@article {pmid42184943,
year = {2026},
author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Zhang, J},
title = {In situ assembly of the humic acid-protein conductive network facilitates chain elongation for medium-chain fatty acids anaerobic production from waste activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134964},
doi = {10.1016/j.biortech.2026.134964},
pmid = {42184943},
issn = {1873-2976},
abstract = {Biosynthesis of medium-chain fatty acids (MCFAs) from waste activated sludge (WAS) is primarily limited by intracellular reductive stress (NADH accumulation) and energy shortages. This work demonstrates that humic acid (HA), functioning as a redox mediator, effectively enhances the carbon chain elongation (CE) process. Optimal HA supplementation (1000 mg/L) increased the peak MCFAs yield by 98.3%, driving a fundamental shift in the dominant product spectrum from short-chain fatty acids (SCFAs) to MCFAs. Combined metagenomic and electrochemical analyses reveal that this enhancement originates from HA-mediated spatial and metabolic integration across multiple scales. Macroscopically, HA complexes with proteins to construct a conductive biopolymer network. Functioning as a highly efficient extracellular electron sink, this network significantly accelerates transmembrane electron discharge to consume excess intracellular electrons. This rapid electron extrusion alleviates reductive stress and relieves product feedback inhibition on dehydrogenases, concurrently inducing an elevated cellular energy charge (ATP surge). Subsequently, feedback regulation driven by this high-energy state suppresses the competitive acetogenic branch (Pta-ackA pathway), effectively preventing carbon loss. Dominated by the highly enriched CE taxon Candidatus_Microthrix, the microbial consortium exhibits a robust metabolic potential to channel carbon into synergistic RBO and FAB pathways. This metabolic shift, fueled by abundant precursors and energy, effectively circumvents acidic toxicity by rapidly consuming SCFAs. These findings elucidate the critical role of HA in reshaping microbial redox homeostasis, providing a robust mechanistic foundation for high-value carbon recovery engineering from complex solid wastes.},
}

@article {pmid42185267,
year = {2026},
author = {Zhou, YL and Feng, JC and Lu, R and Chen, Z and Mara, P and Tao, X and Liu, J and Huang, Y and Hu, J and Yao, J and Edgcomb, VP and Teske, A and Wang, X and Zhang, S},
title = {Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73573-4},
pmid = {42185267},
issn = {2041-1723},
support = {42494884//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42325603//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Anaerobic methanotrophic (ANME) archaea have been primarily documented by metagenomic analysis of environmental samples. The mechanisms that drive their diversification and speciation are poorly understood. Here we analyse the phylogenomic diversity at the species and strain levels of clade ANME-1 from deep-sea cold seeps, as a model system with a well-studied phylogenetic framework. We reconstruct high-quality circular metagenomic-assembled genomes (cMAGs) and identify highly variable genomic hotspots that distinguish them. Genomic differentiation and diversification in ANME-1 is associated with genes involved in prokaryotic defense systems, transport mechanisms and methane metabolism. In addition, heterologous expression of ANME-1 hicAB operons supports their proposed role as toxin/antitoxin systems, possibly involved in mediating responses to environmental stresses.},
}

@article {pmid42185302,
year = {2026},
author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R},
title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01021-8},
pmid = {42185302},
issn = {2055-5008},
support = {2020/06077-9//São Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//São Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; },
abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.},
}

@article {pmid42185318,
year = {2026},
author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR},
title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73524-z},
pmid = {42185318},
issn = {2041-1723},
support = {U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R35GM137828//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.},
}

@article {pmid42185326,
year = {2026},
author = {Hoggard, M and Gios, E and Tee, HS and Geoghegan, JL and Handley, KM},
title = {DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73439-9},
pmid = {42185326},
issn = {2041-1723},
abstract = {Viruses are ubiquitous albeit individually constrained by host-range. Less well understood are environmental limitations on virus proliferation. To investigate estuarine viral diversity, niche constraints, and traits of environmental adaptation, we analyse metagenomic and metatranscriptomic data from an estuarine salinity gradient, including water and sediment. We then expand our analysis to globally-distributed viral genomes. Viral distributions vary by estuary habitat, reflecting prokaryote community patterns, and highlighting that virus-host interactions are strongly influenced by environment. Viral lineages, up until approximately the rank of genus, are largely partitioned by ecological niche based on factors such as salinity and the aquatic-terrestrial divide. Across habitat boundaries, viruses feature osmoadaptive traits similar to their prokaryote hosts. These include slightly elevated ratios of acidic to basic amino acids and decreased protein isoelectric points at higher salinities, particularly in virus major tail and capsid proteins, which are not solely explained by reliance on host machinery. Further studies are needed to determine the primary driver of these modifications in viruses (e.g. environment or host) and whether these traits restrict virus distributions beyond host-range limitation. Overall, our findings indicate that successful proliferations of viruses into distinct biomes (e.g. freshwater, saline, terrestrial) are rare, with viruses constrained to specific ecological niches.},
}

@article {pmid42185942,
year = {2026},
author = {Wang, Y and Peng, Y and Wang, B and Di, M and Xi, M and Yao, Z and Shi, C and Feng, Q and Yin, D and Li, J and Xu, X and Zhang, R and Peng, X},
title = {A preliminary metagenomic and metabolomic investigation into the effects of Aspergillus niger cultures on microbial homeostasis and antibiotic resistance gene profiles in the rumen of fattening sheep.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42185942},
issn = {1674-9782},
abstract = {BACKGROUND: Under high-concentrate feeding conditions, ruminants often experience rumen microecological imbalance and dysfunction, which can impair growth performance and increase the risk of antibiotic resistance gene (ARG) dissemination.

RESULTS: To evaluate the ameliorative effects of Aspergillus niger (A. niger) cultures, fattening sheep were randomly allocated into the following five groups: a control group (CON), a control diet supplemented with 250, 500, or 1,000 mg/kg A. niger cultures (designated as LA, MA, and HA, respectively); and an antibiotic group supplemented with 5,000 mg/kg chlortetracycline premix (AN). Microbial community analysis indicated that several bacterial taxa, including Succinivibrio sp900317105, Prevotella sp002353485, Quinella sp017515635, Quinella sp015206805, and Prevotella sp900320255, were significantly enriched in the A. niger culture-supplemented groups (P < 0.05). ARG profiling showed that the abundance of tetracycline resistance genes was significantly lower in all A. niger groups compared with the CON and AN groups (P < 0.05), while β-lactam resistance genes were significantly reduced in the HA group (P < 0.05). Furthermore, the abundances of Rank I and Rank II ARGs were significantly higher in the AN group than in the other groups, whereas the abundances of Rank II and Rank IV ARGs were significantly lower in the A. niger culture groups than in the CON and AN groups. Metabolomic analysis further demonstrated that supplementation with A. niger cultures significantly decreased the concentration of N-decanoyl-L-homoserine lactone (P < 0.05) while increasing the levels of N-3-oxotetradec-7Z-enoyl-L-homoserine lactone, indole-3-methyl acetate, and indole-3-propionic acid (P < 0.05).

CONCLUSIONS: These findings suggest that A. niger cultures can reduce the abundance of ARGs and mitigate the risk of ARG dissemination by modulating the rumen microbial community and associated metabolites.},
}

@article {pmid42185948,
year = {2026},
author = {Michalik, A and Majewska, E and Andriienko, V and Nowak, KH and Stroiński, A and Łukasik, P},
title = {Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12986-3},
pmid = {42185948},
issn = {1471-2164},
support = {2021/41/B/NZ8/04526//Narodowe Centrum Nauki/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; },
abstract = {BACKGROUND: Ancient nutritional symbioses underpin the ecological success of many sap-feeding insects. In 'true hoppers' - the hemipteran suborder Auchenorrhyncha, obligate bacterial partners provide essential amino acids lacking in plant phloem diets. However, the stability and persistence of such associations across the diversity of hoppers are poorly understood, and investigations are often complicated by insufficiently resolved host identity.

RESULTS: Here, we combined multitarget amplicon sequencing, metagenomics, and microscopy to assess the compositional and functional diversity of the microbiota across Polish, Swedish, and Austrian populations of leafhoppers morphologically identified as Verdanus abdominalis. Host COI data revealed pronounced cryptic genetic diversity, indicating several deeply divergent lineages within the characterized collection, but limited microbiota variation among populations. 16S rRNA amplicon data confirmed the consistent presence of the ancient bacterial endosymbionts Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola, and metagenomics showed that their reduced but complementary genomes jointly encode the complete set of essential amino acid biosynthesis pathways required by the host. Other microbes were uncommon in these symbioses. Microscopy corroborated these findings, revealing conserved bacteriome organization and spatial separation of Sulcia and Nasuia within distinct bacteriocytes.

CONCLUSIONS: Our results demonstrate that the Sulcia-Nasuia dual symbiosis remains evolutionarily stable across cryptic Verdanus diversity, underscoring the robustness of ancient nutritional partnerships despite ongoing host diversification.},
}

@article {pmid42186028,
year = {2026},
author = {Larroya, A and Romera-Giner, S and Tolosa-Enguís, V and Rodríguez-Ruano, SM and Andrés-García, S and Soro-Conde, I and Codoñer, P and Sanz, Y},
title = {Gut microbiota and western dietary patterns associated with behavioral problems in children and adolescents: a cross-sectional study.},
journal = {Nutrition journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12937-026-01335-5},
pmid = {42186028},
issn = {1475-2891},
abstract = {BACKGROUND: Childhood and adolescence are crucial periods for brain development, during which multiple environmental factors, including gut microbiota and dietary habits, play important roles. However, the combined impact of those factors on neurodevelopment and mental disease risk remains largely unexplored. Here, we aimed to investigate the relationships between gut microbiota and diet and their role in classifying behavioral problems that may precede mental disorders in children and adolescents.

METHODS: We performed a cross-sectional study, including data from 335 subjects, including 202 children (5-10 years) and 133 adolescents (11-17 years). Gut microbiota was analysed in stools by shotgun metagenomics. Dietary habits, lifestyle factors and emotional and behavioral difficulties were screened using validated questionnaires. Penalized Logistic Regression models were trained to classify individuals into Healthy and Behavioral Problem groups based on microbial diversity, differential abundance of bacterial species, dietary patterns, and food and nutrient intakes. Mediation analyses were applied to assess whether gut microbiota mediates the effect of diet on behavioral problems.

RESULTS: A Western diet characterized by poor adherence to dietary recommendations was consistently associated with behavioral problems in all age groups. Individuals with behavioral problems exhibited distinct gut microbiota profiles characterized by lower levels of short-chain fatty acid-producing bacteria (particularly butyrate-producing species) and higher levels of potential pathogens (e.g., Campylobacter coli and Lautropia mirabilis), linked to poor dietary choices. Furthermore, we evidenced the mediation role of the gut microbiota in the association between dietary patterns and food groups and behavioral problems. In adolescents, L. mirabilis was identified as a mediator of the relationship between a Western diet and behavioral problems, while Anaerostipes rhamnosivorans mediated the relationship between fish consumption and behavioral problems. Gut microbiota data enhanced the classification accuracy of logistic regression models for identifying individuals with behavioral problems over models based solely on dietary data.

CONCLUSION: Integrating dietary habits and gut microbiota data enables more accurate stratification of children and adolescents at risk for behavioral problems. Our findings may help to refine dietary interventions targeting the gut microbiota to improve mental health outcomes in these vulnerable populations.},
}

@article {pmid42186092,
year = {2026},
author = {Wang, L and Li, F and Ma, Z and Ungerfeld, EM and Zhang, T and Zhang, Z and Liu, X and Zhang, Q and Zhang, X},
title = {Yeast culture promotes butyrate produced fibrolytic bacteria as intracellular hydrogen sink in the rumen.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02436-3},
pmid = {42186092},
issn = {2049-2618},
support = {32308686//The National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Yeast culture (YC) supplementation is widely adopted to mitigate rumen pH depression and alleviate the inhibition of fiber degradation under starch-rich diets. Yet, the underlying microbial mechanisms, particularly how yeast culture orchestrates fibrolytic communities and affects metabolic hydrogen flow in the rumen, remain a critical knowledge gap. Accordingly, elucidating the microbial basis by which yeast culture modulates fiber degradation and hydrogen utilization under starch-rich diets is of both theoretical and practical importance.

METHODS: We conducted a study with growing lambs receiving starch-rich diets that differed only in yeast culture supplementation (CON 0%, YC 1%). We evaluated their growth performance, apparent total-tract digestibilities, rumen fermentation end-products, and the rumen metagenome.

RESULTS: The YC treatment increased the lambs' final body mass (P = 0.02), average daily gain (P = 0.03), digestibilities of neutral detergent fiber (P < 0.001) and acid detergent fiber (P < 0.001), and rumen pH (P < 0.05), and tended to increase organic matter digestibility (P = 0.09). In addition, total VFA concentrations, particularly butyrate, were higher at 6 h post-morning feeding (P = 0.01). Fibrolytic and hydrogenotrophic taxa (e.g., Ruminococcus_E and Quinella) and CAZyme families, including GH43, GH31, GH9, and GH35, were enriched by the YC treatment, as were bacteria involved in fiber degradation and butyrate production. Furthermore, none of the top five YC treatment-enriched bacterial genomes contained any hydrogenase genes, which indicates that this butyrogenic fibrolytic consortium is significantly different from the hydrogen-producing fiber-degrading microorganisms we are familiar with.

CONCLUSION: Yeast culture supplementation promoted the proliferation of a distinct butyrogenic consortium that degrades fiber while apparently disposing intracellularly metabolic hydrogen generated during fermentation, rather than releasing it as H2. These findings provide a microbial basis for understanding how yeast culture improves fermentation efficiency under starch-rich diets and suggest that selecting yeast culture products capable of promoting butyrogenic fibrolytic bacteria may be beneficial for ruminant performance and rumen stability. Video Abstract.},
}

@article {pmid42186552,
year = {2026},
author = {Méndez-Sánchez, D and Pomahač, O and Valt, M and Bourland, WA and Čepička, I},
title = {An extensive morphological and molecular characterization of the neglected class Odontostomatea (Ciliophora).},
journal = {Marine life science & technology},
volume = {8},
number = {2},
pages = {289-323},
pmid = {42186552},
issn = {2662-1746},
abstract = {UNLABELLED: Odontostomatid ciliates, known for over a century, were historically classified within various taxonomic groups of Ciliophora Doflein, 1901 until their reclassification into the class Odontostomatea. Despite the recognition of 25 valid species, most descriptions predate the advent of silver impregnation and sequencing methods. Consequently, many species were described based solely on observations of live specimens, leading to incomplete or ambiguous records. To date, redescriptions of only three species include 18S rRNA gene sequences data, and their evolutionary relationships remain unresolved. In this study, we investigated 32 populations representing 15 species-including three newly described-across the genera Discomorphella, Epalxella, Limnomylestoma gen. nov., Mircalla gen. nov., Mylestoma, Pelodinium, Saprodinium, and Tostonella gen. nov. Comprehensive analyses were conducted using in vivo microscopy, silver impregnation, and scanning electron microscopy. We also designed specific primers to amplify the partial 18S rRNA gene of various odontostomateans and retrieved additional 18S rRNA sequences from environmental metatranscriptomic and metagenomic datasets. This study represents the most extensive investigation of Odontostomatea to date, confirming the monophyly of the class by revealing the position of Epalxella, reconstructing its internal phylogeny, identifying two main odontostomatean lineages, and revealing its remarkable diversity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-026-00352-x.},
}

@article {pmid42186601,
year = {2026},
author = {Zhang, Z and Jia, Z and Zhang, X and Zou, W and Chen, J},
title = {Late-onset cytomegalovirus pneumonia after autologous stem cell transplantation for angioimmunoblastic T-cell lymphoma: a case report.},
journal = {Therapeutic advances in infectious disease},
volume = {13},
number = {},
pages = {20499361261450721},
pmid = {42186601},
issn = {2049-9361},
abstract = {This case report illustrates a diagnostic and therapeutic challenge in a highly immunocompromised host: severe pneumonia occurring late after autologous hematopoietic stem cell transplantation (auto-HSCT). A 57-year-old male with angioimmunoblastic T-cell lymphoma (AITL) presented with hypoxemic respiratory failure 1 year post-auto-HSCT, a timeline extending beyond the typical high-risk period for opportunistic infections. A profoundly low CD4+ T-cell count (172/µL) was identified as the key predisposing factor. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) enabled rapid, unbiased pathogen detection, confirming cytomegalovirus (CMV) pneumonia (viral load: 3.0 × 10[4] copies/mL) with Klebsiella pneumoniae coinfection. An integrated management strategy was instituted, comprising early empiric coverage for Pneumocystis jirovecii pneumonia, targeted therapy with ganciclovir and levofloxacin, and adjunctive immunomodulation using intravenous immunoglobulin and corticosteroids. This comprehensive approach resulted in full recovery, highlighting that the severity of immune suppression-rather than time since transplantation alone-determines infection risk. This case challenges the conventional time-based risk paradigm and supports immune-guided surveillance. It underscores the transformative role of mNGS in diagnosing complex infections in immunocompromised patients and advocates for a management paradigm that concurrently addresses pathogen eradication and host immune dysfunction.},
}

@article {pmid42186944,
year = {2026},
author = {Patin, NV and Pitz, K and Kimbrough, K and Archer, F},
title = {Beyond Biodiversity: Incorporating Uncertainty Into Metabarcoding Data for Improved Inference of Ecological Relationships.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70160},
doi = {10.1111/1755-0998.70160},
pmid = {42186944},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Bayes Theorem ; },
abstract = {Metabarcoding sequence data from environmental DNA (eDNA) is rapidly expanding as a powerful method for biodiversity surveys. In order to interpret these data, tools are needed that account for the uncertainty associated with eDNA sampling, sequencing and analysis. The data resulting from eDNA marker gene analysis differ from many traditional methods of biodiversity surveys because they are highly complex, sparse and compositional. Methodological biases produce uncertainty at every step of the sampling and sequencing process. Thus, it is critical that users have a way of interpreting eDNA results that accounts for their compositional nature and models the uncertainty resulting from factors like patchy sampling, PCR amplification biases and variable sequencing depth. Here, we introduce MAMBO: Metabarcoding Analysis using Modeled Bayesian Occurrences. MAMBO simulates in silico replication and models the uncertainty surrounding the sequencing and analysis process. Further, it uses these modelled sequence count data to correlate two sets of marker genes with a Bayesian regression, facilitating the linkage of different groups targeted by these assays. Compared with correlational network analyses, MAMBO overcomes many of the limitations to robust statistical analyses of eDNA marker gene data and provides an opportunity for new insight into ecological patterns over space and time.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
*DNA, Environmental/genetics
*Metagenomics/methods
*Computational Biology/methods
Bayes Theorem

@article {pmid42187250,
year = {2026},
author = {Liu, X and Kwok, L-Y and Zhang, W},
title = {Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0024426},
doi = {10.1128/spectrum.00244-26},
pmid = {42187250},
issn = {2165-0497},
abstract = {UNLABELLED: Post-stroke cognitive impairment (PSCI) is significantly exacerbated in individuals with type 2 diabetes mellitus (T2DM), yet the underlying gut microbial and metabolic mechanisms remain unclear. In this study, baseline fecal samples from 28 diabetic PSCI (PSCI-DM) patients and 29 matched non-PSCI non-diabetic controls were subjected to deep metagenomic sequencing and untargeted metabolomics. Although alpha diversity was preserved, subtle but meaningful shifts were observed in bacterial and fungal composition. The PSCI-DM group exhibited depletion of beneficial butyrate-producing taxa, including Lachnospira spp. and Butyribacter intestini, and enrichment of Butyricimonas virosa. Five fungal species, including Torulaspora globosa and Pichia kudriavzevii, were significantly reduced. Metabolomic profiling identified 45 differentially abundant metabolites, with decreases in neuroprotective compounds, such as 9-oxononanoic acid, C16-ceramide, and nootkatone, and increases in metformin and bile acid derivatives. Abundances of microbial functional pathways linked to energy metabolism were elevated, while those involved in cofactor and neurotransmitter precursor synthesis were reduced. Significant correlations were found between specific microbes and metabolites, suggesting coordinated dysregulation across kingdoms. However, only a limited subset of microbial features remained independently associated with cognitive performance. Specifically, metabolites Nb-palmitoyltryptamine and pipecolic acid, and fungal species Pichia kudriavzevii showed significant correlations with Montreal cognitive assessment (MoCA) scores for cognitive impairment. These findings reveal a tripartite gut ecosystem signature in PSCI-DM and provide a mechanistic foundation for microbiota-targeted therapeutic strategies.

IMPORTANCE: In the context of type 2 diabetes, post-stroke cognitive impairment represents a clinically prevalent yet mechanistically underexplored condition with limited therapeutic options. This study combined metagenomic sequencing with non-targeted metabolomics to reveal the coordinated dysregulation of bacteria, fungi, and host-related metabolites in the gut of type 2 diabetes mellitus with post-stroke cognitive impairment (PSCI-DM) patients. The research indicates that cognitive impairment is not solely related to the overall decline in microbial diversity, but also involves the targeted reduction of neuroprotective butyrate-producing bacteria, the absence of specific gut fungi, and the corresponding reduction in neural activity and lipid metabolites. These findings collectively establish the gut microbiota-metabolite characteristics of PSCI-DM patients, providing a theoretical basis for targeted probiotic intervention measures to prevent or alleviate cognitive decline in diabetic patients after stroke.},
}

@article {pmid42187318,
year = {2026},
author = {Tang, Y and Lin, Z and Liu, Z and Guo, J and Yang, C and Feng, L and Wang, Y and Zhang, P and Chen, Y},
title = {Impact of Corneal Microbial Latency Detected by Metagenomic next-generation sequencing on Postoperative Recovery Following Keratorefractive lenticule extraction.},
journal = {Journal of cataract and refractive surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/j.jcrs.0000000000001979},
pmid = {42187318},
issn = {1873-4502},
abstract = {PURPOSE: To investigate the microbial species latent in corneas of healthy individuals and determine whether small incision lenticule extraction (SMILE) serves as a risk factor for pathogen reactivation.

SETTING: The Ophthalmology Department of Peking University Third Hospital, Beijing, China.

DESIGN: Prospective Cohort Study.

METHODS: Metagenomic next-generation sequencing (mNGS) was employed to analyze the microbial composition of corneal lenticules from SMILE. Based on the results, patients were categorized into Viral Group (VG) and Non-Viral Pathogen Group (NVPG). Two Matched Groups (MG1 and MG2) were established by selecting pathogen-negative individuals at a 1:4 ratio relative to two positive groups. Using SPSS to analyze baseline characteristics, preoperative ocular parameters and postoperative ocular parameters among groups.

