@article {pmid42242079,
year = {2026},
author = {Yang, F and Zhang, M and Tan, Y and Yuan, Z and Liu, W and Wu, Y and Li, F},
title = {Alkaline woody peat shifts CO2 emissions to CH4 by modulating microbial cross-feeding in Cd-contaminated paddy soil.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142498},
doi = {10.1016/j.jhazmat.2026.142498},
pmid = {42242079},
issn = {1873-3336},
abstract = {Alkaline organic amendments are widely used to remediate cadmium (Cd)-contaminated paddy soils by alleviating acidification and reducing Cd bioavailability, yet their impacts on greenhouse gas emissions remain unclear. Here, we examined how alkaline woody peat (WP) regulates carbon fluxes and microbial interactions in Cd-contaminated paddy soil. Anaerobic incubation and greenhouse pot experiments, together with in situ methane monitoring and metagenomic analyses, were used to compare alkaline-modified WP with acidic WP, CaO alone, and unamended controls. Alkaline WP (AWP-2) increased soil pH from 5.5 to 7.35 and decreased exchangeable Cd from 32% to 13%, confirming its remediation effectiveness. However, this was accompanied by marked changes in greenhouse gas emissions: methane production increased by up to 3.9-fold, while carbon dioxide emissions declined. Metagenomic analyses showed that alkaline WP strongly enriched methanogenic archaea, particularly Methanosarcina, whose relative abundance reached 26.6% compared with 4.2% in the control, while suppressing microbial populations associated with CO2-generating pathways. Functional gene profiles revealed increased abundance of mcrA and reduced representation of genes involved in complete acetate oxidation (maeA, pdc, sucA, porA, aceE, and icd). Genome-resolved analysis further showed that some microbes positively associated with methanogens lacked key genes involved in acetate oxidation to CO2 (e.g., aceE), suggesting a reduced capacity for CO2 generation from acetate and a greater tendency to retain carbon as acetate, thereby potentially favoring acetoclastic methanogenesis. Overall, these results highlighting a potential trade-off between Cd remediation and greenhouse gas mitigation and the need to incorporate microbially driven carbon fluxes into environmental risk assessments of alkaline amendments in contaminated paddy soils.},
}

@article {pmid42242448,
year = {2026},
author = {Ammar, M and Fang, Y and Saqib, M and Xiao, J and Sial, AU and Wu, Q and Mansoor, MK and Wu, X and Moaaz, M and Butt, MU and Hafeez, R and Iqbal, K and Zohaib, A and Shen, S and Deng, F},
title = {Metagenomic and serological evidence of emerging tick-borne viruses in livestock, humans, and rats in Pakistan.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.06.001},
pmid = {42242448},
issn = {1995-820X},
abstract = {Tick-borne viruses (TBVs) pose significant emerging threats to public and veterinary health worldwide. In Pakistan, the potential threats posed by TBVs extend far beyond Crimean-Congo hemorrhagic fever virus (CCHFV), which causes outbreaks and severe hemorrhaging with a high fatality rate among humans each year. However, the full extent of the tick-borne virome remains largely unexplored. This study presents the metagenomic profiling of viruses in livestock-associated ticks from Pakistan. Eighty-seven ticks belonging to the genera Ixodes, Rhipicephalus, Haemaphysalis, and Hyalomma species from livestock in Punjab. These ticks were subsequently grouped into 11 pools for RNA sequencing. Our analysis revealed extensive viral diversity, identifying sequences related to 31 viruses spanning at least 11 families. New strains of Jingmen tick virus (JMTV), brown dog tick phlebovirus 2 (BDTPV-2), and Liman tick virus (LMTV) were characterized, confirming their presence in the region. Serological surveys performed among 319 livestock, 253 humans, and 214 rats detected antibodies against these viruses, indicating host exposure. Notably, the presence of JMTV-neutralizing antibodies was confirmed in two livestock animals, one human, and one rat, providing evidence of productive infection. Our findings significantly expand the known diversity and distribution of TBVs in Pakistan, establish the preliminary baseline of the tick virome in the country, and provide serological evidence of cross-species exposure to emerging TBVs. This study highlights the underestimated risk of tick-borne viral zoonoses in Pakistan and underscores the urgent need for enhanced surveillance and risk assessment.},
}

@article {pmid42242497,
year = {2026},
author = {Han, J and Lisco, A and Che, Y and Anderson, MV and Laidlaw, E and Kim, CS and Hou, P and Conlan, S and Proctor, DM and Lee-Lin, S and Amirkhani, A and Holmes, CJ and Suh, GS and Brownell, I and , and Segre, JA and Sereti, I and Kong, HH},
title = {Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.05.019},
pmid = {42242497},
issn = {1523-1747},
abstract = {The microbiome and host immune system maintain a dynamic homeostatic equilibrium at the skin interface. Prior studies have shown that the skin microbiome is profoundly altered in immunodeficient conditions. Patients with idiopathic CD4 lymphopenia (ICL), a rare clinical syndrome with obscure cause, and people living with HIV (PLWH) are two etiologically distinct groups of individuals with CD4 T-cell lymphopenia. We conducted shotgun metagenomic sequencing, metagenome assembly, and read-based mapping to characterize the multi-kingdom taxonomic diversity of skin microbiomes in patients with ICL and PLWH who were followed longitudinally before and after antiretroviral therapy (ART) initiation. Compared with healthy individuals, the skin microbiomes of patients with ICL and ART-naïve PLWH showed greater inter-individual variation and higher relative abundances of eukaryotic viruses. Both patient groups carried pathogenic microbes, including high-oncogenic-risk human papillomaviruses (HPVs) and dermatophytes such as Trichophyton rubrum, which were rarely seen in healthy individuals. In PLWH, high-oncogenic-risk HPV types persisted after 2 months of ART but were mostly cleared after 14 months. The loss of peripheral blood CD4 T-cells was associated with shifts in the skin microbiome and a relative expansion of pathogenic microbes. Investigating microbiome dynamics during immunodeficiency and subsequent immune reconstitution provides additional insights into host-microbial interactions.},
}

@article {pmid42243106,
year = {2026},
author = {Lee, M and Kim, D and Song, JH and Park, SJ and Chang, JY},
title = {Efficacy of Lactococcus lactis WiKim0124 in Fat-, Sucrose-, and Fat/Sucrose-Induced Obesity Models.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00915-3},
pmid = {42243106},
issn = {2396-8370},
support = {KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; },
abstract = {Lactococcus lactis WiKim0124 (WiKim0124), a probiotic strain isolated from kimchi, has previously shown anti-obesity effects in high-fat diet (HFD) models. This study investigated whether WiKim0124 and its formulated version, SW01, exert consistent anti-obesity efficacy across distinct diet-induced obesity models through modulation of host lipid metabolism and gut microbial function. In 3T3-L1 adipocytes and FFA-treated HepG2 cells, both treatments inhibited lipid accumulation and modulated lipid metabolism-related markers, indicating enhanced fatty acid oxidation and reduced lipogenesis. In C57BL/6 J mice fed HFD, high-sucrose (HSuc), or HFD + HSuc diets, daily oral administration of WiKim0124 or SW01 significantly reduced body weight gain, adipose tissue mass, and hepatic lipid accumulation. WiKim0124 and SW01 significantly enhanced fatty acid oxidation pathways, as evidenced by increased expression of the markers PPARα, CPT-1α, and UCP2. Gut microbiota analysis showed increased Bacteroidetes and enrichment of Akkermansia muciniphila in treated groups. Shotgun metagenomic functional profiling revealed enhanced short-chain fatty acid-related pathways and enzymes, with distinct patterns depending on treatment and dietary stressors. Microbial functional responses were most pronounced in the HFD + HSuc model, supporting a diet-dependent mode of probiotic action. Together, these findings demonstrate consistent anti-obesity efficacy of WiKim0124 and support the translational potential of its formulated application through integrated modulation of host metabolism and gut microbial function.},
}

@article {pmid42243452,
year = {2026},
author = {Das, R and Medhi, MC and Tamang, B},
title = {Microbial diversity and its links to retinol pathways and aroma compounds in ethnic fermented rice beverages of Assam.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02062-0},
pmid = {42243452},
issn = {2191-0855},
abstract = {Traditional fermented rice beverages are produced through complex microbial fermentation processes that influence their physicochemical characteristics and metabolite composition. In this study, metagenomic sequencing and GC-MS/MS-based metabolomics were integrated to characterize four indigenous rice beverages: Black Rohi Modh (BR), Rohi Modh (RH), Jou Bidwi (JOU), and Sai Mod (SM). All beverages were mildly acidic, with pH values ranging from 4.1 to 4.5 and titratable acidity between 0.58 and 0.72% lactic acid. Ethanol content varied among samples, with BR showing the highest concentration (8.13% v/v), followed by JOU and RH (approximately 5.5% v/v), while SM exhibited the lowest level (4.28% v/v). Antioxidant activity differed across beverages, with RH and BR demonstrating higher DPPH radical scavenging activity and SM showing the highest ferric reducing antioxidant power (96.93 µmol/mL). Metagenomic analysis generated 57.69 Mb of assembled sequences, identifying 48 microbial phyla and 1,785 species, with Eukarya accounting for 66.12% of the total community. Ascomycota predominated in BR and JOU, whereas Bacillota was more abundant in RH. The genus Saccharomyces was consistently dominant across samples. Functional annotation indicated enrichment in metabolic pathways related to carbohydrate and amino acid metabolism, as well as genes associated with ethanol biosynthesis and retinol metabolism pathways, reflecting microbial metabolic potential rather than direct vitamin production. Metabolomic profiling identified 113-167 metabolites per beverage, with 93 compounds shared among all samples. Correlation analysis revealed significant associations between Saccharomyces cerevisiae and short-chain fatty acids (ρ = 0.62-0.71, FDR < 0.05), indicating a strong positive relationship between microbial abundance and metabolite production.},
}

@article {pmid42243513,
year = {2026},
author = {Yi, J and Zhao, Y and Li, Z and Chen, A and Tang, Z and Zheng, L and Ge, H and Yu, Q and Liu, W and Xiang, J and Tang, J},
title = {M.globosa promotes lung cancer progression and M2 macrophage polarization through oxidative phosphorylation.},
journal = {NPJ precision oncology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41698-026-01528-5},
pmid = {42243513},
issn = {2397-768X},
support = {2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2403084//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; },
abstract = {The lungs are colonized by a variety of microbes which play a significant role in lung cancer progression. In this study, we conducted an in-depth analysis of metagenomic sequencing data obtained from alveolar lavage fluid (ALF) samples of patients with non-small-cell lung cancer (NSCLC) at different clinical stages. The nested qPCR was used to validate the abundance of key fungi and establish a correlation between fungi abundance and patient prognosis. We found that elevated levels of M.globosa correlated with patients at stage1B-3 and worse prognosis. M.globosa enhanced the proliferation of lung cancer cells and promoted tumor growth in vivo by promoting M2-like macrophage polarization, which was primarily driven by oxidative phosphorylation (OXPHOS) activation. The inhibition of OXPHOS in tumor-bearing mice using metformin significantly retarded the tumor growth induced by M. globosa. Together, our clinical observations and experimental findings suggest that intracellular M. globosa infection may contribute to lung cancer progression through immunometabolic remodeling of macrophages.},
}

@article {pmid42243631,
year = {2026},
author = {Bauer, C and Reger, N and Rustem, HAL and Tisza, M and Triosi, CL and Javornik Cregeen, S and Ghobrial, L and Gitter, A and Wu, F and Surathu, A and Deegan, J and Mena, KD and Petrosino, J and Boerwinkle, E and Hanson, BM and Maresso, AW},
title = {SeqBoard: a genomics-based data dashboard for comprehensive wastewater virome monitoring.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {},
number = {},
pages = {},
doi = {10.1093/jamia/ocag088},
pmid = {42243631},
issn = {1527-974X},
support = {//S.B. 1780, 87th Legislature, 2021 Reg. Sess./ ; U19 AI44297/NH/NIH HHS/United States ; //Anonymous Foundation/ ; //UTHealth Houston Seed/ ; //Baylor College of Medicine/ ; //Alkek Foundation Seed/ ; },
abstract = {OBJECTIVES: To develop the first public-facing dashboard that translates genomic sequencing data from wastewater into accessible and actionable community information concerning human pathogenic viruses, representing a shift to sequencing-based public health wastewater monitoring.

MATERIALS AND METHODS: We developed SeqBoard, a user-friendly dashboard that displays sequencing information from the total wastewater virome. The dashboard integrates diverse expertise and components, including data processing and analysis, visualization and management, security, and stakeholder engagement and feedback. We implemented a 3-tiered system for user interactions, customized to the general public, public health officials, and genomics experts.

RESULTS: SeqBoard provides an intuitive interface for presenting genomic information as species-specific trend lines, level indicators, and all-site aggregates. It translates complex sequencing data into public health insights, including reporting on dozens of viruses of concern with modules for detections, variant information, and genomic context.

DISCUSSION: The prevention of the next pandemic will require comprehensive pan-monitoring of deadly viruses and their evolution. Genomics-based dashboards will be essential for early detection of viral activity before significant clinical manifestation, thereby allowing public health systems to provide warnings, ready actions, and develop vaccines.

CONCLUSION: SeqBoard shows that sequencing data can be translated into useful public health information, serving as a model for future sequencing-based pathogen dashboards. The dashboard is publicly available at https://tephi-ww.uth.edu/public-dashboard and represents the first publicly available dashboard providing pan viral genomic detection data for wastewater monitoring.},
}

@article {pmid42243719,
year = {2026},
author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS},
title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09123-3},
pmid = {42243719},
issn = {1471-2229},
support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; },
abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.

RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.

CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).},
}

@article {pmid42243998,
year = {2026},
author = {Li, S and Sun, Y and Tong, X and Zhang, Z and Ma, X and Li, D and Min, L},
title = {Near-complete inhibition of rumen methanogenesis via microbial and enzymatic modulation using a low dose of Asparagopsis taxiformis combined with 3-nitrooxypropanol.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42243998},
issn = {1674-9782},
support = {SKXRC2025487//Youth S&T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 2024CXTD13//Guangdong Modern Agro-industry Technology Research System/ ; 202408440440//China Scholarship Council/ ; NYQS202613//Special Funding for the Construction of the High-Level Academy of Agricultural Sciences/ ; 2026A1515010802//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {BACKGROUND: Enteric methane (CH4) from ruminants represents a major contributor to agricultural greenhouse gas emissions. The red seaweed Asparagopsis taxiformis (A. taxiformis) is a highly effective CH4 emission inhibitor, but its large-scale application is restricted by limited biomass availability. This study evaluated whether reducing the inclusion level of A. taxiformis (0.32% dry matter, DM) combined with 3-nitrooxypropanol (3-NOP; 0.05% DM) could maintain a high inhibitory efficacy, and elucidated the underlying microbial mechanisms through in vitro fermentation and metagenomics analysis.

RESULTS: The combined treatment decreased CH4 production by 98.21% (P < 0.01) without impairing DM degradation, and markedly shifted rumen fermentation towards propionate, lowering the acetate-to-propionate ratio (1.59 vs. 2.65; P < 0.01). Metagenomic profiling revealed substantial reductions in the abundance of Methanobrevibacter and Ruminococcus, along with increased levels of propionate-associated bacteria such as Prevotella, Treponema, Eubacterium, and Selenomonas (P < 0.01). Functionally, the combined treatment downregulated key enzymes in hydrogenotrophic and methylotrophic methanogenesis, including methyl-coenzyme M reductase (EC:2.8.4.1) and tetrahydromethanopterin S-methyltransferase (EC:2.1.1.86), thereby blocking terminal methanogenic steps.

CONCLUSIONS: Collectively, these results demonstrate that co-supplementation with A. taxiformis and 3-NOP achieves near-complete methanogenesis inhibition at drastically reduced seaweed dosage through coordinated changes in fermentation patterns, microbial community structure, and methanogenic enzymatic pathways. This approach provides a practical strategy to overcome biomass limitations of A. taxiformis and warrants validation in long-term in vivo trials.},
}

@article {pmid42244002,
year = {2026},
author = {Ansari, MH and Staubach, F and Alacatli, N and Obbard, DJ},
title = {A diverse gut virome in natural populations of Drosophila melanogaster.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00585-2},
pmid = {42244002},
issn = {2524-4671},
abstract = {BACKGROUND: Drosophila melanogaster is not only one of the most important models of antiviral immunity in invertebrates, but is also a powerful model for research of the gut microbiome. Although recent studies have continued to improve our knowledge of the fly gut microbiota, the viral component of the microbiome has remained unexplored.

RESULTS: Here we explore the viral component of the Drosophila melanogaster gut microbiome using deep metagenomic DNA sequencing. We recovered 3040 non-redundant viral contigs, most of which were bacteriophage-associated sequences, resulting in 167 viral Metagenome-Assembled Genomes. Many of these sequences showed limited similarity to reference viruses and included bacteriophages related to tailed double-strand DNA phage lineages, with putative links to major gut-associated bacteria of D. melanogaster, including Lactobacillus, Acetobacter, and Gluconobacter. Our functional annotation and discovery of auxiliary metabolic genes suggested that these bacteriophages encode putative functional potential related to microbial metabolism and genetic information processing. We also identified evidence of known fly pathogens Drosophila Kallithea nudivirus, Vesanto bidna-like virus, and Drosophila Linvill Road densovirus, some of which were common in our studied populations.

