogenous thiosulfate (S2O3[2-]) in Sb(V) immobilization and the underlying mechanisms by integrating microcosm incubations, speciation analyses, and genome-resolved metagenomic analyses. We found that during the oxic-anoxic-oxic transition, Sb(V) was immobilized under anoxic condition and was released under oxic condition. However, thiosulfate amendment significantly inhibited Sb release through facilitating the sulfur-dependent reduction of Sb(V) to Sb(III) and formation of Sb2O3 precipitates. Complete Sb(V) immobilization was achieved within 14 days, concurrently with the oxidation of S2O3[2-] to SO4[2-], indicating thiosulfate is the primary electron donor for microbial reduction of Sb(V). Key microorganisms, including Ramlibacter (Bin.5), Thiomonas (Bin.105), and Unclassified (Bin.112 and Bin.123), which harbor antimonate/arsenate respiratory reductase gene (arrA) and sulfur oxidation pathway (Sox system), drive the sulfur-dependent Sb immobilization, as evidenced by metagenome-assembled genomes (MAGs) results. These findings enhance our understanding of the coupled cycling of Sb and S in alternating oxic-anoxic environments and provide a potential approach for Sb remediation.},
}

@article {pmid42134371,
year = {2026},
author = {Govender, KN and Street, TL and Sanderson, ND and Leach, L and Morgan, M and Eyre, DW},
title = {Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101333},
doi = {10.1016/j.lanmic.2025.101333},
pmid = {42134371},
issn = {2666-5247},
abstract = {BACKGROUND: Metagenomic sequencing can potentially transform clinical microbiology by enabling rapid pathogen identification and antimicrobial resistance (AMR) prediction in critically ill patients with bloodstream infections. However, the clinical use of metagenomic sequencing has been constrained by its speed, accuracy, and technical feasibility. Our aim was to develop and evaluate a direct-from-positive blood culture workflow using Oxford Nanopore sequencing that overcomes these limitations and delivers rapid, accurate results.

METHODS: In this metagenomic pipeline analysis, 211 positive (130 aerobic and 81 anaerobic) and 62 negative (30 aerobic and 32 anaerobic) randomly selected blood cultures were processed from Oxford University Hospitals for comparing species identification, AMR detection, and time-to-result against standard culture-based diagnostics performed by the hospital's routine microbiology laboratory. Species prediction was performed using Kraken2 with a comprehensive standard database, applying heuristic and random forest classification models. Additionally, we benchmarked AMR classification tools and databases, including ResFinder, CARD, and NCBI AMRFinderPlus.

FINDINGS: Across all samples, our method achieved 97% sensitivity and 94% specificity for species identification compared with that of routine culture and matrix-assisted laser desorption ionisation time-of-flight-based diagnostics; both sensitivity and specificity increased to 100% after adjudication of plausible additional infections. We detected 19 additional infections (13 polymicrobial, five previously unidentifiable, and one in a culture-negative sample) and delivered species identification results within 3 h 20 min (IQR 3 h 7 min-3 h 27 min), approximately 10 h earlier than routine diagnostic methods. For the ten most common clinically relevant pathogens, our method yielded AMR results 20 h earlier than current antimicrobial susceptibility testing, with an overall sensitivity of 88% and specificity of 93%. Performance varied by species. For Staphylococcus aureus, the AMR prediction sensitivity was 100% and specificity was 99%, and for Escherichia coli, the prediction sensitivity was 91% and specificity was 94%.

INTERPRETATION: These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to close diagnostic gaps, reduce empirical antibiotic use, and enable rapid targeted treatment. Nonetheless, improvements in AMR prediction for some species and drugs, along with further multisite validation, are required before clinical implementation.

FUNDING: National Institute for Health Research (NIHR) Oxford Biomedical Research Centre.},
}

@article {pmid42134579,
year = {2026},
author = {Zhao, C and Hu, Z and Wang, D and Xu, M and Hao, Z and Fu, C and Zhang, J and Zhuang, L},
title = {Metagenomic insights into the enhancement of doxycycline hydrochloride removal in constructed wetlands under moderate lead stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134878},
doi = {10.1016/j.biortech.2026.134878},
pmid = {42134579},
issn = {1873-2976},
abstract = {Constructed wetlands (CWs) serve as an important ecological barrier preventing contaminated water from entering surface waters and are frequently exposed to antibiotic-heavy metal co-contamination under real operating conditions. However, how heavy metal stress regulates antibiotic removal through microbial processes in CWs remains poorly understood. Here, CWs subjected to doxycycline hydrochloride (DOX) and lead (Pb) co-contamination were established to elucidate the effects of different Pb stress levels on DOX removal performance and the underlying microbial mechanisms. The results showed that DOX removal was maximized under moderate Pb stress (1 mg/L), reaching a highest removal efficiency of 95.8%. Consistent toxicity responses were observed, with moderate Pb exposure significantly reducing effluent biotoxicity, alleviating plant stress, and improving overall system stability. Mass balance analysis demonstrated that microbial transformation dominated DOX removal, accounting for over 79% of total removal. Metagenomic analyses further revealed the underlying microbial mechanisms, showing that moderate Pb stress reshaped microbial community structure, promoted the enrichment of key functional microorganisms, and increased the abundance of DOX degradation-related functional genes. Representative functional taxa included Sphingomonas, Propionibacterium, and Candidatus Woesearchaeota archaeon. In contrast, high Pb stress (10 mg/L) imposed strong metal toxicity that suppressed the activity and diversity of core functional microorganisms, resulting in reduced DOX degradation capacity accompanied by toxicity accumulation. Collectively, this study clarifies how heavy metal stress regulates antibiotic removal through microbial pathways in CWs, and provide a reference for understanding CWs performance under co-contamination.},
}