RESULTS: Among the detected pathogens, latent Herpesviruses were identified in 9 cases (4.31%), Papillomavirus were 4 cases (1.91%), and non-viral pathogens were 20 cases (9.57%). Both VG and NVPG groups showed no significant differences in baseline characteristics or preoperative ocular parameters compared with MG groups. In postoperative ocular parameters, no significant differences were found between VG and MG1, though intergroup variations in intraocular pressure and corneal thickness were observed (p>0.05). However, NVPG demonstrated significantly poorer results than MG2 in 1 month-spherical equivalent (p=0.033) and corneal epithelial staining (p=0.044).

CONCLUSION: These findings indicate pathogen latency does not affect ocular status and SMILE surgery is unlikely to reactivate latent viruses or exerts minimal influence. Viral latency has almost no impact on postoperative recovery, while latent non-viral pathogens may interfere with postoperative recovery.},
}

@article {pmid42187703,
year = {2026},
author = {Sun, Q and Li, J and Xu, G and Zhou, C and Lei, K and Jiang, W},
title = {Source-Specific Nitrogen Inputs Are Associated with Pathway Partitioning Between Denitrification and DNRA in River Water.},
journal = {Biology},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biology15100741},
pmid = {42187703},
issn = {2079-7737},
support = {Lishui City Key R&D Program Projects.(2023zdyf03)//Lishui Ecological and Environmental Monitoring Center of Zhejiang Province/ ; },
abstract = {Understanding how external nitrogen sources regulate nitrogen fate in river water is critical for improving nitrogen removal and reducing greenhouse-gas risk. Here, short-term microcosm incubations were conducted using source water as the background matrix and seven representative source inputs. By integrating hydrochemical analyses, bacterial community profiling, metagenomics, RT-qPCR, and process-rate measurements, we evaluated source-dependent shifts in nitrogen-cycling pathways. Manure-related inputs generated the highest organic and nitrogen loading, suppressed nitrification, enhanced nrfA (cytochrome c nitrite reductase) abundance and transcription, and promoted DNRA, indicating a shift toward nitrogen retention via ammonium regeneration. In contrast, sewage-related inputs maintained relatively high NO3[-] availability, elevated nirS (cytochrome cd1 nitrite reductase) and nosZ (nitrous oxide reductase) expression, and enhanced denitrification, but also increased N2O production. Metagenomic, transcriptional, and rate-based evidence consistently identified 12 h as a critical window for source-dependent pathway redistribution, highlighting the importance of short-term monitoring for detecting rapid nitrogen-cycle responses following pollution inputs. These findings support source-oriented nitrogen management that considers both nitrogen loading and hydrochemical controls on nitrate fate.},
}

@article {pmid42187710,
year = {2026},
author = {Singh, S and Tiwari, H and Singh, M and Gautam, V and Gautam, A and Gautam, HK},
title = {Expanding the Microbial Genomic Landscape and Biotechnological Applications of CRISPR-Cas Systems.},
journal = {Biology},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biology15100748},
pmid = {42187710},
issn = {2079-7737},
support = {(File No.: ANRF/IRG/2025/000135/LS)//Anusandhan National Research Foundation (ANRF)/ ; CST/D-1187//Council of Science and Technology, Uttar Pradesh, India (CST-UP)/ ; },
abstract = {The CRISPR-Cas systems, identified initially as adaptive immune mechanisms in bacteria and archaea against viral threats, have rapidly evolved into transformative tools in genetic engineering and biotechnology. These RNA-guided systems are broadly classified into Class 1, comprising multi-subunit complexes, and Class 2, characterized by compact single-effector protein, such as Cas9, Cas12, and Cas13. Their remarkable structural and functional diversity enables microorganisms to adapt to diverse ecological niches, offering a vast repertoire of genome-editing strategies. Beyond their natural role in maintaining genome integrity and defense, CRISPR-Cas systems have been extensively repurposed for precise genome modification, transcriptional regulation, epigenetic editing, and nucleic acid detection. Recent advances in computational mining of microbial genomes and metagenomes have uncovered a broad range of novel CRISPR effectors with unique properties, distinct protospacer adjacent motif (PAM) requirements, RNA-targeting capabilities, miniature architectures, and promiscuous cleavage activities that significantly expand the molecular biology toolkit. The development of CRISPR-based technologies such as base editing, prime editing, gene knock-in/out, and live-cell DNA/RNA imaging exemplifies the versatility of these systems. Despite the challenges associated with delivering complex Class 1 systems, both classes are now being actively harnessed across diverse microbial platforms. Concurrently, the CRISPR-Cas research, particularly for guide RNA (gRNA) design and activity prediction, has revolutionized target specificity and editing efficiency. This review presents a comprehensive overview of CRISPR-Cas system diversity, their genomic landscape in microorganisms, and their cutting-edge biotechnological applications. It also emphasizes the transformative potential of CRISPR in synthetic biology, therapeutics, diagnostics, environmental remediation, and agriculture, while also addressing the ethical and biosafety considerations surrounding its deployment. As CRISPR-Cas systems continue to evolve, they stand at the forefront of innovations that bridge natural microbial immunity with engineered precision tools for next-generation biotechnology.},
}

@article {pmid42187714,
year = {2026},
author = {Peng, D and Huang, T and Kang, W},
title = {Evolutionary Strategies for Heavy Metal Resistance: Genomic Plasticity in Pseudomonas Versus Stability in Aeromonas and Bacillus.},
journal = {Biology},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biology15100751},
pmid = {42187714},
issn = {2079-7737},
support = {2025QT02//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2024FY100200//Science & Technology Fundamental Resources Investigation Program/ ; },
abstract = {Heavy metal resistance represents a critical microbial trait shaped by lineage-specific evolutionary pressures, yet its genomic foundations and diversification across major bacterial taxa remain poorly resolved. This study presented a comparative pangenomic analysis of Aeromonas (n = 32), Bacillus (n = 123), and Pseudomonas (n = 350)-three phylogenetically and ecologically distinct genera frequently enriched in metal-contaminated environments and exhibiting notable differences in resistance architectures. All three genera exhibited open pangenomes, with fitted expansion indices of 0.003 (Aeromonas), 0.03 (Bacillus), and 0.04 (Pseudomonas), each showing strong model fit (R[2] > 0.98). Pseudomonas harbored a significantly greater number of resistance genes, with copper and zinc resistance genes exceeding 25 per strain in some cases. Most heavy metal resistance genes across the three genera were subject to purifying selection (dN/dS < 1), and no significant expansion or contraction of these gene families was observed (p > 0.05). The presence of these genera and their lineage-specific resistance determinants may serve as bioindicators of heavy metal exposure, offering valuable references for assessing contamination levels through environmental metagenomics.},
}

@article {pmid42187862,
year = {2026},
author = {Mills, N and Mills, N and Suwannarach, N and Noirungsee, N and Kumla, J and Inwongwan, S and Yongsawas, R and Saksunwiriya, C and Domethong, V and Shoocongdej, R and Disayathanoowat, T},
title = {Fungal Communities Associated with Wooden Coffins in a Prehistoric Burial Cave.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/jof12050380},
pmid = {42187862},
issn = {2309-608X},
support = {2021//U.S. Ambassador's Fund for Cultural Preservation/ ; },
abstract = {Phi Man Long Long Rak Cave, located in Mae Hong Son Province, northern Thailand, is a prehistoric burial site containing ancient wooden coffins that have undergone biodeterioration, likely due to fungal activity. Both culture-dependent and culture-independent approaches were employed to characterize fungal communities and assess their roles in wood degradation. Culture-dependent analysis identified five Aspergillus isolates from the wooden coffins, most of which produced cellulolytic and hemicellulolytic enzymes; some isolates also produced organic acids, indicating significant degradative potential. Culture-independent analysis revealed a community dominated by Aspergillus, together with additional taxa such as Penicillium and Ceriporia that were not detected by cultivation, highlighting greater community diversity and demonstrating the complementarity of the two methods. Functional prediction indicated a predominance of saprotrophic fungi. The presence of shared dominant taxa between soil and coffin-associated substrates suggests ecological connectivity at the soil-coffin interface, although the direction of dispersal cannot be determined from the present data. All tested fungicides inhibited fungal growth, with the highest efficacy observed in the formulation containing the highest proportion of active components. Taken together, these findings provide insights into fungal biodeterioration processes and inform conservation strategies.},
}

@article {pmid42188011,
year = {2026},
author = {Li, X and Deng, W and Zhang, Z and Tong, H and Cao, Y},
title = {Revealing the Formation Mechanism of Key Metabolites During Japonica Rice Storage Driven by Microbial Functional Genes.},
journal = {Metabolites},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/metabo16050302},
pmid = {42188011},
issn = {2218-1989},
support = {2023010714-JH3/107//Liaoning Provincial Science and Technology Plan Project General Project/ ; 254358.//China Postdoctoral Science Foundation Project/ ; },
abstract = {BACKGROUND: To elucidate the evolution of metabolites and fungal communities during storage of fragrant japonica rice (Liaoxiangjing 1396), and to investigate the biosynthetic mechanisms of key compounds and their association with quality deterioration, this study examined rice samples stored under simulated conditions for 16 months.

METHOD: Samples were collected at 4-month intervals (designated R20, R14, R13, R12, and R11). Metabolites were identified using GC-MS non-targeted metabolomics, while fungal community structure was analyzed through metagenomics. Core mechanisms were further elucidated via PLS-DA, KEGG pathway enrichment, and multiomics association analysis.

RESULT: Results demonstrated that the fatty acid content of rice increased initially and then stabilized (from 12.24 mg/g in R20 to 17.63 mg/g in R12). A total of 263 metabolites were identified, with oxygenated organic compounds (38 species) and lipids/lepidid molecules (24 species) as the predominant categories. Twelve key differential metabolites were screened from the R20 and R12 groups, involving five major metabolic pathways, including amino acid metabolism and lipid metabolism. In the fungal community, Pseudomonas (60.2%) and Pantoea (38.19%) were dominant taxa, with a specific Pantoea species (Pantoea sp.) identified as a core potential biomarker. Multiomics association analysis revealed that Klebsiella dominated the ndhB energy metabolism pathway, while multiple bacteria cooperatively regulated the mcp chemotaxis pathway, interacting with monosaccharide and amino acid accumulation.

CONCLUSIONS: This study reveals that the storage quality deterioration of fragrant japonica rice is driven by the "metabolite-microbe-pathway" chain regulation, and the dynamic changes in key metabolites and fungal communities can serve as quality early warning targets.},
}

@article {pmid42188051,
year = {2026},
author = {Deng, H and Zhang, R},
title = {TCM-Derived Natural Compounds Targeting the Gut Microbiota in Metabolic Dysfunction-Associated Steatotic Liver Disease: Gut-Liver Axis Mechanisms, Safety Considerations, and Translational Challenges.},
journal = {Metabolites},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/metabo16050342},
pmid = {42188051},
issn = {2218-1989},
abstract = {The occurrence and development of metabolic dysfunction-associated steatotic liver disease (MASLD) are closely related to intestinal flora imbalance, intestinal barrier damage, and gut-liver axis dysfunction. Due to their multi-target regulatory effects and advantages in intestinal microecological intervention, Chinese herbal monomers have shown promising application prospects in the prevention and treatment of MASLD. However, basic research on their toxicity still lags behind, and issues related to safety and clinical translation urgently need attention. This article systematically reviews the research progress on how flavonoids, triterpenoids, alkaloids, and polysaccharides improve hepatic steatosis, inflammatory responses, and metabolic disorders from a toxicological perspective by reshaping the intestinal microbiota, repairing the intestinal mucosal barrier, regulating short-chain fatty acid and bile acid metabolism, and synergistically acting on signaling pathways such as TLR4/NF-kB, FXR, TGR5, SIRT1, and the NLRP3 inflammasome. Furthermore, by combining methods such as 16S rRNA sequencing, metagenomics, metabolomics, and multi-omics integration, the article analyzes their application value and limitations in toxicological mechanism research, and discusses the translational bottlenecks faced by Chinese herbal monomers in pharmacokinetics, bioavailability, quality standardization, targeted delivery, and toxicological safety. Existing evidence indicates that Chinese herbal monomers have a three-in-one intervention advantage of microecological remodeling-metabolic regulation-inflammation inhibition, but their long-term medication safety, toxic target organs, dose-effect/toxicity relationships, and potential drug interactions still need further clarification. This article aims to provide a systematic reference for the safety evaluation and clinical translational research of Chinese herbal monomers in the prevention and treatment of MASLD.},
}

@article {pmid42188128,
year = {2026},
author = {Sontigun, N and Thanawan, N and Fungwithaya, P},
title = {Epidemiology and Antimicrobial-Resistant Genes of Family Staphylococcaceae in Musca domestica: Case Studies from Chicken Farm, Pig Farms, and Residential Areas in Southern Thailand.},
journal = {Insects},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/insects17050461},
pmid = {42188128},
issn = {2075-4450},
support = {KREF186729//King Mongkut's Institute of Technology Ladkrabang Research Fund/ ; },
abstract = {The major Staphylococcaceae family is recognized as opportunistic pathogens colonizing human and animal skin, mucous membranes, and environments. Musca domestica, the house fly, plays a role in the transmission of AMR bacteria. This study focused on examining the epidemiology and antimicrobial-resistant genes of the family Staphylococcaceae in M. domestica through metagenomic analysis, using samples collected from three animal farms and two residential areas in southern Thailand. Fifty M. domestica were collected from five places surrounding Walailak University, including one chicken farm (CF1), two pig farms (PF2 and PF3), and two residential areas (H1 and H2). All samples were dispatched for analysis using shotgun metagenomic sequencing and analyzed using FastQC, MultiQC, FASTQ, MEGAHIT, QUAST, ABRicate, AMRFinderPlus, ResFinder, ARG-ANNOT, MEGARES, PlasmidFinder, VFDB, Kraken2, Krona and Python. Our findings describe the taxonomic composition of Staphylococcaceae taxa in M. domestica from different environments; the representation of the family Staphylococcaceae in CF1, PF2, PF3, H1, and H2 was recorded at 2%, 0.7%, 0.2%, 0.2%, and 2% of this phylum, respectively. The average populations discovered were Staphylococcus (37.4%), Mammaliicoccus (17.4%), and Macrococcus (10.3%), respectively. Trimethoprim-resistant genes (dfrG and dfrE) were found only in CF1, PF2, and H1. Interestingly, fosfomycin-resistant genes were found only in M. domestica within residential areas. Our findings pertain to the Staphylococcaceae population in M. domestica within residential areas, which exhibited varying multidrug-resistance genes, particularly those resistant to fosfomycin.},
}

@article {pmid42188162,
year = {2026},
author = {Tao, M and Zhang, J and Fan, Y},
title = {Metagenomic Analysis of Gut Microbiome Across Developmental Stage of Asian Corn Borer (Ostrinia furnacalis).},
journal = {Insects},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/insects17050495},
pmid = {42188162},
issn = {2075-4450},
support = {Grant No. 32402469//National Natural Science Foundation of China/ ; },
abstract = {Ostrinia furnacalis is one of the most important agricultural pests in Asia. Previous studies utilizing 16S rRNA sequencing have established a foundational understanding of the taxonomic composition of its gut microbiota; however, the dynamic functional transitions across the host's entire life cycle remain poorly understood. In this study, we used metagenomic sequencing to systematically characterize the gut microbiome across six groups representing different life stages and sexes of O. furnacalis: first-instar, third-instar, and fifth-instar larvae, pupae, and adults (both males and females). Microbial richness and evenness vary significantly across six groups representing different life stages and sexes. Species richness is highest in the first-instar larvae (L1D2), while evenness is relatively high in both first- and third-instar larvae (L1D2 and L3D2). Additionally, no sex-based differences were observed in either indicator during the adult stage. Enterococcus mundtii is the primary species driving community succession and rapidly achieves dominance after the third-instar stage. Co-occurrence network analysis revealed that the first-instar larval network exhibits the highest complexity, with positive correlations accounting for 96.6% of all edges. Conversely, the fifth-instar larvae exhibits the greatest proportion of negative correlation edges at 29.13%, while the pupal stage network is the most dispersive, indicating microbial reorganization during metamorphosis. Functional annotation reveals that carbohydrate and amino acid metabolism pathways are significantly enriched during the larval stage. In contrast, the pupal stage is characterized by enrichment in environmental information processing and a notable increase in polysaccharide lyases (PLs). This shift indicates that the microbiota transitioned from degrading plant polysaccharides to foraging host-derived glycans. The number of resistance genes in the first-instar larvae is significantly higher than that in all other groups representing different life stages and sexes. Collectively, this study systematically reveals the dynamic succession patterns of the gut microbiome throughout the life cycle of O. furnacalis and provides a theoretical foundation for the development of microbiome-based pest management strategies.},
}

@article {pmid42188886,
year = {2026},
author = {Yi, C and Nicolas, CS and Sun, Z and Wang, Q and Dong, T and Wu, Y},
title = {Effects of a Novel Prebiotic and Postbiotic Dietary Supplement on Gut Microbiota, Intestinal Barrier Markers, and Inflammation in Healthy Dogs.},
journal = {Veterinary sciences},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/vetsci13050417},
pmid = {42188886},
issn = {2306-7381},
support = {202404810411350//Virbac China/ ; },
abstract = {Although prebiotics and postbiotics support gastrointestinal health, evidence for their combined effects in dogs remains limited. This study evaluated a novel prebiotic and postbiotic supplement in healthy dogs undergoing a dietary transition. Thirty-six healthy adult dogs were randomly assigned to control group (CON, high-protein basal diet with placebo chew) or treatment group (TRT, the same basal diet with chew containing prebiotics [baobab fruit pulp and acacia gum] and postbiotics [inactivated Lactobacillus acidophilus and selected yeast fractions]) for a 28-day formal trial following a 7-day adaptation period. The primary outcomes evaluated included clinical fecal scores, specific biomarkers of intestinal barrier function and inflammation, fecal short-chain fatty acids, and microbiota structure. Following the 7-day adaptation, formal trial baseline, fecal scores were already within the healthy range and remained optimal without differing between groups throughout the study. Compared with CON, the TRT group showed lower fecal calprotectin and serum diamine oxidase levels, and higher fecal butyrate (p < 0.05). Metagenomic analysis revealed increased abundances of Bacteroidota, Oscillospiraceae, Prevotellaceae, and Prevotella in TRT (p < 0.05). Overall, in healthy dogs, this supplementation was associated with favorable microbiota modulation and modulated biomarkers of intestinal barrier and inflammation within normal ranges, without altering clinical fecal endpoints.},
}

@article {pmid42188905,
year = {2026},
author = {Yao, Y and Yang, Z and Xie, T and Zhang, Y and Huang, F and Meng, C and Wu, Y},
title = {Multi-Omics Analyses of the Gut Microbiota and Metabolism in Cats with Different Body Conditions and the Effects of Fecal Microbiota Transplantation.},
journal = {Veterinary sciences},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/vetsci13050436},
pmid = {42188905},
issn = {2306-7381},
abstract = {Obesity is increasingly recognized in domestic cats and is associated with metabolic disturbances such as insulin resistance and dyslipidemia. The gut microbiota is considered an important regulator of host metabolism, yet its role in feline obesity remains unclear. In this study, a multi-omics approach was used to investigate gut microbiota composition and metabolic profiles in cats with different body conditions and to evaluate the effects of fecal microbiota transplantation (FMT) on the feline gut microbiota and overall metabolism. In Experiment 1, twenty-four cats were classified as obese, normal, or lean, and their gut microbiota and serum metabolites were analyzed. In Experiment 2, fecal microbiota from obese or lean donors were transplanted into recipient cats. Although overall microbial diversity and community structure did not differ significantly among groups, Coriobacteriaceae and Collinsella were enriched in obese cats, whereas Enterobacteriaceae-related taxa were more abundant in normal-weight cats. Serum metabolomics revealed alterations mainly related to amino acid and antioxidant metabolism, including O-acetylcarnitine, glutathione, and tryptophan metabolism. FMT shifted the recipient gut microbial communities toward their respective donor profiles (obese or lean) but did not significantly affect body weight or routine serum biochemical parameters during the experimental period. These findings suggest that gut microbiota remodeling may influence metabolic processes prior to detectable phenotypic changes in cats.},
}

@article {pmid42189102,
year = {2026},
author = {Zheng, H and Xie, X and Zhang, L and Cai, Y and Zhang, Q and Yang, F and Liu, X and Basitere, M and Wei, C and Qiu, G},
title = {Intralineage Diversity and Global Biogeography of Ca. Phosphoribacter.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c18078},
pmid = {42189102},
issn = {1520-5851},
abstract = {In wastewater treatment plants (WWTPs), the newly defined polyphosphate-accumulating organism (PAO) "Candidatus Phosphoribacter" demonstrated important contributions to phosphorus removal. However, their phylogenetic and metabolic diversity, as well as ecological distributions, remain largely uncharacterized. By sequencing 81 activated sludge samples from 34 provinces in China and integrating 747 WWTP metagenomes from six continents, we recovered 166 metagenome-assembled genomes (MAGs) of this genus, expanding the number of Ca. Phosphoribacter MAGs by 17 times and identifying 12 novel species. Biogeographical analysis demonstrated their distinct intercontinental distribution. The coexistence of cosmopolitan species and regionally dominant ones was observed globally as a result of metabolic differentiation. Ancestral gene family reconstruction indicated that this genus underwent a streamlining process dominated by gene loss. Vertically inherited ppk2 and horizontally acquired phoU jointly underpinned the genetic basis of a PhoU-dysregulation-driven polyphosphate phenotype. Comparative genomics revealed broad metabolic potential, including versatile carbon utilization, α-glucan metabolism, and three complementary denitrifying phenotypes. Metatranscriptomic analyses further supported glucose uptake and potential α-glucan cycling as a carbon storage polymer. Overall, this study establishes the most comprehensive genomic framework of Ca. Phosphoribacter, elucidates their functional metabolisms, ecological roles, and global distributions, providing new insights into Ca. Phosphoribacter-mediated enhanced biological phosphorus removal (EBPR) for improved engineering implementation and system sustainability.},
}

