@article {pmid42402588,
year = {2026},
author = {Jin, Y and Cui, J and Liu, R and Ma, H and Xu, X and Wu, S and Gan, F and Lu, ZJ and Xu, ZZ},
title = {Conserved 3' stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02454-1},
pmid = {42402588},
issn = {2049-2618},
abstract = {BACKGROUND: Bacterial transcription termination is a critical yet underexplored layer of gene regulation in microbial ecosystems. Existing computational tools, however, primarily focus on predicting transcript 3' ends generated by Rho-independent terminators (RITs) in a few model species, leaving gaps in understanding those generated by Rho-dependent terminators (RDTs) and their diversity across Bacteria.

RESULTS: We developed BATTER (Bacteria Transcript Three Prime End Recognizer), a deep learning-based framework for predicting bacterial transcript 3' termini. BATTER leverages the observation that conserved stem-loop structures are frequently associated with 3' ends of primary transcripts terminated by both RIT and RDT mechanisms across diverse bacterial clades. Compared with existing approaches, BATTER demonstrated superior performance and scalability, enabling a comprehensive analysis of 42,905 representative bacterial genomes. This large-scale application revealed that stem-loop structures exhibit clade-specific properties with greater variations between species than between gene families. Notably, BATTER uncovered that certain Cyanobacteria lineages, despite lacking rho homologs, harbor Rho utilization (RUT)-like sequences near 3' ends, and preliminary experimental validation in E. coli supports their partial functionality in transcription termination. Additionally, BATTER systematically identified pervasive premature termination events in antimicrobial resistance (AMR) genes.

CONCLUSIONS: BATTER enables large-scale comparative genomic analyses of transcription termination, providing a powerful framework to investigate termination-associated transcriptional regulation in microbial communities. The BATTER tool is available at https://github.com/xu-research-lab/BATTER. Video Abstract.},
}

@article {pmid42402612,
year = {2026},
author = {Cao, L and Zhang, G and Zhang, G and Zhang, F and Li, W and Song, Q and He, J and Zhao, J and Zhang, Z},
title = {Cichorium intybus L. polysaccharide improves growth performance and colonic barrier function in weaned piglets via the microbiota-HDCA-TGR5-Akt-NF-κB signaling axis: validation by FMT and in vitro models.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42402612},
issn = {1674-9782},
support = {32302766//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Weaning stress predisposes piglets to intestinal barrier disruption and gut dysbiosis, which contribute to post-weaning diarrhea and poor feed efficiency. Chicory (Cichorium intybus L.) polysaccharide (CLP) is a fructan-rich prebiotic candidate; however, how CLP reshapes the microbiota-metabolite network to protect the colon remains unclear.

METHODS: In Exp. 1, 96 weaned piglets [Duroc × (Landrace × Yorkshire), 28 days old, 8.03 ± 0.2 kg] were fed a basal diet (CON group) or a 0.5% CLP supplemented diet (CLP group). In Exp. 2, fecal microbiota from piglets were transplanted into dextran sulfate sodium (DSS)-induced mice to confirm the causal role of the CLP-remodeled microbiota. Metagenomic and untargeted metabolomic analyses were employed to identify key microbial species and functional metabolites. In Exp. 3, Caco-2 cells were treated with varying concentrations of hyodeoxycholic acid (HDCA) for 24 h to functionally validate the regulatory effects on TGR5 and FXR expression levels.

RESULTS: The results showed that dietary CLP significantly decreased the feed to gain ratio, diarrhea rate and histology index (P < 0.05), but increased goblet cell numbers (P < 0.05). Metagenomic sequencing revealed that CLP significantly increased microbial α-diversity and remodeled the community structure, specifically enriching beneficial microbes, such as Blautia sp., Eubacterium sp., and Ruminococcus sp. To test microbiota causality, fecal microbiota from CON or CLP piglets was transplanted into antibiotic treated mice followed by DSS challenge. The CLP modified microbiota alleviates DSS induced colitis, upregulated Occludin and ZO-1 expression, and reduced colonic IL-1β and TNF-α levels. Mechanistically, the CLP remodeled microbiota promoted the accumulation of HDCA, which functioned as a signaling ligand to activate the colonic TGR5 receptor. This activation subsequently suppressed the phosphorylation of Akt (P < 0.05), leading to the inhibition of the NF-κB signaling pathway through the reduced phosphorylation of IκBα and the p65 subunit (P < 0.05), thereby effectively abrogating the inflammatory response.

CONCLUSION: Dietary CLP supplementation mitigates weaning induced intestinal injury and inflammation by remodeling the colonic microbiota, specifically enriching HDCA-producing species. The subsequent activation of the HDCA-TGR5-Akt signaling axis inhibits the NF-κB pathway, thereby improving host immune responses and intestinal barrier function.},
}

@article {pmid42402715,
year = {2026},
author = {Bellucci, M and Mostofa, MG and Benucci, GMN and Kabir, AH and Khan, I and Lombardi, M and Locato, V and Bonito, G and Loreto, F and Sharkey, TD},
title = {Isoprene-Emitting Transgenic Tobacco Shapes Root Microbiome and Enhances Growth of Co-Cultivated Non-Emitting Plants.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70698},
pmid = {42402715},
issn = {1365-3040},
support = {IOS-2022495//National Science Foundation (NSF)/ ; DE-FG02-91ER20021//Basic Energy Sciences/ ; FIS00000382//Italian Ministry of University and Research (MUR) Future in Science (FIS) 2021 program/ ; 2022ZYCCJJ//MUR - PRIN 2022/ ; P20229ZW4A//MUR - PRIN 2022/ ; DEVTF2210892//The Company of Biologists/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; },
abstract = {Isoprene is the most abundant biogenic volatile organic compound emitted by terrestrial vegetation. Here we report the impact of isoprene on root-associated microbiomes. Using isoprene-emitting (IE) transgenic tobacco and isogenic non-emitting (NE) controls, we performed co-cultivation experiments in natural soil and analysed plant phenotypes and growth alongside bacterial and fungal communities across root, rhizosphere, and soil niches. NE plants co-cultivated with IE neighbours displayed increased shoot and root biomass, suggesting interactive belowground functions of isoprene. Amplicon sequencing revealed more growth-promoting microbiota in root and rhizosphere of IE plants than NE plants. Both bacterial and fungal growth-promoting microbiota were enriched in IE and NE plants grown in the same pot. However, isoprene-fumigated plant-free soils did not replicate these shifts, indicating that plant-microbe interactions are required for the modulation of the soil microbiome. Our results suggest that isoprene acts as a belowground cue influencing microbiome assembly and indirectly enhancing growth in neighbouring plants. This work uncovers a potential ecological role for isoprene, highlighting how plant-derived isoprene can mediate plant-plant-microbiome interactions and contribute to community-level processes in the rhizosphere.},
}

@article {pmid42402854,
year = {2026},
author = {Cai, Y and Yan, H and Qin, J and Qiang, Y and Lin, GQ and Wang, H and He, QL and Zhao, Q},
title = {Heterologous Expression of an Abandoned Termite Mound Fungus Gene Cluster Reveals a Protective Aldehyde-Alcohol Cycle and a Candidate Termiticidal Metabolite.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.6c00101},
pmid = {42402854},
issn = {2161-5063},
abstract = {The medicinal fungus Wulingshen, comprising multiple Xylaria species, inhabits deserted termite mounds as sclerotia. To explore the molecular basis of its niche adaptation, we employed a synthetic biology-driven approach. Metagenomic and transcriptomic mining of wild specimens identified a conserved biosynthetic gene cluster. Its heterologous reconstruction in the fungal host Aspergillus oryzae enabled the characterization of a family of α-pyrone metabolites and, crucially, the elucidation of a spatially separated aldehyde-alcohol cycle. In this self-protection system, an extracellular oxidase (WlsA) converts an alcohol precursor to a reactive aldehyde, while an intracellular reductase (WlsE) catalyzes the reverse reaction. The aldehyde product exhibits potent toxicity against termites in vitro, suggesting a potential role in ecological interactions. This work establishes a functional genomics platform that decodes cryptic ecological metabolism by integrating multiomics with heterologous pathway expression, providing a generalizable strategy for discovering and mechanistically understanding niche-specific natural products.},
}

@article {pmid42402985,
year = {2026},
author = {Asato, Y and Kubo, T and Hashimoto, M and Wakatsuki, T and Sakamoto, H and Tanigawa, T and Kitamura, S and Kadokawa, H},
title = {Bifidobacterium longum BB536 supplementation is associated with increased circulating choline plasmalogen concentrations in non-pregnant, non-lactating dairy cows.},
journal = {Reproduction, fertility, and development},
volume = {38},
number = {10},
pages = {},
doi = {10.1071/RD26107},
pmid = {42402985},
issn = {1448-5990},
mesh = {Animals ; Female ; Cattle ; *Plasmalogens/blood ; Pregnancy ; *Probiotics/administration & dosage ; Dietary Supplements ; Lactation ; *Bifidobacterium ; Animal Feed ; },
abstract = {CONTEXT: Plasmalogens are ether phospholipids implicated in neuroendocrine regulation, including reproductive function. Recent studies have suggested that circulating plasmalogen concentrations are associated with reproductive performance in dairy cows; however, practical strategies to increase these concentrations remain limited.

AIMS: We hypothesised that supplementation with Bifidobacterium longum increases circulating choline plasmalogen concentrations and that this response depends on physiological state.

METHODS: Commercial probiotic products were screened using liquid chromatography-mass spectrometry and metagenomics to identify candidates containing plasmalogen-producing bacteria. A product containing the characterised strain B. longum BB536 and products containing other B. longum strains were selected for in vivo evaluation. Selected products were administered to Holstein cattle, and circulating choline plasmalogen concentrations were measured using an enzyme-based fluorometric assay.

KEY RESULTS: In long-term non-pregnant, non-lactating dairy cows, supplementation with B. longum BB536 significantly increased circulating choline plasmalogen concentrations, with a detectable rise approximately 1 week after the start of treatment and peak concentrations during Days 8-14 (P < 0.05). In contrast, no consistent increase was observed in pregnant, lactating dairy cows. Cross-sectional analysis across pregnancy stages showed significant variation in circulating choline plasmalogen concentrations, with lower concentrations during mid- to late gestation. No adverse effects were observed in ruminal pH, blood lactate concentrations, or bodyweight.

CONCLUSION: These findings suggest that supplementation with B. longum BB536 increases circulating choline plasmalogen concentrations in a state-dependent manner.

IMPLICATIONS: This study has provided new insight into the regulation of plasmalogens in cattle and suggests a potential nutritional approach for modulating reproductive function.},
}

Animals
Female
Cattle
*Plasmalogens/blood
Pregnancy
*Probiotics/administration & dosage
Dietary Supplements
Lactation
*Bifidobacterium
Animal Feed

@article {pmid42403142,
year = {2026},
author = {Zheng, Y and Ruan, P and Chen, H},
title = {Severe <em>Pneumocystis Jirovecii </em>Pneumonia in a Non-HIV Infant: The Diagnostic Value of Metagenomic Next-<br /> Generation Sequencing.},
journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP},
volume = {36},
number = {7},
pages = {961-962},
doi = {10.29271/jcpsp.2026.07.961},
pmid = {42403142},
issn = {1681-7168},
mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology ; *Pneumocystis carinii/genetics/isolation & purification ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Infant ; },
abstract = {Null.},
}

Humans
*Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology
*Pneumocystis carinii/genetics/isolation & purification
*Metagenomics/methods
High-Throughput Nucleotide Sequencing
Infant

@article {pmid42403487,
year = {2026},
author = {Calvanese, CM and Valentino, V and Sequino, G and De Vivo, A and Buzzanca, D and Prencipe, S and Demarinis, C and Perri, G and Pontonio, E and Ferrocino, I and Ercolini, D and De Filippis, F},
title = {Lactobacilli, best allies of mental health: a probiogenomic approach to identify potential psychobiotic strains.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101490},
pmid = {42403487},
issn = {2665-9271},
abstract = {Targeted dietary strategies and supplements represent a promising approach for the treatment of cognitive problems. Multi-omic approaches may facilitate and accelerate the discovery of new psychobiotic strains and their applications. In this work, we applied metagenomics and comparative genomics to guide the isolation and screening of novel psychobiotic strains from fermented foods. Metagenomes of 1185 fermented food were screened, revealing the occurrence of genes coding for the biosynthesis of neuroactive molecules, supporting the isolation of 73 novel Lactic Acid Bacteria (LAB) strains. Comparative genomic analysis highlighted species-specific patterns, identifying Levilactobacillus brevis, Lactiplantibacillus plantarum, Limosilactobacillus fermentum as potential psychobiotics. In vitro functional screening for the production of neuroactive metabolites confirmed four strains, Lactiplantibacillus plantarum TUCC00000144, Limosilactobacillus fermentum TUCC00000777, Levilactobacillus brevis TO10, Lentilactobacillus diolivorans B92, as the most promising candidates for the development of dietary supplements or innovative fermented food products aimed at supporting mental health.},
}

@article {pmid42403498,
year = {2026},
author = {Leprohon, H and Tannir, B and Jolicoeur, G and Domingo, MC and Dufresne, PJ and Morency-Potvin, P and Benoit, P and Grandjean Lapierre, S},
title = {Impact of direct from clinical sample sequencing assays for infectious diseases diagnostics: A single-centre retrospective cohort study.},
journal = {Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada},
volume = {11},
number = {2},
pages = {141-154},
pmid = {42403498},
issn = {2371-0888},
abstract = {BACKGROUND: The analytical performance of bacterial targeted sequencing (BTS), fungal targeted/panfungal sequencing (FTS), and metagenomic next-generation sequencing (mNGS) assays has been previously evaluated and their clinical use is increasing. Limited evidence is available on their true clinical impact on infectious disease diagnosis and treatment.

METHODS: We conducted a 3-year retrospective cohort study including all patients for whom broad-range sequencing assays were performed directly from clinical samples for the detection of bacterial and fungal pathogens. The operational characteristics, diagnostic and therapeutic impacts of the assays were assessed by reviewing patient clinical files and laboratory information system charts.

RESULTS: A total of 279 samples from 185 patients were included. The positivity rates for BTS, FTS, and mNGS were respectively 20.5% (47/229), 20% (9/45), and 20% (1/5). Of these 279 samples, 40 (14.3%) had an impact on patient management. The test results helped to establish a diagnosis in 26 (9.3%) cases and led to treatment modifications in 14 (5%). FTS achieved higher impact rates (26.7%) than both BTS (12.2%) and mNGS (0%). Short turnaround times increase impact rates, and the most impactful tests were those performed on bone and intervertebral disc samples, or in patients with negative culture results due to prior antibiotic administration.

CONCLUSIONS: In this study, the overall diagnostic impact of BTS and FTS was high. Both the diagnostic and treatment impact of those assays can be increased if prescribed in well-selected clinical syndromes and performed on well-selected clinical samples.},
}

@article {pmid42404619,
year = {2026},
author = {Ramani, RR and Baskaran, S and Arun, KV and Alamelu, S and Arumugamnainar, D},
title = {Salivary metagenomic profiling of Neisseria , Dialister , and Filifactor species in periodontal health and disease using next-generation sequencing.},
journal = {Journal of oral biology and craniofacial research},
volume = {16},
number = {4},
pages = {101482},
pmid = {42404619},
issn = {2212-4268},
abstract = {BACKGROUND: Periodontal diseases represent a complex dysbiosis-driven inflammatory condition, where the transition from health to gingivitis and periodontitis is accompanied by distinct microbial shifts. Emerging evidence highlights the significance of less-studied genera such as Neisseria, Dialister, and Filifactor in shaping periodontal outcomes. This study aimed to investigate the salivary distribution of Neisseria, Dialister, and Filifactor species across periodontal health, gingivitis, periodontitis, and gingival recession using next-generation sequencing (NGS).

METHODS: Whole saliva samples were collected from 40 participants (10 per group) classified according to the American Academy of Periodontology criteria. Microbial DNA was extracted and subjected to 16S rRNA sequencing (V3-V4 region, Illumina MiSeq). Species-level classification was performed using the Human Oral Microbiome Database. Frequency distributions were compared across groups using Fisher's exact test, with significance set at p < 0.05.

RESULTS: Distinct patterns were observed. Several commensal Neisseria species, including N. subflava (p = 0.001), N. elongata(p = 0.015), and N. polysaccharea (p = 0.001), showed significantly reduced prevalence in periodontitis compared with health and gingivitis. In contrast, Dialister pneumosintes exhibited a sharp increase in all diseased groups (p = 0.002). Filifactor alocis was markedly enriched in gingivitis, recession, and periodontitis (p = 0.011), suggesting its strong association with disease states.

CONCLUSION: The findings demonstrate a characteristic microbial shift in saliva: health-associated Neisseria species decline with disease progression, while anaerobic taxa such as D. pneumosintes and F. alocis expand. These results align with the polymicrobial synergy and dysbiosis model and underscore the potential of these species as salivary biomarkers for early detection and monitoring of periodontal disease.},
}

@article {pmid42404879,
year = {2026},
author = {Dai, P and Feng, J and Cao, J and Fan, D},
title = {Integrative multi-omics profiling reveals coordinated immunometabolic reprogramming and host-microbiome interactions in acute pancreatitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1828633},
pmid = {42404879},
issn = {1664-3224},
mesh = {Humans ; Multiomics ; *Pancreatitis/metabolism/microbiology/immunology ; Metabolomics ; Gene Expression Profiling ; *Host Microbial Interactions/immunology ; Biomarkers ; Metabolic Reprogramming ; *Gastrointestinal Microbiome/immunology ; Acute Disease ; Female ; Transcriptome ; Male ; Metabolome ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) is a life-threatening inflammatory disorder characterized by diverse etiologies and complex pathophysiological mechanisms involving immune dysregulation, systemic metabolic reprogramming, and gut microbiota disturbances. Although single-omics studies have provided partial insights into AP pathogenesis, comprehensive integrative multi-omics analyses investigating the intricate interactions among immunity, metabolism, and the microbiome in AP remain limited.

METHODS: We conducted an integrative multi-omics analysis of peripheral blood transcriptomics, untargeted plasma metabolomics, and fecal whole-metagenome sequencing in 15 patients with AP and 15 age- and sex-matched healthy controls. Differentially expressed genes (DEGs), metabolites (DEMs), and gut microbial species (DGMs) were identified. Subsequently, functional enrichment analysis, correlation network analysis, and exploratory machine learning approaches were employed to investigate molecular interactions and identify candidate biomarkers.

RESULTS: Transcriptomic profiling identified 4, 776 DEGs, including 409 immune-related genes significantly enriched in the NF-κB, IL-17, and cytokine-cytokine receptor interaction pathways, indicating pronounced inflammatory activation. Metabolomic analysis detected 296 DEMs, with prominent alterations in amino acid and lipid metabolism, mong which 9 metabolites showed potential discriminatory value (AUC > 0.75), with representative metabolites including xanthine, homocarnosine, and tetradecanedioic acid. Metagenomic sequencing revealed significant microbial compositional and functional remodeling, characterized by enrichment of pro-inflammatory taxa such as Escherichia coli and Streptococcus anginosus, alongside depletion of SCFA-producing commensals including Faecalibacterium prausnitzii and Blautia wexlerae. Functional profiling demonstrated disrupted amino acid metabolism, gut-brain signaling, and SCFA synthesis. Multi-omics integration revealed 215 significant correlations between host genes, metabolites, and microbes, highlighting key interaction hubs. An exploratory random forest model identified Lachnospira pectinoschiza, Megamonas funiformis, and SRGN as candidate biomarkers, showing promising classification performance within the current cohort (AUC = 0.951).

CONCLUSIONS: This study provides a systems-level characterization of the immune, metabolic, and microbial alterations in AP. The identified molecular signatures and cross-omics interaction networks offer mechanistic insights into AP pathogenesis and highlight candidate biomarkers that warrant further validation in larger, independent cohorts.},
}

Humans
Multiomics
*Pancreatitis/metabolism/microbiology/immunology
Metabolomics
Gene Expression Profiling
*Host Microbial Interactions/immunology
Biomarkers
Metabolic Reprogramming
*Gastrointestinal Microbiome/immunology
Acute Disease
Female
Transcriptome
Male
Metabolome

@article {pmid42405192,
year = {2026},
author = {Scott, CJR and Caccia, S},
title = {metaLoc: protein localisation prediction workflow.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag169},
pmid = {42405192},
issn = {2635-0041},
abstract = {SUMMARY: metaLoc combines existing tools for signal peptide, localisation, and transmembrane helices prediction from protein sequences into a workflow for rapid evaluation of protein datasets. By accepting both protein and nucleotide sequences, the workflow is especially suitable for in silico screening of the growing volumes of sequencing data. With a single command, metaLoc provides a simple, accessible, and user-friendly tool for the bioinformatic investigation of proteomic or metagenomic datasets.

metaLoc is freely available on the GitHub platform (https://github.com/scottc-bio/metaLoc). The metaLoc workflow is implemented in Nextflow with a modular design utilizing isolated Conda environments for reproducibility. An archived version of this release is permanently available at Zenodo (https://doi.org/10.5281/zenodo.18936772).},
}

@article {pmid42405317,
year = {2026},
author = {Wang, Y and Cai, Y and Peng, Z and Hou, F and Jia, Z},
title = {Molecular insights into atmospheric methane-oxidizing USCγ from desert grassland soil based on metagenome-assembled genome analysis.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag151},
pmid = {42405317},
issn = {2730-6151},
abstract = {Upland Soil Cluster Gamma (USCγ) is a key high-affinity aerobic methanotroph driving atmospheric methane oxidation in grassland soils; however, it has never been obtained in pure culture, and its metabolic processes remain largely unknown. Here, we reconstructed a USCγ metagenome-assembled genome (MAG) containing the complete pmoA gene from desert grassland soil in northwestern China, designated USC_AKS. At the site, USCγ accounted for 9.83% of the microbial community in the 10-20 cm layer. BLASTn of its 16S rRNA gene against the NCBI database (excluding uncultured/environmental sequences) showed 93.03% similarity to the non-methanotroph Thioalkalivibrio sulfidiphilus HL-EbGr7 (order Chromatiales). The closest match among named species was an uncultured bacterium (JN672117) at 97.86% similarity. Its pmoA shares 96.18% similarity with the original USCγ-defining sequence. Phylogenomic analysis placed USC_AKS and seven other USCγ MAGs into a monophyletic group of three subclades, distantly related to culturable Type I methanotrophs. Their genomic average nucleotide identity values are all below 95%, confirming eight distinct species. Like other USCγ MAGs, USC_AKS encodes a complete pmoCAB operon, an XoxF-type methanol dehydrogenase, and enzymes for formaldehyde oxidation to CO2. However, it lacks key ribulose monophosphate (RuMP) cycle genes encoding 3-hexulose-6-phosphate synthase (hps) and 6-phospho-3-hexulose isomerase (phi). The serine cycle also appears incomplete, as these MAGs lack hpr, the gene encoding hydroxypyruvate reductase. Moreover, none encode Rubisco, ruling out the Calvin-Benson-Bassham CO2-fixation pathway. Consequently, the metabolic characteristics of USCγ-particularly its carbon assimilation pathway-remain enigmatic, and obtaining pure cultures or enriched consortia is likely the only route to resolving this mystery.},
}

@article {pmid42405318,
year = {2026},
author = {Modolon, F and Capo, E and Wardle, DA},
title = {Long-term ecosystem development and retrogression drive microbial specialization for complex organic matter degradation.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag157},
pmid = {42405318},
issn = {2730-6151},
abstract = {Long-term ecosystem development includes a build-up phase followed by a decline (retrogressive) phase characterized by reduced plant productivity and belowground process rates due to reduced nutrient availability. In boreal forests, retrogression is accompanied by soil organic matter (SOM) accumulation, especially in the prolonged absence of fire. However, the role of bacterial communities in SOM dynamics during ecosystem retrogression has been little explored. Using a 5000-year post-fire boreal forest chronosequence, we investigated how long-term succession and retrogression shapes soil bacterial community structure and functional specialization. While the Actinomycetota phylum dominated communities across all chronosequence stages, a significant family-level shift within this phylum occurred in the later (retrogressive) phase, characterized by a transition from Mycobacteriaceae to Streptosporangiaceae. The recovery of metagenome-assembled genomes (MAGs) revealed distinct life-history trade-offs between these families. Streptosporangiaceae MAGs were significantly enriched in genes for degrading phenolics, cellulose, and lignin, and exhibited potential for chitin, lipid and peptide degradation. This positions them as potential decomposers of the primary constituents of stored soil carbon, including plant-derived complex carbohydrates and fungal necromass, during retrogression when fungal activity declines. In contrast, Mycobacteriaceae MAGs are likely to prioritize inorganic phosphate (P i) uptake-by pstS gene enrichment, reflecting adaptation to P availability changes during ecosystem development. Collectively, our results demonstrate that long-term ecosystem retrogression drives shifts in the bacterial communities and functions within the Actinomycetota. These shifts may indicate possible divergent strategies, i.e. recalcitrant carbon turnover versus nutrient scavenging, which could explain shifts in the microbial community as the ecosystem transitions toward retrogressive, nutrient-limited states.},
}

@article {pmid42405543,
year = {2026},
author = {Anggraini, D and Yovi, I and Elliyanti, A and Safari, D and Syah, NA and Jati, AP and Sarassari, R and Simatupang, ETM},
title = {Metagenomic Analysis of Thoracic Empyema Etiology Through Next-Generation Sequencing Enhances Conventional Culture Techniques.},
journal = {Infection & chemotherapy},
volume = {58},
number = {2},
pages = {214-223},
doi = {10.3947/ic.2025.0159},
pmid = {42405543},
issn = {2093-2340},
abstract = {BACKGROUND: This study aimed to analyze the microbiome of thoracic empyema using metagenomic methods and compare the results with conventional culture methods to increase diagnostic accuracy and enhance antibiotic therapy.