@article {pmid42134580,
year = {2026},
author = {He, J and Xiang, B and Xu, W and Pan, Z},
title = {Comparative study on microbial mechanisms of denitrification failure in AAO process and air-lift internal circulation process under ultra-low C/N ratios.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134881},
doi = {10.1016/j.biortech.2026.134881},
pmid = {42134580},
issn = {1873-2976},
abstract = {Denitrification failure under low-carbon conditions limits biological nitrogen removal. This study compared the recovery performance of a conventional anaerobic-anoxic-oxic (AAO) process and an air-lift internal circulation reactor (AICR) after carbon supplementation, following long-term operation at ultra-low C/N (≈1). Batch experiments showed that the AICR initiated denitrification more rapidly than the AAO. At C/N = 7, the AICR removed 62% of nitrate nitrogen (NO3[-]-N) within 4.5 h, while the AAO removed only 43%. After 10 h, removal efficiencies reached 78% in the AICR and 69% in the AAO. The AICR also had higher adenosine triphosphate (ATP) levels and greater denitrification enzyme activities. Quantitative polymerase chain reaction (qPCR) confirmed that nirS and nosZ copy numbers in the AICR were approximately twice those in the AAO. Metagenomic analysis revealed distinct genomic architectures in the two systems. The AAO relied on a limited number of versatile strains carrying complete denitrification gene clusters. In contrast, the AICR harbored a distributed network where denitrification steps were partitioned among phylogenetically diverse and functionally specialized strains. These differences in community architecture were linked to the distinct flow regimes of the two reactors and corresponded to enhanced functional modularity and metabolic redundancy in the AICR, which contributed to its faster recovery under carbon fluctuations.},
}

@article {pmid42134588,
year = {2026},
author = {Chauhan, A and Santhiya, D and Sharma, JG},
title = {Microbial consortium driven degradation of mixed microplastics: systematic review on enzymes and omics-based insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134885},
doi = {10.1016/j.biortech.2026.134885},
pmid = {42134588},
issn = {1873-2976},
abstract = {Microplastics (MPs) are among the most persistent pollutants in the environment. Mixed polymer waste further complicates the remediation due to their toxic additives and heterogenous composition. Conventional remediation methods show limited efficiency, especially for mixed MPs. As a result, biological approaches, particularly microbial consortium mediated degradation is a promising alternative. It is gaining increasing attention due to their cooperative metabolism and ability to degrade multiple polymers simultaneously. This review summarizes recent advances in consortium-based degradation of mixed MPs. It compares existing studies and identifies key challenges in translating laboratory findings to real-world. This review further discusses enzymes involved in the degradation of major polymer constituting mixed MPs. In addition, the role of multi-omics approaches like metagenomics, meta-transcriptomics, metabolomics, and integrated systems biology is also highlighted to explain microbial-metabolite interaction, functional pathways, and degradation mechanisms. Further, this review proposed future research directions focusing on green and scalable technologies. These include green biosensors for real-time monitoring, agro based aerogels and biochar for microbial immobilization, and nano-bubble assisted systems to enhance degradation under economic real-world conditions.},
}

@article {pmid42134644,
year = {2026},
author = {Liang, M and Wang, X and Li, J and Li, R and Peng, J and Gao, B and An, R and Chen, X and Zhang, J and Liu, X},
title = {Antibiotic-mediated Gut Microbiota Depletion Partially Attenuates Methamphetamine-induced Reward and Linoleic Acid Metabolic Disturbance.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {111022},
doi = {10.1016/j.neuropharm.2026.111022},
pmid = {42134644},
issn = {1873-7064},
abstract = {Methamphetamine (METH) is a highly addictive psychostimulant that possesses potent toxicity to multiple organs. Emerging evidence has suggested associations between gut microbiota dysbiosis and METH-induced rewarding effects. However, the role and underlying mechanisms of gut microbiota in METH addiction remain poorly understood. Using a mouse conditioned place preference (CPP) model combined with multi-omics profiling of gut microbiota and metabolites, we first investigated how METH exposure affects gut microbiota composition. Then, antibiotic (ABX)-mediated gut microbiota depletion was conducted to explore the role of gut microbiota in the METH-induced associative memory of context-reward (METH reward) and metabolic dynamics. Furthermore, associations among gut microbiota, metabolites, and behavioral phenotypes were determined to reveal the potential key microbial taxa and metabolites in METH reward. Finally, the key metabolite was intervened to reveal the role of it in the METH reward. Our results demonstrated that repeated METH administration induced significant alterations in gut microbiota profiles. ABX-mediated microbiota depletion attenuated METH-induced rewarding effects and metabolic perturbations, especially in linoleic acid (LA) metabolism. METH exposure led to an increase in, while gut microbiota depletion rescued the activation of LA metabolism. Correlation analyses consistently demonstrated associations among specific bacterial species, LA metabolites, and CPP scores. Supplementation of LA could facilitate, while inhibition of it could attenuate the METH-induced CPP. These findings highlight LA metabolism as a potential mechanistic link between gut microbiota dysbiosis and METH reward. Future gut microbiota-targeted therapeutic interventions, particularly those modulating LA metabolism, may improve the treatment of METH use disorder.},
}

@article {pmid41917812,
year = {2026},
author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W},
title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41917812},
issn = {1471-2180},
support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; },
abstract = {UNLABELLED: The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04923-x.},
}

@article {pmid42120383,
year = {2026},
author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW},
title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42120383},
issn = {2041-1723},
support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Carrageenan/metabolism ; *Ruminants/microbiology ; Rumen/microbiology ; Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; Bacteria/metabolism/genetics/classification/isolation & purification ; Seaweed/metabolism ; Bacteroides/metabolism/genetics/isolation & purification ; Metagenomics ; Phylogeny ; },
abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.},
}

Animals
*Gastrointestinal Microbiome/genetics/physiology
*Carrageenan/metabolism
*Ruminants/microbiology
Rumen/microbiology
Glycoside Hydrolases/metabolism/genetics
Feces/microbiology
Bacteria/metabolism/genetics/classification/isolation & purification
Seaweed/metabolism
Bacteroides/metabolism/genetics/isolation & purification
Metagenomics
Phylogeny

