@article {pmid42468699,
year = {2026},
author = {Qing, C and Zhou, Y and Wang, Y and Li, P and Hedlund, B},
title = {Arsenic detoxification mediated by mutualistic cross-feeding in a thermophilic microbial consortium.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135440},
doi = {10.1016/j.biortech.2026.135440},
pmid = {42468699},
issn = {1873-2976},
abstract = {Cyanobacteria-dominated microbial mats thrive in arsenic (As)-rich hot springs, but how they cope with As stress remains unclear. This study explored the As detoxification strategy of a photosynthetic microbial mat from a high-As hot spring in Tibet. The photosynthetic mat oxidized arsenite [As(Ⅲ)] under light without external organic carbon sources or electron acceptors. However, As(Ⅲ) was not oxidized by a pure culture of the dominant cyanobacterium isolated from the mat, "Thermoleptolyngbya sichuanensis" XZ-Cy5. Instead, exposure of a growing culture to 5 mM As(Ⅲ) led to rapid loss of chlorophyll and photosynthetic activity. In contrast, a pure culture of the mat-derived heterotroph Chelatococcus sp. XZ-Ab1 could oxidize As(Ⅲ) quickly with the addition of organic carbon and oxygen. A co-culture system demonstrated mutualistic interactions where "T. sichuanensis" XZ-Cy5 secreted organic carbon to facilitate heterotrophic growth of Chelatococcus sp. XZ-Ab1, while Chelatococcus sp. XZ-Ab1 promoted growth of "T. sichuanensis" XZ-Cy5 by oxidizing toxic As(Ⅲ) to the less toxic arsenate. Following growth of the co-culture using [13]CO2, NanoSIMS isotope tracing provided direct evidence of photoautotroph-derived carbon from "T. sichuanensis" XZ-Cy5 to Chelatococcus sp. XZ-Ab1. Metagenomic and genomic analyses indicated several mechanisms for metabolic complementarity between the two strains, including As detoxification by the heterotroph and fixed carbon and nitrogen provision by the cyanobacterium, in addition to oxygen production. Our findings reveal a cooperative survival strategy in extreme environments and provide a novel model for engineering synthetic microbial consortia for As bioremediation.},
}

@article {pmid42469266,
year = {2026},
author = {Yu, Z and Zhang, K and Zeng, XM and Cheng, X and Zhang, Y and Wang, X and Sun, J and Chen, L and Liu, F and Zhang, Q},
title = {Consequences of agricultural deforestation and subsequent afforestation on soil biodiversity and ecosystem multifunctionality.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75740-z},
pmid = {42469266},
issn = {2041-1723},
support = {32471650,32430068, 31922060, 32130069//National Natural Science Foundation of China (National Science Foundation of China)/ ; Y2022091//Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)/ ; },
abstract = {The Earth is currently in an era where massive deforestation and afforestation coexist. The impact of large-scale agricultural deforestation and the subsequent afforestation on soil biota multidiversity, ecosystem multifunctionality (EMF), and the relationship between soil biota multidiversity and EMF (BEFm) remain unclear. Here, we investigate 405 paired plots along a 4000 km south-north transect, spanning tropical, subtropical, temperate, and boreal zones. We measure 19 ecological functions and sequence soil biota (including bacteria, fungi, archaea, viruses, protists, and invertebrates) and metagenomes. We find that agricultural deforestation reduces soil multitrophic biodiversity by 25% and EMF by 58%, and afforestation has partially restored them, but pristine levels have not been reached. Agricultural deforestation decouples the positive BEFm relationship across four climatic zones, while afforestation restores the positive BEFm relationship in tropics and subtropics but not in temperate and boreal zones. Afforestation in the warmer zone triggers potential multitrophic cascades to enhance EMF, thereby strengthening BEFm relationship. The changes in biogeochemical-cycling genes induced by afforestation exert more significant driving effects on EMF in the warmer zone than the colder zone. Our study provides integrative evidence that climate modulates the recovery of BEFm relationship and offers multitrophic and metagenomic insights into the mechanisms underlying EMF.},
}

@article {pmid42469597,
year = {2026},
author = {Shen, Z and Eckert, JK and Saffery, R and Allen, KJ and Walsh, A and , and Deming, C and Chen, Q and Laky, K and Li, JM and Chatman, L and , and Kong, HH and Perrett, KP and Segre, JA and Frischmeyer-Guerrerio, PA},
title = {Shotgun Metagenomics Reveals Skin Microbiome Composition and Function in Infant Atopic Disease.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70449},
pmid = {42469597},
issn = {1398-9995},
support = {AR084058/NH/NIH HHS/United States ; UM1AI109565/NH/NIH HHS/United States ; APP1146913//National Health and Medical Research Council/ ; GNT2008911//National Health and Medical Research Council/ ; 26-PBII-T1-04//WSU Office of Research/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors underlying distinct atopic phenotypes remain unclear. Although FLG null mutations are major genetic risk factors for AD, they explain only part of disease heritability, suggesting a potential role for the skin microbiome. This study examined how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.

METHODS: We analyzed > 1000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, their co-occurrence, and FLG mutation status.

RESULTS: Within AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA showed decreased Staphylococcus hominis and Lactococcus species, and increased Dermacoccus nishinomiyaensis and Malassezia slooffiae. At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with later development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers showed additional microbial shifts, including reduced Streptococcus species and increased M. slooffiae. Strain-level analyses revealed mother-infant sharing of AD-associated taxa, and microbial genome-wide association analyses identified species-specific genes linked to AD severity.

CONCLUSIONS: Infant atopic phenotypes are associated with distinct, phenotype-specific skin microbiome features that emerge before and after disease onset, highlighting the microbiome as a potential target for early risk stratification.},
}

@article {pmid42469878,
year = {2026},
author = {Li, S and Guo, R and Sun, L and Zhu, P and Wang, T and Zheng, J and Chen, H and Li, H},
title = {Co-production of high-purity floridoside and isofloridoside ameliorates MASH via Parabacteroides goldsteinii-UDCA-FXR enterohepatic axis.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {42469878},
issn = {1749-8546},
support = {No.2024J422//Ningbo Natural Science Foundation/ ; No.2024020919//Ningbo Top Medical and Health Research Program/ ; No.32373099//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatohepatitis (MASH), the progressive form of metabolic dysfunction-associated fatty liver disease (MAFLD), is tightly linked to gut microbiota dysbiosis and disrupted bile acid (BA) homeostasis. Floridoside (Flor), a marine glycoside from the edible seaweed Pyropia haitanensis (P. haitanensis), exerts promising biological activities. However, protocols for its high-purity preparation and the mechanisms underlying its anti-MASH effects remain unclear.

PURPOSE: To develop a protocol for the preparation of high-purity Flor and its isomer isofloridoside (Isoflor) from P. haitanensis, and to elucidate how Flor alleviates MASH via regulating gut microbiota and BA metabolism.

METHODS: High-purity Flor and Isoflor were isolated via integrated chromatography, with their chemical structures confirmed by LC-MS and NMR. Anti-MASH efficacy was evaluated in a high-fat diet (HFD)-induced murine MASH model. The underlying mechanisms were explored using multi-omics analyses, including transcriptomics, gut microbiota metagenomics and BA-targeted metabolomics, and further validated by molecular docking, molecular dynamics simulation and western blotting; the compounds' biosafety was evaluated using zebrafish.

RESULTS: High-purity Flor and Isoflor were successfully isolated, each with a purity of ≥ 99.0%. Both compounds exhibited a favorable biosafety profile and comparable lipid-lowering activity in zebrafish. In HFD-induced murine MASH models, Flor robustly ameliorated HFD-driven obesity, hepatic steatosis, and chronic inflammation, and restored systemic BA homeostasis characterized by a markedly increased non-12-OH/12-OH BA ratio. Meanwhile, Flor treatment dramatically enriched the relative abundance of intestinal Parabacteroides goldsteinii (P. goldsteinii), which showed a significant positive correlation with MASH alleviation and beneficial BAs (e.g., ursodeoxycholic acid (UDCA)). Mechanistically, UDCA exerted its therapeutic effects by antagonizing FXR signaling, upregulating the hepatic protein and mRNA expression of CYP7B1 and CYP27A1, and ultimately promoting the activation of the alternative BA synthesis pathway.

CONCLUSION: High-purity Flor and Isoflor were obtained via an integrated co-production process from P. haitanensis. We hypothesize that Flor may ameliorate MASH by enriching P. goldsteinii and modulating the UDCA-FXR axis to activate the alternative bile acid synthesis pathway, positioning Flor as a promising prebiotic candidate for MASH management.},
}

@article {pmid42470286,
year = {2026},
author = {Nikam, R and Kalani, K and Beverly, M and Kumar, PS},
title = {The Vape, the Mouth, and the Mycobiome: A Comparative Metagenomic Analysis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345261450182},
doi = {10.1177/00220345261450182},
pmid = {42470286},
issn = {1544-0591},
abstract = {Electronic nicotine delivery systems (ENDS), including e-cigarettes, are increasingly marketed as safer alternatives to combustible tobacco, yet their effects on oral health remain underexplored. Although the role of ENDS in creating dysbiotic oral bacterial communities is documented, effects on the oral mycobiome remain underexplored. This study compared the subgingival fungal communities of 123 periodontally and systemically healthy e-cigarette-only users, smokers, dual users, former smokers, and never-smokers using whole-genome shotgun sequencing for functional profiling. Taxonomic assignment using Kraken 2 and the PlusPF database identified 98 fungal taxa, and functional annotation with the Kyoto Encyclopedia of Genes and Genomes identified 2,960 fungal genes. Cross-domain bacterial-fungal interactions were interrogated using a correlation threshold of |r| ≥ 0.7 and P ≤ 0.001. E-cigarette users demonstrated a significantly higher α-diversity than smokers and never-smokers did (P < 0.001; P < 0.005) and a mycobiome enriched with Candida albicans, Aspergillus oryzae, and Schizosaccharomyces pombe. Functional profiling revealed enrichment of genes encoding or DNA repair, xenobiotic degradation, membrane transport, and stress response. The mycobiome of dual users and former smokers using e-cigarettes did not differ from that of e-cigarette users. Cross-kingdom networks identified 5- to 10-fold higher bacterial-fungal connectivity in e-cigarette users, with fungi capable of enhanced stress tolerance, DNA repair capacity, and metabolic adaptability acting as network anchors. Our data support an association between e-cigarette use and remodeling of the oral mycobiome and microbiome, driven by enhanced polymicrobial interactions and increased functional complexity, suggesting that assumptions regarding the biological neutrality of e-cigarette aerosols warrant further investigation.},
}

@article {pmid42470541,
year = {2026},
author = {Ergen, AG and Keskin, E and Akgun, A and Erol, HB and Edis, G and Celik, I and Kaskatepe, B and Erganis, S and Sahin, EA and Gülmez, D and Akdağlı, SA and Ergin, Ç and San Keskin, O and Yardımci, H and Sivri, N and Altug, G and Kalkanci, A},
title = {Environmental Detection of Candidozyma (Candida) auris in Surface Waters of the Gediz Delta, a Critical Coastal Wetland in Türkiye: Expanding One Health Surveillance Perspective.},
journal = {Mycopathologia},
volume = {191},
number = {4},
pages = {},
pmid = {42470541},
issn = {1573-0832},
support = {124S746//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; },
mesh = {*Wetlands ; Temperature ; DNA, Fungal/genetics/isolation & purification ; *Candida auris/isolation & purification/genetics/classification ; Real-Time Polymerase Chain Reaction ; *Water Microbiology ; Hydrogen-Ion Concentration ; *Saccharomycetales/isolation & purification/genetics/classification ; *Candida/isolation & purification/classification/genetics ; },
abstract = {BACKGROUND: Candidozyma auris (syn. Candida auris) is an emerging multidrug-resistant yeast of growing clinical and environmental concern. Despite its increasing detection in healthcare settings worldwide, environmental evidence remains scarce. This study presents the first molecular detection of C. auris DNA in surface waters of Türkiye, within the Ramsar-protected Gediz Delta, as part of the national One Health Surveillance Framework.

METHODS: A total of 80 surface-water samples were collected from five wetland ecosystems Tuz Lake, Kulu Lake, Göksu Delta (Akgöl and Paradeniz Lagoons), Kızılırmak Delta, and Gediz Delta. Physicochemical parameters; temperature, pH, and salinity were recorded in situ using a multi parameter sensor. Environmental DNA was extracted from 2 L of 0.22 µm Sterivex-filtered water and analyzed via qPCR using C. auris-specific (CauF/CauR) and Candida-genus (CauRelF/CauRelR) primer sets. Yeast isolation was performed on CHROMagar™ Candida Plus, and identification was achieved by MALDI-TOF MS.

RESULTS: C. auris DNA was detected in one sample (1.25%), specifically from the Gediz Delta (Sample No. 5651, 38.523° N, 26.892° E), with Ct values 33.8-37.2 confirmed by sequencing. Broader Candida genus signals were observed in 24% of samples. Culture-based analyses yielded no viable C. auris, but 15 yeast isolates were identified, mainly Pichia kudriavzevii (Candida krusei), C. albicans, and Nakaseomyces glabratus (Candida glabrata).

CONCLUSION: The culture-negative yet qPCR-positive finding indicates that C. auris DNA likely persists in aquatic environments as non-viable or residual material. This finding provides early molecular evidence of environmental dissemination and underscores the need for viability assays, culture-based isolation, and metagenomic monitoring integrated within One Health surveillance programmes.},
}

*Wetlands
Temperature
DNA, Fungal/genetics/isolation & purification
*Candida auris/isolation & purification/genetics/classification
Real-Time Polymerase Chain Reaction
*Water Microbiology
Hydrogen-Ion Concentration
*Saccharomycetales/isolation & purification/genetics/classification
*Candida/isolation & purification/classification/genetics

@article {pmid42462951,
year = {2026},
author = {Jin, Y and Liu, J and Liu, Z and Yuan, Y and Cui, H and Dong, Z and Zhang, F and Lv, M and Hu, L and Zhang, L and Zhou, D and Yang, W},
title = {Linking oral microbiota to clinic air during ultrasonic scaling: Quantitative sequencing and CFD modeling reveal pathogenic aerosol emissions, infection risk, and control strategies.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128796},
doi = {10.1016/j.envpol.2026.128796},
pmid = {42462951},
issn = {1873-6424},
abstract = {Microbial aerosols from dental procedures pose a recognized yet unquantified airborne infection risk. During ultrasonic scaling, we performed multi-site sampling (saliva, air, surfaces) and combined metagenomics with quantitative 16S rRNA and ITS amplicon sequencing to profile viral, bacterial, and fungal communities. Using size-resolved aerosol sampling and absolute quantification, we determined the emission strength and size distribution of pathogenic bacterial aerosols (PBA), which were key inputs for computational fluid dynamics (CFD) simulations performed at ventilation velocities of 0.1, 0.2, and 0.4 m/s, corresponding to air exchange per hour (ACH) of 2.4, 4.7, and 9.4 h[-1], respectively. We first linked patient oral microbiota to clinic aerosols, identifying a shared core of 51 viral, 55 bacterial, and 23 fungal families, of which three bacterial families (Streptococcaceae, Pasteurellaceae, Nocardiaceae) were pathogenic. The emission strength of PBA was ∼3.06×10[3] copies/min, with 66.7% concentrated in the 2.1∼4.7 μm fraction, a size associated with higher deposition in the lower respiratory tract. CFD simulations, fed with real pathogen concentrations and aerodynamic size spectra, revealed that increasing ACH from 0.1 to 0.4 m/s reduced PBA suspension (-26.4%) and surface deposition (-12.7%) during scaling, lowering the inhalation infection risk (IIR) at the dentist's position by 80.8% and keeping overall IIR below 25%. After scaling, lower velocity favours particle removal, supporting a dynamic ventilation strategy (high during treatment, low afterwards). This integrated framework provides a direct scientific basis for infection control in dental operatories.},
}

@article {pmid42463489,
year = {2026},
author = {Gao, Z and Wu, J and Lucaci, AG and Ouyang, J and Wang, L and Ryon, KA and Elhaik, E and Probst, AJ and Rodó, X and Velavan, TP and Chasapi, A and Ouzounis, CA and Oliveira, M and Dias-Neto, E and Osuolale, O and Poulsen, M and Meleshko, D and Bhattacharyya, M and Ugalde, JA and Tull, A and Rubins, KH and Sierra, MA and Tierney, BT and Prithiviraj, B and Sharma, NK and Munteanu, V and Mangul, S and Kurt, KC and Ushio, M and Mazur-Panasiuk, N and Kopera, K and Marszałek, K and Kowalski, M and Toscan, RB and Branicki, W and Pyrć, K and Łabaj, PP and Subramanian, B and Frolova, A and Burkhart, JG and Deng, Y and Udekwu, KI and Schriml, LM and Hazrin-Chong, NH and Suzuki, H and Lee, PKH and Camargo, AP and Kyrpides, NC and Liu, D and Wang, LF and Mason, CE and Shi, T and , },
title = {Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42463489},
issn = {2041-1723},
support = {32370720//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; RNA, Viral/genetics ; Cities ; Animals ; },
abstract = {RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments-including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings - across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health.},
}

Humans
*Virome/genetics
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
RNA, Viral/genetics
Cities
Animals

@article {pmid42463504,
year = {2026},
author = {Côrtes, MF and Luna-Muschi, A and Marchi, AP and Noguera, SLV and Hurtado, R and Espinoza, ES and Ferreira, NE and Da-Costa, AC and Berg, MG and Rodgers, MA and Cloherty, GA and Silveira, CGT and Paranhos-Baccalà, G and Kallas, EG and Mendes-Correa, MC and Costa, SF},
title = {Nasopharyngeal metagenomics of symptomatic healthcare workers provides insights into the respiratory microbiome and antimicrobial resistance.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59198-z},
pmid = {42463504},
issn = {2045-2322},
abstract = {Respiratory infections represent a significant risk for healthcare workers (HCWs), particularly during viral outbreaks. This study applied metagenomic sequencing to characterize microbial communities and antimicrobial resistance (AMR) genes in nasopharyngeal swabs from HCWs presenting respiratory symptoms. Samples from 161 HCWs collected at a tertiary hospital in 2020-2021 were screened using FilmArray; negative samples were analyzed by metagenomic sequencing. After removal of human reads, sequences were taxonomically classified into viral, bacterial, and eukaryotic groups, and AMR genes were identified. On average, samples consisted of 5% viral reads, 89% bacterial, and 6% eukaryotic. Detected viruses included Enterovirus, human bocavirus(HBoV1), Alphaherpesvirus, and Coronavirus OC43, with one OC43 infection identified exclusively by metagenomic. Bacteria commonly associated with respiratory infections, such as Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis, were frequently observed. Fungi included Schizophyllum commune, Cryptococcus wingfieldii, Pneumocystis murina, and Cryptococcus neoformans. AMR analysis revealed that 65% of samples harbored at least one resistance gene, totaling 112 distinct genes; ermC was the most prevalent, detected in 28% of samples. Predominant classes included macrolide-lincosamide-streptogramin, beta-lactam, aminoglycoside, and tetracycline. These findings demonstrate the utility of metagenomic sequencing for comprehensive pathogen detection and AMR profiling, supporting improved infection control and clinical management in healthcare settings.},
}

@article {pmid42463700,
year = {2026},
author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S},
title = {Metagenomics-based surveillance identifies possible sources of mastitis-associated organisms in organic and conventional dairy farm environments.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00989-z},
pmid = {42463700},
issn = {2396-8370},
support = {2020-67017-30776//National Institute of Food and Agriculture/ ; },
abstract = {Mastitis is one of the most economically significant diseases of the dairy industry. Although farm environments are recognized reservoirs for mastitis pathogens, comprehensive metagenomic comparisons between organic and conventional systems remain limited. We compared the prevalence, diversity, and functional potential of mastitis-associated organisms in one organic and one conventional dairy farm in Texas using shotgun metagenomics. Of 180 samples collected from six environmental sites (teats, liners, parlor floor mats, feed areas, bedding sands, and water troughs), 126 were retained after quality-control exclusions. Taxonomic analysis revealed the prevalence of Pseudomonas fluorescens, Lactococcus garvieae, Escherichia coli, Citrobacter freundii, Enterococcus faecium, and Streptococcus parauberis. Alpha- and beta-diversity analyses indicated similar pathobiome structure between farm types, with niche-specific clustering observed for teat and liner samples. Functional annotation revealed comparable COG category distributions, with toxin-related genes representing the most abundant virulence-associated signatures, followed by lipopolysaccharide synthesis genes; adhesion and capsular polysaccharide genes were relatively more abundant on the organic farm. Metagenome-assembled genomes affiliated with key species confirmed genes related to toxin secretion, lipopolysaccharide biosynthesis, adhesion, and biofilm formation. Collectively, these farms harbored similar mastitis-associated reservoirs but differed in certain virulence-associated signatures, highlighting the need for environment-specific hygiene interventions.},
}

@article {pmid42464133,
year = {2026},
author = {Chen, Y and Wang, X and Si, Y and Zhang, F and Ding, K and Zhang, J and Wang, J and Zhou, L and Luo, X},
title = {Salt/alkali‑tolerant Streptomyces luteus TRM 45540 improves pepper growth and soil quality in acidic and alkaline soils.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09509-3},
pmid = {42464133},
issn = {1471-2229},
support = {(Grant No. 32560008)//Study on Spatial Heterogeneity of Microbial Community Structure and Function in Tamarix Shrub Sand Dunes of the Tarim Basin/ ; (2025AB005),//Key Technology R&D and Demonstration of Saline-Alkali Tolerant Carbon-Based Slow-Release Functional Fertilizer/ ; (Grant No. 2025DA008)//Green Preparation of High-Efficiency Acaricidal Microbial Technical Concentrates and Development of Controlled-Release Synergistic Technologies"./ ; },
abstract = {This study evaluated the potential of the salt-alkali-tolerant actinobacterium Streptomyces luteus TRM 45540, isolated from Lop Nur saline-alkali soil in Xinjiang, to alleviate pH-related iron deficiency and promote pepper growth. We hypothesized that this strain could mobilize and compete for soil iron via siderophore production, thereby benefiting plants under variable-pH conditions. To test this hypothesis, we compared its effects with conventional iron fertilizers (EDDHA-Fe6, ferrous sulfate) and compound microbial fertilizer on pepper growth, soil physicochemical properties, and rhizosphere microbial communities in acidic (pH 5) and alkaline (pH 7.69) soils. TRM 45540 exhibited good stress tolerance, growing well at 3%-9% NaCl and pH 9-12. In both soil types, it significantly promoted pepper growth: fresh weight was increased by over 44% in acidic soil relative to the control, while root and stem lengths were elevated by 26%-91% in alkaline soil compared with conventional amendment groups. The strain increased the content of indigenous soluble iron in soil, raising soluble iron to 42 mg/kg[- 1] in acidic soil without exogenous iron addition, neutralized acidic soil toward neutral pH, increased total nitrogen to 6.5 g/kg[- 1], and enhanced phosphorus and potassium availability. Redundancy analysis identified pH and total iron as the dominant factors shaping microbial communities in acidic and alkaline soils, respectively. KEGG pathway enrichment revealed significant changes in organic pollutant degradation, nutrient metabolism, and stress response pathways following TRM 45540 inoculation. The strain enriched functional microorganisms related to siderophore secretion and nitrogen fixation, thereby improving soil microbial diversity and richness, while compound microbial fertilizer was associated with relatively lower microbial community activity. These findings demonstrate that S. luteus TRM 45540, with cross-pH adaptability and functional stability, enhances pepper growth and soil quality via synergistic effects of stress tolerance, nutrient activation (especially iron mobilization), and microbial community regulation. This strain provides a promising microbial inoculant for sustainable pepper production in variable-pH soils, especially saline-alkali soils.},
}

@article {pmid42464224,
year = {2026},
author = {Zhang, G and Wang, Y and Liu, S and Wu, X and Fu, H and Sun, D},
title = {Clinical randomized comparative study of Laifu Chengqi Decoction enema for treating postoperative peritonitis in children with complicated appendicitis.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-026-07329-w},
pmid = {42464224},
issn = {1471-2431},
support = {2025KJ061//Tianjin Municipal Education Commission Scientific Research Project/ ; },
abstract = {BACKGROUND: Laifu Chengqi Decoction (LF-CQD) is a traditional Chinese medicine enema rooted in classic heat-clearing and purgative formulas traditionally used to relieve abdominal distention, resolve stasis, and restore bowel motility. Its components (e.g., Laifuzi and Dahuang) provide plausible pro-motility and anti-inflammatory actions, supporting its culturally grounded use as a postoperative adjunct in pediatric perforated appendicitis. This study aimed to evaluate the clinical efficacy of LF-CQD enemas in the treatment of postoperative peritonitis in children.

METHODS: This prospective randomized controlled trial included 118 children with perforated appendicitis complicated by peritonitis. The LF-CQD group received LF-CQD retention enemas for 5 days, whereas the control group was administered saline enemas. The primary outcome was time to first passage of flatus (a core marker of gastrointestinal recovery). Key secondary outcomes included time to bowel sound resumption, time to oral intake, preoperative and postoperative day (POD) 3 and 7 inflammatory marker levels, complication rates at 6-month follow-up, antibiotic use, and length of hospital stay.