@article {pmid42189287,
year = {2026},
author = {Candeliere, F and Busi, E and Cerri, S and Sola, L and Lombardi, M and Greco, S and Pedroni, S and Amaretti, A and Raimondi, S and Chiavelli, C and Vitale, MG and Bertolini, F and Depenni, R and Franchini, G and Dominici, M and Rossi, M},
title = {Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00262-026-04432-w},
pmid = {42189287},
issn = {1432-0851},
support = {PE00000019//NextGenerationEU/ ; },
abstract = {The gut microbiota appears to play a critical role in modulating antitumor immune responses and influencing the efficacy of cancer immunotherapy drugs such as immune checkpoint inhibitors. However, the identification of consistent microbial biomarkers of response remains a significant challenge. This lack of consensus is largely driven by multi-source heterogeneity, including geographic variations in lifestyle, and high inter-individual variability. We hypothesize that these inconsistencies arise because microbiome composition is not uniform but organized into distinct enterotypes. To address this, we performed an integrated metagenomic analysis of 569 fecal samples from oncological patients affected by different tumor types treated with immunotherapy. The samples were clustered into two main enterotypes, E1 and E2, each of them containing two subclusters. A total of 166 species (e.g., Collinsella spp., Blautia spp., Bacteroides spp.) were identified as enterotype-specific biomarkers. A preliminary independent concordance assessment of these biomarkers was conducted in 19 oncologic patients with exceptional response to immunotherapy, providing an initial confirmation of selected enterotype-associated signals. Furthermore, we evaluated the predictive potential of gut microbiota profiles for immunotherapy outcomes through machine learning techniques. The models showed encouraging, albeit moderate, performance in the heterogeneous full dataset, supporting the potential of microbiome-based stratification as an exploratory framework for patient classification, while indicating that further validation is needed before clinical application.},
}

@article {pmid42189388,
year = {2026},
author = {Chen, P and Ma, M and Li, Y and Chen, X and Xu, Z and Guo, J and Hu, X and Lv, L and Guo, J and Liu, G},
title = {Food processing-derived carbon dots disrupt male fertility via the gut-testis axis.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42189388},
issn = {1869-1889},
abstract = {Carbon dots (CDs) are unintentionally formed during thermal processing of food and are emerging environmental pollutants that may pose health risks. We investigated the reproductive toxicity of food-derived CDs via the gut-testicular axis by exposing male mice to environmentally relevant doses (25 and 100 mg kg[-1] d[-1]) for 15 weeks. Multi-omics analysis (including metagenomics, transcriptomics, and metabolomics) revealed that CDs significantly altered the gut microbiota composition, reducing beneficial bacteria (Akkermansia muciniphila, P<0.01) while increasing pathogenic bacteria (Desulfovibrionaceae, P<0.001). Functional analysis revealed upregulation of the lipopolysaccharide (LPS) biosynthesis pathway (P<0.001) and reduced levels of barrier-protective tryptophan metabolites. Time-series studies established a mechanistic sequence: microbiota disruption (days 1-3), intestinal barrier dysfunction (days 3-5), blood-testis barrier damage (days 5-7), testicular inflammation, and reproductive dysfunction. Dose-dependent testicular toxicity included reduced testosterone synthesis (P<0.001), impaired spermatogonial stem cell maintenance due to downregulation of PLZF, and impaired fertility. Testicular transcriptomics analysis revealed activation of the IL-17 signaling pathway and inhibition of steroidogenesis. This study provides comprehensive evidence that CD induces male reproductive toxicity through microbiota-dependent mechanisms, emphasizing the environmental health implications of dietary nanoparticle exposure.},
}

@article {pmid42189604,
year = {2026},
author = {Lopes, F and Martinez-Martinez, D and Späth, MR and Hoyer-Allo, KJR and Strubl, S and Cukoski, S and Knieps, L and Brodesser, S and Göbel, H and Schwarz, G and van den Berg, BM and Rabelink, TJ and Schermer, B and Benzing, T and Müller, RU and Beyer, A and Cabreiro, F and Koehler, FC},
title = {The Interplay between Gut Microbiota and Diet-Induced Kidney Protection.},
journal = {Kidney360},
volume = {},
number = {},
pages = {},
doi = {10.34067/KID.0000001219},
pmid = {42189604},
issn = {2641-7650},
abstract = {BACKGROUND: On the one hand, dietary interventions are known for their pivotal role in regulating diversity, composition as well as function of the gut microbiome. On the other hand, specific diets show an immense potential in preventing kidney injury from various damaging stimuli in rodents and recent findings, in turn, highlight a central role of gut microbiota in kidney health and disease.

METHODS: Three protective dietary regimens - a fasting mimicking diet, a diet depleted in sulfur containing amino acids and caloric restriction - were examined in parallel in a rodent model of ischemia-reperfusion injury. To delineate the diet-induced effect on gut microbiota in response to ischemic kidney damage we used comparative shotgun metagenomics for taxonomic as well as functional profiling. We further examined the renal metabolic response using comparative transcriptomics to unravel the interplay between gut microbiota and kidney protection.

RESULTS: Beneficial dietary preconditioning strategies changed the composition of gut microbiota in an IRI-dependent manner. Using ternary plots to investigate the role of dietary interventions over time before and after ischemic insult, we detected a central role of Lachnospiraceae that commonly expanded in response to renal IRI in dietary-preconditioned mice. Further functional profiling of gut microbiota in our model revealed an increase in plasma levels of bacterial derived short chained fatty acids in diet-induced kidney protection. Comparative bulk transcriptomics in our model, in turn, pointed towards the metabolic use of these bacterial derived short-chained fatty acids in kidneys of protected mice.

CONCLUSIONS: As proximal tubules lack sufficient glycolytic capacity, products of microbial metabolism may serve as an additional energy source to fulfill their high demands when withstanding ischemic damage. Our data shed light on a close interplay between gut microbiota and diet-induced kidney protection calling for further research at the crossroads of microbiology, metabolism and molecular nephrology.},
}

@article {pmid42177063,
year = {2026},
author = {Sélem-Mojica, N and Magaña-Lemus, MÁ and Rosiles-Loeza, PY and Barona-Gómez, F},
title = {Bringing CORASON to Windows: Exploring fungal natural products through biosynthetic gene clusters.},
journal = {Methods in enzymology},
volume = {730},
number = {},
pages = {61-73},
doi = {10.1016/bs.mie.2026.03.001},
pmid = {42177063},
issn = {1557-7988},
mesh = {*Multigene Family ; *Biological Products/metabolism ; *Fusarium/genetics/metabolism ; Phylogeny ; *Software ; Genome, Fungal ; *Biosynthetic Pathways/genetics ; *Computational Biology/methods ; },
abstract = {Biosynthetic gene clusters (BGC) are genomic regions that encode the production of specialized metabolites, including antibiotics, pigments, and toxins. While BGC are traditionally classified into broad categories such as NRPS, PKS, and terpene clusters, these classes often overlook finer relationships among gene clusters that produce structurally or functionally related compounds. Tools like BiG-SCAPE and BiG-SLiCE have been developed to address this issue by organizing BGC into gene cluster families (GCFs). CORASON complements these tools by enabling phylogenetic reconstruction of BGC, identifying conserved core genes, and visualizing GFCs as a continuum of variation in gene presence/absence and sequence identity. Although CORASON is incorporated in BiG-SCAPE visualization, it is also a standalone tool initially designed for bacterial genomes annotated via RAST and implemented through Docker in Linux environments. Here, we demonstrate CORASON's broader applicability using fungal GenBank files and its installation via Conda on Windows. As a case study, we examine metagenome-assembled genomes (MAGs) from Fusarium domesticum, a lesser-known member of the Fusarium genus, which is often present in food-associated microbiomes. Unlike its pathogenic relatives (F. oxysporum, F. graminearum), F. domesticum remains understudied, making it an interesting target for genomic mining. This work expands the accessibility of CORASON for fungal genome analysis and highlights its potential in uncovering novel biosynthetic potential in overlooked microbial taxa.},
}

*Multigene Family
*Biological Products/metabolism
*Fusarium/genetics/metabolism
Phylogeny
*Software
Genome, Fungal
*Biosynthetic Pathways/genetics
*Computational Biology/methods

@article {pmid42177457,
year = {2026},
author = {Zhang, H and Abbas, Z and Li, H and Zhu, Y and Hu, X and Si, D},
title = {Synergistic fungal-enzymatic fermentation of corn straw enhances nutritional value, microbial stability, and bio-feed quality.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05190-6},
pmid = {42177457},
issn = {1471-2180},
support = {2024TSYCTD0016//Xinjiang Uygur Autonomous Region "Tianshan Talents" Cultivation Program/ ; },
abstract = {Valorizing mature, dry corn straw into nutritional animal feed is constrained by its recalcitrant lignocellulosic matrix, while conventional silage methods face stability and logistical limitations. Existing enzymatic and bacterial approaches often lack synergistic efficacy and fail to mitigate pathogen risk in dry biomass systems. We engineered a two-stage fungal-enzymatic fermentation strategy employing a consortium of Aspergillus niger LFB-AN14, Coriolopsis trogii LFB-F1, Bacillus subtilis LFB-BS7, and Pediococcus acidilactici A62, integrated with cellulase, xylanase, and laccase under optimized conditions (1% inoculation, 5:5:1:1 ratio, 37 °C, 21 days). Our results demonstrated that the bacterial-enzyme co-treatment (Group A3) significantly reduced fiber content, with neutral detergent fiber (NDF) and acid detergent fiber (ADF) decreasing by 22.6% and 29.1%, respectively, compared to the control (p < 0.001). Lignin degradation was enhanced, accompanied by a 4.5-fold increase in water-soluble carbohydrates (WSC). The metabolic profile revealed elevated lactic acid production (36.54 g/kg FM) and the suppression of undesirable byproducts such as propionic and butyric acids. Microbial community analysis revealed a dominant shift toward Pediococcus (> 50% abundance) and inhibition of pathogenic Enterobacter spp. Structural analyses (SEM, FTIR) confirmed extensive lignocellulose deconstruction, particularly through carbonyl and hydroxyl functional groups. Metagenomic analysis revealed upregulated Auxiliary Activity (AA) enzymes and cellulosome modules, elucidating the mechanistic basis for enhanced degradation. KEGG enrichment highlighted enhanced aromatic compound metabolism and yeast proliferation, reflecting superior metabolic efficiency. This integrated fungal-enzymatic approach establishes a safe, scalable, and metabolically efficient strategy for transforming agricultural residues into high-quality bio-feed, resolving key challenges in fiber digestibility, pathogen control, and storage stability for sustainable livestock production.},
}

@article {pmid42178356,
year = {2026},
author = {Chen, S and Xu, S and Muhammad, ZUA and Wang, X and Guo, K and Tao, J and Li, M and Wang, H and Zhang, C and Hou, S},
title = {Two-hourly resolved microbial and viral dynamics in the subtropical Daya Bay.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07491-x},
pmid = {42178356},
issn = {2052-4463},
support = {JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; 4241003//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Planktonic microbial and viral communities are fundamental drivers of biogeochemical cycling and energy flow in marine ecosystems. These communities display substantial variability in their composition at daily to sub-daily scales, which cannot be captured by conventional low-frequency monthly or weekly sampling. To reveal these high-resolution dynamics, we performed a time-series sampling of planktonic microbial and viral communities in the subtropical Daya Bay at 2-hour intervals over 3 days. Seawater samples were subjected to metagenomic and metatranscriptomic sequencing for the cellular size fraction (>0.2 μm) and metagenomic sequencing for the viral size fraction (0.02-0.2 μm). This approach enabled us to capture fine-scale temporal variations in the genomic composition and transcriptional activities of microbial and viral communities. The resulting comprehensive dataset, including 700 metagenome-assembled genomes (MAGs) and 118,242 viral operational taxonomic units (vOTUs), provides a valuable resource for investigating the metabolic potentials and dynamic interactions within natural planktonic microbial-viral assemblages in subtropical bay ecosystems, offering insights into their ecological roles that are inaccessible through low-temporal-resolution sampling.},
}

@article {pmid42178395,
year = {2026},
author = {Sharaf, H and Bobay, LM},
title = {MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag340},
pmid = {42178395},
issn = {1367-4811},
abstract = {MOTIVATION: Metagenomics provides broad insights from microbial communities, but more biological relevant phenotypes are attributed to subtle changes at the strain-level rather than species. Despite development of several tools using different algorithms, resolving individual strains from short-read pair-end sequencing data remains challenging.

RESULTS: Here we present MetaStrainer, a tool capable of reconstructing strain genotypes from metagenomic data. Compared with existing approaches, MetaStrainer substantially increases genotype accuracy, correctly identifies the number of strains, and accurately estimates their relative abundances. Accuracy of reconstructed genotypes is robust to choice of mapping reference.

AVAILABILITY: MetaStrainer is implemented in Python 3. Source code and instructions are available on GitHub at www.github.com/lbobay/MetaStrainer and on Zenodo: 10.5281/zenodo.17872331.

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

@article {pmid42178569,
year = {2026},
author = {Garritano, AN and J Hill, L and Ribeiro, B and Damasceno, T and Medeiros, L and Duarte, G and L S Vilela, C and Majzoub, ME and Allen, MA and Nappi, J and S Peixoto, R and Thomas, T},
title = {Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42178569},
issn = {2049-2618},
support = {BAS/1/1095-01-01//KAUST/ ; ANP 21005-4//ANP, Brazil/ ; },
mesh = {Animals ; *Porifera/microbiology ; *Ammonia/metabolism ; *Symbiosis ; Oxidation-Reduction ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Microbiota ; *Carbon/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Autotrophic Processes ; Carbon Cycle ; Seawater/microbiology ; },
abstract = {BACKGROUND: Sponges are important members of shallow-water, benthic ecosystems, where they often rely on their microbial symbionts to acquire organic or inorganic carbon. Sponges are also found in the deep sea, however, how they metabolically interact there with their symbionts remains underexplored. Here, we combined metagenomic, metatranscriptomic and stable-isotope labelling approaches to investigate the metabolic activities of the microbial community of the deep-sea sponge Calyx sp.

RESULTS: Approximately 84% of the total estimated microbial abundance was composed of nine heterotrophic phyla, whilst the remaining 16% consisted of two autotrophic ammonia-oxidising archaea. Metatranscriptomic analysis revealed the high expression of genes involved in the degradation of recalcitrant polysaccharides of algal origin, suggesting that an undegraded fraction of marine snow plays a role in the nutrition of this deep-sea holobiont. Additionally, we detected active ammonia oxidation and carbon fixation pathways in the autotrophic community members and, through ex situ incubations with labelled carbonate show a potential to fix 13.67 mg CO2 per g dry weight in a year.

CONCLUSIONS: This study highlights the mixotrophic lifestyle of a deep-sea sponge microbiome, expanding our knowledge of the sponge-microbe symbiosis in the oligotrophic environment of the deep ocean. Video Abstract.},
}

Animals
*Porifera/microbiology
*Ammonia/metabolism
*Symbiosis
Oxidation-Reduction
*Archaea/metabolism/genetics/classification/isolation & purification
*Microbiota
*Carbon/metabolism
*Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics/methods
Autotrophic Processes
Carbon Cycle
Seawater/microbiology

@article {pmid42178714,
year = {2026},
author = {Zeamer, AL and Lai, Y and Loew, E and Sanborn, V and Tracy, M and Jo, C and Ferdinand, D and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP},
title = {Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2676162},
doi = {10.1080/19490976.2026.2676162},
pmid = {42178714},
issn = {1949-0984},
mesh = {Humans ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Female ; Male ; *Cognition ; Middle Aged ; *Cognitive Dysfunction/microbiology ; Aged, 80 and over ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Cohort Studies ; Metagenomics ; Metabolic Networks and Pathways/genetics ; },
abstract = {Disturbances in the gut microbiome are increasingly correlated with neurodegenerative disorders, including Alzheimer's disease. Multiple lines of emerging evidence are consistent with the microbiome's involvement in disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby influencing disease pathology through the "microbiota-gut-brain axis." Currently, the copathologies contributing to cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in the gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (aged 60 y or older) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiome samples. Subjects were classified as healthy controls, exhibiting mild cognitive impairment, or having dementia based on clinical assessments. Using metagenomic sequencing and gene pathway analyses, we found that certain microbial-encoded metabolic pathways correlated with worse cognitive performance. Specifically, genes involved in the urea cycle, polyamine synthesis, or the metabolism of methionine and cysteine predicted worse cognitive performance. Our study suggests that the gut microbiome composition may be linked to cognitive impairment along the AD continuum and points to microbial metabolic pathways that may potentiate disease.},
}

Humans
*Alzheimer Disease/microbiology
*Gastrointestinal Microbiome/genetics
Aged
Female
Male
*Cognition
Middle Aged
*Cognitive Dysfunction/microbiology
Aged, 80 and over
*Bacteria/classification/genetics/isolation & purification/metabolism
Cohort Studies
Metagenomics
Metabolic Networks and Pathways/genetics

@article {pmid42178721,
year = {2026},
author = {Schulze, K and Goldschmidt, I and Melk, A and Boehne, M and Woltemate, S and Ballmaier, M and Kleiner, S and Lehmann, E and Kramer, M and Vital, M},
title = {Altered SIgA-targeting of gut microbiota is associated with long-term dysbiosis in pediatric solid organ transplant recipients.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2675078},
doi = {10.1080/19490976.2026.2675078},
pmid = {42178721},
issn = {1949-0984},
mesh = {Humans ; *Dysbiosis/microbiology/immunology/etiology ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Immunoglobulin A, Secretory/immunology/genetics ; *Transplant Recipients ; Tacrolimus/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Adolescent ; Immunosuppressive Agents/adverse effects/therapeutic use ; *Organ Transplantation/adverse effects ; Feces/microbiology ; Child, Preschool ; Liver Transplantation/adverse effects ; },
abstract = {The composition of the gut microbiota (GM) is altered in solid organ transplantation (SOT) recipients, where the degree of dysbiosis is associated with long-term survival and is believed to be influenced by immunosuppression therapy. At the interface stands secretory (S)IgA, however, little is known about its role in governing dysbiosis in the context of SOT. We performed quantitative metagenomic analyses of the GM accompanied by SIgA sequencing in 48 pediatric SOT recipients (age = 10.6 ± 4.7 y) receiving either heart (n = 11), kidney (n = 10) or liver transplantation (n = 27), and compared the results to age-matched healthy controls (HC, n = 16). We confirmed compositional and functional dysbiosis in SOT recipients, with the degree of dysbiosis being associated with tacrolimus (TAC) levels. Overall, SOT recipients exhibited higher SIgA levels than HC, along with an increased percentage of bacteria targeted and altered target spectra. Furthermore, altered SIgA responses were associated with the degree of dysbiosis. A mechanistic model connecting immunosuppression, GM composition and SIgA-targeting is proposed, suggesting that GM dysbiosis in SOT recipients is mediated by the immune system through the SIgA response; direct drug-mediated effects on fecal communities were not observed in in vitro experiments. Our study provides new insights into factors that contribute to persisting dysbiosis in SOT recipients.},
}

Humans
*Dysbiosis/microbiology/immunology/etiology
*Gastrointestinal Microbiome
Child
Male
Female
*Immunoglobulin A, Secretory/immunology/genetics
*Transplant Recipients
Tacrolimus/adverse effects
Bacteria/classification/genetics/isolation & purification
Adolescent
Immunosuppressive Agents/adverse effects/therapeutic use
*Organ Transplantation/adverse effects
Feces/microbiology
Child, Preschool
Liver Transplantation/adverse effects

@article {pmid42180198,
year = {2026},
author = {Nnorom, MA and Du, B and Wang, Z and Tian, Z and Hough, R and Avery, L and Saroj, D and Guo, B},
title = {Dynamics of the Microbiome and Antibiotic Resistome in Hyper-Mesophilic Anaerobic Digestion of Cattle Manure Assisted with Granular Activated Carbon.},
journal = {ACS environmental Au},
volume = {6},
number = {3},
pages = {435-448},
pmid = {42180198},
issn = {2694-2518},
abstract = {The use of conductive materials, such as granular activated carbon (GAC), for optimization of the anaerobic digestion (AD) process has garnered attention in recent years; however, its impact on the dynamics of the microbiome and resistome in continuous AD systems remains unclear, especially under temperature variation. This study combined culture-based bacterial enumeration and shotgun metagenomics to investigate the impact of two GAC application strategies, suspended and packed, on the fate of pathogens (viable Escherichia coli) and ARGs during the AD of cattle manure at 40 and 45 °C. The results show that GAC mitigated the process imbalance and shock induced by temperature transition. The microbial community in the AD sludge was highly impacted by temperature but not GAC, while GAC biofilms showed notably higher archaeal abundance. All AD reactors reduced viable E. coli, with the highest reduction occurring in the packed GAC reactors (95.70-96.24%), followed by the suspended GAC (94.53-95.69%), and then the non-GAC (92.77-94.24%). Culturable tetracycline-resistant bacteria were reduced below the quantification limit in all reactors. Reduction of ampicillin-resistant bacteria showed stochastic trends at 40 °C but improved at 45 °C, indicating limited impact by GAC. ARGs and mobile genetic elements (MGEs) were reduced in all reactors at comparable levels, regardless of GAC addition. Temperature transition exerted a mixed effect, with higher reduction of some resistance classes (MLS, tetracycline, and multidrug) and lower reduction of others (bacitracin, aminoglycoside, beta-lactam, and streptothricin). Mantel test and Procrustes analysis revealed a significant correlation between the resistome and the bacterial community, inferring that shifts in the ARG host population were a major determinant of the fate of ARGs. Overall, GAC was beneficial to reactor stability but had a minimal influence on the reduction of E. coli, ARGs, and MGEs. It is highly recommended to monitor antimicrobial resistance using both culture-based and culture-independent methods.},
}

@article {pmid42180259,
year = {2026},
author = {He, J and Ning, Y and Liang, H and Qin, J and Wei, Y and Liang, S and He, Z and Yin, S},
title = {Special pathogen infections presenting with neck mass as the initial manifestation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1767591},
pmid = {42180259},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; Aged ; *Neck/pathology/microbiology ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology/pathology/drug therapy ; *Mycoses/diagnosis/microbiology/pathology/drug therapy ; *Talaromyces/isolation & purification ; Nontuberculous Mycobacteria/isolation & purification ; China ; Lymphadenopathy/microbiology ; },
abstract = {BACKGROUND: The etiology of neck masses is complex. Infections caused by Talaromyces marneffei (TM) and nontuberculous mycobacteria (NTM) are uncommon but often present with insidious clinical manifestations, leading to frequent misdiagnosis.

METHODS: We collected and analyzed data from 13 patients with TM/NTM infections presenting with neck masses at The First Affiliated Hospital of Guangxi Medical University and The Second Affiliated Hospital of Guangxi Medical University. Clinical manifestations, laboratory findings, infection sites, pathogen types, treatments, and outcomes were described and analyzed.

