@article {pmid42886419,
year = {2026},
author = {Bagul, SY and Sarkar, R and Suthar, MK and Kumar, V and S, S and Rana, VS and Sircar, D and Reddy, NRR},
title = {Culturomics and amplicon-based insights into the endophytic microbiome of Kalmegh (Andrographis paniculata (Burm.f.) Nees) and its implications in plant growth promotion.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42886419},
issn = {1573-0972},
support = {NASF/MA-10007/2023-24//ICAR - National Agricultural Science Fund/ ; (NASF/MA-10007/2023-24//ICAR - National Agricultural Science Fund/ ; (NASF/MA-10007/2023-24//ICAR-National Agricultural Science Fund (NASF)/ ; },
mesh = {*Endophytes/classification/isolation & purification/genetics/metabolism ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Microbiota/genetics ; *Andrographis/microbiology/growth & development ; Diterpenes/metabolism ; Plant Leaves/microbiology/chemistry ; Plants, Medicinal/microbiology/growth & development ; Plant Development ; Metagenomics ; Phylogeny ; Plant Stems/microbiology ; Andrographis paniculata ; Plant Extracts ; },
abstract = {Leaf and stem endophytic microorganisms play an important role in plant physiology and secondary metabolite biosynthesis of plants, particularly in medicinal plants. Kalmegh (Andrographis paniculata (Burm.f.) Nees) is an important medicinal plant with liver-protective, anti-inflammatory, ovicidal, larvicidal, and anti-urolithatic properties. The medicinal activities are due to presence of andrographolides. This study investigated the culture-independent diversity of endophytic bacteria associated with Kalmegh at nursery, vegetative, and flowering stages using a metagenomic approach. The results revealed that Sphingomonas was the dominant bacterial genus during nursery and vegetative stages, whereas Halobacterium predominated during the flowering stage. Microbial abundance was highest in the nursery stage, followed by flowering and vegetative stages. Functional analysis showed that flowering stage endophytes were enriched with specialized carbon metabolism and aromatic compound degradation pathways, potentially influencing andrographolide biosynthesis. Chemical analysis supported these findings, showing the highest andrographolide content in leaves during flowering (3.1%). Gene expression analysis further demonstrated that increased andrographolide accumulation was associated with upregulation of methyl erythritol phosphate pathway (MEP) pathway and diterpene biosynthetic genes. Bacterial endophytes isolated from flowering-stage leaves exhibited plant growth-promotion, antifungal, and seed germination-enhancing activities. In vitro assays against Fusarium wilt and Rhizoctonia disease showed that Bacillus cereus strains KL11, KL12, and KL5 inhibited pathogen growth by 60-65%. Biopriming with strains KL3 and KL5 of Bacillus cereus improved seed germination and plant growth. Pot trials with Micrococcus luteus KES1 increased herbage yield, plant height, and andrographolide content by 43%. These findings highlight the potential of leaf and stem endophytes for sustainable improvement of Kalmegh productivity and andrographolide content in the plant.},
}

*Endophytes/classification/isolation & purification/genetics/metabolism
*Bacteria/classification/isolation & purification/genetics/metabolism
*Microbiota/genetics
*Andrographis/microbiology/growth & development
Diterpenes/metabolism
Plant Leaves/microbiology/chemistry
Plants, Medicinal/microbiology/growth & development
Plant Development
Metagenomics
Phylogeny
Plant Stems/microbiology
Andrographis paniculata
Plant Extracts

@article {pmid42886518,
year = {2026},
author = {Sharif, B and Kutschera, VE and Oskolkov, N and Guinet, B and Lord, E and Chacón-Duque, JC and Oppenheimer, J and van der Valk, T and Del-Molino, DD and Heintzman, PD and Dalén, L},
title = {DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag782},
pmid = {42886518},
issn = {1367-4811},
abstract = {MOTIVATION: Ancient DNA (aDNA) research has advanced rapidly with the development of high-throughput sequencing, enabling genome-wide analyses of large collections of prehistoric specimens. However, analysing palaeontological and archaeological material with highly degraded DNA constitutes a major bioinformatic challenge. DNA from such samples is characterized by short fragment lengths, low endogenous content, post-mortem damage, and cross-species contamination, which can increase spurious mapping and reference bias, affecting downstream population genetic inferences.

RESULTS: We present DNAharvester, a modular and reproducible pipeline designed specifically for processing highly degraded DNA from ancient and historical specimens. DNAharvester integrates metagenomic filtering, competitive mapping, adaptive aligner selection (incorporating BWA-aln, BWA-mem, and Bowtie2), and systematic evaluation of reference bias and spurious mapping. By incorporating flexible mapping and filtering strategies, the pipeline can be adapted to varying sample preservation, focusing on maximizing authentic data recovery. DNAharvester features subworkflows for iterative assembly of mitogenomes, identification of genomic repeats and CpG sites, taxonomic classification, microbial/pathogen screening, genetic sex determination, and variant calling. To accommodate varying sequencing depths, the pipeline supports diploid variant calling, genotype likelihood estimation, and pseudo-haploid random allele calling. We validated the pipeline using simulated and empirical datasets, demonstrating its ability to systematically mitigate complex background contamination while preserving authentic genomic signals. By streamlining complex bioinformatic tasks through simple configuration files, DNAharvester establishes a standardized approach for analysing aDNA datasets and makes genomic analyses of ancient remains accessible to the broader research community.

Implemented in Nextflow, DNAharvester provides a highly scalable, containerized framework that enhances reproducibility, portability, and robustness in aDNA analyses. DNAharvester is open source under the GNU General Public License v3.0 and freely available at https://github.com/NBISweden/DNAharvester.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online and Zenodo repository: https://doi.org/10.5281/zenodo.22725211.},
}

@article {pmid42886573,
year = {2026},
author = {Hou, S and Jiang, Y and Zhang, D and Xu, Z and Li, Y and Liu, X and Zhang, H and Zhang, J and Zhai, Q and Zhang, C and Wang, X and Huang, S},
title = {A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748153},
doi = {10.1080/19490976.2026.2748153},
pmid = {42886573},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts/metabolism ; Metagenomics ; *Host Microbial Interactions ; },
abstract = {The spatial organization of the gastrointestinal microbiome is shaped by strong physicochemical gradients along the gut, yet many region-associated microbial niches remain poorly resolved in humans. Here, we used the rhesus macaque (Macaca mulatta) as a spatially resolved primate model to profile 148 luminal and mucosal samples across the gastrointestinal tract using shotgun metagenomics, 2bRAD-M sequencing, and targeted bile acid metabolomics, complemented by comparative human datasets. Microbial communities exhibited strong spatial stratification along the gastrointestinal tract, while host species explained greater variation than anatomical location in our comparative datasets. Despite broad phylum-level similarity between humans and monkeys, substantial divergence emerged at species and functional levels. Monkey-associated Segatella copri encoded expanded carbohydrate-active enzyme (CAZyme) repertoires specialized for degradation of complex plant polysaccharides, consistent with dietary and other host-associated adaptation. Along the gastrointestinal tract, microbial load and diversity followed pronounced spatial gradients, although the low-biomass stomach retained unexpectedly high taxonomic and functional diversity. Mucosal communities largely mirrored luminal microbiota at broad taxonomic scales but exhibited distinct species-level signatures associated with niche-specific functional specialization. The monkey large intestine was further enriched in the immunomodulatory bile acid isoallo-lithocholic acid (isoalloLCA), with candidate biosynthetic genes identified in previously uncharacterized microbial lineages. Together, these findings establish a high-resolution framework of the primate gut microbiome and reveal how spatial organization and host-associated selection shape microbial metabolism and host-microbe interactions relevant to gut health.},
}

Animals
Humans
*Macaca mulatta/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Gastrointestinal Tract/microbiology
Bile Acids and Salts/metabolism
Metagenomics
*Host Microbial Interactions

@article {pmid42887104,
year = {2026},
author = {Yang, S and Luo, Y and Zou, X and Zhang, W and Su, Y and Luo, J and Wang, F},
title = {Thiamphenicol decouples acidogenesis from methanogenesis and redirects carbon flux toward volatile fatty acids in sludge anaerobic digestion.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143930},
doi = {10.1016/j.jhazmat.2026.143930},
pmid = {42887104},
issn = {1873-3336},
abstract = {Antibiotic residues in waste activated sludge (WAS) may disrupt anaerobic carbon conversion, yet how phenicol antibiotics redistribute carbon between acidogenesis and methanogenesis remains unclear. At 10 mg/g TSS, methane production decreased by 63.2% while VFAs reached 131-fold the control. This functional decoupling was underpinned by microbial fates: hydrolytic-acidogenic bacteria were largely retained or enriched, whereas methanogenic archaea and syntrophic bacteria were severely depleted. Concurrently, bacteria-archaea ecological networks underwent reorganization, with positive correlations partially rebounding at moderate TAP exposure. The network collapsed at high TAP, with substantial loss of connector taxa mediating inter-module metabolite exchange. Metagenomic evidence further revealed a functional asymmetry: genes involved in substrate transport and amino acid metabolism were maintained or showed increased relative abundance, while methanogenic genes and AI-2-associated communication genes exhibited decreased relative abundance. PLS-PM revealed that TAP was positively associated with the acidogenic bacterial community (β = 0.960) but negatively with methanogenic potential (β = -0.998). Accordingly, the methane share dropped from 98.7% to 18.1%, while VFAs increased to 81.9% of the COD-equivalent product pool. This work advances the understanding of antibiotic-driven functional imbalance and carbon flux redirection in sludge anaerobic digestion, providing a mechanistic basis for managing antibiotic-laden sludge prior to energy recovery.},
}

@article {pmid42887308,
year = {2026},
author = {Zhang, L and Ye, M and Dong, Y and Yuan, L and Qiu, S and Shao, H and Zhang, D},
title = {Modulation of the gut microbiome and resistome in Taihe Black-Boned Silky Fowls by different dietary selenium forms.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107919},
doi = {10.1016/j.psj.2026.107919},
pmid = {42887308},
issn = {1525-3171},
abstract = {Selenium is a widely utilized supplement in poultry production. Its bioavailability and tissue deposition vary with chemical form and may affect the gut microenvironment. Taihe Black-Boned Silky Fowl (TBSF), a Chinese endemic breed with systemic melanin deposition, exhibit enhanced absorption and enrichment of diverse compounds. As a metalloid, selenium may also promote antimicrobial resistance in microbiomes, including those of the gut. However, its impact on the TBSF gut microbiota and resistome remains unknown. We therefore investigated how selenium chemical form influences the cecal microbiome and resistome. Four dietary treatment groups of TBSF (n = 120 birds per group; 60 males and 60 females) were fed for 80 days: CK (selenium-deficient control), YS (sodium selenite), JS (yeast-derived selenium), and DS (selenomethionine), with measured dietary selenium concentrations of 0.05 ± 0.002, 0.33 ± 0.023, 0.35 ± 0.017, and 0.36 ± 0.042 mg/kg, respectively. We performed metagenomic sequencing analysis to assess alterations in microbial composition and resistome profiles in cecum. Results demonstrated that selenium supplementation significantly modulated cecal microbiota structure in both male and female birds(Bray-Curtis distance-based analysis, Wilcoxon rank-sum test, P < 0.05), with pronounced sex-dependent differences. The relative abundances of three prevalent antibiotic resistance genes (ARGs), bcrA, efrA, and fusA, were significantly elevated in selenium-supplemented groups compared with the CK group (Kruskal-Wallis H test, FDR-adjusted P < 0.05). Selenium supplementation reduced mobile genetic element (MGE) type diversity while increasing overall MGE relative abundance. Transposases and recombinases were the two most abundant MGE-associated functional classes. Mantel correlation analysis revealed strong associations between cecal microbiota composition and both ARG and MGE profiles (r ≥ 0.5, P ≤ 0.001). The sexually dimorphic cecal microbiota composition in TBSF may underlie the observed sex-dependent resistome response: sodium selenite exerted the strongest effect on ARG and MGE enrichment in roosters, whereas yeast-derived selenium induced the strongest effect in hens. Further network analysis revealed that sodium selenite exerted the most pronounced influence on resistome-microbiota co-occurrence patterns. These findings underscored the dual-sided nature of selenium supplementation from the perspective of ARGs, indicating that selenium supplementation may alter the composition of the cecal microbiota, thereby modulating the relative abundance and community structure of ARGs and MGEs in the TBSF cecum. Given selenium's essential role and narrow therapeutic index, its chemical form and dosage must be evidence-based and rigorously optimized to minimize potential unintended contributions to antimicrobial resistance. This represents a potential ecological and antimicrobial resistance concern from a One Health perspective that warrants further investigation.},
}

@article {pmid42887325,
year = {2026},
author = {Cao, X and Zang, Z and Liu, J and Zhan, G and Shi, G and Zhang, L},
title = {Synergistic effects of biochar and organic fertilizer on the regulation of microbial carbon and nitrogen metabolism in paddy soil to reduce net greenhouse gas emissions.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131181},
doi = {10.1016/j.jenvman.2026.131181},
pmid = {42887325},
issn = {1095-8630},
abstract = {Biochar and organic fertilizer have been widely applied to improve soil carbon sequestration and mitigate greenhouse gas (GHG) emissions in rice production systems. However, the synergistic mechanisms through which these amendments regulate microbial carbon/nitrogen (C/N) metabolism, net GHG emissions, and crop productivity in dry direct-seeded rice (DDSR) systems remain insufficiently understood. In this study, a two-year field experiment was conducted with combined treatments of organic fertilizer substitution (0% and 20%) and biochar application (0, 5, and 10 t/hm[2]) to evaluate their integrated effects on GHG emissions, soil properties, rice yield, and microbial functional genes involved in C/N cycling. Biochar and organic fertilizer significantly reduced CH4 and N2O emissions, leading to lower global warming potential (GWP), greenhouse gas emission intensity (GHGI), and net greenhouse gas emissions (NGHGE), while simultaneously increasing rice yield. The combined application of 20% organic fertilizer substitution with 5 t/hm[2] biochar achieved the optimal performance, increasing yield by 11.64%-15.44% and reducing GWP and GHGI by 7.58%-16.56% and 17.21%-27.72%, respectively. Metagenomic analysis revealed that the combined application modified microbial community structure while regulated microbial C/N metabolism by reshaping key functional pathways. The enhancement of Calvin-Benson-Basham (CBB) pathway was related to the increased abundance of PRK and prkB under biochar conditions; meanwhile, reduced abundances of aclA, aclB, and ccsA were associated with suppressed reductive tricarboxylic acid (rTCA) cycle. Concurrently, denitrification and nitrification pathways showed positive correlations with increased abundances of nirK, norB, and nosZ. Redundancy analysis (RDA) and mantel analyses indicated that soil organic carbon (SOC), pH, ammonium nitrogen (NH4[+]-N), and nitrate nitrogen (NO3[-]-N) were the primary drivers shaping microbial functional gene structure. Overall, the synergistic application of biochar and organic fertilizer effectively coordinated carbon sequestration, emission reduction, and yield enhancement, providing a feasible strategy for low-carbon and sustainable management of DDSR.},
}

@article {pmid42887796,
year = {2026},
author = {Liu, L and Liu, L and Qiu, C and Yu, J and Wang, C and Wang, S},
title = {Mechanistic insights into riboflavin-mediated recovery of the single-stage partial nitritation-anammox system under tetracycline stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136039},
doi = {10.1016/j.biortech.2026.136039},
pmid = {42887796},
issn = {1873-2976},
abstract = {Tetracycline (TC) contamination poses a potential threat to the stability of anammox-based wastewater treatment systems, yet effective strategies for accelerating functional recovery remain poorly understood. This study explored the inhibitory effects of 5 mg/L TC on a single-stage partial nitritation-anammox (SPNA) system, and further unraveled its functional potential and underlying mechanisms of exogenous riboflavin for restoring system performance. TC exposure substantially impaired nitrogen removal, with total nitrogen removal efficiency decreasing from 53.39 % to 34.44 %, accompanied by a pronounced decline in anammox activity. Supplementation with 0.5 mg/L riboflavin accelerated system recovery, partially restoring total nitrogen removal efficiency to 48.15 %, by enhancing anammox activity and suppressing nitrite-oxidizing bacteria proliferation. Riboflavin alleviated these disturbances by enhancing electron transfer, mitigating oxidative stress, and restoring nitrogen metabolism-related functional genes. Metagenomic analysis further revealed that riboflavin recovered extracellular electron transfer and amino acid and nucleotide metabolism pathways disrupted by TC stress, while promoting the enrichment of tetracycline resistance and degradation-related genes and putative tetracycline-degrading bacteria, including Sphingobacterium and Bacillus. These responses were accompanied by enhanced tetracycline removal, suggesting potential mechanisms of improved microbial adaptation to antibiotic stress.},
}

@article {pmid42887801,
year = {2026},
author = {Zhang, S and Wang, Q and Zhang, X and Tian, Z and Xu, X and Wang, S and Lv, G and Chen, Y and Ma, Y and Gao, A},
title = {Short-chain perfluorobutyric acid (PFBA) disrupts anaerobic ammonium oxidation in riverbed sediments and reshapes the functional microbial community.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136077},
doi = {10.1016/j.biortech.2026.136077},
pmid = {42887801},
issn = {1873-2976},
abstract = {Perfluorobutanoic acid (PFBA), a representative short-chain perfluoroalkyl carboxylic acid, is increasingly detected in aquatic environments, yet its impacts on anaerobic nitrogen cycling remain poorly understood. Here, a laboratory-scale simulated river sediment system was established to investigate the concentration-dependent effects of PFBA (1 ng/L-50 mg/L) on Anammox performance, microbial communities, functional genes, and PFBA transformation. Low PFBA concentrations (≤1 μg/L) stimulated nitrogen removal, with NH4[+]-N conversion and NO2[-]-N removal increasing by 30.8% and 38.9%, respectively. In contrast, inhibition emerged at 1 mg/L and became pronounced at ≥ 10 mg/L. At 50 mg/L, NO2[-]-N and TN removal rates decreased to 7.58 and 5.22 μg/(g·h), respectively, and remained suppressed during recovery. High PFBA exposure reduced extracellular polymeric substances (EPS) -associated protein content and key Anammox enzyme activities, accompanied by downregulation of hao, hdh, and hzs and increased relative abundance of nrf, indicating a shift from autotrophic Anammox toward heterotrophic dissimilatory nitrate reduction to ammonium (DNRA). Notably, 91.7% of PFBA was apparently transformed at 50 mg/L, with shorter-chain products such as perfluoropropanoic acid and trifluoroacetic acid being qualitatively identified, suggesting sequential dealkylation and decarboxylation. However, a complete mass balance was not established because the transformation products were not quantified. These findings demonstrate that PFBA exerts concentration-dependent effects on sedimentary nitrogen cycling by disrupting Anammox metabolism and reshaping microbial functional pathways, providing new insights into per- and polyfluoroalkyl substances (PFAS) ecological risks and sediment bioremediation.},
}

@article {pmid42887802,
year = {2026},
author = {Liu, H and Li, L and Peng, Y and Peng, X and Li, Z and Zhao, B},
title = {Nitrogen removal mechanisms in improved hybrid activated sludge-membrane aerated biofilm reactor: Insights from metagenomics and metaproteomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136070},
doi = {10.1016/j.biortech.2026.136070},
pmid = {42887802},
issn = {1873-2976},
abstract = {Simultaneous nitrification-denitrification (SND) is a promising process for low C/N wastewater treatment. A hybrid activated sludge-membrane aerated biofilm reactor (H-MABR) capable of achieving two‑stage SND was developed and exhibited satisfactory nitrogen removal performance; however, the underlying mechanisms remain unclear. To address this, an improved H-MABR was developed and integrated metagenomic and metaproteomic analyses were performed to systematically elucidate the spatial distribution of microbial communities and their functions in the reactor. The results showed that the improved H-MABR achieved removal efficiencies of 94.4 ± 0.4% for chemical oxygen demand, 92.9 ± 0.7% for total nitrogen, and 97.8 ± 0.8% for ammonia nitrogen. Multi‑omics analysis identified seven dominant microbial genera and three highly expressed nitrogen metabolic pathways. The outer ring was the primary nitrogen removal zone, where the aerobic zone mainly mediated nitrification and the anoxic zone exhibited significantly upregulated activities of NosZ, NirK, NirS, and NorC (ORA vs. ORO), strongly supporting the denitrification function in this zone. The inner ring served as an important auxiliary nitrogen removal unit, showing particularly strong ammonia nitrogen removal performance, which was attributed to the highly expressed hydroxylamine dehydrogenase. This study provides a foundation for advancing the understanding and application of SND systems.},
}

@article {pmid42888205,
year = {2026},
author = {Hoozemans, JB and de Jonge, PA and Guman, MSS and Haal, S and Aydin, Ö and Meijnikman, AS and Bäckhed, F and de Brauw, M and Acherman, YIZ and Nieuwdorp, M and Groen, AK and Gerdes, VEA},
title = {Understanding pathophysiology of gallstone disease: a multi-omic analysis focused on adult women with obesity.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {42888205},
issn = {1476-5497},
abstract = {BACKGROUND: Gallstone disease has a complex, multifactorial pathophysiology. Both the gut microbiome and the liver have been implicated as potential contributors. Because obesity is associated with alterations in gut microbial composition and is itself a risk factor for gallstone formation, we investigated the relative roles of the gut microbiome, the liver, and adipose tissue in gallstone disease in female patients with obesity.

METHODS: From the BARIA cohort, 108 consecutive female patients with obesity were included, of whom at baseline 39 had ultrasound proven gallstones (cases), whereas 69 did not have gallstones (controls). Fecal shotgun metagenomics, untargeted fasting plasma metabolomic analysis, and bulkRNAseq transcriptome analyses of liver, visceral (VAT), and subcutaneous (SAT) biopsies (taken during surgery) were analyzed.

RESULTS: Especially VAT showed differences in expression of 57 genes, whereas liver gene expression revealed differences only after secondary analysis. In contrast to other publications, in liver "classic" ABC transporter gallstone genes were not identified in this cohort. Instead, the cholesterol transporter ABCG1 emerged, and expression was decreased in patients with gallstone disease. Plasma metabolomic profiling demonstrated increased levels of primary and secondary bile acids in the gallstone group. In contrast, gut microbiome differences between groups were limited.

CONCLUSIONS: This integrated multi-omics analysis suggests that visceral adipose tissue may play a more prominent role in gallstone disease pathophysiology in women with obesity than previously appreciated. The observed selective molecular alterations and persistent bile acid differences highlight the complex metabolic interplay underlying gallstone formation and provide insight into tissue-specific mechanisms associated with obesity-related gallstone disease.},
}

@article {pmid42888449,
year = {2026},
author = {He, P and Zhang, K and Khan, J and Ouyang, H and Hu, S and Qian, S and Shu, B and Li, X and Lin, D},
title = {Metagenomic analysis of developmental-category-associated fungal communities in the gut contents of Achatina fulica, an intermediate host of Angiostrongylus cantonensis.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42888449},
issn = {1756-3305},
support = {18MDZ02//Major Project Cultivation Plan of Xizang Minzu University/ ; XZ202401ZR0017//the Tibet Natural Science Foundation/ ; No. SKXRC2025159//the Youth S&T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 82672963 and 82202560//the National Natural Science Foundation of China/ ; 23360095 and 23360208//College Students' Innovative Entrepreneurial Training Plan Program/ ; },
mesh = {Animals ; Metagenomics ; *Mycobiome ; *Snails/microbiology/parasitology ; *Angiostrongylus cantonensis/physiology ; China ; *Fungi/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: The invasive giant African snail (Achatina fulica) poses serious agricultural and ecological threats and serves as an important intermediate host of the zoonotic parasite Angiostrongylus cantonensis, which causes human eosinophilic meningitis. While its gut bacterial microbiome has been extensively characterized, the gut mycobiome remains largely uncharacterized. In particular, variations in gut fungal communities across developmental stages remain unknown, limiting our understanding of the A. fulica gut holobiont.

METHODS: In November 2025, giant African snails were collected from Guangzhou, Guangdong Province, China. Genomic DNA was extracted from the gut contents of the collected snails. Metagenomic sequencing was conducted to characterize variations in the gut mycobiota across different snail sample types.

RESULTS: Metagenomic sequencing of 18 snail gut samples across three developmental stages showed lower fungal alpha diversity in adults than in juveniles, whereas PCoA visualized differences in community composition among developmental categories and PERMANOVA confirmed that these differences were statistically significant. Ascomycota dominated the mycobiome, with developmental-category-associated differences in taxonomic composition. LEfSe and DESeq2 identified differentially abundant taxa associated with developmental categories, while SIMPER analysis identified several taxa contributing to the observed dissimilarity, including Synchytrium taraxaci, Aspergillus flavus and Cladosporium cladosporioides. These taxa are interpreted as contributors to community dissimilarity rather than as causal drivers of developmental-category-associated differences. Co-occurrence networks analysis identified six highly connected taxa (Hanseniaspora uvarum, Apiospora montagnei, Aureobasidium thailandense, Colletotrichum aenigma, Truncatella angustata, and Calonectria ilicicola) within the inferred fungal association network.