RESULTS: Gastrointestinal function recovery was significantly faster in the LF-CQD group than in the control group [bowel sound resumption (p < 0.001), flatus (p < 0.001), and oral intake (p < 0.001)]. On POD7, the LF-CQD group exhibited significantly lower inflammatory marker levels than the control group (C-reactive protein level: p < 0.001). Exploratory post-hoc analyses showed greater relative reductions (ΔCRP/ΔWBC) in the LFCQD group at all timepoints (all p < 0.05). Complication rates for intra-abdominal abscess (8.5% vs. 25.4%, p = 0.008) and adhesive intestinal obstruction (5.1% vs. 22%, p = 0.003) were reduced, and antibiotic use duration was shorter (p < 0.001).

CONCLUSIONS: LFCQD enema serves as a safe, well-tolerated adjuvant intervention for children with postoperative peritonitis secondary to complicated perforated appendicitis. It accelerates gastrointestinal function recovery and alleviates postoperative inflammation. However, being a single-center trial with a modest sample size, it yielded large treatment effects for intra-abdominal abscess, adhesive intestinal obstruction, and length of hospital stay; thus, these effect sizes warrant cautious interpretation and require validation in large-scale multicenter trials. Exploratory post hoc analyses also indicated reduced systemic inflammatory marker levels in the intervention group. We hypothesize that LFCQD may modulate inflammatory signaling cascades and promote gut microbiota homeostasis to drive these clinical improvements. However, as no direct assessment of these pathways or metagenomic profiling of the intestinal microbiome was performed during this trial, these mechanistic proposed mechanistic pathways remain speculative and unconfirmed. In conclusion, this study demonstrates clinical associations between LFCQD enema and improved postoperative outcomes, but does not establish definitive causal molecular mechanisms.

TRIAL REGISTRATION: International Traditional Medicine Clinical Trial Registry; ITMCTR2025001634. Retrospectively registered on July 24, 2025, which constitutes an methodological limitation of this trial. All primary and secondary outcomes, inclusion and exclusion criteria, and core study procedures were precisely predefined and finalized in 2019 at the study design stage, prior to the initiation of patient enrollment in January 2020. No post-hoc additions, deletions, or modifications to any trial outcomes were made after patient recruitment, data collection, or statistical analysis. The retrospective registration was merely delayed due to institutional administrative procedures for traditional Chinese medicine clinical trials, without any alteration to the originally designed trial endpoints. The updated Supplementary Material 1 provides a detailed item-by-item comparison between the registered protocol and manuscript-reported outcomes, confirming full consistency and integrity of all pre-specified endpoints.},
}

@article {pmid42464266,
year = {2026},
author = {He, C and Du, Y and Lloyd, KG and Vishnivetskaya, TA and Rivkina, EM and Jiang, H and Liang, R},
title = {Diversity and potential ecological roles of viruses in Pleistocene permafrost.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02685-6},
pmid = {42464266},
issn = {1741-7007},
abstract = {BACKGROUND: Ancient permafrost, formed during past glacial periods, is widespread in Siberia and other Arctic regions. Even though these soils have remained below 0 °C over geological time periods, the widespread presence of bacteria and archaea in permafrost is well documented. However, the diversity of viruses in ancient permafrost of different geological ages and their potential ecological roles are still poorly understood.

RESULTS: We applied metagenomics to characterize viruses from Middle to Late Pleistocene permafrost sediments from Siberia. A total of 2697 viral operational taxonomic units (vOTUs) were recovered through metagenomic assembly and virus identification. Viral diversity in the Middle Pleistocene permafrost was much higher than that in the Late Pleistocene. The virus communities at different depths of the Middle Pleistocene permafrost showed great similarity to each other but were significantly different from those of the Late Pleistocene, with Azeredovirinae, Peduoviridae, and Fiersviridae being the predominant viruses in Pleistocene permafrost. The viruses were predicted to carry auxiliary metabolic genes potentially involved in cold adaptation and elemental (C and N) biogeochemical cycling in ancient permafrost. The virus-host prediction revealed that microorganisms such as bacteria and archaea are the main hosts and only a few eukaryotic hosts were identified.

CONCLUSIONS: Our results show that permafrost viral communities in Siberia exhibit remarkable diversity and may have played a significant ecological role in ancient permafrost over geological time. While the release of viruses from thawing deep permafrost could pose a relatively small risk to human health and environment, it could have significant impacts on the carbon cycle, potentially influencing climate change feedback in permafrost regions.},
}

@article {pmid42464281,
year = {2026},
author = {Yu, M and Xiao, Y and Liu, Y and Wang, Z and Zhou, H and Tang, Y},
title = {Sequential Talaromyces marneffei and Legionella pneumophila infections leading to the diagnosis of anti-interferon-γ autoantibody-associated immunodeficiency: a case report.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04455-0},
pmid = {42464281},
issn = {1471-2466},
support = {2024YFHZ0273//Science and Technology Department of Sichuan Province-International Science and Technology Innovation Cooperation Project/ ; },
abstract = {BACKGROUND: Opportunistic infections caused by uncommon intracellular pathogens can serve as important clues to underlying immune dysfunction.

CASE PRESENTATION: We report a 57-year-old male who presented with chronic cough, dyspnea, fever, and weight loss. Chest imaging revealed diffuse pulmonary infiltrates and mediastinal lymphadenopathy, mimicking tuberculosis or lymphoma. Despite empirical anti-tuberculosis and broad-spectrum antibiotic therapy, his condition deteriorated. Metagenomic next-generation sequencing (mNGS) and culture confirmed Talaromyces marneffei infection. During antifungal therapy, he developed Legionella pneumophila pneumonia-an unusual sequential infection that raised suspicion of an immune defect. Comprehensive immunological evaluation revealed anti-interferon-γ (anti-IFN-γ) autoantibodies, supporting the diagnosis of AIGA-associated immunodeficiency. The patient had also shown repeatedly indeterminate interferon-γ release assay (IGRA) results, retrospectively suggesting impairment of the IFN-γ pathway.

CONCLUSIONS: This case illustrates that recurrent or sequential infections with intracellular pathogens, particularly Talaromyces marneffei and Legionella pneumophila, should prompt evaluation for cell-mediated immunodeficiency such as AIGA syndrome. Early recognition may facilitate tailored antimicrobial therapy, immunological follow-up, and consideration of immunomodulatory treatment in selected patients.},
}

@article {pmid42464402,
year = {2026},
author = {Stiffler, AK and Varona, NS and Wallace, BA and Silveira, CB},
title = {Chemical prophage induction selectively removes Vibrio from a pelagic Sargassum-derived multispecies biofilm.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00925-4},
pmid = {42464402},
issn = {2524-6372},
support = {2023349872//National Science Foundation Graduate Research Fellowship Program/ ; 2023353157//National Science Foundation Graduate Research Fellowship Program/ ; 80NSSC23K0676/NASA/NASA/United States ; 2424579//National Science Foundation/ ; },
abstract = {BACKGROUND: Pelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This alga's microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment.

RESULTS: Here, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after Mitomycin C treatment. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to the depletion of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization.

CONCLUSION: Due to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.},
}

@article {pmid42464404,
year = {2026},
author = {Eriksson, CE and Shipley, L and Clark, DA and Levi, T},
title = {Comparing Accuracy and Biases of DNA Metabarcoding, Hybridization Capture, and Metagenomic Sequencing for Quantifying Herbivore Diets.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70175},
doi = {10.1111/1755-0998.70175},
pmid = {42464404},
issn = {1755-0998},
support = {WNP00848//USDA National Institute of Food and Agriculture, McIntire-Stennis Project/ ; F23AF03162//Federal Aid in Wildlife Restoration/ ; 2317537//National Science Foundation/ ; },
mesh = {Animals ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; *Herbivory ; *Diet/methods ; Deer/physiology ; Sequence Analysis, DNA/methods ; *Nucleic Acid Hybridization/methods ; Plants/genetics ; },
abstract = {DNA metabarcoding using relative read abundance (RRA) is commonly applied to estimate herbivore diet composition, yet its quantitative accuracy remains uncertain. We assessed taxonomic resolution and quantitative performance of RRA from DNA metabarcoding compared to metagenomic sequencing and hybridization capture, using deer scats from feeding trials and recreated diet samples using plant tissues. All methods recovered plant composition in recreated diets (R[2] = 0.59-0.82), indicating accurate scaling with biomass in the absence of digestion, with only minor bias from amplicon length in DNA metabarcoding. In contrast, RRA from scat samples performed poorly (R[2] < 0.01) across all methods largely due to differential plant digestibility. Correcting for digestibility, measured with acid detergent lignin and acid-insoluble ash, was strongly supported in mixed-effects models and improved prediction of dietary composition, although species-level variation remained. For metagenomic sequencing and hybridization capture, we also evaluated Relative Genome Coverage (RGC), a novel relative abundance metric quantifying the proportion of each plant's chloroplast genome covered by mapped reads, normalized for genome length. RGC further improved correlations in recreated diets (R[2] = 0.82-0.84) and, with hybridization capture, largely overcame digestibility-related biases in scat samples (R[2] = 0.57) without correction. When such corrections are infeasible, hybridization capture with uncorrected RGC may achieve higher quantitative accuracy in scat samples. Our results provide practical guidance for improving molecular herbivore diet analysis and highlight the importance of accounting for digestion-related biases.},
}

Animals
*Metagenomics/methods
*DNA Barcoding, Taxonomic/methods
*Herbivory
*Diet/methods
Deer/physiology
Sequence Analysis, DNA/methods
*Nucleic Acid Hybridization/methods
Plants/genetics

@article {pmid42464944,
year = {2026},
author = {Hazan, S and Bao, G and Goudzwaard, A and Ichim, T and Martin, L and Vidal, AC},
title = {Gut Microbiome Alterations in Cancer and Non-cancer Adults: A Cross-Sectional Metagenomic Study.},
journal = {Technology in cancer research & treatment},
volume = {25},
number = {},
pages = {15330338261470516},
doi = {10.1177/15330338261470516},
pmid = {42464944},
issn = {1533-0338},
mesh = {Humans ; Female ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Neoplasms/microbiology/pathology ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Aged ; *Bacteria/classification/genetics ; Metagenome ; Retrospective Studies ; },
abstract = {IntroductionPrevious studies found associations between cancer and the gut microbiome. Thus, we aimed to investigate the gut microbiome composition in adults with and without cancer to try to identify specific microbes that may be associated with cancer in a cross-sectional, observational, and retrospective study.MethodsStool samples from sixty participants, n=20 controls, n=25 with aggressive cancer, and n=15 with non-aggressive cancer were analyzed using Metagenomic Next Generation Sequencing. Mann-Whitney U test tests were used to examine differences in the relative abundances of bacterial genera.ResultsCompared to controls, aggressive cancer patients had statistically significantly lower levels of gut Bifidobacterium, Faecalibacterium, and Collinsella, (all p≤0.05), while they had higher levels of gut Bacteroides (p=0.015). Non-aggressive cancer patients had lower levels of gut Bifidobacterium compared to controls, an association that was approaching statistical significance (p=0.054).ConclusionAggressive-cancer patients showed significantly altered levels of key gut microbes compared to controls. These are preliminary associations, and thus further larger studies are needed to confirm these findings.},
}

Humans
Female
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Cross-Sectional Studies
*Neoplasms/microbiology/pathology
Male
Middle Aged
High-Throughput Nucleotide Sequencing
Adult
Aged
*Bacteria/classification/genetics
Metagenome
Retrospective Studies

@article {pmid42465056,
year = {2026},
author = {Li, Q and Chen, M and Lu, Y and Xu, C and Zheng, Y and Zeng, Z and Xu, D and Qin, W and Zhang, Y},
title = {Close spatial and metabolic association between heterotrophic and ammonia-oxidizing marine Nitrososphaerota.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag173},
pmid = {42465056},
issn = {2730-6151},
abstract = {Following the ubiquitous autotrophic ammonia-oxidizing archaea (AOA), heterotrophic representatives of the marine Nitrososphaerota (HMN) form the second most abundant group within this archaeal phylum. However, their eco-evolutionary strategies remain poorly understood. Previous studies have reported a consistent co-occurrence of HMN with marine AOA (MAOA), prompting a detailed investigation into their potential interaction. Through large-scale (meta)genomic and metatranscriptomic analyses, we reveal that HMN possess ultra-streamlined genomes and globally co-occur with marine AOA. The absence of most B vitamin biosynthesis pathways, incomplete citrate cycle and glycolysis, along with the essential requirement for exogenous amino acids, suggest their potential metabolic dependency on AOA. Meanwhile, catalyzed reporter deposition fluorescence in situ hybridization supports a close physical association between HMN and AOA. The nearly synchronous origins of HMN and AOA after oxygen rise, coupled with HMN's dispersive microhabitats (evidenced by dense, shallow subclades) and extensive horizontal gene transfer between these groups, further support their close relationship-although HMN likely acquired heterotrophic capabilities from bacteria. This study reveals a previously unrecognized association between HMN and AOA, implying a tight coupling between autotrophic and heterotrophic processes in deep-sea habitats.},
}

@article {pmid42465060,
year = {2026},
author = {Koike, K and Smith, GJ and Okuda, N and Konno, R and Watanabe, S and Kusunoki, Y and Kawakami, S and van Alen, TA and van Kessel, MAHJ and Yamamoto-Ikemoto, R and Lücker, S and Matsuura, N},
title = {Copper availability controls niche differentiation between comammox Nitrospira and ammonia-oxidizing bacteria.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag135},
pmid = {42465060},
issn = {2730-6151},
abstract = {The biological oxidation of ammonia, the first step of nitrification, is central to biological water purification processes for nitrogen removal. For drinking water treatment, particularly sourced from groundwater, low concentrations of available copper often limit the efficiency of nitrification. Copper dosing both enhances nitrification and affects the composition of the nitrifying microbial community. The mechanisms underlying the effect of copper on nitrifying community composition, ammonia oxidation, and subsequent nitrogen removal processes remain unknown. The objective of this study was to confirm the effects of copper availability on the relative abundance of complete (comammox) and canonical ammonia-oxidizing bacteria (AOB) in nitrifying communities within the drinking water treatment plant and to determine differences in their copper transport mechanisms. Comparative metagenomic analysis revealed that, unlike most AOB, many comammox Nitrospira encode PcoB/CopB-type high-affinity copper uptake systems, indicating that they are more competitive in low-copper environments. This niche adaptation was confirmed in laboratory-scale bioreactors, which showed that comammox Nitrospira became dominant under copper-limited conditions, while AOB dominated at high copper concentrations. Furthermore, specific detection of comammox amoA mRNA by catalyzed reporter deposition-fluorescent in situ hybridization confirmed that the transcriptional activity of comammox Nitrospira was higher compared to AOB under copper limitation. Thus, these results suggest that copper availability may play an important role in shaping the dominant ammonia-oxidizing bacterial guild, with potential implications for engineered water treatment processes.},
}

@article {pmid42465064,
year = {2026},
author = {Zhao, S and Bos, RP and Nakajima, R},
title = {Comparative functional profiles of microbial communities on drifting microplastics and volcanic pumice.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag158},
pmid = {42465064},
issn = {2730-6151},
abstract = {Plastics have been shown in incubation experiments to select for distinct microbial communities from biogenic and inanimate controls, with successional shifts over time. However, few field studies have directly compared microbial communities on free-drifting plastic debris and non-plastic particles. Using shotgun metagenomics, we analyzed the microbial communities adhered to marine microplastics and co-drifting volcanic pumice as a time-tracked control to investigate differences in metabolic potential. Overall, the mature microbial communities on neuston-net collected microplastics and pumice exhibited broad functional and taxonomic similarity, providing suggestive evidence of function convergence. Interestingly, plastic hydrolysis genes, and putative hydrocarbon-degrading bacteria were scarce on both substrates, whereas β-glucan degradation genes were abundant, indicating potential utilization of biofilm-associated carbon sources. Nevertheless, pumice biofilms exhibited substrate-associated enrichment of genes linking to biofilm formation, quorum sensing, nitrogen and phosphonate metabolism, suggesting expanded genomic versatility. Considering the increasing input of anthropogenic and natural inanimate particles may act as environmental perturbations, potentially shaping microbial succession and metabolic potential on floating surfaces. Our findings provide insight into the genomic potential of particle-associated assemblages that stay afloat for months to years, and their metabolic responses to both natural and anthropogenic perturbations.},
}

@article {pmid42465072,
year = {2026},
author = {Li, S and Zeng, H and Wan, X and Chen, Z and Nong, X and Peng, L and Li, Q and Wang, Y},
title = {Characteristics in the uterine cavity microbiota of infertile women with hydrosalpinx or endometrial polyps revealed by shotgun metagenomics.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1825869},
pmid = {42465072},
issn = {2296-858X},
abstract = {Infertility is a global public health issue, and a favorable endometrial environment is essential for successful assisted reproductive treatment. Endometrial polyps (EM) and hydrosalpinx (HD) are common gynecological disorders impairing the intrauterine milieu, but their impacts on uterine cavity microbiota remain unclear. This study enrolled 75 participants [32 fertile controls (C), 32 EM patients, 11 HD patients] to characterize their uterine cavity profiles using shotgun metagenomic sequencing. The C group showed significantly higher microbial alpha diversity than the two patient groups, with no significant difference between EM and HD groups. At the species level, EM group exhibited marked dysbiosis, characterized by elevated pathogenic bacteria, particularly Streptococcus and Streptococcus pneumoniae. HD featured a marked reduction in overall microbial load, decreased absolute abundance of core beneficial bacteria, and a relative increase in Streptococcus and Streptococcus pneumoniae. This study identifies distinct endometrial microbial profiles for EM and HD, providing novel insights into microbiota-mediated mechanisms of infertility. These subtype-specific signatures support the endometrial microbiota as a potential biomarker for infertility, offering clinical targets for antibiotic selection and therapeutic evaluation.},
}

@article {pmid42465457,
year = {2026},
author = {Maier, J and Deshmukh, N and Kleiner, M},
title = {High throughput chromatographic ultra-purification of virus-like particles for downstream viromics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.09.737491},
pmid = {42465457},
issn = {2692-8205},
abstract = {Virus-like particles (VLPs) are an abundant component of microbiomes with critical ecological roles such as population control through viral predation and horizontal gene transfer. Studying the collection of viruses in microbiomes (the virome) through metagenomics has provided important insights into the composition and functions of VLPs in different environments. However, the current gold-standard method for VLP purification, CsCl density gradient ultracentrifugation (CsCl), is low throughput, time consuming and suffers from biases which limits the ability to study viromes in larger sample sets and can interfere with data interpretation. Here we present an anion exchange (AEX) chromatography-based approach for the purification of VLPs from microbiome samples that allows for significant increases in throughput and reproducibility while achieving VLP purity levels similar to or higher than CsCl. We used microbiome samples of known composition to first establish and evaluate the AEX approaches and compare them to CsCl. We implemented the AEX approach both for fast performance liquid chromatography (FPLC) and in multi-well plates. We compared the VLPs purified with CsCl and AEX using shotgun metagenomic sequencing and found that AEX performs similarly to or better than CsCl for purification of VLPs. AEX purified VLP-fractions captured significantly more viral DNA compared to CsCl. We also found that both AEX and CsCl were capable of capturing viruses present at extremely low relative abundances (<0.001%). Additionally, we found that DNase digestion and CsCl may bias against filamentous phage morphologies. Finally, we purified VLPs from conventional murine feces using AEX and CsCl. AEX purified murine fecal VLPs had a much higher viral DNA content (85%) than CsCl (41%). While there were some differences in viral contigs assembled from AEX and CsCl VLP metagenomes, these method unique viral contigs made up only small proportions (<8%) of the relative abundance in the VLP metagenomes. AEX, particularly in the multi-well format, enables the ultrapurification of VLPs from tens to hundreds of samples in a single day thus facilitating virome studies with the large sample numbers needed for translational and clinical research.},
}

@article {pmid42465472,
year = {2026},
author = {Deka, N and Nawrocki, EM and Brauer, AL and Chakraborty, S and Cooper, VS and Armbruster, CE},
title = {Optimized Urine Metagenomic Methods Reveal Longitudinal Microbial Community Dynamics and Predictors of Transition from Asymptomatic Colonization to CAUTI.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.06.736792},
pmid = {42465472},
issn = {2692-8205},
abstract = {BACKGROUND: Urinary tract infections (UTIs) rank among the most common infections globally, with many linked to indwelling urinary catheters. Our prior culture-based longitudinal evaluation of long-term catheterized nursing home residents revealed persistent asymptomatic colonization by pathogens and demonstrated that CAUTI onset was not necessarily due to new pathogen acquisition. In this study, we optimized metagenomics methods to examine the ecological structure underlying persistent colonization and the transition to infection.

RESULTS: We present a comprehensive longitudinal metagenomic analysis of catheterized urine specimens, revealing colonization dynamics of 69 microbial species across 198 samples from 9 individuals. Descriptive ecological metrics were combined with Bayesian mixed-effects models that accounted for repeated within-participant sampling to identify clusters of co-occurring species, determine the impact of perturbations such as antibiotic exposure and catheter changes on community structure, and identify taxa predictive of infection sign and symptom onset. Longitudinal specimens clustered into three main ecological phenotypes: 1) moderate diversity, unstable communities (3 participants); 2) high diversity, stable communities that resisted disruption even after multiple catheter changes (3 participants); and 3) low diversity, pathogen-dominated communities (3 participants). Catheter changes alone did not significantly disrupt community composition, while antibiotic exposures induced major shifts often followed by re-colonization with the same genera within subsequent weeks. Six clusters of species were identified for which relative abundances correlated across perturbations to the microbial community, including a mutually exclusive Enterobacterales cluster and fastidious-anaerobe group cluster. 24 species were found to correlate with onset of signs and symptoms of infection, 11 of which were missed by standard urine culture.

CONCLUSIONS: The catheterized urinary tract represents a novel ecosystem that is resilient to disruption by catheter changes but susceptible to antibiotic perturbation. Antibiotic exposure did deplete all species associated with signs and symptoms but also depleted potentially benign microbes. Our findings have direct implications for catheter management protocols and antibiotic stewardship in long-term catheterized patients. Prospective evaluation using this framework in a larger cohort can help translate these ecological insights into clinical decision-making tools.},
}

@article {pmid42465527,
year = {2026},
author = {Vega Brizneda, M and Lum, J and Wang, H and Yetmar, ZA},
title = {Pulmonary Nocardiosis Diagnosed by Plasma Metagenomic Next-Generation Sequencing in a Patient With Recurrent Febrile Neutropenia.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {2832247},
pmid = {42465527},
issn = {2090-6625},
abstract = {BACKGROUND: Nocardiosis disproportionately affects immunocompromised hosts. Early identification of Nocardia infections is critical as delays can lead to worse outcomes. Species such as N. farcinica are associated with increased risk of dissemination and resistance. Diagnosis of opportunistic infections in immunocompromised populations relies on culture, antigen, or serologic methods that often have limited sensitivity or specificity. Plasma microbial cell-free DNA metagenomic next-generation sequencing (mNGS) offers a noninvasive approach for early diagnosis of opportunistic infections.

CASE PRESENTATION: We report a case of pulmonary nocardiosis in an 87-year-old man with myelodysplastic syndrome and prolonged neutropenia diagnosed by plasma mNGS. He had been hospitalized multiple times with recurrent febrile neutropenia and respiratory symptoms. Standard noninvasive microbiologic workup was unrevealing, but lower respiratory specimens could not be readily obtained. Due to elevated risk of complications from invasive testing, plasma mNGS was used as a complementary tool and identified N. farcinica. Anti-Nocardia therapy was initiated, and his fevers resolved.

CONCLUSION: mNGS is an emerging diagnostic tool that may identify Nocardia species from clinical specimens with a faster turnaround time than culture and enables rapid species identification. Although culture is still recommended for susceptibility testing, mNGS may expedite diagnosis in particular situations. This case supports the role of plasma mNGS as a complementary tool in the evaluation of febrile neutropenia and highlights its diagnostic potential.},
}

@article {pmid42465693,
year = {2026},
author = {Vaher, K and Kenny, A and Lusarreta Parga, P and Jiménez-Sánchez, L and Turner, H and Smikle, R and Corrigan, A and Cruickshank, H and Rudnicka, M and Fletcher-Watson, S and Bogaert, D and Boardman, JP},
title = {From microbes to milestones: Gut bacterial abundances and functional pathways associate with neurodevelopment following preterm birth.},
journal = {Gut microbiology},
volume = {2},
number = {},
pages = {None},
pmid = {42465693},
issn = {3051-1720},
abstract = {The early life gut microbiome has been identified as a potential driver of neurocognitive development. Evidence for this relationship in preterm children, who are at increased risk of both gut microbiome disruptions and neurodevelopmental impairment, is scarce. In a sample of 73 very preterm infants drawn from a prospective birth cohort, we assessed associations between the neonatal gut microbiome and neurodevelopmental outcomes at 9 months and 2 years. The gut microbiome taxonomic and functional profiles were obtained from stool samples collected prior to NICU discharge using shotgun metagenomics. Neurodevelopment was assessed using a battery of outcome measures. We took a consensus-based analytic approach, applying several different methods to investigate microbiome-outcome relationships and focussing on results which were consistently significant across methods. We found the most robust evidence for associations between the abundances of several gut bacterial species and measures related to autistic traits (e.g. Klebsiella spp.), socio-emotional development, including temperament (e.g. Enterobacter cloacae complex, Veillonella parvula), and executive functioning (Clostridium perfringens). The abundances of functional modules involved in gut-brain signalling, particularly those involved in histamine and quinolinic acid metabolism, were associated with outcome measures related to executive functioning and cognitive-behavioural flexibility. This study provides evidence that the neonatal gut microbiome composition may affect longer-term neurodevelopmental profiles following preterm birth, particularly those related to socio-emotional development, autistic traits and executive functioning.},
}

@article {pmid42465842,
year = {2026},
author = {Sun, Y and Yang, S and Wang, M and Xu, H and Wang, S},
title = {Predictors for identifying autoimmune encephalitis in pediatric patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1827367},
pmid = {42465842},
issn = {2235-2988},
mesh = {Humans ; Female ; Child ; *Encephalitis/diagnosis/cerebrospinal fluid/immunology ; Retrospective Studies ; Child, Preschool ; Male ; Risk Factors ; ROC Curve ; *Hashimoto Disease/diagnosis/cerebrospinal fluid ; Infant ; Nomograms ; Adolescent ; },
abstract = {OBJECTIVES: This study aimed to identify the independent predictors and develop a predictive model for autoimmune encephalitis (AE) in pediatric populations.