MATERIALS AND METHODS: This study involved 30 patients with thoracic empyema from hospitals in Riau Province, Indonesia. Pleural fluid samples were collected for culture analysis and identification using the Vitek 2 compact system and metagenomic analysis. Patient clinical data were also collected.

RESULTS: Culture methods showed a 40.0% positive rate, with Gram-negative bacteria (Klebsiella pneumoniae and Pseudomonas aeruginosa) predominating. Metagenomics showed a 56.7% positive rate, identifying a more diverse microbiome, including fungi (29.4% abundance), other Gram-negative bacteria (26.5%), and anaerobic bacteria (22.5%). Comparison of the two methods showed 36.7% complete agreement and 23.3% partial agreement, with 40% disagreement, with a Kappa coefficient of 0.416 and P-value of 0.016 (P<0.050).

CONCLUSION: Metagenomic NGS offers significant advantages in detecting the microbiome of thoracic empyema, particularly fungi and anaerobic bacteria, which are often missed by conventional culture methods. This has the potential to improve diagnostic accuracy and optimize antibiotic therapy. Further research with larger sample sizes is needed.},
}

@article {pmid42405768,
year = {2026},
author = {Berryhill, BA and Gil-Gil, T and Burke, KB and Fontaine, J and Brink, CE and Harvill, MG and Goldberg, DA and Navas, JN and Grabowicz, M and Konstantinidis, KT and Levin, BR and Woodworth, MH},
title = {Enteric populations of Escherichia coli are likely to be resistant to phages due to O antigen expression.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0038626},
doi = {10.1128/msphere.00386-26},
pmid = {42405768},
issn = {2379-5042},
abstract = {Metagenomic data provide evidence that bacteriophage (phage) abound in the enteric microbiomes of humans. However, the contribution of these viruses in shaping the bacterial composition of the gut microbiome and how these phages are maintained remain unclear. We performed experiments with 756 combinations of 54 Escherichia coli and nine phage isolates from four fecal microbiota transplantation (FMT) doses and five laboratory phages as samples of non-dysbiotic human enteric microbiota. We also developed a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our experiments predict that as a consequence of the production of the O antigen, most of the E. coli in the human enteric microbiome will be resistant to infections with the array of co-occurring phages. Our modeling suggests that phages are maintained in these enteric communities due to the high rates of transition between the O antigen-resistant and -sensitive states. Based on our observations and predictions from this theory, we postulate that the phage found in the human gut are likely to play a little role in shaping the strain composition of E. coli of healthy individuals. Although we only investigated E. coli, the mechanism of resistance described here is shared among most of the gram-negative bacteria. Evidence is provided that, as a consequence of O antigen-mediated resistance, the genetically diverse array of bacteriophage in the gut microbiome of humans plays little or no role in determining the densities and distribution of the genetically diverse strain E. coli in this habitat. Our mathematical model predicts and our experiments support the hypothesis that the phage present in the gut microbiome are maintained by replication on the minority of sensitive bacteria generated by the leakiness of O antigen-mediated resistance.IMPORTANCEBacteriophages (phages) are abundant in the human gut, yet whether these viruses shape the bacterial communities living there remains unresolved. Using Escherichia coli and phages isolated from the stool of healthy fecal microbiota transplantation (FMT) donors, together with a mathematical model, we show that the vast majority of gut E. coli are resistant to co-occurring phages because they express the O antigen, a surface structure that masks the receptors phages use to attach. Despite this widespread resistance, phages persist by replicating on a small, continually regenerated subpopulation of sensitive cells, a phenomenon we term leaky resistance. These findings suggest that phages play a little role in determining which E. coli strains dominate the healthy human gut. Because the O antigen is broadly expressed across gram-negative bacteria, this mechanism likely extends well beyond E. coli and helps explain why isolating therapeutic phages against many pathogens is difficult.},
}

@article {pmid42406122,
year = {2026},
author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B},
title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02817-z},
pmid = {42406122},
issn = {1432-184X},
support = {REIG-FPS-2025/038//UCSI University/ ; },
abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.},
}

@article {pmid42407310,
year = {2026},
author = {Jiang, ZQ and Xing, RK and Peng, D and Ren, YH and Wei, TY and Guo, WB and Shen, ZM and Wang, CN and Zhang, FL and Yuan, T},
title = {Compartment-specific host association and mobility shape ARG risk in aquaculture systems.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142895},
doi = {10.1016/j.jhazmat.2026.142895},
pmid = {42407310},
issn = {1873-3336},
abstract = {Antimicrobial resistance in aquaculture threatens environmental and public health, but the risk of ARGs cannot be inferred from abundance alone; host context and mobility potential are essential. Here, we investigated how ecological compartments shape ARG host background, mobility, and risk in aquaculture systems. We analyzed 437 metagenomes from water and sediment in freshwater and marine aquaculture across China using resistome profiling, host assignment, genetic localization, ARG-MGE co-occurrence, a four-tier risk framework, and machine learning. We detected 1413 nonredundant ARG subtypes (28 classes). Water had higher ARG diversity, stronger associations with opportunistic pathogens, and stronger mobility-related signals than sediment. High-risk ARGs were concentrated in water: Rank I ARGs were exclusive to water, and water-specific Rank II ARGs accounted for 7.2% (freshwater) and 6.9% (marine) of total ARG diversity, versus 4.2% (freshwater sediment) and 2.9% (marine sediment). The LightGBM model identified salinity, temperature, and pH as key mobility predictors. Together, these results show that ARG risk in aquaculture is jointly shaped by the ecological compartment, host association, and mobility potential, with water acting as the principal high-risk interface. This risk-oriented analytical framework provides a transferable basis for prioritizing surveillance and intervention in aquaculture environments.},
}

@article {pmid42407426,
year = {2026},
author = {Dong, F and Hou, A and Hu, X and Wei, L and Sun, F and Xiao, X and Su, X},
title = {Process-dependent niches of rpf-harboring microorganisms regulate nitrogen and carbon functional networks in full-scale activated sludge.},
journal = {Environmental research},
volume = {306},
number = {Pt 2},
pages = {125198},
doi = {10.1016/j.envres.2026.125198},
pmid = {42407426},
issn = {1096-0953},
abstract = {Resuscitating viable but non-culturable (VBNC) microorganisms offers a strategy to unlock hidden metabolic capabilities, enhancing pollutant degradation and system stability in wastewater bioreactors. However, the ecological mechanisms underlying VBNC resuscitation in activated sludge, particularly the role of resuscitation-promoting factor (Rpf) gene-harboring microbial consortia, remain elusive. Here, metagenomic profiling of full-scale anaerobic/anoxic/oxic (A[2]/O) and oxidation ditch processes demonstrates the widespread distribution of rpf-harboring microorganisms in wastewater treatment plants (WWTPs). A[2]/O systems enriched for taxa associated with denitrification and ammonification, while oxidation ditches showed higher abundance of microorganisms involved in nitrification and dissimilatory nitrate reduction to ammonium (DNRA). The two processes configuration harbored distinct sets of rpf-carrying taxa, with Chloroflexota dominating in A[2]/O systems and Nitrospira and Kouleothrix in oxidation ditches. Network analysis further reveals that rpf-harboring taxa may act as ecological connectors between dormant and metabolically active populations, thereby enhancing community cohesion and resilience under fluctuating operational conditions. These findings uncover process-dependent resuscitation ecology shaping activated sludge communities and nutrient transformation pathways, providing a mechanistic foundation for engineering Rpf-mediated microbial interactions to improve biological wastewater treatment.},
}

@article {pmid42409195,
year = {2026},
author = {Yan, M and Yang, C and Huang, J and Qi, P and Tang, L and Lu, H},
title = {Reactor performance and microbial responses of sulfate-reducing bacteria sludge under stepwise polyvinyl chloride microplastic exposure.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135334},
doi = {10.1016/j.biortech.2026.135334},
pmid = {42409195},
issn = {1873-2976},
abstract = {Plastic pollution, particularly microplastic contamination, poses potential risks to biological wastewater treatment processes. However, the response of sulfate-reducing bacteria (SRB) sludge systems to polyvinyl chloride (PVC) microplastics remains poorly understood. In this study, a laboratory-scale sulfate-reducing up-flow sludge bed (SRUSB) reactor was operated under stepwise PVC microplastic exposure at 0, 20, 100, and 500 particles/L. COD removal and sulfate reduction showed limited changes at 20 and 100 particles/L, whereas 500 particles/L caused transient inhibition followed by gradual recovery within the same reactor. PVC exposure increased intracellular reactive oxygen species (ROS) levels and lactate dehydrogenase (LDH) release, while live/dead staining indicated no marked increase in cell mortality across the operational stages. Stepwise PVC exposure was also accompanied by enrichment of protein-rich loosely bound extracellular polymeric substances (LB-EPS) and accumulation of PVC-derived additives, including BPA and ATBC. Microbial community analysis showed that the relative abundance of SRB-related genera increased from 8.7% to 24.9%, mainly involving increased abundances of Desulfobacter, Desulfococcus, and Desulforhabdus. Metagenomic annotation further revealed genes associated with EPS precursor supply, polysaccharide assembly/export, protein secretion, antioxidant response, aromatic metabolism, ester-bond hydrolysis, and dissimilatory sulfate reduction. Overall, this study provides a longitudinal characterization of reactor performance and associated physiological, chemical, microbial, and community-level genetic responses of SRB sludge under stepwise PVC microplastic exposure, offering useful insights for evaluating sulfate-reducing saline wastewater treatment systems facing microplastic contamination.},
}

@article {pmid42409199,
year = {2026},
author = {Agostini, F and Baruzzo, V and Fernandez, FR and Satta, A and Raga, R and Penzo, D and Modesti, M and Valerin, MC and Campanaro, S and Treu, L and Zampieri, G},
title = {Discovering hidden candidate plastic-degrading enzymes: Combined multi-omics and machine learning strategy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135332},
doi = {10.1016/j.biortech.2026.135332},
pmid = {42409199},
issn = {1873-2976},
abstract = {Plastic pollution poses a major threat to the stability of natural ecosystems as well as human health. Microbial enzymes have long been considered a potential resource for targeted biodegradation but, except for a few successful cases, the discovery of efficient enzymes has proved challenging. Aiming to accelerate the process, we propose an approach combining metagenomics, metatranscriptomics and semi-supervised learning that selects promising plastic-degrading candidate enzymes from the proteome of relevant microorganisms. Tested on a dataset of over 10,000 microbial proteins, ranking models consistently prioritize known plastic-degrading enzymes, achieving an area under the cumulative distribution function curve above 0.96, with leave-one-family-out cross-validation indicating that performance is largely retained across protein families. As a case study, this work focuses on mixed microbial cultures exposed for extended periods to polyethylene, polyethylene terephthalate, and polyurethane substrates. The prevalent species after selective enrichment were functionally characterized, finding Rhodococcus aetherivorans as the most relevant species in two of the five cultures under investigation. Among the top-ranked proteins, several have high structural similarity with known enzymes despite not being identified by sequence similarity search. Moreover, according to metatranscriptomics results, several of these enzymes were found to be expressed at the same level or above that of annotated enzymes, suggesting that they may have functional relevance. Overall, this work highlights the potential of integrating multi-omics with data-driven methods for enzyme discovery and for accelerating the development of biotechnological solutions to plastic pollution.},
}

@article {pmid42409336,
year = {2026},
author = {Wu, J and Lin, M and Fan, Y},
title = {An Unusual Cause of Chronic Hematochezia.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.06.025},
pmid = {42409336},
issn = {1528-0012},
}

@article {pmid42409355,
year = {2026},
author = {Nguyen, HT and Bez, C and Tran, MQ and Tran, LT and Pham, VT and Bertani, I and Venturi, V and Dinh, HT},
title = {Rhizospheric Fungal Communities and Their Role in Biocontrol of Fusarium in Robusta Coffee (Coffea canephora) in Vietnam.},
journal = {The plant pathology journal},
volume = {},
number = {},
pages = {},
doi = {10.5423/PPJ.OA.12.2025.0186},
pmid = {42409355},
issn = {1598-2254},
abstract = {Rhizospheric microbial communities are critical to the health and productivity of coffee plantations. This study investigated the microbiome of robusta coffee (Coffea canephora) across three major cultivation areas in Vietnam (Dak-Nong, Dak-Lak, and Gia-Lai) to assess its role in Fusarium suppression. Using ITS ampliconbased metagenomics and culture-dependent approaches, we analyzed fungal community structure in relation to location, plant age, and health status. Metagenomic analysis revealed no significant differences in bacterial communities between healthy and diseased rhizospheres, whereas fungal communities showed clear distinctions, particularly in young plants (<2 years). These differences diminished in mature plants (≥2 years) but continued to vary with age (2-10 years). Healthy rhizospheres were enriched with beneficial fungi, while diseased soils contained more phytopathogenic genera. Fusarium was prevalent in all regions, with higher abundance in diseased soils, whereas Trichoderma, a known biocontrol agent, was more abundant in healthy soils but declined with plant age. Of 343 fungal isolates, 46 strains exhibited strong antagonistic activity against Fusarium, representing 10 genera, including Aspergillus, Penicillium, Gongronella, and Talaromyces. Although Trichoderma isolates were less frequent, they showed promising biocontrol potential. These findings underscore the role of rhizospheric fungi in managing Fusarium wilt and identify candidate biocontrol agents for sustainable robusta coffee cultivation.},
}

@article {pmid42409501,
year = {2026},
author = {Huang, C and Zhao, Y and Gu, M and Li, Z and Li, X and Huang, Y and Zhang, C and Zhang, D},
title = {Metagenomic-metabolomic integration elucidates stage-specific dynamics of microbial communities and metabolites driving pork spoilage in commercial supply chains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {240},
number = {},
pages = {119678},
doi = {10.1016/j.foodres.2026.119678},
pmid = {42409501},
issn = {1873-7145},
abstract = {Microbial-metabolic axis drives meat quality deterioration and shelf-life changes along commercial supply chains. This study tracked pork quality and freshness from postmortem processing to retail sale by integrating untargeted metabolomic and metagenomic analyses. Over the first 1700 min postmortem, pork showed a decline in pH and increases in L*, a* and b* values, cooking loss, shear force, total volatile basic nitrogen and total viable counts. At the point of sale, the meat remained in rigor mortis and retained acceptable freshness. Metabolic profiles remained dynamic after warehousing and were further modified by ambient exposure during transport and retail sale. Results revealed that differential metabolites were predominantly enriched in purine metabolism, nucleotide metabolism, lysosome pathway, as well as alanine, aspartate and glutamate metabolism. Likewise, several genera potentially associated with spoilage or contamination-associated bacteria were influenced by commercial condition along the supply chain, with increased abundance of Acinetobacter, Bacillus, Listeria, Psychrobacter, Salmonella andEnterobacter during transport and retail sale, while Listeria, Salmonella andEnterobacter may originate from environmental or processing-associated sources. These findings identify stage-specific metabolic and microbial signatures shaped by commercial handling, such as temperature, relative humidity and provide insights for improving pork quality and safety management during the early postmortem period.},
}

@article {pmid42409516,
year = {2026},
author = {Moon, SH and Yang, X and Kim, J and Leighton, E and Jun, SR and DiCaprio, E and Gale, C and Chen, S and Li, X and Huang, E},
title = {Comprehensive analyses of carbapenem-resistant and ESBL-producing bacteria in fresh vegetables and their resistome in the United States.},
journal = {Food research international (Ottawa, Ont.)},
volume = {240},
number = {},
pages = {119552},
doi = {10.1016/j.foodres.2026.119552},
pmid = {42409516},
issn = {1873-7145},
abstract = {Carbapenem-resistant and extended-spectrum beta-lactamase (ESBL)-producing bacteria, once largely confined to healthcare settings, are increasingly detected in community environments. Food and the environment may act as important reservoirs for clinically relevant antibiotic-resistant bacteria. A large-scale surveillance study was conducted from 2022 to 2023 to assess antibiotic resistance in retail fresh vegetables across three U.S. regions: the Midsouth, Midwest, and West Coast. A total of 1218 samples representing five vegetable categories (carrots, lettuce, spinach, sprouts/microgreens, and salads) were analyzed for carbapenem-resistant bacteria and ESBL-producing Enterobacterales. Culture-based methods included selective isolation on CHROMagar, antibiotic susceptibility testing, phenotypic evaluation of ESBL and carbapenem resistance, and carbapenemase detection and typing. Whole-genome sequencing of phenotypically resistant isolates was used to identify beta-lactamase genes. Overall, 62 carbapenem-resistant isolates (5.09%) and 70 ESBL-producing Enterobacterales isolates (5.74%) were recovered. Carbapenemase-producing Enterobacterales included 30 Enterobacter strains and one Kluyvera strain, with carbapenem-resistant Enterobacter most frequently isolated from sprouts and microgreens. ESBL-producing strains included 39 Serratia, 20 Enterobacter, 6 Klebsiella, 3 Raoultella, and 2 Rahnella isolates. Comparative genomic analyses showed close similarity between vegetable isolates and human clinical strains. Notably, the carbapenemase gene blaIMI-6 identified in Enterobacter asburiae from microgreens was transferable to Escherichia coli by conjugation. Shotgun metagenomics of 40 samples further confirmed diverse resistance genes. These findings highlight vegetables as potential reservoirs of clinically important antibiotic resistance and emphasize the need for ongoing surveillance in both vegetable products and their production environments.},
}

@article {pmid42409884,
year = {2026},
author = {Studer Silva Gutierrez, FAO and Morandi, SC and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Influence of smoking on the human ocular surface microbiome and tear proteome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60743-z},
pmid = {42409884},
issn = {2045-2322},
abstract = {The ocular surface hosts microbes of low abundance and their genomes, collectively called the ocular surface microbiome (OSM). The OSM is involved in maintaining health and protecting the eye from infection. Although disruption of this microbial balance has been linked to various eye diseases, the effect of smoking, a known risk factor for ocular conditions, on the OSM remains unclear. We analysed ocular samples from smokers (n = 17) and non-smokers (n = 24) using metagenomic sequencing and proteomics approaches to assess both microbial composition and functions, as well as the host protein profiles. Microbial DNA was examined for bacterial, fungal, and viral taxa, with contaminants removed using microDecon. Statistical analyses showed no significant differences in microbial diversity or tear proteins between groups, apart from one bacterial gene. No bacterial, fungal, or viral species were uniquely associated with smoking status. While no clear smoking-related effects were observed in microbial communities or tear proteome composition, the overall stability of tear proteins may reflect intrinsic resilience dynamics that maintain low microbial abundance on the ocular surface.},
}

@article {pmid42401772,
year = {2026},
author = {Afonso, AC and Lema, JM and Trueba-Santiso, A},
title = {Metaproteomics for Water Biotechnology: Considerations and Study Cases.},
journal = {Advances in experimental medicine and biology},
volume = {1510},
number = {},
pages = {21-44},
pmid = {42401772},
issn = {0065-2598},
mesh = {*Proteomics/methods ; *Biotechnology/methods ; Multiomics ; *Water Purification/methods ; Water Microbiology ; Wastewater/microbiology ; Biofilms ; },
abstract = {This chapter summarizes the current knowledge on the practical, methodological, and interpretative aspects of applying metaproteomics in water biotechnology. We outline the full metaproteomic workflow-from sampling and protein extraction to LC-MS/MS acquisition, database construction, quantitative analysis, and bioinformatic interpretation-and emphasize critical considerations specific to complex matrices such as EPS-rich biofilms, granular sludge, and low-biomass drinking water. Case studies illustrate how metaproteomics can clarify mechanisms of micropollutant degradation, nitrogen-transforming pathways, biofilm functional architecture, and microbial resilience under operational stress. Recent advances in data-independent acquisition, metagenome-informed databases, and integrative multi-omics are shown to substantially improve depth, reproducibility, and functional resolution. Finally, we discuss emerging applications in wastewater-based epidemiology, where metaproteomics complement nucleic-acid-based surveillance by enabling the detection of large biomolecule biomarkers of population health and industrial activity. Although metaproteomics is already being applied across a wide range of water cycle contexts and is producing promising, robust results, several challenges, including limitations in analytical chemistry, database completeness, and bioinformatics workflows, continue to hinder its broader implementation. Continued technical research and innovation are therefore essential to fully unlock its potential in water biotechnology.},
}

*Proteomics/methods
*Biotechnology/methods
Multiomics
*Water Purification/methods
Water Microbiology
Wastewater/microbiology
Biofilms

@article {pmid42401776,
year = {2026},
author = {Zapata-Peñasco, I and Herrera-Díaz, J},
title = {Proteomic Sample Preparation for the Petroleum Industry: A Biocorrosion Case Study.},
journal = {Advances in experimental medicine and biology},
volume = {1510},
number = {},
pages = {121-145},
pmid = {42401776},
issn = {0065-2598},
mesh = {*Proteomics/methods ; *Petroleum/microbiology ; Corrosion ; *Oil and Gas Industry ; Biodegradation, Environmental ; Biofilms/growth & development ; *Bacterial Proteins/metabolism ; Sewage/microbiology ; *Bacteria/metabolism/genetics ; },
abstract = {Petroleum-associated environments are among the most chemically complex and biologically extreme systems encountered in the field of industrial biotechnology. Here, microbial activity plays a pivotal role in hydrocarbon biodegradation, reservoir souring, and microbiologically influenced corrosion (MIC). In these systems, proteins constitute the functional interface between microbial metabolism and physicochemical processes affecting infrastructure integrity and environmental impact. This chapter presents an integrated proteomics-based workflow for the characterization of microbial communities inhabiting oil pipeline sludges, with particular emphasis on sample preparation strategies tailored to hydrocarbon-rich, metal-laden, and saline matrices. Optimized phenol-based extraction, electrochemical in vitro corrosion assays, two-dimensional gel electrophoresis, and high-resolution mass spectrometry are combined with metagenomic information to enable robust identification and functional interpretation of proteins involved in redox metabolism, biofilm formation, extracellular electron transfer, sulfur and nitrogen cycling, and stress adaptation. The approach is illustrated through a biocorrosion case study of marine pipeline sludge, revealing key enzymatic systems, including oxidoreductases, hydrolases, cytochromes, ABC transporters, and biofilm-associated structural proteins that mediate metal dissolution and microbial energy conservation. By integrating proteomics with electrochemical measurements and systems-level analysis, this chapter highlights how tailored sample preparation and functional protein profiling can overcome the limitations of culture-dependent methods, providing mechanistic insight into complex petroleum microbiomes. These advances establish proteomics as a critical tool for monitoring, predicting, and ultimately mitigating biocorrosion, as well as for guiding the development of biotechnology-based strategies in the oil and gas industry.},
}

*Proteomics/methods
*Petroleum/microbiology
Corrosion
*Oil and Gas Industry
Biodegradation, Environmental
Biofilms/growth & development
*Bacterial Proteins/metabolism
Sewage/microbiology
*Bacteria/metabolism/genetics

@article {pmid42401984,
year = {2026},
author = {Pangga, GM and Richmond, A and Hughes, C and Psifidi, A and Xia, D and Blake, D and Ijaz, UZ and Gundogdu, O},
title = {Integrated metabolomics and metagenomics reveal divergent caecal metabolic signatures following commercial gut health interventions in broilers.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00596-z},
pmid = {42401984},
issn = {2524-4671},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
abstract = {BACKGROUND: The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience.

RESULTS: We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA p > 0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. Bacteroides fragilis emerged as a dominant associate, correlating positively with a diverse range of metabolites (n = 271). Functional gene analysis suggested a link between Mediterraneibacter spp. and soyasaponin deglycosylation, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps.