CONCLUSIONS: Gut fungal community composition differed significantly among the sampled developmental categories of A. fulica, although the cross-sectional design does not establish that the host development itself causes these differences. The identified developmental-category-associated and highly connected taxa provide a baseline for gut mycobiota ecology and a foundation for future controlled studies investigating their functional roles and potential relevance to A. cantonensis infection.},
}

Animals
Metagenomics
*Mycobiome
*Snails/microbiology/parasitology
*Angiostrongylus cantonensis/physiology
China
*Fungi/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology

@article {pmid42888864,
year = {2026},
author = {Schlager, JG and Stiefel, D and Patzer, K and Schloter, M and Foesel, BU and Zelzer, NM and French, LE and Gschwendtner, S and Hartmann, D},
title = {Basal Cell Carcinoma May Be Associated With Staphylococcus Dysbiosis.},
journal = {Experimental dermatology},
volume = {35},
number = {10},
pages = {e70371},
doi = {10.1111/exd.70371},
pmid = {42888864},
issn = {1600-0625},
support = {//Verein zur Förderung von Wissenschaft und Forschung an der Medizinischen Fakultät der LMU München e.V. (WiFoMed)/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/complications ; *Basal Cell Carcinoma/microbiology ; *Skin Neoplasms/microbiology ; Skin Microbiome ; *Staphylococcus/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Male ; Middle Aged ; Skin/microbiology ; Aged, 80 and over ; Microbiota ; },
abstract = {There is growing evidence that a dysbiosis of the skin microbiome has an impact on carcinogenesis in cutaneous squamous cell carcinoma. However, the role of the microbiome in basal cell carcinoma (BCC) remains unclear due to limited, inconsistent, ex vivo studies. Here, we analysed the skin microbiome of patients with BCC, including the tumour lesion as well as perilesional skin from the same subject. Skin swabs from BCC and perilesional skin were taken prior to tumour surgery. After DNA extraction, we used a metabarcoding approach based on 16S rRNA gene amplicon sequencing to analyse the cutaneous bacterial communities. In total, 63 patients with BCC were included for analysis. Most tumour lesions were located on sun-exposed, sebaceous areas such as the nose, cheeks, and forehead. The genera Corynebacterium, Cutibacterium, and Staphylococcus predominated both in BCC and perilesional skin. However, the microbiome of BCC was reduced in overall bacterial richness, with a significant overabundance of amplicon sequence variants (ASV) assigned to the genus Staphylococcus, resulting in a reduced complexity in microbial networks. The dominating ASV assigned to Staphylococcus was also detected in perilesional skin regions, indicating that the microbial dysbiosis in BCC affected regions is caused by natural members of the healthy skin microbiome. The BCC microbiome is characterised by microbial dysbiosis, reflected by a reduced overall bacterial richness, fewer microbe-microbe interactions and a significant over-representation of Staphylococcus species compared with perilesional skin. Further long-read metagenomics and cultivation-based studies are needed to identify Staphylococcus species driving dysbiosis.},
}

Humans
*Dysbiosis/microbiology/complications
*Basal Cell Carcinoma/microbiology
*Skin Neoplasms/microbiology
Skin Microbiome
*Staphylococcus/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Female
Aged
Male
Middle Aged
Skin/microbiology
Aged, 80 and over
Microbiota

@article {pmid42888868,
year = {2026},
author = {Xie, S and Yang, Y and Tang, S and Zhou, L and Wang, J and Chan, JWY and Or, B and Li, N and Gong, S and He, Z and Ni, J and Liu, Y and Zhang, J and Chan, PKS and Chen, Z and Wong, SH and Mok, VCT and Chan, NY and Chau, SWH and Wing, YK and Huang, B},
title = {Habitual Diet, Gut Microbiome Dysbiosis, and α-Synucleinopathy Conversion in Isolated Rapid Eye Movement (REM) Sleep Behavior Disorder.},
journal = {Movement disorders : official journal of the Movement Disorder Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/mds.70562},
pmid = {42888868},
issn = {1531-8257},
support = {05162876//Health and Medical Research Fund/ ; 06170676//Health and Medical Research Fund/ ; C4044-21G//Research Grants Council of Hong Kong/ ; //Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong/ ; },
abstract = {BACKGROUND: Accumulating evidence indicates that habitual diet, including plant-based dietary patterns, is associated with neurodegenerative α-synucleinopathy risk. However, the role of diet and its correlation with the gut microbiome in prodromal α-synucleinopathy, specifically among patients with isolated rapid eye movement (REM) sleep behavior disorder (iRBD), remains unclear.

OBJECTIVE: To evaluate dietary patterns, their interplay with gut microbial dysbiosis, and longitudinal effects on neurodegenerative progression in iRBD patients.

METHODS: We recruited 287 iRBD patients and 208 age- and sex-matched controls. Plant-based diet indices (PDIs) were derived from food frequency questionnaires. Shotgun metagenomic sequencing was performed in 456 subjects for diet-microbiome analyses. After a median follow-up of 4.2 years, 45 (15.7%) iRBD patients converted to α-synucleinopathies. Cox proportional hazards models assessed the associations between diet and neurodegenerative outcomes.

RESULTS: We found that iRBD patients exhibited lower healthful PDIs (adjusted odds ratio [aOR] 95% confidence interval [95% CI]: 0.48 [0.29-0.80], P = 0.005) but higher consumption of unhealthful plant-based foods (refined grains, sweets, and sweeteners). Diet-microbiome interaction analysis identified dietary associations for 84.3% of iRBD-related gut microbes, including co-occurrence between healthful PDI and Clostridium sp. AF20-17LB. Longitudinally, four dietary factors and five iRBD-related microbes were associated with neurodegenerative outcomes; specifically, higher coffee consumption was linked to a lower risk of progression to α-synucleinopathy (aHR [95% CI]: 0.30 [0.11-0.78], P = 0.01). Furthermore, mediation analyses indicated that the iRBD-enriched species Ruthenibacterium lactatiformans mediated the association between unhealthful PDI and dementia-first conversion.

CONCLUSIONS: Habitual diet in iRBD is associated with gut microbiome dysbiosis and predicts neurodegenerative progression. These findings highlight diet-microbiome interactions as modifiable targets for intervention in prodromal α-synucleinopathy. © 2026 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.},
}

@article {pmid42888920,
year = {2026},
author = {Hardy, SMC and Aguilar-Pine, EJ and Gulick, S and Ahmad, A and Baker, BJ and Scott, N and Aitolo, G and Felton, N and Cockell, CS},
title = {Impact Crater Hydrothermal Systems Support Rapid Microbial Enrichment and Diverse Metabolic Potential.},
journal = {Geobiology},
volume = {24},
number = {6},
pages = {e70070},
doi = {10.1111/gbi.70070},
pmid = {42888920},
issn = {1472-4669},
support = {73592LPI//Simons Foundation/ ; LI-SIAME-00002001//Simons Foundation/ ; ST/V000586/1//Science and Technology Facilities Council/ ; ST/Y001788/1//Science and Technology Facilities Council/ ; },
mesh = {*Hydrothermal Vents/microbiology ; *Bacteria/metabolism/classification/genetics ; Germany ; *Archaea/metabolism/classification/genetics ; },
abstract = {Impact crater hydrothermal systems, formed after asteroid and comet impacts, have been proposed as promising habitats for life on early Earth and as key targets in the search for life on planetary bodies such as Mars, since they provide liquid water and active geochemical turnover. Because no newly formed impact structures exist on Earth, studies of microbial establishment in impact-crater hydrothermal systems have largely relied on the direct observation of fossil microbial life or its isotopic signatures. To address this limitation, we established simulated microcosm hydrothermal systems in the laboratory using melt-bearing impact breccia (suevite) from the Ries impact structure, Germany, and temperate soils. Within weeks, these systems hosted taxonomically diverse communities, with broad metabolic potential, partitioned among oxidized impact glass, endolithic suevite habitats, and sedimentary environments. Dominant taxa included thermophiles from primarily heterotrophic lineages (e.g., Meiothermus and Aneurinibacillus spp.), as well as lineages with potentially chemolithotrophic metabolisms (e.g., Brockia spp.). Metagenomic annotations identified genes associated with methane, iron, and sulfur cycling, including sulfate-reduction, indicating metabolic potential for biogeochemically relevant processes under hydrothermal conditions. These results show that impact-generated hydrothermal systems can rapidly support diverse thermophilic microbial communities with habitat-specific community structure and metabolic potential, supporting their relevance as analogue environments for studying early microbial establishment and biosignature formation in planetary impact settings.},
}

*Hydrothermal Vents/microbiology
*Bacteria/metabolism/classification/genetics
Germany
*Archaea/metabolism/classification/genetics

@article {pmid42888984,
year = {2026},
author = {Wei, E and Shang, P and Li, F and Yan, K and Zhang, M and Fang, X and Jia, P and Wang, J and Zhao, J and Li, N and Wang, H and Xie, N},
title = {Clinical and metagenomic characterization of HHV-6 versus HHV-7 encephalitis in immunocompetent children.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1909287},
doi = {10.3389/fcimb.2026.1909287},
pmid = {42888984},
issn = {2235-2988},
mesh = {Humans ; *Herpesvirus 7, Human/genetics ; *Herpesvirus 6, Human/genetics ; Male ; Female ; Child, Preschool ; Child ; Infant ; *Encephalitis, Viral/virology/cerebrospinal fluid/diagnosis ; Retrospective Studies ; *Roseolovirus Infections/virology/cerebrospinal fluid/diagnosis ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Adolescent ; Immunocompetence ; DNA, Viral/cerebrospinal fluid ; Cerebrospinal Fluid/virology ; },
abstract = {BACKGROUND: Human herpesvirus 6 (HHV-6) and human herpesvirus 7 (HHV-7) are betaherpesviruses that can cause encephalitis/encephalopathy in immunocompetent children. However, early clinical manifestations, routine laboratory tests, and neuroimaging findings often lack specificity, making etiological characterization challenging. This study aimed to characterize the clinical features and metagenomic findings of HHV-6 and HHV-7 encephalitis in immunocompetent children.

METHODS: This single-center retrospective cohort study included children (<18 years) with suspected central nervous system infection who underwent lumbar puncture and cerebrospinal fluid (CSF) next-generation sequencing (mNGS) testing at The First Affiliated Hospital of Zhengzhou University between January 2020 and December 2024. Patients with HHV-6 or HHV-7 sequences detected in CSF by mNGS, together with compatible clinical features and exclusion of other more likely etiologies, were included. Demographic characteristics, clinical manifestations, laboratory and CSF findings, neuroimaging features, mNGS results, treatments, and short-term outcomes were analyzed.

RESULTS: A total of 20 children with CSF HHV-6 or HHV-7 sequence detection were included (HHV-6, n=5; HHV-7, n=15). HHV-6 cases mainly occurred in infants and young children, whereas HHV-7 cases were predominantly observed in older children. Fever and seizure-related symptoms were the most common clinical manifestations. Peripheral inflammatory markers, CSF parameters, and neuroimaging findings showed heterogeneous patterns among patients. CSF mNGS detected HHV-6 or HHV-7 sequences in all included cases, with variable sequencing read counts (HHV-6: median 257 reads, range 55-52, 686; HHV-7: median 2, 635 reads, range 457-26, 355). The median turnaround time of mNGS reporting was 1 day (range, 1-2 days). All patients received antiviral therapy, with some receiving adjunctive corticosteroids and/or intravenous immunoglobulin. Short-term outcomes at discharge were generally favorable, and only one patient developed secondary autoimmune encephalitis.

CONCLUSIONS: HHV-6 and HHV-7 encephalitis in immunocompetent children share overlapping clinical characteristics and lack specific early laboratory or imaging features. CSF mNGS enabled rapid and unbiased detection of HHV-6 and HHV-7 sequences and provided complementary etiological information when interpreted together with clinical and ancillary findings.},
}

Humans
*Herpesvirus 7, Human/genetics
*Herpesvirus 6, Human/genetics
Male
Female
Child, Preschool
Child
Infant
*Encephalitis, Viral/virology/cerebrospinal fluid/diagnosis
Retrospective Studies
*Roseolovirus Infections/virology/cerebrospinal fluid/diagnosis
Metagenomics
High-Throughput Nucleotide Sequencing
Adolescent
Immunocompetence
DNA, Viral/cerebrospinal fluid
Cerebrospinal Fluid/virology

@article {pmid42889167,
year = {2026},
author = {Zhao, C and Chen, J and Wu, P and Zhang, W and Ning, S},
title = {Viral metagenomic characterization of HAdV-B-related signals in bronchoalveolar lavage fluid from pediatric and adult clinical cohorts.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1961482},
doi = {10.3389/fpubh.2026.1961482},
pmid = {42889167},
issn = {2296-2565},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/virology ; *Metagenomics ; *Adenoviruses, Human/genetics/isolation & purification ; Phylogeny ; Child ; Adult ; Female ; Male ; Child, Preschool ; High-Throughput Nucleotide Sequencing ; *Adenovirus Infections, Human/virology ; Cohort Studies ; Infant ; },
abstract = {Human adenovirus (HAdV) is an important respiratory virus in children, but sequence-level evidence for HAdV-related signals in lower respiratory tract samples remains limited. In this study, we analyzed metagenomic next-generation sequencing data from 189 bronchoalveolar lavage fluid (BALF) libraries from pediatric and adult clinical cohorts, including 30 pediatric and 159 adult patients, together with laboratory environmental controls. MEGAN read-level classification was used to screen for Adenoviridae-related signals. HAdV-related contigs were further reviewed, and a BALF-derived HAdV-B-related representative contig was selected for read recruitment and coverage analysis. Phylogenetic trees were reconstructed using penton base, hexon, and fiber protein sequences. Adenoviridae-classified signals were more apparent in pediatric BALF libraries than in adult BALF libraries or environmental controls. Several pediatric BALF libraries showed broad read coverage across the HAdV-B-related representative contig, whereas adult libraries and environmental controls mainly showed low-coverage-breadth signals. Phylogenetic analysis placed BALF-derived penton base, hexon, and fiber sequences within HAdV-B-related lineages. Twenty-seven capsid protein sequences from 12 pediatric samples had best BLASTp matches to references annotated as HAdV-B3 (n = 23) or HAdV-B7 (n = 4). These findings provide sequence evidence for HAdV-B-related sequence signals in clinically selected pediatric BALF samples and support further investigation using targeted assays and genome sequencing.},
}

Humans
*Bronchoalveolar Lavage Fluid/virology
*Metagenomics
*Adenoviruses, Human/genetics/isolation & purification
Phylogeny
Child
Adult
Female
Male
Child, Preschool
High-Throughput Nucleotide Sequencing
*Adenovirus Infections, Human/virology
Cohort Studies
Infant

@article {pmid42889534,
year = {2026},
author = {Al-Fatlawi, A and Schroeder, M},
title = {UniProt data pruning and the growing invisibility of the dark proteome.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {4},
pages = {lqag115},
doi = {10.1093/nargab/lqag115},
pmid = {42889534},
issn = {2631-9268},
mesh = {*Proteome/genetics ; *Databases, Protein ; Proteomics/methods ; },
abstract = {The protein resource UniProtKB has undergone a major, multi-stage reorganization of its protein space, implemented from release 2025_04 through release 2026_02. Analysis of UniProtKB and UniParc records accessed on 20 January 2026 showed that 125.9 million entries were last present in UniProtKB in 2025 and are now represented in UniParc, while ~200.0 million entries remained in UniProtKB at the access date. Of these, 58.9 million were designated for removal in release 2026_02, whereas 141.2 million were classified as retained. The reorganization retains all reviewed UniProtKB/Swiss-Prot entries (the expert-curated subset of UniProtKB), along with proteins from selected reference proteomes and unreviewed entries with additional biologically important data, including experimentally determined three-dimensional structures. The expected benefits include reduced redundancy, easier navigation, and a protein set that is more tractable for annotation and routine searches. However, the reorganization may reduce the visibility of protein sequences from uncultured microorganisms and metagenomic surveys, phylogenetically underrepresented lineages, particularly many archaeal groups, proteins belonging to the so-called "dark proteome," and strain-level variants of well-studied species such as Escherichia coli. We argue that the main consequence is not the loss of the sequences themselves, because affected proteins remain recoverable through UniParc and related resources, but a reduction in their discoverability, annotation context, and accessibility within routine workflows. These effects are likely to be most important for biodiversity-oriented analyses, retrospective reuse of older datasets, studies of specialized protein families, and downstream pipelines that rely on UniProtKB as an annotation hub. As UniProt shifts toward a more explicitly reference-proteome-centered model, a critical question arises: What are the implications of UniProtKB contraction for the representation of evolutionary diversity across the tree of life, particularly in under-sampled and uncultured lineages?},
}

*Proteome/genetics
*Databases, Protein
Proteomics/methods

@article {pmid42890506,
year = {2026},
author = {Yang, X and Chen, J and Song, J and Liu, H and Wang, L and Li, T and Yan, H and Gao, X and Ding, S},
title = {A nested case-control study on the relationship between gut microbiota and non-alcoholic fatty liver disease.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1917815},
doi = {10.3389/fendo.2026.1917815},
pmid = {42890506},
issn = {1664-2392},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/epidemiology ; Female ; Male ; *Gastrointestinal Microbiome ; Case-Control Studies ; Middle Aged ; Biomarkers/analysis ; Adult ; Metagenomics ; Boosting Machine Learning Algorithms ; },
abstract = {BACKGROUND: The gut microbiota plays an important role in non-alcoholic fatty liver disease (NAFLD). This study aimed to explore gut microbiota-associated biomarkers for incident NAFLD and evaluate their predictive value, providing preliminary evidence for early risk identification.

METHODS: From an initial cohort of 1,772 participants, 404 were included in the final analysis, comprising 101 incident NAFLD cases and 303 age-matched controls (1:3). Gut microbiota composition and function were characterized by metagenomic sequencing. Microbial features were compared between participants who developed NAFLD (NAFLD -/+) and those who did not (NAFLD -/-). A CatBoost model integrating gut microbiota, functional pathways, and clinical indicators was constructed to predict NAFLD, with a random forest (RF) model on the same features for comparison. Progressively enriched feature sets assessed the incremental value of microbiota-related features beyond clinical indicators, and SHapley additive exPlanations (SHAP) values interpreted the model outputs.

RESULTS: The NAFLD (-/+) group had significantly lower species-level beneficial gut microbiota (P < 0.05), and the two groups differed markedly in gut microbiota metabolic enrichment. The CatBoost model achieved an area under the curve (AUC) of 0.762, indicating moderate predictive performance for incident NAFLD. We also identified significant intergroup differences in gut microbiota composition within the diagnostic model, including the key species Coprobacillus unclassified and the metabolic pathway PWY-5030.

CONCLUSION: Gut microbiota alterations may serve as potential early biomarkers for incident NAFLD and contribute to its pathogenesis. The CatBoost model integrating multi-omics and clinical data shows moderate predictive ability, supporting the potential of gut microbiota-based approaches for non-invasive risk stratification.},
}

Humans
*Non-alcoholic Fatty Liver Disease/microbiology/epidemiology
Female
Male
*Gastrointestinal Microbiome
Case-Control Studies
Middle Aged
Biomarkers/analysis
Adult
Metagenomics
Boosting Machine Learning Algorithms

@article {pmid42890539,
year = {2026},
author = {Yao, H and Chen, J and Liu, C and Huang, J and Liu, L and Wang, Q and Wang, F},
title = {Structural and functional characterization of the gut microbiota in women with early pregnancy loss in Northwest China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1895733},
doi = {10.3389/fmicb.2026.1895733},
pmid = {42890539},
issn = {1664-302X},
abstract = {BACKGROUND: Early pregnancy loss (EPL) is a common adverse pregnancy outcome with a complex and incompletely understood etiology. Moreover, metagenomic studies of the gut microbiota in women with EPL in Northwest China remain limited.

OBJECTIVE: This study aimed to characterize differences in gut microbial composition and predicted functional potential between women with EPL (EPL group) and normal controls (NCs) using shotgun metagenomic sequencing.

METHODS: We collected fecal samples from 216 women in Northwest China (EPL group, n = 72; NCs, n = 144). Shotgun metagenomic sequencing was performed to analyze gut microbiota composition and assess the functional potential of the microbiota.

RESULTS: Our study revealed significant differences in the composition of the gut microbiota between the EPL group and NCs, as assessed by alpha and beta diversity analyses (p < 0.001). Bacteroides was significantly more abundant in the EPL group, whereas Coprococcus, Bifidobacterium, and Roseburia were significantly more abundant in NCs. Compared to NCs, the EPL group had higher relative abundances of species such as Bacteroides stercoris, Bacteroides plebeius, and Bacteroides uniformis, but lower relative abundances of Bifidobacterium adolescentis, Megamonas funiformis, and Fusicatenibacter saccharivorans. Partial correlation analysis showed that Bacteroidetes was positively correlated with EPL at the phylum level. At the genus level, Odoribacter, Parabacteroides, and Haemophilus were positively correlated with EPL, whereas Corynebacterium, Lactobacillus, and Roseburia were negatively correlated with EPL. Metabolic pathway analysis revealed that pathways such as L-rhamnose degradation I, L-arginine biosynthesis III and 2-oxobutanoate degradation I exhibited significant positive correlations with EPL. In contrast, pathways including purine nucleobases degradation I (anaerobic) and chitin derivatives degradation showed significant negative correlations with EPL.

CONCLUSION: The results of our study revealed significant differences in gut microbiota composition and metabolic pathways between the EPL group and NCs, indicating that gut microbiome alterations are associated with EPL.},
}

@article {pmid42890753,
year = {2026},
author = {Li, Y and Liu, Y and Chen, Y and Xiang, B and Fu, H and Pan, H and Xu, T and Li, Z and Zhang, Y and Yuan, H and Zhang, C},
title = {High-fiber diet altered gut microbiota, improved glycemic control, and reduced body weight in newly diagnosed type 2 diabetes and obesity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1972983},
doi = {10.3389/fmicb.2026.1972983},
pmid = {42890753},
issn = {1664-302X},
abstract = {Type 2 diabetes and obesity commonly coexist, making glycemia and body weight both central treatment goals. Few trials have directly compared a high-fiber dietary intervention with metformin. The factors associated with individual responses to high-fiber diet also remain unclear. In this single-center, open-label, head-to-head clinical trial, 48 adults with newly diagnosed type 2 diabetes and overweight or obesity were randomized to a high-fiber dietary intervention without glucose-lowering medication (n = 36) or metformin (n = 12) monotherapy for 84 days; 46 completed the trial. Clinical outcomes and 184 fecal samples were assessed longitudinally using shotgun metagenomic and metabolite profiling. At Day 84, the high-fiber group had greater reductions in glycated hemoglobin and body mass index and lower glycemic variability than the metformin group. The diet altered gut microbiota by Day 28, enriching genomes from Bifidobacterium and Lactobacillus and depleting genomes from Bilophila wadsworthia, but metformin produced little detectable microbiota change. These changes included increased acetate-production functions and decreased hydrogen sulfide-production functions; fecal hydrogen sulfide was lower at Days 28 and 56, although short-chain fatty acid concentrations did not differ between groups at matched time points. Within the high-fiber group, participants with increased fecal acetate (25 of 34) had larger glycated hemoglobin reductions at Days 28 and 56, and baseline microbial features differed between acetate-response subgroups. These findings support high-fiber diet as a non-pharmacologic strategy for diabesity, with baseline microbial features as candidate markers of response. Clinical trial registration: ChiCTR-INR-17011752.},
}

@article {pmid42890803,
year = {2026},
author = {Yang, Y and Yang, J and Zhang, W and Zhou, L and Zhu, C and Zhang, X and Mao, Y and Zhang, M},
title = {Host-microbiota interaction drives 5-hydroxyindole-3-acetic acid production to promote linear growth in infant mice.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70062},
doi = {10.1002/imo2.70062},
pmid = {42890803},
issn = {2996-9514},
abstract = {This study discovered that Lactiplantibacillus plantarum Hi188 promoted linear growth in postweaning mice. Transcriptomic analysis, untargeted metabolomics, and in vitro experiments showed that the elevated levels of 5-hydroxyindole-3-acetic acid (5-HIAA) activated the hepatic aryl hydrocarbon receptor (AhR) and subsequently promoted insulin-like growth factor-1 (IGF-1) production via the IRS1/PI3K/Akt pathway. Integrated metagenomics and reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis of host colonic genes revealed that 5-HIAA was cooperatively produced by the gut microbiota and the host. These findings offered novel perspectives on the therapeutic potential of microbiota-targeted interventions for growth regulation.},
}

@article {pmid42890805,
year = {2026},
author = {Coche-Miranda, J and Arros, P and Canales, N and Berríos-Pastén, C and Azziz, G and Lagos, R and Orlando, J and Chávez, FP and Marcoleta, AE},
title = {Antarctic soil microbiomes encode structurally conserved and phylogenetically diverse beta-lactamases.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70118},
doi = {10.1002/imo2.70118},
pmid = {42890805},
issn = {2996-9514},
abstract = {Antimicrobial resistance is a major global health threat shaped not only by clinical settings but also by environmental reservoirs, in line with the One Health framework. Antarctic and Subantarctic soils represent a largely unexplored component of the environmental resistome, particularly beta-lactamases, whose diversity, structural features, and biogeographic patterns remain poorly resolved. Here, we applied an integrative metagenomic approach combining sequence-, structure-, and function-based similarity to systematically identify putative beta-lactamase orthologs across an extensive collection of Antarctic and Subantarctic soil metagenomes. We detected multiple beta-lactamase classes and families, with a predominance of class A serine beta-lactamases and subclass B3 metallo-beta-lactamases. Several previously uncharacterized families and divergent variants were identified, many of which retain conserved catalytic architectures. Beta-lactamase diversity and relative abundance were strongly patterned across three major biogeographic clusters: Subantarctic islands, the Antarctic Peninsula and surrounding islands, and continental cold deserts, mirroring shifts in microbial community composition. The Antarctic Peninsula and maritime Antarctica exhibited the highest overall beta-lactamase abundance. Analysis of more than 3500 metagenome-assembled genomes indicated that most beta-lactamases were encoded by members of p_Pseudomonadota and p_Bacteroidota, with additional representatives distributed across other bacterial phyla. A subset was linked to mobile genetic elements, suggesting a latent but limited potential for horizontal gene transfer. Together, these findings reveal a geographically organized and compositionally diverse repertoire of beta-lactamases in (sub)Antarctic soils, underscoring the evolutionary persistence of conserved catalytic frameworks in cold environments and highlighting the contribution of remote ecosystems to global resistome diversity.},
}

@article {pmid42890814,
year = {2026},
author = {Chen, P and Taylor, JW and Gao, C},
title = {Arbuscular mycorrhizal fungal community abundance, functions, and symbiotic interactions revealed by root metatranscriptomes.},
journal = {iMetaOmics},
volume = {3},
number = {2},
pages = {e70087},
doi = {10.1002/imo2.70087},
pmid = {42890814},
issn = {2996-9514},
abstract = {Arbuscular mycorrhizal (AM) fungal communities are often profiled by metabarcoding, but this approach can bias abundance estimates and provide limited insight into community function and interactions with the host. Here, using weekly, field-based multi-omics, we find metatranscriptomes and metagenomes increase estimates of AM fungal relative abundance 6-15-fold over rDNA metabarcoding and that root AM fungal relative abundance correlates strongly with sorghum forage yield (R > 0.9) and moderately with grain yield/quality. AM fungal relative abundance is impacted directly by sorghum development and indirectly by drought via suppressed sorghum fatty acid gene expression. Gene co-expression network revealed coordinated plant and AM fungal functions in structural reorganization, resource exchange, and signal communication between the symbiotic partners. We found that early-season co-transcriptions of AM fungal and host genes feature cytoskeletal genes essential for arbuscule formation, the fungal-plant organs of nutrient and mineral exchange. Late-season plants downregulate cytoskeletal genes, but AM fungi continue their upregulation, which is associated with fungal sporulation and putative mating. Our study identifies previously ignored massive underestimation of AM fungal relative abundance, highlights the predictive role of AM fungal relative abundance for crop productivity, and uncovers symbiotic life history dynamics underpinned by coupled and decoupled co-expression of plant and AM fungal genes.},
}

@article {pmid42890823,
year = {2026},
author = {Han, Y and Peng, Y and Li, M and Wei, X and Chai, J and Zhao, J and Li, Y and Deng, F},
title = {Evidence tiers for strain-resolved long-read metagenomics.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70130},
doi = {10.1002/imo2.70130},
pmid = {42890823},
issn = {2996-9514},
abstract = {Long-read metagenomics links variants, repeats, and mobile elements across individual molecules and can reveal lineage turnover that is obscured at the species level. The strength of the resulting inference, however, depends on the type and genomic span of the recovered linkage. We distinguish four evidence units-strain profiles, local haplotype blocks, genome-scale strain candidates, and host-linkage evidence-and describe the diagnostics appropriate to each. Confidence is reported separately as candidate, supported, or high confidence in context, based on read assignment, allele coherence, coverage continuity, boundary support, and independent confirmation. Ambiguous placement, contamination, consensus collapse, coverage breaks, reference bias, or unresolved linkage should prompt more conservative terminology. Aligning terms with the available evidence reduces overstatement in claims of strain reconstruction, host assignment, persistence, replacement, and engraftment, while making analyses easier to compare and review.},
}

