@article {pmid42108288,
year = {2026},
author = {Yan, C and Zhang, F and Long, C and Yin, Y and Wang, L},
title = {A Brief Review of Microbial Omics: Methods and Perspectives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {1-20},
pmid = {42108288},
issn = {1940-6029},
mesh = {*Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; Single-Cell Analysis/methods ; Artificial Intelligence ; Transcriptome ; Metagenomics/methods ; },
abstract = {Microbial omics has progressed from isolated genomic analyses into a comprehensive, integrated multi-omics framework, profoundly advancing our understanding of microbial complexity and functionality. This mini-review systematically outlines the core technologies within microbial omics-including genomics, transcriptomics, proteomics, and metabolomics-by introducing their fundamental principles, common experimental workflows, and state-of-the-art bioinformatic strategies. We particularly highlight the emergence of single-cell microbial omics as a transformative methodology that resolves molecular and functional heterogeneity within communities, enabling the identification of rare taxa, strain-level microdiversity, and specialized functional roles that are obscured in bulk analyses. Furthermore, we discuss how artificial intelligence (AI)-driven tools are revolutionizing the interpretation of high-dimensional omics data, uncovering latent biological patterns, improving predictive modeling of microbial behavior, and facilitating the translation of microbiome insights into clinical and environmental applications. The review concludes by comparing the strengths, limitations, and optimal use cases of each omics layer and single-cell approach while also addressing ongoing technical challenges and future directions in the field.},
}

*Genomics/methods
*Metabolomics/methods
*Proteomics/methods
*Microbiota/genetics
*Computational Biology/methods
Single-Cell Analysis/methods
Artificial Intelligence
Transcriptome
Metagenomics/methods

@article {pmid42108289,
year = {2026},
author = {Li, B and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y},
title = {Standardized Protocols for Environmental Sample Collection: Minimizing Contamination and Preserving Microbial Community Integrity.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {21-42},
pmid = {42108289},
issn = {1940-6029},
mesh = {*Specimen Handling/methods/standards ; Humans ; *Microbiota ; *Environmental Microbiology ; Soil Microbiology ; *Environmental Monitoring/methods ; Water Microbiology ; },
abstract = {Accurate microbial community assessment begins with reliable sample collection. Environmental matrices, such as soil, water, and human-associated habitats, each present unique challenges that can introduce contamination or alternative microbial structures in samples. This chapter provides an overview of standardized sampling strategies for these environments, emphasizing principles for minimizing external contamination and preserving the integrity of microbial communities. Key considerations in field practice, sample handling, preservation, and transport are summarized, along with common pitfalls and practical solutions.},
}

*Specimen Handling/methods/standards
Humans
*Microbiota
*Environmental Microbiology
Soil Microbiology
*Environmental Monitoring/methods
Water Microbiology

@article {pmid42108291,
year = {2026},
author = {Li, B and Yang, X and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y},
title = {Metagenomic Assembly and Gene Prediction.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {63-89},
pmid = {42108291},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Metagenome ; *Computational Biology/methods ; Molecular Sequence Annotation ; Contig Mapping/methods ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.},
}

*Metagenomics/methods
*Metagenome
*Computational Biology/methods
Molecular Sequence Annotation
Contig Mapping/methods
Software
Microbiota/genetics
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods

@article {pmid42108292,
year = {2026},
author = {Guo, JX and Gao, YZ},
title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {91-103},
pmid = {42108292},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.},
}

*Microbiota/genetics
*Bacteria/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/methods
Humans
DNA, Bacterial/genetics
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid42108293,
year = {2026},
author = {Liu, J and Li, Y and Huang, T},
title = {Network Analysis in Microbiome Research: Methods, Tools, and Applications.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {105-115},
pmid = {42108293},
issn = {1940-6029},
mesh = {Humans ; *Microbiota ; *Computational Biology/methods ; Algorithms ; },
abstract = {The human microbiome operates as a complex, interconnected ecosystem where microbial interactions dictate community stability, host health, and disease progression. Understanding these dynamics requires moving beyond simple taxonomic catalogs to systems-level network analyses. This chapter reviews network methodologies in microbiome research, progressing from traditional correlation-based approaches to advanced artificial intelligence techniques. We systematically cover co-occurrence, protein-protein interaction, metabolic, multi-omics integrated, and evolutionary transmission networks. Computational tools-spanning general platforms and specialized pipelines-are compared alongside topology metrics and community detection algorithms. Furthermore, we highlight the integration of graph neural networks and protein language models, discussing current challenges in data standardization, model interpretability, and the merging of mechanistic and data-driven paradigms.},
}

Humans
*Microbiota
*Computational Biology/methods
Algorithms

@article {pmid42108295,
year = {2026},
author = {Peng, B and Chang, X},
title = {Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {147-164},
pmid = {42108295},
issn = {1940-6029},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung/metabolism ; *Metabolomics/methods ; Lung Diseases/metabolism/microbiology ; Metagenomics/methods ; Dysbiosis ; Animals ; *Genomics/methods ; Proteomics/methods ; },
abstract = {The complex, bidirectional communication between the gut and the lungs, known as the "gut-lung axis," profoundly influences host immune homeostasis and the pathogenesis of respiratory diseases. In recent years, multi-omics approaches, including metagenomics, metabolomics, and metatranscriptomics, have emerged as the core driving force for unraveling the complexity of this interorgan cross talk network. This review aims to systematically summarize the current omics-based evidence in the field of the gut-lung axis. We highlight key communication mechanisms discovered through multi-omics integration, particularly how gut microbiota-derived metabolites, exemplified by short-chain fatty acids (SCFAs), mediate distal immune regulation. Concurrently, we consolidate omics evidence from the contexts of respiratory infectious diseases, chronic lung disorders, and aging, systematically delineating the impact of gut dysbiosis on pulmonary pathophysiology via the gut-lung axis and emphasizing the feasibility of disease management in patients with lung diseases by modulating the gut microbiota. Although omics technologies have significantly advanced our understanding of this field, the challenge of effectively integrating vast, heterogeneous data and transitioning from "correlation" to "causation" remains a primary hurdle. By reviewing and discussing the current omics evidence in the gut-lung axis, this paper aims to provide new perspectives for future mechanistic explorations and clinical translation strategies.},
}

Humans
*Gastrointestinal Microbiome
*Lung/metabolism
*Metabolomics/methods
Lung Diseases/metabolism/microbiology
Metagenomics/methods
Dysbiosis
Animals
*Genomics/methods
Proteomics/methods

@article {pmid42108298,
year = {2026},
author = {Song, Q},
title = {Infection-Associated Microecology and Hepatocellular Carcinoma.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {209-215},
pmid = {42108298},
issn = {1940-6029},
mesh = {*Carcinoma, Hepatocellular/etiology/microbiology/pathology ; *Liver Neoplasms/etiology/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Hepatitis B, Chronic/complications/virology ; Animals ; Aflatoxins ; },
abstract = {Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality worldwide and remains one of the few malignancies with steadily increasing incidence and death rates over recent years. Globally, major etiological drivers of HCC include chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, consumption of aflatoxin-contaminated food, heavy alcohol intake, obesity, cigarette smoking, and type 2 diabetes mellitus. In China, however, the exceptionally high burden of HCC is primarily attributable to chronic HBV infection and aflatoxin exposure, with approximately 80% of Chinese HCC patients testing positive for HBV. The natural history of the disease generally progresses from chronic hepatitis to liver cirrhosis and ultimately to HCC. Throughout this trajectory, the infection-associated microecological environment exerts a crucial influence on hepatocarcinogenesis. This chapter will examine the role and mechanistic underpinnings of infection-related microecology-particularly the gut microbiome-in the development of HCC and highlight the clinical relevance of infection-associated microbial components in liver cancer treatment.},
}

*Carcinoma, Hepatocellular/etiology/microbiology/pathology
*Liver Neoplasms/etiology/microbiology/pathology
Humans
*Gastrointestinal Microbiome
*Hepatitis B, Chronic/complications/virology
Animals
Aflatoxins

@article {pmid42108392,
year = {2026},
author = {Kou, R and Zheng, J and Hou, S and Qiao, L and Liu, X},
title = {The Effect of SO2 Pulse on Synergistic Interaction of Postharvest Quality and Fungal Community During Thin-Skinned Grape Storage.},
journal = {Journal of food science},
volume = {91},
number = {5},
pages = {e71021},
doi = {10.1111/1750-3841.71021},
pmid = {42108392},
issn = {1750-3841},
support = {2024YFD2100800//China Rural Technology Development Center/ ; 32402194//National Natural Science Foundation of China/ ; 6202512184//Agriculture and Rural Affairs Bureau of Dabancheng District, Urumqi/ ; },
mesh = {*Vitis/microbiology/drug effects ; *Sulfur Dioxide/pharmacology ; Food Storage ; Fruit/microbiology/drug effects ; *Fungi/drug effects/classification ; *Food Preservation/methods ; Catechol Oxidase/metabolism ; },
abstract = {SO2 is commonly used to control postharvest grape mold, but the technology of low-residue usage and the regulatory effects on the grape microbial community are still to be explored. In this research, slow-release SO2 pads (SR) and intermittent high SO2 pluses (IHP) were adopted to treat Daqing grapes during low-temperature storage. The results showed that IHP maintained the best appearance, grape-skin integrity, and reduced the SO2 residue by 49.9% compared to SR group. Meanwhile, the grapes of IHP significantly reduced the decay, inhibited the browning and weight loss, and maintained higher firmness than the control. To explain the reason, the activities of enzymes associated with the immune resistance system, including superoxide dismutase (SOD), peroxidase (POD), phenylalanine ammonia (PAL), and polyphenol oxidase (PPO) were found a higher level in IHP during storage. More importantly, changes in fungi communities were analyzed using internal transcribed spacer (ITS) in the IHP and control groups. The changes in fungal communities showed that IHP preserved the richness of OTU and diversity of fungi communities, effectively inhibiting the relative quantity of the primary pathogens: B. cinerea, C. chasmanthicola, and A. alternata. Furthermore, correlation analysis suggested that microbial communities and immune resistance independently regulate grape postharvest quality while being interrelated, collectively influencing the postharvest quality of Daqing grapes and forming "short-term stress-grape immune resistance (the postharvest quality)-the postharvest grape surface microbiome" a novel interaction system. Thus, we inferred that IHP could induce grape resistance, inhibit surface pathogens, modify surface microbiome, and maintain the postharvest quality of the grapes.},
}

*Vitis/microbiology/drug effects
*Sulfur Dioxide/pharmacology
Food Storage
Fruit/microbiology/drug effects
*Fungi/drug effects/classification
*Food Preservation/methods
Catechol Oxidase/metabolism

@article {pmid42108513,
year = {2026},
author = {Huang, Q and Wen, C and Gu, S and Jie, Y and Li, G and Yan, Y and Wu, G and Yang, N},
title = {Gut microbiota and their metabolites contribute to the heterosis of breast muscle yield in broilers.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42108513},
issn = {1674-9782},
support = {2022YFF1000204//the National Key Research and Development Program of China/ ; ZDYF2023XDNY036//the Key Research and Development Program of Hainan province/ ; GK AA23062049//the Guangxi Science and Technology Major Program/ ; 6262015//Beijing Natural Science Foundation/ ; },
abstract = {BACKGROUND: Breast muscle yield is a key economic trait in broilers, directly affecting carcass value and profitability, and has been significantly improved by intensive selection and exploiting heterosis through crossbreeding. Our previous work showed that synergy between the gut microbiota and host genome underlies breast muscle heterosis in crossbred progeny (CR) derived from Cornish (CC) and White Plymouth Rock (RR) lines. However, the molecular mechanisms by which the gut microbiota contributes to heterosis in breast muscle yield remain poorly understood. Here, we integrated cecal microbiome, metabolome, and transcriptome data from 266 birds at 42 days of age to elucidate the potential gut microbiota-mediated molecular mechanisms underlying breast muscle yield heterosis.

RESULTS: To assess whether heterosis extends beyond productive traits to the gut microbiota and their metabolites in broilers, we compared the cecal microbial and metabolic profiles of CR with those of their parental lines. The gut microbiota of CR were clearly distinct from those of both parental lines and exhibited heterosis characteristics, with 88 genera displaying heterotic patterns that collectively accounted for approximately 85% of the total microbial abundance. Heterosis was also evident in the cecal metabolites of CR birds. Differential abundance analysis across groups identified 868 cecal metabolites, and abundance-pattern classification showed that approximately 75% exhibited nonadditive patterns in the crossbred progeny. These nonadditive metabolites were predominantly host-microbiota co-metabolites and were mainly enriched in amino acid and lipid metabolic pathways. Importantly, seven of the nine genera previously identified in association with breast muscle yield exhibited heterosis in the crossbred progeny. At the metabolomic level, yield-associated genera were linked to a distinct set of 35 cecal metabolites, dominated by sphingolipids, ether-linked phospholipids, and acyl-homoserine lactones. These metabolites formed coordinated associations with the expression of 269 host genes, which were functionally enriched in MAPK signaling and focal adhesion pathways.

CONCLUSIONS: These findings suggest that heterosis exists not only in productive traits but also in gut microbiota and their metabolites, the latter in turn contributed to breast muscle yield, which offers valuable guidance for elucidating the molecular basis of heterosis in animals.},
}

@article {pmid42108623,
year = {2026},
author = {Kashkouli, M and Fathipour, Y},
title = {Cross-kingdom signaling manipulation by insect-associated microbial symbionts: Linking molecular mechanisms to pest management strategies.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70885},
pmid = {42108623},
issn = {1526-4998},
abstract = {Microbial symbionts associated with herbivorous insects can modulate plant hormone networks and reconfigure induced defenses during feeding. This review synthesizes current knowledge on how symbiont effectors converge on conserved jasmonic acid (JA)/salicylic acid (SA)/ethylene (ET) signaling hubs to suppress or reprogram plant immunity. These microbial partners secrete a diverse arsenal of bioactive molecules, including effector proteins (e.g., the histidine-rich Ca[2+]-binding protein ApHRC from Serratia symbiotica in pea aphids), enzymes (e.g., gut microbiome-derived proteases in Anticarsia gemmatalis larvae), and host metabolite mimics (e.g., cytokinin production induced by Wolbachia in the apple leaf-mining moth). Through these mechanisms, symbionts selectively manipulate plant hormonal pathways, a form of molecular interference that often enhances herbivore performance by increasing feeding efficiency, fecundity, and host plant range, thereby increasing plant susceptibility to biotic stress. These physiological alterations trigger cascading ecological effects, reshaping multitrophic interactions: symbiont-mediated changes in herbivore-induced plant volatiles (HIPVs) and secondary metabolites influence the behavior of natural enemies, alter competitive outcomes among herbivores, and disrupt plant-insect communication. Consequently, microbial symbionts act as hidden ecological engineers, driving community dynamics and evolutionary trajectories. By integrating molecular, ecological, and evolutionary perspectives, we propose a unified framework that explicitly links symbiont effector function to plant immune modulation and its ecosystem-level consequences. Ultimately, this synthesis underscores the potential of targeting insect-microbe partnerships through approaches such as effector blocking, microbiome augmentation, or symbiont disruption, for developing sustainable pest management strategies and advancing the field of plant defense ecology. © 2026 Society of Chemical Industry.},
}

@article {pmid42108649,
year = {2026},
author = {Hermanson, JB and Tolba, SA and Gazi, MA and Chrisler, EA and Kaur, M and Sidebottom, AM and Liu, Y and Martinez-Boggio, G and Lucas, LN and Amador-Noguez, D and Rey, FE and Leone, VA},
title = {Gut microbes mediate the synergistic effects of dietary cholesterol and saturated fat in driving fibrosing MASH.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2668121},
doi = {10.1080/19490976.2026.2668121},
pmid = {42108649},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Cholesterol, Dietary/adverse effects/metabolism ; Mice ; Humans ; Diet, High-Fat/adverse effects ; Male ; *Dietary Fats/adverse effects/metabolism ; *Fatty Acids/metabolism/adverse effects ; Mice, Inbred C57BL ; Bile Acids and Salts/metabolism ; *Fatty Liver/microbiology/metabolism/pathology ; Specific Pathogen-Free Organisms ; *Liver Cirrhosis/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Hepatic Stellate Cells/metabolism ; Liver/pathology ; Germ-Free Life ; Non-alcoholic Fatty Liver Disease ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) affects approximately one-third of the global population and can progress to metabolic dysfunction-associated steatohepatitis (MASH) with fibrosis, increasing the risk of cirrhosis, hepatocellular carcinoma, and mortality. Gut microbes driven by diets high in saturated fat, simple sugar, and cholesterol contribute to disease progression, yet the underlying mechanisms remain undefined. We explored the independent and synergistic effects of dietary saturated fat and cholesterol on MASH development using specific pathogen-free (SPF) and germ-free (GF) mice. We demonstrate that (1) both dietary cholesterol and saturated fat are required to induce fibrosing MASH in SPF mice, whereas GF mice are protected, (2) saturated fat and cholesterol individually alter gut microbial membership, potentially via altered bile acid metabolism, while their combination promotes a distinct composition, including an increase in Parasutterella spp. which correlates with hepatic fibrosis, and (3) diluted cecal contents from SPF, but not GF, mice fed high-fat, high-cholesterol diets are enriched in deoxycholic acid and activate human hepatic stellate cells in vitro, suggesting a mechanistic link between dietary lipid-induced microbiota and liver fibrogenesis. These findings reveal how specific Western dietary components shape the gut microbiota and contribute to hepatic fibrosis via stellate cell activation, offering potential targets for therapeutic interventions against MASLD/MASH.},
}

Animals
*Gastrointestinal Microbiome
*Cholesterol, Dietary/adverse effects/metabolism
Mice
Humans
Diet, High-Fat/adverse effects
Male
*Dietary Fats/adverse effects/metabolism
*Fatty Acids/metabolism/adverse effects
Mice, Inbred C57BL
Bile Acids and Salts/metabolism
*Fatty Liver/microbiology/metabolism/pathology
Specific Pathogen-Free Organisms
*Liver Cirrhosis/microbiology
Bacteria/classification/genetics/isolation & purification/metabolism
Hepatic Stellate Cells/metabolism
Liver/pathology
Germ-Free Life
Non-alcoholic Fatty Liver Disease

@article {pmid42108651,
year = {2026},
author = {Xu, Z and Mu, L and Su, H and Zhang, X and Shang, H and Li, Z and Tak Vai Chan, M and Ka Kei Wu, W and Chen, H},
title = {Probiotics in colorectal cancer: mechanisms, biomarkers, and adjunct strategies.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2026.0133},
pmid = {42108651},
issn = {2095-3941},
support = {24103225//RGC-GRF Hong Kong/ ; 14104924//RGC-GRF Hong Kong/ ; C4008-23W//RGC-CRF Hong Kong/ ; C4042-24GF//RGC-CRF Hong Kong/ ; 82573882//National Natural Science Foundation of China [NSFC]/ ; 82272989//National Natural Science Foundation of China [NSFC]/ ; 22210032//Health and Medical Research Fund [HMRF]/ ; 2025.090//CUHK Direct Grant for Research/ ; },
abstract = {Colorectal cancer (CRC) is among the most common malignant tumors and remains a leading cause of cancer-related mortality worldwide. The gut microbiota and metabolites, which are modulated by host genetics and environmental exposures, have emerged as key contributors to the pathogenesis of CRC. A key feature of gut dysbiosis in CRC is the enrichment of pathogenic bacteria alongside the depletion of beneficial commensals. Probiotic supplementation has been shown to counteract this imbalance and suppress tumor progression. Mechanistically, probiotics suppress CRC development through multifaceted actions, including directly inhibiting tumor cell growth, reducing inflammation, reinforcing the intestinal barrier, and reprogramming host immunity. This review summarizes evidence on the inhibitory role of probiotics in CRC, evaluates the potential of probiotics as predictive biomarkers, and discusses microbiome-modulation strategies designed to enhance immunotherapy and chemotherapy, thereby offering a complementary paradigm for CRC prevention and treatment.},
}

@article {pmid42108693,
year = {2026},
author = {van Heule, M and Heil, B and Norris, JK and Gedye, K and Lin, X and De Spiegelaere, W and Daels, P and Dini, P},
title = {Vaginal host-microbe signatures linked to placental outcomes in mares.},
journal = {Equine veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1002/evj.70185},
pmid = {42108693},
issn = {2042-3306},
support = {//Special Research Fund at the University of Ghent (BOF)/ ; //New Zealand Equine Research Foundation/ ; //John P. Hughes Endowment/ ; },
abstract = {BACKGROUND: Ascending placentitis is a leading cause of late-term pregnancy loss in mares. Although pathogens are presumed to ascend from the caudal reproductive tract, the association between the vaginal microbiome and placentitis has not been systematically examined.

OBJECTIVES: To characterise microbial and host gene expression in the equine vagina during gestation and to identify taxa or transcripts that were associated with the presence of an abnormal placenta at birth.

STUDY DESIGN: Prospective, paired observational study.

METHODS: Vaginal wall swabs were collected from 49 multiparous Thoroughbred mares at days 42-46 and 118-133 of gestation (first and second trimester). Pregnancies were monitored to term, and placentas were classified as normal (healthy) or abnormal. Complete data was available for 37 mares, and 13 were included in this study: normal (n = 6), abnormal (n = 5), and ascending placentitis (n = 2). Total RNA underwent deep dual RNA-sequencing. Alpha- and beta-diversity metrics, differential expression, and microbe-host correlation analyses were performed.

RESULTS: Global vaginal microbial diversity did not differ between mares with healthy or abnormal placentas. Several microbes from the phyla Actinomycetota and Pseudomonadota showed altered activity in mares with abnormal placentas. Vaginal transcriptome showed a subtle inflammatory response in the second trimester in the abnormal placenta group in the absence of clinical signs. Correlation analysis suggested an interaction between bacterial survival and virulence genes and host inflammation and apoptosis genes.