CONCLUSION: Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.},
}

@article {pmid42402030,
year = {2026},
author = {Qi, K and Zhang, S and Su, X and Chen, J and Huang, S and Chen, Y and Li, W and Ni, G and Duo, J and Yang, S and Shen, Q and Wang, X and Liu, Y and Wu, P and Yang, H and Ji, L and Wang, X and Zhang, W},
title = {Comparative analysis of gut viromes in four penguin species reveals diverse novel viruses and host-associated differences.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0084825},
doi = {10.1128/msphere.00848-25},
pmid = {42402030},
issn = {2379-5042},
abstract = {Penguins, as distinctive marine birds, play important roles in polar and sub-Antarctic ecosystems, yet the diversity and species-specific distribution of their gut viromes remain insufficiently understood. Here, we used viral metagenomics to characterize the cloacal viromes of four penguin species-Spheniscus humboldti (S. humboldti), Pygoscelis papua (P. papua), Pygoscelis adeliae (P. adeliae), and Aptenodytes forsteri (A. forsteri)-collected at Chimelong Ocean Kingdom. A total of 219 viral sequences representing potentially novel lineages were identified, with more than 94% sharing <80% amino acid similarity with previously known viruses. These sequences were assigned to several viral families, including Parvoviridae, Caliciviridae, Anelloviridae, Circoviridae, and Microviridae, among others. Marked interspecies differences in virome composition were observed: Parvoviridae dominated in S. humboldti, Microviridae were enriched in P. papua, Caliciviridae accounted for a substantial proportion in A. forsteri, and P. adeliae displayed the greatest overall virome diversity. Multiple-virus co-detections, particularly involving Parvoviridae, were frequent in S. humboldti. Phylogenetic analyses showed that many penguin-associated viruses clustered with viruses infecting other avian and fish hosts, suggesting possible dietary or environmental origins of some detected viral sequences. These findings expand current knowledge of penguin gut virome diversity and host-associated differences and provide a valuable foundation for evaluating the ecological roles, health implications, and transmission risks of penguin-associated viruses.IMPORTANCEThis study uncovers significant diversity in the gut viromes of four penguin species, revealing over 219 viral sequences representing potentially novel lineages, many of which showed host-associated distribution patterns. Using viral metagenomics, we identified notable interspecies differences, with Parvoviridae predominating in Spheniscus humboldti and Microviridae being enriched in Pygoscelis papua. These findings highlight the complexity of viral community structures in penguins, including frequent viral co-detections, which could impact host health and ecological adaptation. Additionally, novel bacteriophage communities were identified, emphasizing their potential role in shaping the gut microbiome and influencing viral dynamics. This work provides new insights into viral diversity in wildlife and lays the groundwork for future studies on viral transmission risks and ecological conservation.},
}

@article {pmid42402034,
year = {2026},
author = {Wu, Y and Wang, Y and Qin, R and Liu, L and Wang, L and Liu, Y and Wang, W and Diao, Q},
title = {Dietary supplementation with fermented compound Chinese herbal medicine reshapes the gastrointestinal microbiota and enhances growth in suckling lambs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0388925},
doi = {10.1128/spectrum.03889-25},
pmid = {42402034},
issn = {2165-0497},
abstract = {UNLABELLED: This study investigated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth performance, antioxidant capacity, immune function, and gastrointestinal microbiota in suckling lambs. FCHM consisted of 10 herbs fermented with Candida utilis and Bacillus subtilis. Sixty twin Hu lambs (15 days) were randomly fed a basal diet (CON) or the diet supplemented with 0.6% FCHM (Treat) for 45 days. The results indicated that the Treat group exhibited a significant increase in average daily gain (ADG) (P < 0.05). Serum analyses revealed elevated levels of growth hormone (GH), insulin-like growth factor-1 (IGF-1), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glucose (GLU), whereas malondialdehyde (MDA) and pro-inflammatory cytokines (IL-6 and TNF-α) were reduced (P < 0.05). In the duodenal mucosa, SOD and GSH-Px activities and T-AOC levels were significantly elevated, while MDA content was notably decreased (P < 0.05). Ruminal fermentation profiles showed increased concentrations of propionate and total volatile fatty acids (TVFA) in the Treat group (P < 0.05). Microbiome analysis revealed that FCHM supplementation selectively modulated the ruminal microbial community, enriching beneficial genera such as Prevotellaceae_UCG-003 and Butyrivibrio, while reducing the abundance of potentially harmful genera like Streptococcus, despite no significant changes in the overall community diversity. Metagenomic sequencing further demonstrated the enrichment of KEGG enzymes and carbohydrate-active enzyme genes involved in carbohydrate metabolism and propionate biosynthesis. Correlation network analyses revealed significant associations among specific microbial taxa, serum antioxidant, immune biomarkers, and growth performance. In conclusion, dietary FCHM supplementation improves growth performance in suckling lambs by optimizing ruminal fermentation patterns, selectively regulating gastrointestinal microbiota, and enhancing systemic antioxidant capacity. These findings support the potential of FCHM as a functional feed additive in lamb production systems.

IMPORTANCE: Enhancing growth performance and ensuring gastrointestinal health during the suckling period are critical for lamb productivity and welfare. In the context of the antibiotic-free mandate in animal feed, we evaluated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth, antioxidant status, immune parameters, and gastrointestinal microbiota in lambs. Our findings demonstrate that FCHM improves average daily gain, enhances systemic and mucosal antioxidant capacity, and modulates ruminal and hindgut microbiota by enriching beneficial taxa and suppressing potentially harmful bacteria. These effects are linked to upregulated microbial functions in carbohydrate metabolism and propionate biosynthesis. This study provides a microbial-based mechanism for FCHM as a natural feed additive to promote lamb growth and gastrointestinal resilience, offering a sustainable strategy to support early-life development in ruminant production systems.},
}

@article {pmid42402279,
year = {2026},
author = {Jiang, C and Wang, Z and Xie, B and Huang, H and Zhan, M and Kim, Y and El-Kady, AA and Su, Y},
title = {Fructose-Induced bioenergetic surplus Unlocks fatty acid biosynthesis pathway dominance over reverse β-Oxidation: Mechanistic insights into High-Caproate production from food waste.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135298},
doi = {10.1016/j.biortech.2026.135298},
pmid = {42402279},
issn = {1873-2976},
abstract = {Chain elongation (CE) is an effective strategy for converting organic wastes into value-added medium-chain fatty acids (MCFAs), wherein electron donors (EDs) dictate process efficiency. However, beyond substrate toxicity and limited reducing power, conventional EDs such as ethanol and lactate impose a chronic bioenergetic constraint: their minimal net ATP yield thermodynamically restricts CE strictly to the energy-neutral reverse β-oxidation (RBO) pathway. To overcome this bioenergetic bottleneck, this study investigated fructose as a high-energy-yielding multidimensional ED to drive n-caproate production from food waste in a mixed-culture system. Herein, the results demonstrated a dose-dependent enhancement of n-caproate, peaking at 12.38 g/L with a remarkable selectivity of 63.0 % (50 g/L fructose dosage). Mechanistically, fructose fermentation established an in-situ synergistic multi-ED microenvironment (fructose, ethanol, and lactate) that buffered toxicity and sustained robust reducing power. More critically, intensive glycolytic flux induced a hyper-energetic intracellular state characterized by abundant ATP and elevated NADH/NAD[+] ratio. Meanwhile, the activities of key enzymes (e.g., phosphofructokinase and butyrate kinase) were significantly stimulated, redirecting carbon flow toward butyrate and n-caproate. This favorable energetic and metabolic environment further selectively enriched Limosilactobacillus spp., which glycolyzed fructose into essential carbon intermediates for CE. Finally, metagenomic profiling revealed that the fructose-induced ATP surplus profoundly enriched genes associated with the ATP-dependent fatty acid biosynthesis (FAB), while suppressing RBO-related genes. This uncovers a paradigm shift from the RBO-dominated route to a FAB-driven mechanism. These findings unravel how a targeted carbohydrate structurally rewires the thermodynamic hierarchy of CE pathways, providing novel mechanistic blueprints for upgrading complex organic wastes into high-value biochemicals.},
}

@article {pmid42402284,
year = {2026},
author = {Dar, RA and Tsui, TH and Du, Z and Zhang, L and Smoliński, A and Xiang, G and Liu, R},
title = {Integrated metagenomic and metaproteomic insights into current-carrying-coil magnetic field enhanced synergistic methanogenic system and antibiotic resistance gene reduction in cow manure anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135326},
doi = {10.1016/j.biortech.2026.135326},
pmid = {42402284},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a sustainable strategy for valorizing cow manure (CM). However, the high ammonia (NH3) concentration and low biodegradability of CM limit hydrolysis and methane production. This study investigated the application of a current-carrying-coil-based magnetic field (CCC-MF) to AD of CM. The CCC-MF digesters showed higher soluble chemical oxygen demand and attained 16.59 % higher ammonium nitrogen reduction, contributing to a 37.50 % higher average methane yield than the control. Further, CCC-MF digesters showed higher enzyme activities (alkaline protease + 30 %, acetate kinase + 22 % and hydrazine dehydrogenase + 26 %) and increased microbial metabolic indices (dehydrogenase activity + 17 % and electron transport system activity + 10 %) than the control. Metagenomics analysis revealed that abundances of the bacterial genera Mesotoga, Aminobacterium, Xiashengella, unclassified Candidatus Cloacimonadota, Advenella, Pseudomonas, and Comamonas increased, whereas the acetoclastic methanogen Methanothrix decreased by 2.58 %, accompanied by 2.07- and 1.64-fold increases in hydrogenotrophic methanogens Methanospirillum and Methanobacterium, respectively, in CCC-MF digesters. The abundance of nitrogen dissimilation and assimilation genes NirK, NorB, NarB, NapA, nmo, and GLT1 were enhanced by 1.14, 1.04, 2.30, 1.32, 1.17, and 1.29-fold in CCC-MF digesters compared to the control. Moreover, metaproteomics revealed higher up-regulated differentially expressed proteins in NH3 reduction-related amino acid metabolism pathways in CCC-MF digester compared to control. Additionally, reduced abundances of bacitracin, polymyxin, sulfonamide, and multidrug antibiotic resistance (MAR) gene types were observed in the CCC-MF digesters. The findings suggest that applying CCC-MF may be associated with higher methane production and ammonium reduction, potentially linked to a more favorable synergistic methanogenic system and nitrogen transformation pathways.},
}

@article {pmid42402338,
year = {2026},
author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandón, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR},
title = {Pre-treatment Gut Microbiome Diversity and Function Linked to Cytotoxic and Natural Killer Cell Immune Responses after N-803 Treatment in People with HIV.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciag369},
pmid = {42402338},
issn = {1537-6591},
abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.

METHODS: In this exploratory longitudinal metagenomic study, we analyzed fecal microbiomes from 10 ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.

RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were nominally enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii showed a nominal increase after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8+ and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA+ cells. MaAsLin2 analyses further identified potentially important associations between short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.

CONCLUSIONS: These findings in a limited Phase 1B clinical study suggest that gut microbiome diversity prior to immunotherapy may influence host response. These results provide a basis for further investigation into microbiome-based strategies to improve efforts to cure HIV.},
}

@article {pmid42399687,
year = {2026},
author = {Wang, X and Wang, H and Wang, X and Liao, H and Yang, J and Jin, H and Hoffnagle, E and Jeon, MK and Cui, Y and Li, X and Liu, X and Chen, X and Liao, L and Dong, Y and Jiang, L and Xiu, Z and Yang, Y},
title = {Fermentative iron reduction by a psychrotolerant Clostridium-dominant consortium enriched from Antarctic penguin-impacted soils.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10434-2},
pmid = {42399687},
issn = {2399-3642},
abstract = {Microbial iron cycling regulates nutrient availability and redox balance in global ecosystems, yet its pathways remain underexplored in ice-free Antarctic terrestrial ecosystems. This study reports the enrichment of a psychrotolerant microbial consortium from penguin-impacted soils on Beaufort Island, Antarctica, capable of reducing Fe(III) to Fe(II) at 4 °C via an anaerobic (likely fermentative) iron-reducing pathway. The consortium was dominated by Clostridium sensu stricto 13 and completely reduced 230 mg L[-1] Fe(III) citrate within three months and drove the biogenic formation of magnetite (Fe3O4). Metagenomic binning yielded four high-quality Clostridium genomes harboring multiple hydrogenases and cold-shock proteins (csp), revealing genomic strategies for energy conservation and psychrotolerance. Hydrogen production was strongly suppressed in the presence of Fe(III) citrate, indicating an intimate coupling of fermentation-derived electron flow to Fe(III) reduction. Our findings reveal a previously unrecognized low-temperature iron reduction mechanism and highlight the ecological significance of anaerobic (likely fermentative) iron reducers in ornithogenic soils-microhabitats enriched in organic matter and metals by penguin guano. This work expands the known diversity of Fe(III)-reducing microorganisms, demonstrates their role in magnetite biomineralization under extreme conditions, and provides insights into microbial modulation of iron speciation in Antarctic ornithogenic soils.},
}

@article {pmid42399871,
year = {2026},
author = {Du, W and Pan, F and Lan, P and Xie, L and Zheng, C and Wu, H},
title = {Metagenomic next-generation sequencing-guided management of descending mediastinitis and empyema caused by Segatella baroniae: a case report.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04465-y},
pmid = {42399871},
issn = {1471-2466},
abstract = {BACKGROUND: Deep neck infections can rapidly progress to descending mediastinitis and empyema, both of which are associated with high morbidity and mortality. Early diagnosis and timely intervention are essential but can be challenging, particularly in infections caused by rare anaerobic pathogens.

CASE PRESENTATION: We report a case of a 63-year-old man presenting with fever and neck pain. Computed tomography revealed extensive cervical emphysema and pneumomediastinum with a large right-sided empyema. The patient developed respiratory failure requiring endotracheal intubation. Endoscopic examination identified a retropharyngeal fistula, and thoracoscopic exploration confirmed communication between the mediastinum and pleural cavity. Combined cervical, mediastinal, and thoracic drainage was performed. Metagenomic next-generation sequencing identified Segatella baroniae as the predominant pathogen, guiding targeted antimicrobial therapy. The patient showed gradual clinical and radiological improvement and was discharged in good condition.

CONCLUSION: This case highlights the importance of early recognition and aggressive surgical management in deep neck infections complicated by descending mediastinitis. Metagenomic next-generation sequencing may facilitate rapid pathogen identification and guide targeted therapy in complex anaerobic infections.},
}

@article {pmid42399943,
year = {2026},
author = {Fu, Y and Song, X and Wang, H and Sun, J and Chen, J and Liu, T and Qi, K and Shi, Y and Li, F and Huang, X and Yang, H and Zhang, W},
title = {Viral metagenomic analysis of the blood virome in patients with multiple autoimmune diseases.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42399943},
issn = {1743-422X},
support = {No.SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; F202322//Jiangsu Province Maternal and Child Health Research Project/ ; JC-2023-004//Clinical Research Project of the Jiangsu University Affiliated People's Hospital/ ; No. 82341106 and 82550118//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Virome ; *Autoimmune Diseases/virology/blood ; *Metagenomics ; Female ; *Viruses/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Lupus Erythematosus, Systemic/virology ; },
abstract = {Autoimmune diseases are chronic and heterogeneous disorders resulting from the breakdown of immune tolerance and subsequent tissue damage. Beyond genetic predisposition, viral infections are increasingly recognized as pivotal environmental contributors to disease onset. In this study, we performed comprehensive viral metagenomic profiling of blood samples from 205 patients with systemic lupus erythematosus (SLE), Sjögren's syndrome (SS), ankylosing spondylitis (AS), and undifferentiated connective tissue disease (UCTD). A total of approximately 103.98 million sequencing reads were analyzed, revealing 44 viral families, including 30 DNA and 14 RNA families. RNA viruses dominated the virome composition, accounting for 71% of total reads, with Picobirnaviridae being consistently prevalent and abundant across all disease groups. Alpha and beta diversity analyses revealed significant heterogeneity in viral community structures among different disease groups, with a marked diversity skew observed in the SS group. Disease-specific viral composition patterns were prominent, and the number of core viral species shared across the four groups was limited. Of particular note, Anelloviridae was significantly enriched in the AS and UCTD groups, suggesting its potential as a biomarker for immunosuppressive states. Furthermore, bacteriophages such as Microviridae exhibited differential abundance across groups, reflecting the potential role of virus-microbe-host immune interactions in disease pathogenesis. In conclusion, this study provides a comprehensive profile of the blood virome in four autoimmune diseases, highlighting the potential role of viral communities in immune regulation and offering new perspectives for the development of related biomarkers.},
}

Humans
*Virome
*Autoimmune Diseases/virology/blood
*Metagenomics
Female
*Viruses/classification/genetics/isolation & purification
Male
Adult
Middle Aged
Lupus Erythematosus, Systemic/virology

@article {pmid42400043,
year = {2026},
author = {Wang, Y and Xue, X and Usyk, M and Sharma, A and Anastos, K and Post, WS and Hodis, HN and Wang, Z and Witt, MD and Rinaldo, CR and Brown, TT and Palella, FJ and Gange, S and Kuniholm, MH and Sha, BE and Caron, P and Gerszten, RE and Clish, CB and Guillemette, C and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB and Peters, BA},
title = {Multi-omics profiles of sex hormone-binding globulin are associated with subclinical atherosclerosis in men with HIV.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01709-8},
pmid = {42400043},
issn = {1756-994X},
support = {R01HL095129/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; R01HL148094/HL/NHLBI NIH HHS/United States ; R01HL140976/HL/NHLBI NIH HHS/United States ; K01HL137557/HL/NHLBI NIH HHS/United States ; K01HL160146/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Sex hormones and HIV infection both influence cardiovascular health. However, the association between sex hormones and subclinical atherosclerosis is not fully understood, especially in the context of HIV.

METHODS: Among 321 men (65% with HIV) from the MACS/WIHS Combined Cohort Study, we measured 14 serum sex hormones and sex hormone-binding globulin (SHBG), assessed carotid artery plaque (IMT > 1.5 mm) using high-resolution B-mode ultrasound, and performed metagenomic sequencing on stool samples. In 312 men, we measured 986 plasma metabolites via liquid chromatography-tandem mass spectrometry and 2883 plasma proteins using the Olink Explore 3072 platform. In stratified analyses of men with (MWH) and without HIV (MWOH) and adjusting for covariates and multiple testing, we (1) examined associations of sex hormones with plaque; (2) characterized multi-omics profiles related to sex hormones; and (3) generated sex hormone-related omics scores via linear combination of related species, metabolites, and proteins, respectively, to explore whether these sex hormone-related multi-omics profiles were associated with plaque.

RESULTS: Median age of participants was 62 years (interquartile range: 58-68), and 31.5% had carotid artery plaque. Sex hormones were differentially associated with plaque in MWH and MWOH. In MWH, an inverse association was observed between SHBG and plaque (OR = 0.60 per 1-SD increase, 95% CI: 0.41, 0.90). Furthermore, higher SHBG levels were associated with overall gut microbial composition, lower abundance of species from genera Prevotella, Fibrobacter and Coprococcus, higher levels of certain metabolites (primarily lipid and carnitine metabolites) and proteins enriched in the cell-cell adhesion pathway. Some SHBG-related species (e.g., Mediterranea massiliensis), metabolites (e.g., phosphatidylcholine-based lipids) and proteins (e.g., enriched in immune response pathway) were also associated with plaque in MWH. All three SHBG-related omics scores were inter-correlated and inversely associated with plaque in MWH. In MWOH, estrone-sulfate was positively associated with plaque (OR = 3.80, 95% CI: 1.41, 10.22) but not with any species, metabolites or proteins.

CONCLUSIONS: Higher SHBG, and related microbial species, circulating metabolites, and proteins, were inversely associated with carotid artery plaque. These findings suggested that SHBG may play a protective role in subclinical atherosclerosis in MWH.},
}

@article {pmid42400260,
year = {2026},
author = {Kim, D and Li, M and Nguyen, TH and Choi, YJ and Jang, S and Kim, M and Kim, YK and Shin, MK and de Guzman, ACV and Park, S},
title = {Vitamin B6 produced by gut microbiome regulates host behavioral phenotypes through dopaminergic metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2695485},
doi = {10.1080/19490976.2026.2695485},
pmid = {42400260},
issn = {1949-0984},
mesh = {Animals ; Caenorhabditis elegans/microbiology/metabolism ; Humans ; *Dopamine/metabolism ; *Gastrointestinal Microbiome ; *Vitamin B 6/metabolism/biosynthesis ; *Parkinson Disease/microbiology/metabolism/genetics ; Mice ; Pyridoxal Phosphate/metabolism ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism ; Phenotype ; Escherichia coli/genetics/metabolism ; alpha-Synuclein/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Male ; Mice, Inbred C57BL ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {The gut microbiome modulates host neuropathology, but the mechanisms linking specific microbial genes and metabolites to host phenotypes remain poorly defined. Here, we identify microbiome-derived vitamin B6 (VB6) and its biosynthesis gene as key regulators of host dopaminergic homeostasis. Metagenomic analysis of fecal samples from Parkinson's disease (PD) patients revealed enrichment of biosynthetic pathways for pyridoxal-5'-phosphate (PLP), the active form of VB6, and tyrosine decarboxylase genes. Using E. coli-C. elegans symbiotic models, we demonstrate that the bacterial pdxJ gene, encoding a key enzyme in de novo VB6 synthesis, is essential in regulating host dopaminergic homeostasis. Colonization with pdxJ-deficient bacteria led to reduced host VB6 and dopamine levels, reduced dopaminergic enzyme activity, and altered motor behavior, which were all rescued by VB6 supplementation. In PD-relevant C. elegans models, bacterial PLP biosynthesis modulated α-synuclein aggregation and behavioral deficits associated with human LRRK2 mutations. In mice, colonization with pdxJ-deficient bacteria reduced serum VB6 levels, decreased tyrosine hydroxylase staining in the substantia nigra, and impaired motor coordination, which were rescued by VB6 supplementation. Overall, our results define a bacterial pdxJ-PLP-dopamine axis that links gut microbial metabolism to host dopaminergic phenotypes and suggest bacterial VB6 biosynthesis as a potential modifier of PD risk and a context-dependent therapeutic target.},
}

Animals
Caenorhabditis elegans/microbiology/metabolism
Humans
*Dopamine/metabolism
*Gastrointestinal Microbiome
*Vitamin B 6/metabolism/biosynthesis
*Parkinson Disease/microbiology/metabolism/genetics
Mice
Pyridoxal Phosphate/metabolism
Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism
Phenotype
Escherichia coli/genetics/metabolism
alpha-Synuclein/metabolism
Bacteria/genetics/metabolism/classification/isolation & purification
Male
Mice, Inbred C57BL
Feces/microbiology
Disease Models, Animal

@article {pmid42400618,
year = {2026},
author = {Yu, J and Jiang, C and Sakai, Y and Mino, S and Sawabe, T},
title = {The Sea Cucumber Holobiont and Probiotics: Recent Progress on Apostichopus japonicus.},
journal = {Current microbiology},
volume = {83},
number = {8},
pages = {},
pmid = {42400618},
issn = {1432-0991},
support = {JP19K22262//MEXT Kaken/ ; },
mesh = {Animals ; *Symbiosis ; *Probiotics ; *Stichopus/microbiology/physiology/genetics ; *Sea Cucumbers/microbiology/physiology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {After the first definition of the term "Holobiont" by Margulis in the introduction of symbiosis as "Association throughout a significant portion of the life history" in 1991 [1], the understanding of holobiont has become an important goal in modern biology today [2]. Recent advances in microbial collection, genome/metagenome/transcriptome sequencings, and bioassays for host-microbes interactions push us towards a fuller understanding of holobiont in various aspects of life on Earth. Historically, holobiont and related hologenome concepts have been tested and expanded through research on marine organisms such as coral, fish, sea cucumber, sponge, and squid. In particular, the sea cucumber Apostichopus japonicus is a physiologically and ecologically unique marine invertebrate in which the holobiont can be studied with its significant capability of organ regeneration, presence of microbes in coelomic fluid, their mysterious nutrition connected to slow growth, and improvements in seed production for the bio-conservation of endangered and essential fisheries resources. The animals are also important in evolutionary terms on a branch of the Deuterostomia clade sharing ancestry with humans, so we can also compare to and learn from knowledge on the human-microbes interactions. In this review, recent progress in the sea cucumber A. japonicus holobiont studies, and the discovery of probiotics candidates among its pioneer microbiomes are described. By understanding this recent progress, we expect to stimulate new and further perspectives on basic biology, bio-conservation, and sustainable aquaculture of sea cucumber.},
}