@article {pmid42890888,
year = {2026},
author = {Bian, P and Han, B and Zhu, H and Zhou, Y and Qi, Z and Gao, W and Wang, Y and Chen, N},
title = {Effects of cultivation of herbaceous perennials on soil microbial community structure and nitrogen cycling functions.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1961532},
doi = {10.3389/fpls.2026.1961532},
pmid = {42890888},
issn = {1664-462X},
abstract = {This study aimed to elucidate the impacts of cultivating different herbaceous perennials on the rhizosphere microenvironment, nitrogen-cycling microbial communities, and functional genes in black soils of urban green spaces in Northeast China, thereby providing a scientific basis for rational urban plant configuration and interspecific differences in soil nutrient cycling. Focusing on five commonly utilized herbaceous perennials in Changchun (Lycopus lucidus [P-LL], Salvia japonica [P-SJ], Hemerocallis fulva [P-HF], Hosta ensata [P-HE], and Pseudolysimachion spicatum [P-PS]), this study integrated conventional physicochemical analyses, metagenomic sequencing, co-occurrence networks, and Random Forest modeling to analyze rhizosphere soil nutrient profiles, nitrogen-cycling microbial community structures, and key functional gene abundances after two years of continuous cultivation. Different floral treatments significantly altered rhizosphere nutrient status and microbial community composition. The P-LL treatment exhibited relatively higher contents of total nitrogen (TN), soil microbial biomass nitrogen (SMBN), available phosphorus, and available potassium, demonstrating a high-level soil multifunctionality index (SMI). The P-PS treatment showed higher available nitrogen and ammonium nitrogen but lower SMBN, accompanied by a higher relative abundance of Actinomycetota and the assembly of a microbial co-occurrence network with enhanced connectivity and robustness, indicating a potent organic nitrogen mineralization potential in its rhizosphere. The composition of nitrogen-cycling genes remained broadly stable across treatments, dominated by ammonia assimilation genes (glnA and gltB), with a relatively low abundance of denitrification genes (nirK). Multivariate and Random Forest analyses revealed that SMBN exerted the strongest positive regulatory effect on nitrogen-sensing genes (e.g., ntrY and ntrX), whereas TN, nitrate nitrogen (NO3 [-]-N), and available potassium (AK) emerged as the paramount direct drivers determining the abundance variations of core ammonia assimilation genes. Different herbaceous perennials shaped species-specific rhizosphere nutrient and microbial functional profiles. P-LL and P-PS exhibited superior comprehensive nutrient traits and potential nitrogen mineralization characteristics, respectively, making them excellent candidate species for urban green space configuration and future mixed-planting trials in cold regions.},
}

@article {pmid42890922,
year = {2026},
author = {Lee, DH and Kim, YS and Kim, DW and Kim, DS and Cha, CJ},
title = {Long-term spatiotemporal dynamics of β-lactamase resistome in the Han River, South Korea.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1903212},
doi = {10.3389/fmicb.2026.1903212},
pmid = {42890922},
issn = {1664-302X},
abstract = {The global dissemination of antimicrobial resistance, particularly resistance to widely prescribed β-lactam antibiotics, is a critical public health threat worldwide. Aquatic ecosystems act as key reservoirs where antibiotic resistance genes accumulate and are transmitted between environmental bacteria and human pathogens within a One Health framework. To move beyond short-term observations and better understand these cross-sectoral dynamics, we conducted 5-year longitudinal surveillance using shotgun metagenomics across different seasons along the Han River, South Korea. Our analysis revealed a diverse repertoire of β-lactamases, predominantly belonging to Ambler classes A and D, which also accounted for most mobile β-lactamase genes and were enriched in densely populated downstream regions. Furthermore, β-lactamase genes exhibited clear seasonal fluctuations, with a pronounced winter surge in total and mobile β-lactamase gene abundances. We also identified a substantial fraction of novel variants, whose abundance and composition varied across spatial and seasonal gradients. Network analysis revealed that the genera Pseudomonas and Klebsiella acted as primary hosts, with their mobile β-lactamase genes highly connected to multiple taxa, suggesting important roles in β-lactamase gene transmission. These findings suggest that preemptive management of aquatic β-lactamase genes is a fundamental strategy for mitigating future resistance crises within a One Health framework and provide critical evidence for identifying transmission pathways and tracking resistance evolution between natural and clinical environments.},
}

@article {pmid42891027,
year = {2026},
author = {Qian, Q and Mo, F and Xu, F and Fan, L},
title = {Multi-omics datasets of paddy field soils to support functional and ecological analysis of microbial communities.},
journal = {Data in brief},
volume = {69},
number = {},
pages = {113298},
doi = {10.1016/j.dib.2026.113298},
pmid = {42891027},
issn = {2352-3409},
abstract = {Soil microbial communities are essential for ecosystem functioning and crop productivity. This dataset consists of 8 soil samples collected from four paddy field plots in Zhejiang, China, including organic and conventional management types during the winter fallow period under sunny conditions. For each plot, soil was sampled from two points at 10 cm depth, resulting in a total of 8 samples. Each sample was subjected to both metagenomic and metatranscriptomic sequencing, generating 16 datasets in total. DNA and RNA were extracted using standardized protocols, followed by Illumina PE150 sequencing. The metagenomic and metatranscriptomic data passed quality control and meet standard sequencing metrics, providing high-quality raw reads, assembled contigs, cDNA libraries, and gene expression matrices. These datasets are a reusable resource for studies on rice soil microbial communities and can support integration with other multi-omics data, such as proteomics or single-cell genomics, for broader investigations into soil microbial diversity and function.},
}

@article {pmid42891309,
year = {2026},
author = {Yu, M and Zhao, Z and Li, P and Teng, Y and Xu, F and Li, Z and Yang, Z and Zhao, H and Zhou, H and Xia, L and Lai, J and Xin, B},
title = {Metagenomic mining reveals novel Cas12 subtypes and their evolutionary diversification.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70057},
doi = {10.1002/imo2.70057},
pmid = {42891309},
issn = {2996-9514},
abstract = {We identified 4112 Cas12 Proteins and 6 new Cas12 subtypes, revealed their significant diversity in N-terminal regions, repeat sequences, and sequences motifs. We developed an AI-driven algorithm, Cas12fam, which allows precise annotation of 18 distinct domains in Cas12 proteins. Through detailed structural analysis, we identified two novel glycine residues in the RuvC-like nuclease domains (RuvC-I, RuvC-II), which were experimentally validated to play a critical role in the DNA-cleavage activity of Cas12. Our analyses revealed that Cas12 proteins are enriched in specific environments, with significant variation in their abundance across ecological niches.},
}

@article {pmid42891310,
year = {2026},
author = {Beblavy, R and Monaco, CL and Newkirk, CE and Xiao, J and Sohn, MB},
title = {TSLC: differential abundance analysis method for identifying biologically relevant known microbes.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag297},
doi = {10.1093/bioadv/vbag297},
pmid = {42891310},
issn = {2635-0041},
abstract = {MOTIVATION: Identifying biologically relevant microbes is a crucial task in human microbiome studies. Numerous computational and statistical methods have been proposed for this task. However, most existing methods are based solely on taxonomic information, even when whole-metagenome sequencing data are available, and thus cannot account for the fact that different microbes can perform the same or similar functions (known as functional redundancy) and for the contribution of unknown microbes to functional abundance. Hence, the identified differentially abundant microbes might not be biologically relevant to manifested phenotypes.

RESULTS: To address the issues with existing methods, we propose a two-stage procedure: (i) determining differentially abundant functions between groups; and then (ii) determining microbes significantly associated with each identified differentially abundant function. This procedure involves ℓ 1 -penalized log-contrast models and debiasing procedures to account for the compositional nature of microbiome data and the bias induced by the ℓ 1 penalty. We performed extensive simulation studies to illustrate the consequences of ignoring functional redundancy and the contribution of unknown microbes, and to assess the performance of the proposed method. We applied the proposed method to two whole-metagenome sequencing datasets and showcased substantial differences between the typical taxonomic-based analysis and the proposed method.

An R package for the proposed method is available at https://github.com/rgbeblavy/TSLC.},
}

@article {pmid42879867,
year = {2026},
author = {Gao, Y and Xu, J and Bi, X and Xiang, W and Chen, D and Huo, H},
title = {Iron-functionalized carbonized melamine sponge reinforces aerobic granular sludge and reconfigures nitrogen-metabolic potential.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127128},
doi = {10.1016/j.watres.2026.127128},
pmid = {42879867},
issn = {1879-2448},
abstract = {Aerobic granular sludge (AGS) is limited by slow granulation and structural instability under variable municipal wastewater conditions. Here, an iron-functionalized carbonized melamine sponge (Fe[3+]@CMS) was developed as a three-dimensional scaffold to accelerate granulation and improve nitrogen removal. Fe[3+]@CMS reduced the time required for complete granulation by 20 d and became embedded within the granules as a persistent internal skeleton. It promoted extracellular polymeric substance (EPS) production during granule nucleation, whereas mature Fe[3+]@CMS-supported granules maintained greater structural integrity with lower EPS accumulation, suggesting partial substitution for the native EPS-dependent framework. After transition to real municipal wastewater, the Fe[3+]@CMS reactor maintained an average soluble COD removal of 92.4% and >97% ammonium removal, and achieved a final total nitrogen removal efficiency of 84.45%, compared with 44.10% in the control. Fe[3+]@CMS also suppressed excessive Thiothrix proliferation and favored denitrifying and iron-redox-associated taxa. Metagenomic analysis indicated selective redistribution rather than overall enrichment of nitrogen-cycle genes: napA/napB and nirS showed higher relative abundances, while the DNRA/(nirK + nirS) abundance ratio decreased from 0.184 to 0.107. These findings demonstrate that Fe[3+]@CMS acts as both a persistent structural scaffold and a selective ecological niche, integrating aerobic-granule stabilization with enhanced denitrification under fluctuating wastewater conditions.},
}

@article {pmid42880064,
year = {2026},
author = {Sun, P and Tan, Y and Jia, R and Lian, J and Yang, T and Li, H and Zhu, Z and Xi, C},
title = {Impacts and mechanisms of oyster farming on denitrification and anammox in coastal sediments from Tieshan Bay, China.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108453},
doi = {10.1016/j.marenvres.2026.108453},
pmid = {42880064},
issn = {1879-0291},
abstract = {Oyster aquaculture is widely recognized as an effective way to mitigate coastal eutrophication, but critical knowledge gaps remain regarding how it modulates nitrogen removal processes, which requires further investigation. In this study, sediments from oyster farming (OY) and non-oyster farming (NOY) areas in Tieshan Bay, China, were analyzed to explore the impacts of oyster farming on denitrification and anammox in coastal sediments. OY sediments exhibited significantly higher sediment oxygen demand (SOD), total organic carbon (TOC), ammonium (NH4[+]), ferrous iron (Fe[2+]), and sulfide than NOY sediments (P < 0.05), collectively creating hypoxic conditions favorable for nitrogen removal. Denitrification dominated nitrogen removal in both areas (OY: 91.84%; NOY: 90.19%). Potential denitrification and anammox rates in OY areas were 2.25 and 1.80 times higher than those in NOY areas, respectively (P < 0.01). Redundancy analysis (RDA) identified TOC, SOD, sulfide, Fe[2+], Fe[3+], and NH4[+] as key drivers of these processes. Metagenomic analysis revealed that OY sediments were enriched in Bacillota and Bacteroidota at the phylum level, and key functional genes (nirS, nosZ, hzsB) were significantly more abundant in OY areas (P < 0.05), suggesting enhanced genetic potential for nitrogen removal. The stronger promotion of denitrification over anammox was attributed to the combined effects of TOC (electron donors), Fe[2+] (electron carrier), and sulfide (alternative electron donor for denitrification but inhibitor for anammox). These findings demonstrate that oyster aquaculture enhances the functional capacity for sedimentary nitrogen removal through physicochemical modification, microbial community selection, and enrichment of key functional genes.},
}

@article {pmid42880177,
year = {2026},
author = {Zhong, C and Zhang, J and Wang, Y and Lu, K and Sun, Y and Li, X and Ma, H and Guan, L},
title = {Oudemansiella raphanipes polysaccharide alleviates DSS-induced colitis associated with gut microbiota and ZBP1-associated PANoptosis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158856},
doi = {10.1016/j.phymed.2026.158856},
pmid = {42880177},
issn = {1618-095X},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease with limited preventive options. The edible mushroom Oudemansiella raphanipes produces polysaccharides with reported bioactivity, but the effects of its purified fraction Oudemansiella raphanipes polysaccharide (UAE-ORP) on colitis remain unknown.

PURPOSE AND METHODS: UAE-ORP was evaluated in mice with sodium dextran sulphate (DSS)-induced colitis using metagenomic and metabolomic analysis, as well as histological, ELISA and Western blot analysis of intestinal barrier function, ZBP1-associated PANoptosis-related proteins, and FFAR2/FFAR3 expression.

RESULTS: UAE-ORP alleviated DSS-induced colonic injury, reducing the DAI scores to 1.7 ± 0.3-2.7 ± 0.5 across treatment groups and restoring colon length to 6.2 ± 0.9-8.2 ± 0.8 cm across doses. UAE-ORP was associated with attenuated ZBP1-associated PANoptosis-related protein expression, increased Lachnospiraceae abundance, and restored acetic acid and 3,4-dihydroxyphthalate levels. UAE-ORP also restored the protein expression levels of FFAR2 and FFAR3. Correlation analysis suggested a potential association between Lachnospiraceae-related metabolites and FFAR2/FFAR3 signaling.

CONCLUSION: UAE-ORP alleviates DSS-induced colitis in mice. The protective effects coincide with altered gut microbiota composition, elevated microbial metabolites, restored FFAR2/FFAR3 expression, and concomitant changes in ZBP1-associated PANoptosis-related protein. These observations identify several candidate pathways warranting further investigation and provide preliminary mechanistic context for the anti-colitic activity of this mushroom polysaccharide.},
}

@article {pmid42880330,
year = {2026},
author = {Forrest-Hammond, R and Kopec, A and Alcolea-Medina, A and Batra, R and Brown, K and Enne, V and Edgeworth, J and Hemingway, J and Hoskote, A and Torres Montaguth, OE and Morfopoulou, S and Peters, M and Robertson, H and Ray, S and Schmidt, A and Snell, LB and Storey, N and Ward, D and De, S and Dixon, G and Hatcher, J and Soothill, J and Breuer, J and Brown, JR},
title = {Implementation of rapid pan-microbial metagenomics in paediatric intensive care: a single-centre, prospective, observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101461},
doi = {10.1016/j.lanmic.2026.101461},
pmid = {42880330},
issn = {2666-5247},
abstract = {BACKGROUND: Few clinical metagenomics studies have reported rapid results with associated clinical impact or described deployment of protocols beyond centres in which they were developed. We aimed to assess the feasibility and clinical impact of implementing a previously validated rapid pan-microbial respiratory metagenomic service in paediatric intensive care, reporting protocol modifications, feasibility, diagnostic performance, clinical impact, and staff perspectives.

METHODS: This single-centre, prospective, observational study was carried out at a general paediatric intensive care unit (ICU) and a cardiac paediatric ICU in Great Ormond Street Hospital (London, UK) between Nov 4, 2024, and Feb 28, 2025. Respiratory samples were obtained from patients selected by intensive care staff based on clinical suspicion of lower respiratory tract infection, with no exclusion criteria. Samples were analysed by a well-established published metagenomic workflow that simultaneously detects bacteria, fungi, and DNA and RNA viruses and provides same-day preliminary results and next-day final results; separate aliquots were sent for concurrent culture and PCR testing. Clinical impact (change in antimicrobials, diagnosis, or infection control) was evaluated through electronic health record review. Clinical staff were surveyed for their feedback via an anonymous online semistructured questionnaire.

FINDINGS: 177 samples from 122 patients (median age 3·4 months [IQR 1·2-36·0]; 54% male) were tested. 174 (98%) samples passed quality control. Sensitivity at 16-h sequencing was 89% (95% CI 80-95) for bacteria, 100% (70-100) for fungi, and 87% (76-93) for viruses, with specificities greater than or equal to 99% across all kingdoms. 42 (24%) of 174 samples analysed by metagenomics yielded 50 organisms that were not detected by routine diagnostics, all of which were confirmed by orthogonal PCR testing. Clinical impact was observed in 51 (29%) of 174 samples, comprising changes in antimicrobial therapy in 46 (26%) samples. Of these 46 samples, 15 (33%) resulted in cessation of antibiotics, ten (22%) in initiation of antibiotics, six (13%) in a change of antibiotic therapy, and 15 (33%) provided confidence to continue an empirical antibiotic choice. Of the 33 ICU staff members surveyed, 23 (72%) reported a positive view of metagenomics, none reported negative views, and 22 (67%) perceived additional benefits over routine testing.

INTERPRETATION: This clinical pilot of rapid respiratory metagenomics in paediatric intensive care showed high specificity and good sensitivity. Protocols developed for an adult population were adapted to a paediatric population, including adaptations for polymicrobial upper respiratory tract samples, which are more common in children. However, increased sensitivity and antimicrobial resistance prediction will be required for broader clinical implementation. Although changes in patient management were observed, particularly for antimicrobial stewardship, delineating the true contribution of metagenomic results offered by this study is difficult. Multicentre studies over multiple winter seasons, with control arms and predefined selection of patients and sample types, are needed to assess the impact on patient outcomes and cost-effectiveness.

FUNDING: NHS Respiratory Metagenomics Network (NHS England).},
}

@article {pmid42880389,
year = {2026},
author = {Yang, Z and Zhang, X and Zheng, S and Huang, Y and Wei, X and Zhang, Y},
title = {Gut Microbiota Remodeling Correlates with Pentose Phosphate Pathway Activation and Steroid Hormone Biosynthesis Dysregulation in Polystyrene Nanoplastic-Induced Hepatic Lipotoxicity.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {112378},
doi = {10.1016/j.cbi.2026.112378},
pmid = {42880389},
issn = {1872-7786},
abstract = {Polystyrene nanoplastics (PS-NPs) have been detected in human tissues, but the systemic consequences of chronic oral exposure remain unclear. Female Sprague-Dawley rats received environmentally relevant PS-NP concentrations of 5 or 50 mg/L in drinking water for 42 days. Gut-liver-endocrine interactions were assessed by 16S rRNA sequencing, shotgun metagenomics, fecal metabolomics, hepatic transcriptomics, and biochemical validation of selected nodes. PS-NP exposure caused notable dysregulation of serum and hepatic lipids and produced histopathological damage in the liver. The exposure was also associated with gut dysbiosis dominated by Bacteroidia, along with hepatic glucose-6-phosphate dehydrogenase (G6PD) upregulation and pentose phosphate pathway (PPP) activation, as well as NADPH accumulation. Low-dose exposure was associated with adaptive redox responses (elevated hepatic superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX)) and lipid clearance signatures, whereas high-dose exposure correlated with GSH-PX depletion, elevated 8-iso-prostaglandin (8-iso-PG), and transcriptomic evidence of mitochondrial impairment and ferroptosis vulnerability. Steroid hormone biosynthesis (SHB) disruption-declining estradiol and rising cortisol-was observed across both doses, with ovarian Cyp19a1/Cyp11a1 downregulation at low dose and additional adrenal Cyp21a2 upregulation at high dose. Multi-omics integration linked Bacteroidia enrichment to the PPP intermediate deoxyribose 5-phosphate and to reduced estrogen metabolites. Collectively, these findings outline a Gut Microbiota-PPP-SHB (GMPS) axis as a candidate integrative framework for understanding PS-NP-associated hepatic lipotoxicity. This work offers an integrative resource that identifies candidate pathways and testable hypotheses for future investigation of metabolic risks from chronic nanoplastic exposure.},
}

@article {pmid42880476,
year = {2026},
author = {Li, P and Ge, J and Wang, Y and Han, Y and Zheng, T and Liu, J and Li, L},
title = {Molecular insights into microbial transformation of dissolved organic matter from a wastewater treatment plant.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125936},
doi = {10.1016/j.envres.2026.125936},
pmid = {42880476},
issn = {1096-0953},
abstract = {Dissolved organic matter (DOM) in treated wastewater influences effluent reactivity and ecological risks. How biological treatment configurations reshape DOM at the molecular level remains unclear. This study integrated molecular characterization, metagenomic microbial community analysis and metatranscriptomic functional profiling, machine-learning interpretation, and dynamic Partial Mantel Distance network analysis to compare DOM transformation in full-scale anaerobic-anoxic-oxic process (A2O) and oxidation ditch process (OD). The A2O exhibited a stronger redox-stage-dependent DOM remodeling than the OD. In the A2O, the final aerobic effluent showed a reduced mean molecular weight of 411.45, higher O/C, and lower H/C, with lipid-like and protein-like compounds decreasing from 35.13% to 15.39% and from 35.70% to 21.44%, respectively, whereas the lignin/CRAM-like fractions increased to 47.64%, indicating preferential removal of labile aliphatic and proteinaceous molecules and enrichment of refractory DOM. The OD retained a higher final molecular weight of 451.43 and a lipid-like fraction of 33.94%, suggesting gradual stabilization under continuous circulation and mixed redox microenvironments. The microbial communities differed significantly between the processes, whereas the enzyme profiles showed weaker separation, indicating functional redundancy. The Random Forest models effectively predicted the DOM molecular fate in both processes, with macro AUC values of 0.8913 and 0.8923 for the A2O and OD, respectively. The dPMD networks revealed intermediate-mediated cascade transformations. The treatment configuration governed DOM persistence, microbial ecological control, and the refractory character of the residual effluent DOM. This study provides a molecular-level theoretical basis for optimizing biological wastewater treatment processes, regulating refractory DOM, and reducing the ecological risks associated with treated wastewater discharge.},
}

@article {pmid42880507,
year = {2026},
author = {Shirazi, MMA and Dilorom, O and Baxtiyorovna, SG and Smerat, A},
title = {Zoonotic Viral Spillover: From Reservoir Ecology and Viral Evolution to Pandemic Prevention.},
journal = {Virus research},
volume = {},
number = {},
pages = {199818},
doi = {10.1016/j.virusres.2026.199818},
pmid = {42880507},
issn = {1872-7492},
abstract = {Zoonotic viral spillover represents a major global health challenge arising from complex interactions among viral evolution, reservoir ecology, host biology, environmental disruption, and human activities. Successful emergence requires viruses to overcome successive ecological, cellular, and immunological barriers, including receptor compatibility, cellular tropism, replication efficiency, and innate immune restriction. Reservoir hosts such as bats, rodents, birds, and livestock contribute to viral maintenance and diversification through distinct ecological and physiological characteristics, while deforestation, agricultural expansion, wildlife trade, intensive farming, urbanization, and climate variability can increase opportunities for cross-species transmission. Following spillover, viral adaptation and host susceptibility determine whether infections remain sporadic or progress to sustained human transmission. This review integrates ecological, molecular, immunological, and anthropogenic determinants of zoonotic emergence and examines major historical spillover events involving coronaviruses, influenza viruses, filoviruses, henipaviruses, and arboviruses. We further evaluate genomic and metagenomic surveillance, wastewater monitoring, artificial intelligence, ecological modeling, and integrated One Health approaches for early risk assessment and pandemic preparedness. Major knowledge gaps include limited characterization of global viral diversity, surveillance bias, inadequate functional validation of newly identified viruses, fragmented data systems, and limited predictive capacity. Future prevention requires integration of technological innovation with ecological conservation, equitable surveillance capacity, responsible biotechnology governance, and sustainable One Health Planetary Health strategies.},
}

@article {pmid42880575,
year = {2026},
author = {Li, X and Xue, R and Hu, L and Jiang, Y and Zhu, F and Xiang, C and Jiang, J and Wu, C and Jiang, G and Xue, S},
title = {Coupled and decoupled antimony-arsenic mobility along environmental gradients in a mining soil: Links to geochemical contexts and microbial functional potential.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129334},
doi = {10.1016/j.envpol.2026.129334},
pmid = {42880575},
issn = {1873-6424},
abstract = {Distinct redox behavior, surface-binding affinities, and microbial transformation pathways of antimony (Sb) and arsenic (As) complicate sustainable remediation of mining soils. Understanding how these differences shape field mobility is essential for nature-based remediation that avoids unnecessary inputs. Yet whether natural gradients produce generalizable Sb-As mobility patterns and mechanisms remains unclear. Here, we integrated physicochemical, metagenomic, and statistical analyses to determine how field gradients shaped microbial functional potential and Sb-As mobility at a single Sb smelting site. We identified two Sb-As mobility modes, further supported by external validation across 60 published studies. In the decoupled mode, along resource-driven gradients including moisture, soil organic carbon, and slope-associated light exposure, water-extractable Sb increased whereas As decreased. In the coupled mode, along pH-redox gradients, especially in alkaline and oxic soils, water-extractable Sb and As increased together. The decoupled mode was generally characterized by Sb(V) and As(V) species with Sb redistribution into more labile pools but As retention in stable fractions. Metagenomic profiles linked this decoupling to heterogeneous C-N-S-Fe geochemical contexts that reshaped microbial functional potential related to electron transfer and mineral-associated reactions. By comparison, the coupled mode was characterized by redistribution of Sb and As into reactive fractions under direct pH/Eh control. Hierarchical partitioning identified environmental factors as the dominant explanatory domain for Sb and As (62.5% and 53.1% of adjusted-R[2]-based relative importance), with metagenomic functional variables contributing 18.5% and 9.3%, respectively. These contrasting mobility modes help distinguish when Sb and As may require joint or separate management, thereby supporting targeted nature-based remediation.},
}

@article {pmid42880576,
year = {2026},
author = {Liu, J and Chen, S and Huang, J and Lin, D and Zhang, L},
title = {Size-dependent Effects of Polystyrene Micro- and Nanoplastics on Gastrointestinal Microbiota in Mice: Overlooked Axial Site-Specific Heterogeneity and Radial Mucosal-Luminal Compartment Divergence.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129351},
doi = {10.1016/j.envpol.2026.129351},
pmid = {42880576},
issn = {1873-6424},
abstract = {Accumulating evidence links micro- and nanoplastics (MNPs) exposure to gastrointestinal (GI) health impairment, especially via gut microbiota disruption. However, most studies focus on fecal or cecal luminal microbiota, neglecting the inherent spatial heterogeneity of the GI tract and distinct mucosal versus luminal microbial niche responses. In this study, multi-omics was applied to investigate the effects of polystyrene nanoplastics (PS-NPs, 100 nm) and microplastics (PS-MPs, 5 μm) on mouse GI microbiota following 4-week drinking water exposure. 16S rDNA sequencing revealed that MNPs altered mucosal microbiota across the stomach, jejunum, and cecum in a size- and site-specific manner: PS-MPs predominantly disrupted gastric mucosal communities, while PS-NPs dominated perturbations in the jejunal and cecal mucosa. Correlation analysis showed that these microbial dysbioses were significantly associated with hepatorenal functional impairment, as evidenced by elevated serum γ-glutamyl transferase, alanine aminotransferase, and lactate dehydrogenase activities. Strikingly, metagenomic sequencing showed that, in stark contrast to mucosal microbiota, PS-MPs exerted more pronounced effects on the structural and functional profiles of cecal luminal microbiota than PS-NPs. Consistently, untargeted metabolomics identified more differential metabolites in cecal contents of PS-MPs-exposed mice (288) than PS-NPs-exposed counterparts (213). Our results demonstrate that microbial niche heterogeneity and size-dependent effects are critical determinants of MNP gastrointestinal toxicity, which must be incorporated into health risk assessment to guide evidence-based pollution management.},
}

