@article {pmid42960658,
year = {2026},
author = {Zeng, XQ and Xiong, JQ and Wang, P},
title = {Metagenomic next-generation sequencing rescues a case of imported visceral leishmaniasis masquerading as hemophagocytic lymphohistiocytosis.},
journal = {Tropical biomedicine},
volume = {43},
number = {3},
pages = {367-371},
doi = {10.47665/tb.43.3.018},
pmid = {42960658},
issn = {2521-9855},
mesh = {Humans ; Male ; *Leishmaniasis, Visceral/diagnosis/drug therapy/parasitology/pathology ; *Lymphohistiocytosis, Hemophagocytic/diagnosis ; Middle Aged ; Amphotericin B/therapeutic use ; Antiprotozoal Agents/therapeutic use ; *High-Throughput Nucleotide Sequencing ; Diagnosis, Differential ; *Metagenomics/methods ; *Leishmania/genetics/isolation & purification/classification ; },
abstract = {This paper reports a case of imported visceral leishmaniasis (VL; also known as kala-azar) in a nonendemic area (Wuhan). The patient was a 63-year-old male who had recurrent fever for more than 5 months and failed to respond to multiple treatments for hemophagocytic syndrome (HLH). No pathogen was detected by traditional bone marrow aspiration smear microscopy. Finally, 12347 standardized sequence count of Leishmania species complex were detected in peripheral blood via metagenomic next-generation sequencing (mNGS), confirming the diagnosis of VL. The patient's condition was relieved after treatment with liposomal amphotericin B. This case suggests that mNGS should be used as a powerful tool for early pathogen screening in patients with fever of unknown origin accompanied by HLH in non-endemic areas.},
}

Humans
Male
*Leishmaniasis, Visceral/diagnosis/drug therapy/parasitology/pathology
*Lymphohistiocytosis, Hemophagocytic/diagnosis
Middle Aged
Amphotericin B/therapeutic use
Antiprotozoal Agents/therapeutic use
*High-Throughput Nucleotide Sequencing
Diagnosis, Differential
*Metagenomics/methods
*Leishmania/genetics/isolation & purification/classification

@article {pmid42961048,
year = {2026},
author = {Sabirova, D and Rayko, M and Vinichenko, V and Shikov, A and Altinbaev, R and Antonets, K and Yunusbaeva, M and Yunusbayev, B},
title = {Genomic insights into the human gut commensal Megasphaera elsdenii: relatedness and metabolic potential compared to animal isolates.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0163726},
doi = {10.1128/spectrum.01637-26},
pmid = {42961048},
issn = {2165-0497},
abstract = {UNLABELLED: Megasphaera elsdenii is best known as a prominent lactate consumer within the rumen microbial community in livestock, and its metabolic properties are relatively well studied. In humans, it can be isolated from healthy donors' feces and, more often, from patients' feces with diverse inflammatory conditions. Genetic diversity of this species is poorly understood, and it is currently unclear whether human and animal gut isolates are genetically related and perform the same metabolic function. In this study, we compared 86 M. elsdenii genomes from human feces (as a proxy for the human gut) to those of animal gut isolates. Phylogenetic analysis revealed that human and animal gut lineages intermingle within a single, genetically homogeneous branch, lacking any host-specific clustering. Human gut lineages shared most of their genes and biochemical pathways with those of swine and cattle gut isolates, despite differences in their digestive tracts. Neither unsupervised nor supervised approaches identified any notable differences in encoded pathways between different host-specific gut lineages. Genome-scale metabolic modeling suggests that human and animal gut lineages likely share identical carbon and energy source requirements. Moreover, the requirements for lactate and acetate were conserved across all studied samples, regardless of the host. Finally, we found no virulence genes, and lactate utilization remains a plausible explanation for M. elsdenii accumulation in the host intestine.

IMPORTANCE: Megasphaera elsdenii is considered a commensal in the human gut and animal rumen. However, M. elsdenii tends to be more abundant in patients' feces with diverse inflammatory conditions. As we know little about the strain diversity and biology of human gut lineages, comparisons with better-studied animal isolates can be informative. In this study, we compared human gut M. elsdenii genomes to those from better-studied isolates from ruminant and non-ruminant animal hosts. Human gut samples associated with patients and healthy donors were genetically very similar to gut isolates from animals and may have shared a common origin. We found that human and animal gut lineages have a similar genomic makeup and metabolic potential and that neither group harbors virulence genes. We hypothesize that M. elsdenii is a benign commensal that grows in response to lactate accumulation in the inflamed gut.},
}

@article {pmid42961364,
year = {2026},
author = {Alghafri, M and Edwards, L and Moyes, D and Nibali, L},
title = {Antimicrobial Resistance in Periodontal Disease: Rethinking Adjunctive Therapy in the Metagenomics Era, the Pressing Need for Precision Treatment and Periodontal Resistome Mapping.},
journal = {Journal of cellular and molecular medicine},
volume = {30},
number = {21},
pages = {},
pmid = {42961364},
issn = {1582-4934},
mesh = {Humans ; *Metagenomics/methods ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Microbiota/drug effects ; *Periodontal Diseases/microbiology/drug therapy ; *Precision Medicine ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial ; },
abstract = {Systemic antibiotics are effective when used as adjunctive therapy in the treatment of periodontitis; however, their use must be balanced against antimicrobial resistance, which is a major threat to global public health. This review provides an expert synthesis of the literature and a field-level overview of antimicrobial resistance in periodontal therapy, highlighting current knowledge and emerging directions, while examining how adjunctive antibiotic protocols may contribute to resistance within the periodontal microbiome through emerging metagenomic insights. To provide this synthesis, the PubMed database was searched for English-language publications using combinations of the terms periodontitis, systemic antibiotics, antimicrobials, resistance, resistome, therapeutic adjuncts, resistance genes, susceptibility, antibacterial and drug resistance, and the findings are presented as a narrative review. The evidence indicates that a substantial proportion of patients with periodontitis harbour subgingival microbiota that are non-susceptible to at least one antibiotic used in periodontal therapy. Across the included studies, antimicrobial resistance was most frequently reported in Prevotella and Porphyromonas species, while some studies also identified virulence-associated factors in Staphylococcus aureus, a non-classical periodontal organism detected within the subgingival microbiota. Overall, current evidence indicates a high prevalence of antibiotic resistance genes in the subgingival microbiota of patients with periodontitis and highlights the ecological consequences of adjunctive antibiotic use. These findings reinforce the need to optimize antibiotic prescribing protocols within an antibiotic stewardship framework and support further metagenomic investigations to refine understanding of resistance patterns, gene-transfer mechanisms and microbiome disruption, with the aim of advancing precision-based periodontal care.},
}

Humans
*Metagenomics/methods
*Anti-Bacterial Agents/therapeutic use/pharmacology
Microbiota/drug effects
*Periodontal Diseases/microbiology/drug therapy
*Precision Medicine
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial

@article {pmid42961615,
year = {2026},
author = {Dolker, S and Ghosh, A and Singh, VK and Joshi, BD and Sharma, LK and Thakur, M},
title = {Exploring sex- and captivity-associated gut microbial diversity in Bengal Tigers (Panthera tigris tigris).},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42961615},
issn = {1573-4978},
mesh = {Animals ; *Tigers/microbiology/genetics ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Feces/microbiology ; Bacteria/genetics/classification ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Endangered Species ; },
abstract = {BACKGRO UND: The gut microbiome plays a critical role in host nutrition, immune regulation, metabolic stability, and overall physiological health in wildlife. However, gut microbiome data from large carnivores remain limited, particularly for endangered tiger populations. This study conducted a comparative analysis of fecal microbiomes from captive and wild Bengal tigers, integrated with publicly avai lable datasets from Amur, Malayan, and South China tigers, to understand how captivity and host factors influence microbial assembly. ME THOD S AND RESULTS: Across all tiger subspecies, Firmicutes and Proteobacteria dominated as core bacterial phyla, with Actinobacteriota, Bacteroidota, and Fusob acteriota forming a conserved microbial backbone. Wild Bengal tigers exhibited higher microbial richness and diversity than captive tigers . Beta diversity analyses demonstrated clear clustering by habitat (captive versus wild), but substantial overlap between male and female captive Bengal tigers, indicating that captivity-associated conditions exert influences on gut microbiome structure than sex. Comparative analyses among tiger subspecies revealed broad overlap in microbial community composition, suggesting limited phylogenetic influence. South China and Amur tigers displayed the lowest richness compared to Bengal and Malayan tigers. Furthermore, analysis identified an enrichment of protein fermentation-associated taxa in captive tigers, whereas wild tigers showed a greater abundance of environmentally associated taxa. CONCLUSIONS: The study provides evidences that captivity promotes reduction in gut microbial diversity in Bengal tigers, and highlights the potential utility of microbiome-informed captive management. Integrating gut microbiome monitoring into conservation breeding, zoo exchange and reintroduction programmes may improve adaptive fitness in endangered tiger populations.},
}

Animals
*Tigers/microbiology/genetics
Female
Male
*Gastrointestinal Microbiome/genetics
Phylogeny
Feces/microbiology
Bacteria/genetics/classification
Biodiversity
RNA, Ribosomal, 16S/genetics
Sex Factors
Endangered Species

@article {pmid42962471,
year = {2026},
author = {Zou, D and Fu, Y and Lv, Z and Liu, Z and Huang, Z and Yan, B and Liu, J and Kuang, Y and Li, M and Lin, L and He, M and Jing, T and Huang, S},
title = {Associations of environmental phenols exposure with gut microbiota in a general population from Shenzhen, China.},
journal = {Ecotoxicology and environmental safety},
volume = {326},
number = {},
pages = {120990},
doi = {10.1016/j.ecoenv.2026.120990},
pmid = {42962471},
issn = {1090-2414},
abstract = {The gut microbiota is considered an important target for the toxicity of environmental phenols, yet the epidemiological evidence elucidating their associations in adults remains limited. This study investigated associations between phenol exposure and gut microbiota in 241 adults from Shenzhen, China. We quantified 38 urinary phenols via ultrahigh performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) and profiled the gut microbiome via shotgun metagenomics. Linear regression, permutational multivariate analysis of variance (adonis), and Multivariable Association with Linear Models 2 (MaAsLin2) were used to assess links with α-diversity, β-diversity, microbial taxa, and functional pathways. We found that exposure to environmental phenols was significantly associated with altered gut microbiota diversity, composition and function. Bisphenol C was negatively associated with α-diversity, whereas benzylparaben and ethylparaben were positively associated with it. Exposure to methylparaben, triclosan, isopropylparaben and propylparaben was significantly associated with altered gut microbial community structure. Taxa analysis showed that methylparaben was negatively associated with the relative abundance of two beneficial species, Bacteroides salyersiae and Anaerostipes caccae. Additionally, functional profiling revealed that parabens inhibited amino-acid, carbohydrate and terpenoid metabolism, whereas triclosan up-regulated pathways for aromatic compound degradation and mixed-acid fermentation. Further prospective investigations are warranted to validate our findings.},
}

@article {pmid42962573,
year = {2026},
author = {Fang, K and Zhu, Q and Zhu, Y and Yao, G and Zhao, J and Xia, S},
title = {From substrate composition to microbial metabolism: performance, molecular, taxonomic and functional insights into sludge-derived hydrothermal carbon sources for denitrification.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127226},
doi = {10.1016/j.watres.2026.127226},
pmid = {42962573},
issn = {1879-2448},
abstract = {Liquid recovered from hydrothermal sludge treatment is an attractive denitrification carbon source, but it carries nitrogen that raises effluent total nitrogen and recalcitrant organics that leave residual chemical oxygen demand (COD). Thermal hydrolysis (TH), wet air oxidation (WAO) and two-stage WAO with catalytic WAO (WAO-CWAO) liquids were compared with sodium acetate in sequencing batch reactors, and the mechanisms were resolved by Fourier transform ion cyclotron resonance mass spectrometry, 16S rRNA gene sequencing and metagenomics. TH and WAO liquids failed as carbon sources, with effluent COD and nitrogen above the Chinese discharge standard, whereas the WAO-CWAO liquid converted the recalcitrant organics into volatile fatty acids (VFAs), removed ammonia, and approached, but did not match, the sodium acetate control. An apparent nitrogen balance showed that residual nitrogen reflected the load introduced with the carbon source, and residual COD was traced to a CHON-rich pool unique to these effluents. Community composition followed carbon source quality, shifting from a diverse consortium sustained by slowly biodegradable organics to a streamlined assemblage of VFAs-utilizing denitrifiers. Genome-resolved analysis of the recovered metagenome-assembled genomes indicated a substrate-based division of labor: the dominant Saprospiraceae carried an expanded hydrolytic arsenal but no nitrate reductase, whereas Thauera carried complete denitrification and VFA-utilization gene sets but no polysaccharide hydrolases. A second, catalytic stage at higher temperature and oxygen pressure therefore alleviates the trade-off between nitrogen release and incomplete oxidation, yielding a sludge-derived carbon source that approaches sodium acetate.},
}

@article {pmid42962635,
year = {2026},
author = {Ma, Y and Ye, Z and Xu, S and Liu, Z},
title = {Copper valence dynamics link microbial redox functions to humification during composting.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143962},
doi = {10.1016/j.jhazmat.2026.143962},
pmid = {42962635},
issn = {1873-3336},
abstract = {Organic-waste composting supports resource recovery, but microbial links between Cu transformation and humification remain insufficiently resolved. We combined XPS-Auger analysis, metagenomics, day-4 metatranscriptomics, and genome-resolved analysis to compare Cu(I), Cu(II), and mixed-valence treatments receiving equal Cu inputs with a control without added Cu (CK) during lignocellulosic composting. By day 30, surface Cu(I) proportions reached 55.63% and 59.04% in Cu(I) and mixed-valence treatments, respectively, whereas the Cu(II) treatment remained Cu(II)-dominated. On day 4, AA1 accounted for 1.331% of the exported CAZy expression total in CK and 2.085-2.931% in Cu treatments, alongside distinct substrate-transformation and redox profiles. Cu treatments showed higher day-4 transcript levels of carbohydrate-associated MAG204 and Cu-homeostasis-associated MAG674. The Cu(I) treatment had the greatest humic acid (HA) concentration gain (60.09 g kg[-1]), whereas the mixed-valence treatment had the highest final HA concentration (122.45 g kg[-1]). The findings support a Cu-valence-associated working model of redox-active humification; extracellular electron transfer remains to be verified by direct electrochemical measurements.},
}

@article {pmid42962640,
year = {2026},
author = {Osborn, KP and Zhang, Y and Ray, S and Kong, Y and Levy, S and Jun, S and Chang, M and Lin, J and Vuong, J and Ives, C and Jones, A and Henning, L and Dickerson, C and Mahendra, S and Bodeau, W and Casillas, A and Chowdhry, R and Chung, J and Curristan, N and Espinoza, A and Alejo, GF and Jennings, I and Lakhanpal, T and Jay, JA},
title = {Widespread antibiotic resistance and multidrug resistance in Escherichia coli from surface waters near dairies and a calf ranch in Wisconsin: Implications for hotspot screening and multi-method monitoring.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143938},
doi = {10.1016/j.jhazmat.2026.143938},
pmid = {42962640},
issn = {1873-3336},
abstract = {Although concentrated animal feeding operations (CAFOs) are known sources of antimicrobial resistance (AMR), gaps remain regarding AMR dissemination to environments and monitoring methods. Impacts of large dairies and a calf ranch in Wisconsin on the environmental resistome were assessed at nine surface water sites near CAFOs and two nearby unimpaired sites. 1297 Escherichia coli (EC) isolates were tested against a suite of antibiotics by Kirby-Bauer disk diffusion. Up to 68% of EC isolates at dairy-impacted sites and 70% downstream of the calf ranch exhibited multidrug resistance (MDR), versus up to 8% at the unimpaired sites. Fecal indicator bacteria kits modified with antibiotics detected elevated extended-spectrum beta-lactamase-producing (ESBL) EC at the site exhibiting highest MDR, suggesting use as a screening tool. Metagenomic analysis showed elevated antibiotic resistance genes (ARGs), abundance, diversity, and human health risk scores at the calf ranch-impacted site. Follow-up sampling just upstream and downstream of the calf ranch showed dramatic increases in multiple measures, indicating calf ranches may warrant additional monitoring and elucidate more complex processes such horizontal gene transfer. Culture-based results revealed pronounced AMR hotspots and differences among sampling events only partially reflected by metagenomic analysis and a limited quantitative PCR (qPCR) panel, underscoring the importance of monitoring through complementary methods.},
}

@article {pmid42962650,
year = {2026},
author = {Luo, J and Dong, S and Yuan, M and Wen, W and Li, YA and Li, Y and Zhao, R},
title = {From environmental gradients to putative intrinsic resistance: Deciphering the soil resistome across Mongolian Plateau grasslands.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144040},
doi = {10.1016/j.jhazmat.2026.144040},
pmid = {42962650},
issn = {1873-3336},
abstract = {Soils are important reservoirs of antibiotic resistance genes (ARGs), yet the ecological differentiation and host associations of grassland resistomes remain poorly understood. We investigated topsoil resistomes across desert steppe, typical steppe, and meadow steppe of the Mongolian Plateau using short- and long-read metagenomics. The resistome comprised 28 ARG types and 819 subtypes, dominated by rifamycin, vancomycin, and multidrug resistance genes. ARG abundance increased from desert steppe to meadow steppe. Soil pH, total organic carbon, total nitrogen, and climatic variables were strongly associated with resistome turnover, whereas grazing showed weaker associations. Mobile genetic element (MGE) abundance correlated positively with ARG abundance, but only 3.37% of ARG-carrying contigs contained detectable MGEs. An operational multi-indicator framework distinguished putative intrinsic and putative acquired ARGs with contrasting host and environmental associations. Both fractions were dominated by Actinomycetota, although Pseudomonadota contributed relatively more to putative acquired ARGs. Putative intrinsic ARGs were associated mainly with nutrient-related soil variables, whereas putative acquired ARGs showed stronger climatic and edaphic associations. Long-read assemblies markedly reduced the unclassified fraction. Among 195 ARG-carrying metagenome-assembled genomes, 65.6% represented reference-poor or previously uncultured lineages. These findings reveal spatially structured and heterogeneous grassland resistomes linked to ARG composition, host affiliation, and genomic context.},
}

@article {pmid42962651,
year = {2026},
author = {Zhu, X and Wang, H and Li, S and Ni, L and Li, Y and Zhang, D},
title = {Distribution patterns of PFASs in intertidal sediments and the effects on reductive dehalogenating bacteria: A nationwide study in China.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144063},
doi = {10.1016/j.jhazmat.2026.144063},
pmid = {42962651},
issn = {1873-3336},
abstract = {Per- and polyfluoroalkyl substances (PFASs) are of great concern because of their environmental persistence. The intertidal zone sequesters various halogenated organic pollutants (HOPs) in sediments. Microbial reductive dehalogenation is crucial for HOPs detoxification. However, the nationwide distribution characteristics of PFASs in intertidal sediments and their impact on reductive dehalogenators (RDGs) remain poorly understood. We investigated PFAS distribution profiles in 128 intertidal sediments across China and analyzed their impact on potential RDGs. Sedimentary PFAS concentrations ranged 0.049-2.58 ng/g, with legacy PFASs being dominant. Amplicon sequencing and Spearman rank correlation analysis revealed positive correlation between total organic halogens and relative abundance and/or α-diversity of Anaerolineae and Desulfobacterota (p < 0.05), whereas no correlation was observed for Dehalococcoidia. Despite low ecological risks, Cl-PFESAs showed significant negative correlations with their relative abundance and α-diversity. Cl-PFESAs negatively correlated with abundance of the module associated with elemental cycles (p < 0.05), rather than those linked to organohalide utilization in the co-occurrence network. Microbial cultivation and metagenomic analysis reinforced the crucial role of Desulfobacterota and Anaerolineae in intertidal microbial dehalogenation and the negligible effect of 6:2 Cl-PFESA (0.1 mg/L) on reductive dehalogenating activity. This study provides critical insights into bioremediation strategies for HOPs in intertidal zones co-contaminated with PFASs.},
}

@article {pmid42962791,
year = {2026},
author = {Wang, Z and Pan, X and Li, Y and Wang, L},
title = {Decoding dissolved organic matter reorganization and multitrophic regulation of biogeochemical cycling in effluent-dominated hyporheic sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126046},
doi = {10.1016/j.envres.2026.126046},
pmid = {42962791},
issn = {1096-0953},
abstract = {Continuous wastewater effluent discharge sustains pronounced redox heterogeneity in the hyporheic zone (HZ), with consequences for dissolved organic matter (DOM) transformation and sediment biogeochemistry. However, the ecological pathways linking redox-dependent DOM transformation to multitrophic organization and coupled nitrogen (N) and sulfur (S) cycling remain poorly understood. We integrated fluorescence and molecular DOM characterization, bacterial and eukaryotic community profiling, metagenomics, ecological network analysis, and structural equation modeling across oxic and anoxic zones. The summed relative contribution of protein-like fluorescence did not differ significantly between zones, while tyrosine-like fluorescence was 31% higher in the oxic zone and the median tryptophan/tyrosine ratio was 52% higher under anoxia. FT-ICR MS analysis showed that formulas positively associated with HIX had higher O/C ratios and a median NOSC of 0.35, whereas negatively associated formulas had a median NOSC of -0.90, linking optical humification to molecular carbon oxidation characteristics. Bacterial genera exhibited broader estimated niche breadths than eukaryotic genera, with median Levins' B values of 7.19 and 5.86, respectively. Under oxic conditions, DOM was associated with basal communities within a connected sequence of bacterial, protozoan, and metazoan associations. Bacterial and algal communities were primarily associated with N and S cycling potentials, respectively. Under anoxia, significant DOM associations with basal groups and the bacteria-to-protozoa association were not detected, while both cycling potentials shifted toward bacteria-centered regulation. N and S cycling potentials remained strongly coordinated, while modeled network robustness was 20.5% lower under anoxia. These findings reveal that redox-associated DOM reorganization shifts multitrophic regulation of coupled N and S cycling, thus providing a framework for integrating DOM composition and multitrophic organization when assessing aquatic interfaces exposed to sustained organic matter loading and redox heterogeneity.},
}

@article {pmid42963302,
year = {2026},
author = {Bravo, JE and Sapoval, N and Han, Y and Kokroko, N and Nakhleh, L and Noyes, NR and Treangen, TJ and Boucher, C},
title = {Advancing microbial pangenomics through human pangenomics.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2026.10.002},
pmid = {42963302},
issn = {0168-9525},
abstract = {Although the term pangenome originated in the study of microbial species, recent advances in eukaryotic pangenomics have been driven largely by the need to manage the substantial computational challenges posed by population-scale eukaryotic datasets. This review evaluates the extent to which existing eukaryotic pangenome tools and methods can be extended to microbial species. We first survey current eukaryotic and microbial pangenomic approaches and then examine opportunities and challenges in adapting eukaryotic methods to microbial genomes, with particular emphasis on scalability, data quality, evolutionary complexity, and benchmarking. Finally, we highlight areas where existing approaches generalize well and where substantive redesign and redevelopment are needed.},
}

@article {pmid42963371,
year = {2026},
author = {Li, S and Huang, J and Lin, D and Luo, D and Fu, W and Liu, J},
title = {Electroacupuncture alleviates chronic pain and comorbid depression through Gut-Metabolite-Brain axis remodeling to restore mPFC Glu/GABA balance.},
journal = {Translational psychiatry},
volume = {16},
number = {1},
pages = {},
pmid = {42963371},
issn = {2158-3188},
mesh = {Animals ; *Electroacupuncture ; *gamma-Aminobutyric Acid/metabolism ; Rats ; *Chronic Pain/therapy/metabolism ; Male ; *Glutamic Acid/metabolism ; *Gastrointestinal Microbiome/physiology ; *Depression/therapy/metabolism ; *Prefrontal Cortex/metabolism ; Rats, Sprague-Dawley ; Disease Models, Animal ; Comorbidity ; },
abstract = {The comorbidity of chronic pain and depression is increasingly recognized as a systemic disorder involving dysregulated microbiota-gut-brain communication. Although electroacupuncture (EA) has demonstrated therapeutic efficacy for both pain and depression, the mechanisms linking peripheral microbial-metabolic remodeling to central neurotransmitter regulation remain incompletely understood. Here, we employed an integrated multi-omics approach in a spared nerve injury (SNI) rat model to investigate the gut-metabolite-brain mechanisms underlying EA's efficacy. EA significantly alleviated mechanical hypersensitivity and depressive-like behaviors while restoring mPFC Glu/GABA balance, accompanied by normalization of the glutamate transporter EAAT2 and the GABA-synthesizing enzyme GAD67. Metagenomic analysis showed that EA remodeled the gut microbial ecosystem by increasing microbial diversity, suppressing opportunistic pathobionts, including Bacillus cereus, Alistipes onderdonkii, while enriching SCFA-associated genera, including Butyricimonas and Romboutsia. These alterations were accompanied by coordinated remodeling of amino acid and butanoate metabolism. Correlation network analysis identified Pipecolic acid as a central metabolic node linking gut microbial alterations with mPFC GABAergic neurotransmission and behavioral recovery. Although individual bacterial genera did not significantly mediate its restoration, causal mediation analysis demonstrated that the Pipecolic acid-GABA axis significantly mediated improvements in both mechanical allodynia and anhedonia, supporting Pipecolic acid as a functional metabolic hub linking peripheral metabolic remodeling to central GABAergic regulation. Collectively, these findings identify peripheral metabolic remodeling as a key mechanistic interface through which EA coordinates gut microbial ecology and central neurochemical homeostasis, providing a systems-level framework for understanding the therapeutic mechanisms of acupuncture in pain-depression comorbidity.},
}

Animals
*Electroacupuncture
*gamma-Aminobutyric Acid/metabolism
Rats
*Chronic Pain/therapy/metabolism
Male
*Glutamic Acid/metabolism
*Gastrointestinal Microbiome/physiology
*Depression/therapy/metabolism
*Prefrontal Cortex/metabolism
Rats, Sprague-Dawley
Disease Models, Animal
Comorbidity