METHODS: This retrospective study comprised 88 pediatric patients with encephalitis (37 AE cases and 51 non- AE cases) at Children's Hospital Affiliated to Shandong University between May 2020 and April 2025. Lasso regression analysis, univariate and multivariate logistic analysis was used to identify autoimmune encephalitis associated risk factors. The nomogram visualized the results. Receiver operating characteristic (ROC) curves, calibration plots, Brier scoring and decision curve analysis (DCA) were used to evaluate the diagnostic model.

RESULTS: 16 clinical variables significantly differed between the autoimmune encephalitis and non-autoimmune encephalitis groups. Lasso regression analysis, univariate and multivariate logistic analysis identified four significant independent predictors: age (OR: 1.44; 95% CI: 1.09-1.91; P = 0.010), proteins in the cerebrospinal fluid/100(C.Protein.100) (OR: 0.80; 95% CI: 0.65-1.00; P = 0.049), chloride in the cerebrospinal fluid(C. Chloride) (OR: 1.38; 95% CI: 1.00-1.92; P = 0.050), and spontaneous remission (OR: 21.14; 95% CI: 3.17-141.17; P = 0.002) were risk factors for autoimmune encephalitis. The predictive model demonstrated excellent discrimination (AUC 0.976, 95% CI 0.947-1.000) and calibration (Hosmer-Lemeshow p = 0.886, R²=0.9796, Brier score 0.052).

CONCLUSIONS: This study established and validated a high-performance predictive model incorporating four clinically accessible parameters for the diagnosis of pediatric autoimmune encephalitis.},
}

Humans
Female
Child
*Encephalitis/diagnosis/cerebrospinal fluid/immunology
Retrospective Studies
Child, Preschool
Male
Risk Factors
ROC Curve
*Hashimoto Disease/diagnosis/cerebrospinal fluid
Infant
Nomograms
Adolescent

@article {pmid42465845,
year = {2026},
author = {Luo, L and Zhan, J and Wang, Z and Du, X and Li, N},
title = {Application of metagenomic next-generation sequencing in HIV-negative hematogenous disseminated tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1851741},
pmid = {42465845},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; C-Reactive Protein/analysis ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Procalcitonin/blood ; Tuberculosis, Extrapulmonary ; Fibrin Fibrinogen Degradation Products/analysis ; },
abstract = {BACKGROUND: Hematogenous disseminated tuberculosis (Hematogenous disseminated tuberculosis, HDTB) is a rare, critical form of tuberculosis with a high case fatality ratio and is uncommon in HIV-negative patients. Early recognition of this disease is difficult, and limitations of traditional testing methods often lead to delayed diagnosis. This study aims to investigate the value of metagenomic Next-Generation Sequencing (metagenomic Next-Generation Sequencing, mNGS), as a promising tool, in the diagnosis of hematogenous disseminated tuberculosis in HIV-negative (Human Immunodeficiency Virus, HIV) patients.

METHODS: A retrospective analysis was conducted of the clinical data of 10 HIV-negative patients with hematogenous disseminated tuberculosis confirmed by mNGS.

RESULTS: All patients had pre-existing diseases that could lead to impaired immune function. Common symptoms included hyperpyrexia, cough, and dyspnea, and 6 patients developed respiratory failure. C-reactive protein (C-reactive protein, CRP) and procalcitonin (procalcitonin, PCT) levels were both elevated, and PCT was markedly elevated in more than half of the patients, using 0.5 ng/mL as the cutoff value. Most patients had markedly elevated D-dimer levels accompanied by thrombotic events, including 3 patients with concomitant pulmonary embolism. Chest imaging showed patchy pulmonary opacities, and 2 patients had atypical bilateral pleural effusion; these nonspecific findings were easily confused with those of other diseases. Blood mNGS detected Mycobacterium tuberculosis within 2 to 3 days. According to the presence or absence of concomitant pulmonary tuberculosis, the patients were divided into the pulmonary tuberculosis subgroup (pulmonary tuberculosis subgroup, PTB) and the non-pulmonary tuberculosis subgroup (non-pulmonary tuberculosis subgroup, non-PTB). The oxygenation index was significantly lower in the pulmonary tuberculosis subgroup than in the non-pulmonary tuberculosis subgroup (P = 0.037). All cases of pulmonary embolism occurred in the pulmonary tuberculosis subgroup, but the difference was not statistically significant.

CONCLUSIONS: HIV-negative patients with hematogenously disseminated tuberculosis have atypical clinical manifestations and are prone to incorrect diagnosis. The application of mNGS helps shorten diagnostic delays and accelerate disease control, providing an effective supplementary diagnostic pathway when conventional testing methods cannot identify the pathogen.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Male
Female
*Metagenomics/methods
Adult
Middle Aged
C-Reactive Protein/analysis
*Mycobacterium tuberculosis/genetics/isolation & purification
Procalcitonin/blood
Tuberculosis, Extrapulmonary
Fibrin Fibrinogen Degradation Products/analysis

@article {pmid42466125,
year = {2026},
author = {Li, H and Gao, H and Tian, J and Wang, X and Jiang, R and Chen, T and Chen, H and Yang, Y and Zhu, C},
title = {tsAMP: a strain-level antimicrobial peptide identification framework based on large language models and pathogen genomic variation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1842380},
pmid = {42466125},
issn = {1664-302X},
abstract = {INTRODUCTION: Facing the global threat of multidrug-resistant bacteria, antimicrobial peptides (AMPs) represent a promising alternative to conventional antibiotics.

METHODS: To improve computational AMP identification and accuracy of strain-level MIC prediction, we developed tsAMP, a comprehensive framework integrating the ESM-1v protein language model with multidimensional feature extraction. The model was trained on AMP and metagenome-derived non-AMP sequences.

RESULTS: tsAMP achieved an F1-score of 0.958 for AMP identification, outperforming state-of-the-art tools. For bacterial inhibition prediction, tsAMP consistently maintained F1-scores above 0.8 across 33 pathogenic species. In strain-specific MIC prediction, it attained high performance (MSE = 0.214, R [2] = 0.634) for 10 bacterial species' strains. To assess predictive reliability, the model was benchmarked against published experimentally determined MIC values for AMPs targeting Micrococcus luteus, yielding low prediction error (MSE = 0.1489) and strong ranking consistency (NDCG = 0.791). Computational benchmarking against published relative MIC data for diverse E. coli strains further demonstrated the model's ranking accuracy (NDCG > 0.85) and consistent strain-level differentiation. Applied to the Mgnify_genome database, tsAMP identified 8,277 putative AMP candidates in silico and revealed distinct predicted antimicrobial activity patterns across pathogens.

DISCUSSION: tsAMP provides a computational framework to facilitate the identification of AMP candidates and support prioritization for downstream experimental characterization. The code is available on GitHub at https://github.com/YangLab-BUPT/tsAMP.},
}

@article {pmid42466130,
year = {2026},
author = {Kumar, V and Ahmad, F and Rai, A and Kushwaha, A and Parmar, K and Singh, R and Tomar, A and Kumar, C},
title = {Multi-omics and synthetic microbial ecology for engineering climate-resilient phytobiomes in cold-arid agroecosystems: current advances and future perspectives.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1876810},
pmid = {42466130},
issn = {1664-302X},
abstract = {Extreme environmental stressors, including freezing temperatures, strong ultraviolet radiation, and nutrient scarcity, pose a serious threat to global food security in high-altitude cold-arid agroecosystems. Ecological stability depends on the phytobiome, which is made up of plant hosts, their microbiomes, and the edaphic environment. Although plant-associated microbiomes are important in providing stress tolerance, existing management strategies predominantly employ descriptive single-strain inoculants, which often fail under open field conditions due to competitive exclusion and environmental drift. The review summarizes recent mechanistic insights into how psychrotolerant microorganisms modify host physiology to alleviate low-temperature stress. We examine the biophysical and biochemical processes involved, with a particular emphasis on the microbial impact on the host plant's internal ICE1-CBF-COR transcriptional cascade and redox homeostasis, the role of biofilm-mediated extracellular polymeric substances (EPS) in root-zone thermal buffering, and the kinetic inhibition of ice crystallization by antifreeze proteins. Furthermore, we evaluate how genome-scale metabolic modeling can be combined with sophisticated integrated multi-omics approaches, particularly metagenomics, metatranscriptomics, and metabolomics, to create structurally stable synthetic microbial communities (SynComs), going beyond traditional isolation methods. Lastly, we discuss how regional microbial biobanks and ecological network modeling can maximize consortia persistence, addressing the translational obstacles that prevent laboratory-scale efficacy from reproducing in the field. This synthesis presents a methodical approach for creating robust phytobiomes in vulnerable mountain agroecosystems by moving the emphasis from descriptive cataloging to predictable, function-driven synthetic ecology.},
}

@article {pmid42466390,
year = {2026},
author = {Buro, AW and Gomez, MF and Kim, Y and Ward, NP and Umbarger, M and Ma, L and Vala, A and Hogue, S and Silva, WV and Bailey, A and Pierce, CM and Kim, Y and DeNicola, GM and Byrd, DA and Robinson, LA},
title = {Metagenomic and Metabolomic Correlates of Immunotherapy Response in Non-Small Cell Lung Cancer.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10107631/v1},
pmid = {42466390},
issn = {2693-5015},
abstract = {Background The gut microbiome may influence cancer treatment response, perhaps by immune system interactions, but studies are limited among non-small cell lung cancer (NSCLC) patients. We investigated associations of the pre-treatment gut microbiome and serum metabolome/lipidome with immune checkpoint inhibitor (ICI) response among patients with stage III-IV NSCLC. Methods We conducted an observational cohort study with fecal and blood collection among 66 patients with stage III-IV NSCLC undergoing ICI therapy, using an updated definition of clinical benefit. Fecal whole genome sequencing, plasma untargeted metabolomics, and serum lipidomics were conducted using liquid chromatography mass spectrometry. Multivariable logistic regression estimated associations of alpha/beta diversity, microbial abundance, metabolites, and lipids with clinical benefit. Microbial taxa, metabolites, lipids, and significant lipids correlations were examined. Results Microbiome composition (beta diversity) differed between participants with and without clinical benefit (P = 0.03). Those with higher relative abundance of Bifidobacterium were less likely (OR per 1-SD = 0.51, 95%CI = 0.25-0.92, P = 0.04) to have clinical benefit. Those with higher Ruminococcus prevalence were more likely (OR = 7.00, 95%CI = 1.80-34.47, P = 0.01) to have clinical benefit. Clinical benefit participants had higher serum concentration of 4-Imidazoleacetate (OR = 6.34, 95%CI = 2.36-22.29, P = 0.001), 6-Bromotryptophan (OR = 3.84, 95%CI = 1.80-10.17, P = 0.002), and lyso-phosphatidylcholines (OR = 4.52, 95%CI = 1.59-17.19, P = 0.01) compared to no clinical benefit, though these findings were not statistically significant after multiple corrections. Conclusions This hypothesis-generating study found Ruminococcus was positively, and Bifidobacterium inversely, associated with ICI response among NSCLC patients. The gut microbiome and related metabolites/lipids were found to be associated with ICI clinical benefit among NSCLC patients. Larger, diverse longitudinal studies are needed to clarify the associations of the microbiome and related metabolites with ICI response among NSCLC patients.},
}

@article {pmid42466699,
year = {2026},
author = {Touati, A and Boufahja, F and Ben Hamadi, N and Touaitia, R and Idres, T},
title = {Artificial Intelligence Applications in Antimicrobial Resistance: Comprehensive Review of Predictive Models, Diagnostic Innovations, and Clinical Integration.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {10766294261467803},
doi = {10.1177/10766294261467803},
pmid = {42466699},
issn = {1931-8448},
abstract = {Antimicrobial resistance (AMR) represents a critical global health crisis, driving increased mortality, treatment failure, and economic burden. Artificial intelligence (AI) offers transformative potential to counter this threat by enhancing detection, diagnostics, and therapeutic precision. This narrative review synthesizes recent advances in AI-based approaches for AMR prediction, antimicrobial discovery, and clinical decision support, drawing on representative peer-reviewed studies published between January 1, 2015, and April 24, 2026. Models such as Deeparg-LS, XGBoost, and vision transformers achieved remarkable predictive accuracy using genomic, spectroscopic, and clinical data (AUC > 0.90; sensitivity/specificity >95%). AI-driven clinical decision support systems reduced antibiotic mismatches by up to 67%, while generative algorithms accelerated antimicrobial peptide discovery with 76% validation success. Deep learning frameworks improved metagenomic resistance profiling, and microscopy-based diagnostics shortened antimicrobial susceptibility testing by 50-70%. However, major challenges persist, including dataset heterogeneity, computational intensity, limited model transferability, and ethical concerns related to data privacy, bias, and interpretability. Emerging strategies such as explainable AI and federated learning show promise in addressing these issues. Overall, AI stands as a pivotal enabler in the fight against AMR, with future progress hinging on interdisciplinary collaboration, standardized validation, and responsible integration into clinical practice.},
}

@article {pmid42466871,
year = {2026},
author = {Jin, C and Chen, Q and Liu, X and Liu, H and Wang, Y},
title = {The functional structure of foxtail millet rhizoplane microbiome and its association with yield.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0070726},
doi = {10.1128/spectrum.00707-26},
pmid = {42466871},
issn = {2165-0497},
abstract = {UNLABELLED: Root-associated microbial communities profoundly influence plant growth and productivity. Although the rhizosphere microbiome has been extensively studied, the functional distinctiveness and host-specific role of the closely adhering rhizoplane microbiota remain unclear. In this study, we performed deep metagenomic sequencing of both the rhizosphere and rhizoplane microbiomes in foxtail millet (Setaria italica). We constructed a comprehensive non-redundant gene catalog, reconstructed 595 metagenome-assembled genomes (MAGs), and analyzed the co-occurrence networks. Our results revealed that the rhizoplane sustains a core microbial network with greater complexity and connectivity than rhizospheres. Metabolically, the rhizoplane microbiome is enriched in the functions underlying host adaptation, including ammonium production and polysaccharide decomposition. Our results showed that the associations between microbial features (taxonomic and functional) and yield were significantly stronger in the rhizoplane than in the rhizosphere. We identified 22 yield-positive MAGs, primarily from Bacillales, harboring genes for plant growth-promoting traits, such as nutrient solubilization and phytohormone synthesis. Collectively, our findings illustrate that the rhizoplane is not only a subset of the rhizosphere but also a critical host-microbe interface and functional hotspot where specialized microbial processes are directly coordinated to enhance plant performance and yield.

IMPORTANCE: Plant roots selectively recruit diverse and beneficial microorganisms from the surrounding soil, assembling a distinctive rhizosphere microbiome. Substantial research, primarily utilizing amplicon sequencing, has elucidated the taxonomic composition of these rhizosphere communities across a wide range of plant species. The functional architecture, assembly processes, and coexistence mechanisms of the rhizoplane microbiome remain poorly understood, and their link to host plant traits is unclear. We elucidate the taxonomic and functional structural disparities between the rhizosphere and rhizoplane microbiomes, thereby clarifying the composition and functional roles of the rhizoplane microbiome, and further examine the association between the rhizoplane microbiome and millet yield. A deeper understanding of root-associated microbial communities may inform the development of effective agricultural probiotics, thereby enhancing sustainable farming practices. Additionally, the candidate biomarkers identified in this work offer potential targets for improving cultivation practices and supporting the long-term agricultural sustainability of foxtail millet.},
}

@article {pmid42466883,
year = {2026},
author = {Han, H and Qian, Q and Wu, W and Yang, J and Zhou, J and Sun, W},
title = {Diabetes-associated Parvimonas enrichment and altered lung microbiota profiles in lower respiratory tract infection: an analysis of 632 metagenomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0404825},
doi = {10.1128/spectrum.04048-25},
pmid = {42466883},
issn = {2165-0497},
abstract = {The homeostasis of pulmonary microbiota is crucial in maintaining human health and modulating disease progression. The stability of pulmonary microbial flora may be associated with diabetes, yet the specific alterations remain poorly characterized. This retrospective observational study aims to analyze the profiles in pulmonary microbiota between individuals with and without diabetes, using metagenomic next-generation sequencing (mNGS). A total of 632 patients were sequentially enrolled, including 77 patients with both pneumonia and diabetes, 46 patients without either pneumonia or diabetes, 499 patients with pneumonia but without diabetes, and 10 diabetic patients without pneumonia. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA). The lung microbiota of diabetic individuals significantly differs from that of non-diabetic individuals in the non-lower respiratory tract infection (non-LRTI) cohort. Parvimonas was more abundant in the diabetic group. Compared to non-diabetic patients with LRTI, those with diabetes and LRTI showed an increased relative abundance of Parvimonas, but decreased relative abundances of Prevotella and Malassezia. Our analysis revealed a negative correlation between Parvimonas and Malassezia, alongside a positive association of Parvimonas with the expression of antimicrobial resistance genes ICR-Mc and RbpA. This suggests a potential association between Parvimonas enrichment and microbial dysbiosis during infection, although the underlying host-microbe interactions require further validation. Interestingly, Parvimonas abundance showed no significant association with HbA1c levels. Our findings suggest that Parvimonas enrichment is associated with diabetes-related alterations in lower respiratory tract microbiota. Whether microbiota-associated alterations represent clinically actionable targets in diabetic patients with pulmonary infections remains to be determined in prospective and interventional studies.IMPORTANCEThis study reveals significant differences in lung microbiota between diabetic and non-diabetic individuals. Parvimonas was enriched in the diabetic lung, and its abundance correlated with the expression of antimicrobial resistance genes, such as ICR-Mc and RbpA. Surprisingly, microbial dysbiosis was independent of HbA1c levels, indicating that mechanisms other than glycemic control contribute to infection progression. This study suggests that Parvimonas enrichment may be a diabetes-associated microbial feature in bronchoalveolar lavage fluid (BALF) microbiota, but its potential diagnostic or clinical relevance requires validation in future studies. Our work provides a scientific foundation for optimizing infection prevention and advancing precision anti-Parvimonas therapies.},
}

@article {pmid42466908,
year = {2026},
author = {Fairusya, N and Wang, R and Honda, R},
title = {Plasmid-mediated antimicrobial resistance across One Health sectors: transmission dynamics and surveillance needs.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0019226},
doi = {10.1128/msphere.00192-26},
pmid = {42466908},
issn = {2379-5042},
abstract = {Antimicrobial resistance (AMR) is increasingly recognized as a One Health challenge driven by the continuous exchange of resistant bacteria and resistance determinants across human, animal, and environmental sectors. While genomic surveillance has substantially improved detection of antimicrobial resistance genes (ARGs), most monitoring frameworks remain gene- or isolate-centric, limiting insight into the mechanisms that govern resistance transmission and persistence. Recent evidence indicates that plasmids, self-replicating mobile genetic elements (MGEs) capable of horizontal transfer across bacterial species, play an important role in disseminating clinically relevant resistance determinants across sectors. In this mini-review, we synthesize genomic and ecological evidence demonstrating that a limited number of plasmid incompatibility (Inc) groups recur across human, animal, and environmental reservoirs, often independent of bacterial host lineages. We highlight how plasmid transmission dynamics are shaped by host-independent mobility, ecological generalism, co-selection with accessory traits, and persistence in engineered and natural environments. We further examine why current AMR surveillance approaches, including ARG-centric metagenomics and isolate-based monitoring, systematically overlook these plasmid-mediated processes. Furthermore, we propose that plasmid-resolved analysis represents a critical and currently underutilized complementary layer for One Health AMR surveillance. Integrating plasmid classification and genomic reconstruction into wastewater-based epidemiology and cross-sector monitoring frameworks can improve attribution of transmission pathways, enhance early detection of high-risk resistance, and provide a mechanistic foundation for risk-informed intervention strategies.},
}

@article {pmid42467010,
year = {2026},
author = {Umekage, S},
title = {Shallow shotgun metagenomic sequencing of wild yeast communities enriched in ethanol-containing koji extract medium.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0034626},
doi = {10.1128/mra.00346-26},
pmid = {42467010},
issn = {2576-098X},
abstract = {I report the shallow shotgun metagenomic sequencing data of three ethanol-enriched wild yeast communities cultured in an ethanol-containing koji extract medium.},
}

@article {pmid42467174,
year = {2026},
author = {Zhao, M and Shi, Q and Zhao, L and Wang, M and Li, J and Wan, Z and Ouyang, T and Yu, Y},
title = {Severe pneumonia and acute respiratory distress syndrome caused by avian influenza A (H10N3) in a young female: a case report.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42467174},
issn = {1439-0973},
abstract = {BACKGROUND: Human infection with avian influenza A (H10N3) is a rare but severe emerging zoonotic disease. To date, only a limited number of cases have been reported, which restricts a comprehensive understanding of its clinical features and public health risks. We report the fourth documented case of human H10N3 infection, which is the first to be identified in a female patient. Additionally, we compared the clinical and genomic characteristics of all four cases.

CASE PRESENTATION: A 23-year-old female with no prior comorbidities developed severe pneumonia and acute respiratory distress syndrome due to infection with avian influenza A (H10N3) virus. The patient, working in a fresh market with recent training at a slaughterhouse, presented a one-week history of high fever, cough, and dyspnea. Despite initial broad-spectrum antibiotics, her condition rapidly worsened, requiring mechanical ventilation and veno-venous extracorporeal membrane oxygenation (V-V ECMO). Metagenomic next-generation sequencing of bronchoalveolar lavage fluid, confirmed by the Centers for Disease Control and Prevention, identified avian influenza A (H10N3). Following approximately three months of intensive treatment, the patient recovered and was discharged. Phylogenetic analyses showed that her virus strain was closest to the third human H10N3 case (Kunming, China, 2024). In addition, this strain had a human-adapted substitution (P221) but lacked the G228S substitution in the haemagglutinin protein, suggesting that the latter is not essential for human infection.