@article {pmid42120665,
year = {2026},
author = {Chen, LG and Zhou, L and Wang, BW and Javed, M and Liu, YF and Yang, SZ and Gu, JD and Mu, BZ},
title = {Microbial assembly and metabolic restructuring following CO2 injection in subsurface oil reservoir.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02066-w},
pmid = {42120665},
issn = {2191-0855},
support = {Grant No. 42473082//National Natural Science Foundation of China/ ; No. 42173076//National Natural Science Foundation of China/ ; No. 52074129//the National Natural Science Foundation of China/ ; 21ZR1417400//the Natural Science Foundation of Shanghai/ ; JKJ01231714//the Fundamental Research Funds for the Central Universities of China/ ; },
abstract = {Carbon dioxide (CO2) injection into oil reservoirs is a well-established and promising strategy for enhancing oil recovery while simultaneously sequestering carbon, whose effectiveness is increasingly recognized to be influenced by microbial-mediated mechanisms and biogeochemical processes. However, the impact of CO2-injected and storage on functional microbial communities and their metabolic potential remains poorly understood. The study employed high-throughput sequencing to analyze the composition and diversity of microbial communities in produced water from three production wells with a long-term (> 20 years) history of CO2 injection and two adjacent water-flooding ones in Xinli Oilfield, China. The results showed that CO2-injected wells had significantly higher microbial diversity and distinct metabolic potential relative to the adjacent water-flooding wells. A metabolic difference in the archaeal communities towards hydrogenotrophic and heterotrophic metabolisms, alongside an enrichment of bacterial taxa associated with sulfur and nitrogen cycling was observed. Correlation analysis revealed that microbial differentiation was strong associated with geochemical alteration (especially pH and some inorganic ions), with NH4[+] and S[2-] identified as key factors in this process. Metagenomic analysis based on high-quality metagenome-assembled genomes (MAGs) further demonstrated that CO2 injection led to a different profile of microbial metabolic functions relative to the water-flooding condition, characterized by significantly enhancing hydrogenotrophic methanogenesis, dissimilatory sulfate reduction, and denitrification, while diminishing methylotrophic methanogenesis and Wood-Ljungdahl pathway activity. These findings provide new insights into the microbial mechanisms driving carbon transformation in CO2-flooded oil reservoirs.},
}

@article {pmid42120930,
year = {2026},
author = {Huang, L and Zhang, X and Wu, Y and Li, H and Li, M and Shao, C and Yang, Q and Jin, G and Hu, X},
title = {The gut microbiota and metabolomics in the pathogenesis of type 2 diabetes mellitus combined with coronary atherosclerotic heart disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51805-3},
pmid = {42120930},
issn = {2045-2322},
support = {Grant No.202204295107020049)//the Clinical Translation Project of Anhui Province/ ; Grant No. 2208085MH216//the Natural Science Foundation of Anhui Province/ ; Grant No. 2020byfy004//the Major Natural Science and Technology Project of Bengbu Medical Uuniversity/ ; Grant No. AHWJ2023BAc10028//The Scientific Research Program of Anhui Provincial Health Commission/ ; },
abstract = {To investigate the characteristics of intestinal bacteria and their metabolites in healthy controls (CONs) compared with individuals with type 2 diabetes mellitus (T2DM) and individuals with type 2 diabetes mellitus combined with coronary atherosclerotic heart disease (T2DM-CAD). Thirty samples were collected from 10 healthy people, 10 T2DM patients, and 10 T2DM-CAD patients. We determined the gut bacterial composition via metagenomic sequencing analysis and analyzed the gut microbes and their metabolomic changes via metabolomics. The potential key gut microbes and metabolites were explored with random forest and receiver operating characteristic (ROC) curve analyses. Finally, Spearman correlation analysis and linear regression were used to identify the correlations between the gut bacteria and metabolites. Eight gut microorganisms with diagnostic significance were screened out, including Prevotella disiens, Bacteroides sp._AM25_34, Paraprevotella clara, Bacteroides sp._CAG_875, Sutterella wadsworthensis, Prevotella sp. 885, Ruminococcus sp. AM42_11 and Anaerobutyricum hallii. Meanwhile, eight characteristic metabolites were identified, including fructose, salicyluric acid, 12-ketoLCA, pyroglutamic acid, glutamic acid, suberic acid, gallic acid and adipic acid. Additionally, the correlations between the above differential gut microbiota and characteristic metabolites were clarified. Our study revealed that gut flora such as g-Bacteroides, Alistipes_putredinis_CAG_67, and Alistipes_putredinis may be key flora, and that fructose, gallic acid, sebacic acid, and 12-ketoLCA may be key metabolites involved in the pathology of T2DM and T2DM-CAD.},
}

@article {pmid42121077,
year = {2026},
author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X},
title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.},
journal = {BMC neurology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12883-026-04958-7},
pmid = {42121077},
issn = {1471-2377},
abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.},
}

@article {pmid42121260,
year = {2026},
author = {Zhou, Z and Lamanna, A and Halder, R and Pansart, E and Narayanasamy, S and Boussoufa, B and Kerkour, T and Wilmes, P and Williams, E},
title = {Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02369-x},
pmid = {42121260},
issn = {2049-2618},
support = {PRIDE21/16749720/NEXTIMMUNE2//Luxembourg National Research Fund/ ; },
abstract = {BACKGROUND: The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.

RESULTS: We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730 days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering > 300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC = 0.84 for CD, 0.79 for HF) and chronological age (AUC = 0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.

CONCLUSIONS: Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC = 0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC = 0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.},
}

@article {pmid42121284,
year = {2026},
author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C},
title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02410-z},
pmid = {42121284},
issn = {2049-2618},
support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; },
abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.

RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4 + T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.

CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.},
}

@article {pmid42121750,
year = {2026},
author = {Moharam, I and Brüggemann, J and Schmitt, F and Schade, B and Böhm, B and Kappe, E and Emmrich, F and Najar, FZ and El-Mayet, FS},
title = {Molecular Epidemiology of Enteric Viral Infections in Poultry Flocks in Southern Germany and the First Complete Genome Sequence of Avian Sicinivirus.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091331},
pmid = {42121750},
issn = {2076-2615},
abstract = {Enteric viral infections represent a major concern for poultry production, causing growth retardation, impaired feed conversion, and increased mortality, particularly in young birds. To investigate the involvement of RNA and DNA enteric viruses in flocks exhibiting growth problems, seven poultry farms in southern Germany, including broiler, pullet, and breeder operations, were examined for the presence of chicken astrovirus (CAstV), avian reovirus (ARV), and fowl adenovirus-1 (FAdV-1) by means of RT-PCR. All farms exhibited growth retardation, diarrhea, and enteritis-associated lesions. Histopathology revealed features of runting-stunting syndrome in most of the broiler farms and depletion of lymphatic tissue in most of the pullet farms. CAstV was detected in all flocks, ARV in six, and FAdV-1 in four farms. To further characterize the viral agents, metagenomic sequencing of cecal tonsils from one severely affected broiler flock confirmed the presence of a CAstV strain identical (100%) to CAV/Belgium/4134_001/2019. In addition, the complete genome of avian Sicinivirus was assembled for the first time in Germany, showing 96.8% nucleotide identity with a Dutch strain (Chicken/NLD/2019/V_M_056_picorna_2). These findings demonstrate the widespread circulation and co-infection of enteric viruses on German poultry farms and underline the transboundary nature of these infections, emphasizing the need for enhanced surveillance and biosecurity measures to mitigate their impact on poultry health and productivity.},
}

@article {pmid42121788,
year = {2026},
author = {Gao, F and Zuo, Z and Wu, Q and Xiao, H and Peng, Z and Zou, L and Jiang, G and Tian, X and Feng, Z and Xie, X and Tian, L},
title = {Analysis of Ochetobibus elongatus (Kner) Dietary Habits Based on Digestive System Morphology, Histology, and Intestinal Content Sequencing Technology.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091369},
pmid = {42121788},
issn = {2076-2615},
support = {HARS-07//Hunan Provincial Modern Agriculture (Aquaculture) Industry Technology System Project/ ; },
abstract = {Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures.},
}

@article {pmid42122064,
year = {2026},
author = {Hussain, A and Abbas, Q and Nadeem, M and Nazar, A and Athar, A and Rahman, HUU},
title = {Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/diagnostics16091360},
pmid = {42122064},
issn = {2075-4418},
abstract = {Meat serves as a prime medium for the growth of foodborne pathogens due to its rich protein content and high water activity, contributing significantly to the global burden of foodborne illnesses. This review synthesizes current advances in meat-borne bacterial pathogen detection with particular emphasis on emerging artificial intelligence (AI)-enabled applications. Major pathogens of concern, including Salmonella, Listeria monocytogenes, Escherichia coli, Campylobacter, Clostridium, and Staphylococcus aureus, are examined in relation to their relevance across the meat supply chain. Recent progress in biosensors (clustered regularly interspaced short palindromic repeats), CRISPR-based assays, isothermal amplification, and metagenomics is evaluated alongside the growing role of AI in automating signal interpretation, enhancing image-based diagnostics, and supporting early contamination prediction. AI-based systems have proved 96.4-104% recovery and 100% bacterial capture ability. Embedding AI methods in a wet lab demands technical and logical modeling, as well as learning and calibration decorum. Nonetheless, AI readiness and full-scale application for meat-borne pathogens surveillance are on the way. Furthermore, additional focus is aligned on meat-borne bacterial pathogen genomic databases, i.e., (NCBI Pathogen Detection, EnteroBase, VFDB, ComBase, and GenBank), which serve as critical training resources for AI models for outbreak tracking, virulence profiling, and antimicrobial resistance (AMR) prediction. By integrating molecular methods, genomic surveillance, and AI-driven analytics, this review presents a framework for strengthening meat safety systems. This will improve early detection capabilities and support data-driven public health interventions in the future.},
}

@article {pmid42122249,
year = {2026},
author = {Dragomir, RD and Saftescu, S and Sandu, DL and Dulan, A and Croitoru-Cazacu, IM and Croitoru, AE and Croitoru, VM and Vornicu, V and Nagy, DE and Perva, IT and Sirca, D and Popovici, DI},
title = {Artificial Intelligence-Guided Personalized Gut Microbiome Modulation for Persistent Secondary Gastrointestinal Symptoms in Oncology Patients: Clinical Efficacy and Biological Correlates from a Prospective Validation Study.},
journal = {Cancers},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/cancers18091453},
pmid = {42122249},
issn = {2072-6694},
support = {No Grant Number//Victor Babeș University of Medicine and Pharmacy Timișoara/ ; },
abstract = {Background/Objectives: Persistent gastrointestinal (GI) symptoms following oncologic treatment represent a major unmet need in survivorship care, often managed symptomatically without addressing underlying biological mechanisms. This study aimed to evaluate the clinical efficacy and biological correlates of an artificial intelligence (AI)-guided, personalized microbiome modulation strategy in oncology patients with chronic secondary GI dysfunction. Methods: We conducted a prospective, single-arm, open-label validation study including 29 adult female oncology patients with persistent GI symptoms lasting ≥3 months. Participants underwent baseline multidimensional assessment integrating shotgun metagenomic sequencing, inflammatory and nutritional biomarkers, and clinical symptom profiling. An AI-guided platform generated individualized dietary, supplement, and lifestyle recommendations. Outcomes were assessed at baseline and after a 3-month intervention, focusing on intra-individual changes in stool frequency (primary endpoint), self-reported energy, microbiome composition, and metabolic biomarkers. Paired statistical analyses, correlation testing, and multivariable regression were performed. Results: After three months, stool frequency significantly decreased (4.69 ± 2.41 to 2.07 ± 1.19 episodes/day; p < 0.0001), accompanied by a marked increase in energy levels (4.00 ± 1.04 to 7.24 ± 1.12; p < 0.0001). Microbiome analysis revealed consistent enrichment of butyrate-producing and barrier-supportive taxa, including Faecalibacterium prausnitzii, Eubacterium rectale, Roseburia intestinalis, Akkermansia muciniphila, and Bifidobacterium longum. Butyrate-related biomarkers and vitamin-associated parameters (B-complex, vitamin D) showed significant improvement, while lactate levels normalized. Changes in Bifidobacterium longum were independently associated with stool frequency reduction (β = -0.783, p = 0.0082). Conclusions: AI-guided personalized microbiome modulation was associated with significant clinical improvement and biologically coherent microbial and metabolic shifts in oncology patients with persistent GI symptoms. These findings support a precision supportive-care approach targeting microbiome restoration, warranting further validation in randomized controlled trials.},
}