@article {pmid42963482,
year = {2026},
author = {Chaves, VA and Alegria, OVC and Dantas, CWD and Ferreira, VBC and Martins, DT and Joseph, RC and Almeida, LS and de Souza, SD and Gomes, PWP and da Silva, JKR and Ramos, RTJ},
title = {Influence of Gliricidia sepium living support on rhizosphere bacterial recruitment and fruit metabolomics in black pepper (Piper nigrum).},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42963482},
issn = {1573-0972},
mesh = {*Rhizosphere ; Soil Microbiology ; *Piper nigrum/microbiology/metabolism/chemistry ; Metabolomics ; *Fruit/metabolism/microbiology/chemistry ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics ; Plant Roots/microbiology ; },
abstract = {The ability of the rhizosphere to recruit beneficial microorganisms is central to the sustainable management of crops. Here, we investigated, through shotgun metagenomic sequencing and mass spectrometry techniques, the microbial composition, antimicrobial resistance (AMRs), and metabolomic profiles of Piper nigrum cultivated under two support systems: living Gliricidia sepium support (SL/RL) and dead wooden support (SD/RD). Bulk and rhizosphere soils were sequenced to assess taxonomic structure and ARGs, with emphasis on Actinobacteria due to their relevance in antibiotic production. Actinobacteria were highly represented across the samples (~ 35%). Dead-support rhizospheres exhibited a broader ARG repertoire and greater abundance of taxa known to include antibiotic-producing members, whereas living-support rhizospheres showed reduced ARG diversity. Metabolomic analysis further revealed support-dependent physiological responses in the host plant. PLS-DA distinguished the two cultivation systems, and three defense-related flavonoids, such as sakuranetin, isovitexin, and orientin, which were enriched in fruits of plants grown with dead support, indicating activation of stress - and defense - associated metabolic pathways. Their low abundance in living-support plants suggests reduced physiological stress, likely linked to improved nutrient cycling and rhizosphere stability provided by G. sepium. However, the volatile and total phenolic profile did not display significant chemical alterations in the samples. Together, these results suggest that support type influences both microbial functions and plant secondary metabolism. Dead support creates a more stressful ecological context that enriches antimicrobial resistance genes ARGs and defense metabolites, whereas living support promotes a more balanced soil-plant-microbe environment, supporting the use of G. sepium as a sustainable and biologically advantageous cultivation strategy for black pepper.},
}

*Rhizosphere
Soil Microbiology
*Piper nigrum/microbiology/metabolism/chemistry
Metabolomics
*Fruit/metabolism/microbiology/chemistry
*Bacteria/classification/genetics/isolation & purification/metabolism
Metagenomics
Plant Roots/microbiology

@article {pmid42963941,
year = {2026},
author = {Ghiotto, G and Chasapi, IN and De Bernardini, N and Fraulini, S and Ndela, EO and Baltoumas, FA and Treu, L and Kyrpides, NC and Pavlopoulos, GA and Campanaro, S},
title = {CAnDi: a global catalogue of anaerobic digestion microbiomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1088},
pmid = {42963941},
issn = {1362-4962},
support = {//U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science User Facilities/ ; 23592-EMISSION//Hellenic Foundation for Research and Innovation/ ; 28787-VIROMINE//Hellenic Foundation for Research and Innovation/ ; 101084405//European Union's Horizon 2020 Research and Innovation Programme/ ; //Fondazione Cariverona through the Bando Ricerca e Sviluppo project AI4AD/ ; //University of Padua/ ; },
abstract = {Methanogenic environments harbour complex prokaryotic consortia that drive the anaerobic conversion of organic matter into methane and carbon dioxide. Beyond being key to the global carbon cycle, such processes have been steered into powerful biotechnologies for energy production in bioreactors. Decoding the functional and taxonomic landscape of these communities requires comprehensive surveys, including bacteriophages and plasmids, which, however, remain vastly underrepresented in current databases. Here, we present the microbial Catalogue of Anaerobic Digestion (CAnDi), a database comprising 36 480 prokaryotic genomes spanning 11 149 species recovered from 1256 metagenomic samples collected across bioreactors worldwide. The reconstructed metagenomes also encode ∼1.9 million viral and over 130 000 plasmid sequences. Identity clustering revealed ∼536 000 candidate viral species, of which 85% are novel relative to existing databases, as well as over 15 000 unique plasmids. Clusters of viral and plasmid proteins were generated de novo, totalling 1 721 182 and 123 813 distinct protein families, respectively. Together, these resources substantially advance previous systematic approaches to characterize anaerobic digestion microbiomes, providing an expanded foundation for investigating the ecological and evolutionary roles of the virome and plasmidome in methane-producing ecosystems. CAnDi is accessible via https://www.candi-db.org/.},
}

@article {pmid42963942,
year = {2026},
author = {Pirtskhalava, M and Alimbarashvili, E and Grigolava, M and Chubinidze, M and Vishnepolsky, B and Zaalishvili, G and Karaputadze, R and Samsonidze, N and Rosenthal, A and Hurt, DE and Tartakovsky, M and Gabrielian, A},
title = {DBAASP V4: condition-resolved bioactivity and chemical structures for data-driven peptide and peptidomimetic discovery.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1050},
pmid = {42963942},
issn = {1362-4962},
support = {HHSN316201300006W/HHSN27200002//National Institute of Allergy and Infectious Diseases/ ; G-2102//International Science and Technology Center/ ; FR-25-412//Shota Rustaveli National Science Foundation of Georgia/ ; G-2102//International Science and Technology Center/ ; },
abstract = {The current peptide renaissance-driven by metagenomic and proteomic mining, molecular de-extinction, protein language models, and generative or evolutionary design-is producing millions of candidates, but useful machine learning depends on experimentally anchored, context-rich labels. The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is a manually curated resource linking peptides and peptidomimetics to quantitative antimicrobial, antibiofilm, anticancer, hemolytic, and mammalian-cell cytotoxicity measurements and their experimental conditions. DBAASP v4 contains >25 000 entries and extends the resource from a sequence-centered database to a structure-aware repository. Major additions include systematic SMILES representations, enhanced annotation of intrachain bonds and ring architectures, dedicated antibiofilm, and synergy records, PubChem links, >9200 molecular-dynamics trajectories, and new prediction services. The condition-resolved data support supervised learning, strain-, and target-specific models, model calibration, and surrogate fitness functions for genetic algorithms. SMILES representations further enable modeling of noncanonical peptides and peptidomimetics that cannot be adequately described by sequence alone. DBAASP therefore complements large peptide catalogues by providing the experimentally curated activity and structure layers, needed to convert sequence information into testable predictions, design, and optimization of biologically active compounds. DBAASP v4 is freely available at https://dbaasp.org.},
}

@article {pmid42964029,
year = {2026},
author = {Zhang, Y and Zhang, Z and Ying, S and Wang, S and Xiang, R},
title = {Co-occurrence and genetic contexts of NDM-1, KPC-2, IMP-1, and AFM-1 carbapenemase genes in a critically ill patient.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1973471},
pmid = {42964029},
issn = {2235-2988},
mesh = {Humans ; *beta-Lactamases/genetics ; *Bacterial Proteins/genetics ; Critical Illness ; Microbial Sensitivity Tests ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Whole Genome Sequencing ; Klebsiella pneumoniae/genetics/isolation & purification/drug effects ; Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; },
abstract = {BACKGROUND: Carbapenem-resistant organisms are increasingly reported in clinical settings, yet the simultaneous detection of multiple carbapenemase genes within a single specimen remains rare.

METHODS: Metagenomic next-generation sequencing (mNGS) and whole-genome sequencing (WGS) were performed on a bronchoalveolar lavage fluid (BALF) sample from a patient with severe pneumonia.

RESULTS: Four carbapenemase genes-bla AFM-1, bla NDM-1, bla IMP-1, and bla KPC-2-were simultaneously detected in a single specimen. Three carbapenem-resistant isolates were recovered: an ST11 K. pneumoniae carrying bla KPC-2 and virulence-associated genes, an S. algae strain with an assembly-based tandem chromosomal bla NDM-1 arrangement, and a P. stutzeri strain co-harboring bla AFM-1 and bla IMP-1. Genomic analysis revealed complex mobile genetic contexts associated with these resistance determinants.

CONCLUSION: The coexistence of four carbapenemase genes within one clinical sample highlights the complexity of polymicrobial carbapenem resistance and underscores the importance of genomic surveillance.},
}

Humans
*beta-Lactamases/genetics
*Bacterial Proteins/genetics
Critical Illness
Microbial Sensitivity Tests
Bronchoalveolar Lavage Fluid/microbiology
High-Throughput Nucleotide Sequencing
Whole Genome Sequencing
Klebsiella pneumoniae/genetics/isolation & purification/drug effects
Carbapenems/pharmacology
Anti-Bacterial Agents/pharmacology
Metagenomics

@article {pmid42964044,
year = {2026},
author = {Hao, W and Zhou, X and Wang, M and Yang, W and Cheng, T},
title = {Case Report: Sporadic Creutzfeldt-Jakob disease initially misdiagnosed as ischemic stroke: a diagnostic challenge and biomarker-based clarification.},
journal = {Frontiers in cellular neuroscience},
volume = {20},
number = {},
pages = {1938627},
pmid = {42964044},
issn = {1662-5102},
abstract = {BACKGROUND: Sporadic Creutzfeldt-Jakob disease (sCJD) is a rare and uniformly fatal prion disorder characterized by rapidly progressive dementia and heterogeneous neurological manifestations. Early sCJD may be misinterpreted as cerebrovascular disease, particularly when focal neurological deficits, unilateral diffusion abnormalities, and vascular risk factors coexist.

CASE PRESENTATION: We report a 76-year-old man with a history of hypertension who initially presented with dizziness and gait instability, followed by progressive right-sided weakness, and was initially diagnosed with ischemic stroke in the setting of intracranial arterial stenosis. Despite antiplatelet and vascular management, the patient experienced rapid cognitive decline, psychiatric disturbances, aphasia, and progressive hemiparesis. Follow-up MRI demonstrated progressive, non-territorial cortical ribbon-like diffusion restriction predominantly involving the left insular, parietal, frontal, and temporal cortices. CSF analysis revealed markedly elevated total tau (4553.50 pg/mL; laboratory-reported cutoff: < 399 pg/mL), phosphorylated tau (66.93 pg/mL; laboratory-reported cutoff: < 50 pg/mL), and 14-3-3γ protein (50515 AU/mL; laboratory-reported cutoff: < 20,000 AU/mL). Autoimmune encephalitis antibodies and metagenomic next-generation sequencing were negative. PRNP genetic testing detected no pathogenic variant in the patient and his son. EEG showed diffuse slowing without periodic sharp wave complexes. According to the 2017 International CJD Surveillance Network criteria, the diagnosis was classified as probable sCJD on the basis of rapidly progressive cognitive impairment, two clinical features (documented cerebellar ataxia and pyramidal signs), characteristic MRI abnormalities, and positive CSF 14-3-3; the typical EEG criterion was absent and RT-QuIC was not performed.

CONCLUSION: This case highlights the diagnostic challenge of early sCJD initially misdiagnosed as ischemic stroke in the presence of coexisting vascular pathology. Recognition of non-vascular diffusion patterns, careful reassessment of atypical clinical progression, and adjunctive CSF biomarker assessment may facilitate timely diagnostic reconsideration and help avoid unnecessary interventions.},
}

@article {pmid42964076,
year = {2026},
author = {Pandey, S and Skidmore, J and Dhillon, J},
title = {A systematic review of the effects of diet on the gut microbiota in individuals at elevated risk for colorectal cancer.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1818522},
pmid = {42964076},
issn = {2296-861X},
abstract = {BACKGROUND: Colorectal cancer (CRC) poses a major public health concern, with emerging evidence highlighting the critical role of the gut microbiota in CRC progression. Considering that diet is a major modifiable factor influencing CRC risk, partly through its interaction with the gut microbiome, this systematic review evaluated the effects of dietary intervention RCTs, including supplements, functional foods, whole foods, and dietary patterns, on the gut microbiome in elevated-risk individuals.

METHODS: A search of PubMed, Scopus, and Web of Science, and manual sourcing of systematic reviews, meta-analyses, and reference lists of relevant papers identified 5,558 records.

RESULTS: Following screening, seven studies met inclusion criteria, focusing on microbial diversity and taxonomic composition. Findings demonstrate that effects on microbial diversity metrics were minimal and were observed only with a general healthy eating dietary pattern, navy bean powder interventions, and with one rice bran intervention. No consistent patterns emerged by intervention type (functional compounds, whole foods, or dietary pattern), intervention duration, or by diversity metric. In contrast, genus-level compositional shifts were more frequently reported, although directionality varied by dietary exposure. Enrichment of Faecalibacterium, Bifidobacterium, and Lactobacillus was reported in some rice bran and navy bean interventions, whereas reductions in Akkermansia, Ruminococcus, Bacteroides, Prevotella, and Porphyromonas were observed in others. Among the four trials assessing microbial-derived metabolites, some were associated with increased short-chain fatty acids and plant-derived metabolites while others reported reductions in secondary bile acids, p-cresol sulfate, and branched-chain bacterial fatty acids.

CONCLUSION: Overall, this review highlights the potential of dietary strategies to modulate the gut microbiome in populations at risk for CRC, while also addressing critical gaps in the current evidence and offering direction for the development of evidence-based dietary interventions that incorporate microbiome assessment. Limited RCTs and heterogeneity in outcomes limit generalizability. Future research should conduct rigorous RCTs across the lifespan, using microbiome and metabolite analyses such as shotgun metagenomics, meta-transcriptomics, or metabolomics and examining understudied dietary patterns to guide CRC prevention.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024530038, identifier CRD42024530038.},
}

@article {pmid42964355,
year = {2026},
author = {Zhang, Y and Cidan, Y and Xu, J and Li, B},
title = {Correction: CRC-TrustBench: benchmarking cross-study and cross-country generalization in gut metagenomic colorectal cancer prediction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {2021752},
doi = {10.3389/fmicb.2026.2021752},
pmid = {42964355},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1971707.].},
}

@article {pmid42964722,
year = {2026},
author = {He, L and Wang, J and Bai, T and Hou, X and Ran, D and Yang, J},
title = {Does the mouth seed the small bowel? Mechanisms and hypothesis-generating framework via the oral-gut axis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2735085},
doi = {10.1080/20002297.2026.2735085},
pmid = {42964722},
issn = {2000-2297},
abstract = {BACKGROUND: As the starting segment of the digestive tract, the oral cavity harbors a complex microbial community that closely interacts with the distal gut microbiota. Recent evidence suggests that oral hygiene status and oral dysbiosis may correlate with gut microbial homeostasis and play a potential role in the initiation or exacerbation of small intestinal bacterial overgrowth (SIBO).

OBJECTIVE: This review aims to integrate existing evidence, outline a hypothesis-generating framework, identify critical knowledge gaps, and provide new perspectives for future interdisciplinary mechanistic research and clinical translation in SIBO and related gastrointestinal disorders.

DESIGN: This narrative review synthesizes and evaluates preliminary clinical correlations, metagenomic surveys, and animal models that support the oral microbiota as a potentially modifiable factor associated with SIBO, and discusses the proposed underlying molecular pathways.

RESULTS: Existing evidence supports the oral microbiota as a potentially modifiable factor associated with SIBO. However, direct high-level evidence testing oral hygiene interventions against definitive SIBO outcomes is currently lacking.

CONCLUSIONS: The oral-gut axis may play a critical role in SIBO pathogenesis. Future research requires high-quality clinical trials to validate the impact of oral hygiene interventions on SIBO outcomes, bridging the current critical knowledge gaps.},
}

@article {pmid42964741,
year = {2026},
author = {Krishnavajhala, A and Gingras, MC and Santiago-Rodriguez, TM and Chen, Y and Bandaranaike, D and Bhamidipati, S and Qin, X and Kottapalli, K and Momin, Z and Santhanam, A and Walker, K and Wang, Q and Griffin, SM and Masternak, MM and Ross, MC and Muzny, D and Wu, J and Urquieta, E and Gibbs, RA and Doddapaneni, H},
title = {Microbial dynamics across commercial spaceflights of varying duration.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117988},
doi = {10.1016/j.isci.2026.117988},
pmid = {42964741},
issn = {2589-0042},
abstract = {Spaceflight introduces environmental stressors that can alter human microbiomes and immune responses. We analyzed 259 and 17 biospecimens for microbiome and single-cell studies from n = 6 astronauts across two commercial International Space Station (ISS) missions: Axiom 2 (10-day mission) and Axiom 3 (21-day mission). Samples included saliva, stool, urine, and body swabs from 10 anatomical sites, profiled via 16S ribosomal RNA (rRNA) gene amplicon sequencing. Gut and oral microbiomes remained stable, while skin-associated communities exhibited transient diversity shifts post-flight. Taxonomic analysis revealed individual and site-specific patterns, as well as from the spaceflight/ISS environment. Cytokine profiling from single-cell data indicated immune activation, with IL-32 and IL-16 transcripts elevated in Axiom 2 and Axiom 3. Microbiome and interleukin correlation analyses found 14 significant associations in Axiom 2 data. These findings provide an integrated view of microbiome individuality. Our study represents a descriptive comparison of two missions, informing strategies for crew health on future long-duration missions.},
}

@article {pmid42965315,
year = {2026},
author = {Sauvestre, C and Garrigue, I and Arcourt, A and Thevenon, J and Burrel, S and Guichoux, J and Trimouille, A},
title = {From genetic investigation to viral diagnosis: HSV-1 detection through genome sequencing analysis in neonatal intensive care.},
journal = {Genetics in medicine : official journal of the American College of Medical Genetics},
volume = {},
number = {},
pages = {102782},
doi = {10.1016/j.gim.2026.102782},
pmid = {42965315},
issn = {1530-0366},
abstract = {PURPOSE: Neonatal sepsis and genetic disorders share overlapping clinical presentations in critically ill neonates, making differential diagnosis challenging. We report an incidental detection of herpes simplex virus 1 (HSV-1) through human genome sequencing (GS) initially performed for suspected genetic disease.

METHODS: A 7-day-old male infant presented with fever and failure to gain weight. Initial investigations revealed inflammatory response and gram-positive cocci in urine; CSF and respiratory microbiological analyses were negative. Trio-based GS was performed under the French Genomic Medicine Plan 2025. Soft-clipped reads from BAM files were analyzed using IGV visualization and NCBI BLAST homology search. Retrospective virological testing was performed on archived samples.

RESULTS: GS variant calling initially identified an apparent de novo insertion in NRROS. Manual BAM file inspection revealed that flanking soft-clipped sequences aligned with the HSV-1 UL47 gene rather than the human genome. Retrospective PCR confirmed HSV-1 in blood and nasopharyngeal samples, despite initially negative CSF testing. The patient died at 14 days of age from disseminated HSV-1 infection with multiorgan failure.

CONCLUSION: Human GS can incidentally detect pathogen sequences through systematic analysis of unmapped reads, highlighting its potential dual diagnostic utility in neonatal intensive care.},
}

@article {pmid42965683,
year = {2026},
author = {Li, S and Cheng, R and He, M and Hu, Q and Xu, H and Wu, X and Liu, X and Cai, X and Miao, Z},
title = {Exploring the relationship among nutrition, gut microbiota and musculoskeletal health in children with Duchenne muscular dystrophy: a cross-sectional study.},
journal = {European journal of nutrition},
volume = {65},
number = {8},
pages = {},
pmid = {42965683},
issn = {1436-6215},
support = {S23053//Sichuan Medical Association Foundation/ ; 2024-YF05-00493-SN//Foundation of Chengdu Municipal Science and Technology/ ; 82404268//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Male ; Child ; Female ; *Gastrointestinal Microbiome/physiology ; *Nutritional Status ; Bone Density ; *Muscular Dystrophy, Duchenne/physiopathology/microbiology/complications ; Body Composition ; China ; Energy Intake ; Child, Preschool ; Adolescent ; Diet ; },
abstract = {AIMS: This study was aimed to explore the nutritional risk standards and nutritional support strategies in Chinese children with DMD.

METHODS: This cross-sectional study included 217 children with DMD. Nutritional status was determined by measuring body composition and clinical testing indicators. Three-day 24-h diet recalls were used to assess nutrient intake. Metagenomic sequencing was performed to detect gut microbiota.

RESULTS: Children with obesity or high body fat percentage (BF%) had higher levels of caloric intake and lower levels of bone mineral density (BMD) and osteocalcin. Age increased the risk of low muscle mass (95% confidence interval [CI] 1.053‒2.152). Overweight (95% CI 0.078‒0.658), obesity (95% CI 0.003‒0.139), low BF% (95% CI 0.015‒0.524) and high levels of calories from protein (95% CI 0.001‒0.001) were protective factors for low muscle mass. The GC exposure (95% CI 1.03‒1.53) increased the risk of low BMD, whereas low body fat percentage (95% CI 0.11‒0.71) decreased the risk of low BMD. Gut microbiota was closely associated with the BMD Z-score, body fat percentage (P < 0.01), age, GC exposure, and P1NP (P < 0.05). DMD children with low BMD had a higher abundance of Bacteroides vulgatus and a lower abundance of Prevotella copri (P < 0.05).

CONCLUSION: BF% rather than obesity was the risk factor for low muscle mass in DMD. SMI may be a more accurate index for muscle mass assessment than SMM. High level of calories from protein may be benefit to SMI. Treatments targeting gut microbiota may alleviate glucocorticoid-induced low BMD in DMD.},
}

Humans
Cross-Sectional Studies
Male
Child
Female
*Gastrointestinal Microbiome/physiology
*Nutritional Status
Bone Density
*Muscular Dystrophy, Duchenne/physiopathology/microbiology/complications
Body Composition
China
Energy Intake
Child, Preschool
Adolescent
Diet

@article {pmid42965699,
year = {2026},
author = {Kurt, H and Tütüncü, HE and Vardar-Yel, N and Sarı, C and Akçok, İ and Hoş, BH and Kurt, KC and Akarsubaşı, AT and Sürmeli, Y},
title = {Identification and in silico characterization of a thermophilic GH10 xylanase from hot spring metagenomes.},
journal = {Archives of microbiology},
volume = {209},
number = {1},
pages = {},
pmid = {42965699},
issn = {1432-072X},
mesh = {*Hot Springs/microbiology ; *Metagenome ; *Endo-1,4-beta Xylanases/genetics/chemistry/metabolism ; Enzyme Stability ; Molecular Dynamics Simulation ; Hot Temperature ; Molecular Docking Simulation ; Amino Acid Sequence ; },
abstract = {This study sought to identify xylanases by mining metagenomic reads from high-temperature environments across multiple geographic regions. It also aimed to conduct an in-silico characterization of a promising thermophilic GH10 xylanase, analyzing its sequence, structural features, and dynamic properties. BLASTp results indicated that potentially thermophilic xylanases from different hot spring environments share high sequence similarity with xylanases from diverse phyla, including Cyanobacteria, Dictyoglomi, Bacteroidota, Bacillota, Pseudomonadota, and Acidobacteriota. Additionally, eighteen complete xylanase sequences with melting temperatures above 65 °C showed instability index values below 40 (ranging from 22.32 to 39.13) and aliphatic index values greater than 72 (ranging from 72.04 to 95.54). Molecular docking analysis revealed that the catalytic residues E164 and E270 of HSWMetXyn15 participated in noncovalent interactions within the HSWMetXyn15-X7 docked complex. Molecular dynamics simulations indicated stable behavior of both HSWMetXyn15 and the HSWMetXyn15-X7 complex. Structural analysis confirmed that HSWMetXyn15 belongs to the GH10 family and differs from the reference xylanase XynAS9 in several secondary structural elements. Moreover, P77 and E78 may contribute to the thermal stability of HSWMetXyn15 through their involvement in local noncovalent interactions. Therefore, the favorable structural and dynamic properties of HSWMetXyn15 compared with the reference xylanase XynAS9 highlight its potential as a promising candidate for high-temperature industrial applications, including biofuel production, animal feed processing, paper and pulp manufacturing, and food processing.},
}

*Hot Springs/microbiology
*Metagenome
*Endo-1,4-beta Xylanases/genetics/chemistry/metabolism
Enzyme Stability
Molecular Dynamics Simulation
Hot Temperature
Molecular Docking Simulation
Amino Acid Sequence

@article {pmid42965706,
year = {2026},
author = {Haferkamp, S and Schilling, B and Baumgart, L and Gesierich, A and Glutsch, V and Drexler, K and Wein, L and Morak, M and Erdmann, M and Berking, C and Piccinno, G and Derosa, L and Zitvogel, L and Wang, Y and Heinzerling, L},
title = {Microbiome-derived TOPOSCORE is associated with response to immune checkpoint inhibitor re-induction after chemotherapy in primary resistant metastatic melanoma.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {11},
pages = {},
pmid = {42965706},
issn = {1432-0851},
support = {70113416//German Cancer Aid / Stiftung Deutsche Krebshilfe/ ; },
mesh = {Humans ; *Melanoma/drug therapy/microbiology/pathology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Male ; *Drug Resistance, Neoplasm ; Female ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Prospective Studies ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; },
abstract = {BACKGROUND: Primary resistance to immune checkpoint inhibitors (ICIs) remains a major challenge in metastatic melanoma. The prospective multicenter PROMIT trial showed that intermittent chemotherapy could restore sensitivity to ICI re-induction in a subset of patients. We investigated whether gut microbiome ecosystem states characterized by TOPOSCORE were associated with tumor response in this setting.

METHODS: In the phase II PROMIT trial (NCT04225390), 24 patients with longitudinal stool samples were included in this exploratory microbiome analysis. ICI-resistant patients received two cycles of dacarbazine followed by ICI re-induction. Stool samples underwent shotgun metagenomic sequencing. Microbiome ecosystem states were classified into SIG1- or SIG2-associated ecosystem states using the TOPOSCORE framework, which is based on species-interacting groups (SIGs) defined by ecological co-abundance patterns.

RESULTS: Baseline TOPOSCORE distributions and s-scores were not associated with clinical outcome. In the nine patients with complete BL-CTX-ICI sampling, six retained the same TOPOSCORE category throughout treatment and three changed category. Of the two patients with PR, one remained SIG2 throughout, whereas the other changed from SIG2+ to SIG1+ after chemotherapy and returned to SIG2+ during ICI re-induction. Analyses using all available samples at each phase likewise did not show significant differences in s-score among PR, SD, and PD groups.