CONCLUSIONS: Our findings reveal a complex and diverse phage community in the D. melanogaster gut microbiome, paving the way to study host-phage related research in the natural microbial communities.},
}

@article {pmid42244030,
year = {2026},
author = {Wang, Y and Zhang, Y and Feng, L and Han, Q and Yu, Q and Li, H},
title = {Host Ecology Shapes Gut Pathogen Evolution: An Eco-Evolutionary Trade-Off in Plateau Wildlife.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70344},
doi = {10.1111/1462-2920.70344},
pmid = {42244030},
issn = {1462-2920},
support = {32471575//National Natural Science Foundation of China/ ; },
abstract = {The intestinal tracts of plateau wildlife function as crucial reservoirs for diverse pathogens. However, the mechanisms through which host ecology influences pathogen community assembly and their interactions remain unclear. By comparing the subterranean-living plateau zokor (Eospalax baileyi) with the aboveground plateau pika (Ochotona curzoniae) across a two-and-a-half-year study, this work provides evidence that the distribution and transmission dynamics of pathogens, virulence factor genes (VFGs), and pathogen-host interaction (PHI) genes are determined by animals' distinct niches. The results demonstrate a clear eco-evolutionary trade-off: the plateau zokor, inhabiting stable yet pathogen-enriched burrow systems, exhibited higher abundances of pathogens, VFGs, and PHI genes in its gut, and formed complex co-occurrence networks. In contrast, the plateau pika, under diverse environmental exposure, possessed higher pathogen and gene diversity but lower overall abundance, alongside simpler interaction networks indicative of opportunistic colonization. Metagenomic binning indicated a close association among VFGs, PHI genes, and mobile genetic elements (MGEs), pointing to their possible joint transfer. Additionally, animal weight and precipitation were identified as key drivers of pathogen dynamics. These findings indicate that the gut sits at the crossroads of animal and environmental health, highlighting how host-mediated pathogen evolution across distinct niches shapes the broader One Health dynamics of the plateau ecosystem.},
}

@article {pmid42244179,
year = {2026},
author = {Wang, Y and Zhu, Z and Zhang, Y and Luo, Q and Niu, T and Liu, Y and Chen, J and Yang, R and Zhu, S and Chen, H},
title = {Dynamic microbiome turnover and glycerol-3-phosphate-linked metabolic adjustments underlie resilience to desiccation in intertidal algae.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71330},
pmid = {42244179},
issn = {1469-8137},
support = {2021Z103//Major Scientific and Technological Project of Ningbo/ ; CARS -50//China Agriculture Research System of MOF and MARA/ ; 32373099//National Natural Science Foundation of China/ ; //Ningbo Yongjiang Talent Program/ ; 2021C02069 -9//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural (Aquaculture) Varieties/ ; },
abstract = {Tolerance to extreme dehydration has emerged across the tree of life, yet current understanding relies heavily on terrestrial host traits. Marine lineages facing rapid, tide-driven hydration oscillations remain largely unexplored. We used Pyropia haitanensis as a model to determine if intertidal resilience arises from a coordinated holobiont strategy. We integrated time-resolved microbiome profiling and metagenomics. Mechanisms were validated through multi-omics of desiccation-stressed bacterial isolates, inoculation, and antibiotic-depletion experiments, and host physiological assessment. Rapid drying reshaped the microbiome through selective loss of osmosensitive taxa and occupation by stress-tolerant lineages, whereas rehydration promoted selective recolonization and network recovery. Metagenomic analysis revealed enrichment of functional potential for microbial antioxidant, osmoprotective, and extracellular polysaccharide pathways, alongside enrichment of glycerol-3-phosphate (G3P) ABC transporter modules. Host G3P secretion increased, creating a selective nutrient niche that recruited symbionts possessing specialized G3P transporters. Inoculation and microbiota-depletion experiments established a causal role for the microbiome in host resilience. Keystone isolates Sulfitobacter sp. and Alteromonas sp. utilized host-derived G3P to fuel complementary protective mechanisms, with their combination outperforming either taxon alone. These findings highlight an integrated host-microbiome partnership shaped by tidal filtering, a cross-domain strategy that buffers hydration stress and supports intertidal resilience and mariculture practices.},
}

@article {pmid42244577,
year = {2026},
author = {Ettinger, CL and Eisen, JA},
title = {Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.28.596327},
pmid = {42244577},
issn = {2692-8205},
abstract = {Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has only recently begun to be described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though we were only able to recover low quality MAGs of abundant taxa, we found preliminary evidence that taxa associated with phoronids and their tubes likely participate in sulfur cycling pathways. Future work should perform more robust metagenomic sequencing and chemical analysis to assess if there is a link between known phoronid chemical defenses and microorganisms. Overall, this study provides foundational insight into the microbial communities associated with phoronids and these initial findings suggest that these communities may play an important role in sulfur cycling in marine sediments.},
}

@article {pmid42244712,
year = {2026},
author = {Iranzo, J and Wolf, YI and Koonin, EV},
title = {Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.25.727639},
pmid = {42244712},
issn = {2692-8205},
abstract = {BACKGROUND: Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome?

RESULTS: We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors.

CONCLUSIONS: Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks', typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving grounds for emerging defense systems, which might eventually become cost-effective once optimized by selection.},
}

@article {pmid42244725,
year = {2026},
author = {Steinberger, AJ and Nickodem, CA and Leite de Campos, J and Kates, AE and Goldberg, TL and Safdar, N and Sethi, AK and Shutske, JM and Ruegg, PL and Suen, G and Hite, JL},
title = {Antimicrobial use contributes to resistance gene enrichment across cattle groups on commercial dairy farms.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.22.726633},
pmid = {42244725},
issn = {2692-8205},
abstract = {Antimicrobial use (AMU) in agricultural systems is frequently linked to antimicrobial resistance (AMR). Yet, the scale at which AMU reshapes host-associated resistomes remains unclear. This gap arises, in part, from the scarcity of farm-level AMU data from commercial production systems. Here, we combine detailed AMU records from commercial dairy farms with metagenomic analyses of bovine fecal resistomes from calves, lactating cows, sick cows, and cull cows. At a broad level, resistome profiles were similar regardless of farm AMU. Resistance associated with historically common antibiotics, such as tetracyclines, was frequent on low- and high-AMU farms, indicating that some resistance classes are ubiquitous in dairy systems regardless of current AMU. In contrast, resistance to other drug classes varied systematically with AMU. Higher AMU was associated with increased resistance to aminoglycosides, β-lactams, and macrolides, drug classes that are critical for treating mastitis and bovine respiratory disease. Resistance gene richness and diversity were highest in calves, underscoring the importance of accounting for host traits alongside AMU when evaluating resistance patterns. Together, these findings underscore the need for detailed, farm-level AMU data to understand how management practices shape AMR and to inform strategies for sustaining the effectiveness of existing antimicrobials in agricultural and public-health contexts.},
}

@article {pmid42244773,
year = {2026},
author = {Espinoza, JL and Dupont, CL and Phillips, A},
title = {Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.14.664802},
pmid = {42244773},
issn = {2692-8205},
abstract = {Functional profiling of metagenomes and metatranscriptomes is essential for understanding microbial community capabilities, yet current methods require computationally expensive translated-search alignments that scale poorly to the large genome-resolved reference databases now common in the field. We introduce Leviathan, an open-source software package for integrated taxonomic and functional profiling that operates at both genome and pangenome resolution. Leviathan combines Sylph for ultra fast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA-space against genome-resolved gene catalogs, bypassing the translated-search step that dominates runtime in existing approaches. For each (pan)genome, Leviathan functional profiling produces dual metrics: pathway abundance from aggregated gene-level quantification and pathway coverage from graph-based assessment of enzymatic step completeness. On CAMI-I and CAMI-II datasets, Leviathan achieved up to 74-fold faster runtimes and 14-fold lower memory usage compared to HUMAnN, while improving genome-level assignment accuracy by up to 12% and pangenome-level accuracy by up to 5%. We demonstrate Leviathan's applicability through two case studies: a marine plastisphere metagenomics dataset where differential coverage analysis revealed metabolic shifts between early and mature biofilm communities and a dental caries metatranscriptomics dataset where pangenome-resolved co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.},
}

@article {pmid42245494,
year = {2026},
author = {Hu, Z and Chen, C},
title = {Revealing gut microbiota profiles and their influencing factors in commercial boars of three breeds by a large-scale metagenome study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1825304},
pmid = {42245494},
issn = {1664-302X},
abstract = {Boars play a critical role in pig production. Numerous studies have reported important effects of the gut microbiota on pig production traits. However, whether the gut microbiota is associated with reproduction traits in boars remains largely unknown. Understanding the gut microbial composition and its influencing factors in large-scale boar populations is an essential first step to investigate this association. In this study, shotgun metagenomic sequencing was performed on fecal samples of 1,651 commercial boars from three breeds raised in three pig farms to uncover their gut microbial structures. We observed significant differences in boar gut microbial compositions across three breeds, even when raised in the same farm. Permutational multivariate analysis of variance (PERMANOVA) within-farm breeds and with-age stages found that the effect size of each factor on boar gut microbial composition varied across farms and age stages. Breeds accounted for 2% ~ 9% of the variance of boar gut microbial compositions in different farms. We then identified gut microbial taxa enriched in each boar breed using MaAsLin2. Lactic acid and butyrate-producing taxa, such as Lactobacillus amylovorus and Faecalibacterium prausnitzii, were enriched in Duroc boars; Akkermansia muciniphila and Lactobacillus reuteri showed the enrichment in Landrace boars, accompanied by increased relative abundance of Enterobacteriaceae members. Meanwhile, the species from Bacteroides, Prevotella, and Treponema had higher abundances in the gut of Large White pigs than in the other two pig breeds. We also identified bacterial species enriched in each of the three age stages. These breed and age-associated microbial enrichment patterns might reflect the combined effects of long-term genetic selection of pig breeds, age, and differences in feeding diets. The results of this study provide important insights for further investigating the effects of gut microbiota on boar reproductive traits and for developing strategies to modulate the gut microbiota to improve boar health and production performance.},
}

@article {pmid42245495,
year = {2026},
author = {Kuźniar, A and Das, AP and Goraj, W},
title = {Editorial: Unveiling microbiome interactions and functions in soil hotspots.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1820854},
doi = {10.3389/fmicb.2026.1820854},
pmid = {42245495},
issn = {1664-302X},
}

@article {pmid42245502,
year = {2026},
author = {Abdulsamad, MA and Bardaa, S and Elleuch, M and Mathlouthi, NEH and Ben Ali, M},
title = {Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1825173},
pmid = {42245502},
issn = {1664-302X},
abstract = {This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including mecA and the mexAB-oprM efflux system, in clinically non-infected wounds. In the Libyan cohort, four major opportunistic pathogens were identified: Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, and Corynebacterium striatum. From sample M13, a high-quality P. aeruginosa MAG (99.68% completeness, 0.89% contamination) was reconstructed, classified as ST664 and carrying 220 virulence factors, 60 antibiotic resistance genes (all confirmed by RGI v6.0.2), and 213 mobile genetic elements. These findings represent the first genomic evidence of ST664 in a North African DFU and underscore the need for metagenomics-guided antimicrobial stewardship in chronic wound management.},
}

@article {pmid42245511,
year = {2026},
author = {Otto, SJG and McLeod, L and McCarthy, EL and Funk, T and Lacoste, SR and Chai, Z and Links, MG and Barlow, LD and Gow, SP and Ramsay, D and Zaheer, R and McAllister, TA and Stothard, P and Hill, JE and Waldner, CL},
title = {Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1806062},
pmid = {42245511},
issn = {1664-302X},
abstract = {INTRODUCTION: The risk to humans and animals from antimicrobial resistance (AMR) has increased the emphasis on antimicrobial stewardship in food animal agriculture. Current stewardship recommendations include increasing diagnostic laboratory testing to inform antimicrobial use for bovine respiratory disease (BRD) management in beef feedlot production, yet the performance of newer molecular and sequencing-based diagnostic tests in commercial settings remains poorly characterized.

METHODS: Using nasopharyngeal swabs collected from commercial feedlot calves as part of Canadian surveillance, this study evaluated diagnostic laboratory testing approaches for detecting key bacterial BRD pathogens (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasmopsis bovis) and associated AMR genes. Bayesian latent class models (BLCMs) were applied to compare traditional culture and antimicrobial susceptibility testing (AST) or qPCR with long-read metagenomic sequencing and recombinase polymerase amplification (RPA). Differences in detection of target bacteria and phenotypic or genotypic AMR were assessed across the early feeding period and between age cohorts.

RESULTS: This represents the first large-scale field evaluation of a recently developed, long-read metagenomic sequencing protocol implemented by a commercial laboratory for detecting BRD bacteria and AMR in respiratory samples (n = 760) collected by private veterinarians from western Canadian beef feedlots. Detection patterns for BRD bacteria and AMR using culture/AST and metagenomics were often similar between fall-placed calves and yearlings, but with differences from RPA. Detection of BRD bacteria had low sensitivity (< 65% for most organisms/tests), but higher specificity (>90% for all organisms/tests). Detection of macrolide and tetracycline resistance had low but variable sensitivity, with higher estimates for AST compared to metagenomics and RPA, and higher but variable specificity (>90% for most resistance outcomes/tests). Despite not using any targeted enrichment, metagenomic sequencing detected M. bovis although with a sensitivity lower than qPCR or RPA. Estimates of predictive value were most informative across the largest range of prevalence for AST, followed by metagenomics and then RPA.

DISCUSSION: This work demonstrates the potential for large scale implementation of long-read metagenomic sequencing to support antimicrobial stewardship and AMR surveillance for feedlot cattle. The estimates of clinical diagnostic performance and predictive values provide evidence-based guidance for three different laboratory tests for BRD management.},
}

@article {pmid42245748,
year = {2026},
author = {Li, JZ and Guan, SY and Zhang, JF and Zheng, JN},
title = {Acute Q Fever in an Elderly Traveler with Multiple Comorbidities Diagnosed by Blood mNGS and Resolved with Omadacycline.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {610202},
pmid = {42245748},
issn = {1178-6973},
abstract = {This article reports a case of acute Q fever in a 61-year-old man. The patient mainly presented with high fever and cough. Extensive multi-system investigations failed to identify an etiology. On the fourth day of admission, the diagnosis of acute Q fever was confirmed by rapid detection of Coxiella burnetii nucleic acid sequence by blood metagenomic Next-Generation Sequencing (mNGS). With the treatment of intravenous omadacycline, the fever was controlled within 24 hours and the clinical symptoms significantly improved. Subsequent sequential therapy with oral doxycycline was administered, and the patient was discharged successfully. This case highlights the value of mNGS in the rapid diagnosis of rare or zoonotic pathogens in patients with fever of unknown origin, especially in patients with potential exposure to endemic areas. Furthermore, the novel tetracycline antibiotic omadacycline, demonstrating favorable efficacy and safety despite the patient's liver dysfunction, offers a valuable treatment option for rapid control of acute Q fever symptoms, especially in severe cases or those intolerant to doxycycline.},
}

@article {pmid42245929,
year = {2026},
author = {Yan, W and Wang, X and Shi, K and Wang, L},
title = {Atypical Legionella pneumophila encephalopathy lacking respiratory symptoms and radiographic lesions: A Case Report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1828042},
pmid = {42245929},
issn = {2296-858X},
abstract = {This report details an unusual case of Legionella pneumophila encephalopathy in a 29-year-old male who presented with acute altered consciousness and extreme agitation, notably lacking any respiratory symptoms or typical meningeal signs. Extensive imaging, including chest CT and cranial MRI, revealed no pulmonary infiltrates or structural brain lesions. Cerebrospinal fluid (CSF) analysis demonstrated an aseptic profile with elevated protein, and CSF metagenomic sequencing returned negative. The diagnostic dilemma was ultimately resolved using whole-blood targeted next-generation sequencing (tNGS), which detected Legionella sequences. The patient achieved a rapid and complete neurological recovery following a combined regimen of levofloxacin and high-dose glucocorticoids. This case underscores that Legionella infection can manifest as an isolated, toxin- and immune-mediated encephalopathy without preceding clinical pneumonia. It highlights the critical rescue value of early molecular screening (such as tNGS) in unexplained encephalopathy and supports the judicious use of early steroid intervention to halt the aseptic neurotoxic cascade.},
}

@article {pmid42246002,
year = {2026},
author = {Ren, JM and Zhang, XY and Liu, XP and Pei, LH and Jiang, WP and Zhang, XM and Ding, H and Huang, JS},
title = {Specimen-specific differences in clinical metagenomic sequencing reporting patterns in hospitalized patients: a single-center retrospective observational study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1823283},
pmid = {42246002},
issn = {2235-2988},
abstract = {Clinical metagenomic next-generation sequencing (mNGS) is increasingly used in hospitalized patients, but finalized reporting patterns vary across specimen types in routine practice. We conducted a single-center retrospective observational study using routine clinical mNGS data from January 1, 2024, to December 31, 2025. A specimen-specific first-order design retained only the first eligible mNGS order per patient within each specimen category during the study window. Orders were grouped as bronchoalveolar lavage fluid (BALF), blood, cerebrospinal fluid (CSF), and tissue for primary comparisons; heterogeneous "Other" specimens were described separately. The primary endpoint was report-interpreted any-positive at the order level. We summarized specimen-specific report-interpreted positivity, pathogen-group detection, the most frequently reported organisms ranked by order-level report presence, and mixed detections among positive orders. ICU-associated analyses were included as contextual descriptive stratification only. The cohort included DNA-only orders and a subset of PMseq-RNA-tested orders; RNA virus analyses were restricted to PMseq-RNA-tested orders, and DNA-only orders were treated as not tested for RNA virus fields. Among 1, 981 included specimen-specific first orders, BALF accounted for 973, blood 473, CSF 240, and tissue 122. Report-interpreted any-positive differed by specimen type, with BALF highest (876/973, 90.0%; 95% CI, 88.0-91.8%), followed by tissue (95/122, 77.9%; 95% CI, 69.7-84.3%), blood (343/473, 72.5%; 95% CI, 68.3-76.3%), and CSF (63/240, 26.2%; 95% CI, 21.1-32.2%). Among positive orders, at least 2 distinct standardized pathogens were reported in 672/876 BALF orders (76.7%), 182/343 blood orders (53.1%), 39/95 tissue orders (41.1%), and 8/63 CSF orders (12.7%). Across the four primary specimen groups, the most frequently reported organisms included Epstein-Barr virus (n = 485), Candida albicans (n = 285), and cytomegalovirus (n = 262), together with Klebsiella pneumoniae and Acinetobacter baumannii; these rankings reflect report-level frequency rather than adjudicated pathogenic roles, particularly for latency- or reactivation-prone viruses. Of included orders, 277 (14.0%) underwent PMseq-RNA testing. These findings characterize specimen-specific differences in clinical mNGS reporting patterns and provide a specimen-context-aware reference for interpreting routine inpatient reports.},
}

@article {pmid42246191,
year = {2026},
author = {Das, D and Dixit, R and Pandey, M},
title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70462},
pmid = {42246191},
issn = {1440-1746},
abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.

METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.

RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7α-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.

CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.},
}

@article {pmid42247317,
year = {2026},
author = {Zeng, Y and Wang, S and Zhang, Q and Miao, H and Xu, J and Li, W},
title = {Successful management of Legionella pneumonia in an immunocompromised infant presenting with generalized pustular rash: A case report.},
journal = {Science progress},
volume = {109},
number = {2},
pages = {368504261458101},
doi = {10.1177/00368504261458101},
pmid = {42247317},
issn = {2047-7163},
abstract = {Legionella infection is rare in children, and extrapulmonary manifestations are even less commonly reported. Cutaneous involvement, particularly in the form of generalized pustular eruptions, may present significant diagnostic and therapeutic challenges, especially in immunocompromised patients. We report a male infant under 6 months with X-linked severe combined immunodeficiency (XL-SCID) who presented with a disseminated pustular rash as the predominant clinical feature. Initial blood and pus cultures were negative, and empirical antimicrobial therapy showed limited clinical response. Metagenomic next-generation sequencing (mNGS) was subsequently performed and identified Legionella as the causative pathogen. Based on this finding, the antimicrobial regimen was adjusted to include a macrolide antibiotic combined with trimethoprim-sulfamethoxazole (TMP-SMX), resulting in significant clinical improvement and eventual recovery. This case highlights the atypical presentation of Legionella infection with predominant cutaneous manifestations in children, particularly in the context of primary immunodeficiency, and underscores the diagnostic value of mNGS in cases with inconclusive conventional testing. Early application of advanced molecular diagnostics and timely optimization of targeted antimicrobial therapy are crucial for improving outcomes in rare and complex pediatric infections.},
}

@article {pmid42247440,
year = {2026},
author = {Levade, I and Delisle, B and Fournier, É and Therrien, C},
title = {RNA metagenomic profiling of mosquito viromes associated with Vector-Borne diseases in Quebec, Canada.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350663},
doi = {10.1371/journal.pone.0350663},
pmid = {42247440},
issn = {1932-6203},
abstract = {Mosquitoes harbor diverse viral communities, including both medically important arboviruses and insect-specific viruses, yet the viromes of mosquito populations in northern temperate regions remains poorly characterized. In this study, we used metagenomic sequencing to analyse pools of archived mosquito samples from Québec, Canada representing multiple species previously identified as arbovirus carriers. Our analyses identified 60 viral species, including three arboviruses, several insect-specific viruses, and multiple dual-host non-pathogenic viruses, revealing the rich viral diversity present in these mosquito populations. Phylogenetic analysis of complete viral genomes demonstrated genetic relationships with viruses reported from diverse geographic regions. We describe, a newly proposed bipartite Culex tombus-like virus and report the complete resolution of thirty-five viral genomic sequences. These results highlight the utility of metagenomic approaches for comprehensive characterization of the mosquito virome and underscore their potential to enhance surveillance of emerging arboviruses, including West Nile virus, in Québec and similar northern ecosystems.},
}

@article {pmid42247515,
year = {2026},
author = {Piñero, M and Librado, P},
title = {Genomic evidence for limited entomophagy in ancient Europeans.},
journal = {Science advances},
volume = {12},
number = {23},
pages = {eaec6939},
doi = {10.1126/sciadv.aec6939},
pmid = {42247515},
issn = {2375-2548},
abstract = {To meet the rising food demands of our growing population, the Food and Agriculture Organization proposed edible insects as sustainable sources of animal protein. Although hundreds of million people already consume insects around the tropics, western societies remain averse to entomophagy. To trace whether ancient Europeans consumed insects, we here apply two complementary genomic approaches. Metagenomic screening on 745 ancient anatomically modern human dental calculus returned limited insect DNA traces, with read abundances well below those observed in Neanderthals, western chimpanzees, and gorillas. In addition, genes encoding stomach-expressed chitinases show two of the most significant signatures of latitudinal differentiation genome-wide. Clines are consistent with evolutionary benefits of entomophagy in tropical regions and with expression quantitative trait locus data supporting low chitin digestibility in present-day Europeans. Ancient genomes confirm that both clines already existed at the onset of agriculture and persisted despite massive migrations. Together, our findings support occasional and possibly incidental insect consumption in Europe over the past ~9000 years.},
}

@article {pmid42247592,
year = {2026},
author = {Boulay, A and Németh, V and Criel, B and Stock, M and De Baets, B and Galiez, C and Rousseau, E and Briers, Y and Vázquez, R},
title = {PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
doi = {10.1093/database/baag033},
pmid = {42247592},
issn = {1758-0463},
support = {#325947//FRQNT/ ; //NSERC/ ; 1S91526N//FWO/ ; 1S38519N//FWO/ ; #307935//FRQS/ ; 01P10022//BOF/ ; },
abstract = {As biology becomes increasingly data-driven, so does the field of phage lysins, enzymes that degrade bacterial cell walls and offer promising alternatives to traditional antibiotics. Five years ago, we introduced PhaLP, a centralized resource for Phage Lytic Protein sequences and associated metadata to support global research efforts. Here, we present PhaLP 2.0, an enhanced database designed to address key challenges in computational lysin research by integrating newly identified lysins from thousands of metagenomes. To expand the known diversity of lysins beyond that of cultured phages, we developed SUBLYME, a protein-embedding-based machine-learning Software designed to Uncover and classify Bacteriophage Lysins from Metagenomic datasets. Using embeddings derived from the well-curated sequences of the original PhaLP database, we trained support vector machines to distinguish lysins from non-lysins in viromes and classify them as endolysins or virion-associated lysins. The models achieved an average F1 score of 98% on held-out clusters. SUBLYME enabled the discovery of 743 000 new lysin sequences from EnVhogDB, a virome-derived protein database, increasing the number of known lysin clusters 40-fold, from 1000 to 40 000. SUBLYME and PhaLP 2.0 are accessible online at https://github.com/Rousseau-Team/sublyme and https://phalp.ugent.be, respectively. Together, these advances establish PhaLP 2.0 as a comprehensive and scalable portal for lysin discovery, classification, and sequence analysis, paving the way for future antibacterial applications and evolutionary insights.},
}

@article {pmid42247807,
year = {2026},
author = {Sadia, H and Amin, A and Khalid, N and Ahmed, I},
title = {Antimicrobial resistance and virulence in polymicrobial chronic wound infections: A metagenomic perspective.},
journal = {Journal of infection and public health},
volume = {19},
number = {8},
pages = {103280},
doi = {10.1016/j.jiph.2026.103280},
pmid = {42247807},
issn = {1876-035X},
abstract = {BACKGROUND: Chronic wound infections represent a significant clinical and public health challenge due to their polymicrobial nature and the increasing burden of antimicrobial resistance (AMR). Conventional culture-based diagnostics often fail to capture the full microbial diversity and resistance potential associated with these infections.

METHODS: Chronic wound samples persisting for more than 15 days were collected from patients at a tertiary-care hospital in Pakistan. Samples are categorized into five groups: lower leg (ll-H1), upper leg (ul-H2), foot (ft-H3), chest (ct-H4) and catheter (ca-H5). Shotgun metagenomic sequencing was employed alongside routine culture-based methods to characterize microbial communities, antimicrobial resistance genes, and virulence determinants. Taxonomic and functional profiling were performed to assess microbial diversity and resistance patterns across wound subgroups.

RESULTS: Metagenomic analysis revealed a predominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Clinically relevant pathogens, including Achromobacter xylosoxidans, Staphylococcus aureus, and Pseudomonas aeruginosa, were frequently detected, along with less commonly reported taxa such as Achromobacter insolitus and Stenotrophomonas maltophilia. Multiple antimicrobial resistance gene clusters and biofilm-associated virulence factors were identified, indicating substantial multidrug resistance potential. Site-specific analysis showed that Pseudomonas aeruginosa dominated ul-H2 (∼32%), while Enterobacter hormaechei was most abundant in ft-H3 (∼40%). Culture-based methods primarily recovered common aerobic pathogens, whereas metagenomics detected additional opportunistic and unculturable taxa, highlighting the limitations of routine diagnostics. Resistome analysis identified ARGs conferring resistance to β-lactams, aminoglycosides, fluoroquinolones, tetracyclines, and macrolides.

CONCLUSIONS: Chronic wound infections in Pakistan harbor diverse polymicrobial communities with substantial antimicrobial resistance and virulence potential. Shotgun metagenomics provides a more comprehensive characterization than culture-based methods by detecting additional pathogens and resistance determinants across wound sites. These findings support the integration of metagenomic diagnostics to improve clinical decision-making, strengthen antimicrobial stewardship, and guide infection control strategies in resource-limited healthcare settings.},
}

@article {pmid42248018,
year = {2026},
author = {Park, S and Shin, JH and Lee, HH and Lee, JG},
title = {Cover crop incorporation maintains the methane oxidation potential and lowers methane emissions in plastic-film-mulched upland arable soils.},
journal = {Journal of environmental management},
volume = {410},
number = {},
pages = {130115},
doi = {10.1016/j.jenvman.2026.130115},
pmid = {42248018},
issn = {1095-8630},
abstract = {Plastic film mulching can transform upland arable soils from sinks for methane (CH4) into sources by limiting gaseous exchange and creating hypoxic microsites. We explored whether incorporating cover crops can help reduce CH4 emissions by maintaining methanotroph functional potential in the presence of mulching. We conducted a field experiment in an upland maize field to compare NPK fertilization and cover crop incorporation, both with and without mulching. We combined CH4 flux measurements with methane oxidation potential (MOP) assays and shotgun metagenomics to analyze CH4-cycling communities and functional gene profiles. Cover crop incorporation under mulching (M-CC) reduced cumulative CH4 emissions by 55% compared with NPK fertilization under mulching (M-NPK) and maintained 17% higher MOP. By contrast, particulate methane monooxygenase (pMMO) genes did not show a uniform enrichment under M-CC. However, M-CC demonstrated higher abundances of genes associated with hydrogenase activity, single-carbon (C1) metabolism, electron transport, and antioxidant biosynthesis. Specifically, there was a 21% to 67% increase in hydrogenase genes, a 14% to 55% rise in C1 metabolism genes, a 28% to 54% increase in electron transport genes, and a remarkable 280% elevation in the antioxidant biosynthesis gene egtD. Using plastic film mulching with incorporated cover crops maintained MOP and promoted greater microbial biomass and metabolic flexibility. These effects were linked to lower CH4 emissions and reduced yield-scale CH4 emissions, all without compromising maize yield.},
}

@article {pmid42248101,
year = {2026},
author = {Xu, Z and Zhang, L and Zhu, D and Zhi, S and Ashbolt, NJ and Li, G and Luo, W and Nghiem, LD},
title = {Optimising composting to reduce plasmid and integrative conjugative element conjugation to minimise antibiotic resistomes in livestock manure for safe organic fertilisation.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142573},
doi = {10.1016/j.jhazmat.2026.142573},
pmid = {42248101},
issn = {1873-3336},
abstract = {Antimicrobial resistance is a critical threat to organic fertilizer production from livestock manure by composting. This study provides new insights to the dynamics of antimicrobial resistance genes (ARGs) during composting to propose strategies for their elimination. Results from genome-resolved metagenomics, meta-analysis, and quantitative assessment showed temperature and moisture content as key factors governing ARG dynamics during composting. Although integrative conjugative elements (ICE) could be transferable by some thermophilic bacteria, composting temperature to above 60 °C reduces mobile ARGs driven by plasmid conjugation for elimination. Further controlling moisture content to low than 60% inhibits the secretion of extracellular polymeric substances to restrain ARG rebound by ICE conjugation, particularly at the maturation stage of composting. These results are significantly useful for China, where swine manure accounted for most of livestock manure-derived ARGs (91.5%). Applying findings from this study to optimise the composting of livestock manure could reduce ARG proliferation by up to 59.3% in China.},
}

@article {pmid42248258,
year = {2026},
author = {Guo, Y and Jia, X and Chen, Y and Xu, S and Ming, T and Kong, F and Xu, J},
title = {Inhibiting methanogenesis with medium-chain fatty acids: strategy for rapid start-up and stable operation of food waste chain elongation systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135078},
doi = {10.1016/j.biortech.2026.135078},
pmid = {42248258},
issn = {1873-2976},
abstract = {Converting food waste (FW) into medium-chain fatty acids (MCFAs) via chain elongation (CE) is an economical and eco-friendly approach, but methanogenic competition remains a key challenge limiting CE efficiency. Traditional inhibition methods (e.g., pH regulation, hydraulic/solids retention time control, chemical additives) require strict operation or external inputs, causing non-specific microbial inhibition, high costs and environmental risks. Innovatively, MCFAs can inherently suppress methanogens with obvious advantages. However, their inhibition mechanisms and dependence on concentration and carbon chain length remain unclear. This study investigated the effects of butyric acid (C4), caproic acid (C6), and caprylic acid (C8) at different concentrations on methane production, medium- and short-chain fatty acids accumulation, and microbial dynamics in FW anaerobic fermentation. The results indicated that the inhibitory effect was primarily driven by undissociated fatty acids, with the potency increasing with longer carbon chain lengths. Notably, C8 at a low undissociated concentration (0.05 mM) completely inhibited methanogenesis. Higher concentrations of C4, C6, and C8 effectively sustained hydrolysis and acidogenesis while promoting CE and leading to the accumulation of caproic acid and caprylic acid. Metagenomic analysis showed that a decline in methanogenesis-related functional genes was accompanied by an increase in reverse β-oxidation related functional genes. These findings provide a feasible strategy for rapid start-up and stable operation of FW-based CE systems, and present a sustainable route for FW valorization toward high-value biochemicals.},
}

@article {pmid42248259,
year = {2026},
author = {Gai, T and Zhang, J and Zhang, S and Zhang, L and Li, X and Wu, Y and Yang, Y and Liu, X and Shi, G and Yang, M},
title = {Performance and mechanisms of a biochar-enhanced partial nitritation/anammox process for the treatment of silane tower wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135083},
doi = {10.1016/j.biortech.2026.135083},
pmid = {42248259},
issn = {1873-2976},
abstract = {The increasing discharge of silane tower wastewater, characterized by high ammonia (NH4[+]-N) and the presence of silane derivatives, poses significant challenges to biological nitrogen removal processes. In this study, a partial nitritation/anammox (PN/A) sludge system was enhanced through the addition of sludge-derived biochar (SBC). The results demonstrated that SBC effectively improved the nitrogen removal performance of PN/A sludge during the treatment of silane tower wastewater. Under low-proportion silane tower wastewater conditions, SBC rapidly promoted R2 sludge granulation within 19 d during phase I. During phase IV, when 100% silane tower wastewater was used as the influent, the NH4[+]-N and total nitrogen removal efficiencies of R2 were stably maintained at 80%-83%. These improvements were mainly attributed to the ability of SBC to promote sludge granulation, enrich functional microorganisms, and enhance extracellular electron transfer (EET) performance. SBC addition enabled the sludge to maintain higher levels of tightly bound extracellular polymeric substances rich in hydrophobic amino acids (HAAs). This study found that SBC-promoted EET was more strongly associated with anammox bacteria than with ammonia-oxidizing bacteria, resulting in a more pronounced enhancement of specific anammox activity than specific ammonia oxidation rate. Metagenomic and metatranscriptomic analyses further revealed that SBC enhanced the biosynthetic pathways and transcriptional expression of genes associated with HAA synthesis in PN/A sludge. Overall, this study provides a novel enhancement strategy for the application of PN/A processes in the treatment of complex industrial wastewater with high NH4[+]-N concentrations.},
}

@article {pmid42248305,
year = {2026},
author = {Janes, VA and Stalenhoef, JE and Van der Putten, B and Koster, L and Jakobs, ME and Van Dissel, JT and De Jong, MD and Schultsz, C and Mende, DR},
title = {Metagenomic sequencing as a diagnostic tool for urine culture negative febrile urinary tract infection.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106783},
doi = {10.1016/j.jinf.2026.106783},
pmid = {42248305},
issn = {1532-2742},
abstract = {OBJECTIVES: The diagnosis of febrile urinary tract infection (fUTI) by urine culture is hampered by antibiotic pre-treatment. We investigated urine metagenomics to diagnose fUTI in patients with positive blood but negative urine cultures.

METHODS: We performed shotgun metagenomic sequencing on 41 culture-positive and 19 culture-negative urine samples from fUTI patients, comparing urine metagenomics to blood and urine culture including antimicrobial susceptibility testing (AST). mOTUs3.1 performed metagenomic pathogen detection and ResFinder2.0 antimicrobial drug resistance (AMR) gene detection (standard settings). Whole genome sequencing (WGS) was performed on blood culture isolates from culture-negative urine samples. BWA-MEM and sylph aligned metagenomic pathogen reads to their respective WGS assemblies.

RESULTS: Metagenomics detected the blood culture isolate in 39/41 culture-positive and 17/19 culture-negative urine samples. 11/19 urine culture-negative patients were pre-treated with antibiotics, versus 8/41 urine culture-positives. The blood culture isolate was the most abundant pathogen in 33/41 culture-positive and 15/19 culture-negative urine samples. A median of 93.2% of pathogen-specific metagenomic reads mapped to their WGS assemblies with a median ANI of 98.7% (n=11). Genotypic AMR detection and phenotypic AST matched in 38-96% of cases.

CONCLUSIONS: Urine metagenomics successfully detected the causative pathogen in urine culture-negative fUTI patients. Genotypic AMR prediction requires further investigation.},
}

@article {pmid41551460,
year = {2026},
author = {Cornman, RS and Hepner, MJ and Otto, CRV},
title = {The Appalbees menu: a multiyear, multilocus metagenetic assessment of pollen foraging by Appalachian Bombus affinis workers.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20284},
pmid = {41551460},
issn = {2167-8359},
mesh = {Animals ; Bees/physiology ; *Pollen/genetics/classification ; Virginia ; West Virginia ; DNA Barcoding, Taxonomic ; Appalachian Region ; *Feeding Behavior ; Metagenomics ; Pollination ; },
abstract = {BACKGROUND: Detailed studies of foraging behavior are needed for scientific management of the endangered rusty-patched bumblebee (Bombus affinis) in the disjunct and ecologically differentiated habitats it presently occupies. Current knowledge gaps hinder recovery planning but are challenging to redress through direct observation of rare interactions in the field.