MAIN LIMITATIONS: Samples were obtained from clinical cases, limiting the availability of a complete history.

CONCLUSIONS: Although overall vaginal microbial diversity was similar between outcome groups, distinct host vaginal transcriptional and microbial activity signatures distinguished mares with an abnormal placenta at birth. These findings warrant targeted investigation of the vaginal immune response and bacterial virulence factors as early biomarkers and therapeutic targets.},
}

@article {pmid42108760,
year = {2026},
author = {Pereira, EC and Bell, CA},
title = {Observing the invisible: X-ray CT for plant-microbe interactions.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71252},
pmid = {42108760},
issn = {1469-8137},
support = {BB/X009823/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Plant-microbe interactions are inherently spatial, yet the physical structure of the soil and rhizosphere is rarely treated as a mechanistic variable in experimental design. X-ray computed tomography (X-ray CT) enables nondestructive, three-dimensional, and time-resolved imaging of intact root-soil systems, providing direct access to the structural context in which plant-microbe interactions occur. Rather than a secondary imaging technique, X-ray CT can offer a wealth of data as a primary experimental platform for future plant-microbe research. Here, we highlight key structural traits that X-ray CT can quantify and discuss how they may shape microbial behaviour, plant immune responses, and disease outcomes. We expand on how X-ray CT could be employed in future to provide a framework to disentangle direct microbial effects from indirect, structure-mediated feedbacks. For breeding and management, it could enable selection for root traits and soil practices that engineer favourable microhabitats rather than targeting organisms in isolation. Despite this potential, broader adoption will require overcoming current limitations related to access to instrumentation, analytical expertise, and the integration of structural data with biological measurements. Overall, we suggest that resolving these issues will enable the integration of X-ray CT-derived structure with molecular, microbiome, and modelling approaches to enable the development of digital rhizospheres, offering a pathway from descriptive observations to predictive, structure-aware in silico frameworks in plant-microbe research.},
}

@article {pmid42108828,
year = {2026},
author = {Pylro, VS and Morais, DK},
title = {Rethinking Alpha Diversity in Marker-Gene Microbiome Studies: Dominance Matters More Than Richness.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70325},
doi = {10.1111/1462-2920.70325},
pmid = {42108828},
issn = {1462-2920},
support = {441346/2023-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 406658/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; RED-00181-23//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; RED-00330-16//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-04011-24//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-08335-25//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APD-01038-25//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 2649/22//FINEP/ ; },
mesh = {*Microbiota/genetics ; *Biodiversity ; *Bacteria/genetics/classification ; Genetic Markers ; },
abstract = {In the era of widespread marker-gene sequencing, alpha diversity metrics are increasingly used to infer ecological responses and biodiversity patterns in microbial communities. We highlight key conceptual and methodological limitations underlying these metrics, particularly the open-ended nature of microbial richness and the uneven detectability of taxa. We argue that, in marker-gene-based studies, alpha diversity often reflects shifts in dominance rather than true richness. We discuss why common assumptions fail, outline the risks of misinterpretation and propose a dominance-centred perspective to improve ecological inference in microbiome research.},
}

*Microbiota/genetics
*Biodiversity
*Bacteria/genetics/classification
Genetic Markers

@article {pmid42108955,
year = {2026},
author = {Yoon, EC and Seok, J and Kim, YK and Yoon, HY},
title = {A harmonized respiratory-gut microbiome cohort framework for idiopathic pulmonary fibrosis.},
journal = {Tuberculosis and respiratory diseases},
volume = {},
number = {},
pages = {},
doi = {10.4046/trd.2026.0032},
pmid = {42108955},
issn = {1738-3536},
}

@article {pmid42109051,
year = {2026},
author = {Zhang, L and Che, X and Zhang, X and Sun, X and Wang, Y and Zhang, R},
title = {Fabricating Blackened Jujube Polysaccharide-Zn (II) Complex to Enhance its Anti-Inflammatory Effect: Structural Characterization and Biological Evaluation.},
journal = {Journal of food science},
volume = {91},
number = {5},
pages = {e71128},
doi = {10.1111/1750-3841.71128},
pmid = {42109051},
issn = {1750-3841},
support = {//Central Government Guiding Local Science and Technology Development Fund of Shandong Province, China (YDZX2025029)/ ; //Science & Technology Cooperation Program of Shandong (2025KJHZ017)/ ; //Taishan Industrial Experts Program (TSCY20241184)/ ; //Haoxiangni Health Food Co.,Ltd. Horizontal Research Project (SSH20250428)/ ; //The grants from Key R&D Program of Shandong Province, China (2024TZXD064, CJZBCZGQXTHG02, 2024TZXD015, 2024TZXD007)/ ; },
mesh = {*Polysaccharides/chemistry/pharmacology ; Animals ; *Anti-Inflammatory Agents/chemistry/pharmacology ; *Zinc/chemistry/pharmacology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Ziziphus/chemistry ; Colitis/drug therapy/chemically induced ; Male ; Dextran Sulfate/adverse effects ; *Plant Extracts/chemistry/pharmacology ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Polysaccharides extracted from blackened jujubes (BP) demonstrate remarkable pharmacological activities. Chelation with zinc ions represents an effective strategy for enhancing their biological functions. In this study, a novel polysaccharide-Zn (II) complex derived from blackened jujube (BP-Zn) was successfully synthesized, and its structural characteristics as well as anti-inflammatory effects were comprehensively evaluated in a dextran sulfate sodium (DSS)‑induced colitis model. The results indicated that -OH and -COOH groups in BP interacted with zinc ions through ligand bonds. Zinc chelation enhances the structural stability and molecular properties of BP. The BP-Zn complex demonstrated significant anti-inflammatory properties by a reduction in body weight loss, an increased thymus index, and the restoration of intestinal barrier integrity. Furthermore, microbiome analysis revealed that the BP-Zn complex modulated the gut microbiota, boosting beneficial bacteria while inhibiting pathogenic species. Metabolomic profiling demonstrated that BP-Zn modulated key metabolic pathways involved in inflammation and immune regulation, particularly amino acid and flavonoid metabolism. These results suggested that BP-Zn complex has strong potential as natural anti-inflammatory agents.},
}

*Polysaccharides/chemistry/pharmacology
Animals
*Anti-Inflammatory Agents/chemistry/pharmacology
*Zinc/chemistry/pharmacology
Mice
Gastrointestinal Microbiome/drug effects
*Ziziphus/chemistry
Colitis/drug therapy/chemically induced
Male
Dextran Sulfate/adverse effects
*Plant Extracts/chemistry/pharmacology
Mice, Inbred C57BL
Disease Models, Animal

@article {pmid42109217,
year = {2026},
author = {Tsaousis, AD and Gentekaki, E and Al, FD},
title = {Blastocystis and chronic urticaria: the evidence reviewed does not justify routine testing or treatment.},
journal = {Journal of medical microbiology},
volume = {75},
number = {5},
pages = {},
pmid = {42109217},
issn = {1473-5644},
mesh = {Humans ; *Chronic Urticaria/parasitology/diagnosis/drug therapy ; *Blastocystis Infections/diagnosis/drug therapy/complications/parasitology ; *Blastocystis/isolation & purification ; Diagnostic Tests, Routine ; Feces/parasitology ; Prevalence ; },
abstract = {Ulusan Bagci et al. propose Blastocystis spp. as a hidden cause of chronic urticaria and suggest routine stool testing and treatment in positive cases. We argue that this conclusion is not supported by the current evidence, which is dominated by heterogeneous diagnostics, cross-sectional prevalence comparisons prone to misclassification and non-randomized treatment-response reports lacking clearance-linked endpoints. We outline minimum standards for interpretable inference, including quantitative detection, longitudinal sampling and trials linking confirmed clearance vs. persistence to validated urticaria outcomes.},
}

Humans
*Chronic Urticaria/parasitology/diagnosis/drug therapy
*Blastocystis Infections/diagnosis/drug therapy/complications/parasitology
*Blastocystis/isolation & purification
Diagnostic Tests, Routine
Feces/parasitology
Prevalence

@article {pmid42109313,
year = {2026},
author = {Duval, H and Knox, K and Fairfield, H and Chai, RC and Corr, AP and Qiang, YW and Belknap, K and Abayomi, K and Schimelman, A and Nestor, B and Karam, M and Jachimowicz, E and Stohn, PJ and Guan, X and Lynes, MD and Hamidi, H and Croucher, PI and Ryzhov, S and Reagan, MR},
title = {Microenvironmentally derived fatty acid-binding proteins 4 and 5 are novel therapeutic vulnerabilities in multiple myeloma.},
journal = {Blood neoplasia},
volume = {3},
number = {2},
pages = {100229},
pmid = {42109313},
issn = {2950-3280},
abstract = {Multiple myeloma (MM) is an incurable cancer of monoclonal plasma cells. Despite its dependency on the bone marrow (BM), therapies targeting the BM microenvironment are lacking, barring immunotherapies. Obesity is associated with worse outcomes in MM, and although antiobesity treatments may benefit patients with MM, this is not yet known. Moreover, those treatments have side effects, and their specific mechanisms of action are elusive because of the interconnectedness of obesity, metabolic syndrome, diet, fiber intake, gut microbiome, inflammation, and the immune system. Fatty acid-binding proteins (FABPs) play a role in obesity and other diseases, but no studies of microenvironmentally derived FABPs' effects on cancer progression exist. Therefore, we tested the hypothesis that microenvironmentally derived FABPs support MM progression using single-cell sequencing data, in vivo models, and MM Research Foundation Relating Clinical Outcomes in MM to Personal Assessment of Genetic Profile data. We found that global Fabp4/Fabp5 double-knockout (Fabp4/5 [dKO]) mice have modifications in body composition, immune cells, and skeletal parameters. Murine myeloma cell (Vk12598) engraftment and growth (tumor incidence) were higher in wild-type (WT) vs Fabp4/5 [dKO] mice. High-fat diet-fed Fabp4/5 [dKO] mice were further protected from metabolic and skeletal diseases, and tumor incidence was reduced, whereas survival was increased in Fabp4/5 [dKO] vs WT mice. Finally, low FABP5 expression in granulocyte-monocyte progenitors, typically considered immunosuppressive, is associated with improved survival of patients with MM, implicating reduced immunosuppression and improved immune-mediated tumor eradication as one mechanism of action. Overall, the data suggest that tumor-extrinsic FABP4/5 support MM progression, which, combined with previous myeloma cell-intrinsic findings, suggests targeting FABP4/5 may cause a 2-pronged attack in MM.},
}

@article {pmid42109325,
year = {2026},
author = {Murella, S and Kaur, H and Gunti, V and Polakala, T and Kanani, R and Juttu, GK},
title = {Breaking the habit: Evidence-based approaches to smoking cessation.},
journal = {Bioinformation},
volume = {22},
number = {2},
pages = {800-805},
pmid = {42109325},
issn = {0973-2063},
abstract = {Smoking is a major public health concern that significantly impacts the oral cavity, the primary site of exposure. Tobacco consumption has been linked to conditions such as leukoplakia, oral cancer and impaired wound healing and severe periodontal disease. At the same time, vaping disrupts the oral microbiome and compromises implant stability, both influenced by social, economic, behavioral and political determinants. Evidence suggests that multicomponent interventions, including dental-based programs combined with community initiatives, behavioral strategies such as Motivational Interviewing and the 5Rs framework and pharmacotherapies such as varenicline, bupropion or NRTs are essential for improving cessation outcomes and reducing tobacco-related oral health risks. Thus, we show the consequences of conventional smoking and vaping on oral tissues, periodontal structures, sensory perception, dental implants and saliva.},
}

@article {pmid42109673,
year = {2026},
author = {Srivastava, K and Srivastava, R},
title = {Explainable deep learning approaches and clinical insights for cancer biomarker identification.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1810793},
pmid = {42109673},
issn = {2234-943X},
abstract = {Biomarkers play a pivotal role in contemporary cancer immunotherapy by guiding diagnosis, patient stratification, therapeutic decision-making, and longitudinal assessment of treatment responses. Despite the transformative impact of immune checkpoint inhibitors, adoptive cell therapies, and neoantigen-based vaccines, durable clinical benefit is achieved in only a subset of patients, highlighting the critical need for accurate predictive and prognostic biomarkers. Technological advances are rapidly expanding the biomarker repertoire through high-resolution approaches such as single-cell and spatial omics, circulating tumor DNA analysis, immune-related gene expression signatures, and microbiome profiling. These platforms enable deeper characterization of immune dynamics, resistance mechanisms, and therapeutic responsiveness. Recent advances in artificial intelligence, machine learning, and deep learning have fundamentally reshaped immunotherapy biomarker discovery by enabling the integration of complex, high-dimensional multiomics, radiomic, and clinical datasets into unified predictive frameworks. Deep learning models have demonstrated superior performance in predicting immune checkpoint inhibitor responses, immune-related adverse events, and mechanisms of therapeutic resistance across multiple cancer types. The incorporation of explainable AI approaches further enhances clinical interpretability by linking algorithmic predictions to biologically validated immune processes. Future progress will depend on multimodal biomarker integration, analytical standardization, and rigorous prospective validation, alongside addressing regulatory, economic, and implementation challenges to advance precision cancer immunotherapy.},
}

@article {pmid42109721,
year = {2026},
author = {Zhu, Y and Li, Y},
title = {Gut microbiota in perimenopausal atherosclerosis: the estrogen-gut-vascular axis and personalized cardiovascular prevention.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1815352},
pmid = {42109721},
issn = {1664-2392},
mesh = {Humans ; *Perimenopause/metabolism ; *Gastrointestinal Microbiome/physiology ; Female ; *Estrogens/metabolism ; *Atherosclerosis/prevention & control/microbiology/metabolism ; Precision Medicine ; *Cardiovascular Diseases/prevention & control ; },
abstract = {The risk of atherosclerosis rises markedly in perimenopausal women. The observed discrepancy between the traditional "estrogen cardioprotection hypothesis" and the complex effects of hormone replacement therapy in clinical practice suggests the existence of intermediary mechanisms that are not yet fully understood. Recent research indicates that the gut microbiota may play a pivotal role in this "estrogen paradox". By integrating current evidence, this review systematically elucidates the core driving function of the "estrogen-gut-vascular axis" in disease progression: declining estrogen levels lead to intestinal barrier dysfunction and associated imbalances in microbial metabolites (e.g. reduced short-chain fatty acids and increased pro-inflammatory metabolites), collectively accelerating atherogenesis. Targeting this axis through dietary modification, microbial therapeutics, and precision hormone interventions may break this pathological cycle. Notably, effective nutritional strategies must consider food matrix, individual microbial metabolic capacity, and timing of intervention. Furthermore, building on extensive research into age-related shifts in gut microbiota, this review proposes the novel concept of 'gut microbial age' based on functional metabolic profiles, to quantify the functional state of host-microbiome interactions. This concept aims to provide new perspectives and tools for personalized cardiovascular risk assessment and precise intervention in perimenopausal women.},
}

Humans
*Perimenopause/metabolism
*Gastrointestinal Microbiome/physiology
Female
*Estrogens/metabolism
*Atherosclerosis/prevention & control/microbiology/metabolism
Precision Medicine
*Cardiovascular Diseases/prevention & control

@article {pmid42110058,
year = {2026},
author = {Gomez, AM and Palencia, CJ},
title = {Granulomatosis With Polyangiitis Unmasked by COVID-19 Infection: A Case Report.},
journal = {Cureus},
volume = {18},
number = {4},
pages = {e106729},
pmid = {42110058},
issn = {2168-8184},
abstract = {Granulomatosis with polyangiitis (GPA) is a type of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), in which small- to medium-sized vessels are targeted. The incidence increases with age, and the most commonly affected systems include the sinonasal tract, lungs, and kidneys. Etiology remains unclear, although exposure to environmental triggers, including infections, has been hypothesized to initiate or unmask autoimmunity in genetically predisposed individuals. The nasal microbiome is also hypothesized to play a role in the disease process, although research is still ongoing. In this report, we present a case of a 65-year-old female with a long history of nonspecific musculoskeletal, sinus, and gastrointestinal complaints, who developed multifocal pneumonia with hemoptysis and progressive pulmonary disease shortly after COVID-19 infection.},
}

@article {pmid42110391,
year = {2026},
author = {Mazic de Sonis, A and Granger, C},
title = {Non-pharmacological pain treatments as neuro-epigenetic revalidation strategies: integrating chronobiology, acupuncture, and pharmaco-nutrition.},
journal = {Frontiers in pain research (Lausanne, Switzerland)},
volume = {7},
number = {},
pages = {1786367},
pmid = {42110391},
issn = {2673-561X},
abstract = {BACKGROUND: Chronic pain is increasingly conceptualized as a disorder of maladaptive neural plasticity sustained by central sensitization, neuroinflammation signalling, disrupted biological rhythms, metabolic dysregulation and environmentally mediated epigenetic modulation, and altered gut-brain interactions. While pharmacological approaches remain central to pain management, their long-term efficacy is limited by tolerance, adverse effects, opioid-induced hyperalgesia, and inter-individual variability. Growing evidence suggests that non-pharmacological interventions may modulate pain not only symptomatically, but through deeper neurobiological and epigenetic mechanisms.

HYPOTHESIS: We propose that selected non-pharmacological pain treatments, particularly chronobiology-informed acupuncture and targeted pharmaco-nutrition, may be considered as neuro-epigenetic revalidation strategies. These interventions may restore adaptive gene expression profiles and neural, immune, metabolic and circadian regulation disrupted in chronic pain, thereby reducing nociceptive sensitization and improving treatment responsiveness.

RATIONALE: Acupuncture has been shown to modulate central pain networks, including prefrontal, limbic, and sensorimotor regions, with effects distinct from sham procedures. Chronobiological regulation of sleep-wake cycles, hormonal rhythms, and feeding timing influences inflammatory pathways and epigenetic regulation. In parallel, the gut-brain axis, through intestinal barrier integrity, microbiome composition, and immune-glial signalling, plays a critical role in pain chronification and drug metabolism. Nutritional and nutraceutical interventions can influence these pathways and have been associated with changes in inflammatory tone, opioid tolerance, and neuroimmune interactions.

TESTABLE PREDICTIONS: This framework generates testable predictions linking multimodal interventions to dynamic modulation of epigenetic signatures (DNA methylation, microRNA expression), chronobiological and sleep parameters, inflammatory mediators, gut-brain markers and clinically meaningful outcomes. Longitudinal, multimodal study designs are required to evaluate association between regulatory recalibration and sustained clinical improvement.

CONCLUSION: Viewing non-pharmacological pain treatments within a neuro-epigenetic revalidation model provides a coherent system-level perspective model that bridges neuroscience, chronobiology, epigenetics, and integrative pain medicine. This integrative model supports the development of personalized, mechanism-based strategies for chronic pain management while encouraging biomarker-informed translational research.},
}

@article {pmid42110445,
year = {2026},
author = {Carrouel, F and Kanoute, A and Faye, D and Rhanoui, M and Lan, R and Bourgeois, D},
title = {Oral prophylaxis for the reduction of interdental dysbiosis-associated red complex pathogens during pregnancy: a randomized clinical trial.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1798508},
pmid = {42110445},
issn = {2296-858X},
abstract = {INTRODUCTION: Periodontal disease during pregnancy is associated with adverse outcomes such as preterm birth, low birth weight, and preeclampsia. Socransky's red complex pathogens including Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, are key risk factors for these complications. This study aims to evaluate whether daily use of calibrated interdental brushes, in addition to conventional tooth brushing, reduces the bacterial load these pathogens in pregnant women.

METHODS: A randomized controlled trial was conducted in six obstetric clinics in Senegal between March 2022 and January 2023. One hundred pregnant women, aged 18-40 and in their third month of pregnancy, were randomized into a test group using interdental brushes plus tooth brushing and a control group using tooth brushing alone. The outcome was the change in bacterial load from the third to eighth month of pregnancy, quantified using real-time polymerase chain reaction techniques.

RESULTS: By the eighth month, the test group demonstrated a statistically significant reduction in total bacterial load compared to the control group, with a mean reduction of 36.6% (95% CI: 31.2-41.1%, p < 0.001). Notably, T. denticola load decreased by 92.1% (95% CI: 87.1-95.6%, p < 0.001) in the test group, while it increased in the control group. Reductions were also observed for P. gingivalis and T. forsythia, although these differences were not statistically significant (p = 0.061 and p = 0.148, respectively).

DISCUSSION: These findings suggest that adding calibrated interdental brushes to a conventional tooth brushing routine is more effective in lowering the bacterial load of harmful red complex pathogens in pregnant women.