@article {pmid42881160,
year = {2026},
author = {Fernandes, N and Cai, M and Warren, FJ and Duncan, A and Harris, H and Serrano Contreras, JI and Sidorczuk, K and Bernal, A and Castillo, A and Petropoulou, K and Blunt, D and Perez-Moral, N and Garcia-Perez, I and Edwards, C and Hildebrand, F and Holmes, E and Wist, J and Frost, G},
title = {Effect of dietary chickpea structures on the small intestine metabolome and microbiome: a randomised crossover trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881160},
issn = {2041-1723},
support = {BB/X018857/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; Cross-Over Studies ; *Metabolome ; Glucagon-Like Peptide 1/metabolism ; Postprandial Period ; *Cicer/chemistry ; *Intestine, Small/metabolism/microbiology ; Peptide YY/metabolism ; Female ; Adult ; Gastric Inhibitory Polypeptide/metabolism ; *Gastrointestinal Microbiome/physiology ; Ileum/microbiology/metabolism ; *Diet ; Young Adult ; },
abstract = {The human gastrointestinal tract (GIT) is central to human physiology, yet our understanding of the metabolite, microbial, and hormonal spatiotemporal dynamics in humans is limited. How these environments respond to complex food structures and homeostatic mechanisms they generate is unknown in humans. In this randomised study, ten participants consumed chickpea-based meals with intact versus broken cellular structures, with sampling of oral, gastric, duodenal and ileal fluids. The primary outcome was the postprandial enteroendocrine hormone responses (GIP, GLP-1 and PYY); secondary outcomes were GIT metabolite profiles ([1]H NMR) and ileal microbiota (shotgun metagenomics). We observed that food structure markedly altered the spatiotemporal trajectories of metabolites and dominant microbe, driving distinct enteroendocrine hormone responses. Broken-cell meals produced early GIT glucose and maltose peaks associated with rapid GIP responses, whereas intact-cell meals elevated duodenal amino acids and ileal sugars, amino acids and formate, enhancing GLP-1 and PYY responses. Microbial profiles exhibited rapid spatial reorganisation, with evidence that oral bacterial strains transmitted to the ileum, where their abundance was associated with local metabolites and PYY responses. These findings identify food structure as a determinant of postprandial gastrointestinal metabolism and enteroendocrine responses and suggest an underappreciated route for oral bacteria to reach the ileum via the food bolus and impact metabolism. ISRCTN registration: ISRCTN18097249.},
}

Humans
Cross-Over Studies
*Metabolome
Glucagon-Like Peptide 1/metabolism
Postprandial Period
*Cicer/chemistry
*Intestine, Small/metabolism/microbiology
Peptide YY/metabolism
Female
Adult
Gastric Inhibitory Polypeptide/metabolism
*Gastrointestinal Microbiome/physiology
Ileum/microbiology/metabolism
*Diet
Young Adult

@article {pmid42881180,
year = {2026},
author = {Anjur-Dietrich, MI and Jones, KG and Mullet, JI and Vo, NN and Castro, KG and Parker, SM and Chisholm, SW},
title = {Biofilm formation and dynamics in the marine cyanobacterium Prochlorococcus.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881180},
issn = {2041-1723},
support = {984601//Simons Foundation/ ; },
mesh = {*Prochlorococcus/physiology/genetics/growth & development/metabolism ; *Biofilms/growth & development ; Seawater/microbiology ; Carbon/metabolism ; Photosynthesis ; },
abstract = {The picocyanobacterium Prochlorococcus is responsible for ~10% of annual marine carbon fixation and plays a role in the global carbon budget. While these phototrophs are primarily considered free-living and neutrally buoyant in the euphotic zone, we observe that they can form biofilms on diverse substrates. This trait is conserved across Prochlorococcus ecotypes, and populations continuously transition between planktonic and biofilm states via a non-genetic heritable mechanism. Throughout their growth, cells in biofilms retain a reversible, dynamic attachment state, and measurements of growth, photosynthesis, and carbon exudation rates reveal that cells in biofilms exude more organic carbon than their planktonic counterparts. Estimates of the fraction of Prochlorococcus cells attached to particles in the ocean-obtained through metagenomic analysis of serially-fractionated samples-reveal that a significant adherent population exists throughout the euphotic and mesopelagic zones. This work describes a dimension of Prochlorococcus's ecological niche and suggests a role in carbon export to the deep sea.},
}

*Prochlorococcus/physiology/genetics/growth & development/metabolism
*Biofilms/growth & development
Seawater/microbiology
Carbon/metabolism
Photosynthesis

@article {pmid42882385,
year = {2026},
author = {Zhang, X and He, J and Zhai, Z and Zhaoyifan, X and Pei, X and Li, Y and Hou, M},
title = {Tropheryma whipplei as the Dominant Organism in Bronchoalveolar-Lavage Metagenomic Next-Generation Sequencing: A Single-Centre Case Series of 28 Patients.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/diagnostics16193230},
pmid = {42882385},
issn = {2075-4418},
support = {TJSQNYXXR-D2-119//Tianjin Municipal Commission of Health/ ; },
abstract = {Background/Objectives: Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) increasingly reports Tropheryma whipplei (T. whipplei) in patients without classical Whipple disease, but the significance of these detections is often uncertain. We aimed to quantify relative sequencing abundance, characterise the accompanying clinical, radiological, and routine laboratory phenotype, and develop a structured framework for interpretation. Methods: We retrospectively reviewed 944 consecutive BALF-mNGS tests performed at Tianjin Chest Hospital between October 2022 and March 2026. T. whipplei was detected in 47 tests; the primary analytic cohort comprised the 28 patients in whom it was the most abundant detected microorganism. Demographics, comorbidities, symptoms, chest computed tomography findings, co-detected organisms, species-level read counts, and routine laboratory indicators were summarised descriptively. Results: T. whipplei was detected in 47/944 tests (4.98%) and was the predominant (most abundant) detected microorganism in 28/47 (59.6%). In these 28 patients, the mean age was 60.2 ± 12.3 years and 15 (53.6%) were women. Cough (18/28, 64.3%) and expectoration (14/28, 50.0%) predominated, whereas fever occurred in 4/28 (14.3%); pulmonary nodules were the most common CT finding (15/28, 53.6%). T. whipplei was the sole microorganism in 11/28 (39.3%) and was co-detected in 17/28 (60.7%); it was sole or ≥10-fold more abundant than the strongest co-detected organism in 25/28 (89.3%). Leukocyte counts were within reference in 26/28, C-reactive protein was ≤5 mg/L in 19/25, and procalcitonin was at or below the assay limit in 12/14. Conclusions: Predominant (most-abundant) BALF-mNGS detection of T. whipplei commonly accompanied nonspecific respiratory presentations and a relatively indolent laboratory phenotype. Because sequence dominance cannot by itself distinguish infection from heavy carriage, interpretation should integrate read burden, orthogonal confirmation, competing pathogens and diagnoses, and systemic features.},
}

@article {pmid42882956,
year = {2026},
author = {Aksomaitiene, J and Novoslavskij, A and Kasparaviciene, B and Malakauskiene, S and Sinkevicius, R and Serniene, L},
title = {Feeder- and Drinker-Associated Microbiota Differ from Host-Associated Fecal Microbiota During a Commercial Broiler Production Cycle with Age-Associated Changes in Taxonomic Composition.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16192987},
pmid = {42882956},
issn = {2076-2615},
support = {No. 963864//Research Council of Lithuania/ ; },
abstract = {Broiler chickens are continuously exposed to microorganisms in the production environment, but the relationship between microorganisms on bird-contact surfaces and fecal microbiota remains unclear. In this exploratory observational study, shotgun metagenomic sequencing was used to compare microbial communities in feeder- and drinker-associated surface samples and individual fecal samples during one production cycle in a single commercial system housing Ross 308 broilers. The dataset comprised 22 individual fecal samples collected on days 1, 7, 19, 27, and 39 and four composite feeder- or drinker-associated environmental surface samples collected on days 1, 19, 27, and 39. Taxonomic composition, alpha and beta diversity, differential taxonomic signatures, and genus-level co-abundance patterns were evaluated. Environmental samples had greater richness and were dominated by Proteobacteria and Bacteroidetes, whereas host-associated fecal samples were dominated by Firmicutes and lactobacilli. Sample type explained 20.0% of variation in Bray-Curtis distances and 15.5% in Binary Jaccard distances (both p = 0.001). Within host-associated samples, Firmicutes increased from 51.4% on day 1 to 93.6% on day 39, while Proteobacteria decreased from 26.5% to 1.4%. Despite these taxonomic changes, host-associated communities did not form statistically distinct clusters by sampling day. Within the investigated production system, host-associated fecal microbial communities differed from those detected on the sampled feeder and drinker surfaces, while the relative abundance of dominant fecal taxa varied across sampling days. These findings are specific to the investigated production system and production cycle.},
}

@article {pmid42882996,
year = {2026},
author = {Shao, KY and Han, F and Chen, PH and Zhu, HB and Liu, BR and Xu, M and Liu, LL},
title = {Effects of Dietary Digestible Energy Levels on Milk Performance, Rumen Fermentation, and Rumen Microbiota in Lactating Bactrian Camels from Southern Xinjiang.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193027},
pmid = {42882996},
issn = {2076-2615},
support = {XJARS-11//Xinjiang Uygur Autonomous Region Dairy Industry Technology System/ ; },
abstract = {This study aimed to investigate the effects of different dietary digestible energy (DE) levels on lactation performance, rumen fermentation, and rumen microbiota in lactating Bactrian camels in southern Xinjiang. Twenty-four mid-lactation Bactrian camels were randomly assigned to four groups, with six camels per group, and were fed diets containing DE levels of 12.25 (CK), 12.49 (LE), 12.74 (ME), and 12.99 MJ/kg (HE), respectively. The experiment lasted 60 days, including a 15-day adaptation period and a 45-day experimental period. Metagenomic sequencing was performed to characterize the composition and functional gene profiles of the rumen microbiota. The results showed that increasing dietary DE significantly increased milk yield, milk fat yield, and lactose yield (p < 0.05), while decreasing ruminal NH3-N concentration. Propionate and butyrate concentrations were significantly higher in the HE group (p < 0.05). No significant differences were detected in rumen pH or the concentrations of acetate, valerate, and total volatile fatty acids among treatments (p > 0.05). No significant differences were detected in rumen microbial α-diversity or overall community structure among dietary DE treatments, although several bacterial genera showed differential enrichment. No significant differences were detected in the relative abundances of genes assigned to the major KEGG pathways or CAZy families among dietary treatments. In conclusion, within the dietary range examined in this study, higher DE was associated with greater lactation performance and changes in rumen fermentation, while no significant differences were detected in the overall rumen microbial community structure or the relative abundances of genes assigned to the major KEGG pathways and CAZy families.},
}

@article {pmid42883021,
year = {2026},
author = {Bao, J and Li, H and Jiang, K and Xu, J and Wu, Y and Ji, W and Li, S and Qi, B and Niu, H},
title = {Comparative Study on Growth Performance and Rumen Digestive Metabolism Between Cull Beef Cows and Fattening Bulls.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193052},
pmid = {42883021},
issn = {2076-2615},
support = {(32460813)//National Natural Science Foundation of China/ ; (2025YFDZ0123, 2025ZY0111, YZ2023010, TL20205TW004)//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; (GXKY26Z082).//Inner Mongolia University for Nationalities/ ; },
abstract = {Culled beef cows may retain practical value for fattening after reproductive use, but the rumen and host physiological characteristics associated with this response remain incompletely characterized. This study compared culled beef cows (CBC; n = 9) with fattening bulls (CON; n = 9) using 18 healthy Simmental crossbred cattle fed the same experimental total mixed ration (TMR) under identical feedlot conditions. Growth performance, body condition score (BCS), apparent nutrient digestibility, economic outcomes, blood indices, rumen fermentation, ruminal enzyme activities, rumen metagenomes, and plasma untargeted metabolomes were assessed. Compared with CON, CBC had higher final body weight, average daily gain, feed intake, and apparent digestibility of dry matter, crude protein, and neutral detergent fiber, whereas the feed-to-gain ratio did not differ significantly between groups (p = 0.692). BCS increased significantly from day 0 to day 60 within both cattle categories. Because different, non-cross-calibrated BCS reference frameworks were used, no between-group comparison of BCS was made. Economic analysis indicated that the value attributable to actual live-weight gain was similar between groups when within-category prices were held constant, whereas the relative economic outcome varied with feed costs and changes in live-cattle market prices. CBC also showed more propionate-oriented fermentation, greater fibrolytic enzyme activities, distinct carbohydrate-active enzyme profiles, higher insulin and leptin, and lower non-esterified fatty acids and β-hydroxybutyrate. Because lean and fat mass were not directly measured, the tissue basis of the greater weight gain remains unresolved. Overall, CBC exhibited a stronger fattening response accompanied by coordinated differences in rumen function and host metabolic profiles.},
}

@article {pmid42883035,
year = {2026},
author = {Shahbaz, GM and Ashraf, Z and Chen, S and Wang, C and He, C and Sun, H and Zhu, L and Liu, L and Wang, M and Wu, L and Gu, R and Li, W and Xing, F},
title = {Emerging and Novel Ovine Viruses: Molecular Diagnostics, Genomic and Metagenomic Surveillance, and One Health Perspectives.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193066},
pmid = {42883035},
issn = {2076-2615},
support = {No. U25A20699//Joint Funds of the National Natural Science Foundation of China/ ; No. TDZKCX202401//President's Fund Project of Tarim University/ ; No. 2024A02004-3//the Major Science and Technology Special Project of Xinjiang Uygur Autonomous Region/ ; No. BTYJXM-2024-S23//the Postgraduate Practical Innovation Project of Xinjiang Production and Construction Corps/ ; },
abstract = {Emerging and novel ovine viruses pose increasing threats to animal health, livestock productivity, trade, food security, and public health preparedness. Their emergence is driven by complex interactions among animal movement, mixed-species production systems, wildlife-livestock interfaces, arthropod vectors, environmental changes, and viral evolution. This review critically compares current strategies for identifying major, emerging, re-emerging, zoonotic, and newly recognized ovine viruses, with emphasis on their analytical sensitivity, turnaround time, throughput, operational cost, accessibility, field applicability, validation status, and capacity for novel-virus detection. Conventional diagnostic approaches, including virus isolation, serology, antigen detection, histopathology, and immunohistochemistry, remain essential for confirmation and flock-level surveillance but may be limited by slow turnaround, dependence on specialized facilities, reduced sensitivity at low viral loads, and an inability to identify highly divergent or unknown viruses. Targeted molecular assays, including PCR, RT-PCR, qPCR, multiplex assays, digital PCR, isothermal amplification, and CRISPR-based diagnostics, have improved detection speed and sensitivity but generally require prior knowledge of viral genomic targets. Genomic and metagenomic approaches, including whole-genome sequencing, next-generation sequencing, nanopore sequencing, viral metagenomics, bioinformatics, and phylogenetic analysis, provide broader detection capabilities by enabling characterization of viral diversity, outbreak tracing, co-infection identification, and discovery of previously unrecognized viruses. However, their interpretation remains challenging due to low viral abundance, poor sample quality, host nucleic acid background, contamination, incomplete reference databases, limited computational capacity, and the inability of sequence detection alone to confirm disease causality. Therefore, future ovine virus surveillance requires integration of molecular diagnostics with active, passive, outbreak-based, risk-based, vector, wildlife, and animal-movement surveillance within a One Health framework. Linking genomic information with ecological, epidemiological, and environmental data will be essential for transforming ovine virus surveillance from reactive diagnosis toward proactive preparedness. Advances in standardized sampling, validated field diagnostics, affordable sequencing, curated databases, bioinformatics capacity, and cross-sector data sharing will strengthen early recognition, risk assessment, and preparedness against emerging viral threats in sheep.},
}

@article {pmid42883377,
year = {2026},
author = {Kakimova, AB and Zaparina, YG and Zayadan, BK and Sandybayeva, SK and Kelden, D and Dauletova, AA and Piazza, S},
title = {Comparative Shotgun Metagenomics of Microbial Communities Associated with Two Geothermal Systems in Kazakhstan.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191704},
pmid = {42883377},
issn = {2079-7737},
support = {АР26194471//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Geothermal-associated microbial communities remain poorly characterized in Central Asia. Here, shotgun metagenomics was used to compare microbial communities associated with thermally influenced substrates from the Chundzha and Rakhman geothermal systems in Kazakhstan. Six metagenomes representing three spatial replicates per site yielded approximately 6.5-7.3 Gb of clean sequence data per sample. Species-level richness showed a directional trend toward higher values in Chundzha, whereas Shannon diversity was similar between sites. Genus-level Bray-Curtis ordination showed apparent site-associated separation, with sampling site explaining 87.3% of the variation, although the effect was not statistically significant (PERMANOVA, R[2] = 0.873, p = 0.10). Chundzha showed greater relative representation of several halophilic and halotolerant taxa, whereas Rakhman showed greater representation of soil-associated lineages. Broad COG and KEGG functional profiles were largely shared between sites. Several hydrogenase-, nitrogenase-, and RuBisCO-associated genes showed higher relative representation in Rakhman, whereas selected fermentation- and photosynthesis-associated functions were relatively higher in Chundzha; however, none of the targeted KO comparisons remained significant after FDR correction. These results indicate candidate taxonomic and functional patterns that should be regarded as exploratory because of the limited replication. The dataset provides a baseline for future genome-resolved and metatranscriptomic studies of geothermal-associated microbial communities in Kazakhstan.},
}

@article {pmid42883560,
year = {2026},
author = {Tong, T and Wu, J and Jia, S and Liao, C and Zhang, H and Xie, J and Chen, W and Huang, Y and Wang, X and Wu, X and Zhou, Y and He, Y and Zhao, K},
title = {Polyphenol Bioconversion and Volatile Aroma Production by Meyerozyma sp. C3 Isolated from Kombucha in the Theaflavin-Sucrose Fermentation Model.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/foods15193453},
pmid = {42883560},
issn = {2304-8158},
abstract = {This study integrated metagenomic and untargeted metabolomics analysis to characterize differences in kombucha communities and metabolites between black tea-sucrose and theaflavin-sucrose systems. Theaflavins selectively enriched yeasts, particularly Meyerozyma and Lodderomyces, and increased the annotated abundance of carbohydrate-metabolism genes, glycoside hydrolases, and glycosyltransferases. Based on these community-level findings, the newly isolated Meyerozyma sp. C3 was employed to establish a simplified single-strain fermentation model to investigate the biotransformation potential of the enriched yeast taxon. The strain exhibited stable growth and sustained acidification throughout fermentation, with a theaflavin conversion rate of 39.5% after 7 days. Metabolomic analysis revealed substantial changes in oligosaccharides (e.g., maltotriose, raffinose), flavonoids/flavanes (e.g., epigallocatechin gallate, (+)-gallocatechin, (-)-epigallocatechin, and catechin derivatives), and organic acids (e.g., citric and isocitric acid), while volatile profiling identified 2-phenylethanol and 4-ethylphenol as newly dominant aroma compounds after fermentation. These results indicate that a yeast-driven route for theaflavin transformation and flavor formation, supporting targeted strain mining and functional fermented-tea development.},
}

@article {pmid42883692,
year = {2026},
author = {Zhang, W and Zhu, Y and Chu, X and Zhang, X and Pan, Z and Li, A},
title = {Co-Enrichment of Desulfovibrio and Erysipelotrichaceae and Dysregulation of Multiple Amino Acid Pathways in HFpEF: Insights into TXG-Associated Metabolic Changes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198445},
pmid = {42883692},
issn = {1422-0067},
support = {82174080//National Natural Science Foundation of China/ ; H2022423333//Hebei Provincial Department of Science and Technology/ ; },
mesh = {Animals ; *Amino Acids/metabolism/blood ; *Heart Failure/metabolism/microbiology/drug therapy ; *Desulfovibrio/genetics/isolation & purification ; Mice ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Male ; *Eubacteriales/genetics ; Diet, High-Fat/adverse effects ; Metabolome ; Metagenomics ; },
abstract = {Gut enrichment of Desulfovibrio and Erysipelotrichaceae may be associated with systemic amino acid metabolic dysfunction, myocardial injury, and heart failure with preserved ejection fraction (HFpEF). These taxa appear to influence host amino acid metabolism through distinct processes, but the functional implications of their co-enrichment in HFpEF remain unclear. Total xanthones from Gentianella acuta (TXG) have documented cardioprotective effects, although their effects on gut microbiota and systemic metabolism remain unexplored. We established a mouse model of HFpEF using a high-fat diet (HFD) combined with Nω-nitro-L-arginine methyl ester (L-NAME). We integrated 16S rRNA sequencing, fecal metagenomics, and targeted serum amino acid metabolomics to examine microbe-metabolite associations, with echocardiography and histopathology providing complementary phenotypic evidence. Microbial and metabolomic analyses revealed pronounced enrichment of Desulfovibrio and Erysipelotrichaceae (particularly Dubosiella), accompanied by elevated serum isoleucine, tryptophan, and homocysteine levels. TXG treatment was associated with lower abundance of both taxa, altered serum amino acid profiles, preserved colonic barrier integrity, and reduced myocardial inflammation and fibrosis. These changes coincided with improved diastolic function. Together, these findings associate co-enrichment of the two taxa with dysregulation of multiple amino acid pathways in HFpEF. TXG treatment was accompanied by attenuated cardiac and metabolic injury as well as shifts in gut-microbiota profiles, with these correlative observations motivating further investigation of Gentianella acuta for metabolic heart failure.},
}

Animals
*Amino Acids/metabolism/blood
*Heart Failure/metabolism/microbiology/drug therapy
*Desulfovibrio/genetics/isolation & purification
Mice
Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Male
*Eubacteriales/genetics
Diet, High-Fat/adverse effects
Metabolome
Metagenomics

@article {pmid42883703,
year = {2026},
author = {Pérez-Castro, S and Carballo-Quinta, M and Rodríguez-Costas, N and Freire-Rodríguez, A and Davina-Nunez, C and Bellas-Pereira, A and Taboada-Rodríguez, P and Pérez-Schoch, M and Cabrera-Alvargonzález, JJ and Muller-Arteaga, CA and Sánchez-García, JF and Cespón-Outeda, E and López-Díez, ME},
title = {Gut Microbiota Signatures Associated with Metastatic Prostatic Cancer Treated with Androgen Receptor Pathway Inhibitor (ARPI) Therapy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198454},
pmid = {42883703},
issn = {1422-0067},
support = {Leonardo de la Peña 2022 Grant//Urological Research Foundation/ ; GAIN IN607B-2022-19//Axencia Galega de Innovacion/ ; },
mesh = {Humans ; Male ; *Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Androgen Receptor Antagonists/therapeutic use/pharmacology ; *Receptors, Androgen/metabolism ; Neoplasm Metastasis ; Aged ; Disease Progression ; Metagenomics/methods ; },
abstract = {Metastatic prostate cancer (MPCa) remains an aggressive disease despite the introduction of androgen receptor pathway inhibitors (ARPIs), and biomarkers predicting progression are still lacking. The aim of this study was to investigate gut microbiota (GM) composition and functional potential associated with advanced disease and progression under ARPI therapy. The GM of 15 patients with metastatic PCa receiving ARPIs, including 5 patients with disease progression, was compared with that of 39 patients with untreated (UT) PCa using shallow shotgun metagenomic sequencing. The metastatic PCa cohort receiving ADT plus ARPI therapy showed reduced microbial alpha diversity and significant taxonomic and functional differences compared with the untreated, clinically localized PCa reference cohort. In patients with advanced disease, microbial functions related to dietary carbohydrate utilization, fermentation, epithelial interaction, and microbial structural maintenance were predominantly underrepresented, whereas stress-responsive and redox-associated functions were overrepresented. These alterations may reflect reduced metabolic and ecological versatility alongside increased adaptation to host-associated stress conditions. Compared with the UT group, in patients with progression we found that Bifidobacterium longum, Anaerobutyricum hallii, Ruminococcus sp., and Blautia obeum (LinDA coefficients 5.7, 2.6, 2.6 and 2.4, respectively) were enriched, whereas Sutterella wadsworthensis, Butyricimonas, Bilophila wadsworthia, Alistipes indistinctus, and Intestinimonas were depleted (LinDA coefficients -8.4, -5.9, -5, -5 and -3, respectively). Together, these findings identify distinct taxonomic and functional features associated with metastatic PCa under systemic therapy and microbial features observed in patients experiencing progression during ARPI treatment, providing potential candidates for biomarker development and generating testable hypotheses regarding microbiome-host metabolic interactions in treatment resistance. The GM may therefore represent a potential source of biomarkers for advanced PCa and progression under ARPI therapy, although longitudinal and multi-omics studies are required to determine their predictive value and functional relevance.},
}

Humans
Male
*Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/drug effects
*Androgen Receptor Antagonists/therapeutic use/pharmacology
*Receptors, Androgen/metabolism
Neoplasm Metastasis
Aged
Disease Progression
Metagenomics/methods

@article {pmid42883729,
year = {2026},
author = {Liu, N and Zhang, S and Li, Y},
title = {Molecular Mechanisms of the Gut-Liver-Placenta Axis in Intrahepatic Cholestasis of Pregnancy: Microbiota-Associated Pathogenesis and Next-Generation Therapeutic Strategies.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198481},
pmid = {42883729},
issn = {1422-0067},
support = {XLYC2412033//LiaoNing Revitalization Talents Program/ ; },
mesh = {Humans ; Female ; *Cholestasis, Intrahepatic/metabolism/microbiology/therapy/etiology/pathology ; Pregnancy ; *Pregnancy Complications/metabolism/microbiology/therapy/etiology ; *Placenta/metabolism ; Bile Acids and Salts/metabolism ; Animals ; *Liver/metabolism/pathology ; *Gastrointestinal Microbiome ; Dysbiosis ; },
abstract = {Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder characterized by elevated maternal bile acid concentrations and an increased risk of adverse perinatal outcomes. Genetic susceptibility, hormonal changes, and impaired bile acid transport contribute to its development but do not fully explain the variability in disease severity and fetal outcomes. Increasing evidence suggests that gut microbiota dysbiosis and altered bile acid metabolism are associated with ICP and may participate in disease development through the gut-liver-placenta axis. In this review, we integrate evidence on bile acid-microbiota interactions during pregnancy, ICP-associated microbial and metabolic alterations, and their possible links to placental and fetal outcomes. Human studies primarily support associations among microbial alterations, bile acid profiles, and disease severity, whereas the microbiota-mediated effects on placental function and fetal injury proposed to date are supported largely by experimental models. We further discuss potential links among gut microbial dysfunction, placental oxidative stress, fetal cardiac injury, neurodevelopmental risk, offspring metabolic susceptibility, and iatrogenic prematurity. Although ursodeoxycholic acid (UDCA) improves maternal pruritus and selected biochemical indices, its effect on major perinatal outcomes remains uncertain. Ileal bile acid transporter (IBAT) inhibitors and microbiota-targeted interventions remain investigational, with insufficient pregnancy-specific evidence regarding their efficacy and maternal-fetal safety. Future studies should clarify the associated causal mechanisms and integrate metagenomic, metabolomic, and placental data to identify clinically relevant biomarkers and therapeutic targets.},
}