@article {pmid42122826,
year = {2026},
author = {Pardo, JM and Suwannarach, N and Malichan, S and Cuellar, WJ and Siriwan, W},
title = {Mixed-Pathogen Infections in Vegetatively Propagated Crops: From Biological Synergism to Integrated Management.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/plants15091332},
pmid = {42122826},
issn = {2223-7747},
support = {000//Ministry of Higher Education, Science, Research and Innovation/ ; 000//Kasetsart University/ ; CROP-2023-157//Australian Centre for International Agricultural Research/ ; 000//National Research Council of Thailand/ ; },
abstract = {Vegetatively propagated crops, including cassava, sweet potato, banana, and potato, are susceptible to mixed-pathogen infections resulting from the continuous use of clonal planting material and infrequent seed replacement. A diverse array of viruses, bacteria, and fungi can accumulate within these materials over successive cultivation cycles, precipitating seed degeneration and complex disease syndromes that complicate diagnosis and management. Mixed infections frequently trigger synergistic interactions that exacerbate disease severity and yield losses. This review synthesizes data on mixed-pathogen complexes in vegetatively propagated crops, with particular focus on vascular and systemically colonizing pathogens and analyzing starch crops to highlight the epidemiological, biological, and ecological drivers of synergism and antagonism. Furthermore, the review examines host defense responses during coinfection, including the modulation of plant immune pathways, and evaluates how interpathogen dynamics influence pathological outcomes. Although advancements in molecular diagnostics-notably next-generation sequencing and metagenomics-have revolutionized the detection of mixed infections, they have also introduced challenges in differentiating causal agents from commensal microorganisms. Finally, we discuss the implications for integrated disease management, emphasizing clean seed systems, resistance breeding, and phenotyping strategies tailored to multipathogen environments. The dynamics of mixed infections is critical for resilient and sustainable management strategies amidst increasingly complex agricultural and climatic shifts.},
}

@article {pmid42122957,
year = {2026},
author = {Terry, C and Hall, LA and Halle-Smith, J and Edwards, LA and Sivakumar, S and Chapple, I and Beggs, A and Iqbal, T and Roberts, KJ},
title = {Pancreatic Cancer in the Holobiont and Therapeutic Targets: A Review.},
journal = {Journal of clinical medicine},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/jcm15093225},
pmid = {42122957},
issn = {2077-0383},
abstract = {Increasing evidence suggests pancreatic cancer develops within a host-microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome-tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes.},
}

@article {pmid42123237,
year = {2026},
author = {Liu, JW and Ma, X and Qian, YT and Wang, JW and Zhu, CY and Ma, DL},
title = {Detection of Nontuberculous Mycobacterial Skin Infection by Next-Generation Sequencing: A Pilot Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/jcm15093504},
pmid = {42123237},
issn = {2077-0383},
support = {2022- PUMCH-161//National High Level Hospital Clinical Research Funding/ ; 3332024006//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {Background: Nontuberculous mycobacteria (NTM) skin infections pose significant diagnostic challenges in clinical practice, due to nonspecific clinical/histopathological features and limitations of conventional pathogenic detection methods. Metagenomic next-generation sequencing (mNGS) offers a promising approach but requires further evaluation. Methods: A prospective pilot study at Peking Union Medical College Hospital enrolled 20 patients with cutaneous NTM infection, confirmed by positive skin culture or mNGS. All patients underwent thorough clinical assessment, skin biopsy for histopathology and culture, and mNGS testing of skin tissue. Treatment was based on identified species and disease extent. Treatment outcomes were tracked. Results: Among 20 patients (median age 45.5 years), fingers were the most common site affected (n = 10), followed by forearms (n = 7), hands (n = 4), and face (n = 4). Mycobacterium marinum was the predominant pathogen (n = 12), associated with fish bone puncture, followed by M. abscessus (n = 4). mNGS demonstrated a substantially higher positivity rate than culture (95% [19/20] vs. 30% [6/20]) and delivered results faster. Histopathology revealed granulomatous inflammation in all cases. Nineteen patients presented with non-disseminated disease; one immunocompromised patient (GATA2 deficiency) had disseminated M. abscessus infection. Treatment success was achieved in 17 patients (85%) with tailored antibiotic regimens. Adverse drug effects occurred in seven patients. Conclusions: In this pilot study of cutaneous NTM infections, mNGS enabled more rapid diagnosis relative to conventional culture. Clinical presentation and exposure history correlate with specific NTM species. Integrating mNGS with clinical assessment significantly improves diagnosis and management.},
}

@article {pmid42123326,
year = {2026},
author = {Zaman, S and Ali, N and Ullah, W and Taimur, N and Akbar, NU and Waheed, A and Muhammad, N and Khan, MS},
title = {Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093741},
pmid = {42123326},
issn = {1422-0067},
mesh = {Animals ; Chickens/microbiology ; *Manure/microbiology ; *Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Microbiota/genetics ; Biodiversity ; },
abstract = {Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects.},
}

Animals
Chickens/microbiology
*Manure/microbiology
*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Metagenome
Microbiota/genetics
Biodiversity