RESULTS: Of the 13 patients, six were male and seven female, with a median age of 57 years (range, 27-73 years). All patients were residents of Guangxi and tested positive for anti-interferon-γ autoantibodies (AIGAs), with titers of 1:2500 in 12 patients and 1:500 in one. The median time from symptom onset to diagnosis was 5 months (range, 1-19 months). Common clinical features included lymphadenopathy (13/13), fever (11/13), respiratory symptoms (10/13), and rash or skin ulceration (8/13). Frequent laboratory abnormalities included leukocytosis (11/13), neutrophilia (11/13), elevated erythrocyte sedimentation rate (12/13), and elevated C-reactive protein (13/13). Coinfection with two or more pathogens was observed in 12 patients. The lungs and lymph nodes were involved in all 13 patients, followed by bone (11/13), skin or soft tissue (8/13), bloodstream or bone marrow (3/13), and nasopharynx (3/13). Neck mass specimens yielded NTM in nine cases and TM in four. NTM was most frequently identified by metagenomic next-generation sequencing (mNGS), whereas TM was detected by culture. The median follow-up duration was 28 months (range, 1-86 months). During follow-up, 6 patients (46.2%) experienced disease exacerbations. Among the 13 patients, 12 achieved clinical improvement after pathogen-directed antimicrobial therapy, while one patient died.

CONCLUSION: Neck masses have diverse etiologies. TM and NTM infections presenting initially as neck masses are rare and easily misdiagnosed as tuberculosis, malignancy, or lymphoma. Culture and mNGS are crucial diagnostic tools for TM and NTM, respectively. Clinicians should maintain a high index of suspicion for these infections, particularly in immunocompromised patients in endemic regions.},
}

Humans
Male
Female
Middle Aged
Adult
Aged
*Neck/pathology/microbiology
*Mycobacterium Infections, Nontuberculous/diagnosis/microbiology/pathology/drug therapy
*Mycoses/diagnosis/microbiology/pathology/drug therapy
*Talaromyces/isolation & purification
Nontuberculous Mycobacteria/isolation & purification
China
Lymphadenopathy/microbiology

@article {pmid42180316,
year = {2026},
author = {Chen, X and Zhang, M and Yang, L and Chen, Y and Chi, Y and Zhao, Y and Ma, Z and Li, Y and Wang, X},
title = {CRISPR spacer profiling and prophage mining reveal diverse bacteriophages associated with Streptococcus Mutans.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2674332},
pmid = {42180316},
issn = {2000-2297},
abstract = {BACKGROUND: Streptococcus mutans is a key cariogenic bacterium. Current antimicrobials lack species specificity, while phage-based approaches remain experimental and require more S. mutans phage isolates.

OBJECTIVE: To profile the diversity of S. mutans-associated phages and strain-level heterogeneity in phage exposure using genome-informed CRISPR spacer and prophage analyses.

MATERIALS AND METHODS: We compiled 944 publicly available S. mutans genomes and dereplicated them into 735 non-redundant strains. CRISPR-Cas systems, spacers, spacer targets, and putative prophages were identified, quality-assessed, and functionally annotated. Phylogenetic relationships of (pro)phages were evaluated using terminase large subunit proteins, and comparative genomics compared spacer-positive and spacer-negative strains.

RESULTS: CRISPR systems were detected in 548/735 strains, yielding 14,263 spacers, 1,864 phage-targeting spacers mapped to 110 viral genomes, including 41 cultured isolates, 51 metagenome-assembled phages, and 18 uncultured viral genomes. The most frequently targeted cultured phage was phiKSM96, whereas metagenome-assembled Caudoviricetes ctNo011 showed broader targeting. Prophage mining identified 186 regions in 130 strains, including 37 of ≥ medium quality and elements related to ctNo011 and phiKSM96. TerL phylogeny showed that most high-quality endogenous prophages clustered with phiKSM96 and ctNo011.

CONCLUSION: These findings reveal a vast, uncultivated phage repertoire targeting S. mutans, providing a critical genomic roadmap to guide the future isolation of novel phages for caries prevention.},
}

@article {pmid42180431,
year = {2026},
author = {Mallawaarachchi, V and Bouras, G and Wick, RR and Grigson, SR and Papudeshi, B and Edwards, RA},
title = {agtools: a software framework to manipulate assembly graphs.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag126},
pmid = {42180431},
issn = {2635-0041},
abstract = {MOTIVATION: Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler in constructing longer genomic fragments. Apart from their core use in assemblers, assembly graphs have become increasingly important in a range of downstream applications such as metagenomic binning, plasmid detection, viral genome resolution, and haplotype phasing. However, there is a need for a comprehensive tool that allows programmatic access to manipulate assembly graphs (e.g. parse, convert, filter, and analyze) across different assembly graph formats.

RESULTS: Here we present agtools, an open-source Python framework to manipulate assembly graphs produced by commonly used assemblers. agtools provides a command-line interface for tasks such as assembly graph format conversion, segment filtering, and component extraction. It also exposes a Python package interface to load, query, and analyze assembly graphs from popular genome and metagenome assemblers. This enables streamlined assembly-graph-based analyses that can be integrated into other bioinformatics software and workflows.

The source code of agtools is hosted on GitHub at https://github.com/Vini2/agtools and the documentation is available at https://agtools.readthedocs.io/. agtools can also be installed from Bioconda (https://anaconda.org/bioconda/agtools) and PyPI (https://pypi.org/project/agtools/).},
}

@article {pmid42180728,
year = {2026},
author = {Wang, T and Wang, M and Zhao, L and Tang, G and Hou, L},
title = {Case Report: Pulmonary brucellosis presenting as multiple cavitary lung lesions on imaging.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1814731},
pmid = {42180728},
issn = {2296-858X},
abstract = {Pulmonary brucellosis is a rare focal manifestation of human brucellosis with non-specific clinical features. Predominant imaging findings include pneumonia, pleural effusion, pulmonary nodules, abscesses, and interstitial changes. Multiple cavitary lesions are exceptionally rare. Herein, we report a case of bilateral multiple pulmonary cavities in a 76-year-old man with a 2-year history of intermittent cough, sputum production, and progressive dyspnea that acutely worsened 10 days prior to admission with intermittent fever, anorexia, and fatigue. Chest computed tomography (CT) revealed bilateral upper lobe irregular mass-like opacities and multiple nodules with heterogeneous density, punctate calcifications, and cavitation; multiple microcavitations in the right middle and lower lobes and the left lower lobe; and enlarged, calcified hilar and mediastinal lymph nodes. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Brucella species, which was confirmed by positive serology. After 3 days of doxycycline (0.1 g bid po) and rifampicin (0.6 g qd po), followed by 140 days of doxycycline (0.1 g bid po), rifapentine (0.6 g biw po), and levofloxacin (0.5 g qd po), along with silibinin meglumine tablets 0.1 g tid po for hepatoprotective therapy, the patient became afebrile with significant symptomatic improvement. Repeat chest CT demonstrated reduction in the right upper lobe consolidation/cavity and left upper lobe consolidation, resolution of the right lower lobe cavity, and complete resolution of the microcavitations. This case underscores that pulmonary brucellosis should be considered in the differential diagnosis of cavitary lung lesions in patients with livestock exposure and that prolonged combination antibiotic therapy can achieve favorable clinical and radiological outcomes.},
}

@article {pmid42181109,
year = {2026},
author = {Wunderer, M and Mullaymeri, A and Wagner, AO and Prem, EM},
title = {Comparative phenotypic and genomic analysis of the methanogen Methanomethylovorans thermophila L2FAW and its phylogenomic placement within the Genome Taxonomy Database.},
journal = {Access microbiology},
volume = {8},
number = {5},
pages = {},
pmid = {42181109},
issn = {2516-8290},
abstract = {The genome of the methylotrophic methanogen Methanomethylovorans thermophila L2FAW is not included in the Genome Taxonomy Database (GTDB) so far, even though the strain was first described in 2005. To evaluate its genomic characteristics and placement in the GTDB, we sequenced the genome of M. thermophila L2FAW via Illumina shotgun and Oxford Nanopore sequencing and subsequently did hybrid assembly. The assembled genome consists of 2.25 Mbp (contigs ≥500 bp) with a G+C content of 40 mol%. The quality of the genome is good, which is already apparent from the low L50 (=1) and L90 (=2) metrics. Our assembled genome was highly similar to the metagenome-assembled genome Methanomethylovorans sp014361205 (GCA_014361205.1_ASM1436120v1_genomic) with an average nucleotide identity of 99.9%. Even though KEGG Mapper Reconstruction results revealed that M. thermophila L2FAW harbours all the enzymes necessary for acetoclastic and hydrogenotrophic methanogenesis and gapseq predicted formate as a potential substrate for M. thermophila L2FAW, no metabolic activity could be observed on acetate, H2-CO2 (80:20 vol/vol, 2,000 mbar) and on a mixture of H2-CO2 and formate in lab tests; thus, the obligate methylotrophic lifestyle of the phenotype was confirmed.},
}

@article {pmid42181159,
year = {2026},
author = {Bressuire, C and Thirion, F and Chiaravano, L and Ngom, SI and Marion, R and Gilles, M and Quinquis, B and Mathieu, E and Berland, M and Blottière, HM and Le Bourgot, C and Béra-Maillet, C},
title = {Short-chain fructo-oligosaccharides modulate gut microbiota composition and metabolism: dose-response assessment in an ex vivo gut model.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2674335},
pmid = {42181159},
issn = {2993-3935},
abstract = {Short-chain fructo-oligosaccharides (scFOS) are prebiotic fiber rapidly fermented in the colon and known to stimulate beneficial bacteria, such as Bifidobacterium spp. and Lactobacillaceae. While their overall effects on the gut microbiota are established, the dose-response relationship remained only partially characterized. This study aimed to determine the minimum effective dose of scFOS required to modulate gut microbiota composition and functions. An ex vivo chemostat model was used to simulate colonic fermentation with different doses of scFOS (1 to 10 g/d). Microbiota composition and metabolic activity were assessed by qPCR, short-chain fatty acid (SCFA) quantification, and shotgun metagenomics. An increase in scFOS dose led to higher SCFA levels, particularly acetate and butyrate, along with a modification in microbial composition, with a minimum significant effective dose of 2.5 g/d. Significant increase in Bifidobacterium adolescentis, Anaerostipes hadrus, and Clostridium innocuum was observed at the same dose. Functional analysis revealed an enrichment of GH32 genes in the pangenomes of species positively impacted by scFOS. These findings demonstrate that low doses of scFOS can effectively modulate the gut microbiota and enhance SCFA production, supporting their use in dietary interventions aimed at improving intestinal health.},
}

@article {pmid42182002,
year = {2026},
author = {Chen, S and Hu, X and Pan, W and Chen, T and Xie, X and Zhang, Y},
title = {Integrated metagenomic and culture-dependent profiling reveals electric shavers as selective reservoirs for multidrug-resistant opportunistic pathogens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1839764},
pmid = {42182002},
issn = {1664-302X},
abstract = {INTRODUCTION: Personal care items are commonly viewed as passive vehicles for microbial transfer; however, the physicochemical stresses they impose may actively shape microbial persistence, community composition, and the distribution of resistance-associated determinants. Electric shavers may therefore constitute an underrecognized anthropogenic niche for the enrichment of clinically relevant antimicrobial resistance traits.

METHODS: We sampled electric shavers from 10 individuals at early (day 2) and mature (day 21) usage stages, generating 8 high-quality metagenomes and recovering 97 viable isolates spanning 16 bacterial species. Deep metagenomic sequencing, combined with whole-genome sequencing of 45 representative isolates, was used to resolve the ecological, functional, and evolutionary features of shaver-associated microbiomes.

RESULTS: Shaver-associated community assembly was dominated by stringent environmental filtering, which promoted the repeated enrichment of stress-adapted lineages across hosts, notably Acinetobacter ursingii MLST3244 and Klebsiella pneumoniae MLST995 and MLST23. We further identified recurrent mobile genetic element-associated resistance islands and plasmid backbones in different host cohorts, suggesting repeated selection under shared anthropogenic pressures rather than direct evidence of de novo convergent evolution. Importantly, viable Klebsiella pneumoniae isolates co-carried extended-spectrum β-lactamase genes such as bla SHV and major virulence determinants, while metagenomic profiling detected reads assigned to mcr- and tet(X)-like gene variants at the community level, targeted PCR further confirmed the presence of these resistance determinants.

DISCUSSION: Because routine shaving can generate barrier-disrupting micro-abrasions, electric shavers may function as selective reservoirs for multidrug-resistant bacteria. Our findings reveal a previously overlooked exposure interface through which everyday personal care practices may promote the enrichment and persistence of clinically important resistance and virulence determinants.},
}

@article {pmid42182003,
year = {2026},
author = {Li, F and Liu, X and Hou, W and Dong, H and Hu, J and Chen, H and Zhong, Y and Wu, Y and Xu, X and Ding, Y},
title = {Archaeal communities as indicators of hydrothermal influence in the Tianxiu vent field, Northwest Indian Ocean.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1837947},
pmid = {42182003},
issn = {1664-302X},
abstract = {Deep-sea hydrothermal sediments represent critical zones for archaea-driven biogeochemical cycling, yet the ecological differentiation of archaeal communities across hydrothermal gradients remains poorly understood. Here, we used 16S rRNA gene amplicon sequencing of sediment cores from two contrasting sites in the Tianxiu hydrothermal field of the Northwest Indian Ocean, and performed metagenomic analysis on the near-vent BC12 sediments, to investigate archaeal community composition, co-occurrence patterns, and metabolic potential in response to the hydrothermal activity. Comparative analysis revealed marked divergence between near-vent site BC12 and far-vent site JL218P. The site BC12, under stronger hydrothermal influence, was enriched in Hydrothermarchaeia, along with Nanoarchaeia and Thermoplasmata, and exhibited a more complex, highly connected co-occurrence network. Correlation analyses further showed that Hydrothermarchaeia abundance was significantly associated with hydrothermal-related geochemical gradients, supporting this lineage as a potential indicator of hydrothermal influence. Metagenomic analysis of BC12 further revealed Hydrothermarchaeia genomes encoding the Wood-Ljungdahl carbon fixation pathway, while genome-centric functional inference suggested enhanced potential for methanogenesis and hydrogen oxidation. In contrast, JL218P was dominated by Nitrososphaeria, showed limited vertical variation, and formed a simpler network structure, with predicted functional profiles more closely associated with nitrification and aerobic ammonia oxidation. Together, these findings identify hydrothermal-related geochemical heterogeneity as a major driver of archaeal community composition, ecological organization, and metabolic differentiation in deep-sea sediments, and advance our understanding of the ecological drivers structuring deep-sea hydrothermal ecosystems.},
}

@article {pmid42182018,
year = {2026},
author = {Abilda, Z and Isgandarov, I and Kanat, R and Daurov, D and Sapakhova, Z and Zhambakin, K and Daurova, A and Begaliyeva, D and Choi, K and Shamekova, M},
title = {Genome-resolved metagenomics reveals co-selection of antibiotic and metal resistance in chronically polluted industrial soils.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1829529},
pmid = {42182018},
issn = {1664-302X},
abstract = {INTRODUCTION: Chronic heavy metal contamination can restructure soil microbiomes and may co-select for antibiotic resistance, yet genome-resolved evidence from industrial soils remains limited.

METHODS: In this study, we applied Oxford Nanopore long-read metagenomic sequencing to soil samples collected across industrially influenced sites in East Kazakhstan to characterize strain-level community composition, profile antibiotic resistance genes and metal resistance genes, and relate these patterns to soil physicochemical properties.

RESULTS: Across all samples, we identified 3,053 strains, with Actinobacteria and Proteobacteria together accounting for 94.1% of the total community. Heavy metal concentrations varied markedly among sites. The resistome comprised antibiotic resistance genes from several drug classes and 238 distinct metal resistant genes, with aminoglycoside, glycopeptide, and multidrug resistance dominating the antibiotic resistance gene profile, while czcA, ruvB, arsM, and arsT were among the most abundant Metal resistant genes. Multivariate analyses showed that heavy metals, particularly Zn, significantly shaped microbial community structure as well as antibiotic resistance gene and metal resistance gene composition, and redundancy analysis identified Zn and soil pH as the principal environmental drivers. Network analyses further revealed that Bradyrhizobium icense and Conexibacter woesei acted as key super-hosts linking ARGs and MRGs, supporting heavy metal-driven co-selection within the soil microbiome.

DISCUSSION: Together, these findings show that long-read genome-resolved metagenomics can uncover how chronic industrial pollution maintains metal-adapted microbial communities while promoting the persistence and potential dissemination of antibiotic resistance in soil ecosystems.},
}

@article {pmid42182023,
year = {2026},
author = {Duan, J and Chen, Y and Zhang, X and Li, C and Gao, T and Li, K},
title = {Metagenomic analysis suggests that tomato root-knot nematode infestation disrupts rhizosphere microbial networks, consistent with reduced disease suppression.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798902},
pmid = {42182023},
issn = {1664-302X},
abstract = {INTRODUCTION: The rhizosphere microbiome serves as a critical line of defense for plant health and soil-borne disease suppression. However, the underlying mechanisms by which root-knot nematodes (RKN), a devastating soil-borne pathogen, undermine putative disease-suppressive function through destabilizing microbial interaction networks remain poorly understood.

METHODS: This study employed metagenomic sequencing coupled with microbial co-occurrence network analysis to systematically compare the community structure, interaction network topology, and functional gene profiles of the rhizosphere microbiome between healthy and RKN-infected tomato plants.

RESULTS: Our findings revealed that RKN infection significantly altered the community structure of bacteria, fungi, and viruses. This disturbance was associated with a systematic simplification and loss of modularity within microbial interaction networks. Specifically, intra-domain bacterial networks exhibited reduced scale and connectivity, whereas fungal networks showed strengthened internal cohesion. Cross-kingdom interactions (e.g., bacteria-fungi) were severely weakened, resulting in a topological imbalance characterized by "tight within domains, loose between domains." Functional profiling further indicated a distinct metabolic reprogramming in the infected rhizosphere, with a shift in resource allocation from growth and biosynthesis toward core energy acquisition and stress response.

DISCUSSION: Collectively, our results suggest that the putative decline in disease-suppressive function following RKN infection may be mechanistically rooted in the destabilization of microbial cooperative networks and the consequent loss of functional redundancy. This study provides a novel network-level ecological framework for understanding plant-microbe-pathogen interactions and lays a theoretical foundation for microbiome-based ecological management strategies against soil-borne diseases.},
}

@article {pmid42182035,
year = {2026},
author = {Qian, W and Han, A and Al Hatmi, AMS and Wang, Y and Rafiq, M and Cui, G and Zhou, S and Li, S and Kang, Y},
title = {Concordance between environmental resistomes and pathogenic phenotypes: a case study of multidrug-resistant Klebsiella pneumoniae in a drinking water source in Guizhou, China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1810806},
pmid = {42182035},
issn = {1664-302X},
abstract = {INTRODUCTION: The persistence of antibiotic resistance in aquatic environments poses a public health concern, particularly when drinking water sources act as reservoirs for multidrug-resistant opportunistic pathogens. However, the linkage between environmental resistomes and the resistance phenotypes of cultivable bacteria remains under-characterized. This case study investigated this relationship in a karst drinking water source in Guizhou, China.

METHODS: Surface water samples from seven sites were analyzed for antibiotic residues using LC-MS/MS. Metagenomic sequencing was conducted on selected contamination hotspots to characterize microbial communities and antibiotic resistance genes (ARGs). Cultivable bacteria were isolated, identified via 16S rRNA sequencing, and tested for antimicrobial susceptibility. To validate resistance mechanisms, a multidrug-resistant Klebsiella pneumoniae isolate was analyzed for tetA expression using RT-qPCR.

RESULTS: Antibiotic residues were detected across all sites, with sulfonamides and tetracyclines being the most prevalent. Consistent with this chemical pressure, metagenomic analysis identified corresponding ARGs, including sul1 and tet(Q), which functionally clustered with mobile genetic elements. From the contaminated matrix (sample W2), a multidrug-resistant Klebsiella pneumoniae strain (B8) was recovered. Mechanistic validation revealed a 2.78-fold upregulation of the tetA efflux pump gene in this strain.