Humans
Female
*Cholestasis, Intrahepatic/metabolism/microbiology/therapy/etiology/pathology
Pregnancy
*Pregnancy Complications/metabolism/microbiology/therapy/etiology
*Placenta/metabolism
Bile Acids and Salts/metabolism
Animals
*Liver/metabolism/pathology
*Gastrointestinal Microbiome
Dysbiosis

@article {pmid42883733,
year = {2026},
author = {Abdulkhakov, SR and Safina, DD and Markelova, MI and Ponomareva, ER and Siniagina, MN and Khusnutdinova, DR and Kupriyanova, OV and Abdulkhakov, RA and Grigoryeva, TV},
title = {Metagenomic and Metabolomic Signatures of Gut Microbiota After Helicobacter pylori Eradication Therapy Supplemented with Butyric Acid and Inulin: Observational Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198485},
pmid = {42883733},
issn = {1422-0067},
support = {12/2025-PD-KFU//Tatarstan Academy of Sciences/ ; },
mesh = {Humans ; *Inulin/pharmacology/therapeutic use/administration & dosage ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/metabolism ; Adult ; *Butyric Acid/pharmacology/therapeutic use/administration & dosage ; Middle Aged ; Metagenomics/methods ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Female ; Male ; Fatty Acids, Volatile/metabolism ; Metabolomics/methods ; *Metabolome ; Young Adult ; Anti-Bacterial Agents/therapeutic use ; Metagenome ; },
abstract = {The long-term impact of eradication therapy for Helicobacter pylori on the gut microbiota is a subject of significant interest. To evaluate the influence of the bismuth-based quadruple H. pylori eradication therapy supplemented with butyrate and inulin on functional alterations within the gut microbial community, metagenomic and metabolomic profiling were performed. Fecal samples were collected from 15 patients (aged 19-64 years) prior to the treatment, immediately after the treatment, and one month after the therapy. A significant decrease in the relative abundance of Actinobacteria, such as Bifidobacterium and Collinsella, was observed after the therapeutic intervention. In contrast, the levels of Faecalibacterium prausnitzii remained consistent, while Roseburia faecis levels exhibited a substantial decline, suggesting a disruption in key butyrate-producing bacteria. A moderate increase in the relative abundance of opportunistic Proteobacteria, Firmicutes, and Bacteroides was observed. A comprehensive analysis of short-chain fatty acids (SCFAs) levels in the feces of the patients revealed a decline in the butyric acid concentration in response to the therapy, followed by a return to baseline levels. However, the level of valeric acid declined, and there was no tendency for it to increase after a month-long course of therapy. It is important to note that these shifts persisted for a period of four weeks. Consequently, the H. pylori eradication therapy intervention promotes a persistent microbial reorganization, and the observed recovery is unlikely to be spontaneous and probably reflects the protective effect of butyrate and inulin supplementation. To confirm the conclusions, a larger sample size and longer-duration studies are required.},
}

Humans
*Inulin/pharmacology/therapeutic use/administration & dosage
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology/metabolism
Adult
*Butyric Acid/pharmacology/therapeutic use/administration & dosage
Middle Aged
Metagenomics/methods
*Gastrointestinal Microbiome/drug effects
Feces/microbiology
Female
Male
Fatty Acids, Volatile/metabolism
Metabolomics/methods
*Metabolome
Young Adult
Anti-Bacterial Agents/therapeutic use
Metagenome

@article {pmid42883741,
year = {2026},
author = {Zhukov, IS and Alnefeesi, Y and Gladyshev, NS and Zolkin, A and Zalicheva, AB and Chalabiani, Y and Miklya, I and Ermolenko, EI and Gainetdinov, RR},
title = {Gut Microbiome Alterations in TAAR5 Knockout Mice and In Silico Ligand Prediction.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198493},
pmid = {42883741},
issn = {1422-0067},
support = {148723091//St Petersburg University/ ; },
mesh = {Animals ; *Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry ; Mice, Knockout ; Trace Amine-Associated Receptors ; Mice ; *Gastrointestinal Microbiome/genetics ; Molecular Docking Simulation ; Ligands ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Trace amine-associated receptors (TAARs) are a class of G protein-coupled receptors with roles in olfaction, behaviour, and immunity. Known best as an olfactory receptor, TAAR5 has been linked to emotional behaviour and hippocampal neurogenesis, yet its peripheral mechanisms remain poorly understood. Given bidirectional influences between the gut microbiota and the host, we investigated whether TAAR5 deletion alters the gut microbiome in mice. Using 16S rRNA sequencing, we compared the gut microbiota of TAAR5-knockout (TAAR5-KO) and wild-type mice. While alpha-diversity remained unchanged, beta-diversity analysis revealed significant separation between genotypes, with TAAR5-KO mice exhibiting markedly increased inter-individual variability. Taxonomically, KO mice showed a significant reduction in Ruminococcus and ASF356, alongside an enrichment of specific Lachnospiraceae and Prevotellaceae lineages. Functional metagenomic prediction (PICRUSt2) implied a reduction in the metagenomic capacity for central metabolic pathways (glycolysis, TCA cycle, fatty acid β-oxidation) and an increase in the capacity for guanosine nucleotide degradation pathways; these hypotheses remain untested. Molecular docking identified candidate microbial metabolites, including small amines (2-aminophenol, aminoacetone, butan-1-amine), with ligand efficiencies comparable to the known TAAR5 agonist trimethylamine. These findings suggest that TAAR5 may influence gut microbiome composition and function, with particular impact on Ruminococcus-a genus linked to intestinal inflammation. The increased compositional variability in TAAR5-KO mice suggests that TAAR5 may act as a homeostatic gatekeeper in gut microbial ecology. Our in silico results offer testable hypotheses for future validation of microbial metabolites as novel TAAR5 ligands.},
}

Animals
*Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry
Mice, Knockout
Trace Amine-Associated Receptors
Mice
*Gastrointestinal Microbiome/genetics
Molecular Docking Simulation
Ligands
RNA, Ribosomal, 16S/genetics

@article {pmid42883855,
year = {2026},
author = {Dessalegn, B and Debelo, M and Palmieri, N and Dublecz, K and Hess, M and Awad, WA},
title = {Early-Life Oat Supplementation Is Associated with Altered Cecal Microbiota and Microbial Metabolic Profiles and Reduced Campylobacter jejuni Colonization in Broiler Chickens.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198607},
pmid = {42883855},
issn = {1422-0067},
support = {FWF; P 36720//FWF Austrian Science Fund/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology/metabolism ; *Campylobacter jejuni ; *Avena/chemistry ; *Dietary Supplements ; *Campylobacter Infections/veterinary/microbiology ; Animal Feed ; *Gastrointestinal Microbiome/drug effects ; Amino Acids/metabolism ; Fatty Acids, Volatile/metabolism ; Diet ; *Metabolome ; *Poultry Diseases/microbiology/prevention & control ; },
abstract = {Campylobacter jejuni is a leading foodborne pathogen that commonly colonizes the intestinal tract of broiler chickens and represents a significant food safety concern. Dietary intervention may provide a practical approach to modulate the gut microbiota and reduce pathogen colonization. This study investigated the effects of oat supplementation on C. jejuni colonization and dissemination, cecal microbiota and predicted functions, and cecal short-chain fatty acids (SCFAs) and ileal amino acid profiles during early-life infection in broiler chickens. One-day-old Ross 308 broiler chickens were fed a basal diet or diets containing 10% oat (MDF) or 20% oat (HDF) and orally infected with C. jejuni at 2 days of age. C. jejuni loads in the cecum, jejunum, liver, and spleen were quantified by culture. Cecal microbiota composition and predicted functional profiles were characterized by shotgun metagenomic sequencing, while cecal SCFAs and ileal amino acids were quantified at 21 and 35 dpi using gas chromatography and an automatic amino acid analyzer, respectively. Oat supplementation reduced intestinal C. jejuni loads and limited dissemination to the liver and spleen, with the MDF diet reducing cecal loads by up to 3.3 log10 CFU/g at 35 dpi (p < 0.05). Infection altered cecal microbial diversity and community structure, while oat supplementation modified these infection-associated microbial patterns, with MDF showing the most consistent effects. Differential abundance analysis identified changes in taxa, including Bacteroides, Parabacteroides, and Phocaeicola, together with changes in predicted functions related to motility and chemotaxis, iron acquisition, and dormancy/sporulation. These microbial changes coincided with alterations in cecal isobutyrate and ileal amino acids, particularly glutamate, serine, proline, and aspartate, in MDF-fed infected chickens. Overall, MDF supplementation was most consistently associated with reduced C. jejuni colonization and dissemination and concurrent changes in the developing cecal microbial and metabolic profiles.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology/metabolism
*Campylobacter jejuni
*Avena/chemistry
*Dietary Supplements
*Campylobacter Infections/veterinary/microbiology
Animal Feed
*Gastrointestinal Microbiome/drug effects
Amino Acids/metabolism
Fatty Acids, Volatile/metabolism
Diet
*Metabolome
*Poultry Diseases/microbiology/prevention & control

@article {pmid42884044,
year = {2026},
author = {Ravin, NV and Gureeva, MV and Beletsky, AV and Grabovich, MY},
title = {The Genomic Characterization of a Novel Candidatus Genus of the Family Gallionellaceae, a Novel Candidatus Species of the Genus Gallionella and Their Metabolic Potential for Iron Oxidation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198801},
pmid = {42884044},
issn = {1422-0067},
support = {25-14-00062//Russian Science Foundation/ ; },
mesh = {Oxidation-Reduction ; *Iron/metabolism ; Phylogeny ; *Genome, Bacterial ; *Gallionellaceae/genetics/metabolism/classification ; Genomics/methods ; },
abstract = {The family Gallionellaceae includes neutrophilic, aerobic, iron-oxidizing bacteria, many of which remain uncultured and known only from metagenomic data. In this study, two high-quality Gallionellaceae genomes were assembled from a ferruginous spring in the Voronezh region, Russia. Phylogenetic analysis based on 120 concatenated proteins, ANI (average nucleotide identity), and AAI (average amino acid identity) indicates that BG-057 belongs to the genus Gallionella and BG-364 to the genus 39-52-133. We propose the names "Candidatus Gallionella aquifuscii" sp. nov. for BG-057 and "Candidatus Dubininella ochracea" gen. nov., sp. nov. for BG-364. Both genomes encode genes for the Calvin-Benson-Bassham (CBB) cycle. Both are potentially capable of aerobic respiration due to the presence of electron transfer chain components. Both genomes encode the iron oxidase Cyc2, and BG-057 also encodes MtoA. BG-057 is potentially capable of lithotrophic growth in the presence of H2 and H2S. BG-364 is potentially capable of growth via Mn (II) oxidation; arsenite oxidation; the direct oxidation of thiosulfate; H2S, elemental sulfur, and sulfite oxidation. BG-364 encodes denitrification genes (narGHI, nirS, norBC). BG-057 possesses systems for the biosynthesis and export of siderophores, while BG-364 lacks these systems but retains Ton-dependent receptors, suggesting the use of exogenous siderophores.},
}

Oxidation-Reduction
*Iron/metabolism
Phylogeny
*Genome, Bacterial
*Gallionellaceae/genetics/metabolism/classification
Genomics/methods

@article {pmid42884152,
year = {2026},
author = {Jenkins Sánchez, L and Poppe, J and Baudot, A and Vu, LD and Villella, W and Van den Abbeele, P},
title = {Impact of Triacetin- and Tributyrin-Based Formulations on IBS Microbiome Composition and SCFA Profiles: A Preclinical Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198910},
pmid = {42884152},
issn = {1422-0067},
mesh = {Humans ; *Triglycerides/pharmacology ; *Fatty Acids, Volatile/metabolism ; *Triacetin/pharmacology ; *Irritable Bowel Syndrome/microbiology/drug therapy/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Adult ; Male ; Prebiotics/administration & dosage ; Female ; Butyrates/metabolism ; },
abstract = {Irritable bowel syndrome (IBS) is a prevalent yet poorly understood functional gut disorder frequently associated with microbial dysbiosis, making microbiome-targeting interventions a promising management strategy. In this study, we evaluated the microbiome-modulating potential of three doses of triacetin (TA; ReBiome™; 100, 200 and 300 mg/day) and two finished formulations containing TA and/or tributyrin (TB): Active Biome™ (AB) and Bio Complete 3™ (BC3). Inulin served as a benchmark prebiotic. The validated ex vivo Systemic Intestinal Fermentation Research (SIFR[®]) technology pipeline was applied using fecal microbiota from eight adults with IBS. TA dose-dependently increased short-chain fatty acid (SCFA) levels from 100 mg/day, significantly increasing acetate and butyrate while maintaining low gas formation. In addition to acetate and butyrate, AB and BC3 also promoted propionate while BC3 induced a particularly pronounced butyrate increase. Overall, both formulations induced stronger SCFA but milder gas increases than inulin. TA, AB and BC3 enriched IBS-depleted, butyrate-associated OTUs related to Faecalibacterium and Anaerobutyricum species. AB and BC3 increased microbial diversity (community modulation score (CMS)) by promoting Bifidobacteriaceae, Lachnospiraceae and Bacteroidaceae. Overall, TA and TA/TB-containing formulations promoted butyrate production, potentially helping mitigate IBS symptom severity by inducing a favorable fermentation profile with limited gas formation.},
}

Humans
*Triglycerides/pharmacology
*Fatty Acids, Volatile/metabolism
*Triacetin/pharmacology
*Irritable Bowel Syndrome/microbiology/drug therapy/metabolism
Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Fermentation
Adult
Male
Prebiotics/administration & dosage
Female
Butyrates/metabolism

@article {pmid42884177,
year = {2026},
author = {Rodríguez-Costas, N and Rodríguez-Blanco, A and Expósito, CR and Cubiella, J and Stompel, ES and Fernández-de-Ana Portela, C and Martín, AID and Taboada-Rodríguez, P and Silva, BF and Fernández, MDR and Zarraquiños, S and Remedios, D and Gómez, CAS and Lorenzo, SA and Poceiro, RF and Parga, MLC and Ramírez, VH and Pérez-Castro, S},
title = {Beyond Taxonomy: Fungal Nutraceutical Supplementation Modifies the Functional Potential of the Gut Microbiome in Colorectal Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198936},
pmid = {42884177},
issn = {1422-0067},
support = {N.º Solicitud SOL-00105490, N.º Expediente EXP0010549//Centre for Industrial Technological Development/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Fungi/chemistry ; Female ; Male ; Feces/microbiology ; Metagenomics/methods ; Middle Aged ; Aged ; },
abstract = {The gut microbiome is increasingly recognized as an important determinant of host immune regulation, intestinal homeostasis, and recovery after colorectal cancer (CRC) surgery. Although our previous randomized, double-blind, placebo-controlled clinical trial demonstrated that fungal nutraceutical supplementation with Micodigest[®] was associated with favorable taxonomic and systemic inflammatory changes in patients undergoing CRC surgery with curative intent, the functional consequences of this intervention remain poorly understood. Here, we performed a functional metagenomic analysis of fecal samples collected from patients enrolled in the original clinical trial to investigate whether Micodigest[®] supplementation was associated with changes in the functional potential of the gut microbiome. A total of 37 patients were analyzed, including 24 receiving Micodigest[®] and 13 receiving placebo, with paired samples collected before supplementation and after 4-6 weeks of intervention. Shallow shotgun metagenomic sequencing was performed, and microbial functional potential was characterized using KEGG Orthologues (KOs). Differential abundance analysis identified 14 significantly different KOs between groups at baseline and 23 after intervention, with no overlap between the two sets of orthologues. Following supplementation, Micodigest[®]-treated patients exhibited increased representation of functions related to CRISPR-associated systems, bacteriophage biology, and chitin-derived carbohydrate utilization, together with reduced representation of nutrient acquisition systems, conjugative transfer, sulfur metabolism, and components of the Wood-Ljungdahl pathway. These functional signatures suggest coordinated changes in microbial ecological adaptation, nutrient utilization, genetic exchange, and metabolic activity following fungal nutraceutical supplementation. Integration with previously reported taxonomic and inflammatory findings supports the hypothesis that Micodigest[®] may promote coordinated remodeling of the gut microbiome and host-microbiota interactions during the perioperative period. Although the present study cannot establish causality or directly infer microbial activity from metagenomic potential, these findings provide novel functional insights into the microbiome response to fungal nutraceutical supplementation in patients with CRC and highlight functional metagenomics as a valuable complement to taxonomic profiling.},
}

Humans
*Colorectal Neoplasms/microbiology
*Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Fungi/chemistry
Female
Male
Feces/microbiology
Metagenomics/methods
Middle Aged
Aged

@article {pmid42884562,
year = {2026},
author = {Xu, Z and Lau, RI and Qi, H and Wong, MCS and Chan, KHN and Lau, ISF and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC},
title = {Synbiotic HQP08 Supplementation for Hair Loss and Depressive Symptoms: An Open-Label Pilot Study of Clinical Outcomes and Gut Microbiome Changes.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193111},
pmid = {42884562},
issn = {2072-6643},
support = {//InnoHK/ ; },
mesh = {Humans ; Pilot Projects ; *Alopecia/microbiology/therapy ; Female ; Male ; Adult ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Synbiotics/administration & dosage ; Treatment Outcome ; *Depression/therapy/microbiology ; *Bifidobacterium longum ; Dietary Supplements ; Young Adult ; },
abstract = {Background: Gut microbiota dysregulation has been implicated in hair loss via the gut-skin axis, but human interventional data are limited. We previously showed that Bifidobacterium longum HK003 reverses alopecia-like phenotypes in mice. Methods: We conducted an open-label, single-arm pilot study to evaluate an HK003-containing synbiotic (HQP08) in 32 adults with self-reported hair loss over 8 weeks. The primary endpoint was the proportion of participants reporting improvement on the Patient Global Impression of Change (PGI-C) scale at week 8. Secondary outcomes included changes in hair loss severity, 60 s hair count, depressive symptoms (PHQ-9), safety, and gut microbiome composition (Chinese Clinical Trial Registry ChiCTR2500112698). Results: At week 8, 62.5% (20/32) of participants reported PGI-C improvement. Significant reductions were observed in hair loss severity (p = 0.0008), 60 s hair count (p = 0.0048), and PHQ-9 scores (p = 0.002). Younger age was associated with PGI-C response (OR per year 0.86, 95% CI: 0.73-0.98, p = 0.037). Metagenomic analysis identified engraftment of B. longum HK003-like profiles in a subset of participants at week 12. Changes in microbial pathways related to thiamine metabolism, vitamin B12 salvage, and lipopolysaccharide biosynthesis were associated with ΔPHQ-9 (FDR-adjusted p < 0.05), but not with hair-related endpoints. No serious adverse events occurred. Conclusions: This first-in-human pilot study suggests that HQP08 was well tolerated and was associated with within-participant changes in hair-loss measurements and PHQ-9 scores. Randomized controlled trials are warranted to confirm efficacy and further elucidate mechanisms within the gut-brain-skin axis.},
}

Humans
Pilot Projects
*Alopecia/microbiology/therapy
Female
Male
Adult
*Gastrointestinal Microbiome/drug effects
Middle Aged
*Synbiotics/administration & dosage
Treatment Outcome
*Depression/therapy/microbiology
*Bifidobacterium longum
Dietary Supplements
Young Adult

@article {pmid42884650,
year = {2026},
author = {Zhao, X and Yang, C and Gao, L and Gao, Y and Qian, W and Liu, H and Sun, Z and Wang, G and Zhao, F},
title = {Heat-Inactivated Lacticaseibacillus paracasei PC-01 Alleviates DSS-Induced Colitis in Mice by Modulating Gut Microbiota and Intestinal Barrier Function.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193199},
pmid = {42884650},
issn = {2072-6643},
support = {23402050//National Natural Science Foundation of China/ ; 2024YFA1307002//National Key Research and Development Program of China/ ; 2024QN03052//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; SPKJ202206//Science and technology project of the Food Science and Engineering College, Inner Mongolia Agricultural University/ ; },
mesh = {Animals ; Mice, Inbred C57BL ; *Lacticaseibacillus paracasei/physiology ; *Gastrointestinal Microbiome ; Mice ; Intestinal Barrier Function ; Dextran Sulfate ; *Colitis/chemically induced/microbiology/therapy ; Cytokines/blood/metabolism ; Disease Models, Animal ; Male ; Hot Temperature ; *Probiotics/pharmacology ; Intestinal Mucosa/microbiology/metabolism ; },
abstract = {Background: Inflammatory bowel disease (IBD) is a chronic, progressive, immune-mediated inflammatory disorder of the gastrointestinal tract. Methods: This study used C57BL/6J mice induced by DSS to construct an intestinal inflammation model, and explored the alleviating effect and potential mechanism of heat inactivated Lactobacillus paracasei PC-01 (PC-01) on intestinal inflammation. Results: The results showed that heat-inactivated PC-01 significantly decreased the Disease Activity Index and H&E histopathological scores (p < 0.05). It also reduced the serum levels of pro-inflammatory cytokines, including IL-6, IL-1β, TNF-α, and malondialdehyde (p < 0.01), increased the levels of the anti-inflammatory factor IL-10 (p < 0.001) and antioxidant enzymes SOD and GSH-Px (p < 0.01), and restored the integrity of the intestinal epithelial barrier in DSS-induced colitis mice. Metagenomic analysis showed that PC-01 treatment restored the abundance of beneficial bacteria, including Barnesiella and Muribaculum, and reduced the enrichment of opportunistic pathogens such as Angelakisella and Lawsonibacter (p < 0.05). Further functional annotation of the microbial community indicated that PC-01 significantly enriched pathways related to the TCA cycle, riboflavin metabolism, Toll and Imd signaling, and lipopolysaccharide biosynthesis. In addition, the relative abundances of auxiliary activities, polysaccharide lyases, and S-layer homology modules were lower than those in the DSS group, whereas those of glycoside hydrolases, glycosyltransferases, and carbohydrate esterases were higher. At the transcriptional level, intervention with heat-inactivated PC-01 resulted in a downward trend in the expression of TLR4, Nfkb1, and Rela, accompanied by reduced expression of the chemokines MCP-1 and Cxcl10, and inflammasome-related genes NLRP3, Casp1, and IL-1β. Conclusions: In summary, heat-inactivated Lacticaseibacillus paracasei PC-01 effectively alleviated intestinal inflammatory injury in mice by regulating gut microbiota homeostasis and suppressing intestinal inflammatory responses.},
}

Animals
Mice, Inbred C57BL
*Lacticaseibacillus paracasei/physiology
*Gastrointestinal Microbiome
Mice
Intestinal Barrier Function
Dextran Sulfate
*Colitis/chemically induced/microbiology/therapy
Cytokines/blood/metabolism
Disease Models, Animal
Male
Hot Temperature
*Probiotics/pharmacology
Intestinal Mucosa/microbiology/metabolism

@article {pmid42884898,
year = {2026},
author = {Li, J and Wang, Q and Li, X and Zhang, Z and Liu, Y and Meng, Q and Zou, J and Liu, X and Luo, Y and Guo, Z},
title = {Long-Term Fertilisation Regimes, Crop Yield and Rhizosphere Microecology in a Wheat-Soybean Rotation System.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/plants15193034},
pmid = {42884898},
issn = {2223-7747},
support = {2023YFD1500700//National Key Research and Development Program of China/ ; },
abstract = {Long-term fertilisation must sustain crop yield and rhizosphere microbial functions in wheat-soybean rotations, but interannual responses remain unclear. We examined 12 treatments in a long-term field experiment established in 1979 and continuing through 2025 in Heilongjiang, China; three within-plot soil composites per treatment represented the 2025 microbiome snapshot. Long-term wheat and soybean grain and straw yield, rhizosphere and non-rhizosphere metagenomes, bacterial diversity, functional gene profiles, taxonomic composition, yield-microbe correlations, and structural equation modelling were assessed. The displayed wheat grain yields differed among treatments, with the median approaching 2500 kg ha[-1] under manure plus medium-rate mineral fertiliser. Soybean grain yield exceeded 2000 kg ha[-1] under manure plus low- or medium-rate mineral fertiliser and was higher than under high-rate mineral fertiliser alone. Separate exploratory treatment-only PERMANOVAs returned R[2] values of 0.7578 and 0.8227 for rhizosphere and non-rhizosphere functional profiles, respectively; the profiles were within-plot subsamples. Mesorhizobium, Lysobacter, Gemmatirosa, and Pseudolabrys were positively correlated with crop yield. Structural equation modelling linked available phosphorus to wheat yield and rhizosphere diversity and linked available potassium to soybean yield. These descriptive findings suggest crop-specific fertilisation patterns and possible associations of yield with soil nutrients and rhizosphere microbiota, indicating that productivity and microbial responses should inform long-term nutrient management.},
}

@article {pmid42885240,
year = {2026},
author = {Ghosh, SK and Wassel, MA and Wong, MK and Hyodo, S and Hamasaki, K},
title = {Functional Metagenomics Reveals Gut Microbial Biosynthetic Potential for Essential Nutrients in Juvenile Chum Salmon.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70448},
doi = {10.1111/1462-2920.70448},
pmid = {42885240},
issn = {1462-2920},
support = {//University of Tokyo/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Animals ; *Oncorhynchus keta/microbiology/metabolism/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Amino Acids/biosynthesis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; },
abstract = {The fish gut microbiota contributes to host nutrition, immunity and homeostasis, yet how its metabolic capacity relates to gaps in the host genome remains poorly characterized. Here we used shotgun metagenomic sequencing and KEGG module completion analysis to compare the biosynthetic potential of the gut microbiome with that of the host genome in juvenile chum salmon (Oncorhynchus keta) at 35 days posthatching, when exogenous feeding begins. Because small juvenile guts yield low microbial biomass and a high proportion of host DNA, we first optimized a protocol combining enzymatic lysis with NEBNext-based host DNA depletion. This raised the bacterial sequence fraction from 11.3% to 41.2% and increased the number of KEGG Orthology identifiers mapped to modules from 1128 to 1532. Module Completion Ratio analysis revealed complementation in functional potential: the chum salmon genome was incomplete for de novo biosynthesis of essential amino acids (threonine, leucine, valine/isoleucine, lysine) and B-vitamins (thiamine, riboflavin, biotin), whereas the gut metagenome encoded complete or near-complete modules for these pathways. Sequences assigned to Bartonella-like, Acinetobacter and Enterococcus lineages contributed most. These observations indicate that the gut microbiome encodes biosynthetic potential the host genome lacks, although demonstrating a nutritional benefit to the host will require experimental manipulation.},
}