METHODS: We used genetic metabarcoding to characterize the taxonomic composition of pollen collected by B. affinis workers in the Appalachian mountains of Virginia and West Virginia from 2021-2023. We developed a custom sequence database of the regional flora and compared results for two independent genetic loci, internal transcribed spacer 1 and internal transcribed spacer 2 (ITS1 and ITS2).

RESULTS: While ITS2 consistently detected more plant diversity, results from the two loci were broadly concordant with a few notable exceptions. The plant genera Hydrangea, Actaea, Rhododendron, Tilia, and (unexpectedly) Laportea were prominent in midsummer samples, with Rubus a consistent contributor in late spring and early summer. Pea flowers (family Fabaceae) were relatively infrequent but the genera Securigera and Trifolium were detected before the Hydrangea bloom and again in late summer afterwards. The diversity of forage plants was highest in late summer, driven primarily by various genera of Asteraceae. Comparing the current data with previous work indicates regional differentiation in forage plants between Appalachia and the upper Midwest, but also allows 'consensus' forage sources that are supported by multiple lines of evidence and shared between regions to be tabulated. These results should help managers focus survey efforts for this endangered species and plan habitat enhancements.},
}

Animals
Bees/physiology
*Pollen/genetics/classification
Virginia
West Virginia
DNA Barcoding, Taxonomic
Appalachian Region
*Feeding Behavior
Metagenomics
Pollination

@article {pmid42012700,
year = {2026},
author = {Chen, J and Xi, M and Hu, W and He, R and Zhang, W and Zhang, Y and Chen, X and Chen, J},
title = {Adult Onset of MSMD Caused by IL-12Rβ1 Variants: Report of a Young Woman with NTM Infection Lacking Bacille Calmette-Guérin (BCG)-induced Diseases.},
journal = {Journal of clinical immunology},
volume = {46},
number = {1},
pages = {},
pmid = {42012700},
issn = {1573-2592},
support = {23141901900//the Shanghai Science and Technology Innovation Action Plan，experimental animal research project/ ; 23PJD073//the Shanghai Pujiang Program/ ; ynms202306//Basic Research Project of the Sixth People's Hospital of Shanghai/ ; },
abstract = {UNLABELLED: Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by increased susceptibility to infections caused by weakly virulent mycobacteria (such as nontuberculous mycobacteria (NTM) or the Bacillus Calmette–Guérin (BCG) vaccine) in otherwise healthy individuals. In this study, we described a 29-year-old patient with MSMD due to NTM infection identified using metagenomic next-generation sequencing (mNGS) testing. The patient showed a poor response to standard antimycobacterial treatment. Therefore, we performed whole-exome sequencing (WES) and identified three heterozygous variants in IL-12Rβ1 (Ala131Thr, Arg323* and Arg561*). The two deleterious IL-12RB1 variants, Arg323* and Arg561*,were shown to be in trans (paternal and maternal, respectively). Further investigation revealed that two of these variants (Arg323* and Arg561*) could affect the binding between IL-12Rβ1 and IL-12Rβ2, leading to a weakened response of CD4[+] T cells to stimulation with IL-12 plus tuberculosis antigen (TbAg), with reduced expression levels of IFN-γ and its downstream target p-STAT4. However, these variants did not affect the CD4[+] T-cell response to glucan stimulation, as the three heterozygous variant loci do not interfere with the aggregation of IL-12Rβ1 and IL-23R. This autosomal recessive, partial IL-12Rβ1 deficiency ultimately resulted in the patient developing disseminated NTM infection. In clinical treatment, we combined IFN-γ with standard antimycobacterial therapy. The patient showed only a partial response to therapy. Therefore, as detection techniques continue to advance, it is important for clinicians to increase their understanding of MSMD to enable faster and more accurate diagnosis and treatment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10875-026-02009-x.},
}

@article {pmid42235671,
year = {2026},
author = {Peng, D and Liu, X and Wang, L and Pan, Y and Kang, B and Liu, X and Xu, R and Cheng, Y},
title = {A multi-omics signature of microplastic exposure and its clinical, metabolic, and microbial correlates in colorectal cancer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128426},
doi = {10.1016/j.envpol.2026.128426},
pmid = {42235671},
issn = {1873-6424},
abstract = {Microplastics (MPs) are emerging environmental contaminants with potential human health implications, yet their distribution and biological effects in colorectal cancer (CRC) remain unclear. Here, we investigate the presence of MPs in blood, tumor, and peri-tumor tissues from CRC patients using a multi-omics approach. We find that MPs, particularly polyvinyl chloride (PVC) and polyethylene (PE), are more abundant in tumor and peri-tumor tissues than in blood. Tissue-specific MPs were associated with clinical traits, serum metabolites, and gut microbes. Functional analysis suggested MP-related alterations in microbial pathways involving carbohydrate metabolism, fatty acid degradation, and bile acid biosynthesis. Our findings provide the first integrative evidence suggesting potential links between MPs exposure to metabolic and microbial dysregulation in CRC patients.},
}

@article {pmid42235696,
year = {2026},
author = {Tang, P and Shuai, H and Yang, Z and Cen, Q and Mao, Y and Wang, J and Zhou, Y},
title = {Contributions and mechanisms of bioclogging-induced oxygen-limited microsites to nitrogen removal in porous media.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135059},
doi = {10.1016/j.biortech.2026.135059},
pmid = {42235696},
issn = {1873-2976},
abstract = {Nitrate (NO3[-]-N) in wastewater treatment plant (WWTP) effluents has become a contributing factor to the increasing eutrophication risk in receiving waters, whereas the relatively high dissolved oxygen (DO, approximately 7-8 mg L[-1]) in effluents constrains NO3[-]-N removal. Constructed wetland systems based on porous media are major technologies for advanced treatment of WWTP effluents. Although bioclogging in such systems is usually regarded as a negative phenomenon, it may create favorable anoxic microenvironments for denitrification through transport confinement. In this study, vertical saturated flow-through porous-media columns were established to systematically elucidate how bioclogging reshapes oxygen transport and drives microbial functional reorganization under bulk-oxic conditions. The results showed that hydraulic conductivity (k) decreased from 27.5 and 18.1 cm s[-1] in Groups A and B, respectively, to < 0.03 cm s[-1], while NO3[-]-N removal increased from 61 to 64% during start-up to 88-91% at day 24. The two-dimensional plate experiment directly captured the full evolution of pore-scale oxygen-limited microenvironments from discrete patches to connected structures. DO heatmaps further showed that bioclogging-induced transport confinement generated nested confined oxygen-limited microsites within an otherwise bulk-oxic flow field. Denitrification-related genes were enriched in the clogging-affected upper and intermediate layers, indicating that efficient denitrification was more likely associated with bioclogging-induced confined oxygen-limited microsites than simply with medium depth. Metagenomic analysis further revealed a metabolic division of labor within the microbial community, with Ectobacillus mainly associated with upstream nitrate reduction, Nitrospira and Chitinophagaceae playing complementary roles in downstream steps, and Ignavibacterium exhibiting genomic signatures consistent with enhanced organic-carbon metabolism and potential reducing-equivalent generation. Overall, bioclogging coupled bulk-oxic and locally oxygen-limited functions through transport confinement and community-level metabolic partitioning, providing new mechanistic insights into stable nitrogen removal under high-DO effluent conditions.},
}

@article {pmid42235698,
year = {2026},
author = {Zhou, X and Yu, Z and Liao, H and Wang, Y and Zhuang, L and Zhou, S},
title = {Bacteria and viruses associated with antibiotic resistome in hyperthermophilic co-composting of cow manure and mushroom residue.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135075},
doi = {10.1016/j.biortech.2026.135075},
pmid = {42235698},
issn = {1873-2976},
abstract = {Antibiotic resistance in livestock-derived wastes represents a critical environmental and public health concern. Here, we applied genome-resolved metagenomic analysis to characterize antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and associated viral communities during co-composting of cow manure and mushroom residue. By day 20, hyperthermophilic composting (HTC) achieved markedly higher ARG removal (93%) than conventional thermophilic composting (TC, 84%). This enhanced performance was associated with the enrichment of thermophilic taxa (e.g., Bacillaceae and Sporolactobacillaceae) and the suppression of mesophilic ARG reservoirs (e.g., Enterobacteriaceae and Pseudomonadaceae). Genome-resolved analysis further revealed that a majority of multidrug-resistant ARB were eliminated during HTC, particularly Klebsiella pneumoniae and Escherichia coli harboring diverse ARGs and virulence factor genes. These high-risk pathogens were predicted to be targeted by a subset of lytic phages, including those affiliated with Autographiviridae and Schitoviridae, suggesting a potential role of lytic phages in suppressing resistance- and virulence-associated ARB. Collectively, these findings provide genome-resolved insights into the coordinated roles of thermophile-driven suppression and phage-mediated predation of ARB in ARG removal, highlighting HTC as a promising strategy for safer manure recycling and resistance risk mitigation.},
}

@article {pmid42235960,
year = {2026},
author = {Chongdar, N and Goyal, A and Damare, SR},
title = {Genomic Survey of Carbon Monoxide Dehydrogenases Reveals Their Widespread Distribution in Marine Habitats.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70375},
doi = {10.1111/1758-2229.70375},
pmid = {42235960},
issn = {1758-2229},
support = {DST/INSPIRE/04/2021/002518//Department of Science and Technology, Govenrnment of India/ ; },
abstract = {Most carbon monoxide (CO) produced in the ocean is consumed by microorganisms encoding carbon monoxide dehydrogenases (CODHs), thereby significantly reducing the flux of CO from the ocean to the atmosphere. CODHs are of two types based on the metal content of their active sites: the oxygen-sensitive, nickel-containing Ni-CODH and the oxygen-tolerant, molybdenum-copper-containing Mo-CODH. Although CODHs have been reported from specific marine environments, their combined distribution across ocean ecosystems remains unclear. Here, we analyzed the NCBI non-redundant protein database and identified 1969 Ni-CODH and 864 Mo-CODH genes from marine prokaryotes spanning diverse oceanic ecosystems. Using metagenomic analyses across three marine biomes, we showed that oxygen availability selectively constrains Ni-CODH gene abundance, but not Mo-CODHs. Thus, Ni-CODHs are restricted to oxygen-limited niches, while Mo-CODHs occur across both oxygenated and oxygen-limited marine environments. Phylogenetic analyses indicated that all previously described CODH clades are represented in the marine ecosphere, highlighting their evolutionary diversity. Genome context analyses suggest that approximately 50% of the marine Ni-CODH potentially participate in carbon fixation via the Wood-Ljungdahl pathway, whereas most marine Mo-CODH likely contribute to the supplementary energy conservation. Together, these results provide an integrated view of CODH distribution and potential function in marine ecosystems.},
}

@article {pmid42236101,
year = {2026},
author = {Borghi, E and Tassi, L and d'Orsi, G and Uzzau, S and Pivari, F and Ricci, E and Longoni, G and Mingarelli, A and Previtali, R and Berardi, R and De Diego, L and Vigano', I and Olivotto, S and Compierchio, E and Veggiotti, P and Canevini, MP and Vignoli, A},
title = {Microbiota-gut-brain axis and treatment resistance in epilepsy: a multicentre prospective study protocol (CARE).},
journal = {BMJ open},
volume = {16},
number = {6},
pages = {e111607},
doi = {10.1136/bmjopen-2025-111607},
pmid = {42236101},
issn = {2044-6055},
abstract = {INTRODUCTION: Approximately one-third of people with epilepsy (PWE) experience resistance to treatment, including pharmacological therapies, epilepsy surgery, vagus nerve stimulation (VNS) and dietary interventions such as the ketogenic diet (KD). Emerging evidence suggests that the gut microbiota may influence seizure susceptibility and treatment response through the microbiota-gut-brain axis, potentially contributing to treatment resistance. The MiCrobiota-gut-brain Axis in Resistant Epilepsy project investigates how gut microbial features and associated host epigenetic signatures affect clinical outcomes in PWE undergoing diverse treatment strategies.

METHODS AND ANALYSIS: This is a multicentre, prospective, longitudinal study involving four clinical centres in Italy and one self-financing partner. Participants aged 3-50 years will be enrolled and stratified into four intervention cohorts: newly diagnosed drug-naïve epilepsy scheduled to start anti-seizure medications, focal drug-resistant epilepsy (DRE) undergoing epilepsy surgery, DRE receiving VNS, and DRE initiating KD. Clinical assessments (including body mass index calculation, self-reported monthly seizure count, dietary evaluation, quality of life scale and gastrointestinal symptoms scale), electroencephalography, MRI and biological sample collection (stool and blood) will be obtained at baseline and longitudinally at two or three timepoints over a 12-month observation period. Gut microbiota changes over time will be assessed via metagenomics (using 16S ribosomal RNA sequencing) and metaproteomics; the associated host DNA methylation profiles will be obtained from blood using Illumina EPIC arrays. Primary endpoints include identification of microbial or host methylation changes predictive of therapeutic response (ie, reduction from baseline in monthly seizure count) to the intervention. Data will be analysed using multivariate models and mixed-effect regression. Further, omics data and corresponding metadata will be integrated using multi-omics approaches to identify molecular signatures biomarkers predictive of treatment response and prognosis in PWE.

ETHICS AND DISSEMINATION: The study received ethical approval from the Research Ethic Board (Comitato Etico Territoriale Lombardia 3, ID 4896 - parere numero 4896_17.07.2024_N_bis). All participants or their legal guardians will provide written informed consent. Results will be disseminated through peer-reviewed publications, conference presentations or lay summaries targeting patient organisations.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier NCT07010445, registered on 2 May 2025.},
}

@article {pmid42236489,
year = {2026},
author = {Kehl, AJ and Taylor-Kearney, L and Jaffe, AL and Pereira, JH and Lee, J and Hammel, M and Waldburger, LM and Yeow, C and Valentin-Alvarado, L and Adams, PD and Banfield, JF and Siegel, JB and Prywes, N and Shih, PM},
title = {Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73982-5},
pmid = {42236489},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of subclades. Recent advances in metagenomics have dramatically reshaped our understanding of both microbial and rubisco diversity; however, biochemical characterization of these sequences has not kept pace with the exponential growth in sequence data. To better survey the functional and structural diversity of rubisco, we systematically sample and synthesize a library of diverse rubisco sequences with an emphasis on clades that are sparsely represented in the biochemical literature. Our updated phylogenetic analysis reveals that many deep‑branching rubiscos assemble as dimers, supporting a dimeric origin for the superfamily - in contrast to the ecologically dominant hexadecameric form I. Additionally, we discover and structurally characterize an unusually large catalytic subunit among characterized rubiscos, originating from a early-branching subclade with secondary structural elements not present in canonical rubisco architectures.},
}

@article {pmid42236734,
year = {2026},
author = {Wei, Y and Xiao, J and He, J and Zhang, K and Xu, C and Zhang, N and Cheng, L},
title = {An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07581-w},
pmid = {42236734},
issn = {2052-4463},
support = {32501490//National Natural Science Foundation of China/ ; 32501489//National Natural Science Foundation of China/ ; 32571850//National Natural Science Foundation of China/ ; 32430070, 32025024 and 92251305//National Natural Science Foundation of China/ ; LQ24C030001//Zhejiang Provincial NSFC/ ; LQ21C030009//Zhejiang Provincial NSFC/ ; LZ24C030001//Zhejiang Provincial NSFC/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
abstract = {Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.},
}

@article {pmid42237168,
year = {2026},
author = {Hou, X and Fu, Y and Jia, Z and Hou, L and Yin, Y and Xu, K},
title = {Multi-omics elucidates the regulatory mechanisms of tryptophan in gut health of weaned piglets.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00586-1},
pmid = {42237168},
issn = {2524-4671},
support = {CARS-35//China Agriculture Research System of MOF and MARA/ ; 2023JJ20043//Natural Science Foundation of Hunan Province Project/ ; 32372913//National Natural Science Foundation of China/ ; 2023RC3204//Science and Technology Innovation Program of Hunan Province/ ; },
abstract = {Tryptophan (Trp), an essential amino acid (AA) implicated in diverse physiological and pathological processes, remains incompletely characterized in its mechanisms regulating intestinal health in weaned piglets. In this study, 27 weaned Bama miniature pigs with highly homogeneous genetic characteristics (6.200 ± 0.242 kg) were randomly divided into three groups and fed a basal diet, a diet supplemented with 0.5-fold Trp, or a diet supplemented with 1.5-fold Trp for 21 days. We used multi-omics approaches to investigate the mechanisms by which Trp regulates intestinal health through dietary interventions with different concentrations. Both Trp-supplemented groups exhibited significantly reduced diarrhea incidence (P = 0.012) and improved intestinal morphology compared to the control group (P < 0.05). While Trp-targeted metabolomics showed no statistically significant alterations, metagenomic analysis revealed Trp-driven microbial remodeling, characterized by increased α-diversity, elevated abundances of Deferribacteres, Turicibacter, Clostridials_Bacteria, and Turicibacter_Sanguinis, alongside decreased Tenericutes and Chryseobacterium. Transcriptome analysis further identified immune-related pathways as central targets of Trp action. Subsequent cytokine quantification confirmed Trp's immunomodulatory effects: pro-inflammatory cytokines (IL-1β, IL-6, IL-17) decreased, while anti-inflammatory IL-10 increased. Collectively, our findings demonstrate that Trp alleviates weaning-associated intestinal dysfunction by reshaping microbial ecosystems and regulating immune homeostasis.},
}

@article {pmid42237383,
year = {2026},
author = {Zhang, J and Shi, X and Peng, S and Zhang, C and Qiao, S and Yu, H},
title = {Icariin shapes post-withdrawal fecal resistome dynamics in layer hens.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42237383},
issn = {1674-9782},
support = {B2024064//Hubei Provincial Department of Education Scientific Research Project/ ; 2025RZ026//Research and Innovation Initiatives of Wuhan Polytechnic University/ ; 202409//Open Fund of Hubei Province Key Laboratory of Animal Nutrition and Feed Science/ ; 32402807//Young Scientists Fund of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: While the livestock industry actively seeks alternatives to antibiotics, residual low-dose exposures continue to drive the spread of antibiotic resistance genes (ARGs). Icariin, a plant-derived compound, is recognized for improving poultry growth and immunity. However, it remains unclear how this compound influences the environmental persistence of ARGs, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) during the vulnerable recovery phase after antibiotic withdrawal.