DISCUSSION: These findings demonstrate a concordance among chemical selection pressures, environmental resistomes, and active resistance phenotypes. The results indicate that drinking water sources can harbor and maintain clinically relevant resistant bacteria, supporting the implementation of integrated surveillance strategies to evaluate biological risks.},
}

@article {pmid42182110,
year = {2026},
author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G},
title = {Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.15.725570},
pmid = {42182110},
issn = {2692-8205},
abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable, in part because existing computational models do not fully capture the metabolic compatibility between donor and recipient communities. Here, we present a metagenome-scale metabolic modeling framework that quantifies metabolic niche complementarity between donor and recipient microbiomes to predict transplantation outcomes. Using MICOM-derived community metabolic models, we show that donor taxa whose metabolic flux profiles are more dissimilar from the recipient community engraft at significantly higher rates in both murine and human FMT cohorts. In a human IBS trial, metabolic models accurately predicted post-FMT community composition via leave-one-out cross-validation and recapitulated disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to demonstrate a platform for personalized donor screening. This screen identified super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition, as quantified by a flux-derived ecological network balance index that strongly predicted engraftment potential. This framework provides a mechanistic, scalable tool for rational donor-recipient matching that could guide personalized microbiome-based therapies.},
}

@article {pmid42182295,
year = {2026},
author = {Kumar, A and Keerthipati, P and Lotana, H and White, T and Jones, E and Prescrille, J and Webb, T and Zhu, Y and Somakhin, A and Johnson, D and Tsymbalyuk, O and Simard, M and Qin, X and Ge, Y and Zhang, H and Dilipkumar, S and Gonzalez-Juarbe, N and Drake, WP},
title = {The Vagus Nerve conducts viable translocation of gut flora to the lungs that impacts interstitial lung disease severity in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.15.725489},
pmid = {42182295},
issn = {2692-8205},
abstract = {Communication between gut microbiota and extraintestinal organs is increasingly recognized, yet elucidation of relevant translocation mechanism(s) remains enigmatic. Vagus neuroanatomy and reports of vagal protein transfer to extraintestinal organs suggest that this "superhighway" could translocate bacteria. Here we explore whether the vagus superhighway can translocate bacteria to extraintestinal organs. Gavage of green fluorescent protein-expressing Escherichia coli (GFP- E. coli) into germ-free (GF) or specific-pathogen free (SPF) C57BL/6 mice yielded high bacillary loads in the stomach and lungs, followed by the heart, stool and peripheral muscles, despite negative blood cultures. Notably, confocal microscopy and culture revealed GFP- E. coli within the vagus nerve within five minutes of gavage suggesting rapid translocation. Metagenomic analysis of stool, lung, heart, vagus nerve, and muscle from non-gavaged SPF mice demonstrated significant microbial overlap, supporting that bacterial translocation occurs despite the presence of endogenous microflora. Remarkably, subdiaphragmatic vagotomy performed prior to GFP- E. coli gavage resulted in marked reductions of bacterial transduction in the lungs and other extraintestinal organs, except muscle. Furthermore, vagotomy significantly reduced lung fibrosis in SPF mice following intranasal bleomycin administration. In lung cancer patients undergoing lobectomy, vagotomy inhibited postsurgical reductions in forced vital capacity. These findings identify the vagus nerve as a literal gut-lung axis, facilitating viable bacterial translocation and influencing lung severity.},
}

@article {pmid42182444,
year = {2026},
author = {Wright, JT and Yendluri, S and Thomas, NC and Butterfield, CN and Dangerfield, TL and Taylor, DW},
title = {Structural and kinetic insights into a metagenomics-derived Cas12a with high specificity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.13.724879},
pmid = {42182444},
issn = {2692-8205},
abstract = {CRISPR-Cas12a nucleases provide an attractive alternative to Cas9 due to their compact RNA scaffold, T-rich PAM requirement, and improved target specificity. However, the mechanistic features that govern activity and discrimination across Cas12a orthologs remain incompletely understood. Here, we characterize Cas12a-MG29-1, a highly active and specific nuclease identified through metagenomic mining, using cryogenic electron microscopy, mutational analysis, and kinetic modeling. The Cas12a-MG29-1 structure reveals repositioned flexible loops near the distal end of the R-loop, including reduced engagement of one loop region and additional contacts formed by a second distal loop. Structure-guided mutagenesis and loop-swap experiments indicate that distal R-loop architecture modulates target discrimination in a context-dependent manner. Single-turnover cleavage and stopped-flow measurements show that Cas12a-MG29-1 and AsCas12a form reversible R-loops with similar kinetics but differ in strand cleavage following R-loop formation. Global kinetic modeling demonstrates that Cas12a-MG29-1 exhibits accelerated non-target strand cleavage, shifting kinetic partitioning toward product formation. This faster irreversible commitment provides a mechanistic explanation for enhanced activity and specificity without altering initial target interrogation. Together, these findings identify distal R-loop interactions and catalytic commitment as key determinants of Cas12a function and provide a framework for interpreting and engineering next-generation Cas12a orthologs.},
}

@article {pmid42182637,
year = {2026},
author = {Cai, X and Pang, S and Tang, C and Li, S},
title = {Relationship between airway stents and airway microorganisms: a literature review.},
journal = {Journal of thoracic disease},
volume = {18},
number = {4},
pages = {418},
pmid = {42182637},
issn = {2072-1439},
abstract = {BACKGROUND AND OBJECTIVE: Airway stent placement is widely used for the management of airway stenosis; however, it can be associated with complications such as granulation, stent migration, and infection, all of which affect patient outcomes. Among these complications, infection is a major concern, yet the relationship between airway stents and microbial colonization remains insufficiently studied. This review aims to summarize the current evidence on the effects of airway stents on the airway microbiome and to discuss their potential clinical implications.

METHODS: A literature search was conducted in PubMed for relevant studies published from database inception to December 31, 2025. Search terms included "airway stent", "tracheal stent", "bronchial stent", "airway microbiome", "biofilm", and "respiratory infection". Relevant studies were screened according to predefined criteria, and the available evidence was narratively synthesized.

KEY CONTENT AND FINDINGS: Available evidence suggests that airway stents can alter the airway microenvironment and facilitate microbial colonization, most commonly involving Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Klebsiella pneumoniae (K. pneumoniae). Both metallic and silicone stents lead to similar microbial profiles, dominated by P. aeruginosa and S. aureus. Although microbial colonization frequently occurs after stent implantation, colonization does not necessarily reflect clinically significant infection, and microbiological findings should be interpreted in the clinical context. Most clinical studies report an increased risk of respiratory infection following airway stent placement. In certain specific clinical situations, such as patients with tracheoesophageal fistula, infection rates may decrease after stenting due to restoration of airway integrity. Conventional culture-based methods remain adequate for detecting common respiratory pathogens, while emerging techniques such as metagenomic next-generation sequencing (mNGS) enable broader characterization of airway microbial communities.

CONCLUSIONS: Airway stents appear to alter the airway's microbial environment by promoting the growth of potentially pathogenic microorganisms. Different stent materials, including silicone stents and self-expanding metallic stents (SEMS), seem to affect the biofilm formation on the stents' surface, which may influence microbial colonization. More studies with larger sample sizes, standardized methodologies, and advanced techniques like metagenomic sequencing are needed to further clarify the microbial changes and improve clinical management.},
}

@article {pmid42182855,
year = {2026},
author = {Jia, Y and Zhu, Y and Cai, H},
title = {Polymicrobial Multidrug-Resistant Infection and Fatal Bowel Ischemic Perforation After Urgent Heart Transplantation in a VA-ECMO-Bridged Recipient: A Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {604688},
pmid = {42182855},
issn = {1178-6973},
abstract = {Post-transplant infection caused by multidrug-resistant organisms (MDROs) is a major challenge in heart transplantation, especially in recipients requiring veno-arterial extracorporeal membrane oxygenation (VA-ECMO) before surgery. We describe a 52-year-old man with non-ST-elevation myocardial infarction and refractory cardiogenic shock who required VA-ECMO, intra-aortic balloon pump support, continuous renal replacement therapy, and mechanical ventilation before urgent heart transplantation. Before transplantation, he had active pneumonia. Donor respiratory culture grew Acinetobacter baumannii, Pseudomonas aeruginosa, and Staphylococcus aureus, whereas donor blood culture and blood metagenomic next-generation sequencing (mNGS) were negative. After transplantation, serial mNGS and conventional cultures revealed rapidly progressive polymicrobial infection involving Stenotrophomonas maltophilia, Burkholderia multivorans, carbapenem-resistant Acinetobacter baumannii, carbapenem-resistant Klebsiella pneumoniae, and vancomycin-resistant Enterococcus faecium. Antimicrobial therapy was repeatedly adjusted, and VA-ECMO was successfully discontinued on postoperative day 13. However, on postoperative day 16, the patient developed bowel ischemia with gastrointestinal perforation, followed by feculent peritonitis, persistent septic shock, progressive multiorgan dysfunction syndrome, and death on postoperative day 24. This case shows that perioperative infection control in VA-ECMO-bridged urgent heart transplant recipients requires more than broad-spectrum antimicrobial escalation. It requires careful assessment of preoperative infection controllability, interpretation of mNGS in conjunction with culture-based susceptibility testing, and early investigation of occult abdominal ischemia when clinical deterioration is unexplained.},
}

@article {pmid42183063,
year = {2026},
author = {Zhang, J and Chen, C and Hu, Y and Jia, S and Li, B and Hu, W and Jia, Y and Li, D and Liu, Y},
title = {Interaction between microorganisms and flavour products during cigar fermentation promoted by citrus Reticulata-"Chenpi" derived Enterobacter G5Z-2: based on multi-omics studies and microbial profiles.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1785975},
pmid = {42183063},
issn = {2296-4185},
abstract = {INTRODUCTION: Cigar fermentation is crucial for developing its characteristic aroma, exogenous microorganisms can be used to enhance fermentation. It is reported that the citrus reticulata 'Chachi' (Chenpi, a traditional fermented ingredient) extract can improve the flavor of cigarette. However, there is no report on the influence of Chenpi-derived microorganisms on the fermentation process and flavor quality of cigar tobacco leaves (CTLs) till now.

METHODS: A fermentation strain (Enterobacter hoffmannii, G5Z-2) was isolated from Chenpi, and it was applied as a bioaugmentation agent in CTLs fermentation. A multi-omics approach, including metagenomics and metabolomics, was employed to investigate its impact.

RESULTS: Inoculation with G5Z-2 significantly altered the microbial community structure, suppressing native Pseudomonas and reducing overall alpha diversity while enriching beneficial genera like Aspergillus and Staphylococcus. Metabolomic analysis revealed substantial restructuring of metabolic pathways, particularly the enrichment of amino acid metabolism (such as arginine biosynthesis and phenylalanine metabolism) and nicotinate/nicotinamide metabolism. This led to accelerated degradation of proteins and amino acids, providing precursors for Maillard reaction, and a marked increase (57.5%) in total volatile flavour compounds, including key aroma constituents from carotenoid and cembranoid degradation.

CONCLUSION: The Chenpi-derived E. hoffmannii G5Z-2 optimises the fermentation process by modulating the microbial consortium and driving metabolic shifts towards favourable flavour development, demonstrating significant potential for improving the quality of Chinese-style cigars.},
}

@article {pmid42184066,
year = {2026},
author = {Al Awawdeh, S and Shafie, NH and Ishak, AH and Mohd Esa, N and Loh, SP and Nurdin, A},
title = {Green tea polyphenol-iron oxide chitosan nanoparticles modulate gut microbiota and regulate metabolic pathways.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42184066},
issn = {1573-0972},
support = {GP-IPS/2023/9772000//Universiti Putra Malaysia/ ; FRGS/1/2018/SKK10/UPM/02/5//Ministry of Higher Education, Malaysia/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polyphenols/pharmacology/chemistry/administration & dosage ; Rats, Sprague-Dawley ; Male ; Rats ; *Chitosan/chemistry ; *Tea/chemistry ; *Metabolic Networks and Pathways/drug effects ; Liver/metabolism/drug effects ; *Nanoparticles/chemistry ; *Ferric Compounds/chemistry ; Proteome ; Proteomics ; Bacteria/classification/genetics/drug effects ; },
abstract = {Green tea polyphenols (GTPP) exhibit antioxidants, anti-inflammatory, and anticancer properties; however, their poor bioavailability limits clinical translation. Nanoparticle-based formulations may enhance absorption and therapeutic potential. This study investigates the therapeutic effects of GTPP encapsulated in iron oxide chitosan nanoparticles (GTPP-IOCHNP) on gut microbiota and hepatic proteome, with particular attention to pathways relevant to inflammation, drug metabolism, and tumorigenesis. Male Sprague Dawley rats were administered a single oral dose of GTPP or GTPP-IOCHNP (200 mg/kg). Cecal microbiota composition was analyzed by metagenomic sequencing, while liver proteome alterations were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metagenomic analysis revealed that GTPP-IOCHNP promoted Actinobacteriota and Collinsella, both linked to reduced inflammation and improved gut health, while inhibiting Bacteroides and Ruminococcus genera associated with intestinal barrier dysfunction, inflammation, and nephropathy. Blautia was significantly enriched (p < 0.05), supporting short chain fatty acid production, modulation of lipid and carbohydrate metabolism, and transformation of polyphenols into bioactive antioxidant metabolites. Proteomics profiling identified 20 differentially expressed hepatic proteins (p < 0.05). GTPP-IOCHNP significantly downregulated cytochrome P4502D26 (CYP2D6), indicating modulation of CYP2D6 mediated drug metabolism, and suppressed glutamate dehydrogenase 1, implicating inhibition of glutamine-driven energy metabolism linked to cancer and hyperinsulinism. Conversely, significant upregulation of elongation factor 1-alpha-1 (eEF1A1), albumin, and adenosine kinase (ADK) highlighted improved GTPP absorption, systemic transport, and regulation of hepatic energy metabolism. The integrative metagenomic and proteomic analyses reveal that GTPP-IOCHNP improves polyphenol bioavailability by modulating gut microbial ecology and hepatic metabolic pathways, offering a mechanistically driven platform for therapeutic advancement.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Polyphenols/pharmacology/chemistry/administration & dosage
Rats, Sprague-Dawley
Male
Rats
*Chitosan/chemistry
*Tea/chemistry
*Metabolic Networks and Pathways/drug effects
Liver/metabolism/drug effects
*Nanoparticles/chemistry
*Ferric Compounds/chemistry
Proteome
Proteomics
Bacteria/classification/genetics/drug effects

@article {pmid42184159,
year = {2026},
author = {Pavlovska, M and Prekrasna-Kviatkovska, Y and Zotov, A and Dzhulai, A and Dykyi, E and Huettel, B and Fuchs, BM and Amann, RI and Teeling, H and Sidhu, C},
title = {Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag053},
pmid = {42184159},
issn = {1574-6941},
abstract = {Seasonal changes in Antarctic coastal waters trigger pronounced shifts in microbial community composition and function, yet sparse spatial and temporal coverage currently limits our understanding of phytoplankton-bacterioplankton coupling. This study combines metagenomic and metatranscriptomic analyses of marine bacterioplankton with environmental data to address the functional dynamics of planktonic communities off the Western Antarctic Peninsula during the austral summer-autumn transition. Diatoms dominated the phytoplankton community, with generally low biomass and abundance, yet a species-specific succession was observed. The bacterioplankton community structure shifted from dominance of copiotrophic taxa (e.g. Polaribacter) towards oligotrophic lineages (e.g. SAR11) adapted to low-nutrient conditions, accompanied by a decrease in microbial carbohydrate-degradation activity. The capacity to degrade algal-derived polysaccharides varied between community members, with ß-glucan, α-glucan, chitin, and host glycan utilization present in all, and fucose, β-galactan and trehalose degradation restricted to specific taxa. DMSP metabolism also showed taxonomic specificity and was shaped by both physical (ice melt and fluctuations in solar irradiation) and biological factors (phytoplankton succession). Together, these findings reveal a complex, taxon-specific coupling between bacterioplankton and phytoplankton communities in the Western Antarctic Peninsula, linking community structure to likely functional gene expression and highlight how Antarctic bacterioplankton drives carbon and sulfur turnover in a polar marine ecosystem.},
}

@article {pmid42184529,
year = {2026},
author = {Wang, R and Chen, H},
title = {Metagenomic insights into vertical migration of soil antibiotic and metal(loid) resistance genes under long-term organic fertilizer application and irrigation.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142479},
doi = {10.1016/j.jhazmat.2026.142479},
pmid = {42184529},
issn = {1873-3336},
abstract = {Agricultural irrigation is associated with antibiotic resistance gene (ARG) transmission and resistome succession through the integration of exogenous and indigenous soil communities. However, the long-term field-scale impacts of organic irrigation on vertical resistome migration and its ecological consequences remain underexplored. This study employed metagenomic analyses and field surveys to bridge these knowledge gaps. The results showed that ARGs and metal(loid) resistance genes (MRGs) were most abundant and diverse at 0-20 cm depth, with distinct characteristics in deeper layers depending on manure type. Cattle manure-irrigated soils exhibited a greater potential for vertical ARG diffusion than chicken manure-irrigated soils, despite lower surface-level enrichment. ARG distribution was more strongly associated with groundwater and soil background factors than with organic fertilizer inputs. Mobile genetic elements (MGEs) and heavy metal concentrations were key factors associated with resistome succession. Compared to the control, contigs associated with both ARGs and MRGs increased 5.8-fold and 3.1-fold in chicken and cattle manure-irrigated soils, respectively, suggesting a potentially important role for prophages. While control contigs were distributed in deeper layers, irrigated soils showed pronounced surface enrichment. Irrigation was linked to increased network density and complexity, with chicken manure-irrigated soils exhibiting higher levels of antibiotic-resistant bacteria (ARB). Notably, opportunistic pathogens carrying ARGs, including Ralstonia pickettii and Stenotrophomonas maltophilia, were enriched in irrigated profiles. Microbiome, MGEs, and abiotic factors were collectively associated with resistome succession, with deterministic processes contributing substantially to community assembly. This study provides new insights into the vertical distribution and inferred succession of the resistome in organically irrigated soils.},
}

@article {pmid42184535,
year = {2026},
author = {Ma, B and Li, F and Zhang, C and Deng, Y and Sekar, R and Chen, Z and Wang, M and Zamyadi, A and He, S and Huang, T and Guo, J and Zhang, H},
title = {Multivalent manganese-mediated synergistic aerobic denitrification boost nitrogen removal in oligotrophic aquatic systems: Insight into microbial functional and metabolic complementarity.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142496},
doi = {10.1016/j.jhazmat.2026.142496},
pmid = {42184535},
issn = {1873-3336},
abstract = {Efficient nitrogen removal from oligotrophic lakes and reservoirs necessitates the development of innovative, eco-friendly strategies to mitigate the limitation of organic electron donors. We engineered four multivalent manganese (Mn) composite-functionalized bioreactors for oligotrophic water remediation, which demonstrated a sustained total nitrogen removal efficiency exceeding 97.66% over five operational cycles. Manganese powder-doped activated carbon achieved the highest nitrate removal rate, ranging from 0.29956 to 0.39831 mg/L/d. Immobilization with sodium alginate has mitigated manganese oxidative corrosion, thereby resulting in more sustained long-term reactive performance. Furthermore, denitrifying bacteria synergistically promote the enrichment of phosphorus-accumulating microorganisms and manganese-oxidizing bacteria (Burkholderiaceae, Methylophilaceae, and Azospirillaceae), which play pivotal roles in denitrification and manganese cycling, within Mn addition (MNA) reactors. Correlation analyses revealed stronger co-occurrence patterns between denitrification genes and manganese-oxidizing genes in the MNA reactors compared to the control. The abundance of ATP-binding cassette transporter genes, particularly encoding lipopolysaccharide transport (wzt) and lipoprotein release (lolD), increased by 1.37-1.90-fold and 1.31-1.80-fold, respectively, in the MNA reactors relative to the control reactor. Furthermore, the metabolic complementarity network suggested that MNA not only promoted community metabolic competition and complementarity effects but also enhanced higher energy production and respiratory activity. These findings establish a manganese-driven microbial enhancement strategy for sustainable nitrogen removal from polluted surface waters, offering new opportunities for eco-engineered water treatment.},
}

@article {pmid42184563,
year = {2026},
author = {Hull, R},
title = {RNA viruses are an integral part in evolution of all organisms.},
journal = {Virology},
volume = {621},
number = {},
pages = {110950},
doi = {10.1016/j.virol.2026.110950},
pmid = {42184563},
issn = {1096-0341},
abstract = {RNA viruses are intracellular symbiotic obligate parasites, needing host factors and energy for their replication with forms of symbiosis ranging from antagonism (pathogenic, not contributing to host metabolism) to mutualism (contributing benefits to the host as well as making demands on host metabolism). As a group, they have several unusual features: a) metagenomic studies suggest that they are probably are the most common group of viruses infecting all organism species and are the most abundant biological entity on earth; b) they have existed ever since the Last Universal Common Ancestor from which all living organisms have evolved; c) a high proportion of their species have + strand RNA genomes, or are retroviruses, that replicate without proof-reading creating many variants (quasispecies); d) they replicate in organelles within the endoplasmic reticulum and other membranes which connect to other organelles and to membrane and metabolic network systems. This paper brings together these facts presenting the hypothesis that RNA viruses and retroviruses form host/mutualistic virus symbionts as an evolutionary unit with the viral responses to evolutionary stresses being rapid and linking closely with the slower host genomic responses. The hypothesis is presented with a background of evolution of organisms and viruses, drivers of evolution, and the evolutionary natural selection pathway from the sources of stresses to impact and molecular reactions to stresses entering the basic organism body, the cell.},
}

@article {pmid42184767,
year = {2026},
author = {Chen, D and Ibrar, M and Yan, F and Sun, G and Xue, R and Jia, A and Zhou, J and Gao, Y and Ma, C and Wang, M and Zhang, J and Ma, Z and Liu, L},
title = {The rising power of females: Dioecious shrub enhances soil organic carbon sequestration via fungal necromass in chronosequence of desertified alpine grassland restoration.},
journal = {Journal of environmental management},
volume = {409},
number = {},
pages = {130022},
doi = {10.1016/j.jenvman.2026.130022},
pmid = {42184767},
issn = {1095-8630},
abstract = {Desertification-induced soil organic carbon (SOC) loss poses a major environmental threat to the alpine grasslands of the Qinghai-Tibet Plateau, jeopardizing ecological security and sustainability. While pioneer shrub introduction has yielded positive ecological outcomes, the mechanisms of SOC recovery remain poorly understood. We investigated the effects of a widely used dioecious shrub on rhizosphere SOC dynamics across a 20-year restoration chronosequence, employing a comprehensive framework that combined root exudation measurements, soil physicochemical analysis, metagenomics, and biomarker profiling to decipher the mechanism. Our results reveal that microbial-derived carbon dominated rhizosphere SOC accrual, contributing 20.1-22.0% to the total SOC pool, over 50 times more than plant-derived carbon (0.1-0.4%). The microbial pool was predominantly fungal necromass (>93%), correlated with declining root exudation and suppressed carbon-degrading gene abundance during restoration. In the 20th year after recovery, a striking divergence in the effects of male and female shrubs on rhizosphere SOC became apparent, with female shrubs sustaining 15% more microbial necromass and 47% more lignin phenols than males. Our findings highlight that SOC restoration in the rhizosphere of pioneer shrubs is predominantly driven by a fungal-mediated microbial carbon pump. Moreover, the preferential use of female shrubs offers a dual benefit: enhancing long-term rhizosphere SOC sequestration and controlling shrubs encroachment. This sex-informed strategy therefore provides a scalable framework for degraded alpine grasslands and serves as a transferable model for other drylands undergoing warming-wetting transitions, where alleviated water limitation increasingly enables vegetation-microbe-mediated carbon stabilization.},
}

@article {pmid42174665,
year = {2026},
author = {Nolan, S and Trego, A and Waters, N and Thorn, C and Fenton, O and Richards, KG and O'Flaherty, V and Ijaz, UZ and Abram, F},
title = {Using feeding regime as a microbial selective pressure to optimise biogas production and digestate sanitisation from slurry-based anaerobic digestion.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00902-x},
pmid = {42174665},
issn = {2524-6372},
support = {14 F847//Irish Department of Agriculture, Food and Marine/ ; },
abstract = {BACKGROUND: The urgent need to adopt sustainable agricultural practices has positioned anaerobic digestion (AD) as a pivotal technology. Indeed, slurry-based AD can mitigate agricultural pollution by capturing greenhouse gas from stored slurry and converting it into biomethane, a valuable source of renewable energy, while generating digestate that can be used as fertiliser. For such a strategy to be effectively and widely deployed however, AD must be optimised. To this end, efforts have typically focused solely on biogas yields, yet improvements in pathogen load reduction may potentially negate the need for a costly pasteurisation step. Hence, optimisation of AD for sanitisation as well as improved biogas output is desirable. To address this, we set up triplicate 10-L CSTR bioreactors, which were fed with a combination of slurry and fats, oils and grease for 216 days. An organic loading rate (OLR) of 2 g VS L[-1] d[-1] was used throughout the trial, with a retention time of 21 days. For the first 98 days, bioreactors were fed each weekday (Monday to Friday), with 3 × feedstock on Fridays to maintain the OLR over the weekend. On Day 99 and for the remainder of the trial, the feeding regime was changed to every three days, still maintaining the 2 g VS L[-1] d[-1] OLR. The change in feeding regime was prompted by a noticeable increase in E. coli removal on Mondays, indicating that feeding regime could potentially function as a controllable ecological selection pressure.