Animals
*Oncorhynchus keta/microbiology/metabolism/genetics
Metagenomics
*Gastrointestinal Microbiome
Amino Acids/biosynthesis
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenome

@article {pmid42885446,
year = {2026},
author = {Deng, Q and Lv, L and Feng, H and Liu, D and Wang, F and Wang, J and Liu, X and Sun, S and Huang, B},
title = {Effects of a bioherbicide and a chemical herbicide on soil microbial community structure, diversity, and nitrogen cycling functions.},
journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/03601234.2026.2745422},
pmid = {42885446},
issn = {1532-4109},
abstract = {The fermentation broth of the bioherbicidal fungus Aspergillus versicolor D5 shows efficacy against dicotyledonous weeds in tobacco fields. However, little is known about its impact on the soil ecological environment of tobacco fields, particularly in comparison with chemical herbicides. This study compares the effects of a bioherbicide (BIO) and rimsulfuron (CHE) on tobacco field soil ecology. Both show comparable weed control efficacy and increase urease and dehydrogenase activities, although BIO causes a smaller urease increase. Unlike CHE, BIO does not inhibit nitrite reductase. Metagenomics shows that BIO slightly alters community structure without reducing diversity, whereas CHE decreases it. BIO increases the abundance of Luteitalea (involved in decomposing complex organic carbon and nitrogen cycling) and Chloracidobacterium (light-assisted carbon metabolism) within the phylum Acidobacteria, whereas CHE significantly reduces the abundance of these bacteria. BIO decreases the abundance of arbuscular mycorrhizal fungi Rhizophagus and Funneliformis, while CHE increases them. Nitrogen cycling analysis shows that BIO only significantly reduces the anammox pathway, causing little overall disturbance, whereas CHE strongly promotes dissimilatory/assimilatory nitrate reduction and nitrate/nitrite uptake pathways. These findings indicate that the fermentation extract of A. versicolor D5 affects soil ecology less than rimsulfuron, causing less disturbance to soil microbial diversity in this study.},
}

@article {pmid42885648,
year = {2026},
author = {Pinson, M and Croville, G and Crispo, M and Gaide, N and Walch, M and Viloux, N and Bourgeois, C and Sraka, B and Belloc, C and Guerin, JL},
title = {Emerging enteric coronaviruses in captive-bred red-legged partridges (Alectoris rufa), France.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/03079457.2026.2723911},
pmid = {42885648},
issn = {1465-3338},
abstract = {Enteritis syndrome in French red-legged partridge flocks.Detection of novel enteric coronaviruses (ParCoVs).ParCoVs are phylogenetically close to French TCoVs.Significant genetic variability of ParCoVs ruled out a clonal cluster of cases.Avian coronavirus RNA detected in intestinal sections by RNAscope ISH.},
}

@article {pmid42885911,
year = {2026},
author = {Xu, C and Wu, X and He, Q and Yang, L and Talib, S and Li, K},
title = {The Qing Chang Hua Shi Formula combined with allicin alleviates Cryptosporidium parvum infection in immunosuppressed mice and is associated with restoration of NLRP6, IL-18, IFN-γ, and intestinal microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0366225},
doi = {10.1128/spectrum.03662-25},
pmid = {42885911},
issn = {2165-0497},
abstract = {Cryptosporidium parvum is a highly pathogenic zoonotic parasite with limited therapies. Current study explored the anti-C. parvum effect of Qing Chang Hua Shi Formula (QHF) and allicin in vitro in immunosuppressed mice. In vitro, QHF and allicin inhibited over 90% of C. parvum. In vivo, the 8-day treatment reduced fecal oocyst shedding to 12.88% of the model group. Infection disrupted intestinal homeostasis, reduced tight-junction protein expression, and downregulated NLRP6, while inducing systemic inflammation and elevating IL-18/IFN-γ levels, which were further increased by treatment. Treated mice also showed increased abundance of Archangium and Corallococcus and decreased abundance of Clostridioides and Butyricimonas. Predicted microbial functional pathways revealed enrichment of glycolysis-related genes (L-lactate dehydrogenase [LDH], glyceraldehyde-3-phosphate dehydrogenase [GAPDH]) in infected mice, with treatment-associated shifts in amino acid synthesis pathways. Molecular docking suggested potential binding of benzoylpaeoniflorin, baicalin, and wogonoside to C. parvum LDH, ATP/ADP translocase, and gp40/15. Together, these findings indicate that QHF combined with allicin alleviates C. parvum infection in immunosuppressed mice and is associated with restoration of intestinal barrier markers, immune responses, and gut microbiota composition, suggesting a potential therapeutic approach for cryptosporidiosis.IMPORTANCECurrent study demonstrates that Qing Chang Hua Shi Formula (QHF) combined with allicin effectively inhibits Cryptosporidium parvum proliferation and concurrently mitigates intestinal damage and dysbiosis induced by C. parvum infection. QHF treatment was associated with upregulation of NLRP6, improved gut microbiota profiles, and elevated IFN-γ levels. These changes correlated with reduced parasite burden and alleviated intestinal injury, suggesting a potential immunomodulatory role that warrants further mechanistic investigation. Metagenomics disclosed that QHF and allicin were associated with changes in predicted microbial functional pathways, including those involved in glycolysis and amino acid metabolism, and with enrichment of certain bacterial taxa, such as Corallococcus and Archangium. Molecular dynamics simulations suggested that benzoylpaeoniflorin and baicalin may bind stably to C. parvum L-lactate dehydrogenase (LDH) and ATP/ADP translocase, raising the hypothesis that they could interfere with parasite energy metabolism. However, enzymatic validation is required to confirm this possibility. These findings suggest a potential therapeutic approach for cryptosporidiosis and highlight alterations associated with C. parvum infection.},
}

@article {pmid42885945,
year = {2026},
author = {Shremo Msdi, A and Begum, K and Hu, C and Shaw, N and Mai, A and Alam, MJ and Bassères, E and Eubank, T and Yu, XY and Mortin, LI and Silverman, MH and Garey, KW},
title = {The effects of novel oral preclinical PolC inhibitor antibiotic candidates on the gut microbiome in a murine thigh infection model.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0114326},
doi = {10.1128/spectrum.01143-26},
pmid = {42885945},
issn = {2165-0497},
abstract = {UNLABELLED: Antibiotics can negatively affect gut microbiome composition and function. However, preclinical evaluations of antibiotic effects on the microbiome are rarely undertaken. The purpose of this study was to characterize pharmacokinetics and metagenomic profiles of PolC inhibitor compounds compared to linezolid in a neutropenic murine thigh infection model. Neutropenic mice thighs were inoculated with methicillin-resistant Staphylococcus aureus (MRSA) and dosed orally starting 1 h later with ACX-728, ACX-801, ACX-978, or linezolid. Untreated control mice were euthanized at 1 h for baseline data, and a second untreated group were euthanized at 24 h after the start of dosing, when all remaining mice were euthanized. At euthanasia, thigh muscles were excised for MRSA quantification, and fecal pellets, colon tissue, and plasma samples were collected for drug concentration and microbiome analyses. All PolC inhibitors were detectable in plasma and feces at 25 h. Compared with linezolid, PolC inhibitors maintained greater gut microbial richness and diversity in this acute murine infection model. PolC-treated samples preserved overall community structure and Bacteroidota dominance, whereas linezolid induced marked disruption, with secondary expansion of Pseudomonadota, primarily Escherichia coli. Microbial pathway analysis showed preservation of community-level metabolic function for PolC inhibitors but marked disruption by linezolid. Compared to controls, linezolid produced a 4.4 log reduction in MRSA colony-forming unit per gram, while the PolC inhibitors produced a mean log reduction of 0.4-2.5 per group. In these exploratory studies, PolC inhibitor compounds preserved anaerobic community structure and fermentative capacity, whereas linezolid induced depletion of healthy commensals and expansion of aerotolerant taxa. These findings highlight the importance of microbiome-informed antibiotic evaluation in preclinical studies. Larger preclinical and clinical studies are warranted to confirm these findings.

IMPORTANCE: This study evaluated the class effect of PolC inhibitors on the microbiome as part of the preclinical development plan for systemic PolC inhibitors. Similar to the non-absorbable antibiotic, ibezapolstat, a narrow effect on the microbiome was observed with these novel compounds.},
}

@article {pmid42874258,
year = {2026},
author = {Zhang, J and Li, J and Qi, J and Zhang, L and Wang, Y and Cheng, D and Zhou, G and Yang, G and Liu, H},
title = {Operational reliability of full-scale activated sludge systems under carbon-source substitution with fermentation-derived yellow water: organic risk attenuation and microbial community stability.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131175},
doi = {10.1016/j.jenvman.2026.131175},
pmid = {42874258},
issn = {1095-8630},
abstract = {Fermentation-derived waste streams have attracted increasing attention as sustainable alternative carbon sources for biological nitrogen removal in municipal wastewater treatment plants (WWTPs). However, their operational reliability remains insufficiently understood because previous evaluations have focused primarily on conventional treatment performance while overlooking the fate of complex organic constituents and microbial responses to chemically heterogeneous carbon inputs. In this study, a full-scale municipal WWTP was investigated to evaluate carbon-source substitution with fermentation-derived yellow water. Carbon-source substitution maintained stable COD, NH4[+]-N, TN, and TP removal throughout operation, with effluent quality consistently meeting the Chinese Class IA discharge standard. Fifteen representative organic constituents with different predicted hazard potentials were identified in yellow water, all of which exhibited substantial attenuation (approximately 50-99%) during biological treatment, including compounds with relatively higher predicted toxicity. Microbial community composition remained relatively stable during carbon-source substitution, while genes associated with nitrogen cycling, aromatic compound degradation, and oxidative stress response remained consistently represented. Genome-resolved metagenomic analysis further demonstrated that representative microbial populations encoded genes spanning these three functional categories. These findings demonstrate the feasibility of using fermentation-derived yellow water as an alternative external carbon source in full-scale WWTPs and extend current evaluation of waste-derived carbon sources beyond conventional treatment performance by incorporating organic risk attenuation and microbial functional adaptation.},
}

@article {pmid42874260,
year = {2026},
author = {Ghaly, TM and McPherson, VJ and Rajabal, V and Ghaly, ME and Taws, N and Gallagher, RV and Le Roux, JJ and Tetu, SG},
title = {Soil microbial traits shift on contrasting timescales following restoration of former grazing lands.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131161},
doi = {10.1016/j.jenvman.2026.131161},
pmid = {42874260},
issn = {1095-8630},
abstract = {Native vegetation restoration is a key strategy for restoring degraded lands globally. While this process can reshape belowground microbial communities, the extent to which such changes restore soil ecosystem functions, and whether different microbial traits recover synchronously or on distinct timescales remains less clear. Understanding the sequence of functional recovery is essential for evaluating restoration success, as distinct microbial traits drive different ecosystem services, from carbon storage to plant growth promotion, and serve as meaningful indicators of long-term ecological recovery. To address this, we applied deep metagenomic sequencing to characterise soil microbial responses following native vegetation restoration (spanning 1-31 years prior to sampling) on grazing agricultural lands. We found that microbial functional changes occurred in distinct phases: an early, rapid restructuring of core soil health processes, detectable as early as three years, including enrichment of nutrient retention and carbon fixation pathways, followed by a more gradual development of plant growth-promoting traits as the plant community matures. Genome-resolved analyses of nearly 500 metagenome-assembled genomes revealed a fundamental shift in dominant microbial life history strategies. Specifically, communities transitioned from a resource-scavenging and stress tolerance profile in grazing soils to strategies that prioritise biosynthesis and growth yields in restored soils. These lifestyle shifts have important implications for enhancing the microbial biomass and carbon sink potential of soils. Together, these findings show that microbial functional shifts following restoration are temporally structured - informing expectations for when key restoration targets may be achieved, and providing a practical framework for monitoring ecosystem recovery.},
}

@article {pmid42874465,
year = {2026},
author = {Orf, GS and Berg, MG and Pantsulaia, M and Vardiashvili, M and Galdavadze, K and Biswas, RSR and Bishop, J and Sequeira, AF and Khoperia, A and Alkhazashvili, M and Cloherty, GA},
title = {Disparate tetraparvovirus species linked to hepatitis.},
journal = {Virology},
volume = {625},
number = {},
pages = {111096},
doi = {10.1016/j.virol.2026.111096},
pmid = {42874465},
issn = {1096-0341},
abstract = {The role of human tetraparvoviruses (PARV4) in cases of acute illness is poorly characterized, and the contribution of animal-associated tetraparvoviruses to human disease is unknown. In this study, we applied metagenomic and viral-enrichment next-generation sequencing to plasma from patients with diagnostically unresolved acute illness in Georgia (non-A-C hepatitis) and Bangladesh (acute febrile illness), and two tetraparvovirus genomes were recovered. Specimen HEP004 from a Georgian patient with acute hepatitis contained a virus clustering within Tetraparvovirus ungulate4, a species associated with sheep and goats, representing the first detection of this species in human plasma. Specimen 39HEP0432 from a Bangladeshi patient with fever and jaundice contained a human PARV4 grouping within a clade of genotype 2 previously reported in pediatric acute encephalitis cases in South Asia. Within-host minor variation was detected in both genomes, raising the possibility of ongoing replication. Phylogenetic and ancestral sequence analyses of human PARV4 genotype 2 identified lineage-defining capsid amino acid substitutions in the South Asian clade (which 39HEP0432 shared), situated in surface-exposed positions that may influence viral tropism or host immune interactions. These findings expand the known diversity of tetraparvoviruses detected in humans, including an ungulate-associated species with possible zoonotic potential, and provide sequence data to support targeted screening in cases of unexplained hepatitis and febrile illness.},
}

@article {pmid42874540,
year = {2026},
author = {Dara, M and Calabrisotto, LS and Bisanti, L and Torreagrossa, N and La Corte, C and Bertini, F and Catania, V and Quatrini, P and Parrinello, D and Piazzese, D and Cammarata, M and Banni, M and Parisi, MG},
title = {Integrated assessment of bioplastic materials effects on microbial communities and macroinvertebrate model, Mytilus galloprovincialis, in marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120459},
doi = {10.1016/j.marpolbul.2026.120459},
pmid = {42874540},
issn = {1879-3363},
abstract = {The increasing use of biopolymer derivatives raises concerns about their actual environmental sustainability, which remains insufficiently understood. In this study, we adopted an integrated approach combining microbial and ecotoxicological perspectives to evaluate their impact in marine ecosystems. We investigated the plastisphere composition of conventional petroleum-based High Density Polyethylene (HDPE) and polyhydroxyalkanoates (PHA), polyhydroxybutyric acid (PHB), and polylactic acid (PLLA) scaffolds after 60 days of exposition in marine ecosystem or microcosm, by high throughput metagenomics 16S rRNA gene sequencing and culture dependent approach. A variation in terms of composition and abundance of plastisphere, between petroleum-derived and bio-based degradable scaffolds, was observed. A high abundance of Proteobacteria was detected in all polymers, with Alpha and Gamma Proteobacteria dominant. At the genera level, high abundance of sequences assigned to hydrocarbon-degrading bacteria (i.e. Oleibacter, Labrenzia, Alcanivorax) was detected in biopolymeric plastic compared to petroleum-based plastic. To link microbial colonization and material degradation with biological effects on marine fauna, the impact of biopolymer-derived micro- and nanoparticles on the mussel Mytilus galloprovincialis was assessed. Both in vitro and in vivo assays demonstrated immune system activation through phagocytosis and encapsulation, while in vivo exposures influenced several biomarkers (phagocytosis, haemocyte density, lysozyme, glutathione peroxidase, phenoloxidase, alkaline phosphatase, esterase), suggesting potential detrimental effects after 72 h. By bridging microbial ecology with immunological responses in a bioindicator species, this multidisciplinary study provides novel insights into the complex ecological footprint of biodegradable plastics in marine environments.},
}

@article {pmid42874563,
year = {2026},
author = {Ako, BAA and Assohoun, SE and Diplo, BFT and Coulibaly, TGS and Acquah, JQ and Touré, AO and Kadjo, HAA and Gbonon, CV and Djaman, JA and Dosso, M},
title = {Establishing a genomic lab during COVID-19: A perspective from Institut Pasteur in Côte d'Ivoire.},
journal = {Cell genomics},
volume = {6},
number = {10},
pages = {101385},
doi = {10.1016/j.xgen.2026.101385},
pmid = {42874563},
issn = {2666-979X},
mesh = {Cote d'Ivoire/epidemiology ; Humans ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics ; *Genomics ; *Laboratories/organization & administration ; Pandemics ; *Academies and Institutes/organization & administration ; },
abstract = {Africa bears a disproportionate burden of epidemic threats, exemplified by COVID-19. Drawing on lessons from the pandemic, we describe how Institut Pasteur de Côte d'Ivoire transitioned from limited capacity to established expertise in genomic surveillance. This institutional strengthening provides a strategic blueprint for enhancing Africa's resilience against emerging health threats.},
}

Cote d'Ivoire/epidemiology
Humans
*COVID-19/epidemiology/virology
*SARS-CoV-2/genetics
*Genomics
*Laboratories/organization & administration
Pandemics
*Academies and Institutes/organization & administration

@article {pmid42874851,
year = {2026},
author = {Wangprapa, P and Nagy-Szakal, D and Wells, HL and Fidler, G and Techasathit, W and Couto-Rodriguez, M and Danko, DC and Mason, CE and O'Hara, NB and Sangtian, M and Viangteeravat, T and Sriswasdi, S},
title = {Potential clinical actionability of metagenomic next-generation sequencing for antimicrobial stewardship for urinary tract infections: a retrospective, single-centre, BI-Biotia UTI cohort study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {109181},
doi = {10.1016/j.ijid.2026.109181},
pmid = {42874851},
issn = {1878-3511},
abstract = {OBJECTIVES: Culture and antimicrobial susceptibility testing (AST) take 48-72 hours, leaving empirical therapy for urinary tract infections (UTIs) without resistance data. Metagenomic next-generation sequencing (mNGS) reports resistance within hours, but its potential clinical actionability for prescribing is underexplored.

METHODS: In a retrospective single-centre cohort (Bangkok tertiary hospital, 2018-2020), BIOTIA-DX results were compared with culture and AST in 251 culture-paired samples. Potential clinical actionability was assessed for 54 same-day empirical prescriptions and a post hoc ablation estimated what a rule-based policy would have prescribed under different information from mNGS.

RESULTS: Twenty-two of 54 prescriptions (40·7%, 95% CI 28·7-54·0) were potentially actionable: treatment failure prevention 9 (16·7%) and de-escalation 13 (24·1%). Excluding blaEC and blaACT raised cephalosporin specificity from 25·6% to 78·9% with a small tradeoff in sensitivity. NPVs were at least 89·7% for carbapenems, cephalosporins, trimethoprim/sulfamethoxazole, aminoglycosides and the fluoroquinolone classifier reached 100·0% PPV in Escherichia coli. Our refined resistance classification rules achieved a good tradeoff between the risk of ineffective antibiotics and the use of broad-spectrum carbapenem, compared with observed prescribing.

CONCLUSIONS: In a high-resistance setting, a same-day mNGS report was potentially actionable for two in five empirical prescriptions, mainly through resistance calling. However, the findings rest on a small number of cases.},
}

@article {pmid42874903,
year = {2026},
author = {Zhang, Y and Liu, H and Wang, P and Liu, H and Jing, H},
title = {Ecological partitioning and functional specialization of Thermoproteota across multiple trench sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125897},
doi = {10.1016/j.envres.2026.125897},
pmid = {42874903},
issn = {1096-0953},
abstract = {Thermoproteota (formerly referred to as Thaumarchaeota) are phylogenetically divided into ammonia-oxidizing archaea (AOA) affiliated with Nitrososphaeria and basal non-ammonia-oxidizing archaea (non-AOA). While both groups co-existed in the hadal trenches, their differentiations across multiple trenches remain poorly understood. Here, 25 medium- and high-quality metagenome-assembled genomes (MAGs), including 18 AOA and 7 non-AOA representatives, were generated from metagenomics of Diamantina, Kermadec, Mariana-Yap trench sediments. AOA MAGs of Nitrosopumilales encompassing CSP1-1, DRGT01 and Nitrosopumilus exhibited chemoautotrophic potential with broader niche widths and higher diversity across trenches. Potential nitrification rates (PNR) were predominantly associated with AOA activity and exhibited clear depth-/trench-dependent patterns, driven by NH4[+] availability. In contrast, the non-AOA lineage diverged approximately earlier (∼2.66 Ga), whereas the divergence between B1T1B5 and JAPUIC01 was estimated at ∼1.91 Ga during the Paleoproterozoic. B1T1B5 harbored auto/mixotrophic traits, whereas JAPUIC01 exhibited a metabolically flexible, heterotrophic strategy potentially suited to anaerobic niches. The pronounced niche partitioning and functional specialization of AOA and non-AOA Thermoproteota across geographically isolated trenches were based on their genomic traits, likely an integrated consequence of microbial ecological adaptation and strong purifying selection of the local environmental condition. The findings provide a unified ecological and evolutionary framework for understanding Thermoproteota diversification in the deep ocean and reveals how functional specialization and genomic adaptive evolution shape nitrogen cycling in Earth's deepest ecosystems.},
}

@article {pmid42875116,
year = {2026},
author = {Díaz Escandón, D and Acton, A and Coppins, BJ and Thai, T and Spribille, T},
title = {The lichen symbiont Wadeana represents an independent origin of hysterothecial fungi in the Eurotiomycetes.},
journal = {Fungal biology},
volume = {130},
number = {7},
pages = {101841},
doi = {10.1016/j.funbio.2026.101841},
pmid = {42875116},
issn = {1878-6146},
mesh = {*Symbiosis ; Phylogeny ; *Lichens/microbiology/physiology ; *Ascomycota/classification/genetics/physiology/isolation & purification ; Sequence Analysis, DNA ; DNA, Fungal/genetics/chemistry ; Genome, Fungal ; },
abstract = {The genus Wadeana was erected almost fifty years ago to accommodate an unusual pair of lichen fungal symbionts with hysterothecial ascomata and polysporous asci associated with the algal genus Trentepohlia. The evolutionary position of Wadeana has long been unclear, and the genus has variably been treated as a dothideomycete, as incertae sedis or, recently, within the subclass Acarosporomycetidae of the Lecanoromycetes. Here we present multilocus evidence from metagenome-assembled genomes from the generitype, Wadeana dendrographa, that place it with strong support as sister to all genera currently treated in the order Sclerococcales in the subclass Sclerococcomycetidae of the Eurotiomycetes. Wadeana represents the first confirmed case of hysterothecial ascomata in Eurotiomycetes. We compare evidence for its status as a lichen symbiosis with examples of fungal-algal interactions in other members of the Sclerococcomycetidae. Finally, we also describe a new family (Wadeanaceae) and order (Wadeanales) to accommodate Wadeana and a new subclass (Xylobotryomycetidae) to accommodate the order Xylobotryales in the Eurotiomycetes.},
}

*Symbiosis
Phylogeny
*Lichens/microbiology/physiology
*Ascomycota/classification/genetics/physiology/isolation & purification
Sequence Analysis, DNA
DNA, Fungal/genetics/chemistry
Genome, Fungal

@article {pmid42875131,
year = {2026},
author = {Kang, C and Zheng, X and Liu, Z and Wang, W and Zeng, W and He, Y and Huang, J and Nie, W and Wang, J and Wang, F},
title = {Cryptic microheterogeneity of the casing-layer microbiome and metabolome is associated with primordium fate in Phallus rubrovolvatus.},
journal = {Fungal biology},
volume = {130},
number = {7},
pages = {101864},
doi = {10.1016/j.funbio.2026.101864},
pmid = {42875131},
issn = {1878-6146},
mesh = {*Microbiota ; *Metabolome ; *Agaricales/growth & development/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Multiomics ; },
abstract = {Commercial cultivation of Phallus rubrovolvatus relies on casing layers, yet yields remain unstable, with primordium development varying among individual microsites. This cryptic microheterogeneity is masked by conventional bulk sampling, limiting insight into casing-layer performance. Here, we combined phenotype-guided back-tracing with multi-omics to characterize microecological signatures associated with primordium fate. We identified two contrasting ecological regimes associated with reproductive outcomes. Productive microsites were characterized by a "Cooperative state" enriched in oligotrophic bacteria (e.g., Hyphomicrobium) and basidiomycetes (e.g., Clathrus columnatus). Productive microsites also showed lower available potassium (K[+]) and elevated catalase activity. Conversely, non-productive microsites were characterized by a Rhizopus-dominated "Disruptive state". This state was associated with elevated urease activity, lower catalase activity, and stress-associated metagenomic functional signatures. Overall, primordium fate was associated with distinct local microbial, functional, and metabolic configurations that were not fully explained by bulk physicochemical properties. We propose the "Cooperative vs. Disruptive" model as a conceptual framework and identify candidate microbial and metabolic features for future validation in microbiome-informed cultivation management.},
}

*Microbiota
*Metabolome
*Agaricales/growth & development/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Multiomics

@article {pmid42875451,
year = {2026},
author = {Aguilar, A and Miranda Perez, I and Nadel, O and Nayfach, S and Ruiz Pestana, L and Segall, AM and Rohwer, FL and Roux, S and White, S and Luque, A},
title = {Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42875451},
issn = {2041-1723},
support = {GBMF9871//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2424579//National Science Foundation (NSF)/ ; },
mesh = {*Capsid/metabolism/chemistry ; *Evolution, Molecular ; Genome, Viral ; Phylogeny ; Models, Molecular ; *DNA Viruses/genetics ; *Capsid Proteins/genetics/chemistry/metabolism ; Protein Folding ; },
abstract = {The HK97-fold is an ancient, conserved protein structure that assembles protein shells, forming the capsids of Duplodnaviria viruses and prokaryotic biochemical compartments called encapsulsins. It has been proposed that encapsulins evolved from HK97-fold viruses. But the higher complexity of viral capsids represents a biophysical paradox in the evolution of HK97-fold protein shells. To resolve this problem, we hypothesize the existence of simpler HK97-fold viral capsids associated with smaller genomes than those of known HK97-fold viruses. Such small viral genomes are searched in environmental metagenomes across public databases, including IMG/M and MGnify. Using hidden Markov models and protein language models, we identify and characterize small viral genomes encoding HK97-fold proteins that exhibit molecular similarities to encapsulins yet lack portal and tail genes. The phylogenetic analyses of HK97-fold proteins reveal independent mixed groups of viruses and encapsulins, and structural analyses identify similarities between encapsulins and procapsids, the immature state of viral capsids. The observations support a bidirectional evolution between encapsulins and HK97-fold viruses enabled by the viral procapsid state. Using biophysical and genomic arguments, we introduce an evolutionary model of HK97-fold protein shells, predicting that they emerged as lower-symmetry biochemical compartments and that HK97-fold viral capsids may retain biochemical functions.},
}

*Capsid/metabolism/chemistry
*Evolution, Molecular
Genome, Viral
Phylogeny
Models, Molecular
*DNA Viruses/genetics
*Capsid Proteins/genetics/chemistry/metabolism
Protein Folding

@article {pmid42876496,
year = {2026},
author = {Yue, C and Xia, B},
title = {Case Report: Necrotizing fasciitis caused by Vibrio vulnificus without recalled seafood or seawater exposure diagnosed by metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1963954},
pmid = {42876496},
issn = {2296-858X},
abstract = {Vibrio vulnificus is a highly virulent marine Gram-negative pathogen that rapidly induces soft tissue necrosis and fatal septic shock, with infections generally linked to raw seafood ingestion or open wound contact with seawater. We report an atypical severe case of V. vulnificus septic shock in a 60-year-old male patient without recalled seafood or seawater exposure and without classic underlying high-risk diseases such as liver cirrhosis and diabetes mellitus. The patient presented with rapidly progressive swelling and subcutaneous ecchymosis of the right lower limb, which quickly deteriorated into refractory septic shock within 24 h. Conventional empiric broad-spectrum antibiotics failed to halt disease progression before pathogen identification. Metagenomic next-generation sequencing (mNGS) rapidly detected V. vulnificus sequences on the second admission day, and the diagnosis was further confirmed by blood culture. Multidisciplinary interventions including repeated radical surgical debridement, vacuum sealing drainage (VSD), targeted anti-infective therapy and comprehensive organ support finally achieved complete recovery. The patient recovered normal walking function during six-month outpatient follow-up. This rare occult infection case reminds clinicians to maintain high suspicion of V. vulnificus infection for rapidly advancing necrotizing fasciitis combined with septic shock, even when no aquatic exposure is recalled. Meanwhile, this work validates the critical value of mNGS for early pathogen identification in unexplained life-threatening sepsis.},
}

@article {pmid42876542,
year = {2026},
author = {Starikova, EV and Kuzmichenko, PA and Fedorov, DE and Vvedensky, AV and Pavlenko, AV and Arkhipova, AL and Kovalchuk, SN and Ilina, EN},
title = {Gut microbiome resistotypes reflect chronological age and Enterobacteriaceae relative abundance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1869983},
pmid = {42876542},
issn = {1664-302X},
abstract = {BACKGROUND: Surveillance of antibiotic resistance genes (ARGs) in the human gut microbiota is critical for informing public health interventions and antibiotic stewardship strategies, taking into account sociodemographic, behavioral, and health-related factors. Although metagenomics research has grown exponentially, few studies have described resistome dynamics over time. In this study, we investigated resistome profiles over a 5-year interval (between 2016-2017 and 2022) in adult residents of Arkhangelsk, Northwestern Russia.