Animals
*Symbiosis
*Probiotics
*Stichopus/microbiology/physiology/genetics
*Sea Cucumbers/microbiology/physiology
Bacteria/genetics/classification/isolation & purification

@article {pmid42400712,
year = {2026},
author = {Song, Y and Mao, C and Liu, P and Yang, G and Kang, L and Li, Z and Zhou, W and Liu, X and Yao, S and Yang, Y},
title = {Microbial community structure and function and their linkages with methane production in sediments of thermokarst lakes on the Tibetan Plateau.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42400712},
issn = {1869-1889},
abstract = {Thermokarst lakes represent a critical source of atmospheric methane (CH4), owing to large amounts of microbially generated CH4 in sediments. However, the structure and function of lake sediment microbiota, as well as their roles in mediating CH4 production, remain poorly understood across broad geographic scales. Here, we combined high-throughput sequencing, a 224-d anaerobic incubation, and stable isotopic analyses to investigate sediment microbiota and CH4 production across 30 thermokarst lakes along a 1,100 km permafrost transect on the Tibetan Plateau. Our results revealed that lake characteristics (i.e., lake depth and salinity-alkalinity) shaped sediment microbial composition and function. Deeper lakes exhibited enriched methanogenic taxa and pathways. In contrast, shallower lakes with higher salinity-alkalinity were dominated by microbial consortia that suppress net CH4 production via methanotrophs consuming CH4 and sulfate reducers competing with acetoclastic and hydrogenotrophic methanogens. Accordingly, cumulative CH4 production decreased by one order of magnitude from deeper lakes (2.5 log10CH4-C µg/g) to shallow and alkaline lakes (1.3 log10CH4-C µg/g) or salinity-alkalinity lakes (1.1 log10CH4-C µg/g). This variation was modulated by both key microbial consortia and sediment organic carbon and nitrogen supply. Overall, these results disentangled how lake characteristics restructured microbial dynamics to alter sediment CH4 production, and identified critical microbial consortia that could predict spatial variations in sediment CH4 production across thermokarst lakes.},
}

@article {pmid42401057,
year = {2026},
author = {Zheng, Y and Wang, C and Niu, X and Han, C and Zhang, Z and Yang, H and Zhang, S and Ye, X and Li, L and Lv, J and Ma, Z and Liu, H and Ma, Y and Su, X},
title = {Coupled geochemical profiling and metagenomics reveal controls on phosphine preservation and emission in a eutrophic Estuary.},
journal = {Water research},
volume = {304},
number = {},
pages = {126393},
doi = {10.1016/j.watres.2026.126393},
pmid = {42401057},
issn = {1879-2448},
abstract = {Matrix-bound phosphine (MBP) represents a critical yet poorly constrained component of aquatic phosphorus cycling, and the controls governing its preservation and emission in eutrophic estuarine systems remain incompletely resolved. The spatial controls on MBP preservation and atmospheric phosphine emission across the Pearl River Estuary (PRE) were investigated by integrating sediment phosphorus fractionation, sub-millimeter diffusive gradients in thin films (DGT) profiling, and metagenomic sequencing. Sedimentary MBP was detected at all sites and varied markedly along the estuarine gradient, ranging from 2.38 to 36.85 ng kg[-1] ww, with significant positive correlations with Org-P and TP (p < 0.05). The PRE acted as a net atmospheric source of PH3 during summer, with air-water interface (AWI) fluxes ranging from -5.35 ± 0.63 to 28.90 ± 4.67 ng m[-2] h[-1] and highest emissions concentrated at inner-estuarine nearshore sites. DGT-derived labile P-Fe-S coupling patterns and systematic shifts in microbial metabolic functional potential (e.g., dsrA, mcrA, and ptxD genes) were broadly consistent with the spatial distribution of MBP, suggesting that microscale redox conditions and microbial community function may collectively contribute to reduced-P preservation. The accumulation of Org-P and OM in nearshore depositional zones, driven by terrestrial inputs and local hydrological conditions, may progressively shift sedimentary phosphorus cycling toward pathways that favor reduced-P preservation and sustained atmospheric PH3 emissions. Collectively, these findings offer new insights into the spatial controls on MBP preservation and atmospheric PH3 emission in eutrophic estuarine systems, which are essential to understanding the complex biogeochemical processes that regulate nutrient cycling in these fragile ecosystems.},
}

@article {pmid42401342,
year = {2026},
author = {Zeng, Y and Zhang, L and Zou, Y and Liu, L and Chen, B},
title = {Enhancing catalytic efficiency of a deep-sea alkaline lipase through integrated engineering of lid-associated dynamics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135300},
doi = {10.1016/j.biortech.2026.135300},
pmid = {42401342},
issn = {1873-2976},
abstract = {A deep-sea alkaline lipase, MyLip2, fromMoritella yayanosiiwas identified from a metagenomic library of 1,048,576 genes. The wild-type enzyme preferred medium- to long-chain p-nitrophenyl esters, with optimal activity at pH 10.5 and 40 °C, but its specific activity was only 2.93 U/mg toward p-nitrophenyl palmitate. To improve performance, we used a structure- and sequence-guided strategy targeting noncatalytic residues around the catalytic center and lid region. Combinatorial engineering produced triple A271F/V250L/L231P and quadruple A271F/V250L/L231P/T300K (4 M), with comparable specific activities of 743.4 and 745.4 U/mg; 4 M was chosen for its high activity and improved thermal tolerance. This variant showed ∼ 196-fold higher catalytic efficiency (kcat/Km) toward p-nitrophenyl palmitate, with increasedVmax and kcat. Molecular docking, kinetics, and simulations indicated that the substitutions support a more open and catalytically accessible lid conformation, facilitating substrate access and turnover. Comparison with reported lipases indicated that MyLip2 and 4 M combine alkaline preference, medium- to long-chain activity, and improved performance. This work provides a high-performance deep-sea alkaline lipase and suggests that catalytic efficiency can be improved by tuning noncatalytic residues that influence the catalytic-center microenvironment and lid dynamics, without mutating the catalytic triad or redesigning the lid.},
}

@article {pmid42401346,
year = {2026},
author = {Ping, Q and Chen, X and Jin, Y and Chen, Y and Zheng, M and Wang, L and Li, Y},
title = {Deciphering the structural and stoichiometric regulation of anaerobic digestion: A cross-scale perspective from molecular thermodynamics to methanogenic pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135314},
doi = {10.1016/j.biortech.2026.135314},
pmid = {42401346},
issn = {1873-2976},
abstract = {Proteins and polysaccharides are the predominant organic fractions of waste activated sludge (WAS). However, the regulation mechanisms of their distinct molecular structures and compositional ratios on the efficiency of anaerobic digestion (AD) remain unclear. This study comprehensively investigates their impacts on AD performance, focusing on molecular thermodynamics and functional gene regulation involved in electron transfer, energy conversion, and methanogenic pathways. The results demonstrate that molecular structure is a key factor determining substrate bioavailability. The protein with a mainly β-structure (xylanase) and randomly coiled polysaccharide (pullulan) exhibited superior hydrolysis, acidification, and methanogenic efficiency due to increased enzyme binding affinity. Conversely, α-helical protein and triple-helix polysaccharide displayed restricted enzymatic accessibility. Further studies revealed the combination of xylanase and pullulan at the optimal C/N ratio (35) effectively balanced nutrition, thereby achieving the highest cumulative methane yield. Metagenomic and metatranscriptomic analyses revealed that the optimal structures and C/N stoichiometry not only enriched GH13 enzymes, but also shifted the metabolic pathway from acetoclastic to hydrogenotrophic methanogenesis. Moreover, it enhanced interspecies electron transfer and energy conversion efficiency by promoting NADH dehydrogenases, formate dehydrogenase and heterodisulfide reductase, thereby establishing a highly efficient and stable metabolic network in AD system. These findings provide novel insights into the microbial and biochemical regulation driven by substrate structure and stoichiometry from cross-scale perspective, thereby offering a theoretical basis and regulatory strategy for the efficient resource recovery of waste activated sludge.},
}

@article {pmid42401622,
year = {2026},
author = {Real, MVF and Vitousek, MN and Sheehan, MJ and Moeller, AH},
title = {The mouse gut microbiota responds to predator odor and predicts host behavior.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01028-1},
pmid = {42401622},
issn = {2055-5008},
support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; },
abstract = {Chronic stressors can alter the mammalian gut microbiota in ways that mediate host stress responses, but the impacts of acute stressors on these interactions are less well understood. Here, we show that brief exposure of wild-derived mice to predator odor altered gut-microbiota composition, which in turn predicted host behavior. We investigated the individual and combined effects of 15-minute exposures to synthetic fox fecal odor and 30 days of chronic social isolation, an established chronic stressor. Using ethological assays, visceral adipose tissue transcriptomics, and genome-resolved metagenomics, we found that predator-odor exposure significantly affected mouse behavior, gene expression, and gut microbiota. Predator odor-responsive bacteria were associated with the expression of genes involved in anti-microbial defense, and host behavioral responses were predicted by random forest models trained on gut-microbiota profiles. These findings indicate interactions between the gut microbiota and wild-mouse responses to the threat of predation, an ecologically relevant acute stressor.},
}

@article {pmid42401690,
year = {2026},
author = {Ribero, MN and Schiaffino, MR and Filloy, J},
title = {Grassland afforestation more than forestry intensification shapes soil multifunctionality via microbial compositional change under abiotic constraints.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60845-8},
pmid = {42401690},
issn = {2045-2322},
support = {UBACyT 2018//Universidad de Buenos Aires/ ; },
abstract = {Soil ecosystem multifunctionality (EMF) is driven by the interplay of abiotic and biological factors, yet how these interactions respond to anthropogenic pressures remains poorly understood. Here, we evaluated how grassland afforestation and its intensification shape soil edaphic conditions, microbial diversity, and EMF along a 200 km grassland-eucalypt plantation transect in Argentina. EMF was estimated, accounting for six ecosystem functions related to nutrient provisioning, organic matter cycling, and pathogen control. Microbial diversity was studied through the taxonomic, functional, and phylogenetic dimensions of prokaryotes, mycorrhizae, and fungal saprotrophs. Abiotic and biotic drivers of individual ecosystem functions and EMF were assessed using correlations, linear mixed models, structural equation models, and Multiple Regressions on distance Matrices. Individual ecosystem functions responded differentially to environmental drivers: functions linked to soil physicochemical processes were primarily associated with edaphic conditions, whereas biologically mediated functions were more closely linked to climate and grassland afforestation. Soil multifunctionality, however, was driven by edaphic and climatic conditions, particularly soil sand percentage and precipitation, with no direct association with microbial alpha diversity or afforestation. In contrast, similarity in fungal composition explained similarity in EMF, suggesting a coupling between microbial composition and soil conditions associated with grassland afforestation. Grassland conversion to commercial forest, rather than forestry intensification, altered individual soil functions and microbial functional composition without further reducing EMF. Overall, our findings indicate that afforestation influences soil EMF through changes in microbial composition, but that these effects are constrained by abiotic drivers.},
}

@article {pmid41738567,
year = {2026},
author = {Ma, M and Liu, B and Zhou, J and Zhang, J and Zhang, Y and Li, W and Liu, X and Xu, D},
title = {Viral Community Profiling of RNA Viruses in Lesion Tissues From Hyriopsis cumingii With Epidemic Disease via Metatranscriptomics and VirID-Based RdRP Mining.},
journal = {Journal of fish diseases},
volume = {49},
number = {8},
pages = {e70143},
doi = {10.1111/jfd.70143},
pmid = {41738567},
issn = {1365-2761},
support = {2024SKLBC-KF02//National Key Laboratory of Aquatic Animal Disease Control and Healthy Aquaculture, 2024 Open Research Projects/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification/physiology ; Phylogeny ; *Unionidae/virology ; RNA-Dependent RNA Polymerase/genetics ; Metagenomics ; Transcriptome ; Epidemics/veterinary ; *Virome ; Hepatopancreas/virology ; },
abstract = {To identify enriched pathogens and characterise the viral community associated with epidemic disease outbreaks in the freshwater mussel Hyriopsis cumingii, we performed metatranscriptomic sequencing combined with VirID-driven RNA-dependent RNA polymerase (RdRP) mining and phylogenetic analysis using hepatopancreas and intestinal samples from six severely infected individuals. Clinical observations were consistent with hallmark features of epidemic outbreaks. The sequencing yielded 86.2 Gb of raw data, of which 97.1% passed quality control, resulting in 77.7 Gb of high-quality clean data. Taxonomic annotation identified 182 viral species, predominantly unclassified viruses (45% Transcripts Per Million, TPM), followed by members of the phyla Lenarviricota (28%) and Uroviricota (17%). Phylogenetic analysis of RdRP sequences revealed 13 viral supergroups, with the Picorna-Calici supergroup showing the highest abundance (26.2% of annotated viruses) and reaching a prevalence of 39.3% in sample HcAV3. Notably, 89.6% of the identified viral RdRPs exhibited less than 70% amino acid identity to known viral sequences, highlighting the presence of extensive "viral dark matter" in this host species. This study establishes the first viral profile associated with epidemic disease in H. cumingii, providing a baseline for further etiological research on this high-mortality aquaculture disease.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification/physiology
Phylogeny
*Unionidae/virology
RNA-Dependent RNA Polymerase/genetics
Metagenomics
Transcriptome
Epidemics/veterinary
*Virome
Hepatopancreas/virology

@article {pmid42392820,
year = {2026},
author = {Li, H and Deng, XF and Chen, H and Wang, P and Xu, HY},
title = {[Metabolomics and metagenomics reveal mechanism of Xinglou Chengqi Decoction in preventing cerebral ischemia-reperfusion injury].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {9},
pages = {2652-2664},
doi = {10.19540/j.cnki.cjcmm.20260107.707},
pmid = {42392820},
issn = {1001-5302},
mesh = {Animals ; *Drugs, Chinese Herbal/administration & dosage ; *Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics ; Rats ; Male ; Metabolomics ; Metagenomics ; Rats, Sprague-Dawley ; *Brain Ischemia/metabolism/drug therapy/genetics ; Humans ; Oxidative Stress/drug effects ; Blood-Brain Barrier/drug effects/metabolism ; Brain/metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; },
abstract = {This study uses a rat model of middle cerebral artery occlusion and reperfusion(MCAO/R) to investigate the mechanism by which Xinglou Chengqi Decoction treats cerebral ischemia-reperfusion injury, employing metabolomics and metagenomics approaches. A rat model of MCAO/R was established to evaluate the neurological function and modified neurological severity scores. Then, the brain tissue pathology, inflammatory mediators, oxidative stress, blood-brain barrier integrity, cerebral edema, and intestinal barrier function were examined to assess the pharmacological effects of Xinglou Chengqi Decoction. Metabolomics analysis of the brain tissue and metagenomics analysis of the intestinal contents were conducted to investigate the metabolism and gut microbiota regulatory mechanisms of Xinglou Chengqi Decoction. The results suggested that Xingluo Chengqi Decoction improved the neural function, reduced the severity of cerebral infarction, attenuated oxidative stress and inflammatory factor levels, boosted blood-brain barrier factor levels, minimized cerebral edema, and strengthened intestinal mucosal barrier protection, thus treating cerebral ischemia-reperfusion injury in rats. Metabolomic analysis of the brain tissue revealed that Xinglou Chengqi Decoction primarily treated ischemic stroke through 14 potential metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism. Metagenomic analysis revealed that administration of Xinglou Chengqi Decoction increased the relative abundance of Firmicutes, Clostridia and Bacilli, Clostridiales and Lactobacillales, and Lachnospiraceae and Oscillospiraceae. In addition, it influenced the biosynthesis of aminoacyl-tRNA, valine, leucine, and isoleucine, along with peptidoglycan synthesis, thereby enhancing the regulatory function of the gut microbiota. Simultaneously, Xinglou Chengqi Decoction exerts therapeutic effects through the gut-brain crosstalk mediated by substances such as amino acids and fatty acids, which act within the biosynthetic and metabolic pathways.},
}

Animals
*Drugs, Chinese Herbal/administration & dosage
*Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics
Rats
Male
Metabolomics
Metagenomics
Rats, Sprague-Dawley
*Brain Ischemia/metabolism/drug therapy/genetics
Humans
Oxidative Stress/drug effects
Blood-Brain Barrier/drug effects/metabolism
Brain/metabolism/drug effects
Gastrointestinal Microbiome/drug effects
Disease Models, Animal

@article {pmid42393176,
year = {2026},
author = {Gordon, LM and Sevigny, JL and Buck, CB and Murray, MJ and Sidor, IF and Newton, AL and Palisoul, SM and Kelly, M and Nigatu, AS and Simpson, SD and Popov, VL and Waltzek, TB and Tsongalis, GJ and Frasca, S and Thomas, WK},
title = {A novel adomavirus from proliferative skin lesions of a broadnose sevengill shark (Notorynchus cepedianus).},
journal = {Npj viruses},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44298-026-00210-8},
pmid = {42393176},
issn = {2948-1767},
support = {P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; 5P30CA023108-37/CA/NCI NIH HHS/United States ; 5P30CA023108-37/CA/NCI NIH HHS/United States ; },
abstract = {In May of 2022, an aquarium-maintained broadnose sevengill shark (Notorynchus cepedianus) developed proliferative skin lesions that prompted pathologic and molecular investigation. Histopathologic examination revealed epidermal hyperplasia consisting of proliferation of spinous epithelial cells with mild dysplasia. Metagenomic sequencing identified a novel adomavirus with an 18,834 base pair circular double-stranded DNA genome. The virus, provisionally named broadnose sevengill shark adomavirus (7AdoV), contains two bidirectionally expressed protein-coding gene sets. Genomic annotation and structural predictions of proteins were used to contextualize 7AdoV phylogenetically and functionally. Transcriptomic analysis showed that expression of the structural late gene set was higher than the replicative early gene set at the time of diagnostic sampling. In situ hybridization using RNAscope technology localized transcripts of the adomavirus Wasp gene to epithelial cells of the hyperplastic epidermis. Infection by this novel adomavirus was associated with superficial and proliferative lesions that were self-limiting and resolved in this shark.},
}

@article {pmid42393215,
year = {2026},
author = {Nthuku, S and Mordecai, J and Babajide, AA and Makoko, D and Sawadogo, Y and Awe, OI},
title = {The Kenyan Human Gut Virome Catalogue reveals extensive viral diversity and age-dependent community structure.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60183-9},
pmid = {42393215},
issn = {2045-2322},
abstract = {The human gut virome is a critical yet understudied component of the microbiome that shapes microbial community structure and host-microbe interactions. However, most existing human gut virome reference databases have been constructed predominantly from populations in high-income countries, resulting in the substantial underrepresentation of African populations. To help address this disparity, we developed the Kenyan Human Gut Virome Catalogue (KHGVC), the first comprehensive human gut virome resource for Kenya and the first country-specific human gut virome catalogue from Africa. Using a standardized viromics pipeline applied to 626 fecal metagenomes spanning infants and adults across three Kenyan counties, we reconstructed 116,968 viral operational taxonomic units (vOTUs). Cross-catalogue comparisons revealed extensive novelty where 65.6% of KHGVC's vOTUs larger than 10 kb lacked matches in five major human gut virome databases, and 95% remained unique relative to the Unified Human Gut Virome (UHGV). Temperate bacteriophages accounted for ~ 70% of vOTUs, supporting a major role for lysogeny in gut ecosystem stability. Functional annotation assigned putative roles to ~ 27% of predicted viral proteins, primarily structural and replication-associated functions. Application of KHGVC revealed pronounced age-dependent virome structuring in which infant viromes were less diverse and enriched in Bifidobacterium-infecting phages, including Bifidobacterium longum, whereas adult viromes exhibited greater diversity and expansion of Prevotella-associated phages. Together, the KHGVC substantially expands known human gut viral diversity and provides a foundational reference for Kenyan and African virome research. The KHGVC can be accessed freely through a publicly available interactive web interface (https://igmr.org/software/kenyavirocat).},
}

@article {pmid42394019,
year = {2026},
author = {Dicko, A and Barro, SG and Sombie, S and Séré, R and Bonkoungou, I},
title = {Applications of Metagenomics and Artificial Intelligence in Characterizing Antimicrobial Resistance in Livestock: A Systematic Review.},
journal = {Studies in health technology and informatics},
volume = {338},
number = {},
pages = {328-332},
doi = {10.3233/SHTI260857},
pmid = {42394019},
issn = {1879-8365},
mesh = {Animals ; *Metagenomics/methods ; *Livestock/microbiology/genetics ; *Artificial Intelligence ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Humans ; One Health ; Machine Learning ; },
abstract = {Antimicrobial resistance (AMR) is an urgent global health threat, intensified by the widespread use of antimicrobials in livestock production. This study synthesizes the current landscape of combining metagenomic sequencing with artificial intelligence (machine learning and deep learning) to characterize, surveil, and predict AMR within the One Health framework. A comprehensive multi-database literature search was conducted, and, following PRISMA guidelines, 10 peer-reviewed studies meeting the inclusion criteria were selected for full synthesis. Metagenomic shotgun sequencing significantly surpasses conventional culture-based methods by directly capturing antimicrobial resistance genes (ARGs) from complex biological communities. AI algorithms substantially outperform traditional bioinformatic tools, achieving high predictive accuracy (AUC-ROC > 0.90) and revealing consistent ARG transfer pathways that link livestock, human, and environmental compartments. Integrating metagenomics with AI delivers a paradigm shift for proactive AMR surveillance. However, standardization, interpretability, and technological adaptation to resource-limited settings-especially in sub-Saharan Africa-remain urgent priorities to inform effective public health policy.},
}

Animals
*Metagenomics/methods
*Livestock/microbiology/genetics
*Artificial Intelligence
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Humans
One Health
Machine Learning

@article {pmid42394335,
year = {2026},
author = {Sun, X and Ding, M and Li, Y and Mu, D and Wu, J and Yu, X and Zhu, M and Sun, G and Xiang, X},
title = {[Effects and Mechanisms of a multi-strain probiotic on the gut microbiota of healthy mice].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {55},
number = {3},
pages = {491-498},
doi = {10.19813/j.cnki.weishengyanjiu.2026.03.019},
pmid = {42394335},
issn = {1000-8020},
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Male ; Mice ; Mice, Inbred C57BL ; Lactobacillus acidophilus/physiology ; Tryptophan/metabolism ; Indoles/metabolism ; Bifidobacterium animalis/physiology ; Lacticaseibacillus rhamnosus/physiology ; Feces/microbiology ; *Microbiota ; },
abstract = {OBJECTIVE: Systematic evaluation of the regulatory effects of compound probiotics containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 and their ratios on gut microbiota composition and the tryptophan-indole metabolic pathway.

METHODS: 30 male C57BL/6 mice were randomly divided into three groups of ten mice each: Control group, Mix-A group(Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101 and Lactobacillus rhamnosus JL1, in a 1∶1∶1 ratio) and Mix-B group(same bacterial strains, in a 10∶1∶1 ratio). The composite probiotic group received daily oral administration of 0.2 mL probiotic suspension at a total concentration of 1.5 × 10~(10) CFU/mL. The control group received daily oral administration of an equal volume of PBS solution. The experimental intervention lasted for 3 weeks. At the end of the experiment, colon tissues were collected from mice to measure superoxide dismutase(SOD)and catalase(CAT)levels. Fecal samples were collected from mice at mid-and end-experiment time points for metagenomic sequencing and targeted metabolomics analysis.

RESULTS: There were no significant differences in body weight or organ indices among the three groups of mice. CAT levels were significantly higher in the Mix-B group compared to the control group(P<0.05). Metabolomic analysis revealed significantly elevated levels of indole-3-acetic acid(IAA), indole-3-lactic acid(ILA), and indole-3-carbaldehyde(IAld) in fecal samples from the Mix-B group(P <0.05). By day 22, β-diversity analysis revealed distinct microbial community structures across all 3 groups. The Mix-B group exhibited decreased Richness indices and increased dominance of specific bacterial taxa. LEfSe analysis indicated enrichment in Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Bifidobacterium animalis in Mix-A; while Mix-B group showed enrichment in Akkermansia muciniphila, Bacteroides acidifaciens, Clostridium cocleatum, and Anaerotruncus colihominis. Correlation analysis revealed significant positive correlations between Bacteroides thetaiotaomicron, Bacteroides acidifaciens, and Akkermansia muciniphila with indole metabolites including IAA, ILA, and IAld.