RESULTS: We designed a two-phase feeding trial with laying hens, using longitudinal metagenomic sequencing to track post-withdrawal resistance dynamics. Following initial exposure to a low-dose antibiotic mixture that established a baseline of elevated resistance, hens received either a basal diet, an icariin-supplemented diet, or a copper sulfate-supplemented diet. The data indicate that icariin supplementation consistently reduced the burdens of both ARGs and MGEs. It also suppressed the potential for HGT and restricted the diversity of microbial hosts harboring these resistance elements. Conversely, copper sulfate-a traditional metal-based additive-exacerbated resistance risks by expanding both the abundance and the host range of ARGs and MGEs. Across all treatments, the population of Escherichia and the prevalent ARG subtype bacA correlated strongly with total resistance loads, tracking the overall resistome burden.

CONCLUSIONS: Compared to conventional copper sulfate treatments, icariin facilitates a safer ecological recovery in the poultry gut by actively lowering ARG and MGE reservoirs after antibiotic withdrawal. These genomic insights, combined with its known physiological benefits, support icariin as a sustainable feed additive. Furthermore, the Escherichia-bacA correlation provides a reliable, streamlined indicator for monitoring resistance risks in farm environments. However, as these findings rely on short-term fecal metagenomic tracking, further validation through multi-environment studies is warranted.},
}

@article {pmid42237400,
year = {2026},
author = {Liu, J and Huang, W and Wu, X and Ma, Y},
title = {Coronavirus disease 2019-associated encephalitis and concomitant subdural hematoma: a case report.},
journal = {Journal of medical case reports},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13256-026-06148-y},
pmid = {42237400},
issn = {1752-1947},
support = {82171350//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents a global pandemic with evolving viral variants. In addition to respiratory symptoms, a growing trend of reports indicates that the central nervous system could also be affected in COVID-19 patients.

CASE PRESENTATION: Herein, we reported a case of a 61-year-old Chinese male with fever, psychiatric symptoms, and concomitant subdural hemorrhage. Although naso-oropharyngeal swab tests for SARS-CoV-2 ribonucleic acid detections were negative, the metagenomic next-generation sequencing from cerebrospinal fluid (CSF) samples showed the exclusive positive finding of SARS-CoV-2. The patient was diagnosed with probable COVID-19-associated encephalitis, and was recovered after receiving anti-infection medications, high-dose methylprednisolone pulses (1 g/day for 5 days), and subsequent intravenous immunoglobulin (0.4 g/kg body weight for 5 days) therapies.

CONCLUSION: Our case underscores the importance that for patients with fever and unexplained neuropsychiatric symptoms, it is recommended to conduct CSF testing to screen for possible pathogen infections, and to perform cranial imaging promptly to detect concomitant lesions.},
}

@article {pmid42237409,
year = {2026},
author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X},
title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02433-6},
pmid = {42237409},
issn = {2049-2618},
support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; },
abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.

RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.

CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.},
}

@article {pmid42237424,
year = {2026},
author = {Yang, L and Chen, J},
title = {mPower: a real data-based power analysis tool for microbiome study design.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02427-4},
pmid = {42237424},
issn = {2049-2618},
support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; },
abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/. Video Abstract.},
}

@article {pmid42237575,
year = {2026},
author = {Tilves, C and Xiao, S and Tanaka, T and Differding, MK and Spira, AP and Ferrucci, L and Mueller, NT},
title = {Longitudinal associations of the gut microbiome with arterial stiffness in US adults: findings from the Baltimore Longitudinal Study of Aging.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwag119},
pmid = {42237575},
issn = {1476-6256},
abstract = {The gut microbiome affects arterial stiffness in experimental murine models; however, evidence in human longitudinal studies is lacking. In this study, we investigated longitudinal between-person (average) and within-person (change) associations of microbiome features with arterial stiffness. We assessed the fecal microbiome using whole genome metagenomic sequencing, and arterial stiffness using carotid-femoral pulse wave velocity (cfPWV). Our analytic sample consisted of 349 adults from the Baltimore Longitudinal Study of Aging, who contributed 915 visits between 2013-2019. Using linear mixed models, we found higher microbiome evenness and butyrate-producing bacteria were associated with lower cfPWV on average (between-person), but changes in diversity were not associated with changes in cfPWV (within-person). Several potentially pathogenic bacteria were positively associated with cfPWV, both between- and within-person. Butyrate-production pathways were inversely associated with cfPWV between-person and borderline within-person. Trimethylamine-production genes were positively associated with cfPWV between-person and borderline within-person. In addition, changes in other functional pathways including peptidoglycan biosynthesis and L-arginine biosynthesis were associated with changes in cfPWV. In conclusion, cfPWV was associated with both between-person and within-person differences in gut microbiome features, with strength and consistency depending on the feature. These results can inform which microbiome features to target in interventions to improve arterial stiffness.},
}

@article {pmid42237904,
year = {2026},
author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH},
title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01505},
pmid = {42237904},
issn = {1520-5851},
abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.},
}

@article {pmid42237982,
year = {2026},
author = {Utreja, S and Andreani, GA and Mahmood, S and Patel, MS and Buck, MJ and Rideout, TC},
title = {Dietary pulse prebiotic fibre intake in a rat obese pregnancy model alters maternal caecal microbiome and protects against steatosis in newly weaned offspring.},
journal = {Journal of nutritional science},
volume = {15},
number = {},
pages = {e37},
pmid = {42237982},
issn = {2048-6790},
abstract = {We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.},
}

@article {pmid42238272,
year = {2026},
author = {Gallina, G and Pizzi, C},
title = {Reference-free k-mer based dissimilarity measures for metagenomes comparison.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1788907},
pmid = {42238272},
issn = {2673-7647},
abstract = {MOTIVATION: Metagenomics plays a crucial role in unraveling the relationship between microbial communities and the environment in which they live, allowing the development of food and environmental control techniques. Similarly, the study of microbial environments within the human body plays a crucial role towards precision medicine. In these contexts, the problem of metagenomic samples comparison is among the most challenging from the computational point of view due to the size of the datasets and to the incompleteness of microbial databases. Thus, the ability to define and efficiently compute reference-free dissimilarity measures is key to the development of effective and practical tools for metagenomes comparison.

RESULTS: In this work, we present a systematic experimental validation of reference-free k -mer-based dissimilarity measures. To this purpose, we investigate the correlation between two popular ecological dissimilarity measures, Bray-Curtis and Jaccard, computed using reference-free and reference-based k -mer approaches, for 12 ≤ k ≤ 31 . Our experiments cover both simulated and real metagenomics settings (samples from the human body and the oceans), and consider both linear and ranking correlation between the computed values. Our results support the hypothesis that the two definitions are indeed correlated for a wide range of values of k , and promote the development of efficient reference-free computational tools based on k -mer statistics for metagenomes comparison.},
}

@article {pmid42238651,
year = {2026},
author = {Zhang, Q and Zhang, X and Cao, M and Ma, J and Yan, R and Wang, H and Jia, S},
title = {Study on the Role and Mechanism of γδ T Cells in Atherosclerosis Under a High-Fat Diet.},
journal = {Reviews in cardiovascular medicine},
volume = {27},
number = {5},
pages = {48002},
pmid = {42238651},
issn = {2153-8174},
abstract = {BACKGROUND: This study aimed to investigate the effects of γδ T cell inhibition under a high-fat diet (HFD) on metabolic function, immune inflammation, gut microbiota, and atherosclerosis (AS) progression in ApoE [-/-] mice.

METHODS: ApoE [-/-] mice were assigned to three groups: a control group (normal diet), a model group (HFD), and an intervention group (HFD + γδ T cell receptor (TCR) monoclonal antibody). After 12 weeks, flow cytometry was used to assess γδ T cell levels, and cytokines (interferon-gamma (IFN-γ), IL-17A) were measured. Inflammatory markers in blood and adipose tissue were quantified, gut microbiota composition was analyzed via fecal metagenomics, and atherosclerosis was evaluated using Oil Red O, Masson's trichrome, and hematoxylin and eosin (HE) staining methods.

RESULTS: The HFD activated γδ T cells and increased pro-inflammatory cytokines in ApoE [-/-] mice. Treatment with the γδ TCR monoclonal antibody suppressed γδ T cells, reduced IFN-γ and IL-17A expression, improved lipid profiles, and decreased tumor necrosis factor-alpha (TNF-α), IL-1β, and IL-6 levels. Gut microbiota analysis showed an increase in beneficial bacteria, and histological staining (Oil Red O, HE, and Masson's trichrome) confirmed a reduction in atherosclerotic lesion burden.

CONCLUSION: The γδ T cells contribute to AS development under the HFD. Inhibition of γδ T cells reduces inflammation, improves gut microbiota composition, and attenuates atherosclerosis progression.},
}

@article {pmid42238901,
year = {2026},
author = {Zhao, T and Chen, Y and Sun, H},
title = {A case of severe Legionella pneumonia treated with omadacycline and nemonoxacin.},
journal = {Respiratory medicine case reports},
volume = {62},
number = {},
pages = {102437},
pmid = {42238901},
issn = {2213-0071},
abstract = {Severe Legionella pneumophila pneumonia carries high mortality, and treatment is challenged by emerging resistance to conventional fluoroquinolones/macrolides and diagnostic delays. Novel agents such as omadacycline and nemonoxacin show theoretical promise, yet robust clinical evidence in legionellosis is lacking. We report a 59-year-old man with severe community-acquired pneumonia(sCAP) who initially received empiric ceftazidime-avibactam plus nemonoxacin. Respiratory failure did not improve, and the inflammatory markers did not decline. Subsequent bronchoalveolar lavage fluid metagenomic next-generation sequencing(BALF-mNGS) and urinary Legionella antigen confirmed Legionella pneumonia. We then switched to dual therapy with omadacycline and nemonoxacin. The combination led to rapid improvements in inflammatory markers, hypoxemia, and creatine kinase levels. This case provides a clinical rationale for using omadacycline plus nemonoxacin as salvage therapy in severe Legionella pneumonia when conventional regimens fail.},
}

@article {pmid42239023,
year = {2026},
author = {Tang, F and Liu, H and Xi, L and Li, C and Wang, X and Wang, B},
title = {Solid-phase enrichment uncovers a hidden Salmonella transmission chain in a recurrent pediatric household cluster: a case report.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1820049},
pmid = {42239023},
issn = {2296-2565},
abstract = {OBJECTIVES: To describe a household cluster of recurrent pediatric non-typhoidal Salmonella (NTS) infection and compare the yield of conventional culture, solid-phase enrichment, and shotgun metagenomic sequencing across symptomatic children and household contacts.

METHODS: Longitudinal fecal specimens from a 4-year-old boy (Mo) with three discrete NTS episodes in 2 months, his monozygotic twin (TB), and three adult co-residents were processed by conventional culture; specimens from Episode 2 onwards and all contact specimens additionally received solid-phase enrichment, and a subset shotgun metagenomics. Isolates were characterized by VITEK 2, XbaI-PFGE, and whole-genome sequencing.

RESULTS: None of Mo's episodes met sepsis criteria (peak WBC 12.52 × 10?/L, CRP 5.46 mg/L, PCT 1.14 ng/mL); TB had one self-limited episode, both parents had brief symptomatic periods, and the grandmother was asymptomatic. Conventional culture was positive only at Mo's first episode, whereas solid-phase enrichment recovered Salmonella from three culture-negative pediatric acute-phase specimens (Mo 4.12, TB 4.16, Mo 5.1). Adult contacts were negative by both culture-based methods, but metagenomic sequencing detected Salmonella reads in all three. Mo_0412 and TB_0416 were S. enterica serovar Enteritidis ST11, with identical cgMLST, 99.9966% ANI, and 97% PFGE similarity, indicating a clonal household source. Mo received antibiotics across four classes during his recurrences, vs. two sequential agents in TB.

CONCLUSION: Conventional culture, solid-phase enrichment, and metagenomic sequencing functioned as complementary modalities, each recovering Salmonella the others missed, supporting a tiered diagnostic strategy for household NTS investigation. Cumulative antibiotic exposure may have contributed to Mo's differential susceptibility, a hypothesis warranting prospective study.},
}

@article {pmid42239051,
year = {2026},
author = {Lalgudi, C and Kotaka, M and Yaffe, E and Lopez, JA and Yu, FB and Ng, K and Sonnenburg, JL and Good, BH and Huang, KC and Shi, H},
title = {Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.22.727306},
pmid = {42239051},
issn = {2692-8205},
abstract = {Recovery of the gut microbiome after antibiotic exposure is often incomplete and variable, and the processes underlying this variation remain unclear. We performed longitudinal shotgun metagenomic sequencing of 2876 daily fecal samples from replicated humanized and conventional mouse cohorts exposed to controlled antibiotic perturbations. Metagenomic profiling recapitulated ecological trajectories previously observed by 16S sequencing, while revealing extensive strain-level dynamics, including reproducible sweeps of standing variants and de novo mutations in antibiotic target sites and regulatory loci. We also identified genetic changes whose effects depended on community composition, competitive release, and perturbation history. Cross-housing experiments revealed bidirectional strain transfer, with antibiotic-induced niche clearance enabling replacement of resident strains. In parallel, phage dynamics were heterogeneous and clustered by cage. Together, these findings show that post-antibiotic microbiome recovery is a path-dependent process shaped by selection, transmission, and phage activity, producing divergent outcomes even among closely matched communities exposed to the same perturbations.},
}

@article {pmid42239166,
year = {2026},
author = {Ghadermazi, P and Emerson, JB and Olm, MR},
title = {ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.726564},
pmid = {42239166},
issn = {2692-8205},
abstract = {Strain-resolved metagenomics characterizes microbial communities at nucleotide-level resolution, enabling researchers to differentiate identical from closely related organisms and characterize population structure and gene content variation. Here we introduce ZipStrain, a program that performs highly accurate strain-resolved metagenomics over 500× faster than available methods while offering superior RAM management. Applied to a dataset of 2,754 samples spanning human populations, we identify a strain-sharing gradient across social relationships, reveal striking variation in clonal structure across bacteria and bacteriophage, and pinpoint genes whose nucleotide identity deviates from genome-wide expectations. ZipStrain is distributed as an open-source Python package and accompanying Nextflow pipeline at https://github.com/OlmLab/ZipStrain .},
}

@article {pmid42239183,
year = {2026},
author = {Cirolia, G and Gustafson, JT and Aswani, A and Wolf, A},
title = {Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.21.727052},
pmid = {42239183},
issn = {2692-8205},
abstract = {Microbiome-based machine learning classifiers show increasing promise for disease identification across gastrointestinal, metabolic, and immune-mediated conditions. Inflammatory bowel disease (IBD), a chronic immune-mediated disorder associated with disruption of the gut microbiome, has been a particularly successful application area. However, while many predictive models achieve high performance within individual datasets, their ability to generalize across independent populations and geographic contexts remains unclear. Here, we tested whether model class and training dataset composition influence model generalizability across geographically diverse evaluation studies. We compiled seven publicly available shotgun metagenomic studies spanning five geographic regions, comprising 697 individuals with IBD or healthy controls. We trained 246,986 model configurations across seven model classes and five distinct training dataset combinations and evaluated top-performing models on independent studies from the USA, Ireland, Germany, Israel and China. Extreme gradient boosting and random forest models showed the highest and most consistent performance across training datasets, a ranking that was maintained on independent evaluation studies. However, models trained on geographically diverse datasets did not outperform those trained on USA-only datasets. Instead, model performance was strongly dependent on the evaluation study itself, with consistent differences in achievable accuracy across studies. Despite most models achieving similar AUC scores, there was limited overlap in the key microbial species identified. Furthermore, even for the small set of disease predictive microbes shared between models, the direction of enrichment between IBD or healthy subjects often varied in opposing directions across study populations. These findings suggest that study-specific factors constrain generalization and may help explain the lack of consistent microbiome-based biomarkers for IBD.},
}

@article {pmid42239221,
year = {2026},
author = {Keown, RA and Sikkema, AP and Barbone, VA and Ferrell, BD and Donnelly, OB and Iredell, SC and Zatopek, KM and Brumm, PJ and Mead, DA and Lohman, GJS and Wommack, KE and Polson, SW},
title = {Single amino acid substitution in DNA Polymerase I dramatically alters infection dynamics of bacteriophage T7.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.726624},
pmid = {42239221},
issn = {2692-8205},
abstract = {UNLABELLED: Viruses constitute a significant proportion of Earth's genetic diversity, yet most remain uncharacterized beyond their sequences in viral metagenomes. Linking viral genotypes to phenotypes-especially enzyme function to phage infection dynamics-is challenging due to the lack of cultured virus-host systems. DNA polymerase I (PolA), essential for genome replication in ∼25% of dsDNA phages, provides an opportunity to explore these connections. In phage T7, residue 526 is critical for nucleotide incorporation, with previous in vitro evidence indicating impacts on enzyme efficiency and fidelity. Previous analyses identified three substitutions at this position (Tyr/Y, Phe/F, Leu/L) linked with deeply rooted viral PolA clades. Mutation impacts at residue 526 were tested in vitro and in vivo . The Y526F protein exhibited a 50% reduction in specific activity, and when introduced via High Complexity Golden Gate Assembly into T7 demonstrated a 53% decrease in burst size and significantly longer latent period compared to wild type. The Y526L protein exhibited a 97% decrease in activity, and the Y526L phage was incapable of completing its lifecycle. These findings confirm historical biochemical data, provide in vivo context for these mutations in the T7- E. coli system, and offer experimental support for genotype-to-phenotype associations in viral PolA, informing viral metagenomics studies.