@article {pmid42123473,
year = {2026},
author = {Cheng, R and Liu, T and Liao, C and Wu, X and Zhu, L and Zhang, S},
title = {Integrating Protein Language Models with Multimodal Embeddings to Accelerate Function Prediction of Uncharacterized Proteins.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093891},
pmid = {42123473},
issn = {1422-0067},
support = {No. 32401056//National Natural Science Foundation of China/ ; 2024RC3144//Hunan Province Science and Technology Innovation Program/ ; },
mesh = {*Proteins/chemistry/metabolism ; *Computational Biology/methods ; Databases, Protein ; Humans ; Molecular Sequence Annotation ; },
abstract = {Accurate prediction of protein function is fundamental to progress in biotechnology and biomedicine, yet progress remains severely hampered by the widening chasm between exponentially growing genomic data and the limited capacity for functional annotation. High-throughput sequencing and metagenomics have driven an explosion in sequence data that far outstrips experimental characterization. UniProt now contains over 203 million protein entries, of which only ~2% have been experimentally validated. This widening "sequence-function gap" exceeds the reach of traditional homology-based tools such as BLAST (v2.17.0) and HMMER (v3.2), which are inherently constrained by sequence identity thresholds. The emergence of Protein Language Models (PLMs), including ESM and ProtTrans, has introduced a transformative paradigm, thereby shifting functional inference from similarity-based retrieval to geometric reasoning within learned semantic spaces. Nevertheless, current approaches remain largely confined to unimodal or narrowly bimodal frameworks, failing to capture the inherently multidimensional determinants of enzymatic function, including active-site geometry, chemical reaction logic, and literature-embedded semantic context. This review systematically adopts a multimodal global-fusion perspective, elucidating how three-dimensional geometric features, chemical reaction semantics, and textual knowledge graphs are synergistically integrated around PLMs as a core backbone. We delineate complementary mechanisms and integration strategies that together enable fine-grained protein function annotation beyond the performance ceiling of single-sequence methods. Furthermore, we survey the translational potential of such frameworks from computational prediction to real biological applications, and critically examine persistent bottlenecks including activity cliffs, transition-state inference, and conformational dynamics. We identify the integration of physics-informed machine learning with dynamics-aware architectures as a pivotal direction toward a causal, mechanism-level understanding of protein function.},
}

*Proteins/chemistry/metabolism
*Computational Biology/methods
Databases, Protein
Humans
Molecular Sequence Annotation

@article {pmid42123477,
year = {2026},
author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M},
title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093893},
pmid = {42123477},
issn = {1422-0067},
mesh = {Humans ; *Mineral Waters/therapeutic use ; Balneology/methods ; Animals ; Skin/drug effects ; },
abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.},
}

Humans
*Mineral Waters/therapeutic use
Balneology/methods
Animals
Skin/drug effects

@article {pmid42123517,
year = {2026},
author = {Nguyen-DeMary, K and Vascellari, S and Mastinu, M and Melis, M and Bastiaanssen, TFS and Tomassini Barbarossa, I and Tepper, BJ},
title = {Cranberry Polyphenol Extract (CPE) Oral Rinse Improves Salivary Microbiome in 6-n-Propylthiouracil (PROP) Non-Tasters and Palatability of Aronia Juice.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
doi = {10.3390/ijms27093935},
pmid = {42123517},
issn = {1422-0067},
support = {10180//United States Department of Agriculture/ ; },
mesh = {Humans ; *Saliva/microbiology/drug effects ; Female ; Male ; *Vaccinium macrocarpon/chemistry ; *Polyphenols/pharmacology/administration & dosage/chemistry ; *Microbiota/drug effects ; Adult ; Propylthiouracil ; *Plant Extracts/pharmacology/chemistry/administration & dosage ; *Photinia/chemistry ; Taste/drug effects ; *Mouthwashes/pharmacology/chemistry ; *Fruit and Vegetable Juices ; Young Adult ; },
abstract = {Sensitivity to the bitterness of 6-n-propylthiouracil (PROP) is controlled by variations in the TAS2R38 gene. This phenotype is often used as a marker for individual differences in taste perception. Previous findings show that PROP taster status is associated with differences in the salivary microbiome. It is well known that diet and environmental factors influence the risk of oral disease, but there is far less evidence showing how genetic differences play a role. Forty-seven young, healthy, PROP taster-classified adults rinsed with a cranberry polyphenol extract (CPE) oral rinse (0.75 g/L CPE powder in spring water) twice daily for 11 days. Saliva was collected pre- and post-intervention for microbiome analysis using shotgun metagenomic sequencing. At the same time points, participants evaluated two astringent juices (cranberry and aronia berry) for key attributes. At baseline, PROP taster groups differed in their salivary microbiome compositions, but post-intervention, the groups had more similar bacterial compositions. Post-intervention, non-tasters showed decreases in the relative abundance of 15 bacterial species, including a significant reduction (p = 0.037) in Eikenella corrodens, which is one bacterium, among several others, involved in oral biofilm formation. Additionally, after the intervention, sourness was reduced, and overall liking increased significantly for aronia juice. Oral dysbiosis, a risk factor for oral disease, may be controlled by bactericidal mouthwashes. Our results suggest that CPE, a natural alternative to traditional bactericidal rinses, may selectively target pathobionts while preserving salivary microbiota diversity. CPE might also provide greater benefits to non-tasters, who are at greater risk for oral disease.},
}

Humans
*Saliva/microbiology/drug effects
Female
Male
*Vaccinium macrocarpon/chemistry
*Polyphenols/pharmacology/administration & dosage/chemistry
*Microbiota/drug effects
Adult
Propylthiouracil
*Plant Extracts/pharmacology/chemistry/administration & dosage
*Photinia/chemistry
Taste/drug effects
*Mouthwashes/pharmacology/chemistry
*Fruit and Vegetable Juices
Young Adult