CONCLUSION: The results support the inclusion of interdental cleaning in prenatal oral health care guidelines as a strategy for managing periodontal risk during pregnancy.},
}

@article {pmid42110460,
year = {2026},
author = {Wu, F and Chen, Y and Ni, X and Yi, T and Tan, S},
title = {The oral-gut-liver axis: linking periodontal microbiota to the pathogenesis of liver diseases.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1810114},
pmid = {42110460},
issn = {2296-858X},
abstract = {Oral microbiota plays a critical role in linking oral and systemic health, with dysbiosis closely associated with the onset and progression of chronic liver diseases. This review systematically examines the central role of the "oral-gut-liver axis" in hepatic pathophysiology. Epidemiological evidence has identified periodontitis and specific oral pathogens, such as Fusobacterium nucleatum (F. nucleatum), as independent risk factors for the progression of non-alcoholic fatty liver disease (NAFLD), development of cirrhosis, and incidence of hepatocellular carcinoma (HCC). The underlying mechanisms primarily involve four interrelated pathways: (1) direct bacterial translocation, where pathogens such as F. nucleatum colonize the liver via bacteremia and activate oncogenic pathways; (2) systemic dissemination of bacterial metabolites, such as lipopolysaccharides (LPS), driving hepatic inflammation, oxidative stress, and fibrosis via Toll-like receptor 4 (TLR4) signaling and reactive oxygen species (ROS)-mediated pathways; (3) systemic immune inflammation, wherein periodontitis acts as a chronic inflammatory focus that continuously releases pro-inflammatory mediators into the circulation; and (4) indirect effects mediated by gut microbiota dysbiosis, whereby oral bacteria compromise the intestinal barrier, facilitating the influx of gut-derived toxins into the liver. These findings underscore the significant impact of oral health on hepatic status. In the short term, oral microbial profiles represent promising noninvasive diagnostic and prognostic biomarkers. Preliminary clinical trials indicate that periodontal therapy can improve metabolic parameters in patients with NAFLD. In the long term, promoting interdisciplinary collaboration between hepatology and oral medicine and strategically integrating oral health interventions into the comprehensive management framework for liver diseases hold significant public health potential for mitigating the global burden of hepatic disorders.},
}

@article {pmid42110505,
year = {2026},
author = {Li, J and Zhang, H and Zhang, P and Hu, J},
title = {Potential Benefits of Gut Microbiota Modulation in Chronic Obstructive Pulmonary Disease.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {21},
number = {},
pages = {594405},
pmid = {42110505},
issn = {1178-2005},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy/physiopathology/metabolism ; Animals ; Humans ; *Dysbiosis/therapy ; Disease Models, Animal ; *Lung/physiopathology/microbiology/metabolism/pathology ; *Fecal Microbiota Transplantation ; Male ; Mice, Inbred C57BL ; Metabolomics/methods ; Anti-Bacterial Agents ; Female ; *Bacteria/genetics/metabolism/drug effects/growth & development/classification ; Middle Aged ; Ribotyping ; Aged ; Case-Control Studies ; Mice ; RNA, Ribosomal, 16S/genetics ; T-Lymphocytes, Regulatory/immunology/metabolism ; },
abstract = {BACKGROUND: The gut-lung axis is increasingly recognized. This study aimed to find out whether and how the gut microbiome involved in the pathogenesis of chronic obstructive pulmonary disease (COPD).

METHODS: Gut microbiota was characterized via 16S rRNA gene sequencing in COPD patients and a smoking-induced mouse model. Gut dysbiosis was induced by antibiotic cocktail (ABX) and restored by fecal microbiota transplantation (FMT). Plasma metabolomics was conducted using liquid chromatography-mass spectrometry (LC-MS), and pathway analysis was performed with MetaboAnalyst 5.0. Differentially expressed genes were identified by RNA sequencing and functionally interpreted through gene set enrichment analysis (GSEA).

RESULTS: Both COPD patients and mice showed altered gut microbiota, characterized by a unique microbial composition and reduced diversity. ABX induced gut dysbiosis exacerbated pathological lung changes, impaired lung function, and promoted Treg cell exhaustion in COPD mice. Restoration of gut homeostasis via FMT attenuated these alterations. Higher plasma levels of acetylcholine (ACh) were observed in COPD mice, while the highest ACh levels were found in ABX treated COPD mice compared to controls. Notably, ACh levels correlated positively with genus Parasutterella, which was more abundant in COPD mice, and inversely with genera Candidatus Saccharimonas and Lactobacillus, which were predominant in control mice. Metabolomic pathways analysis revealed enrichment in unsaturated fatty acids biosynthesis and purine metabolism in COPD mice relative to controls.

CONCLUSION: These findings highlight the involvement of the gut microbiome in COPD development and suggest that maintaining gut homeostasis may represent a novel therapeutic strategy for COPD.},
}

*Gastrointestinal Microbiome/drug effects
*Pulmonary Disease, Chronic Obstructive/microbiology/therapy/physiopathology/metabolism
Animals
Humans
*Dysbiosis/therapy
Disease Models, Animal
*Lung/physiopathology/microbiology/metabolism/pathology
*Fecal Microbiota Transplantation
Male
Mice, Inbred C57BL
Metabolomics/methods
Anti-Bacterial Agents
Female
*Bacteria/genetics/metabolism/drug effects/growth & development/classification
Middle Aged
Ribotyping
Aged
Case-Control Studies
Mice
RNA, Ribosomal, 16S/genetics
T-Lymphocytes, Regulatory/immunology/metabolism

@article {pmid42110624,
year = {2026},
author = {Liu, Z and Liu, Z and Sun, W and Zhu, L and Lyu, T},
title = {Causal association between oral microbiome and chronic kidney disease: two-sample Mendelian randomization.},
journal = {Archives of medical science : AMS},
volume = {22},
number = {1},
pages = {377-386},
pmid = {42110624},
issn = {1734-1922},
abstract = {INTRODUCTION: Chronic kidney disease (CKD) contributes to 1.2 million deaths annually. Oral dysbiosis may influence CKD, highlighting the need for further research on its role as a risk factor and preventive target.

MATERIAL AND METHODS: We obtained summary statistics for genome-wide association studies (GWAS) of the oral microbiome from the GWAS Catalog and CKD from the CKDGen Consortium. Inverse variance weighting (IVW) was used as the principal analysis method, supplemented by MR-Egger, weighted median, and weighted mode to assess causal relationships. Sensitivity analyses, including MR-PRESSO and Cochran's Q, validated the robustness of the results.

RESULTS: The IVW results showed that Veillonella species was causally associated with CKD (OR = 0.96, 95% CI (0.93-0.99)), Order Fusobacteriales (OR = 1.01, 95% CI (1-1.01)) and Rothia species (OR = 0.99, 95% CI (0.99-1)) were causally associated with urinary albumin-to-creatinine ratio (UACR); Order Bacteroidales (OR = 0.97, 95% CI (0.94-1)) and Species micronuciformis (OR = 0.95, 95% CI (0.91-0.99)) were causally associated with CKDi25; and Streptococcus species was causally associated with dialysis (OR = 0.82, 95% CI (0.69-0.97)). There was no significant causal association between other oral microbiome features and CKD at the genetic level. Sensitivity analysis indicated that the results were robust.

CONCLUSIONS: Our study suggests that there are associations between the oral microbiome and CKD. To better understand its mechanism of action and to develop broader strategies for preventing chronic kidney disease, further research is required.},
}

@article {pmid42110715,
year = {2026},
author = {Rumão, MS and Andrade, MT and Costa, RJ and Santana, GJ and Cerqueira, JPC and Lima, GSO and Garcia, NC and Heller, D and Espinosa, CN and Arantes, RME and Moraes, MM and Mendes, TT},
title = {Human Microbiome Alterations in Antarctic Isolated, Confined, and Extreme (ICE) Environments: A Systematic Review and Meta-Regression.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {3405549},
pmid = {42110715},
issn = {1687-918X},
abstract = {Antarctica is one of the most extreme and isolated environments on Earth, serving as a natural laboratory for studying human physiological and microbial adaptation under stress. This systematic review and meta-regression evaluated how exposure to Antarctica's isolated, confined, and extreme (ICE) environments impacts the human microbiome, considering environmental and behavioral factors that may modulate these alterations. Following PRISMA guidelines and being registered with PROSPERO (CRD42024558423), comprehensive searches were conducted in PubMed, Scopus, Embase, Cochrane, and LILACS without language or date restrictions. Seven studies conducted between 2014 and 2024, enrolling 77 healthy participants in total, investigated oral, gut, or skin microbiota changes under Antarctica's ICE conditions at field camps, research stations, or shipboard environments. The findings suggest that ICE environments could induce measurable changes in microbial composition, relative abundance, and diversity across gut, oral, and skin sites, with age, type of accommodation, and sampling site emerging as significant predictors. Specifically, older individuals and those stationed at research bases exhibited greater odds of microbial alterations, while the gut microbiota showed greater stability compared to skin and oral sites. Although some studies explored the effects of probiotic supplementation and physical activity as modulators, evidence remains limited. The review highlights that environmental stressors such as confinement, duration of stay, extreme climate, diet, and physical exertion may collectively influence microbiome dynamics. These findings highlight the influence of age, accommodation type, and sampling site on microbial shifts in ICE environments, while underscoring the need for standardized longitudinal studies to clarify the biological and operational relevance of these changes.},
}

@article {pmid42110826,
year = {2026},
author = {Garcia, BA and Dornelas-Figueira, LM and Katrak, C and Roesch, LFW and Tomar, SL and Adams, G and Oliveira, D and Nascimento, MM and Abranches, J},
title = {Co-infection with Cbp[+] Streptococcus mutans and Candida albicans is associated with root caries in older adults.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2667029},
pmid = {42110826},
issn = {2000-2297},
abstract = {BACKGROUND: Gingival recession increases with age, exposing root surfaces and raising susceptibility to root caries. As the global population ages, root caries prevalence is expected to rise, underscoring the need to better understand its risk factors.

OBJECTIVE: To investigate the association between co-infection with Cbp[+] Streptococcus mutans and Candida albicans and root caries in older adults with gingival recession, while characterizing the root plaque microbiome and evaluating multifactorial risk factors.

DESIGN: This cross-sectional study included 117 adults ≥65 years; 56 with root caries and 61 without. Saliva and site-specific supragingival plaque samples were collected to assess Mutans streptococci and Candida spp., along with microbiome composition. Demographic, behavioral, biological, dental, and medical factors were also evaluated.

RESULTS: Participants with root caries had higher salivary levels of Mutans streptococci and Candida spp. (p = 0.0122 and p = 0.0013). Co-infection with Cbp[+] S. mutans and C. albicans was significantly associated with root caries (p = 0.0003). Microbiome analysis showed enrichment of Capnocytophaga leadbetteri in diseased root surfaces. Individuals with root caries were more likely to report xerostomia and less likely to use an electric toothbrush or floss daily.

CONCLUSIONS: These findings highlight microbial and behavioral factors associated with root caries, offering insights into potential prevention and management strategies.},
}

@article {pmid42110914,
year = {2026},
author = {Zhao, YQ and Kuang, BF and Dusenge, MA and Liu, Q and Zhang, FY and Zhou, YH},
title = {Sex-specific variations in subgingival microbiome of elderly patients with moderate periodontitis: an exploratory study.},
journal = {Frontiers in genetics},
volume = {17},
number = {},
pages = {1791446},
pmid = {42110914},
issn = {1664-8021},
abstract = {INTRODUCTION: Periodontitis, a leading cause of alveolar bone destruction and tooth loss, is associated with oral microbiota dysbiosis and shows higher susceptibility in males than in females. This study investigated sex-specific variations in the subgingival microbiome of elderly patients with moderate periodontitis.

METHODS: Subgingival plaque samples were collected from 25 patients with moderate periodontitis (8 males, 17 females; aged 50-73 years). The microbial composition was analyzed using 16S rRNA gene sequencing (V3-V4 region). Functional prediction was conducted utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

RESULTS: Males exhibited higher Chao1 diversity, and beta diversity analysis revealed sex-based clustering. Wilcoxon rank-sum tests and LEfSe analysis identified Lactobacillus was enriched in females. KEGG analysis predicted a trend of enrichment of Immune system and Metabolic pathways in females.

CONCLUSION: This exploratory study observed sex-specific subgingival microbiome variations of elderly patients with moderate periodontitis. Females exhibited specific enrichment of Lactobacillus, which may be associated with predicted Immune system and Metabolic pathways. These findings suggest that sex-specific microbiome differences may be a relevant biological variable in future periodontitis research, and their potential link to alveolar bone loss deserves further exploration.},
}

@article {pmid42110957,
year = {2026},
author = {Skidmore, AM and Goodfellow, SM and Nofchissey, RA and Jiang, L and Dunnum, J and Cook, JA and Guo, Y and Mali, I and Bradfute, SB},
title = {Characterization of the gut microbiome of wild Peromyscus sonoriensis in New Mexico, USA.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1672092},
pmid = {42110957},
issn = {2813-4338},
abstract = {The microbiome is highly important to the physiologies of all multicellular organisms, particularly metazoans. However, the microbiomes of many wild animals remain understudied and poorly understood. Peromyscus mice are commonly used as models of adaptation, mental health, and human disease in biomedical research, and are also common in the environment across North America, frequently coming into close contact with humans. Additionally, Peromyscus sonoriensis are implicated as the primary reservoir for Sin Nombre hantavirus, a rare but severe disease of high morbidity and mortality in humans. Here we characterize the fecal microbiomes of 311 Peromyscus sonoriensis, the western deer mouse, collected from across New Mexico, USA, which will further their usefulness as models of disease and behavior as well as increase our understanding of their ecology. The animals used in this study are geographically diverse, collected from multiple ecoregions, and encompass mice of all ages and sexes. We sequenced the entire 16S rRNA gene in a PCR independent approach and characterized the microbiomes with Shannon entropy, Faith phylodiversity, and weighted UNIFRAC. We found that these mice have diverse microbiomes, with individuals varying in the presence and proportions of various identified bacteria. We analyzed the total population of mice according to age, sex, and trapping location, and found that trapping location was the only condition to significantly impact the microbiome. When the mice were subdivided by the location of collection, there were mild effects of age and sex. When comparing mice from archival museum storage, storage of samples in 95% ethanol resulted in significant alterations to the microbiome when compared to cryopreservation. Differential bacterial family presence was determined using ANCOMBC at the 0.05 significance threshold, and there were many differentially abundant families across all groups of mice. This data set can now be used as a reference for further research into the microbiomes of related Peromyscus species, enhance the use of P. sonoriensis as model laboratory animals, and as a source of novel research questions regarding the physiology of these rodents.},
}

@article {pmid42111177,
year = {2026},
author = {Liu, X and Wen, C and Gu, S and Hao, Y and Xiong, Y and Chen, C and Zeng, S and Zhang, P},
title = {Gut microbial-host isozymes: A novel perspective on gut microbiota-host interactions.},
journal = {iScience},
volume = {29},
number = {5},
pages = {115226},
pmid = {42111177},
issn = {2589-0042},
abstract = {The interaction between gut microbiota and host health has garnered significant attention since its initial discovery. Dysbiosis of the gut microbiota is implicated in various diseases, particularly metabolic disorders such as diabetes, as well as neuro-, cardiovascular-, and hepatic-metabolic diseases. In recent years, the concept of microbial-host isozymes (MHIs) has emerged as a novel research area within the microbiome field. These enzymes, encoded by intestinal microbiota, can replicate the functions of host enzymes and contribute to disease development, presenting potential new therapeutic targets. In this review, we examine the current understanding of the discovery, function, and potential applications of MHIs. We summarize the distribution and functional enrichment of identified MHIs, provide examples of MHI-targeted interventions aimed at optimizing diabetes treatment, and discuss existing challenges and future research directions in this area.},
}

@article {pmid42111183,
year = {2026},
author = {Rastelli, E and Tangherlini, M and Corinaldesi, C and Dell'Anno, A and Lo Martire, M and Giorgetti, A and De Luca, P and Bakran-Petricioli, T and Kipson, S and Pajusalu, L and Rinde, E and Tunka Bengil, EG and Tüney, İ and Danovaro, R},
title = {Seagrasses host unique and vulnerable microbiomes, structured by inter-domain microbial interactions.},
journal = {iScience},
volume = {29},
number = {5},
pages = {115757},
pmid = {42111183},
issn = {2589-0042},
abstract = {Seagrass meadows are vital for coastal ecosystems but are declining worldwide due to human impacts. Microbes play key roles in seagrass health, yet their diversity and functions remain poorly understood. We investigated prokaryotes and microbial eukaryotes associated with different seagrass species across multiple regions by analyzing leaves, roots, and surrounding sediments. Microbiome similarity was minimal among seagrass and sediments (<5% shared small subunit (SSU|)-rRNA amplicon sequence variants -ASVs), among species (<2%), and between leaves and roots within species (<12%). Seagrass species, rather than environmental factors, primarily shaped microbiome composition. Network analysis revealed all seagrass microbiomes as highly vulnerable to the loss of keystone microbes, including bacterial taxa potentially supporting seagrass health through nutrient supply and detoxification processes. Although microbial eukaryotes have been traditionally linked to seagrass diseases, we found mostly positive interactions with keystone bacteria, suggesting overlooked roles in holobiont stability. These findings provide a benchmark for integrating microbiomes into seagrass conservation.},
}

@article {pmid42111202,
year = {2026},
author = {Abrahamsson, T and Wejryd, E and Pujolassos, M and Calle, ML and Sverremark-Ekström, E and Jenmalm, MC and Martí, M},
title = {Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial.},
journal = {iScience},
volume = {29},
number = {5},
pages = {115802},
pmid = {42111202},
issn = {2589-0042},
abstract = {Preterm birth is associated with a high risk of long-term neurological deficits. Although research underscores the role of the gut microbiome in the gut-brain axis, the mechanisms of neurodevelopmental impairment remain elusive. In this prospective observational study (PROPEL), we evaluated whether early gut microbiota development and Limosilactobacillus reuteri supplementation to extremely preterm infants with extremely low birth weight (EPT-ELBW) are associated with neurodevelopment at 2 years. Gut microbiota was characterized by 16S sequencing, and neurodevelopment was assessed by Bayley-III score. Microbiota composition constellations and lower microbial diversity, but not single bacteria, are associated with impaired neurodevelopment. Microbial maturation over the first month was discriminative for motor development, with higher abundance of E. coli and Enterococcus relative to Cutibacterium associated with impairment. L. reuteri supplementation did not seem to affect neurodevelopment via the gut microbiome. In conclusion, dynamics of gut microbiota maturation during early life may impact neurodevelopment in EPT-ELBW infants.},
}

@article {pmid42111290,
year = {2026},
author = {Serrana, JM and Tian, R and Nascimento, FJA and Broman, E and Dessirier, B and Posselt, M},
title = {Pollutant biodegradation profile mediated by multi-trophic microbial dynamics in rivers.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag089},
pmid = {42111290},
issn = {2730-6151},
abstract = {Microbial communities and environmental conditions are closely linked to ecosystem functions and directly govern the biodegradation of pollutants in aquatic environments. However, the role of multi-trophic interactions and their spatiotemporal dynamics in these processes remains poorly understood. Here, we examined how seasonal and spatial variations, mediated by trophic interactions within benthic microbial communities, influence their composition, functional capacity, and collective potential to degrade a diverse array of organic pollutants in rivers. By characterizing both prokaryotic (i.e. archaea and bacteria) and eukaryotic taxa (i.e. algae, fungi, protists, and metazoans), and inferring metabolic pathways, we explored the connections between community composition and pollutant degradation in wastewater-receiving rivers across four seasons. Mediation analysis revealed that variation in multi-trophic community structure statistically mediates the total effect of environmental factors on the biodegradation profiles of 96 organic pollutants, with prokaryotic communities explaining 60% of the total environmental influence. Eukaryotic groups also showed significant indirect mediation effects, with fungal, protistan, algal, and metazoan communities accounting for 56%, 53%, 26%, and 38% of the mediated effect, respectively. Across the two rivers studied, spatial variation explained more of the variance in community composition than seasonality did over the sampled year. Together, these results provide ecosystem-level insights into how multi-trophic microbial community organization is associated with pollutant biodegradation potential in dynamic river environments and support the development of predictive frameworks for sustainable water management.},
}

@article {pmid42111291,
year = {2026},
author = {Marcos, S and Odriozola, I and Aizpurua, O and Eisenhofer, R and Mak, SST and Martin-Bideguren, G and Kale, V and Baldi, G and Richardson, LJ and Finn, RD and Tarradas, J and Estonba, A and Gilbert, MTP and Alberdi, A},
title = {Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag091},
pmid = {42111291},
issn = {2730-6151},
abstract = {The early-life development of the gut microbiome in broiler chickens is a dynamic ecological process with significant implications for host physiology and productivity. Using 388 genome-resolved metagenomic and 61 metatranscriptomic samples across two replicated trials, we analysed the compositional and functional succession of the caecal microbiome in chickens from hatching to slaughter age. We reconstructed 822 bacterial genomes and distilled gene annotations into comprehensive metabolic traits that captured the functional capacities of each genome. We observed that the increase in microbial diversity with chicken age was accompanied by a decline in community-level average metabolic capacity, driven by a shift from metabolically versatile generalists (Lachnospiraceae) to hitherto uncultured, genome-reduced specialists (RF39, RF32, and UBA1242). However, the specific identity of the dominant genome-reduced specialists varied among individuals, resulting in contrasting associations with host body weight. At slaughter age, only 10 UBA660 (RF39) bacteria were positively associated with body weight, while other genome-reduced lineages, such as UBA1242 (Christensenellales), were among 190 negatively associated bacteria. Gene expression analyses revealed that despite their reduced functional repertoire, UBA660 exhibited greater metabolic activity than UBA1242, particularly in the production of two key metabolites for host nutrition and intestinal homeostasis: the essential amino acid lysine and the signaling molecule indole-3-acetate. These findings provide new insights into the functional ecology of the chicken gut microbiome and highlight the relevance of cultivation approaches to retrieve underexplored and uncultured bacterial taxa, which could open new avenues for microbiome-based strategies aimed at improving poultry growth and health in intensive production systems.},
}