GRAPHICAL ABSTRACT: Created in BioRender. Keown, R. (2026) https://BioRender.com/mhrmup3.},
}

@article {pmid42239239,
year = {2026},
author = {Cho, Y and Tsuboyama, K and Litberg, TJ and Jung, MD and Obisesan, A and Wang, Q and Phoumyvong, CM and Thibeault, J and Ovchinnikov, S and Rocklin, GJ},
title = {Accurate protein stability prediction for small domains using mega-scale experiments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.19.726285},
pmid = {42239239},
issn = {2692-8205},
abstract = {Predicting absolute protein folding stability is a long-standing challenge in biophysics, with broad applications in protein design and in understanding genetic variation and evolution. Physics-based simulations have shown limited success at predicting stability and are often computationally intractable, and machine learning methods have been constrained by the lack of sufficiently large experimental datasets. We recently introduced cDNA display proteolysis, a cell-free approach that can measure folding stability for nearly one million protein domains in parallel. Here, we applied this method to measure stability for 1.8 million diverse protein domains 60-80 amino acids in length primarily taken from the MGnify metagenomic database and spanning over 200,000 sequence families. Using this new "MGnify Stability dataset", we developed the predictive models SaProtΔG and ESM3ΔG, which accurately predict absolute folding stability for small domains with root mean squared error of 0.8 kcal/mol over a 6 kcal/mol range (Spearman rank correlation of 0.88). These predictors show high accuracy at predicting effects of substitutions, insertions, and deletions, successfully identify global trends toward higher stability in thermophilic organisms, and improve discrimination of stable and unstable computationally designed proteins. Our results illustrate how megascale biophysical measurements can complement existing evolutionary and structural data to enable accurate absolute stability prediction for small domains.},
}

@article {pmid42239480,
year = {2026},
author = {Qian, J and Ghadermazi, P and Maret, S and Kemp, JF and Frank, D and Melanson, EL and Hendricks, AE and Krebs, N and Tang, M and Olm, MR},
title = {IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.19.726352},
pmid = {42239480},
issn = {2692-8205},
abstract = {BACKGROUND: IgA is the dominant antibody in the human gut and a key regulator of host-microbe interactions. Infants begin to produce IgA at around 6 months old and receive large quantities of IgA via human milk, but technical limitations have prevented species-level characterization of IgA binding in early life. This has left basic knowledge gaps about which species are targeted by IgA in infancy, and how modifiable lifestyle factors like breastfeeding and complementary feeding impact IgA targeting.

RESULTS: Here we adapt Metagenomic Immunoglobulin Sequencing (MIg-Seq) for low-biomass infant fecal samples and apply this optimized protocol to 32 longitudinal samples from 16 infants enrolled in the MINT trial, a four-arm randomized controlled trial comparing meat-based, dairy-based, plant-based, and reference complementary feeding patterns, with fecal sampling at 6 and 12 months (pre and post intervention). Infant IgA targeting mirrors adults at the phylum level, with both age groups showing significantly higher IgA targeting of Pseudomonadota and lower targeting of Bacteroidota relative to other phyla. During the substantial microbiome compositional shifts noted between 6 and 12 months, IgA targeting is significantly more stable than the microbiome itself. Among persistent colonizers, IgA targeting strengthens significantly from 6 to 12 months, with the most pronounced effect observed for Bifidobacterium , a finding robust across all dietary arms and feeding modes. The feeding arm to which infants were enrolled was not significantly associated with IgA binding, but several nutrient-specific associations were discovered. Animal-derived nutrients, particularly cholesterol, are strongly positively correlated with IgA targeting of Bifidobacterium longum , while plant-derived carotenoids are positively associated with IgA targeting of Flavonifractor plautii and Ruminococcus gnavus .

CONCLUSIONS: This study introduces an experimental and computational framework for species-level IgA profiling in the infant gut. The progressive strengthening of IgA targeting of Bifidobacterium and other beneficial persistent colonizers suggests a role for IgA in reinforcing beneficial microbes during infancy. The nutrient-specific dietary effects on IgA targeting reveal the immunological consequences of the complementary feeding period, and highlight a contrast between animal-versus plant-based diets. Together, these findings point to early nutritional interventions and IgA-based therapeutics as promising tools for promoting healthy immune-microbiome development.},
}

@article {pmid42239539,
year = {2026},
author = {Jiang, X and Chen, B and Wang, Q and Liu, Y and Li, N and Zhang, L},
title = {Structural variation analysis suggests strain-level maternal-infant microbial transmission in early life.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1765801},
pmid = {42239539},
issn = {2235-2988},
abstract = {INTRODUCTION: Structural variations (SVs)-large, functionally consequential genomic alterations-serve as high-resolution markers for strain-level differentiation in the human microbiome, yet their relevance to vertical transmission of the maternal microbiota and early-life colonization remains unclear.

METHODS: Using metagenomic data from a 98-pair longitudinal mother-infant cohort and a 25-pair multi-niche cohort, we profiled microbial taxa, functions, and SVs, characterized variable SVs (vSVs), deletion SVs (dSVs), and transmitted SVs (tSVs), and evaluated the potential influence of delivery mode, feeding regimen, and maternal ecological niches.

RESULTS: We identified 5,578 SVs across 51 reference strains, with infants showing increasing SV diversity during the first year of life, and observed significantly greater SV similarity within mother-infant pairs than unrelated pairs. Abundance-based analysis identified 90 microbial species shared between mothers and infants. However, when incorporating SV-based tracking, only 14 strains showed patterns consistent with sustained maternal contribution across time points. Furthermore, exploratory subgroup analyses suggested that both delivery mode and feeding regimen may influence the vertical transmission patterns of maternal microbial strains and transmitted SVs. Functionally, tSVs were enriched in pathways linked to carbohydrate, amino acid, and lipid metabolism, as well as transport and environmental adaptation modules such as T4SS. Multi-niche analysis further suggested that the maternal gut showed the strongest inferred signal of SV-supported strain sharing with both the infant gut and oral microbiota.

DISCUSSION: Together, these findings suggest that microbial SVs can serve as complementary markers for investigating maternal contribution and vertical transmission-related strain-level patterns in early-life microbiome development, providing new insights into microbial inheritance and early-life health trajectories.},
}

@article {pmid42239987,
year = {2026},
author = {Zhao, C and Zhang, L and Wang, Y and Yang, G and Ren, C and Cao, X and Yu, Q and Jin, B and Men, Y and Liu, H and Zhang, J},
title = {Microbial Dehalogenation of 3,5,6-Trichlorooctafluorohexanoic Acid under Different Reducing Conditions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c17496},
pmid = {42239987},
issn = {1520-5851},
abstract = {Chlorinated polyfluoroalkyl substances (Cl-PFAS) have emerged as promising alternatives to legacy PFAS due to their enhanced microbial reactivity and improved environmental degradability. However, their transformation mechanisms under environmentally relevant reducing conditions remain poorly characterized. This study investigated the microbial dehalogenation of 3,5,6-trichlorooctafluorohexanoic acid (CTFE3), a representative Cl-PFAS, under nitrate-, sulfate-, iron-reducing, and methanogenic conditions. Microbial defluorination was observed across all reducing environments, with higher total defluorination efficiencies (∼60%) under nitrate- and sulfate-reducing conditions compared to iron-reducing and methanogenic conditions (∼30%) under the tested experimental conditions. Proposed biotransformation pathway analysis suggested that CTFE3 underwent more diverse and sequential hydrolytic dechlorination under nitrate- and sulfate-reducing conditions, which was associated with more extensive defluorination. Genes associated with hydrolytic dechlorination were consistently enriched under these conditions, but not in iron-reducing or methanogenic environments. Metagenomic binning further identified key taxa (e.g., Methyloversatilis discipulorum, Herbaspirillum seropedicae, Paracoccaceae, and Rhodobacteraceae-related bacteria) harboring both hydrolytic dechlorination and nitrate/sulfate-reduction genes, suggesting their involvement in CTFE3 hydrolytic dechlorination and subsequent defluorination. This study demonstrates that reducing conditions play an important role in shaping CTFE3 transformation patterns and highlight hydrolytic dechlorination as a viable pathway associated with extensive microbial defluorination, thereby offering insights for sustainable Cl-PFAS remediation.},
}

@article {pmid42240391,
year = {2026},
author = {de Sousa, LP and Calderon Fajardo, AA and Brandão, MM and Maia de Oliveira, V and Romero, GQ},
title = {Metagenome-assembled genomes of four novel bacterial species from Atlantic rainforest stream sediments in Brazil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0033626},
doi = {10.1128/mra.00336-26},
pmid = {42240391},
issn = {2576-098X},
abstract = {Here, we report draft genome sequences of four novel bacterial species from Atlantic rainforest stream sediments in southeastern Brazil. The genomes represent distinct lineages within Nitrospirota and Pseudomonadota (average nucleotide identity <95% to known species) and encode diverse metabolic capabilities, including nitrification, denitrification, and aromatic compound degradation.},
}

@article {pmid42240519,
year = {2026},
author = {Gharbi, M and Abbassi, MS},
title = {Bacteria as anticancer agents: bioactive metabolites, engineered platforms, and translational mechanisms.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag050},
pmid = {42240519},
issn = {1472-765X},
abstract = {Bacteria represent a vast and underexplored reservoir of bioactive compounds with significant anticancer potential. Numerous bacterial taxa, particularly actinomycetes, Bacillus, Pseudomonas, and marine-derived species, produce structurally diverse metabolites exhibiting cytotoxic, cytostatic, pro-apoptotic, immunomodulatory, and anti-angiogenic activities against cancer cells. Clinically established agents such as actinomycin D and bleomycin highlight the therapeutic relevance of bacterial natural products, while recent discoveries continue to expand the repertoire of bioactive polyketides, peptides, alkaloids, and proteins. These compounds act through multiple mechanisms, including DNA intercalation, induction of apoptosis, cell cycle arrest, metabolic disruption, and modulation of the tumor microenvironment. Advances in metagenomics, genome mining, and synthetic biology have enabled the identification and activation of previously silent biosynthetic gene clusters, significantly enhancing drug discovery potential. In addition to metabolite-based anticancer agents, advances in synthetic biology have enabled the development of engineered bacterial platforms capable of selectively colonizing tumors, delivering therapeutic molecules, and activating prodrug therapies within the tumor microenvironment. Despite ongoing challenges related to toxicity, limited yield, selectivity, and clinical translation, bacterial-derived compounds remain a promising frontier in oncology. This review summarizes bacterial sources, bioactive metabolites, molecular mechanisms, preclinical and clinical applications, and future prospects for developing effective and safe anticancer strategies.},
}

@article {pmid42240631,
year = {2026},
author = {Hernández-Velázquez, R and Hernández-Avilés, JS},
title = {Metagenomic insight into the diversity and biogeochemical functions of microbial communities in the maar tropical Lake Atexcac.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {6},
pages = {},
pmid = {42240631},
issn = {1465-2080},
abstract = {Warm monomictic maar lakes in tropical regions represent dynamic systems where thermal stratification generates strong vertical gradients in oxygen availability and redox conditions, shaping microbial community structure and function. Lake Atexcac (Puebla, Mexico) undergoes seasonal stratification and episodic whiting events that provide a framework to examine microbial responses to changing hydrodynamic conditions. In this study, we applied deep shotgun metagenomic sequencing to characterize the taxonomic composition and functional potential of microbial communities across the epilimnion, metalimnion and hypolimnion during two contrasting stratification phases: early stratification associated with a whiting event and a later, well-established stratification period.Metagenomic profiles revealed a clear vertical organization of microbial communities, with samples clustering primarily according to thermal strata and the metalimnion displaying the highest genetic differentiation. Genome-resolved analyses enabled the recovery of a large number of metagenome-assembled genomes, with marked differences in their vertical distribution between hydrodynamic phases. The recovered genomes encompassed diverse metabolic pathways related to carbon, nitrogen and sulphur transformations, reflecting the heterogeneous redox conditions along the water column. Notably, sulphur-related metabolisms were widespread across strata, and Chlorobiota-affiliated genomes and metagenomic reads were consistently detected in suboxic layers. These organisms were found to harbour diverse thiosulphate disproportionation pathways and are thought to play an important role in the sulphur cycle that has not previously been reported in this type of lacustrine system.Overall, this study provides a genome-resolved perspective on microbial diversity and metabolic potential in a stratified tropical maar lake and establishes a baseline for future comparative and process-oriented studies integrating water column and sediment microbial communities.},
}

@article {pmid42241759,
year = {2026},
author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Robinson, K and Hauck, R},
title = {Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations[1].},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107151},
doi = {10.1016/j.psj.2026.107151},
pmid = {42241759},
issn = {1525-3171},
abstract = {This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.},
}

@article {pmid42241815,
year = {2026},
author = {Zhang, S and Liu, X and Cheng, R and Huang, C and Zhang, Z and Long, S and Yang, Q},
title = {Elucidating the Feammox nitrogen transformation pathway: Key intermediates and putative multi-species metabolic cooperation in a long-term Feammox-dominant system.},
journal = {Water research},
volume = {303},
number = {},
pages = {126223},
doi = {10.1016/j.watres.2026.126223},
pmid = {42241815},
issn = {1879-2448},
abstract = {The emerging Fe(Ⅲ) reduction coupled to anaerobic ammonia oxidation (Feammox) process offers a promising approach toward carbon neutrality in wastewater treatment. However, its nitrogen transformation pathway and metabolic mechanism remain unclear. This study established a Feammox-dominant sequencing batch reactor (Fe-SBR) and operated it for 515 days, achieving an ammonia removal efficiency of 97.9 ± 4.5% during the stable phase. Feammox was confirmed as the dominant process for NH4[+]-N conversion, accounting for 83.2% of ammonia transformation. NH2OH, NO, and N2O were identified as key intermediates in the Feammox nitrogen transformation pathway. By integrating metagenomic analysis of functional gene dynamics with metagenome-assembled genomes (MAGs), a potential coupled iron-nitrogen (Fe-N) metabolic pathway was proposed. This pathway suggested that the Feammox process might be accomplished through multi-species metabolic cooperation, with MtrC-mediated extracellular electron transfer potentially serving as the key link coupling nitrogen transformation to the iron redox cycle. These findings provide novel insights into the Feammox metabolic pathway and lay a theoretical foundation for the future precise control and optimization of this process.},
}

@article {pmid42241861,
year = {2026},
author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L},
title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.},
journal = {Journal of environmental management},
volume = {410},
number = {},
pages = {130128},
doi = {10.1016/j.jenvman.2026.130128},
pmid = {42241861},
issn = {1095-8630},
abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.},
}

@article {pmid42241983,
year = {2026},
author = {Bettera, L and Buzzanca, D and Levante, A and Cirlini, M and Saadoun, JH and Martinengo, N and Chiarini, E and Faccia, M and Zeppa, G and Calasso, M and Alessandria, V and Gatti, M},
title = {Cheeseomics of Grana Padano PDO cheese: Microbial diversity and flavour profiles compared to non-PDO cheeses.},
journal = {International journal of food microbiology},
volume = {459},
number = {},
pages = {111881},
doi = {10.1016/j.ijfoodmicro.2026.111881},
pmid = {42241983},
issn = {1879-3460},
abstract = {Protected Designation of Origin (PDO) schemes define technological constraints that may shape cheese microbiota and, consequently, volatilome and sensory quality. Here, a "cheesomics" approach to compare Grana Padano PDO (n = 13) with hard cooked cheeses of the same type and ripening time (9 months) produced outside the PDO framework (non-PDO; n = 15). Shotgun metagenomics was used to characterize bacterial and fungal communities and functional profile, while the volatilome was profiled by HS-SPME/GC-MS and sensory attributes were evaluated by trained ONAF panelist. A subset of samples (4 PDO and 4 non-PDO) was further analysed by flash profiling. Lactic acid bacteria dominated all samples, but distinct community and functional signature differentiated PDO and non-PDO cheeses. Grana Padano PDO showed higher sensory scores for odor/aroma and taste (p-value < 0.05), together with a more consistent microbiological profile. Non-PDO cheeses were more heterogeneous and displayed higher abundance of lipid-derived volatiles, including short- to medium-chain free fatty acids and methyl ketones, whereas PDO samples were associated with compounds such as pentanal and 2,5-dimethylpyrazine. Multivariate integration of taxa, VOCs and sensory data revealed partial separation between groups, supporting group-specific co-variation patterns. Functional profiling showed higher contributions (p-value < 0.05) of fermentation-related functions and cellular/extracellular polysaccharides in PDO cheeses, suggesting that sensory performance is not driven by VOC abundance alone. Fungal DNA was detected at very low level and showed limited relevance from a dairy microbiology perspective. Overall, the PDO production framework was associated with a measurable microbiological and metabolic imprint and with enhanced sensory performance relative to comparable non-PDO cheeses.},
}

@article {pmid42242027,
year = {2026},
author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M},
title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128569},
doi = {10.1016/j.micres.2026.128569},
pmid = {42242027},
issn = {1618-0623},
abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.},
}

@article {pmid42242076,
year = {2026},
author = {Bai, H and He, LY and Qiao, LK and Gao, FZ and Liu, YS and Ying, GG},
title = {Human-associated microbial inputs and bacterial-fungal ecological coupling shape antibiotic resistance risk in environmental dust.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142602},
doi = {10.1016/j.jhazmat.2026.142602},
pmid = {42242076},
issn = {1873-3336},
abstract = {Environmental dust represents a critical exposure matrix, yet the relationships between multi-kingdom dust microbiomes and antimicrobial resistance (AMR)-associated health risks remain insufficiently characterized. We applied shotgun metagenomics to dust samples from pharmaceutical factories, a dairy farm, railway stations, and schools to comprehensively characterize bacterial, fungal, and viral communities, alongside resistome structure. Microbial community composition exhibited significant differences across all three domains among the sampled environments. Specifically, dust from railway stations displayed the strongest human-associated microbial signal and harbored the highest diversity of antibiotic resistance genes (ARGs), and MetaCompare-derived AMR risk. Functional analyses revealed shared bacterial-fungal metabolic organization, with cross-domain taxonomic and functional associations pointing to structured ecological coupling. Variation partitioning analysis showed that shared explanatory components accounted for most of the variation in MetaCompare-based human-health AMR risk, particularly the overlap among bacterial composition, humanization, and fungal functional structure. Notably, Candida and Aureobasidium emerged as divergent fungal indicators, tracking microbiome humanization and resistome risk in opposite directions. By contrast, viral auxiliary metabolic genes accounted for only 3.92% of the abundance-weighted virome, consistent with a host-linked auxiliary layer rather than a dominant independent pathway. Collectively, these findings demonstrate that AMR-related signatures in environmental dust are shaped by the interplay of human-associated microbial inputs and ecologically coupled bacterial-fungal interactions.},
}