CONCLUSIONS: This case highlights the potential for severe human infection by the H10N3 virus. It is imperative that surveillance is enhanced in both human and animal populations.},
}

@article {pmid42467233,
year = {2026},
author = {Liu, W and Tang, Q and Shen, M and Zhang, L and Jia, X},
title = {Conditional superiorities and unaddressed bottlenecks: a critical review of artificial intelligence for waterborne microbial detection.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13917-8},
pmid = {42467233},
issn = {1432-0614},
abstract = {Although conventional microbial detection approaches for water samples are widely applied, they still suffer from prolonged assay durations (24-72 h), low sensitivity, and the absence of real-time monitoring capacity. Artificial intelligence (AI) has demonstrated conditional advantages in specific experimental environments, such as achieving a sensitivity of 99% for detecting Cryptosporidium and Giardia in low turbidity water (based on approximately 12,000 annotated images, using fivefold cross validation, completed under laboratory conditions); however, such advantages tend to diminish or vanish in high-turbidity water matrices or when training datasets are insufficient. This review critically evaluates four categories of AI-driven approaches: image-based analysis, spectroscopic techniques, genome, and metagenomic sequencing, as well as predictive pollution modeling. While AI helps boost detection efficiency, precision, and analytical capacity, a set of long-standing obstacles restrict its real-world deployment. The main issues involve non-standardized datasets, low model interpretability, weak generalization over various water substrates, and a substantial gap between lab-based performance and on-site operational outcomes. In summary, to fully exploit the capabilities of AI in aquatic microbial detection, greater emphasis should be placed on on-site validation, unified data specifications, and practical performance benchmarks, rather than further algorithmic innovation. This review seeks to provide practical references for scholars and practitioners working in the fields of microbiology, AI and water quality monitoring and management. KEY POINTS: • AI shows favorable performance for microbial detection under lab conditions. • Model performance declines greatly in complex water with many practical barriers. • Standardized data and validation will advance real-world application.},
}

@article {pmid42467464,
year = {2026},
author = {Savin, M and Hayer, JJ and Mutters, NT and Erler, T and Simon, S and Griesdorn, L and Steinhoff-Wagner, J and Hammerl, JA and Heinemann, C and Probst, AJ},
title = {Lineage-aware comparison of extended-spectrum β-lactamase-producing Escherichia coli from unweaned dairy calves and human references reveals host-structured plasmidomes and co-selection.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001783},
pmid = {42467464},
issn = {2057-5858},
mesh = {Animals ; Cattle ; *Plasmids/genetics ; *Escherichia coli/genetics/isolation & purification/classification/drug effects/enzymology ; *beta-Lactamases/genetics/metabolism ; Humans ; *Escherichia coli Infections/microbiology/veterinary ; Phylogeny ; Germany ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial resistance in Escherichia coli is shaped not only by resistance genes themselves but also by their chromosomal or plasmid localization and co-occurrence with biocide/metal resistance genes (BMRGs), virulence-associated genes and mobile genetic elements. We applied chromosome- and plasmid-resolved genomics to 109 extended-spectrum β-lactamase-producing E. coli isolates from unweaned dairy calves (n=484) in Germany and compared them with 479 human-associated reference genomes. Calf isolates were polyclonal and dominated by phylogroups A and B1. Resistance was predominantly plasmid-borne: 41% of isolates carried antibiotic resistance genes (ARGs) exclusively on plasmids, whereas only 4.6% carried ARGs exclusively on chromosomes. The chromosomal-versus-plasmid distribution of acquired ARGs differed significantly across phylogroups (P<0.05) and sequence types (all P<0.01). Conjugative plasmids accounted for 94.6% of plasmid-borne ARG occurrences and carried significantly more ARGs than mobilizable plasmids (P=3.66×10[-42]). ARG and BMRG counts were strongly correlated at the plasmid level (ρ=0.574, P=8.0×10[-41]), and class 1 integrons marked enriched multidrug plasmids with increased ARGs (P=6.22×10[-34]) and BMRGs (P=3.00×10[-29]). At the isolate level, calf isolates carried more acquired ARGs in unadjusted comparisons, but this host-associated difference was largely explained by population structure. At the plasmid level, however, host-associated differences persisted after adjustment: human plasmids carried more ARGs (IRR 1.66, P=0.0017) and showed a strong host×mobility interaction (IRR 4.61, P=4.9×10-8), stronger ARG-BMRG coupling and a higher prevalence of integrons. These findings show that antimicrobial resistance ecology in E. coli is shaped not only by which resistance genes are present, but by where they are located, what they are linked to and how readily their genomic carriers can disseminate.},
}

Animals
Cattle
*Plasmids/genetics
*Escherichia coli/genetics/isolation & purification/classification/drug effects/enzymology
*beta-Lactamases/genetics/metabolism
Humans
*Escherichia coli Infections/microbiology/veterinary
Phylogeny
Germany
Anti-Bacterial Agents/pharmacology

@article {pmid42467473,
year = {2026},
author = {Donoso, A and Pérez, AB and Lopez-Dosil, M and Vázquez, A and Gámbaro, F and Sánchez-Seco, MP and Martinez-Martinez, L and Cabrerizo, M and Tarragó, D and Fernandez-Garcia, MD},
title = {Human pegivirus, Toscana virus and herpesviruses identified in cerebrospinal fluid from adults with unexplained neurologic disease, Spain, 2022-2023.},
journal = {The Journal of general virology},
volume = {107},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002302},
pmid = {42467473},
issn = {1465-2099},
mesh = {Humans ; Spain/epidemiology ; Male ; Female ; Adult ; Retrospective Studies ; *Sandfly fever Naples virus/isolation & purification/genetics ; *Pegivirus/genetics/isolation & purification ; Middle Aged ; *Nervous System Diseases/virology/cerebrospinal fluid ; Aged ; *Herpesviridae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; *Flaviviridae Infections/cerebrospinal fluid/virology ; *Cerebrospinal Fluid/virology ; },
abstract = {Viral central nervous system (CNS) infections in adults frequently remain unresolved after routine diagnostic testing. We applied probe-based viral metagenomic next-generation sequencing (vmNGS) to cerebrospinal fluid samples from adults with suspected CNS infection and negative conventional diagnostics in a retrospective multicentre study conducted in Spain between 2022 and 2023. Among 40 idiopathic cases, vmNGS detected viral sequences in 6 patients without evidence of coinfection: human pegivirus (HPgV, n=3), Toscana virus (TOSV, n=1), herpes simplex virus type 1 (HSV-1, n=1) and varicella-zoster virus (VZV, n=1). Two HPgV-positive patients were transplant recipients, with neurological disease occurring more than 2 years after transplantation, compatible with possible long-term viral persistence in immunocompromised hosts. TOSV genotype B was identified in a patient residing in central Spain, supporting consideration of TOSV in selected cases of unexplained aseptic meningitis during the vector season, including outside traditionally recognized Mediterranean coastal regions. Furthermore, the failure of syndromic panel testing to detect HSV-1 and VZV highlights the need for complementary diagnostic strategies when clinical suspicion remains high. Overall, the detection of unexpected viral sequences, together with missed clinically actionable infections, supports the use of complementary molecular testing in selected cases of unexplained CNS syndromes when routine diagnostics are negative. These findings highlight the added diagnostic value of vmNGS and provide sequence-level data for future studies of viral diversity and molecular epidemiology in neurological disease.},
}

Humans
Spain/epidemiology
Male
Female
Adult
Retrospective Studies
*Sandfly fever Naples virus/isolation & purification/genetics
*Pegivirus/genetics/isolation & purification
Middle Aged
*Nervous System Diseases/virology/cerebrospinal fluid
Aged
*Herpesviridae/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing
*Flaviviridae Infections/cerebrospinal fluid/virology
*Cerebrospinal Fluid/virology

@article {pmid42467734,
year = {2026},
author = {Dai, G and Yao, S and Chen, W and Zhang, J and Du, X and Zhao, Y and Jin, Z and Zhang, G},
title = {Ephrin B2 and Ephrin B3 are receptors for a novel putative henipavirus with zoonotic potential.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {7},
pages = {e0014557},
doi = {10.1371/journal.pntd.0014557},
pmid = {42467734},
issn = {1935-2735},
abstract = {Next-generation sequencing has accelerated the discovery of novel putative viruses in wildlife reservoirs, while identifying those with zoonotic potential remains challenging. In this study, we report the identification and characterization of Ailong virus, a novel putative henipavirus from previous bat metagenomes in China that utilizes human ephrin B2 (EFNB2) and EFNB3 as functional receptors. Using an integrated approach combining phylogenetic analysis, pseudotyped virus entry assays, antibody blockade assays, and structural modeling, we demonstrate that Ailong virus glycoprotein binds human EFNB2 and EFNB3 with high specificity, mediating pseudovirus entry into both human neuronal and respiratory epithelial cells. Structural analysis revealed the Ailong virus glycoprotein-EFNB2 interface closely resembling that of Nipah virus (NiV), with conservation of all critical receptor-binding residues. Moreover, AiV encodes an exceptionally large phosphoprotein, 1,033 amino acids in length, which is larger than any other known phosphoprotein in the subfamily Paramyxoviridae. Given its receptor usage, structural similarities to NiV, and efficient entry in human airway epithelia, Ailong virus is believed to pose a spillover risk.},
}

@article {pmid42467857,
year = {2026},
author = {Majumdar, A and Upadhyay, MK and Ghosh, A and Biswas, R and Loizou, IK and Buck, M and Tibbett, M and Giri, B and Moulick, D and Kumar Jaiswal, M and Roychowdhury, T},
title = {Revolutionising Agricultural Sustainability: New 'Furrow Tillage' can Mitigate Short-Term Soil-to-Atmosphere CO2 Flux and Promote Soil-Plant-Microbe Health.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76645},
doi = {10.1002/advs.76645},
pmid = {42467857},
issn = {2198-3844},
support = {PDF/2022/001418/LS//National Postdoctoral Fellowship scheme, Ministry of Education, Government of India/ ; 101152605//Marie Skłodowska-Curie-UKRI Postdoctoral Fellowship scheme, United Kingdom/ ; EP/Z002664/1//Marie Skłodowska-Curie-UKRI Postdoctoral Fellowship scheme, United Kingdom/ ; },
abstract = {Global agricultural carbon loss demands refined tillage practices. This study evaluates a hybrid furrow tillage field (FTF) approach that combines the bed geometry of conservation tillage with controlled, localised disturbance of conventional tillage. Distinct from strip-tillage and permanent-bed planting, FTF is designed for puddled, lowland rice systems, featuring a continuously water-filled furrow and an alternately wet-dry mid-bed. A two-year, twelve-site field trial across the Gangetic deltaic plain of West Bengal, India, assessed FTF through agronomy, geochemistry, crop physiology, and molecular microbiology, and presented all CO2-flux and labile-carbon results as short-term responses. FTF produced CO2 efflux comparable to no-tillage (3.94-4.38 vs. 2.43-2.84 g C m[-] [2] d[-] [1]) while sustaining nutrient bioavailability close to conventional deep tillage (6.29-7.11 g C m[-] [2] d[-] [1]), demonstrating that hybrid bed-and-furrow geometry can decouple short-term CO2 flux from nutrient-mineralisation benefits. Microbial diversity and gene-ontology profiles indicate active microbial interactions with reduced soil-to-atmosphere CO2 transfer. Molecular modelling identifies AmtB and HypC-HypD as candidate CO2-handling routes; mid-bed physical properties independently contribute to flux reduction. Long-term SOC stability requires multi-year, multi-soil-order validation with isotopic partitioning. The study integrates CO2 flux chambers, Kriging interpolation, elemental bioavailability analysis, plant ultrastructural observation, metagenomics, and molecular modelling.},
}

@article {pmid42467901,
year = {2026},
author = {Zhang, M and Yu, Y and Zhang, X and Qu, F and Chen, N},
title = {Climate-Driven Harmful Algal Blooms Impair the Coastal Nitrogen Filter and Shift Denitrification Pathways toward N2O Accumulation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01472},
pmid = {42467901},
issn = {1520-5851},
abstract = {Climate change is expanding harmful algal blooms (HABs) beyond nutrient-driven paradigms, yet their effects on coastal nitrogen cycling remain poorly understood. Here, we investigated a climate-driven dry-season Phaeocystis globosa bloom in Xiamen Bay, a subtropical coastal embayment, using field observations, isotopic incubations, and metagenomics. Contrary to the conventional view that HABs stimulate denitrification, the bloom suppressed sedimentary denitrification by ∼70% and reduced total dissolved excess gaseous nitrogen (ΔN2 + ΔN2rO) by ∼50% relative to the pre-bloom period. Despite this decline in nitrogen removal, N2O yield (ΔN2O/(ΔN2 + ΔN2O)) increased by approximately an order of magnitude from 0.04% to 0.30%, indicating a shift toward incomplete denitrification. This shift was linked to a sulfur-mediated microbial reorganization. In seawater, sulfur-metabolizing denitrifiers, particularly Roseobacter, capable of utilizing algal-derived sulfur compounds (e.g., DMSP), were enriched and became dominant. These taxa harbored clade I nosZ, whose sensitivity to oxygen and pH likely constrained N2O reduction. In sediments, chemolithoautotrophic sulfur-oxidizing denitrifiers, particularly Sulfurovum, became dominant and were associated with reduced N2 production. Together, these compartment-specific responses weakened denitrification and shifted its end-product composition toward a higher N2O share, revealing a sulfur-coupled microbial mechanism by which climate-driven HABs impair the coastal nitrogen filter.},
}

@article {pmid42468181,
year = {2026},
author = {Zhang, H and Zhu, L and Zhao, X and Wu, Z},
title = {Metagenomic next-generation sequencing identifies Ureaplasma parvum in culture-negative peritoneal dialysis-associated peritonitis complicated by COVID-19: a case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {3},
pages = {117554},
doi = {10.1016/j.diagmicrobio.2026.117554},
pmid = {42468181},
issn = {1879-0070},
abstract = {Ureaplasma parvum is a fastidious, cell wall-deficient urogenital commensal that is rarely reported in peritoneal dialysis-associated peritonitis (PDAP) and often missed by routine culture. We describe a 43-year-old woman with stage 5 chronic kidney disease receiving maintenance peritoneal dialysis who presented with abdominal pain, diarrhea, fever, and cloudy effluent. The effluent nucleated cell count was 223/μL, with 85.3% neutrophils, and CT showed abdominopelvic fluid with mild irregular peritoneal thickening. Empirical broad-spectrum therapy failed, while repeated blood and effluent cultures remained negative. Metagenomic next-generation sequencing (mNGS) of peritoneal effluent identified U. parvum, confirmed by species-specific nucleic acid testing. Doxycycline therapy and catheter removal led to defervescence. Although coronavirus disease 2019 (COVID-19), inflammatory pulmonary changes, and colitis complicated the course, she recovered with targeted and supportive treatment. No recurrence occurred during 2 years of follow-up. However, because paired genital and intestinal specimens were not analyzed, the exact route of infection remains unconfirmed, which is a limitation of this study. CLINICAL TRIALS REGISTRATION: ChiCTR2600120155.},
}

@article {pmid42468189,
year = {2026},
author = {Wan, S and Huang, W and Zhang, Z and Liu, X and Dong, W and Chen, Y and Ke, L and Yang, Q and Chen, S and Hu, Y and Zhang, Y},
title = {Microbial succession and flavor-related metabolic potential during industrial eight-round mechanized stacking fermentation of Maotai-flavor Baijiu.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111975},
doi = {10.1016/j.ijfoodmicro.2026.111975},
pmid = {42468189},
issn = {1879-3460},
abstract = {Mechanized production of Maotai-flavor Baijiu (MFB) is increasingly adopted in the Baijiu industry; however, microbial succession and flavor-related metabolic potential throughout the complete eight-round mechanized stacking fermentation (SF) process remain insufficiently understood. In this study, microbial communities, functional genes, physicochemical properties, and volatile compounds during SF were investigated using metagenomic sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC/MS). A total of 168 volatile compounds were detected, of which 41 representative compounds were selected for further analysis. Among them, 15 differential volatiles were identified by PLS-DA, with furfural showing the highest abundance. Microbial profiling revealed pronounced community differentiation and continuous succession across fermentation rounds. Acidity, starch, and reducing sugars were significantly associated with microbial community variation, with acidity and starch exhibiting the strongest associations. In the initial round (R1), microbial communities were mainly derived from raw materials and Daqu. Bacterial communities shifted from lactic-acid-bacteria-enriched communities to those characterized by Kroppenstedtia and Bacillus, whereas fungal communities transitioned from yeast-enriched stages to mold-enriched and mold-yeast coexistence stages. Metagenome-inferred functional annotation, co-occurrence network, and correlation analyses suggested potential links between microbial succession and flavor-related metabolic pathways. Yeasts were mainly associated with ethanol- and organic-acid-related metabolism during the early stage, whereas Bacillus and Kroppenstedtia were linked to predicted starch-degradation and organic-acid-related pathways during the middle and late stages. Overall, this study provides a comprehensive characterization of microbial succession and metagenome-inferred flavor-related metabolic potential during mechanized SF and offers reference data for process monitoring and quality management in MFB production.},
}

@article {pmid42468214,
year = {2026},
author = {Wei, T and Chen, J and Zhang, Q and Song, M and Lin, Z and Qiu, R and Luo, C},
title = {Effects of maize and peanut cultivation on microbial degradation of dibutyl phthalate in agricultural soil.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120510},
doi = {10.1016/j.ecoenv.2026.120510},
pmid = {42468214},
issn = {1090-2414},
abstract = {Phthalate esters (PAEs) widely contaminate agricultural soils. Although microbes can degrade PAEs, how plants influence this process remains unclear. Using DNA-stable isotope probing and metagenomics, this study investigated the influence of plants on microbial degradation of PAEs by soil bacteria. Our results revealed that maize and peanut, representing non-legumes and legumes, exerted contrasting impacts on PAE microbial degradation. Specifically, peanut cultivation significantly enhanced PAE biodegradation efficiency by 26.53% compared to unplanted soil, whereas maize inhibited the process by 33.97%. Mechanism-driven analyses indicated that peanut facilitated PAE biodegradation by enriching active degraders and key degrading genes (e.g., pcaF, xylF, and benB-xylY) involved in biodegradation pathway II, recruiting Bacteroidetes, and alleviating nitrogen limitation (evidenced by increased abundances of nrfH, rhlA, and gspD). Furthermore, peanut cultivation promoted synergistic microbial interactions by increasing the diversity of taxa positively correlated with PAE degraders. In contrast, maize inhibited biodegradation by disrupting these processes and energy metabolism. This study sheds light on the plant-specific mechanisms driving PAE dissipation in soil.},
}

@article {pmid42458280,
year = {2026},
author = {Wu, L and Wang, J and Zhu, J and Li, T and Chen, Y and Luo, L and Zhang, Y and Ning, S and Li, B},
title = {Rare primary small intestinal infection: a case report of Mycobacterium kansasii enteropathy in an immunocompetent patient and literature review.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13817-2},
pmid = {42458280},
issn = {1471-2334},
abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) are important opportunistic pathogens that most commonly infect the lungs. Primary involvement of the gastrointestinal tract-especially the small intestine-is exceedingly rare, and small-bowel infection caused by Mycobacterium kansasii (M. kansasii) has seldom been reported.

CASE PRESENTATION: We describe an extremely rare case of primary small-intestinal M. kansasii infection in an immunocompetent young man who presented with prolonged chronic diarrhea and fever. After an extensive but unrevealing diagnostic work-up, the etiology was finally established by microbial metagenomic sequencing of tissue obtained by double-balloon endoscopy. Building on the initial regimen of ethambutol hydrochloride, rifampicin, and clarithromycin-and with subsequent antibiotic adjustments tailored to the patient's evolving symptoms-clinical symptoms resolved completely, and follow-up endoscopy showed mucosal improvement.

CONCLUSION: This case underscores that NTM infection should be considered in the differential diagnosis of unexplained chronic gastrointestinal symptoms and highlights the pivotal role of modern molecular techniques in reaching a precise diagnosis. Detailed analysis of the case together with a review of the literature aims to raise clinicians' awareness and improve management of this rare entity.},
}

@article {pmid42458473,
year = {2026},
author = {Gupta, E and Sharma, S and Tikar, SN and Dash, PK},
title = {Exploration of viral diversity in Aedes mosquitoes employing different shotgun metagenomic data analysis pipelines.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03249-4},
pmid = {42458473},
issn = {1743-422X},
abstract = {Metagenomics or metaviromics is emerging as a powerful technology for pathogen surveillance and pandemic preparedness. Mosquitoes are important vectors for transmission of many emerging viruses responsible for numerous outbreaks. Monitoring mosquitoes becomes essential to investigate its virome which leads to understanding of disease dynamics and allow preventive actions. In this study, shotgun metagenomic methodology using Ion GeneStudio S5 System was optimized for exploration of viral diversity. A total of 1913 Aedes larvae were collected from Central India during post monsoon season of 2024. Aedes larvae reared to adulthood and processed for sequencing using Ion Torrent S5 platform. Computational analyses were performed using three bioinformatic pipelines: Chan Zuckerberg ID (CZ ID), Genome Detective Platform and the Galaxy Platform. A mock database of 11 known viruses was created as well as publicly available NCBI Sequence Read Archive (SRA) datasets were used to validate all three pipelines. In terms of detection accuracy, Genome Detective and CZ ID performed exceptionally well and therefore may be suitable for future mosquito virome surveillance studies. We found presence of viruses viz. Alphamesonivirus cavallynense and Phasivirus phasiense dominating in all samples. Dengue virus was detected in one sample by CZ ID, whereas Wenzhou sobemo-like virus, Hubei mosquito virus 2, Cell fusing agent virus found most commonly among samples. Other viruses found like Aedes anphevirus (AeAV; genus Glybovirus), Aedes totivirus, Verdadero virus and Chaq-like virus. Variation in the result among different pipelines are likely attributable to incorporation of different viral reference databases, classification algorithms, metrics and analysis parameters. To the best of our knowledge, this study represents the first metagenomic study of mosquitoes using Ion GeneStudio S5 platform in India. The findings provide a comparative evaluation of the metagenomic pipelines and elucidates detailed information of each pipeline and its working for future studies.},
}

@article {pmid42458483,
year = {2026},
author = {Jiang, Q and Nian, F and Xu, L and Wu, S and Zhang, F and Meng, F and Chen, Z and Tang, W and Shen, X and Dong, L},
title = {Helicobacter pylori promotes hepatocarcinogenesis by abrogating the protective effect of intestinal Bacteroides acidifaciens in females.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08590-4},
pmid = {42458483},
issn = {1479-5876},
support = {NSFC82273027//National Natural Science Foundation of China/ ; 24YF2704900//Shanghai Sailing Program/ ; },
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) exhibits sexual dimorphism, with a lower incidence observed in females. However, the mechanisms underlying the disruption of this protective effect remain inadequately understood. Helicobacter pylori (Hp) is associated with HCC and can cause gut microbiota imbalances that promote HCC progression. This study explored how Hp might influence female susceptibility to HCC via the gut-liver axis, focusing on gut bacteria and their metabolites.

METHODS: A Hp-infected DEN + CCl₄-induced HCC mouse model was established, and a cohort of 186 HCC patients was analyzed. Fecal metagenomics and serum metabolomics were employed to identify Hp-responsive gut microbes and metabolites. The therapeutic potential of Bacteroides acidifaciens (Ba) and its metabolite 4‑hydroxybenzyl alcohol (4‑HBA), alone or combined with Hp eradication, was evaluated in mouse models and in mechanistic cell-based assays.

RESULTS: Hp increased tumor burden and fibrosis especially in female mice. Hp-positive female patients exhibited larger tumors, more advanced disease stages, higher cirrhosis incidence, and poorer overall survival compared to Hp-negative females. Hp also reduced gut microbiota diversity and decreased female-enriched Ba. The Ba-specific metabolite 4-HBA, which is higher in females and reduced by Hp, suppressed TGF‑β/SMAD signaling by binding to TGFBR2, thereby inhibiting hepatic stellate cell activation and HCC cell proliferation. Ba/4-HBA alleviated Hp-induced liver pathology in both sexes, with the combination of Hp eradication and Ba/4-HBA treatment proving more effective than eradication alone in females.