CONCLUSIONS: Baseline TOPOSCORE classification was insufficient to predict treatment outcome in this cohort. Longitudinal TOPOSCORE patterns were heterogeneous, and the small number of complete longitudinal profiles precludes conclusions that chemotherapy induced a favorable microbiome transition. These exploratory findings support further evaluation of microbiome ecosystem dynamics in larger prospective cohorts.},
}

Humans
*Melanoma/drug therapy/microbiology/pathology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Male
*Drug Resistance, Neoplasm
Female
*Gastrointestinal Microbiome/drug effects
Middle Aged
Prospective Studies
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Aged

@article {pmid42966027,
year = {2026},
author = {Kim, B and Joe, HI and Yang, AI and Lee, JY and Kim, HS and Bae, JW and Shin, NR},
title = {Senimuribacter muris sp. nov., a butyrate-producing bacterium isolated from mouse feces, and reclassification of members of the family Eubacteriaceae into the family Anaerovoracaceae.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126782},
doi = {10.1016/j.syapm.2026.126782},
pmid = {42966027},
issn = {1618-0984},
abstract = {Two strictly anaerobic, Gram-stain-positive, non-motile, and rod-shaped bacterial strains, designated rT4E-8[T] and mB4P-1, were isolated from the feces of specific-pathogen-free Mus musculus (C57BL/6J). Both strains were catalase- and oxidase-negative and produced butyrate as a major fermentation product, with optimal growth at 37 °C and pH 7. The two strains shared 100% pairwise 16S rRNA gene sequence similarity and showed high similarity to Senimuribacter intestinalis DSM 106208[T] (95.1-95.3%). Genome sizes of strains rT4E-8[T] and mB4P-1 were 2.9 Mbp and 2.8 Mbp, with genomic DNA G+C contents of 44.9% and 45.1%, respectively. Orthologous average nucleotide identity and digital DNA-DNA hybridization values between strain rT4E-8[T] and S. intestinalis were 75.9% and 25.4%, respectively, supporting their classification as a novel species. Based on the phenotypic, chemotaxonomic, and genomic evidence, strains rT4E-8[T] and mB4P-1 represent a novel species, for which the name Senimuribacter muris sp. nov. is proposed. The type strain is rT4E-8[T] (=KCTC 25664[T] =JCM 36407[T]). Phylogenomic analyses supported the reassignment of Senimuribacter and several related taxa from the family Eubacteriaceae to the family Anaerovoracaceae. In addition, Eubacterium sulci and Eubacterium infirmum are reclassified into Pareubacterium gen. nov., with Pareubacterium sulci comb. nov. and Pareubacterium infirmum comb. nov. Amplicon sequence variant analysis of mouse fecal microbiome datasets revealed that sequences corresponding to strain rT4E-8[T] exhibited a significant positive correlation with host age and were detected exclusively in C57BL/6J mice from a specific vendor. Large-scale metagenomic screening further supported the association of the novel strains with mouse gut environments.},
}

@article {pmid42966099,
year = {2026},
author = {Liu, Q and Yang, R and Yang, C and Xiang, Y and Chen, Z and Cui, J and Mao, Y and Zhang, H and Chen, M},
title = {Spatial distribution and microbial degradation potential of microplastics and nanoplastics along a 134-year proglacial chronosequence.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144076},
doi = {10.1016/j.jhazmat.2026.144076},
pmid = {42966099},
issn = {1873-3336},
abstract = {Glacier retreat increasingly exposes proglacial soils to micro- and nanoplastic (MNP) pollution, yet long-term MNP dynamics and associated microbial plastic-degradation potential remain unclear. Along a 134-year chronosequence at Hailuogou Glacier, we combined µ-FTIR, Py-GC/MS, and metagenomics to characterize MNP pollution, ecological risk, and microbial degradation potential. MP abundance followed a non-linear trajectory, peaking at 270 items kg[-1] at 66 yr, whereas NP abundance increased from 1.54 to 4.17 mg kg[-1] . MPs were dominated by PA, PE, PET, and Rayon, while NPs shifted from PMMA to PE dominance (>78%) in mature soils. Ecological risk was non-monotonic and polymer-dependent: MP-associated PERI reached Level IV at 66 yr, whereas NP-associated PERI peaked at 94 yr despite increasing NP mass. This decoupling suggested that risk was strongly influenced by polymer-composition turnover rather than abundance or mass alone. Gene-based microbial plastic-degradation potential increased during succession through enrichment of plastic-degradation-related genes. PLS-PM identified a sequence of positive associations linking glacier retreat age, soil development, MNP pollution, and microbial plastic-degradation potential. Random Forest analysis further highlighted retreat age and Ca among the leading predictors of degradation-gene abundance. These findings provide insights into MNP risk and gene-based microbial plastic-degradation potential in rapidly deglaciating high-altitude ecosystems.},
}

@article {pmid42954932,
year = {2026},
author = {Plisko, OL and Chapel, VS and Sekela, JJ and Talbert, JA and Townsend, SD and Zemel, BS and Wu, GD and R Redinbo, M},
title = {Human milk oligosaccharides are distinctly processed by early life gut microbial sialidases.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748788},
doi = {10.1080/19490976.2026.2748788},
pmid = {42954932},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Oligosaccharides/metabolism/chemistry ; *Neuraminidase/metabolism/genetics/chemistry ; Infant ; Adult ; Lactose/analogs & derivatives/metabolism ; *Bacteria/enzymology/genetics/classification ; Metagenome ; },
abstract = {The infant gut microbiome in early life is shaped by numerous factors, including feeding method. Exclusively breastfed and formula-fed infants exhibit distinct microbiome compositions. While these effects are well-established, the underlying mechanisms that drive these differences are not fully understood. Here, we examine the removal of sialic acid from human milk oligosaccharides (HMOs) influenced by human microbial sialidases in early life. We identify 351 and 214 unique sialidase sequences from adult and infant microbiome metagenomes, respectively, and characterize a diverse, representative set in vitro using sialylated HMOs normally present in human breastmilk. We find these proteins exhibit distinct abilities to metabolize 3'- and 6'-sialyllactose, which are the most abundant sialylated HMOs in breastmilk, and distinctly process other more complex substrates, as well. We provide structural insights into these functional differences by pinpointing active site features uniquely present in efficient enzymes and show that these results extend to activities on complex mixtures of sialylated HMOs purified from human breastmilk. Finally, we demonstrate in human clinical data that distinct profiles of sialidase-encoding bacterial taxa are observed in breastfed and formula-fed infants at 1 and 4 months of age, prior to the introduction of solid foods. Together, these findings show that specific bacterial sialidases are influential in shaping the early gut microbiome, data that may improve the supplementation of infant formulas for enhanced developmental outcomes.},
}

Humans
*Milk, Human/chemistry/metabolism
*Oligosaccharides/metabolism/chemistry
*Neuraminidase/metabolism/genetics/chemistry
Infant
Adult
Lactose/analogs & derivatives/metabolism
*Bacteria/enzymology/genetics/classification
Metagenome

@article {pmid42955188,
year = {2026},
author = {Saqr, A and Mohamed, ME and Staley, C and Onyeaghala, G and Vo, D and Remmel, RP and Teigen, L and Guan, W and Oetting, WS and El-Rifai, R and Dorr, CR and Gupta, K and Matas, AJ and Israni, AK and Jacobson, PA},
title = {Microbiome-Mediated Pharmacokinetics and Informed Dosing of Mycophenolate in Kidney Transplantation.},
journal = {Clinical pharmacokinetics},
volume = {},
number = {},
pages = {},
pmid = {42955188},
issn = {1179-1926},
support = {5R01AI140303//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND AND OBJECTIVES: The gut microbiome contributes to interindividual variability in drug pharmacokinetics; however, its role in guiding dose adjustments remains unclear. Mycophenolic acid (MPA), the active metabolite of the immunosuppressant mycophenolate mofetil (MMF), exhibits high pharmacokinetic variability, potentially linked to microbial activity. This study aimed to characterize the gut microbiome effect on MPA pharmacokinetics and determine if these effects necessitate dose modifications.

METHODS: In 84 kidney transplant recipients, plasma and urine concentration-time profiles for MPA and its glucuronide metabolites were characterized using population pharmacokinetic modeling in NONMEM[®]. Stool samples were collected within 2 days of pharmacokinetic sampling for microbiome shotgun metagenomic sequencing. Machine learning was used to identify microbial species associated with pharmacokinetic variability. The impact of these species and clinical covariates was evaluated using full fixed-effect modeling. Simulations were conducted to assess the effect of microbial relative abundance on MPA therapeutic target attainment across various MMF doses.

RESULTS: Five bacteria were associated with the magnitude or duration of enterohepatic circulation (EHC). High relative abundance of Eubacterium callanderi increased EHC and MPA exposure by 29-63%, requiring a 17% lower MMF dose. Conversely, high Faecalibacterium SGB15315 abundance reduced EHC and MPA exposure by 13-26%, requiring a 50-75% higher dose. While Gemmiger formicilis and Eisenbergiella tayi prolonged EHC by >100% and Anaerostipes caccae decreased it by 30%, these taxa did not clinically impact therapeutic target attainment.

CONCLUSION: We identified several stool microbial species affecting MPA pharmacokinetics. Specifically, Eubacterium callanderi and Faecalibacterium SGB15315 may identify patients who require additional therapeutic drug monitoring or possible dose modifications to reach target concentrations.

CLINICAL TRIAL REGISTRATION: Clinicaltrials.gov, NCT04953715.},
}

@article {pmid42955203,
year = {2026},
author = {Sagawa, T and Hirakawa, M and Nagashima, H and Fujikawa, K},
title = {Gut Microbiome Signatures and Immune Checkpoint Inhibitor Response in Gastrointestinal Cancers: Reproducibility and Translational Readiness.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42955203},
issn = {1534-6269},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Neoplasms/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; Reproducibility of Results ; Translational Research, Biomedical ; },
abstract = {PURPOSE OF REVIEW: Gut microbial features have been associated with immune checkpoint inhibitor (ICI) outcomes, but whether these signatures are robust across gastrointestinal (GI) tumor types, treatment regimens, and populations remains uncertain. This critical narrative review assesses human evidence, experimental mechanisms, longitudinal sampling, and the criteria needed for clinical implementation.

RECENT FINDINGS: A gastric cancer cohort showed different response-associated microbial features for immunotherapy alone, chemotherapy alone, and combined treatment. Cross-cancer strain-resolved analyses found that signature transportability was strongly conditional on matching ICI regimens. A large primary liver cancer cohort analyzed 315 patients and 777 serial samples and explored a baseline score derived from on-treatment species selection; later samples were available only in a selected subgroup, complicating interpretation. Experimental studies link selected microbes and metabolites with antitumor immunity, but these mechanistic findings do not establish therapeutic efficacy in humans. Fecal microbiota transplantation (FMT) studies in melanoma demonstrate feasibility yet do not establish benefit in GI malignancies. Stool profiles may not represent mucosal or tumor-adjacent communities in upper GI cancer. No stool microbiome signature is currently validated to select ICI therapy in GI oncology. Meaningful translation requires standardized assays, non-ICI comparators to establish treatment-effect prediction, strict separation of discovery and external validation, prospectively handled missingness, and randomized clinical-utility studies.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Neoplasms/drug therapy/microbiology/immunology
*Gastrointestinal Microbiome/drug effects/immunology
Reproducibility of Results
Translational Research, Biomedical

@article {pmid42956103,
year = {2026},
author = {Mariotto, P and Baldan, M and Di Camillo, B and Baruzzo, G},
title = {From 16S rDNA-seq count data to microbial interactions: A comprehensive benchmark of co-occurrence network inference methods.},
journal = {PLoS computational biology},
volume = {22},
number = {10},
pages = {e1014898},
doi = {10.1371/journal.pcbi.1014898},
pmid = {42956103},
issn = {1553-7358},
abstract = {The study of the ecological interactions within microbial communities is crucial for gaining deeper insights into community ensemble and evolution, enabling targeted modification of the community's functionality. Many inference approaches have been developed to derive ecological associations. Here, we focus on co-occurrence computational methods, in which associations are inferred from metagenomic abundance data by measuring the statistical dependence between species counts across different sampled populations. The limitations in culture-based experiments have hindered the ability to assess these methods' validity, leading to scarce application in metagenomics studies. To provide a comprehensive assessment of network inference method performance, we benchmark 18 different computational approaches across a broad spectrum of experimental scenarios. We use synthetic 16S rDNA-seq count data generated from known underlying interaction networks, enabling systematic and controlled evaluation. The benchmark spans scenarios varying in numbers of species and samples, sample richness, sequencing depth, and interaction network structure. We evaluated the performance of the methods both in terms of accuracy of the inferred network, using various metrics from binary classification theory and metrics coming from network science, and in terms of computational burden. We found that methods have valid results only in a restricted, and often unrealistic, field of application, whereas their effectiveness diminishes with more realistic simulation parameters. Our findings highlight the limits of the co-occurrence-based approach and the need for further development in microbial ecological association inference.},
}

@article {pmid42956390,
year = {2026},
author = {Abbatemarco, JR and Begum, F and Villalba, JA and Davis, E and Bhatnagar, J and Brault, AC and Calvert, AE and Chomyk, A and Gould, CV and Isada, CM and Jung, JU and Jones, SE and Kang, S and Ko, Y and Li, Y and Nakamura, K and Najm, L and Staples, EJ and Trapp, BD and Tipping, P and Yeaney, GA and Fox, RJ},
title = {Establishing Potosi Virus as a Human Pathogen: Fatal Neuroinvasive Disease in a B-Cell-Depleted Patient.},
journal = {Neurology},
volume = {107},
number = {10},
pages = {e218683},
doi = {10.1212/WNL.0000000000218683},
pmid = {42956390},
issn = {1526-632X},
mesh = {Humans ; Female ; Fatal Outcome ; Adult ; *B-Lymphocytes/pathology ; *Meningoencephalitis/virology ; Multiple Sclerosis/drug therapy/complications ; Brain/pathology/virology ; },
abstract = {OBJECTIVES: To establish Potosi virus, a mosquito-borne member of the family Peribunyaviridae, as a neuroinvasive human pathogen.

METHODS: Case report.

RESULTS: A 37-year-old woman with multiple sclerosis on long-term rituximab developed rapidly progressive dementia. Serial MRI demonstrated progressive generalized atrophy. CSF showed transient, minimal lymphocytic pleocytosis. Extensive infectious, autoimmune, and prion evaluations were unrevealing, but CSF metagenomic sequencing detected all 3 genome segments for Potosi virus. Postmortem examination revealed diffuse meningoencephalitis with T-cell-predominant leptomeningeal and perivascular inflammation. Molecular analyses confirmed multiple nucleotide sequences with >99+% concordance with a known Potosi strain, with widespread viral infection confirmed by immunohistochemistry demonstrating intracellular and extracellular viral antigen. Electron microscopy demonstrated particles of a size consistent with the Peribunyaviridae family. Metagenomic sequencing of RNA extracted from frozen brain tissue identified all 3 Potosi virus gene segments without other infectious entities. Findings were concordant across multiple laboratories and institutions.

DISCUSSION: Potosi virus can cause fatal neuroinvasive disease in humans, as evidenced by convergent postmortem neuropathologic, molecular, and ultrastructural evidence. Chronic B-cell depletion may increase susceptibility to severe disease with arboviral infections, which may present without conventional CNS inflammatory markers. CSF metagenomic sequencing should be considered in immunocompromised patients with unexplained progressive neurologic decline.},
}

Humans
Female
Fatal Outcome
Adult
*B-Lymphocytes/pathology
*Meningoencephalitis/virology
Multiple Sclerosis/drug therapy/complications
Brain/pathology/virology

@article {pmid42956707,
year = {2026},
author = {Xie, T and Lin, D and Du, S and Wu, D and Zhu, D},
title = {Cascading effects of nano-biochar mitigate antibiotic resistance via phage-host interactions in the soil-crop ecosystem.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144071},
doi = {10.1016/j.jhazmat.2026.144071},
pmid = {42956707},
issn = {1873-3336},
abstract = {Controlling the spread of antibiotic resistance genes (ARGs) in agroecosystems is central to One Health, yet whether nano-biochar-amended organic fertilizers can mitigate phage-mediated ARG dissemination along the fertilizer-soil-crop continuum remains poorly understood. Here, we analyzed 120 viral metagenomes to examine how biochar-amended organic fertilizers modulate ARG dynamics, phage-associated functions, and phage-host interactions across the fertilizer-soil-lettuce continuum. The lettuce phyllosphere served as a key endpoint for ARG accumulation, exhibiting 4.1-4.9 times the total ARG abundance and 56.8-66.3% higher phage-encoded ARG abundance compared with rhizosphere and non-rhizosphere soils. Source-tracking analysis indicated that manure and soil inputs accounted for 50.8-57.0% of phyllosphere ARGs, while 111 manure-associated viral populations were shared with the phyllosphere at the viral cluster level. Notably, nano-biochar-amended vermicompost exerted a cascading mitigation effect, reducing manure- and soil-derived ARG inputs to the phyllosphere by 20.4-21.6% and manure-associated viral sharing by 51.6%. Meanwhile, nano-biochar-amended vermicompost reduced lysogenic phage-host interactions, phage-encoded ARGs, and auxiliary metabolic genes associated with antibiotic-resistant bacteria, which may contribute to reduced phage-associated ARG dissemination potential. Consequently, total ARG abundance in the phyllosphere decreased by 68.9-76.3%, while lettuce biomass increased by 54.1-61.5%. This work suggests that nano-biochar-amended vermicompost may mitigate antibiotic resistance risks and enhance crop productivity partly by attenuating phage-associated ARG dissemination across the fertilizer-soil-crop continuum, highlighting its potential for One Health-oriented resistance-risk control in agricultural production.},
}

@article {pmid42956850,
year = {2026},
author = {Wang, H and Xu, J and Cao, Y and Liu, J and Liu, K and Gong, Y and Xu, X and Zhi, S and Zhang, K and Wijffels, RH},
title = {Strain-dependent carbon partitioning and community-level functional responses during microalgae-based dairy wastewater treatment under CO2 enrichment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136162},
doi = {10.1016/j.biortech.2026.136162},
pmid = {42956850},
issn = {1873-2976},
abstract = {BACKGROUND: Microalgae-bacteria consortia offer a route for coupling dairy-wastewater treatment with carbon conversion, yet strain-dependent differences in carbon partitioning and microbial functional responses remain insufficiently resolved.

METHODS: Chlorella vulgaris, Tetradesmus obliquus, and Synechocystis sp. were cultivated in dairy wastewater under air or a one-time 4% CO2 gas charge followed by closed-loop recirculation. Biomass production, nutrient removal, liquid-solid-gas carbon inventories, biochemical composition, bacterial succession, metagenomic profiles, and entropy-weighted TOPSIS were integrated.

RESULTS: Synechocystis sp. treatment S1 showed the greatest liquid-phase total-carbon drawdown (72.1%), as carbon transferred to the suspended-solid pool, the proportion of liquid inorganic carbon within the instantaneous carbon inventory declined from 54.18% to 8.85%. T. obliquus treatment T1 achieved the highest biomass concentration (0.99 ± 0.01 g·L[-1]), NH4[+]-N removal (84.89%), and comparatively high carbohydrate and lipid accumulation, yielding the highest integrated TOPSIS score. Metagenomic analyses revealed treatment-associated shifts in CBB/TCA-related functions in C. vulgaris communities and late enrichment of glycogen-associated genes in Synechocystis sp. communities. RDA further linked central-carbon gene profiles with TC, TN, TP, EPS, and biochemical pools, while bacterial succession showed marked strain- and gas-condition dependence.

CONCLUSIONS: This divergence shows that maximizing biomass recovery and maximizing liquid-carbon drawdown represent different operational objectives rather than a single strain-independent response. The results identify distinct operational advantages among the tested phototrophs: T. obliquus favored biomass and resource recovery, whereas Synechocystis sp. promoted stronger short-term inorganic-carbon conversion. Together, carbon partitioning and community functional patterns indicate that tested-strains identity, carbon availability, nutrient demand, extracellular-carbon exchange, and phycosphere succession jointly shape system performance.},
}

@article {pmid42956856,
year = {2026},
author = {Fan, Y and Guo, D and He, Y and Zhai, X and Zhao, Z and Fan, G},
title = {Hydrogen nanobubbles overcome metabolic bottlenecks and remodel transcriptional networks for high-rate methanogenesis in the anaerobic digestion of Paulownia leaf litter.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136136},
doi = {10.1016/j.biortech.2026.136136},
pmid = {42956856},
issn = {1873-2976},
abstract = {Volatile fatty acid (VFA) accumulation limits anaerobic digestion (AD) of lignocellulosic biomass by causing acidification and microbial metabolic imbalance. Paulownia leaf litter (PLL), an underutilized lignocellulosic residue with potential for renewable energy recovery, was selected as the substrate. This study evaluated hydrogen nanobubble water (H2-NBW) as a strategy to alleviate VFA inhibition and investigated associated microbial responses using integrated multi-omics analyses. H2-NBW increased cumulative methane yields by 26.4-34.5% compared with controls, accelerated VFA turnover, improved acid-base stability and buffering capacity, and enhanced extracellular hydrolytic enzyme activities by 12.7-42.4%. Coenzyme F420 fluorescence intensity increased by 11.5-30.7%, indicating enhanced methanogenic activity. Amplicon sequencing suggested that H2-NBW enriched microorganisms associated with carbohydrate degradation and fermentation, while overall community restructuring remained limited. Metagenomic analysis revealed increased functional potential for lignocellulose degradation, reflected in carbohydrate-active enzyme and H2 metabolism genes. Meta-transcriptomic analysis further showed increased transcription of genes associated with hydrolysis, acetate-forming metabolism, the Frh/Mvh-Hdr hydrogenase system, and hydrogenotrophic methanogenesis. These responses suggest that H2-NBW may support carbon conversion and hydrogenotrophic methanogenesis, accompanied by enhanced transcription of genes involved in substrate degradation, H2 metabolism, and methane formation. The observed improvements may be associated with exogenous H2 availability, microbial metabolic responses, and potential nanobubble-associated physicochemical effects. Overall, this study links improved AD performance with coordinated microbial functional and transcriptional responses, highlighting the potential of H2-NBW to improve lignocellulosic biomass conversion and methane recovery.},
}

@article {pmid42956874,
year = {2026},
author = {Wang, S and Yang, Q and Chen, X and Liu, H and Wu, R and Yang, R and Li, W},
title = {Structural characterization of longan polysaccharide and its modulation of gut microbiota and metabolic profiles.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {155105},
doi = {10.1016/j.ijbiomac.2026.155105},
pmid = {42956874},
issn = {1879-0003},
abstract = {The present work characterized the structure of longan polysaccharide (LP) and investigated its fermentation behavior and modulatory effects on pooled human gut microbiota. LP was composed predominantly of glucose with minor arabinose and galactose in molar ratios of 97.49%: 1.65%: 0.87%, with an average molecular weight of 7.34 × 10[7] g/mol (PDI 1.09). The LP main chain consists of →6)-α-D-Glcp-(1→ linkages with sparse branches at O-3/O-4 of Glcp and O-2 of Galp. LP selectively enriched saccharolytic species including Bacteroides thetaiotaomicron, B. ovatus, Prevotella copri, and Parabacteroides distasonis that harbor GH97 and other co-enriched CAZyme families. These changes suggest a potential role in LP degradation and potential ABC/PTS-dependent uptake. Functionally, this selective microbiota modulation may drive enhanced short-chain fatty acid production and nitrogen metabolism, generating metabolites including GABA, taurine, and tryptophan/indole derivatives. Collectively, LP functions as a slow-fermentable, microbiota-targeted α-glucan that reshapes gut microbial metabolism toward SCFA and immune-relevant metabolite signature.},
}

@article {pmid42957028,
year = {2026},
author = {Wang, Y and Qing, Y and Luo, S and Tao, M and Yang, Y and Chen, Z and Zhang, X},
title = {Intracity-scale study reveals spatiotemporal variation of urban airborne microbiota and dynamics of antibiotic resistance/virulence genes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126045},
doi = {10.1016/j.envres.2026.126045},
pmid = {42957028},
issn = {1096-0953},
abstract = {Airborne microbiota are critical to urban air quality and public health, yet their spatiotemporal differentiation, community assembly, and profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) across urban functional zones remain poorly characterized. In this study, monthly 16S rRNA amplicon sequencing was combined with seasonal metagenomic profiling of 12 composite samples and environmental data to investigate airborne microbiota at three sites representing commercial, industrial, and recreational zones in Changsha, China. Airborne communities showed similar spatial patterns among the investigated functional zones but strong seasonal variation, with Shannon diversity below 2.0 in July and above 6.0 in January. Proteobacteria dominated most samples, while key seasonal taxa shifted among Delftia, Cupriavidus, and Achromobacter. Neutral community modeling supported stochastic dominance (R[2] = 0.664, Nm = 1,200), with 92.6% of operational taxonomic units within the 95% confidence interval. However, βNTI and RCbray analyses indicated increased deterministic selection in autumn-winter, coinciding with high pressure and pollutant accumulation. Metagenomics identified 25 ARG, 14 VFG, and 6 mobile genetic element (MGE) categories, with season explaining 53.9% of VFG compositional differences. Exploratory structural equation modeling identified associations between MGE abundance and ARG/VFG abundances (β = 0.75 and 1.09, respectively; both P < 0.001). Binning and contig co-localization showed that ARG-VFG-MGE co-harboring fragments were potentially affiliated with opportunistic pathogens such as Pseudomonas aeruginosa and Klebsiella pneumoniae, indicating potential biosafety concerns. These findings identify season as a key driver of urban airborne microbiota and genetic risk factors, providing a basis for atmospheric biosafety monitoring and assessment.},
}

@article {pmid42957112,
year = {2026},
author = {Jin, M and Hu, Y and Ding, M and Cheng, J and Liu, M and Liu, X and Bai, X and Fan, X},
title = {A pectic polysaccharide from Lonicera japonica alleviates DNCB-induced atopic dermatitis-like inflammation associated with gut microbial and metabolic alterations and reduced cutaneous JAK2/STAT3 activation and Th17 responses.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {122553},
doi = {10.1016/j.jep.2026.122553},
pmid = {42957112},
issn = {1872-7573},
abstract = {Lonicera japonica Thunb. (Jin Yin Hua) is a traditional medicinal herb widely used in East Asia for inflammatory disorders and is commonly included in herbal prescriptions for atopic dermatitis (AD). WLJP-025p, a homogeneous pectic polysaccharide isolated from Lonicera japonica, has shown anti-inflammatory and anti-AD potential, but its underlying mechanisms remain unclear.

