@article {pmid41629563,
year = {2026},
author = {Suksa, W and Li, WJ and Luo, ZH and Jiao, JY and Ponce, V and Nuñez-Montero, K and Arce-Johnson, P and Sharma, NR and Thamchaipenet, A and Narsing Rao, MP},
title = {Metagenomic analysis revealed the presence of novel Actinomycetota "Candidatus Solincola uaceae" sp. nov., obtained from a hot spring.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37544-5},
pmid = {41629563},
issn = {2045-2322},
support = {PHD/0136/2561//The Royal Golden Jubilee Ph.D. Program (RGJ Ph.D.), Thailand Research Fund, National Research Council of Thailand (NRCT)/ ; },
abstract = {Metagenomic analysis of the hot spring led to the recovery of a high-quality metagenome-assembled genome (MAG), MPNR_HS_01, affiliated with the phylum Actinomycetota. Taxonomy analysis assigned the MAG to "Candidatus Solincola", clustering closely with "Candidatus Solincola tengchongensis". MPNR_HS_01 was 2.82 Mb in size, assembled into 27 contigs, with a G+C content of 63.4%, 49 tRNAs, 4 rRNAs, 98.7% completeness, and no detectable contamination. Functional annotation revealed the presence of complete glycolysis and nonoxidative pentose phosphate pathways, while the tricarboxylic acid cycle was incomplete. Notably, MPNR_HS_01 encoded Wood-Ljungdahl pathway, suggesting carbon assimilation. Energy conservation was supported by hydrogenases, heterodisulfide reductase, Rnf complex, and V-type ATPase. Stress adaptation traits included genes for heat shock proteins, proline biosynthesis, and ion transporters involved in osmotic homeostasis. Although lacking flagellar machinery, MPNR_HS_01 possessed type IV pili and genes associated with twitching motility. Secondary metabolite analysis identified a betalactone biosynthetic gene cluster. Genome-relatedness analyses showed that MPNR_HS_01 was distinct from "Candidatus Solincola" species, with both average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values falling below the established species threshold (95-96% ANI and 70% for dDDH), supporting its designation as a novel species, for which we propose the name "Candidatus Solincola uaceae" sp. nov.},
}

@article {pmid41629364,
year = {2026},
author = {Spörri, L and Studer, JM and Kreuzer, M and Rotzetter, J and Schärer, D and Largiadèr, CR and Jaggi, D and Zinkernagel, MS and Zysset-Burri, DC},
title = {Linking the microbiome to the complement system in geographic atrophy.},
journal = {NPJ genomic medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41525-026-00550-7},
pmid = {41629364},
issn = {2056-7944},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
abstract = {Age-related macular degeneration (AMD) is the leading cause of vision loss in the aged population with the late stage geographic atrophy (GA). Risk factors for AMD include age, genetic variants in the complement system, nutritional factors, and alterations in the gut microbiome (GM). To identify taxonomic and functional differences in the microbiome associated to disease pathophysiology and genetic risk factors, this study investigated the GM and the ocular surface microbiome (OSM) of GA patients compared to healthy controls by whole-metagenome shotgun sequencing. 16 AMD-associated SNPs were genotyped from blood samples using TaqMan assays and Sanger sequencing. While GA patients showed differences in the GM, and altered metabolic pathways including inosine 5'-phosphate degradation, NAD salvage, and ketogenesis, no alterations in the OSM were found. Genetic analysis associated SNP rs1061170 in the complement factor H gene with GA. These findings suggest that microbial alterations may contribute to GA through inflammation and oxidative stress.Registry: ClinicalTrials.gov, NCT02438111, Registration date: 28 April 2015, and NCT04658238, Registration date: 01 December 2020.},
}

@article {pmid41629097,
year = {2026},
author = {Lyu, WT and Jia, QQ and Tong, X and Fan, H},
title = {[STAT1 gain-of-function mutation leading to disseminated Talaromyces marneffei infection combined with hemophagocytic syndrome: a case report].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {49},
number = {2},
pages = {184-187},
doi = {10.3760/cma.j.cn112147-20250730-00456},
pmid = {41629097},
issn = {1001-0939},
mesh = {Humans ; Male ; Talaromyces ; Adult ; *Lymphohistiocytosis, Hemophagocytic/genetics/complications/microbiology ; *STAT1 Transcription Factor/genetics ; *Gain of Function Mutation ; *Mycoses/genetics/complications/microbiology ; Antifungal Agents/therapeutic use ; Mutation ; },
abstract = {This study reports a 28-year-old HIV-negative male with a STAT1 gain-of-function mutation who presented with a systemically disseminated Talaromyces marneffei (TM) infection, which was complicated by hemophagocytic lymphohistiocytosis (HLH). The patient presented with recurrent fever, weight loss, oral mucosal ulcers, as well as lymphopenia and markedly elevated inflammatory markers during the acute phase of the illness. Imaging revealed scattered ground-glass opacities and nodular shadows in both lungs, as well as localized bronchiectasis, and splenomegaly. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and bone marrow aspirate specimens revealed TM-specific sequences. Whole-exome sequencing was performed to elucidate the underlying mechanism of recurrent fungal infections. This revealed a de novo heterozygous dominant mutation in the STAT1 gene (c.1151G>A, p.Gly384Asp), localized to the DNA-binding domain at amino acid position 384. This confirmed a STAT1 gain-of-function (STAT1-GOF) variant, which is consistent with the clinical phenotype of impaired antifungal immunity. Over the clinical course, the patient developed HLH. Following a two-week course of intravenous amphotericin B liposome (5 mg/kg per day), followed by oral voriconazole maintenance therapy (200 mg, twice daily), the patient exhibited significant improvements in clinical symptoms and laboratory parameters. Notably, the marked resolution of HLH was closely linked to the successful eradication of the fungal infection. This case highlights three critical clinical implications: (1) Patients with a predisposition to primary immunodeficiency disorders (e.g., STAT1-GOF mutations) should be evaluated for disseminated TM infections, even if they are HIV-negative; (2) mNGS is instrumental in etiological diagnosis and facilitates early intervention for fungal infections; (3) early identification of genetic defects establishes a theoretical basis for precision medicine and guides targeted therapeutic strategies.},
}

Humans
Male
Talaromyces
Adult
*Lymphohistiocytosis, Hemophagocytic/genetics/complications/microbiology
*STAT1 Transcription Factor/genetics
*Gain of Function Mutation
*Mycoses/genetics/complications/microbiology
Antifungal Agents/therapeutic use
Mutation

@article {pmid41628881,
year = {2026},
author = {Sun, G and Guo, S and Yao, Y and Lin, Z and Gao, H and Stauber, RH and Li, BC and Ding, GB},
title = {Facile immobilization of an unstable recombinant α-L-rhamnosidase on magnetite nanoparticles for efficient naringin biotransformation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150652},
doi = {10.1016/j.ijbiomac.2026.150652},
pmid = {41628881},
issn = {1879-0003},
abstract = {α-L-Rhamnosidase is a significant biocatalyst that specifically cleaves terminal α-L-rhamnose group from natural flavonoid diglycosides, enabling the biocatalytic production of high-value flavonoid glucosides like prunin from naringin. Compared to its precursor naringin, prunin exhibits superior solubility and bioavailability, making this enzymatic conversion commercially valuable for the food and pharmaceutical industry. However, the industrial application of free α-L-rhamnosidases faces significant challenges, including enzyme instability, difficulty in recovery, and unsatisfactory reusability. To address these issues, this study developed an innovative magnetically recoverable biocatalyst (Fe3O4-Rha) through covalent immobilization of recombinant α-L-rhamnosidase from human fecal metagenome onto Fe3O4 nanoparticles using EDC/NHS chemistry, and the immobilization parameters were systematically optimized. The successful preparation of Fe3O4-Rha was verified by TEM, FTIR, TGA, and SQUID analysis. Fe3O4-Rha retained the catalytic property of free Rha in terms of optimal pH and temperature but exhibited superior tolerance on organic solvent especially ethanol and isopropanol. Moreover, Fe3O4-Rha could effectively biotransform naringin to prunin and maintained 61.34% of initial activity after 5 cycles. In a scaled-up reaction system, Fe3O4-Rha also efficiently converted naringin into prunin and the complete conversion was achieved within 10 h. This work successfully developed a magnetically recoverable immobilized α-L-rhamnosidase system for the efficient and reusable biotransformation of naringin, offering a promising approach for the enzymatic modification of bioactive small molecules using biological macromolecular catalysts.},
}

@article {pmid41628768,
year = {2026},
author = {Frizzera, A and Vázquez, N and Sacristán, H and Tapella, F and Lovrich, G and Khalaf, A and Bojko, J and Cremonte, F},
title = {Patagonian king crabs (Lithodes santolla and Paralomis granulosa) and their diseases: Pathogen survey and taxonomic clarification of Areospora rohanae (Microsporidia).},
journal = {Journal of invertebrate pathology},
volume = {216},
number = {},
pages = {108560},
doi = {10.1016/j.jip.2026.108560},
pmid = {41628768},
issn = {1096-0805},
abstract = {Lithodid crabs constitute a valuable natural resource with commercial interest; however, their health status in South America is scarcely studied. The presence of pathogens may have a negative impact on affected populations, endangering the fishery. This study surveys the symbionts present in populations of the king crab, Lithodes santolla, and the stone/false king crab, Paralomis granulosa, using histology, transmission electronic microscopy, and molecular analyses to characterise various symbionts. The histological and molecular data revealed a wide range of infections in L. santolla, including prokaryotic microorganisms, Areospora rohanae (Microsporidia), apicomplexan gregarines, ciliated protozoans, ectoparasitic crustaceans, and various epibiotic associations. In the case of P. granulosa, apicomplexan gregarines, ciliated protozoans, and various ectoparasites were observed. Molecular analyses confirmed the presence of the microsporidian A. rohanae, occurring at high prevalences (30%) in L. santolla, and some bacterial associations. We use metagenomic tools to extract a partial genome of this parasite to aid in its identification and taxonomic position, which leads us to erect the taxonomic orders Astathelohaniida and Areosporida and further clarify the previously assigned: "Glugeida+". The results of this study represent the first broad survey for symbionts in both king crab species and take us another step forward to a more accurate microsporidian taxonomy.},
}

@article {pmid41628665,
year = {2026},
author = {Hartog, M and Korsten, SGPJ and Popa, CD and Pelle, T and Gavriilidou, A and van den Bemt, BJF and Willemsen, LEM and Koenders, MI and Vermeiden, JPW and Smidt, H and van den Ende, CHM},
title = {Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: a proof-of-concept placebo-controlled randomized trial.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2026.01.630},
pmid = {41628665},
issn = {1522-9653},
abstract = {OBJECTIVE: This study primarily assessed effects of Sustained Release Calcium Butyrate (SRCaBu) on gut microbiome composition and function in hand OA patients. Secondary objectives included its impact on hand pain and function, markers of intestinal permeability, systemic inflammation, and safety.

METHOD: A participants, researchers, and pharmacy assistants blinded, randomized, placebo-controlled proof-of-concept trial compared 600mg daily dose SRCaBu with placebo over 4-5 weeks. The primary domain was microbiome composition and function, assessed via fecal 16S rRNA gene- and metagenome sequencing, and short-chain fatty acid analysis. Secondary outcomes included parameters for intestinal barrier function, clinical outcomes and adverse events. Primary analyses followed the per-protocol principle.

RESULTS: 35 participants (mean age 62.5±6.9 years, 82% female) were randomized to SRCaBu (n=18) or placebo (n=17). Two SRCaBu participants discontinued treatment for pre-existing liver impairment and need for pain medication. SRCaBu tended to reduce the relative abundance of Streptococcus (regression coefficient:-0.67, 95%CI:-1.46,0.13) and Faecalibacterium -0.38(-0.83,0.07), increase fecal acetate (median between-group difference: 9.5, [IQR]: [-3.5,22.5]), and was inversely associated with microbial LPS biosynthesis- and virulence genes. SRCaBu increased toxin-related genes, primarily from beneficial Blautia species, without association to pathogenicity. SRCaBu did not significantly affect biomarkers of intestinal permeability, inflammation, or clinical outcomes. Adverse events were mild and comparable between groups.

CONCLUSION: Our study yielded indicative findings that SRCaBu supports microbiome health in patient with hand OA by improving compositional and functional characteristics of the microbiome. Although the treatment was well tolerated, effects on serum markers for intestinal barrier function and systemic inflammation, and clinical symptoms remained unclear.

TRIAL REGISTER: 2020-001071-33 / NL73382.091.21.},
}

@article {pmid41627741,
year = {2026},
author = {Castañeda, S and Ramírez, JD and Poveda, C},
title = {Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {265-297},
pmid = {41627741},
issn = {1940-6029},
mesh = {*Chagas Disease/microbiology/parasitology ; Animals ; Mice ; Trypanosoma cruzi ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {Chagas disease, caused by Trypanosoma cruzi, leads to chronic cardiac and gastrointestinal complications. Emerging evidence shows the gut microbiome plays a key role in modulating disease severity, with shifts in microbial composition influencing immune responses and metabolic pathways. Here, we describe a workflow for microbiome analysis in T. cruzi-infected mice. Methods included sample collection from feces and gastrointestinal tissues, DNA extraction, sequencing, and quality control. Then, we outline bioinformatic analyses covering taxonomic profiling, diversity assessment, and microbial network construction. Finally, protocols for functional prediction tools are also included to explore microbial capabilities and the identification of signatures associated with disease progression.},
}

*Chagas Disease/microbiology/parasitology
Animals
Mice
Trypanosoma cruzi
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
*Microbiota
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid41627733,
year = {2026},
author = {Hałakuc, P and Maciszewski, K and Karnkowska, A},
title = {Euglenid Extrachromosomal DNA: Assembly and Annotation.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {109-120},
pmid = {41627733},
issn = {1940-6029},
mesh = {*Computational Biology/methods ; *Molecular Sequence Annotation/methods ; DNA, Ribosomal/genetics ; Genome, Mitochondrial ; *Euglenozoa/genetics ; Genome, Plastid ; DNA, Mitochondrial/genetics ; Phylogeny ; Genomics/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Euglenids (Euglenozoa) contain several forms of extrachromosomal DNA (ecDNA) in their cells, including the ribosomal DNA operon (rDNA), the mitochondrial genome (mtDNA), and, in photosynthetic species, the plastid genome (ptDNA). These ecDNA elements can be easily and accurately assembled and annotated even from limited sequencing data, such as single-cell genomic or metagenomic datasets. They are an important source of information for phylogenomic analyses, metabarcoding and evolutionary studies. In this chapter, we present a robust and adaptable bioinformatics pipeline for the identification, assembly, and annotation of extrachromosomal DNA from whole-genome datasets. The pipeline was developed with euglenids in mind and takes into account their unique genomic features, but can also be adapted for other Euglenozoa (and protists). This approach enables the recovery of organellar and rDNA sequences with high confidence and supports both targeted studies and large-scale environmental analyses.},
}

*Computational Biology/methods
*Molecular Sequence Annotation/methods
DNA, Ribosomal/genetics
Genome, Mitochondrial
*Euglenozoa/genetics
Genome, Plastid
DNA, Mitochondrial/genetics
Phylogeny
Genomics/methods
Sequence Analysis, DNA/methods

@article {pmid41627460,
year = {2026},
author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT},
title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {167},
pmid = {41627460},
issn = {1432-072X},
support = {DTDLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; Infant ; Vietnam ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation & purification/virology ; *Bacteriophages/genetics/isolation & purification/classification ; Child, Preschool ; Male ; Female ; Metagenome ; Diarrhea/microbiology ; Southeast Asian People ; },
abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.},
}

Humans
Infant
Vietnam
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Bacteria/classification/genetics/isolation & purification/virology
*Bacteriophages/genetics/isolation & purification/classification
Child, Preschool
Male
Female
Metagenome
Diarrhea/microbiology
Southeast Asian People

@article {pmid41627458,
year = {2026},
author = {Jiang, F and Gu, H and Song, P and Zhang, J and Cai, Z and Liang, C and Gao, H and Zhang, R and Zhang, T},
title = {Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {53},
pmid = {41627458},
issn = {1432-0614},
support = {32200408//National Natural Science Foundation of China/ ; 2023-ZJ-952Q//Natural Science Foundation of Qinghai Province/ ; 2023M743743//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Forests ; DNA, Bacterial/genetics ; Endangered Species ; Conservation of Natural Resources ; Time Factors ; Sequence Analysis, DNA ; },
abstract = {In endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time on microbial composition and function remains unclear, constraining data accuracy and reliability. To address this, we investigated the time-gradient effect in the globally endangered forest musk deer (Moschus berezovskii). Using non-invasive sampling under standardized captive conditions, fecal samples were collected at six storage times: (0, 1, 2, 4, 6, 8 days). Gut microbiota composition, diversity, enterotypes, and functional differences were assessed through 16S rRNA gene sequencing on the Illumina MiSeq platform. In total, 147,013 valid ASVs (amplicon sequence variants) were obtained showing significant shifts in microbial composition with storage time. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Increasing storage time led to declining α-diversity, reduced community stability, and more unique genera. PCoA (principal coordinates analysis) and NMDS (non-metric multidimensional scaling) indicated progressive separation of experimental groups from control groups, with Anosim and Adonis confirming progressive separation with storage time. Structurally, Firmicutes decreased while Proteobacteria, specifically the Acinetobacter genus, increased with storage time. Community assembly shifted from deterministic to stochastic processes, reflecting stronger environmental disturbance effects. These results demonstrate that the gut microbiota composition, diversity, and ecological functions in forest musk deer feces are highly sensitive to storage time. Thus, preservation duration must be strictly controlled as a critical variable in microbiome studies. This work establishes methodological standards for non-invasive fecal metagenomics in endangered species, providing theoretical insights and practical guidance for improving scientific rigor in conservation-related microbiome research. KEY POINTS: Fecal microbiota diversity and stability decline significantly with longer storage. Firmicutes decrease while Proteobacteria, especially Acinetobacter, increase over time. Storage duration strongly impacts microbiome data, requiring strict sampling control.},
}

Animals
*Deer/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Metagenomics
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Forests
DNA, Bacterial/genetics
Endangered Species
Conservation of Natural Resources
Time Factors
Sequence Analysis, DNA

@article {pmid41627236,
year = {2026},
author = {Yu, M and Wang, Y and Huangfu, K and Wu, S and Huang, H and Ma, Z and Wang, Y and Qiu, Y and Liu, S},
title = {Oxygen Vacancy-Engineered High-Entropy Oxide Nanozymes for Spatiotemporal Cascading Antifouling in Marine Environments.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e13363},
doi = {10.1002/smll.202513363},
pmid = {41627236},
issn = {1613-6829},
support = {52272271//National Natural Science Foundation of China/ ; },
abstract = {The catalytic versatility and compositional tunability of oxidative attack-based nanozymes offer a promising strategy for marine antifouling, yet their performance is often constrained by insufficient active-site accessibility, transient catalytic intermediates and restricted diffusion. Inspired by haloperoxidases (HPOs) in marine organisms, this study reports oxygen vacancy (Vo)-enriched high-entropy oxides (Vo-HEO) as multifunctional nanozymes to address these challenges. The entropy-stabilized multicomponent lattice, synergistically coupled with abundant Vo sites, reconfigures electronic structures and diversifies catalytic pathways, enabling efficient HPO-mimetic generation of hypobromous acid (HOBr), which is a selective and long-lived biocide (half-life > 36 days) capable of disrupting bacterial quorum sensing (QS) signals and oxidizing key biomolecules. By further integrating persistent HOBr with highly reactive hydroxyl radicals, Vo-HEO establishes a spatiotemporally cascading protective regime at the substrate interface, combining long-range QS suppression in the bulk phase with rapid oxidative eradication at the nano-biological interface, ultimately reducing bacterial adhesion by 90%. Microbiological characterization and metagenomic sequencing analyses further verify that Vo-HEO systematically collapses the coordination of microbial communication and energy metabolism across temporal and spatial scales. Collectively, this work demonstrates intelligent regulation of marine microecology and establishes a paradigm for adaptive antifouling design.},
}

@article {pmid41628276,
year = {2026},
author = {Habib, I and Hernandez-Valencia, JC and Martinu, J and Novakova, E},
title = {Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {2},
pages = {e0013576},
doi = {10.1371/journal.pntd.0013576},
pmid = {41628276},
issn = {1935-2735},
abstract = {Kissing bugs (Triatominae) are hematophagous insects and the principal vectors of Trypanosoma cruzi, the causative agent of Chagas disease. While their bacterial microbiomes have received considerable attention, the diversity of viruses associated with these insects remains poorly understood. To address this gap, we investigated the metavirome of five Triatominae species from the southern United States (Triatoma rubida, T. sanguisuga, T. gerstaeckeri, T. indictiva, and Hospesneotomae protracta), sampled in Texas, New Mexico, and Arizona. We sequenced 23 samples, including abdomen, gut and reproductive tissues from 13 field-collected individuals and assembled 41 viral operational taxonomic units (vOTUs), 40 of which are novel and together constitute 13 viral families, including Chuviridae, Arenaviridae, Orthomyxoviridae, Partitiviridae, Solemoviridae, Circoviridae, Rhabdoviridae, Microviridae, Xinmoviridae, Astroviridae, Narnaviridae, Tombusviridae, and the order Elliovirales. The vOTUs composition and abundance analysis examined variables including species, sex, tissue type, blood meal, and T. cruzi infection status, showing that metavirome diversity varied significantly among Triatominae species. Our findings demonstrate a species-specific metavirome and the presence of virus taxa linked to insects, plants, and vertebrates, highlighting the complex ecological interactions between viruses and triatomines. This study uncovers a diverse and largely novel set of metaviromes within North American Triatominae, providing a foundation for future research on virus-vector interactions.},
}