CONCLUSIONS: Hp exacerbates hepatic fibrogenesis and HCC in females by depleting Ba and its metabolite 4-HBA, which inhibits TGF-β/SMAD signaling through binding to TGFBR2. Supplementation with Ba/4-HBA, particularly when combined with Hp eradication, tend to be a promising microbiota-metabolite-targeted strategy for attenuating female HCC progression.},
}

@article {pmid42459144,
year = {2026},
author = {Sriram, S and Alsafar, H and Lusa, R and Wang, Y},
title = {Single-Thallus Genomics of Ejectosporus trisporus, an Unculturable Stonefly Gut Fungal Symbiont.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70380},
pmid = {42459144},
issn = {1462-2920},
support = {RGPIN-2020-04293//Natural Sciences and Engineering Research Council of Canada/ ; DGECR-2020-00154//Natural Sciences and Engineering Research Council of Canada/ ; //TD Undergraduate Research Fellowship/ ; //Centre for Environmental Research in the Anthropocene Undergrad Research Fund/ ; //Mitacs Globalink Research Internship Award/ ; },
mesh = {Animals ; *Symbiosis ; Phylogeny ; *Genome, Fungal ; *Insecta/microbiology ; Genomics ; Gastrointestinal Tract/microbiology ; Canada ; },
abstract = {Microorganisms play essential roles in global ecosystems, yet much of their diversity, particularly among fungi, remains unexplored due to challenges in culturing and genomic characterisation. Trichomycetes, an early-diverging lineage of obligate gut symbionts of aquatic insects, exemplify this 'microbial dark matter', as most taxa cannot be maintained in axenic culture. Here, we present the first culture-independent genome assembly of Ejectosporus trisporus, an unculturable Harpellales fungus isolated from the hindgut of a winter stonefly (Allocapnia sp.) in Rouge National Urban Park, Canada. Using a single-thallus genomic approach based on multiple displacement amplification and Illumina short-read sequencing, we generated a 29.3 Mb genome assembly with 76.6% BUSCO completeness, comparable to existing culture-based Harpellales genomes. Phylogenomic analyses using 1241 conserved orthologs placed E. trisporus in a well-supported clade with Zancudomyces culisetae and Capniomyces stellatus, confirming its taxonomic position. Scanning electron microscopy further revealed detailed ultrastructural features of thalli, trichospores, and zygospores. This study demonstrates the feasibility of single-thallus genomics for unculturable fungi and provides the first genomic resource for an unculturable trichomycete species. Our study establishes a valuable basis for future large-scale genomic investigations of early-diverging fungi, enabling further exploration of the symbiosis and ecological roles of these cryptic gut-dwelling fungi.},
}

Animals
*Symbiosis
Phylogeny
*Genome, Fungal
*Insecta/microbiology
Genomics
Gastrointestinal Tract/microbiology
Canada

@article {pmid42459798,
year = {2026},
author = {Cao, D and Huang, L and Zhang, X and Zhang, X and Zhao, Z and Long, X and Zhu, X and Li, Y},
title = {Lentinan alleviates metabolic dysfunction implicating Parabacteroides goldsteinii-enriched gut microbiota and hepatic lipid metabolism reprogramming through gut-liver axis-associated mechanisms.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1841358},
pmid = {42459798},
issn = {2296-861X},
abstract = {Metabolic disorders represent a global health challenge requiring novel therapeutic strategies targeting the gut-liver axis. This study investigates the protective effects and mechanisms of lentinan, a bioactive polysaccharide from Lentinus edodes, against high-fat diet (HFD)-induced metabolic dysfunction. HFD-fed mice were treated with lentinan. Comprehensive phenotypic assessments, metagenome sequencing, hepatic transcriptomics, and correlation analyses were performed to elucidate mechanisms. Lentinan intervention significantly ameliorated dyslipidemia, hepatic steatosis, systemic inflammation, and intestinal barrier dysfunction in HFD-fed mice. Mechanistically, lentinan induced taxonomically selective gut microbiota remodeling, characterized by substantial enrichment of Parabacteroides goldsteinii (positively correlated with hepatic Plppr3 expression) and reduction of Romboutsia ilealis (negatively correlated with Dgkh and Nfat5), while paradoxically decreasing Akkermansia muciniphila despite metabolic improvements. Hepatic transcriptomics revealed significant downregulation of glycerolipid metabolism and oxidative phosphorylation pathways, directly correlating with reduced lipid accumulation and improved serum biochemistry. Unlike conventional prebiotics, lentinan functions as a precision modulator of specific microbial metabolic functions, particularly L-arginine and uridine 5'-monophosphate (UMP) biosynthesis pathways, which interface with host inflammatory and lipid metabolism. These findings establish lentinan as a promising therapeutic candidate for metabolic syndrome management through coordinated gut microbiota-liver axis modulation, providing a conceptual framework for developing precision microbiome-targeted interventions.},
}

@article {pmid42459877,
year = {2026},
author = {Romero-Arguelles, R and Ruiz-Ayma, G and Rodriguez-Castro, VA and Gonzalez-Rojas, JI and Gomez-Govea, MA},
title = {Next-generation soil monitoring: linking metagenomics, biosensors, and ecological modeling for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1861333},
pmid = {42459877},
issn = {1664-302X},
abstract = {Soils represent one of the most complex and dynamic biological systems on Earth, where microbial communities play a central role in regulating ecosystem functions, including nutrient cycling, carbon sequestration, and plant productivity. However, increasing pressures from land-use intensification and climate change threaten soil health and biodiversity, highlighting the need for innovative monitoring and management approaches. In this review, we synthesize current advances in soil microbial ecology, sustainable soil management, environmental sensing technologies, and metagenomics to propose an integrative framework for soil monitoring and prediction. This review integrates environmental sensing, microbiome characterization, ecological modeling, and AI-based analytics into a unified framework for next-generation predictive soil monitoring systems. We discuss how high-resolution environmental sensors enable real-time characterization of soil physicochemical dynamics, while metagenomic approaches provide unprecedented insights into the taxonomic and functional diversity of soil microbiomes. Furthermore, we explore the role of microbial network analysis and ecological modeling in uncovering interaction patterns and predicting ecosystem responses to environmental change. The integration of these tools through machine learning and data-driven approaches is transforming soil science from a descriptive to a predictive discipline. We also address key challenges, including data standardization, scalability, and the interpretation of complex biological datasets. Finally, we highlight emerging directions such as microbiome-informed precision agriculture, microbiome engineering, and the development of soil digital twins. Together, these advances pave the way toward sustainable soil management strategies that enhance ecosystem resilience and agricultural productivity in the face of global change.},
}

@article {pmid42460235,
year = {2026},
author = {Barthman, B and Klassen, M and Ressing, A and Danielson, K},
title = {Disseminated Culture-Negative Periprosthetic Knee Infection With Multifocal Septic Arthritis Associated With Mycoplasma pneumoniae: A Case Report.},
journal = {Case reports in orthopedics},
volume = {2026},
number = {},
pages = {9426714},
pmid = {42460235},
issn = {2090-6749},
abstract = {We report a case of a 72-year-old woman with Waldenström macroglobulinemia who developed a culture-negative periprosthetic joint infection (PJI) of the right knee following total knee arthroplasty. Despite multiple debridements and broad-spectrum antibiotics, she developed systemic signs of infection and hematogenous spread to multiple native joints, including the contralateral knee, ankle, wrist, and lumbar facet joints. All intraoperative cultures remained negative. A respiratory PCR was performed, which detected Mycoplasma pneumoniae, and metagenomic next-generation sequencing (mNGS) of plasma supported the diagnosis of the pathogen. Based on these findings, therapy was narrowed to doxycycline, resulting in clinical improvement and deferral of further surgery. This case highlights the importance of considering atypical pathogens in culture-negative PJI and demonstrates the utility of mNGS in guiding targeted antimicrobial therapy.},
}

@article {pmid42460558,
year = {2026},
author = {Fan, L and Sun, F},
title = {Composition and function of biofilm microbial communities reveal high efficiency potential in carbohydrate metabolism in the mariculture.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {94},
number = {1},
pages = {60-69},
pmid = {42460558},
issn = {0273-1223},
support = {ZDYF2021XDNY131//Key Research and Development Project of Hainan Province/ ; },
mesh = {*Biofilms ; *Carbohydrate Metabolism ; Bacteria/metabolism/genetics ; Citric Acid Cycle ; },
abstract = {Biofilms on composite carriers may contribute to organic matter transformation in mariculture effluents, but the taxa and carbon-metabolic functions underlying this process remain unclear. This study employed metagenomic sequencing and functional annotation to comprehensively analyze the microbial composition and metabolic potential involved in glycoside hydrolase (GH), glycolysis, and the tricarboxylic acid (TCA) cycle in biofilms, revealing the functional characteristics of microbial communities in carbon metabolism. The results showed high microbial diversity in various carbon metabolism pathways, with Bacteroidota, Proteobacteria, and Planctomycetota being the dominant phyla, and Flavobacteriales and Planctomycetales being the predominant orders across all metabolic pathways. Functional analysis indicated that key enzymes involved in polysaccharide hydrolysis, glycolysis, and the TCA cycle exhibited high abundance. Core functional genes included polysaccharide hydrolases (GH33, GH109), glycolytic enzymes (glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase), and TCA cycle enzymes (succinate dehydrogenase, pyruvate dehydrogenase). These profiles suggest that carrier-associated biofilm communities harbor coordinated genetic potential for carbohydrate depolymerization and downstream central carbon metabolism in mariculture effluents. This study offers theoretical and practical guidance for developing efficient and sustainable biofilm-based wastewater treatment systems.},
}

*Biofilms
*Carbohydrate Metabolism
Bacteria/metabolism/genetics
Citric Acid Cycle

@article {pmid42461001,
year = {2026},
author = {Zhang, Q and Niu, Z and Li, J and Wei, M and Wang, R and Zhao, J},
title = {Emergent Macrophytes Specifically Regulate Ammonia-Oxidizing Microbial Communities and Functions: Comammox Dominance and N2O Emission Effects.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag178},
pmid = {42461001},
issn = {1365-2672},
abstract = {AIMS: Emergent macrophytes regulate nitrogen-cycling microbial processes in lake riparian zones, though the mechanisms underlying these species-specific effects remain to be fully elucidated. This study investigated the structure, functional activity, and environmental drivers of three ammonia-oxidizing microbial communities in sediments with different emergent macrophytes (Phragmites australis, Typha orientalis, and Thalia dealbata) in Meixi Lake, Changsha.

METHODS AND RESULTS: Metagenomic sequencing, quantitative PCR (qPCR), potential nitrification rate, and N2O yield were integrated to reveal the influence of riparian vegetation on the structural dynamics and ecological effects of ammonia-oxidizing microorganisms. The results indicated that the emergent macrophytes altered the sediment physicochemical properties, thereby exerting certain selective effects on specific ammonia-oxidizing microbial communities. The microbial community structure was similar in the P. australis and T. orientalis sediments, whereas significantly different in the T. dealbata sediment. Comammox Nitrospira dominated across all sediments, with a maximum absolute abundance of 2.10 × 109 copies g-1. Notably, the T. orientalis sediment exhibited the highest comammox-driven potential nitrification rate (1.196 mg N kg⁻¹ d⁻¹), while the T. dealbata sediment showed the highest N2O production rate (3.042 ng N g-1 h-1). Environmental factor analysis revealed that organic matter and plant biomass facilitated N2O emissions driven by comammox and ammonia-oxidizing archaea (AOA), respectively. Furthermore, AOA abundance was positively regulated by pH whereas negatively regulated by ammonium nitrogen (NH₄⁺-N).

CONCLUSIONS: This study demonstrates that different emergent macrophytes influence the nitrogen transformation processes by modulating the abundance and activity of key microbial communities, providing a scientific basis for optimizing plant configuration in ecological restoration to mitigate greenhouse gas emissions.},
}

@article {pmid42461036,
year = {2026},
author = {Munford, KE and Grégoire, DS and Hug, LA},
title = {Tracking interlinked microbial and geochemical succession over decades in landfilled municipal solid waste.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0031126},
doi = {10.1128/aem.00311-26},
pmid = {42461036},
issn = {1098-5336},
abstract = {Landfills are heterogeneous built environments embedded in natural freshwater systems. They pose increasing risks of groundwater contamination from metal-bearing leachates over time. The interlinked succession of waste decomposition processes, microbial community membership, and metal cycling across a landfill's lifespan has not been explored, reducing our ability to predict the long-term environmental impacts of landfills. Working with 1,647 metagenome-assembled genomes from a single landfill, from samples spanning over 39 years of waste decomposition, we identified changes in landfill biogeochemistry and connected these changes to shifts in microbial community composition and predicted functions over time. Comparing Older (aged 31-39 years) and Newer (aged 3-20 years) waste cells identified significant shifts in the availability of labile carbon, redox-associated processes, and concentrations of mobile metals-all higher in Newer cells. Newer cells were dominated by chemoorganoheterotrophs, while Older cells contained higher proportions of chemolithoautotrophs and organisms with higher metabolic versatility. Metal resistance and metal cycling genes were significantly more abundant in Older cells. Using geochemical data from the time of filling to the present and microbial membership data across six landfill cells of different ages, we developed a conceptual model of landfill characteristics across time. This model connects redox conditions and metal fate, highlighting leachate recirculation as a key process impacting many geochemical parameters and defining site chemistry. Our work highlights the substantial changes occurring over the stabilization phase and provides a conceptual model for understanding this critical, final stage in a landfill's life cycle.IMPORTANCEAging landfills pose significant risks to environmental stability and are currently poorly modeled beyond ~20 years. Our examination of a single landfill across 39 years of waste degradation was a unique opportunity to examine the impact of time within a connected system. Our work connects geochemical data, microbial membership, and predicted function, as well as physical processes (e.g., leachate recirculation). Our conceptual model interlinks these facets across the lifespan of a landfill, providing an empirical data-based model of landfill aging. Previous models were extrapolated from younger waste and did not include the microbial dimension-a critical facet of the landfill ecosystem. Our model clarifies processes taking place in older wastes (30+ years), including oxygen infiltration, that have important implications for methane emission and metal mobility and fate over the longer term.},
}

@article {pmid42461050,
year = {2026},
author = {Wozniak, KJ and Pan, L and Zhu, D and Corver, J and Kuijper, EJ and Smits, WK and Britton, RA},
title = {Acquisition of a gene cluster in Clostridioides difficile PCR ribotype 023 strains enables xylitol utilization.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0026326},
doi = {10.1128/msphere.00263-26},
pmid = {42461050},
issn = {2379-5042},
abstract = {Hundreds of ribotypes of the gastrointestinal pathogen Clostridioides difficile have emerged over the last three decades, yet the factors driving their emergence are poorly understood. Recently, there has been an increase in infections caused by PCR ribotype 023 (RT023) strains in Europe. We profiled the growth of seven RT023 strains in 190 unique carbon sources and found they were able to grow in xylitol, a sugar alcohol used as a food additive in humans and animals. Other ribotypes of C. difficile tested (n = 19) displayed little to no growth in 0.5% xylitol and were growth-inhibited in higher concentrations of xylitol. Genome sequencing identified that RT023 strains acquired a putative xylitol dehydrogenase (xdh) gene in a mobile genetic element (MGE) that is absent from other C. difficile ribotypes. We created a deletion of xdh in the RT023 strain PRB1128 and observed poor growth in xylitol, indicating that the xdh is necessary for xylitol utilization. Complementation of the xdh mutant with a plasmid-based inducible copy of the xdh gene restored growth in xylitol. We performed competition assays in minibioreactor arrays (MBRAs) and observed that PRB1128 outcompeted the non-xylitol-utilizing strain CD2015 (RT027) in the presence of xylitol. These data support that the xdh gene within RT023 strains provides a fitness benefit for growth in xylitol. Interestingly, the chromosomal locus where the MGE inserted appears to be a hotspot for genetic insertions across clades of C. difficile. Together, this work improves our understanding of the molecular basis for niche adaptation of C. difficile.IMPORTANCEGenetic factors aiding in the emergence of the opportunistic pathogen Clostridioides difficile are poorly understood. Infections with clade 3 (PCR ribotype 023) strains causing severe disease have increased since 2008. Here, we show RT023 strains have the unique ability to utilize xylitol, a sugar alcohol used as a food additive in humans and animals, due to the presence of a xylitol dehydrogenase (xdh) gene within a mobile genetic element (MGE). This xylitol utilization ability confers a fitness benefit in competition against other C. difficile ribotypes, as well as in a fecal community in vitro. Research investigating the underlying genetic factors driving the physiology of C. difficile will improve our understanding of colonization and hypervirulence.},
}

@article {pmid42461222,
year = {2026},
author = {Schwartz, M and Ladeira, R and Neiers, F and Nicolaï, A and Hocquet, D and Loupiac, C},
title = {Next-Generation Food Enzymology: From Metagenomic Discovery to AI-Driven Biocatalyst Design.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c04349},
pmid = {42461222},
issn = {1520-5118},
abstract = {Food enzymology is entering a new era driven by the convergence of metagenomics, artificial intelligence, and synthetic biology. While traditional food processes rely on a limited repertoire of established biocatalysts, metagenomic and multiomics approaches now provide access to vast reservoirs of unexplored enzymatic diversity. Simultaneously, advances in protein structure prediction, functional modeling, and de novo protein design are transforming enzyme discovery from a largely empirical process to a predictive discipline. In this Perspective, we discuss how these technologies will enable the development of tailored biocatalysts for sustainable, precise, and next-generation food processing applications.},
}

@article {pmid42461231,
year = {2026},
author = {Liu, S and Li, Y and Zeng, X and Sun, Y and Li, L and Jia, Y},
title = {Reversible Control of Microbial As(III) Oxidation by Nitrous Oxide Availability in Flooded Paddy Soils.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04988},
pmid = {42461231},
issn = {1520-5851},
abstract = {The persistence of arsenite (As(III)) oxidation in flooded paddy soils is difficult to explain once canonical oxidants are rapidly depleted under anoxia. Here we tested whether nitrous oxide (N2O), a prevalent nitrogen-cycle intermediate, reversibly regulates microbial As(III) oxidation and arsenic (As) partitioning in flooded soils. Using two paddy soils with low and high As contents, we conducted (i) three-generation serial-transfer enrichments with exogenous As(III) addition and (ii) continuous-cessation-readdition N2O exposure microcosms targeting native As pools. Across transfer generations, N2O consistently promoted As(III) oxidation under strictly anoxic conditions, while sterilized controls showed no As(III) loss, indicating biological mediation. In native-soil microcosms, porewater As(III) declined during N2O input, rebounded upon N2O withdrawal, and decreased again after N2O readdition, demonstrating reversible control. N2O exposure also shifted As toward amorphous Fe (hydr)oxide-associated operational fractions, consistent with reduced porewater mobility. Metagenomic analyses further showed enrichment of functional genes for As oxidation (aioA, aioB) and N2O reduction (nosZ), with the strongest responses in the high-As soil at day 70 (1 mM vs 0 mM N2O: aioA 13.9-fold, aioB 1.68-fold, nosZ 3.26-fold). These results indicate that N2O availability can act as a reversible control point associated with microbially mediated As(III) oxidation and As redistribution under anoxia, with implications for As mobility and exposure risk in flooded paddy systems.},
}

@article {pmid42462345,
year = {2026},
author = {Wang, Y and Ye, L and Cao, C and Che, G and Zhang, C and Wei, Q and Hong, Y and Jiang, K},
title = {Metagenomics indicates new taxa in Candidatus Saccharimonadia and proposal of Parviradicicola hetaonensis gen. nov. sp. nov. and Parviputeicola dengkouensis gen. nov. sp. nov. following the rules of the SeqCode.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {5},
pages = {126751},
doi = {10.1016/j.syapm.2026.126751},
pmid = {42462345},
issn = {1618-0984},
abstract = {Candidatus Saccharimonadia is a core lineage within the phylum Patescibacteriota (formerly the bacterial candidate phyla radiation, CPR), yet the class has long lacked a standardized, complete taxonomic framework. This nomenclatural gap severely hinders consistent academic exchange and global research into its diversity, evolutionary history, and ecological roles. Here, we recovered 29 medium- to high-quality Ca. Saccharimonadia metagenome-assembled genomes (MAGs) from groundwater, rhizosphere soil, and saline-alkali soil in the Hetao Irrigation District, Inner Mongolia, China, and performed integrated phylogenomic, genome size evolution, and metabolic analyses alongside reference genomes from the GTDB r220 database. Based on robust polyphasic taxonomic evidence (multi-dimensional phylogenetic analyses, widely accepted genome-wide ANI/AAI thresholds) and SeqCode rules, we formally propose two novel taxa: Parviradicicola hetaonensis gen. nov., sp. nov. (type material: txb011_bin.8.strict[TS]) and Parviputeicola dengkouensis gen. nov., sp. nov. (type material: sgl022_bin.19.orig[TS]), plus two novel families and one novel order. We further identified potential drivers and important associations related to Ca. Saccharimonadia genome size evolution and adaptive metabolic traits. This work refines the Ca. Saccharimonadia taxonomic framework, providing critical genomic references for follow-up research.},
}

@article {pmid42462650,
year = {2026},
author = {Liu, J and Wang, H and Wang, Y},
title = {Iron limitation induced siderophores production drives interspecies competition in anammox consortia.},
journal = {Water research},
volume = {305},
number = {},
pages = {126446},
doi = {10.1016/j.watres.2026.126446},
pmid = {42462650},
issn = {1879-2448},
abstract = {Anaerobic ammonium oxidation (anammox) relies heavily on iron to sustain the metabolism of its functional bacteria. However, actual wastewater systems are typically characterized by bioavailable iron scarcity, threatening the long-term stability of the nitrogen removal process. To understand how anammox bacteria utilize insoluble ferric iron and how iron availability dictates microbial interactions, we investigated the ecological dynamics of anammox consortia under iron-limited conditions (< 1 mg/L) using combined microbial network and metagenomic analyses. Results revealed that anammox bacteria could utilize endogenous siderophores to acquire trace iron, a strategy that initially sustained high anammox activity and achieved a nitrogen removal efficiency exceeding 70%. Quantitative PCR and functional genes analyses identified the AcsABCDEF and MbnBH systems as the potential siderophores synthesis pathways of anammox bacteria, predominantly attributed to catechol and carboxylate types. Notably, while this siderophore-mediated iron acquisition initially promoted the proliferation of both anammox and denitrifying bacteria, it subsequently triggered intense interspecies competition and cell apoptosis for the scarce iron pool. This competitive exclusion eventually disrupted the stability of the system, causing the nitrogen removal efficiency to plummet below 40% after 60 days. These findings uncover the iron uptake strategies of anammox bacteria and highlight iron availability as a critical regulatory lever for managing microbial interactions, offering a new ecological perspective for maintaining stable anammox processes in wastewater treatment.},
}

@article {pmid42462831,
year = {2026},
author = {Qiang, H and Jing, Y and Xu, X and Heo, S and Liu, Z and Yue, X and Zhou, A and Fernández-Morales, FJ and Oleskowicz-Popiel, P},
title = {N-(3-oxohexanoyl)-homoserine lactone-assisted enrichment reshapes functional microbial consortia for chain elongation in electrofermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135425},
doi = {10.1016/j.biortech.2026.135425},
pmid = {42462831},
issn = {1873-2976},
abstract = {The functional microbial consortia supporting chain elongation determine medium-chain carboxylate recovery from organic wastes, but how signal-molecule-assisted enrichment shapes chain-elongating bacteria (CEB), electroactive bacteria (EAB), and competing guilds in electrofermentation remains unclear. Here, three N-acyl-homoserine lactones: N-butyryl-homoserine lactone (C4-HSL), N-octanoyl-homoserine lactone (C8-HSL), and N-(3-oxohexanoyl)-homoserine lactone (3OC6-HSL), were supplied during microbial enrichment, and the subsequent electrofermentation was conducted fed with sludge fermentation broth. Compared with the Control (without signaling molecules), 3OC6-HSL had the strongest response, increasing caproate production by 94.0%, compared with 16.9% and 27.3% for C4-HSL and C8-HSL, respectively. It also increased the apparent caproate electron transfer efficiency by 20.7 percentage points, increased the abundance of CEB (44.9% vs. 33.2%) and EAB (14.3% vs. 6.6%), and reduced the abundance of homoacetogens (12.1% vs. 33.7%). Co-occurrence network analysis revealed more modular and compact inferred associations, with 25.0% more modules and a 34.7-49.3% shorter average path length. Metagenomic analysis revealed enhanced reverse β-oxidation, QS, chemotaxis, and flagellar assembly potentials, and the expression levels of acetyl-CoA acyltransferase (ACAT/fadA) and acyl-CoA dehydrogenase (ACADS/ACADM) increased by 162.1% and 96.6%, respectively. Clostridium kluyveri dominated the ACAT contribution (85.9%). Overall, enrichment-phase 3OC6-HSL supplementation was associated with a caproate-oriented microbial consortium and improved caproate recovery without continuous signal dosing.},
}

@article {pmid42448275,
year = {2026},
author = {Wang, Q and Cui, J and Zhang, X and Zhao, H and Xu, X},
title = {Process-specific inhibition of sediment denitrification by metal oxide nanoparticles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128777},
doi = {10.1016/j.envpol.2026.128777},
pmid = {42448275},
issn = {1873-6424},
abstract = {The continuous accumulation of nanoparticles (NPs) in river sediments poses a potential threat to benthic nitrogen cycling. However, systematic comparisons of their effects on denitrification pathways driven by different electron donors are lacking. This study investigated the impacts of nZVI, nCuO, and nZnO on heterotrophic denitrification (H-DN), iron-based autotrophic denitrification (Fe-AD), and sulfur-based autotrophic denitrification (S-AD) in sediment. An integrated analysis was conducted including denitrification performance, key enzyme activities, extracellular polymeric substance (EPS) responses, microbial community structure, and functional gene abundance. Results revealed process- and particle-specific nanoparticle toxicity. H-DN was sensitive only to nZnO (11.6% reduction in nitrate removal rate). Fe-AD was sensitive to three NPs, with nZnO showing the strongest inhibition (38.7% reduction). In contrast, S-AD exhibited high tolerance. Nitrite reductase (NIR) activity reached 5.1 times that of the control, coupled with lower oxyR abundance, suggesting that sulfide-mediated passivation alleviated oxidative stress. NIR was identified as the common enzymatic target. Microorganisms defended against NP stress by increasing the protein fraction of EPS. nZnO triggered abnormal soluble microbial products (SMP) profiles across all systems, with protein/polysaccharide ratios surging to 45.0-45.3. Metagenomics revealed higher abundances of heavy-metal efflux and oxidative-stress genes in H-DN and Fe-AD under NP stress, imposing an energy trade-off between defense and metabolism; these genes were less abundant in S-AD. Gene abundance-enzyme activity decoupling further cautions that ecological risk assessments based solely on community abundance may underestimate nanoparticle toxicity.},
}

@article {pmid42448379,
year = {2026},
author = {Feng, Y and Lin, G and Jiang, Z and Shi, W and Deng, L and Dong, J},
title = {A Phenotype-Embedded Mapper Framework Links Microbiome-Metabolome Interaction Modules to Colorectal Cancer.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.6c00192},
pmid = {42448379},
issn = {1535-3907},
abstract = {Integrative analysis of the gut microbiome and metabolome can help characterize colorectal cancer (CRC)-associated molecular changes that are difficult to resolve from either omics layer alone. However, microbiome-metabolome data are high-dimensional, heterogeneous, and often contain nonlinear or locally confined associations that may be obscured by global linear models. Here, we propose a phenotype-guided topological framework that extends the Mapper algorithm for local interpretation of paired microbiome and metabolome profiles. Disease-associated variation from each omics block was summarized by partial least-squares regression and used to construct a two-dimensional filter space for Mapper graph construction. We further developed an Extended Spatial Analysis of Functional Enrichment strategy (eSAFE) to evaluate the spatial enrichment of phenotypes, individual features, and feature-pair associations on the resulting graph. Applied to paired fecal metagenomic and metabolomic profiles from a CRC cohort, the framework organized samples into phenotype-aligned neighborhoods and identified localized microbial, metabolic, and cross-omics association patterns linked to CRC. Coenrichment analysis further prioritized disease-associated features and interaction modules that were partly distinct from those obtained by univariate differential analysis or supervised sparse multiblock integration. One disease-localized microbiome-metabolome module showed moderate CRC discrimination in internal cross-validation and was enriched for metabolites involved in butanoate and amino acid-related pathways. These results suggest that phenotype-guided topological analysis can provide a complementary, interpretable view of localized multiomics organization in CRC-associated gut ecosystems.},
}

@article {pmid42448967,
year = {2026},
author = {Sittipo, P and Park, JY and Tiffany, E and Oh, A and Moon, S and Lee, CH and Oh, JS and Kim, TY and Kweon, MN and Choi, J and Song, KH and Lee, DW and Nam, MH and Hong, SJ and Lee, EY and Jeon, SR and Song, HY and Kim, BS and Lee, YK},
title = {Gut microbiome modulation by Veillonella ratti induces resistance to EAE pathogenesis via microbe-derived metabolites.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42448967},
issn = {2092-6413},
support = {2021M3A9I4027993//National Research Foundation of Korea (NRF)/ ; RS-2023-00219563//National Research Foundation of Korea (NRF)/ ; 2021M3A9I4023974//National Research Foundation of Korea (NRF)/ ; },
abstract = {The progression of multiple sclerosis (MS) is potentially influenced by the microbiome. Elucidating host-microbiome interactions in MS may aid in developing microbiome-based applications; however, these interactions remain unclear. Here, we aimed to elucidate how Veillonella ratti MHL0042, isolated from human infant feces, modulates neuroinflammation and disease severity in experimental autoimmune encephalomyelitis, a murine MS model. Whole metagenomic sequencing revealed that V. ratti MHL0042 reshaped disrupted gut microbiota via microbial interactions throughout the intestinal tract. V. ratti MHL0042 administration significantly reduced central nervous system inflammation, notably decreasing CD4[+]IFN-γ[+] T cell populations and activated spinal cord microglia. Mechanistically, V. ratti MHL0042 depleted pldA-containing bacteria, involved in phosphatidylethanolamine metabolism, thus elevating dioleoyl phosphatidylethanolamine (DOPE) levels. Increased DOPE was not only detected in the intestinal tract but also extended systemically and reflected in the central nervous system. Exogenous DOPE administration recapitulated the attenuation of experimental autoimmune encephalomyelitis pathogenesis by suppressing microglial activation. These findings highlight the therapeutic applicability of the microbiome and underscore its potential in human disease treatment.},
}

@article {pmid42449467,
year = {2026},
author = {Gan, L and Yang, Z and Zhang, Y and Wang, S and Meng, F and Liu, Y and Dorji, T},
title = {Beyond diversity: the functional mechanisms of microbial adapations under climate change in alpine deserts.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00928-1},
pmid = {42449467},
issn = {2524-6372},
support = {QYXTZX-AL2022-05//Regional Science and Technology Collaborative Innovation Special Project of Ngari in Tibetan Autonomous Region of China/ ; 2019QZKK0600//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U20A2005//the Joint Key Research Fund under cooperative agreement between the National Natural Science Foundation of China (NSFC) and Tibet Autonomous Region (TAR)/ ; 42122005//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The functional responses of soil microbiomes to concurrent warming and altered precipitation in alpine deserts remain poorly understood, hindering predictions of these fragile ecosystem to climate change. Specifically, the mechanisms by which microbial communities maintain ecosystem function potential despite climate-induced biodiversity changes are unclear.