AIM OF THE STUDY: This study aimed to evaluate the therapeutic effect of WLJP-025p on DNCB-induced AD-like dermatitis in mice and to investigate associated changes in epidermal barrier dysfunction, Th17/IL-17A-associated inflammation, JAK2/STAT3 signaling, and gut microbial and metabolic profiles.

MATERIALS AND METHODS: An AD-like mouse model was established in BALB/c mice by repeated application of 2,4-dinitrochlorobenzene (DNCB). WLJP-025p was orally administered at 30 or 60 mg/kg during the challenge phase, and topical dexamethasone was used as a reference anti-inflammatory control. Disease severity was assessed by skin appearance, dermatitis score, ear thickness, serum biomarkers, and histopathological examination. Skin barrier and inflammation-related proteins were evaluated by immunohistochemistry, immunofluorescence, Western blotting, and flow cytometry. Colonic injury was examined by hematoxylin and eosin (H&E) and Alcian blue-periodic acid-Schiff (AB-PAS) staining. Fecal metagenomic and metabolomic analyses were conducted to characterize gut microbial and metabolic changes.

RESULTS: WLJP-025p significantly alleviated DNCB-induced AD-like lesions, as evidenced by reduced erythema, scaling, excoriation, ear swelling, dermatitis scores, epidermal hyperplasia, and mast cell infiltration. WLJP-025p decreased serum IgE, IL-1β, IL-6, and IL-17A levels. It restored filaggrin (FLG) expression and suppressed thymic stromal lymphopoietin (TSLP) expression in skin lesions, indicating improved epidermal barrier function. WLJP-025p also reduced the proportions of splenic CD3[+]CD4[+]IL-17A[+] T cells and suppressed cutaneous IL-17A-related inflammatory mediators, including CCR6 and CCL20. These changes were accompanied by decreased phosphorylation of JAK2 and STAT3 in lesional skin. In addition, WLJP-025p alleviated DNCB-associated colonic injury and was accompanied by changes in gut microbial and metabolic profiles.

CONCLUSION: WLJP-025p exerted protective effects against DNCB-induced AD-like dermatitis. Treatment was accompanied by restoration of epidermal barrier-related markers, reduced JAK2/STAT3 activation and Th17/IL-17A-associated inflammatory signaling, improved gut barrier integrity, and alterations in gut microbial and fecal metabolite profiles. These findings indicate that oral WLJP-025p treatment is associated with concurrent intestinal and cutaneous changes in this AD-like model.},
}

@article {pmid42957639,
year = {2026},
author = {Lista, S and Emanuele, E and Cuperlovic-Culf, M and Mahdi, A and Singh, V and López-Ortiz, S and Khoramipour, K and Merino-País, M and Minoretti, P and Cisale, GY and Heslegrave, A and Imbimbo, C and Sancesario, GM and Bendlin, BB and Imbimbo, BP and Zetterberg, H and Santos-Lozano, A},
title = {Artificial intelligence applications in microbiota-gut-brain axis research: Implications for Alzheimer's disease.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261500124},
doi = {10.1177/13872877261500124},
pmid = {42957639},
issn = {1875-8908},
abstract = {Alterations in the gut microbiota (GM) are increasingly implicated in Alzheimer's disease (AD) pathogenesis through the microbiota-gut-brain axis (MGBA), influencing neuroinflammation, amyloid-β deposition, and tau aggregation. The inherent complexity of microbiota data necessitates artificial intelligence (AI) and machine learning (ML) to identify novel biomarkers and therapeutic targets. In this narrative review, we examined AI applications in AD-related GM research, including metataxonomic and metagenomic approaches. AI methods facilitate microbial signature identification and enterotype characterization associated with AD progression, enable multi-omics integration clarifying molecular pathways linking GM dysbiosis to neurodegeneration, support predictive modeling for early AD detection, and inform personalized MGBA-targeted interventions. Employed techniques include classical ML (e.g., random forests) for taxonomic classification, deep learning (e.g., neural networks) for complex pattern recognition, and explainable AI for identifying key bacterial taxa and metabolic functions. Significant challenges persist regarding methodological standardization, larger longitudinal cohorts, and ethical considerations in clinical applications. Future priorities include developing interpretable models, integrating longitudinal multi-omics data to establish causality, and validating AI-derived insights for precision AD prevention and treatment. AI uniquely enables high-dimensional, non-linear analyses that advance understanding of microbiome-brain interactions, though clinical translation requires rigorous validation and interdisciplinary collaboration.},
}

@article {pmid42957705,
year = {2026},
author = {Anani, H and Destras, G and Semanas, Q and Martin, FP and Petrier, M and Oddoux, E and Burfin, G and Bulteau, S and Poulain, C and Sinha, D and Motos, A and Gourain, V and Cremet, L and Montassier, E and Bressollette-Bodin, C and Roquilly, A and Josset, L},
title = {Identification of functional bacterial-viral pneumotypes associated with airway inflammation and all-cause mortality in critically ill patients.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957705},
issn = {2041-1723},
mesh = {Humans ; *Critical Illness/mortality ; Female ; Male ; Klebsiella pneumoniae/genetics/virology ; *Lung/microbiology/virology ; Middle Aged ; Bacteriophages/genetics/isolation & purification/pathogenicity ; Aged ; Microbiota/genetics ; Cross Infection/microbiology/mortality/virology ; Metagenomics ; Dysbiosis/microbiology ; Streptococcus/genetics ; },
abstract = {Alterations in lung virome and bacteriome compositions have been associated with hospital-acquired pneumonia in critically ill patients, but data on lung microbiome functions underlying progression to severe complications remain unclear. Here, we analyse 184 endotracheal aspirates (ETAs) collected in 94 intubated critically ill patients enrolled in a clinical trial (NCT04793568). Combining viral-metagenomics with metatranscriptomics analyses, we identify a high-risk functional pneumotype observed before the onset of hospital-acquired pneumonia and associated with lung inflammation and mortality. This unfavourable pneumotype is characterised by enrichment in virulent Streptococcus-bacteriophages and temperate Klebsiella-bacteriophages, decreased transcriptional activity of commensal taxa such as Streptococcus and Alloprevotella, and increased transcriptional activity of Klebsiella pneumoniae. Machine-learning models define two-viral- and four-bacterial-factor signatures predicting unfavourable pneumotype (AUC 0.8 and 0.7, respectively). Validation in an independent cohort (NCT02003196) of 117 ICU patients (239 ETAs) demonstrates the robustness of the association of these signatures with the risk of mortality. Causal inference identifies virulent bacteriophages associated with Streptococcus and host genes including IL18R1, ADM and PTX3, as key regulators of severe lung dysbiosis linked to mortality in critically ill patients.},
}

Humans
*Critical Illness/mortality
Female
Male
Klebsiella pneumoniae/genetics/virology
*Lung/microbiology/virology
Middle Aged
Bacteriophages/genetics/isolation & purification/pathogenicity
Aged
Microbiota/genetics
Cross Infection/microbiology/mortality/virology
Metagenomics
Dysbiosis/microbiology
Streptococcus/genetics

@article {pmid42957707,
year = {2026},
author = {Pulliam, C and Xu, M and Holandez-Lopez, K and Xue, D and Shang, Z and Gupta, G and Dioli, OE and Xiao, H and Gou, L and Wu, C and Brodbelt, JS and Wu, E and Peng, X and Chen, H and Li, J},
title = {Genome mining of the tumor microbiome reveals biosynthetic diversity and potential pathology-modulating metabolites.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957707},
issn = {2041-1723},
support = {1R35GM150565//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM139658//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F-1155//Welch Foundation/ ; },
mesh = {Humans ; *Neoplasms/microbiology/metabolism/pathology ; *Microbiota/genetics ; Multigene Family ; Fusobacterium/genetics/metabolism ; Metagenome ; Biosynthetic Pathways/genetics ; Genome, Bacterial ; },
abstract = {Human tumor-associated microbes - the tumor microbiome - have demonstrated an increasingly important role in human health due to their relevance to cancer progression and treatment response. While the metabolism at the host-microbiota interface, such as in the human gut, has been extensively investigated in recent years, the specialized metabolites from the tumor microbiome remain uncharted territory. To address this knowledge gap, we report a survey of the biosynthetic potential of the human tumor microbiome. Utilizing high-quality microbial metagenome-assembled genomes from 3,526 human tumor tissue samples, we identify 528 biosynthetic gene clusters with the potential to encode specialized metabolites relevant to tumor pathology. We reveal that the tumor microbiome encodes known and unknown metabolites spanning multiple biosynthetic classes. From this diverse biosynthetic landscape, we express a conserved family of biosynthetic genes from the genus Fusobacterium, which has a well-established role in cancer, and discover distinct families of long-chain fatty acyl amides. We subsequently find that one of these fatty acyl amides, oleoyl γ-aminobutyric acid, has immunomodulatory and G-protein-coupled receptor partial agonist activities, potentially supporting the influence of Fusobacterium in tumor pathology. The findings of our investigation lay a foundation for further research into the roles of tumor microbe-derived metabolites in cancer.},
}

Humans
*Neoplasms/microbiology/metabolism/pathology
*Microbiota/genetics
Multigene Family
Fusobacterium/genetics/metabolism
Metagenome
Biosynthetic Pathways/genetics
Genome, Bacterial

@article {pmid42957714,
year = {2026},
author = {Gray, DA and Nhung, NT and Coertze, RD and Ekwanzala, MD and Waters, N and Järhult, JD and Wenzel, M and Åhrén, C and Fick, J and Flach, CF and Larsson, DGJ},
title = {Widespread selection of antibiotic resistance within hospital sewers.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957714},
issn = {2041-1723},
support = {2018-05771//Vetenskapsrådet (Swedish Research Council)/ ; 2021-00949//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; NA//Adlerbertska Stiftelserna (Adlerbertska Foundations)/ ; },
mesh = {*Escherichia coli/drug effects/genetics/isolation & purification ; *Anti-Bacterial Agents/pharmacology/analysis ; Sweden ; Ciprofloxacin/pharmacology ; Hospitals ; *Sewage/microbiology ; Biofilms/drug effects ; Humans ; Wastewater/microbiology ; Microbial Sensitivity Tests ; Cefotaxime/pharmacology ; *Drug Resistance, Bacterial/genetics ; Fluoroquinolones/pharmacology ; *Selection, Genetic ; beta-Lactams/pharmacology ; },
abstract = {Environmental microbiomes are sources of diverse antibiotic resistance determinants that can be mobilized and transferred to human pathogens under a selection pressure from antibiotics. Hospital sewers contain more antibiotics than most environments and are thus increasingly recognised as potential arenas for resistance evolution. However, it is unknown if resistance selection occurs there and what the drivers are. Here we show selection of antibiotic-resistant bacteria within Swedish hospital sewers. Evidence include; consistent selection of multiple resistances in Escherichia coli exposed to filtered wastewater from ten hospitals, but not to corresponding municipal wastewaters; in-situ enrichment of resistant over sensitive E. coli from wastewater to sewer biofilms at hospitals, but not at municipal sites; and higher resistance in bacteria collected from hospital sewers than from municipal sites as assessed by culturing and metagenomics. Evidence for drivers includes complete rescue of sensitive E. coli by addition of resistance genes to fluoroquinolones and β-lactams, and cellular effects typical for β-lactams. Measured concentrations by liquid-chromatography-tandem-mass-spectrometry compared to selective thresholds identify ciprofloxacin and cefotaxime as principal selective agents. Antibiotic concentrations and use data allow extrapolation of risks beyond Sweden. Given the absence of detectable selection at municipal sites, mitigations of risks in hospital sewers should be prioritized.},
}

*Escherichia coli/drug effects/genetics/isolation & purification
*Anti-Bacterial Agents/pharmacology/analysis
Sweden
Ciprofloxacin/pharmacology
Hospitals
*Sewage/microbiology
Biofilms/drug effects
Humans
Wastewater/microbiology
Microbial Sensitivity Tests
Cefotaxime/pharmacology
*Drug Resistance, Bacterial/genetics
Fluoroquinolones/pharmacology
*Selection, Genetic
beta-Lactams/pharmacology

@article {pmid42957720,
year = {2026},
author = {Ramachandran, PS and Ramesh, A and Cresswell, FV and Wapniarski, A and Narendra, R and Quinn, CM and Tran, EB and Rutakingirwa, MK and Bangdiwala, AS and Kagimu, E and Kandole, KT and Zorn, KC and Tugume, L and Kasibante, J and Ssebambulidde, K and Okirwoth, M and Bahr, NC and Musubire, A and Skipper, CP and Fouassier, C and Lyden, A and Serpa, P and Castaneda, G and Caldera, S and Ahyong, V and DeRisi, JL and Langelier, C and Crawford, ED and Boulware, DR and Meya, DB and Wilson, MR},
title = {Author Correction: Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
doi = {10.1038/s41467-026-79080-w},
pmid = {42957720},
issn = {2041-1723},
}

@article {pmid42957759,
year = {2026},
author = {Nasr, EMT and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, KT and Ferrari, E and Griffin, TJ and Grüning, BA and Hiltemann, S and Hyde, CJ and Jagtap, PD and Kumar, A and Malla, MA and Mehta, S and Métris, KL and Momin, S and Nelson, T and Oba, AJ and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, AP and van Heusden, P and Vohra, M and Zierep, PF and Batut, B},
title = {Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42957759},
issn = {2399-3642},
support = {ANR-11-INBS-0013//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-MPGA-0013//Agence Nationale de la Recherche (French National Research Agency)/ ; U41HG006620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U24AI183870//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 75N92023P00302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U41HG006620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; INV-046492//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV-079648//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 228162/Z/23/Z//Wellcome Trust (Wellcome)/ ; LIBIS/de.NBI Freiburg,//Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg (Ministry of Science, Research and Art Baden-Württemberg)/ ; HORIZON-INFRA-2021-EOSC-01-04//European Commission (EC)/ ; REA.B.3, BGE 101059492//European Commission (EC)/ ; REA.B.3, BGE 101059492//European Commission (EC)/ ; },
mesh = {Reproducibility of Results ; *Microbiology ; *Computational Biology/methods ; Microbiota ; Proteomics ; *Software ; },
abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyse it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab (MGL): a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports the creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbiological data analysis. The MGL enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org , .eu , .org.au , . fr).},
}

Reproducibility of Results
*Microbiology
*Computational Biology/methods
Microbiota
Proteomics
*Software

@article {pmid42957850,
year = {2026},
author = {Roux, S and Neri, U and Bushnell, B and Fremin, BJ and George, NA and Gophna, U and Hug, LA and Camargo, AP and Wu, D and Ivanova, N and Kyrpides, NC and Eloe-Fadrosh, EA},
title = {Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42957850},
issn = {2058-5276},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; ERC-AdG 787514//European Commission (EC)/ ; 2016-03686//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; },
abstract = {Interactions between microorganisms and their mobile genetic elements (MGEs), including viruses and plasmids, impact microbiome dynamics. CRISPR-Cas systems are important regulators of these host-MGE interactions, but a global understanding of the diversity, activity and roles of CRISPR spacers across Earth's biomes is still lacking. Here we develop a computational approach to search short-read data and collect 794 million CRISPR spacers across 367,609 public metagenomes, from which we identified 1.18 billion hits between 41 million spacers and 2.5 million viruses and plasmids. While spacers were highly variable across samples, those matching known viruses were more prevalent and conserved, consistent with a positive selection pressure associated with phage targeting. Among these, however, we find evidence suggestive of recurrent entry of phage genomes into non-host microbial cells, further blurring the line between CRISPR targeting and virus-host interactions. These results highlight key drivers of CRISPR targeting patterns likely to influence strain-level diversification and selection processes in microbiomes.},
}

@article {pmid42958064,
year = {2026},
author = {Hou, Z and Pan, J and Wang, F and Zhao, M and Liu, X and Wang, L},
title = {Coxiella burnetii infective endocarditis involving a valved right ventricle-to-pulmonary artery conduit after Rastelli repair in an adolescent: a case report.},
journal = {BMC cardiovascular disorders},
volume = {26},
number = {1},
pages = {},
pmid = {42958064},
issn = {1471-2261},
mesh = {Humans ; Male ; *Endocarditis, Bacterial/microbiology/drug therapy/diagnostic imaging/diagnosis ; Adolescent ; *Coxiella burnetii/isolation & purification/pathogenicity/immunology ; *Q Fever/microbiology/drug therapy/diagnosis ; Treatment Outcome ; Anti-Bacterial Agents/therapeutic use ; *Prosthesis-Related Infections/microbiology/drug therapy/diagnosis/diagnostic imaging ; *Blood Vessel Prosthesis Implantation/adverse effects/instrumentation ; *Pulmonary Artery/surgery/diagnostic imaging/microbiology ; *Pulmonary Valve/surgery/diagnostic imaging/microbiology ; *Blood Vessel Prosthesis/adverse effects ; *Heart Valve Prosthesis/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; *Heart Valve Prosthesis Implantation/adverse effects/instrumentation ; Doxycycline/therapeutic use ; },
abstract = {BACKGROUND: Coxiella burnetii is an important cause of blood culture-negative infective endocarditis (IE). Pediatric C. burnetii endocarditis is rare, particularly in patients with prosthetic cardiovascular materials.

CASE PRESENTATION: A 13-year-old boy with pulmonary atresia who had undergone Rastelli repair followed by replacement with a valved right ventricle-to-pulmonary artery (RV-PA) conduit presented with recurrent fever and a mobile intraconduit mass. Transthoracic echocardiography (TTE) showed a vegetation in the pulmonary valve/conduit region, and cardiac computed tomography (CT) confirmed a corresponding filling defect without periconduit abscess or pseudoaneurysm. Blood metagenomic next-generation sequencing (mNGS) detected C. burnetii, while indirect immunofluorescence assay (IFA) showed positive phase I and phase II IgG antibodies. The conduit vegetation and blood detection of C. burnetii fulfilled major imaging and microbiological criteria, respectively, under the 2023 Duke-International Society for Cardiovascular Infectious Diseases criteria. An individualized regimen of doxycycline, trimethoprim-sulfamethoxazole (TMP-SMX), and hydroxychloroquine was followed by clinical improvement and reduction in lesion size during hospitalization.

CONCLUSIONS: C. burnetii should be considered in children with prosthetic cardiovascular materials who present with persistent fever and negative conventional blood cultures. Molecular testing, serology, and multimodality cardiac imaging can support diagnosis and early follow-up.},
}

Humans
Male
*Endocarditis, Bacterial/microbiology/drug therapy/diagnostic imaging/diagnosis
Adolescent
*Coxiella burnetii/isolation & purification/pathogenicity/immunology
*Q Fever/microbiology/drug therapy/diagnosis
Treatment Outcome
Anti-Bacterial Agents/therapeutic use
*Prosthesis-Related Infections/microbiology/drug therapy/diagnosis/diagnostic imaging
*Blood Vessel Prosthesis Implantation/adverse effects/instrumentation
*Pulmonary Artery/surgery/diagnostic imaging/microbiology
*Pulmonary Valve/surgery/diagnostic imaging/microbiology
*Blood Vessel Prosthesis/adverse effects
*Heart Valve Prosthesis/adverse effects
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use
*Heart Valve Prosthesis Implantation/adverse effects/instrumentation
Doxycycline/therapeutic use

@article {pmid42958146,
year = {2026},
author = {Pan, W and Li, Y and Wei, C and He, Z and Luo, J and Liao, G and Chen, L and Li, M},
title = {Membranous obliterans bronchitis after hematopoietic stem cell transplantation: case report.},
journal = {BMC pulmonary medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42958146},
issn = {1471-2466},
support = {81360012//National Natural Science Foundation of China/ ; 2016GXNSFAA380269//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology ; Bronchoscopy ; Tomography, X-Ray Computed ; Retrospective Studies ; Male ; Female ; *Bronchiolitis Obliterans/diagnosis/etiology ; *beta-Thalassemia/therapy ; Fatal Outcome ; },
abstract = {BACKGROUND: Pulmonary complications following hematopoietic stem cell transplantation (HSCT) are crucial factors affecting the prognosis of pediatric patients. Among them, membranous obliterative bronchitis (MOB) is rare, lacks sufficient clinical recognition, and is easily confused with bronchiolitis obliterans (BO), often leading to delayed diagnosis and extremely poor treatment outcomes. This study aimed to clarify the clinical characteristics, diagnostic key points of MOB after HSCT and its association with graft-versus-host disease (GVHD), so as to bridge the current knowledge gap regarding this rare fatal complication in clinical practice.

METHODS: A retrospective analysis was conducted, enrolling 2 pediatric patients with severe β-thalassemia who were diagnosed with MOB after HSCT. Data including clinical manifestations, chest computed tomography (CT), pulmonary function, fiberoptic bronchoscopy, pathological biopsy, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, and immune indicators were systematically collected. The diagnosis and treatment processes were summarized, and the pathogenesis was analyzed. The 2 patients developed progressive dyspnea at 7 months and 4 months after HSCT, respectively, both presenting with severe obstructive ventilatory dysfunction in pulmonary function tests (FEV1% predicted: 23.2% and 22.1%, respectively). Fiberoptic bronchoscopy revealed characteristic membranous stenosis or occlusion in segmental/subsegmental bronchi (3rd-4th generation), and bronchiectasis was observed on chest CT in both cases. Both patients were complicated with active GVHD and opportunistic infections. The conditions could not be reversed despite immunosuppressive therapy, anti-infective treatment, and interventional fiberoptic bronchoscopy, and both eventually died of respiratory failure. Immune monitoring indicated excessive activation of CD8 + T cells, persistently lowered CD4/CD8 ratio, and decreased B cell counts.

CONCLUSIONS: MOB after HSCT is a rare fatal complication that may be closely related to GVHD progression, immune dysregulation, and infectious triggers. Membranous occlusion under fiberoptic bronchoscopy is the key to definitive diagnosis, and existing therapeutic measures have limited efficacy. Clinically, early fiberoptic bronchoscopy should be performed for dyspneic patients complicated with GVHD after HSCT, and the prevention and control of GVHD as well as infection prophylaxis should be strengthened. Targeted immune intervention strategies should be explored in the future to improve prognosis.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
*Graft vs Host Disease/etiology
Bronchoscopy
Tomography, X-Ray Computed
Retrospective Studies
Male
Female
*Bronchiolitis Obliterans/diagnosis/etiology
*beta-Thalassemia/therapy
Fatal Outcome

@article {pmid42958270,
year = {2026},
author = {Wu, Z and Youssef, G and Kean, IRL and Zhang, Z and Clark, JA and Pathan, N and Han, N},
title = {Integrated host-microbe biomarkers for early diagnostic classification of paediatric LRTI in mechanically ventilated children.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {},
pmid = {42958270},
issn = {1465-993X},
support = {900240//Addenbrooke's Charitable Trust, Cambridge University Hospitals/ ; 900240//Addenbrooke's Charitable Trust, Cambridge University Hospitals/ ; 900240//Addenbrooke's Charitable Trust, Cambridge University Hospitals/ ; BRC-1215-20014//NIHR Cambridge Biomedical Research Centre/ ; RG91966//LifeArc, United Kingdom/ ; GTL24021-000//National Research Council of Science and Technology/ ; RS-2025-18362970//National Research Foundation of Korea/ ; RS-2025-25456722//Korea Health Industry Development Institute/ ; RS-2025-25427881//Brain Pool Plus Fellowship Program, South Korea/ ; },
mesh = {Humans ; *Respiration, Artificial/trends/adverse effects ; Biomarkers/metabolism ; *Respiratory Tract Infections/diagnosis/microbiology/classification/genetics ; Male ; Female ; Early Diagnosis ; Prospective Studies ; Child, Preschool ; Infant ; Child ; *Host-Pathogen Interactions/physiology ; Bronchoalveolar Lavage Fluid/microbiology ; Intensive Care Units, Pediatric/trends ; },
abstract = {BACKGROUND: Early diagnosis of paediatric lower respiratory tract infection (LRTI) in intensive care is difficult because clinical features overlap with non-infectious respiratory failure and conventional microbiology has limited sensitivity. We aimed to integrate airway microbial and host-response signals to identify early diagnostic biomarkers in mechanically ventilated children.

METHODS: We re-analysed airway metagenomic sequencing and tracheal aspirate transcriptomics from 261 ventilated paediatric intensive care unit (PICU) patients using differential expression, protein-protein interaction network analysis, and machine-learning feature selection. Findings were evaluated in an exploratory assessment of biologically related cytokine markers within an independent prospective cohort (RASCALS; n = 100 enrolled, n = 78 analysed) using non-bronchoscopic mini-bronchoalveolar lavage (mini-BAL), plasma cytokines, and clinician-adjudicated diagnoses.

RESULTS: Respiratory syncytial virus and Haemophilus influenzae were the only pathogens consistently enriched in LRTI. Host transcriptomics showed activation of interferon, cytokine, and chemokine signalling. Network-guided feature selection identified a seven-gene panel (IRF7, FFAR3, GZMB, FABP4, FN1, CXCL5, BCAR1) with high diagnostic performance in cross-validation (median F1 0.94), comparable to a published 14-gene model. In RASCALS, a logistic model using mini-BAL IL-1β, IL-4, and IL-8 classified bacterial LRTI with 65% accuracy (sensitivity 70%, specificity 63%), while blood IL-6 and TRAIL achieved 82% accuracy (sensitivity 79%, specificity 83%).