@article {pmid42111293,
year = {2026},
author = {Stewart, JD and Klein, M and Jaupitre, S and Oyarte-Galvez, L and Dong, L and Bouwmeester, HJ and Kiers, ET and Kokkoris, V and Weedon, JT},
title = {Root traits correlate with crop rhizosphere microbiome diversity independent of legume relatedness.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag087},
pmid = {42111293},
issn = {2730-6151},
abstract = {Predicting the composition of rhizosphere microbiomes has become increasingly important for sustainable agriculture. A key open question is whether a plant's rhizosphere community is shaped more by the specific traits or host phylogeny, under different soil conditions. We conducted a greenhouse experiment on 15 legume species, including three pairs of crop-wild relative pairs, under different phosphorus conditions. We then sequenced the bacterial and fungal rhizosphere communities. Using Bayesian models, we found rhizosphere composition was shaped by individual species identity, independent of host phylogeny (intraclass correlation = 0.40-0.79). This suggests that closely related plants do not necessarily share similar rhizosphere microbiomes. These patterns remained consistent across host intraspecific variation and nutrient treatments. Using a custom-built root imaging platform, we quantified root architectural traits and applied machine learning to correlate with rhizosphere community composition (R[2] = 0.46-0.80). Root diameter and carbon content were the strongest drivers. Notably, these key root traits were largely uncorrelated with phylogeny, yet strongly explained variation in rhizosphere community composition. Our results indicate that even closely related legume species may host divergent rhizosphere communities.},
}

@article {pmid42111294,
year = {2026},
author = {Yergaliyev, T and Enokela, SO and Eberhardt, G and Flisikowski, K and Hornburg, SC and Reyer, H and Tetens, J and Wimmers, K and Zentek, J and Camarinha-Silva, A},
title = {Toward reproducible pig gut microbiome profiling through standardized methodologies.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag097},
pmid = {42111294},
issn = {2730-6151},
abstract = {Reproducible microbiome profiling is essential for linking microbial communities to host health, yet methodological variation continues to undermine reproducibility across studies. This problem is acute in pig microbiome research, where no standardized DNA extraction protocols exist despite the species' importance in agriculture and biomedicine. Here, we benchmark how 12 widely used extraction kits influence microbiome outcomes in 16S rRNA gene amplicon sequencing and shotgun metagenomics of pig fecal samples. We demonstrate that extraction choice biases 16S rRNA gene datasets, affecting DNA yield, diversity, community composition, and spike-in recovery, whereas metagenomic taxonomy and functional profiles are comparatively robust. Kit-dependent recovery of Gram-positive versus Gram-negative taxa revealed systematic biases with direct consequences for biological interpretation. By integrating spike-in controls, taxonomic resolution, and metagenome-assembled genomes, we establish a framework for evaluating DNA extraction methods in animal microbiome research. Our findings demonstrate that 16S rRNA gene amplicon sequencing is more susceptible to extraction-driven artifacts than metagenomics, highlighting the need for standardized protocols to ensure reproducibility and comparability across pig microbiome studies. Moreover, while shotgun metagenomics was comparatively robust to DNA extraction choice, the number of assembled good-quality metagenome-assembled genomes recovered was strongly dependent on the extraction kit selection.},
}

@article {pmid42111446,
year = {2026},
author = {Zulaika, G and Nordgren, R and Agingu, W and Chaudhary, A and Dibondo, E and Wambua, P and van Eijk, AM and Rusie, L and Naqib, A and Otieno, F and Phillips-Howard, PA and Mehta, SD},
title = {Characterizing the bacterial surface profiles of menstrual cups and their association with user characteristics and vaginal microbiomes in an adolescent cohort from western Kenya.},
journal = {Gates open research},
volume = {10},
number = {},
pages = {25},
pmid = {42111446},
issn = {2572-4754},
mesh = {Humans ; Female ; Kenya ; *Vagina/microbiology ; *Microbiota/genetics ; Adolescent ; *Menstrual Hygiene Products/microbiology ; *Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Menstruation ; Escherichia coli/isolation & purification ; },
abstract = {BACKGROUND: Menstrual cups are increasingly promoted in low-resource settings as long-lasting and cost-effective menstrual hygiene solutions. However, no studies have been done among cup users to characterize the bacterial communities found on cups with long-term use when stored. This study sought to comprehensively characterize the bacterial surface profile of the menstrual cup, identify factors associated with putative pathogens, and quantify the vaginal microbiome as potential source for menstrual cup bacterial communities.

METHODS: Over 30 months of follow-up, 369 menstrual cup samples were collected from 172 secondary schoolgirls participating in a randomized controlled trial in western Kenya. Samples were obtained from cups brought to school by girls during study visits. Menstrual cup and vaginal microbiomes were assessed using 16S rRNA gene amplicon sequencing. Mixed effects models were applied to identify factors associated with putative pathogens (Escherichia coli, Staphylococcus aureus, coliform bacteria), and factors associated with vaginal microbiome as potential source environment to bacterial surface profile of the menstrual cup, estimated via fast expectation-maximization for microbial source tracking (FEAST).

RESULTS: Menstrual cup bacterial surface profile composition was primarily comprised of soil and water bacteria. However, taxa specific to the vaginal microbiome (e.g., Lactobacillus crispatus, L. iners, and Gardnerella vaginalis) were also recovered from cups. The mean relative abundance (presence) of E. coli and S. aureus was 0.09% (36%) and 0.36% (24%), respectively, with higher relative abundance among participants with HSV-2 or non-optimal vaginal community state type 4. Damaged cups were also associated with higher relative abundance of putative pathogens, while antibiotic use was inversely associated with E. coli. On average, 25.1% of cup microbiota originated from the vagina, with lower contributions among older participants and those with damaged cups. No serious adverse events related to the menstrual cup were observed in the cohort.

CONCLUSIONS: Interventions focused on improved cleaning and storage tools and methods, and access to clean water and sanitation infrastructure are required to maximize safety of menstrual cup use in low-resource settings.},
}

Humans
Female
Kenya
*Vagina/microbiology
*Microbiota/genetics
Adolescent
*Menstrual Hygiene Products/microbiology
*Bacteria/genetics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Cohort Studies
Menstruation
Escherichia coli/isolation & purification

@article {pmid42111471,
year = {2026},
author = {Balagoni, S and Evelyne, DG and Mathews, A and Dugyala, RR and Biradar, M and Deekshith, V and Goel, A and Verma, A},
title = {Unveiling the Bidirectional Relationship on the Effect of Gut Microbiota and Female Infertility: A Narrative Review.},
journal = {Health science reports},
volume = {9},
number = {5},
pages = {e72399},
pmid = {42111471},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Dysbiosis is the substitution of the normal gut flora with a dysfunctional array of organisms that influences the outcome of multiple inflammatory pathways, contributing to systemic inflammation and various disease states. It has historically been understudied, with outcomes that may directly or indirectly cause pathologies. This review aims to emphasize the understanding of the effects of dysbiosis on female fertility and various approaches to addressing it.

METHODS: A comprehensive review was conducted using databases such as PubMed, Scopus, Cochrane Library, and Google Scholar, applying search terms like "Dysbiosis", "Female Infertility", "Gut-Brain Axis", "Reproductive Health", "Estrobolome", "Polycystic Ovary Syndrome (PCOS)", and "Endometriosis". Articles published in the English language from January 2007 to April 2025, encompassing original research, systematic reviews, randomized controlled studies, and meta-analyses, were included. Studies not pertinent to therapeutic applications, lacking outcome, or restricted to editorials were excluded.

RESULTS: Gut dysbiosis may be associated with female reproductive disorders (PCOS, endometriosis, ovulatory dysfunction), complications during pregnancy, thyroid dysfunction, and infertility. Altered microbial diversity affects estrogen metabolism, which in turn impacts GnRH, LH regulation, and systemic inflammation. An imbalance in Prevotella and other organisms is correlated with hormonal and metabolic dysregulation, poor oocyte quality, and thus infertility.

CONCLUSION: Gut dysbiosis plays a pivotal role in female reproductive health. The current evidence suggests potential benefits of microbiome modulation therapy, including the use of probiotics or dietary modifications. Many of these studies are observational, small-scale, and use different methodologies, which restrict our scope. So, larger and standardized interventional studies are required to establish the gut microbiome as a viable therapeutic target for female infertility.},
}

@article {pmid42111712,
year = {2026},
author = {Sha, Q and He, Q and Zeng, L and Liu, Y and Luo, L and Zhu, H and Hu, M and Huang, Y and Wu, Y and Wang, Q and Deng, X and Tao, L and Zhang, W and Guan, Y and Yuan, W and Shi, N and Li, Y and Qin, Y and Wang, B and Wang, X},
title = {The soil microbiome and metabolome in concert shape the flavor profile of ancient tea plants from Laowu mountain region.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1797648},
pmid = {42111712},
issn = {1664-462X},
abstract = {INTRODUCTION: Ancient tea plants from small tea-producing areas in Yunnan possess irreplicable flavor characteristics, yet the mechanisms underlying flavor formation remain unclear.

METHODS: This study focused on the core production region of ancient tea plants in the Laowu Mountain Region, including Shahe Village, Hetou Village, and Luojia Village. Differences in tea quality among production regions were analyzed, together with soil physicochemical properties and soil microbial communities, using correlation analysis and amplicon sequencing.

RESULTS: Significant differences in tea quality were observed among different production regions, with catechins, amino acids, and caffeine collectively contributing to these variations. Soil organic carbon, organic matter, and nitrate nitrogen showed significant differences between production regions. Correlation analysis revealed that soil organic carbon was significantly positively correlated with epigallocatechin (EGC) (r > 0.8, P < 0.05), while soil nitrate nitrogen and organic matter were significantly negatively correlated with epicatechin (r < -0.8, P < 0.05). Amplicon sequencing indicated that the dominant bacterial phyla in the soil included Chloroflexi, Acidobacteriota, Proteobacteria, and Actinobacteriota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. Spearman correlation analysis showed that g:Streptomyces was negatively correlated with amino acid metabolites but positively correlated with total amino acids (AA) in tea, whereas amino acid metabolites were negatively correlated with AA. Meanwhile, g:Bacillus was negatively correlated with gibberellin A7 and GA, but positively correlated with EGC, while gibberellin A7 was positively correlated with GA and negatively correlated with EGC.

DISCUSSION: These results shed new light on the mechanisms by which soil microorganisms and metabolites collaboratively shape the flavor compounds of ancient tea plants, while also providing a basis for the soil ecological management of Yunnan ancient tea plants.},
}

@article {pmid42111744,
year = {2026},
author = {Tang, S and Chen, X and Ma, J and Tu, P and Shi, X and Chen, G},
title = {Integrating multi-omics and epiphytic microbial communities to decipher the spatiotemporal dynamics of flower color dynamic regulation in Hibiscus mutabilis.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1803034},
pmid = {42111744},
issn = {1664-462X},
abstract = {The dynamic change of flower color is a key trait for plant environmental adaptation and pollinator attraction, yet its spatiotemporal regulatory mechanisms remain poorly understood. Hibiscus mutabilis L., known for its remarkable diurnal color-changing phenomenon, provides an ideal model for deciphering the dynamic regulation of flower color. This study integrated metabolomics, transcriptomics, and epiphytic microbial community analyzes to systematically compare the spatiotemporal differences between petals and the flower base of H. mutabilis. Metabolomic analysis revealed that differential metabolites between petals and the flower base were primarily enriched in pathways such as glycolysis and glutathione metabolism. Differences between morning and afternoon in the flower base were concentrated in flavonoid biosynthesis and amino acid metabolism pathways. Transcriptomic analysis identified MYB114-like was significantly upregulated in the afternoon, with its expression co-enriched with genes from the plant hormone signaling and MAPK pathways, suggesting it participates in the regulatory mechanism of environmental signal responses. Microbial community analysis showed a significant increase in the relative abundance of Actinomycetota in the flower base from morning to afternoon. Functional prediction suggested that these microbes might be involved in processes such as redox metabolism and nucleotide degradation. This study reveals a multidimensional regulatory network involving metabolism, transcription, and microbes governing the dynamic color change in H. mutabilis, from the perspective of spatial heterogeneity and plant-microbe interactions, providing novel insights into the mechanisms of flower color formation and the adaptability of ornamental plants.},
}

@article {pmid42111748,
year = {2026},
author = {Chowdhary, R and Goyal, MK and Arora, K and Sehgal, T and Dawer, P and Anirudh, FNU and Berinstein, J and Bishu, S and Matt-Amaral, L},
title = {Gut Microbiota and Extraintestinal Cancers: Mechanistic Insights and Microbiome-Targeted Interventions.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {10},
number = {},
pages = {e70409},
pmid = {42111748},
issn = {2397-9070},
abstract = {The gut microbiota is a dynamic community of bacteria, viruses, fungi, and archaea that plays a pivotal role in regulating host immunity, metabolism, and systemic homeostasis. Dysbiosis, characterized by an imbalance in the microbial composition, is being increasingly recognized as a contributor not only to gastrointestinal cancers but also to extraintestinal malignancies. Mechanistic studies highlight the gut-microbiota-cancer axis, where microbial metabolites such as bile acids, short-chain fatty acids (SCFAs), and tryptophan derivatives influence genetic, epigenetic, and immune pathways, influencing carcinogenesis. Germ-free models demonstrate that commensal signals are essential for CD4[+] and CD8[+] T-cell differentiation, IgA production, and anti-tumor immunity. Dysbiosis-induced immune dysregulation is believed to impair immune checkpoint inhibitor (ICI) efficacy, while specific taxa such as Bifidobacterium and Akkermansia have been shown to enhance therapeutic responses. Emerging evidence links gut microbiota to breast cancer via estrogen metabolism "estrobolome" to lung cancer through the gut-lung axis and modulation of ICI responses, to melanoma by shaping systemic T-cell function and immunotherapy outcomes, and to prostate cancer through androgen receptor signaling and microbial metabolite interactions. These findings underscore the systemic oncogenic and tumor-suppressive potential of microbial communities. Microbiome-targeted interventions, including fecal microbiota transplantation (FMT), defined live biotherapeutics, probiotics, prebiotics, dietary modulation, and postbiotic delivery, are being actively investigated to optimize cancer treatment. While early trials have demonstrated feasibility, variability between individuals and methodological challenges remain significant hurdles. Hence, understanding how gut microbes influence extraintestinal cancers could revolutionize diagnostics, risk prediction, and treatment strategies.},
}

@article {pmid42112079,
year = {2026},
author = {Kurniawan, and Milanda, T and Kusuma, SAF},
title = {Comparative Profiling of Yeast Communities in Kefir Grains and Liquid Kefir Using ITS Amplicon Next-Generation Sequencing.},
journal = {International journal of food science},
volume = {2026},
number = {},
pages = {2572378},
pmid = {42112079},
issn = {2314-5765},
abstract = {Kefir is a fermented dairy beverage produced by a complex microbial consortium of bacteria and yeasts coexisting within a polysaccharide-protein matrix known as kefir grains. Although the bacterial communities are well-characterized, the distribution of yeast taxa, specifically those transitioning into the fermented liquid phase, remains insufficiently described. This study is aimed at characterizing and comparing the fungal community composition in both the kefir grains and the resulting fermented liquid. Using internal transcribed spacer (ITS) amplicon sequencing on samples from a traditionally propagated culture, we identified 122 yeast taxa in the grains and 221 taxa in the liquid fraction, with 182 taxa shared between both habitats. Crucially, taxonomic profiling of the liquid phase revealed a high diversity of yeasts, with Saccharomyces cerevisiae, Kluyveromyces marxianus, and Pichia kudriavzevii being significantly more abundant compared with the grain matrix. In contrast, grain samples were relatively enriched in Pichia fermentans. Several taxa maintained moderate abundance across both fractions, suggesting ecological persistence during fermentation. These patterns reflect the spatial distribution of yeast taxa within the system rather than functional specialization. Although based on a single culture without biological replication, these findings provide a detailed descriptive map of the kefir mycobiome, distinguishing dominant fermentation-associated yeasts in the liquid phase from low-abundance environmental fungi.},
}

@article {pmid42112126,
year = {2026},
author = {Seo, Y and Jung, JE and Oh, S and Kwon, IG and Park, JS},
title = {Effects of red ginseng on gut microbiome in patients after gastrointestinal cancer surgery: A pilot, randomized controlled trial.},
journal = {Journal of ginseng research},
volume = {50},
number = {3},
pages = {100932},
pmid = {42112126},
issn = {1226-8453},
abstract = {BACKGROUND: The gut microbiome plays diverse roles in human health. Although Korean red ginseng (KRG) has shown therapeutic potential in animal models, its effects on the human gut microbiome after gastrointestinal (GI) cancer surgery remain underexplored. This prospective randomized controlled study aimed to evaluate postoperative safety of KRG and its impact on the gut microbiome and postoperative outcomes after GI cancer surgery.

METHODS: Patients were randomly assigned 1:1 to the red ginseng or control groups. Microbiome analysis of preoperative and postoperative fecal samples was performed using 16S rRNA sequencing. The alpha and beta diversities, taxonomic composition changes of microbiome, nutritional index, clinical symptoms, GI symptoms, and quality of life (QOL) were assessed.

RESULTS: A total of 60 patients were enrolled and 16 patients in the red ginseng group and 25 in the control group were included in the final analysis. Postoperative alpha diversity decreased significantly in the control group, but remained relatively stable in the red ginseng group. Postoperative Lactobacillus levels increased significantly in the red ginseng group compared to the control group (18.34 % vs. 0.23 %; p < 0.001), whereas Bifidobacterium levels decreased (p = 0.002). Serum albumin levels were significantly higher in the red ginseng group at 3 months postoperatively (p = 0.003), and global health status/QOL scores were improved in the red ginseng group (p = 0.047).

CONCLUSION: Red ginseng supplementation may play a protective role in gut microbiome, improving clinical outcomes in patients undergoing GI cancer surgery, as a safe and supportive therapy for enhancing postoperative recovery.},
}

@article {pmid42112348,
year = {2026},
author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H},
title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1782828},
pmid = {42112348},
issn = {1664-3224},
mesh = {Humans ; *Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology ; Dysbiosis/immunology ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Autoimmunity ; },
abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.},
}

Humans
*Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology
Dysbiosis/immunology
Animals
*Microbiota/immunology
*Gastrointestinal Microbiome/immunology
Autoimmunity

@article {pmid42112377,
year = {2026},
author = {Tschang, MA and Deo-Campo Vuong, R and Eilers, B and Chac, D and Waalkes, A and Penewit, K and Easton, A and Schuessler, B and Daniels, R and Weil, AA and Salipante, SJ and Gibbons, SM and Schindler, AG},
title = {If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1816919},
pmid = {42112377},
issn = {1664-3224},
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Mice ; Corticosterone/blood ; *Stress, Psychological/therapy/microbiology ; Male ; Feces/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Anxiety ; Behavior, Animal ; Stress, Physiological ; },
abstract = {BACKGROUND: The microbiome-gut-brain axis is a mediator of stress-related disorders. The number of preclinical studies exploring the potential causal mechanism of this connection using fecal microbiota transplantation (FMT) is growing. However, the most common method for delivering fecal transplants in rodent models is still oral gavage, which creates an adverse experience that may confound stress-related outcomes. Here, we establish an alternative methodology for FMT that decreases stress induced by traditional experimental procedures.

METHODS: We first used preference and anxiety behavior assays to identify antibiotic therapies having maximal tolerability and minimal anxiolytic properties. We then collected feces from donor mice and homogenized them with a microbe-stabilizing buffer to create a slurry, which was frozen into aliquots ("poopsicles") for subsequent FMT. Recipient mice voluntarily consumed the frozen aliquots, and blood was collected to compare corticosterone relative to that after delivery via traditional gavage.

RESULTS: Plasma corticosterone levels were found to be significantly lower in mice receiving frozen aliquots compared to oral gavage. Furthermore, relative to controls, microbial signatures of mice receiving FMT via frozen aliquots were more similar to those of the donors at one week following final FMT and were sustained for up to six weeks, as assessed by comparing Bray-Curtis beta diversity distances.

CONCLUSION: Together, these results establish antibiotic and FMT methods that minimize treatment-induced stress, while effectively transplanting fecal microbes between murine conspecifics.},
}

Animals
*Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome
Mice
Corticosterone/blood
*Stress, Psychological/therapy/microbiology
Male
Feces/microbiology
Disease Models, Animal
Mice, Inbred C57BL
Anxiety
Behavior, Animal
Stress, Physiological

@article {pmid42112384,
year = {2026},
author = {Oyedokun, PA and Oyeleke, BT and Akanji, OO and Oyelaran, AO and O, KP and Akanbi, GB and Oyedokun, PO and Oyedokun, MD and Naomi, CC and Imoleayo, OO and Akhigbe, RE},
title = {The role of the microbiome in gynecological cancers: implications for diagnosis and treatment.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1718883},
pmid = {42112384},
issn = {1664-3224},
mesh = {Humans ; Female ; *Genital Neoplasms, Female/therapy/diagnosis/microbiology/etiology ; *Microbiota ; Dysbiosis ; Animals ; Tumor Microenvironment ; Fecal Microbiota Transplantation ; },
abstract = {Gynecological malignancies such as cancer of the cervix, ovary, endometrium, vulva, and vagina pose a severe global health burden. Although conventionally attributed to genetic mutation, hormonal imbalance, and chronic viral infection, including high-risk human papillomavirus, recent evidence suggests that the human microbiome plays a central role in their pathogenesis and development. This review summarizes existing evidence that microbial dysbiosis, specifically the depletion of beneficial Lactobacillus species and overrepresentation of anaerobic organisms such as Fusobacterium, Atopobium, and Sneathia, is implicated in carcinogenesis pathways. These include chronic inflammation, immune modulation, loss of epithelial barrier integrity, microbial metabolite toxicity, and estrogen metabolism by the estrobolome. Dysbiosis in the gut and reproductive tract has been associated with HPV persistence, tumor microenvironment remodeling, and immune surveillance/therapy resistance. Consequently, microbial signatures are being investigated as a potentially successful non-invasive biomarker for early diagnosis, prognosis, and monitoring of therapy in gynecological oncology. In addition, emergent microbiome-based therapies are being considered as potential adjunct therapies, including probiotics, prebiotics, dietary manipulation, vaginal microbiota transplantation, and fecal microbiota transplantation. This review connects the basic research microbiome research to translational and clinical practice, identifies associated limitations, and highlights how it may transform gynecological cancer prevention, detection, and treatment.},
}

Humans
Female
*Genital Neoplasms, Female/therapy/diagnosis/microbiology/etiology
*Microbiota
Dysbiosis
Animals
Tumor Microenvironment
Fecal Microbiota Transplantation

@article {pmid42112428,
year = {2026},
author = {Du, S and Jia, H and Lu, H and Li, X and Yang, M and Zhang, H and Wu, H and Wang, L and Zhu, B},
title = {Characterization and genomic analysis of DSF2: a novel lytic phage infecting multidrug-resistant Shigella.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1740847},
pmid = {42112428},
issn = {1664-302X},
abstract = {BACKGROUND: Multidrug-resistant Shigella flexneri (MDR S. flexneri) serotype 2a is the predominant cause of shigellosis in China, presenting a major public health challenge amid escalating antibiotic resistance and limited treatment options. Bacteriophages are gradually emerging as a highly promising alternative to antibiotics because of its highly specific bactericidal ability. However, only 113 Shigella phage genomes are available in NCBI as of August 2025, highlighting the need for novel lytic phages targeting prevalent MDR strains.