@article {pmid41626594,
year = {2026},
author = {Sapino, R and Fernández-González, Á and Castresana, J},
title = {Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.},
journal = {Evolutionary applications},
volume = {19},
number = {2},
pages = {e70199},
pmid = {41626594},
issn = {1752-4571},
abstract = {Metagenomic analysis of fecal samples is emerging as a powerful tool for monitoring endangered species, particularly in assessing the burden of pathogens and parasites that can threaten population viability. However, accurate identification in non-model species remains challenging due to the frequent absence of host-specific pathogen reference genomes. In this study, we developed a robust computational framework for detecting potentially pathogenic bacteria from metagenomic sequences by mapping them to available reference genomes in databases. Several key parameters affecting the analysis, including mapping algorithm, database configuration, and identification parameters, were analyzed to optimize detection sensitivity and specificity. Applying this approach to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal, we identified 26 potentially pathogenic bacterial species, with prevalences ranging from isolated cases to nearly half of the individuals examined. Furthermore, our analysis revealed that some desmans had atypical compositions of potential pathogens, suggesting variations in environmental exposure or host genetic factors. This work demonstrates a novel application of fecal metagenomics for species-level detection of microorganisms implicated in disease, providing a powerful approach to gain essential insights into the health and epidemiology of endangered species and to support the development of more effective conservation strategies.},
}

@article {pmid41626263,
year = {2026},
author = {Liu, Y and Fu, H},
title = {Pulmonary Tropheryma whipplei Infection Presenting With Multiple Thick-Walled Cavities on Chest CT: A Case Report and Literature Review.},
journal = {Respirology case reports},
volume = {14},
number = {2},
pages = {e70487},
pmid = {41626263},
issn = {2051-3380},
abstract = {Whipple's disease (WD) is a rare chronic multisystem infectious disease caused by the actinomycete Tropheryma whipplei. Pulmonary involvement is uncommon, and its clinical manifestations lack specificity, with diverse imaging findings, making it prone to misdiagnosis. We report a rare case of a 50-year-old woman who presented with a 2-week history of cough. Chest CT showed multiple thick-walled cavities in both lungs, a highly unusual presentation for WD pneumonia. Routine microbiological tests, including acid-fast staining and culture of bronchoalveolar lavage fluid (BALF), were negative, which made the diagnosis challenging. Metagenomic next-generation sequencing (mNGS) of BALF detected T. whipplei, confirming the diagnosis of WD pneumonia. After oral doxycycline treatment, follow-up chest CT showed complete resolution of the pulmonary cavities. This case demonstrates that multiple thick-walled cavities may be a characteristic imaging manifestation of WD pneumonia, highlights the diagnostic value of mNGS for this rare infection, and supports oral doxycycline monotherapy as an effective treatment option for isolated pulmonary TW infection.},
}

@article {pmid41626090,
year = {2026},
author = {Chen, L and Tang, M and Wang, Q and Jiang, H},
title = {Why a Mycobacterium Avium Infected Patient Showed a Positive Xpert MTB/RIF Result?.},
journal = {Clinical case reports},
volume = {14},
number = {2},
pages = {e71965},
pmid = {41626090},
issn = {2050-0904},
abstract = {This article discusses whether a MAC infected patient with a positive Xpert MTB/RIF test has a co-infection with Mycobacterium tuberculosis (MTB). The patient presented with chronic, indolent pulmonary patchy shadows on imaging but lacked typical symptoms. The MTB antigen-specific interferon-gamma enzyme-linked immunospot assay (T-SPOT.TB) was negative. Bronchoalveolar lavage fluid (BALF) testing yielded conflicting results: Xpert MTB/RIF assay detected trace levels of MTB DNA, whereas reverse dot blot hybridization confirmed the presence of Mycobacterium avium complex (MAC); in contrast, metagenomic next-generation sequencing (mNGS) returned a negative result for all pathogens. Mycobacterial culture ultimately returned positive; however, the MPB64 assay-employed for species identification-yielded a negative result, indicating a probable nontuberculous mycobacterial (NTM) infection. Despite contradictory lab results, the patient's symptoms and culture findings favored MAC infection. However, MTB infection could not be definitively ruled out in this patient, so a treatment regimen combining anti-tuberculosis and anti-MAC medications (isoniazid, rifampicin, ethambutol, and azithromycin) was initiated, leading to significant radiographic improvement. The discordance between the positive Xpert MTB/RIF result and other diagnostic evidence highlights important diagnostic challenges, underscoring the need for integrated clinical interpretation and providing actionable insights for clinicians.},
}

@article {pmid41625985,
year = {2026},
author = {Taboada, S and Riesgo, A and Busch, K and Erpenbeck, D and Hentschel, U and Galià, C and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {15},
pmid = {41625985},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.},
}

@article {pmid41625959,
year = {2026},
author = {de Melo Pereira, GV and da Silva Vale, A and Ribeiro-Barros, AI and Rodrigues, LRS and de França Bettencourt Mirção, GM and Camilo, B and da Piedade Ernesto Tapaça, I and de Mello Sampaio, V and Brar, SK and Soccol, CR},
title = {Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100344},
pmid = {41625959},
issn = {2666-5662},
abstract = {Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (Leuconostoc-Hanseniaspora-Galactomyces axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.},
}

@article {pmid41625836,
year = {2025},
author = {Matsukawa, M and Sakai, Y and Aoki, K and Ishii, Y},
title = {Urinary Microbiome Profiling by Shotgun Metagenomic Sequencing in Women Having Acute Cystitis-Like Symptoms With Negative Urine Cultures.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e100451},
pmid = {41625836},
issn = {2168-8184},
abstract = {BACKGROUND: Women presenting with typical symptoms of acute cystitis but with negative urine cultures, termed acute cystitis-like symptoms with negative urine cultures (ACNCs) in this study, are not uncommon. Despite previous attempts to detect bacterial DNA in urine, the etiology remains unclear. Although alterations in the urinary microbiome have been linked to other urological disorders, its involvement in ACNC has not been thoroughly investigated.

METHODS: Between September 2016 and December 2017, midstream urine samples were collected from women aged ≥16 years who had at least one typical symptom of acute cystitis and a negative urine culture. Samples were obtained at the initial (V1) and follow-up (V2) visits. Shotgun metagenomic sequencing (SMG) was performed via an Illumina MiSeq system. Taxonomic analysis at the genus level included taxa with ≥10 assigned reads in samples with ≥10,000 human-subtracted reads (HSRs).

RESULTS: Of 206 eligible women, 15 (7.3%; median age, 65 years) met the ACNC criteria and were enrolled. SMG was conducted for 15 samples at V1 and nine samples at V2. At V1, the HSR varied widely, and only five samples met the criteria for reliable interpretation. Seven samples, particularly those with high-grade pyuria, contained fewer than 1,000 HSRs, indicating potentially very low microbial loads or technical limitations. ACNC microbiomes demonstrated marked interindividual variation in taxonomic composition. The predominant taxa most frequently observed were Lactobacillus spp., Gardnerella spp., and JC polyomavirus. Conventional uropathogens, such as Escherichia spp., were not identified at interpretable levels. At V2, microbial diversity remained heterogeneous, but eight samples yielded sufficient read counts for interpretation.

CONCLUSIONS: While conventional uropathogens below interpretable criteria are unlikely to be responsible for most ACNCs, it is not necessarily recommended to regard the leading taxon in each case as the cause or to exclude microbiological involvement simply due to a low HSR because no validated metagenomic signature distinguishes pathogens from commensals. However, the observed diversity in ACNC microbiome profiles may reflect a heterogenous group of microbial conditions, including potentially viral, and nonmicrobial etiologies.},
}

@article {pmid41625740,
year = {2025},
author = {Su, J and Liu, K and Wu, X and Lin, B and Ying, F and Zhu, Y and Li, M and Guo, P},
title = {Case Report: Confocal microscopy in the early diagnosis of microsporidial keratitis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1745070},
pmid = {41625740},
issn = {2296-858X},
abstract = {This report describes a rare case of microsporidial stromal keratitis (MSK) complicated by corneal perforation in a 69-year-old male farmer with a 5-month history of ocular redness, pain, photophobia, and epiphora. In vivo confocal microscopy (IVCM) revealed pathognomonic findings-hyperreflective double-walled spore casings and vesicular clusters, providing the earliest diagnostic clues for microsporidia infection. Subsequent metagenomic next-generation sequencing (mNGS) and histopathology confirmed Microsporidia species. The patient underwent therapeutic penetrating keratoplasty followed by targeted anti-microsporidial therapy, achieving globe preservation and visual improvement. This case underscores IVCM's pivotal role in diagnosing MSK, particularly in atypical presentations. Because MSK remains a rare corneal disorder, its insidious progression necessitates high clinical vigilance. In summary, IVCM's ability to detect microsporidial structures in real-time significantly enhances early diagnosis, complementing molecular methods like mNGS. We conclude that IVCM, as a non-invasive and rapid diagnostic tool, provides a convenient and efficient means for the early differentiation of challenging corneal infections.},
}

@article {pmid41625489,
year = {2026},
author = {Zhou, L and Liu, J and Li, S and Xiong, Y and Qin, F and Luo, Z and Huang, D and Chen, H and Wang, X},
title = {Association between anxiety symptoms on risky e-biking riding behavior among adolescents: based on gut-brain axis.},
journal = {Comprehensive psychoneuroendocrinology},
volume = {25},
number = {},
pages = {100337},
pmid = {41625489},
issn = {2666-4976},
abstract = {OBJECTIVE: This study aimed to investigate the association between anxiety symptoms and risky e-bike riding behavior (RERB) among adolescents and to explore whether gut microbiota mediates this relationship.

METHODS: Adolescents using e-bikes were recruited through a combined online and offline recruitment approach. Data collection involved supervised electronic questionnaire completion in face-to-face settings, with biological samples collected independently by participants. Anxiety symptoms were assessed using the Generalized Anxiety Disorder-7 scale. RERB were evaluated via a structured questionnaire, yielding separate scores for aggressive behaviors (ABS), violation behaviors (VBS), and negligent behaviors (NES), along with total behavior scores (TBS). Fecal samples were obtained for metagenomic sequencing to characterize gut microbiota composition. Multiple linear regression was employed to elucidate the associations between anxiety symptoms and RERB. Partial Least Squares Path Modeling (PLS-PM) was applied to evaluate the potential mediating role of gut microbiota in these associations.

RESULTS: A total of 71 adolescents were included in this cross-sectional study. Anxiety symptoms were significantly associated with RERB, including TBS and VBS (both P < 0.05). Among the 15 microbial genera identified from fecal samples, 17 species showed significant association with both anxiety symptoms and RERB. PLS-PM modeling revealed a significant mediating effect of specific gut microbiota in the anxiety→behavior pathway, particularly for TBS and VBS. In contrast, for ABS, a reverse pathway-microbiota→anxiety→behavior-was found significant.

CONCLUSIONS: Anxiety symptoms were significantly associated with RERB among adolescents. Specific gut microbiota may mediate these associations, suggesting a potential microbiota-brain-behavior pathway.},
}

@article {pmid41624871,
year = {2025},
author = {Zhu, H and Hu, L and Feng, Z and Zhang, Z and Zhu, H and Li, H},
title = {Case Report: Murine typhus complicated by symmetrical peripheral gangrene: first report and diagnostic insights from metagenomic next-generation sequencing.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1746919},
pmid = {41624871},
issn = {1664-3224},
mesh = {Humans ; Female ; High-Throughput Nucleotide Sequencing ; Aged ; *Gangrene/diagnosis/etiology ; Metagenomics/methods ; *Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Rickettsia typhi/genetics ; Doxycycline/therapeutic use ; },
abstract = {BACKGROUND: Murine typhus, a flea-borne infection caused by Rickettsia typhi, often presents with nonspecific symptoms that delay diagnosis. While usually self-limiting, it can rarely progress to multiple organ dysfunction syndrome (MODS). We report the first case of murine typhus complicated by symmetrical peripheral gangrene (SPG), in which metagenomic next-generation sequencing (mNGS) enabled rapid diagnosis and guided timely doxycycline therapy.

CASE PRESENTATION: A 69-year-old female from South China was hospitalized with persistent abdominal pain and low-grade fever. She was a farmer and had suspected animal exposure. Laboratory investigations revealed hypoxia, abnormal coagulation profile, hepatorenal impairment, and thrombocytopenia. Despite empirical antibiotic therapy, her condition deteriorated progressively, manifested as hemodynamic instability, respiratory failure, and the emergence of purpuric-petechial cutaneous eruptions. Immediate interventions were initiated, including administration of vasoactive agents and mechanical ventilation. Based on mNGS, R. typhi was confirmed, she received targeted antibiotic treatment with intravenous doxycycline (100 mg twice daily). On the hospital day 16, gangrene of all four extremities became evident. The patient underwent amputation of all four extremities and survived, with systemic symptoms gradually resolving during 6-months follow-up.

CONCLUSION: This first reported case of murine typhus complicated by symmetrical peripheral gangrene (SPG) establishes its potential to cause life-threatening multiorgan failure. Metagenomic next-generation sequencing (mNGS) resolved the diagnostic challenge by rapidly identifying Rickettsia typhi, guiding life-saving doxycycline therapy and underscoring its value in severe zoonotic infections.},
}

Humans
Female
High-Throughput Nucleotide Sequencing
Aged
*Gangrene/diagnosis/etiology
Metagenomics/methods
*Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications/microbiology
Anti-Bacterial Agents/therapeutic use
*Rickettsia typhi/genetics
Doxycycline/therapeutic use

@article {pmid41624426,
year = {2026},
author = {Santi, I and Pavloudi, C and Abagnale, M and Azua, I and Baña, Z and Bastianini, M and Belser, C and Berg, K and Bilbao, J and Bird, K and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Cunliffe, M and Daguin, C and Deneudt, K and Díaz de Cerio, O and Exter, K and Fauvelot, C and Fontana, Y and Frada, MJ and Galand, PE and Gallia, R and Garczarek, L and González Fernández, J and Guillou, L and Heynderickx, H and Koplovitz, G and Labrune, C and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhães, C and Margiotta, F and Moal, H and Moussy, A and Not, F and Percopo, I and Paredes Rosendo, E and Péru, E and Poulain, J and Praebel, K and Rigaut-Jalabert, F and Romac, S and Rzeznik-Orignac, J and Sarno, D and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Tramontano, F and Trano, AC and Wincker, P and Pade, N},
title = {Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e178484},
pmid = {41624426},
issn = {1314-2828},
abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.},
}

@article {pmid41623646,
year = {2025},
author = {Thagulisi, F and Baatjies, L and Sharma, A and Ngom, JT and Nyambo, K and Jooste, T and Tapfuma, KI and Mavumengwana, V},
title = {Antimycobacterial activity of intertidal sediment-derived bacteria from False Bay, South Africa.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745248},
pmid = {41623646},
issn = {1664-302X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a global health burden due to the pathogen's ability to develop resistance to current treatment options. Consequently, drug discovery studies are essential for identifying new antimycobacterial agents with novel mechanisms of action. This study investigated the antimycobacterial activity of crude extracts derived from mixed culturable bacteria isolated from intertidal marine sediments. The bacterial diversity of the bioactive mixed cultures was characterized using 16S rRNA gene-based metagenomic analysis. Their pathogen-targeted effects were evaluated against Mycobacterium smegmatis mc[2]155 and M. tuberculosis H37Rv, and THP-1-derived macrophages infected with M. smegmatis mc[2]155. Of the 48 mixed bacterial crude extracts derived from 17 intertidal marine sediments, five-PPB1, GCR1, BB1, PPB2, and CR1-demonstrated strong antimycobacterial activity against M. smegmatis mc[2]155 and M. tuberculosis H37Rv with minimum inhibitory concentrations ranging from 31.25 to 62.50 μg/mL and 7.8125 to 15.625 μg/mL, respectively. At 62.50 μg/mL, CR1 significantly reduced the intracellular M. smegmatis mc[2]155 burden in THP-1-derived macrophages, resulting in 28.08 ± 4.25% mean decrease in bacterial survival (p < 0.0001) and 94.4% ± 1.14 mean growth inhibition. From the CR1 mixed cultures, nine axenic bacterial isolates were cultivated, and their resulting crude extracts were evaluated for bioactivity. The identified isolates included Marinobacter maritimus, Psychrobacter celer, Pseudomonas benzenivor, Bacillus altitudinis, Bacillus aerius, Bacillus stratosphericus, and Paenibacillus glucanolyticus. Metabolite profiling of axenic crude extracts identified several compounds, including tenacibactin B, maremycin D1, and tubercidine. These findings suggest that South African intertidal marine sediments host diverse microbial communities capable of producing novel antimycobacterial agents.},
}

@article {pmid41623642,
year = {2025},
author = {Kuang, HF and Jiang, XY and Tie, SY and Lian, K and Hao, MY and Xu, H and Huang, X and Yang, Y and Guo, Q and Li, J and Chen, LL},
title = {Global research trends in bacteriophage and gut microbiota: a bibliometric and visual analysis from 2012 to 2025.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1738456},
pmid = {41623642},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota constitutes a complex microbial ecosystem that plays a fundamental role in host metabolism and immune homeostasis. As the most abundant viral entities in the gut, bacteriophages are increasingly recognized as key modulators of microbial community structure and function. Nevertheless, the global research landscape and thematic evolution of bacteriophage-gut microbiota studies have not been systematically evaluated.

METHODS: Publications related to bacteriophages and the gut microbiota published between 2012 and 2025 were retrieved from the Web of Science Core Collection and Scopus databases. Bibliometric and visual analyses were conducted using CiteSpace, VOSviewer, and Scimago to examine publication trends, countries/regions, institutions, authors, journals, references, and research hotspots.

RESULTS: A total of 687 articles and reviews were included. The annual number of publications increased steadily, with accelerated growth after 2018 and a peak in 2023. China ranked first in publication output, while the United States demonstrated strong centrality in global collaboration networks. The University of California, San Diego and the University of Copenhagen were identified as leading institutions. Highly productive authors included Colin Hill, Bernd Schnabl, Zhang Yue, Li Shenghui, and Ross R. Pau. Frontiers in Microbiology and Nature are the most influential journals in this field. Keyword analyses revealed major research hotspots, including viral metagenomics, antimicrobial resistance, phage-microbiota-immune interactions, and the transition from phage therapy toward microecological and immunomodulatory interventions.

CONCLUSION: Research on bacteriophage-gut microbiota interactions has shifted from descriptive profiling to mechanistic and translational studies, driven by advances in viral metagenomics and phage culturomics. Increasing attention has been directed toward disease-associated phage-microbiota interactions, particularly in inflammatory bowel disease, as well as the development of precision interventions such as phage therapy and engineered phages. This bibliometric analysis provides a comprehensive overview of global research trends and highlights emerging directions for future microbiome research.},
}

@article {pmid41623638,
year = {2025},
author = {Kane, Y and Ma, Y and Yan, B and Zhao, X and Ge, T and Li, Y and Cao, L and Zhang, M and Wan, Z and Zhang, T and Zhang, C},
title = {The human plasma anellome exhibits age- and sex-dependent patterns with links to cardiometabolic health in older adults.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1716110},
pmid = {41623638},
issn = {1664-302X},
abstract = {The human plasma virome is dominated by anelloviruses which are increasingly associated with several clinical conditions including among others HIV-1, COVID-19, autoimmune diseases, and cardiovascular and metabolic diseases. Due to their high genetic divergence, most studies investigated human anellome at broad family or genus level. These approaches obscure the contributions of specific anellovirus species to clinical conditions. We conducted plasma metagenomics in 218 individuals from young (0-16 years) and old (63-100 years) cohorts to resolve the anellome at the species level and examine its patterns across age, sex, and associations with cytokines and cardiometabolic outcomes. Older adults exhibited near-universal anellovirus detection and significantly higher abundance compared with youth. Species-specific analysis revealed that Alphatorquevirus_homin1 and Alphatorquevirus_homin13 were markedly enriched in diseased older adults. Predictive modeling based on machine learning algorithms distinguished disease status in the young cohort with high accuracy (AUC = 0.86), but performance was limited in the elderly (AUC = 0.58), suggesting a lack of diagnostic value in advanced age. Specific species abundances and diversity were associated with stroke and coronary heart disease, while cytokine correlations revealed module-specific immune signatures: Gammatorquevirus-dominated modules associated positively with pro-inflammatory cytokines and growth factors (e.g., IL-1β, IL-15, VEGF), whereas Beta- and some Alphatorquevirus-dominated modules showed predominantly negative correlations with several inflammatory and regulatory mediators (e.g., IL-6, TNF-α, IL-10). These findings demonstrate that the anellome is influenced by age and immune status and shows associations with cardiometabolic health, although these relationships do not guarentee diagnostic or causal significance. Additonally, we found no significant differences of Human endogenous retrovirus K Env expression between disease and healthy controls. This work underscores the importance of resolving human anollome to species level in future longitudinal studies to strengthen their clinical significance and biomarker potential.},
}

@article {pmid41623634,
year = {2025},
author = {Zeng, J and Gong, L and Qin, S and Fang, P and Shu, F and Zhang, W and Zhou, Y and Li, X and He, Q and Sun, P and Deng, H},
title = {Multi-omics reveals glutinous rice varieties shape Baijiu flavor via microbial and metabolic modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721127},
pmid = {41623634},
issn = {1664-302X},
abstract = {INTRODUCTION: Glutinous rice significantly influences Baijiu flavor, yet standardized brewing-specific indicators are lacking.