CONCLUSIONS: Integrating airway microbial profiles with host-response biomarkers supports earlier and more specific LRTI diagnostic classification in ventilated children. The seven-gene panel and cytokine combinations are candidates for rapid PCR- or immunoassay-based bedside tests to inform antimicrobial stewardship.},
}

Humans
*Respiration, Artificial/trends/adverse effects
Biomarkers/metabolism
*Respiratory Tract Infections/diagnosis/microbiology/classification/genetics
Male
Female
Early Diagnosis
Prospective Studies
Child, Preschool
Infant
Child
*Host-Pathogen Interactions/physiology
Bronchoalveolar Lavage Fluid/microbiology
Intensive Care Units, Pediatric/trends

@article {pmid42958435,
year = {2026},
author = {Rao, B and Liu, S and Cui, G and Jiang, J and Li, N and Hu, J and Sun, R and Li, A and Zhang, R and Lu, H and Wen, P and Xue, J and Aji, T and Wang, H and Chen, X and Zheng, S and Yu, Z and Ren, Z},
title = {Multikingdom and functional gut microbiota markers for cholangiocarcinoma.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42958435},
issn = {1756-994X},
support = {82570691//National Natural Science Foundation of China/ ; 81672422//National Natural Science Foundation of China/ ; 82470654//National Natural Science Foundation of China/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2025ZD01906305//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; HNCMS202423//Henan Province "Three 100" Program, Special Project for Clinical Medical Scientist Cultivation/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/diagnosis ; Female ; Metagenomics/methods ; Male ; Middle Aged ; Feces/microbiology ; Liver Neoplasms/microbiology/diagnosis ; Biomarkers, Tumor ; Metagenome ; Carcinoma, Hepatocellular/microbiology ; Aged ; },
abstract = {BACKGROUND: While the association between gut microbiota and cholangiocarcinoma (CCA) has been explored, existing research has been limited to bacterial components. The alterations in non-bacterial members (fungi, archaea, and viruses) and their functional characteristics in CCA remain unclear. This study aimed to comprehensively characterize the multi-kingdom gut microbiota and functional profiles in CCA patients and develop a non-invasive diagnostic model.

METHODS: We performed metagenomic sequencing on 700 fecal samples collected from three distinct regions in China, comprising 289 CCA patients, 312 healthy controls, and 99 hepatocellular carcinoma (HCC) patients. Multi-kingdom microbial composition and functional profiles were analyzed. We integrated multiple machine learning algorithms to generate 117 distinct modeling schemes for constructing and screening the optimal CCA diagnostic model. The model was validated across three independent cohorts and tested for specificity against HCC. We also benchmarked the model against established diagnostic approaches by reviewing 15 CCA clinical practice guidelines/consensus statements and their cited evidence and by evaluating model detection in CA19-9-positive and CA19-9-negative patients.

RESULTS: Extensive alterations were identified in CCA patients across multi-kingdom and functional layers, including 198 archaeal, 154 bacterial, 78 fungal, and 120 viral species, as well as 278 genes, 99 pathways, and 151 carbohydrate-active enzymes (CAZymes). A panel of 21 multi-kingdom and functional markers demonstrated superior diagnostic accuracy with an average AUC of 91% across three validation cohorts, outperforming any single-kingdom model. The model exhibited high specificity in distinguishing CCA from HCC, achieving an AUC of 99.74% with a false positive rate of 11.11%. Benchmarking supported a complementary role as a noninvasive screening aid, the model showed pooled sensitivity and specificity of 96.2%, and 78.5%, respectively, and detected 97.6% of CA19-9-negative CCA cases.

CONCLUSIONS: This study represents the first comprehensive characterization of multi-kingdom gut microbiome and functional markers in cholangiocarcinoma. Gut multi-kingdom and functional microbial signatures represent a promising noninvasive tool that may aid the screening and early identification of cholangiocarcinoma in high-risk populations, complementing existing diagnostic approaches.},
}

Humans
*Cholangiocarcinoma/microbiology/diagnosis
*Gastrointestinal Microbiome
*Bile Duct Neoplasms/microbiology/diagnosis
Female
Metagenomics/methods
Male
Middle Aged
Feces/microbiology
Liver Neoplasms/microbiology/diagnosis
Biomarkers, Tumor
Metagenome
Carcinoma, Hepatocellular/microbiology
Aged

@article {pmid42958437,
year = {2026},
author = {Zhao, WS and Cui, NQ and Lu, XY and Zhang, XY and Li, SZ and Guo, QG and Ma, P},
title = {Effect of low-density polyethylene microplastics on incidence of cotton Verticillium wilt and the structure and function of rhizosphere microbial community.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42958437},
issn = {2524-6372},
support = {CARS-15-19//China Agriculture Research System of MOF and MARA/ ; },
abstract = {Microplastics have become a global environmental concern, but the impact of microplastics on plant disease remains poorly understood. The primary objective of this study was to evaluate the effects of low-density polyethylene (LDPE) microplastics on cotton Verticillium wilt (CVW), as well as the structure and function of the soil microbial community. Metagenomic sequencing was performed to characterize the microbial community composition of the cotton rhizosphere. The experiment consisted of five treatments: a control group, and four LDPE groups with concentrations set at 0.1%, 0.5%, 1.0%, and 2.5%, respectively. The results demonstrated that high-dose LDPE treatments reduced the cotton emergence rate by 1.47-4.41% and plant biomass by 14.58-34.64%. These findings suggest that high-dose LDPE may exert pronounced phytotoxic effects on cotton plants. Although the populations of Verticillium dahliae did not differ significantly across treatments, LDPE microplastics at concentrations of 0.5-2.5% significantly exacerbated CVW, elevating the disease index by 54.29-71.67%. Statistical analysis revealed that LDPE microplastics altered the contents of soil nitrate nitrogen (NO3[-]-N) and available phosphorus (AP), with NO3[-]-N increasing by 16.86%-85.63% and AP by 51.16-69.77%. Meanwhile, LDPE microplastics triggered substantial alterations in the structure of rhizosphere microbial communities, as well as in their functional potential (assessed via KEGG pathway annotation). Microbial community structure and KEGG pathways were both significantly changed by soil nutrients (NO3[-]-N, NH4[+]-N, AP, AK). Moreover, partial least squares path modeling (PLS-PM) suggested that LDPE treatment indirectly influenced DI through two pathways: one was a positive effect mediated by alternations in fungal community structure and function, and the other was a negative effect driven by changes in soil nutrients. The exacerbation of CVW was closely linked to LDPE-induced dysbiosis in the cotton rhizosphere microenvironment.},
}

@article {pmid42958549,
year = {2026},
author = {Sheng, Y and Yan, C and Yin, Y and Zeng, Z and Pei, X and Ma, C and Rao, J and Sun, H and Xue, Y},
title = {From microbial dysbiosis to putative epigenetic locking: a hypothesis-driven framework for the pathogenesis and future therapeutic perspectives of gastric intestinal metaplasia.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42958549},
issn = {1479-5876},
support = {32372302//National Natural Science Foundation of China/ ; 82405210//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Epigenesis, Genetic ; Metaplasia ; *Dysbiosis/microbiology/genetics/therapy ; Animals ; *Intestines/pathology ; *Stomach/pathology/microbiology ; Helicobacter pylori/physiology ; *Models, Biological ; },
abstract = {BACKGROUND: Intestinal metaplasia (IM) is a key precancerous lesion connecting chronic atrophic gastritis and gastric cancer in the Correa cascade, and its risk of progression has significant individual heterogeneity. A potential explanatory framework for this heterogeneity involves interactions between gastric microbiota imbalance and host epigenetic remodeling. Current research needs to clarify the relationship between microbial community stratification and IM reversibility, particularly whether high-risk microbial signatures and putative epigenetic "silencer locking" states are associated with IM regression or persistence.

METHOD: This hypothesis-driven narrative review synthesizes representative findings from metagenomic, metabolomic, transcriptomic, and epigenomic studies to develop a conceptual framework for how interactions between Helicobacter pylori (H. pylori), non-H. pylori microorganisms, and host mucosal responses may be associated with the initiation and progression of IM, potentially through microbiota-associated, host-derived, and mixed-origin metabolic signals that converge on epigenetic and transcriptional regulation.

RESULT: Available evidence suggests that microbial networks in IM may include potential pro-inflammatory interactions between H. pylori and taxa such as Fusobacterium nucleatum (F. nucleatum), as well as possible protective associations involving beneficial bacteria such as Lactobacillus. Based on this, we propose a three-stage working model, H. pylori initiation, putative microbial network amplification, and silencer remodeling-associated progression, and discuss a candidate intervention framework involving probiotics, miR-185, and Wnt/β-catenin signaling, which should be regarded as a testable hypothesis rather than a clinically validated reversal strategy.

CONCLUSION: These findings may provide candidate mechanistic targets and a theoretical basis for future risk stratification, dynamic monitoring, and individualized intervention of IM, pending validation in prospective clinical studies.},
}

Humans
*Epigenesis, Genetic
Metaplasia
*Dysbiosis/microbiology/genetics/therapy
Animals
*Intestines/pathology
*Stomach/pathology/microbiology
Helicobacter pylori/physiology
*Models, Biological

@article {pmid42959031,
year = {2026},
author = {Songel-Sanchis, B and Cosín-Roger, J},
title = {Gut mycobiome dysbiosis in inflammatory bowel disease: a systematic review and meta-analysis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1960101},
pmid = {42959031},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/microbiology/immunology ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Mycobiome/immunology ; *Fungi/classification/genetics ; },
abstract = {BACKGROUND: The intestinal mycobiome is increasingly recognized as an important component of host-microbiota interactions in inflammatory bowel disease (IBD), yet its contribution to intestinal immune dysregulation remains incompletely characterized. We aimed to characterize alterations in the intestinal mycobiome in patients with inflammatory bowel disease, including Crohn's disease and ulcerative colitis, compared with individuals without IBD, focusing on fungal diversity, taxonomic composition, and relative abundance, as well as their potential associations with disease phenotype and inflammatory activity.

METHODS: A systematic review and meta-analysis was conducted according to PRISMA 2020 guidelines. PubMed/MEDLINE, Embase, and Cochrane Central Register of Controlled Trials were systematically searched from inception to March 2026, with no language or publication-date restrictions. The review was not prospectively registered. Human studies assessing gut fungal communities by internal transcribed spacer (ITS)-based sequencing or shotgun metagenomics were eligible. Alpha and beta diversity, taxonomic composition, and clinically relevant fungal alterations were extracted. Study quality was assessed independently by two reviewers using the Newcastle-Ottawa Scale (NOS), and quantitative analyses were performed using standardized effect estimates and pooled prevalence.

RESULTS: Twenty-eight studies were included in the qualitative and quantitative synthesis. CD was consistently associated with reduced fungal alpha diversity compared with healthy controls, with a pooled weighted mean difference in Shannon diversity of -0.84 (p<0.001), whereas the reduction in UC was more modest (-0.31, p=0.04). Fungal beta diversity consistently differed between IBD and healthy controls. Expansion of Candida spp. was the most reproducible taxonomic alteration, occurring in 82.1% of analyzed cohorts, while depletion of Saccharomyces cerevisiae was reported in 71.4%. Malassezia enrichment was also associated with mucosal inflammation and CARD9-related immune responses. Cross-kingdom interactions involving Candida, Escherichia coli, and Serratia marcescens further highlighted potential fungal-bacterial mechanisms underlying persistent inflammation. Persistent fungal dysbiosis despite clinical remission supported the concept of a "mycobiotic scar."

CONCLUSION: IBD is characterized by substantial disruption of the intestinal mycobiome, particularly in CD, with reduced fungal diversity, expansion of potentially pathogenic Candida spp., and depletion of protective fungal taxa. These alterations may contribute to immune dysregulation and therapeutic refractoriness and support the mycobiome as a potential source of biomarkers and therapeutic targets in IBD.},
}

Humans
*Dysbiosis/microbiology/immunology
*Inflammatory Bowel Diseases/microbiology/immunology
*Gastrointestinal Microbiome/immunology
*Mycobiome/immunology
*Fungi/classification/genetics

@article {pmid42959082,
year = {2026},
author = {Zhang, Y and Pei, C and Zhang, D and Liu, J},
title = {Microbiome-driven precision psychiatry: integrating multi-omics, artificial intelligence, and personalized interventions along the gut-brain axis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1957715},
pmid = {42959082},
issn = {2296-858X},
abstract = {INTRODUCTION: This scoping review maps evidence for microbiome-driven precision psychiatry in depression and anxiety.

METHODS: Following JBI guidance and PRISMA-ScR, we searched PubMed/MEDLINE and PubMed Central from inception to July 2026, supplemented by Google Scholar and backward citation searching. Human primary studies were screened and charted; findings were synthesized narratively.

RESULTS: Of 58 identified records, 49 remained after deduplication, 35 full texts were assessed, and 28 studies were included. The evidence was predominantly observational. Taxonomic findings varied across populations, while studies of microbial functions, metabolites, multi-omics signatures, and treatment response suggested potential for biological stratification. Microbiome-targeted interventions and artificial intelligence models remain exploratory.

DISCUSSION: Microbiome-derived biomarkers and predictive models require standardized methods, independent validation, and prospective evidence of clinical utility before routine psychiatric use.},
}

@article {pmid42959182,
year = {2026},
author = {Zhang, Y and Zhang, X and Wei, X and Yu, W and Ma, N and Liu, W and Zheng, Y and Jia, H},
title = {Metagenomic next-generation sequencing confirmed pseudorabies virus encephalitis complicated with central visual impairment: a case report.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1954544},
pmid = {42959182},
issn = {1664-2295},
mesh = {Humans ; Male ; Middle Aged ; *Pseudorabies/complications/diagnostic imaging ; *Encephalitis, Viral/complications/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; *Herpesvirus 1, Suid/genetics ; Metagenomics ; *Vision Disorders/etiology/diagnostic imaging/virology ; },
abstract = {Pseudorabies virus (PRV) is an alphaherpesvirus for which domestic swine serve as the sole natural reservoir. Human PRV infection has historically been regarded as extremely rare. Since 2017, however, an increasing number of severe human PRV encephalitis cases have been identified in China, pre-dominantly among individuals with occupational exposure to pigs or pork products. The condition has been associated with substantial morbidity and mortality and remains under recognized in clinical practice. We report a 53-year-old male dockworker who presented with a 9-day history of fever followed by progressive severe headache. PRV infection was confirmed by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). Brain magnetic resonance imaging revealed signal abnormalities involving the right insular cortex, temporal lobe, hippocampus, and amygdala, consistent with encephalitis. The patient received intravenous acyclovir (500 mg every 8 h for 23 days), corticosteroids, and intravenous immunoglobulin. Although his level of consciousness gradually improved, he developed permanent bilateral blindness with no light perception. At 1-year follow-up, he remained alive but with persistent blindness; neuroimaging demonstrated encephalomalacia in the right temporal and insular regions. PRV can cause devastating human encephalitis with visual impairment as a frequent and serious complication, reported in up to 60% of published cases. Our case is notable in that bilateral blindness emerged after recovery of consciousness, without evidence of peripheral ocular pathology, suggesting a pre-dominantly central visual pathway injury. CSF mNGS has become a key tool for timely diagnosis of rare viral encephalitides. Clinicians should consider PRV encephalitis in patients with unexplained encephalitis and a history of swine exposure, and pursue early mNGS testing to facilitate prompt aetiological diagnosis and antiviral therapy.},
}

Humans
Male
Middle Aged
*Pseudorabies/complications/diagnostic imaging
*Encephalitis, Viral/complications/diagnostic imaging
High-Throughput Nucleotide Sequencing
*Herpesvirus 1, Suid/genetics
Metagenomics
*Vision Disorders/etiology/diagnostic imaging/virology

@article {pmid42959280,
year = {2026},
author = {Lee, Y and Min, EK and Park, YJ and Kim, DG and Joo, DJ and Kim, MS and Shin, S and Lee, ST and Lee, JG and Jeong, SJ},
title = {Plasma microbial cell-free DNA metagenomic sequencing for early detection of infection after liver transplantation: a prospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1930701},
pmid = {42959280},
issn = {2235-2988},
mesh = {Humans ; *Liver Transplantation/adverse effects ; Prospective Studies ; Female ; *Metagenomics/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Male ; High-Throughput Nucleotide Sequencing ; Middle Aged ; Adult ; Early Diagnosis ; Aged ; DNA, Bacterial/blood ; },
abstract = {INTRODUCTION: Microbial cell-free DNA (mcfDNA) metagenomic next-generation sequencing (mNGS) is a promising technique for diagnosing infectious diseases. However, research on mcfDNA-based mNGS for diagnosing infections in liver transplantation (LT) recipients remains limited. The aim of this study was to evaluate the diagnostic performance and clinical utility of plasma mcfDNA mNGS during the early post-LT period.

METHODS: In this prospective diagnostic cohort study, adult LT recipients underwent plasma mcfDNA mNGS on postoperative days 7 and 14. The findings were compared with results of the blood cultures and other conventional microbiological tests at the species level.

RESULTS: Among 193 LT recipients, mNGS positivity was observed in 14.5% on day 7 and 21.8% on day 14. The concordance between mNGS and blood culture for bacterial pathogens was modest on days 7 (35.0%) and 14 (14.3%) but increased substantially when other clinically relevant specimens were included (80.0% and 71.4%, respectively). mNGS identified additional pathogens not detected using blood culture in 59.3% and 74.2% of cases on days 7 and 14, respectively. Viral pathogens, including cytomegalovirus, herpes simplex virus, varicella-zoster virus, and roseolovirus, were also detected. Among the 13 discordant cases (blood culture-positive and mNGS-negative), two (15.4%) were classified as contamination/colonization, five (38.5%) as weak positives, and six (46.2%) as not detected by mNGS.

CONCLUSION: Plasma mcfDNA mNGS demonstrated substantial concordance with conventional microbiological testing when clinically relevant specimens were considered. mNGS may serve as a useful adjunct tool for early pathogen detection and clinical assessment of LT recipients.},
}

Humans
*Liver Transplantation/adverse effects
Prospective Studies
Female
*Metagenomics/methods
*Cell-Free Nucleic Acids/blood/genetics
Male
High-Throughput Nucleotide Sequencing
Middle Aged
Adult
Early Diagnosis
Aged
DNA, Bacterial/blood

@article {pmid42959430,
year = {2026},
author = {Hua, X and Grimaud, GM},
title = {A Two-Stage ESM-Based Machine Learning Pipeline for Robust Hierarchically Evaluated Enzyme Function Prediction.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0246},
pmid = {42959430},
issn = {2001-0370},
abstract = {Accurate enzyme annotation remains a major bottleneck in translating rapidly growing protein sequence data into biological knowledge. Enzyme Commission (EC) prediction is particularly challenging because enzyme functions are organized hierarchically, annotations are often imbalanced across classes, and sequence similarity alone may be insufficient to resolve functional differences. To address these challenges, we developed ESM-ECForest, a 2-stage framework that combines protein embeddings generated by the pretrained language model ESM-2 (Evolutionary Scale Modeling 2) with random forest classifiers. The first stage distinguishes enzymes from nonenzymes, whereas the second assigns one or more EC numbers to proteins predicted to be enzymatic. On an external benchmark comprising 25,778 protein sequences, ESM-ECForest achieved competitive weighted F1 scores among the evaluated off-the-shelf methods, decreasing from 0.94 at Level 1 to 0.90 at Level 4. The largest relative improvements were observed for lyases (EC 4), ligases (EC 6), and translocases (EC 7), although EC 6 and EC 7 remained the most difficult classes internally. Uniform manifold approximation and projection of the ESM-2 embedding space showed clustering patterns that broadly reflected enzyme functional relationships, suggesting that the pretrained representations capture functionally relevant information. These results support the use of pretrained protein language model embeddings as an effective foundation for enzyme annotation. By combining pretrained protein representations with a lightweight supervised classifier, ESM-ECForest provides a scalable approach for EC prediction and may facilitate functional annotation of proteins from large microbial genomic and metagenomic datasets within the taxonomic and EC-label space represented during model development.},
}

@article {pmid42959609,
year = {2026},
author = {Trubitsyn, VE and Rusanov, II and Rechkina, VI and Kadnikov, VV and Zasko, DN and Beletsky, AV and Pimenov, NV and Ravin, NV and Shcherbakova, VA and Karnachuk, OV},
title = {Archaeal methanogenesis in a deep terrestrial aquifer driven by Methanothermobacter tomskensis sp. nov.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1973590},
pmid = {42959609},
issn = {1664-302X},
abstract = {Methanogenic archaea, capable of producing organic matter from hydrogen and CO2 emanating from the mantle, constitute one of the key functional groups of microorganisms in the deep subsurface. Although the diversity of methanogenic inhabitants of the deep biosphere has been studied in detail, the activity of methanogens in these biotopes remains virtually uncharacterized. We have measured the rate of hyrogenotrophic methanogenesis in water from the model borehole 3P (2.7 km deep), located near the small town of Parabel in the Tomsk Region. The potential rate of hydrogenotrophic methanogenesis, measured using [14]C-labeled sodium bicarbonate, was 5.45 ± 0.528 nmol CH4/dm[3]/day (0.00545 ± 0.0005 nmol CH4/cm[3]/day) - a value compatible to the methanogenic archaeal activity known for anaerobic sediments of surface water bodies. The 16S rRNA gene profiles of water from well 3P were dominated by s single phylotype assigned to the genus Methanothermobacter; it accounted for 25.54% of the total microbial community. A MAG (metagenome assembled genome) designated 3P-20-051 and belonging to the genus Methanothermobacter was assembled from the water metagenome of well 3P. According to GTDB taxonomy, this MAG represents a novel species within the genus. The closest validly described relative of MAG 3P-20-001 was Methanothermobacter marburgensis with an ANI of 92.66%. Following the characterization of this MAG, a strain of methanogenic archaea designated as K4[T] was isolated in pure culture. Morphological, physiological, genotypic, and phylogenetic data indicate that this strain represents a new species of the genus Methanothermobacter, for which we propose the name Methanothermobacter tomskensis sp. nov. Comparison of the strain K4[T] genome with MAG 3P-20-051 showed that they were nearly identical: the ANI value was 99.96%. Thus, M. tomskensis sp. nov. indeed, represents a dominant methanogenic lineage revealed by metagenomics. Strain K4[T] is characterized by an obligately hydrogenotrophic metabolism and possibly represents the main producer of organic matter in the deep horizons of the thermal aquifer.},
}

@article {pmid42959625,
year = {2026},
author = {Shen, Y and Yang, Y and Sun, J and Han, Z and Sun, Y and Li, R and Zhang, Y and Yu, Y},
title = {Why does apical periodontitis persist? A shotgun metagenomic survey of the microbial community in primary and persistent periapical granulomas.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2741866},
pmid = {42959625},
issn = {2000-2297},
abstract = {OBJECTIVE: This cross‑sectional observational study used shotgun metagenomic sequencing to compare the microbiomes of periapical granulomas from primary and persistent apical periodontitis to identify microbial taxa and functional pathways associated with persistent lesions.

METHODS: Seventeen patients with untreated primary apical periodontitis (UA), 19 with persistent apical periodontitis (PA), and 19 healthy gingival reference samples (HC) were enrolled. Periapical granuloma and healthy gingival samples were collected during tooth extraction for whole-metagenome shotgun sequencing. Alpha diversity was assessed by the Shannon and Chao1 indices. Beta-diversity was evaluated using PERMANOVA based on Bray‑Curtis distances. Differential abundance analysis of species and predicted functional pathways between UA and PA was performed using the Mann‒Whitney U test with Benjamini‒Hochberg false discovery rate (FDR) correction. Clinical associations were examined using Spearman's correlation. The HC group served as a descriptive reference.

RESULTS: Alpha diversity showed a significant difference in species richness (Chao1, p < 0.05) but not overall diversity (Shannon, p > 0.05). Beta diversity revealed a trend toward separation but did not reach statistical significance (PERMANOVA, R[2]  = 0.05085, p = 0.051). Metagenomic sequencing revealed differences in species composition and functional potential between UA and PA. Taxonomic profiling identified 503 species in UA versus 255 in PA. At the species level, several taxa showed nominal differences between UA and PA (p < 0.05), but none remained significant after FDR correction (q > 0.05). Functionally, several KEGG pathways showed nominal differences between UA and PA (p < 0.05, q > 0.05), with the top three pathways all below 3% relative abundance. Swelling duration correlated negatively with several taxa and pathways (p < 0.05), while lesion diameter showed little association with microbial abundance.

CONCLUSIONS: Persistent apical periodontitis granulomas showed lower species richness and abundance, but similar predicted functional capacity, compared with primary infections. Further longitudinal and multi‑omics studies are needed to investigate the associations.},
}

@article {pmid42959809,
year = {2026},
author = {Reysenbach, AL and St John, E and Catchpole, R},
title = {Expanding the global diversity of Nanobdellales from deep-sea hydrothermal vents.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag280},
pmid = {42959809},
issn = {2730-6151},
abstract = {The archaeal symbiotic Nanobdellales have been isolated with their hosts from a shallow hot marine vent off Iceland and from terrestrial hot springs in Yellowstone National Park and Japan. They have highly reduced genomes and rely on their archaeal hosts for most of their metabolic needs. Here, to provide further insights into the ecology and evolution of this order, we greatly expand their phylogenomic distribution using metagenome-assembled genomes from deep-sea hydrothermal vents in the Atlantic, Pacific and Indian Oceans, and the Gulf of California. We show that at least 11 novel genus-level lineages occur at deep-sea vents. We conservatively propose two new genera with their nomenclatural types, Nanoprofundum liuii Rb-1[Ts] gen. nov. sp. nov. and Nanojejuna irisiana Rb-38[Ts] gen. nov. sp. nov. We also describe a second species of Nanoarchaeum, N. abyssimaris 17S-22[Ts] sp. nov. Our genomic and metabolic characterization of the high-quality metagenome-assembled genomes confirm their highly reduced metabolic capabilities and likely symbiotic lifestyle. With the exception of Nanoarchaeum, all deep-sea genera resemble their terrestrial relatives in that they have genes that encode for archaella and RNAase P protein subunits, and have several genes involved in glycolysis and gluconeogenesis. Using an inferred lateral gene transfer analysis, our data suggest that deep-sea Nanobdellales may potentially associate with a greater taxonomic breadth of hosts than previously reported, spanning members of the Sulfolobales (Ignicoccaceae), the Archaeoglobales and Methanococcales.},
}

@article {pmid42960201,
year = {2026},
author = {Luo, L and Zhao, J and Zhuge, J and Fang, H and Yuan, L and Wang, J and Hua, Z and Cui, Y},
title = {BALF-mNGS-Derived Microbial Detection Profiles and Their Associations with Clinical Severity in Immunocompromised Patients with Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {657668},
pmid = {42960201},
issn = {1178-6973},
abstract = {BACKGROUND: Immunocompromised patients with community-acquired pneumonia (CAP) have heterogeneous pulmonary microbial profiles and frequently experience a severe clinical course. Whether bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS)-derived microbial features are associated with clinical severity in this population remains unclear.