RESULTS: A three-year field manipulation experiment in an alpine desert grassland on the Qinghai-Xizang Plateau showed that warming and watering acted as distinct ecological drivers. Warming restructured prokaryotic and fungal communities, favored stress-associated taxa, and increasing interkingdom network complexity, indicating tighter microbial associations under climate stress. Although warming reduced microbial richness and diversity, it did not diminish the overall potential for soil nutrient cycling. Instead, functional stability was associated with sustained microbial abundance, network reorganization, and selective changes in nutrient-cycling genes, particularly those involved in nitrogen and phosphorus transformation hosted by specific bacterial phyla. In contrast, watering did not significantly increase mean soil moisture, but altered soil nutrient availability, affecting key microbial groups and their functions, showing an indirect regulation pathway.

CONCLUSIONS: Functional stability in alpine deserts under climate change was maintained not by taxonomic diversity alone, but through abundance-based compensation, community reorganization, and pathway-specific functional shifts. This study provides a mechanistic framework linking climate drivers to microbial community structure and nutrient-cycling potential, offering predictive insights into the responses of cold-arid ecosystems to future climate change.},
}

@article {pmid42449846,
year = {2026},
author = {Sun, Y and Wang, F and Mao, L and Lu, W and Wu, H and Mao, H and Zhang, Y},
title = {Optimization of Metagenomic Library Construction for Influenza A Virus and SARS-CoV-2: Systematic Comparison of rRNA Depletion Strategies and Fragmentation Orders.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/diagnostics16132065},
pmid = {42449846},
issn = {2075-4418},
support = {2024YFC2309905//National Key R&D Program of China/ ; },
abstract = {Background/Objectives: RNA virus metagenomic sequencing is a core technology for emerging infectious disease prevention and control, as well as for rapid pathogen identification. However, two major bottlenecks hinder its clinical application: the low fraction of informative sequencing reads caused by host rRNA contamination, and insufficient viral genome coverage. This study aimed to optimize the experimental parameters of RNA virus metagenomic sequencing, address the above bottlenecks, and establish a standardized workflow. Methods: Forty-five clinically positive samples (20 influenza virus-positive; 25 SARS-CoV-2-positive) were investigated in three parallel comparative experiments: rRNA depletion versus no depletion; probe-mediated RNase H digestion versus rRNA blocking; and two fragmentation timing strategies (fragmentation before versus after reverse transcription). Sequencing was performed on the GeneMind platform, and key performance metrics were systematically analyzed. Results: Following rRNA depletion, the host sequence proportion in the influenza virus and SARS-CoV-2 samples decreased from 39.5 to 90.5% to 3.6 to 32.2%, while the 10× genomic coverage increased from 0 to 99.4% to 98.1 to 100.0%. The proportion of host sequences captured by probe capture depletion (0.3-16.2%) was significantly (p < 0.05) lower than that captured by rRNA blocking module (14.3-92.3%). No significant differences were observed in the 10× genomic coverage (96.5-100.0%) or the fraction of effective viral reads between the two fragmentation strategies (p > 0.05). rRNA depletion is key to improving library quality, with post-capture probe digestion being optimal. Conclusions: The suggested optimization process will enhance sequencing efficiency and support the standardization of clinical RNA virus identification.},
}

@article {pmid42449918,
year = {2026},
author = {Smirne, C and Romano, G and Ravanini, P and Crobu, MG and Palumbo, A and Ferrari, G and Mercandino, A and Grossini, E and Pirisi, M and Piralla, A},
title = {Phylogenetic and Genomic Characterization of Whole Genome Sequences of a Herpes Simplex Virus Type 1 Isolate Identified Genomic Variant Characteristics in a Human Subject with Fulminant Hepatitis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135640},
pmid = {42449918},
issn = {1422-0067},
support = {PE00000007//European Union/ ; },
mesh = {Humans ; Phylogeny ; *Genome, Viral ; *Herpesvirus 1, Human/genetics/isolation & purification/classification ; Whole Genome Sequencing ; Polymorphism, Single Nucleotide ; *Liver Failure, Acute/virology ; Genomics/methods ; *Herpes Simplex/virology/complications ; },
abstract = {Herpes simplex virus 1 (HSV-1) is a rare cause of acute hepatitis, especially in patients with chronic immunosuppression. We performed whole-genome HSV-1 sequencing with a metagenomics approach on peripheral blood samples from an Italian case of fatal acute liver failure with high circulating HSV-1 (1,129,900,000 copies/mL), followed by phylogenetic analysis. After multiple sequence alignment, a final dataset of 182 whole-genome sequences was selected. The sequenced HSV-1 strain belonged to a phylogenetic clade isolated in Florida in 2002 (OQ724868.1). A characterization of single nucleotide polymorphisms and indels was performed to determine their effects on the viral genome: only one variant, classified as an indel, was detected with a high impact effect (c.905_906insGTTTT) in the UL49A gene, which is known to encode a membrane protein regulating virion morphogenesis, replication and assembly. In addition, this study also detected variants in other genes involved in crucial steps of the HSV-1 life cycle, like alpha-regulation (US7), capsid transport (UL36) and viral polymerase function (UL30). In conclusion, the results of this variant analysis confirmed that in HSV-1 hepatitis, some viral regions may be hotspots for adaptive mutations with a substantial impact on viral replication or immune evasion.},
}

Humans
Phylogeny
*Genome, Viral
*Herpesvirus 1, Human/genetics/isolation & purification/classification
Whole Genome Sequencing
Polymorphism, Single Nucleotide
*Liver Failure, Acute/virology
Genomics/methods
*Herpes Simplex/virology/complications

@article {pmid42449941,
year = {2026},
author = {Wojtyś, M and Górska, EB and Osińska, E and Stępień, W and Gozdowski, D and Gworek, B and Cunha, A and Garcia, INS and Kondras, M and Hewelke, E and Fidler-Jarkowska, J and Chmielewski, J and Orzechowski, S},
title = {Integrating Microbiological Indicators and Shotgun Metagenomics for the Assessment of the Rhizosphere Microbiome of Medicinal Plants.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135665},
pmid = {42449941},
issn = {1422-0067},
support = {UID/50006 + LA/P/0094/2020//Foundation for Science and Technology/ ; 8762E-385/SPUB /2018/31.07.2018//Ministry of Science and Higher Education/ ; },
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Soil Microbiology ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Medicinal plants are rich sources of bioactive secondary metabolites, yet their long-term effects on the rhizosphere (RS) microbial communities remain poorly understood, particularly with respect to microbial selection and functional potential. This study evaluated the number of selected groups of microorganisms culturable in vitro in the RS and bulk soil (BS) within 10-year monocultures of 11 medicinal plant species, and as a targeted case study, we performed shotgun metagenomic profiling for Allium ursinum. The abundance of microorganisms differed markedly among plant species, indicating species-specific RS selection. Azotobacter spp. showed the strongest variation: they were not detected in the RS of Allium ursinum, Thymus vulgaris, and Carum carvi, whereas higher counts were observed under Artemisia dracunculus (135.1 × 10[2] CFU g[-1] DM), Melissa officinalis (67.1 × 10[2] CFU g[-1] DM) and Calendula officinalis (38.8× 10[2] CFU g[-1] DM). Azotobacter spp. may serve as a sensitive candidate indicator of RS imbalance. Metagenomic analysis of the A. ursinum-associated soil revealed fine-scale taxonomic restructuring, while major functional categories remained broadly similar between the RS and BS. The novelty of this study lies in the development of the Integrated Microbiological Health Soil Index (IMHSI) and the proposal of a Nitrogen Enrichment Index (NEI) as exploratory composite metrics that integrate selected functional microbial groups.},
}

*Rhizosphere
*Metagenomics/methods
*Microbiota/genetics
*Plants, Medicinal/microbiology
*Soil Microbiology
Bacteria/genetics/classification
Metagenome

@article {pmid42450074,
year = {2026},
author = {Sheng, L and Wang, Y and Lu, P and Han, G and Hao, Z and Hou, S},
title = {The Composition and Differentiation of the Seed-Associated Microbiome in Rapeseed Seeds as Studied Through 218 Rapeseed Transcriptomes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135801},
pmid = {42450074},
issn = {1422-0067},
support = {CARS-12//China Agriculture Research System/ ; },
mesh = {*Seeds/microbiology/genetics ; *Transcriptome ; *Microbiota/genetics ; *Brassica rapa/microbiology/genetics ; Gene Expression Profiling ; Stress, Physiological ; *Brassica napus/microbiology/genetics ; },
abstract = {Rapeseed is one of the most important oil crops in the world. Its yield and quality are severely restricted by biotic stress and abiotic stress. Rapeseed seeds play a crucial role in the propagation process, and the microorganisms in the seeds can be vertically passed on to the next generation, which greatly affects the quality, yield and growth of rapeseed. However, from a group perspective, there is currently a lack of systematic research on the composition of seed-associated microbiome within rapeseed seeds. This study utilized the transcriptome data of 218 rapeseed seeds that have been published, focusing on analyzing and comparing the dynamic changes and functional differences in the composition of seed-associated microbiome in rapeseed seeds under normal growth and development, biologic stress and abiotic stress conditions. Since we used public transcriptome data without surface sterilisation control, we refered to the detected microorganisms as seed-associated microbiome. The advantage of this study lies in its application of this method to a large-scale sample of rapeseed populations, which systematically revealed the response characteristics of seed-associated microbiome under different stress conditions. Interestingly, some widely distributed genera were not detected, while rare taxa were found under specific conditions, warranting further verification. Since these microorganisms originated from the seeds, their compatibility with plants and colonization ability may far exceed those of soil-derived agents. In the future, high-throughput screening of strains with excellent antagonistic or repellent effects against major diseases and pests of rapeseed can be conducted from these unique seed-associated microbiome. These strains that were confirmed by culture-based, amplicon or metagenomic approaches can then be used to develop seed coating agents or soil inoculants.},
}

*Seeds/microbiology/genetics
*Transcriptome
*Microbiota/genetics
*Brassica rapa/microbiology/genetics
Gene Expression Profiling
Stress, Physiological
*Brassica napus/microbiology/genetics

@article {pmid42450138,
year = {2026},
author = {Getsina, M and Tsyba, N and Chernevskaya, E},
title = {Modern Approaches to Diagnosis and Evaluation of Survival Prognosis in Patients with Pancreatic Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135867},
pmid = {42450138},
issn = {1422-0067},
mesh = {*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism ; Humans ; Prognosis ; *Biomarkers, Tumor/metabolism ; Microbiota ; Metabolomics/methods ; Circulating Tumor DNA/blood ; Early Detection of Cancer ; },
abstract = {Pancreatic cancer is among the most aggressive malignancies, and late diagnosis remains a key challenge. For a systematic review of pancreatic cancer diagnosis and prognosis, Scopus and Web of Science databases were used for the period from 2016 to 2026. The search query included the following keywords and their combinations: pancreatic cancer, diagnosis, early detection, prognosis, biomarkers, metabolomic profiling, CA19-9, microbiome, metagenomic changes, circulating tumor DNA, genomic analysis. Inclusion criteria included only articles published in English. Exclusion criteria included case reports and studies that did not examine pancreatic cancer. Our analysis demonstrates that integrating multi-omics data, particularly combining traditional CA19-9 with circulating tumor DNA (ctDNA) and metabolomic profiles (lipids, amino acids, carbohydrates), significantly improves diagnostic accuracy. Microbiome composition and genomic alterations further refine risk stratification and prognostic assessment. The synergistic use of these biomarkers may facilitate the development of screening, early diagnosis, risk stratification, and treatment optimization. However, the introduction of new diagnostic approaches into clinical practice requires additional verification, standardization and prospective clinical studies.},
}

*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism
Humans
Prognosis
*Biomarkers, Tumor/metabolism
Microbiota
Metabolomics/methods
Circulating Tumor DNA/blood
Early Detection of Cancer

@article {pmid42450507,
year = {2026},
author = {Xu, M and Ma, B and Zhu, K and Tu, W and Li, C and Hao, P and Zhang, M},
title = {Research Progress in Multi-Omics Analysis of Dairy Products: Nutritional Quality, Safety Evaluation, and Health Functions.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/foods15132389},
pmid = {42450507},
issn = {2304-8158},
support = {2023YFF1104704//National Key Research and Development Program of China/ ; 2025SNJF021//Zhejiang Provincial Department of Agriculture and Rural Affairs Project/ ; },
abstract = {This review evaluates multi-omics applications in dairy research across nutrition, safety, and health. Through multi-omics integration, we reveal nutrient differences driven by species, rearing practices, and processing techniques, identify protein patterns and allergen profiles, and construct adulteration detection fingerprints and species-specific peptide markers, thereby improving the timeliness and accuracy of safety assessment. The coupling of metagenomics and metabolomics effectively predicts spoilage-related microbial risks, enabling better risk control. Furthermore, multi-omics approaches systematically elucidate the functional mechanisms of bioactive peptides (e.g., ACE-inhibitory peptides), clarify the prebiotic effects of functional oligosaccharides, and build interaction networks between dairy components and gut microbiota. The introduction of machine learning enables origin and shelf-life prediction, as well as the discovery of novel biomarkers, promoting personalized nutrition and precision fermentation strategies. However, the field is currently constrained by severe reproducibility issues arising from the absence of standardized operating procedures, excessive optimism regarding machine learning models that rarely generalize across laboratories or product matrices, and a persistent disconnect between laboratory-scale biomarker discovery and industrial implementation. Without rigorous cross-platform validation and openly shared multi-omics reference datasets, most published markers remain unfit for regulatory or industrial application. Future efforts should establish standardized workflows and expand the evidence base to drive the dairy industry toward safer, healthier, and more traceable directions.},
}

@article {pmid42450525,
year = {2026},
author = {Oo-Puthinan, S and Limpeanchob, N and Pichitsiri, W and Wangteeraprasert, A and Trisat, K and Chumee, S and Sutheerawattananonda, M},
title = {Safety, Tolerability, and Gut Microbiota Impact of Sericin-Derived Oligopeptides (SDOs) from Yellow Silk Cocoons in Healthy Adults: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/foods15132405},
pmid = {42450525},
issn = {2304-8158},
support = {CRP6105022920//Agricultural Research Development Agency/ ; CRP6105022920//Ministry of Agriculture and Cooperatives/ ; },
abstract = {Sericin-derived oligopeptides (SDOs) from the Bombyx mori yellow silk cocoons show strong bioactive properties. However, clinical safety data on SDOs produced by specific enzymatic hydrolysis with a particular serine-rich (20.5%) and aspartic acid-rich (16.9%) composition is required to obtain regulatory approval as a novel food ingredient. This Phase 0 randomized, double-blind, placebo-controlled trial evaluated the short-term safety, tolerability, and gut microbiota effects of SDOs supplementation in healthy adults. Forty-two healthy volunteers were randomized (1:1:1) to receive daily doses of placebo, 0.9 g SDOs or 1.8 g SDOs for eight weeks. Primary safety endpoints included vital signs, hematology, and comprehensive clinical chemistry (renal and hepatic functions). Secondary outcomes included lipid profiles, oxidative stress markers (hs-CRP, TAC, SOD, MDA) and gut microbiota composition analyzed by 16S rRNA metagenome sequencing. Forty-one participants (97.6%) completed the study with high compliance (>98%). No serious adverse events were reported. All primary clinical parameters remained within clinically normal ranges, and no significant differences between groups were observed throughout the study (p > 0.05). No adverse effects on fasting blood glucose, lipid profiles or systemic oxidative stress were observed after SDOs supplementation. Importantly, 16S rRNA sequencing analysis showed that SDOs maintained gut microbial homeostasis throughout the 8-week intervention period, with Bacteroidetes and Firmicutes as the predominant phyla in the core community structure. Oral intake of enzymatically generated SDOs up to 1.8 g/day in healthy adults was well-tolerated with only occasional mild and transient gastrointestinal symptoms that did not appear to be dose-dependent. These first preliminary findings suggest a favorable safety profile for this unique peptide preparation, supporting its potential evaluation as a novel food ingredient and providing a reasonable basis for future, larger-scale trials to evaluate its efficacy in metabolic health.},
}

@article {pmid42450613,
year = {2026},
author = {Jiang, Z and Chen, J and Ren, Y and Lin, T and Li, S and Shen, F and Qin, B and Li, L and Li, C and Ying, N and Zheng, H},
title = {Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk.},
journal = {Biology},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/biology15131066},
pmid = {42450613},
issn = {2079-7737},
support = {2024TD08//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2025QT04//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2025ZX03//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; SF2407//Lianyungang Key Research and Development Program/ ; },
abstract = {The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome-mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater-seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG-MGE associations. Risk assessment should therefore move beyond ARG abundance toward host-ARG-MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons.},
}

@article {pmid42450643,
year = {2026},
author = {Han, Y and Yuan, Z and Liu, B and Liu, T and Zhang, Q and Zhang, Z and Zhang, F and Yuan, H},
title = {Effects of Dietary Nucleotides on Growth Performance, Antioxidant Capacity, Intestinal Morphology and Gut Microbiota of Swamp Eel (Monopterus albus).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16131936},
pmid = {42450643},
issn = {2076-2615},
support = {2022CFB314//Natural Science Foundation of Hubei Province of China/ ; },
abstract = {This study evaluated how graded dietary nucleotide supplementation (0, 0.25, 0.5, 0.75, 1.0, and 2.0 g/kg) affects growth performance, antioxidant capacity, intestinal morphology, and gut microbiota in swamp eel (Monopterus albus) (initial body weight 10.07 ± 0.92 g). Three hundred sixty fish were randomly assigned to six diets, each in triplicate, for eight weeks. Compared with the control, nucleotide addition significantly increased final body weight, weight gain rate, and specific growth rate, and decreased feed conversion ratio (p < 0.05), with optimal results at 0.75 g/kg (HS3). Survival was 100% in all groups. Supplemented fish showed lower serum and intestinal malondialdehyde levels and higher superoxide dismutase and catalase activities (p < 0.05). Serum total protein, albumin, and triglycerides increased, whereas alanine aminotransferase, aspartate aminotransferase, and γ-glutamyl transpeptidase decreased (p < 0.05), pointing to improved hepatic and lipid metabolism. Intestinal trypsin, lipase, and amylase activities also rose markedly (p < 0.05), peaking in HS3. Histological examination revealed greater mucosal thickness and villus height (p < 0.05); in HS3, these values reached approximately 0.95 mm and 0.87 mm, respectively. Metagenomic analysis showed that 0.75-1.0 g/kg nucleotides increased alpha diversity and restructured the microbial community, enriching Bacteroidetes- and Prevotella-related taxa while reducing Proteobacteria, including Acinetobacter baumannii and Escherichia coli. LEfSe identified dose-specific discriminant taxa, and refined KEGG Level 3 pathway analysis predicted enhanced butyrate and propanoate biosynthesis, starch utilization, and purine/pyrimidine interconversion at moderate doses. Genus-level abundances of Prevotella and Bacteroides correlated inversely with serum oxidative and hepatic stress markers. Quadratic regression estimated the optimal dietary nucleotide level at 764 mg/kg (0.76 g/kg), consistent with the best-performing 0.75 g/kg group. Collectively, 0.75-0.76 g/kg dietary nucleotides optimize growth and intestinal health in M. albus through coordinated improvements in antioxidant status, digestive function, mucosal architecture, and beneficial gut microbiota remodeling.},
}

@article {pmid42450707,
year = {2026},
author = {Dai, Y and Qiao, Y and Xie, N and Zhu, J and Lin, Q and Xu, B and Dai, Y},
title = {Contrasting Roles of Mobile Genetic Elements and Metal Resistance Genes in Shaping the Gut Resistome of Wild Fish from the Qiantang River.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16132000},
pmid = {42450707},
issn = {2076-2615},
support = {LHZY24C190001//Zhejiang Provincial Natural Science Foundation/ ; },
abstract = {The dissemination of antibiotic resistance genes (ARGs) in riverine ecosystems poses a pressing public health threat, while the mechanisms governing the assembly of the gut resistome in wild fish remain poorly elucidated. This study aimed to elucidate the distributional patterns of ARGs across multiple environmental compartments and to identify factors associated with their variation, particularly the contributions of mobile genetic elements (MGEs) and metal resistance genes (MRGs) to gut resistome variation. Metagenomic sequencing was conducted on 60 samples, comprising water, sediment, and gut contents from three wild fish species (Megalobrama terminalis, Aristichthys nobilis, and Coilia nasus) with distinct feeding habits, collected from four reaches of the Qiantang River basin. A total of 305 ARG subtypes belonging to 23 classes were identified. ARG composition differed significantly across environmental media and host species (permutational multivariate analysis of variance, PERMANOVA; p < 0.01), with host species identity as the primary structuring factor. Variance partitioning analysis (VPA) revealed that MGEs independently explained the largest fraction of ARG variation in A. nobilis (33.8%, p = 0.006), whereas MRGs dominated in C. nasus (33.3%, p = 0.005); in M. terminalis, MGEs and MRGs together accounted for 47.9% of the variation. Metagenomic assembly recovered 2622 ARG-carrying contigs, of which 28.3% (743) were predicted as plasmid sequences; physical co-localization among ARGs, MGEs, and MRGs was detected on both chromosomes and plasmids. Metagenomic binning validated the physical co-localization of ARG-MGE-MRG modules in genera such as Morganella and Burkholderia at the genome level, while plasmid-borne high-risk ARGs were identified in Aeromonas. Risk ranking further revealed significant enrichment of Rank II potentially high-risk ARGs (e.g., mcr-7.1, blaZ) in fish guts, carried by potential pathogens. These findings suggest that horizontal gene transfer involving MGEs and co-selection related to MRGs are closely associated with the fish gut resistome composition in a manner dependent on host ecology, providing a scientific basis for shifting riverine resistance management from concentration-based control toward the interruption of dissemination pathways.},
}

@article {pmid42450796,
year = {2026},
author = {Wei, Q and Chen, Y and Yang, H and Du, J and Li, H and Song, Z},
title = {Host-Associated and Environmental Microbiota of Hatchery-Reared Sichuan Taimen (Hucho bleekeri): Community Structure and Functional Profiling.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16132089},
pmid = {42450796},
issn = {2076-2615},
support = {BL2023/D-88//the Sichuan Zumuzu River Hydropower Development Company, Ltd./ ; NJTCSC25-2//the Open Project of Sichuan Provincial Key Laboratory of Fish Resources Conservation and Utilization in the Upper Reaches of the Yangtze River/ ; YSCX2035-011//the Project of Original Innovation 2035/ ; SCCXTD-2026-15//the Sichuan Fresh Water Fish Innovation Team/ ; },
abstract = {The diversity and complexity of symbiotic microbiota in fish may significantly influence the host's physiological, metabolic and immunological functions. In order to understand the microbial assembly in Sichuan taimen (Hucho bleekeri), an endangered fish species in the upper reaches of the Yangtze River, the microbiota of the skin, oral cavity and feces of artificially reared individuals and the microbiota of the rearing water were characterized through metagenomic sequencing. The results demonstrated that Pseudomonadota were shared across the skin, oral cavity, feces and rearing water, suggesting that they may constitute a shared microbial group connecting the aquatic environment and host mucosal surfaces. Based on functional prediction analyses, these taxa were potentially associated with organic matter degradation, nutrient cycling, and microbial and immune homeostasis. Likewise, Actinomycetota and Bacillota were consistently detected across multiple mucosal tissues and were predicted to be associated with nutrient transformation, antimicrobial defense, and the maintenance of mucosal microbial stability. Fusobacteriota were detected solely in feces, suggesting a strong tissue-specific colonization capacity. The alpha diversity of the microbiota did not differ significantly among tissues, and the beta diversity revealed strong clustering of host-associated samples and clear separation from water samples. Functional annotation further revealed that the water microbiota exhibited broader yet more dispersed functional potential, whereas host-associated microbiota showed stronger functional specialization closely aligned with host physiological demands. Collectively, the findings are better presented as baseline information for future comparative and hypothesis-driven studies in Sichuan taimen.},
}

@article {pmid42451140,
year = {2026},
author = {Ibor-Miguel, M and Pérez-Sánchez, D and Marques-Martínez, L and Aura-Tormos, JI and Guinot-Barona, C and Miralles, EG},
title = {Influence of Early Feeding Practices on Oral Microbiota Composition During Infancy and Potential Implications for Early Childhood Caries: A Systematic Review.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132138},
pmid = {42451140},
issn = {2072-6643},
mesh = {Humans ; Infant ; *Dental Caries/microbiology/epidemiology ; *Microbiota ; *Mouth/microbiology ; Breast Feeding ; Child, Preschool ; Infant, Newborn ; Female ; *Feeding Behavior ; Child ; Infant Nutritional Physiological Phenomena ; Milk, Human ; Infant Formula ; },
abstract = {BACKGROUND: Early feeding practices are among the most influential determinants of the infant oral microbiota during the first years of life. Breastfeeding provides bioactive components-immunoglobulins, human milk oligosaccharides (HMOs), and commensal bacteria-that may shape microbial colonisation patterns with long-term implications for oral health. However, the nature, magnitude, and clinical relevance of these effects remain poorly characterised, particularly with regard to early childhood caries (ECC) risk.