CONCLUSION: The compound probiotic combination containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 can safely modulate gut microbiota composition and enhance tryptophan-indole metabolism, which may provide a potential strategy for maintaining gut health.},
}

Animals
*Probiotics/pharmacology/administration & dosage
Male
Mice
Mice, Inbred C57BL
Lactobacillus acidophilus/physiology
Tryptophan/metabolism
Indoles/metabolism
Bifidobacterium animalis/physiology
Lacticaseibacillus rhamnosus/physiology
Feces/microbiology
*Microbiota

@article {pmid42394341,
year = {2026},
author = {Stenger, PL and Majorel, C and Valette, L and Ihage, W and Jardin-Camps, M and Jourand, P and Anton-Leberre, V},
title = {Spatial structuring dominates over seasonality in tropical coastal microbiomes: Insights from New Caledonia's Indo-Pacific lagoon.},
journal = {Journal of environmental quality},
volume = {55},
number = {4},
pages = {e70215},
doi = {10.1002/jeq2.70215},
pmid = {42394341},
issn = {1537-2537},
support = {//CRESICA (Consortium for Research, Higher Education, and Innovation in New Caledonia)/ ; //MITI-CNRS (Mission pour les initiatives transverses et interdisciplinaires)/ ; },
mesh = {New Caledonia ; Seasons ; *Seawater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Bacteria/classification ; Tropical Climate ; *Environmental Monitoring ; Archaea ; Ecosystem ; },
abstract = {Tropical coastal ecosystems harbor diverse microbes essential for biogeochemical cycling and serve as sentinels of environmental change. However, microbial community profiles remain largely undocumented across the Southwest Pacific. We investigated bacterial communities in coastal and lagoonal waters surrounding Nouméa, New Caledonia, an area under increasing urban pressure. Our objective was to determine whether spatial heterogeneity or seasonal variation primarily structures these communities and how anthropogenic activities shape microbial diversity. Forty-two seawater samples were collected from seven sites spanning anthropized bays, mangrove estuaries, and offshore lagoon waters during hot and cold seasons. We found that spatial gradients explained significantly more variation in community structure (R[2] = 0.25) than seasonal changes (R[2] = 0.04), revealing distinct microbial signatures along the land-to-sea continuum. Coastal and mangrove sites harbored more copiotrophic taxa and elevated levels of predicted pathogen-associated functional pathways, though these predictions are based on 16S rRNA data, and require validation with metagenomic or functional assays. Seasonal shifts mainly involved Cyanobacteria (Synechococcus↑, Prochlorococcus↓ in warm season) and archaeal Marine Group II, reflecting temperature-mediated niche partitioning. This study establishes the first spatial and seasonal microbial inventory for New Caledonian coastal ecosystems, suggesting associations between anthropogenic influence and microbial community health. Spatial dominance highlights the potential value of local management, while temperature sensitivity of key taxa underscores the importance of integrating microbial monitoring into coastal conservation and One Health frameworks.},
}

New Caledonia
Seasons
*Seawater/microbiology
*Microbiota
RNA, Ribosomal, 16S/analysis
Bacteria/classification
Tropical Climate
*Environmental Monitoring
Archaea
Ecosystem

@article {pmid42394361,
year = {2026},
author = {Queiroz, VF and Tatara, JM and Jivaji, AM and Given, CJ and Dutra, LAL and Abbas, W and Ricky, Z and Stokke, R and Stensvåg, K and Abrahao, JS and Almeida, GMF},
title = {Isolation of a Cohort of Giant Viruses From Above the Arctic Circle in Northern Norway.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70366},
doi = {10.1111/1462-2920.70366},
pmid = {42394361},
issn = {1462-2920},
support = {311192/A65276//Tromsø Forskningsstiftelse/ ; 101150485//Horizon 2020 Framework Programme/ ; 101162830/ERC_/European Research Council/International ; 315427//Norges Forskningsråd/ ; TMS2020TMT13//Trond Mohn stiftelse/ ; },
mesh = {*Giant Viruses/isolation & purification/classification/genetics ; Arctic Regions ; Norway ; Phylogeny ; *Acanthamoeba/virology ; Mimiviridae/isolation & purification/classification/genetics ; *Seawater/virology ; Fresh Water/virology ; },
abstract = {Viruses are the most abundant biological entities on Earth. Metagenomic data indicates a higher viral abundance of viruses of unicellular eukaryotes in the polar regions, information still not matched by broad isolation efforts using samples collected in these regions. Here we describe a prospection effort using diverse samples collected above the Arctic circle, including freshwater and marine samples from urban areas, deep-sea hydrothermal vents and sea ice samples from the Nansen Basin. We isolated 10 giant viruses capable of infecting Acanthamoeba spp., five representing the Marseilleviridae family and five representing the Mimiviridae family. These viruses are the northernmost isolates found so far in the Nordic countries and consist of a unique cohort of Arctic viruses that differs geographically and temporarily from a cohort already described from the Siberian permafrost. Despite an apparent viral diversity in the samples, the uniqueness of the samples themselves and the use of additional non-amebozoan strains as hosts, our viruses are still representatives of known viral families. In conclusion, here we show the isolation of giant viruses in Northern Norway and highlight the potential host bias towards Acanthamoeba in giant virus prospection, indicating the need to break this bias to diversify the isolation of environmental viruses.},
}

*Giant Viruses/isolation & purification/classification/genetics
Arctic Regions
Norway
Phylogeny
*Acanthamoeba/virology
Mimiviridae/isolation & purification/classification/genetics
*Seawater/virology
Fresh Water/virology

@article {pmid42394639,
year = {2026},
author = {Zhu, H and Yang, P and Tu, Y and Fu, X and Yang, X and An, N},
title = {A Case Report of Meningitis with Possible Coinfection by Listeria monocytogenes and Mycobacterium tuberculosis (Detected by Metagenomic Next-Generation Sequencing) and Literature Review.},
journal = {Case reports in critical care},
volume = {2026},
number = {},
pages = {9615951},
pmid = {42394639},
issn = {2090-6420},
abstract = {RATIONALE: The study is aimed at exploring the complex clinical scenario of a patient with systemic lupus erythematosus who developed a rare coinfection with Listeria monocytogenes and Mycobacterium tuberculosis. The rationale is to highlight the diagnostic and therapeutic challenges in managing such a case, particularly in the context of immunosuppression and the need for effective antimicrobial therapy. This case underscores the importance of advanced diagnostic techniques like metagenomic next-generation sequencing in identifying coinfections and the critical balance required in treating both infections while managing the underlying autoimmune condition.

PATIENT CONCERNS: This case report presents a 58-year-old female patient who initially manifested thrombocytopenia and was diagnosed with SLE in an external hospital. After treatment, her condition did not improve. On the contrary, she developed a fever and a headache, and her disturbance of consciousness gradually worsened. The patient was admitted to our hospital with a suspected diagnosis of lupus encephalopathy and central nervous system infection.

DIAGNOSES: MRI plain scan showed linear enhancement shadows in the right temporal pole and bilateral cerebellar hemisphere regions on the fluid-attenuated inversion recovery three-dimensional volumetric fluid-attenuated inversion recovery contrast-enhanced scan. Subsequently, NGS of the cerebrospinal fluid detected L. monocytogenes and M. tuberculosis, suggesting a possible mixed infectious meningitis caused by these two pathogens.

INTERVENTIONS: The patient underwent a comprehensive treatment regimen including antiListeria and antituberculosis therapies. Unfortunately, this was followed by the development of liver failure and various other complications. In response, we administered interventions such as blood purification and liver support measures. Furthermore, we organized a multidisciplinary consultation to address the complex medical needs of the patient.

OUTCOMES: Despite aggressive medical interventions, the patient's condition deteriorated. She developed multiorgan failure, which significantly impacted her prognosis. The patient's family elected to withdraw life-sustaining treatment, and the patient passed away within 24 h after discharge.

LESSONS: This case underscores the importance of early and accurate diagnosis, particularly for immunocompromised patients with complex clinical presentations. Identifying mixed infections is crucial, and it also poses a significant challenge in selecting appropriate antimicrobial agents and conducting relevant tests.},
}

@article {pmid42394779,
year = {2026},
author = {Wishahi, M and Badawy, M},
title = {Letter to the Editor: Urinary infection in European guidelines 2025 vs microbiology culture results in the management of urinary infection.},
journal = {World journal of experimental medicine},
volume = {16},
number = {2},
pages = {115894},
pmid = {42394779},
issn = {2220-315X},
abstract = {We read with great interest the study by Yadav et al published in the World Journal of Experimental Medicine, which postulated a nomogram including patient's critical factors, other than urine sample. European Association of Urology (EAU) published the guidelines on urological infection 2025. The EAU guidelines 2025 of urinary infections (UIs) has classified in two distanced categories: Localized UTs and systemic UTs according to specific patient's symptoms and clinical signs, this new practical classification replaced previous concept of non-complicated urinary tract infection (UTI) against complicated UTI. The new EAU classification categorizes UIs as either localized or systemic, according to the presence of specific clinical signs and symptoms, this new practical classification replaced previous concept of non-complicated UTI against complicated UTI, irrespective of the results of bacteriological findings. In the new classification of UIs, the classification is based on clinical set-up on which the practitioner or urologist will manage the patient. Management of UIs is crucial to consider the urinary and gut microbiota. It was established recently that antibiotic use affects microbiota homeostasis in the gut and urinary tract that will initiate dysbiosis.},
}

@article {pmid42394824,
year = {2026},
author = {Wu, Y and Cai, H and Wu, Q and Wu, J and Hu, J and Huang, E and Li, Z and Liang, S and Hu, X and Dai, J and Liao, R},
title = {The CRISPR-Cas toolkit for mosquito-borne virus surveillance: detection, tracing, and discovery.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1873187},
pmid = {42394824},
issn = {2235-2988},
mesh = {Animals ; *CRISPR-Cas Systems ; Humans ; *Mosquito-Borne Diseases/virology ; *Epidemiological Monitoring ; *Culicidae/virology ; *Mosquito Vectors/virology ; *Viruses/genetics/isolation & purification/classification ; *Virus Diseases/virology/transmission/diagnosis ; },
abstract = {Mosquito-borne virus surveillance increasingly requires rapid, distributed detection of co-circulating pathogens, serotypes, and lineages across clinical and vector-sampling sites. CRISPR-Cas platforms offer a programmable toolkit for this purpose, but their readiness differs substantially across surveillance functions. Here, we review CRISPR-Cas methods for mosquito-borne virus surveillance across detection, tracing, and discovery-supporting targeted screening. Detection is the most advanced application: selected Cas12- and Cas13-based assays for dengue, Zika, chikungunya, West Nile, Japanese encephalitis, and related mosquito-associated viruses report sub-hour workflows, portable readouts, and targeted serotype- or lineage-marker discrimination. However, performance remains assay-, target-, and sample-matrix-dependent, and validation in pooled mosquito samples and field settings is still limited. Tracing currently relies mainly on validated portable amplicon-sequencing workflows, whereas CRISPR-aided sample-preparation methods such as DASH, FLASH, RAPID-DASH, and Cas9-targeted enrichment remain transferable opportunities for host depletion or target enrichment rather than established mosquito-borne virus genomic-surveillance workflows. For discovery-oriented surveillance, multiplex CRISPR-Cas systems such as CARMEN can support targeted screening of known or near-neighbor viruses represented by predesigned crRNAs, while metagenomic next-generation sequencing remains necessary for divergent or previously unknown viruses. Across these functions, CRISPR-Cas programmability may accelerate parts of assay redesign, but practical retargeting still requires compatible amplification primers, effector-specific target constraints, cross-reactivity assessment, and analytical revalidation. Routine surveillance use will require integrated demonstrations with clinical and pooled-vector samples, comparison against established molecular and sequencing methods, cost validation, and regulatory evidence.},
}

Animals
*CRISPR-Cas Systems
Humans
*Mosquito-Borne Diseases/virology
*Epidemiological Monitoring
*Culicidae/virology
*Mosquito Vectors/virology
*Viruses/genetics/isolation & purification/classification
*Virus Diseases/virology/transmission/diagnosis

@article {pmid42394849,
year = {2026},
author = {Ding, J and Liu, F and Zhao, Y and He, Z and Shi, Y and Shu, L},
title = {Protists show high resilience and thrive under multiple chemical stressors.},
journal = {mLife},
volume = {5},
number = {3},
pages = {388-392},
pmid = {42394849},
issn = {2770-100X},
abstract = {Protists are an underexplored but functionally important component of aerobic-activated granular sludge under pollution stress. Using metagenomics, we profiled protistan responses to ciprofloxacin, triclosan, and Cu[2+] (alone or in combination). Protists remained a stable 6.35%-7.88% of the bacterial community, and the consumers were the most abundant groups. Ciprofloxacin showed little effect on protist abundance, while Cu[2+] increased protist abundance, especially consumers. Stress conditions also strengthened predominantly positive protist-bacteria associations, suggesting cross-domain interactions that may enhance community resilience. These results demonstrate that protists are key determinants in stabilizing microbial communities under multiple stressors.},
}

@article {pmid42395046,
year = {2026},
author = {Kumar, A and Ghosh, D},
title = {Letter to the Editor: Dengue virus as an underrecognized cause of encephalitis in tropical Asia - Bridging diagnostic and surveillance gaps.},
journal = {World journal of virology},
volume = {15},
number = {2},
pages = {118082},
pmid = {42395046},
issn = {2220-3249},
abstract = {Arboviral encephalitis remains a major public health concern in tropical Asia, where the etiology of a substantial proportion of central nervous system infections remains undetermined despite endemic circulation of dengue virus (DENV) and Japanese encephalitis virus. Laboratory confirmation is frequently absent in clinically suspected encephalitis. Perera et al recently published a study in World Journal of Virology, highlight this diagnostic gap by identifying DENV infection in 6.06% of encephalitis cases, including molecular evidence of DENV-3 neuroinvasion. These findings add to the growing evidence that DENV can cause encephalitis and meningoencephalitis across age groups. However, encephalitis in endemic settings is etiologically heterogeneous, and dengue represents only one of several infectious and immune-mediated contributors. Neurological dengue is likely under-recognized due to overlapping clinical presentations and limited diagnostic capacity. The identification of DENV-3 is noteworthy given its recurrent association with neurological disease. Limited concordance between reverse transcription polymerase chain reaction and immunoglobulin M assays reflects challenges related to viral kinetics, timing of specimen collection, and flaviviral serological cross-reactivity. Strengthening surveillance through integrated molecular and serological diagnostic strategies, including multiplex polymerase chain reaction and metagenomic next-generation sequencing, is essential to reduce undiagnosed encephalitis and improve clinical management and public health preparedness in tropical Asia.},
}

@article {pmid42395425,
year = {2026},
author = {Shih, JB and Zhao, C and Pollard, KS and Lind, AL},
title = {Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.24.734308},
pmid = {42395425},
issn = {2692-8205},
abstract = {Microbial eukaryotes are prevalent members of host-associated and free-living microbial communities, but are routinely excluded from studies of these communities. Existing methods for eukaryote detection from whole metagenome sequencing are limited by contamination of eukaryotic reference genomes and incomplete taxonomic coverage. Our previously published tool EukDetect addressed these challenges using a curated database of universal BUSCO marker genes, but lacked validated quantitative abundance metrics and was built from a limited number of genomes. Here we present EukDetect2, incorporating a database containing 6,948 microbial eukaryotic genomes representing 6,594 unique species, 2,339 of which are newly added since EukDetect version 1, alongside quantitative metrics for estimating absolute and relative abundance of microbial eukaryotes. Using simulated data, we demonstrate accurate abundance estimation, no false positives from bacterial or host-derived reads, and equivalent or greater sensitivity and specificity than alternative taxonomic profiling tools across a range of microbial abundances and community compositions. Applying EukDetect2 across globally distributed human gut microbiome cohorts, we find that Blastocystis spp. and Dientamoeba fragilis are the most prevalent gut eukaryotes across cohorts, while host-associated fungi are consistently less prevalent than commensal protists. Blastocystis abundance is positively associated with a gut microbial community enriched for fiber-fermenting microbes and depleted for pro-inflammatory and industrialization-associated taxa. EukDetect2 provides sensitive, accurate, and quantitative metrics for investigating microbial eukaryotes from metagenomic samples.},
}

@article {pmid42395547,
year = {2026},
author = {Kokroko, N and Jayanti, R and Sapoval, N and Nute, MG and Nakhleh, L and Treangen, TJ},
title = {Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.22.733643},
pmid = {42395547},
issn = {2692-8205},
abstract = {MOTIVATION: Horizontal gene transfer (HGT) shapes bacterial evolution and microbial ecosystems, yet detecting HGT within microbiomes remains a challenge due to fragmented metagenomic assemblies, reference bias, reliance on gene boundaries, and limited ability to model structural mosaicism and patterns across genomes.

METHODS: We present Kente, a novel pangenome graph-based framework designed for HGT detection that aligns metagenomic assembly contigs to a curated database of >600 genus-level bacterial pangenome graphs constructed using minigraph. Kente infers local taxonomic composition along contigs using alignment evidence and classifies candidate transfers using structured clade-transition topologies (e.g., A-B-A sandwich, open tips, and mosaic patterns). A complementary intra-genus module detects inter-species transfers within a single genus graph using segment-level clade annotations.

RESULTS: Across simulated intra- and inter-genus transfer scenarios, Kente achieves higher precision and comparable recall relative to existing gene-centric microbiome HGT detection approaches while reducing false positives from fragmented assemblies. Application to real human gut metagenomes (HMP2, n = 26) demonstrates Kente's ability to detect candidate cross-lineage transfer regions in complex microbial communities. Runtime profiling shows near-linear scaling with input size, enabling efficient analysis of large metagenomic assemblies.

https://github.com/treangenlab/Kente.},
}

@article {pmid42395643,
year = {2026},
author = {Yang, S and Yu, Q and Zeng, Y and Lu, Y and Xia, C and Cheng, F and Liu, Y and Liu, M and Chen, Y},
title = {Direct viral invasion and tumor-like pulmonary nodules: A fatal case of mpox in a patient with advanced HIV disease.},
journal = {Biosafety and health},
volume = {8},
number = {3},
pages = {228-233},
pmid = {42395643},
issn = {2590-0536},
abstract = {While mpox is typically a self-limiting zoonosis, individuals with advanced human immunodeficiency virus type 1 (HIV-1) infection are at increased risk for severe visceral complications and high mortality. We report a fatal case of fulminant mpox pneumonia in a 38-year-old male with advanced HIV-1 Infection and severe immunosuppression (CD4[+] T-cell count <100 cells/µL). The patient initially presented with characteristic cutaneous lesions but rapidly progressed to dyspnea and respiratory failure. Serial chest imaging revealed diffuse, solid perivascular nodules and patchy consolidations were highly suggestive of pulmonary malignancy. While initial microbiological cultures and clinical presentation (Day 4) suggested bacterial and fungal superinfections, metagenomic next-generation sequencing (mNGS) of lung tissue biopsy identified an overwhelming burden of mpox virus (MPXV; 260,840 sequence reads), cytomegalovirus (CMV) and Epstein-Barr virus (EBV), confirming direct viral invasion of the pulmonary parenchyma. Despite comprehensive treatment with antibiotics, antifungals, CMV-targeted therapy, and mechanical ventilation (specific anti-orthopoxvirus agents were unavailable), the patient succumbed to progressive respiratory failure on Day 31. This case highlights that mpox can manifest as severe necrotizing pneumonia with tumor-like radiological features in patients with acquired immunodeficiency syndrome (AIDS). It underscores the necessity of early pulmonary imaging and molecular testing in high-risk populations to differentiate mpox pneumonia from malignancy or opportunistic infections.},
}

@article {pmid42395675,
year = {2026},
author = {Almuhanna, AA and Vatte, C and Guo, Q and Elsalamouni, TS and Al-Muhanna, FA and Aboalrihy, AM and Alhabib, HA and Almomen, MF and Alali, RA and Habara, AH and Alrubaish, MA and Alfalah, KM and Cyrus, C and Abdul-Rahman, IS and Keating, BJ and Al-Ali, AK and Wang, C},
title = {Gut microbiota in a Saudi population with chronic kidney disease.},
journal = {World journal of nephrology},
volume = {15},
number = {2},
pages = {118343},
pmid = {42395675},
issn = {2220-6124},
abstract = {BACKGROUND: The gut microbiota (GM) plays an important role in chronic kidney disease (CKD) progression, and dialysis modalities can differentially impact the GM composition and function. There is also limited information on the GM in Arab populations.

AIM: To investigate the distinct microbial profiles and functional alterations associated with hemodialysis (HD) and peritoneal dialysis (PD) in a Saudi Arabian cohort.

METHODS: We performed whole-genome metagenomic sequencing on fecal samples from 189 participants (controls and CKD, HD, and PD patients).

RESULTS: We detected distinct microbial profiles across all patient groups compared with that of the controls. Microbial risk scores derived from differentially abundant taxa accurately distinguished CKD, PD, and HD patients from controls, with area under the curves exceeding 0.9. Compared with HD patients, PD patients exhibited reduced species richness, an increased abundance of opportunistic pathogens (particularly Proteobacteria), and increased virulence. Functional analysis revealed suppressed energy metabolism and activated proinflammatory pathways in PD patients. Cooccurrence network analysis demonstrated decreased microbial community resilience in PD patients, with increased Proteobacteria interactions. Conversely, the HD group showed partial recovery of microbial balance and beneficial metabolic functions, including increased short-chain fatty acid metabolism and reduced lipopolysaccharide biosynthesis.

CONCLUSION: The findings of this study highlight the potential of the microbial profile as a robust biomarker for CKD classification and underscore the differential impacts of different dialysis modalities.},
}

@article {pmid42395905,
year = {2026},
author = {Li, H and Li, N and Wang, C and Yang, J and Dong, Z and Cai, Z and Li, J and Chen, Y and Zheng, J and Zhu, J},
title = {Dysbiosis and unsustainable delayed gut microbiota development as non-invasive biomarkers for predicting autism spectrum disorder in Chinese children.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753665},
pmid = {42395905},
issn = {1664-302X},
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social impairment, restricted interest, repetitive behavior, and stereotypical behavioral patterns. Diagnosing ASD presents considerable challenges; a previous large-sample study in children linked ASD and intestinal flora imbalances.

METHODS: To explore the composition and functional changes of the gut microbiota in children with ASD, shotgun metagenomic sequencing was used to evaluate the gut microbiota of 78 Chinese children (34 with ASD and 44 with typical development [TD] children).

RESULTS: We observed differences in the gut microbiota composition and richness between children with ASD and TD in this cohort. The α-diversity of the gut microbiota in the ASD group fluctuated more with age than that in the TD group, based on cross-sectional data. Age-related dynamic changes in the gut bacteria of TD children were not clearly observed in children with ASD. Gut microbiota of children with ASD showed a higher number of antibiotic resistance genes compared to TD. Additionally, the functional gene pathways related to carbohydrate-active enzymes and amino acid metabolism and synthesis appeared reduced in the ASD group.