OBJECTIVE: To characterize pulmonary microbial features in immunocompromised patients with CAP and evaluate their association with ICU admission and length of hospital stay (LOHS).

METHODS: This multicenter retrospective study included 1072 patients with CAP who underwent BALF-mNGS at five hospitals (August 2021-June 2025), including 362 immunocompromised and 710 immunocompetent patients. Microbial diversity, composition, and differentially enriched taxa were compared by immune status. Among immunocompromised patients, taxon-outcome associations were assessed using adjusted logistic and negative binomial regression, with sensitivity analyses additionally adjusting for antibiotic and antifungal exposure before BALF.

RESULTS: Immunocompromised patients had higher alpha diversity (P<0.001), with limited overall community separation. Five taxa were enriched: Burkholderia multivorans, Klebsiella pneumoniae, Candida glabrata, Candida tropicalis, and Streptococcus pseudopneumoniae. In primary analyses, B. multivorans abundance was associated with ICU admission (adjusted odds ratio [aOR] 1.400, 95% CI 1.088-1.801; false discovery rate [FDR]-adjusted P=0.045) and longer LOHS (adjusted incidence rate ratio [aIRR] 1.108, 95% CI 1.036-1.186; FDR-adjusted P=0.014). C. glabrata was associated with longer LOHS (aIRR 1.101, 95% CI 1.023-1.185; FDR-adjusted P=0.026). K. pneumoniae showed a nominal ICU association that did not survive FDR correction (FDR-adjusted P=0.084). After additional adjustment for antibiotic and antifungal exposure, the associations of B. multivorans and C. glabrata with longer LOHS remained significant (both FDR-adjusted P=0.044), whereas the association between B. multivorans and ICU admission did not (FDR-adjusted P=0.168).

CONCLUSION: BALF-mNGS-derived microbial features showed limited overall community differences but distinct taxon-specific associations with clinical severity. These exploratory findings require further validation before their prognostic or clinical utility can be established.},
}

@article {pmid38651906,
year = {2024},
author = {Qin, B and Jia, L and Chen, J and Liu, W},
title = {Balamuthia Amebic Encephalitis Cured and Discharged.},
journal = {The Journal of craniofacial surgery},
volume = {35},
number = {6},
pages = {e496-e497},
doi = {10.1097/SCS.0000000000010123},
pmid = {38651906},
issn = {1536-3732},
mesh = {Humans ; Male ; Middle Aged ; *Infectious Encephalitis/parasitology/diagnostic imaging/drug therapy/diagnosis/therapy ; *Amebiasis/drug therapy/diagnosis ; Magnetic Resonance Imaging ; },
abstract = {Intracerebral granulomatous infectious encephalitis caused by Baboon Balamuthia amoeba is a rare form of infectious granulomatous amoebic encephalitis. There are very limited case reports of cured discharges. The authors report a 59-year-old male patient who met the diagnostic criteria for granulomatous infection caused by Baboon Balamuthia amoeba. After treatment, the patient's condition improved, and he was discharged from the hospital. The authors reviewed the data of this patient, analyzed relevant imaging information, and summarized our experience to enhance understanding of this condition.},
}

Humans
Male
Middle Aged
*Infectious Encephalitis/parasitology/diagnostic imaging/drug therapy/diagnosis/therapy
*Amebiasis/drug therapy/diagnosis
Magnetic Resonance Imaging

@article {pmid42948400,
year = {2026},
author = {Yu, Y and Wang, J and Yuan, Q and Yu, L and Zhang, C},
title = {Evaluating traditional Chinese medicine modulation of the gut microbiota-bile acid axis in metabolic and inflammatory diseases: mechanistic evidence and translational priorities.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1977691},
pmid = {42948400},
issn = {1664-302X},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD), obesity, type 2 diabetes mellitus (T2D), and inflammatory bowel disease (IBD) are clinically distinct disorders that share perturbations in intestinal ecology, bile-acid composition, epithelial barrier function, and immune-metabolic regulation. Traditional Chinese medicine (TCM) may modify these interconnected processes, but the translational significance of reported effects remains uncertain. Changes in microbial composition are often interpreted as mechanisms without evidence of altered microbial function, bile-acid profiles or concentrations, receptor engagement, or clinical benefit. Here, we present a structured narrative review that uses the gut microbiota-bile acid axis to evaluate TCM in metabolic and inflammatory disease. We describe how microbial bile salt hydrolases, the bile acid-inducible (bai) operon, hydroxysteroid dehydrogenases, and amino-acid conjugation diversify the bile-acid pool and influence farnesoid X receptor (FXR), Takeda G protein-coupled bile acid receptor 1 (GPBAR1, also known as TGR5), and immune pathways. We then assess evidence for defined TCM constituents and formulae in MASLD, obesity/T2D, and IBD. Across these settings, the most informative studies combine a standardized intervention with longitudinal metagenomic and targeted bile-acid profiling, host-signaling measurements, and an outcome that is attenuated by microbiota depletion, fecal microbiota transplantation, or functional microbial manipulation. Only one eligible human trial, of Qushi Huayu in adults enrolled under the historical NAFLD designation, reported both clinical and microbiota-related outcomes. Evidence for obesity/T2D and IBD was predominantly preclinical or observational, and the framework is therefore a translational assessment tool rather than a clinically validated model. We therefore propose an evidence hierarchy and a minimum translational package that integrates chemical quality control, dietary and co-medication assessment, strain- and gene-resolved microbiome analysis, targeted bile-acid metabolomics, and pathway-directed validation. TCM should be considered a potential precision adjunct to standard care only when reproducible microbial-metabolic phenotypes are linked to clinically meaningful benefit.},
}

@article {pmid42949018,
year = {2026},
author = {Gilbert, NE and Coffey, NR and McCall, N and Kimbrel, JA and Carlson, CA and Halewood, E and Ramon, CE and Diep, P and Weber, PK and Mayali, X and Boiteau, RM and Stuart, RK},
title = {Iron limitation reduces diatom carbon flow to bacteria through shifts in exometabolite consumption.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag274},
pmid = {42949018},
issn = {1751-7370},
abstract = {Iron is required for photosynthesis and thus affects carbon fixation rates in widespread aquatic regions where availability is limited. Turnover of aquatic photosynthetically derived fixed carbon is largely constrained by bacterial activity, but it is unknown how algal iron limitation alters dissolved organic matter composition and subsequent processing through the microbial loop. We examined a bacterial community dependent on carbon from the diatom Phaeodactylum tricornutum to investigate how iron limitation alters bacterial carbon processing. By quantifying activity at single-cell-resolution with nanoSIMS, we found that iron limitation led to a 43% reduction in carbon-fixation but an 80% reduction in carbon transfer into bacterial biomass. Ultra-high-resolution exometabolomics revealed that iron limitation led to bacterial consumption of less labile compounds including aromatics, specific lipids, and nucleobases. A population of bacteria specific to the iron-deplete condition exhibited high anabolic activity yet low incorporation of newly fixed carbon, supporting a shift to consumption of compounds with longer residence times. From metagenome assembled genomes we identified candidate taxa and gene pathways responsible for this carbon processing shift. These results provide a mechanistic link between decreased carbon flow to bacteria under iron limitation and consumption of less labile exometabolites responsible for this decreased flow. This has implications for predicting organic matter composition and turnover in iron deplete surface oceans and manipulating algal-bacterial interactions in engineered systems.},
}

@article {pmid42949282,
year = {2026},
author = {Ivashin, D and Glascock, A and Lydon, EC and Langelier, CR},
title = {Near-complete genome sequence of a GII.P7-GII.7 norovirus from a 2026 California outbreak.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0098326},
doi = {10.1128/mra.00983-26},
pmid = {42949282},
issn = {2576-098X},
abstract = {We report a 7,456-bp near-complete norovirus GII.P7-GII.7 genome recovered by metagenomic RNA sequencing from a pediatric stool swab collected during a 2026 gastroenteritis outbreak in Northern California. The genome expands the public genomic record of norovirus diversity and is available under GenBank accession PZ705759.},
}

@article {pmid42949298,
year = {2026},
author = {Möbius, P and Wibberg, D},
title = {Complete genome sequence of Mycobacterium avium subsp. hominissuis strain Jp1289, isolated from a lymph node of a pig in Germany.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0103326},
doi = {10.1128/mra.01033-26},
pmid = {42949298},
issn = {2576-098X},
abstract = {Here, we provide the complete genome sequence of the Mycobacterium avium subsp. hominissuis strain Jp1289 isolated from an enlarged lymph node of a slaughtered pig in southern Germany. The strain has a 5,061,038 bp circular chromosome. Genome annotation predicted 4,081 coding genes and 59 RNA genes.},
}

@article {pmid42949848,
year = {2026},
author = {Arboleda, A and Joye, A and Goodman, D and Denny, MR and Doan, T and Seitzman, GD},
title = {False-Positive Acanthamoeba Keratitis From Multiplex Polymerase Chain Reaction Diagnostics, a Case Series.},
journal = {Cornea},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICO.0000000000004271},
pmid = {42949848},
issn = {1536-4798},
abstract = {PURPOSE: The purpose of this study was to describe a series of cases in which multiplex polymerase chain reaction (PCR) suggested false-positive Acanthamoeba keratitis (AK).

METHODS: Four patients without traditional risk factors for AK were referred after multiplex PCR (HealthTrackRx, Denton, TX) returned positive for Acanthamoeba. Clinical history, slitlamp examination, confocal microscopy, microbiologic cultures, viral PCR, and metagenomic deep sequencing (MDS) were reviewed. Clinical course and response to therapy were assessed.

RESULTS: Three patients had corneal involvement, and 1 had anterior scleritis without any corneal pathology. In all cases, corneal cultures were negative for Acanthamoeba. For the case with no corneal involvement, conjunctival culture was negative for Acanthamoeba. For all 4 cases, MDS was negative for Acanthamoeba. Two patients received a brief course of antiamoebic therapy, which was subsequently discontinued. The other 2 never received antiamoebic treatment. All patients recovered fully with therapy directed toward different underlying conditions. Final diagnoses included staphylococcal marginal keratitis, recurrent herpes simplex virus keratitis, undifferentiated anterior scleritis, and a chronic neurotrophic epithelial defect within a penetrating keratoplasty.

CONCLUSIONS: These cases illustrate the potential for false-positive multiplex PCR results for Acanthamoeba in patients without classic risk factors or expected clinical findings. Molecular diagnostic results should be interpreted alongside clinical assessment and adjunctive testing. Treating the patient rather than a single-test result remains essential in managing suspected AK.},
}

@article {pmid42949890,
year = {2026},
author = {Wang, H and Chang, X and Han, S and Guo, J and Xia, Z and Xiong, W},
title = {Multi-omics Integration Reveals L-arginine as a Key Mediator Linking Dietary Protein to Weight Change in Cats: An Exploratory Study.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag287},
pmid = {42949890},
issn = {1525-3163},
abstract = {Cats exhibit an insufficient endogenous capacity for arginine synthesis, making dietary protein a core factor in nitrogen homeostasis. In this study, we investigated whether protein level-induced body weight change is mediated by host-microbiome interactions and serum metabolites. A 180-day trial was conducted on 30 cats fed three isocaloric diets with varying crude protein levels (LP: 28%, MP: 36%, HP: 46%). Fecal shotgun metagenomic sequencing, serum short-chain fatty acid analysis, untargeted metabolomics, and targeted amino acid profiling were integrated and then subjected to causal mediation analysis. The HP diet improved protein digestibility (HP: 93.29% vs. LP: 89.36%, P = 0.027) and attenuated body weight loss (HP: -3.43% vs. -14.52%, P = 0.031) without compromising fecal scores (all groups: 2.5-3.0 throughout the trial) or intestinal barrier integrity, as indicated by unchanged serum DAO, D-LA, and LPS levels. The MP group significantly enhanced humoral immunity, as evidenced by higher serum IgA, IgG, and IgM concentrations (P < 0.05 vs. LP and HP), while the HP group boosted antioxidant capacity, with significantly increased SOD and T-AOC activities (P < 0.05 vs. LP and MP). High protein increased the abundance of Phocaeicola and decreased that of Megasphaera. Serum arginine biosynthesis pathways and branched-chain amino acids were significantly enriched in MP and HP groups compared with the LP group (P < 0.05 for both comparisons). Crucially, multi-omics network and causal mediation analysis identified L-arginine as a statistically confirmed key regulatory node in the protein-weight relationship, as evidenced by a significant indirect effect (ACME = 0.208, P = 0.006) and a non-significant direct effect (ADE = 0.31, P = 0.23). These results suggested that L-arginine may serve as a key regulatory node mediating this process linking dietary protein to body weight in cats, providing a novel mechanistic target for precision nutritional interventions in feline weight management.},
}

@article {pmid42949970,
year = {2026},
author = {Pigani, E and Simoens, K and Bernardi, D and Campese, L and Iudicone, D and Azaele, S and Suweis, S},
title = {Scaling laws link conserved gene-abundance distributions to adaptive expression in diatom communities worldwide.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {44},
pages = {e2615743123},
doi = {10.1073/pnas.2615743123},
pmid = {42949970},
issn = {1091-6490},
support = {862923//AtlantECO/ ; 101059915//Biocean5D/ ; C53D23003420001//NRRP/ ; C93C22002810006//NRRP/ ; 101082021//MARCO-BOLO/ ; },
mesh = {*Diatoms/genetics ; Ecosystem ; Oceans and Seas ; Transcriptome ; Metagenomics ; },
abstract = {Marine microbes sustain Earth's major biogeochemical cycles, yet how they maintain stable ecosystem functions across diverse environments remains unclear. We analyzed metagenomic and metatranscriptomic data from diatom communities sampled during the Tara Oceans global expedition. While gene abundance distributions remain statistically similar across sample, gene expression varies systematically across geographical locations, a global pattern we show reflects predictable scaling laws. Global distributions, scaling relationships, and variability among sampling stations are captured by a stochastic model linking gene abundance dynamics to gene expression. While colder waters are associated with higher transcriptional activity and warmer regions show more selective gene usage, we find that transcript abundance increases nonlinearly with transcript richness. This general scaling is captured by our model and suggests that diatom communities balance high expression of core genes with specific functional diversity. These scaling relationships hold consistently across ocean basins, with temperature, used as an effective large-scale environmental descriptor whose signature cannot be fully disentangled from spatial structure, sufficing to predict transcriptional patterns from genetic composition. Our findings reveal how the stability of gene-abundance structure in diatom ecosystems coexists with transcriptional variability, enabling flexible functional responses.},
}

*Diatoms/genetics
Ecosystem
Oceans and Seas
Transcriptome
Metagenomics

@article {pmid42950681,
year = {2026},
author = {Xie, T and Lin, D and Tong, SQ and Wang, Q and Ni, N and Wang, N and Yang, Z and Liu, XH and Zhu, D},
title = {Chiral antibiotics amplify the phage-associated antibiotic resistome in salinized soil.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144003},
doi = {10.1016/j.jhazmat.2026.144003},
pmid = {42950681},
issn = {1873-3336},
abstract = {Anthropogenic global change is intensifying antibiotic pollution and soil salinization, yet how salinity shapes bacteria-phage interactions to drive the dissemination of antibiotic resistance genes (ARGs) under chiral antibiotic pressure remains poorly understood. Using viral metagenomic analyses and laboratory validation, we show that salinity amplifies the enrichment of total and high-risk ARGs along gradients of racemic ofloxacin and its S-enantiomer levofloxacin, concomitant with the parallel accumulation of mobile genetic elements and virulence factors. High-concentration antibiotic treatment in saline soils selected for stress-tolerant, fast-growing antibiotic-resistant bacteria (ARBs) carrying abundant prophages and diverse defense systems, thereby promoting tight ARB-phage interactions. Under these dual extreme stresses, lysogenic phages were enriched, enhancing their carriage of ARGs, auxiliary metabolic genes (AMGs) that bolster host survival, and antidefense genes via a "piggyback-the-winner" strategy, thereby increasing ARG dissemination potential. Notably, high-concentration levofloxacin exerted stronger selective pressure than ofloxacin, increasing virus-to-host ratios and phage-associated ARG accumulation, as supported by incubation assays. Collectively, our findings support a mechanistic framework in which soil salinization interacts with chiral antibiotic exposure, particularly levofloxacin, to increase phage-associated ARG dissemination potential. This highlights a long-underappreciated, Anthropocene-driven pathway intensifying environmental resistance risks and posing new challenges for the One Health framework.},
}

@article {pmid42950786,
year = {2026},
author = {Li, MM and Liu, MC and Lv, AP and Ortúzar, M and OuYang, YT and Chen, LB and Chen, Y and Bian, BR and Yuan, Y and Gao, L and Liu, L and Jiao, JY and Li, WJ},
title = {Metagenome-assembled genomes reveal Labilithrix thermalis sp. nov., an uncultured microorganism in hot springs.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126780},
doi = {10.1016/j.syapm.2026.126780},
pmid = {42950786},
issn = {1618-0984},
abstract = {Geothermal environments harbor diverse microbial communities, including numerous phylogenetically novel lineages that remain largely unexplored. This study characterized two high quality metagenome assembled genomes (MAGs) from hot spring sediments in Yunnan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences indicated that the two MAGs (JZ-3_bin_45[TS] and QQ_bin_234) should be assigned to the genus Labilithrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two MAGs and other genomes of the genus Labilithrix were below the recommended species thresholds (95% and 70%, respectively), indicating that the two MAGs represent a novel species within the genus Labilithrix. Genome annotation suggested an aerobic, chemoheterotrophic, and motile lifestyle, with the genetic potential for oxidative phosphorylation, tricarboxylic acid (TCA) cycle, starch degradation, assimilatory sulfate reduction, arsenic detoxification, geothermal adaptation, and diverse biosynthetic gene clusters (BGCs). Based on genomic and phylogenetic analysis, these MAGs should be classified as a novel species within this genus, for which the name Labilithrix thermalis sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This study expands the known diversity of the genus Labilithrix and highlights the value of metagenomics for uncovering previously uncultivated microbial taxa and function.},
}

@article {pmid42950998,
year = {2026},
author = {Al-Joary, YIMA and Al-Mashhadany, ZZI and Al-Hamadany, MAM and Altai, ZMAAA and Moslawi, MAAA and Hasan, MYMHA and Almiemari, WMAH},
title = {Shotgun Metagenomic Profiling of Phlebotomus papatasi (Diptera: Psychodidae, Phlebotomine) in Zoonotic Cutaneous Leishmaniasis Endemic Foci of Iraq: Microbiota, Resistome, and Virulome.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108385},
doi = {10.1016/j.actatropica.2026.108385},
pmid = {42950998},
issn = {1873-6254},
abstract = {This study aims to develop a regional baseline for future individual-level and comparative studies of microbial ecology and symbiont-based vector control. Phlebotomus papatasi is a major vector of Leishmania major and an important component of the transmission cycle of zoonotic cutaneous leishmaniasis (ZCL) in Iraq, although the internal microbial communities of this vector are poorly characterised in the region. In this study, shotgun metagenomic sequencing was employed to investigate the microbial communities of a pooled sample of 129 blood-fed female Ph. papatasi collected from ZCL-endemic foci in Nineveh Governorate, Iraq, from 2024 to 2025. Approximately 32.9 million raw reads were obtained from sequencing, with the quality-filtered, host-removed, and low-diversity-filtered reads analysed for taxonomic and functional profiles. The data revealed a complex microbial community inside blood-fed Ph. papatasi dominated by bacteria. Moreover, several species of Proteobacteria in blood-fed Ph. papatasi were detected, which accounted for 98.32% of the classified reads, with Enterobacter cloacae as the most common species (74.34% of classified reads). Strains associated with Wolbachia were also detected (approximately 8.96% of classified reads). The microbial data further revealed the presence of genes associated with antimicrobial resistance including oqxA/oqxB-associated efflux and AmpC-type β-lactamase families, and virulence factors associated with motility, iron acquisition, and secretion systems. Nevertheless, the data represented the distribution of sequencing reads within the pooled sample (single sample), rather than the prevalence or average abundance among individual sand flies.},
}

@article {pmid42951153,
year = {2026},
author = {Zhou, L and Peng, L and Rousk, J and Deng, H and Mu, L and Wang, Z and Dai, W and Gao, M},
title = {Biochar-immobilised phosphate-solubilising bacteria enhance soil available phosphorus by affecting phosphorus fraction transformation and phosphorus-acquiring microbiota.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136141},
doi = {10.1016/j.biortech.2026.136141},
pmid = {42951153},
issn = {1873-2976},
abstract = {Phosphate-solubilising bacteria (PSB) play an important role in phosphorus (P) transformation and plant P uptake. However, their effectiveness is often limited by environmental instability and soil poor survival. Biochar has been proposed as a suitable carrier for microbial immobilisation; however, the effects of biochar-immobilised PSB on soil P fractions and the microbial mechanisms underlying P transformation remain unclear. In this study, we developed a biochar-immobilised PSB using Klebsiella sp. N107 and assessed its effects on soil P availability, P fraction transformation, and microbial processes regulating P cycling. A pot experiment was conducted: no fertilisation, conventional fertilisation (NPK), NPK + pristine biochar (NPKB), NPK + PSB (NPKP), and NPK + biochar-immobilised PSB (NPKBP). Soil properties, P fractions, organic acids, enzyme activities, and metagenomic characteristics were analysed. Compared with NPKB and NPKP, NPKBP enhanced plant P uptake and soil available P. It also increased labile P fractions, organic acid concentrations, and the activities of P acquiring enzymes. Genes associated with P transport (pit, ugpB, ugpQ, and ugpE), polyphosphate degradation (ppk1 and ppk2), organic P mineralisation (phoA and phoD), and inorganic P solubilisation (gcd, ppa, and ppx) were upregulated. P acquiring taxa, including Sphingomonas, Gaiella, and Bradyrhizobium, were enriched and contributed functionally to P cycling. Overall, biochar-immobilised PSB improved soil P availability by promoting P fraction transformation and restructuring microbial communities involved in P cycling. Soil pH, organic acids, and available nitrogen were identified as key drivers of these processes, highlighting the potential of biochar-immobilised PSB to improve soil P utilisation and management.},
}

@article {pmid42951945,
year = {2026},
author = {Park, H and Dhand, A},
title = {Beyond Blood Cultures and Echocardiography: Emerging Diagnostics for Infective Endocarditis.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
pmid = {42951945},
issn = {1538-4683},
abstract = {Management of infective endocarditis (IE) is often confounded by the presence of prosthetic valves, transcatheter prostheses, and cardiovascular implantable electronic devices, as well as by changing epidemiologic risks and antimicrobial resistance patterns. For the diagnosis of IE, blood cultures and echocardiography remain foundational, but important gaps persist, particularly in culture-negative and prosthetic/device-associated infections. Contemporary diagnostic criteria and guidelines now support a multimodality approach incorporating molecular microbiology and advanced imaging. This review summarizes emerging technologies including broad-range 16S/18S/28S rRNA polymerase chain reaction and sequencing, fluorescence in situ hybridization coupled with sequencing, targeted and shotgun metagenomic next-generation sequencing (mNGS), plasma microbial cell-free DNA, cardiac computed tomography, and 18F-fluorodeoxyglucose positron-emission tomography/computed tomography. We also examine the potential role of artificial intelligence in echocardiographic interpretation and of large language models in multimodal data integration. Current evidence suggests that tissue-based molecular testing generally provides greater microbiologic yield than valve culture in culture-negative IE, while blood-based mNGS and microbial cell-free DNA may extend pathogen detection after antibiotic exposure and reduce reliance on tissue-based diagnosis. However, heterogeneity in specimen handling, sequencing pipelines, contamination control, reporting thresholds, and clinical interpretation remains a major barrier to implementation. Future progress should move beyond pathogen detection toward rapid, reproducible, clinically actionable diagnosis that integrates organism identification, anatomic localization, disseminated disease, and personalized treatment. Prospective outcome trials, standardized workflows, cost-effectiveness studies, and multidisciplinary Endocarditis Team integration can help determine whether these technologies translate into better antimicrobial stewardship, procedural decision-making, and patient outcomes.},
}

@article {pmid42952710,
year = {2026},
author = {Ji, W and Tang, X and Liu, X and Su, W and Chai, W and Chen, K and Ge, J and Wang, B},
title = {Environment-dependent responses of soil physicochemical properties, microbial communities and functional gene profiles to protected and open-field cultivation of Stropharia rugosoannulata.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1912245},
pmid = {42952710},
issn = {1664-302X},
abstract = {The cultivation of Stropharia rugosoannulata involves substantial organic substrate input and fungal mycelial activity, which may influence soil nutrient transformation, microbial communities and functional gene profiles. However, whether these responses differ between protected and open-field cultivation settings remains unclear at the metagenomic level. In this study, four treatments were investigated: protected cultivation soil (NT), protected uncultivated soil (NK), open-field cultivation soil (ZT) and open-field uncultivated soil (ZK). Soil physicochemical properties, enzyme activities and shotgun metagenomes were analyzed to compare cultivation-associated soil responses under the two sampled cultivation settings. Protected cultivation showed more evident biochemical responses than open-field cultivation. Compared with NK, NT had significantly higher NH 4 + -N content and sucrase activity, together with lower soil salinity and electrical conductivity, whereas no significant differences in the measured soil properties were detected between ZT and ZK. Exploratory two-way ANOVA indicated setting-associated variation in several soil variables and significant interaction effects for NH 4 + -N and NO 3 - -N. Metagenomic analysis showed treatment-associated variation in specific classified genera, with Cellvibrio and Flavobacterium showing higher relative abundances in cultivated soils. However, PERMANOVA did not detect significant separation in the overall genus-level community structure. KEGG functional profiles remained broadly stable across treatments, although protected cultivation showed more evident variation in selected functional categories. Antibiotic resistance gene profiles also exhibited treatment-specific patterns. Overall, S. rugosoannulata cultivation did not induce uniform microbial community restructuring or consistent soil improvement, but was associated with context-dependent responses in soil biochemical properties, specific microbial taxa, functional potential and resistome composition. These findings provide metagenomic insights for soil health management and resistome monitoring in continuous edible mushroom cultivation systems.},
}

@article {pmid42952836,
year = {2026},
author = {Bidzhieva, SK and Tourova, TP and Grouzdev, DS and Soloveva, SR and Sokolova, DS and Tereshina, VM and Poltaraus, AB and Mardanov, AV and Nazina, TN},
title = {Phenotypic and genomic characterization of a halophilic sulfate-reducing bacterium Desulfoplanes aerotolerans sp. nov. from a petroleum reservoir and its possible implication in pipeline corrosion.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1968038},
pmid = {42952836},
issn = {1664-302X},
abstract = {INTRODUCTION: The issue of biogenic corrosion of steel equipment is especially pressing for petroleum reservoirs with high-salinity formation water containing sulfate. The predominance of sulfate-reducing bacteria of the genus Desulfoplanes in formation water samples from petroleum reservoirs in Tatarstan (Russia) was previously demonstrated using 16S rRNA gene amplicon sequencing and metagenomic analysis. The present study is devoted to the isolation, phenotypic and genomic characterization of the sulfate-reducing bacterial strain Desulfoplanes sp. PS50[T] and its involvement in steel corrosion. Studying the composition of sulfidogenic prokaryotes and their corrosion activity is necessary in order to find a way to suppress their growth and minimize corrosion of oilfield equipment.