RESULTS: Over 5 years, we observed an increase in ARGs richness and abundance along with the prevalence changes in genes conferring resistance to aminoglycosides (aph2, aph3, ant9), lincosamides (lnuC), chloramphenicol (cat, catA), and macrolides (ermG, ermB). We have identified two resistotypes in our data that differed in the number of identified ARGs. The less frequent resistotype 2, characterized by a higher number of ARGs, was associated with higher participants' chronological age and increased Enterobacteriaceae abundance. Approximately one-third of the participants have shifted from one resistotype to another within a 5-year period. Temporal changes in resistome profiles occurred unevenly among participants, with the greatest changes noted for 41-45 and 61-65 age groups. No associations were found between COVID-19 history and resistome composition.

CONCLUSIONS: We showed an increase in overall ARG richness, ARG abundance, and the prevalence of certain ARGs in microbiomes of adult residents of Arkhangelsk over a 5-year period. We have identified two resistotypes; the one with higher ARGs richness was linked to higher chronological age and Enterobacteriaceae family relative abundance. These findings underscore the necessity for further antibiotic resistance surveillance to address the accelerating global dissemination of ARGs, while highlighting age as an underrecognized factor contributing to resistome dynamics.},
}

@article {pmid42876655,
year = {2026},
author = {Shi, X and Xu, H and Li, W and Wang, J and Song, Y and Yang, M and Wang, B and Liu, CQ},
title = {Evolution of lake microbial structure and function under climatic and anthropogenic forcings: Insights from sedimentary ancient DNA.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117760},
pmid = {42876655},
issn = {2589-0042},
abstract = {Structure and function of lake microorganisms are sensitive to environmental disturbances; yet their differential responses to climatic and anthropogenic forcings over centennial scales remain poorly understood. Here, we analyzed a sediment core from Lake Daihai in northern China, combining metagenomics and stable isotope analyses. Our results revealed that microbial community assembly was dominated by deterministic processes, whereas stochasticity increased notably after 1850, coinciding with the termination of the Little Ice Age and intensified human impacts. Notably, microbial community structure evolved at a rate approximately one order of magnitude faster than community function. This decoupling was mediated by functional redundancy associated with bacterial keystone taxa, ultimately resulting in more negative sedimentary carbon and nitrogen isotopic compositions nearly a century later. Gene-level functional redundancy further buffered ecosystem function variability across biological scales. Collectively, our findings integrate omics and geochemical approaches to advance the understanding of lake ecological evolution under complex multi-forcing regimes.},
}

@article {pmid42876743,
year = {2026},
author = {Tie, X and Sun, X},
title = {Pneumococcal meningitis secondary to chronic orbital inflammation with skull base erosion: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1918613},
pmid = {42876743},
issn = {2296-858X},
abstract = {This case report describes a 32-year-old female patient who developed acute pneumococcal meningitis following six-year chronic orbital inflammatory changes after strabismus corrective surgery. The patient experienced gradual deterioration of right-eye vision and recurrent retro-orbital headache; serial magnetic resonance imaging (MRI) from 2021 to 2023 demonstrated diffuse intraconal retrobulbar abnormalities and extraocular-muscle thickening. She subsequently presented with high fever, generalized seizures and impaired consciousness. Cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) detected Streptococcus pneumoniae and low-abundance Epstein-Barr virus (EBV) DNA; Active EBV-associated central nervous system infection could not be confirmed in the absence of CSF quantitative EBV polymerase chain reaction (PCR), EBV serology and immune-status testing. The patient received broad-spectrum intravenous antimicrobial, antiviral and glucocorticoid therapy, followed by endoscopic endonasal resection of inflammatory lesions at the ethmoid-skull-base complex. Histopathological examination of surgical specimens revealed non-specific inflammatory granulation tissue, and Langerhans cell histiocytosis was excluded. At six-month follow-up, the patient remained seizure-free; infectious foci showed near-complete resolution on imaging, yet mild residual orbital-leptomeningeal abnormalities persisted with modest visual improvement. This case demonstrates the potential for delayed intracranial extension from long-standing chronic orbital inflammation and highlights both the diagnostic utility and interpretive limitations of CSF-mNGS in clinical practice.},
}

@article {pmid42876779,
year = {2026},
author = {Cleanclay, WD and Kernyuy, FB and Kintung, IF and Yensii, NG and Obi, AMM and Nguema, OAM},
title = {The mosquito gut microbiome and Plasmodium development: a scoping review of molecular approaches and implications for malaria vector control.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1906816},
pmid = {42876779},
issn = {2235-2988},
mesh = {Animals ; *Malaria/prevention & control/transmission/parasitology ; *Plasmodium/growth & development ; *Mosquito Vectors/microbiology/parasitology ; *Gastrointestinal Microbiome ; *Anopheles/microbiology/parasitology ; *Mosquito Control/methods ; Metagenomics ; Humans ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Malaria remains a major health burden, with an estimated 282 million cases and approximately 610,000 deaths recorded in 2024. The increasing prevalence of insecticide-resistant Anopheles vectors and drug-resistant Plasmodium strains has substantially eroded the efficacy of conventional control strategies, underscoring the critical need for innovative approaches. Accumulating evidence suggest that the mosquito midgut microbiome exerts a significant influence on Plasmodium sporogonic development; however, no scoping investigation has fully mapped the metagenomic evidence base in this field.

METHODS: Adhering to the Arksey and O'Malley framework and PRISMA-ScR guidelines, a systematic search was conducted across PubMed, Scopus, and Web of Science for publications from January 2000 to April 2026. Studies that used microbiological, molecular, or metagenomic techniques to study the gut microbiota of mosquito species related to Plasmodium were included. Descriptive mapping was used to synthesize the data in a thematic manner.

RESULTS: Thirteen primary studies met the inclusion criteria, comprising both observational field surveys and experimental infection studies. Four themes emerged: (1) gut microbiota diversity and composition are associated with Plasmodium infection status, though the direction varies by mosquito species, geography, and season; (2) several taxa, including Burkholderia, Asaia, Sphingomonas, Pseudomonas, and Serratia, are consistently associated with reduced infection or are experimentally inhibitory; (3) the Enterobacteriaceae and Serratia spp. show context-dependent, bidirectional relationships with Plasmodium that are best explained by strain-level variation; and (4) a smaller set of taxa, including Elizabethkingia, Chryseobacterium, Methylobacterium, and Pantoea, is positively associated with infection, on observational evidence only. The evidence relied predominantly on 16S rRNA amplicon sequencing, with a minority of studies adding whole-genome sequencing, transcriptomics, or metabolomics; none used shotgun metagenomics.

CONCLUSIONS: The mosquito gut microbiome exerts a net inhibitory effect on Plasmodium development, with translational potential for microbiome-based vector control, including paratransgenesis. However, the microbiota is not uniformly antagonistic to the parasite, and taxa positively associated with infection remain observational. The field is limited by a near-exclusive reliance on 16S rRNA profiling, few functional and longitudinal studies, and geographically narrow evidence. Multi-omics approaches, longitudinal designs, and broader geographic coverage will be essential to translate these associations into sustainable malaria control.},
}

Animals
*Malaria/prevention & control/transmission/parasitology
*Plasmodium/growth & development
*Mosquito Vectors/microbiology/parasitology
*Gastrointestinal Microbiome
*Anopheles/microbiology/parasitology
*Mosquito Control/methods
Metagenomics
Humans
Bacteria/classification/genetics

@article {pmid42876851,
year = {2026},
author = {Xie, W and Lu, S and Liu, Z and Zheng, J and Mo, F and Zhang, K and Huang, Z},
title = {Gut microbiome profiles of two limestone forest-dwelling langurs show stronger influence of host-associated factors than environment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1953526},
pmid = {42876851},
issn = {1664-302X},
abstract = {BACKGROUND: Host-associated factor and the environment play crucial roles in shaping the composition and function of the gut microbiome. Considerable debate exists regarding the relative influence of host-associated and environmental factors on the gut microbiome. To determine the relative importance of host-associated factors and environmental factors in langurs, we employed metagenomic sequencing to examine differences in the gut microbiome of the white-headed langurs (Trachypithecus leucocephalus) and François' langurs (T. francoisi).

RESULTS: The results revealed that the alpha diversity of the gut microbiome significantly differed between white-headed langurs and François' langurs in similar habitats. However, there was no significant variation in the alpha diversity between the wild and captive François' langurs. Similarly, the proportion of Bacillota differed between the langur species, with a higher proportion in the white-headed langurs than the François' langurs. In addition, significant separation in gut microbiome functions also occurred between the two species. The functional genes related to metabolism (e.g., carbohydrate metabolism and amino acid metabolism) and Glycoside Hydrolases in wild François' langurs were more abundant than in the other langurs. The results of PCoA showed that the pathways were significantly separated between white-headed langurs and François' langurs at four levels in the KEGG database, whereas the pathways showed no significant differences between the wild and captive François' langurs except for module level. The proportion of ARGs related to multidrug resistance was higher in wild François' langurs, likely associated with the utilization of poultry manure and antibacterial biocides in the langur's habitat.

CONCLUSION: Our study demonstrates that the host-associated factors have stronger influence on shaping the gut microbiome of langurs than environmental factors. These findings provide data on the relative contributions of host-associated factors and environmental factors to the gut microbiome of langurs and identify potential driving factors for antibiotic resistance genes. In addition, these findings provide crucial insights into the influence of host-associated factors on the gut microbiome, offering a theoretical basis for future langur conservation strategies.},
}

@article {pmid42877015,
year = {2026},
author = {Gao, W and Han, W and Chen, J and Gao, Z and Gao, J and Zhen, R and Yuan, Y and Gu, Y and Huang, C and Liu, C and Wang, G and Zhang, X and Zhao, Z and Xiong, G and Li, X and Zhu, P and Liu, J and Hu, C and Gong, Y and Zhang, Z},
title = {Targeted next-generation sequencing: a promising approach for pathogen and antimicrobial resistance gene detection in urinary tract infections.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1945070},
pmid = {42877015},
issn = {1664-302X},
abstract = {OBJECTIVE: Urinary tract infections (UTIs) are common and frequently recurrent. As traditional diagnostic methods fail to meet clinical needs, this study aimed to construct and evaluate the performance of targeted next-generation sequencing (tNGS) for detecting pathogens and antimicrobial resistance genes (ARGs) in urine specimens.

METHODS: A total of 446 urine samples from patients with suspected UTIs were tested by tNGS, routine culture, and antimicrobial susceptibility testing (AST), with discordant results resolved by metagenomic NGS (mNGS) and whole-genome sequencing (WGS). The performance of tNGS was evaluated against culture and a composite reference standard (CRS) for pathogen detection, and against AST and WGS for resistance prediction.

RESULTS: tNGS achieved limit of detections of 500-1,000 CFU/mL, with high precision. Compared to culture, tNGS achieved a higher positive rate (62.78%), along with an overall sensitivity of 90.05% and specificity of 56.28%, whereas against the CRS the sensitivity and specificity reached 99.54% and 97.49%, respectively. For the seven common UTI bacteria, both metrics exceeded 90% regardless of the reference standard. Additionally, tNGS outperformed culture in detecting hard-to-culture microbes and polymicrobial infections. Among 132 samples with available AST results, ARG-based prediction showed strong concordance with resistance phenotypes for carbapenems (100.00%) and third generation cephalosporins + β-lactamase inhibitors (91.67%). Factors including sex and urine leukocyte count > 10 cells/μL were found associated with positive tNGS results.

CONCLUSION: tNGS enables rapid, sensitive and comprehensive detection of UTI pathogens and ARGs, covering hard-to-culture pathogens and mixed infections, thereby showing promise in improving diagnosis. However, it complements rather than replaces phenotypic AST, particularly for penicillin-class antibiotics.},
}

@article {pmid42877059,
year = {2026},
author = {Xue, Y and Cai, S and Ji, L and Ji, L and Shen, Q and Wang, X and Wu, P and Liu, Y and Wang, Y and Zhang, W and Yang, S},
title = {Identification and characteristics of multiple viruses in snow leopard fecal samples using viral metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1946718},
pmid = {42877059},
issn = {1664-302X},
abstract = {Metagenomic studies on the fecal virome of snow leopards, rare apex predators on the Qinghai-Tibet Plateau (QTP), remain limited. In this study, we utilized metagenomic sequencing to characterize the fecal viral community in captive QTP snow leopards. We assembled 22 complete viral genomes across the families Anelloviridae, Circoviridae, Parvoviridae, Picornaviridae, Genomoviridae, and Smacoviridae. Phylogenetic analyses indicated substantial sequence novelty. We identified 9 anellovirus genomes in the genera Tettorquevirus and Etatorquevirus, 3 candidate novel parvoviruses in Bocaparvovirus, Chaphamaparvovirus, and Dependoparvovirus, 3 circovirus genomes representing 2 candidate novel species, and 1 candidate novel sakobuvirus species. Another kobuvirus genome represented a divergent strain of a known species. In addition, 4 divergent genomoviruses showed phylogenetic relationships with sequences reported from diverse animal and environmental sources. Notably, one candidate novel porprismacovirus (family Smacoviridae) displayed a marked discordance between its highly conserved replication-associated protein (96.7% amino acid identity), divergent capsid protein (maximum identity, 59.7%), and low whole-genome identity (63.6%). Recombination analysis suggested it might be a recombinant virus. In summary, this study expands current knowledge of the diversity and evolutionary characteristics of viruses detected in snow leopard fecal samples and provides baseline genomic data for future investigation of captive snow leopard viromes.},
}

@article {pmid42877104,
year = {2026},
author = {Tang, H and Xiong, Q and Qian, G},
title = {Exploratory microbiota-metabolite alterations associated with cognitive impairment after repeated low-dose sevoflurane exposure in mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1869293},
pmid = {42877104},
issn = {2235-2988},
mesh = {Animals ; *Sevoflurane/adverse effects/administration & dosage ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Cognitive Dysfunction/chemically induced/microbiology ; Mice, Inbred C57BL ; Metabolomics ; Disease Models, Animal ; Maze Learning/drug effects ; *Microbiota/drug effects ; *Metabolome/drug effects ; },
abstract = {BACKGROUND: Repeated low-dose sevoflurane exposure may affect cognition, but the relationship between such exposure, gut microbial composition, and circulating metabolites remains unclear. This study examined an experimental proof-of-concept exposure model and treated microbiota-metabolite findings as exploratory associations.

METHODS: Mice were exposed to 100 ppm sevoflurane for 2 h/day over 7 consecutive days, followed by Morris water maze testing without a long-term recovery follow-up. Gut microbiota and serum metabolites were profiled by shotgun metagenomic sequencing and LC-MS metabolomics, respectively, and machine-learning analyses were used only for exploratory feature ranking.

RESULTS: Sevoflurane-exposed mice exhibited poorer Morris water maze performance (Day 6 escape latency: 28.6 ± 3.4 s vs. 12.5 ± 1.8 s in controls, p < 0.01), although interpretation is limited by unequal behavioral sample sizes. Serum metabolomics suggested nominal and exploratory alterations in bile acid- and sphingolipid-related pathways. Shotgun metagenomics (n = 3/group) identified preliminary relative-abundance shifts, including a lower Bacteroidota/Bacillota ratio and lower relative abundance of Akkermansia.

CONCLUSIONS: In this proof-of-concept model, repeated low-dose sevoflurane exposure was associated with impaired spatial learning and memory and with exploratory serum metabolic and gut microbial alterations. The findings do not establish persistent long-term deficits, routine occupational risk, or causal microbiota-metabolite mediation. Larger cage-aware studies, an ambient-air comparison group, targeted validation, and interventional experiments are required.},
}

Animals
*Sevoflurane/adverse effects/administration & dosage
Mice
Male
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Cognitive Dysfunction/chemically induced/microbiology
Mice, Inbred C57BL
Metabolomics
Disease Models, Animal
Maze Learning/drug effects
*Microbiota/drug effects
*Metabolome/drug effects

@article {pmid42877189,
year = {2026},
author = {},
title = {Correction: Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag274},
doi = {10.1093/ismeco/ycag274},
pmid = {42877189},
issn = {2730-6151},
abstract = {[This corrects the article DOI: 10.1093/ismeco/ycag081.].},
}

@article {pmid42877214,
year = {2026},
author = {Kalendar, R and Daniyarov, A and Kairov, U and Kozhakhmetov, S and Yerezhepov, D and Yermekbayeva, B and Sarbassov, D and Kushugulova, A},
title = {Targeted long-read eukaryotic profiling of human stool by broad-range 18S-28S rRNA gene amplicon sequencing on Oxford Nanopore Technologies: a proof-of-concept study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1904425},
pmid = {42877214},
issn = {1664-302X},
abstract = {The gut eukaryome, comprising the protists and fungi that fall within the strict definition of the microbiota together with the macroscopic helminths and arthropods that lie outside it, is under-detected by clinical microscopy and by short-read 16S/18S sequencing, yet is increasingly implicated in inflammatory and autoimmune disorders, including psoriasis. Existing 18S V4/V9 primers either lack cross-kingdom universality or fail to discriminate closely related species. We designed and evaluated broad-range PCR primers anchored in conserved blocks of nuclear 18S and 28S ribosomal genes, flanking a 1.0-3.5 kb cassette spanning the 3'-end of 18S, ITS1, 5.8S, ITS2, and the 5'-end of 28S. Stool samples from 91 plaque-psoriasis patients and 92 matched controls were collected; a subset of 32 samples was profiled by Oxford Nanopore amplicon sequencing using the EPI2ME wf-metagenomics pipeline (Kraken + Bracken) against the NCBI core_nt database. The gut eukaryome was dominated by Ascomycota and Protista, with 51 species-level entries assigned to Candida (37 named binomials), 27 entries assigned to Blastocystis (12 subtype-labelled entries), 20 entries assigned to Malassezia (15 named species), and 37 entries assigned to Cladosporium recovered from a single PCR tube. Blastocystis hominis was detected in 37.5% of subjects (≥50-read threshold; mean 7.5% in carriers), with concurrent detection of 12 subtype-labelled entries (ST1-ST4, ST7, ST10-ST15, ST24) and 11 named isolate entries. Psoriasis-relevant Candida species, such as C. albicans (34.4%), C. tropicalis (34.4%), C. parapsilosis (31.2%), and Malassezia restricta (9.4%; up to 12.1%) were co-detected. Long-read sequencing of a broad-range 18S -28S rRNA gene cassette provides a single-tube workflow for the simultaneous recovery of fungal, protistan, and plant-derived eukaryotic sequences from human stool.},
}

@article {pmid42877526,
year = {2026},
author = {Fang, YH and Liu, HN and Chen, YJ and Hsu, TW and Chiu, CA and Chiang, PN and Huang, CL},
title = {Metagenomic profiling reveals that divergent fire-adaptive strategies drive distinct fungal succession in pine litter decomposition.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e201414},
pmid = {42877526},
issn = {2210-6340},
abstract = {Decomposing litter is a critical driver of fuel bed formation and forest fire regimes, yet how divergent plant fire-adaptive strategies influence litter chemistry and subsequent fungal decomposition dynamics remains poorly understood. Here, we conducted a 6-month reciprocal litterbag experiment by incubating litter from two contrasting pine species-the fire-tolerant Pinus taiwanensis and the fire-avoiding P. morrisonicola-in both their own native habitat and that of the other species, coupled with genome-resolved metagenomics to track fungal succession and lignocellulolytic functional profiles. We found that the fire-avoiding P. morrisonicola exhibited significantly accelerated decomposition, driven by inherently lower initial C:N ratio and less recalcitrant litter, whereas the fire-tolerant P. taiwanensis exhibited slower decomposition rates. Metagenomic profiling revealed a distinct functional succession underlying this process. Early decomposition was dominated by Ascomycota (e.g., Leotiomycetes), which rapidly colonized the litter to initiate biopolymer breakdown. As easily decomposable substrates depleted, a functional shift occurred. Specifically, the highly recalcitrant P. taiwanensis litter selectively recruited Basidiomycota (e.g., Agaricales and Trechisporales) equipped with diverse lignin-modifying enzymes, reflected by a late-stage temporal surge in ligninolytic gene abundances. Ultimately, these findings demonstrate that plant fire-adaptive strategies act as a strong filter, shaping litter chemistry to drive specific taxonomic and functional fungal succession. This study provides a mechanistic understanding of the eco-evolutionary linkage between plant traits, microbiome assembly, and ecosystem-level fire dynamics.},
}

@article {pmid42877629,
year = {2026},
author = {Metzler-Zebeli, BU and Balfanz, F and Vollrath, F},
title = {Fibrolytic capacity of the gut microbiome in captive African elephants (Loxodonta africana): a pilot study.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1933152},
pmid = {42877629},
issn = {2297-1769},
abstract = {African elephants (Loxodonta africana) depend on the fibrolytic capacity of their gut microbiome (GMB) to efficiently utilize fibrous plant material. However, knowledge is missing on the temporal stability and functional dynamics (especially fibrolytic capacity) of their GMB. Likewise, information on the associated volatile fatty acids (VFA) production in the elephant's hindgut is scarce. In this pilot study, we collected feces from five captive African elephants on two occasions separated by 12 months to explore the GMB composition and its changes over time. We characterized the GMB's fibrolytic potential based on total microbial numbers and metagenome composition, including carbohydrate-active enzymes (CAZy), and fecal VFA, at individual and group level. Elephants received a roughage-based diet, which contained more carrots at the second than at the first sampling. Bacteria, specifically fibrolytic Prevotella, Bacteroides, Ruminococcus and Fibrobacter dominated the GMB, while archaea, fungi and protozoa were less present. Treponema was highly abundant, which might be an adaptation to maximize energy gain from cellulose-rich food. The elephants showed individual shifts in GMB composition from the first to second sampling. The shift in functional gene composition from the first to the second sampling was similar among elephants. It showed distinct clustering of CAZy families between fecal collections and discriminated features related to breakdown of carrot pectin for the second sampling. Sparse partial least squares-discriminant analysis identified (hemi-)cellulolytic genera within Prevotellaceae as discriminant taxa, which positively associated with CAZy families but negatively with VFA. At group level, fecal VFA concentrations were similar among elephants. However, opposite shifts from the first to the second sampling were detected among elephants at individual level. It may be speculated whether feeding decisions of three related females might explain the increase of VFA in their feces at the second compared to the first sampling, whereas VFA were lower in feces of the non-related female at the second sampling. We assert that this pilot study on GMB taxonomy and carbohydrate breakdown in captive African elephants may be helpful for feeding management at zoological gardens.},
}

@article {pmid42878130,
year = {2026},
author = {Lamarca, AP and Silveira, MC and Azevedo, RC and Guimarães, MAAM and de Mello, CMB and Camargo, AC and de Souza, LM and Gerber, AL and Guimarães, APC and Cavalcanti, AC and Vasconcelos, ATR},
title = {First Phylodynamic Analysis of HRSV-A and HRSV-B in Rio de Janeiro, Brazil, Reveals Recurrent Dispersals From the Megalopolis Center to Suburban Cities.},
journal = {Journal of medical virology},
volume = {98},
number = {10},
pages = {e71177},
doi = {10.1002/jmv.71177},
pmid = {42878130},
issn = {1096-9071},
support = {E-26/210.717/2025//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; SEI260003/001621//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/200.095/2026//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 00x0ma614//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil/ ; },
mesh = {Brazil/epidemiology ; Humans ; *Phylogeny ; *Respiratory Syncytial Virus Infections/epidemiology/virology/transmission ; Genetic Variation ; Cities/epidemiology ; *Respiratory Syncytial Virus, Human/genetics/classification/isolation & purification ; Female ; Infant ; Genome, Viral ; Respiratory Tract Infections/virology/epidemiology ; },
abstract = {Human respiratory syncytial virus (HRSV) is the leading cause of acute lower respiratory tract infections in infants and represents a major burden to public health systems worldwide. Despite its epidemiological relevance, genomic surveillance of HRSV in Brazil remains limited. Here, we investigated the genetic diversity and dispersal dynamics of HRSV-A and HRSV-B in the state of Rio de Janeiro, Brazil, during the period immediately preceding the implementation of maternal vaccination and prophylactic monoclonal antibodies. A total of 136 near-complete HRSV genomes were recovered from respiratory samples collected between May 2024 and June 2025 using metagenomic sequencing. Phylogenetic analyses identified 11 HRSV-A and five HRSV-B lineages, with most sequences belonging to the A.D.3 and B.D.E.1 clades. Phylodynamic reconstructions revealed multiple independent introductions into the state, with the city of Rio de Janeiro acting as the primary within-state dispersal hub. Viral dispersal routes originating from the capital also showed greater mean transmission distances than those from other municipalities. Coinfections with additional respiratory viruses were frequently detected, and most HRSV-positive patients were children under 1 year of age. These results demonstrate that HRSV circulation in Rio de Janeiro is shaped by repeated introductions and strong spatial structuring centered around highly connected urban areas. Our findings underscore the importance of continuous genomic surveillance to monitor viral evolution, characterize transmission dynamics, and support science-based public health strategies against HRSV. Establishing robust monitoring systems will be critical to evaluate the impact of newly implemented immunization programs in Brazil.},
}