METHODS: A novel lytic phage, vB_SflP_DSF2 (DSF2), was isolated from untreated sewage at the 305 Hospital of PLA using MDR S. flexneri 2a strain 301 as host. Morphology was examined by transmission electron microscopy. Host range and efficiency of plating were determined against 41 bacterial strains (33 Shigella, 6 Escherichia coli, and others) using double-layer agar spot assays. One-step growth curves, pH and thermal stability, and biological properties were assessed using standard plaque assays. The complete genome was sequenced via Illumina NovaSeq, with comparative genomic and phylogenetic analyses performed using VIRIDIC, TerL phylogeny, AlphaFold structural predictions, and Swiss-Model for protein structure comparisons.

RESULTS: The DSF2 is a Schitoviridae phage with an elongated prolate head, short non-contractile tail. It produces haloed 1-2 mm plaques indicating depolymerase activity, with a 60-min latent period and 115 PFU/cell burst size. The DSF2 remains stable from 4 °C to 50 °C and active at pH 4-10, selectively lysing all S. flexneri serotype 2/X strains. Genomic analysis revealed that DSF2 possesses a 72,532 bp dsDNA genome with a G+C content of 44.89%, containing 89 predicted open reading frames. The DSF2 harbors no virulence or antibiotic resistance genes. Closest relative Shigella virus Moo19 shares 94.1% identity, defining the DSF2 as a new species. The prolate head of DSF2 closely resembles that of Escherichia coli phage PH444, driven by divergent Hoc-like head decoration, despite the conservation of capsid and portal proteins when compared to Shigella virus Moo19.

CONCLUSION: The DSF2 represents a novel Schitoviridae species that expands the limited Shigella phage repertoire, offering precision biocontrol against MDR S. flexneri serotype 2/X with minimal microbiome disruption. Hoc-like head decoration likely drives DSF2's unique prolate morpholog through intercapsomer angular constraints.},
}

@article {pmid42112429,
year = {2026},
author = {Mbaraka, A and Meena, RR and Menghani, E and Verma, N},
title = {Targeting biofilm-driven antibiotic resistance: emerging mechanisms and next-generation therapeutic interventions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1823476},
pmid = {42112429},
issn = {1664-302X},
abstract = {Biofilm mediated antimicrobial resistance (AMR) has become a critical global health and economic challenge, affecting both community and healthcare settings. Microbial Biofilms significantly enhance the antibiotic tolerance and cause the persistent and device-associated infections via limited drug penetration, degradation of antibiotics, and assist horizontal gene transfer. Biofilm-mediated antimicrobial resistance remains a major obstacle to treating infectious diseases today. Biofilms can boost antibiotic tolerance by up to 1,000 times and lead to chronic, persistent, and device-associated infections. The lack of FDA-approved anti-biofilm drugs highlights the urgent need for new therapeutic strategies and mechanistic insights. Redefining the treatment landscape and improving outcomes for resistant infections could be achieved through a multi-platform therapeutic approach. This review summarizes recent developments in our knowledge of how biofilms contribute to antibiotic resistance and highlights new therapeutic strategies, such as nanotechnology, antimicrobial peptides, bacteriophage-derived enzymes, quorum-sensing inhibitors, CRISPR-based tools, microbiome engineering, and AI-driven drug discovery.},
}

@article {pmid42100955,
year = {2026},
author = {Alsheikh, ZSA and Qingsong, T and Qinjie, L and Youkun, C},
title = {Re-arming checkpoint blockade in MSS colorectal cancer: A precision-microbiome playbook from mechanisms to clinic.},
journal = {Turkish journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.47717/turkjsurg.2026.2025-8-3},
pmid = {42100955},
issn = {2564-6850},
abstract = {Immune checkpoint blockade transforms outcomes for the 15% of colorectal cancers (CRCs) with mismatch-repair deficiency; yet most tumours remain refractory. Beneficial gut microbes can change this. Akkermansia muciniphila, Bacteroides fragilis, and short-chain fatty acid producers prime dendritic cells to produce interleukin (IL)-12, polarise Th1 cells, and reinvigorate CD8[+] T-cells. Antibiotics, Western-style diets, and Fusobacterium nucleatum foster myeloid suppression and β-catenin- or IL-17-mediated signalling, which blunt checkpoint activity. Multi-omics analyses link biosynthetic genes for inosine, riboflavin, and folate to durable clinical benefit. Faecal microbiota transplantation from responders has produced objective regressions in otherwise refractory microsatellite-stable disease. This narrative review maps CRC-microbiota-immune crosstalk, evaluates biomarkers and interventions, and proposes a CRC-specific, three-tiered clinical algorithm. We outline standards for trial design and manufacturing processes to facilitate the translation of microbiota-guided therapy into routine practice.},
}

@article {pmid42101034,
year = {2026},
author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM},
title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70354},
pmid = {42101034},
issn = {1758-2229},
support = {NA19NOS4190106//Texas General Land Office/ ; },
mesh = {*Estuaries ; *Fresh Water/chemistry/microbiology/virology ; Salinity ; *Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; Temperature ; Metagenomics ; Ecosystem ; },
abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.},
}

*Estuaries
*Fresh Water/chemistry/microbiology/virology
Salinity
*Viruses/genetics/classification/isolation & purification
Bacteria/genetics/classification/isolation & purification
Temperature
Metagenomics
Ecosystem

@article {pmid42101085,
year = {2026},
author = {El Sehrawy, AAMA and Aljumaili, OI and Axmedov, U and Khasawneh, MAS and Alanazi, MA and Smerat, A and Basunduwah, TS},
title = {Personalized Medicine in Autism Spectrum Disorder: Integrating Epigenomics, Microbiome Research and Early Diagnostics.},
journal = {International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience},
volume = {86},
number = {3},
pages = {e70128},
doi = {10.1002/jdn.70128},
pmid = {42101085},
issn = {1873-474X},
mesh = {Humans ; *Autism Spectrum Disorder/diagnosis/genetics/therapy/microbiology ; *Precision Medicine/methods ; *Epigenomics/methods ; *Microbiota/physiology ; Early Diagnosis ; Biomarkers ; *Gastrointestinal Microbiome ; },
abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by persistent difficulties in social communication together with restricted, repetitive patterns of behaviour and sensory-processing differences. Growing evidence suggests that ASD is shaped by complex interactions among genetic susceptibility, epigenetic regulation, immune signalling, maternal and early-life exposures and gut microbiome-related pathways. However, many of these associations remain biologically plausible rather than definitively causal, particularly when findings from experimental models are considered alongside human clinical data. This narrative review examines recent advances across these interconnected domains, with particular emphasis on maternal immune activation, prenatal nutrition, gut microbial imbalance, epigenetic and molecular mechanisms, emerging therapeutic directions and developing biomarker platforms. We also discuss current diagnostic limitations and evaluate the potential of salivary microRNAs, perinatal metabolic and epigenetic markers, oxidative stress-related measures and microbiome-based profiles as early and biologically informative indicators of ASD risk. Special attention is given to the need for biologically informed stratification, although current subgrouping frameworks remain preliminary and not yet sufficiently validated for routine clinical use. Likewise, candidate biomarkers remain investigational and require stronger evidence for reproducibility, external validation, longitudinal performance and clinically meaningful sensitivity and specificity before they can be considered for screening or precision-guided care. Emerging therapeutic strategies targeting immune, epigenetic and microbiome-related pathways are also reviewed, but most remain preclinical or early-stage and face substantial translational barriers. The convergence of epigenomics, microbiome research and early diagnostic science may help advance a more personalized medicine framework for ASD, provided that future studies improve cross-cohort reproducibility, clarify brain relevance of peripheral signals and develop practical multiomics models that can support clinically meaningful integration.},
}

Humans
*Autism Spectrum Disorder/diagnosis/genetics/therapy/microbiology
*Precision Medicine/methods
*Epigenomics/methods
*Microbiota/physiology
Early Diagnosis
Biomarkers
*Gastrointestinal Microbiome

@article {pmid42101126,
year = {2026},
author = {Azarkan, SY and Ünal, HSA and Akçay, S},
title = {Pharmacomicrobiomics in Precision Pharmacotherapy: Bidirectional Microbial-Drug Interactions as a Key Determinant of Therapeutic Response.},
journal = {Drug metabolism reviews},
volume = {},
number = {},
pages = {1-31},
doi = {10.1080/03602532.2026.2671428},
pmid = {42101126},
issn = {1097-9883},
abstract = {Interindividual variability in drug efficacy and toxicity remains a major challenge in clinical pharmacotherapy. Although pharmacogenomics has substantially advanced personalized medicine, host genetic variation alone cannot fully explain differences in drug disposition, response, and adverse effects. Increasing evidence identifies the human gut microbiotaas an additional, functionally relevant metabolic layer that complements host drug-metabolizing enzymes, giving rise to the field of pharmacomicrobiomics. This discipline examines bidirectional interactions between drugs and microbial communities that influence absorption, metabolism, enterohepatic circulation, and pharmacodynamic outcomes. The gut microbiota can directly biotransform or sequester drugs through diverse enzymatic reactions, including deconjugation, reduction, and decarboxylation, thereby modifying systemic drug exposure and toxicity. In parallel, microbially derived metabolites and bile acid-mediated signaling pathways regulate host drug-metabolizing enzymes and transporters, including cytochrome P450 enzymes and ATP-binding cassette transporters. Conversely, many commonly used medications-such as antibiotics, chemotherapeutic agents, targeted therapies, immunotherapies, psychotropic drugs, and proton pump inhibitors-can substantially reshape microbial composition and function, resulting in dysbiosis that feeds back onto drug metabolism and therapeutic outcomes. This review summarizes the mechanistic basis and clinical relevance of microbiota-drug interactions across key therapeutic areas, including oncology (chemotherapy and immunotherapy), neuropsychiatric disorders, and metabolic diseases. Well-established examples, including microbial β-glucuronidase-mediated reactivation of irinotecan, microbiota-dependent modulation of levodopa and antidepressant pharmacokinetics, and microbiota-driven variability in immune checkpoint inhibitor efficacy, are discussed to illustrate causality. Emerging microbiome-informed strategies-such as selective inhibition of microbial enzymes, microbiota modulation, and microbial biomarker-based patient stratification-are highlighted. Finally, we examine integration of pharmacomicrobiomics with pharmacogenomics within multi-omic and systems pharmacology frameworks, emphasizing implications for predictive modeling and precision drug metabolism.},
}

@article {pmid42101202,
year = {2026},
author = {Yashar, M and Thigale, UY and Karakus, S},
title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICU.0000000000001228},
pmid = {42101202},
issn = {1531-7021},
abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.

RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced α-diversity and shifts in dominant taxa. Genera such as Staphylococcus, Corynebacterium, and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.

SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.},
}

@article {pmid42101281,
year = {2026},
author = {Wang, Z and Mao, J and Ma, L},
title = {A Tree-Based Model for Addressing Sparsity and Taxa Covariance in Microbiome Compositional Count Data.},
journal = {Statistics in medicine},
volume = {45},
number = {10-12},
pages = {e70584},
pmid = {42101281},
issn = {1097-0258},
support = {R01-GM135440/GM/NIGMS NIH HHS/United States ; DMS-2013930//National Science Foundation/ ; DMS-1749789//National Science Foundation/ ; },
mesh = {Humans ; Bayes Theorem ; *Microbiota ; *Models, Statistical ; Computer Simulation ; Logistic Models ; Infant ; Normal Distribution ; Multivariate Analysis ; },
abstract = {Microbiome compositional data are often high-dimensional, sparse, and exhibit pervasive cross-sample heterogeneity. We introduce the "logistic-tree normal" (LTN) model, a generative model that allows flexible covariance among the microbiome taxa, enables scalable computation, and effectively captures other key characteristics of microbiome compositional data such as the abundance of zeros. LTN incorporates a tree-based decomposition for effective aggregation over sparse taxa counts and models the relative abundance at the tree splits jointly using a (multivariate) logistic-normal distribution. The latent Gaussian structure allows a wide range of multivariate analysis and modeling tools for high-dimensional data-such as those enforcing sparsity or low-rank assumptions on the covariance structure-to be readily incorporated. As a general-purpose, fully generative model, LTN can be applied in a wide range of contexts, while at the same time, efficient computational recipes for Bayesian inference under LTN are available through conjugate blocked Gibbs sampling enabled by pólya-gamma augmentation. We demonstrate the use of LTN in a compositional mixed-effects model for differential abundance analysis through both numerical experiments and a reanalysis of the infant cohort in the DIABIMMUNE study. We explain and showcase through numerical experiments and the case study how LTN, through adequately accounting for the cross-sample heterogeneity, is capable of generating the appropriate proportion of zeros without incurring an explicit zero-inflation component. This confirms a recent viewpoint that "zero-inflation" in count-based sequencing data are often results of unaccounted cross-sample variation.},
}

Humans
Bayes Theorem
*Microbiota
*Models, Statistical
Computer Simulation
Logistic Models
Infant
Normal Distribution
Multivariate Analysis

@article {pmid42101372,
year = {2026},
author = {Zhang, H and Zhang, S and Zhu, J},
title = {Molecular-level host-microbe interactions: mechanisms, molecules, and modeling toward precision probiotics.},
journal = {Expert opinion on therapeutic targets},
volume = {},
number = {},
pages = {},
doi = {10.1080/14728222.2026.2671689},
pmid = {42101372},
issn = {1744-7631},
abstract = {INTRODUCTION: Advancing next-generation probiotics (NGPs) as precision therapeutics depends on a detailed understanding of host - microbe molecular interactions, as these organisms exert targeted effects through defined bioactive molecules rather than broad, nonspecific mechanisms. This review addresses the need to systematically organize emerging knowledge on microbe-derived molecules (MDMs) that underpin NGP efficacy.

AREAS COVERED: This narrative review summarizes recent discoveries of MDMs isolated from NGPs and classifies them based on three principal molecular interaction interfaces: protein - protein/peptide, protein - lipid or glycopeptide, and protein - metabolite interactions. We discuss how these molecules - encompassing proteins/peptides, lipids, glycoconjugates, and small metabolites - modulate host immune and metabolic pathways to maintain homeostasis. The literature was identified through targeted searches of recent peer-reviewed studies focusing on host - microbe molecular mechanisms and probiotic-derived bioactives. We also review the application of molecular docking, molecular dynamics simulations, and artificial intelligence - based tools in predicting host - microbe interactions and accelerating therapeutic discovery.

EXPERT OPINION: By integrating experimental insights with computational strategies, we propose a framework to guide the development of precision microbiome-based interventions tailored to specific diseases and individual microbiome profiles. These advances lay the foundation for rational design of targeted NGP therapies for metabolic, inflammatory, infectious, and neurodegenerative disorders.},
}

@article {pmid42101618,
year = {2026},
author = {Nguyen, PN and Rehan, SM},
title = {Microbial Communities Across Social Roles in Small Carpenter Bee Nests.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02787-2},
pmid = {42101618},
issn = {1432-184X},
abstract = {Bee microbiota form important symbiotic relationships with their hosts, but microbial communities vary across bee species, sociality, and environment. Comparing the microbiome of bees with different social roles and foraging behaviours may uncover the ways in which microbiota are environmentally acquired and subsequently introduced and spread into the nest environment. Here, we performed metabarcoding of the 16S rRNA, ITS, and ribulose biphosphate carboxylase large (rbcL) regions on mothers, dwarf eldest daughters, and regular daughters in nests of the facultatively social, small carpenter bee, Ceratina calcarata, contrasting bacteria, fungi, and plant associates. We also performed two different sampling types by characterizing the microbiome using whole-guts and whole-bodies. Social role in nest impacted the microbial community composition and mothers were found to demonstrate increased plant diversity compared to their daughters, more specifically in whole-bodies, highlighting the ability to determine plants that bees are visiting during foraging through DNA metabarcoding. We also found that metabarcoding of the whole-body recovered increased fungal and plant diversity compared to whole-guts, suggesting that including microbiota from beyond the gut offers an opportunity to characterize uncommon associates that bees encounter, particularly through plant-pollinator relationships. As the transmission of beneficial symbionts and pathogens between individuals are studied for its impact on bee health, microbial analyses of bees across different environments and levels of sociality provides unique biomonitoring that can indicate the health of the larger bee community.},
}

@article {pmid42101639,
year = {2026},
author = {Makkar, P and Singh, CK and V, N and Narang, PK and Sodhi, KK},
title = {Insect immunity unveiled: exploring the molecular and cellular defenses against microbial threats.},
journal = {Archives of microbiology},
volume = {208},
number = {8},
pages = {},
pmid = {42101639},
issn = {1432-072X},
mesh = {Animals ; *Immunity, Innate ; *Insecta/immunology/microbiology ; Receptors, Pattern Recognition/immunology ; Microbiota/immunology ; Hemocytes/immunology ; Symbiosis ; Drosophila melanogaster/immunology/microbiology ; Bombyx/immunology/microbiology ; },
abstract = {Insects, as diverse and ecologically dominant organisms, rely exclusively on innate immunity to defend against a wide array of microbial threats. This paper presents an integrative review of insect immune mechanisms, highlighting the molecular, cellular, and systemic components that underpin host defense. The immune response is orchestrated through physical barriers, cellular processes and humoral factors. Evolutionarily conserved pattern recognition receptors (PRRs) are essential to these processes. Emphasis is laid on pivotal functions of hemocytes, the significance of microbiome interactions in immune regulation, and the emerging influence of non-coding RNAs. Furthermore, the paper explores defensive symbiosis, environmental and evolutionary influences on immune dynamics, and applications in biotechnology and pest management. Model organisms, such as Drosophila melanogaster and Bombyx mori, serve as critical systems for unravelling innate immunity, with translational relevance to vertebrate immunology and vector control strategies. Understanding these mechanisms offers valuable insights into conserved immune pathways and holds promise for advancing strategies in human disease prevention, therapeutic innovation, and global health.},
}

Animals
*Immunity, Innate
*Insecta/immunology/microbiology
Receptors, Pattern Recognition/immunology
Microbiota/immunology
Hemocytes/immunology
Symbiosis
Drosophila melanogaster/immunology/microbiology
Bombyx/immunology/microbiology

@article {pmid42101655,
year = {2026},
author = {Miwa, T and Hsu, CL and Shimizu, M and Bloom, PP and Schnabl, B},
title = {Covert hepatic encephalopathy as a multi-organ syndrome: the gut-liver-muscle-brain axis, diagnosis, treatment, and multidisciplinary care.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42101655},
issn = {1435-5922},
support = {JP24K18908//Japan Society for the Promotion of Science/ ; },
abstract = {Covert hepatic encephalopathy (CHE) is a highly prevalent complication of liver cirrhosis. Despite the absence of overt symptoms, CHE is strongly associated with impaired quality-of-life, overt hepatic encephalopathy, and mortality. Over the past two decades, evidence regarding the pathophysiology, diagnosis, and treatment of CHE has accumulated considerably, and clinical guidelines recommend screening in patients with cirrhosis. Nevertheless, diagnostic and therapeutic algorithms have not been fully implemented in real-world practice, and many patients remain undiagnosed and untreated. Understanding the natural history of CHE is essential to improve cirrhosis care, as it provides a framework for appropriate screening, treatment decision-making, and patient counseling. CHE is a multi-organ syndrome with complex interactions between the liver, gut, skeletal muscle, kidneys, and brain, with impaired ammonia handling and systemic inflammation acting as central drivers of this organ crosstalk. Hyperammonemia induces astrocytic dysfunction, brain edema, and neuroinflammation, while systemic inflammation, oxidative stress, sarcopenia, gut dysbiosis, and altered microbial metabolites, including bile acids and short-chain fatty acids, further modulate disease expression. In this review, we summarize current understanding of CHE pathophysiology, diagnostic testing, including psychometric batteries and point-of-care tools, such as the Stroop test and animal naming test, and therapeutic options, ranging from lactulose and rifaximin to microbiome-targeted approaches, including fecal microbiota transplantation. We also highlight major challenges in CHE management, including limited implementation of testing, inadequate biomarkers, diagnostic difficulties in geriatric cirrhosis, and unmet needs in fall and driving risk management, and emphasize the importance of multidisciplinary team-based approaches to improve patient outcomes.},
}