METHODS: A new sulfate-reducing bacterial strain Desulfoplanes sp. PS50[T] was studied using polyphase taxonomy approaches, including genome sequencing and functional annotation. The ability to cause corrosion of the steel coupon and the effect of three biocides on the growth of the strain were tested.

RESULTS: Sulfate-reducing strain Desulfoplanes sp. PS50[T] isolated from an Arkhangelskoe petroleum reservoir (Tatarstan, Russia) was phenotypically characterized. The optimal growth of the strain PS50[T] was observed at a temperature of 25-30 °C, in the presence of 40-50 g NaCl·L[-1] and at pH 7.5. The strain utilized formate, lactate, yeast extract, and H2/CO2/acetate as carbon and energy sources for reduction of sulfate to sulfide. The strain exhibited both anaerobic and microaerophilic growth (in the presence of 5% O2 (v/v). Based on physiological features and genomic and phylogenomic analyses, strain PS50[T] (=VKM B-4014[T] = KCTC 35101[T]) has been assigned to a new species, Desulfoplanes aerotolerans sp. nov. Genomic analysis revealed genes of sulfate reduction, hydrogenase, and iron uptake, which confirms the strain's ability to participate in the steel biocorrosion. The genome also contains the genes that determine the main metabolic pathways and the strain's adaptation to the high-salinity conditions of its habitat.

DISCUSSION: This study provides experimental proofs on the ability of sulfate-reducing bacteria of the genus Desulfoplanes to participate in general and pitting corrosion, confirmed by deep genome-resolved detection of corrosion-determining genes.},
}

@article {pmid42952981,
year = {2026},
author = {Tyagi, A and Rajput, M and Mishra, S},
title = {One health perspectives on pharmaceutical and clinical effluents driving multidrug resistance in aquatic ecosystems: a comprehensive review.},
journal = {Frontiers in systems biology},
volume = {6},
number = {},
pages = {1890380},
pmid = {42952981},
issn = {2674-0702},
abstract = {Antimicrobial resistance (AMR) has emerged as one of the most pressing global health challenges, yet the contribution of environmental reservoirs to the spread of multidrug resistance (MDR) remains insufficiently integrated into mainstream discussions. This systematic review synthesizes evidence from 167 peer-reviewed studies published between 2000 and 2026 to examine how pharmaceutical manufacturing effluents and clinical waste drive the dissemination of antibiotic resistance genes (ARGs) and multidrug-resistant bacteria in aquatic ecosystems. The literature was systematically identified and selected from major scientific databases using predefined inclusion and exclusion criteria. The reviewed evidence consistently shows that aquatic environments receiving inadequately treated pharmaceutical and healthcare waste which creates environmental hotspots characterized by elevated antibiotic residues, mobile genetic elements, and resistant microbial communities. Sub-inhibitory antibiotic concentrations, biofilm-mediated horizontal gene transfer and quorum-sensing dynamics collectively accelerate resistance gene dissemination beyond what direct selective killing alone would predict. Heavy metals, including copper, zinc, mercury, cadmium, and arsenic, further reinforce resistance through co-selection mechanisms, sustaining clinically important determinants such as blaNDM-1, blaKPC, and mcr-1 even in environments with limited antibiotic exposure. The review also highlights the role of non-pathogenic environmental bacteria as genetic reservoirs that facilitate the movement of resistance traits into pathogenic microorganisms. Metagenomic evidence confirms bidirectional exchange of resistance determinants between environmental and clinical bacterial populations, firmly situating the environmental resistome within a One Health framework. Despite growing evidence, important knowledge gaps remain regarding environmental-to-clinical transmission pathways, long-term ecological impacts, and the effectiveness of current mitigation strategies under diverse environmental conditions. Future research should prioritize longitudinal surveillance, multi-omics and systems biology approaches, metagenomic resistome profiling, and machine-learning-based predictive frameworks to better understand resistance dynamics across interconnected ecosystems. The findings support the integration of ARG monitoring into environmental management programs and underscore the need for advanced wastewater treatment technologies, harmonized discharge regulations, and coordinated One Health policies to curb the environmental amplification of antimicrobial resistance. These insights also contribute directly to achieving multiple Sustainable Development Goals, particularly SDG 1, 2, 3, 6, 9, 12, and 17 by fostering sustainable and integrated approaches to AMR mitigation.},
}

@article {pmid42952990,
year = {2026},
author = {Zhao, R and Na, H and Miao, W and Liu, L and Zhang, J and Miao, Y and Zhao, Y and Li, X},
title = {Comparative evaluation of metagenomic and targeted next-generation sequencing for pathogen detection in bronchoalveolar lavage fluid from patients with lower respiratory tract infections: a retrospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1877320},
pmid = {42952990},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Aged ; Sensitivity and Specificity ; Adult ; Bacteria/genetics/isolation & purification/classification ; },
abstract = {BACKGROUND: Rapid and precise pathogen identification is crucial for managing lower respiratory tract infections (LRTIs). While metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) are emerging as valuable diagnostic tools, large-scale studies directly evaluating their real-world impact on antimicrobial stewardship remain scarce.

METHODS: We conducted a retrospective cohort study encompassing 941 patients with suspected LRTIs who underwent bronchoalveolar lavage fluid (BALF) sequencing. Patients were evaluated in either an mNGS cohort (n = 479; DNA-only sequencing) or a tNGS cohort (n = 462; DNA and RNA sequencing). Diagnostic performance, pathogen spectrum, and clinical utility were compared against a composite final clinical diagnosis, which served as the reference standard.

RESULTS: Both sequencing platforms demonstrated diagnostic efficacy superior to traditional laboratory tests. In the tNGS cohort, polymicrobial infections were highly prevalent (93.5%). Furthermore, tNGS demonstrated high sensitivity for fastidious pathogens, identifying 54 cases of Mycobacterium tuberculosis (a cohort in which routine smears missed 77.8% of cases) and effectively detecting Pneumocystis jirovecii. The overall diagnostic sensitivity was 90.6% (95% CI: 87.5-93.1%) for mNGS and 73.4% (95% CI:69.2%-77.3%) for tNGS. Guided by tNGS results, clinicians escalated antimicrobial therapy in 22.6% of positive cases. The clinical improvement rate following this targeted escalation was 66.2%, comparable to the 66.7% improvement rate observed in patients receiving appropriate initial empirical therapy (P = 0.946).

CONCLUSION: Both tNGS and mNGS offer substantial diagnostic value for LRTIs, with tNGS showing particular utility in identifying fastidious and low-titer pathogens. Sequencing-guided diagnostics frequently informed antimicrobial adjustments and were associated with favorable clinical progress; however, future prospective paired-testing studies are required to isolate the direct impact of sequencing on patient survival outcomes.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology
Retrospective Studies
*Respiratory Tract Infections/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Female
Male
Middle Aged
Aged
Sensitivity and Specificity
Adult
Bacteria/genetics/isolation & purification/classification

@article {pmid42953187,
year = {2026},
author = {Di Bartolo, I and Sebastiano, M and Vaccari, G and Suffredini, E and Boni, A and Costantini, D and De Sabato, L},
title = {Metagenomic characterization of microbial communities associated with alphaherpesvirinae detection in magnificent frigatebirds from French Guiana.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1866497},
pmid = {42953187},
issn = {2297-1769},
abstract = {INTRODUCTION: A population of Magnificent Frigatebirds (Fregata magnificens, Suliformes) inhabiting French Guiana has been under investigation since 2005 due to high chick mortality rates associated with nodular proliferative skin lesions, characterized by featherless areas on the body. An initial study conducted in 2009 reported the presence of an alphaherpesvirus detected in a crust from a single individual in the same frigatebird population. However, the cause of the outbreaks and the associated high mortality in the frigatebird population remained undetermined.

METHODS: Almost 15 years later, in 2024, we collected beak swabs, cloacal swabs, and blood samples from 14 animals. Six animals were clinically healthy, while eight showed clinical signs including skin crusts, hyperkeratosis on the eyes, corneal thickening, and signs of distress. To investigate the potential causes of those signs, we screened the samples for herpesviruses. To characterize bacterial and viral communities and investigate potential co-infections, we selected four beak swabs for metagenomic analysis: two from herpesvirus-positive individuals and two from herpesvirus-negative controls (one healthy and one with clinical signs), and sequenced them using metagenomic Next Generation Sequencing (NGS).

RESULTS AND DISCUSSION: Two individuals tested positive for herpesviruses in beak swabs, one healthy and one with clinical signs. Analysis of the bacterial community revealed that the most abundant phyla were Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Fusobacteria, which typically inhabit the gut microbiota. All reported bacterial phyla were detected in every sequenced sample. At the viral level, among non-bacteriophage viruses, Orthoherpesviridae showed the highest abundance in PCR-positive animals, followed by Adenoviridae- and Hepadnaviridae-related sequences. Sequence analysis of the DNA-directed DNA polymerase (DdDp) region of Orthoherpesviridae identified two sequences: one with 98.1% nucleotide identity to sequences reported in the same geographic area in 2005, and the other with 72.1% identity to a vulture herpesvirus from India. The bacterial and viral populations detected were largely similar between animals with and without clinical signs. Due to the limited sample size, it was not possible to determine whether the detected microorganisms were associated with the observed clinical signs.},
}

@article {pmid42953211,
year = {2026},
author = {Manrique, EI and Sciglitano, L and Ortega-Santos, CP},
title = {Gut microbiome and gut-derived metabolites to identify the transition from metabolically healthy to unhealthy obesity: a mini review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1989174},
pmid = {42953211},
issn = {2296-861X},
abstract = {Obesity is a metabolically heterogeneous condition with distinct metabolic phenotypes, ranging from metabolically healthy obesity (MHO) to metabolically unhealthy obesity (MUO). Although individuals with MHO initially lack cardiometabolic dysfunction, many transition to MUO over time, exponentially increasing their risk for type 2 diabetes and cardiovascular disease. In this mini-review, we synthesize recent evidence from multi-omic cohort studies evaluating gut microbiome composition and gut-derived metabolites as functional biomarkers of obesity heterogeneity and drivers of metabolic decline. While microbial diversity yields inconsistent signatures across cohorts, MHO is generally characterized by higher relative abundance of Ruminococcaceae, Oscillospira, Akkermansia, and Bifidobacterium and enrichment of other taxa predicted to be short-chain fatty acid-producers. Conversely, circulating gut-derived metabolomic signatures including altered secondary bile acid pools, elevated branched-chain amino acids, and trimethylamine N-oxide more reliably discriminate MUO from MHO than traditional measures, and correlate strongly with visceral adiposity, insulin resistance, and systemic inflammation. Furthermore, new systems biology approaches, such as integrating high-dimensional metagenomics and metabolomics via machine learning models, offer a potentially superior early indicators tool in precision medicine for identifying obesity phenotypes compared with traditional metrics (e.g., body mass index, fasting glucose). Overall, current evidence remains predominantly cross-sectional and based on secondary analyses of large cohort studies, underscoring the need for prospective longitudinal studies to validate these multi-omic biomarkers for precise phenotype identification and clinical risk assessment.},
}

@article {pmid42953364,
year = {2026},
author = {Liu, L and Kong, F and Li, J and Wang, J and Li, W and Jiang, Y and Liu, L and Qin, X},
title = {Cryptococcal meningitis-associated cerebrovascular injury presenting with sequential multifocal cerebral infarctions and prominent autonomic dysfunction in a non-HIV patient: a case report and focused literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1970390},
pmid = {42953364},
issn = {2296-858X},
abstract = {Cryptococcal meningitis (CM) can occur in patients without human immunodeficiency virus (HIV) infection and may be complicated by genuine cerebral infarction, creating a powerful diagnostic anchor toward primary cerebrovascular disease. We report a 66-year-old non-HIV man with type 2 diabetes mellitus and no documented major immunosuppressive condition who initially presented with dizziness and mild headache. Brain MRI showed restricted diffusion in the left brainstem, and acute ischemic stroke was diagnosed. Over the following weeks, neurological deterioration continued despite stroke-directed treatment. Repeat MRI demonstrated new infarctions involving the left cerebellar vermis, corpus callosum, and left thalamus, while the patient developed rapid cognitive decline and prominent autonomic manifestations, including orthostatic hypotension, urinary retention, constipation, vomiting, and severe sleep disturbance. Cerebrospinal fluid (CSF) examination revealed an opening pressure >300 mmH2O, leukocytes 128 × 10[6]/L, protein 964 mg/L, and glucose 1.28 mmol/L. India ink staining was suspiciously positive, and Cryptococcus neoformans was confirmed by fungal culture and metagenomic next-generation sequencing. Serial lumbar punctures and antifungal treatment with amphotericin B and fluconazole were followed by substantial clinical improvement. To contextualize the case, we conducted a focused review of published non-HIV or apparently immunocompetent reports of CM-associated cerebral infarction. The literature shows a recurring pattern of deep perforator, brainstem, cerebellar, callosal, and multifocal ischemic injury, with both small- and large-vessel mechanisms reported. However, sequential infarctions across multiple territories accompanied by a prominent progressive autonomic syndrome remain poorly documented. This case supports early CSF investigation when recurrent infarction, encephalopathic progression, and multisystem neurological features are discordant with an isolated vascular diagnosis.},
}

@article {pmid42953614,
year = {2026},
author = {Liu, Y and Bian, X and Wang, H and Tang, D},
title = {Metagenomic Next-Generation Sequencing Enhances Pathogen Detection and Prognostic Stratification in Hematopoietic Stem Cell Transplantation Recipients.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {617255},
pmid = {42953614},
issn = {1178-6973},
abstract = {BACKGROUND: As an emerging detection technique, metagenomic next-generation sequencing (mNGS) provides superior genomic resolution and enhances detection precision relative to conventional pathogen detection methods. Patients with malignant hematological disorders are susceptible to infections following hematopoietic stem cell transplantation (HSCT). mNGS demonstrates a significantly higher positivity rate compared with conventional testing.

METHODS: A total of 100 patients who had undergone HSCT were retrospectively enrolled in this study. The detection rates and patient mortality rates associated with conventional diagnostic methods and mNGS were analyzed and compared. Additionally, the impact of mNGS results on the adjustment of antibacterial therapy was investigated, and the receiver operating characteristic (ROC) curve was utilized to assess the predictive value of mNGS for mortality.

RESULTS: mNGS detected pathogens in 81% of patients (viruses 71.0%, with herpes simplex virus type 1 [HSV-1] at 26.7%; bacteria 25.0%, predominantly Enterobacteriaceae at 61.5%), outperforming conventional testing (P < 0.001). The results indicated that C-reactive protein (CRP), age, length of hospital stay, transplantation modality, and granulocyte reconstitution time were independent predictors of mNGS-only positive results (P < 0.05). Antibiotic adjustment strategies aligned with mNGS findings were implemented in 59% of patients. The area under the curve (AUC) values for procalcitonin (PCT), CRP, granulocyte reconstitution time, megakaryocyte reconstitution time, and mNGS positivity alone in predicting mortality were 0.657, 0.756, 0.743, 0.724, and 0.539, respectively. The combined AUC of these five indicators was 0.812 (95% CI: 0.694-0.929).

CONCLUSION: Compared with conventional methods, mNGS has a broader pathogen detection spectrum, which may improve the overall detection rate of unknown, uncommon, and mixed infectious pathogens. The selection of diagnostic modalities may be guided by patient-specific factors including CRP levels, age, length of hospital stay, transplantation modality, and granulocyte reconstitution time. mNGS informs antibiotic adjustment, while combined biomarkers (AUC = 0.812) provide prognostic value.},
}

@article {pmid42953986,
year = {2026},
author = {Shum-Tim, C and Islam, P and Boyajian, JL and Abosalha, A and Kassab, A and Santos, M and Khan, KA and Stern, K and Emad, A and Prakash, S},
title = {Artificial Intelligence-Driven Graph Methods for Microbiome Research: A Systematic Review.},
journal = {WIREs mechanisms of disease},
volume = {18},
number = {6},
pages = {},
doi = {10.1002/wsbm.70016},
pmid = {42953986},
issn = {2692-9368},
support = {252743//Canadian Institute of Health Research/ ; 335999//Fonds de Recherche du Québec-Santé/ ; 351337//Fonds de Recherche du Québec-Santé/ ; 2020-245622//Islamic Development Bank Scholarship/ ; //Ministry of Higher Education of the Arab Republic of Egypt/ ; 504933//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {*Microbiota/genetics ; *Artificial Intelligence ; Humans ; Animals ; },
abstract = {The complexity of high-throughput sequencing data in microbiome research necessitates advanced analytical methods to decipher microbial community structures and interactions. Graph-based methods, which model taxa as nodes and their relationships as edges, have emerged as a powerful framework for this purpose. However, the rapid evolution of these techniques, from classical network analysis to modern graph representation learning, has created a fragmented and complex methodological landscape. This systematic review provides a comprehensive synthesis and structured overview of the field. We systematically review the literature and propose a three-part classification to categorize the primary contribution of each study: (1) novel methods for microbial network representation, (2) applications of classical graph analysis, and (3) the emerging use of graph representation learning for predictive modeling. We summarize the most frequent applications within each class, including keystone species identification, community clustering, and graph-based disease classification. Furthermore, we identify critical cross-cutting challenges, such as the lack of standardized tools and the need for improved model interpretability. By structuring the current landscape of graph-based methods, this review serves as a crucial guide for researchers to select appropriate models and highlights key gaps to direct future research.},
}

*Microbiota/genetics
*Artificial Intelligence
Humans
Animals

@article {pmid42954463,
year = {2026},
author = {Wozniak, KJ and Corver, J and Kuijper, EJ and Smits, WK and Britton, RA},
title = {Genome sequence of Clostridioides difficile PRB1128, a RT023 strain containing a mobile genetic element allowing for xylitol utilization.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0090726},
doi = {10.1128/mra.00907-26},
pmid = {42954463},
issn = {2576-098X},
abstract = {Clade 3 strains of Clostridioides difficile, dominated by PCR ribotype 023 (RT023) strains, remain the least well studied in the phylogeny. We sequenced a strain of RT023 C. difficile (PRB1128) to gain molecular genetic insights and add to the limited repository of RT023 genomes in existence.},
}

@article {pmid42954465,
year = {2026},
author = {Pan, X and Chen, X and Xie, H and Zhang, Y and Dai, Y and Yuan, C and Kong, F and Luo, F},
title = {From saccharides to methane: substrate-driven microbial diversity and methanogenesis in anaerobic digestion revealed by 390 MAGs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0285426},
doi = {10.1128/spectrum.02854-26},
pmid = {42954465},
issn = {2165-0497},
abstract = {UNLABELLED: Anaerobic digestion (AD) is a key technology for organic waste treatment and renewable energy production, yet its microbial processes remain poorly understood. This study employed genome-centric metagenomics to investigate synthetic AD systems fed with five substrates: starch, glucose, butyrate, propionate-valerate, and acetate. A total of 390 high-quality metagenome-assembled genomes (MAGs) were reconstructed, 64.36% of which represent potentially novel species. Substrate-driven selection shaped distinct functional consortia, with Bifidobacterium enriched in starch hydrolysis and Syntrophomonas enriched in butyrate oxidation. A complete set of acetoclastic methanogenesis-associated genes was identified in a bacterial MAG (Armatimonadota UBA5829). A complete CO2 reduction pathway was also identified in Methanothrix soehngenii. Glycine cleavage systems were prevalent in high-abundance MAGs, while key Wood-Ljungdahl pathway enzymes were absent. These findings provide genomic insights into substrate-driven assembly and methanogenic pathway distribution in synthetic AD systems.

IMPORTANCE: Anaerobic digestion is a key technology for converting organic waste into renewable energy, yet the microbial processes underlying its efficiency remain largely hidden. By reconstructing 390 microbial genomes from digestion systems fed with different sugar-derived substrates, this study unveils how specific substrates shape microbial communities and reveals unexpected metabolic pathways for methane production. These findings challenge long-standing assumptions about which organisms perform key steps in the process, provide a valuable genomic resource for the field, and offer concrete targets for improving waste-to-energy systems through microbiome engineering.},
}

@article {pmid42954466,
year = {2026},
author = {Liu, J and Li, W and Qi, M and Zhao, J and Wu, J and Wang, Y and Yang, Y and Song, X},
title = {Gut microbiome and metabolomics reveal the role of thioproline in attenuating colorectal cancer-associated inflammation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0054826},
doi = {10.1128/msystems.00548-26},
pmid = {42954466},
issn = {2379-5077},
abstract = {Colorectal cancer (CRC) is one of the top three cancers globally in terms of both incidence and mortality, and its development may be influenced by an inflammatory environment in the intestines, often associated with gut microbiota dysbiosis. Food bioactives could modulate gut microbiota through anti-inflammatory and epigenetic mechanisms. Given the significant role of thioproline as a food bioactive with antioxidant properties, its potential to modulate gut microbiota and mitigate CRC remains largely unexplored. This study aims to understand the effects of thioproline on gut microbiota community and investigate the mechanisms through which thioproline regulates gut microbiota and exerts its anticancer effects. Fecal and intestinal tissue samples were collected from health, CRC, and thioproline-treated CRC mice. The metagenome and metabolome data revealed that thioproline treatment significantly altered the gut microbiota community composition and metabolism in CRC mice. These CRC-associated gut microbiota and bacterial metabolites returned to normal levels. Moreover, under thioproline treatment, the microbial-metabolite interactions in CRC mice shifted toward patterns more closely resembling those observed in healthy mice. Thioproline treatment increased linoleic acid levels in mice, indicating its role in promoting linoleic acid metabolism to therapeutically restore homeostasis and alleviate inflammation in CRC. This was further supported by hematoxylin and eosin staining, which demonstrated that thioproline alleviated inflammation in CRC mice. Our study highlights thioproline's dual role in regulating the gut microbiota community and bacterial metabolism, modulating bacteria-host interactions, and ultimately reducing inflammation in CRC. These findings offer valuable insights for future research and therapeutic applications.IMPORTANCEColorectal cancer (CRC) is associated with gut microbiota dysbiosis and intestinal inflammation. While food bioactives can modulate the microbiome, whether thioproline exerts inhibitory effects against CRC through microbial regulation remains unknown. Using integrated metagenomics and metabolomics, we show that thioproline treatment restores the gut microbiota composition and bacterial metabolites disrupted by CRC to near-normal levels. Importantly, thioproline remodels microbial metabolite interaction networks, elevates linoleic acid levels, and alleviates intestinal inflammation. This study provides a systems-level perspective on how a single dietary bioactive compound reshapes the gut microbial ecosystem and its metabolic landscape to reduce inflammation in CRC. Our findings suggest a potential role for microbiome-targeted nutritional strategies in protecting against CRC progression through modulation of the gut microbiota and intestinal microenvironment.},
}

@article {pmid42954653,
year = {2026},
author = {Busturia, I and Martín-Cardoso, H and Domingo, C and Garcia-Molina, A and San Segundo, B},
title = {Decoding microbial diversity in roots of rice plants under flooded conditions: influence of the host genotype, root compartment, and mycorrhizal association.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0167126},
doi = {10.1128/aem.01671-26},
pmid = {42954653},
issn = {1098-5336},
abstract = {UNLABELLED: Rice is a vital staple for more than half of the world's population, uniquely adapted to grow under flooded conditions. Our current understanding of root-associated microbiomes in rice plants under flooded conditions (anaerobic rice) is, however, limited. While rice plants are capable of establishing symbiotic associations with arbuscular mycorrhizal (AM) fungi, also under flooded conditions, little is known about the impact that mycorrhizal associations might have on the root microbiome. Here, we used metagenomic sequencing to characterize the root-associated microbiomes of cultivated rice grown under flooded conditions. The root endosphere and rhizosphere compartments were found to harbor distinct microbial communities, with bacterial taxa comprising approximately 95% of the total microbial community. At the phylum level, the root bacteriome was primarily composed of Pseudomonadota (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria), followed by Actinomycetota. The fungal microbiome was dominated by Ascomycota (Sordariomycetes, Eurotiomycetes, and Dothideomycetes) and Basidiomycota. Both root compartment and host genotype significantly influenced microbiome composition, with most genotype-specific recruitment occurring at the species level. These associations were further reshaped in plants pre-inoculated with the AM fungus Rhizophagus irregularis. Co-occurrence networks revealed a genotype-dependent effect in the complexity of microbial taxa in mycorrhizal rice plants. Key microbial species primarily involved in methane production and nutrient cycling (e.g., phosphate-solubilizing bacteria and nitrogen-cycling bacteria) residing in roots of flooded rice were identified. Functional analysis of gene abundance related to those microbial communities revealed compartmentalization, with nutrient-cycling bacteria being more prevalent at the endosphere. Overall, this study demonstrated that the rice genotype, root compartment, and mycorrhizal condition shape the root microbiome in rice plants, ultimately influencing holobiont dynamics in flooded rice fields.