METHODS: In this study, metagenomic, metaproteomic, and non-targeted GC-MS analyses of Zaopei, along with HS-SPME-GC-MS analysis of Baijiu, were used to compare the effects of three glutinous rice varieties with distinct nutritional profiles on microbial diversity and flavor formation.

RESULTS: The Wuliangye-specific variety Dajiugu, with high sucrose, high amino acids, and low fatty acids, promoted early growth and metabolic activity of Saccharomycopsis, Enterobacter, and Klebsiella. Functional genera such as Saccharopolyspora, Pediococcus, and Clostridium enhanced fatty acid and amino acid accumulation in Zaopei and increased ethyl acetate, 4-vinylphenol, and dimethyl trisulfide in Baijiu.

DISCUSSION: These findings highlight the pivotal role of glutinous rice variety in shaping Baijiu flavor and offer a scientific basis for breeding brewing-specific glutinous rice.},
}

@article {pmid41484707,
year = {2026},
author = {Zhou, Z and Zheng, X and Yang, W and Cui, Y and Gao, Y and Xia, J and Wang, Y and Gao, Y and Lu, M and Zhang, D and Wang, H and Chen, L},
title = {A rare case of peritoneal dialysis-associated peritonitis caused by Coxiella burnetii diagnosed by mNGS.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {233},
pmid = {41484707},
issn = {1471-2334},
abstract = {We report a rare case of peritoneal dialysis (PD)-associated peritonitis caused by Coxiella burnetii, an intracellular pathogen typically associated with Q fever. A 28-year-old female with lupus nephritis and end-stage kidney disease on PD presented with cloudy effluent and abdominal pain after consuming undercooked lamb. Despite initial empirical broad-spectrum antibiotic therapy (cefazolin/ceftazidime protocol), clinical symptoms persisted. Conventional bacterial, fungal, and mycobacterial cultures were negative. Metagenomic next-generation sequencing (mNGS) of the peritoneal effluent identified C. burnetii DNA. The treatment was transitioned to doxycycline and hydroxychloroquine resulted in clinical improvement and normalization of inflammatory markers. This case underscores the diagnostic value of mNGS in culture-negative peritonitis and emphasizes C. burnetii as an emerging pathogen in immunocompromised PD patients, particularly with zoonotic exposure histories.},
}

@article {pmid41623622,
year = {2025},
author = {Li, Y and Cheng, Y and Liu, W and Li, J and Li, S and Suriguga, and Ma, T and Kwok, LY and Cai, Z and Sun, Z},
title = {Gut microbial and functional signatures in breast cancer: an integrated metagenomic and machine learning approach to non-invasive detection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722632},
pmid = {41623622},
issn = {1664-302X},
abstract = {INTRODUCTION: Breast cancer is associated with significant restructuring of the gut ecosystem. Gut microbial composition and function may influence cancer development and progression through immune modulation, metabolic regulation, and inflammation-related pathways.

METHODS: Using shotgun metagenomic sequencing of fecal samples from 38 stage I-III breast cancer patients and 36 age- and body mass index-matched healthy controls. Machine learning models were constructed to evaluate the diagnostic potential of integrated microbial and metabolic features.

RESULTS: Significant alterations were observed in gut microbiota composition, including depletion of beneficial taxa (Limosilactobacillus fermentum, Blautia sp.) and enrichment of Prevotella copri. Pathways involved in short-chain fatty acid and purine metabolism were reduced. The gut phageome exhibited structural changes and altered correlations with bacterial hosts. Predictive analysis revealed depletion of short-chain fatty acids (butyrate, propionate), purine intermediates (hypoxanthine, xanthine), and nicotinate in patients. A machine learning model integrating microbial and predicted metabolic features achieved an area under the curve values of 0.78 in the discovery cohort and 0.73 (recall = 0.74) in an independent validation cohort.

DISCUSSION: Coordinated gut microbiome, phageome, and metabolome alterations characterize breast cancer, offering potential non-invasive biomarkers and mechanistic insights for disease detection and intervention.},
}

@article {pmid41623619,
year = {2025},
author = {Wei, T and Qian, N and Wang, H and Song, Y and Wang, W and Li, Y and Zhao, Z and Xu, F and Yang, W},
title = {Wilson's disease-associated gut dysbiosis: novel insights into microbial functional alterations, virulence changes, and resistance markers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1714276},
pmid = {41623619},
issn = {1664-302X},
abstract = {BACKGROUND: Although the gut microbiota is associated with a variety of metabolic, inflammatory, and neurological disorders through microbial dysbiosis, current studies on the gut microbiota in Wilson's disease (WD) remain limited. Critical gaps exist in understanding the roles of key functional microbial factors in WD pathogenesis, which hinders the acquisition of mechanistic insights into this disease.

OBJECTIVE: This study aims to characterize alterations in the gut microbiome associated with WD, with a particular emphasis on virulence factors (VFs) and antibiotic resistance genes (ARGs), as well as functional mobile genetic elements (MGEs), in order to elucidate their potential roles in disease progression and clinical manifestations.

METHODS: We analyzed fecal samples from 37 patients with WD and 33 healthy controls (HCs) using metagenomic sequencing, with a specific focus on examining virulence gene profiles and antibiotic resistance patterns and MGE composition in relation to liver function markers.

RESULTS: Beta diversity analysis revealed significant differences in the gut microbial community structure between patients with WD and HCs, and a distinct set of microbial taxa was identified that showed significant associations with clinical indicators. A gut microbial co-occurrence network identified key species playing central roles in the microbial community structure, including Prevotella stercorea, Firmicutes bacterium CAG 110, Bacteroides salyersiae, Lactococcus petauri, Streptococcus cristatus, Actinomyces sp. HMSC035G02, and Streptococcus viridans. Widespread functional dysbiosis was detected across multiple biological levels in patients with WD, with significant correlations identified between these microbial alterations and clinical indicators. Significant disruptions were identified in key metabolic pathways, including the Pentose Phosphate Pathway, Pyruvate Metabolism, and Starch and Sucrose Metabolism, which were associated with the dysregulation of carbohydrate-active enzymes (CAZymes). These alterations showed significant correlations with clinical markers of liver dysfunction (e.g., procollagen III N-terminal peptide PIIINP, aspartate transaminase/alanine transaminase AST/ALT). A total of 54 virulence factor (VF) genes exhibited differential abundance in WD, with 36 genes depleted and 18 enriched. Notably, these included colibactin genes (clbB, clbH) from Escherichia coli and type IV secretion system genes (aec19, pilB). These VFs were significantly associated with indicators of liver function (e.g., bilirubin levels) and coagulation abnormalities. Among the detected antibiotic resistance genes (ARGs), 21 exhibited disease-specific patterns in WD, notably tetQ (encoding tetracycline resistance), ErmB (conferring macrolide resistance), and cfxA6 (mediating cephamycin resistance). Furthermore, ARG profiles were associated with Bifidobacterium enrichment and showed significant correlations with lipid metabolism markers [e.g., triglycerides (TG), high-density lipoprotein cholesterol (HDL-C)]. Critically, we identified significant enrichment of 60 functional mobile genetic elements (MGEs) in WD, spanning categories involved in DNA replication/repair, phage activity, and conjugative transfer, indicating heightened genomic plasticity and horizontal gene transfer potential. Strikingly, correlation network analysis revealed strong and specific co-occurrence between key ARGs (e.g., ErmX) and defined suites of MGEs, suggesting MGE-facilitated dissemination of resistance determinants.

CONCLUSION: Wilson's disease (WD) patients exhibit significant alterations in gut microbial community structure and functional dysbiosis, wherein the enrichment of virulence genes (such as colibactin genes clbB/clbH) and the specific antibiotic resistance genes (such as tetQ and ErmB), and the activation of mobile genetic elements are closely associated with clinical indicators including liver function impairment, coagulation abnormalities, and lipid metabolism disorders.},
}

@article {pmid41623458,
year = {2026},
author = {Li, QM and He, LS and Wang, Y},
title = {Small proteins from prokaryotes in the marine water column at full ocean depth.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114585},
pmid = {41623458},
issn = {2589-0042},
abstract = {Small proteins (SPs, ≤50 aa) are often overlooked in genomics. We conducted the first systematic analysis of prokaryotic SPs across the full ocean-depth gradient. From 433,311 short open reading frames (sORFs) predicted from 71 western Pacific metagenomes, we identified 193,281 SP clusters. Filtration yielded 75,581 prevalent SPs, including 4,307 high-confidence clusters (RfSPs). Notably, 87.09% of RfSPs lacked non-marine homologs, and ∼70% contained unknown domains. While most (65.57%) were phylum-specific, twelve were distributed across ≥5 phyla, and some were prophage-associated. Geographically, twenty-three core RfSPs were universally present. Co-occurrence analysis revealed that interacting RfSPs typically originated from the same or adjacent zones. Finally, we confirmed the transcription of 8.20% RfSP clusters in deep-sea metatranscriptomes. The zone-specific transcription of certain RfSPs suggests adaptive functions, such as stress response and molecular chaperoning, in distinct marine environments. Our study reveals SPs as a critical strategy for prokaryotic adaptation to deep-sea stressors.},
}

@article {pmid41623309,
year = {2026},
author = {Luo, Y and Ding, H and Pan, J and Xu, G},
title = {Use of metagenomic next-generation sequencing to diagnose Tropheryma whipplei infection-related pneumonia: A case report.},
journal = {Experimental and therapeutic medicine},
volume = {31},
number = {3},
pages = {75},
pmid = {41623309},
issn = {1792-1015},
abstract = {Whipple's disease is caused by Tropheryma whipplei (T. whipplei), an uncommon pathogen that is often related to gastrointestinal symptoms. Extraintestinal involvement, particularly pulmonary manifestations, is rare and poses notable diagnostic challenges. An objective technique for identifying undiscovered infections is the application of metagenomic next-generation sequencing (mNGS). The present case report described a 55-year-old female presenting with community-acquired pneumonia (CAP), who received empirical treatment with moxifloxacin, ultimately diagnosed through mNGS performed on bronchoalveolar lavage fluid. The results indicated that the patient was infected with T. whipplei and that the patient exhibited notable clinical improvement within 2 weeks following intravenous moxifloxacin during hospitalization and continuation of oral moxifloxacin following discharge. The present case report highlighted the utility of mNGS in diagnosing atypical infections and identified T. whipplei as a potential etiological agent of CAP in immunocompetent hosts.},
}

@article {pmid41622335,
year = {2026},
author = {Ota, C and Bamba, M and Sato, S and Tsuchimatsu, T},
title = {Soil microbial composition and abundance influence the growth of Lotus japonicus.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {41622335},
issn = {1618-0860},
abstract = {In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume-rhizobia interactions could trigger a positive plant-soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.},
}

@article {pmid41622302,
year = {2026},
author = {Li, S and Zhang, J and Han, L and Yu, Y and Mousa, AA and Zhu, W and Leng, J and Xie, F and Mao, S},
title = {Comparative metagenomic and metatranscriptomic analyses reveal the role of the gayal rumen and hindgut microbiome in high-efficiency lignocellulose degradation.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {18},
pmid = {41622302},
issn = {1674-9782},
support = {U2202203//Joint Funds of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The gayal (Bos frontalis), a semi-domesticated bovine species, demonstrates exceptional adaptability to lignocellulose-rich diets dominated by bamboo, suggesting the presence of a specialized gastrointestinal microbiome. However, the functional mechanisms underlying this host-microbiome interaction remain poorly understood. Here, we conducted integrated metagenomic and metatranscriptomic analyses of rumen, cecum, and colon digesta from yellow cattle and gayal raised on the same bamboo-based high-fiber diet.

RESULTS: The results showed that gayal exhibited superior fiber-degrading capacity relative to yellow cattle, evidenced by significantly higher (P < 0.05) fiber digestibility, cellulase and xylanase activities, and increased volatile fatty acids production despite identical feed intake. Microbial community analysis revealed distinct composition in both the rumen and hindgut of gayal compared to yellow cattle, with notable enrichment of taxa specialized in lignocellulose degradation. Metatranscriptomic profiling further identified upregulation of key lignin-modification enzymes, particularly AA6, AA2, and AA3, primarily encoded by Prevotella, Cryptobacteroides, Limimorpha, and Ventricola. These enzymes are known to modify lignin structure to increase polysaccharide accessibility. These results demonstrate that gayal hosts a unique and metabolically active gastrointestinal microbiome capable of efficient lignocellulose deconstruction through a coordinated enzymatic cascade, especially effective in dismantling lignin barriers.

CONCLUSIONS: This study provides novel insights into host-microbiome co-adaptation to fibrous feeds and highlights the potential of gayal-derived microbial consortia and enzymes for improving roughage utilization in ruminant agriculture.},
}

@article {pmid41622108,
year = {2026},
author = {Deng, Z and Sanchis-López, C and Hernández-Plaza, A and Davín, AA and Huerta-Cepas, J},
title = {TreeProfiler: Large-scale metadata profiling along gene and species trees.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag028},
pmid = {41622108},
issn = {1537-1719},
abstract = {Profiling biological traits along gene or species tree topologies is a well-established approach in comparative genomics, widely employed to infer gene function from co-evolutionary patterns (phylogenetic profiling), reconstruct ancestral states, and uncover ecological associations. However, existing profiling tools are typically tailored to specific use cases, have limited scalability for large datasets, and lack robust methods to aggregate or summarize traits at internal tree nodes. Here, we present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes. TreeProfiler supports the profiling of custom continuous and discrete traits, as well as ancestral character reconstruction and phylogenetic signal tests. It also integrates commonly used genomic features, including multiple sequence alignments, protein domain architectures, and functional annotations. We demonstrate TreeProfiler's utility beyond traditional phylogenetic profiling, as well as its ability to efficiently handle massive datasets, by analyzing the functional diversification of the methyl-accepting chemotaxis protein (MCP) family comprising over 400,000 genomic and metagenomic sequences, and by profiling the relative abundance of 124,295 bacterial and archaeal species across 51 biomes. TreeProfiler is open-source and freely available at https://github.com/compgenomicslab/TreeProfiler.},
}

@article {pmid41621540,
year = {2026},
author = {Sun, H and Han, Y and Ren, S and Zhang, X and Li, X and Bi, P and Chen, L and Zhu, L and Yang, G and Ma, J and He, Q},
title = {Convergent enrichment of communities involved in Fe-N metabolism in anammox and activated sludge: Insights into genome-resolved metagenomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134125},
doi = {10.1016/j.biortech.2026.134125},
pmid = {41621540},
issn = {1873-2976},
abstract = {The coupled process of ferric ammonium oxidation (Feammox) and nitrate-dependent ferrous oxidation (NDFO) is a cost-effective nitrogen removal strategy, yet insufficient molecular evidence supports its microbial mechanisms. This study successfully established anaerobic Fe-N coupling systems using anammox sludge and activated sludge as inoculum. Batch experiments and microbial community analysis revealed that two systems achieved similar nitrogen removal, dominated by anammox and Feammox performed by anammox bacteria (AnAOB), with a minor NDFO contribution, and convergently enriched core functional guilds under identical environmental pressures. Genome-resolved metagenomics further indicated that the porin-cytochrome protein complex associated with extracellular electron transfer co-occurred with anammox genes in Brocadia sapporoensis, suggesting its potential Feammox capability. Meanwhile, the iron oxidation gene Cyc2 co-occurred with mtr pathway homologs and complete denitrification genes in IGN3 sp900696555, suggesting its role in NDFO. This genomic evidence supports their dual metabolic capabilities, providing new insights into nitrogen removal in the coupled Feammox-NDFO process.},
}

@article {pmid41621514,
year = {2026},
author = {Ren, X and Zhang, W and Liu, M and Ge, J and Yang, H and Chi, G},
title = {Colon-targeted probiotic delivery system based on oxidized konjac glucomannan/thiolated chitosan/bacterial cellulose: Enhanced survival, mucoadhesion, and gut microbiota modulation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150646},
doi = {10.1016/j.ijbiomac.2026.150646},
pmid = {41621514},
issn = {1879-0003},
abstract = {Probiotics play a critical role in maintaining human health homeostasis, yet their oral delivery faces challenges due to poor gastrointestinal survival, uncontrolled release, and inefficient targeted colonization. To address these limitations, we developed colon-targeted mucoadhesive (sCS-BC)/OKGM-SA microspheres using a W1/O/W2 double emulsion technique combined with ionic crosslinking, employing oxidized konjac glucomannan (OKGM), thiolated chitosan (sCS), and bacterial cellulose (BC). In vitro digestion assays revealed that the microspheres effectively shielded probiotics under simulated gastric and bile salt, while enabling pH- and enzyme-responsive release in the intestinal, achieving a viable probiotic count of 1.5 × 10[8] CFU/mL. Rheological characterization and in vivo gastrointestinal transit studies demonstrated that the microspheres enhanced colonic colonization through interactions with the intestinal mucus layer. Histological analysis further indicated that the microspheres stimulated colonic goblet cell proliferation and mucus layer formation. Metagenomic and metabolomic profiling confirmed that oral administration of the probiotic-loaded microspheres markedly enriched gut microbial diversity and helped preserve intestinal barrier integrity, showing potential in modulating gut immune function. The (sCS-BC)/OKGM-SA system integrates upper gastrointestinal protection, colon-targeted delivery, mucus adhesion, and probiotic proliferation, offering a novel strategy for targeted probiotic delivery. This work establishes a foundational framework for designing next-generation colon-targeted probiotic carriers and underscores their therapeutic promise in modulating intestinal ecosystems.},
}

@article {pmid41621269,
year = {2026},
author = {Li, J and Dong, W and Kong, A and Wang, G and Yang, J and Zhou, Y and Song, K and Kong, L and Tong, L},
title = {Floating macrophyte growth and decomposition greatly affects the exogenous antimony mobility and microbial community functions in water-sediment system.},
journal = {Water research},
volume = {293},
number = {},
pages = {125448},
doi = {10.1016/j.watres.2026.125448},
pmid = {41621269},
issn = {1879-2448},
abstract = {Anthropogenic antimony (Sb) contamination in aquatic systems poses persistent ecological risks, yet the role of floating macrophyte life-cycle processes in regulating Sb migration and speciation remains poorly understood. In this study, a mesocosm experiment was conducted to investigate how the growth and decomposition of Alternanthera philoxeroides (AP) influence Sb mobility and transformation following exogenous Sb(V) input. Results show that Sb was ultimately sequestered in sediments, which acted as a dynamic regulator rather than a passive sink, controlling Sb retention and long-term reactivity. Rapid surface adsorption was followed by progressive downward migration driven by redox-sensitive remobilization and re-adsorption onto deeper mineral phases, with Sb predominantly associated with amorphous and poorly crystalline Fe/Al (hydr)oxides (67.3-84.1%). Growth of AP accelerated Sb removal from the water column mainly through indirect, DOM-mediated sequestration rather than direct plant uptake, while simultaneously enhancing the vertical redistribution of bioavailable Sb within sediments. In contrast, AP removal followed by decomposition caused pronounced physical and biogeochemical disturbances. These disturbances induced transient reducing conditions, organic matter release, and a marked increase in pH (up to 9.14), collectively promoting Sb remobilization and Sb(III) release into the overlying water. As a result, Sb(III) concentrations were up to 67-fold higher than those in the unvegetated control. Exogenous Sb strongly reshaped sediment microbial communities, selectively enriching metal-tolerant taxa such as Actinomycetota (genus Streptomyces) and favoring functional traits related to Sb detoxification and elemental cycling. Metagenomic evidence indicates that Sb resistance, coupled with coordinated C, N, P, and S cycling functions, enables the indigenous microbiome to actively regulate Sb speciation and mobility, particularly under organic matter inputs derived from macrophyte growth and decomposition. These findings demonstrate that floating macrophytes exert process-level control over Sb cycling, with life-cycle-mediated biogeochemical feedbacks governing its mobility, speciation, and persistence in water-sediment systems.},
}

@article {pmid41620987,
year = {2026},
author = {Tian, H and Liu, J and Li, L and Ge, J},
title = {From Interface to Cell: The Complex Interaction and Transfer Process Coupling Mechanism between Microplastics and Antibiotic Resistance Genes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11841},
pmid = {41620987},
issn = {1520-5851},
abstract = {Microplastic-phase interfaces (MPPIs) were established as critical vectors for accelerating antibiotic resistance gene (ARG) dissemination. Through integrated anaerobic/aerobic wastewater treatment system experiments combined with physicochemical characterization, metagenomic sequencing, and molecular dynamics simulations (MD), we elucidated MP-ARG interaction mechanisms from the interfacial to the cellular scale. Polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) MPPIs underwent significant aging during 60 days of exposure, resulting in elemental enrichment (C/O/P), the formation of C═C/C-H/C-O/C-OH functional groups, and elevated oxidation. These transformations enhanced extracellular polymeric substance production (184.81 mg/g MLSS) and selectively enriched antibiotic-resistant bacteria, ARGs, and mobile genetic elements (MGEs), promoting horizontal gene transfer. XDLVO theory revealed spontaneous microbial adhesion (ΔGadh = -23.63 mJ/m[2]) driven by Lifshitz-van der Waals (LW) and acid-base interactions. MD demonstrated direct MP penetration into the membrane via dominant LW forces (-1200 kJ/mol) and increased permeability. Concurrently, compared with sewage water (SW), MPPIs induced a 2.06-fold overproduction of reactive oxygen species, which upregulated genes encoding efflux pumps (acrF, 3.2-fold), outer membrane porins (OmpF, 4.1-fold), and conjugative transfer genes (traF, 3.8-fold). Material-specific (PET > PE > PP) and oxygen-driven redox mechanisms governed ARG dissemination: aerobic conditions favored radical-driven oxidation and MGE entrapment, whereas anaerobic systems enhanced hydrophobic adhesion.},
}

@article {pmid41620752,
year = {2026},
author = {Sharma, A and Küsel, K and Wegner, CE and Pérez-Carrascal, OM and Taubert, M},
title = {Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02325-1},
pmid = {41620752},
issn = {2049-2618},
support = {218627073//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; },
abstract = {BACKGROUND: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood.