OBJECTIVES: The primary objective was to evaluate the association between early feeding practices and oral microbiota composition during infancy. A secondary exploratory objective was to assess whether feeding-associated microbiota differences had been linked to subsequent dental caries outcomes.

METHODS: A systematic review was conducted in accordance with PRISMA 2020 guidelines. PubMed, Scopus, Web of Science, and Embase were searched from January 2010 to June 2026. Eligible studies compared at least two feeding groups and measured oral microbiota directly using culture-independent methods (16S rRNA gene sequencing, metagenomics, or quantitative PCR targeting multiple taxa). Study selection, data extraction, and risk of bias assessment using the ROBINS-E tool were performed independently. Qualitative synthesis was conducted given clinical and methodological heterogeneity.

RESULTS: Of 8582 records identified, 12 studies met the inclusion criteria (sample size range: 12-448 participants; age range at microbiota assessment: 2 days-14 years, although eligibility was based on feeding exposure during infancy; six countries). Most included studies reported differences in oral microbiota composition associated with feeding type. During the first months of life, breastfed infants generally showed lower oral microbial diversity and higher abundance of Lactobacillus, the Streptococcus mitis group and Bifidobacterium compared with formula-fed infants, who exhibited greater alpha diversity, higher transmission of maternal oral bacteria, and higher abundance of Prevotella and Actinomyces. Effects were most pronounced in the first three months of life and attenuated by 12 months in most cohorts. Only one study reported subsequent dental caries outcomes after early-life microbiota assessment, finding that Streptococcus cristatus abundance at three months was associated with dental caries at nine years of age, and that longer breastfeeding duration (≥12 months) was associated with a distinct microbiota profile and lower caries rates in this single available longitudinal study. Risk of bias was low in two studies, moderate in six, and high in four. Publication bias could not be formally evaluated.

CONCLUSIONS: Early feeding practices are associated with measurable differences in oral microbiota composition during infancy, particularly during the first months of life. However, evidence linking these microbiota differences to subsequent dental caries outcomes remains extremely limited, with only one included study assessing later caries development. Therefore, the clinical significance of feeding-associated microbiota profiles remains uncertain and should be investigated through well-designed prospective longitudinal studies.},
}

Humans
Infant
*Dental Caries/microbiology/epidemiology
*Microbiota
*Mouth/microbiology
Breast Feeding
Child, Preschool
Infant, Newborn
Female
*Feeding Behavior
Child
Infant Nutritional Physiological Phenomena
Milk, Human
Infant Formula

@article {pmid42451600,
year = {2026},
author = {Garcia, J and Silva, J and Alves, MJ and Gouvinhas, I},
title = {Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host-Microbe Mechanisms and Paths to Clinical Translation.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {13},
pages = {},
doi = {10.3390/molecules31132229},
pmid = {42451600},
issn = {1420-3049},
mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota ; Chronic Disease ; *Host Microbial Interactions ; Animals ; Probiotics/therapeutic use ; Skin Microbiome ; Biofilms ; Translational Research, Biomedical ; },
abstract = {Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption-often combined with persistent biofilm formation-drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host-microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools-advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance.},
}

Humans
*Wound Healing/drug effects
*Microbiota
Chronic Disease
*Host Microbial Interactions
Animals
Probiotics/therapeutic use
Skin Microbiome
Biofilms
Translational Research, Biomedical

@article {pmid42451744,
year = {2026},
author = {Yan, S and Li, J and Chen, K and Ren, C and Zhang, S and Chen, Q and Gao, Y and Liu, B},
title = {Metagenomic and Metabolomic Insights into Volatile Flavor Changes and Microbial Community Shifts in Physalis pubescens L. Fermentation by Lactiplantibacillus plantarum.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {13},
pages = {},
doi = {10.3390/molecules31132377},
pmid = {42451744},
issn = {1420-3049},
support = {CZKYF2025-1-B013//Provincial Research Institutes Scientific Research Operating Funds Project of Heilongjiang Province/ ; },
mesh = {*Fermentation ; *Metagenomics/methods ; *Metabolomics/methods ; *Volatile Organic Compounds/metabolism/analysis ; *Physalis/microbiology/metabolism/chemistry ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Metabolome ; Fruit/microbiology/chemistry ; *Flavoring Agents/metabolism ; Metagenome ; },
abstract = {Physalis pubescens L. is a seasonal fruit with high nutritional value but a short shelf life that limits its processing and utilization. This study integrated metagenomics and metabolomics to investigate the comparative effects of Lactiplantibacillus plantarum fermentation on volatile flavor metabolites and microbial community composition of P. pubescens by comparing initial (0 h) and post-fermentation (24 h) states. After 24 h of fermentation, 1316 volatile compounds were putatively identified by GC-MS, with 592 metabolites significantly changed and 501 upregulated and 91 downregulated. Key flavor compounds that impart citrus, floral, fruity, and rose notes including D-limonene, geraniol, D-carvone, and phenylethyl alcohol were markedly increased. Metagenomic analysis revealed that L. plantarum rapidly dominated the microbial community (relative abundance surged from <0.05% to ~72%) while effectively suppressing potential spoilage bacteria such as Escherichia coli. Functional gene annotation demonstrated significant enrichment of amino acid, carbohydrate, and fatty acid metabolism pathways, with key enzyme genes (L-lactate dehydrogenase, pyruvate oxidase, acetyl-CoA carboxylase) predominantly assigned to L. plantarum, suggesting their potential contribution to the generation of organic acids, ethanol, and esters. Spearman correlation analysis indicated that Lactobacillaceae genera were significantly positively correlated with terpenoids, phenols, alcohols, and aldehydes. This study provides the first metagenomics-metabolomics insight into the microbial and molecular mechanisms associated with flavor formation in LAB-fermented P. pubescens, offering a theoretical foundation for developing stable and controllable fermented fruit products.},
}

*Fermentation
*Metagenomics/methods
*Metabolomics/methods
*Volatile Organic Compounds/metabolism/analysis
*Physalis/microbiology/metabolism/chemistry
*Microbiota
Gas Chromatography-Mass Spectrometry
Metabolome
Fruit/microbiology/chemistry
*Flavoring Agents/metabolism
Metagenome

@article {pmid42452294,
year = {2026},
author = {Huang, J and Zhang, X and Tian, Y and Luo, G and Xie, D and Li, J and Duan, B and Peng, S},
title = {Moss Cover Redirects Soil Organic Carbon from Active Turnover to Mineral-Associated Stabilization in Subalpine Forests.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/plants15132098},
pmid = {42452294},
issn = {2223-7747},
support = {N5132112023000495//Huanglong Nature Reserve/ ; },
abstract = {Understory mosses modify near-surface soil conditions, but how elevation regulates their influence on active and mineral-associated soil organic carbon (SOC) remains unclear. We compared independently selected moss-covered and non-moss-covered soils across a 3200-3500 m elevational gradient and integrated soil physicochemical measurements, microbial biomass (MB), dissolved organic matter (DOM), microbial necromass carbon (MNC), particulate organic carbon (POC), mineral-associated organic carbon (MAOC), metagenomic profiling, and piecewise structural equation modeling. Moss-covered soils consistently contained higher SOC and MAOC, but lower DOM, MB, and generally lower POC, than non-moss-covered soils. MNC showed an elevation-dependent reversal, with higher values under moss cover at 3200 m but lower values under moss cover at 3300-3500 m. Elevation was not a significant uniform driver of MB, DOM, MNC, POC, or MAOC; instead, its influence was mainly reflected in interactions with surface cover and in elevation-related changes in moss-layer structure, diversity, and hydrothermal conditions. Core carbon-fixation and degradation functions remained broadly stable, whereas specific functional modules shifted within moss-covered soils: acetate and acetyl-CoA metabolism genes (ackA and abfD) were relatively abundant at 3300-3400 m, while the polysaccharide-reprocessing gene SGA1 and oxidative-transformation gene katG increased toward higher elevations, and pmoC/amoC rebounded at 3500 m. Structural equation models linked the microbial functional gene system more strongly to POC, whereas MNC was positively associated with MAOC, and the direct POC-to-MAOC pathway was not significant. These findings indicate that moss cover is associated with contrasting SOC allocation patterns and stronger microbial necromass-MAOC coupling, while elevation modulates these relationships indirectly through changes in moss communities, soil microenvironment, and microbial functional potential.},
}

@article {pmid42453369,
year = {2026},
author = {Cui, Y and Li, Q and Liu, Z and Yu, Y},
title = {Induced Sputum Microbial Diversity and Function Changes in Patients with Acute Exacerbations of Chronic Obstructive Pulmonary Disease by Metagenomic Sequencing: A Cross-Sectional Study.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {21},
number = {},
pages = {600218},
pmid = {42453369},
issn = {1178-2005},
mesh = {Humans ; *Sputum/microbiology ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Male ; Female ; Aged ; Cross-Sectional Studies ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Disease Progression ; *Microbiota ; Middle Aged ; *Lung/microbiology/physiopathology ; High-Throughput Nucleotide Sequencing ; China ; Phenotype ; Ribotyping ; },
abstract = {PURPOSE: The underlying pathogenesis of acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is closely related to airway microbiota dysregulation. Currently, there is a lack of systematic elaboration based on deep metagenomic sequencing regarding the species-level and functional characteristics of the microbiota during AECOPD, as well as its correlation with clinical phenotypes of the host. This study aims to systematically analyze the taxonomic composition and functional profile changes of the microbiota in induced sputum samples from COPD patients during the stable and acute exacerbation periods using metagenomic next-generation sequencing and to explore their correlations with clinical indicators through metagenomic methods.

PATIENTS AND METHODS: A total of 66 patients with COPD were recruited from the Department of Respiratory and Critical Care Medicine at Jiading District Central Hospital in Shanghai, China. Of these, 49 induced sputum samples were obtained from 47 patients (17 in the stable group; 30 in the acute exacerbation group) after the quality control with DNA extraction and deep metagenomic sequencing. The species annotation and functional analysis were conducted using bioinformatics procedures, and microbial α-diversity analysis, LEfSe analysis was performed to identify differentially expressed markers. Spearman correlation analysis was used to evaluate the correlation between microbial/functional characteristics and a series of clinical indicators.

RESULTS: The α-diversity of the sputum microbiota in AECOPD patients was significantly lower at the species level compared to the stable stage (p < 0.01), and the community structure also underwent significant changes. Functional annotation and comparative analysis further identified 9 KEGG pathways (ko00970, ko04112, ko03420, ko03440, ko03060/ko03070, ko03410, ko04930, and ko00680) and 1 eggNOG functional category (M: Cell wall/membrane/envelope biogenesis) that differed significantly between the two groups. Among them, pathways such as methane metabolism were downregulated in the exacerbation period.

CONCLUSION: This study revealed significant dysregulation of the airway microbiome in AECOPD patients at species-level diversity, community structure, and functional metabolism, providing a molecular basis for the discovery of functional biomarkers and therapeutic targets in the microbiome.},
}

Humans
*Sputum/microbiology
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis
Male
Female
Aged
Cross-Sectional Studies
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Disease Progression
*Microbiota
Middle Aged
*Lung/microbiology/physiopathology
High-Throughput Nucleotide Sequencing
China
Phenotype
Ribotyping

@article {pmid42453735,
year = {2026},
author = {Shulga, S and Tigunova, O and Andriiash, H and Yemets, A and Blume, Y},
title = {Harnessing plant microbiomes to enhance crop resilience and restore war-affected soils in Ukraine.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1868751},
pmid = {42453735},
issn = {1664-462X},
abstract = {This review presents the current understanding of the rhizosphere microbiome and its potential application for the regeneration of damaged soils. The aim was to examine the issues of soil degradation associated with military actions and the latest developments in microbiome engineering for their application in the bioremediation of damaged lands. The review analyses recent developments and achievements in the study of the microbiome, its role in soil fertility, and plant protection against stress. Various directions and approaches to microbial profiling and addressing relevant pollution issues using developed bioengineered models and constructs have been examined. It has been shown that the most common explosive organic compounds - TNT, hexogen, and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine - and heavy metals - lead, cadmium, zinc, and antimony - account for the greatest soil contamination. The restoration of soils damaged as a result of military actions is feasible through the engineering of a specific soil microbiome (including genera Bacillus, Pseudomonas, and Arthrobackter, as well as arbuscular mycorrhiza). Military-related stress on soil is exerted by a mixture of organic pollutants and heavy metals, and the use of microbial consortia is a promising approach for mitigating their impact. The main economic advantage of such associations is that a consortium not only degrades toxic contaminants but also contains strains capable of nitrogen fixation and phosphorus mobilisation. The economic feasibility of applying synthetic microbial consortia and microbial engineering in war-affected regions is based on balancing the initial costs of research and development against substantial savings in capital investments compared with conventional land remediation methods.},
}

@article {pmid42454139,
year = {2026},
author = {Wang, Q and Tang, C},
title = {Diagnosis and treatment of severe tuberculosis complicated by ARDS and MODS in a young immunosuppressed host: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1846671},
pmid = {42454139},
issn = {2296-858X},
abstract = {BACKGROUND: Severe tuberculosis (TB) presents with complex clinical manifestations and high mortality. Immunosuppressed hosts are at high risk for TB infection and prone to progress to severe disease.

CASE PRESENTATION: A young female patient was admitted to our Respiratory Intensive Care Unit with fever, cough, and progressive dyspnea. She had a history of nephrotic syndrome and was on long-term corticosteroids and immunosuppressive agents, but without TB screening at baseline. Following admission, she rapidly developed acute respiratory distress syndrome (ARDS), diffuse alveolar hemorrhage, and multiple organ dysfunction syndrome (MODS). While providing broad-spectrum anti-infective therapy, invasive mechanical ventilation, continuous renal replacement therapy, and supportive care to maintain vital signs, we achieved an early definitive diagnosis of disseminated tuberculosis through rapid sputum acid-fast bacilli staining, Mycobacterium tuberculosis nucleic acid testing, and metagenomic next-generation sequencing (mNGS). A multidisciplinary team collaborated to formulate an individualized anti-tuberculosis treatment plan, leading to a favorable clinical outcome.

CONCLUSION: This case highlights the necessity of TB screening in immunosuppressed hosts, early recognition of severe TB, the importance of precise etiological diagnosis, and emphasizing the application of comprehensive treatment strategies in such patients.},
}

@article {pmid42454225,
year = {2026},
author = {Kafaie, S and Naseri, S and Mahoney, DBJ and Gagie, T and Beiko, RG and Maguire, F},
title = {Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag066},
pmid = {42454225},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Drug Resistance, Bacterial/genetics ; *Software ; Humans ; },
abstract = {Antimicrobial resistance (AMR) is a major global challenge to human and animal health. The genomic element (e.g. chromosome, plasmid, and genomic islands) and neighbouring genes associated with an AMR gene play a major role in its function, regulation, evolution, and propensity to undergo lateral gene transfer. Therefore, characterizing these genomic contexts is vital for effective AMR surveillance, risk assessment, and stewardship. Metagenomic sequencing is widely used to identify AMR genes in microbial communities but fragmentary short-read data do not directly provide this critical contextual information. Assembly of these reads provides some contextual information but fails to recover many mobile genetic elements. Here, we introduce Sarand, a method retaining some of the sensitivity of read-based methods while providing the genomic context of assembly by extracting AMR genes and their associated context directly from metagenomic assembly graphs. Sarand uses BLAST-based homology searches with coverage statistics to identify and visualize AMR gene contexts while filtering false chimeric contexts. Using both real and simulated metagenomic data, we show that Sarand outperforms metagenomic assembly and other recently developed graph-based tools in terms of precision and sensitivity for this problem. Sarand enables effective extraction of metagenomic AMR gene contexts to better characterize AMR evolutionary dynamics within complex microbial communities.},
}

*Metagenomics/methods
*Drug Resistance, Bacterial/genetics
*Software
Humans

@article {pmid42454401,
year = {2026},
author = {Pettinga, D and Fonseca-García, C and Krause, G and Ploemacher, H and Wheeler, T and Clendinen, CS and Handakumbura, P and Egbert, R and Coleman-Derr, D},
title = {Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant-microbe interactions.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71425},
pmid = {42454401},
issn = {1469-8137},
support = {2019-67019-29306//National Institute of Food and Agriculture/ ; DE-AC05-76RL01830//Pacific Northwest National Laboratory/ ; CRIS 2030-12210-003-000D//Agricultural Research Service/ ; DE-AC05-76RL0183//Biological and Environmental Research/ ; },
abstract = {Plant growth is influenced by the composition of its associated microbiome. The inherent complexity and functional redundancy of natural plant microbiomes present a formidable barrier to understanding the myriad biological interactions therein. Efforts have been made to develop synthetic microbial communities (SynComs) that can provide a rigorous and generalizable framework for the rational design of next-generation microbial products for sustainable agriculture. We test multiple strategies for stable, plant growth promoting SynCom design and evaluate the phenotypic and molecular impacts of a successful plant-SynCom interaction. We designed four distinct, reduced-complexity variants of SynCom Sorghum Root Consortium 1 and assessed their capacities for colonization, stability, and plant growth promotion (PGP). To understand the impact on plant performance of our highest performing SynCom variant, we characterized the host's longitudinal transcriptional response to SynCom inoculation and corroborated the results with metabolomics analysis. The top-performing SynCom stably colonized Sorghum bicolor roots and rhizospheres, elicited PGP, and induced dynamic spatiotemporal gene transcription in S. bicolor roots and shoots defined by modulation of growth-defense trade-off machinery and enhanced flavonoid production. The resultant reduced-complexity SynCom is a highly stable, soil-independent, plant growth promoting, and demonstrates the utility of colonization-based selection criteria, integrated with longitudinal transcriptomic and metabolomic characterization.},
}

@article {pmid42454923,
year = {2026},
author = {Shen, J and Hu, Y and Zou, X and Zhao, X and Li, S and Jiang, Y and Zhu, F},
title = {Impact of corticosteroids on lung antibiotic resistance genes in patients with lower respiratory tract infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0208025},
doi = {10.1128/spectrum.02080-25},
pmid = {42454923},
issn = {2165-0497},
abstract = {UNLABELLED: Lower respiratory tract infections (LRTIs) are a major global health concern, complicated by rising antibiotic resistance driven by antibiotic resistance genes (ARGs). Despite its role in the treatment of respiratory diseases, the impact of corticosteroids on ARGs in LRTI patients remains underexplored. Bronchial alveolar lavage (BAL) samples were collected from LRTI patients from two intensive care units (ICUs). Patients were classified into the corticosteroid group (CS group) and the non-corticosteroid group (NCS group) based on corticosteroid use. Next-generation sequencing assessed ARGs and associated microbes, with multivariable logistic regression analyzing the relationship between corticosteroid therapy and ARG accumulation. Ninety-one patients were recruited; the CS group (n = 57) exhibited a distinct ARG profile, marked by higher alpha-diversity and increased prevalence of ARGs than the NCS group (n = 34). The duration of corticosteroid therapy was positively associated with ARG accumulation, with individuals receiving treatment for more than 30 days exhibiting the highest ARG burden. The duration of corticosteroid therapy and the underlying hematological diseases were two independent risk factors for ARG accumulation. Our data provide new evidence that, in patients with LRTIs, extended corticosteroid use is associated with the accumulation of ARGs and modifications in the microbial composition of the lower respiratory tract.

IMPORTANCE: This research provides new evidence that prolonged use of corticosteroid drastically increases antibiotic resistance genes (ARGs) in the lungs of LRTI patients. It reveals a duration-dependent accumulation of ARGs, notably for common broad-spectrum antibiotics. These findings highlight the need to consider ARG burden when evaluating corticosteroid prescribing practices in patients with lower respiratory tract infections.},
}

@article {pmid42454926,
year = {2026},
author = {Davies, J and Ireland-Hughes, J and Stronati, S and Smith, RP and Oastler, C and Nunez-Garcia, J and Anjum, MF and AbuOun, M},
title = {Exploratory analysis of livestock waste treatment impacts on microbial diversity and antimicrobial resistance gene abundance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0147626},
doi = {10.1128/spectrum.01476-26},
pmid = {42454926},
issn = {2165-0497},
abstract = {UNLABELLED: The potential spread of antimicrobial resistance (AMR) through agricultural waste is underexplored and may contribute to the dissemination of AMR genes into the environment. This pilot study used metagenomic sequencing to investigate how anaerobic digestion (AD) and on-farm slurry lagoon treatment affect microbial community composition and relative AMR gene abundance in livestock waste. Samples were collected before and after treatment from three AD sites and two on-farm slurry lagoon sites. Taxonomic profiles and diversity metrics were generated from short-read Illumina sequencing, and AMR gene presence and relative abundance were assessed using APHA SeqFinder, an in-house analysis pipeline. AD treatment led to decreased microbial richness and evenness, and reduced the relative abundance of several high-prevalence taxa, including members of the Enterobacteriaceae. On-farm slurry lagoon treatment had a comparatively minor effect on microbial composition. AD was also associated with significant reductions in the relative abundance of genes conferring resistance to macrolides, aminoglycosides, fusidic acid, and beta-lactams. These findings suggest that AD and on-farm slurry lagoon treatment exert distinct effects on microbial communities and AMR gene profiles. The results provide preliminary evidence that AD may contribute to reducing AMR gene burden in agricultural waste, although further investigation across broader temporal scales and treatment methods is needed.