IMPORTANCE: Plant roots harbor a large diversity of microorganisms that strongly influence plant health and improve stress tolerance. Among them, root colonization by arbuscular mycorrhizal (AM) fungi enhances mineral nutrition and mitigates environmental stress. Although most rice cultivated worldwide is grown under anaerobic conditions (flooded fields), investigation of microbial communities inhabiting root-associated compartments of flooded rice, including AM fungi, has received only little attention. Here, we demonstrated that the rice genotype, root compartment, and mycorrhizal condition markedly influence the microbiome in roots of rice plants in flooded conditions, thus illustrating the potential of the rice plant to shape its root-associated microbiome. Differential root-associated microbiomes of commercial rice varieties include microbes primarily associated with methane production and nutrient cycling. Elucidation of factors influencing root-associated microbiomes in flooded rice systems, including their association with AM fungi, offers practical guidance for exploiting root-associated microbial communities for sustainable rice cultivation while reducing reliance on agrochemicals.},
}

@article {pmid42945246,
year = {2026},
author = {Wang, Y and Qu, G and Huang, ZYX and Zhang, X and Li, H and Wei, X and Hu, L and Xu, S and Becker, DJ and Wei, F and Xu, Y},
title = {Viral metagenomics reveals heterogeneity in mammalian virus hosting, sharing, and spillover.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {44},
pages = {e2610672123},
doi = {10.1073/pnas.2610672123},
pmid = {42945246},
issn = {1091-6490},
mesh = {Animals ; *Metagenomics/methods ; Humans ; *Mammals/virology ; Phylogeny ; Zoonoses/virology ; *Virome/genetics ; *Viruses/genetics/classification ; Chiroptera/virology ; },
abstract = {Zoonotic viruses originating from mammals pose a persistent threat to global health. While rodents and bats are often considered "special reservoirs," it is debated if spillover risk is driven by specific taxa or merely reflects mammalian species richness. However, most tests have focused on published host-virus association datasets, which can reflect systematic biases in host and virus sampling effort. To address this limitation, we analyzed a comprehensive repository of 4,685 metagenomic datasets, minimizing bias toward any one viral taxon and spanning 296 species across 14 mammalian orders. We characterized the global mammalian virome and found substantial heterogeneity in the capacity of different mammalian orders to harbor and share human-associated viruses. Counter to conventional wisdom, carnivores exhibited significantly higher propensities to carry human-associated viruses, with bats ranked lower in this metric of zoonotic risk. Network analyses of viral sharing further revealed higher cross-order virus sharing among specific mammalian orders (e.g., carnivores and artiodactyls). Phylogenetic comparative analyses revealed that host life-history traits (e.g., longevity) and anthropogenic factors (e.g., urban land use) were key ecological drivers of both virus richness and transmission centrality. Our study provides a data-driven framework that challenges prevailing narratives of zoonotic risk and offers a refined strategy for prioritizing surveillance and mitigating emerging zoonotic threats.},
}

Animals
*Metagenomics/methods
Humans
*Mammals/virology
Phylogeny
Zoonoses/virology
*Virome/genetics
*Viruses/genetics/classification
Chiroptera/virology

@article {pmid42945300,
year = {2026},
author = {Andrade, B and Ramírez, M and Reyes, G},
title = {Microbial community structure of Penaeus vannamei post-larvae naturally infected with multiple viruses in hatchery tanks.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0361576},
pmid = {42945300},
issn = {1932-6203},
mesh = {Animals ; *Penaeidae/virology/microbiology ; Larva/virology/microbiology ; Aquaculture ; *Microbiota ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This study offers an observational evaluation of how viral and bacterial infections co-occur with alterations in the microbiome and survival of Penaeus vannamei post-larvae, one of the most economically important species in global aquaculture.

METHODS: Eleven commercial larval production tanks were classified into three distinct infection scenarios using histology and PCR: Baculovirus penaei (BP) monoinfection, mixed infections (BP, white spot syndrome virus [WSSV], and acute hepatopancreatic necrosis disease [AHPND]-causing bacteria), and non-infected controls. High-molecular-weight DNA was subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform, followed by evaluation of microbial diversity, community structure, and infection-associated microbial signatures.

RESULTS: Although BP was the most abundant viral genus across infected groups, severe mortality was observed only under mixed-infection conditions, which were closely associated with AHPND-causing bacteria presence and microbiome disruption rather than with BP alone. Deep metagenomic sequencing revealed reduced, distinct microbiome structures in shrimp infected with BP and in those with mixed infections, compared to non-infected individuals. Non-infected post-larvae maintained complex and well-balanced bacterial communities, predominantly composed of Donghicola and Muricauda. Nudiviridae and Oscillospiraceae showed comparable relative abundances in BP-only and mixed-infection groups. In contrast, mixed infections were characterized by a relative increase in Vibrio, together with the PCR-detection of PirAB toxin genes, whereas WSSV remained detectable in the metagenomic dataset despite its comparatively low relative abundance, while the infection remained thermally suppressed and asymptomatic in the larvae. Functionally, infected larval microbiomes were enriched for transposases, retrotransposons, and virulence-factor genes. The near-complete BP-GR25 genome (119,245 bp) was assembled and annotated from larval metagenomes.

CONCLUSION: These results highlight the value of high-throughput sequencing in the early detection of pathogens in aquaculture, where subtle microbial shifts during postlarval stages can be valuable indicators of health status for production.},
}

Animals
*Penaeidae/virology/microbiology
Larva/virology/microbiology
Aquaculture
*Microbiota
Metagenomics
Metagenome

@article {pmid42945345,
year = {2026},
author = {Zang, C and Tang, L and Deek, RA},
title = {Supervised and covariate-adjusted dimension reduction for prediction and visualization using microbiome data.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
pmid = {42945345},
issn = {1477-4054},
support = {R56LM014522/LM/NLM NIH HHS/United States ; S10OD028483/OD/NIH HHS/United States ; //University of Pittsburgh's CTSI Trans-disciplinary Collaboration Pilot Award/ ; RRID:SCR_022735//University of Pittsburgh Center for Research Computing and Data/ ; },
mesh = {Humans ; Principal Component Analysis ; Algorithms ; *Microbiota ; Dimensionality Reduction ; *Gastrointestinal Microbiome ; *Computational Biology/methods ; Prediction Algorithms ; },
abstract = {Given that the gut microbiome has been shown to play a critical role in human health, discerning the relationship between microbial taxa and disease outcomes or phenotypes is of interest. Often, this involves association testing, predictive modeling, and visualizing trends in the data. Principal coordinates analysis (PCoA) is a commonly used dimension reduction technique in microbiome studies. PCoA relies on pairwise distances between samples and serves as a nonlinear alternative to the classic principal component analysis when non-Euclidean distances are used. Its low-dimensional embeddings provide intuitive visualizations but do not incorporate outcome-related information. Therefore, the low-dimensional principal coordinates may have poor performance in visualizing outcome differences, as well as in downstream disease prediction tasks. Additionally, covariates, such as demographics, lifestyle factors, and technical artifacts, can obscure true biological signals, leading to masked or spurious associations and limited generalizability. To address these limitations, we propose a supervised and covariate adjusted PCoA algorithm. By utilizing outcome information, while simultaneously minimizing the influence of nuisance variables, our method produces low-dimensional embeddings that better separate disease outcomes in visualizations and result in improved accuracy in downstream regression and classification tasks. We demonstrate the effectiveness of the proposed method and highlight its ability to extract important associations between the microbiome and disease outcomes while mitigating nuisance variation through simulations and application to real microbiome profiling studies.},
}

Humans
Principal Component Analysis
Algorithms
*Microbiota
Dimensionality Reduction
*Gastrointestinal Microbiome
*Computational Biology/methods
Prediction Algorithms

@article {pmid42945621,
year = {2026},
author = {Brîncuș, AV and Angebault, C and Wesner, N and Leonard-Louis, S and Le Joncour, A and Blandin, C and Richette, P and Poirier, P and Benveniste, O and Rodriguez, C and Botterel, F and Allenbach, Y},
title = {Pathogen identification by shotgun metagenomics in inflammatory myopathies: a prospective observational study reporting the first European case of Anncaliia algerae myositis.},
journal = {Neuromuscular disorders : NMD},
volume = {69},
number = {},
pages = {107458},
doi = {10.1016/j.nmd.2026.107458},
pmid = {42945621},
issn = {1873-2364},
abstract = {This study highlights the utility of shotgun metagenomics (SMg) in the diagnosis of infectious myositis, focusing on a rare case of Anncaliia algerae infection in an immunocompromised patient. This is among the first reports of SMg application in inflammatory myopathies. We conducted a monocentric prospective observational study at Pitié-Salpêtrière Hospital (2021-2024), including patients with inflammatory myopathies and suspected infectious etiologies. Diagnosis was based on clinical symptoms, paraclinical findings, myopathological examination, and SMg performed using DNA/RNA sequencing with the Illumina NextSeq 500® sequencing system and the MetaMIC® bioinformatics pipeline. Among nine patients, SMg identified A. algerae in a kidney transplant recipient with severe myositis and myocarditis. Standard microbiological techniques, including blood tests and muscle biopsy staining, failed to accurately identify the pathogen. Despite specific therapy (albendazole), the infection was fatal, underscoring the pathogen's aggressiveness in immunocompromised hosts. Other patients either recovered spontaneously or with immunosuppressants. This study demonstrates the diagnostic advantage of SMg in infectious myopathies, especially for rare pathogens like A. algerae. The unbiased nature of SMg enables pathogen identification when conventional methods fail, guiding targeted treatments. Early SMg use could improve outcomes in immunocompromised patients and warrants integration into diagnostic workflows for inflammatory myopathies. As an unbiased and culture-free pan-pathogenic method, SMg enables the identification of pathogens, including unexpected ones, and can be used in addition to routine procedures for inflammatory myopathy diagnosis.},
}

@article {pmid42945792,
year = {2026},
author = {An, Z and Ma, WJ and Hou, Y and Gao, L and Tian, Y and Zhang, H},
title = {Macro-scale oxygen pulsing engineers dynamic microbial niches and endogenous carbon cycling for energy-efficient nitrogen removal from low C/N high-strength wastewater.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127163},
doi = {10.1016/j.watres.2026.127163},
pmid = {42945792},
issn = {1879-2448},
abstract = {Low-cost and efficient nitrogen removal from low-C/N high-strength ammonium wastewater remains challenging. Herein, a novel macro-scale oxygen pulsing-driven anaerobic/micro-aerobic/anoxic (MOP-AMA) system was developed to treat low-C/N high-strength ammonium wastewater, achieving TN, NH4[+]-N, and COD removal efficiencies of 97.0 ± 2.2%, 99.1 ± 1.9%, and 97.5 ± 1.6%, respectively, with a specific aeration energy consumption of 20.0 Wh L[-1]. Functional gene analysis revealed strong enrichment of denitrification-related genes (1635.79 RPKM), while concurrent enrichment of glycogen degradation genes and gltA indicated coordinated glycogen metabolism and TCA cycle activity supplying reducing power and energy for polyhydroxyalkanoates (PHAs) synthesis. At KEGG Level 3, "Metabolic pathways" was the dominant functional category, accounting for 16.78% of the total RPKM-normalized functional abundance. Metagenome-assembled genomes and metatranscriptomics showed that glycogen-accumulating organisms (GAOs) (Candidatus Contendobacter and Candidatus Competibacter) had the highest transcriptional activity in the anaerobic phase (18.57% and 4.73%), while synergistic interactions among AOB, Candidatus Nitrospira defluvii (NOB), and Candidatus Competibacter denitrificans (GAOs) enabled coupled nitrification and endogenous denitrification. Nitrification genes peaked under micro-aerobic conditions, whereas denitrification genes (narGHI, nirKS, norB, nosZ) were highly expressed in the micro-aerobic (930.81, 864.93, 122.59, 277.11 TPM) and anoxic phases (756.21, 688.40, 142.64, 128.22 TPM). These findings demonstrate that macro-scale oxygen pulsing can temporally steer redox processes and electron partitioning for carbon-efficient nitrogen removal, thereby providing guidance for the treatment of carbon-limited high-strength ammonium wastewater.},
}

@article {pmid42946178,
year = {2026},
author = {Li, JT and Zhang, SM and Jiang, X and Liu, DL and Wang, ZG and Zhao, HX},
title = {Exploration of the therapeutic mechanisms of nuciferine in polyendocrine metabolic ovarian syndrome treatment based on multi-omics approaches.},
journal = {Genomics},
volume = {},
number = {},
pages = {111333},
doi = {10.1016/j.ygeno.2026.111333},
pmid = {42946178},
issn = {1089-8646},
abstract = {Polyendocrine metabolic ovarian syndrome (PMOS) is one of the most common reproductive endocrine and metabolic diseases affecting women's health. Here, we investigated the effect of nuciferine (NUC) on PMOS in vivo experiments. For transcriptome sequencing analysis and verification results, NUC mainly affected PI3K-AKT and MAPK pathways in liver tissue and affected PI3K-AKT and NF-κB pathway in adipose tissue, respectively. Molecular dynamics simulations indicated that the binding of PI3K to NUC is more effective. Meanwhile.Indole-3-acetic acid and Tryptamine were the key production of intestinal flora regulated by NUC after integrating metagenomics and non-targeted metabolomics analysis. The study confirmed the efficacy of NUC in DHEA - induced PMOS mice. PI3K might be the key target protein and Indole-3-acetic acid and Tryptamine were the key production regulated by NUC in PMOS treatment.},
}

@article {pmid42946188,
year = {2026},
author = {Liu, W and Song, B and Chen, Q and Du, M and Xu, N and Huang, R and Wei, H and Bai, H and Zhang, S},
title = {Meta-omic insight into the community-level tolerance of the activated sludge to limited-dose ionizing radiation (LimDIR).},
journal = {Environmental research},
volume = {},
number = {},
pages = {126020},
doi = {10.1016/j.envres.2026.126020},
pmid = {42946188},
issn = {1096-0953},
abstract = {Ionizing radiation is a promising advanced oxidation process for wastewater treatment, yet the community-level tolerance mechanisms of conventional activated sludge (CAS) under limited-dose ionizing radiation (LimDIR, 2-50 Gy) remain poorly characterized. To address this knowledge gap, we investigated such tolerance mechanisms by integrating batch experiments, 16S rRNA profiling, metagenomics, metatranscriptomics, and metagenome-assembled genome (MAG)-resolved analyses of glucose-fed communities receiving a single acute X-ray dose. Under LimDIR, the CAS community maintained NH4[+]-N removal despite transient inhibition at 2-15 Gy and recovery at higher doses, and progressively enhanced carbon removal (from 64.5% to 71.6%, R[2] = 0.85 with dose), while community diversity and the dominant phylogenetic framework were preserved even though genus-level composition shifted. In contrast, transcriptional profiles responded sensitively to irradiation, indicating that resilience was mainly driven by functional regulation rather than compositional turnover. Mechanistically, the dose-dependent increase in repair transcripts was carried by RecA-mediated homologous recombination together with the SOS/translesion damage-tolerance set, and enzymatic antioxidant systems constituted the major defense against oxidative stress. Community-level tolerance was further supported by quorum sensing, two-component systems, biofilm/extracellular polymeric substance (EPS)-related protection, and syntrophic carbon and nitrogen metabolism. MAG-resolved analysis suggested a core-partner cooperative tolerance model. In this model, self-protective core taxa encoded integrated DNA repair, antioxidant defense, and stress-responsive regulatory functions, whereas partner populations supplied essential structural components, including lipopolysaccharide biosynthesis, and metabolic complementarity required for community-level stability. Functional redundancy across taxa further buffered irradiation stress and sustained process performance. These findings indicate LimDIR tolerance in activated sludge as a cooperative, multilayer community property and provide a mechanistic basis for the resilience of biological wastewater treatment under irradiation stress.},
}

@article {pmid42946190,
year = {2026},
author = {Chen, H and Chai, Z and Song, C and Zheng, Y and Chen, J and Zheng, M},
title = {Revitalizing simultaneous nitrification, endogenous denitrification and phosphorus removal under carbon starvation: Redox mediator-modulated electron transfer and metabolic coordination.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126032},
doi = {10.1016/j.envres.2026.126032},
pmid = {42946190},
issn = {1096-0953},
abstract = {The simultaneous nitrification, endogenous denitrification and phosphorus removal (SNEDPR) process provides a resource-efficient paradigm for synergistic nutrient removal. However, its efficacy can be severely constrained by limited electron-donor availability and inefficient intracellular electron transfer under low carbon-to-nitrogen (C/N) ratios. Herein, we demonstrate that anthraquinone-2-sulfonate (AQS) serves as an effective redox mediator to alleviate these electron-transfer limitations. Under severe carbon-limited conditions, with an influent C/N ratio of 3.24±0.11, supplementation with 0.3 mmol/L AQS successfully restored the deteriorated system, recovering total inorganic nitrogen (TIN) removal efficiency to 96.57±0.87% while sustaining robust phosphorus removal (96.47±2.68%). Batch kinetic assays showed that AQS increased electron transfer system activity (ETSA) by over 100%, accompanied by enhanced nitrification-related activity, endogenous denitrification and phosphorus uptake. Integrated metagenomic and metatranscriptomic analyses further revealed transcriptional responses consistent with an electron-shuttling role of AQS, including enhanced ETC-associated electron-transfer potential and increased transcription of downstream denitrification enzymes. ATP synthase-related transcription was also enhanced, indicating an increased potential for PMF-coupled cellular energy conservation. Consequently, increased transcription was observed for key functional genes involved in nitrification (amoABC, nxrAB), denitrification (narGHI, napAB, nirKS, nosZ), and polyphosphate synthesis (ppk). Furthermore, AQS-amended operation was associated with microbial community succession toward a more specialized consortium, in which comammox, Thauera and Candidatus Accumulibacter clade ⅡC were associated with nitrification, endogenous denitrification, and denitrifying phosphorus removal, respectively. Although practical translation will require effective retention or recovery of soluble AQS, these findings demonstrate the potential of AQS-enhanced SNEDPR under carbon-limited conditions and provide multi-omics evidence linking improved nutrient removal with increased electron-transfer activity and coordinated microbial metabolic responses.},
}

@article {pmid42946193,
year = {2026},
author = {Lu, P and Chen, A and Feng, Y and He, S and Han, G and Hu, S},
title = {Microbial-Mediated Degradation of Aflatoxin B1 in Agricultural Soil.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126028},
doi = {10.1016/j.envres.2026.126028},
pmid = {42946193},
issn = {1096-0953},
abstract = {Aflatoxin B1 (AFB1) is commonly present in agricultural soil and poses severe threats to soil ecosystems due to its high toxicity, yet its environmental fate and microbial-mediated degradation mechanisms remain insufficiently studied. In this study, the environmental behavior of AFB1 in an agricultural soil was investigated. Metagenomic analysis showed that exposure to a higher concentration of AFB1 (5.0 mg kg[-1]) altered soil bacterial community structure and reduced community diversity. After 30 days of incubation, AFB1 was slowly removed from natural soil microcosms but persisted in sterilized soil microcosms, indicating that indigenous soil microorganisms make a major contribution to AFB1 dissipation. Exposure to high-concentration AFB1 significantly enriched the genus Nocardioides, and a novel AFB1-degrading strain, Nocardioides sp. N13 (phylum Actinomycetota), was isolated from the agricultural soil. Strain N13 harbors three genes encoding putative F420H2-dependent reductase (FDR) homologs, which are hypothesized to be involved in the initial degradation of AFB1. Bioinformatics analysis revealed that putative FDR homolog-carrying bacteria are mostly assigned to the phylum Actinomycetota and are widely distributed across diverse soil environments worldwide. These findings provide a theoretical basis and potential microbial resources for mitigating AFB1 contamination in soil ecosystems.},
}

@article {pmid42946251,
year = {2026},
author = {Charles, DW and Alkabab, Y and Sharma, D and Adekunle, RO and Catalano, J and Colven, R and Curry, SR and Dorman, SE and Meissner, EG and Mills, A and Patterson, L and Teixeria, CS and Tyler, RS and Salgado, CD and Harris, CE},
title = {Clinical Utility of Plasma Microbial Cell-Free DNA Sequencing in Adult Immunocompromised Patients: A Real-World Cohort Study.},
journal = {The American journal of the medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjms.2026.10.011},
pmid = {42946251},
issn = {1538-2990},
abstract = {BACKGROUND: Plasma metagenomic next generation sequencing (mNGS) enables noninvasive pathogen detection independent of organism viability. Although analytic performance has been described, the real-world clinical impact in immunocompromised hosts remains incompletely defined.

METHODS: We conducted a retrospective cohort study of immunocompromised adults undergoing plasma mNGS testing from January 2022 through November 2024 at the Medical University of South Carolina. Immunocompromised conditions included solid organ transplantation, hematopoietic stem cell transplantation, active hematologic malignancy, HIV, or biologic immunosuppressants. Clinical impact was adjudicated by infectious disease physicians as positive, negative, or neutral. Positive results were classified as definite, probable, possible, or unlikely infectious based on clinical correlation and concordance with conventional microbiologic testing (CMT).

RESULTS: Ninety-eight patients were included (median age 60 years [range 18-76]; 63% male), including solid organ transplant (31%), hematopoietic stem cell transplant (8%), HIV (13%), active malignancy (42%), corticosteroids (3%), and biologic therapy (10%). At testing, 85% were receiving antimicrobials and 88% were hospitalized. Plasma mNGS was positive in 62% of cases, with CMT concordance in 30%. Thirty-two percent of tests had positive clinical impact, identifying unrecognized infection or antimicrobial optimization. Sixty-six percent had no treatment impact and 2% had potential negative impact. More than half of discordant positives were deemed possible or unlikely infections. False-negative cases included invasive mold and nontuberculous mycobacterial infections.

CONCLUSIONS: In this antimicrobial-exposed immunocompromised cohort, plasma mNGS frequently detected organisms but less often influenced clinical management. Discordant positives were common, and false negatives occurred in selected syndromes, supporting cautious interpretation and stewardship-guided use.},
}

@article {pmid42946473,
year = {2026},
author = {Pradhan, M and Molinaro, A and Ginanni Corradini, S and Silecchia, G and Ferri, F and Capoccia, D and Lv, B and Wu, H and Huber-Schönauer, U and Völkerer, A and Mischitelli, M and Parlati, L and Bergström, G and Datz, C and Leonetti, F and Tilg, H and Tremaroli, V and Bäckhed, F},
title = {Gut microbiome profiles associated with simple liver steatosis in MASLD.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337572},
pmid = {42946473},
issn = {1468-3288},
}

@article {pmid42946695,
year = {2026},
author = {Dahal, A and Chang, WC and Grashel, B and Morgan, D and Spagna, D and Kim, DH and Sachdeva, S and Phelan, KJ and Satish, L and Biagini, JM and Haslam, DB and Ollberding, NJ and Khurana Hershey, GK},
title = {Longitudinal Skin Bacterial Cluster Associated With Protection Against Allergic Co-Morbidity in Pediatric Atopic Dermatitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70554},
pmid = {42946695},
issn = {1398-9995},
support = {U19AI070235//National Institute of Allergy and Infectious Diseases/ ; F30AI181481//National Institute of Allergy and Infectious Diseases/ ; T32GM149200/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is an inflammatory skin condition that often portends the development of allergic comorbidities. Despite evidence supporting the role of the skin microbiome in AD, its temporal patterns and associations with risk or protection for allergic co-morbidity remain unclear. Our objective is to characterize core species of the pediatric AD bacterial microbiome, assess microbial networks and clusters, and identify global microbial changes relevant to AD and the atopic march.

METHODS: We performed metagenomic shotgun sequencing on 353 non-lesional skin samples from children in the Mechanisms of Progression of Atopic Dermatitis to Asthma in Children (MPAACH) cohort across 5 annual visits. We assessed taxonomic composition and analyzed longitudinal skin microbial patterns with progression to allergic co-morbidities.

RESULTS: We identified 436 distinct species. Shannon diversity and richness declined with age, and socioeconomic factors explained the variance in species composition. Staphylococcus aureus (SA) was more abundant in severe AD. Cluster 5, comprised of typically gut-associated microbes, was more abundant in non-sensitized children who did not develop allergic co-morbidities over time.

CONCLUSIONS: Our analyses revealed key patterns in core taxa, diversity and abundance of the skin microbiome over time in early life and highlighted previously unexplored factors such as socioeconomic status as key contributors to the variability in species composition. Abundance of SA confers risk, while gut-associated microbes may offer protection, influencing the clinical trajectory of AD and the atopic march. Thus, these results provide a novel and comprehensive understanding of the temporal dynamics of the skin microbiota in pediatric AD.},
}

@article {pmid42946708,
year = {2026},
author = {Wang, Y and Kim, H and Malmuthuge, N and Zhou, M and Chen, Y and Alexander, TW and Timsit, E and Yao, J and Liang, G and Guan, LL},
title = {Early-life bovine respiratory virome analysis reveals phage-driven adaptation and cross-host evolutionary signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42946708},
issn = {2041-1723},
mesh = {Animals ; Cattle ; *Virome/genetics ; *Bacteriophages/genetics/physiology ; Phylogeny ; Humans ; Genome, Viral ; *Respiratory System/virology ; Metagenomics ; Respiratory Tract Infections/virology/veterinary ; Evolution, Molecular ; },
abstract = {Past outbreaks of zoonotic viral infections highlight the importance of understanding respiratory virome ecology. As major food-producing animals with frequent human contact, cattle represent a critical host at the human-animal interface; however, the early-life establishment of their respiratory virome and its evolutionary connections to viruses from other hosts remain underexplored. Here, we longitudinally profile the upper respiratory tract (URT) virome of beef calves from birth to weaning using an optimized viral enrichment procedure and metagenomic workflow. Viral communities exhibited increased richness and turnover, reflecting ecological structuring during early life. Temperate phages dominate the URT phage community and share virulence- and mobility-associated genes with bacterial hosts, likely contributing to host adaptation and colonization persistence. Vertebrate-associated viruses emerge after the first week of life. Targeted reassembly from bovine URT viromes recovers near-complete betacoronavirus-like (CoV-D180) and adenovirus-like (AdV-D56) genomes positioned phylogenetically between bovine and human viral lineages. Competitive mapping of bovine-derived CoV-D180 and AdV-D56 to human respiratory metatranscriptomic datasets reveals genome-specific, regionally structured coverage patterns distinct from reference viruses, supporting shared sequence features in conserved genomic regions across host-associated viral lineages. Collectively, these findings reveal early-life assembly dynamics of the bovine respiratory virome and highlight cross-host signatures in a One Health framework.},
}

Animals
Cattle
*Virome/genetics
*Bacteriophages/genetics/physiology
Phylogeny
Humans
Genome, Viral
*Respiratory System/virology
Metagenomics
Respiratory Tract Infections/virology/veterinary
Evolution, Molecular