Brazil/epidemiology
Humans
*Phylogeny
*Respiratory Syncytial Virus Infections/epidemiology/virology/transmission
Genetic Variation
Cities/epidemiology
*Respiratory Syncytial Virus, Human/genetics/classification/isolation & purification
Female
Infant
Genome, Viral
Respiratory Tract Infections/virology/epidemiology

@article {pmid42878177,
year = {2026},
author = {Vliex, LMM and Godinho Mimoso, IF and Le, GN and Blaak, EE and Penders, J},
title = {Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2746814},
doi = {10.1080/19490976.2026.2746814},
pmid = {42878177},
issn = {1949-0984},
mesh = {Humans ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Vancomycin/administration & dosage/therapeutic use ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Obesity/microbiology/drug therapy ; *Trisaccharides/administration & dosage ; Double-Blind Method ; *Overweight/microbiology/drug therapy ; Female ; Adult ; Male ; Middle Aged ; Prebiotics/administration & dosage ; Feces/microbiology ; Drug Resistance, Bacterial ; },
abstract = {Antibiotics are widely used to treat bacterial infections, yet overuse and misuse causes disruption of the gut microbiome and spread of antibiotic-resistant bacteria. Presence of antibiotic resistance genes (ARGs) could be a determinant of the response to antibiotics. Supplementation with prebiotics may limit the detrimental antibiotic-induced effects on the microbiome, but whether this results in changes in the gut resistome is unclear. This study investigated the impact of eight-week 2'-fucosyllactose (2'-FL) supplementation after seven-day vancomycin use in 18 adults with overweight/obesity, a subset from a double-blind placebo-controlled randomized intervention. Whole-metagenome shotgun sequencing was used to characterize the gut microbiome and resistome at baseline, after vancomycin use and after supplementation. Seven-day vancomycin use disrupted microbial richness and diversity (p < 0.001) and changed microbial composition. No improvements in microbial recovery were detected after eight week 2'-FL supplementation compared to placebo. Resistome richness and diversity were not affected by vancomycin use, although the presence of specific ARGs changed. No differential impact of 2'-FL supplementation on resistome richness, diversity and composition was detected. While vancomycin use disrupted the gut microbiome and affected the resistome, the detectable effects of 2'-FL supplementation were limited. Future research should investigate antibiotic- and prebiotic-induced changes in the gut resistome in more detail.},
}

Humans
*Anti-Bacterial Agents/administration & dosage/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Vancomycin/administration & dosage/therapeutic use
*Bacteria/genetics/drug effects/classification/isolation & purification
*Obesity/microbiology/drug therapy
*Trisaccharides/administration & dosage
Double-Blind Method
*Overweight/microbiology/drug therapy
Female
Adult
Male
Middle Aged
Prebiotics/administration & dosage
Feces/microbiology
Drug Resistance, Bacterial

@article {pmid42878179,
year = {2026},
author = {Shin, MG and Park, SJ and Kang, W and Bae, Y and Kim, S and Yoo, D and Yoon, S and Park, SM and Kwon, ES and Chang, J and Yoon, JH and Park, DG and Lee, EJ},
title = {Escherichia coli hns and methylglyoxal link gut microbial metabolism to host neuronal gene regulation in Parkinson's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2739674},
doi = {10.1080/19490976.2026.2739674},
pmid = {42878179},
issn = {1949-0984},
mesh = {Animals ; *Parkinson Disease/metabolism/microbiology/genetics ; Humans ; *Escherichia coli/metabolism/genetics ; Caenorhabditis elegans/genetics/microbiology ; *Gastrointestinal Microbiome ; *Pyruvaldehyde/metabolism/blood ; Dopaminergic Neurons/metabolism ; *Escherichia coli Proteins/metabolism/genetics ; Gene Expression Regulation ; Male ; Disease Models, Animal ; Female ; Neurons/metabolism ; Feces/microbiology ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss in the substantia nigra (SN). Although the gut microbiota has been implicated in PD pathogenesis, how defined bacterial genes and their metabolites influence host neuronal gene regulation remains unclear. Here, we identify a gut microbial hns-methylglyoxal (MG) pathway linking Escherichia coli (E. coli) metabolism to host neuronal gene regulation. In the stool metagenomic cohort, hns, a bacterial gene encoding the histone-like nucleoid structuring protein and primarily derived from E. coli, was enriched particularly in body-first PD, a subtype associated with gut-originating pathology. In a separate plasma MG cohort, plasma levels of MG, a reactive metabolite whose bacterial production was hns-dependent in our model system, were higher in body-first than in brain-first PD and were nominally inversely associated with cardiac meta-iodobenzylguanidine (MIBG) uptake within the body-first group. Using Caenorhabditis elegans (C. elegans) PD models, we found that feeding with Δhns E. coli protected dopaminergic neurons, whereas exogenous MG abolished this neuroprotection. Transcriptomic and neuronal RNAi analyses identified rig-5 as a host mediator of hns deletion-induced neuroprotection. Cross-species analyses identified LSAMP as a candidate mammalian ortholog of rig-5. MG suppressed LSAMP expression in human neuronal cells, and LSAMP expression was reduced in the post-mortem SN of patients with PD. Conversely, Lsamp expression was increased in the SN of mice colonized with Δhns E. coli. Together, these findings delineate a microbial gene-metabolite-host gene pathway through which E. coli hns and MG modulate rig-5-dependent dopaminergic vulnerability in C. elegans, with corresponding changes of LSAMP expression in mammalian systems.},
}

Animals
*Parkinson Disease/metabolism/microbiology/genetics
Humans
*Escherichia coli/metabolism/genetics
Caenorhabditis elegans/genetics/microbiology
*Gastrointestinal Microbiome
*Pyruvaldehyde/metabolism/blood
Dopaminergic Neurons/metabolism
*Escherichia coli Proteins/metabolism/genetics
Gene Expression Regulation
Male
Disease Models, Animal
Female
Neurons/metabolism
Feces/microbiology

@article {pmid42878386,
year = {2026},
author = {Vojtková, M and Baltušis, M and Martiny, HM and Baral, A and Pyrounakis, N and Beleon, A and Freitag, R and Pico-Tomàs, A and Kaas, RS and Petersen, TN and Munk, P},
title = {PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag776},
pmid = {42878386},
issn = {1367-4811},
abstract = {MOTIVATION: Antimicrobial resistance databases are central to genomic surveillance, but resistance determinants remain distributed across resources with different scopes, structures, and annotations.

RESULTS: We developed PanRes, a curated resistance database of 11 717 genes integrating acquired and latent determinants of antibiotic, biocide, and metal resistance within a unified ontology. We predicted representative protein structures and clustered them by structural similarity, grouping proteins into 505 high-confidence structurally conserved clusters coherent despite sequence divergence. Their structure-guided alignments were used to build Hidden Markov Models (HMMs) for remote homology search. In seven wastewater metagenomes from five European cities, PanRes 3D-based HMMs expanded detection beyond what was possible with BLAST, with 35.3% of retained hits identified only by the HMMs and generally showing greater divergence from known proteins. For beta-lactamases, several proteins retained beta-lactamase-like folds and catalytic geometry despite weak sequence similarity.

PanRes is available through an interactive web platform (https://panres.rambio.dk/), a structure-informed resource for exploring the whole resistome. The database, HMM profiles, and ontology are available at Zenodo (10.5281/zenodo.22876216).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42878464,
year = {2026},
author = {Gonzalez, C and Ali, J and Román-Reyna, V and Vasco-Correa, J},
title = {Metagenome-assembled genomes from methane-fed bottle incubations under variable moisture and pH conditions.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0104126},
doi = {10.1128/mra.01041-26},
pmid = {42878464},
issn = {2576-098X},
abstract = {Methane-oxidizing microorganisms mitigate methane emissions in natural and engineered environments. We report 63 metagenome-assembled genomes recovered from methane-fed compost incubations under contrasting moisture and pH conditions, including 62 bacterial metagenome-assembled genomes (MAGs) and 1 archaeal MAG. The MAGs include methanotrophs and microorganisms involved in complementary carbon, nitrogen, sulfur, and carbohydrate metabolic functions.},
}

@article {pmid42878705,
year = {2026},
author = {Keuschnig, C and Feord, H and Broadwell, ELM and Zervas, A and Tranter, M and Anesio, AM and Benning, LG},
title = {Aerobic anoxygenic phototrophs are widespread and active members of Greenland Ice Sheet microbiomes.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag116},
pmid = {42878705},
issn = {1574-6941},
abstract = {The Greenland Ice Sheet (GrIS) hosts diverse microbial communities where glacier ice algae, snow algae, and cyanobacteria act as key primary producers across bare ice, snow, and cryoconite habitats, yet the ecological roles of associated heterotrophic prokaryotes remain poorly understood. Aerobic anoxygenic phototrophs (AAPs), known to couple light harvesting to heterotrophy and enter trophic relationships with algae in marine systems, suggesting they may represent an important but underexplored functional group in supraglacial ecosystems. Using genome-resolved analyses of supraglacial metagenomes and metatranscriptomes from Greenland, we recovered nine AAP metagenome-assembled genomes (MAGs) (4% of the 229 recovered MAGs) consistently enriched in bare ice and cryoconite communities, but nearly absent in snow. A meta-analysis of 2 451 public metagenomes supported this cryospheric habitat association. AAP_MAGs were disproportionally enriched in thiosulfate oxidation and bicarbonate-dependent carbon assimilation pathways relative to other MAGs. Iron and CO oxidation pathways were broadly distributed across the GrIS microbiome, including in AAPs, together suggesting adaptation strategies in supraglacial ecosystems. Genomic evidence for algal coupling via sulfoquinovose degradation was limited. Overall, we document that AAPs are active and widespread in weathering crust habitats, highlighting their potential contributions to biogeochemical cycling in supraglacial ecosystems.},
}

@article {pmid42879678,
year = {2026},
author = {Lin, ZR and Shi, JC and Qiu, CC and Wu, ZX and Lin, XQ and He, GQ and Liu, SD and Du, QW and Lin, HB and Wu, LP and Sun, F and Jiang, XG},
title = {Metagenomic insights into the pulmonary microbiome of drug-sensitive and multidrug-resistant tuberculosis patients.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2720327},
doi = {10.1080/07853890.2026.2720327},
pmid = {42879678},
issn = {1365-2060},
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Female ; Male ; Metagenomics ; *Lung/microbiology ; Middle Aged ; Adult ; Prospective Studies ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {BACKGROUND: While the pulmonary microbiota may influence TB pathogenesis, direct comparisons between drug-sensitive (DS-TB) and multidrug-resistant (MDR-TB) patients remain scarce. This study explored microbiome differences between these groups.

METHODS: Bronchoalveolar lavage fluid (BALF) from 30 prospective patients (11 DS-TB, 19 MDR-TB) was analysed via metagenomic sequencing.

RESULTS: Patients with MDR-TB showed lower α-diversity and distinct β-diversity compared with patients with DS-TB. Streptococcus and Prevotella were relatively enriched in DS-TB, whereas Staphylococcus, Cutibacterium, and Mycobacterium were more abundant in MDR-TB. DS-TB showed enrichment of 45 carbohydrate-active enzyme families and core metabolic annotations, whereas MDR-TB showed enrichment of infection- and immunity-related functional annotations and a less connected taxonomic network. An exploratory random forest analysis identified six candidate genera and yielded an internally cross-validated AUC of 0.957.

CONCLUSIONS: MDR-TB was associated with lower pulmonary microbial diversity, altered community composition, and shifts in predicted microbial functions. These findings characterise lower-airway microbiome differences between DS-TB and MDR-TB and provide a basis for further validation.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Tuberculosis, Multidrug-Resistant/microbiology/drug therapy
Female
Male
Metagenomics
*Lung/microbiology
Middle Aged
Adult
Prospective Studies
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid42879864,
year = {2026},
author = {Scott, WT and Jácome, LAP and Nijsse, B and Wang, J and Stouten, GR and Koehorst, JJ and Smidt, H and Edwards, EA and Schaap, PJ and Kleerebezem, R},
title = {Resolving metabolic interdependencies during chlorobenzene dechlorination in a Dehalobacter-containing community.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127036},
doi = {10.1016/j.watres.2026.127036},
pmid = {42879864},
issn = {1879-2448},
abstract = {Chlorinated benzenes are persistent groundwater contaminants whose anaerobic transformation can depend on organohalide-respiring microorganisms embedded within metabolically interconnected communities. Here, we asked which microorganisms and metabolic functions characterize a Dehalobacter-containing dechlorinating community, and whether bioinformatics and genome-resolved metabolic modeling could identify candidate interactions supporting organohalide respiration. To address these questions, we integrated dechlorination data from related Dehalobacter-containing enrichment lineages with genome-resolved metagenomics and constraint-based modeling. Transformation of 1,2,4-trichlorobenzene (TCB) to dichlorobenzenes and monochlorobenzene (MCB) was observed in one enrichment lineage, whereas MCB transformation to benzene was observed in a related lineage; in the latter, benzene increased from 0 to 62.3μmol bottle[-1] as MCB decreased from 88.3 to 22.0μmol bottle[-1] over 120 days. These experiments comprised one observation unit per lineage rather than independent biological reactor replicates and therefore do not establish continuous TCB-to-benzene conversion within a single culture. Genome-resolved reconstruction identified two Dehalobacter populations among 12 community members selected for metabolic modeling. Following structural, phenotypic, and thermodynamic quality control, pairwise random flux sampling predicted a metabolically differentiated exchange network: Methanobacterium consumed H2 in all 11 pairwise models (median model-normalized flux, 22.36 mmol gDW[-1] h[-1]), whereas Methanothrix consumed acetate in all 11 (10.16 mmol gDW[-1] h[-1]) and released CH4 (9.51 mmol gDW[-1] h[-1]), distinguishing hydrogenotrophic and acetoclastic methanogenic functions. Model-guided community reduction across 39 sensitivity scenarios produced objective-minimal candidate communities in 34 scenarios, predominantly bicultures with condition-dependent recruitment of a third member. A Dehalobacter member occurred in every candidate community and Methanothrix recurred across all evaluated scenarios, defining a compact model-predicted Dehalobacter-methanogen backbone rather than demonstrating biological indispensability. Together, these results distinguish observed dechlorination from genome-inferred metabolic potential and model-predicted interactions, providing experimentally testable hypotheses for metabolic dependencies that could inform more predictable anaerobic bioremediation strategies.},
}

@article {pmid41603601,
year = {2026},
author = {Stairs, B and Johnson, H and Mondron, K and Syring, KC and Guerrero, A and Ballou, ER and King, JS and Pawlowska, TE and Adeleke, R and Stevens, DA and Uehling, JK},
title = {Genomic analyses of globally distributed Rhizopus microsporus populations indicate clinical isolates derived from environmental diversity reservoirs.},
journal = {Mycologia},
volume = {118},
number = {2},
pages = {316-329},
doi = {10.1080/00275514.2025.2594974},
pmid = {41603601},
issn = {1557-2536},
support = {NSF 2202410//National Science Foundation/ ; NSF 2030338//National Science Foundation/ ; BB/W002760/1//BBSRC/ ; },
mesh = {Humans ; *Disease Reservoirs/microbiology ; DNA, Environmental/genetics/isolation & purification ; DNA, Fungal/genetics/isolation & purification ; Genome, Fungal ; *Mucormycosis/microbiology ; Polymorphism, Single Nucleotide ; *Rhizopus/genetics/isolation & purification ; *Soil Microbiology ; Whole Genome Sequencing ; Metagenomics ; },
abstract = {Mucormycosis is a group of diseases that is increasing in frequency. A common opportunistic human fungal pathogen in this group is Rhizopus microsporus, which is a globally distributed species present in soil-associated environments. A subset of isolates in this species host endobacteria that are hypothesized to influence fungal pathogenicity in both clinical and environmental settings. We have limited understanding of how clinically and environmentally derived isolates are related or how physiological attributes, including thermotolerance and endosymbiosis, are correlated with population structure. Traditional molecular barcodes used to assess intraspecific relationships, such as ribosomal DNA internal transcribed spacer (ITS-rDNA)-based markers, do not provide species-level resolution, necessitating analyses of whole genome data. In this study, we generated novel whole genome sequencing data for six R. microsporus isolates and combined these data with publicly available whole genome sequences of 46 R. microsporus isolates. We evaluated these sequences to understand the evolutionary relationships among clinical and environmental isolates using phylogenomic and single nucleotide polymorphism (SNP)-based population genomics methods. We further studied their relationships by quantifying and comparing potential physiological differences and endosymbiont presence in a subset of 16 isolates with live cultures. We found that clinical isolates that originate from environmental settings contain higher molecular diversity than subpopulations isolated from clinical settings. We observed that environmental isolates grow faster than clinical isolates at temperatures between 22 and 37 C and that 7 of 16 (44%) contain endobacteria in the genus Mycetohabitans (Burkholderiales). Lastly, we observed that genome assembly size in R. microsporus is variable and that long-read sequencing technologies greatly enhance our ability to investigate the underlying genomic features. Our study provides a valuable backdrop for probing the basic biology and applied biomedical importance of Rhizopus and related fungi that cause mucormycosis.},
}

Humans
*Disease Reservoirs/microbiology
DNA, Environmental/genetics/isolation & purification
DNA, Fungal/genetics/isolation & purification
Genome, Fungal
*Mucormycosis/microbiology
Polymorphism, Single Nucleotide
*Rhizopus/genetics/isolation & purification
*Soil Microbiology
Whole Genome Sequencing
Metagenomics

@article {pmid42868942,
year = {2026},
author = {Shu, W and Wang, P and Yang, J and Ding, M and Qin, L and Huang, G and Zhang, H and Ge, Y},
title = {Linking microbial community reassembly to multi-element metabolic potential across community and genome scales in rivers impacted by ion-adsorption rare earth mining.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127131},
doi = {10.1016/j.watres.2026.127131},
pmid = {42868942},
issn = {1879-2448},
abstract = {Ion-adsorption rare earth element (REE) mining can create a composite pollution environment characterized by acidification and enrichment of NH4[+], SO4[2][-], and REEs, yet its effects on riverine microbial community assembly and multi-element metabolic potential remain poorly understood. Here, we combined 16S rRNA amplicon sequencing, metagenomic sequencing, and metagenome-assembled genomes (MAGs) to characterize microbial community assembly and functional reorganization across a mining-disturbance gradient. At the community level, bacterial and archaeal richness and diversity declined significantly with increasing pollution, accompanied by clear community differentiation. Compared with bacteria, archaea exhibited greater environmental specificity, with larger contributions of homogeneous selection and dispersal limitation to community assembly. Meanwhile, microbial functional genes formed a modular network linking carbon, nitrogen, sulfur, iron, arsenic, and methane transformation processes, with particularly prominent cross-module associations among carbon-, nitrogen-, and sulfur-related functions. At the genome level, mining-associated MAGs showed multifunctional integration within individual genomes and potential functional division of labor and complementarity among different microbial members. Together, the community- and genome-level results revealed a cross-scale organization of multi-element metabolic potential, extending from functional network connectivity at the community level to functional configuration at the genome level. Such mining-driven reorganization of microbial communities and metabolic functions may further influence greenhouse-gas-related processes and the mobility and transformation of metal(loid)s, providing new insights into microbial ecological processes and potential ecological risks in mining-impacted rivers.},
}

@article {pmid42868958,
year = {2026},
author = {Yan, C and Liu, J and Ma, S and Cheng, Z and Xu, H and Shangguan, YX and Liu, H},
title = {Rhizosphere functional microbiome remodeling by Streptomyces and jasmonic acid mitigates cadmium accumulation in rice.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128761},
doi = {10.1016/j.micres.2026.128761},
pmid = {42868958},
issn = {1618-0623},
abstract = {Cadmium (Cd) contamination poses a serious threat to rice production and food safety because of its high mobility in soil and its accumulation in edible rice tissues. Although beneficial microorganisms and plant signaling regulators have individually shown potential for alleviating Cd stress, whether their combined application can reduce Cd accumulation by restructuring rhizosphere microbial functions remains poorly understood. This study investigated the effects of two Cd-tolerant, plant growth-promoting Streptomyces strains, alone or in combination with jasmonic acid (JA), on Cd stress, Cd accumulation, and rhizosphere microbial communities and functions in rice. The results indicated that Streptomyces co-inoculation improved rice growth, photosynthetic performance, antioxidant defense, and osmotic regulation. It also reduced soil Cd bioavailability and altered Cd partitioning within rice plants. JA alone exerted relatively limited effects on the rhizosphere microbiome but strengthened Streptomyces-mediated physiological and microbial responses when applied in combination. Metagenomic analysis showed that the treatments altered microbial community composition and enriched COG functions associated with inorganic ion transport, signal transduction, and cell envelope biogenesis. KEGG analysis further revealed changes in pathways associated with environmental sensing and Cd detoxification, particularly the two-component system and glutathione metabolism. BacMet analysis identified 37 Cd-related resistance genes. Streptomyces co-inoculation broadly enriched resistance modules involved in metal sensing, transport, efflux, and detoxification, whereas the combined treatment selectively enriched core resistance genes, including czcA, czcP, zntA, and nccB. These changes were consistent with the reduced bioavailable Cd in rhizosphere soil and lower Cd accumulation in rice. Rather than increasing the number of responsive genes, the addition of JA to Streptomyces co-inoculation was associated with a more focused Cd resistance gene response, particularly involving metal transport and efflux. Overall, the reduction in Cd accumulation was associated with coordinated changes in rhizosphere microbial communities, metabolic pathways, and Cd resistance genes. These findings highlight the potential of combining Streptomyces co-inoculation with JA as a microbiome based strategy for rice cultivation in Cd contaminated soils.},
}

@article {pmid42869245,
year = {2026},
author = {Ríos-Castro, R and Allen, A and Itoh, N and Long, A and Bower, S and Joseph, A and Kim, E and Collins, C and Wickramanayaka, DN and Lynch, S and Culloty, S and Hill, R and Bignell, J and Green, M and Ward, GM and Tidy, A and Kerr, R and White, P and Cano, I},
title = {Surveillance, genetic diversity, and virulence characterisation of Francisella halioticida in blue mussels from the United Kingdom and Ireland.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108763},
doi = {10.1016/j.jip.2026.108763},
pmid = {42869245},
issn = {1096-0805},
abstract = {Francisella halioticida is a recently recognized pathogen affecting molluscs. In Europe, its presence has been documented within mussel populations in both France and England. At present, data concerning its genetic variability in mussels remain scarce. Between 2024 and 2025, a comprehensive monitoring programme was implemented to assess F. halioticida prevalence in southern England, alongside analyses of archived samples from Scotland and Ireland. The findings indicated a low prevalence of the pathogen within the surveyed populations, primarily associated with mild or localized infections. Phylogenetic analyses based on multi-locus sequence analysis showed genetic variability of F. halioticida in mussels across surveyed locations and years, however a distinct F. halioticida cluster from mussels separated from F. halioticida infecting scallops and abalone was identified. A F. halioticida metagenome assembled genome was obtained from an infected mussel from southern England, with 3666 predicted ORFs, and a ~14.2 kb region containing a putative Francisella Pathogenicity Island, including genes associated with Type VI secretion system components (TssK, DotU, IglE, and IglH), together with several hypothetical proteins, and flanked by IS3 family transposases. Additional virulence-associated genes were detected, including transcriptional and global regulators, oxidative stress and detoxification genes, and metallopeptidases. These findings improve understanding of the occurrence, diversity, and genomic features of F. halioticida in wild mussel populations, highlighting the need for expanded surveillance and higher-resolution genomic data to better understand its epidemiology and pathogenic potential. This improved resolution enhances risk assessment, enables early detection of emerging lineages, and supports more targeted monitoring strategies for wild mussel populations.},
}

@article {pmid42869256,
year = {2026},
author = {Pan, LL and Liang, W and Ren, Z and Yang, J and Jia, K and Wang, Q and Ma, Y and Tian, H and Zou, H and Liu, H and Wang, L and Wu, M and Li, B and Yang, S and Zuo, J and Wang, Z and Yang, Q and Dong, X and Bhatia, M and Peng, S and Zhou, C and Zou, WB and Liao, Z and Zou, D and Diana, J and Sun, J},
title = {HtpG-High-Expressing Escherichia coli Promotes Fibrosis in Chronic Pancreatitis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.09.025},
pmid = {42869256},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Chronic pancreatitis (CP) is a progressive fibroinflammatory disease with rising global incidence and no curative therapy. Gut dysbiosis has been associated with CP, but its causal contribution to disease pathogenesis remains unclear. We intended to identify specific pathogenic microbial species that promote CP and to delineate the underlying pathogenic mechanisms.

METHODS: Multi-omics analyses were used to identify key microbial signatures in CP patients and mice. Novel pathogenic Escherichia coli strains were isolated and bioengineered for functional studies. In vitro and in vivo assays, along with macrophage-specific knockout mice, adenoviral tools, and pharmacological inhibitors, were employed to dissect host-microbe mechanistic pathways. Therapeutic intervention included administering a screened next-generation probiotic.

RESULTS: Metagenomic sequencing identified HtpG-high-expressing E. coli (HHEC) enrichment as a dominant microbial signature in CP patients. Prevention of HHEC adherence and colonization alleviated CP, whereas recolonization with a new patient-derived HHEC strain PS718 exacerbated it. Mechanistically, E. coli-derived HtpG upregulated protein arginine methyltransferase 5 (PRMT5) in pancreatic macrophages. Pharmacological inhibition of PRMT5 or macrophage-specific deletion of PRMT5 mitigated pancreatic fibrosis and CP progression. PRMT5 methylated Krüppel-like factor 4 (KLF4) at residues R387/R389, stabilizing it, which promoted M2 polarization and pancreatic fibrosis. Therapeutic intervention with Akkermansia muciniphila, which is reduced in CP, suppressed HHEC colonization and ameliorated CP.

CONCLUSION: These findings provide novel evidence for a pathogenic HHEC-HtpG-macrophage axis in CP, highlighting the potential of microbiota-targeted therapies for the condition.},
}