IMPORTANCE: Antimicrobial resistance is a major global health challenge, and agricultural waste is a key environmental reservoir of resistance genes. This study examined how two livestock waste treatments (anaerobic digestion and on-farm slurry lagoon storage) affect microbial communities and relative antimicrobial resistance gene (ARG) abundance. The findings show that anaerobic digestion reduces both microbial diversity and the relative abundance of several resistance genes, while on-farm slurry lagoon treatment has a limited impact. These results highlight the potential for treatment strategies to reduce the environmental spread of resistance.},
}

@article {pmid42454932,
year = {2026},
author = {Li, J and Xue, S and Hou, L and Zhang, Z and Yuan, K and Chen, X and Kong, C and Wang, L and Gu, B and Liu, X},
title = {Construction and validation of a phenotypic prediction model for bacterial gentamicin resistance using deep learning with gene sequences.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0190625},
doi = {10.1128/spectrum.01906-25},
pmid = {42454932},
issn = {2165-0497},
abstract = {The emergence of bacterial resistance to antibiotics poses a significant threat to human health; thus, there is an urgent need for new strategies in understanding the mechanisms of resistance and further fast prediction of it. Deep learning models offer promising solutions through analyzing genetic sequences in the prediction of bacterial resistance patterns. This study develops and validates a transformer-based deep learning model, DNABERT-2-117M, to predict gentamicin resistance in Klebsiella pneumoniae directly from whole-genome sequences. Our central methodological advance investigates the impact of the DNA tokenization strategy on predictive performance. We prospectively compared a dynamic tokenization approach against conventional fixed-length tokenization. Evaluated through rigorous fivefold cross-validation and on a hold-out test set, the model employing dynamic tokenization achieved superior performance, with a mean F1-score of 0.95 and an area under the curve of 0.97. Our findings establish that optimizing sub-sequence tokenization is crucial for model accuracy, and this dynamic tokenization approach significantly enhances model accuracy for antibiotic resistance prediction from genomic data. This genome-based predictive model represents a scalable and rapid alternative to traditional antibiotic susceptibility testing, offering the potential to accelerate clinical decision-making and improve patient outcomes in managing K. pneumoniae infections.IMPORTANCEThis study addresses a critical gap in diagnostic technologies for hypervirulent, antibiotic-resistant Klebsiella pneumoniae. We introduce a transformer-based deep learning framework that utilizes dynamic tokenization strategies to predict drug resistance directly from genomic sequences. The core significance of our work is the development of a robust genomic prediction model that serves as a foundational component for future diagnostic paradigms. The significance of this work lies in its potential to fundamentally alter clinical timelines. By decoupling resistance prediction from the requirement for phenotypic growth, our approach is a critical step toward next-generation workflows (e.g., clinical metagenomics) that could deliver a complete diagnostic and susceptibility report directly from a patient sample within hours. This represents a scalable, rapid diagnostic platform that promises to accelerate the administration of targeted treatment for high-risk K. pneumoniae infections, with a clear trajectory toward same-day, specimen-to-result diagnostics in the near future.},
}

@article {pmid42454939,
year = {2026},
author = {Sen, P and Oliver, LL and Makarova, KS and Wolf, YI and Pavloudi, C and Shlafstein, M and Saw, JH},
title = {Hawaiian geothermal fumaroles contain diverse and novel viruses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156726},
doi = {10.1128/spectrum.01567-26},
pmid = {42454939},
issn = {2165-0497},
abstract = {UNLABELLED: Viral community structure is known to influence the evolution of microbes in diverse and complex environments. While the diversity of microbes and their viruses have been metagenomically explored in terrestrial hot springs and hydrothermal vent systems, other volcanic features remain remarkably understudied. Fumaroles (steam vents) are geothermal features that heat groundwater with magma, releasing heated water vapor and volcanic gases, such as CO2 and H2S. Fumaroles are physicochemically dynamic compared to terrestrial hot springs-temperatures and gas emissions fluctuate rapidly with volcanic activity. The viral community structures and diversity have never been systematically characterized or explored. We hypothesize that viruses facilitate microbial community adaptation to the harsh and dynamic fumarole environment. Using a sensitive profile-based approach for identification, we identify 383 viral operational taxonomic units (vOTUs) from 46 metagenomes of biofilms hosted near basaltic fumaroles. We estimate two previously undescribed order-level clades of Caudoviricetes (tailed phages), and find evidence of phylogenetic diversification within the fumarole systems. Read-mapping analysis of three sampled geothermal regions shows unexpected diversity and community structure within the geologic system: 99.7% of fumarole vOTUs are shared between distant fumaroles, and 40°C-60°C biofilms have high viral richness and evenness that do not correspond to biofilm microbial composition or diversity. Lastly, we provide the first description of a terrestrial environment dominated by Microviridae, which has only been described in viral communities of deep-ocean hydrothermal vents. Our study offers a unique geological system for the exploration of viral ecology in extreme environments.

IMPORTANCE: Geothermal environments serve as natural laboratories for studying adaptations to extreme conditions that challenge the limits of microbial life and offer insight into early life on Earth. Exploring microbial diversity in these systems reveals how ecological factors shape complex communities in extreme environments. Evidence increasingly shows that viruses influence microbial diversity in terrestrial hot springs and oceanic hydrothermal vents, yet the biogeography of viruses across these systems remains largely unexplored. We present the first metagenomic characterization of viral diversity and ecology in Hawaiian terrestrial volcanic fumaroles. Our results indicate extensive viral dispersal, in contrast to the typically more constrained dispersal observed in hot springs and hydrothermal vent systems. Furthermore, we observe a dominance of ssDNA viruses in fumarole viral communities, a pattern not previously reported in terrestrial systems. Our comprehensive analyses indicate that Hawaiian fumaroles are a valuable system for studying community patterns and the ecological determinants of viral biogeography.},
}

@article {pmid42454945,
year = {2026},
author = {Oworae, KO and Rabacal, W and Hu, A and Wychrij, DA and Rayens, E and Chapman, TI and Bahl, J and Norris, KA},
title = {Evaluating the impact of immunization with the "pan-fungal" vaccine, NXT-2, on the gut mycobiome and microbiome in non-human primates (NHPs).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0104726},
doi = {10.1128/spectrum.01047-26},
pmid = {42454945},
issn = {2165-0497},
abstract = {Fungal infections remain a significant public health concern with high mortality, morbidity, and increasing associated health costs. This burden is projected to rise due to expansion of at-risk populations, limited therapeutics, increasing drug resistance, and the emergence of new fungal pathogens. Even with these challenges, there are currently no approved vaccines. We previously developed a "pan-fungal" vaccine candidate, NXT-2, that confers protection against multiple invasive fungal infections such as pulmonary aspergillosis, pneumocystosis, and invasive candidiasis, as well as non-invasive vulvovaginal candidiasis. NXT-2 is a 90 amino acid consensus peptide designed from a conserved region of the fungal antigen (KEX1). We assessed the effect of NXT-2 immunization on gut microbial diversity, composition, and functional capacity in non-human primates. To do this, we monitored changes in the gut mycobiome and microbiome pre- and post-vaccination using ITS2 and metagenomic sequencing, respectively, in Japanese and rhesus macaque cohorts. NXT-2 elicited a robust antibody response without disrupting the gut microbial communities in both macaque species. The mycobiome exhibited stability with no significant changes in alpha and beta diversity, taxonomic composition, or functional guild distributions. The relative abundance of gut resident Candida and Aspergillus species remained stable and was not significantly altered following vaccination. The microbiome showed stability with preserved alpha and beta diversities, taxonomic composition, and functional capacity. Results from this study show the first cross-kingdom analysis demonstrating that antifungal vaccination can achieve protective immunity without perturbing gut microbial communities. This establishes a framework for microbiome-informed vaccine assessment beyond conventional immunogenicity and adverse effect monitoring.IMPORTANCEFungal infections cause millions of deaths annually, yet no vaccines are approved despite growing drug resistance and limited treatment options. NXT-2 is a pan-fungal vaccine that protects against multiple fungal infections such as pneumocystosis, candidiasis, and aspergillosis. Here, we demonstrate in NHPs that NXT-2 elicits robust protective antibody responses without altering gut bacterial or fungal communities. This is the first study to assess antifungal vaccination across both microbial kingdoms and establish that protective antifungal immunity can be achieved while preserving resident microbiota. This work provides a framework for incorporating microbiome assessment into vaccine development beyond conventional immunogenicity and adverse event monitoring.},
}

@article {pmid42455045,
year = {2026},
author = {Deng, L and Ju, Z and Chen, J and Lin, Y and Zhou, W and Lee, SS and Yung, CCM and Liu, H},
title = {Sulfur-cycling diazotrophs dominate nitrogen fixation in seagrass sediments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0099326},
doi = {10.1128/aem.00993-26},
pmid = {42455045},
issn = {1098-5336},
abstract = {Diazotrophs, the microbes capable of fixing dinitrogen, are essential for providing bioavailable nitrogen that supports marine primary production. Traditionally, nitrogen fixation in seagrass sediments has been linked primarily to heterotrophic sulfate reduction, leaving the roles of other metabolic processes, like sulfur oxidation, largely unexplored. Here, we employed metagenomic and metatranscriptomic approaches to explore the distribution, metabolic capabilities, and activity of diazotrophs in sediments dominated by the seagrass Halophila ovalis in a subtropical bay in Hong Kong. Our results revealed significantly higher nitrogen fixation rates in seagrass-vegetated sediments compared to adjacent bare sediments, with peak rates occurring in subsurface layers, suggesting that seagrass sediments may serve as hotspots for nitrogen fixation. We recovered 305 metagenome-assembled genomes, including those of diazotrophic sulfur-cycling bacteria. Notably, sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Desulfobacterota emerged as the dominant and active members of the diazotroph community in seagrass sediments, expressing specific genes related to both nitrogen and sulfur metabolic pathways. Furthermore, our findings suggest that sulfate-reducing Desulfobacterota likely drive the high nitrogen fixation rates observed in deeper sediment layers, while sulfur-oxidizing Gammaproteobacteria may play a crucial role in surface layers. This study underscores the important roles of both sulfate-reducing and sulfur-oxidizing bacteria in nitrogen fixation within seagrass sediments, revealing a complex interplay between nitrogen fixation and sulfur metabolism.IMPORTANCESeagrass meadows are vital blue carbon ecosystems found in coastal and estuarine regions, playing a crucial role in carbon sequestration and supporting marine diversity. Traditionally, biological nitrogen fixation, an essential process for supplying bioavailable nitrogen to living organisms, has been primarily associated with heterotrophic sulfate reduction in these ecosystems. Our research offers novel insights into the nitrogen-fixing microorganisms present in the sediments dominated by the seagrass Halophila ovalis. We found that both sulfur-oxidizing and sulfate-reducing bacteria contribute to nitrogen fixation processes in seagrass sediments. This study highlights the intricate connections between nitrogen and sulfur metabolic pathways, providing a more comprehensive understanding of nutrient cycling in coastal ecosystems.},
}

@article {pmid42455624,
year = {2026},
author = {Signorelli, T and Walker, M and Robertson, J and Quizon, K and Zhang, Y and Reimer, AR and Eagle, SHC},
title = {Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001738},
pmid = {42455624},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Benchmarking ; *DNA, Bacterial/isolation & purification/genetics ; Humans ; Microbiota/genetics ; Feces/microbiology ; Nanopores ; *DNA/isolation & purification ; },
abstract = {Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.},
}

*Metagenomics/methods
*Nanopore Sequencing/methods
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
Benchmarking
*DNA, Bacterial/isolation & purification/genetics
Humans
Microbiota/genetics
Feces/microbiology
Nanopores
*DNA/isolation & purification

@article {pmid42456224,
year = {2026},
author = {Zhang, Y and Wang, D and Su, N and Lu, H and Xu, H and Wan, W and Li, Z and Li, W},
title = {Chronic prosthetic joint infection caused by Coxiella burnetii diagnosed by metagenomic next-generation sequencing: A case report and literature review.},
journal = {Journal of infection and public health},
volume = {19},
number = {9},
pages = {103301},
doi = {10.1016/j.jiph.2026.103301},
pmid = {42456224},
issn = {1876-035X},
abstract = {Prosthetic joint infection (PJI) caused by Coxiella burnetii (C. burnetii) remains a rare but clinically significant diagnostic challenge due to its culture-negative characteristics and nonspecific clinical manifestations. Metagenomic next-generation sequencing (mNGS) has emerged as a valuable tool for identifying fastidious pathogens in culture-negative PJI cases. A patient with a history of joint arthroplasty presented with persistent joint pain and swelling. Despite multiple surgical interventions and prolonged empirical antibiotic therapy, routine bacterial cultures remained negative and the infection recurred. mNGS performed on periprosthetic tissue detected C. burnetii in two independent specimens, while all conventional cultures remained negative. Targeted antimicrobial therapy with doxycycline combined with levofloxacin was initiated, resulting in gradual symptom resolution and sustained clinical improvement during follow-up. This case highlights C. burnetii as an underrecognized cause of culture-negative PJI and demonstrates the clinical value of mNGS for early pathogen identification when conventional diagnostics fail. Repeated detection in independent specimens strengthened diagnostic confidence and enabled timely targeted therapy. Our findings support the early incorporation of mNGS into the diagnostic algorithm for suspected culture-negative PJI. In the present case, targeted doxycycline-levofloxacin therapy following mNGS-based pathogen identification was associated with sustained clinical improvement.},
}

@article {pmid42456442,
year = {2026},
author = {Wills, OC and Chua, XY and McEvoy, C and Fitzmaurice, M and El-Assaad, F and El-Omar, E and Probst, Y},
title = {A case-control study of the oral microbiome among Australian female adults with relapsing-remitting multiple sclerosis: A pilot study.},
journal = {Multiple sclerosis and related disorders},
volume = {113},
number = {},
pages = {107383},
doi = {10.1016/j.msard.2026.107383},
pmid = {42456442},
issn = {2211-0356},
abstract = {BACKGROUND: There is growing evidence investigating the role of the gut microbiome in the onset and progression of multiple sclerosis (MS). However, the role of the oral microbiome in MS is poorly understood, despite its importance in immune regulation and systemic health.

METHODS: A cross-sectional, case-control, pilot study comparing the oral microbiome among adults with relapsing-remitting MS to matched controls based on age, sex and body mass index (BMI), was conducted. Participants provided fasting oral swabs where DNA was extracted and shotgun metagenomic sequencing performed. Comparative analyses between cases and controls explored alpha-and beta-diversities including differential abundance testing.

RESULTS: Across 24 oral microbiome samples, 355 species from 12 phylum were detected. Alpha diversity was lower in MS at the species level, however, did not reach statistical significance for either richness or Shannon diversity. Beta diversity demonstrated a significant difference using Bray-Curtis dissimilarity with group status accounting for ∼6.7% of the total variation in microbial community structure. Differential abundance testing highlighted Veillonella parvula as the most enriched species among cases (coef=2.56, stderr=0.74, FDR=0.17), while Porphyromonas pasteri (coef=-3.57, stderr=1.02, FDR=0.17) and s__GGB4936_SGB6889 (coef=-4.29, stderr=1.30, FDR=0.17) were predominant among controls.

CONCLUSION: The oral microbiome of Australian females with RRMS differs in a subtle but detectable manner from those without MS, characterised by a non-significant trend towards reduced microbial diversity and distinct compositional clustering based on Bray-Curtis dissimilarity. Findings support the emerging concept of an oral-immune axis in MS, underscoring the need for longitudinal and functional studies to explore causality.},
}

@article {pmid42456685,
year = {2026},
author = {Steriade, C and Segata, N and Saxena, D},
title = {The role of the gut microbiome in mediating neuroinflammation in immune-based neurological disorders.},
journal = {The Lancet. Neurology},
volume = {25},
number = {8},
pages = {764-780},
doi = {10.1016/S1474-4422(26)00193-6},
pmid = {42456685},
issn = {1474-4465},
abstract = {The gut microbiome can influence brain health by modulating neuroinflammation through various mechanisms, including immune regulation, the production of metabolites that affect neural function, gut and blood-brain barrier integrity, upstream effects via the vagus nerve, upstream migration of gut-resident lymphocytes to the brain, bile acid signalling, and endocrine activity. Changes in gut microbiota have been observed in demyelinating conditions, autoimmune encephalitis, and epilepsy. Gut microbiota composition changes can affect neuroinflammation, disease progression, and treatment outcomes. Advances in microbiome research have improved the potential for clinical translation of findings; but limitations persist, driven by the largely correlational nature of clinical studies and the complexity of microbiome sequencing and interpretation. At present, only the ketogenic diet is routinely recommended by clinicians, whereas other microbiome-based interventions remain investigational. Multiple strategies for manipulating the gut microbiome, including dietary changes, prebiotics, probiotics, postbiotics, and faecal microbiota transplantation, might be used as disease-modifying therapies in the future.},
}

@article {pmid42456986,
year = {2026},
author = {Yang, C and Xu, Y and Nie, Y and Li, Y and Zeng, XC},
title = {Beyond arsenite: Arsenite-oxidizing prokaryotes drive sulfur compound oxidation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135419},
doi = {10.1016/j.biortech.2026.135419},
pmid = {42456986},
issn = {1873-2976},
abstract = {Arsenite oxidation prokaryotes (AsOPs) contribute significantly to the biogeochemical processes governing arsenic cycling. Since AsOPs can oxidize As[III] to As[V], markedly reducing arsenic toxicity and decreasing its migration potential, they have been widely utilized in the restoration of As[III]-affected sites and in the design of bioreactors for treating As[III]-polluted groundwater. However, it is still unclear whether AsOPs possess additional catalytic activities that may interfere with their bioremediation capacity, highlighting a critical knowledge gap that warrants further investigation. Because arsenic often coexists with sulfur, it was hypothesized that AsOPs may also oxidize reduced sulfur compounds. To verify this hypothesis, an AsOP-enriched culture was successfully established. Metagenomic analysis revealed that ∼ 96.1% of the AsOP metagenome-assembled genomes (MAGs) contained at least one pathway for the oxidation of reduced sulfur compounds, including sulfide, thiosulfate, or sulfite. Functional assays using both the AsOP community and three cultivable AsOP strains demonstrated that AsOPs actively catalyzed anaerobic sulfide oxidation coupled with nitrate reduction to ammonium, leading to complete sulfide oxidation to sulfate and a marked decrease in pH from ∼ 7 to ∼ 3. In addition, AsOP also directly degraded arsenopyrite, releasing As[V] and sulfate and causing acidification (pH 2.5). The findings from this study, for the first time, reveal that AsOP possesses not only As[III] oxidation capability but also anaerobic reduced sulfur compound oxidation activity that may lead to environmental acidification, highlighting the need for extreme caution when applying AsOPs in arsenic bioremediation.},
}

@article {pmid42456987,
year = {2026},
author = {Zhu, Y and Guo, J and Sun, H and Zhu, M and Shan, W and Lv, X and Qu, Z and Zhang, S and Liu, Y},
title = {Perfluorobutane sulfonate reshapes microbial metabolism and enhances antibiotic resistance and pathogen dissemination in anammox systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135422},
doi = {10.1016/j.biortech.2026.135422},
pmid = {42456987},
issn = {1873-2976},
abstract = {As the use of short-chain per- and polyfluoroalkyl substances, particularly perfluorobutane sulfonate (PFBS), continues to increase, their accumulation in wastewater treatment plants (WWTPs) and the associated ecological risks have attracted growing attention. Nevertheless, the impacts of PFBS on the anaerobic ammonium oxidation (anammox) process, as well as its role in the dissemination of antibiotic resistance genes (ARGs) and the proliferation of pathogens, remain poorly understood. In this study, metagenomic analysis combined with multidimensional data integration was employed to systematically investigate the effects of PFBS exposure on anammox performance, microbial metabolism, and ARG dynamics. The results revealed that PFBS exposure significantly deteriorated nitrogen removal, leading to a 10.16% reduction in total nitrogen removal efficiency. Carbon metabolism was inhibited, whereas microbial communities adapted by enhancing antioxidant capacity and electron transport activity. The relative abundance of key anammox functional genes (hzs and hdh) decreased by 54.65% and 57.32%, respectively. Molecular docking analysis demonstrated a strong binding affinity between PFBS and hydrazine dehydrogenase (-8 kcal/mol), suggesting potential interactions. Moreover, PFBS exhibited notable interactions with denitrification-related enzymes, suggesting potential perturbations to denitrification pathways. Additionally, PFBS facilitated the enrichment of ARG and mobile genetic elements (MGE), thereby increasing the potential for MGE-mediated ARG dissemination. PFBS enriched potential pathogenic microorganisms and strengthened their associations with ARGs. Collectively, these findings demonstrate that PFBS exposure compromises anammox performance while simultaneously elevating antimicrobial resistance dissemination and pathogen-associated risks, highlighting its ecological implications in WWTPs.},
}

@article {pmid42457325,
year = {2026},
author = {Zhang, YY and Gan, MY and Zhu, YQ and Wu, BB and Zhou, WH},
title = {[Application of metagenomic next-generation sequencing in the pathogen spectrum analysis of suspected infections in neonatal blood and cerebrospinal fluid].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {28},
number = {7},
pages = {824-831},
doi = {10.7499/j.issn.1008-8830.2511025},
pmid = {42457325},
issn = {1008-8830},
abstract = {OBJECTIVES: To evaluate the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens in suspected neonatal sepsis and central nervous system infections.

METHODS: This retrospective study included 648 neonates with suspected sepsis or central nervous system infections, with 734 cerebrospinal fluid and 733 blood samples collected. The pathogen spectra detected by mNGS and traditional culture were compared. Using clinical diagnosis as the gold standard, the diagnostic efficacy of the two methods was analyzed.

RESULTS: The positive rates of pathogen detection by mNGS in cerebrospinal fluid and blood samples were 15.3% and 40.0%, respectively, significantly higher than those of traditional culture (1.4% and 10.7%, respectively). mNGS identified 25 and 40 distinct pathogenic species from cerebrospinal fluid and blood, respectively, exceeding the 4 and 24 species detected by culture. Ureaplasma, Mycoplasma, and other fastidious pathogens difficult to culture were detected exclusively by mNGS. Using clinical diagnosis as the reference, mNGS showed sensitivities of 50.4% (cerebrospinal fluid) and 46.7% (blood), compared to 5.8% and 18.0% for culture.

CONCLUSIONS: mNGS significantly improves pathogen detection rates in neonatal infections compared with traditional culture, provides more comprehensive pathogen information, and holds important clinical value for the precise diagnosis and treatment of neonatal infections.},
}

@article {pmid42457685,
year = {2026},
author = {Wei, L and Cui, Z and Mu, Z and Li, Y and Deng, F},
title = {Comparative fecal microbiome and metabolome reveal enhanced lignocellulose-degrading potential in Cervus elaphus yarkandensis.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-01002-3},
pmid = {42457685},
issn = {2396-8370},
support = {ygzbhly2025102//School-level project fund of Chongqing Medical and Pharmaceutical College/ ; QN[2025]100//Guizhou Provincial Basic Research Program (Natural Science) Youth Guidance Project/ ; },
abstract = {Reed is rich in lignocellulose and is therefore challenging for many ruminants to use efficiently. The endangered Tarim red deer subspecies Cervus elaphus yarkandensis (TH) inhabits the Tarim Basin, where reed represents an important forage resource, whereas captive observations suggest that the closely related Cervus elaphus songaricus (TS) may exhibit poorer tolerance to reed-rich diets. Here, we compared fecal microbial composition, metagenomic functional potential, metagenome-assembled genome (MAG)-level carbohydrate-active enzyme (CAZyme) profiles, fecal enzymatic activities, in vitro reed-straw degradation capacity, and fecal and serum metabolomic profiles between TH and TS under the same reed-containing feeding conditions. Compared with TS, TH showed higher fecal microbial diversity and increased abundances of fiber-associated taxa, including Ruminococcaceae, Lachnospiraceae, and Alistipes. Shotgun metagenomics and MAG-level CAZyme analysis indicated that TH-associated microbial communities carried a broader repertoire of functions related to lignocellulose degradation and plant-polysaccharide deconstruction. Consistent with these functional profiles, TH fecal samples exhibited higher cellulase and hemicellulase activities, and TH fecal inocula showed greater reed-straw degradation capacity than TS fecal inocula in vitro. Untargeted metabolomics revealed group-specific fecal and serum metabolites related to carbohydrate fermentation, short-chain fatty-acid-related metabolism, and lipid metabolism, which were associated with TH-enriched fiber-degrading taxa and microbial functional pathways. In an exploratory mouse colonization experiment, TH-derived fecal microbiota was associated with changes in fiber-associated microbial taxa, metabolic pathways, fecal metabolites, body weight, and intestinal morphology in antibiotic-treated mice fed a reed-containing diet. Together, these results indicate that TH harbors fecal microbial and metabolic features associated with enhanced lignocellulose and reed-straw degradation capacity. These findings suggest candidate microbiome-associated pathways relevant to reed-rich forage utilization and may help identify microbial and enzymatic resources for lignocellulose bioconversion.},
}

@article {pmid42457990,
year = {2026},
author = {Danielsson, H and Portlock, T and Hellström, A and Nilsson, A and Sävman, K and Wackernagel, D and Hansen-Pupp, I and Ley, D and Shoaie, S and Uhlén, M and Brusselaers, N and Elfvin, A},
title = {Supplementation with long-chain polyunsaturated fatty acids to extremely preterm infants associates with development of the intestinal microbiota.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42457990},
issn = {1530-0447},
abstract = {BACKGROUND: Supplementation with arachidonic acid (AA) and docosahexaenoic acid (DHA) to extremely preterm infants reduces the risk of severe retinopathy of prematurity (ROP). The main aim of this study was to explore the involvement of AA:DHA supplementation in the developing gut microbiome, and its possible contribution to the ROP-protective effect. Secondly, additional covariates for microbiome maturation were evaluated.

METHODS: Longitudinal gut microbiome profiles and bacterial gene pathways were characterised using shot-gun metagenomics in 75 extremely preterm infants who participated in a randomized clinical trial on AA:DHA supplementation. Serum protein levels quantified using proximity extension assays were merged with the microbiome data.

RESULTS: AA:DHA supplementation was linked to an increase in relative abundance of Citrobacter koseri and associated with changes in proteins and metabolic pathways. Occurrence of severe ROP was associated with microbiome alpha diversity (Shannon and Evenness) and beta diversity (Bray-Curtis). Additionally, study centre and gestational age at birth impacted the microbiome composition.

CONCLUSION: We conclude that AA:DHA supplementation impacts the microbiome. However, the current study could not determine the causality between the supplementation, microbiome and ROP-decrease. Nonetheless, these findings highlight the complex interplay between external interventions, including nutritional supplements, and the gut microbiome development in extremely preterm infants.

IMPACT: Longitudinal gut microbiome profiles, bacterial gene pathways and serum protein expressions were determined using shotgun metagenomics and proximity extension assays in 75 extremely preterm infants included in a multicentre randomized clinical trial investigating enteral fatty acid supplementation. Dynamic shifts in microbiome and pathway composition were seen from birth to 34 weeks gestational age. Arachidonic acid (AA) and docosahexaenoic acid (DHA) supplementation was linked to an increase in relative abundance of Citrobacter koseri and associated with changes in proteins and metabolic pathways. However, the causality between the supplementation, microbiome, and ROP-decrease could not be determined.},
}