@article {pmid42101775,
year = {2026},
author = {Szpytma, M and Dobrzyński, J},
title = {Interactions of PGPR from the phylum bacillota with native rhizosphere microbiota: current insights and future perspectives.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42101775},
issn = {1573-0972},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics ; Crops, Agricultural/microbiology/growth & development ; Plant Development ; Soil/chemistry ; Plant Roots/microbiology ; Agriculture ; },
abstract = {The intensive use of synthetic fertilizers and pesticides has increased crop productivity but also contributed to soil degradation and biodiversity loss, highlighting the need for more sustainable agricultural strategies. Among emerging solutions, plant growth-promoting rhizobacteria (PGPR), particularly members of the Bacillota phylum, are gaining attention as effective bioinoculants that enhance plant growth and tolerance to biotic and abiotic stresses. However, introduced strains do not function in isolation. They enter complex microbial communities, shaped by plant type and developmental stage, influenced by soil properties and environmental conditions. While the positive effects of PGPR on plant performance are well documented, their impact on indigenous rhizosphere microbiota remains less studied. This review synthesizes current knowledge on how Bacillota-based inoculants influence native microbial communities in cereals, vegetables, orchard crops, and fiber plants. Most studies report shifts toward plant-beneficial taxa and reduced abundance of potential pathogens following Bacillota application. Frequently enriched genera include Bacillus, Pseudomonas, Lysobacter, Sphingomonas, Streptomyces, Azotobacter, Arthrobacter, Pseudarthrobacter, Bradyrhizobium, Devosia, Flavobacterium, Klebsiella, Herbaspirillum, and Rhodanobacter. These changes are often associated with improved plant growth and yield, and stress resilience. However, responses strongly depend on strain, plant and methodological approach. We summarize commonly applied approaches used to assess these interactions. Despite technological advances, limitations remain, such as single time-point sampling, simplified experimental systems, and insufficient integration of inoculant persistence with community analyses. Standardized, multi-site experimental frameworks, with multiple sampling terms are needed to improve predictability and ensure the safe implementation of PGPR-based solutions in sustainable agriculture.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
*Bacteria/classification/genetics
Crops, Agricultural/microbiology/growth & development
Plant Development
Soil/chemistry
Plant Roots/microbiology
Agriculture

@article {pmid42101879,
year = {2026},
author = {Theys, C and Decaestecker, E and Stoks, R},
title = {Extending space-for-time substitutions: the missing role of the gut microbiome.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voag032},
pmid = {42101879},
issn = {1420-9101},
abstract = {The space-for-time substitution (SFTS) approach is widely used to predict evolutionary trait responses to global warming. The current approach ignores the explicit role of the gut microbiome in shaping the future host phenotype, despite its strong influence on thermal adaptation and its ability to show more rapid adaptation than the host. We propose integrating reciprocal gut microbiome transplants into SFTS and identify a set of contrasts between treatment combinations to disentangle host and gut microbiome contributions to thermal adaptation under future warming. To illustrate our approach, we apply the proposed contrasts between treatment groups to re-interpret data on immune functioning of Ischnura elegans damselfly nymphs of which the gut microbiome was reciprocally transplanted between nymphs from warm-adapted low-latitude and cold-adapted high-latitude populations reared at both the cold (high-latitude) and warm (low-latitude) thermal regime. By disentangling the contributions of the host and its gut microbiome, our conceptual approach shows that gut microbiome adaptation can buffer against immune suppression in the high-latitude populations under future warming, while adaptation of the host will not. Incorporating the gut microbiome into SFTS may enhance realism in predicting species resilience to climate change and better inform conservation strategies under future climates.},
}

@article {pmid42102024,
year = {2026},
author = {Abu, BAZ and Zhang, L and Beblavy, R and Wu, Y and Lu, X and Fiscella, K and Sohn, MB and Xiao, J},
title = {Effects of pica practice on oral bacteriome and mycobiome profiles among pregnant women: A comparative study.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0328198},
pmid = {42102024},
issn = {1932-6203},
mesh = {Humans ; Female ; Pregnancy ; Adult ; *Pica/microbiology ; Cross-Sectional Studies ; *Mycobiome ; *Microbiota ; *Mouth/microbiology ; Saliva/microbiology ; Young Adult ; Bacteria/genetics/classification ; },
abstract = {INTRODUCTION: Pica, the excessive craving and consumption of non-food substances such as clay, and ice, is common among pregnant women but may pose risks for oral and systemic infections.

OBJECTIVE: Assessed the comparative effect of pica practice on the oral microbiome (bacteriome and mycobiome) profiles of pregnant women.

METHODS: A cross-sectional study was conducted in Upstate New York among pregnant women. Demographic, socioeconomic, pica practices (current and past), and oral hygiene practices were collected via questionnaires. The medical history of anemia was self-reported and verified using electronic records. A calibrated dentist assessed dental caries, periodontal status, and a comprehensive oral examination (plaque index, bleeding on probing). Oral samples (saliva and supragingival plaque) and pica samples were collected for the microbiome for Genomic DNA using I6S rRNA and ITS DNA sequencing and analyzed using linear regression with and without anemia as a covariate.

RESULTS: Of the 20 pregnant women in the study, 17 were minority women (75% non-white). The mean age of participants was 29 years, and 29 weeks of gestational age. Eight participants (40.0%) reported practicing pica, and six provided samples, namely ice (and popsicles), and chalk. Streptococcus, Actinomyces, and Prevotella dominated in both saliva and plaque samples, but the microbial compositions differed. Between the pica and the non-pica groups, two differentially abundant (DA) bacterial taxa were identified in saliva samples with and without anemia namelyOribacterium sinus (p < 0.05). In plaqueseven identical DA bacterial taxa including Prevotella nigrescens were seen except for Leptotrichia goodfellowii, which was unique to when anemia was controlled for (p < 0.05). Network analysis showed the co-occurrence of Candida albicans and Lactobacillus in the pica group.

CONCLUSION: Pica practice was associated with specific oral taxa abundance change in saliva and supragingival plaque, reflecting distinct microbiome distributions. In the regression model, including anemia as a covariate had almost no impact on the overall DA results. These findings are preliminary, indicating that future large prospective cohort studies are warranted to thoroughly assess the impact of pica practice on oral flora.},
}

Humans
Female
Pregnancy
Adult
*Pica/microbiology
Cross-Sectional Studies
*Mycobiome
*Microbiota
*Mouth/microbiology
Saliva/microbiology
Young Adult
Bacteria/genetics/classification

@article {pmid42102421,
year = {2026},
author = {Li, X and Liu, J and Yue, W and Yang, W and Zhang, L and Guo, C and Qing, W},
title = {Chronic endometritis and reproductive failure: The paradigm shift from microbial eradication to ecological restoration.},
journal = {Journal of reproductive immunology},
volume = {175},
number = {},
pages = {104906},
doi = {10.1016/j.jri.2026.104906},
pmid = {42102421},
issn = {1872-7603},
abstract = {Despite advancements in assisted reproductive technologies, such as preimplantation genetic testing, clinical success rates have plateaued, thereby increasing the clinical focus on the endometrial factor. Chronic endometritis (CE), a persistent and often asymptomatic mucosal inflammation, is an underdiagnosed condition associated with reproductive failure, particularly in cohorts with repeated implantation failure (RIF) and recurrent pregnancy loss (RPL). This review examines the evolving understanding of CE pathophysiology, transitioning from a traditional infection model toward a framework involving endometrial dysbiosis and potential bacterial biofilm formation. These microbial alterations are hypothesized to trigger maladaptive immune activation and may induce persistent epigenetic modifications that desynchronize endometrial receptivity. We critically evaluate current diagnostic modalities, addressing controversies regarding CD138 immunohistochemistry thresholds and the interpretive limitations of molecular microbiome screening associated with relic DNA. Therapeutically, while antibiotic regimens remain the standard of care, there is conflicting evidence regarding their universal clinical efficacy. Consequently, we review the rationale for transitioning from generalized broad-spectrum microbial eradication toward antibiotic stewardship and targeted ecological restoration using biotherapeutics. Synthesis of current evidence, including data from euploid embryo transfers, suggests that resolving histopathological inflammation improves live birth rates in specific high-risk cohorts. The future management of CE necessitates the implementation of risk-stratified algorithms and therapeutic strategies that focus on functional endometrial recovery rather than isolated histological clearance.},
}

@article {pmid42102504,
year = {2026},
author = {IJdema, F and Broeckx, L and Deruytter, D and Frooninckx, L and van Miert, S and De Smet, J},
title = {Short communication: The persistent influence of host lineage on the gut microbiomes of black soldier fly and yellow mealworm.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {5},
pages = {101828},
doi = {10.1016/j.animal.2026.101828},
pmid = {42102504},
issn = {1751-732X},
abstract = {Production insects such as the black soldier fly (BSF) and yellow mealworm (YM) are increasingly recognised as sustainable protein sources, and selective breeding of genetically distinct lines offers opportunities to improve production efficiency. However, insect performance is also influenced by the gut microbiome, which provides essential metabolic and protective functions. Despite this, current breeding programmes typically focus on host genetics and phenotypes, assuming that microbiome composition remains stable under consistent rearing conditions. However, this hypothesis remains largely untested. We examined gut bacterial communities in ten distinct BSF and YM populations reared for multiple generations under identical conditions. Each species shared a distinct set of ten zero-radius operational taxonomic units (zOTUs) across all populations, but their relative abundances varied, indicating host-specific effects on microbiome composition. Strain-specific zOTUs also persisted despite uniform environments. These findings suggest that host genetic background exerts a more persistent influence on gut microbiome composition than previously assumed.},
}

@article {pmid42102652,
year = {2026},
author = {Al-Salihy, AAS},
title = {Toward an immunological classification of autism spectrum disorder: A PRISMA-ScR-compliant scoping review.},
journal = {Journal of neuroimmunology},
volume = {417},
number = {},
pages = {578962},
doi = {10.1016/j.jneuroim.2026.578962},
pmid = {42102652},
issn = {1872-8421},
abstract = {Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental condition increasingly linked to disturbances in immune signaling and neuroimmune cross-talk. This PRISMA-ScR-guided scoping review synthesizes contemporary evidence to propose a structured immunological classification of ASD comprising six immune-related subtypes: immune overactivation, immune deficiency, autoimmunity-linked ASD, gut-immune axis dysregulation, post-infectious or immune-triggered onset patterns, and maternal immune activation. Each subtype is defined by characteristic neuroimmune features - including cytokine imbalances, aberrant microglial activation, altered microbiome-immune communication, and prenatal immune priming - reflecting distinct biological pathways through which immune dysfunction may influence neurodevelopment. Based on 42 mapped sources identified through a search strategy that primarily emphasized literature published between 2020 and 2025, while incorporating selected foundational earlier studies through citation chaining when necessary for conceptual and mechanistic context, and spanning human clinical and epidemiological studies, animal models, and integrative neuroimmune reviews, this synthesis identifies candidate biomarkers and immune signatures relevant to each subtype, including systemic and CNS-localized inflammation, autoantibodies, disrupted gut-immune-brain pathways, and maternal cytokine profiles. The framework also clarifies ongoing debates by distinguishing immune-mediated vulnerability and timing-dependent unmasking of susceptibility from assumptions of direct causation regarding environmental or infectious exposures. Conceptualizing ASD along immune-related subtypes provides a foundation for precision-based diagnostic and therapeutic approaches, highlighting opportunities for targeted immunomodulation, microbiome-informed interventions, and biomarker-driven stratification, thereby advancing translational efforts at the interface of immunology, neuroscience, and developmental psychopathology.},
}

@article {pmid42102900,
year = {2026},
author = {Hamerlinck, H and Boelens, J and De Looze, D and Messiaen, AS and Vandendriessche, S and Holvoet, T and Verhasselt, B},
title = {Seven years of stool banking: clinical and microbiological insights from the Ghent Stool Bank.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108744},
doi = {10.1016/j.ijid.2026.108744},
pmid = {42102900},
issn = {1878-3511},
abstract = {OBJECTIVES: The Ghent Stool Bank (GSB) was founded in 2018 at Ghent University Hospital to provide safe, ready-to-use faecal suspensions for faecal microbiota transplantation (FMT), primarily targeting recurrent Clostridioides difficile infection (rCDI) and supporting clinical trials.

METHODS: This retrospective cohort study explores the relationship between donor characteristics and rCDI treatment outcomes following FMT.

RESULTS: Between 2018 and 2024, 12.0% of screened candidates qualified as donors after rigorous evaluation, resulting in 159 approved donations. Forty-four FMT procedures were carried out in forty rCDI patients, achieving a primary cure rate of 77.1%, which increased to 85.7% following a second treatment. Donor microbiome diversity did not show association with treatment outcomes, and no statistically significant differences in taxa abundance were observed. Notably, faecal suspensions stored for up to five years were as effective as those stored for shorter periods. Additionally higher donor age did not appear to negatively impact treatment success in rCDI patients.

CONCLUSION: These findings support the role of stool banks like the GSB in ensuring safe FMT procedures. Allowing higher donor age and longer storage periods may help sustain sufficient high‑quality donor availability. Future efforts should focus on improving safety, enhancing donor-recipient compatibility through microbiome profiling and increasing public awareness.},
}

@article {pmid42103091,
year = {2026},
author = {Todua, I},
title = {Management of salt-sensitive hypertension in clinical settings: how should we approach it?.},
journal = {The American journal of medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjmed.2026.05.003},
pmid = {42103091},
issn = {1555-7162},
abstract = {Salt sensitivity is a major component of highly prevalent uncontrolled hypertensive disease. Multiple disease determinants, such as age, sex, genetic predisposition, pro-inflammatory factors, renal and vascular dysfunction, disrupted blood-brain barrier integrity, as well as gut microbiome health, effectively regulate sodium turnover and associated adverse outcomes. Salt sensitive blood pressure can be commonly observed in patients with both primary and secondary hypertension. Furthermore, patients suffering from obesity and insulin-resistant states, heart failure, chronic kidney disease, as well post-menopausal females and senior citizens, may be particularly sensitive to excessive salt exposure. Despite paramount importance, diagnosis or treatment of salt sensitive blood pressure remain challenging, often pushing clinicians into complicated management labyrinths. Significant discordance between objective findings, such as degree of thirst and edema on presentation, and results of laboratory testing, such as serum sodium, potassium, NT-proBNP, or RAAS essay, is often observed delaying the provision of appropriate care. This review offers detailed description of underlying pathophysiology, diagnosis and treatment of salt sensitive blood pressure in clinical settings, intending to ameliorate the burden of uncontrolled hypertension.},
}

@article {pmid42103112,
year = {2026},
author = {Kumwan, B and Meachasompop, P and Adisornprasert, Y and Rajitdumrong, C and Chaemlek, P and Srisapoome, P and Phaksopa, J and Buncharoen, W and Thangsunan, P and Thangsunan, P and Rodkhum, C and Paankhao, N and Kingwascharapong, P and Uchuwittayakul, A},
title = {Sequential nanoimmersion and hydrogel-based multivalent vaccination induce durable multilayered immunity against four bacterial pathogens in Nile tilapia (Oreochromis niloticus).},
journal = {Fish & shellfish immunology},
volume = {175},
number = {},
pages = {111398},
doi = {10.1016/j.fsi.2026.111398},
pmid = {42103112},
issn = {1095-9947},
abstract = {Bacterial infections caused by Flavobacterium oreochromis, Aeromonas veronii, Streptococcus agalactiae, and Edwardsiella tarda represent major threats to Nile tilapia aquaculture. This study evaluated a multistage mucosal vaccination strategy combining sequential nanoemulsion immersion priming with oral hydrogel-based boosters against these four pathogens in Oreochromis niloticus. Vaccination was associated with significant enhancement of both mucosal and systemic humoral immunity, as evidenced by elevated pathogen-specific IgM levels in gills, skin mucus, intestine, and serum across three successive challenge rounds. Immune-related gene expression analysis revealed significant upregulation of ighm, ighd, and ight in key immune tissues, consistent with broad activation of B cell-mediated responses. Label-free quantitative proteomic profiling demonstrated extensive immune remodeling in vaccinated fish, characterized by increased abundance of antigen-presentation molecules, complement factors, lysozyme, serpins, and mucosal defense-associated enzymes. Intestinal microbiome analysis revealed that vaccination reshaped microbial community composition toward a more stable and pathogen-resistant structure, with markedly reduced colonization by all four target pathogens. These immunological and microbial changes were associated with significantly higher survival rates under both immersion and intraperitoneal challenge conditions. Taken together, these findings suggest that multistage sequential vaccination may induce broad-spectrum, durable, multilayered protection in Nile tilapia through synergistic enhancement of humoral immunity, immunoglobulin gene expression, proteomic remodeling, and microbiome stabilization, providing a promising framework for sustainable disease management in intensive aquaculture.},
}

@article {pmid42103122,
year = {2026},
author = {Dhayalan, A and Manoharan, S and Waheeb, MQ and Rabbee, MF and Govindasamy, B and Selvan, ST and Pachiappan, P},
title = {An examination of the microbiome of Bacillus cereus (PS5) isolated from Puntius sarana (Olive barb) for α-amylase production, optimization, macromolecule extraction, and structural characterization with industrial and agricultural applications.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152420},
doi = {10.1016/j.ijbiomac.2026.152420},
pmid = {42103122},
issn = {1879-0003},
abstract = {The α-amylase enzyme plays a vital role in enzyme therapy and the intestinal digestive system, and is widely utilized in the food and pharmaceutical industries. Thus, this study aimed to isolate intestinal bacterial strains that produce α-amylase, optimize enzyme production, and characterize the molecular properties of the produced proteins. A total of 11 strains were isolated from the fish gut; 9 strains were positive for α-amylase production. The PS5 strain exhibited the highest enzymatic activity and was confirmed as Bacillus cereus. Optimization of B. cereus culture conditions revealed parameters of pH 7.0, temperature 35 °C, incubation time 40 h, and starch and yeast extracts of 1.5% and 2.53%, respectively. The bacterial protein was extracted, purified, and shown to have a molecular weight of 55 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. FTIR spectroscopy confirmed the presence of functional groups, such as phenols, alkanes, amides, and aromatic and aliphatic amines. Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)-tandem mass spectrometry (MS/MS) analysis identified 12 peptides, with the major peptide sequence being SVGLLLVLLLPMLGAAAPLTTQMLDSGWQFR (m/z 2383.97; S/N 69.3). The α-amylase protein sequence (513 amino acids) was used for structural prediction, while protein-protein interaction analysis revealed a significant interaction with pullulanase (interaction score 0.945). Molecular docking analysis showed strong binding energy of propoxur (-7.2 kcal/mol) and the hormone indole-3-acetic acid (-6.9 kcal/mol) with α-amylase protein. These findings indicate that Bacillus cereus (PS5) is a promising source of α-amylase for diverse industrial and agricultural applications. Further investigation into the activity and stability of these enzymes in natural environments could enhance the associated potential biotechnological applications.},
}

@article {pmid42103208,
year = {2026},
author = {Abdelhalim, KA and Wang, Y and Amirkhani Namagerdi, A and Alfuraiji, N and Mburu, D and Hassan, HA},
title = {Gut Oxalate Transport and Gut Microbiome as Potential Therapeutic Targets for Hyperoxaluria and Hyperoxalemia: Implications for Related Human Disease.},
journal = {Mayo Clinic proceedings},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mayocp.2026.04.020},
pmid = {42103208},
issn = {1942-5546},
abstract = {Besides kidney stones (KS), oxalate potentially contributes to chronic kidney disease (CKD) and its progression, CKD- and end stage kidney disease (ESKD)-associated cardiovascular diseases, and poor kidney transplant survival. KS affect about 1 in 5 men and 1 in 11 women and the recurrence rate remains high (50% in 5 years and up to 80% in 10-20 years), reflecting that current interventions are inadequate, and novel therapies are needed. 70-80% of KS are composed of calcium oxalate and small increases in urine oxalate enhance the KS risk. The gastrointestinal tract (gut) plays a major role in oxalate homeostasis by acting as a site for oxalate absorption and secretion. Therefore, the gut potentially represents a novel therapeutic pathway for body oxalate elimination. Strategies aiming at reducing the gut's ability to absorb oxalate and/or enhancing its ability to secrete oxalate can lead to decreased plasma and urinary oxalate levels and therefore can serve as novel approaches for the prevention and/or treatment of hyperoxalemia and hyperoxaluria. Humans lack oxalate metabolizing enzymes, and they rely on gut bacteria referred to as oxalate-degrading bacteria (oxalobiome) for gut oxalate degradation. This limits net gut oxalate absorption, thereby helping with maintaining normal oxalate homeostasis. This review focuses on the role of gut oxalate transport and gut microbiome in overall oxalate homeostasis and how they can be therapeutically targeted. Importantly, the majority of evidence for gut oxalate transport is derived from animal studies, but the relevance of these findings to human gut oxalate transport remains to be established.},
}

@article {pmid42103277,
year = {2026},
author = {Yan, J and Jin, N and Xu, C and Wu, H and Jiang, Q and Liu, H and Yuan, J and Yin, D and Lin, F and Wang, R and Liang, Y and Feng, Y and Lan, Y and Lin, X and Wang, Y and Zhang, N and Dai, L and Li, T and Dong, S and Cheng, L and Sun, X},
title = {Multi-omics landscape and machine learning predictors of acute and chronic coronary syndrome diagnosis in young patients.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.05.015},
pmid = {42103277},
issn = {2090-1224},
abstract = {BACKGROUND: Acute coronary syndrome (ACS) is a leading global cause of death, and its incidence is increasingly rising in young adults, who exhibit distinct clinical characteristics from elderly patients. However, multi-omics studies focusing specifically on young coronary heart disease (CHD) patients remain scarce, hindering precise diagnosis and mechanism exploration.

METHODS: Here, we enrolled 206 young chest pain patients (18-45 years old), including 122 ACS patients, 38 chronic coronary syndrome (CCS) patients, and 46 individuals with healthy coronary arteries (NC). We performed integrated analyses of peripheral blood mononuclear cell transcriptomics, serum metabolomics, stool metabolomics, and gut microbiome metagenomics to characterize CHD subtypes and develop targeted diagnostic tools.