RESULTS: After an initial period of adaptation to the new operating conditions (from day 99-150), the change in feeding regime resulted in improved E. coli removal, achieving consistently the required reduction in numbers to satisfy EU sanitisation standards (< 1000 CFU g[-1]). Additionally, methane production increased significantly in all bioreactors with an average of 58% higher methane yield per gram VS fed when compared to the previous 5-day feeding regime. Interestingly, process optimisation led to a more tailored microbial community as revealed by metagenomics. Specifically, we observed selection for improved carbon oxidation, syntrophic acetate oxidation and methanogenesis, as well as overall reduced microbial richness and decreased functional diversity. This could potentially lead to a reduced ecosystem stability however the emergence of Methanosarcina prevalence, known for its robustness, together with the detection of the two main methanogenic pathways-acetoclastic and hydrogenotrophic-after process optimisation might confer some resistance against future perturbations. The impact of microbial shifts on ecosystem stability needs to be further assessed experimentally.

CONCLUSIONS: Taken together, we demonstrate that feeding regime can function as a microbial selection pressure in anaerobic digestion. The switch from a 5-day to a 3-day feeding regime led to shifts in microbial pathways, underpinning the simultaneous improvement in methane production and E. coli removal. While further research is required to assess the impact of the observed microbial community dynamics on system stability, our findings suggest that full scale on-farm AD operators could explore the effects of feeding intervals on their process performance.},
}

@article {pmid42175291,
year = {2026},
author = {Dicko, A and Barro, SG and Somda, NS and Sombie, S and Bandaogo, O and Sanou, G and Esona, MD and Bonkoungou, JIO},
title = {Application of Metagenomics and Artificial Intelligence for Pathogen Characterization in Domestic Animals and Epizootic Prediction: A Systematic Review and Meta-Analysis.},
journal = {Studies in health technology and informatics},
volume = {336},
number = {},
pages = {2095-2096},
doi = {10.3233/SHTI260622},
pmid = {42175291},
issn = {1879-8365},
mesh = {Animals ; *Metagenomics/methods ; *Artificial Intelligence ; *Animals, Domestic/microbiology ; *Disease Outbreaks/veterinary/prevention & control ; *Animal Diseases/diagnosis/microbiology ; },
abstract = {Sub-Saharan Africa suffers devastating animal health losses exceeding $20 billion each year. By combining metagenomics with artificial intelligence (AI), a promising path emerges for faster diagnostics and proactive disease prediction. Our PRISMA-guided review of 1,225 studies reveals that metagenomics achieves 94.2% diagnostic sensitivity (compared to 67.3% with conventional methods), while AI dramatically shortens turnaround from 48-72h to just 4-8h, offering a valuable 14-18 day early warning window for epizootics.},
}

Animals
*Metagenomics/methods
*Artificial Intelligence
*Animals, Domestic/microbiology
*Disease Outbreaks/veterinary/prevention & control
*Animal Diseases/diagnosis/microbiology

@article {pmid42175403,
year = {2026},
author = {Tang, R and Wang, R and Han, Y},
title = {Mycobacterium avium complex pulmonary disease in rheumatoid arthritis-associated interstitial lung disease under non-biologic immunomodulatory therapy: A case report.},
journal = {Medicine},
volume = {105},
number = {21},
pages = {e48801},
doi = {10.1097/MD.0000000000048801},
pmid = {42175403},
issn = {1536-5964},
mesh = {Humans ; Male ; *Lung Diseases, Interstitial/complications/drug therapy/etiology ; Aged ; *Arthritis, Rheumatoid/complications/drug therapy ; *Mycobacterium avium-intracellulare Infection/drug therapy/diagnosis/complications/etiology ; Mycobacterium avium Complex/isolation & purification ; },
abstract = {RATIONALE: Rheumatoid arthritis (RA) is a well-recognized risk factor for nontuberculous mycobacterial infections, especially among patients receiving glucocorticoids or biological disease-modifying antirheumatic drugs. However, cases of Mycobacterium avium complex (MAC) pulmonary disease in RA patients without such immunosuppressive therapies are rarely reported, which challenges the conventional risk stratification.

PATIENT CONCERNS: A 78-year-old male with a 3-year history of RA and interstitial lung disease (ILD) presented with progressive dyspnea and chest tightness. He had no fever, joint swelling, or typical infection flares. Before admission, he was treated with Tripterygium Glycosides and Iguratimod (non-biologic, non-glucocorticoid agents).

DIAGNOSIS: The patient had chest tightness and weight loss. Chest high-resolution computed tomography showed asymmetric progression of ILD, along with tree-in-bud signs, centrilobular nodules, and suspicious fibrocavities. Bronchoscopy revealed necrotizing granulomatous inflammation, and quantitative metagenomic sequencing of bronchoalveolar lavage fluid confirmed MAC (no drug-resistant genes detected).

INTERVENTIONS: The patient was put on a 4-drug anti-MAC regimen (rifampicin, azithromycin, ethambutol, amikacin). However, he was lost to follow-up after being transferred to a tuberculosis specialist hospital. He eventually died of unknown causes, and there were prior reports of his nonadherence to treatment.

OUTCOMES: For RA patients with ILD who show asymmetric imaging progression or discordant inflammatory markers, it is crucial to actively screen for atypical pathogens like MAC, even in the absence of glucocorticoid or biologic exposure. This case highlights the necessity of expanding nontuberculous mycobacterial infection risk assessment beyond traditional immunosuppressive therapies in RA-ILD patients.

LESSONS: For patients with autoimmune disease-associated interstitial pneumonia, particularly those with progressive interstitial lung disease (ILD) despite stable autoimmune serology, proactive screening for atypical pathogens such as nontuberculous mycobacteria is critical. When imaging shows asymmetric lesions, tree-in-bud opacities, centrilobular nodules, or fibrocavitary changes, clinicians should prioritize comprehensive etiological evaluation - including bronchoscopy and histopathology - to avoid misdiagnosing these opportunistic infections.},
}

Humans
Male
*Lung Diseases, Interstitial/complications/drug therapy/etiology
Aged
*Arthritis, Rheumatoid/complications/drug therapy
*Mycobacterium avium-intracellulare Infection/drug therapy/diagnosis/complications/etiology
Mycobacterium avium Complex/isolation & purification

@article {pmid42175735,
year = {2026},
author = {Li, J and Liu, Q and He, C and Zhu, Y and Yin, C and Pang, X},
title = {Microbial Life-History Strategies and Functional Gene Regulation Drive Soil Nitrogen and Phosphorus Bioavailability During Succession in an Arid Valley Ecosystem.},
journal = {Molecular ecology},
volume = {35},
number = {10},
pages = {e70408},
doi = {10.1111/mec.70408},
pmid = {42175735},
issn = {1365-294X},
support = {32572029//National Natural Science Foundation of China/ ; 2025ZYD0007//Sichuan Province Science and Technology Support Program/ ; XZ202501JX0012//Science and Technology Projects of Xizang Autonomous Region, China/ ; DJ-ZDXM-2024-28//Power Construction Corporation of China/ ; },
mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Phosphorus/metabolism ; *Ecosystem ; *Soil/chemistry ; Microbiota/genetics ; Tibet ; Metagenomics ; Bacteria/genetics ; },
abstract = {Arid valley ecosystems are highly vulnerable to environmental change and face accelerating degradation due to climate warming and anthropogenic disturbance. Although soil microorganisms are known to drive nutrient cycling during succession, their adaptive strategies under persistent nutrient limitation remain poorly understood. This study integrated metagenomics, enzymatic stoichiometry and co-occurrence network analysis to investigate microbial community composition, life-history strategies, and nitrogen (N) and phosphorus (P) cycling functional genes along a successional gradient in an arid valley on the southeastern Tibetan Plateau. We found that microbial communities experienced consistent N limitation throughout succession, which shaped their functional potential and biogeochemical roles. Notably, during the transition from bare soil to biological soil crusts (BSCs), shifts in microbial life-history strategies towards resource acquisition (A-strategy) were accompanied by increased network complexity. Key functional genes, particularly those involved in nitrification (nxrB, amoC), dissimilatory nitrate reduction (nirB, nifH, nirD), inorganic P solubilization (gcd, ppk) and organic P mineralization (phnJ, phoA, phnM, phnI), were significantly upregulated during the BSCs stage. These genetic traits facilitated the transformation of organic and mineral nutrients into bioavailable forms, thereby supporting ecosystem development. This is manifested as a higher bioavailability of DON (+110%) and Bio-P (+97%) in the BSCs stage compared to bare land. Our results demonstrate that microbial communities adapt to resource constraints through trait-based strategies and functional gene regulation, highlighting the BSCs stage acts as a critical biogeochemical trigger in early succession. These insights advance our understanding of microbial-mediated nutrient cycling in arid ecosystems and inform restoration strategies under global change.},
}

*Nitrogen/metabolism
*Soil Microbiology
*Phosphorus/metabolism
*Ecosystem
*Soil/chemistry
Microbiota/genetics
Tibet
Metagenomics
Bacteria/genetics

@article {pmid42175741,
year = {2026},
author = {Yuan, S and Wang, X and Chang, Z and Zhang, B and Wang, M and Yu, J and Chen, Z},
title = {Climate Change Elevates the Risk of Antibiotic Resistance in Global Surface Ocean.},
journal = {Global change biology},
volume = {32},
number = {5},
pages = {e70929},
doi = {10.1111/gcb.70929},
pmid = {42175741},
issn = {1365-2486},
support = {42277386//National Natural Science Foundation of China/ ; 24JCYBJC01900//Tianjin Natural Science Foundation/ ; },
mesh = {*Climate Change ; *Drug Resistance, Microbial/genetics ; Oceans and Seas ; *Microbiota ; Virulence Factors/genetics ; *Seawater/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Understanding how climate change affects antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in marine microbiomes is critical to safeguarding global health, yet a systematic, global-scale analysis of their responses and associated health risks remains lacking. Here, we analyzed 890 surface-ocean metagenomic samples, the largest dataset collected using a standardized sampling pipeline to date. Our analysis revealed distinct biogeographical patterns in the composition of ARGs and VFGs across spatial and temporal gradients. Using machine learning, we mapped global distributions of ARGs and VFGs across the surface ocean by leveraging their strong associations with climate-releated environmental factors, revealing clear differences between polar and low-latitude areas. We then quantified the community-level antibiotic resistance risk and identified global risk zones, finding that high-risk regions are the least extensive and occur primarily at low latitudes. Furthermore, we estimated how this risk would change under future climate scenarios, suggesting that anthropogenic climate change is projected to increase the antibiotic resistance risk index of the surface ocean by altering environmental factors, most notably carbonate concentrations. Under the SSP5-8.5 scenario, which respresents a high greenhouse gas emissions pathway, the risk index is projected to rise across 33.0% (95% CI: 32.2%-33.5%) of the surface ocean by 2100, mainly in low-latitude regions, driven by an increase in genes involved in antibiotic efflux, inactivation, and motility. In contrast, effective greenhouse-gas mitigation would limit this increase to 3.7% (95% CI: 3.4%-4.1%). This study advances our understanding of how climate shapes marine antibiotic resistome and underscores the urgency of climate mitigation.},
}

*Climate Change
*Drug Resistance, Microbial/genetics
Oceans and Seas
*Microbiota
Virulence Factors/genetics
*Seawater/microbiology
Anti-Bacterial Agents/pharmacology

@article {pmid42176010,
year = {2026},
author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E},
title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02785-4},
pmid = {42176010},
issn = {1432-184X},
abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.},
}

@article {pmid42176043,
year = {2026},
author = {Khan, I and Naeem, I and Ali, S and Gulbin, M and Iqbal, A and Shafiq, M},
title = {Metagenomic surveillance identifies a high-risk antibiotic resistance profile in community wastewater: a pilot study from Pakistan.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42176043},
issn = {1432-1912},
abstract = {Environmental antimicrobial resistance surveillance in low- and middle-income countries (LMICs) faces critical data gaps, particularly in Pakistan, where approximately 90% of municipal wastewater is discharged untreated. In the absence of systematic monitoring in regions like Khyber Pakhtunkhwa, we conducted a pilot shotgun metagenomic sequencing study on two strategically selected community wastewater sites in Mardan. To translate complex metagenomic data into actionable public health intelligence, we developed the Antibiotic Resistance Risk Index (ARRI), a novel framework integrating antibiotic resistance gene (ARG) proportional abundance, pathogen taxonomic expansion, and WHO priority weighting. Our analysis revealed that the urban site (MCW2) exhibited a "critical" resistance profile, characterized by a 54% increase in ARG allelic richness (628 unique variants) despite a 19.9% decline in total relative ARG abundance. Taxonomic compositional changes consistent with an aerobic shift, including a 34-fold decline in Thermodesulfobacteria and a 46% increase in Pseudomonadota, were observed alongside an increased proportion of WHO priority pathogens, including Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. This site served as a reservoir for last-resort resistance determinants, including blaNDM, blaIMP, blaCTX-M, and mcr, which emerged exclusively in the urban drainage environment. The resistome contained 159 ARG families and 26 MGE types. Network analysis showed that 90.8% of ARG-MGE pairs exhibited coordinated increase in relative abundance, with all carbapenemase-linked pairs showing parallel trends. Consequently, ARRI scores escalated from 8.7 (moderate risk) to 34.2 (critical risk) at the urban site. These findings reveal the environmental circulation of hospital-associated resistance through decentralized sanitation infrastructure, representing a convergence of hospital-associated and community resistance profiles in LMIC settings. This study demonstrates that risk-weighted surveillance enables high-resolution, actionable AMR monitoring, providing a baseline methodology for environmental AMR surveillance in resource-limited settings.},
}

@article {pmid42176229,
year = {2026},
author = {Cagle, GA and Baiser, B and Bernardin, JR and Bittleston, LS and Young, EB and Gray, SM and Freedman, ZB},
title = {Carbon regime structures functional trait trajectories during primary succession in microorganisms.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag134},
pmid = {42176229},
issn = {1751-7370},
abstract = {Primary succession is a foundational process in ecology, but how microbial communities shift functionally during succession, and whether these dynamics follow predictable patterns, remains unresolved. We conducted a systematic review of functional primary succession in microorganisms and applied a consistent metagenomic pipeline to evaluate functional richness, rRNA operon copy number (RRN), and average genome size (AGS) over time. We also explored the yield-acquisition-stress (Y-A-S) life-history framework using functional gene annotations. Across autotrophic systems, RRN tended to decrease and AGS tended to increase during succession, whereas heterotrophic systems exhibited more variable trajectories. These consistent shifts in autotrophic systems suggest a transition from early colonization by copiotrophic taxa with small genomes and high RRN toward later-stage communities with larger genomes, lower RRN, and greater functional versatility. In contrast, heterotrophic systems showed heterogeneous trait trajectories, likely reflecting variation in the timing and predictability of organic inputs. Topic modeling further revealed that early successional stages were enriched in stress-tolerance genes, followed by shifts toward other strategies over time. While certain trait patterns such as RRN and AGS appeared broadly conserved, changes in life-history strategies during succession were context dependent and shaped by resource dynamics and system type. These findings suggest that microbial successional trajectories are structured by differences in resource availability, particularly whether systems are driven by autotrophic inputs or constrained by externally supplied carbon sources.},
}

@article {pmid42176246,
year = {2026},
author = {Chen, Y and Wang, S and Chen, A and Lin, Z and Wang, H and Li, W and Liu, J and Yao, J and Tian, D and Lei, Y and Liu, M},
title = {Multi-omics Analysis Reveals the Protection of a Quadruple Probiotic Mixture in Experimental Autoimmune Hepatitis.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42176246},
issn = {1867-1314},
support = {2025M782000//China Postdoctoral Science Foundation/ ; 2023AB006//Shangrao Science and Technology Bureau/ ; 202303021221195//Fundamental Research Program of Shanxi Province/ ; 82270558//National Natural Science Foundation of China/ ; },
abstract = {Autoimmune hepatitis (AIH) is a chronic progressive inflammatory liver disease with a rising global incidence. The treatment of AIH remains challenging because first-line drugs show limited efficacy and systemic side effects. Gut microbiota plays a crucial role in the pathogenesis of AIH, leading to growing interest in developing probiotic-based therapies. In this study, we used multi-omics analysis to investigate the therapeutic effects of a quadruple probiotic mixture (Probiotic-quad) consisting of Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus in a well-established chronic AIH murine model. Our results showed that Probiotic-quad treatment significantly alleviated AIH progression, as evidenced by lower serum liver enzyme levels, ameliorated hepatic inflammatory infiltration and histopathological damage. Metagenomic sequencing results showed that gut dysbiosis in AIH mice was partially reversed after Probiotic-quad administration. Additionally, the integrity of the intestinal epithelial barrier was restored, accompanied by a reduction in serum lipopolysaccharide levels. Untargeted metabolomic and transcriptomic analysis revealed that Probiotic-quad treatment was linked to alterations in hepatic metabolism, including the citrate cycle and tryptophan metabolism, and was associated with reduced activation of the NF-κB and NOD-like receptor signaling pathways. These findings suggest that Probiotic-quad treatment ameliorates AIH severity and is potentially associated with changes in hepatic immune responses, metabolism, gut microbiota, and intestinal barrier function, highlighting its potential as an adjuvant therapy for AIH.},
}

@article {pmid42176375,
year = {2026},
author = {Zhang, Y and Wang, R and Su, X and Lang, T and Li, D},
title = {Freeze-thaw specifically regulates microbiome patterns and phosphorus acquisition strategies in the lake-groundwater interaction zone.},
journal = {Water research},
volume = {302},
number = {},
pages = {126129},
doi = {10.1016/j.watres.2026.126129},
pmid = {42176375},
issn = {1879-2448},
abstract = {Freeze-thaw regulates phosphorus cycling in lake-groundwater interaction zones (LIZ) of seasonally frozen regions, where microorganisms and their functional traits play indispensable roles. However, the spatiotemporal dynamics of phosphorus pools and their driving mechanisms in the LIZ remain poorly understood, especially with insufficient quantitative evidence. Using absolute quantitative metagenomics, this study investigated the LIZ of Lake Chagan, a typical eutrophic lake in the seasonally frozen region. Results showed that Losses of Fe-P (44.69%) and Res-P (35.47%) dominated sediment phosphorus dynamics. Freeze-thaw induced opposing trends in diversity and similarity of PCGs-microbial communities between sediment and the lake-groundwater. The assembly of PCGs-microbial communities shifted from stochastic to deterministic processes in lake-groundwater, while stochastic processes persisted in sediments. DIP and DOP in lake-groundwater were driven by genes involved in P-uptake and transport (r = 0.65 and 0.40, respectively, P<0.05), while phosphorus release from sediments was co-regulated by inorganic P-solubilization and organic P-mineralization genes (r = 0.89 and -0.36, respectively, P<0.05). Microbial taxa harboring complete phosphorus cycling pathways (42.2%) and organic P-mineralization genes (48.1%) were relatively rare, with Pseudomonadota as the dominant phylum (65.2% and 57.0%, respectively). This study reveals medium-specific adaptive strategies of microorganisms and PCGs-mediated phosphorus cycling mechanisms, providing scientific support for predicting eutrophication risks and managing lake ecosystems in seasonally frozen regions.},
}

@article {pmid42176511,
year = {2026},
author = {Li, K and Jin, F and Tan, S and Zeng, X and Yuan, D and Shu, F and Chen, J and Ouyang, JM and Zhang, L and Li, C and Zhu, J},
title = {Cinchonain Ia inhibits uric acid reabsorption by binding to the TRP-459 residue of the GLUT9 protein.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {157},
number = {},
pages = {158292},
doi = {10.1016/j.phymed.2026.158292},
pmid = {42176511},
issn = {1618-095X},
abstract = {BACKGROUND: Hyperuricemia, a chronic metabolic disorder resulting from purine metabolism abnormalities, imposes a substantial burden on patients, their families, and society. Consequently, discovering more efficient prevention strategies and treatment drugs is of crucial importance. Polygonum capitatum (Buch.-Ham. ex D. Don) H. Gross is a plant belonging to the Polygonaceae family and Polygonum genus. Polygonum capitatum can reduce uric acid levels and alleviate gouty arthritis; However, whether its aqueous extract contains other uric acid-lowering active components besides quercetin and gallic acid still requires further research.

PURPOSE: This study aims to investigate the protective effects and potential mechanisms of Polygonum capitatum aqueous extract on liver and kidney function, while also identifying new potential pharmacologically active components for hyperuricemia within the extract.

METHODS: This study established a hyperuricemia rat and mice model and a uric acid-induced renal injury cell model. Liquid chromatography-tandem mass spectrometry was employed to analyze the active components of Polygonum capitatum aqueous extract. The target was analyzed by proteomics. Metagenomics and spatial metabolome were used to analyze gut microbes and metabolites associated with liver and kidney injury. Finally, SPR, DARTS, and CETSA were used to assess the binding potential of active components to targets. Additionally, mutant plasmids were constructed to analyze the binding sites between pharmacologically active components and their targets.

RESULTS: The aqueous extract of Polygonum capitatum significantly reduced serum uric acid levels and alleviated renal injury in the hyperuricemia rat model, with no apparent damage on liver tissue morphology or hepatic function indicators. Metagenomic and spatial metabolomics analyses demonstrated that the extract increased the relative abundance of beneficial gut microbiota and decreased that of harmful bacteria. It also modulated the levels and distribution of renal metabolites such as l-arginine and N-acetylglucosamine, reduced lipid oxidation in the kidney. Proteomics analysis suggests that renal GLUT9 may be one of the action targets of this extract. LC-MS/MS analysis indicated that the chemical composition of the extract underwent significant changes after entering rat blood and undergoing renal metabolism. Specifically, serves as a new active component in Polygonum capitatum aqueous extract, Cinchonain Ia was found to bind to the TRP-459 residue of GLUT9, inhibiting its expression and thereby reducing uric acid reabsorption in vivo and in vitro, and alleviated oxidative stress, inflammation, and tissue damage. However, overexpression of GLUT9 markedly reversed the inhibitory effects of Cinchonain Ia on inflammation and injury.