@article {pmid42229597,
year = {2026},
author = {Fard, MB and Kwon, S and Vrieze, J and Wu, D},
title = {Long-term inhibition under continuous perfluorooctanoic acid exposure during anaerobic digestion of waste microalgal-bacterial aerobic granular sludge: Metagenomic-metatranscriptomic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135056},
doi = {10.1016/j.biortech.2026.135056},
pmid = {42229597},
issn = {1873-2976},
abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but the effect of residual perfluorooctanoic acid (PFOA) on the anaerobic digestion of waste MB-AGS (WMB-AGS) remains poorly understood. This study evaluated PFOA effects (100, 500, and 1000 µg/L) on anaerobic digestion of WMB-AGS by comparing short-term single-exposure batch assays with long-term semi-continuous digestion. Under control conditions, methane production reached 76 ± 2 mL CH4/g volatile solids. Relative to the control, methane yield changed marginally in the presence of PFOA, indicating no measurable inhibition in a single-exposure biochemical methane potential (BMP) assay. In contrast, during continuous exposure in the semi-continuous digester, biogas output decreased after introducing 1000 µg/L PFOA (31 ± 1 to 19 ± 1 mL/day) and coincided with increased residual soluble chemical oxygen demand. During 3-day hydrolysis-acidogenesis tests, total volatile fatty acids increased from 82 ± 9 mg/L (control) to 122 ± 12 mg/L (1000 µg/L), suggesting greater accumulation of fermentation intermediates in the early digestion phase. The PFOA distribution showed substantial partitioning into extracellular polymeric substance fractions and sludge solids, with 28.3% remaining in supernatant, 23.2% in loosely bound extracellular polymeric substances, 16.0% in tightly bound extracellular polymeric substances, and 32.6% in sludge solids with no transformation products. Multi-omics analysis supported that dominant microbial communities remained broadly stable, whereas reduced transcription of glycolysis and pyruvate-to-acetyl-coenzyme A conversion genes was consistent with soluble organic accumulation and reduced biogas production. Overall, single-exposure BMP assays underestimated the long-term operational impact of continuous PFOA exposure during anaerobic digestion of WMB-AGS.},
}

@article {pmid42229598,
year = {2026},
author = {Dong, C and Pan, J and Li, Y and Liu, M and Li, Y and Zhao, Z and Zhang, Y},
title = {Direct interspecies electron transfer-based simplified microbial consortia for high-efficiency conversion of lignocellulose to methane: Construction, metabolic pathway and performance optimization.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135043},
doi = {10.1016/j.biortech.2026.135043},
pmid = {42229598},
issn = {1873-2976},
abstract = {Establishing direct interspecies electron transfer (DIET)-based methanogenic pathway is likely to address the technical bottlenecks involved in long periods and low rates of methanogenesis during anaerobic digestion of lignocellulose. However, the efficiency of DIET is limited by low abundance of electroactive bacteria and electron competition with conventional methanogenic pathway. Here, we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a 'top-down' selection. Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level) and increased methane production rates (ca. 32 vs 10-25 mL/gVS·d). Lowering pH dramatically increased conductivity of both DIETsimp, similar to that was found in electrically conductive pili of Geobacter sulfurreducens. Meanwhile, the intensities of characteristic peaks in electrochemical Fourier transform infrared spectra associated with c-type cytochrome in both DIETsimp dramatically increased. Metagenomic analysis showed that, Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively. The potential DIET-based methanogenic pathway during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane was proposed. At last, we optimized culture conditions (including inoculum ratio, C/N and period) to maximize the performances of both DIETsimp via combining the single-factor experiments with response surface methodology.},
}

@article {pmid42229914,
year = {2026},
author = {Li, H and Yang, L and Chen, B and Zhang, L and Zhu, J and Zhang, H and Lin, L},
title = {Pneumococcal Rib Osteomyelitis With Concurrent Lung and Chest Wall Abscess in an Infant.},
journal = {Pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1542/peds.2025-073077},
pmid = {42229914},
issn = {1098-4275},
abstract = {We present a rare case of a 7-month-old infant with a complex invasive Streptococcus pneumoniae infection involving rib osteomyelitis, a pulmonary abscess, and a chest wall abscess. The patient presented with persistent fever and no respiratory symptoms. On day 9, chest radiography was performed because of persistent fever and marked leukocytosis, consistent with the American College of Radiology Appropriateness Criteria that recommend imaging in febrile infants with high fever (≥39°C) or elevated white blood cell counts (≥20 000/mm3). On day 14, the emergence of a chest wall mass prompted escalation to ultrasonography, which provided noninvasive assessment of soft tissue involvement. Subsequent contrast-enhanced computed tomography scans were undertaken to delineate the extent of contiguous spread, evaluate rib destruction, and exclude alternative diagnoses. Microbiological cultures of sputum and aspirated pus, along with metagenomic sequencing, confirmed the presence of macrolide-resistant S. pneumoniae. Because of benzylpenicillin and cephalosporin allergy, intravenous linezolid was selected, resulting in rapid clinical improvement. A 6-week course (intravenous infusion followed by oral) led to complete resolution on imaging, with no recurrence over 5 years. This case underscores the importance of appropriate imaging modalities in febrile infants without respiratory symptoms and the need to consider extrapulmonary spread in chest wall masses. It highlights the diagnostic value of metagenomic sequencing and susceptibility testing in guiding individualized antimicrobial therapy, particularly in macrolide-resistant settings.},
}

@article {pmid42230119,
year = {2026},
author = {Alexander, JL and Mullish, BH and Thomas, L and Weersma, RK and Sokol, H and Roberts, LA and Edwards, LA and Emmanuel, A and Gerasimidis, K and Hall, LJ and Iqbal, TH and Kinross, JM and McIlroy, J and Monaghan, TM and Sergaki, C and Shawcross, DL and Stewart, CJ and Lamb, CA and Williams, HRT and Hansen, R and Hold, G},
title = {Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338252},
pmid = {42230119},
issn = {1468-3288},
abstract = {At around 10 years ago, at the time of the first publication by the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology, recognition of the gut microbiome's importance in health and disease was transitioning from fringe interest towards major global pursuit. A decade on, we appraise the considerable progress made in the field, while acknowledging ongoing challenges. Earlier human work characterising the 16S rRNA gene amplicon signature of particular conditions in small cohorts has been superseded by larger, multicentre studies with extensive metadata. Studies increasingly employ shotgun metagenomics and other 'omic' techniques-coupled with refined bioinformatic tools and disease models-to better characterise perturbation in gut microbiome functionality. The arrival of 'gold standard' pipelines for microbiome analysis and increased mechanistic validation of signals are key developments towards more clinically-translatable outcomes. Novel clinical areas where the gut microbiome has relevance have emerged, including early life and the efficacy of certain treatments (including immune checkpoint inhibitors and vaccination). Enthusiasm for 'microbiome diagnostics and treatments' has grown, but barriers to widespread adoption remain. Faecal microbiota transplant (FMT) is established for treating recurrent Clostridioides difficile infection, with donor-derived 'next generation' FMT products licensed for this condition in certain countries. Beyond FMT, other microbial therapeutic techniques-including nutritional, bacteriophage and probiotic therapies-show promise, but have not fulfilled their high expectations yet. Gut microbiome research is now well-established and shows significant translational potential; the future focus will be translational work to drive its utility in clinical diagnostics, prognostics and therapeutics.},
}

@article {pmid42230654,
year = {2026},
author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F},
title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01029-0},
pmid = {42230654},
issn = {2055-5008},
abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.},
}

@article {pmid42230804,
year = {2026},
author = {Linh, LTK and My, TN and Thi Tran, N and Song, LH and Nurjadi, D and Boutin, S and Velavan, TP},
title = {Metagenomic profiling reveals shared resistome signatures between humans and pigs in Vietnamese smallholder farms.},
journal = {npj antimicrobials and resistance},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44259-026-00223-6},
pmid = {42230804},
issn = {2731-8745},
support = {PACE-UP; DAAD Project ID: 57592343//Deutscher Akademischer Austauschdienst/ ; },
abstract = {Antimicrobial resistance (AMR) is a global health concern, yet the extent of resistant genes and microbial exchange between humans and livestock in low- and middle-income countries remains underexplored. Vietnam, an AMR hotspot, was studied using shotgun metagenomic sequencing of paired faecal samples from pigs and caretakers across 50 small-scale farms. Results revealed 10,270 antimicrobial resistance genes (ARGs) representing 550 unique types, including clinically relevant mcr, blaOXA-58, and optrA genes. Pigs showed higher total AMR abundance, while workers harboured richer resistomes. Approximately 52% (288/550) of ARGs were shared between hosts, dominated by aminoglycoside, β-lactam, and tetracycline resistance genes, often co-located with mobile genetic elements, indicating horizontal transfer potential. Closely related Escherichia coli strains were identified in both hosts, consistent with strain sharing or exposure to common sources beyond individual farms. These findings highlight the human-pig interface as an important setting for shared AMR signatures and support the need for integrated One Health surveillance and antimicrobial stewardship.},
}

@article {pmid42231385,
year = {2026},
author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N},
title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.},
journal = {Nutrition journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12937-026-01343-5},
pmid = {42231385},
issn = {1475-2891},
support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; },
abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.

METHODS: A total of 102 male Han participants was randomized to curcumin (812 mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.

RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P = 0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P < 0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P < 0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P < 0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.

CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.

TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.},
}

@article {pmid42231497,
year = {2026},
author = {Vayena, G and Giangeri, G and Gaspari, M and Ghofrani-Isfahani, P and Tsapekos, P and Kougias, PG and Angelidaki, I},
title = {Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02443-4},
pmid = {42231497},
issn = {2049-2618},
abstract = {BACKGROUND: Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.

RESULTS: Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.

CONCLUSIONS: This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.},
}

@article {pmid42231509,
year = {2026},
author = {Sarhan, MS and Samadelli, M and Zink, A and Maixner, F},
title = {The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42231509},
issn = {2049-2618},
support = {FESR1078-MummyLabs//European Regional Development Fund/ ; },
abstract = {BACKGROUND: The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.

RESULTS: By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.

CONCLUSIONS: Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.},
}

@article {pmid42231528,
year = {2026},
author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA},
title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2679516},
doi = {10.1080/19490976.2026.2679516},
pmid = {42231528},
issn = {1949-0984},
abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.},
}

@article {pmid42232316,
year = {2026},
author = {Webster, NS and Bell, SC and Luter, HM and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {211},
pmid = {42232316},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Rhopaloeides odorabile (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.42 kilobases. From the metagenome data, we recovered 162 bins, of which 96 were high-quality MAGs. R. odorabile displays a characteristic high microbial abundance sponge profile, with MAGs representing diverse phyla (i.e., Acidobacteriota, Pseudomonadota, and Chloroflexota) and candidate phyla (i.e., Ca. Latescibacteria, Ca. Poribacteria, and Ca. Tectomicrobia).},
}

@article {pmid42232360,
year = {2026},
author = {Li, Y and Yi, G and Han, Z and Fu, J and Xu, L},
title = {Comparison of mNGS microbial detection profiles between percutaneous lung aspiration biopsy and bronchoalveolar lavage fluid in infective pneumonia.},
journal = {Open medicine (Warsaw, Poland)},
volume = {21},
number = {1},
pages = {20261445},
pmid = {42232360},
issn = {2391-5463},
abstract = {OBJECTIVES: To compare the mNGS-based microbial detection profiles of percutaneous lung aspiration biopsy (PLAB) and bronchoalveolar lavage fluid (BALF) in patients with infective pneumonia under real-world clinical sampling strategies.

METHODS: The study included 166 patients with infective pneumonia, of whom 54 underwent PLAB to obtain unfixed fresh lung tissue from the lesion site, while 112 underwent fiberoptic bronchoscopy to obtain BALF.

RESULTS: In the BALF group, 3 pathogens of high concern and 5 suspected pathogens, totaling 8 types of pathogens, were detected. In contrast, in the PLAB group, 1 pathogen of high concern and 1 suspected pathogen, totaling 2 types of pathogens were detected. Cumulatively, 348 pathogens were identified in the BALF group. In the PLAB group, 96 pathogens were identified cumulatively, p<0.001. In the BALF group, the most frequently detected pathogen was Streptococcus pneumoniae, with 19 strains of Mycobacterium tuberculosis among the special pathogens. In the PLAB group, the most frequently detected pathogen was Epstein-Barr virus (EBV) (14.58 %).

CONCLUSIONS: BALF and PLAB showed different mNGS microbial detection patterns under different clinical sampling strategies. Because of the retrospective non-paired design, these findings should be interpreted as descriptive comparative data rather than proof of the superior diagnostic performance of either sampling method.},
}

@article {pmid42232489,
year = {2026},
author = {Huang, Y and Yang, M and Liu, J and Zhang, M and Penttinen, P and Zhang, L and Ge, L and Zhang, X and Zhao, N},
title = {Phage succession and putative mechanisms of microbial community regulation in Sichuan radish paocai (traditional Chinese fermented vegetable).},
journal = {Food chemistry: X},
volume = {36},
number = {},
pages = {103997},
pmid = {42232489},
issn = {2590-1575},
abstract = {Spontaneous fermentation of Sichuan paocai is shaped by complex microbial and environmental factors, yet phage communities remain understudied. This study presents integrated viromic and metagenomic analysis of radish paocai combined with metabolite profiling to elucidate phage diversity, dynamics, ecological roles, and sources. Time-series metagenomics revealed Lactiplantibacillus increasing from 11% to 71%, while viromics showed phages comprising 78% of viral contigs, with Uroviricota reaching 88% by day 5. Host prediction indicated that 89% of phages targeted Lactiplantibacillus, mainly L. plantarum. Correlation analysis suggested that core phages were associated with fermentation-related metabolites, including volatile compounds (e.g., decanal), implicating that phages might influence metabolism by modulating host activity. Functional annotation showed phage encoded amino acid and carbohydrate metabolism genes, suggesting auxiliary metabolic roles. Source analysis suggested that most phages in radish paocai may be derived from bacterial prophages. This work advances understanding of phage diversity and ecological function in fermented vegetable ecosystems.},
}

@article {pmid42232626,
year = {2026},
author = {Han, X and Zhang, L and Zhang, R and Liu, W},
title = {Case Report: Multiple organ dysfunction syndrome in a preterm infant secondary to respiratory syncytial virus and bacterial co-infection.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1825002},
pmid = {42232626},
issn = {2296-2360},
abstract = {This article reports a case of a 1-month 11-day-old preterm infant, born at 36 + 6 weeks gestation, who presented to an outside hospital emergency department with a persistent cough that had not improved over four days. During this period, the infant progressively developed respiratory distress and lethargy. The infant subsequently developed cardiopulmonary arrest, underwent cardiopulmonary resuscitation, and was transferred to our hospital under endotracheal intubation with positive pressure ventilation. Respiratory pathogen polymerase chain reaction testing of a throat swab was positive for respiratory syncytial virus (RSV), while sputum and bronchoalveolar lavage fluid culture and blood metagenomic next-generation sequencing (mNGS) detected Haemophilus influenzae and S. pneumoniae. After 22 days of hospitalization and treatment including invasive mechanical ventilation, antibiotic adjustment, intravenous immunoglobulin (IVIG), and dexamethasone, the infant was discharged without further complications. Metagenomic next-generation sequencing provides rapid diagnostic evidence for mixed infections, while integrated interventions, including IVIG, short-course corticosteroids, and nutritional support, effectively modulate immune responses.},
}

@article {pmid42232631,
year = {2026},
author = {Gao, L and Wen, Y and Jing, X},
title = {Case Report: Cervical lymphadenitis resulting from Pseudomonas aeruginosa diagnosed by metagenomic next-generation sequencing.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1795457},
pmid = {42232631},
issn = {2296-2360},
abstract = {Pediatric cervical lymphadenitis is usually caused by Staphylococcus aureus and Streptococcus pyogenes. Cases resulting from Gram-negative bacteria are rare. Herein, we report the case of an 11-year-old boy who developed cervical lymphadenitis. He was diagnosed with a Pseudomonas aeruginosa infection through metagenomics next-generation sequencing of blood and biopsy. After treatment with meropenem, the patient's condition improved and he was discharged. Lymphadenitis may be caused by Gram-negative opportunistic pathogens. Metagenomic next-generation sequencing can help identify the underlying cause.},
}

@article {pmid42232653,
year = {2026},
author = {Fan, F and Wang, B and Jia, R and Lyu, J and Han, F},
title = {Amelioration of tic disorder by Jujuboside A via gut microbiota remodeling and intestinal 5-HT signaling.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1760647},
pmid = {42232653},
issn = {1662-4548},
abstract = {BACKGROUND: Tic disorder (TD) is a common chronic neuropsychiatric condition manifesting during childhood and adolescence. Jujuboside A (JuA) may alleviate TD symptoms; however, the mechanisms underlying its therapeutic effects remain unclear.

METHODS: We established a rat model of TD and used histological techniques to evaluate the effects of JuA on pathological changes. We also measured 5-hydroxytryptamine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels and assessed tryptophan hydroxylase 1 (TPH1) mRNA expression. Finally, we analyzed the gut microbiota composition in fecal samples using 16S rRNA metagenomic sequencing.

RESULTS: JuA administration alleviated pathological changes in rats with TD, increased 5-HT and 5-HIAA levels, and upregulated TPH1 mRNA expression. Compared with no treatment, JuA treatment increased the proportion of Bacteroidia, Muribaculaceae, Bacteroidales, and Bacteroidota, while reducing that of Bacilli, Lactobacillaceae, Lactobacillus, Lactobacillales, and Firmicutes.