RESULTS: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (> 90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances.

CONCLUSIONS: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO2 fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.},
}

@article {pmid41620643,
year = {2026},
author = {Ratcliff, JS and Kumari, M and Varga-Weisz, P and O'Gorman, R},
title = {Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2623356},
doi = {10.1080/19490976.2026.2623356},
pmid = {41620643},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Socioeconomic Factors ; Bacteria/classification/genetics/isolation & purification ; *Social Class ; },
abstract = {Evidence suggests that socioeconomic position (SEP) may shape the gut microbiota (GM), representing a mechanism through which social and environmental factors may drive health inequalities, yet no systematic review has examined this association. In this narrative systematic review, we searched PubMed, Web of Science, and Scopus up to 30 November 2024 for observational studies examining associations between measures of SEP and GM diversity, composition, or function in participants of any age, ethnicity, or location. We identified 1,479 unique studies, of which 26 met the inclusion criteria for this review. Associations were observed between SEP indicators and GM features, including alpha (α) and beta (β) diversity, taxonomic composition, and functional pathways. Notably, socioeconomic patterns in α-diversity differed by context, with greater diversity observed in advantaged groups in high-income countries (HICs) but in disadvantaged groups in low- and middle-income countries (LMICs). Differences in β-diversity suggest that advantaged and disadvantaged groups have distinct GM profiles. Furthermore, considerable heterogeneity was evident across studies, particularly in sampling, sequencing, and analytical methods. Overall, socioeconomic-related differences in the GM are evident globally, highlighting the microbiota as a potential target for interventions aimed at reducing health disparities. Further research employing larger and more diverse cohorts, longitudinal designs, metagenomic sequencing approaches, and comprehensive measurement and adjustment of key covariates is needed to deepen understanding of this relationship.},
}

*Gastrointestinal Microbiome
Humans
*Socioeconomic Factors
Bacteria/classification/genetics/isolation & purification
*Social Class

@article {pmid41620544,
year = {2026},
author = {Kirsche, L and Leary, P and Blaser, MJ and Scharl, M and Negussie, A and Müller, A},
title = {Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09639-2},
pmid = {41620544},
issn = {2399-3642},
support = {310030_192490//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.},
}

@article {pmid41620049,
year = {2026},
author = {Xia, Q and Li, J and Li, Q and Hu, Z and Wu, H and Xie, H and Lu, J and Liu, H and Zhang, J},
title = {Immobile iron-rich particles enhance simultaneous nitrogen removal and phosphorus retention in treatment wetlands.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134129},
doi = {10.1016/j.biortech.2026.134129},
pmid = {41620049},
issn = {1873-2976},
abstract = {Eutrophication control requires cost-effective and sustainable technologies capable of simultaneously removing nitrogen and phosphorus from wastewater treatment plant (WWTP) effluents. Widely used post-treatment systems, treatment wetlands (TWs) typically exhibit limited nutrient removal because of imbalances in electron supply and demand, and rapid saturation of substrate adsorption capacity. In this study, immobile iron-rich particles (IIRPs) were introduced into TWs via a drainage-injection strategy to enhance nutrient removal from municipal WWTP effluent. Following the start-up phase, the IIRP-amended TWs consistently achieved effluent concentrations that met the target quasi-Class IV surface water quality standards (TN ≤ 10 mg L[-1]; TP ≤ 0.3 mg L[-1]) for 300 days of continuous operation. The enhanced NH4[+]-N and TN removal with iron-rich particles amendment could not be attributed to nitrification or anammox, as evidenced using qPCR, metagenomic binning, and removal profiles. Instead, Fe-N redox-coupling processes, including Fe(III) reduction-driven and Fe(II) oxidation-driven nitrogen-removal pathways, contributed to enhanced nitrogen removal. The IIRPs amendment increased the equilibrium phosphorus adsorption capacity of wetland substrate by threefold, and the improved phosphorus retention was attributed to Fe-P interactions. These findings reveal a coupled Fe-N-P mechanism that enables efficient and stable nutrient removal and provide a mechanistic foundation for developing low-carbon, sustainable strategies to upgrade existing TWs for advanced wastewater polishing.},
}

@article {pmid41620043,
year = {2026},
author = {Chang, XL and Xing, BS and Qin, Y and Xie, J and Li, ZB and Wang, XC and Chen, R and Li, YY},
title = {Sustained performance and microbial succession in novel artificial rumen system coupling dynamic membrane with methanogenic granules for acid absorption.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134119},
doi = {10.1016/j.biortech.2026.134119},
pmid = {41620043},
issn = {1873-2976},
abstract = {Artificial rumen systems promise for converting lignocellulosic biomass into renewable products but face challenges in long-term operation. This study developed a novel artificial rumen system combined fermentation with acid absorption using methanogenic granules and a dynamic membrane. Over 480 days, volatile fatty acids (VFAs) were effectively separated by the dynamic membrane and immediately absorbed by granules, simulating natural ruminant acid absorption. Despite increasing the organic loading rate from 3.27 to 8.18 g-VS/L/day, stable VFA yields of 0.21-0.24 g-COD/g-VS were maintained. After 440 days, removal efficiencies for cellulose, hemicellulose, and lignin reached 62.7 %, 52.1 %, and 40.7 %, respectively. The acid absorption unit efficiently converted VFAs into biomethane (302-304 mL/g COD), showing high bioenergy potential. Metagenomic analysis confirmed key rumen microbes (Firmicutes, Bacteroidetes) were dominant, with enrichment of low-abundance species like Prevotella and Solobacterium that secreted lignocellulose-degrading enzymes. The system enables long-term biomass conversion and supports future high-load artificial rumen engineering.},
}

@article {pmid41619990,
year = {2026},
author = {Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Qin, Y and Liu, S and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H},
title = {Antimicrobial Resistance and Genomic Characterization of Escherichia coli Isolated from Mink in Northern China.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108328},
doi = {10.1016/j.micpath.2026.108328},
pmid = {41619990},
issn = {1096-1208},
abstract = {Escherichia coli (E. coli) is one of the most common commensal bacteria in the intestinal tract of humans and animals. It serves as a major reservoir of antimicrobial resistance genes and may facilitate their horizontal transfer among different hosts. In this study, 212 fecal samples were collected from mink across four northern provinces of China, a total of 110 E. coli isolates were recovered (isolation rate, 51.89%). Preliminary antimicrobial screening was conducted using four clinically critical antibiotics, including ceftazidime (CAZ), polymyxin B (PMB), meropenem (MEM), and tigecycline (TGC), with CAZ resistance being the most prevalent, followed by PMB, MEM, and TGC. Further antimicrobial susceptibility testing against ten commonly used antibiotics in 49 representative isolates revealed universal multidrug resistance (MDR), including 100% resistance to imipenem, tetracycline, enrofloxacin, florfenicol, and sulfamethoxazole. Genetic screening identified multiple resistance genes such as aac(3')-IIa, blaCTX-M, tet(A), and mcr-1. Conjugation assays demonstrated that CAZ resistance was the most transferable. Virulence profiling revealed a low prevalence of classical pathogenic virulence factors, with only six virulence gene types detected, consistent with the results of Galleria mellonella infection assays. Whole-genome sequencing of 41 representative isolates revealed 87 unique antibiotic resistance genes (ARGs) types spanning 14 antibiotic classes including alinically important determinants such as blaCTX-M, tet, and mcr, and 71 unique virulence genes assigned to 65 functions. Metagenomic analysis further identified diverse ARGs within the mink gut microbiota, with 21 shared between whole-genome and metagenomic sequencing. Correlation analysis suggested co-occurrence patterns among ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs), particularly between ARGs and MGEs. Overall, mink-derived E. coli exhibited extensive MDR but limited classical pathogenic virulence, and the mink gut microbiota may represent an important reservoir and transmission hub for resistance genes in intensive farming ecosystems.},
}

@article {pmid41619833,
year = {2026},
author = {Tran, LNB and Zhuo, R and Singha, M and Sekhon, H and Yang, S and Fishbein, GA and Tymchuk, C and Allyn, PR},
title = {First Reported Case of Capnocytophaga cynodegmi Infective Endocarditis: A Diagnostic Odyssey.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108446},
doi = {10.1016/j.ijid.2026.108446},
pmid = {41619833},
issn = {1878-3511},
abstract = {Capnocytophaga cynodegmi, a commensal of canine and feline oral flora, is rarely implicated in human infections, with most cases limited to localized soft tissue infections. We present the first case of C. cynodegmi-associated infective endocarditis (IE) in a 39-year-old man with bicuspid aortic valve and alcohol use disorder. The patient presented with sepsis, aortic valve vegetations, and systemic complications, including heart failure and shock liver. Despite negative blood and valve cultures, metagenomic sequencing of plasma (Karius test) initially detected Capnocytophaga canimorsus, while targeted Next-Generation Sequencing (NGS) of explanted valve tissue confirmed C. cynodegmi (100% match). The patient underwent valve replacement and completed a 6-week course of ampicillin-sulbactam with clinical recovery. This case underscores the diagnostic challenges of fastidious pathogens and demonstrates the potential of C. cynodegmi to cause life-threatening IE. It highlights the necessity of advanced molecular diagnostics, such as NGS, in atypical cases of IE. Clinicians should consider zoonotic Capnocytophaga spp. in culture-negative IE, particularly in high-risk patients with animal exposure or valvular abnormalities.},
}

@article {pmid41619830,
year = {2026},
author = {Zheng, C and Zhang, Y and Wang, Y and Sun, Y and Wei, F and Zhang, Y and Ma, Y and Cai, M},
title = {Two-case cluster of rapidly progressive influenza B and Staphylococcus aureus pneumonia with one death.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108442},
doi = {10.1016/j.ijid.2026.108442},
pmid = {41619830},
issn = {1878-3511},
abstract = {The synergistic interaction between Panton-Valentine leukocidin (PVL)-positive methicillin-susceptible Staphylococcus aureus (MSSA) and influenza virus can cause fulminant necrotizing pneumonia. We report a cluster of two cases involving epidemiologically linked construction workers illustrating this life-threatening synergy. After shared occupational exposure, one patient died of rapidly progressive pneumonia, while the other survived after prolonged intensive care. As conventional diagnostics failed, metagenomic next-generation sequencing (mNGS) of sputum and bronchoalveolar lavage fluid (BALF) identified co-infection with PVL-positive sequence type 22 (ST22) MSSA and influenza B virus (IBV) in case 2, guiding a successful shift to targeted therapy. This report demonstrates the extreme virulence of PVL-positive MSSA-influenza co-infection, highlights the diagnostic value of mNGS in severe treatment-refractory pneumonia, and emphasizes the need for effective respiratory protection in high-risk occupational environments.},
}

@article {pmid41619556,
year = {2026},
author = {Xiao, Y and Ke, C and Wang, D and Chen, N and Chen, G and Qu, L and Liu, Y},
title = {Atractyloside-A ameliorates spleen deficiency diarrhea in mice via modulating Lactobacillus johnsonii-butyric acid-GPR43 axis and NF-κB -NLRP3 signaling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {152},
number = {},
pages = {157875},
doi = {10.1016/j.phymed.2026.157875},
pmid = {41619556},
issn = {1618-095X},
abstract = {BACKGROUND: Spleen deficiency diarrhea (SDD) is regarded as a common gastrointestinal dysfunction in Traditional Chinese Medicine (TCM), which may lead to intestinal barrier damage and trigger intestinal inflammation. Previous studies have shown that Atractylenolide-A (AA) can effectively treat SDD by regulating intestinal flora. However, it remains uncertain whether AA can increase the levels of short-chain fatty acids (SCFAs) by restoring intestinal microbiota, thereby activating specific signaling pathways to regulate target protein and subsequently alleviate issues related to intestinal barrier function and inflammation.

PURPOSE: This study focused on examining the function of the signaling pathway involving microbiota, SCFAs, and G protein-coupled receptors (GPRs) in the anti-SDD effects of AA.

METHODS: The effects of AA on the Senna (SE) - induced SDD mouse model were assessed through various methods, including diarrhea scoring, H&E staining, qRT-PCR, and ELISA analysis. Subsequently, targeted metabolomics was employed to pinpoint essential metabolites that influence the intestinal microenvironment, while western blotting was utilized to measure the expression of GPRs and the NLRP3 inflammasome. Additionally, experiments involving dietary supplementation with SCFAs and AAV-shGPR43 were performed to determine whether the pharmacological effects of AA operate through SCFAs and rely on GPR43. Key bacterial species that play a role in AA's modulation of SCFAs' pharmacological effects were identified through metagenomic sequencing and single-strain experiments.

RESULTS: The findings of this research revealed that AA is capable of significantly reducing the intestinal inflammatory response, reversing damage to mucin synthesis, and alleviating the pathological symptoms linked to SDD. Furthermore, the use of Lactobacillus johnsonii, sodium butyrate (NaB), and SCFAs individually can lead to notable enhancements in various phenotypes related to SDD. In terms of mechanism, AA achieves its anti-SDD effects by elevating the levels of Lactobacillus johnsonii, facilitating the concentration of butyric acid, boosting GPR43 expression, and modulating the TLR4/NF-κB signaling pathway, which in turn inhibits the assembly of the NLRP3 inflammasome. Nonetheless, following the injection of AAV-shGPR43, the advantageous effects of both AA and NaB were negated, underscoring the significance of this target.

CONCLUSIONS: Gut microbiota-SCFAs-GPRs axis and NF-κB-NLRP3 pathway involve in the alleviation of diarrhea and inflammation in SDD mice intervened with AA, AA promotes the production of butyrate by influencing Lactobacillus johnsonii, stimulates GPR43, and suppresses the formation of the NLRP3 inflammasome via the regulation of the TLR4/NF-κB signaling pathway, which subsequently improves SDD in mice.},
}

@article {pmid41619541,
year = {2026},
author = {Shayo, MJ and Kuchaka, D and Beti, M and Kimu, P and Wadugu, B and Jensen, EEB and Kumburu, H and Kazyoba, P and Ali, M and , and Clausen, PTLC and Muro, F and Mmbaga, BT and Alifrangis, M and Aarestrup, FM and Sonda, T},
title = {Genomic diversity of human adenoviruses in Tanzanian children under five: Insights into F40, F41, B, and rare A18 genotypes.},
journal = {Virology},
volume = {617},
number = {},
pages = {110813},
doi = {10.1016/j.virol.2026.110813},
pmid = {41619541},
issn = {1096-0341},
abstract = {Human adenoviruses (HAdVs) are important pathogens that are associated with a wide array of clinical diseases, particularly in the pediatric population. Despite numerous reports of HAdV infections in Tanzania, there are currently no whole genome sequences from this region available in global public databases. This gap presents challenges to our efforts to understand their dissemination and evolution over time. This study employed nanopore-based metagenomic sequencing to detect and sequence the whole genomes of HAdV strains in Tanzanian infants with diarrhea. We present the first whole genome of HAdV-A18 from Africa, representing only the third worldwide. Additionally, it includes the first complete genomes of HAdV-F40, HAdV-F41, and HAdV-B3 obtained from Tanzania. In addition, this study provides information on the enteric adenovirus lineages circulating in Tanzania. These findings provide crucial genomic insights into the diversity of viruses in sub-Saharan Africa and underscore the importance of genomic surveillance to deepen our understanding of adenovirus transmission and evolution.},
}

@article {pmid41619490,
year = {2026},
author = {Deng, S and Zheng, X and Chu, H and Hong, L and Zhang, J and Yang, H and Gu, L and Pu, L},
title = {Antibiotic-free Wenchang chickens may promote blood levels of B vitamins by modulating the gut microbiota: An integrated analysis of cecal content metagenomics and serum metabolomics.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106506},
doi = {10.1016/j.psj.2026.106506},
pmid = {41619490},
issn = {1525-3171},
abstract = {Through the selective breeding of superior strains, livestock and poultry can achieve enhanced disease resistance and production performance, thereby improving farming efficiency and increasing chicken meat yield. This study analyzed the expression of gut health-related genes, cecal microbiota, and untargeted serum metabolomics in Wenchang chickens from the NS strain (Normal strain) and the AFS strain (Antibiotic-free strain), and explored the relationships between their cecal microbiota and serum metabolites. Our results show that in the ileum, antioxidant-related indicators T-AOC (P < 0.05), T-SOD (P < 0.05), and GSH-PX (P < 0.05) were significantly higher in the AFS strain than in the NS strain, while MDA (P < 0.05) was significantly lower in the AFS strain than in the NS strain. The mRNA expression level of RORγt/FoxP3, which is related to immune regulation, was significantly lower in the AFS strain than in the NS strain (P < 0.05). The differential microorganisms in the cecum primarily included Muribaculum, Cryptobacteroides, Blautia, Enterocloster, Lachnoclostridium, Hydrogenoanaerobacterium, Ruminococcus, Subdoligranulum, Clostridioides, and Evtepia. The main differential metabolites in serum included folinic acid, biotin, lysophosphatidic acid (LPA), 3-hydroxy-3-methylbutanoic acid, 3-hydroxybutyric acid, and others. The differential metabolites are primarily enriched in the following metabolic pathways: gap junction, glycolipid metabolism, and fatty acid biosynthesis. In addition, the Pearson correlation analysis between the gut microbiota and serum metabolites showed that Blautia was positively correlated with folinic acid (P < 0.05) and biotin (P < 0.05); Lachnoclostridium was positively correlated with biotin (P < 0.01); and Ruminococcus was positively correlated with 3-hydroxybutyric acid (P < 0.05). This study mainly elucidates the metabolic characteristics of the antibiotic-free Wenchang chicken strain by analyzing gut microbiota and serum metabolites.},
}