@article {pmid42124595,
year = {2026},
author = {Mejía-Pitta, A and Zhang, Z and Hossain, AA and Bartosik, K and Baca, CF and Peralta, C and Molina, H and Teplova, M and Brady, SF and Micura, R and Patel, DJ and Marraffini, LA},
title = {A 5-hydroxymethylcytosine DNA glycosylase provides defense against T-even bacteriophages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.25.707755},
pmid = {42124595},
issn = {2692-8205},
abstract = {The most abundant prokaryotic mechanisms of defense against phage predation involve the recognition and destruction of the infecting DNA. One method of counter-defense is the incorporation of modified nucleobases into the phage genome to avoid interaction with enzymes that target the viral DNA. T-even coliphages replace cytosine with 5-hydroxymethylcytosine (5hmC) that in some cases are further decorated with glucosyl groups. To explore the diversity of immunity genes that recognize 5hmC, we infected a library of metagenomic DNA inserts from uncultured, non-sequenced soil bacteria with a mutant T4 phage that harbored only non-glucosylated 5hmC on its genome. Bacteria that resisted infection carried a DNA glycosylase, Brig3, that specifically excises 5hmC nucleobases to generate abasic sites in the phage genome and prevent viral proliferation. The crystal structure of Brig3 bound to its substrate revealed a catalytic mechanism in which the 5hmC nucleobase is flipped out of the DNA into the active site and replaced by an asparagine residue that inserts into the double helix to contact the complementary guanosine. Brig3 is encoded within an operon that also encodes BapA, a hydrolase that removes glucosyl groups from glucosyl-5hmC present in the genome of otherwise Brig3-resistant T-even phages carrying this hypermodified base. Our results uncover a defense strategy in which the combined action of BapA and Brig3 widens the immune response to restrict the infection of T-even phages with genomes that are either partially or completely glucosylated.},
}

@article {pmid42125129,
year = {2026},
author = {Khantsi, M and Babalola, OO},
title = {Influence of Cowpea Plants on Soil Bacterial Community and Soil Quality: Effects of the Rhizosphere.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {7},
number = {},
pages = {e70157},
pmid = {42125129},
issn = {2575-6265},
abstract = {Cowpea (Vigna Unguiculata), a vital legume for suitable agriculture and food security in sub-Saharan Africa, plays a crucial role in improving soil health through intricate plant-microbe interactions in the rhizosphere. This review synthesizes current knowledge on the microbial interactions in the rhizosphere, focusing on soil health, microbial diversity, and their contributions to nutrient cycling and plant growth. Cowpea roots foster a diverse microbial consortium, including nitrogen-fixing rhizobia, phosphate-solubilizing bacteria and organic matter decomposers, which enhance soil fertility and structure. The microbial community in the cowpea rhizosphere is shaped by complex soil physiochemical properties, such as potential of hydrogen (pH), nutrient availability, and salinity, which significantly influence plant-microbe interactions. However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa. Advanced techniques, including metagenomic analyses, have provided deeper insights into the taxonomic and functional composition of rhizosphere microbiomes, uncovering both abundant and rare microbial taxa involved in these processes. Despite these advancements, gaps remain in understanding the dynamic responses of microbial communities to environmental stresses. Bridging these gaps through integrative multi-omics approaches will enable the development of microbiome-informed strategies to improve cowpea productivity and promote sustainable agricultural practices, ensuring resilience in the face of climate variability.},
}

@article {pmid42125266,
year = {2026},
author = {Nõlvak, H and Dang, NP and Truu, M and Peeb, A and Devarajan, AK and Petrich, C and O'Sadnick, M and Tiirik, K and Truu, J},
title = {Microbial succession and hydrocarbon-degrading potential in Arctic sea ice exposed to dispersed crude oil and chemical dispersant.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag022},
pmid = {42125266},
issn = {2633-6685},
abstract = {The increasing oil exploration and transport activities in the Arctic amplify the risk of oil spills in ice-containing marine environments. Chemical dispersants, intended to promote oil biodegradation by breaking hydrocarbons into small droplets, are potential tools in cold marine oil spill mitigation; however, their fate and effectiveness within sea ice remain uncertain. This study examined the influence of dispersed crude oil and the chemical dispersant (FinasolOSR 51) on microbial community dynamics and hydrocarbon-degrading potential compared to clean ice during an 89-day sea-ice mesocosm experiment using shotgun metagenomics and metagenome-assembled genomes. Dispersant addition markedly reshaped microbial communities in both dispersed-oil and dispersant containing ice, causing similar shifts toward psychrophilic hydrocarbon degraders such as Oleispira, Bermanella, and Pseudoalteromonas. Although aliphatic hydrocarbon degradation genes were enriched, several dominant taxa exhibited limited hydrocarbon metabolic capacity yet possessed extensive stress-response traits. Oil hydrocarbon loss in ice remained modest despite the presence of degraders, likely due to the very low microbial abundance. These findings demonstrate that dispersants can strongly shape microbial communities in Arctic sea ice, without necessarily enhancing the biodegradation of oil hydrocarbons. This highlights the need for careful evaluation of dispersants as remediation tools in ice-containing Arctic marine environments.},
}

@article {pmid42125370,
year = {2014},
author = {, },
title = {Schmallenberg virus: State of Art.},
journal = {EFSA journal. European Food Safety Authority},
volume = {12},
number = {5},
pages = {3681},
pmid = {42125370},
issn = {1831-4732},
abstract = {This scientific report provides an overview of all research carried out on Schmallenberg virus (SBV), reviewing the current knowledge on SBV regarding genotyping findings, susceptible species, pathogenesis, transmission routes, immunity, seroprevalence, geographical and temporal SBV spread, improved within-herd transmission model, SBV impact assessment and within-herd and regional spread models. Metagenomic analysis identified SBV as a novel orthobunyavirus emerged in 2011 and it has been detected in domestic cattle, sheep, goats and 12 wild species. Seroprevalence studies indicate that SBV has probably spread over the whole of Europe, showing high seroprevalence at national scale, while larger variability is observed at regional scales. Clinical disease frequency is low and experimental infection on pregnant ewes and cows suggest that SBV rarely induces malformations. SBV may be detected from semen with a low frequency though there is no scientific evidence of transmission through insemination. Vector competence studies suggest that Culicoides are likely to be able to transmit SBV but found no evidence that mosquitoes are likely to be able to transmit it. SBV vertical transmission has not yet been identified as a major route. SBV has successfully overwintered, despite lengthy period of minimal vector activity and duration of immunity in cattle lasts for at least one year. A farm-to-farm spread model for SBV shows a rapid spread of infection across the study region and latent period, duration of viraemia, probability of transmission from host to vector and virus replication are sufficient to account for the rapid SBV spread. The between-farm SBV transmission model indicates that the application of movement restrictions has little effect on SBV spread. An impact assessment based on limited data suggests a probable effect of SBV infection on abortion, short gestation, non-return and the number of artificial inseminations required per animal. International trade restrictions by third countries represent the main SBV impact.},
}