CONCLUSION: These findings indicate that JuA mitigates TD progression, potentially by remodeling the gut microbiota and regulating 5-HT levels.},
}

@article {pmid42232910,
year = {2026},
author = {Oskolkov, N},
title = {Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1603339},
pmid = {42232910},
issn = {1664-302X},
abstract = {Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.},
}

@article {pmid42232914,
year = {2026},
author = {Chamberlain, EJ and Boulton, W and Connors, E and Calianos, T and Bowman, JS and Creamean, JM and Mock, T and Kim, HH},
title = {From microbial diversity to functional potential using dimensionality reduction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786397},
pmid = {42232914},
issn = {1664-302X},
abstract = {The high dimensionality of microbial diversity data from 'omics observations can be reduced using Machine Learning, with many recent studies showcasing ML utility for exploratory ecological feature finding and process prediction. Here, we compare the Self Organizing Map (SOM) dimensionality reduction method to the well-documented sample-based Principal Coordinate Analysis (PCoA) and taxa-based Weighted Gene Correlation Network Analysis (WGCNA) using near daily 16S rRNA gene amplicon sequencing data from the 2019 to 2020 MOSAiC International Arctic Drift Expedition. We then map k-means clustering outputs from each method to available metagenomes, extracting functionally distinct seasonal microbial ecotypes in the surface Arctic Ocean. Our results indicate the SOM method better represented expected seasonal transitions and identified a greater number of metabolically distinct functional groups than the more traditional PCoA ordination. Ultimately, we identified four community ecotypes with distinct taxonomic and functional cut-offs driven by seasonality, water mass, and substrate turnover, highlighting the importance of succession in functional diversity for the central Arctic Ocean. These results reinforce ML dimensionality reduction as a meaningful translator in the mining of historical amplicon datasets to address modern mechanistic questions and potentially provide 'omics informed ecotype diversity to leverage in mechanistic biogeochemical models.},
}

@article {pmid42233252,
year = {2026},
author = {Hashmi, L and Rehman, SU and Jabeen, F and Kayani, MUR},
title = {GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
doi = {10.1093/database/baag029},
pmid = {42233252},
issn = {1758-0463},
support = {//Metagenomics Discovery Lab at the SINES/ ; //NUST/ ; },
abstract = {Gut dysbiosis is widely recognized as a contributor to autoimmune diseases, as it can lead to the expression of microbial antigens that disrupt immune regulation through specific molecular mechanisms. However, existing resources do not systematically link gut microbial antigen sequences to the specific autoimmune mechanisms through which they act. Here, we present GUTAID (Gut Microbes in Autoimmune Disorders), a literature-curated database of gut microbial antigens annotated with experimentally supported autoimmune mechanisms. Peer-reviewed studies published from October 1970 to September 2024 were manually screened, yielding 73 potential antigens that operate through nine molecular mechanisms, including protein citrullination, epitope spreading, molecular mimicry, and immune modulation, amongst others. The corresponding protein sequences were retrieved from UniProtKB, and redundancy was removed with MMseqs2. For the database implementation, data were delivered through a lightweight LAMP (Linux-Apache-MySQL/MariaDB-PHP) stack with server-side HTML/Bootstrap rendering, MySQL indexing, and HTTPS-secured downloads. Users can browse, keyword-search, or bulk-download sequence archives via a five-tab interface (Home, Downloads, Search, Team, and About). GUTAID thus enables mechanism-oriented exploration of gut microbial antigens and supports downstream biomarker and therapeutic discovery in autoimmune research. Database URL: https://gutaid.mgdiscoverylab.com/.},
}

@article {pmid42233644,
year = {2026},
author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M},
title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149825},
doi = {10.1128/msystems.01498-25},
pmid = {42233644},
issn = {2379-5077},
abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.},
}

@article {pmid42233648,
year = {2026},
author = {Hu, J and Zhang, H and Miao, H and Chang, W and Zheng, J and Hu, F and Zhang, D and Guo, W and Hu, P and Han, R and Wang, J and Li, L and Wang, X},
title = {Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0399325},
doi = {10.1128/spectrum.03993-25},
pmid = {42233648},
issn = {2165-0497},
abstract = {UNLABELLED: This study aimed to compare the analytical characteristics and diagnostic performance of short-read next-generation sequencing (NGS) and long-read third-generation sequencing (TGS) for metagenomic pathogen detection, using defined mock communities and clinical bronchoalveolar lavage fluid (BALF) samples. Mock evaluations included microbe-host gradient mixtures (D1/D2) and six complex microbial panels (M1-M6). Sequencing was performed on Illumina, MGI, and Oxford Nanopore Technologies (ONT) platforms. Clinical validation was conducted on 62 BALF samples. Diagnostic performance was assessed against culture, clinical microbiological tests (CMT), and a composite reference standard (CRS). Turnaround times for Illumina and MGI were approximately 18-20 h and 14-19 h, respectively, whereas the ONT workflow was completed within 4-6 h. The microbe-to-host DNA ratio significantly influenced sequencing performance. Depletion of host DNA notably enhanced ONT detection, reducing the false-negative rate for low-abundance microorganisms from 43.3% to 6.7%. For all mock samples, both the Illumina and MGI platforms demonstrated 100% sensitivity and showed highly concordant detection profiles. In clinical specimens, when evaluated against the composite reference standard, the positive percent agreement (PPA) values of NGS and TGS were 93.3% and 90.7%, respectively, with corresponding negative percent agreements (NPAs) of 77.6% and 83.3%. Both platforms identified numerous pathogens that were missed by culture, especially in polymicrobial infections. Among 22 CRS-defined polymicrobial samples, culture identified all pathogens in only 2 cases, whereas NGS and TGS achieved full pathogen recovery in 18 and 17 cases, respectively. Within the evaluated workflows, short-read sequencing showed slightly higher sensitivity and overall stability, whereas host-depleted ONT offered a substantial turnaround-time advantage and may serve as a useful complementary approach in complex or time-sensitive clinical scenarios.

IMPORTANCE: Rapid and accurate identification of the microbes causing pneumonia is essential for choosing effective treatment, yet current diagnostic tests are slow and often miss important pathogens. We systematically compared two major DNA sequencing strategies-established short-read platforms and newer long-read nanopore sequencing-using both carefully designed mock communities and real bronchoalveolar lavage samples from patients. We show when removal of human DNA is essential, how mixed infections are best captured, and what trade-offs exist between speed and sensitivity. Our results provide practical guidance on how hospitals can implement sequencing-based diagnostics, when rapid nanopore testing can complement conventional short-read workflows, and how to interpret sequencing read counts in day-to-day clinical decision-making.},
}

@article {pmid42233650,
year = {2026},
author = {Kane, M and Moukaha Doukanda, SF and Sankhé, S and Sow, B and Ndione, MHD and Mhamadi, M and Dieng, M and Diop, SMBS and Seye, S and Mbanne, M and Faye, O and Barry, MA and Sembene, PM and Loucoubar, C and Fall, G and Diallo, A and Diagne, CT and Dia, N and Diagne, MM},
title = {Evaluating myxovirus resistance protein A-based rapid testing combined with pathogen sequencing for arboviral and incidental viral infection surveillance in Senegal.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0339225},
doi = {10.1128/spectrum.03392-25},
pmid = {42233650},
issn = {2165-0497},
abstract = {Accurate differentiation between viral and bacterial infections remains challenging in resource-limited, arbovirus-endemic settings, leading to antibiotic misuse and diagnostic uncertainty. Myxovirus resistance protein A (MxA), an interferon-induced host biomarker, may offer a pathogen-agnostic approach to improve rapid diagnosis and clinical triage. We evaluated the performance of an MxA rapid diagnostic test (RDT) using archived samples from febrile patients collected during dengue virus (DENV) and chikungunya virus (CHIKV) outbreaks in Senegal. We tested 171 blood samples from patients with acute febrile illness using an MxA RDT and RT-qPCR for DENV and CHIKV. Samples with discordant results (MxA-positive and RT-qPCR-negative) underwent metagenomic and hybrid-capture Illumina-based sequencing to detect missed infections. Sequencing data were analyzed using maximum-likelihood phylogenetics to assess viral lineage placement. The MxA RDT demonstrated moderate-to-high sensitivity (70.0%-85.1%, depending on virus) and moderate specificity (70.2%) for detecting primary arboviral infections. Among discordant samples, sequencing revealed previously missed pathogens, including DENV serotype 3 (genotype III), Parvovirus B19 (B19V), and Torque teno virus (TTV). Detection of B19V and TTV highlights the broader clinical utility of host-response biomarkers to uncover unexpected viral pathogens in high-diversity settings. MxA's longer persistence than viral RNA enables detection of recent infections missed by PCR. Combined with sequencing, this broadens the diagnostic window, improves clinical triage, and supports identification of underdiagnosed viruses. Future research should integrate MxA testing into routine clinical care and surveillance protocols to enhance outbreak responses in resource-limited regions.IMPORTANCETimely and equitable viral diagnosis is vital in outbreak-prone regions where advanced laboratories are scarce. This study shows how a simple, rapid test for the host biomarker myxovirus resistance protein A can provide real-time detection of viral infections such as dengue and chikungunya, even in remote or frontline health centers. When paired with pathogen sequencing, the test also uncovers infections that standard PCR may miss. This integrated approach demonstrates how field-deployable diagnostics can operate both during and between epidemics, strengthening outbreak preparedness, improving patient triage, and advancing laboratory equity worldwide.},
}

@article {pmid42233654,
year = {2026},
author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H},
title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0318325},
doi = {10.1128/spectrum.03183-25},
pmid = {42233654},
issn = {2165-0497},
abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.

IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.},
}

@article {pmid42233680,
year = {2026},
author = {Grettenberger, CL and Macalady, JL and Hamilton, TL},
title = {Metabolic diversity of Ferrovaceae and potential contributions to iron oxidation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0070026},
doi = {10.1128/aem.00700-26},
pmid = {42233680},
issn = {1098-5336},
abstract = {Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovaceae are Fe-oxidizing bacteria observed in AMD globally and thus could be an asset for bioremediation strategies. To better understand the potential for Ferrovaceae to contribute to AMD bioremediation, we analyzed 240 genomes and metagenome-assembled genomes from Ferrovaceae, including sequences from AMD sites with high iron oxidation rates. Based on our analyses, the phylogenetic and physiological diversity of this group is greater than previously known. We found that while all taxa are likely capable of iron oxidation using a cyc-2 like protein, some may also be capable of iron oxidation using an Mto-like protein. We also identified Ferrovaceae that are likely capable of anoxygenic phototrophy. Our findings indicate that multiple Ferrovaceae populations co-occur and suggest that differences in physiology may promote niche differentiation along resource axes. Physiologically diverse iron oxidizer communities could support a more resilient microbial community, resulting in higher iron oxidation rates and potentially more efficient bioremediation, and thus our results also indicate that future studies that link taxonomy with iron oxidation activity are warranted.IMPORTANCEAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation because they drive biogeochemical processes in these ecosystems. In AMD streams, iron-oxidizing microbial populations remove iron from the AMD effluent by precipitating iron oxides, which absorb other metals. These communities vary across sites and differ in how rapidly they oxidize iron. The factors that contribute to iron oxidation rates are not well understood, making it difficult to design effective bioremediation strategies. Ferrovaceae populations are widespread in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovaceae to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovaceae in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovaceae as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity leads to co-occurrence of multiple Ferrovaceae species at the same sites. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.},
}

@article {pmid42233768,
year = {2026},
author = {Éles, ZB and Rahmani, L and Gyöngyösi, E and Szarka, K and Rebenku, I and Veress, G and Major, T and Kónya, J and Szalmás, A},
title = {Sublineage-Specific A45S Polymorphism Alters the Biological Function of the Human Papillomavirus 11 E7 Protein.},
journal = {Journal of medical virology},
volume = {98},
number = {6},
pages = {e70997},
doi = {10.1002/jmv.70997},
pmid = {42233768},
issn = {1096-9071},
support = {FK125038//National Research, Development and Innovation Office/ ; //Hungarian Academy of Sciences/ ; //Faculty of Medicine, University of Debrecen/ ; //Richter Gedeon Talentum Foundation/ ; },
abstract = {The E7 oncoprotein of human papillomavirus (HPV) plays a crucial role in viral pathogenesis and replication. Although it is generally highly conserved across HPV genotypes, naturally occurring E7 variants can display functional differences that may affect viral persistence, oncogenic potential, and host cellular responses. The prevalent HPV11 A2 sublineage is characterized by a distinctive amino acid substitution at position 45 (A45S) within the E7 protein. In comparative analyses of transfected primary keratinocytes and HPV-negative cancer cells, we here demonstrate that the A45S substitution enhances the interaction of HPV11 E7 with key cellular targets, including pRb family proteins and PTPN14. A further consequence is an increased ability to target both PTPN14 and pRb family proteins for degradation. Functionally, these differences are exemplified by the S45 variant's enhanced ability to activate E2F-driven gene expression, particularly resulting in elevated mRNA levels of key factors involved in homologous recombination-mediated repair of DNA double-strand breaks, a pathway critical for preserving genomic integrity. Together, these findings indicate that the A45S substitution imparts high-risk-like molecular properties to the low-risk HPV11 E7 oncoprotein. To our knowledge, this is the first report to identify a functionally significant alteration in HPV11 E7 activity resulting from a naturally occurring sequence variation. Understanding the underlying mechanisms could provide new strategies for targeting the therapeutically challenging HPV-associated conditions, such as recurrent respiratory papillomatosis.},
}

@article {pmid42234268,
year = {2026},
author = {Hoseini, R and Hoseini, Z and Heydarpour, B and Faraji, M},
title = {A systematic review of molecular signaling in the muscle-brain-gut axis: exercise-induced myokines and microbial metabolites as key mediators.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42234268},
issn = {1573-4978},
abstract = {Exercise physiology is evolving from an organ-based framework toward a systems-level understanding, where molecular interactions between muscle, brain, and the gut microbiome critically influence performance and health. This review systematically examines the genetic, molecular, and cellular bases of this triad, with a focus on translational insights for disease prevention and human optimization. A systematic search of PubMed, Embase, and Web of Science was conducted up to October 2023 to identify studies exploring molecular pathways linking skeletal muscle, cognitive/affective function, and gut microbiota in exercise contexts. Inclusion criteria were original research articles investigating at least two components of the muscle-brain-gut axis. Exclusion criteria included non-English articles, conference abstracts, and studies without molecular data. The PRISMA 2020 guidelines were followed. The search strategy is detailed in Supplementary Material. Evidence was categorized into Grades 1 through 4 based on methodological rigor, omics integration, reproducibility, and translational relevance to human physiology and disease models. Analysis included 154 studies encompassing 987 molecular associations. Among these, 59 associations (Grades 1-2) provided robust evidence for genetically and functionally validated pathways, including myokine-mediated (e.g., irisin, BDNF) and microbially derived metabolites (e.g., SCFAs, tryptophan derivatives) that modulate neuroplasticity, mitochondrial function, inflammation, and HPA axis activity. Psychobiological factors influenced microbial composition, illustrating bidirectional gut-brain-muscle signaling. Most associations (n = 952) were limited by methodological variability or insufficient mechanistic depth. The integration of multi-omics platforms (metagenomics, metabolomics, proteomics) emerges as a key tool for personalized exercise interventions and biomarker discovery. This review synthesizes molecular evidence for the muscle-gut-brain axis as an integrative determinant of exercise responsiveness and disease resilience. We highlight genetic and metabolic pathways with diagnostic and therapeutic potential, aligning with the development of molecular tools for precision medicine. Future interdisciplinary research should leverage artificial intelligence and longitudinal omics to translate these mechanisms into targeted strategies for performance enhancement and disease prevention.},
}

@article {pmid42234577,
year = {2026},
author = {Faure, R and Faure, U and Truong, T and Derzelle, A and Lavenier, D and Flot, JF and Quince, C},
title = {SNooPy: a statistical framework for long-read metagenomic variant calling.},
journal = {Nucleic acids research},
volume = {54},
number = {10},
pages = {},
doi = {10.1093/nar/gkag556},
pmid = {42234577},
issn = {1362-4962},
support = {101088572//ERC/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; },
abstract = {Current long-read single-nucleotide variant callers were designed primarily for genomic data-particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inherent complexity of metagenomic samples. To date, no long-read variant caller has been purpose-built for metagenomic applications. To address this gap, we present SNooPy, a single nucleotide polymorphism (SNP)-calling tool that implements a new statistical framework tailored to long-read metagenomic data. Unlike previous genomic methods, our approach makes no assumptions about the number of haplotypes present, their evolutionary relationships, or their sequence divergence. We demonstrate that SNooPy outperforms both traditional statistical and deep learning-based SNP callers. Our results suggest that future integration of this framework with deep learning approaches could further enhance variant-calling performance. SNooPy is freely available on github.com/rolandfaure/snoopy.},
}

@article {pmid42234710,
year = {2026},
author = {Liu, F and Lai, T and Xu, W and Li, G},
title = {ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0349393},
doi = {10.1371/journal.pone.0349393},
pmid = {42234710},
issn = {1932-6203},
abstract = {Accurate functional annotation of viral proteins is essential for genomic surveillance, yet rapid viral evolution causes "functional drift" that challenges conventional sequence-only models. These models often lack interpretability and struggle with fragmented sequences from complex environmental samples such as wastewater. We developed ViralMultiNet, a structure-aware multimodal framework that integrates multi-scale k-mer encodings (4-7-mers) with functional semantic embeddings derived from UniProt annotations. Using a curated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) dataset of 66,011 samples from wastewater metagenomics (NCBI SRA: SRX28474964), we implemented gated multimodal fusion and triple knowledge distillation to transfer structural insights from a teacher to a student model. Model performance was evaluated via 5-fold cross-validation and external validation on emerging variants. Training efficiency was optimized using Low-Rank Adaptation and Flash Attention. ViralMultiNet achieved robust classification performance with a macro F1 score of 0.921 ± 0.004, accuracy of 0.928 ± 0.003, and AUC of 0.983 in cross-validation. The distilled student model matched teacher performance within a negligible margin (<0.003 F1 difference) while reducing training time by 40.4% (from 94.3 to 56.2 minutes per epoch). Interpretability analysis revealed that model attention peaks consistently aligned with experimentally validated functional domains of the SARS-CoV-2 Spike protein, including the receptor-binding domain (residues 319-541), S1/S2 cleavage site (681-685), and fusion peptide (816-835). ViralMultiNet offers a scalable, interpretable solution for viral protein function prediction. Its ability to generalize across variants and map attention to critical biological regions supports deployment in wastewater-based early warning systems, enhancing global pandemic preparedness.},
}