DISCUSSION: This exploratory study describes key compositional and functional characteristics of the gut microbiota in Chinese children with ASD. Our preliminary findings identify differential bacterial taxa that may be considered as potential candidates for further investigation as fecal markers, and suggest differences in age-related gut microbiota patterns between ASD and TD children. However, due to the modest sample size, cross-sectional design, and lack of external validation, these results should be regarded as a preliminary exploration and require confirmation in larger, independent cohorts.},
}

@article {pmid42396176,
year = {2026},
author = {Deb, D and Liguori, F and Shuster, BM and Huang, R and Shoreibah, S and Wang, S and Rojas Ocampo, NE and Murray, KP and Danino, T},
title = {Toward development of soil-derived Bacillus isolates as lung cancer cytotoxic agents.},
journal = {Biodesign research},
volume = {8},
number = {2},
pages = {100074},
pmid = {42396176},
issn = {2693-1257},
abstract = {The wide-ranging impact of the human microbiome on health and disease has sparked growing interest in employing bacteria as live therapeutics. Natural properties of bacteria have been enhanced using synthetic biology to treat diverse diseases, from infections to inflammation and cancer. However, a major obstacle in this area is identifying specific bacterial hosts and molecular payloads that are both safe and effective for specific diseases or cancers. In this study, we explored environmental microbial diversity as a promising source of new therapeutic agents that could be engineered for bacterial drug delivery systems. We collected and characterized soil bacteria from 25 urban public parks, then evaluated their secreted metabolites for anti-cancer activity using both monolayer and three-dimensional spheroid models of lung cancer. Metagenomic analysis, toxicity profiling, and co-culture assays revealed that several Bacillus species isolated from Manhattan park soils produced compounds with strong, dose-dependent cytotoxic effects on lung cancer cells. Furthermore, we demonstrated that Bacillus subtilis-a well-characterized, gram-positive model organism-was capable of colonizing lung tumor spheroids, suggesting its potential as a safe and effective chassis for bacterial cancer therapy. Complementing these experiments, we developed a mechanistic ordinary differential equation (ODE) model of the bacteria-spheroid co-culture that is consistent with our bacterial and spheroid growth data. Overall, our findings highlight a discovery platform for the screening of environmental microbes as chassis or payload sources for microbial cancer therapies.},
}

@article {pmid42396177,
year = {2026},
author = {Ross, DAN and Lauzon, J and Makarenkov, V and Kembel, SW},
title = {Metagenome-assembled genomes from the temperate forest phyllosphere in Eastern Canada.},
journal = {Access microbiology},
volume = {8},
number = {7},
pages = {},
pmid = {42396177},
issn = {2516-8290},
abstract = {The phyllosphere is host to diverse microbial communities surviving in dynamic environmental conditions and which form important relationships with their hosts. Here, we constructed metagenome-assembled genomes (MAGs) from 25 temperate forest phyllosphere samples collected in Eastern Canada. We found 423 dereplicated MAGs with completeness ≥50% and contamination ≤10%, using a combination of co-assembly strategies. The MAGs were predominantly classified into the bacterial phyla Pseudomonadota (n=197), Actinomycetota (n=88) and Acidobacteriota (n=50) and included two archaeal MAGs in the phylum Thermoproteota. These genomes can help to improve reference database entries of phyllosphere-affiliated microbes, increasing our understanding of phyllosphere microbial phylogenomic and community dynamics and the ecological roles of phyllosphere microbiomes.},
}

@article {pmid42396572,
year = {2026},
author = {Campos, PE and Collins, PC and Ruane, A and Carlsson, JE and Carlsson, J},
title = {Instance of a Heteroplasmic Mitogenome in Alvinocaridid Shrimp Mirocaris fortunata (Martin & Christiansen 1995) Found at the Moytirra Deep-Sea High-Temperature Hydrothermal Vent Field.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e73956},
pmid = {42396572},
issn = {2045-7758},
abstract = {In this study, we report the complete mitochondrial genome of the deep-sea hydrothermal vent shrimp Mirocaris fortunata (Alvinocarididae) from shotgun sequencing data on an individual tail tissue. The 15,923-bp-long sequence displays 98.72% pairwise identity with its closest relative, Mirocaris indica. A significant proportion of the mitochondrial genome (0.63%) corresponds to heteroplasmic sites that were found on 14 of the 37 genes, including cox1, though all such sites induce synonymous mutations. This level of heteroplasmy may serve as the first step for recombination of the mitogenome by paternal leakage and/or a less effective purifying selection in somatic tissues. We also take advantage of the shotgun deep sequencing strategy to assess the metagenomic composition of the sample and are able to detect other deep-sea hydrothermal vent species present at the vent system.},
}

@article {pmid42397430,
year = {2026},
author = {Liu, Y and Jiang, W and Wang, J and Cheng, S and Cheng, C and Zhang, C and Zhang, J and Liu, C and Zhao, J and Wang, H},
title = {A special multifiber dietary mixture ameliorates Crohn's-like colitis in an IL-10[-]/[-] mouse model by promoting treg differentiation through the ETS1/RUNX1/Foxp3 axis.},
journal = {European journal of nutrition},
volume = {65},
number = {5},
pages = {},
pmid = {42397430},
issn = {1436-6215},
mesh = {Animals ; Proto-Oncogene Protein c-ets-1/metabolism/genetics ; *T-Lymphocytes, Regulatory/metabolism ; Mice ; *Crohn Disease/diet therapy/metabolism ; *Colitis/diet therapy ; Forkhead Transcription Factors/metabolism/genetics ; *Interleukin-10/genetics/metabolism/deficiency ; Disease Models, Animal ; Cell Differentiation/drug effects ; Core Binding Factor Alpha 2 Subunit/metabolism/genetics ; Mice, Knockout ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory disorder characterized by immune dysregulation. Regulatory T cells (Tregs) play a pivotal role in maintaining mucosal tolerance, and their dysfunction directly contributes to CD pathogenesis.

METHODS: We used interleukin-10[-]/[-] mice to evaluate the therapeutic effects of a special multifiber mixture (MF) on colitis. T cell phenotypes, transcriptional profiles, gut microbiota composition, and N[6]-methyl adenosine (m6A) ribonucleic acid (RNA) methylation were analyzed using flow cytometry, RNA sequencing, metagenomics, and methylated RNA immunoprecipitation-quantitative polymerase chain reaction.

RESULTS: MF significantly reduced intestinal inflammation, restored epithelial barrier function, and promoted Treg differentiation while suppressing Th1/Th17 polarization. Integrated transcriptomic and proteomic analyses identified ETS1 as a negative regulator of Treg differentiation, modulated by gut microbiota-derived S-adenosylmethionine (SAM) through methyltransferase-like protein 3-mediated m6A methylation. MF feeding reduced SAM levels and m6A enrichment on ETS1 messenger RNA, leading to decreased ETS1 expression. Silencing of ETS1 enhanced Foxp3 expression and expanded the Treg population. RUNX1 was identified as a functional interactor of ETS1, with reciprocal expression patterns validated in both mouse models and colonic tissues from patients with CD.

CONCLUSION: MF alleviates colitis by reshaping the gut microbiota and suppressing SAM-dependent m6A methylation, resulting in ETS1 downregulation and the restoration of Treg homeostasis through the ETS1/RUNX1/Foxp3 axis. These findings reveal a mechanistic link between microbiota, epigenetics, and immunity, highlighting MF feeding as a promising nutritional intervention for CD treatment.},
}

Animals
Proto-Oncogene Protein c-ets-1/metabolism/genetics
*T-Lymphocytes, Regulatory/metabolism
Mice
*Crohn Disease/diet therapy/metabolism
*Colitis/diet therapy
Forkhead Transcription Factors/metabolism/genetics
*Interleukin-10/genetics/metabolism/deficiency
Disease Models, Animal
Cell Differentiation/drug effects
Core Binding Factor Alpha 2 Subunit/metabolism/genetics
Mice, Knockout
Mice, Inbred C57BL
Gastrointestinal Microbiome
Male

@article {pmid42397535,
year = {2026},
author = {Sharma, R and Gupta, V and Pal, V and Sen, J and Meghvansi, MK and Goel, AK},
title = {Influence of inoculum-to-substrate ratio on process stability and microbial community structure in anaerobic digestion of human faecal matter.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42397535},
issn = {1614-7499},
abstract = {Anaerobic digestion is a pivotal technology for modern sanitation. This study investigates the impact of inoculum-substrate ratio (ISR) on anaerobic digestion of human faecal matter (HFM). To determine the anaerobic digestion efficiency of HFM, the experiments were conducted using an automatic biomethane potential test system with ISRs ranging from 0.33 to 3. Higher ISRs (1, 2, and 3) resulted in improved volatile solids reduction, increased hydrolysis rates, and higher cumulative methane production compared to lower ISRs. Kinetic modelling revealed that an ISR of 3 exhibited the highest hydrolysis rate constant and shortest lag phase. Analysis of volatile fatty acids showed that higher ISRs mitigated acid accumulation and maintained pH stability. Microbial community analysis demonstrated shifts in bacterial and archaeal populations across different ISRs, with higher ratios fostering greater diversity and abundance of hydrolytic and methanogenic microorganisms. The findings offer essential insights for enhancing the anaerobic digestion of HFM, promoting sustainable waste management and renewable energy production.},
}

@article {pmid42397700,
year = {2026},
author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D},
title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001778},
pmid = {42397700},
issn = {2057-5858},
mesh = {Humans ; *Enterococcus faecium/genetics/isolation & purification/classification ; *Vancomycin-Resistant Enterococci/genetics/isolation & purification/classification ; *Metagenomics/methods ; *Gram-Positive Bacterial Infections/microbiology/transmission ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Metagenome ; },
abstract = {Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity and can miss transmission involving low-abundance and co-colonizing strains. Here, we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures obtained between 2020 and 2025 at a single hospital. GI tract populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters including 6 clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.},
}

Humans
*Enterococcus faecium/genetics/isolation & purification/classification
*Vancomycin-Resistant Enterococci/genetics/isolation & purification/classification
*Metagenomics/methods
*Gram-Positive Bacterial Infections/microbiology/transmission
Gastrointestinal Tract/microbiology
Genetic Variation
Metagenome

@article {pmid42397950,
year = {2026},
author = {Karthik, Y and Nanjareddy, K and Arthikala, MK},
title = {Deciphering soybean-microbiome interactions: from rhizosphere dynamics to sustainable yield enhancement.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2693436},
doi = {10.1080/15592324.2026.2693436},
pmid = {42397950},
issn = {1559-2324},
mesh = {*Glycine max/microbiology/growth & development/metabolism ; *Rhizosphere ; *Microbiota/physiology ; Soil Microbiology ; Plant Roots/microbiology ; },
abstract = {The soybean plant (Glycine max L.) is an important crop for valuable food source because of its high levels of protein and oil, thus contributing greatly to a sustainable system for producing food through biological nitrogen fixation. Recent research supports the theory that the soybean-associated microbiome located in the rhizosphere is a crucial regulatory mechanism governing plant growth, nutrient acquisition, and stress tolerance. Additionally, advances in metagenomics, metatranscriptomics, metabolomics, and root exudate profiling via LC‒MS have shown that soybean roots alter the microbial communities found in their rhizosphere by utilizing dynamic chemical signaling and targeted microbial recruitment, thereby enhancing the ecological interpretation of the processes that drive microbiome assembly. Microbial consortia (AMF & PGPR) assess cycling through nutrients, phytohormones, suppressing diseases, as well as having a legacy effects on the productivity of agroecosystems. Factors such as plant genotype, physical and chemical soil properties, and environmental conditions greatly affect the assembly and functioning of the soybean microbiome, thus this is difficult to transfer this information to field applications. Unlike previous reviews focused primarily on biological nitrogen fixation, this review integrates recent advances in multi-omics technologies, species-level microbiome characterization, root exudate chemistry, microbiome-assisted breeding, and translational microbiome engineering approaches to provide a systems-level perspective of soybean-microbiome interactions. while also identifying significant knowledge gaps and future areas of research within this aspect of agriculture.},
}

*Glycine max/microbiology/growth & development/metabolism
*Rhizosphere
*Microbiota/physiology
Soil Microbiology
Plant Roots/microbiology

@article {pmid42397959,
year = {2026},
author = {Umezawa, K and Tsuji, JM and Tani, Y and Nohara, S and Amann, RI and Fukui, M},
title = {Isolation of Allocrenothrix methanica reveals distinct ecophysiologies of filamentous methanotrophs and adaptations to O2 limitation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag178},
pmid = {42397959},
issn = {1751-7370},
abstract = {Ferdinand Cohn observed abundant filamentous bacteria in drinking water wells in 1870 that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metabolism of Crenothrix bacteria and their disproportionately high activity in stratified lakes compared to unicellular methanotrophs, yet laboratory cultivation has proven elusive, leaving the ecophysiology of Crenothrix bacteria largely unknown. Here we report the isolation of two methanotrophic strains of the "lacustrine Crenothrix" clade from an iron-rich wetland and reveal their unique cell biology and ecology. We demonstrate that the strains are microaerobic and grow as filaments of cells, which are connected by unidirectionally oriented structures. The strains have broad genomic repertoires for addressing O2 limitation that are uniquely associated with lacustrine Crenothrix compared to related clades based on genome data. Aligning with laboratory observations, we identify lacustrine Crenothrix bacteria along potential redox gradients in the wetland at iron-rich snow sites, and we also detect such bacteria in diverse global ecosystems based on public metagenome searches. Together, our data strongly point to an ecophysiology of lacustrine Crenothrix bacteria that is tightly linked to O2 limitation, and we propose that the strains uniquely store or share metabolic intermediates between cells in filaments to thrive under such conditions. Our cultivation-based findings for these strains, which we name Allocrenothrix methanica, provide new insights into the diversity, evolution, and ecology of filamentous methanotrophs, connecting over 150 years of microbiology research and opening vast new opportunities to investigate bacteria contributing to the global methane cycle under O2 limitation.},
}

@article {pmid42398003,
year = {2026},
author = {Robinson, CRP and Dolezal, AG and Liachko, I and Newton, ILG},
title = {Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.},
journal = {Genome biology and evolution},
volume = {18},
number = {7},
pages = {},
doi = {10.1093/gbe/evag152},
pmid = {42398003},
issn = {1759-6653},
support = {//Costco/Project Apis m/ ; 2005306//NSF IOS Collaborative Research/ ; 2022049//NSF DBI Biology Integration Institutes/ ; //Bill and Melinda Gates Foundation to Phase Genomics/ ; },
mesh = {Animals ; Bees/virology/microbiology ; *Bacteriophages/genetics ; *Host Specificity/genetics ; Genetic Variation ; Evolution, Molecular ; Genome, Viral ; Phylogeny ; Selection, Genetic ; Metagenome ; },
abstract = {Bacteriophages can evolve rapidly. Mutation and recombination via horizontal gene transfer allow them to counter adaptive responses by microbial hosts. However, little is known about the genomic processes underlying phage evolution within an ecological context-especially within natural microbial communities. This is due in part to the difficulty in resolving aspects of phage ecology, such as host range. To better understand the interplay of phage ecology and evolution within natural microbial communities, we combined measures of phage host range in vivo with measures of genome evolution in order to infer the evolutionary pressures acting on phage genomes within individual honeybee worker microbiomes. We show that near-identical phage genomes, cooccurring across multiple honeybee colonies, exhibit large variation with respect to gene modules, despite retaining a highly similar core genome. Estimates of genic diversity suggest deviations from neutral evolutionary models and identify loci under putative diversifying selection. We then use HiC-resolved metagenomics and show that the honeybee gut contains a dense phage community that exhibits a wide degree of host range variation. This variation differed across individual metagenomes in both the number and phylogenetic distance of potential hosts. We show that common measures of genetic variation positively correlate with host range in bee-associated phages and that functional targets of diversifying selection are partitioned differently between broad or narrow host range phages. Our work underscores the high host range variation associated with phages within host-associated microbial communities and provides evidence that this variation impacts rates of phage evolution.},
}

Animals
Bees/virology/microbiology
*Bacteriophages/genetics
*Host Specificity/genetics
Genetic Variation
Evolution, Molecular
Genome, Viral
Phylogeny
Selection, Genetic
Metagenome

@article {pmid42398208,
year = {2026},
author = {Yi, Y and Li, D and Li, Y and Wang, H and Yang, D and Yang, S and Xing, S and Wei, S and Yang, J and Guo, H and Luo, Z},
title = {Abrus cantoniensis α-glucan-like polysaccharide alleviates influenza via gut microbial acetate to activate free fatty acid receptor 2/ mitochondrial antiviral signaling protein/interferon-beta pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {159},
number = {},
pages = {158533},
doi = {10.1016/j.phymed.2026.158533},
pmid = {42398208},
issn = {1618-095X},
abstract = {BACKGROUND: The gut microbiota is critical for host defense against influenza. Polysaccharides are known for their microbiota-modulating and immunomodulatory activities; however, the anti-influenza efficacy of homogeneous Abrus cantoniensis polysaccharides (ACP) remains unexplored.

PURPOSE: The present study seeks to clarify the protective role of ACP in influenza and explore its underlying molecular mechanisms.

METHODS: Initially, crude polysaccharides were extracted via ethanol precipitation and subsequently purified by gel chromatography. Systematic structural characterization of ACP was then performed using carbohydrate chemistry techniques, including scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), ultraviolet (UV) spectroscopy, and nuclear magnetic resonance (NMR). The therapeutic efficacy of ACP was assessed by monitoring various indicators such as body weight, survival rate, viral load, and pulmonary pathological changes in mouse models. Furthermore, to elucidate the biological mechanism underlying ACP's anti-influenza activity via regulation of pulmonary interferon-beta (IFN-β) immune networks by intestinal acetate-producing microbiota, multi-omics analyses integrating metagenomics, metabolomics, gene knockout, immunofluorescence, and Western blot were conducted. Finally, the potential anti-influenza effects of ACP via the gut-lung axis were evaluated based on in vivo and in vitro detection of protein expression of IFN-β, free fatty acid receptor 2 (FFAR2), and mitochondrial antiviral signaling protein (MAVS), as well as antiviral interferon-stimulated genes (ISGs).

RESULTS: In this study, we purified a novel polysaccharide, ACP-A1, with a backbone of→4)-α-D-Glcp-(1→,→4)-β-D-Galp-(1→, and →4,6)-α-D-Glcp-(1→ linkages and α-D-Glcp-(1→ branches at O-6. In H1N1-infected mice, oral ACP-A1 alleviated weight loss, increased survival, and reduced lung inflammation and viral load. Metagenomic and targeted metabolomic analyses showed that ACP-A1 enriched Limosilactobacillus reuteri and elevated acetate levels. Fecal microbiota transplantation, FFAR2 inhibition, and MAVS knockout experiments demonstrated that ACP-A1 enhances the FFAR2/MAVS/IFN-β antiviral pathway via microbial-derived acetate.

CONCLUSION: Collectively, our findings elucidate that ACP mitigates influenza virus-induced lung dysfunction by promoting the proliferation of acetate-producing gut microbiota, particularly Limosilactobacillus reuteri, and activating the FFAR2/MAVS/IFN-β antiviral axis in pulmonary immune cells. These findings establish ACP-A1 as a natural polysaccharide regulating IFN-β homeostasis, highlighting its potential for influenza prevention.},
}

@article {pmid42398246,
year = {2026},
author = {Zhang, Y and Tang, Z and Shangguan, H and Zhu, R and Xie, A and Huang, Q and Su, J and O'Connor, P and Jiang, Y and Sun, X},
title = {Invasive giant African snails as potential reservoirs of antimicrobial resistance and bacterial pathogens in urban park.},
journal = {Journal of environmental management},
volume = {413},
number = {},
pages = {130396},
doi = {10.1016/j.jenvman.2026.130396},
pmid = {42398246},
issn = {1095-8630},
abstract = {Urban parks serve millions of visitors annually, yet antimicrobial resistance (AMR) surveillance programs rarely consider invasive species as environmental reservoirs. Here, we investigated antibiotic resistance genes (ARGs) and potential zoonotic pathogens in invasive giant African snails (Lissachatina fulica) across 23 urban parks in Xiamen, China, with comparative analysis of dog feces and earthworm casts collected from the same parks. Metagenomic profiling revealed that snails harbored extensive ARG diversity (1222 subtypes) comparable to dogs (1,393) and substantially exceeding earthworms (492), with 936 ARG subtypes shared between invasive snails and dogs. Invasive snails also carried substantial relative abundances of potential zoonotic pathogens (mean 15.7% relative abundance), including clinically relevant taxa such as Escherichia, Pseudomonas, and Enterococcus. Phenotypic testing of representative isolates confirmed the presence of antibiotic-resistant bacteria in snail and dog fecal samples. The convergence of broad ARG diversity, substantial potential zoonotic pathogen burdens, and coprophagous behavior suggests that invasive snails may represent previously unmonitored environmental hosts associated with AMR in urban parks. Field observations of snails consuming dog feces, together with the greater resistome similarity between snails and dogs than between snails and earthworms, are consistent with exposure to animal feces as a potential source of ARGs. This study underscores the need to integrate invasive species into One Health AMR surveillance and urban environmental management strategies.},
}

@article {pmid42398311,
year = {2026},
author = {Guleria, A and Bagal, D and Mishra, S and Mehrotra, S and Srivastava, V},
title = {Phytomicrobiome-based approaches for sustainable crop performance and environmental resilience.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128605},
doi = {10.1016/j.micres.2026.128605},
pmid = {42398311},
issn = {1618-0623},
abstract = {The plant microbiome refers to the dynamic microbial communities including bacteria, fungi, protists, viruses, and nematodes that colonize diverse plant tissues and coevolve intimately with their host. The primary objective of microbiome engineering is to improve plant performance by enhancing tolerance to biotic and abiotic stresses, increasing plant fitness, and boosting crop productivity. By discovering the modern approaches and plant-microbe interactions, many experts can design artificial microbial consortia and other biotechnological tools suited to specific crops and environmental conditions. Therefore, in current work special attention is given to the goals, applications, and advanced tools-such as genome editing, synthetic biology, metagenomics, and AI-driven modelling used to optimize plant-microbe interactions for sustainable agriculture and ecosystem restoration. Further, recent advances in ecological, biochemical, and molecular approaches have also introduced a new paradigm for addressing microbiome-based challenges in agricultural management. In this context, microbiome engineering has emerged as a promising biotechnological strategy aimed at the targeted addition, removal, or modification of microbial community traits to achieve greater specificity and efficacy.},
}

@article {pmid42398436,
year = {2026},
author = {Funk, T and Zaheer, R and Wobeser, B and Conrad, C and McLeod, L and Gow, S and Otto, SJG and Waldner, CL and McAllister, T},
title = {Evaluating detection of Histophilus somni immunoglobulin-binding protein A DR2 Fic: A species-specific gene target for recombinase polymerase amplification relative to long-read sequencing of respiratory samples from feedlot calves.},
journal = {Research in veterinary science},
volume = {210},
number = {},
pages = {106315},
doi = {10.1016/j.rvsc.2026.106315},
pmid = {42398436},
issn = {1532-2661},
abstract = {Histophilosis is an important cause of morbidity and mortality as well as antimicrobial use in feedlot cattle across North America. Detection of Histophilus somni by culture is challenging, and there is no standardized tool for distinguishing isolates that carry virulence factors most likely to contribute to disease. The DR2 repeat of H. somni-associated virulence factor 'immunoglobulin-binding protein A' (ibpA DR2) harbors a Fic domain that mediates host cell cytotoxicity and is essential for histophilosis. For rapid detection of ibpA DR2 in extracted DNA, we developed a real-time recombinase polymerase amplification (RPA) assay with a runtime of 24 min at 39 °C. DNA from H. somni-RPA-positive respiratory swabs (n = 73) was screened for ibpA DR2 using the novel RPA assay and long-read metagenomic sequencing, as well as nanopore whole-genome sequencing (WGS) of H. somni isolated from the same samples. IbpA DR2 was identified in 71% and 70% of tested samples using RPA and WGS, respectively, and in ≤41% of samples using metagenomic sequencing. The likelihood of detection by RPA did not differ (OR 1.1, 95% CI (0.42, 2.9), P > 0.99) from WGS; however, agreement between these assays was only fair (κ = 0.31). Conversely, RPA (OR 3.4, 95% CI (1.6, 8.2)) and WGS (OR 8.0, 95% CI (2.4, 42)) were more likely (P < 0.001) to detect ibpA DR2 than metagenomic sequencing, likely reflecting limited coverage of H. somni by metagenomics. This study demonstrated that RPA and long-read WGS detected ibpA DR2 with similar frequencies in extracted DNA and H. somni isolates, respectively. Further testing of non-target isolates confirmed the analytical specificity of ibpA DR2 to H. somni. Further investigation of the diagnostic validity for RPA-based ibpA DR2 detection is required in a larger cohort of field samples, as a rapid screening tool for H. somni most likely to contribute to disease.},
}

@article {pmid42398457,
year = {2026},
author = {Fonseca, A and Kenney, S and Bierly, S and Boney, J and Ganda, E},
title = {Assessing the impact of dietary interventions on the resistomes of broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107343},
doi = {10.1016/j.psj.2026.107343},
pmid = {42398457},
issn = {1525-3171},
abstract = {Antimicrobial resistance (AMR) is a major One Health concern, and while natural feed additives such as probiotics and phytotherapeutics are increasingly used as alternatives to antimicrobial growth promoters (AGPs) in poultry production, their potential effects on the selection of antibiotic resistance genes remain poorly understood. Therefore, our objective was to characterize the effects of a probiotic and an essential oils blend on the broiler resistome. Cobb 500 1-day-old chicks (N=320) were randomly allocated in 32 cages, with eight replicates of ten broilers per cage per treatment and were raised until day 21. Treatments consisted of four diets: a basal diet (negative control), a basal diet with Bacitracin Methylene Disalicylate (BMD) at 50 g/ton, a basal diet with an essential oil blend at 100 g/ton, and a basal diet with a probiotic (Bacillus subtilis) at 226.8 g/ton. Excreta samples were collected at three-time points (1, 10, and 21 days) to characterize broilers' resistome. The DNA extracted from these samples was sequenced using shotgun metagenomics on the NovaSeq platform and statistical analyses were done using Kruskal-Wallis and PERMANOVA to assess gene diversity. Across all samples, 823 unique ARGs were identified. These genes spanned a broad spectrum of classes, including multi-compound, metals, drugs, and biocides resistance. No significant differences in alpha diversity of these genes (P = 0.51) were observed between treatment groups; however, AMR gene diversity varied by age (P < 0.001). A statistically significant difference was observed in beta diversity across ages (P = 0.001), but not between treatments (P = 0.95). While age impacted AMR gene diversity, under our experimental conditions, antibiotics or other in-feed additives did not significantly alter broiler resistomes. This study advances poultry AMR surveillance by demonstrating that resistome diversity and composition in broiler chickens are predominantly shaped by age-dependent microbial succession, while neither in-feed antibiotics nor non-antibiotic feed additives induced persistent or treatment-specific alterations in ARG profiles under the conditions tested.},
}