@article {pmid41619482,
year = {2026},
author = {Wang, M and Ye, X and Hsu, CY and Fugate, H and Zhang, X and Adhikari, PA and Fan, P and Elliott, K and Macklin, K and Zhang, L},
title = {Application of culturomics to explore the cultivable microbiota and enable targeted bacterial isolation from the ceca of broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106527},
doi = {10.1016/j.psj.2026.106527},
pmid = {41619482},
issn = {1525-3171},
abstract = {Metagenomic analyses have significantly advanced our understanding of microbial composition in the poultry gut. However, many microbes identified through metagenomic studies remain uncultured, largely due to the lack of understanding of their cultivation conditions, which hinders efforts to explore their functional roles in gut health and metabolism. In this study, we performed culturomics, a culture-dependent approach that combines diverse culture conditions with high-throughput 16S rRNA gene sequencing, to comprehensively assess the cultivability of chicken cecal microbiota and provide guidance for isolating target species of interest. Microbial profiling was performed using both culture-dependent (CD) and culture-independent (CI) approaches. For CI, genomic DNA (gDNA) was directly extracted from six broiler chicken cecal samples and subjected to full-length 16S rRNA gene sequencing. For CD, the same samples were cultured under 28 conditions, yielding 161 colony mixtures for sequencing. Based on diversity profiles of the colony mixtures, 10 conditions were selected for single-colony isolation and analysis. Results showed that CD and CI approaches identified 350 and 502 bacterial species, respectively, with 160 species detected by both methods. The dominant species recovered by the CD approach,including Escherichia coli, Proteus mirabilis, Limosilactobacillus reuteri, Enterococcus faecalis, and Ligilactobacillus salivarius, were detected at much lower abundances in the CI analysis, highlighting the capacity of culturomics to enrich and recover minority taxa that are often poorly detected by CI apparoach. Cultivation profiling showed that MRS selectively enriched Limosilactobacillus and Ligilactobacillus as well as Lactobacillus, whereas CNAB and MSA enriched Enterococcus and Bacillus, respectively. Community diversity and structure were significantly influenced by culture conditions (P < 0.01), with medium as the primary factor and air condition as a secondary factor. Subsequent single-colony analysis from 10 selected culture conditions identified 150 single-species isolates belonging to 14 distinct bacterial species. This study provides foundational insight into the cultivability of chicken cecal microbiota, facilitating future research to isolate specific strains and characterize their roles in poultry health and nutrition.},
}

@article {pmid41619464,
year = {2026},
author = {Umunnawuike, C and Abutu, D and Nwaichi, PI and Nyah, F and Agi, A},
title = {Thermophilic biohydrogen production from reservoir residual hydrocarbons using palm oil mill effluent-derived microbial consortia.},
journal = {The Science of the total environment},
volume = {1016},
number = {},
pages = {181482},
doi = {10.1016/j.scitotenv.2026.181482},
pmid = {41619464},
issn = {1879-1026},
abstract = {Residual crude oil remaining in depleted reservoirs represents a largely untapped carbon source for biological hydrogen generation. Previous studies have relied on indigenous bacteria present in oil reservoirs but reported low hydrogen yields, as not all reservoir microorganisms are hydrogen-producing. Therefore, in this study, external mixed culture bacterial consortia obtained from palm oil mill effluent (POME) were used to degrade crude oil for hydrogen production. Morphological changes in microbial communities were assessed using field emission scanning electron microscopy. Metagenomic profiling was conducted to identify the dominant microbial taxa capable of producing biohydrogen. Thereafter, a high-temperature and high-pressure (800 °C/30 MPa) stainless-steel bioreactor containing crude oil was inoculated with mixed culture consortia to simulate an oilfield reservoir for hydrogen production. Box-Behnken design was applied to systematically examine the effects of exposure time (6-90 h), crude oil volume (10-40 mL), and temperature (35-70 °C) on continuous hydrogen production. Statistical analysis of variance was used to evaluate model parameters. Heat pretreatment selectively enriched hydrogenogenic spore-formers (Clostridium and Bacillus), resulting in a ~ 4-fold increase (97.40 ± 0.02 mL/L) in hydrogen yield compared to 25.68 ± 0.04 mL/L POME for untreated sludge. In the presence of crude oil, the optimum hydrogen production was 152.50 ± 0.01 mL/L at 50 °C, compared to 125.45 ± 0.03 mL/L and 29.95 ± 0.01 mL/L crude oil at 35 °C and 70 °C, respectively. Predicted hydrogen production, with R[2] value of 97.4% close to unity, indicates that the model was highly consistent with the experimental results, with high precision and reliability. Thermodynamic analysis shows negative Gibbs free energy changes of -122 to -236 kJ/mol, demonstrating that hydrocarbon-to‑hydrogen conversion was energetically favorable and feasible across all tested temperatures. Overall, the experimental, statistical, and thermodynamic analyses establish the technical and energetic feasibility of microbial enhanced hydrogen recovery in depleted oil reservoirs.},
}

@article {pmid41619271,
year = {2026},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Functional Pathways of the Gut Microbiome Associated with SCFA Profiles in Preclinical Alzheimer's Disease.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.1539},
pmid = {41619271},
issn = {2152-5250},
abstract = {Functional activities of the gut microbiome, particularly those contributing to short-chain fatty acid (SCFA) metabolism, play a central role in host-microbe interactions and are linked to neuroinflammatory mechanisms underlying Alzheimer's disease (AD). How microbial metabolic functions relate to SCFA concentrations and cerebral amyloid-β (Aβ) burden during the preclinical stage of AD remains poorly understood. In this study, faecal metagenomes from 87 cognitively unimpaired adults were profiled using HUMAnN3 to generate MetaCyc pathway abundance data, normalised and filtered to retain pathways present in at least 30% of participants. A keyword-based search identified 362 SCFA-related pathways spanning acetate, propionate, butyrate, isobutyrate, valerate and isovalerate metabolism. Associations between microbial functions, SCFA concentrations and Aβ status were evaluated using Spearman correlations, Kruskal-Wallis tests across SCFA quartiles, and multivariable linear regression with false discovery rate correction, supported by canonical correspondence analysis and network modelling. A total of 38 significant SCFA pathway correlations were identified. Acetate, butyrate and total SCFA levels showed positive associations with biosynthetic pathways, including L-arginine biosynthesis II, peptidoglycan biosynthesis and flavin biosynthesis, whereas fermentative pathways such as pyruvate fermentation to acetone and lysine fermentation to butanoate were negatively correlated. Butyrate quartiles demonstrated dose-dependent increases in biosynthetic functions and declines in fermentative routes. Canonical Correspondence Analysis (CCA) confirmed a significant multivariate association, and network analysis revealed enhanced fermentative and methanogenic connectivity among Aβ High participants. These findings indicate that amyloid burden is associated with a shift from anabolic to fermentative microbial metabolism and may inform future studies examining potential mechanistic links in preclinical AD.},
}

@article {pmid41619244,
year = {2025},
author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS},
title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.},
journal = {Tropical biomedicine},
volume = {42},
number = {4},
pages = {435-445},
doi = {10.47665/tb.42.4.010},
pmid = {41619244},
issn = {2521-9855},
mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/classification ; Animals ; *Microbiota ; Male ; *Lice Infestations/epidemiology/parasitology ; Female ; Child ; Child, Preschool ; *Genetic Variation ; RNA, Ribosomal, 16S/genetics ; Vulnerable Populations ; Infant ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.},
}

Humans
Malaysia/epidemiology
*Pediculus/genetics/classification
Animals
*Microbiota
Male
*Lice Infestations/epidemiology/parasitology
Female
Child
Child, Preschool
*Genetic Variation
RNA, Ribosomal, 16S/genetics
Vulnerable Populations
Infant
Bacteria/classification/genetics/isolation & purification

@article {pmid41619209,
year = {2026},
author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z},
title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116930},
doi = {10.1016/j.celrep.2026.116930},
pmid = {41619209},
issn = {2211-1247},
abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units). Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.},
}

@article {pmid41618858,
year = {2026},
author = {Yang, T and Gao, Z and Huang, H and Zhang, C and Tang, Y and Qu, Q and Li, H and Ke, J and Chen, Z and Feng, M and Zhou, H and Shu, Y and Yuan, W},
title = {Gut-Metabolome-Proteome Interactions in Age-Related Hearing Loss: Insights from Fecal Microbiota Transplantation and Multi-Omics Analyses.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e14269},
doi = {10.1002/advs.202514269},
pmid = {41618858},
issn = {2198-3844},
support = {81873702//National Natural Science Foundation of China/ ; 81470694//National Natural Science Foundation of China/ ; 82225014//National Natural Science Foundation of China/ ; 82171114//National Natural Science Foundation of China/ ; 2024NF008//National Clinical Research Center for Otolaryngologic Diseases/ ; CSTB2023TIAD-KPX0059//Chongqing Technology Innovation and Application Development Special Project/ ; 2022DBXM006//Major Programs of Chongqing Science and Health Union/ ; cstc2022ycjh-bgzxm0126//Chongqing Talent Project/ ; CSTB2022NSCQ-MSX0553//Chongqing Natural Science Foundation/ ; },
abstract = {Age-related hearing loss (ARHL) is a prevalent sensory disorder lacking disease-modifying interventions. The biological drivers, particularly the contribution of the gut microbiota and gut-inner ear crosstalk, remain poorly defined. Here, we utilize germ-free (GF) mice and fecal microbiota transplantation (FMT) to isolate microbiota-dependent effects on ARHL progression. Through integrated metagenomic, metabolomic, and proteomic profiling, we map molecular signatures of auditory aging and uncover functional gut-inner ear network, prioritizing 5-hydroxytryptophan (5-HTP) as a key intermediate metabolite within this network. Furthermore, in an aging-like House Ear Institute-Organ of Corti 1 (HEI-OC1) model, 5-HTP exhibits protective effects, potentially mediated through the PI3K/Akt-antioxidant signaling axis. Collectively, this study provides a valuable multi-omics resource and highlights microbiota-derived metabolic regulation as a promising avenue for biomarker discovery and therapeutic development in ARHL.},
}

@article {pmid41618766,
year = {2026},
author = {Yan, Y and Li, F and Huang, T and Cheng, Y and Liao, Y and Liu, H},
title = {Intraocular infection of Moraxella nonliquefaciens accompanied by secondary angle-closure glaucoma: A case report.},
journal = {The Journal of international medical research},
volume = {54},
number = {1},
pages = {3000605251411736},
doi = {10.1177/03000605251411736},
pmid = {41618766},
issn = {1473-2300},
mesh = {Humans ; *Glaucoma, Angle-Closure/microbiology/etiology/diagnosis ; *Moraxellaceae Infections/microbiology/complications/drug therapy/diagnosis ; *Moraxella/isolation & purification ; *Endophthalmitis/microbiology/complications ; Trabeculectomy/adverse effects ; Anti-Bacterial Agents/therapeutic use ; *Eye Infections, Bacterial/microbiology/complications ; Male ; Female ; Aged ; Vitrectomy ; Vancomycin/therapeutic use/administration & dosage ; },
abstract = {Infectious endophthalmitis after ocular surgery is a rare complication that can result in severe vision loss. Moraxella nonliquefaciens is an opportunistic pathogen that rarely causes ocular infections. We report a rare case of Moraxella nonliquefaciens endophthalmitis complicated by secondary angle-closure glaucoma occurring years after trabeculectomy and cataract surgery. Cycloplegia resulted in deepening of the anterior chamber and opening of the angles. Metagenomic next-generation sequencing of the aqueous humor identified Moraxella nonliquefaciens. Following multiple intravitreal vancomycin injections and vitrectomy with posterior capsulectomy, direct communication between the anterior chamber and the vitreous cavity was established, leading to resolution of the condition. The patient's visual acuity was fully restored. We hypothesize that persistent infection with Moraxella nonliquefaciens may damage the lens zonules, resulting in zonular laxity and weakness; however, this represents only one possible mechanistic explanation and may play a secondary role in the development of secondary angle-closure glaucoma. Ophthalmologists should be aware that patients with Moraxella nonliquefaciens endophthalmitis may be at risk of zonular laxity and secondary angle-closure glaucoma, particularly years after trabeculectomy and cataract surgery. Prompt recognition and intervention may be vision-saving.},
}

Humans
*Glaucoma, Angle-Closure/microbiology/etiology/diagnosis
*Moraxellaceae Infections/microbiology/complications/drug therapy/diagnosis
*Moraxella/isolation & purification
*Endophthalmitis/microbiology/complications
Trabeculectomy/adverse effects
Anti-Bacterial Agents/therapeutic use
*Eye Infections, Bacterial/microbiology/complications
Male
Female
Aged
Vitrectomy
Vancomycin/therapeutic use/administration & dosage

@article {pmid41618437,
year = {2026},
author = {Chong-Nguyen, C and Artiles, RF and Pilgrim, T and Yilmaz, B and Döring, Y},
title = {The gut-heart axis in coronary artery disease: a scoping and narrative review of sex-based microbial and metabolic disparities.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00824-w},
pmid = {41618437},
issn = {2042-6410},
abstract = {BACKGROUND: The gut microbiota significantly influences cardiovascular health by regulating host metabolism and generating bioactive compounds like trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), both linked to coronary artery disease (CAD). Emerging research indicates sex-based differences in microbial composition and metabolite production, yet their impact on CAD pathophysiology remains unclear. This scoping review summarizes current findings on sex-specific microbial and metabolic differences in individuals with CAD.

METHODS: A systematic search of PubMed and EMBASE was conducted through March 2025 for peer-reviewed studies comparing gut microbiota or metabolite profiles between male and female patients with CAD. Eligible studies used 16S rRNA sequencing, shotgun metagenomics, or metabolite profiling to analyze microbial communities and atherosclerosis-associated metabolites. Mechanistic links from genetics, epigenetics, and hormone-microbiota interactions were integrated to provide a more comprehensive understanding of how gut microbiota may contribute to sex differences in CAD.

RESULTS: Eleven studies met the inclusion criteria for this review. Men with CAD exhibited increased relative abundances of taxa such as Prevotella, Clostridia_UCG_014, UCG_010, and other pro-inflammatory genera, whereas women microbiota was comparatively enriched in Barnesiella, Bifidobacteriales, and other potentially beneficial taxa. Parallel differences emerged in microbial metabolite profiles: men demonstrated elevated plasma levels of TMAO and IS, both associated with heightened cardiovascular risk and disease burden. Conversely, women with CAD had higher circulating levels of secondary bile acids and lower TMAO concentrations.

CONCLUSION: Preliminary studies suggest sex-related differences in gut microbiota composition and metabolite profiles in CAD patients. Integrating mechanistic links from microbial metabolism, genetics, epigenetics, and hormones supports a potential role of the microbiota in sex-dependent disease pathways. Current evidence is limited and mostly observational; well-designed studies are needed to clarify mechanisms, clinical relevance of sex-specific microbiome signatures and specifically assess whether these sex-specific microbial and metabolic differences influence CAD progression and outcomes.},
}

@article {pmid41618433,
year = {2026},
author = {Wang, Y and Zuo, W and Huang, J and Sun, F and Du, Y},
title = {Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03970-x},
pmid = {41618433},
issn = {1474-760X},
support = {EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; },
abstract = {BACKGROUND: Metagenomics combined with High-throughput Chromosome Conformation Capture (Hi-C) provides a powerful approach to study microbial communities by linking genomic content with spatial interactions. Hi-C complements shotgun sequencing by revealing taxonomic composition, functional interactions, and genomic organization within a single sample. However, aligning Hi-C reads to metagenomic contigs is challenging due to variable insert sizes of Hi-C paired-end reads, multi-species complexity, and gaps in assemblies. Although several benchmark studies have evaluated general alignment tools and Hi-C data alignment, none have specifically focused on metagenomic Hi-C data.

RESULTS: We evaluated seven alignment strategies commonly used in Hi-C analyses: BWA MEM -5SP, BWA MEM default, BWA aln default, Bowtie2 default, Bowtie2 -very-sensitive-local, Minimap2 default, and Chromap Hi-C default. We benchmarked these tools on one synthetic dataset and seven real-world environments. Performance was assessed based on the number of inter-contig Hi-C read pairs and their impact on downstream tasks, such as binning quality.

CONCLUSIONS: We show that BWA MEM -5SPgenerally outperformed all other tools across most environments in terms of inter-contig read pairs and binning quality, followed by BWA MEM default. Chromap and Minimap2, while less effective in these metrics, demonstrated the highest computational efficiency.},
}

@article {pmid41618383,
year = {2026},
author = {Pérez-Pérez, L and Arguello, H and Cobo-Díaz, JF and Galisteo, C and Puente, H and Gómez-Martínez, S and Carvajal, A},
title = {From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {25},
pmid = {41618383},
issn = {1297-9716},
support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; EDU-1868-2022//Junta de Castilla y León/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; *Swine Diseases/microbiology ; *Gram-Negative Bacterial Infections/veterinary/microbiology ; *Brachyspira hyodysenteriae/physiology ; Feces/microbiology ; Disease Susceptibility/veterinary/microbiology ; },
abstract = {Restrictions on antibiotics use have increased interest in the gut microbiota relationship to host health, particularly in enteric infections. The present field study, performed on two farms with endemic swine dysentery (SD) infection, characterises the faecal microbiota in 102 faecal samples from 13 diseased and 13 non-diseased pigs by shotgun metagenomic sequencing. The samples were collected during four samplings, which allowed us to monitor the animals before, during and after the clinical disease to investigate the role of the gut microbiota in disease outcome, assess the impact of infection on microbial composition and evaluate the microbiota evolution following recovery. Samples collected before disease demonstrated that SD susceptible pigs had lower microbial diversity, with significantly lower abundance of Treponema rectale, Prevotella spp. or Ruminiclostridium E compared with SD resistant pigs, which remained healthy. Marked alterations in microbial species composition and their functional profiles were evident during clinical disease. Brachyspira hyodysenteriae, Dysosmobacter sp. BX15, Acetivibrio ethanolgignens and Mucispirillum sp. 910586745 were significantly increased in abundance, which was associated with an increase of functions such as Bacteroides capsular polysaccharide transcription antitermination proteins or pterin carbinolamine dehydratase. No changes in the microbiota were observed after the disease when compared with non-diseased pigs, thus evidencing a restoration of the microbiota composition after therapeutic treatment and recovery. The study demonstrates that the microbiota may play a relevant role in SD disease outcome and evidences the changes that occur during clinical disease do not persist over time after pig therapeutic treatment.},
}

Animals
Swine
*Gastrointestinal Microbiome
*Swine Diseases/microbiology
*Gram-Negative Bacterial Infections/veterinary/microbiology
*Brachyspira hyodysenteriae/physiology
Feces/microbiology
Disease Susceptibility/veterinary/microbiology

@article {pmid41618136,
year = {2026},
author = {Liu, J and Elsheikha, HM and Lei, CC and Qin, SY and Liu, Y and Ni, HB and Qin, Y and Yu, HL and Su, JW and Chen, BN and Jiang, J and Sun, HT and Zhang, XX},
title = {Genome-resolved analysis of bile acid-metabolizing microbiota in Tibetan antelope (Pantholops hodgsonii).},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04750-0},
pmid = {41618136},
issn = {1471-2180},
support = {2025ZD01900110//National Science and Technology Major Project for Prevention and Control of Emerging and Re-emerging Infectious Diseases/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
}

@article {pmid41618101,
year = {2026},
author = {Park, SJ and Özdinç, BE and Coker, KG and Walsh, DM and Fox, DJ and Evans, S and Farahnik, J and Moffat, K and Boomgaarden, M and Mischley, LK},
title = {Metagenomics indicates an interplay of the microbiome and functional pathways in Parkinson's disease.},
journal = {NPJ Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41531-026-01271-5},
pmid = {41618101},
issn = {2373-8057},
abstract = {Previous studies suggest there are distinct gut microbial and functional variations in patients with Parkinson's disease (PwPD) that may reveal potential microbiome signatures or biomarkers to aid in early detection of the disease. In this case-control study, we used whole genome sequencing to compare the stool samples of 55 PwPD to 42 healthy controls (HC) from a public database (BioProject Accession PRJEB39223). For bacterial phyla, we observed a greater relative abundance in Firmicutes and Actinobacteria among PwPD, while that of Bacteroidetes was lower. For phages, PwPD had a greater relative abundance of Siphoviridae, Tectiviridae, and Podoviridae, while Microviridae was lower. Moreover, we described 10 functional pathways that most significantly differed between PwPD and HC (all P < 0.0001). In conclusion, significant differences were observed in gut bacteria, phages, and functional pathways between PwPD and HC that both support and conflict with previous case-control studies and warrant further validation.},
}

@article {pmid41617733,
year = {2026},
author = {Thangaraj, S and Sun, J},
title = {Depth Resolved Metagenomic Dataset from Surface and Deep Chlorophyll Maximum Layers in the Western Pacific Ocean.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06706-5},
pmid = {41617733},
issn = {2052-4463},
abstract = {Stratified microbial communities are central to ocean biogeochemical cycles, yet their vertical structure and functional potential remain under characterized in oligotrophic regions. We present a metagenomic dataset from surface ocean and the deep chlorophyll maximum (DCM) layers of the stratified Western Pacific Ocean, sampled at four stations spanning approximately 800 kilometres. Each of the eight samples generated over 22.9 Gb of high-quality Illumina HiSeq 2500 paired end reads (Q20 > 95%, Q30 > 90%). De novo assemblies yielded 1.3-1.9 million contigs per sample, with total assembly sizes of 948 Mb to 1.33 Gb and N50 values of 632-749 bp. Gene prediction identified ~5.26 million non-redundant genes across all samples, reflecting substantial microbial diversity and depth-specific variation. Assembly statistics, taxonomic profiles, and functional annotations of genes are included for technical validation of the dataset, demonstrating data completeness and analytical depth. This dataset offers annotated sequence data and environmental metadata suitable for benchmarking, method development, and comparative studies of marine metagenomes.},
}