@article {pmid42125413,
year = {2026},
author = {Wang, J and Qiu, J and Zhang, C},
title = {Crusted scabies complicated by septic shock: a fatal case report with incidental detection of Sarcoptes scabiei DNA in peripheral blood.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02577},
pmid = {42125413},
issn = {2214-2509},
abstract = {Crusted scabies is a severe form of scabies characterized by massive mite burden and profound immune dysregulation. Secondary bacterial infection is common and may progress to sepsis with fatal outcomes. We report a fatal case of crusted scabies complicated by septic shock in a 58-year-old man with diabetes mellitus and chronic dermatitis. The patient presented with diffuse erythroderma, extensive hyperkeratotic crusts, and deep skin fissures, and several household members had similar pruritic skin lesions. Laboratory investigations revealed marked eosinophilia, extremely elevated serum immunoglobulin E levels, and multiorgan dysfunction. Peripheral blood metagenomic next-generation sequencing identified multiple bacterial pathogens and incidentally detected Sarcoptes scabiei DNA. Despite broad-spectrum antimicrobial therapy, antiparasitic treatment, and intensive supportive care, the patient deteriorated and died. This case highlights crusted scabies as a potentially lethal condition when complicated by severe bacterial infection and underscores the need for cautious interpretation of parasitic DNA detected in blood, particularly in non-invasive ectoparasitic diseases.},
}

@article {pmid42125597,
year = {2026},
author = {Pasaribu, B and Herawati, T and Purba, NP and Lewaru, MW and Sofyana, NT and Dilens, CVM and Dewanti, LP and Alina, DN and Agung, MUK},
title = {Shotgun metagenomic dataset of microbial communities in the water column of the Flores Sea, Indonesia.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112791},
pmid = {42125597},
issn = {2352-3409},
abstract = {The Flores Sea is a crucial component of the Indonesian Throughflow (ITF) pathway, which influences the transport of carbon, oxygen, and nutrients that support marine ecosystems. Here, we present the first dataset of microbial communities from the Flores Sea, Indonesia, generated using shotgun metagenomic sequencing of water column samples. Taxonomic analysis revealed that Proteobacteria (86%) was the most abundant phylum. In the dataset, the most abundant taxa identified through metagenomic analysis demonstrated Pseudoalteromonas lipolytica, Chromohalobacter salexigens, Marinobacter nauticus, Halopseudomonas aestusnigri, Pseudomonas mendocina, Flavobacterium beibuense, and Flavobacterium rakeshii, respectively. Functional annotation indicated that metabolism was major functional category in the microbial community. This metagenomic dataset provides valuable baseline information on microbial communities that may support future ocean monitoring and conservation strategies in the Flores Sea.},
}

@article {pmid42125669,
year = {2026},
author = {Szaraz, D and Bohm, J and Machacek, C and Salokova, G and Gachova, D and Ruzicka, F and Danek, Z and Gheit, T and Zavadil, J and Borilova Linhartova, P},
title = {Bacteriome-based oral dysbiosis index in patients with oral squamous cell carcinoma.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2668149},
pmid = {42125669},
issn = {2000-2297},
abstract = {BACKGROUND: Oral dysbiosis plays an important role in the pathogenesis of oral squamous cell carcinoma (OSCC). Our study aimed to perform a pairwise comparison of the oral microbiota, especially the bacteriome, from OSCC tumoral surface vs other oral samples and evaluate the association of a novel bacteriome-based Oral Dysbiosis Index (bbODI) with the OSCC surface.

MATERIALS AND METHODS: This pilot observational study used 84 patient-matched samples from the OSCC tumoral surface (swabs and biopsies), healthy oral mucosa (tongue and buccal swabs), and supragingival dental plaque swabs. Bacteriomes were analyzed by 16S rRNA amplicon sequencing. The presence of microscopic fungi and selected viruses was also evaluated.

RESULTS: The relative abundance of the genus Fusobacterium, the ratio of the relative abundances of gram-negative to gram-positive bacterial genera, and the bbODI on the tumour surface significantly differed from patient-matched healthy oral mucosa (both buccal and tongue swabs) and supragingival dental plaque samples. Oral candidosis was found in 25% of patients; all patients were negative for cytomegalovirus and Epstein-Barr virus.

CONCLUSIONS: Certain characteristics of the bacteriome composition of the OSCC surface differ from patient-matched samples of healthy oral mucosa and supragingival dental plaque. The proposed bbODI appears to be a promising non-invasive tool for the identification of bacteriome disruption on the OSCC surface.},
}

@article {pmid42125783,
year = {2026},
author = {Hu, X and Han, L and Ochoa-Hueso, R and Song, J and Yang, X and Wang, G},
title = {From Microbes to Molecules: Biodegradable Microplastics Reshape Soil Carbon Metabolism and Composition of Dissolved Organic Matter.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01030},
pmid = {42125783},
issn = {1520-5118},
abstract = {Microplastics (MPs) are ubiquitous in the environment, yet how conventional MPs (CMPs) and biodegradable MPs (BMPs) alter microbial carbon (C) metabolism and dissolved organic matter (DOM) remains unclear. Using metagenomic sequencing and Fourier transform ion cyclotron resonance mass spectrometry, we found that BMPs altered microbial C cycling profiles more profoundly than CMPs. This was driven by a significant enrichment of functional genes involved in aerobic respiration, C fixation, intracellular C decomposition, and fermentation. In addition, BMPs exerted stronger influences on prokaryotic and viral community structures than CMPs. Notably, BMPs specifically enriched unique microbial taxa and virus-host linkages carrying diverse C-cycling genes, coregulating key metabolic pathways, and promoting a "viral shuttle" mechanism that accelerated DOM turnover. These effects were mediated through enhanced accumulation of labile and recalcitrant C components in relation to fertilization regimes. These findings revealed mechanisms by which BMPs reshape soil carbon dynamics through microbial-viral interactions.},
}