@article {pmid42398478,
year = {2026},
author = {Gao, Q and Hou, J and Ding, W and Qi, C and Xu, D and Zhou, C and You, G},
title = {Carbon-to-nitrogen stoichiometry shapes divergent intracellular and extracellular antibiotic resistance gene fates through a dissolved organic matter-extracellular polymeric substance-mobile genetic element cascade in cyanobacteria-bacteria co-cultures.},
journal = {Water research},
volume = {304},
number = {},
pages = {126390},
doi = {10.1016/j.watres.2026.126390},
pmid = {42398478},
issn = {1879-2448},
abstract = {The carbon-to-nitrogen (C:N) ratio constrains microbial metabolism, yet whether nutrient stoichiometry controls the differential fates of intracellular (iARGs) versus extracellular antibiotic resistance genes (eARGs) remains unknown. This study aimed to test whether C:N ratios approaching the bacterial threshold elemental ratio (TER) would maximize iARG enrichment through a dissolved organic matter (DOM)-extracellular polymeric substance (EPS)-mobile genetic element (MGE) cascade, while eARG dynamics would be governed by physicochemical processes. Cyanobacteria-bacteria co-cultures at four C:N ratios (5:1, 10:1, 20:1, 40:1) were analyzed using shotgun metagenomics, FTICR-MS, 3D-EEM, untargeted metabolomics, and EPS fractionation. C:N = 10:1 produced the highest iARG abundance (65.1 ± 17.4 TPM, mean ± SD) and a 17-fold iARG/eARG ratio, while eARG showed no significant treatment effect (Kruskal-Wallis p = 0.082, treating triplicate subsamples as observations). FTICR-MS revealed the lowest intensity-weighted O/C (0.334), most negative NOSC (-0.67), and highest molecular diversity (8029 formulas) at C:N = 10:1, indicating a uniquely reduced, aliphatic-enriched DOM pool. (Note: FTICR-MS samples were pooled from triplicate subsamples per treatment, yielding one composite per C:N level; these results are therefore descriptive and unreplicated.) EPS polysaccharide/protein ratios peaked at 2.8, correlating with iARG across treatments (ρ=0.91, p < 0.001) but inversely with eARG (ρ=-0.59, p = 0.044). Guanosine (ppGpp precursor) peaked at C:N = 10:1 (ρ=0.75 with iARG) while UDP-glucose was depleted, confirming active EPS biosynthesis. Piecewise structural equation modeling identified a pathway from C:N through DOM, EPS, and MGE to iARG (R[2]=0.78, Fisher's C p = 0.31), whereas eARG depended on eDNA physicochemical trapping (R[2]=0.41). These findings provide evidence that nutrient stoichiometry acts as a selective control on ARG partitioning, suggesting that C:N monitoring could be incorporated into eutrophic water ARG risk assessment.},
}

@article {pmid42398553,
year = {2026},
author = {Xu, J and Zhang, X and Sun, W and Zhang, X and Wu, P and Wang, A},
title = {Hydroxylamine steers nitrogen metabolism toward dissimilatory nitrate reduction to ammonium by suppressing competitive denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135307},
doi = {10.1016/j.biortech.2026.135307},
pmid = {42398553},
issn = {1873-2976},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is important for nitrogen conservation and resource recovery in wastewater treatment, but its efficiency is often limited by competition for electrons and substrates from denitrifiers. Although hydroxylamine (NH2OH) has been shown to modulate various nitrogen transformation processes, its long-term effects on DNRA systems and the underlying microbial ecological responses remain unclear. In this study, the nitrogen transformation performance, electron transfer characteristics, and microbial community succession in DNRA systems were comprehensively investigated under prolonged exposure to 0-5 mg/L NH2OH. The results demonstrated that, with increasing NH2OH concentrations, the system consistently achieved near-complete nitrate removal without nitrite accumulation, and the effluent NH4[+]-N reached up to 51.5 mg/L, indicating a substantial enhancement of DNRA ammonium production. Functional activity analyses and apparent electron-equivalent balance suggested an increased contribution of DNRA to nitrate-reduction-associated electron consumption. Metagenomic analyses further showed that NH2OH could decrease the relative abundances of denitrification-related genes, including nirS, norB, and nosZ, while increasing those of narG and the nrf gene cluster. Building upon the existing DNRA functionality, NH2OH selectively enriched a tolerant DNRA population, exemplified by Ignavibacteriota, and facilitated cross-feeding interactions and electron transfer network remodeling involving fermentative bacteria. Collectively, these findings suggest that NH2OH can weaken denitrification competition and increase the apparent contribution of DNRA to nitrate-reduction-associated electron consumption, thereby enhancing ammonium production. Moreover, these findings may provide a theoretical basis for the future development of DNRA-Anammox coupled processes for high-level nitrogen removal.},
}

@article {pmid42398606,
year = {2026},
author = {Liu, J and Liu, Y and Zheng, Y and Wang, H and Wang, J and Zhang, Y and Wang, K},
title = {Intestinal metabolic characteristics of Smilax china L. pectic polysaccharide and prediction of its gut microbiota-mediated mechanism.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153348},
doi = {10.1016/j.ijbiomac.2026.153348},
pmid = {42398606},
issn = {1879-0003},
abstract = {This study aimed to investigate the intestinal metabolic characteristics and mechanisms of the pectic polysaccharide isolated from the medicinal plant Smilax china L. (SCLP). Firstly, in vitro simulated digestion confirmed that SCLP remained stable in simulated digestive fluids. Subsequently, in vivo real-time tracking of intestinal metabolism based on fluorescent labeling revealed that SCLP maintained its prototype in the small intestine and began to be degraded into fragments (Mw < 4000 Da) upon reaching the cecum and colon, where it was retained for prolonged periods. Pseudo-sterile mouse experiments indicated the mediating role of gut microbiota in SCLP metabolism. Furthermore, metagenomic sequencing suggested that SCLP increased the proportion of polysaccharide utilization loci (PULs) from Phocaeicola vulgatus and Bacteroides uniformis, elevated the gene numbers of carbohydrate-active enzymes (CAZymes) including GHs, GTs and CBMs, and activated pathways of carbohydrate metabolism. Finally, in vitro bacterial culture study verified the degradation and utilization of SCLP by Phocaeicola vulgatus and Bacteroides uniformis. In summary, this work elucidates the intestinal metabolic profile of SCLP, providing valuable insights for its further development and utilization.},
}

@article {pmid42398615,
year = {2026},
author = {Majeed, A and Javaid, MH and Mahreen, N and Hussain, M and Kang, Y and Hussain, K and Su, J},
title = {Nucleic acid and multi-omics approaches for understanding plant-microbiome interactions in grassland ecosystems.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153356},
doi = {10.1016/j.ijbiomac.2026.153356},
pmid = {42398615},
issn = {1879-0003},
abstract = {Grasslands are among the largest terrestrial biomes and play essential roles in livestock production, carbon sequestration and global food security. The productivity and resilience of these ecosystems are driven by complex molecular interactions between plants and their associated microbiomes. Although recent advances in nucleic acid research and multi-omics approaches have provided new insights into these interactions, the molecular mechanisms underpinning plant-microbiome interactions in these ecosystems remain insufficiently explored. This review synthesizes the latest progress in nucleic-acid and multi-omics approaches to better understand plant-microbiome interactions. It integrates nucleic acid-based technologies with multi-omics frameworks to explain plant-microbiome interactions across molecular, ecological, and management scales. By linking microbial community structure, functional genes, gene expression, metabolite profiles, ecosystem multifunctionality and sustainable grassland management, this review provides a broader framework for translating molecular insights into practical strategies for grassland resilience, productivity, and food security. Advances in amplicon sequencing, shotgun and long-read metagenomics, environmental DNA (eDNA) monitoring, plant and microbiome genome-wide association studies (GWAS) and transcriptomics have provided valuable insights into plant-microbiome interaction. This review highlights how these techniques enable functional and mechanistic understanding by linking microbial diversity with gene expression, nutrient cycling and plant performance. Additionally, long-read sequencing technologies provide genome-resolved analysis, improving the detection of structural and epigenetic variations, which are essential for understanding these interactions. These approaches reveal the role of beneficial microbes in enhancing grassland fertility, ultimately improving grassland productivity. Integrating these findings with metabolomics and phenomics offers a novel approach for predictive modeling in sustainable grassland management. The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.},
}

@article {pmid42399247,
year = {2026},
author = {Liao, H and Cui, HX and Chen, LX and Duan, CS and Li, J and Zhao, S and Zhu, YG and Su, JQ},
title = {Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75234-y},
pmid = {42399247},
issn = {2041-1723},
abstract = {Glacier forelands undergo a transition from oligotrophic to eutrophic conditions during primary succession. Reduced sulfur compounds may serve as an energy source for early microbial colonizers, yet the sulfur oxidation potential and key taxa remain largely unknown. Here, we perform a multi‑omics survey across a 130‑year chronosequence on the Tibetan Plateau. Glacial retreat profoundly reshapes both viral communities (61,394 viral operational taxonomic units, vOTUs) and microbial communities (404 metagenome‑assembled genomes, MAGs). Notably, Oxidative Dissimilatory sulfite reductase (Dsr) operon‑encoding Sulfur‑Oxidizing Bacteria (ODSOB) were specifically enriched within the first 1-5 years after retreat. Their associated viruses predominantly follow a "piggyback‑the‑winner" strategy, influencing host cold shock protein evolution and potentially modulating sulfur oxidation via iron‑sulfur (Fe‑S) cluster assembly. Metatranscriptomics reveals elevated expression of the oxidative Dsr operon and Form‑I ribulose‑1,5‑bisphosphate carboxylase/oxygenase (RubisCO) in early stages, coinciding with higher sulfate, sulfite, sulfide, and dissolved inorganic carbon (DIC)‑to‑dissolved carbon ratios compared to later stages. These findings indicate that ODSOB support DIC fixation and sulfide detoxification during early ecosystem development. Collectively, this study uncovers the eco‑evolutionary dynamics between viruses and microbes in developing ecosystems and provides genomic and functional evidence for ODSOB as key drivers of soil formation and primary succession in glacial forelands.},
}

@article {pmid42399252,
year = {2026},
author = {Dai, D and Wang, P and Zhang, H and Qi, G and Wang, J},
title = {Temporal landscapes of the gut microbiota-host axis reveal mechanisms of age-related eggshell quality decline in laying hens.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01079-4},
pmid = {42399252},
issn = {2055-5008},
support = {32402797//National Natural Science Foundation of China/ ; 32322078//National Natural Science Foundation of China/ ; CARS-40//China Agriculture Research System/ ; ASTIP//Agricultural Science and Technology Innovation Program/ ; },
abstract = {Age-related shifts in the gut microbiota of laying hens significantly affect eggshell quality. However, the temporal interactions of the gut microbiota during the eggshell mineralization cycle remain unclear. Existing research often overlooks the rhythmic synchronization required for mineralization, as well as the specific cellular landscape of the aging intestine that impairs effective host-microbe crosstalk. We integrated 16S rRNA sequencing, metagenomics, untargeted metabolomics, and single-cell RNA sequencing to compare young and aged hens during the initial (7 h post-oviposition) and rapid growth (17 h post-oviposition) phases of eggshell mineralization. Aged hens exhibited significantly lower eggshell strength, thickness, and Ca/P concentrations (P < 0.05), which were associated with mitochondrial cristae disruption and necrocytosis in ileal tissues. 16S and metagenomic analyses revealed that young hens maintain stochastic microbial assembly, whereas aged hens shift toward deterministic processes driven by environmental stress. Rhythmic shifts in Lactobacillus and Ligilactobacillus were observed in young hens, supporting energy metabolism and mineral absorption pathways. In contrast, the aged hen microbiome remained focused on basal survival and oxidative stress responses. scRNA-seq identified nine cell populations, highlighting T cell exhaustion and HIF-1-driven metabolic reprogramming in epithelial cells of aged hens. Mediation analysis identified Ligilactobacillus salivarius as a keystone species that enhances eggshell breaking strength and thickness by increasing rhamnose and tyrosol levels and modulating host CALB1 and BLB2 expression. These findings indicate that aging disrupts proactive host-microbe synergy required for eggshell formation and identify L. salivarius-derived metabolites as promising candidates for restoring mineralization function in aged hens.},
}

@article {pmid42399304,
year = {2026},
author = {Sun, Y and Cheng, X and Zhou, J and Li, R and Wei, Y and Li, H and Qin, Y and Bao, J and Ren, X and Qu, S and Liu, W},
title = {Bio-stimulants improve tomato growth by regulating the rhizosphere microbiome involved in phosphorus and nitrogen cycling.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59808-w},
pmid = {42399304},
issn = {2045-2322},
support = {2024CXPT056//the Key R&D Plan of Shandong Province (Competitive Innovation Platform) Project: Green, Ecological and Efficient Modern Agricultural Biological Product Development/ ; },
abstract = {Bio-stimulants are promising environment friendly alternatives to support sustainable agricultural development, capable of boosting crop growth and yield while cutting down excessive dependence on chemical synthetic fertilizers. Nevertheless, the explicit regulatory mechanisms by which bio-stimulants exert the role of growth-promoting functions still remain largely unclear and require further systematic clarification. In this study, we explored the influences of bio-stimulants (rich in humic acid) on tomato growth performance and rhizosphere microbial community assembly via greenhouse trials, and comparatively analyzed the functional differences between foliar spraying and root irrigation application modes. The results demonstrated that bio-stimulants treatment markedly improved tomato aboveground biomass, plant nitrogen and phosphorus accumulation by 17.1%, 27.4% and 22.7%, respectively. Meanwhile, bio-stimulants application effectively raised soil available nitrogen and soil organic matter levels, and further facilitated phosphorus assimilation in tomato plants. Metagenomic sequencing confirmed that bio-stimulants substantially reshaped the overall structure and composition of tomato rhizosphere microbiome. Specifically, they dramatically enriched the relative abundance of core microbial taxa responsible for soil nitrogen fixation and phosphorus solubilization. Collectively, these results clearly elaborate the underlying action mechanism: bio-stimulants optimize rhizosphere micro-ecological environment, enrich functional nutrient-solubilizing microorganisms, improve soil nutrient availability, and ultimately promote nutrient absorption and vegetative growth of tomato plants. This study confirms that bio-stimulants can serve as efficient and reliable regulators to advance green and sustainable crop production.},
}

@article {pmid42342250,
year = {2026},
author = {Baghbanzadeh, M and Mann, BT and Crandall, KA and Rahnavard, A},
title = {seqLens: Optimizing Language Models for Genomic Predictions.},
journal = {Molecular biology and evolution},
volume = {43},
number = {7},
pages = {},
pmid = {42342250},
issn = {1537-1719},
support = {2109688//National Science Foundation/ ; },
mesh = {*Genomics/methods ; *Models, Genetic ; Large Language Models ; Evolution, Molecular ; Genome ; },
abstract = {Understanding evolutionary variation in genomic sequences through the lens of language modeling has the potential to revolutionize biological research. Yet to maximize the utility of language modeling in genomics, we must overcome computational challenges in tokenization and model architecture adapted to diverse genomic features across evolutionary timescales. In this study, we investigated key elements in genomic language modeling (gLM), including tokenization, pretraining datasets, fine-tuning approaches, pooling methods, and domain adaptation, and applied the language models to diverse genomic data. We gathered two evolutionarily distinct pretraining datasets: one consisting of 19,551 reference genomes, including over 18,000 prokaryotic genomes (115 B nucleotides) and the remainder eukaryotic genomes, and another more balanced dataset with 1,354 genomes, including 1,166 prokaryotic and 188 eukaryotic reference genomes (180 B nucleotides). We trained five byte-pair encoding tokenizers and pretrained 52 gLMs, systematically comparing different architectures, hyperparameters, and classification heads. We introduce seqLens, a family of models based on disentangled attention with relative positional encoding, which outperforms relatively similar-sized models in 13 of 19 benchmarking phenotypic predictions. We further explore continual pretraining, domain adaptation, and parameter-efficient fine-tuning methods to assess trade-offs between computational efficiency and accuracy. Our findings demonstrate that relevant pretraining data significantly boost performance, alternative pooling techniques can enhance classification, tokenizers with larger vocabulary sizes negatively impact generalization, and gLMs are capable of understanding evolutionary relationships. These insights provide a foundation for optimizing genomic language models for identifying diverse evolutionary genomic features and improving genome annotations.},
}

*Genomics/methods
*Models, Genetic
Large Language Models
Evolution, Molecular
Genome

@article {pmid42386120,
year = {2026},
author = {Nancy, N and Sharma, M and Singh, K and Singh, B and Sharma, PK},
title = {Mutation T71R enhanced the structural stability and functional activity of wild type superoxide dismutase cloned from soil metagenome.},
journal = {Gene},
volume = {},
number = {},
pages = {150294},
doi = {10.1016/j.gene.2026.150294},
pmid = {42386120},
issn = {1879-0038},
abstract = {In this study, we report engineering of three mutations m1, m2, and m3 respectively in the wild type SOD, cloned form soil metagenome. Expressed proteins from wild type and mutants were purified to homogeneity using Ni-NTA affinity chromatography. Biochemical characterization of mutants demonstrated enhanced functional activity at varying pH and temperature compared to wild type and other mutant proteins. Additionally, it also showed increased specific activity of 185 ± 0.75 U/mg compared to 150 ± 0.042 U/mg and 168 ± 0.25 U/mg respectively for mutant m1, m2 and m3. Altogether, it was observed that the relative enzyme activity of mutant m1, m2 and m3 enhanced ∼ 30 %, 10 % and 17 % respectively compared to wild type. Biophysical investigation carried out employing circular dichroism and intrinsic tryptophan fluorescence also demonstrated conformational stability in the secondary and tertiary structure of mutant m1 compared to the wild type at varying pH and temperature. Interestingly, in silico molecular simulation dynamics studies carried out at 300 ns demonstrated structural stability, reduced flexibility and attainment of stable conformation in this mutant form. Molecular simulation analysis revealed that mutation T71R in m1 tends to introduce β-sheet like secondary structure at protein surface, which might enhance residue-residue interactions within this protein, leading to allover enhancement in the stability and activity of this mutant.},
}

@article {pmid42386249,
year = {2026},
author = {Arenas-Montes, J and Garcia-Fernandez, H and Alcala-Diaz, JF and Boughanem, H and Allais, A and Gutierrez-Mariscal, FM and Arenas-de Larriva, AP and Ojeda-Rodriguez, A and Malagon, MM and Priego-Capote, F and Delgado-Lista, J and Perez-Martinez, P and Camargo, A and Lopez-Miranda, J},
title = {High postprandial endotoxemia is associated with recurrence of cardiovascular events in patients with coronary heart disease: from the CORDIOPREV randomized clinical trial.},
journal = {The American journal of clinical nutrition},
volume = {124},
number = {1},
pages = {101323},
doi = {10.1016/j.ajcnut.2026.101323},
pmid = {42386249},
issn = {1938-3207},
mesh = {Humans ; *Endotoxemia/complications/blood ; Male ; Female ; *Postprandial Period ; *Coronary Disease/complications/blood ; Middle Aged ; Lipopolysaccharides/blood ; Diet, Fat-Restricted ; Recurrence ; Diet, Mediterranean ; Aged ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/etiology ; },
abstract = {BACKGROUND: The translocation into the systemic circulation of proinflammatory bacterial components such as lipopolysaccharide (LPS) has been linked to cardiovascular disease (CVD).

OBJECTIVES: We aimed to evaluate the association between baseline postprandial endotoxemia and the risk of suffering major adverse cardiovascular events (MACE) in patients with coronary heart disease (CHD), as well as the influence of consuming a low-fat (LF) diet or the Mediterranean (MED) diet on the associated risk.

METHODS: Our research was conducted within the framework of the CORDIOPREV Study, a clinical trial which involved 1002 patients with CHD randomly assigned to consume an LF diet or the MED diet for 7 y. A mixed meal was administered at the beginning of the study and after 3 y of follow-up. LPS plasma concentrations were measured by Limulus Amebocyte Lysate (LAL) colorimetric assay and gut microbiota was analyzed using 16S metagenomics.

RESULTS: Baseline postprandial increase in LPS plasma concentrations were associated with recurrence of MACE after a follow-up of 7 y, using Cox regression analysis [hazard ratio (HR):1.42 (1.01, 2.00)]. Patients with moderate LPS postprandial increase and consuming LF diet had higher risk of suffering MACE compared with the MED diet [HR: 1.45 (1.01, 2.09)]. Both diets reduced LPS plasma concentrations and formed a gut microbiota profile associated with a postprandial LPS decrease.

CONCLUSIONS: Our results suggest that the magnitude of postprandial endotoxemia is associated with suffering new MACE in patients with CHD, with the MED diet exercising a higher preventive role than an LF diet. Our results especially are relevant to clinical practice, supporting the measurement of postprandial endotoxemia as a tool for personalized medicine in secondary prevention. This study was registered at clinicaltrials.gov as NCT00924937.},
}

Humans
*Endotoxemia/complications/blood
Male
Female
*Postprandial Period
*Coronary Disease/complications/blood
Middle Aged
Lipopolysaccharides/blood
Diet, Fat-Restricted
Recurrence
Diet, Mediterranean
Aged
Gastrointestinal Microbiome
*Cardiovascular Diseases/etiology

@article {pmid42387129,
year = {2026},
author = {Kumar, A and Kumar, A and Tyagi, A and Singh, R and Charaya, MU},
title = {A review of bloodstream infections-pathogens, pathogenesis, diagnostic strategies, treatment methods-challenges and future aspects.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42387129},
issn = {1435-4373},
abstract = {PURPOSE: Bloodstream infections (BSIs) remain a major cause of morbidity and mortality worldwide and continue to represent a substantial challenge to modern healthcare systems. These infections arise when pathogenic microorganisms gain access to the bloodstream, triggering systemic inflammatory responses that may progress to sepsis, septic shock, multi-organ dysfunction, and death. This review provides a comprehensive overview of the historical development, epidemiology, pathogenesis, diagnosis, treatment, and future perspectives of BSIs. The major bacterial, fungal, viral, and parasitic pathogens associated with BSIs are discussed, with particular emphasis on their virulence attributes, mechanisms of immune evasion, antimicrobial resistance, and clinical significance.

METHODS: A comprehensive literature review was conducted using peer-reviewed publications, clinical guidelines, surveillance reports, and systematic reviews published between 2010 and mid-2026. Evidence related to bacterial, fungal, viral, and parasitic bloodstream pathogens, host-pathogen interactions, diagnostic modalities, antimicrobial resistance mechanisms, and emerging therapeutic and diagnostic innovations was critically evaluated and integrated.

RESULTS: BSIs continue to impose a substantial healthcare burden, driven by increasing antimicrobial resistance, delayed diagnosis, and diverse pathogen-specific virulence mechanisms. Bacterial pathogens remain the predominant cause of BSIs, whereas Candida species represent the leading fungal agents. Advances in molecular diagnostics, metagenomic sequencing, biomarker-guided testing, and artificial intelligence-assisted analyses have substantially improved rapid pathogen detection and therapeutic decision-making. Precision medicine, genomic surveillance, and novel antimicrobial agents show considerable promise for enhancing clinical management and addressing multidrug-resistant infections.

CONCLUSION: Bloodstream infections remain a major global health challenge due to their complex pathogenesis, increasing antimicrobial resistance, and high associated mortality. Improving patient outcomes requires early and accurate pathogen identification, prompt initiation of targeted antimicrobial therapy, effective antimicrobial stewardship, and continuous epidemiological surveillance. The integration of next-generation diagnostics, artificial intelligence-assisted pathogen detection, genomic surveillance, and precision medicine has the potential to transform BSI diagnosis and management by enabling rapid, individualized therapeutic interventions.},
}

@article {pmid42387141,
year = {2026},
author = {Zou, P and Wang, X and Zhao, H and Yang, K and Ye, J and Sun, Y and Meng, X and Yi, Z and Xiong, X and Li, W},
title = {Mycobacterium Abscessus Infection after Breast Augmentation: Case Reports and Literature Review.},
journal = {Aesthetic plastic surgery},
volume = {},
number = {},
pages = {},
pmid = {42387141},
issn = {1432-5241},
abstract = {BACKGROUND: Mycobacterium abscessus (M. abscessus) infection following breast augmentation is a rare complication, yet evidence and standardized treatments remain limited. Challenges include diagnostic difficulties and prolonged treatment periods.