@article {pmid41617724,
year = {2026},
author = {Dong, Z and Sun, MS and He, YD and Zhou, L and Xiang, W and Li, X and Huang, P and Zeng, JG},
title = {Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06624-6},
pmid = {41617724},
issn = {2052-4463},
abstract = {As symbiotic complexes formed through the association of bacteria or algae with fungi, lichens exhibit exceptional adaptability to extreme environments and function as pioneer species in rocky habitat ecological succession. The absence of high quality chromosome-level genome has constrained investigations into lichen adaptive evolution, while functional contributions of symbiotic bacterial communities remain inadequately explored. This study presents the chromosome-level genome assembly of the mycobiont Cladonia uncialis, comprising 28 chromosomes with a total size of 43.49 Mb, generated through integrated PacBio HiFi and Hi-C methodologies. We characterized the symbiotic microbiota using integrated short and long-read sequencing and constructed 31 metagenome-assembled genomes. The community was dominated by Ascomycota (41.16%), Proteobacteria (17.61%), and Bacteroidota (14.20%). Long-read sequencing significantly enhanced detection sensitivity for low-abundance taxa. This study provides essential genomic resources and comprehensive profiles of the symbiotic microbiota, enabling mechanistic exploration of adaptive evolution within lichen symbiotic systems under extreme environmental conditions.},
}

@article {pmid41617723,
year = {2026},
author = {Pratama, AA and Pérez-Carrascal, O and Sullivan, MB and Küsel, K},
title = {Diversity and ecological roles of hidden viral players in groundwater microbiomes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68914-2},
pmid = {41617723},
issn = {2041-1723},
support = {EXC 2051, Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE-SC0023307//U.S. Department of Energy (DOE)/ ; },
abstract = {Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we analyzed 1.24 terabases of metagenomic and metatranscriptomic data from seven wells in the Hainich Critical Zone Exploratory (CZE) to characterize groundwater viromes. We identified 257,252 viral operational taxonomic units (vOTUs) (≥ 5 kb), with 99% novel at order, family and genus levels against global ocean, freshwater and/or other publicly available datasets. In silico host predictions suggest that vOTUs primarily targeted Proteobacteria, Candidate Phyla Radiation (CPR) bacteria, and DPANN archaea, which reflects abundant and active groundwater microbial members. Patterns of virus-host abundance ratios, CRISPR-spacers, and prophage screening suggest the potential for multi-layer interactions involving CPR/DPANN lineages, their hosts, and viruses. Additionally, we identified 289 KEGG metabolic modules, 31.1% of which were targeted by 3378 vOTUs encoded auxiliary metabolic genes (AMGs) linked to carbon, nitrogen, and sulfur cycling. These findings provide a baseline for exploring how viruses influence microbial community dynamics, metabolic reprogramming and nutrient cycling in groundwater.},
}

@article {pmid41617710,
year = {2026},
author = {Shrestha, B and Romero, MF and Villada, JC and , and Blaby-Haas, CE and Schulz, F},
title = {Global metagenomics reveals plastid diversity and unexplored algal lineages.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68871-w},
pmid = {41617710},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.},
}

@article {pmid41617300,
year = {2026},
author = {Shah, D and Balendra, S and Petrushkin, H and Patel, A},
title = {Paediatric ocular toxocariasis with relentless progression despite negative metagenomic testing.},
journal = {The Lancet. Infectious diseases},
volume = {26},
number = {2},
pages = {e130-e131},
doi = {10.1016/S1473-3099(25)00685-1},
pmid = {41617300},
issn = {1474-4457},
}

@article {pmid41617130,
year = {2026},
author = {Wang, J and Ma, Y and Shi, X and Han, Y and Zhang, Y and Diao, Z and Li, Z and Lai, H and Meng, S and Zhang, C and Zhao, F and Qin, X and Li, J and Zhang, R},
title = {A Multicenter Evaluation of Metagenomic Sequencing for Pathogen Detection in Central Nervous System Infections.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.01.015},
pmid = {41617130},
issn = {1469-0691},
abstract = {OBJECTIVES: Metagenomic next-generation sequencing (mNGS) is a promising tool for diagnosing central nervous system (CNS) infections. However, the low-biomass nature of cerebrospinal fluid (CSF) increases susceptibility to contamination and host-background interference, potentially compromising accuracy. This study aimed to evaluate CSF mNGS performance across multiple laboratories and to identify key factors influencing detection accuracy.

METHODS: A reference panel of fifteen CSF samples was designed to evaluate CSF mNGS performance across laboratories, including three replicate samples, five serial concentration-gradient samples, three anti-interference samples with added human serum albumin or increased host nucleic acids, and three simulated clinical case samples, along with one negative sample. A total of 127 laboratories participated, which apply mNGS in clinical diagnostics or research. Each laboratory used independently developed mNGS workflow, which varied in experimental procedures, bioinformatic pipelines, and positive detection thresholds. Accuracy, repeatability, sensitivity, and anti-interference capability were systematically evaluated, and sources of erroneous results and methodological factors influencing accuracy were analyzed.

RESULTS: Overall performance across 127 laboratories was favorable (average F1-score 0.98, reflecting overall accuracy by balancing sensitivity and specificity). Most false-positive results (83.43%) were due to experimental contamination, while false negatives were mainly attributed to RNA viruses (57.14%). Methodological factors significantly affected detection, with impact varying by microbial type. Generally, pelleting impaired the detection of all microbes. Notably, microbial enrichment through DNase treatment and Kraken2 improved detection accuracy for DNA viruses, bacteria, fungi and atypical pathogens, but had little effect on RNA viruses.

CONCLUSIONS: This large-scale study underscores the need for improved contamination controls, optimized RNA virus detection, and enhancement of key wet-lab procedures to strengthen CSF mNGS reliability. These findings provide actionable insights to refine mNGS workflows and advance its clinical utility for diagnosing CNS infections.},
}

@article {pmid41617120,
year = {2026},
author = {Hu, S and Wang, X and Xu, H and Xiong, J and Gu, Y and Cao, X and Zhou, L and Fan, Y and Wang, S and Bai, X and Shi, H and Zhu, Q and Chen, L and Shi, Z},
title = {Vaginal microbiota in late pregnancy associates with the outcomes of planned induced labor: a multicenter prospective cohort study.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2026.01.026},
pmid = {41617120},
issn = {1097-6868},
abstract = {OBJECT: To explore the impact of the vaginal microbiota prior to delivery on the maternal and fetal outcomes of planned induced labor through metagenomic sequencing and genome-wide association studies (GWAS).

METHODS: From October 2022 to June 2024, a multicenter prospective cohort study of planned sequential induction of labor using cervical balloons in combination with oxytocin in five hospitals was conducted, enrolling 635 pregnant women. The clinical data throughout the entire pregnancy and labor period, as well as samples of vaginal and cervical secretions before the induction of labor were collected. Firstly, the characteristics of the vaginal microbiota in all pregnant women were analyzed through metagenomic sequencing, and then the impact of vaginal microbiota differences on the maternal and fetal outcomes of planned induced labor was studied. Subsequently, a nested case-control study was performed, based on human whole genome sequencing combined with GWAS analysis on vaginal secretion samples, to investigate the role of genetic factors in planned induced labor. Finally, vaginal microbiota transplantation (VMT) in pregnant rats was conducted to verify the effects of vaginal microbiota on the maternal and fetal outcomes of labor.

RESULTS: Among the participants, 167 delivered within 24 h, 318 delivered within 24-72 h, 50 failed induction, and 100 underwent cesarean section for miscellaneous indications. Vaginal microbiota analysis in parturients revealed that the probability of delivery within 24 hours is negatively correlated with Lactobacillus iners (L. iners) abundance, while failed induction is negatively correlated with Ralstonia mannitolilytica abundance. Cesarean section probability is positively correlated with Lactobacillus crispatus (p=0.03). Additionally, the time from balloon placement to delivery is positively correlated with L. iners (p=0.002) and negatively correlated with Lactobacillus crispatus (p=0.08, not fully significant). GWAS analysis shows that SNPs associated with adverse pregnancy outcomes are mainly concentrated on chromosomes 1, 4, 8, and 10. VMT experiments showed that pregnant rats transplanted with vaginal bacteria from women who delivered within 24 hours had the shortest delivery time, while those transplanted with vaginal bacteria from women who failed to induced labor had the longest delivery time and some experienced dystocia.

CONCLUSION: This study reveals that, in addition to genetic factors, the outcomes of planned labor induction, especially the total duration of labor and the success rate of induction, are closely related to the vaginal microbiota in women during the late stages of pregnancy. The study provides new evidence to explain the different outcomes of labor induction.},
}

@article {pmid41616776,
year = {2026},
author = {Liu, C and Sun, S and Ren, X and Geisen, S and Wang, S and Jiang, G and Xu, Y and Shen, Q and Jousset, A and Wei, Z and Xiong, W},
title = {Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.01.006},
pmid = {41616776},
issn = {1934-6069},
abstract = {Many soil protists are bacterivores, yet how protist predation reshapes bacterial metabolic interactions and functions remains poorly understood. Here, we combine global soil samples with microbial metabolic simulations, along with soil microcosm-pot validations, to investigate the influence of protists on bacterial metabolic interactions. Across 3,785 metabolic simulations spanning 757 soils, increased protists predicted higher bacterial metabolic interaction potential and cross-feeding but lower metabolic resource overlap and competition. These patterns were confirmed using an independent rhizosphere dataset and metagenomic analysis. Protist predation selected bacterial communities containing GC-rich genomes, acid-carbon-preferring taxa, and enhanced metabolite exchange. Additionally, exposing a synthetic community (SynCom) to protist predation elevated the expression of bacterial genes associated with plant growth-promoting functions. Consistently, microcosm- and pot-based experiments showed that protist addition increased bacterial cross-feeding over time and improved plant performance. Together, we establish a scalable framework to evaluate protist-driven bacterial cooperation and function to guide rational rhizosphere microbiome engineering.},
}

@article {pmid41616716,
year = {2026},
author = {Breyer, GM and Torres, MC and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Nicoloso, RDS and Dorn, M and Kich, JD and Siqueira, FM},
title = {From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms.},
journal = {Journal of environmental management},
volume = {400},
number = {},
pages = {128747},
doi = {10.1016/j.jenvman.2026.128747},
pmid = {41616716},
issn = {1095-8630},
abstract = {The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework.},
}

@article {pmid41616686,
year = {2026},
author = {Sattari Khavas, D and Schwartz, SK and Bird, P and Truong, A and Silberg, JJ},
title = {Microbial spies and bloggers: programming cells to convert environmental information into discernible signals.},
journal = {Current opinion in biotechnology},
volume = {98},
number = {},
pages = {103436},
doi = {10.1016/j.copbio.2026.103436},
pmid = {41616686},
issn = {1879-0429},
abstract = {Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. In this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.},
}

@article {pmid41616624,
year = {2026},
author = {Sun, Y and Zhang, M and Teng, Y and Yin, Y and Ran, J and Su, H and Li, H and Huang, X and Long, Z and Sun, X and Pan, H and Wang, X and Li, M},
title = {Human activities and horizontal gene transfer shape the resistome landscapes of non-human primates.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141276},
doi = {10.1016/j.jhazmat.2026.141276},
pmid = {41616624},
issn = {1873-3336},
abstract = {Antibiotic resistance represents a growing threat to human, animal, and ecosystem health, yet its dynamics in wildlife remain poorly understood. We conducted a systematic analysis of the gut resistomes in non-human primates (NHPs) and environmental soils in Guizhou Province, China, a biodiversity hotspot. Metagenomic analyses reveal that human activities and horizontal gene transfer (HGT) influence primate resistome landscapes and enhance their dissemination potential. A total of 1927 antibiotic resistance ontologies (AROs) distributed across 1477 species-level genome bins (SGBs), providing a comprehensive genomic catalog of the NHPs resistome. Bacterial genera such as Pseudomonas, Stenotrophomonas, and Comamonas drive ARG mobilization, with a core subset of ARGs that reliably predict overall resistance burdens. Notably, widely distributed primate species, with large habitat ranges and frequent interspecies interactions exhibit the most potential for ARG dissemination. Ecological modeling identifies current and future hotspot regions requiring prioritized monitoring amid ongoing human disturbance and climate change. These findings provide a molecular-indicator-based framework for environmental antibiotic resistance (AR) monitoring and conservation strategies for endangered species. Despite limitations in temporal and spatial coverage, our study highlights the need to integrate wildlife, particularly NHPs, as sentinel species into "One Health" AR surveillance and policy. This approach will strengthen our understanding of ARG transmission dynamics and their long-term impacts on host adaptation, ecosystem stability, and public health.},
}

@article {pmid41615921,
year = {2026},
author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM},
title = {Correction: Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0342098},
pmid = {41615921},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0323382.].},
}

@article {pmid41615602,
year = {2025},
author = {Fedonenko, YP and Grinev, VS and Velichko, NS and Lipatov, NN and Selivanov, NY and Kuzina, MS and Sigida, EN and Konnova, SA},
title = {Isolation and Characterization of Halophilic Bacteria of the Halomonadaceae Family, Promising Producers of Extracellular Polysaccharides.},
journal = {Doklady. Biochemistry and biophysics},
volume = {525},
number = {2},
pages = {653-658},
pmid = {41615602},
issn = {1608-3091},
mesh = {*Polysaccharides, Bacterial/biosynthesis/chemistry ; *Halomonadaceae/metabolism/isolation & purification/genetics ; },
abstract = {Exopolysaccharide (EPS) production is one of the key mechanisms of bacterial survival in hypermineralized environments. Representatives of the Halomonadaceae family are recognized as basic organisms for next-generation industrial biotechnology; however, the range of Halomonas used and information on the structural diversity of their EPSs are rather limited. The results of metagenomic analysis of salt, peloid, and soil samples from the coastal zone of salt lakes in the Volgograd region with subsequent seeding on selective mineral media made it possible to isolate bacteria of the Halomonadaceae family. For taxonomically identified strains, cultivation conditions were optimized and EPSs were obtained, the structure of which was characterized based on chemical analysis data and NMR spectroscopy. The study of the physicochemical properties of EPSs (viscosity, hygroscopicity, emulsifying activity, and antioxidant properties) showed that these polymers are promising for biotechnological applications.},
}

*Polysaccharides, Bacterial/biosynthesis/chemistry
*Halomonadaceae/metabolism/isolation & purification/genetics

@article {pmid41615149,
year = {2026},
author = {Mora-Martínez, C and Molina-Mendoza, G and Cenit, MC and Medina-Rodríguez, EM and Larroya-García, A and Sanchez-Carro, Y and Gonzalez-Blanco, L and Bobes, J and Lopez-Garcia, P and Zandio-Zorrilla, M and Lahortiga-Ramos, F and Gili, M and Garcia-Toro, M and Barcelo, B and Ibarra, O and Sanz, Y},
title = {Gut microbiome signatures associated with depression and obesity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0126325},
doi = {10.1128/msystems.01263-25},
pmid = {41615149},
issn = {2379-5077},
abstract = {UNLABELLED: Depression and obesity are highly comorbid and likely involve common risk factors and pathophysiological mechanisms, which could crosslink to gut microbiome dysfunction. Here, we performed a case-control study with a total of 105 subjects, 43 with major depressive disorder (MDD) and 62 non-depressed controls free from psychiatric comorbidities, to identify gut microbiome signatures associated with MDD and dissect its relation to body mass index (BMI) and lifestyle (diet and exercise). We performed shotgun metagenomics, followed by taxonomic and functional annotations. Using different machine learning methods, we were able to classify subjects into depressed and non-depressed controls with a balanced accuracy of 0.90 and into depressed or non-depressed and normal weight or overweight with a balanced accuracy of 0.78 based solely on taxonomic profiles. We identify novel bacterial taxa associated with depression, including reductions in Butyrivibrio hungatei and Anaerocolumna sedimenticola, and also replicate previously reported associations, such as decreased Faecalibacterium prausnitzii in patients with MDD. Functional annotation of metagenomes shows differences in pathways linked to the synthesis of fundamental nutrients, which have been associated with diet, as well as inflammation. Strikingly, we found an increase in tryptophan degradation and a decrease in queuosine synthesis pathways, both of which are directly related to a decrease in monoaminergic neurotransmitter availability. Additionally, our functional analysis shows that most of the functions that are more abundant in controls than in depressed subjects are encoded by F. prausnitzii. These findings reveal distinct microbial and functional signatures associated with depression, including taxa and pathways linked to neurotransmitter metabolism and independent of other covariates. This suggests that gut microbiome profiling could support diagnosis and the development of gut-directed depression treatments.

IMPORTANCE: This study identifies gut microbiome signatures that are predictive of major depressive disorder (MDD) and explores their links to body mass index (BMI). We uncover bacterial species and metabolic pathways that are associated with MDD, some of them related to neurotransmitter metabolism and inflammation. Among the differences identified, depletion of Faecalibacterium prausnitzii stands out as an important feature in the MDD microbiome, which suggests the possible use of this species to improve depression symptoms. Importantly, we demonstrate shared microbiome features between MDD and BMI, suggesting common underlying mechanisms. This research not only provides a framework for developing microbiome-based diagnostics but also informs future stratified interventions targeting gut microbial functions to improve mental health outcomes.},
}

@article {pmid41615027,
year = {2026},
author = {Jiménez, DJ and Marasco, R and Schultz, J and Rodríguez, CAD and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS},
title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag012},
pmid = {41615027},
issn = {1751-7370},
abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence (AI)-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.},
}

@article {pmid41614733,
year = {2025},
author = {Kim, D and Kim, WJ and Woo, HM and Jeong, H},
title = {PixelCut: A Unified Solution for Zero-Configuration 16S rRNA Trimming via Computer Vision.},
journal = {Current issues in molecular biology},
volume = {47},
number = {12},
pages = {},
pmid = {41614733},
issn = {1467-3045},
support = {ncheon National University Research Grant in 2023. 284//Incheon National University/ ; },
abstract = {16S rRNA amplicon sequencing has been an effective method for profiling microbial taxonomy in microbiome research, as it offers lower per-sample costs and higher sample throughput than shotgun metagenomics. Although 16S rRNA sequencing offers clear advantages over shotgun sequencing, it depends on precise trimming of low-quality bases at the 3' ends of reads. Given the widespread use of 16S rRNA amplicon sequencing, there is an increasing demand for analysis tools that can identify errors in the 3' region of reads and remove erroneous bases. While various algorithms for predicting trim locations are widely employed, most are command-line standalone tools, which pose challenges for users with limited computational background or resources. Furthermore, in the absence of biological or experimental priors such as amplicon size, trim position predictions may be unreliable. Here, we introduce PixelCut, a fully automated trim-position prediction framework that requires no hyperparameters or prior biological information for accurate prediction. Unlike most available algorithms that operate on raw FASTQ data, PixelCut analyzes the per-base quality report generated by FastQC to infer trimming positions. Based on the recommended quality score threshold from the quality report, PixelCut inspects the quality scores across bases and automatically determines the recommended trim position using character recognition techniques based on computer vision. We have also developed a user-friendly web application to make the method accessible to those without programming expertise, while offering a command-line version for advanced users. Through comprehensive computer simulations, we show that PixelCut produces taxonomic profiling results that are consistent with those from popular trim-location prediction algorithms.},
}

@article {pmid41614172,
year = {2026},
author = {Li, Y and Wang, J and Zhang, Z and Zhang, Y and Müller, R and Huo, L},
title = {Deep-Sea Genome Mining Reveals Cooperative ATP-Grasp Ligase-Directed Biosynthesis of Pentacyclic Myxomiditides with Potent Protease Inhibition.},
journal = {JACS Au},
volume = {6},
number = {1},
pages = {607-620},
pmid = {41614172},
issn = {2691-3704},
abstract = {Microviridins are ribosomally synthesized and post-translationally modified peptides, typically featuring a conserved tricyclic structure formed by two ATP-grasp ligases. However, the diversity and evolution of these enzymes remain incompletely understood. Here, we identify a distinct ATP-grasp ligase subclade (MyxF) that specifically modifies the conserved (KxxE)n motif, defining a new subclass of microviridins with the (KxxE)nTxKxPSDx-(D/E)-(D/E) sequence signature. Guided by SSN analysis, we discovered a deep-sea myx biosynthetic gene cluster from 10,000 m sediments and heterologously expressed two pentacyclic microviridin-like peptides, Myxomiditide A and B. Using mass spectrometry and NMR, we fully elucidated their chemical structures, revealing not only the conserved tricyclic core but also two additional N-terminal lactam rings within the KxxEKxxE motif, distinguishing them from known microviridins. Combined in vivo coexpression and in vitro reconstitution uncovered a noncanonical division of labor among four ATP-grasp ligases involved in myxomiditide biosynthesis. MyxF and MyxD1 act as functional isozymes responsible for installation of the N-terminal lactam moieties, whereas MyxD2(?)catalytically inactive on its own(?)requires the synergistic presence of both MyxF and MyxD1 to enable formation of the C-terminal lactone rings. The pathway is finalized by MyxC, which catalyzes the terminal lactam macrocyclization, collectively revealing a highly cooperative enzymatic assembly mechanism governing myxomiditide maturation. Furthermore, MyxF exhibited remarkable catalytic plasticity, catalyzing multiple lactam macrocyclizations beyond its native substrate architecture. Notably, Myxomiditide A potently inhibited elastase with nanomolar IC50 values. Collectively, this study expands the enzymatic landscape of ATP-grasp ligases and highlights the deep sea as a rich source of evolutionary innovation in RiPP biosynthesis.},
}