RESULTS: Our results showed that single omics layers had limited ability to distinguish CHD subtypes, while multi-omics integration significantly improved diagnostic efficacy. We identified unique molecular signatures for different subtypes: STEMI was associated with abnormal amino acid and carbohydrate metabolism, CCS was dominated by amino acid metabolism disturbances, and both STEMI and ACS showed enriched inflammation-related pathways. Novel biomarkers including p-chlorobenzene sulfonamide, cotinine, and the gut bacterium Streptococcus parasanguinis were identified, with Streptococcus parasanguinis validated as an atherogenic pathogen in a murine model. We constructed three multi-omics fusion diagnostic models (ACS vs. NACS, CCS vs. NC, STEMI vs. NSTE-ACS) with AUC values of 0.99, 0.95, and 0.96, respectively, and integrated them into a comprehensive diagnostic pipeline. Furthermore, multi-omics functional analysis unraveled a synergistic "microbiota-metabolism-immunity" regulatory network underlying CHD subtypes, linked to disordered amino acid and carbohydrate metabolism and aberrant inflammatory activation.

CONCLUSION: This study provides a systematic molecular landscape of young CHD, a high-precision diagnostic strategy, and novel targets for mechanism research and targeted intervention, addressing the unmet clinical need for precise management of young CHD patients.},
}

@article {pmid42103586,
year = {2026},
author = {Liu, WC and Chang, TT},
title = {From intratumoral microbiome association to spatial microbiome biology in primary liver cancer: a response and perspective.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.05.021},
pmid = {42103586},
issn = {0929-6646},
}

@article {pmid42103590,
year = {2026},
author = {Fukuda, K and Hozaka, Y and Ohtsuka, T},
title = {Reply to the Letter to the Editor regarding microbiome-genetic interplay in intraductal papillary mucinous neoplasms of the pancreas.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pan.2026.04.016},
pmid = {42103590},
issn = {1424-3911},
}

@article {pmid42103597,
year = {2026},
author = {Fan, Z and Shahgaleh, H and Ding, S},
title = {Nitrous oxide mitigation in hybrid maize mediated by Massilia.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.04.015},
pmid = {42103597},
issn = {1878-4372},
abstract = {Massilia presents a functional paradox in maize heterosis: its enrichment correlates with lower nitrous oxide (N2O) emissions, yet it lacks reduction genes. We propose that Massilia functions as an ecological hub, coordinating the rhizosphere microbiome and engineering the microenvironment to suppress N2O emissions. This paradigm guides new strategies for breeding climate-smart crops.},
}

@article {pmid42103701,
year = {2026},
author = {Wu, H and Wang, M and Ouyang, Q and Zhang, X and Liao, L and Wang, Y and Tang, N and Wang, Z},
title = {Comprehensive analysis of microbiome and transcriptome revealed the mechanisms of Flammulina velutipes stem-base enhance intestinal health in Gymnocypris eckloni.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70490},
pmid = {42103701},
issn = {1095-8649},
support = {23ZR102//Chengdu Agricultural College/ ; 23BS03//Chengdu Agricultural College/ ; },
abstract = {Although Flammulina velutipes residues are increasingly used in fish feeds, their mode of action in the gut is poorly defined. Here, we show that feeding Gymnocypris eckloni diets supplemented with F. velutipes stem-base (FVS) or its polysaccharides (FVP) selectively enhance foregut morphology-increasing both villus height and muscle layer thickness-without affecting mid- or hindgut regions. Transcriptome profiling revealed that 1831 differentially expressed genes (DEGs) were generated by FVS diet in the foregut mainly enriched in the signalling pathways related to DNA replication, fat digestion and absorption and HIF-1 signalling pathway. In addition, the differential genes between the FVP group and the control group were enriched in cell adhesion molecules, MAPK signalling pathway and cytokine-cytokine receptor interaction. Consistent with this, KEGG enrichment highlighted HIF-1α and MAPK as key pathways activated by FVS and FVP, respectively. Importantly, FVP also shifted the gut microbiota composition, boosting Weissella and other putative beneficial bacteria. These findings imply that F. velutipes has the potential to strengthen the intestinal barrier and improve intestinal health, offering valuable insights for the aquaculture of G. eckloni.},
}

@article {pmid42103708,
year = {2026},
author = {Basler, N and De Smet, L and Bouras, G and Swinnen, J and Pranga, K and Brussaard, CPD and Vandamme, P and de Graaf, DC and Matthijnssens, J},
title = {The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72757-2},
pmid = {42103708},
issn = {2041-1723},
support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 817622//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; H2020//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Honey bees (Apis mellifera) contribute to crop production and floral biodiversity via pollination, but their health is increasingly challenged by stressors including pathogens, parasites and agricultural practices. Although the honey bee gut microbiome is relatively simple, its phages are not well studied. Here, we conducted a metagenomic study, providing a comprehensive catalogue of honey bee gut phages from 450 virus-enriched samples from 63 hives, across eight European countries, three seasons and three gut sections. We describe a diverse phageome including many phages that appear to belong to novel taxa, as well as a core set of 97 highly prevalent phages. In addition, we identify potential auxiliary metabolic genes, such as a sulfur metabolism gene carried by phages that are predominantly temperate and likely infect mutualistic honey bee core bacteria. This gene is associated with land use around the sampled hives, indicating complex ecological interactions in the tripartite system of the honey bee, its microbiota and the phages therein.},
}

@article {pmid42103720,
year = {2026},
author = {Easter, QT and Huynh, KLA and Stolf, CS and Xie, J and Matuck, BF and Hasuike, A and Alvarado-Martinez, Z and Kim, WS and Chen, Z and Ribeiro, AA and Pareek, N and Azcarate-Peril, AM and Wu, D and Casarin, R and Ko, KI and Liu, J and Byrd, KM},
title = {CD38[+] endothelial remodeling marks spatially patterned vasculopathy in rapidly advancing periodontitis and peri-implantitis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72452-2},
pmid = {42103720},
issn = {2041-1723},
support = {Volpe Research Scholar Award//ADA Foundation (American Dental Association Foundation)/ ; Large Research Grant//American Academy of Implant Dentistry (AAID)/ ; #1RM1DE035338-01//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; #1R03DE034507-01//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; #5R01DE030415-05//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; startup funds//Virginia Commonwealth University (VCU)/ ; #2021/11082-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; Overseas Researcher Grant//Nihon University/ ; Schoenleber Grant//University of Pennsylvania (Penn)/ ; #P30CA016059//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; #UM1TR004360//U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; },
abstract = {Oral inflammatory diseases affect nearly half of all humans, yet mechanisms underlying rapidly-destructive inflammation remain poorly understood. We compared peri-implantitis with moderate- and high-grade periodontitis using integrated microbial and single-cell sequencing (>967,169-cells; single-cell RNA-seq, spatial proteotranscriptomics). Laser capture microdissection with compartmental microbiome analysis revealed reduced bacterial load and diversity in peri-implantitis. Expansion of the Human Periodontal Atlas with peri-implantitis single-cell RNA-seq data (36-samples; 121,395 cells) identified CD34[+] vascular endothelial cell (VEC) rarefaction and oxidative stress, hypoxia, and NAD[+] metabolism-associated transcriptional programs enriched in a TNFRSF6B[+]/ICAM1[+] post-capillary venule (PC-VEC) subpopulation. NAD[+]-consuming ectoenzyme CD38 was selectively enriched and orthogonally confirmed by spatial transcriptomics (6-samples; 283,377-cells) and proteomics (23-samples; 562,397-cells). Spatial neighborhood analyses demonstrated CD38[+]-high PC-VEC expansion, closer proximity, and higher IL16-CD4 T cell signaling in peri-implantitis. Matched high-grade periodontitis biopsies confirmed spatially restricted CD38[+]-VECs despite similar microbial burden, identifying endothelial vasculopathy underlying rapidly advancing oral inflammation and a potential therapeutic axis.},
}

@article {pmid42103800,
year = {2026},
author = {Bahuguna, M and Diwan, P and Wahlang, J and Gupta, RK},
title = {Comparative microbiome profiling of betel quid chewers and non-chewers to identify dysbiotic microbial signatures.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46533-7},
pmid = {42103800},
issn = {2045-2322},
support = {2019-3072//Indian Council of Medical Research/ ; 2019-3072//Indian Council of Medical Research/ ; 2019-3072//Indian Council of Medical Research/ ; },
abstract = {Recent studies are showing an association between oral microbiome community changes and oral diseases, including oral cancer. The prevalence of betel quid chewing has been linked to the incidence of oral cancer, particularly in the Northeast region of India. Hence, the study to understand the bacterial community shifts induced by betel quid to identify dysbiotic microbial signatures will not only aid in early diagnosis of oral cancers but also facilitate the development of strategies to restore microbial balance and potentially prevent disease progression. The present cross-sectional study evaluated the oral microbiome of 92 adults in Meghalaya, India, using a 16 S rRNA sequencing approach. Significant differences were observed in the bacterial community in betel quid chewers and non-chewers. Alpha diversity, assessed using Chao1 and observed genera metrics, was significantly higher in betel quid chewers as compared to non-chewers, especially among long-term users and male individuals. Beta diversity analysis revealed significant community compositional differences between Betel quid chewers and non-chewers, more notably in males and individuals aged 40-60 years. Betel quid chewers demonstrated a higher number of unique taxa (63 Overall; 102 Male; 123 in 40-60 years old) compared to non-chewer samples. Linear discriminant analysis identified Haemophilus, Fusobacterium, and Lautropia enriched in non-chewers, while Lachnoclostridium, Ottowia, and Prevotella were enriched in chewers. Additionally, Pediococcus pentosaceus and Leuconostoc citrenum were found exclusively in older, long-term chewers; Lactobacillus reuteri and Lactobacillus salivarius in non-chewers. These findings highlight profound BQ-associated oral microbiome dysbiosis.},
}

@article {pmid42103814,
year = {2026},
author = {Petrás, S and Szabó, BV and Kiss, T and Bahar, MA and Csupor, D and Tóth, B},
title = {Prenatal maternal antibiotic use increases the risk of childhood eczema: a systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51441-x},
pmid = {42103814},
issn = {2045-2322},
abstract = {Early-life disruption of microbiome development is known to impair health; however, the long-term effects of pregnancy-related pharmacological alterations to the maternal gut microbiota on offspring health remain unclear. This meta-analysis aimed to evaluate the impact of maternal antibiotic use (either prenatal or intrapartum) on the risk of childhood atopic dermatitis, based on cohort and case-control studies. Literature searches were conducted in EMBASE, PubMed, Cochrane, and Web of Science databases using predefined PICO (patients, intervention, comparison, outcome) criteria. Overall, our meta-analysis included 30 studies with a total of 4,125,143 mothers and 4,346,050 children. Using the random effects model, our study found that prenatal antibiotic use was associated with higher odds of atopic dermatitis in childhood (aOR: 1.32; 95% CI: 1.12; 1.56). This result remained significant after adjusting publication bias by the trim-and-fill method (aOR: 1.22; 95% CI: 1.03; 1.44), highlighting the potential relevance of antibiotic prescribing practices during pregnancy in relation to childhood atopic disease risk. Intrapartum antibiotic use was not associated with elevated risk for atopic dermatitis in the children (OR: 1.64; 95% CI: 0.84; 3.17). Prenatal antibiotic use appears to have a modest effect on atopic dermatitis in offspring.},
}

@article {pmid42103910,
year = {2026},
author = {Lyu, WN and Shen, CY and Tsai, YJ and Chen, LH and Lee, YH and Chen, SK and Lee, JM and Lou, PJ and Chuang, EY and Tsai, MH},
title = {Intratumoral microbial networks as biomarkers for second primary oral cancer risk in esophageal squamous cell carcinoma.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52247-7},
pmid = {42103910},
issn = {2045-2322},
support = {PL-202208034-V//Fu Jen Catholic University Hospital/ ; 115KKZA3T1//Development Center for Medical Devices, National Taiwan University/ ; },
abstract = {Esophageal squamous cell carcinoma (ESCC) survivors remain at elevated risk of developing second primary oral cancer (SPOC), yet the role of intratumoral microbiomes in SPOC emergence is not fully understood. We performed 16 S rRNA V3-V4 sequencing on tumor brushings from 28 ESCC patients (20 SPOC-negative, 8 SPOC-positive) to profile microbial diversity, taxonomic composition, functional potential, and interaction networks. Alpha diversity metrics (Chao1, Shannon) did not differ significantly between groups (p > 0.05), whereas sparse partial least squares-discriminant analysis of beta diversity robustly separated SPOC-positive from SPOC-negative tumors (p < 0.001), identifying 32 discriminant amplicon sequence variants (ASVs) linked to 41 differential KEGG pathways. Intratumoral Spearman correlation networks (|r| > 0.3, p < 0.05) between the ten most abundant genera and these pathways revealed two distinct modules: a SPOC-associated network centered on Prevotella pallens and P. scopos, enriched in carbohydrate metabolism, PI3K-Akt signaling, and glycosaminoglycan degradation; and a non-SPOC network anchored by Alcaligenaceae, Cyanobiaceae, Rhodobacteraceae, and Prevotella oris, associated with macrolide biosynthesis and aminobenzoate degradation. These findings demonstrate that specific intratumoral microbial interaction networks distinguish ESCC patients who develop SPOC, and highlight network-based microbial signatures as promising biomarkers for SPOC risk stratification.},
}

@article {pmid42103925,
year = {2026},
author = {Anil, and Ramesh, KB and Gouda, MNR and Subramanian, S},
title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52250-y},
pmid = {42103925},
issn = {2045-2322},
abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.},
}

@article {pmid42104127,
year = {2026},
author = {Byrne, D},
title = {How a passion for baking fermented a fresh career move.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-026-01390-2},
pmid = {42104127},
issn = {1476-4687},
}

@article {pmid42104135,
year = {2026},
author = {Cheong, KL and Pan, T and Wang, M and Wang, D and Zhong, S},
title = {Impact of prebiotics, probiotics, and postbiotics on maternal and fetal health: mechanisms, efficacy, and safety across pregnancy.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42104135},
issn = {1530-0447},
abstract = {Microbiome-directed biotics are gaining attention in obstetrics. This review clarifies terminology, mechanisms, clinical effects, and safety for prebiotics, probiotics, and postbiotics. Prebiotics are nondigestible substrates that are selectively used by host microbes to confer health benefits. Probiotics are defined as live microorganisms that improve health when given in adequate amounts. Postbiotics are preparations of nonviable microbes or their components that trigger beneficial responses. We summarize how these agents may influence maternal and fetal physiology across gut, immune, metabolic, vaginal, placental, and human milk contexts. In the gut, they reshape short-chain fatty acid and bile acid pools, modulate enteroendocrine hormones, and recalibrate basal immunity. They also tighten epithelial junctions and stimulate goblet cell mucin, which reduces microbial translocation, endotoxemia, and vascular strain. In the vaginal and urogenital niches, lactobacilli maintain acidity, suppress pathobionts, and may lower colonization risk. At the placenta and in milk, microbial metabolites and immune mediators, including human milk oligosaccharides and secretory IgA, carry maternal cues that shape fetal and neonatal development. Safety profiles differ by class. Prebiotics are generally well tolerated, with dose-dependent gastrointestinal symptoms most common. Probiotics require strain-level validation, viability control, and contaminant-free production. Postbiotics need to be verified inactivation and structural characterization. IMPACT: Provides a comprehensive, mechanism-based overview of how prebiotics, probiotics, and postbiotics influence maternal and fetal health across multiple physiological systems. Clarifies definitions, safety profiles, and quality standards for biotics in pregnancy, addressing current inconsistencies in research and commercial products. Integrates emerging evidence on postbiotics and vertical microbial transmission, offering a timely framework for future clinical applications and regulatory guidance.},
}

@article {pmid42104237,
year = {2026},
author = {An, L and Liu, X and Li, X and Chu, Y and Sun, X and Chu, J and Nie, Y},
title = {Contact-mediated bacterial transmission and infection risk dynamics in a newly opened hospital ward.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05030-7},
pmid = {42104237},
issn = {1471-2180},
support = {32500094//National Natural Science Foundation of China/ ; },
abstract = {The hospital microbiome significantly influences patient recovery and clinical outcomes. However, the dynamics of microbial colonization and transmission following initial patient occupancy remain poorly understood. Here, we employed 16 S rRNA gene amplicon sequencing of the V3-V4 region (Illumina platform) to investigate bacterial community dynamics on surfaces within neurosurgery ward and patients as a new hospital became operational. Our results showed that bacterial colonization in hospital wards follows distinct site-specific patterns, after hospital opening, alpha diversity was significantly increased on floors and drawer handles but decreased on bedrails and faucet handles compared to preopening. Beta diversity analysis showed that surfaces frequently contacted by patients exhibited the greatest compositional turnover, such as bedrails, drawer handles, and faucet handles, bacterial communities in after-opening were more homogeneous across sites than preopening, indicating potential bacterial transmission. Moreover, we found that following patient admission, patient hand-derived microbiomes exert a significant influence on the bacterial communities in hospital wards, with a particularly pronounced impact on bedrails. Additionally, the potential pathogenic potential of the microbial community at the taxonomic level of bedrails in post-opening was significantly higher than preopening, which does not reflect direct clinical infection risk. Taken together, these findings underscore the critical role of human contact in shaping hospital microbiomes and highlight the importance of targeted infection control strategies to mitigate potential pathogen transfer.},
}

@article {pmid42104530,
year = {2026},
author = {Bibinger, S and Nosenko, T and Sivaprakasam Padmanaban, PB and Schulz, S and Schroeder, H and Kersten, B and Zimmer, I and Buegger, F and Schloter, M and Schnitzler, JP},
title = {Provenance legacies override species effects in shaping oak rhizosphere microbiomes and metabolomes.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71213},
pmid = {42104530},
issn = {1469-8137},
support = {457330647//Deutsche Forschungsgemeinschaft/ ; 2220WK09A4//German Federal Ministry of Food and Agriculture (BMEL), Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU)/ ; 2220WK09B4//German Federal Ministry of Food and Agriculture (BMEL), Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU)/ ; },
abstract = {As climate change drives more frequent drought-heat extremes, selecting drought-tolerant trees is crucial for future forest resilience. However, the role of tree-microbial associations remains largely unclear. We investigated how geographic origin, species identity, and intrinsic water use efficiency (iWUE) shape the rhizosphere microbiome and root-rhizosphere metabolome of Quercus robur L. and Q. petraea (Matt.) Liebl. In a 6-yr common garden experiment, we analyzed trees from two distinct geographic origins (upper Rhine basin and north German lowland) using 16S/ITS metabarcoding and untargeted metabolomics. We found a consistent legacy effect of seed origin on the prokaryotic rhizosphere microbiome and metabolome, whereas tree species had no significant impact. The bacterial family Pseudonocardiaceae was enriched for trees from the drier origin (NGL), while Blastocatellaceae and Micromonosporaceae were associated with iWUE. Higher iWUE also correlated with lower prokaryotic diversity. Ellagic acid, a polyphenol associated with drought tolerance, was enriched in the drier origin. The rhizosphere fungal community, however, was largely unaffected by origin or species. Our findings suggest that ecotypic adaptation linked to origin can outweigh species-level traits in shaping the oak rhizosphere. These findings emphasize that provenance-driven adaptation influences plant-microbe interactions and underscore the need for provenance-aware selection to strengthen forest drought resilience.},
}

@article {pmid42104576,
year = {2026},
author = {Ii C, JF and Vidal, MJS and Dela Cruz, FSE and Tantengco, OAG and Menon, R},
title = {The Microbiome Signature of the Placenta and its Role in Spontaneous Preterm Birth: A Systematic Review and 16S rRNA Re-Analysis.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {5},
pages = {e70246},
doi = {10.1111/aji.70246},
pmid = {42104576},
issn = {1600-0897},
mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Premature Birth/microbiology/immunology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; },
abstract = {PROBLEM: The advent of high-throughput 16S rRNA sequencing has enabled deeper insights into microbial communities associated with adverse pregnancy outcomes, including spontaneous preterm birth (sPTB). While microbial dysbiosis in the cervicovaginal and oral-gut microbiomes has been implicated in sPTB, the existence of a placental microbiome remains contentious. Traditional paradigms of a "sterile womb" have been challenged by studies suggesting a low-biomass microbial community in the placenta, though recent evidence disputes this claim, attributing findings to contamination or transient microbial DNA signals.

METHOD: This study systematically reviewed placental microbiome studies employing 16S rRNA sequencing and re-analyzed publicly available datasets to determine microbial signatures in term and preterm placentas. Following a comprehensive search of three databases and stringent inclusion criteria, seven studies were included. The risk of bias was assessed using a modified Joanna-Briggs tool, revealing moderate-to-low risk across studies. Methodological heterogeneity, including differences in contamination controls, sequencing regions, and analytical platforms, was a significant limitation.

RESULTS: A re-analysis of sequencing data showed no consistent microbiome signature distinguishing the term from preterm placentas. Beta diversity analysis revealed no group clustering, while alpha diversity indices showed comparable species richness. Bacterial DNA in placental tissues was primarily attributed to contamination from the urogenital tract or laboratory processes.