CONCLUSIONS: The aqueous extract of Polygonum capitatum prevents liver damage and alleviates kidney injury by regulating gut microbiota and renal metabolites. Furthermore, Cinchonain Ia, as one of its active components, can bind to the TRP-459 residue of the GLUT9 protein and inhibit its expression, thereby suppressing uric acid reabsorption and lowering serum uric acid levels.},
}

@article {pmid42176589,
year = {2026},
author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q},
title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128552},
doi = {10.1016/j.micres.2026.128552},
pmid = {42176589},
issn = {1618-0623},
abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.},
}

@article {pmid42176630,
year = {2026},
author = {Wu, Y and Ma, W and Sun, Y and Tang, J and Xu, X and Zhu, J and Miao, J and Li, M and Zeng, J and Gou, K and Song, Y and Zou, J},
title = {From active defense to cross-kingdom alarm: Rhizosphere microenvironment remodeling in soybean under polylactic acid nanoplastics and cadmium Co-stress.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142470},
doi = {10.1016/j.jhazmat.2026.142470},
pmid = {42176630},
issn = {1873-3336},
abstract = {As foundational components of the food web, plants face significant environmental threats caused by the coexistence of micro/nanoplastics (MNPs) and heavy metals. This study investigates the combined effects of cadmium and biodegradable polylactic acid nanoplastics on soybean. Under co-exposure conditions, toxicity progressively diminishes from the roots to the leaves of soybeans. By integrating root transcriptomics, root exudate metabolomics, rhizosphere soil metagenomics, and soil physicochemical analyses within a Bayesian structural equation modeling framework, we identified the Flavonoid biosynthesis pathway as a central mediating hub in the rhizosphere microenvironment under combined stress. Soybean roots modulated this pathway as a response strategy, which concurrently served as a signal for rhizosphere microbes to downregulate energy-intensive processes such as Methane metabolism, facilitating microbial adaptation. The down-regulation of the Flavonoid biosynthesis pathway in root exudates further altered rhizosphere soil properties, creating a feedback loop that amplified the expression of stress-related genes in soybean roots.},
}

@article {pmid42176697,
year = {2026},
author = {Yao, J and Zhu, T and Tian, W and Xu, J and Nie, M and Wan, J},
title = {Artificial reefs alter viral communities and functional traits in coastal waters.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108131},
doi = {10.1016/j.marenvres.2026.108131},
pmid = {42176697},
issn = {1879-0291},
abstract = {Artificial reefs (ARs) are widely deployed as engineered coastal structures to enhance habitat complexity and support marine resource management, yet their impacts on marine viral ecology remain poorly understood. Viruses regulate microbial communities and biogeochemical processes, and their functional traits are sensitive to environmental change. Here, we investigated how artificial reefs influence viral community composition, functional gene profiles, and virus-environment interactions across paired reef and non-reef sites in coastal shelf systems. Using an integrated viromic and metagenomic approach, we compared viral assemblages in both seawater and sediments under artificial reef influence. ARs significantly modified seawater physicochemical conditions, including pH, sulfate concentration, dissolved oxygen, and salinity, whereas sediment properties remained largely unchanged. These environmental differences coincided with distinct virus-environment association patterns across habitats. Notably, artificial reefs were associated with viral functional profiles characterized by a reduced genomic representation of lysis-related genes and an increased representation of genes involved in DNA replication and nucleotide metabolism. Network analyses further showed differences in the balance of positive and negative virus-host correlations between AR and non-AR sites. Together, these results indicate that engineered coastal structures are linked to habitat-specific patterns in viral functional traits and virus-host associations. Our findings highlight viruses as sensitive indicators of anthropogenic habitat modification and underscore the importance of incorporating viral dynamics into assessments of microbial and biogeochemical responses in engineered coastal ecosystems.},
}

@article {pmid42176766,
year = {2026},
author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM},
title = {Neuronutrition In Asd: Involvement Of Gut Microbiota, Oxidative Stress And Inflammatory Markers.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106775},
doi = {10.1016/j.neubiorev.2026.106775},
pmid = {42176766},
issn = {1873-7528},
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.},
}

@article {pmid42176818,
year = {2026},
author = {Dorofeev, A and Pelevina, A and Gruzdev, E and Beletsky, A and Berestovskaya, Y and Litti, Y and Mardanov, A and Pimenov, N},
title = {Development of an Azonexus- and Competibacter-enriched phosphate-accumulating community in the anaerobic/anoxic sequencing batch reactor: Cooperative denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134959},
doi = {10.1016/j.biortech.2026.134959},
pmid = {42176818},
issn = {1873-2976},
abstract = {Denitrifying polyphosphate-accumulating organisms (DPAOs) enable simultaneous N and P removal, however, reliable strategies for enriching stable DPAO communities and their metabolic interactions remain insufficiently understood. In this study, DPAO-enriched cultures were developed in a sequencing batch reactor operated under anaerobic/anoxic conditions with acetate as C source. For three independent experiments, activated sludge, collected at different times, was used as the inoculum. Within 0.5-2 months, all experiments exhibited definitive DPAO phenotype dynamics. After 100-200 days of operation, the microbial community was consistently co-dominated by two genera: Azonexus (19-35 %), representing DPAOs, and Competibacter (23-31 %), representing denitrifying glycogen-accumulating organisms (DGAOs). Metagenomic reconstruction revealed that neither Azonexus nor Competibacter harbored the full complement of denitrification genes. The Azonexus metagenome-assembled genome encoded napAB (nitrate reductase), nirS (nitrite reductase), and nosZ (nitrous oxide reductase), while the Competibacter MAG possessed only norBC (nitric oxide reductase) genes. This genomic complementarity provides evidence that complete denitrification in this system could be achieved through cooperation between DPAOs and DGAOs. Consequently, the observed lower phosphorus removal efficiency, compared to anaerobic/aerobic systems, is attributed to the reduced biomass yield of DPAOs and the high essential abundance of DGAOs. These results clarify the ecological role of Azonexus as a DPAO dependent on partnership with DGAOs. Furthermore, the selective conditions favoring Azonexus development in enhanced nutrient removal systems, are evaluated. This work reveals a possible mechanism of syntrophic cooperation between DPAO and DGAO, which has direct implications for the development of resource-saving biological processes for nutrient removal.},
}

@article {pmid42176923,
year = {2026},
author = {Pi, D and Zhou, F and Huang, S and Yan, H and Pan, J and Yang, Q and Pan, M and Zhang, Y},
title = {Atractylodes lancea (Thunb.) DC polysaccharide alleviates MASH by regulating the 1‑carbon cycle through intestinal flora remodelling.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152668},
doi = {10.1016/j.ijbiomac.2026.152668},
pmid = {42176923},
issn = {1879-0003},
abstract = {Metabolic-associated steatohepatitis (MASH) is a severe stage of Metabolic-associated fatty liver disease (MAFLD). Currently, effective pharmacological therapies for MASH are extremely limited. An Atractylodes lancea (Thunb.) DC polysaccharide (ALP) was isolated from Atractylodes lancea (Thunb.) DC, and its preventive effect on MASH and the potential mechanism were investigated. Mice were fed a high-fat, high-cholesterol, high-fructose diet (HFMCD) to induce MASH. MASH model mice were then treated with ALP at low (50 mg/kg/d) or high (100 mg/kg/d) dosages. Faecal metagenomics, nontargeted metabolomics sequencing, biochemical and pathological analyses, ELISAs, western blotting and other detection techniques were conducted to elucidate the mechanism by which ALP alleviates MASH. The research results indicate that both the low-dose (50 mg/kg/d) and high-dose (100 mg/kg/day) of ALP can effectively alleviate MASH, but the high-dose has a more significant effect. ALP effectively reduced liver lipid accumulation and inflammation in MASH model mice by regulating the 1‑carbon cycle through intestinal flora remodelling. ALP may be a promising natural candidate for the treatment of MASH.},
}

@article {pmid42177038,
year = {2026},
author = {Strobel, KM and Leibel, SL and Bhute, S and Aja, E and Jacobs, JP and Calkins, K},
title = {Gut microbial differences and function in infants with gastroschisis: a pilot prospective cohort study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-14},
doi = {10.1163/18762891-bja00121},
pmid = {42177038},
issn = {1876-2891},
abstract = {Newborns with gastroschisis hospitalised in the neonatal intensive care unit (NICU) are at risk for a disrupted gut microbiome. Infants with gastroschisis are particularly vulnerable to a dysbiotic microbiome; they require prolonged parenteral nutrition (PN) due to intestinal dysmotility, which often leads to growth faltering (GF). This pilot study's goals were to (1) compare the gut microbiome in infants with gastroschisis to infants admitted to the NICU without congenital anomalies, (2) identify differences in the gut microbiome between infants with gastroschisis requiring prolonged PN and those who do not, and (3) compare the microbiome in infants with gastroschisis with GF to those without GF. This was a multi-site prospective cohort study including 17 infants born with gastroschisis and 16 infants with a gestational age greater than 34 weeks admitted to the NICU without congenital anomalies (controls). Prolonged PN was defined as more than 28 days. GF was defined as a decline in weight or length z-score from birth to discharge of ≤-0.8. Stool samples were collected weekly during hospitalisation and analysed by shotgun metagenomics to assess bacterial composition, diversity, and function. Gestational age and birth weight were similar in the gastroschisis group and the control group. Infants with gastroschisis showed increased Staphylococcus aureus and decreased Bifidobacterium longum. Those requiring prolonged PN had a reduced abundance of genes in the glucosidase pathway compared to those who did not. Infants with GF showed a lower abundance of genes involved in the NAD-diphosphatase pathway compared to those without GF. Infants with gastroschisis display a distinct microbial composition and function compared to NICU infants without this condition. Among infants with gastroschisis, differences in bacterial functional capacity were observed in those who required prolonged PN and developed GF.},
}

@article {pmid42177062,
year = {2026},
author = {Adamek, M and Yılmaz, TM and Erdogmus, S and Moore, S and Ziemert, N},
title = {The ARTS toolset: Resistance-based genome mining for systematic prioritization of bioactive gene clusters.},
journal = {Methods in enzymology},
volume = {730},
number = {},
pages = {35-60},
doi = {10.1016/bs.mie.2025.08.023},
pmid = {42177062},
issn = {1557-7988},
mesh = {*Multigene Family ; *Software ; Genome, Bacterial ; Genome, Fungal ; Fungi/genetics/metabolism ; *Bacteria/genetics/metabolism ; *Computational Biology/methods ; Biological Products/metabolism ; Data Mining/methods ; Genomics/methods ; Metagenome ; },
abstract = {Natural products, especially those produced by bacteria and fungi, have been a rich source of antibiotics and other medically important compounds. Advances in genome sequencing have revealed that many microorganisms harbor far more biosynthetic potential than previously known, but identifying which gene clusters are most likely to produce bioactive compounds remains a major challenge. One promising strategy is to look for genes that protect the producing organism from its own toxic products-so-called resistance genes-which often appear near the biosynthetic genes. In this chapter, we introduce the ARTS toolset, a collection of computational tools designed to identify such resistance-linked biosynthetic gene clusters in microbial genomes. ARTS 2.0 allows users to analyze bacterial genomes and metagenomes, ARTS-DB provides access to precomputed results from tens of thousands of genomes, and FunARTS adapts the approach for fungal genomes. We describe how each tool works and provide examples to guide their use, with additional online tutorial videos provided by the authors.},
}

*Multigene Family
*Software
Genome, Bacterial
Genome, Fungal
Fungi/genetics/metabolism
*Bacteria/genetics/metabolism
*Computational Biology/methods
Biological Products/metabolism
Data Mining/methods
Genomics/methods
Metagenome

@article {pmid42171933,
year = {2026},
author = {Xu, Y and Sun, X and Xu, S and Deng, S and Zhang, Y},
title = {Clinical profile of microsporidial keratoconjunctivitis in healthy individuals of China -new species and neglected risk factors.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12348-026-00596-9},
pmid = {42171933},
issn = {1869-5760},
abstract = {OBJECTIVE: To characterize microsporidial keratoconjunctivitis (MKC) in immunocompetent individuals in Mainland China, including novel etiologies and risk factors.

METHODS: A prospective analysis of 20 MKC patients in 2025, including clinical features, pathogens (via corneal scrapings and metagenomic sequencing), risk factors and etc. RESULTS: All patients were misdiagnosed for a median of 1 month. Patients (mean age 28.5 years, 13 F) showed Encephalitozoon hellem (65.0%), E. bieneusi (15.0%, first reported in MKC), and Vittaforma corneae (15.0%). Key risks included bird contact (70.0%, mostly psittacines), contact lens use (40.0%), and water exposure (15.0%). The most common symptom was redness (85.0%); limbal fluorescein positivity occurred in 65.0%. Topical 0.02% PHMB cured 90.0% of 20 cases; one recurrence followed treatment stop. Some E. hellem cases linked to parrots showed potential zoonotic transmission.

CONCLUSION: MKC in China involves E. bieneusi and parrot-associated E. hellem. Limbal staining aids diagnosis; PHMB is effective. Zoonotic risks related to Psittacine birds and contact lens use require clinical attention.},
}

@article {pmid42172047,
year = {2026},
author = {Delgado, LF and Sunyer, JO and Laczny, CC and Hickl, O and May, P and Wilmes, P},
title = {PathoFact 2.0: An Integrative Pipeline for the Prediction of Antimicrobial Resistance Genes, Virulence Factors, Toxins and Toxin-associated Proteins, and Biosynthetic Gene Clusters in Metagenomes.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag062},
pmid = {42172047},
issn = {2047-217X},
abstract = {BACKGROUND: Antimicrobial resistance genes (ARG) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections.

FINDINGS: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGC) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting biosynthetic gene clusters.

CONCLUSIONS: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems.},
}

@article {pmid42172141,
year = {2026},
author = {Long, K and Gravel-Pucillo, K and Waldron, L and Davis, S and Oh, S},
title = {Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42172141},
issn = {1758-0463},
support = {/CA/NCI NIH HHS/United States ; U24CA289073/NH/NIH HHS/United States ; 3U24CA180996-10S1/NH/NIH HHS/United States ; },
mesh = {*Metadata/standards ; Humans ; *Data Curation/methods ; *Neoplasms/genetics ; *Databases, Genetic ; *Metagenomics ; *Genomics ; },
abstract = {Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminologies, and quality issues that severely limit data reusability and cross-study integration. While prospective metadata standards exist, the majority of published omics data remain in non-standardized formats requiring retrospective harmonization. We performed comprehensive manual curation and harmonization of metadata, such as participant characteristics and study conditions, from 212 027 omics samples across 468 studies in two repositories: curatedMetagenomicData (93 studies, 22 588 samples) and cBioPortal (375 studies, 189 438 samples). Through systematic ontology mapping, we consolidated redundant, dispersed information into far fewer harmonized columns, reduced unique values, and increased the completeness of major attributes. This curation process revealed common metadata quality issues, including typos, inconsistent terminologies, misplaced values, conflicting annotations, and inappropriately merged information across attributes. We document the challenges, decisions, and solutions during this large-scale metadata harmonization. The harmonized metadata, accessible through the OmicsMLRepoR Bioconductor package, enables repository-wide queries and cross-study analyses previously challenging with heterogeneous metadata. Our experience provides practical guidance for similar curation efforts and demonstrates the value of investing in retrospective metadata improvement for existing public omics resources.},
}

*Metadata/standards
Humans
*Data Curation/methods
*Neoplasms/genetics
*Databases, Genetic
*Metagenomics
*Genomics

@article {pmid42172324,
year = {2026},
author = {Freschlin, CR and Yang, KK and Romero, PA},
title = {Scalable and cost-efficient custom gene library assembly from oligopools.},
journal = {Science advances},
volume = {12},
number = {21},
pages = {eady2279},
pmid = {42172324},
issn = {2375-2548},
mesh = {*Gene Library ; Software ; *Oligonucleotides/genetics ; Computational Biology/methods ; },
abstract = {Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost and scalability of DNA synthesis. Here, we present OMEGA (Oligo-based Multiplexed Efficient Gene Assembly), a low-cost, accessible method for assembling hundreds to thousands of full-length genes in parallel using standard laboratory techniques. OMEGA computationally fragments target genes into short, high-fidelity Golden Gate-compatible oligonucleotides that can be ordered as a pooled library and assembled across multiplexed subpools. We systematically optimized the number of fragments per gene and orthogonal ligation sites per reaction and determine that OMEGA can assemble up to 2.6-kilobase constructs using as many as 70 Golden Gate sites. To validate the approach, we assembled and functionally screened a library of 810 natural and synthetic green fluorescent protein variants, recovering 94 to 97% of target sequences with high uniformity. OMEGA enables precision library construction at scale, with per-gene costs as low as $1.50, and offers a broadly applicable solution for bridging computational protein design with high-throughput experimental validation. We have developed OMEGA as an open-source software package and an easy-to-use Colab notebook to facilitate community adaptation.},
}

*Gene Library
Software
*Oligonucleotides/genetics
Computational Biology/methods

@article {pmid42172586,
year = {2026},
author = {Singh, R and Gupta, P and Singh, R and Basant, N},
title = {Environmental Antibiotic Contamination and AMR: Integrating Pathways, Impacts, and AI-Driven Mitigation.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/etojnl/vgag115},
pmid = {42172586},
issn = {1552-8618},
abstract = {The widespread contamination of the environment with antibiotic residues is a significant factor contributing to the global crisis of antimicrobial resistance. Antibiotics from various sources, such as effluents from municipal and hospital wastewater treatment plants, agricultural runoffs, discharges from pharmaceutical manufacturing and improper disposal of expired or unused medicines, create selective pressures in the spread of antibiotic resistance genes. These environmental reservoirs act as hotspots for horizontal gene transfer, facilitating the emergence of multidrug-resistant pathogens. Conventional detection methods including culture-based assays, chromatographic quantification, and molecular diagnostics, provide essential insights but are limited by low throughput, reduced sensitivity to new Antibiotic Resistance Genes, and challenges in real-time monitoring across complex environments. Recent advances, such as whole-genome sequencing, metagenomics, and biosensor-based detection, help to address these gaps by enabling more comprehensive surveillance of the resistome. Artificial intelligence further enhances these approaches by improving data interpretation and pattern recognition, thus complementing traditional and molecular methods rather than replacing them. This review examines the pathways of environmental antibiotic contamination, ecological and health impacts of Antimicrobial Resistance (AMR), and limitations of conventional detection methods. It aims to clarify how these pathways contribute to the AMR crisis, assess the effectiveness of existing surveillance techniques, and identify gaps in current research.},
}

@article {pmid42172842,
year = {2026},
author = {Chen, X and Tan, QG and Pan, K and Xiao, A and Cheng, H and Wang, X},
title = {Vegetation of exotic fast-growing species Sonneratia apetala increases the potential of methylmercury production: Insights from carbon bioavailability, microbial metabolism and mercury methylators.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142469},
doi = {10.1016/j.jhazmat.2026.142469},
pmid = {42172842},
issn = {1873-3336},
abstract = {Mangrove sediments are hotspots for neurotoxic methylmercury (MeHg) production, with litter-derived organic carbon strongly affecting mercury (Hg) methylation. However, the specific role of carbon bioavailability in regulating net MeHg production remains unclear. This study investigated sediments vegetated by exotic fast-growing Sonneratia apetala (SA) and native Kandelia obovata (KO) in southern China. Contrary to the expectation that larger carbon pools enhance methylation, MeHg levels were 2.1-2.6 times higher in SA sediments despite KO containing 1.2-4.2 times more total organic carbon. This disparity was driven by carbon bioavailability: SA sediments exhibited a significantly higher proportion of available carbon (34-50%) compared to KO (28-36%), which stimulated microbial activity and enriched Hg-methylating microbes (1.4-3.3 times higher in hgcAB gene abundance). Metagenomics showed that SA not only promoted key Hg-methylating taxa (e.g., Desulfobacterales, Syntrophobacteria) but also upregulated their metabolic pathways for labile carbon use and methyl transfer to Hg. Our results demonstrate that carbon bioavailability, governed by species-specific litter chemistry, is the key driver of net MeHg production. The findings provide an in-depth understanding of Hg biogeochemistry by linking soil carbon quality to microbial metabolic networks, and offer novel insights for evaluating the ecological risks associated with exotic species in mangrove restoration.},
}

@article {pmid42172844,
year = {2026},
author = {Xu, Y and Xie, T and Zhong, W and Yang, G and Zhang, W},
title = {Probable disseminated Mycobacterium avium complex infection in an apparently immunocompetent patient: A case report and literature review.},
journal = {Journal of infection and public health},
volume = {19},
number = {7},
pages = {103245},
doi = {10.1016/j.jiph.2026.103245},
pmid = {42172844},
issn = {1876-035X},
abstract = {Disseminated Mycobacterium avium complex (MAC) infection is rare in immunocompetent hosts. This often leads to diagnostic delays. We report a challenging case of an apparently immunocompetent patient with pulmonary lesions, osteomyelitis, and skin ulcers. While routine cultures were pending, metagenomic next-generation sequencing (mNGS) rapidly identified MAC, enabling timely treatment. Subsequent culture and species identification confirmed the pathogen as Mycobacterium colombiense. Systematic reviews since 2000 have shown that skeletal and pulmonary involvement are common in this population. Diagnosis has gradually incorporated molecular biological techniques, and with timely treatment, patient outcomes are generally favorable. Our findings highlight the limitations of traditional microbiology and demonstrate that mNGS is a vital adjunctive tool for slow-growing pathogens. We conclude that disseminated MAC should be considered in refractory multifocal infections, even without recognized immunodeficiencies. Early molecular diagnosis, individualized multidrug therapy, and rigorous follow-up are essential for clinical remission.},
}

@article {pmid42172850,
year = {2026},
author = {Li, Y and Shi, B and Li, D and Li, YA and Yuan, M and Luo, J and Dong, S and Wen, W and Zhao, R},
title = {Microbial community shift and functional reorganization from influent to effluent in wastewater treatment plants on the Qinghai-Tibet Plateau.},
journal = {Journal of environmental management},
volume = {409},
number = {},
pages = {130036},
doi = {10.1016/j.jenvman.2026.130036},
pmid = {42172850},
issn = {1095-8630},
abstract = {Wastewater treatment plants (WWTPs) on the Qinghai-Tibet Plateau play a critical role in safeguarding fragile high-altitude aquatic ecosystems. However, microbial community structure and functional characteristics in the influent and effluent in high-altitude WWTPs remain poorly understood. Here, we integrated 16S rRNA gene amplicon sequencing with metagenomic gene-centric profiling and genome-resolved reconstruction to investigate influent and final effluent microbiomes from 18 municipal WWTPs across five cities in Qinghai Province. The results showed that alpha diversity was comparable between influent and effluent, whereas microbial community composition differed significantly. Co-occurrence networks revealed a simplified and more modular interaction pattern in effluent, accompanied by fewer keystone taxa compared with influent. Metagenomic analyses showed that major metabolic pathways were retained across treatment stages, but their relative abundances declined toward effluent. Genome-resolved analyses further indicated this treatment-associated functional reorganization primarily reflected shifts in the taxa and genomic coverage supporting these pathways, rather than replacement of pathway categories. Pseudomonadota accounted for the largest proportion of metabolic contributions across carbon, nitrogen, and sulfur transformation pathways, while multiple pathways persisted in effluent but were encoded by fewer genomes with lower coverage. Denitrification-associated steps, particularly nitric oxide and nitrous oxide reduction, constituted major genome-level contributions to nitrogen removal potential. Notably, Patescibacteria were significantly enriched in effluent and exhibited highly simplified genomes dominated by energy-conserving traits. These results reveal treatment-associated microbial and functional reorganization in plateau WWTPs and provide a genome-resolved framework for interpreting microbial metabolic potential in high-altitude wastewater systems.},
}

@article {pmid42172982,
year = {2026},
author = {Yan, S and Zhang, Y and Fan, Q and Jia, W and Dai, Y and Li, X and Lu, S and Sheng, Y and Sun, S and Lin, R and Tang, Y and Zhao, C},
title = {Evodiamine targets ZO-1 to ameliorate cholestatic liver disease: Intestinal homeostasis as the core mediator of gut-liver axis repair and bile acid metabolism remodeling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {157},
number = {},
pages = {158288},
doi = {10.1016/j.phymed.2026.158288},
pmid = {42172982},
issn = {1618-095X},
abstract = {BACKGROUND: Cholestatic liver disease (CLD) is a complex and multifactorial chronic disorder that requires a systematic and integrative management. Evodiamine (EVO), a natural alkaloid derived from Evodiae Fructus, has demonstrated significant therapeutic potential in ameliorating digestive diseases. However, the beneficial effects of EVO on CLD and the underlying mechanisms remain poorly understood.