METHODS: We report two cases of M. abscessus infection following breast augmentation and conducted a structured narrative review of PubMed literature to explore prevention, diagnosis, and treatment strategies associated with this condition.

RESULTS: The two patients underwent different breast augmentation procedures: one received autologous fat transfer, and the other had a prosthetic implant inserted. Following confirmation of M. abscessus infection via metagenomic next-generation sequencing (mNGS), both patients underwent through surgical debridement and drainage with daily amikacin irrigation. Combination antibiotic therapy was administered, including intravenous amikacin and linezolid, plus oral azithromycin. Both patients demonstrated good tolerance to the prescribed antibiotics, achieving effective infection control without recurrence over a 12-month follow-up period. The rigorous debridement and targeted antibiotic therapy significantly enhanced treatment efficacy.

CONCLUSION: This study reports two rare cases of M. abscessus infection occurring after breast aesthetic surgery. Such infections are difficult to diagnose and are often associated with prolonged treatment courses. We successfully identified the causative pathogen through mNGS and implemented a comprehensive treatment strategy that included multiple surgical debridements, local irrigation, and combination antimicrobial therapy with azithromycin, amikacin, and linezolid, which was associated with favorable clinical outcomes. Rather than establishing a definitive management model, this study provides practical, case-based insights into the diagnosis and management of postoperative M. abscessus infections.

LEVEL OF EVIDENCE V: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .},
}

@article {pmid42387381,
year = {2026},
author = {Andersson, O and Fagerström, A and Dannenberg, K and Kekki, J and Rode, J and Rangel, I and Lindqvist, CM and Stenmark, B},
title = {Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42387381},
issn = {1471-2180},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Computational Biology/methods ; *Gene Library ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; DNA, Bacterial/genetics ; Microbiota/genetics ; },
abstract = {BACKGROUND: 16S rRNA gene sequencing is widely used for bacterial community profiling in both clinical and research contexts. The expanding availability of library preparation protocols and bioinformatic pipelines increases analytical flexibility but may also introduce method-dependent biases that affect inferred microbial composition and relative abundance estimates. The relative impact of library preparation protocol, amplicon region, and bioinformatic pipeline on species-level taxonomic inference and compositional agreement remains insufficiently characterised. We therefore compared the Illumina 16S Metagenomic Sequencing Library Preparation protocol (V3-V4) and the Zymo Quick-16S Plus NGS Library Prep Kit (V1-V2 and V3-V4) in combination with two bioinformatic pipelines, nf-core/ampliseq and TRANA. Performance was assessed using defined microbial community standards and human faecal and colonic biopsy samples.

RESULTS: Pipeline choice was the dominant driver of variation in inferred community composition, exceeding the effects of amplicon regions and library preparation protocols. Genus-level profiles were broadly concordant across methods. Species-level resolution and agreement with expected community composition differed systematically between pipelines, with TRANA demonstrating lower Bray-Curtis dissimilarities to expected compositions than nf-core/ampliseq. Amplicon region had a secondary, pipeline-dependent effect, while protocol differences were minor. In clinical samples, inter-individual biological variation exceeded technical variation.

CONCLUSIONS: Bioinformatic processing substantially influenced species-level inference in short-read 16S sequencing, highlighting the importance of pipeline selection for microbiome study design and cross-study comparability.},
}

*RNA, Ribosomal, 16S/genetics
*Computational Biology/methods
*Gene Library
Humans
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Sequence Analysis, DNA/methods
Metagenomics/methods
DNA, Bacterial/genetics
Microbiota/genetics

@article {pmid42387416,
year = {2026},
author = {Ishio, D and Eguchi, H and Hotta, F and Miyamoto, T},
title = {Blepharoconjunctivitis mimicking conjunctival tumor associated with Streptococcus intermedius sinusitis: case report and literature review.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13910-6},
pmid = {42387416},
issn = {1471-2334},
abstract = {Streptococcus intermedius, a commensal bacterium in the human oral cavity, can occasionally cause severe infections in deep tissues. The patient was referred because of a conjunctival tumor. She had severe nasal cavity and periocular tissue inflammation that persisted for over a year. Microbiological examination of the nasal and ocular specimens identified S. intermedius as the pathogenic strain. The inflammation and the conjunctival mass subsided after systemic and topical administration of a susceptible antibiotic. Smear microscopy of the eye and nasal discharge was useful for the differential diagnosis. 16S metagenomic analysis using MinION as an adjunctive diagnostic tool has contributed to the species identification of the pathogenic strain.},
}

@article {pmid42387479,
year = {2026},
author = {Vastolo, A and Tolone, M and Gannuscio, R and Staropoli, A and Giosa, D and Bonomo, A and Vinale, F and Cutrignelli, MI and Todaro, M},
title = {Impact of Opuntia spp. by-product silage on sheep metabolic profile, rumen fermentation and microbial communities.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05646-x},
pmid = {42387479},
issn = {1746-6148},
support = {cod. U-Gov PRJ-1776; CUP: J83C22000830005//National Recovery and Resilience Plan (PNNR) of Italy: project Biometric-Call PNNR a cascata-Università della TUSCIA/ ; },
abstract = {BACKGROUND: Prickly pear (Opuntia ficus-indica) by-products represent a promising alternative feed resource for improving the sustainability of sheep production systems in Mediterranean areas. This study evaluated the effects of prickly pear by-product (PPB) silages on rumen fermentation, metabolic profile, and rumen microbiome in lactating ewes. Twelve Valle del Belice ewes were assigned to three dietary treatments (control, CTR; prickly pear peel silage, PPP; and pastazzo silage, PPS) in a Latin square design. Blood biochemical parameters, rumen volatile fatty acids (VFA), and metagenomic profiles were analysed.

RESULTS: PPB inclusion did not induce significant changes in blood biochemical parameters, which remained within physiological ranges. Rumen fermentation parameters were significantly affected, with the PPP diet increasing total VFA concentration and promoting a more glucogenic profile through higher propionate production. The rumen microbiome was dominated by Prevotella, which showed higher relative abundance in the CTR diet. PPB supplementation was associated with shifts in microbial functional profiles, including pathways related to polyphenol degradation, vitamin K2 biosynthesis, and central carbon metabolism, partially consistent with observed changes in rumen fermentation. No significant effects were observed on methanogenesis-related pathways.

CONCLUSIONS: Prickly pear by-product silages, particularly prickly pear peel, modulate rumen fermentation and microbial functional profiles in lactating ewes without adversely affecting systemic metabolic status.},
}

@article {pmid42387526,
year = {2026},
author = {Bing, Y and Yuan, W and Liang, L and Li, J and Chen, Y and Feng, L and Li, X and Li, H and Zhong, J and Wang, L and Tong, Z and Liu, X},
title = {Alterations in the fecal virome and bacteriome-virome interplay in IPAH.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03797-x},
pmid = {42387526},
issn = {1465-993X},
support = {Nos. 82570072, 82170302//Innovative Research Group Project of the National Natural Science Foundation of China/ ; Nos. Ysbz2025004, Ysbz2025005, Ysbz2025006, Ysbz2025007//the Financial Budgeting Project of Beijing Institute of Respiratory Medicine/ ; },
abstract = {BACKGROUND: Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening cardiovascular disorder characterized by complex multisystem disturbances. Although alterations in the gut microbiota have been reported in IPAH, how the gut virome interacts with bacterial communities and host metabolism remains unclear.

METHODS: We enrolled 28 patients with IPAH and 30 age-matched healthy controls (HCs). Fecal viromes and bacteriomes were profiled by metagenomic sequencing, and serum metabolomic data were integrated to construct virus-bacterium-metabolite interaction networks. Random forest models were used to evaluate the diagnostic potential of virome features.

RESULTS: IPAH patients exhibited markedly reduced gut virome diversity (Shannon, Simpson, and Pielou indices, p < 0.05) and distinct community structures from HCs (p < 0.01). A total of 499 differential viral operational taxonomic units (vOTUs) were identified, accompanied by extensive reorganization of interaction networks. At the phylum level, Hofneiviricota was enriched and Phixviricota depleted, both correlating with clinical indicators. Virus-bacterium associations were markedly increased in IPAH (44,894 vs. 17,920, r > 0.5). Notably, vOTU2967, vOTU1924, and vOTU4522 were elevated and inversely related to Bacteroides, whose depletion was associated with increased lactic acid levels. Mediation analysis confirmed significant indirect virus-bacterium-metabolite effects (p < 0.05). Random forest models based on vOTUs or viral families effectively distinguished IPAH patients from controls, highlighting the exploratory potential of gut virome features for mechanistic insights.

CONCLUSIONS: IPAH is characterized by reduced virome diversity, altered viral taxa, and reorganized virus-bacterium-metabolite networks. These findings suggest that gut viruses may influence disease progression by modulating bacterial metabolism, providing a potential avenue for biomarker discovery and therapeutic intervention.},
}

@article {pmid42387604,
year = {2026},
author = {Hu, Y and Chen, JS and Zhou, MY and Huang, H and Zhou, YF and Zhou, HY and Lv, ZY},
title = {Dynamic alterations and potential roles of gut microbiota and metabolites in Angiostrongylus cantonensis-infected mice and rats.},
journal = {Infectious diseases of poverty},
volume = {15},
number = {1},
pages = {},
pmid = {42387604},
issn = {2049-9957},
support = {NPRC-2019-194-30//National Parasitic Resources Center of China/ ; 22qntd4804//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2021YFC2300800//National Key Research and Development Program of China/ ; 82072303//National Natural Science Foundation of China/ ; YSPTZX202133//Specific Research Fund of the Innovation Platform for Academicians of Hainan Province/ ; ZDYF2020120//Key Research and Development Program of Hainan Province/ ; ZDKJ202003//Major Science and Technology Program of Hainan Province/ ; 2020TTM007//Open Foundation of Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University/ ; },
mesh = {Animals ; Female ; *Angiostrongylus cantonensis/physiology ; Rats, Sprague-Dawley ; *Strongylida Infections/parasitology/microbiology/metabolism ; Rats ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred BALB C ; RNA, Ribosomal, 16S/genetics/analysis ; Biomarkers ; Feces ; },
abstract = {BACKGROUND: Angiostrongyliasis, a food-borne parasitic disease caused by Angiostrongylus cantonensis, is characterized by eosinophilic meningitis or meningoencephalitis, leading to serious central nervous system damage. Current diagnostic methods lack specificity or sensitivity, and the pathogenesis is complex and incompletely understood. This study aimed to comprehensively characterize the dynamic alterations in the gut microbiota and host metabolism in both suitable (rats) and non-suitable (mice) hosts following A. cantonensis infection and to identify potential metabolic biomarkers for early diagnosis.

METHODS: Female BALB/c mice and Sprague Dawley rats (n = 10/group) were infected with 30 or 100 third-stage larvae, respectively. Serum, urine, feces, and brain samples were collected longitudinally. Gut microbiota was analyzed via 16S rRNA gene sequencing and metagenomics. Host metabolism was profiled using untargeted and targeted metabolomics via ultraperformance liquid chromatography-quadrupoles/time of flight-mass spectrometry. Statistical analyses included Wilcoxon rank sum test, linear discriminant effect size analysis, Spearman correlation analysis, orthogonal partial least squares-discriminatory analysis, and receiver operating characteristic curve analysis.

RESULTS: Infection induced significant, host-specific gut microbiota dysbiosis. In infected hosts, Firmicutes decreased (P < 0.05) while Bacteroidetes increased (P < 0.05). A main difference in gut flora structure between infected hosts was observed in Prevotellaceae, which increased significantly in mice (P < 0.05) but decreased in rats (P < 0.05). Metagenomics revealed enhanced carbohydrate metabolism and fatty acid biosynthesis in gut microbes of infected mice, whereas up-regulated amino acid and vitamin metabolism were also observed in infected rats. Infection caused pronounced disruptions in host lipid and bile acid (BA) metabolism, changes in various BA types were closely related to alterations in specific bacterial genera (P < 0.05). Several metabolites, including phosphatidylcholine (16:0/18:1), 2-phenyl acetic acid, 2-octenoylglycine, lysophosphatidylcholine (18:2), O-glucuronide, and 2-carboxylic acid, were identified as potential early diagnostic biomarkers in the mouse model.

CONCLUSIONS: A. cantonensis infection causes profound host-specific dysregulation of the gut microbiome and metabolome, with severe disturbances in Firmicutes, Bacteroidetes, lipid and BA metabolism being central features. These alterations highlight the critical role of the host-gut microbiota-metabolite axis in pathogenesis and offer novel insights for developing diagnostic and therapeutic strategies.},
}

Animals
Female
*Angiostrongylus cantonensis/physiology
Rats, Sprague-Dawley
*Strongylida Infections/parasitology/microbiology/metabolism
Rats
*Gastrointestinal Microbiome
Mice
Mice, Inbred BALB C
RNA, Ribosomal, 16S/genetics/analysis
Biomarkers
Feces

@article {pmid42388191,
year = {2026},
author = {Zhang, J and Fu, C and Tan, S and Lyu, B and Shu, G and Shi, L and Wu, Y and Guo, P},
title = {How Host Phylogeny, Diet, and Habitat Affect Gut Microbial Diversity in Wild Snakes.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e73902},
pmid = {42388191},
issn = {2045-7758},
abstract = {Gut microbiota plays critical roles in host digestion, immune regulation, neurochemical signaling, and metabolic homeostasis. Based on wild snakes (73 individuals from 23 species) from China, we explored the composition, characteristics, and functions of gut microbes across different groups using fecal metagenomic samples; further we explored the relative contributions of host phylogeny, diet, and habitat to the microbial structure. Among 23 wild snake species, the dominant gut microbial phyla were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, with Bacteroides, Salmonella, Citrobacter, and Aeromonas comprising the major genera. Mantel test revealed a significant correlation (r = 0.3173, p = 0.0055) between microbial composition at the genus level and host genetic divergence (p-distance), indicating potential phylogenetic influence on gut microbial profiles. While α-diversity and principal coordinate analysis showed no marked differences across different subgroups. Linear discriminant analysis effect size demonstrated notable differences in the gut microbes of the terrestrial snakes with different diets and vertebrate-feeding snakes with different habitats. Functional annotation of microbial genes indicated enrichment in metabolic processes, as well as environmental and genetic information processing. Carbohydrate-active enzymes were predominantly from GT2, GT4, GT51, and GH23 families. Linear discriminant analysis effect size showed different diets and habitats had distinct differential taxa. Additionally, antibiotic resistance gene profiles varied across groups, with acrB, AcrF, MexB, acrD, and mdtF being most prevalent. Future studies should increase the samples and comprehensively consider different ecological factors to explore the impacts on the composition and functions of snake gut microbes on different evolutionary, which will provide a deeper understanding of the interrelationships between snake gut microbes and their hosts.},
}

@article {pmid42388299,
year = {2026},
author = {Maccario, L and Otani, S and Szarvas, J and Mortensen, LH and Elberling, B and Møller, KE and Madsen, CEK and Aarestrup, FM and Priemé, A},
title = {Microbial composition of archaeological middens: tracing human footprints through centuries in Greenland's ancient settlements.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809037},
pmid = {42388299},
issn = {1664-302X},
abstract = {The history of Greenland is marked by different waves of Paleo-Inuit immigration from North America from 2,500 BC to the 12th century and from the 10th to 15th century, Norse settlers immigrated from Northwest Europe and flourished in Southwest Greenland with the introduction of domestic livestock. The different Inuit and Norse cultures created middens by dumping and accumulating domestic waste; a latent source of microbes, including potential pathogens, that might have been preserved due to the general wet and cold conditions in the region. The aim of this study was to evaluate whether ancient Arctic settlements might be possible hot-spots for pathogenic agents that may spread to the surrounding environment because of current climate changes. Using metagenomics, we compared the microbial communities and resistomes of 78 samples from middens from different ages and locations in West and South Greenland (two Paleo-Inuit, four Norse and one early Colonial-time middens) to 143 soil samples from nearby surroundings. We found that the middens harbor a distinctive microbial signature enriched in human-associated bacteria. Those include opportunistic pathogens such as Clostridium perfringens and Paeniclostridium sordellii. In some early colonial midden layers, C. perfringens and Paraclostridium tenue together accounted for up to ~40%-50% of MetaPhlAn-derived relative abundance in individual samples. Antimicrobial resistance genes representing 17 resistance classes were detected across all sites, dominated by β-lactam and tetracycline resistance. Transect analyses across an actively eroding midden showed that midden-derived bacteria were confined to local erosion layers and were rapidly replaced by native marine communities, indicating limited environmental dispersal.},
}

@article {pmid42388302,
year = {2026},
author = {Cao, H and Wang, Q and Ren, W and Wang, A and Tian, W and Zhang, D and Chen, J},
title = {Characterization of the gastric mucosal microbiota in tumoral and peritumoral mucosa in patients with advanced gastric cancer from Northwest China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1763714},
pmid = {42388302},
issn = {1664-302X},
abstract = {INTRODUCTION: The gastric microbiota affects tumor development and treatment response, yet the characteristics and interactions of mucosal bacteria and fungi in advanced gastric cancer (AGC) remain unclear.

METHODS: Here we analyzed 177 mucosal samples (88 peritumoral and 89 tumoral) from 91 AGC patients in Northwest China using shotgun metagenomic sequencing.

RESULTS: MetaPhlAn4 and Kaiju were used to annotate the gastric mucosal microbial composition. MetaPhlAn4 has identified 12 phyla (no phylum-level differences), 98 genera and 278 species. PERMANOVA revealed age and tumor location significantly influenced microbial composition in tumoral mucosa. Wilcoxon signed-rank test revealed that 10 species including Serratia surfactantfaciens, Pseudomonas protegens, Treponema pectinovorum, Streptococcus anginosus, Bacteroides heparinolyticus, Selenomonas sputigena, and Mogibacterium diversum were significantly enriched in tumoral tissue, whereas five species including Actinomyces graevenitzii, Gemella sanguinis, Porphyromonas pasteri, Helicobacter pylori, and Leptotrichia sp. oral taxon-215 were more abundant in peritumoral mucosa. HUMAnN4 showed tumor-enriched bacteria were involved in metabolic pathways including polysaccharide degradation, biosynthesis of fatty acids, nucleotides, and arginine/histidine/purine/pyrimidine, which were primarily linked to S. surfactantfaciens. Peritumor-enriched bacteria were associated with L-tryptophan biosynthesis, L-arginine degradation, and TCA cycle. Kaiju annotation further revealed 2,429 bacteria, 12 archaea, 74 viruses, 82 fungi, and 63 other eukaryota species, among which the majority of significantly different species were enriched in the tumoral mocusa. Mycobiome analysis revealed eight fungal phyla, 82 genera and 82 species. PERMANOVA revealed that age had a significant effect on fungal composition in peritumoral mucosa, and five species including Saccharomyces cerevisiae, Aspergillus ochraceoroseus, Aspergillus fumigatiaffinis, Mitosporidium daphniae, and Puccinia striiformis were significantly positively correlated with age. Alpha diversity using Shannon index was significantly reduced in peritumoral mucosa at both genus and species levels. Wilcoxon signed-rank test revealed that all the significantly different fungi, including eight phyla, 46 genera, and 42 species were significantly enriched in tumoral mucosa. Correlation analysis indicated tumor-enriched bacteria were positively correlated with tumoral fungi but negatively with peritumoral fungi, suggesting possible synergistic bacteria-fungi interactions.

DISCUSSION: This study comprehensively characterizes the gastric mucosal bacteriome and mycobiome in AGC, illuminates potential microbiota-mediated carcinogenic mechanisms, identifies candidate biomarkers, and fills a regional research gap.},
}

@article {pmid42388305,
year = {2026},
author = {Zhang, H and Ma, L and Jia, L and Li, Y and Wang, Y and Wang, W and Wu, W and Wang, H and Li, H and Zhang, Y and Chen, G and Hou, K and Dong, J},
title = {Multi-omics analysis reveals the potential for fermented Cordyceps militaris mushroom substrate in laying hens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1807060},
pmid = {42388305},
issn = {1664-302X},
abstract = {This study examines how varying levels of fermented Cordyceps militaris mushroom substrate (CMMS) in laying hen diets affect production performance, digestive health, immunity, cecal microbiota, metabolites, and quorum-sensing functions. Fermentation reduced CMMS dry matter, NDF, and phosphorus content (p < 0.05). Replacing 30% of the diet with fermented CMMS significantly improved laying rate, egg weight, feed intake, and feed efficiency (p < 0.05), while enhancing yolk color, Haugh units, and lipase activity. A 20% substitution increased nutrient digestibility and immunoglobulin levels (p < 0.05). Metagenomic analysis revealed increased abundance of Phocaeicola, Alistipes, and Parabacteroides (p < 0.05) with enhanced energy metabolism and specific gene families. Metabolomic analysis identified 1,529 differentially expressed metabolites, with carboxylic acids being most prevalent (21.20%), and enhanced taurine/hypotaurine metabolism and GPI-anchor biosynthesis. Parabacteroides showed negative correlations with certain metabolites, while Alistipes correlated positively with PemK/MazF family genes (p < 0.001). CMMS fermented feed proportions influence cecal microbiota, their metabolites, and quorum sensing in laying hens, affecting production, digestibility, immunity, metabolism, and health, demonstrating CMMS potential as alternative poultry nutrition.},
}

@article {pmid42388398,
year = {2026},
author = {Yu, L and Chong, Z and Yanchun, L and Yingying, H},
title = {The Diagnosis of Human Neurological Infection Caused by Rabies Virus Using Metagenomic Next-Generation Sequencing: Two Case Reports.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {1910139},
pmid = {42388398},
issn = {2090-6625},
abstract = {The rabies virus (RABV) causes acute progressive and fatal encephalomyelitis. Two case studies of RABV neurological infection identified using metagenomic next-generation sequencing (mNGS) are presented in this paper. A total of 39 RABV sequences were detected using mNGS in the cerebrospinal fluid (CSF) in Case 1. The detected sequences were located in the 0%-35% range of the enriched and amplified region and had a 27 × sequencing depth. A total of 75 RABV sequences were detected using mNGS in the CSF in Case 2. These cases illustrate that mNGS use during the early diagnosis of infectious diseases is critical. They also indicate that RABV can remain latent in the human body for many years. Disease prevention education for people who have experienced bites or scratches by rabid animals is therefore crucial.},
}

@article {pmid42388653,
year = {2026},
author = {Zhang, X and Sun, E and Zhao, Z and Li, S and Shen, X and Liu, J and He, Q and Wang, Y and Zhao, F and Zhao, H and Zhang, H},
title = {Intervention With Lacticaseibacillus paracaseiPC-01 Fermented Milk Beverage Ameliorates Functional Dyspepsia and Modulates Gut Microbiome: A Pilot Study.},
journal = {Food science & nutrition},
volume = {14},
number = {7},
pages = {e71928},
pmid = {42388653},
issn = {2048-7177},
abstract = {Functional dyspepsia (FD) is a common chronic gastrointestinal disorder characterized by persistent or recurrent epigastric symptoms in the absence of detectable structural abnormalities. In this pilot study, we explored whether a Lacticaseibacillus paracasei PC-01 (PC-01) fermented milk beverage alleviates FD symptoms. Fifty-five patients with FD were randomized into an experimental group (EP, n = 37) receiving the PC-01 fermented milk beverage (5.0 × 10[8] CFU/mL, 200 mL/day) or a control group (CP, n = 18) receiving the active comparator, an acidified milk beverage (non-fermented, without PC-01) (200 mL/day). The interventions lasted 28 days, with symptom scores on the 7-point Global Overall Symptom Scale (GOSS) and Gastrointestinal Symptom Rating Scale (GSRS), and fecal samples were collected at baseline (day 0), 14, and 28. Consumption of the PC-01 fermented milk beverage in this pilot study was associated with improvements in FD symptoms, and a higher effective response rate was observed in the EP group than in the CP group (p = 0.04). Metagenomic analysis revealed that, compared with the CP group, the EP group exhibited significant enrichment of potentially beneficial bacteria (e.g., Blautia) and a reduction in potentially pathogenic bacteria (e.g., Clostridium paraputrificum), accompanied by significant downregulation of the fatty acid β-oxidation I (FAO-PWY) pathway. We acknowledge that the limitation of this pilot study is that the acidified milk beverage used as the control might also exert certain effects on gastrointestinal symptoms and gut microbiota, which could not be fully avoided due to the lack of a fully inert placebo. Collectively, the findings of this preliminary study indicate that the PC-01 fermented milk beverage may alleviate FD-related symptoms and modulate the gut microbiome and metabolic pathways, highlighting its potential in ameliorating FD-associated symptoms. Further large-sample, multi-center, and long-term clinical studies are warranted to verify these preliminary results and establish the long-term efficacy and safety of FD management.},
}