@article {pmid41614136,
year = {2025},
author = {Zhao, S and Wang, X and Zhu, H and Guo, G and Mustafa, GR and Mustafa, A and Chen, Y and Li, X and Wang, Y and Zhao, B},
title = {Metagenomic analysis revealed the distribution of antibiotic resistance genes of Awang sheep (Ovis aries) gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1740198},
pmid = {41614136},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) in livestock is a major contributor to the global AMR crisis, yet little is known about its dynamics in high-altitude pastoral systems. We performed deep metagenomic sequencing of 100 fecal samples from Tibetan Awang sheep reared under grazing (aw_fm) and captive (aw_qs) conditions. Microbiome profiling revealed striking community shifts: grazing sheep were enriched in Bacteroidetes and Firmicutes, whereas captive sheep showed expansion of Proteobacteria, particularly Acinetobacter, suggesting dysbiosis. The resistome comprised 302 unique ARGs, dominated by rpoB2 (43.3%), Bifidobacterium_adolescentis_rpoB (11.2%), and ugd (10.2%). Grazing sheep carried ARGs mainly against rifamycins and peptide antibiotics, reflecting natural selective pressures, while captive sheep exhibited significantly broader resistance, including tetracyclines, macrolides, and fluoroquinolones (p < 0.05). Enrichment of efflux pump genes (MexK, adeJ) in captive sheep highlighted a shift toward multidrug resistance. These findings demonstrate that rearing practices profoundly restructure the gut resistome, underscoring the need for targeted antibiotic stewardship in high-altitude livestock systems.},
}

@article {pmid41614128,
year = {2025},
author = {Wang, J and Bai, C and Tian, Y and Bao, J and Liu, J},
title = {Intercropping reshapes soil stress resistance and growth promotion capabilities through rhizosphere exudates in conjunction with the microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1708938},
pmid = {41614128},
issn = {1664-302X},
abstract = {Terrestrial plants can affect the growth and health of neighboring plants through interspecific interactions. Long-term monoculture in agricultural and pastoral production can lead to the occurrence of soil-borne diseases, depletion of nutrients, and a decline in soil microbial diversity, thereby affecting the sustainable development of cultivated ecosystems. In this study, we employed three cultivation patterns: monoculture of Melilotus officinalis (L.) Pall. (M. officinalis), monoculture of Avena sativa L. (A. sativa), and intercropping of M. officinalis and A. sativa. To introduce ecologically protective plants into cultivated ecosystems and investigate the effects of plant root exudates on the recruitment of rhizosphere microbiota of neighboring plants, as well as the disease resistance and growth promotion capabilities of intercropping, we conducted non-targeted metabolomics and metagenomics analyses on root exudates and soil microbiota. The sequencing data obtained provided strong evidence for the interaction mechanisms between root exudates and microorganisms in intercropping ecosystems. We observed that in intercropping ecosystems, the abundance and variety of root exudates were more similar to those of the crop plants. The differential metabolites between intercropping and A. sativa were inclined to be chemically defensive, while those between intercropping and M. officinalis were more inclined to promote material synthesis. Compared with A. sativa, intercropping enhances the alpha and beta diversity of soil microbial communities, particularly increasing the enrichment abundance in pathways such as the bacterial secretion system, sulfur metabolism, and phenylpropanoid biosynthesis, which is closely associated with the suppression of soil-borne pathogens. Compared with M. officinalis, intercropping further enhanced the synthesis of plant-available substances in the soil, driving microorganisms to optimize the levels of carbon, nitrogen, and trace elements in the soil. In comparison, intercropping had a significant impact on the aggregation of soil-specific microorganisms, which can optimize nitrogen utilization to promote plant growth and enhance plant defense and stress tolerance. The results of this study will provide a theoretical basis for cultivated ecosystems and sustainable land management.},
}

@article {pmid41614121,
year = {2025},
author = {Shi, M and Guo, A and Qin, S and Kang, Y and Zhang, W and Yang, X},
title = {Metagenomic insights into short-term legume rotation: modulating potato rhizosphere microbiota to enhance tuber yield and quality.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680056},
pmid = {41614121},
issn = {1664-302X},
abstract = {OBJECTIVE: This study aims to investigate the effects of legume crop rotation on the rhizosphere microbiota and its potential to improve potato (Solanum tuberosum L.) productivity and tuber quality. We specifically focus on the microbial functional potential revealed through metagenomic sequencing under different legume rotation systems in the intensive agricultural region of the Chinese Loess Plateau.

METHODS: A five-year field experiment (2018-2022) was conducted to establish three cropping systems: (1) continuous potato monocropping for 5 years (CK), (2) continuous potato cropping for 3 years followed by one-year pea rotation and one-year potato cropping (T1), and (3) continuous potato cropping for 3 years followed by one-year faba bean rotation and one-year potato cropping (T2). The impacts of these rotation regimes on potato yield formation, tuber quality, and rhizosphere microbial communities were systematically evaluated, with a focus on microbial diversity and functional potential, using metagenomic sequencing and network analysis.

RESULTS: Metagenomic analysis demonstrated that legume rotation, particularly the T2 system, significantly enriched the relative abundances of Actinobacteria (38.31%) and Proteobacteria (28.40%) in the potato rhizosphere while reducing Acidobacteria (10.03%). Functional annotation further revealed that T2 promoted the expression of microbial genes involved in carbon fixation (K00626, K01895, etc.), nitrogen assimilation (narB, narA, etc.), and sulfur metabolism (cysNC, cysN, etc.), enhanced potential for nutrient cycling. Co-occurrence networks revealed Actinobacteria and Acidobacteria as keystone taxa forming robust interaction modules potentially linked to soil ecological stability. Compared to CK, T2 increased the commercial tuber rate by 85.82%, overall tuber yield by 28.38%, starch content by 34.85%, and vitamin C content by 30.79%, while reducing sugar levels decreased by 9.35%.

CONCLUSION: Faba bean-potato rotation (T2) effectively mitigated the adverse impacts caused by continuous potato cropping by altering the rhizosphere microbial structure and enhancing microbial functional pathways related to nutrient cycling. This study provides a detailed metagenomic perspective on the microbial mechanisms underlying the benefits of crop rotation and offers a theoretical basis for developing microbiome-informed ecological management strategies to mitigate continuous cropping obstacles in potato production on the Loess Plateau.},
}

@article {pmid41466185,
year = {2025},
author = {Liu, B and Shen, D and Cao, X and Hong, X and Lin, C and Guo, R and Sun, Z and Ning, C and Chen, L and Yu, Y and Li, J and Huang, G},
title = {Clinical evaluation of probe capture-based targeted next-generation sequencing in suspected infected pancreatic necrosis: a prospective pilot diagnostic study.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {215},
pmid = {41466185},
issn = {1471-2334},
support = {2023JJ30885//Natural Science Foundation of Hunan Province/ ; },
abstract = {OBJECTIVE: To evaluate the diagnostic performance of probe capture-based targeted next-generation sequencing (tNGS) in suspected infected pancreatic necrosis (IPN).

METHODS: A prospective study was conducted among patients with suspected IPN at Xiangya Hospital from December 2023 to May 2025. Blood samples were collected and sent for tNGS, metagenomic next-generation sequencing (mNGS), and culture. For patients with indications for surgical interventions, peripancreatic specimens were simultaneously collected for microbial culture during the initial surgical procedure to confirm the presence of IPN. The clinical performance of tNGS, mNGS and culture were compared.

RESULTS: In 51 patients, blood tNGS demonstrated a significantly higher positivity rate compared to blood culture (54.9% vs. 17.7%, P < 0.05), while no statistically significant difference was observed between blood tNGS and blood mNGS (54.9% vs. 51.0%, P = 0.683). tNGS demonstrated superior detection of fungi and Gram-negative bacteria. With peripancreatic culture as the reference standard, tNGS demonstrated superior sensitivity (94.7%), accuracy (81.3%), and concordance rate (78.9%) compared to conventional culture, and exhibited comparable performance to mNGS. tNGS also detected antimicrobial-resistance genes in 7 patients, with findings consistent with available phenotypic susceptibilities. Detection of virulence factors (VF) was associated with higher rates of persistent organ failure (POF) (100.0% vs. 57.1%, P = 0.009) and mortality (77.7% vs. 11.9%, P = 0.022). Firth’s bias-reduced logistic regression identified OF > 7 days as an independent predictor of tNGS positivity (OR 4.259, P = 0.040).

CONCLUSIONS: Blood tNGS demonstrated diagnostic performance comparable to mNGS in suspected IPN, with potentially greater sensitivity for fungal and Gram-negative pathogens. Its ability to detect VF may offer prognostic insights, but clinical utility requires further validation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-12441-w.},
}

@article {pmid41613591,
year = {2025},
author = {Xu, Y and Ma, Y and Huang, Q and Guo, X and Guo, L and Ren, Y and Lu, W and Wu, X and Li, D and Li, S},
title = {The role of bronchoalveolar lavage fluid metagenomic next-generation sequencing in detecting pathogens and optimising antibiotic therapy in paediatric severe community-acquired pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1688473},
pmid = {41613591},
issn = {2235-2988},
mesh = {Humans ; *Community-Acquired Infections/drug therapy/microbiology/diagnosis ; Infant ; Child, Preschool ; *High-Throughput Nucleotide Sequencing/methods ; Child ; Male ; Retrospective Studies ; Female ; *Anti-Bacterial Agents/therapeutic use ; *Metagenomics/methods ; Adolescent ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; ROC Curve ; *Pneumonia/drug therapy/microbiology/diagnosis ; Severity of Illness Index ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) remains a major cause of mortality in the paediatric population, with current diagnostic and treatment approaches often proving insufficient and contributing to the growing challenge of antibiotic resistance. This study explored the potential of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid as a tool to enhance the precision of antibiotic management in children with SCAP.

METHODS: A retrospective cohort study of 202 paediatric patients with community-acquired pneumonia (aged 1 month-18 years) admitted to the First Affiliated Hospital of Xinxiang Medical University (November 2020-March 2023) was conducted. Patients were grouped by severity (intensive care unit [ICU]/non-ICU) and mNGS timing (early: ≤72 hours post-admission; late: >72 hours). The diagnostic efficacy of mNGS versus conventional microbiological techniques (CMT) was evaluated using sensitivity, specificity, positive/negative predictive values and area under the receiver operating characteristic curve (AUC) analysis. Antibiotic adjustments and clinical outcomes were analysed via survival statistics.

RESULTS: Metagenomic next-generation sequencing showed a higher positive detection rate (98.51%) than CMT (47.52%) (AUC = 0.82, 95%CI: 0.76-0.88). Of the 202 patients, 127 (62.87%) were male, with a median age of 1.88 years (interquartile range: 0.29-7 years). Early mNGS was associated with fewer extrapulmonary complications (69.63% vs 55.22% in the late group, p < 0.05), and shorter hospitalisation (median 13 vs 15 days, p <0.01). Antibiotic escalation occurred in 50 (24.75%) cases, de-escalation in 22 (10.89%) and same-level adjustment in 25 (12.38%).

CONCLUSION: Metagenomic next-generation sequencing outperforms CMT in pathogen detection. Early mNGS is associated with improved clinical outcomes, suggesting its potential utility in paediatric SCAP management.},
}

Humans
*Community-Acquired Infections/drug therapy/microbiology/diagnosis
Infant
Child, Preschool
*High-Throughput Nucleotide Sequencing/methods
Child
Male
Retrospective Studies
Female
*Anti-Bacterial Agents/therapeutic use
*Metagenomics/methods
Adolescent
*Bronchoalveolar Lavage Fluid/microbiology/virology
*Bacteria/genetics/isolation & purification/classification
Sensitivity and Specificity
ROC Curve
*Pneumonia/drug therapy/microbiology/diagnosis
Severity of Illness Index
Community-Acquired Pneumonia

@article {pmid41613303,
year = {2025},
author = {Huang, J and Lan, C and Liang, Y and Chen, H and Liang, H and He, H and Che, S and Chen, Y},
title = {Case Report: Metagenomic next-generation sequencing diagnosed a rare case of sternal tuberculosis mimicking a malignant tumour.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1708834},
pmid = {41613303},
issn = {2296-858X},
abstract = {This is a case report of a 17-year-old female patient who presented with a painless, palpable swelling on the anterior chest wall. Imaging studies revealed osteolytic lesions involving the manubrium and adjacent ribs, along with multiple enlarged lymph nodes, raising a high suspicion of malignant tumour with metastasis. An ultrasound-guided needle biopsy revealed the pathological finding of "granulomatous inflammation." Multidisciplinary consultation and clinical indicators, including a strongly positive purified protein derivative (PPD) test and markedly elevated erythrocyte sedimentation rate, were taken to indicate a potential diagnosis of tuberculosis. Consequently, subsequent metagenomic next-generation sequencing (mNGS) of the biopsy specimen identified nucleic acid sequences belonging to the Mycobacterium tuberculosis complex, thereby confirming the rare diagnosis of sternal tuberculosis. Following the administration of standardised anti-tuberculosis therapy, a substantial reduction in the size of the lesion was observed, thereby validating the accuracy of the diagnosis. This case underscores the importance of considering extrapulmonary tuberculosis in the differential diagnosis of bone-destructive lesions and demonstrates the critical value of mNGS technology in confirming challenging infectious diseases.},
}

@article {pmid41612676,
year = {2026},
author = {Asin, J and Carvallo, F and Gonzales-Viera, OA and Macías-Rioseco, M and Streitenberger, N and Abdelrazek, S and Crossley, B and Pesavento, PA and Uzal, FA},
title = {Interstitial pneumonias of undetermined etiology in foals in California, 1990-2020.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {},
number = {},
pages = {10406387251410524},
doi = {10.1177/10406387251410524},
pmid = {41612676},
issn = {1943-4936},
abstract = {Interstitial and bronchointerstitial pneumonias of undetermined etiology in young foals are relatively common in autopsy services with an equine focus. Unknown viruses, toxins, hyperthermia, surfactant or alveolar macrophage function deficiency, certain antibiotics, and aberrant responses to Rhodococcus equi or other bacteria have been proposed as causes. We performed a retrospective study of autopsies on foals with a diagnosis of interstitial or bronchointerstitial pneumonia with an unidentified etiology. Forty-one foals (median age: 3-mo-old) were included. Most were received in summer (n = 28) and spring (n = 10). The most frequently reported clinical signs were dyspnea and/or tachypnea (n = 28) and fever (n = 19). Antibiotic treatment was reported in 21 cases, and the most frequently used antibiotics were penicillin (n = 9) and gentamicin (n = 8). Grossly, most of the lungs were diffusely rubbery-to-firm (n = 35) and did not collapse (n = 22). Histologically, combinations of exudative (E; hyaline membranes), proliferative (P; type II pneumocyte hyperplasia), and fibrotic (F; fibroplasia) phases were common (E + P, n = 15; E + P + F, n = 13) in the interstitial component. Necrosis of the bronchiolar epithelium was rare (n = 4), concurrent suppurative bronchopneumonia was common (n = 22), and a few foals (n = 5) had pulmonary pyogranulomas. Pneumocystis spp. organisms were observed in 8 cases using Grocott-Gomori methenamine silver stain. Bacteria were recovered from the lungs in 22 cases, with R. equi (n = 7) and E. coli (n = 6) being the most common isolates. No unequivocal viral causes were identified during the regular diagnostic work-up and after using novel diagnostic approaches such as herpesvirus consensus PCR and viral metagenomics in a subset of the cases.},
}

@article {pmid41612514,
year = {2026},
author = {Enagbonma, BJ and Pierneef, RE and Modise, DM and Babalola, OO},
title = {Effects of legume-based rotation on subsequent sorghum rhizosphere microbial communities and their drought tolerance-related genes.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00829-9},
pmid = {41612514},
issn = {2524-6372},
support = {CRP/ZAF22-03//ICGEB/ ; },
abstract = {INTRODUCTION: The impacts of incorporating legumes into cereal crops on soil microbial structure, composition, functional genes involved in nitrogen, carbon and phosphorus cycling, signaling pathways and hydraulic conductivity adaptations have been well studied. However, the same cannot be said for functional genes that increase drought tolerance.

OBJECTIVES: Here, we examined the changes in microbial community structure and functional genes involved in drought tolerance in response to legume‒cereal rotation and cereal‒cereal rotation. This study provides a preliminary, exploratory characterization of microbial community and functional gene shifts, without direct evidence of functional impact on plant physiology or productivity.

METHODS: DNA extracted from soil samples collected across cowpea-sorghum treatment (CS) or maize-sorghum treatment (MS) was sequenced via shotgun sequencing.

RESULTS: Nonmetric multidimensional scaling analysis revealed that the microbial communities in the CS treatment significantly differed from those in the MS treatment. Compared with the MS rotation, the CS rotation increased the relative abundances of Pseudomonadota, Acidobacteriota, Chloroflexota, Gemmatimonadota, Euryarchaeota, and Candidatus Bathyarchaeota and reduced the abundances of Actinomycetota, Ascomycota, and Nitrososphaerota at the phylum level. Furthermore, the CS rotation increased the abundance of microbial genera such as Solirubrobacter, Sphingomonas, Nitrosocosmicus, Nitrosotenuis Aspergillus, and Metschnikowia when related to the MS rotation. STAMP analysis revealed that in the CS rotation, genes involved in trehalose biosynthesis, biofilm formation, oxidative stress mitigation (e.g., sodA, katG), stress signaling (e.g., rpoS, ipdC), nutrient provisioning (e.g., nifH, pqqC), membrane fluidity (desA, desB), dormancy (spo0A, spoVF), and ion homeostasis (nhaB, kup) predominated. In the MS rotation, proline biosynthesis (proA, proB, and proC), glycine betaine synthesis (betA and betB), aquaporin (aqpZ), and structural integrity genes (murA and murC) were predominant. The RDA results revealed that crop rotation influenced the soil physicochemical parameters, which in turn impacted both the microbial communities and drought tolerance genes in both treatments, probably creating a favorable environment for resilience under drought.

CONCLUSION: These research findings provide insight into the relationships between cowpea cropping sequences and the soil microbiome and drought-tolerant functional genes fundamental for the productivity of successive crops and this understanding guides sustainable crop selection.},
}

@article {pmid41612472,
year = {2026},
author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y},
title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-026-03892-1},
pmid = {41612472},
issn = {2047-783X},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; },
abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.

METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n = 196) and non-severe (n = 110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.

RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced α-diversity, altered β-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.

CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.},
}

@article {pmid41612232,
year = {2026},
author = {Chen, Q and Yin, Q and Chen, J and Jin, L and Guo, W and Huang, M},
title = {Comparison of the diagnostic value of targeted next-generation sequencing, metagenomic next-generation sequencing, and Xpert MTB/RIF in adult pulmonary tuberculosis.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12673-4},
pmid = {41612232},
issn = {1471-2334},
}

@article {pmid41612194,
year = {2026},
author = {Ballandras, V and McNamara, L and Carolan, JC and Pichon, A and Byrne, S},
title = {Whole genome sequencing of 18 economically important aphid pests with photographic vouchers for taxonomic validation.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-026-01406-w},
pmid = {41612194},
issn = {2730-6844},
}

@article {pmid41611865,
year = {2026},
author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR},
title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36282-y},
pmid = {41611865},
issn = {2045-2322},
abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.},
}

@article {pmid41611767,
year = {2026},
author = {Jain, AG and Agwan, D and Kumar, A and Pancha, I and Rathod, J and Mohapatra, B},
title = {Mixing regimes shape microbial community composition, nutrient regimes, and plant growth attributes in Jeevamrit: metagenomics and culturomics-based insights.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36414-4},
pmid = {41611767},
issn = {2045-2322},
support = {GSBTM/JD(R&D)/661/2022-23/00173054//GSBTM/ ; },
abstract = {Jeevamrit, a microbial inoculant widely used in zero-budget natural farming (ZBNF) that relies on local farm-based resources to enhance overall biological health of soil, is reported for inconsistent crop yield enhancements. This is mainly due to variability in its preparation methods, e.g., mixing intensity, incubation regimes, and quality of ingredients used. Hence, the current study aimed to decipher the effect of mixing intensity (extent of oxygenation) on microbial community composition, nutrient transformation, and plant growth attributes of Jeevamrit, using a combined metagenomics-culturomics approach. Frequent mixing (Constant/Intermediate) enhanced nutrient solubilization (Fe, Zn, Cu, Mn) with higher total N and dissolved organic carbon, while less mixing (Anoxic/No-mix) led to accumulation of soluble Fe and NH4[+]-N with higher microbial diversity. Mixing-driven differential enrichment of taxa were noted, i.e., constant mixing (CM) dominated by Acinetobacter (~ 40%), Comamonas, Pseudomonas, and Lysinibacillus, linked to oxidative C/N cycling and metal dissolution. Whereas, anoxic (AO) favored Clostridium sensu stricto, Lactobacillales, Enterococcus, and Enterobacterales (> 60%), correlating to fermentative metabolism-driven reductive elemental cycling. Co-occurrence network analysis identified Acinetobacter, Pseudomonas, Comamonas, Trichococcus, and Stenotrophomonas as hubs, indicating keystone functions in structuring metabolic interactions. The metagenome-recovered MAGs belonged to Acinetobacter sp., Clostridium saccharobutylicum, Trichococcus flocculiformis, and Enterococcus gallinarum with potential to participate in multiple nutrient cycling. Cultivable members of Shigella, Rhodococcus, and Bacillus spp. showed high IAA production (135-145 µg mL[-][1]), NH3 release (~ 0.12 µg mL[-][1]), and K and P solubilization (~ 55.2 µg mL[-][1]). We hypothesize that oxygenation drives the Jeevamrit's microbial guild assembly, where mixing intensity modulates oxido-reductive metabolism and nutrient mobilization efficiency, indicating the requirement for standardization of formulation aligned to soil-specific conditions.},
}

@article {pmid41611691,
year = {2026},
author = {Srivathsan, A and Arzika, AM and Maliki, R and Abdou, A and Lipsitch, M and Blumberg, S and O'Brien, KS and Porco, TC and Hinterwirth, A and Doan, T and Keenan, JD and Lietman, TM and Arnold, BF},
title = {Geographic spillover of antimicrobial resistance from mass distribution of azithromycin.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68691-y},
pmid = {41611691},
issn = {2041-1723},
abstract = {Large-scale, placebo-controlled, cluster-randomized trials in high-mortality settings in sub-Saharan Africa demonstrated a 14-18% reduction in childhood mortality following twice-annual mass drug administration (MDA) of azithromycin among children aged 1-59 months. Azithromycin MDA also selected for antimicrobial resistance (AMR), particularly macrolide resistance. It is unknown whether the AMR from azithromycin MDA could spill over to neighboring untreated populations. If present, such geographic spillover effects could lead trials to underestimate AMR risks. We assess between-village geographic spillover effects of genotypic macrolide resistance using metagenomic deep sequencing in rectal swabs collected from 300 children in 30 monitoring villages in Niger after two years of MDA in 594 surrounding villages. Conditional permutation tests assess associations between proximal azithromycin treatment intensity and resistance gene abundance. We find no evidence of geographic spillover of macrolide resistance in untreated villages, as the genetic load of AMR remains at baseline levels in placebo-treated villages regardless of surrounding azithromycin treatment intensity (Spearman ρ = -0.05, P = 0.83). Sensitivity analyses confirm robustness across metrics, and no spillover effects are detected for other antibiotic classes. Azithromycin MDA-induced macrolide resistance appears localized to treated villages, mitigating some concerns about geographic spillover of AMR to nearby untreated villages at 24 months.},
}

@article {pmid41611489,
year = {2026},
author = {Li, W and Zhang, N and Li, Z and Cui, L and Wang, X and DU, Y},
title = {[Research progress on nanopore sequencing data alignment analysis methods and reference databases].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {42},
number = {1},
pages = {77-92},
doi = {10.13345/j.cjb.250554},
pmid = {41611489},
issn = {1872-2075},
mesh = {*Nanopore Sequencing/methods ; *Sequence Alignment/methods ; *Nanopores ; *Sequence Analysis, DNA/methods ; *Databases, Genetic ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Nanopore sequencing, as an emerging hotspot in sequencing technology, demonstrates tremendous potential in species identification, genome assembly, variant detection, and transcriptome analysis, owing to its distinctive advantages including extended read lengths, rapid detection capabilities, and compact instrumentation. However, nanopore sequencing data are characterized by high error rates and presence of insertions and deletions, which pose novel challenges for the application of conventional sequence alignment tools and the construction of reference databases. Focusing on the characteristics of nanopore data, this paper systematically sorts out sequence alignment tools suitable for nanopore sequencing, and elaborates on their advantages and limitations in processing sequence data for five different application scenarios: long-read sequencing, real-time sequencing, error rate compatibility, metagenomics, and structural variation detection. Meanwhile, from the perspective of data sources, this paper conducts multi-dimensional classification and organization of reference genome databases, and sorts out the key technologies for constructing high-quality nanopore databases. Through the collaborative analysis of alignment tools and databases, this paper provides references for the optimization and innovation of nanopore sequencing data analysis, and promotes the in-depth transformation of metagenomic sequencing from data generation to functional analysis.},
}

*Nanopore Sequencing/methods
*Sequence Alignment/methods
*Nanopores
*Sequence Analysis, DNA/methods
*Databases, Genetic
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid41611279,
year = {2026},
author = {Ma, XJ and Wang, F and Han, XT and Fang, F and Han, LY and Liu, HX},
title = {[Clinical characteristics and prognostic factors in patients with cerebrospinal fluid torque teno virus positivity after allogeneic hematopoietic stem cell transplantation].},
journal = {Zhonghua yi xue za zhi},
volume = {106},
number = {5},
pages = {455-460},
doi = {10.3760/cma.j.cn112137-20250711-01704},
pmid = {41611279},
issn = {0376-2491},
mesh = {Humans ; *Torque teno virus/isolation & purification ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Retrospective Studies ; Prognosis ; Male ; Female ; Transplantation, Homologous ; Adult ; Adolescent ; Survival Rate ; Young Adult ; *DNA Virus Infections ; },
abstract = {Objective: To investigate the clinical characteristics and prognostic factors for patients with cerebrospinal fluid positivity for torque teno virus (TTV) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods: A retrospective analysis was conducted on the patients who received allo-HSCT at Hebei Yanda Lu Daopei Hospital from 2022 to 2023 year and showed positive cerebrospinal fluid metagenomic next-generation sequencing (mNGS) results post-transplantation, with their clinical data collected accordingly. The patients were categorized into TTV-negative and TTV-positive groups based on the detection of TTV in cerebrospinal fluid. The TTV-positive group was further subdivided into low-RPM [TTV reads per million sequencing reads (TTV-RPM)<1] and high-RPM (TTV-RPM≥1) subgroups using the threshold of TTV-RPM. The patients were followed until December 9, 2025, to investigate the clinical features of cerebrospinal fluid TTV positive patients after allo-HSCT. The survival curve was drawn to compare the difference of survival rate between groups. The influencing factors of patient prognosis were analyzed using a multivariate Cox regression model. Results: A total of 134 patients were enrolled: sixty in the TTV-negative group, including 35 males and 25 females, aged [M (Q1, Q3)] 30 (14, 42) years, and 74 in the TTV-positive group, including 45 males and 29 females, aged 24 (15, 40) years. Within the TTV-positive group, 44 were classified as low-RPM subgroup and 30 as high-RPM subgroup. Baseline characteristics, including gender, age, primary disease, donor type, neutrophil engraftment time, platelet engraftment time, whether acute graft-versus-host disease (aGVHD) occurred, and other microbial infections in cerebrospinal fluid, showed no significant differences between the TTV-negative and TTV-positive groups, or between the low-RPM and high-RPM subgroups (all P>0.05). The median follow-up time was 30.0(18.0, 35.4) months, the median survival period was not reached in the low-RPM subgroup, while that in the high-RPM subgroup was 25.6 months (95%CI: 5.3-45.9), and the 3-year survival rate was lower than that in the low-RPM subgroup (41.1% vs 76.8%, P=0.014). Multivariate Cox regression analysis confirmed high TTV-RPM level (≥1) in cerebrospinal fluid as a risk factor for mortality in allo-HSCT patients (HR=2.57, 95%CI: 1.09-6.08). Conclusions: There is no difference in clinical characteristics among allo-HSCT patients with or without TTV infection or with different TTV viral loads. A high TTV-RPM value (≥1) in cerebrospinal fluid is a risk factor for mortality in allo-HSCT patients.},
}

Humans
*Torque teno virus/isolation & purification
*Hematopoietic Stem Cell Transplantation/adverse effects
Retrospective Studies
Prognosis
Male
Female
Transplantation, Homologous
Adult
Adolescent
Survival Rate
Young Adult
*DNA Virus Infections

@article {pmid41611053,
year = {2026},
author = {Ma, WJ and Ma, ZS and An, ZJ and Zhang, HM and Tian, Y},
title = {Commercial powdered activated carbon achieves high-efficiency nitrogen removal in sulfur-driven autotrophic denitrification at low temperatures.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123882},
doi = {10.1016/j.envres.2026.123882},
pmid = {41611053},
issn = {1096-0953},
abstract = {Sulfur-driven autotrophic denitrification (SAD), a nitrate removal process, is characterized by low carbon emissions and high sustainability. However, its efficiency is notably affected by low temperatures. This study confirmed that the addition of powdered activated carbon (PAC) could enhance denitrification capacity at low temperatures in the SAD process. At 15-10 °C, the nitrogen removal efficiency was 80.38%, 1.38 times higher than that of the blank reactor. At low temperatures, PAC enhanced the activities of nitrate reductase and nitrite reductase. Meanwhile, PAC stimulated EPS secretion and improved bio-electrochemical properties. Concurrently, both extracellular and intracellular electron transfer were enhanced by the addition of PAC. Microbial analysis indicated that the microbial network with PAC addition exhibited greater stability and robustness. Furthermore, PAC increased the relative abundances of denitrifying bacteria at low temperatures, particularly those of Ferruginibacter and Dokdonella. Metagenomic sequencing indicated that PAC enhanced pathways related to nucleotide sugar metabolism and synthesis, tRNA charging, and coenzyme A biosynthesis. At the genes level, the functional genes narIL, nirS, nasE, norCE, nosZ, soxA, soxZ, and dsrA were enriched with PAC addition. This study proposed and validated the feasibility of using PAC to enhance nitrogen removal efficiency in the wastewater treatment process at low temperatures, and further elucidated the underlying mechanisms.},
}

@article {pmid41611051,
year = {2026},
author = {Shi, J and Sun, C and Su, Y and Wu, Y and Zhan, M and Ji, C and Wang, R and Lv, B},
title = {Ecosystem-specific composition and drivers of plastisphere resistome in freshwater and marine environments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123858},
doi = {10.1016/j.envres.2026.123858},
pmid = {41611051},
issn = {1096-0953},
abstract = {Microplastics in aquatic environments facilitate the formation of specific plastisphere microbiomes and serve as potential hotspots for antibiotic resistance genes (ARGs) propagation. However, the systematic comparisons of ARG profiles on microplastics from different aquatic ecosystems remain limited, particularly the prevalent ARGs and their bacterial hosts. This study performed a comparative meta-analysis of existing metagenomic datasets to investigate the resistome between freshwater and seawater microplastics (FMP and SMP) and their driving factors. Our results revealed that the ARG profiles on both FMP and SMP were significantly distinct from their surrounding waterbody. Moreover, FMP exhibited a higher diversity and abundance of ARGs rather than SMP. Ten core ARGs were shared on FMP and SMP, while 23 core ARGs were exclusively detected on FMP. The bacterial community on microplastics exhibited an ecosystem-specific composition, and was identified as the primary determinant shaping the ARG profiles. Notably, more complex bacteria-ARG co-occurrence pattern was identified on FMP, involving a broader spectrum of core genera and potential pathogenic hosts (e.g., Mycobacterium, Streptomyces). Furthermore, a significant and specific correlation between mobile genetic elements and ARGs was identified on FMP but not SMP, suggesting a markedly elevated horizontal gene transfer potential, with mechanistic support from the concurrent enrichment of oxidative stress and SOS response genes on FMP. These findings provide a comprehensive characterization of ARGs on aquatic microplastics, and especially highlight the role of FMP on the ARG dissemination.},
}

@article {pmid41611023,
year = {2026},
author = {Li, W and Li, J and Wu, Y and Chen, M and Fu, Y and Li, W and Liu, S and Wang, J and Chen, Y},
title = {Artificial regulation of aerobic and anaerobic layers interface enhanced efficient nitrogen removal by weaving insulating grid and conductive carbon fiber in membrane aerated biofilm reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134074},
doi = {10.1016/j.biortech.2026.134074},
pmid = {41611023},
issn = {1873-2976},
abstract = {Artificial regulation of aerobic and anaerobic biofilm thickness is crucial for enhancing nitrogen removal efficiency of the membrane aerated biofilm reactor (MABR). In this study, conductive aeration membrane modules were fabricated by physical weaving technology to couple MABR with microbial electrochemistry for efficient nitrogen removal. Insulating grids of different thickness and conductive carbon fibers were woven onto the aeration membrane to form aerobic and anaerobic layers. When the total biofilm thickness reached 254 μm (150 μm aerobic layer and 104 μm anaerobic layer), the TN removal efficiency (89.49 ± 2.89 %) was optimal. 16S rRNA gene sequencing and metagenomics analysis confirmed that the aerobic and anaerobic layers in the biofilm were completely separated, but there was a synergistic effect in nitrogen removal. The composite cathode structure provides a mechanism for efficient spatial coupling between the aerobic and anaerobic layers, establishing a basis for regulating biofilm stratification.},
}

@article {pmid41610602,
year = {2026},
author = {Phusathian, B and Pongmanee, K and Theapparat, Y and Saikhwan, N and Trairatapiwan, T and Chaosap, C and Seemacharoensri, A and Tactacan, GB and Wong, LY and Ruangpanit, Y},
title = {Bacterial xylanase supplementation improves nutrient utilization, gut integrity, and microbial metabolism in broilers fed energy-reduced diets.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106515},
doi = {10.1016/j.psj.2026.106515},
pmid = {41610602},
issn = {1525-3171},
abstract = {This study evaluated the effects of bacterial xylanase supplementation on growth performance, nutrient digestibility, intestinal integrity, and microbial metabolic function in broilers fed energy-reduced diets. A total of 1,050 one-day-old male Ross 308 broiler chicks were randomly assigned to three dietary treatments, each comprising 14 replicates of 25 birds: a positive control (CON; standard corn-soybean meal diet), a negative control with reduced energy (NC; -85 kcal/kg), and an energy-reduced diet supplemented with bacterial xylanase (NCX; 100 g/ton Belfeed Xylanase™). During the starter phase, broilers fed the NC diet exhibited higher feed intake and FCR compared with those fed the CON and NCX diets (P < 0.05), with no significant difference between the CON and NCX diets. Apparent digestibility of dry matter, crude protein, and fat did not differ among dietary treatments (P > 0.05). However, broilers fed the NCX diet showed higher (P < 0.05) digestibility of crude fiber, NDF, and ADF than those fed the CON or NC diets. Apparent metabolizable energy was higher in broilers fed the CON and NCX diets compared with the NC diet. Furthermore, broilers receiving the CON and NCX diets exhibited significantly lower serum fluorescein isothiocyanate-dextran concentrations than those fed the NC diet, indicating improved intestinal barrier integrity. Bacterial xylanase supplementation increased microbial alpha diversity and altered beta diversity clustering, with enrichment of beneficial taxa such as Bifidobacteriaceae and Lactobacillaceae. Functional metagenomic prediction suggested greater representation of carbohydrate metabolism and energy production pathways in the NCX diet, whereas the NC diet was associated with enrichment of stress-related and xenobiotic degradation pathways. Overall, bacterial xylanase supplementation mitigated the adverse effects of dietary energy reduction by improving fiber utilization, maintaining gut integrity, and modulating the cecal microbiota toward a more favorable metabolic profile.},
}

@article {pmid41610548,
year = {2026},
author = {Zafar, S and Alimohammadi, M and Hatami Moghadam, P and Hadei, M},
title = {Investigating the types of bacterial species with antimicrobial resistance genes in Iran's wastewaters: a systematic review.},
journal = {The Science of the total environment},
volume = {1016},
number = {},
pages = {181385},
doi = {10.1016/j.scitotenv.2026.181385},
pmid = {41610548},
issn = {1879-1026},
abstract = {Antimicrobial resistance (AMR) is a major global health threat, with wastewater systems performing as critical reservoirs and dissemination pathways for antimicrobial-resistant bacteria (ARB) and resistance genes (ARGs). Despite rising AMR rates in Iran, a comprehensive understanding of resistance patterns in wastewater remains limited. This systematic review aimed to investigate the prevalence, bacterial diversity, and resistance gene profiles in hospital, municipal, and industrial wastewater across Iran. A systematic search was conducted in Scopus, PubMed, Web of Science, and Iranian databases for studies published between 1990 and September 2024. Data extraction followed PRISMA guidelines, and study quality was assessed using the JBI checklist. A total of 43 studies from 13 provinces met the inclusion criteria, with nearly half originating from Tehran (21/43, 48.8%), indicating uneven national coverage. Hospital wastewater (18 studies, 41.9%) harbored the highest burden of clinically significant AMR, including MRSA (22%), VRE (17%), and ESBL-producing E. coli (17%). Municipal wastewater (31 studies, 72.1%) frequently contained VRE Enterococcus faecium (32%) and Enterococcus faecalis (23%), ESBL-producing E. coli (19%), and MRSA (10%). Industrial wastewater (10 studies, 23.3%), primarily from slaughterhouses, exhibited high ESBL rates in E. coli (80%), with some studies reporting up to 93% ESBL production among isolates. Across studies, the most recurrent ARGs were blaCTX (16.3%), vanA (20.9%), mecA (9.3%), tetracycline genes, and intI1. Detection methods were predominantly culture- and PCR-based, with limited use of qPCR, molecular typing, or metagenomics. The most frequently detected resistance genes included blaCTX-M, mecA, vanA, tetA, and intI1. Most studies used culture and PCR-based detection; molecular typing and metagenomic approaches were rarely applied. The persistent detection of MDR pathogens and high-priority ARGs highlights significant gaps in AMR surveillance. Strengthening national wastewater monitoring through standardized protocols, broader geographic coverage, and integration of advanced molecular tools is essential to support effective One Health based public-health strategies.},
}

@article {pmid41610462,
year = {2026},
author = {Nagy, EZ and Szeredi, L and Földi, D and Belecz, N and Kovács, ÁB and Sulyok, KM and Grózner, D and Wehmann, E and Bányai, K and Marton, S and Tenk, M and Kreizinger, Z and Gyuranecz, M},
title = {Development and efficacy test of a live, attenuated Mycoplasma hyorhinis vaccine candidate strain.},
journal = {Vaccine},
volume = {75},
number = {},
pages = {128278},
doi = {10.1016/j.vaccine.2026.128278},
pmid = {41610462},
issn = {1873-2518},
abstract = {BACKGROUND: Mycoplasma (M.) hyorhinis causes substantial economic losses in swine. Currently, prevention and treatment rely on minimizing risk factors and administering antibiotics, as no vaccines are commercially available in Europe. However, antibiotics often cannot fully eliminate the bacteria. The development of an effective vaccine could lead to a potentially long-term control method.

MATERIALS AND METHODS: A temperature-sensitive M. hyorhinis strain was developed using 1-methyl-3-nitro-1-nitrosoguanidine (NTG) mutagenesis. The immunogenicity and efficacy of this vaccine candidate clone were evaluated in combination with an adjuvant. Three-week-old piglets were immunized with the candidate vaccine strain, and the vaccination site was monitored daily. At six weeks of age, the pigs were challenged intravenously on two subsequent days. Daily clinical examinations were conducted, with blood and nasal swabs collected weekly throughout the study for M. hyorhinis enzyme-linked immunosorbent assay (ELISA), real-time PCR analysis, and isolation. Three weeks post-challenge, the animals were euthanized for gross and histopathological examinations. Body temperature was recorded daily, and body weight was measured upon arrival, and then at six and nine weeks of age.

RESULTS: Vaccination significantly reduced clinical signs (p = 0.03), as well as gross pathological (p = 0.01) and histopathological (p = 0.005) lesions compared with the positive control group. The vaccinated group exhibited an earlier and higher increase in M. hyorhinis-specific IgG antibody levels post-challenge than the positive control group. However, the vaccine candidate did not mitigate the impact of M. hyorhinis infection on the weight gain. After the challenge (days 21-42), both the vaccinated (p = 0.001) and the positive control (p = 0.003) groups exhibited reduced weight gain compared with the negative control group.

DISCUSSION: Overall, the attenuated M. hyorhinis strain, combined with the adjuvant, provided protection against M. hyorhinis infection. These results form a basis for the development of a novel vaccine candidate that offers effective prevention.},
}