OBJECTIVE: This study aims to elucidate the mechanisms through which EVO modulates the progression of CLD, with a particular focus on the regulation of gut-liver axis homeostasis.

METHODS: The therapeutic efficacy of EVO in bile duct ligation (BDL)- and α-naphthyl isothiocyanate (ANIT)-induced CLD rat models was systematically evaluated. An integrative approach combining network pharmacology with multi-omics analyses (transcriptomic, metagenomic sequencing, targeted bile acid metabolomics) was employed to identify significantly altered molecular networks. Fecal microbiota transplantation (FMT) was conducted to validate the functional role of gut microbiota in the hepato-intestinal protective effects. Direct molecular targets as well as the functional validation were confirmed through molecular docking, pull-down assays, surface plasmon resonance and cellular thermal shift assay.

RESULTS: EVO achieved significant synchronous hepato-intestine protection in both CLD rats: it markedly ameliorated hepatic injury and hepatic fibrosis, downregulated pro-inflammatory cytokine levels, while preserving intestinal barrier integrity and alleviating intestinal inflammation. Mechanistically, EVO exerted these protective effects by directly targeting the tight junction protein ZO-1 and enhancing its expression and stability. Furthermore, EVO restored intestinal microbial homeostasis, corrected dysregulated BA metabolism-specifically normalizing deoxycholic acid (DCA) levels. FMT experiments demonstrated that the synchronous hepato-intestinal beneficial effects of EVO were partially mediated by gut microbiota.

CONCLUSION: EVO exerts a protective effect against CLD by directly targeting ZO-1 to strengthen intestinal barrier function, thereby restoring gut microbial balance and rebalancing BAs metabolism (especially DCA levels) in the gut-liver axis. This study uncovers a novel ZO-1-dependent mechanism of EVO in CLD, highlighting EVO as a promising candidate for the treatment of CLD and providing new insights into gut-liver axis-targeted therapies.},
}

@article {pmid42173380,
year = {2026},
author = {Du, S and Ding, S and Zhao, Y and Wang, Y and Ju, F and Wu, D},
title = {Maintaining oxygen above a critical threshold prevents acetate-driven phytotoxicity in industrial-scale aerobic composting: metagenomic, MAG, and enzyme-activity evidence.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134949},
doi = {10.1016/j.biortech.2026.134949},
pmid = {42173380},
issn = {1873-2976},
abstract = {Aerobic composting is a key route for organic-waste valorization, yet product utilization is often constrained by phytotoxicity and low germination index (GI), particularly under oxygen-limited operation. Here, we developed an actionable oxygen-control window (O2 ≥ 10% v/v) to mitigate acetate-associated GI inhibition by integrating process monitoring with inhibitor profiling of GI extracts, metagenomics/metagenome-assembled genomes (MAGs), and pyruvate dehydrogenase (PDH) activity measurements. Three composting modes were implemented to create contrasting oxygen regimes: mechanical composting (MC; well-aerated), forced aeration composting (FC; intermittently oxygen-limited), and static composting (SC; ventilation-supported static aerobic). Chemical profiling and mixed-effects/regression analyses identified acetate as the dominant GI-inhibiting compound relative to other candidates (e.g., ammonium, formate, chloride). A bench-scale oxygen-gradient validation experiment (0-21% O2) confirmed an oxygen dose-response of acetate accumulation: acetate reached 1163.5 and 865.4 mg/L at 0% and 5% O2, but remained near baseline at ≥ 10% O2 (85.8 and 80.2 mg/L at 10% and 21% O2, respectively; 24 h), defining an oxygen window for suppressing acetate build-up. To probe mechanism, KEGG-based pathway mapping showed that acetate-linked functions were dominated by pyruvate metabolism, and high-acetate states were associated with reduced PDH-related functional gene abundance (PDHA/B) and lower PDH activity. MAG co-occurrence and correlation analyses further linked acetate-associated states to specific MAG-level contributors (including Thermobifida fusca). Together, these results support a PDH-linked metabolic constraint under oxygen limitation that promotes acetate persistence and GI inhibition, and provide operational guidance to maintain in-pile O2 ≥ 10% (v/v) to reduce acetate-driven phytotoxicity in industrial composting of readily acidogenic wastes.},
}

@article {pmid42173516,
year = {2026},
author = {Ogasawara, K and Uno, K and Tamahara, T and Asano, N and Sudo, K and Kusano, K and Tanabe, M and Kaise, Y and Shindo, T and Shimoyama, Y and Kanno, T and Koike, T and Shimizu, R and Masamune, A},
title = {Antibiotics treatment promotes squamocolumnar junction tumor progression via tumor immune evasion in K19-Wnt1/C2mE mice fed high-fat diet and acidic bile salts.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00056.2026},
pmid = {42173516},
issn = {1522-1547},
support = {19K08434//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 23K07368//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 24K13105//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; },
abstract = {Clinical studies suggested that antibiotics (ABx) administration might increase esophagogastric junction adenocarcinoma risk, but the underlying mechanisms remain unclear. We previously demonstrated that the administration of a high-fat diet (HFD) and acid bile salts (ABS) to K19-Wnt1/C2mE mice might promote the metabolic-driven tumor growth at the squamocolumnar junction (SCJ) cooperatively with gut dysbiosis. To clarify whether ABx-induced dysbiosis promotes the tumorigenesis, we evaluated the effects of HFD+ABS ± ABx treatment on tumor immune evasion in mice. In HFD+ABS+ABx-treated mice, SCJ tumor growth with increased tumor cell proliferation and infiltration of inflammatory cells positive for CD8, programmed cell death protein 1 and programmed cell death-ligand 1 (PD-L1) were observed along with apoptosis suppression. Protein expressions of interferon-gamma (IFN(?)) and phosphorylated signal transducer and activator of transcription (p-STAT) 3 were upregulated in the tumors of the HFD+ABS+ABx group, whose p-STAT1 expression was equivalent to that of the control group. The mice exhibited insulin resistance and metabolic endotoxemia, and metagenomic analysis of their ileal excrement revealed dysbiosis with a decrease in butyrate-producing bacteria and bacterial butanoate metabolism activity. Moreover, IFN(?) stimulation of human-derived NUGC-4 cells increased the protein expression of PD-L1, p-STAT1 and p-STAT3, all of which decreased in response to STAT inhibitors. Transfection with small interfering RNA targeting STAT1 or STAT3 did not attenuate PD-L1 induction, which was inhibited by the combined knockdown. Therefore, oral HFD+ABS+ABx administration to K19-Wnt1/C2mE mice may promote SCJ tumors through tumor immune evasion via IFN(?)-STAT1/STAT3-PD-L1 signaling, along with metabolic endotoxemia.},
}

@article {pmid42173938,
year = {2026},
author = {van Beek, N and Bargheet, A and Jian, C and Noordzij, HT and Ponsero, A and Pettersen, VK and Korpela, KE},
title = {Metagenomic survey of pathogen prevalence in the infant gut.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47440-7},
pmid = {42173938},
issn = {2045-2322},
support = {101039583//ERC Starting Grant/ ; },
abstract = {The human microbiota impacts our health and well-being from infancy throughout our lives. Besides mutualistic and commensal strains, it also contains opportunistic pathogens. Infants may be especially vulnerable to opportunistic pathogen colonisation due to their immature immune systems and low microbial diversity.The study aims to examine associations between opportunistic pathogen prevalence and factors such as breastfeeding, antibiotic use, birth-mode, and the presence of other bacterial taxa. This study analysed 3981 publicly available shotgun metagenomes collected from 1275 infants and 415 mothers across ten countries to identify species that may be considered opportunistic pathogens in the infant gut. The prevalence of C. difficile was decreased in breastfed infants and in those carrying Faecalibacterium and Dorea spp. S. aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding. K. pneumoniae was acquired later in life and was more prevalent in premature infants, and less commonplace in vaginal deliveries without antibiotics. Our findings indicate that opportunistic pathogen prevalence in the infant gut is influenced by medical and caregiving practices and may be modifiable through targeted interventions. Reducing the spread of these opportunistic pathogens could contribute to global efforts against early life infections.},
}

@article {pmid42174003,
year = {2026},
author = {Kumari, R and Ghosh, C and Kumar, R and Shakya, R and Kumar, S and Saini, AK},
title = {Assessment of water quality and microbial contamination in institutional water resources: a necessity to understand health risks.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53672-4},
pmid = {42174003},
issn = {2045-2322},
support = {project grant MH-32/2024//R&D cell, Miranda House, University of Delhi, India/ ; },
abstract = {Lack of regular monitoring of water sources may lead to undetected contamination, posing serious health risks and necessitating regular water quality assessments. Sampling for physicochemical, microbial analyses, and online surveys across three higher education institutions was done to evaluate water quality. Spatiotemporal variations among physicochemical parameters showed that the pH, EC, and TDS decreased during the wet season, reflecting the dilution effect of rain. However, DO increased from 0.67 to 4.83 ppm, indicating better aeration. PCA showed seasonal variability, whereas the correlation matrix highlighted both positive and negative interrelationships between temperature-pH (- 0.25), DO-ORP (0.11), and TDS-EC (1.00). Potentially toxic metals were either negligible or not detected. Metagenomics revealed the presence of 29 bacterial phyla, 61 classes, 124 orders, 241 families, and 457 genera. Canonical correspondence analysis showed the influence of Mo, EC, salinity, and TDS on Bacteroidota, Chloroflexota, Cyanobacteriota, and Planctomycetota, whereas Verrucomicrobiota, Acidobacteriota, Chlamydiota, Candidatus Melainabacteria, Bdellovibrionota, and Deinococcota were affected by Ni, pH, and COD. Pathogen mapping revealed the presence of Vibrio, Pseudomonas, Enterobacter spp., etc., responsible for diseases such as cholera, diarrhea, and typhoid. Also, occupants' perception about the water quality emphasizes the need for better management of drinking water in HEIs.},
}

@article {pmid42174021,
year = {2026},
author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W},
title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53556-7},
pmid = {42174021},
issn = {2045-2322},
abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.},
}

@article {pmid42174437,
year = {2026},
author = {van Bemmelen, J and Nika, I and Baaijens, JA},
title = {Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12874-w},
pmid = {42174437},
issn = {1471-2164},
abstract = {BACKGROUND: Over the past decades, genome databases have expanded exponentially, often incorporating highly similar genomes at the same taxonomic level. This redundancy can hinder taxonomic classification, leading to difficulties distinguishing between closely related sequences and increasing computational demands. While some novel taxonomic classification tools address this redundancy by selecting a subset of genomes as references, insights regarding the impact of different reference genome selection methods across taxonomic classification tools are lacking.

RESULTS: We systematically evaluate genome selection and dereplication methods on bacterial and viral datasets using simulated metagenomic samples and a bacterial mock community. For bacterial species-level profiling, incorporating all available genomes generally yields the highest accuracy, while having a limited impact on computational resource usage. In contrast, for highly similar bacterial strain-level and SARS-CoV-2 lineage-level datasets we find that selection significantly improves abundance estimation accuracy. Incorporating location-based metadata further enhances viral profiling performance by prioritizing locally relevant genomes. Across viral experiments, smaller reference sets significantly reduce memory and runtime requirements during both indexing and profiling, although this comes at an additional pre-processing cost.

CONCLUSIONS: Reference genome selection influences both accuracy and computational efficiency in taxonomic profiling, but its benefits seem context- and resolution-dependent. Our results demonstrate that reference set design does not have a one-size-fits-all solution, and that selection strategies should be adapted based on the biological and computational setting.},
}

@article {pmid42167521,
year = {2026},
author = {Wolacewicz, M and Decewicz, P and Valdes, ME and Iaconi, OS and Todiras, M and Ferdohleb, A and Rodriguez-Mozaz, S and Borrego, CM and Dziewit, L},
title = {The occurrence and removal of antibiotic residues and antibiotic resistance genes in the largest European constructed wetland at Orhei (Moldova).},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128381},
doi = {10.1016/j.envpol.2026.128381},
pmid = {42167521},
issn = {1873-6424},
abstract = {Constructed wetlands (CWs) are increasingly promoted as low-cost, nature-based solutions for wastewater treatment, particularly in low- and middle-income countries (LMICs), yet their performance in removing pharmaceutical compounds, antibiotic resistance genes (ARGs), and bacterial pathogens remains insufficiently characterized under real-field-scale conditions. Here, we investigated the fate of pharmaceutical compounds (including antibiotic residues), wastewater bacterial communities, and the associated ARGs in the largest European passive treatment system, the vertical-flow CW of Orhei (Moldova), serving nearly 26,000 inhabitants. Metagenomic profiling revealed 783 bacterial families, with a reduction from 33 families in raw sewage to 25 in the final effluent and clear enrichment of autochthonous wetland taxa. A total of 150 ARG types conferring resistance to 16 antibiotic classes were detected. The cumulative ARG load decreased by approximately 78% from influent to effluent. ARGs conferring resistance to fosfomycin, nitroimidazoles, rifamycins, streptothricin, oxazolidinones, and pleuromutilins were not detected in the final effluent, suggesting effective removal to below the detection limit of the applied metagenomic method, while sulfonamide resistance genes (sul1, sul2) persisted across all stages. Out of 29 antibiotic residues analyzed, 13 (including two sulfamethoxazole metabolites) were detected, together with 14 non-antibiotic pharmaceuticals (out of 30 residues analyzed). The removal of individual antibiotics ranged between 85 and 100%, and for other pharmaceuticals between 34 and 100%, although some compounds (e.g., carbamazepine, 10,11-epoxycarbamazepine, alprazolam) showed negative removals. Environmental risk assessment (risk quotients, RQ) indicated no significant risk to freshwater biota (RQ < 0.1) for all detected compounds in the treated effluent. Results demonstrated that a large-scale CW in the LMIC context can substantially reduce antibiotic residues and ARGs, supporting its role as an effective, nature-based component of One Health-oriented wastewater management.},
}

@article {pmid42167540,
year = {2026},
author = {Wang, W and Liu, H and Jiang, K and Posum, W and Lu, Z and Chen, X},
title = {A rare case of Porphyromonas endodontalis lung abscess mimicking lung cancer on imaging: The diagnostic value of postoperative metagenomic next-generation sequencing.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108821},
doi = {10.1016/j.ijid.2026.108821},
pmid = {42167540},
issn = {1878-3511},
abstract = {This case highlights the diagnostic challenge of a Porphyromonas endodontalis lung abscess mimicking lung cancer. A 67-year-old male presented with a right lower lobe mass suggestive of malignancy. Following wedge resection, pathology confirmed an abscess. Metagenomic next-generation sequencing (mNGS) of the tissue revealed a microbial profile dominated by oral anaerobes of Porphyromonas endodontalis. Postoperative mNGS identified the oral origin of infection and prompted periodontal treatment, leading to full recovery. This report reveals the decisive value of postoperative mNGS in correcting a diagnosis of infection mimicking lung cancer. It emphasizes that oral anaerobic infections can present as "tumor-like" pulmonary lesions. This case suggests that oral infection sources should be considered in the differential diagnosis of challenging pulmonary lesions and highlights the potential value of a multidisciplinary approach that includes dental evaluation.},
}

@article {pmid42167986,
year = {2026},
author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S},
title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.},
journal = {Journal of the World federation of orthodontists},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ejwf.2026.03.003},
pmid = {42167986},
issn = {2212-4438},
abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.

METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.

RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri‑implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).

CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri‑implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.},
}

@article {pmid42168196,
year = {2026},
author = {Bowie, KR and Luhung, I and Burke, TR and Roberts, SC and Martinello, RA and Gerstein, M and Peccia, J and Healy, HG},
title = {Disinfection of hospital sink drains enriches pseudomonadota and efflux pump-mediated antibiotic resistance in reestablished biofilms.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73533-y},
pmid = {42168196},
issn = {2041-1723},
support = {1S10OD030363-01A1//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Antimicrobial resistant pathogens and associated infections represent major public health threats affecting healthcare facilities, with sink drain biofilms serving as reservoirs for many of these bacteria. Despite attempts at sink drain biofilm disinfection and removal, drain biofilms inevitably regrow, and disinfection may shape the returning microbial communities and their resistance profiles. We applied culture-based and metagenomic approaches to study these drain disinfection effects on microbial community abundance, taxonomy, and antimicrobial resistance in operational hospital sinks. Drain biofilms regrew to baseline densities in approximately four days. Regrown biofilms contained more viable carbapenem-resistant bacteria and were dominated by Pseudomonadota, including Cupriavidus and Pseudomonas. Long-read sequencing revealed an increase in multidrug efflux pump genes after disinfection, which confer broad resistance to antibiotics and disinfectants. This work provides mechanistic insights into how disinfection influences sink drain biofilm ecology and the enrichment of antimicrobial resistance, with implications for infection prevention strategies in healthcare environments.},
}

@article {pmid42168704,
year = {2026},
author = {Zhang, X and Mallick, H and Rahnavard, A},
title = {Meta-analytic microbiome target discovery for immune checkpoint inhibitor response in advanced melanoma.},
journal = {Communications medicine},
volume = {6},
number = {1},
pages = {},
pmid = {42168704},
issn = {2730-664X},
support = {2109688//National Science Foundation (NSF)/ ; 2109688//National Science Foundation (NSF)/ ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors have transformed melanoma therapy, yet only a subset of patients achieve durable responses. Gut microbes have been linked to response, but reported biomarkers vary across studies. We aim to identify reproducible microbial features and test their generalizability across cohorts and treatment settings.

METHODS: We reprocessed stool metagenomic sequencing data from 15 melanoma cohorts (763 samples from 484 individuals), including 12 cohorts treated with immune checkpoint inhibitors alone and 3 trials combining immune checkpoint inhibitors with fecal microbiota transplantation. Using a unified analysis pipeline, we profiled microbial species, metabolic pathways, and biosynthetic gene clusters, and analyzed their associations with treatment response using Tweedie regression, random-effects meta-analysis, and multimodal integration with leave-one-dataset-out validation.

RESULTS: Here, we show that responders in immune checkpoint inhibitor-only cohorts are enriched for several short-chain fatty acid-producing commensals, whereas non-responders show higher abundance of taxa associated with disrupted gut communities. In fecal microbiota transplantation plus immune checkpoint inhibitor trials, response associates with distinct communities and shifts in amino-acid, nucleotide and cofactor metabolism. Across cohorts, multiview prediction models repeatedly select gene clusters linked to antimicrobial peptides and surface polysaccharides, but cross-study discrimination remains modest.

CONCLUSIONS: Microbiome signatures of response are treatment-context dependent and are not captured by a single universal species. These harmonized findings prioritize microbial taxa and functions for mechanistic studies and future microbiome-informed interventions.},
}

@article {pmid42168837,
year = {2026},
author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T},
title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05157-7},
pmid = {42168837},
issn = {1471-2180},
support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; },
abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.},
}

@article {pmid42168845,
year = {2026},
author = {Zhao, Q and Zuo, S and Liu, S and Wang, J and Tang, J and Zou, X and Leng, Y and Li, X and Zhou, M and Tian, J and Wang, P},
title = {Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05168-4},
pmid = {42168845},
issn = {1471-2180},
support = {2023AFD045//Hubei Provincial Natural Science Foundation / Joint Fund Project Cultivation Project/ ; 2023BCB140//Hubei Provincial plan of science and technology key research project/ ; 2023XKQT1//The Advantages Dicipline Group (Medicine) Project in Higher Education of Hubei Province (2021-2025)/ ; },
abstract = {Alterations in the gut microbiome have been increasingly implicated in Parkinson's disease (PD), but the associated metabolic changes remain incompletely understood. Here, we applied an integrative multi-omics approach combining shotgun metagenomic sequencing and untargeted LC-MS-based plasma metabolomics to investigate host-microbiome alterations in PD. Fecal and plasma samples were collected from 30 PD patients and 30 healthy spouse controls. Significant differences in microbial diversity and taxonomic composition were observed between the two groups. Taxonomic profiling revealed marked gut microbial dysbiosis in PD, including altered abundances of Phocea massiliensis, Bacteroides sp900766005, and Alistipes_A indistinctus. Metabolomic analysis identified 86 significantly altered plasma metabolites, including glycerophospholipids, indoleacetic acid, and kynurenic acid. Integrative pathway analysis suggested links between microbial functional alterations and host metabolic changes. Machine-learning analyses identified three biomarker panels that distinguished PD patients from controls in validation datasets, with the highest area under the curve (AUC) reaching 0.92. In silico molecular docking further suggested potential interactions between several metabolite biomarkers and alpha-2-macroglobulin (A2M) or the human B[act] spliceosome. Overall, these findings provide an integrative view of host-microbiome metabolic alterations associated with PD and highlight candidate biomarkers and exploratory host-metabolite associations for further investigation.},
}