CONCLUSION: Findings underscore the importance of robust contamination control and standardized protocols in low-biomass microbiome research. Future studies should employ advanced techniques, such as metagenomics and fluorescence in situ hybridization, to evaluate the functional relevance of microbial communities in the placenta, as well as rule out microbial DNA deposited in the placenta through circulating bacterial extracellular vesicles (EVs).},
}

Humans
Female
Pregnancy
*Placenta/microbiology
*Premature Birth/microbiology/immunology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics

@article {pmid42104937,
year = {2026},
author = {Kang, X and Hu, L and Song, J and Zhang, Z and Li, Y and Zhang, Q and Luo, C and Pang, Y and Guo, P and Yue, B and Li, P and Fan, Z},
title = {Snake Gut Microbiota as a Source of Anti-Inflammatory Probiotics: Isolation and Functional Characterization of Two Novel Strains.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70118},
pmid = {42104937},
issn = {1749-4877},
support = {2023NSFSC1935//Sichuan Science and Technology Program/ ; },
abstract = {The intestinal microbiome is fundamental to host physiological homeostasis, while deviations from its balanced state have been linked to inflammatory bowel diseases (IBD). To address the limitations of conventional antibiotic therapies, this study explored snake gut microbiota as a novel source of anti-inflammatory probiotics. We explored the gut microbiota of five snake species (Deinagkistrodon acutus, Trimerodytes annularis, Trimerodytes percarinatus, Lycodon rufozonatus, and Trimeresurus stejnegeri) through metagenomic sequencing. Community composition analysis revealed that the phylum-level composition was mainly Proteobacteria, Bacteroidetes, Actinomycetota, and Firmicutes. We further detected some potential probiotic species, such as Enterococcus, Lactobacillus, and Limosilactobacillus. From 196 isolated strains, Lactobacillus johnsonii DA0116 and Limosilactobacillus reuteri DA0218 were selected through rigorous safety and functional assessments, including acid/bile tolerance, pathogen inhibition, and adhesion capacity. In a DSS-induced murine colitis model, both strains significantly reduced disease activity index (DAI), pro-inflammatory cytokines (TNF-α, IL-6, and IL-8), and restored gut microbiota diversity. Additionally, whole-genome analysis identified bacteriocin synthesis clusters (gassericin-S/T) and carbohydrate metabolism genes, explaining their antimicrobial and immunomodulatory properties. This study not only emphasizes the untapped latent value of reptilian gut microbiota for probiotic discovery but also provides two candidate strains with therapeutic promise for IBD and functional food applications.},
}

@article {pmid42105032,
year = {2026},
author = {Saeed, T and Grover, M and Singh, AK and Prasanna, R and Kaushik, R and Meena, MC and Mandal, PK and Kumar, P},
title = {Hydrophyte root microbiome: a novel reservoir of plant growth-promoting bacteria for enhancing lettuce (Lactuca sativa L.) growth and nutritional quality under soilless cultivation.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42105032},
issn = {1573-0972},
mesh = {*Lactuca/growth & development/microbiology ; *Plant Roots/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Biomass ; Plant Growth Regulators/metabolism ; Nutritive Value ; Soil/chemistry ; Germination ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Soilless cultivation is a major component of modern protected agriculture; however, often lack the beneficial microbial communities that support plant health in natural soils. This study explored hydrophyte root microbiomes as an eco-friendly and novel source of plant growth-promoting bacteria (PGPB) for engineering beneficial microbial communities in soilless systems. Bacteria associated with the roots of Eichhornia crassipes, Pistia stratiotes, and Alternanthera philoxeroides, expressing PGP traits were assessed for their growth-promoting potential on lettuce (Lactuca sativa L. cv. 'Lolo Red') using cocopeat-based soilless media and soil under polyhouse conditions. Hydrophyte associated rhizobacteria exhibited diverse PGP functions, including nutrient solubilization and phytohormone production, similar to those exhibited by rhizobacteria associated with terrestrial plants. Under soil and soilless conditions, lettuce crop inoculated with hydrophyte associated rhizobacteria significantly enhanced germination, plant biomass, root architecture, photosynthetic pigments and leaf quality traits, including TSS (total soluble solids), total phenolics, vitamin C, anthocyanins, antioxidant enzyme activities, DPPH (2,2-Diphenyl-1-picrylhydrazyl) radical scavenging and FRAP (Ferric Reducing Antioxidant Power) responses in both the cultivation systems. Two strains viz. Bacillus aerius Aq35 and Pseudomonas protegens Aq45 were particularly very promising. Under soilless cultivation, Aq35 enhanced root fresh weight and surface area by 90.0% and 83.5%, respectively, while Aq35 and Aq45 increased lettuce yield by 39.62% and 28.70%, respectively. Bacterial inoculation significantly enhanced the availability of soil and plant macro (N, P, and K) and micronutrients (Fe, Mn, Zn, and Cu) along with a marked increase in enzymatic activities and microbial biomass carbon (MBC). Under soilless substrate, dehydrogenase activity increased from 43.40 to 64.65 µg TPF g[-1] day[-1], while alkaline phosphatase activity increased from 261.53 to 380.87 µg PNP g[-1]h[-1] inoculated (Aq35) treatment over uninoculated treatment indicating enhanced substrate biological quality. These results demonstrate that hydrophytes as rich, pre-adapted reservoirs of potent PGPB, and strains such as B. aerius Aq35 and P. protegens Aq45 hold strong potential as biostimulants for sustainable soilless agriculture.},
}

*Lactuca/growth & development/microbiology
*Plant Roots/microbiology/growth & development
*Microbiota
Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
Biomass
Plant Growth Regulators/metabolism
Nutritive Value
Soil/chemistry
Germination
RNA, Ribosomal, 16S/genetics

@article {pmid42105271,
year = {2026},
author = {Meijer, GW and Fogliano, V and Lähteenmäki, L and Ahrné, LM and Labbe, D and Forde, CG},
title = {From fiction to facts: on the safety, rules, perception, and role of food additives.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-26},
doi = {10.1080/10408398.2026.2669055},
pmid = {42105271},
issn = {1549-7852},
abstract = {Consumer perceptions of food additives are often negative, driven by unfamiliar terminology, associations with "ultra‑processed food," and concerns about reduced naturalness. Despite this, additives play essential roles in food preservation, sensory quality, and safety, and undergo rigorous safety evaluation in jurisdictions worldwide by authoritative bodies such as JECFA, EFSA, and the (US-)FDA. While some studies suggest possible effects of specific emulsifiers or sweeteners on the microbiome or metabolism, evidence is limited and often not reflective of real dietary exposure. Broader claims-such as additives causing "hyper‑palatability" or "food addiction"-lack scientific support, with research showing that overeating is more closely linked to energy density and food availability than additives themselves. Reducing additives use, without sound scientific justification, may inadvertently worsen nutrient profiles of foods, and increase food waste and health risks. Improving public understanding of additives safety and function is essential to counter misconceptions and avoid counterproductive reformulation decisions.},
}

@article {pmid42105460,
year = {2026},
author = {Ma, C and Chang, M and Zang, S and Shi, K and Sha, Z},
title = {Dual-omics links host genomic variation to gut microbiome restructuring under Mycobacterium marinum challenge in Cynoglossus semilaevis.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101838},
doi = {10.1016/j.cbd.2026.101838},
pmid = {42105460},
issn = {1878-0407},
abstract = {Disease outbreaks caused by Mycobacterium marinum pose a major challenge to marine aquaculture and threaten the sustainable production of Cynoglossus semilaevis. Increasing evidence suggests that host genetic variation and gut microbial communities may jointly influence disease-related phenotypes, yet their interaction under mycobacterial challenge remains poorly understood. In this study, we combined host whole-genome resequencing and gut 16S rRNA sequencing to explore host-microbiome associations in C. semilaevis following M. marinum challenge. Gut microbiota analysis revealed significant differences in community structure and composition between the experimental and control groups, with marked shifts in dominant taxa and differential enrichment of several bacterial genera. Genome-wide association analysis identified nine significant SNPs (λ = 1.02) associated with infection status, distributed across chromosomes 5, 10, 13, 18, and 19. Functional annotation showed that most of these loci were located in non-coding or regulatory regions, including six intronic SNPs, one ncRNA_exonic SNP, one ncRNA_intronic SNP, and one intergenic SNP. Correlation network analysis further linked host genetic variants with changes in gut microbial taxa, suggesting a potential association between host genomic variation and microbiome restructuring under challenge conditions. Overall, these results provide preliminary evidence that host genomic variation may be associated with gut microbiome dynamics during M. marinum infection in C. semilaevis. Although limited by sample size, this dual-omics framework offers a useful basis for future validation of host-microbiome markers relevant to disease-resilience breeding in aquaculture. CONCLUSION: Host genomic variation in C. semilaevis may be associated with gut microbiome restructuring under M. marinum challenge, particularly involving Acinetobacter dynamics. Although limited by sample size, this dual-omics framework provides a preliminary basis for future disease-resilience breeding in aquaculture.},
}

@article {pmid42105533,
year = {2026},
author = {Nizam, A and Shireen, N and Hasan, MR and Singh, S and Farooqui, M and Naithani, D and Farooqi, H},
title = {Artificial intelligence, omics, and biomarkers: Redefining lung cancer early detection.},
journal = {Current problems in cancer},
volume = {63},
number = {},
pages = {101312},
doi = {10.1016/j.currproblcancer.2026.101312},
pmid = {42105533},
issn = {1535-6345},
abstract = {Lung cancer, the leading cause of death worldwide, claims millions of lives yearly, largely due to limited early interventions. Currently used lung cancer screening methods are still limited in their reach and accuracy due to invasiveness, radiation exposure, and low sensitivity, especially in early stages, necessitating the need for innovative technologies. This review examines emerging tools for the early detection of lung cancer, utilizing biomarkers in conjunction with omics approaches and AI technology, which could significantly impact its clinical landscape. Tumor cells release specific biological indicators called biomarkers, which can be cellular components, nucleic acid fragments, protein fragments, or metabolites, detected from bodily fluids through non-invasive methods. The integration of biomarkers with omics technologies (such as proteomics and genomics) or multi-omics provides a comprehensive insight into the molecular profiles of various cancer subtypes and stages. Artificial intelligence, including machine learning and deep learning tools, further increases the accuracy and precision of these techniques. However, challenges still persist in its clinical translation, including technical limitations, regulatory hurdles and ethical concerns. Overcoming these limitations requires standardised protocols, interdisciplinary collaborations, and strategies for equitable access to innovative technologies. Novel, cutting-edge technological interventions, such as advanced imaging techniques, sensor technology, nanotechnology, breathomics, and microbiome analysis, have the potential to enhance early lung cancer diagnosis, ultimately improving patient outcomes and reducing the global burden of this disease.},
}

@article {pmid42105545,
year = {2026},
author = {Shan, X and Wang, H and Liu, X and Li, P and Zhang, F and Wang, R and Xue, M and Li, F},
title = {Remodeling distinct rhizosphere interactions of plant-microbiome by legacy and alternative PFASs: A multi-omics insight and biphasic role of iron plaque.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142313},
doi = {10.1016/j.jhazmat.2026.142313},
pmid = {42105545},
issn = {1873-3336},
abstract = {Rhizosphere microhabitat as a dominant sink for per(poly)fluoroalkyl substances (PFASs) and hotspot for redox reactions and root iron plaque (IP) forming is largely affected by the interactions between plants and bacteria. However, whether PFOA and its substitute (HFPO-DA) modulated distinct rhizosphere symbiotic patterns and what roles IP played remain unclear. This study integrated plant physiology, metabolism and rhizosphere microbiome to systematically elucidate their differences in remodulating plant-microbiome interactions and IP roles. Results showed that PFOA preferred to accumulate in roots and induced serious oxidative stress, while HFPO-DA was more easily transported to shoots directly affecting photosynthesis. Molecular docking suggested higher proteinic affinity of HFPO-DA, inhibiting superoxide dismutase activity. PFOA and HFPO-DA increased organic acids and sugars in root exudates recruiting differential beneficial bacteria. However, HFPO-DA downregulated the glycerophospholipid metabolism, shaped a more vulnerable and simpler bacterial network. Remarkably, PFASs concentration determined the double-edged roles of IP. At environmental levels, IP promoted glycerophospholipids and small peptides release facilitating azotobacter recruitment and photosynthesis. But under high-dose stress, it induced accelerated pollutant migration especially HFPO-DA, thereby exacerbating phytotoxicity. Partial least squares path modeling revealed that PFOA indirectly influenced plant phenotypes via shaping bacterial community, while HFPO-DA not only modified that but also altered root exudates. This work unveils distinct rhizosphere symbiotic patterns and IP biphasic role remodulated by legacy and alternative PFASs, and provides a reference for their risk assessment and control through nature-based solutions.},
}

@article {pmid42105760,
year = {2026},
author = {Fitzpatrick, CR and Allen Smith, R and Hige, J and Law, TF and Russ, D and Ajayi, OE and Eida, AA and Jacob, P and Jowers, M and Kumar, N and Lai, CTU and Anguita-Maeso, M and Peterson, SB and Saha, C and Skelly, T and Zhao, Q and Zhou, W and Grant, SR and Mougous, JD and Jones, CD and Dangl, JL},
title = {Streptomyces enrichment in roots during drought is uncoupled from plant benefit and is driven by host suppression of iron uptake and immunity.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.04.027},
pmid = {42105760},
issn = {1097-4172},
abstract = {Drought reshapes the plant root microbiota, yet the mechanistic drivers and consequences of this observation remain unclear. We discovered that suppression of host immunity and iron homeostasis is required for Streptomyces enrichment in roots during drought across diverse soils. Genetic and physiological manipulation of these host pathways confirmed their requirement in modulating Streptomyces root enrichment. Drought-induced suppression of iron uptake was conserved across the ∼160 mya monocot-eudicot divergence. Some Streptomyces strains enhanced plant growth and rescued iron uptake under drought. These benefits were uncoupled from Streptomyces root enrichment. They were instead shaped by intra-Streptomyces antagonism. We propose a two-step model: drought-driven downregulation of host iron and immune pathways enriches Streptomyces, while intra-genus dynamics fine-tune strain-level assembly and functional outcomes. Our data refine the idea that Streptomyces are enriched in roots during drought in response to a plant "cry for help" and consequently contribute to the alleviation of this abiotic stress.},
}

@article {pmid42105814,
year = {2026},
author = {Khan, YA and Anas, M and Khan, F and Ali, M and Al-Zharani, M and Nasr, FA and Qamar, W and Rahman, S},
title = {Cannabinoids in autoimmune diseases: mechanistic insights and translational challenges.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {118032},
doi = {10.1016/j.bcp.2026.118032},
pmid = {42105814},
issn = {1873-2968},
abstract = {Cannabinoids are traditionally recognized for their effect on the nervous system. Emerging evidence suggests that cannabinoids mitigate inflammation driven by Th1/Th17 responses, which are linked to autoimmune diseases. In addition to their symptomatic, and analgesic effects, cannabinoids suppress the immune response by modulating regulatory T-cell activity, reducing microglial activation, and help in maintaining the integrity of the epithelial barrier. These findings suggest that cannabinoids may be involved in immune, and metabolic regulatory pathways. Despite the promising preclinical data, translating these findings into effective treatments for autoimmune disorders has proven challenging. Current human studies have primarily focused on symptomatic relief such as reducing spasticity, managing pain, improving sleep quality, and boosting appetite. However, few trials have included immune profiling, i.e., assessed cytokine panels, performed immune cell phenotyping, tracked relapses, or utilized inflammation-focused imaging endpoints. Consequently, documented benefits are primarily symptomatic, while potential disease-modifying effects are not yet adequately studied. Cannabinoids interact with CB1, CB2, TRP, and PPAR-γ receptor proteins, suggesting that they may offer targeted immune modulation rather than broad immunosuppression, potentially overcoming limitations of conventional therapies. Moreover, new compounds like cannabigerol (CBG), cannabidivarin (CBV), and CB2-selective agonists with minimal psychoactivity offer expanded therapeutic options. However, challenges persist due to variability in formulations, bioavailability issues, regulatory hurdles, and a lack of long-term safety data. Future clinical development will require standardised GMP-grade preparations, robust pharmacokinetic evaluation, and trials that include immune-related endpoints such as T-cell polarisation, inflammasome markers, oxidative stress profiles, microbiome signatures, and longitudinal imaging, to clarify their therapeutic potential in autoimmune diseases.},
}

@article {pmid42105827,
year = {2026},
author = {Bottaro, F and Enrico, P and Ratti, G and Brambilla, P and Delvecchio, G},
title = {Gut Microbiome Variability and Brain Alterations in Schizophrenia: A Scoping Review of Structural and Functional MRI Studies.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106739},
doi = {10.1016/j.neubiorev.2026.106739},
pmid = {42105827},
issn = {1873-7528},
abstract = {INTRODUCTION: Schizophrenia (SCZ) is increasingly considered a multifactorial disorder involving gut-brain interactions. Current evidence supports gut microbiome alterations in SCZ, along with well-established structural and functional brain abnormalities. However, findings linking gut microbiome variability to neuroimaging alterations in SCZ have not yet been comprehensively integrated.

METHODS: Following the Joanna Briggs Institute methodology for scoping reviews and the PRISMA-ScR checklist, a literature search was performed in PubMed, Scopus, and Web of Science, selecting structural magnetic resonance imaging (sMRI) and resting-state functional MRI (fMRI) studies examining the associations between gut microbiome variability and brain alterations in first-episode and chronic SCZ.

RESULTS: Eight studies (one sMRI-only, one fMRI-only, and six combining sMRI and fMRI) met the inclusion criteria. The sMRI studies primarily showed associations between gut microbiome composition and gray matter volume in frontal, temporal, and limbic regions, while the fMRI studies found microbial variations associated with resting-state activity and functional connectivity across cortico-subcortical and large-scale brain networks. Notably, gut microbiome-neuroimaging associations differed between early and chronic stages of the disorder, suggesting stage-dependent gut-brain relationships.

CONCLUSIONS: Available evidence supports an association between gut microbiome variability and neuroimaging alterations in SCZ, with emerging differences between first-episode and chronic patients. Despite methodological heterogeneity and predominantly cross-sectional designs, these findings highlight the relevance of a multimodal gut-brain framework. Future longitudinal, multimodal studies integrating gut microbiome, neuroimaging, and clinical features may help disentangle biological heterogeneity and improve patient stratification in SCZ.},
}

@article {pmid42105950,
year = {2026},
author = {Kuna, A and Killi, K and Mettu, TR},
title = {Quantum-Enabled Approaches to Precision Nutrition: Linking Molecular Interactions with Metabolic Prediction.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101584},
doi = {10.1016/j.tjnut.2026.101584},
pmid = {42105950},
issn = {1541-6100},
abstract = {Precision nutrition aims to tailor dietary guidance to individual biology, yet current methods struggle to integrate complex molecular and multi-omic data into clinical care. Emerging quantum-driven technologies encompassing quantum computing, quantum chemistry and quantum-enhanced sensors link detailed molecular modelling with real-time metabolic forecasting. Quantum chemical simulations and machine learning model nutrient protein interactions at the atomic level, while quantum algorithms and echo state networks have been applied to create digital metabolic avatars that predict weight and metabolic trajectories from daily diet and activity data. Quantum computing enables rapid integration of genomic, metabolomic and microbiome datasets and supports optimization of personalised diet plans. Advances in computational molecular modelling now allow prediction of molecular structures and properties relevant to food components, and prototype quantum metabolic twins have demonstrated the capacity to forecast weight trends from incomplete real-world data. The clinical implications include proactive dietary interventions, noninvasive nutrient deficiency screening and improved prediction of disease risk from metabolic profiles, all of which can enhance patient outcomes and clinical decision making. This perspective synthesizes recent advances and delineates research directions at the intersection of quantum science, medical diagnostics, metabolism and clinical nutrition, with implications for clinicians, physicians, dietitians and clinical decision support in patient care.},
}

@article {pmid42105976,
year = {2026},
author = {Gomes, J and Rodrigues, ES and Carvalhinho-Lopes, PS and Comis-Neto, AA and Pujol Arena, RV and Birmann, PT and Fidelis, EM and Meus, SS and Rodrigues, BG and Alves de Jesus, GF and Ávila, DS and Pesarico, AP and Ribeiro, AM and Rosa, SG and Pinton, S},
title = {Paraprobiotics attenuate oxidative stress, dopaminergic neuron loss, and gut microbiome imbalance in an intranasal MPTP rat model of Parkinson's disease.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {111011},
doi = {10.1016/j.neuropharm.2026.111011},
pmid = {42105976},
issn = {1873-7064},
abstract = {Intestinal dysbiosis may contribute to the progression of Parkinson's disease (PD) by promoting inflammation and oxidative stress. Paraprobiotics, defined as non-viable microbial cells, have emerged as a promising therapeutic strategy. This study evaluated the neuroprotective, gastroprotective, and microbiota-modulating effects of a paraprobiotic blend comprising Lactobacillus casei CCT 7859, Bifidobacterium lactis CCT 7858, and Streptococcus thermophilus ATCC 19258 in a murine PD model induced via intranasal administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Seventy female Wistar rats received either intranasal MPTP or saline, followed 24 hours later by 14 days of paraprobiotic treatment (100 mg/kg/day, intragastrically). Fecal and tissue samples were collected for microbiota, oxidative stress, dopaminergic neurodegeneration, and physiological parameter analyses. Antioxidant enzymes (superoxide dismutase and catalase), oxidative damage markers (malondialdehyde, reactive oxygen and nitrogen species), gut microbiota composition, immunohistochemistry for tyrosine hydroxylase, and physiological variables such as body weight, intestinal length, fecal water content, and ash levels were assessed. Paraprobiotic administration enhanced antioxidant defenses, reduced oxidative damage in brain and intestinal tissues, preserved dopaminergic neurons within the nigrostriatal pathway, improved fecal hydration (indicating constipation relief), and decreased fecal mineral content, suggesting improved nutrient absorption. Notably, modulation of gut microbiota, including an increased abundance of beneficial families (Lactobacillaceae and Sutterellaceae) and a reduced abundance of potentially harmful families (Clostridiaceae and Peptostreptococcaceae), may have contributed to oxidative stress attenuation, preservation of gut health, and prevention of dopaminergic neuron loss. Collectively, these findings suggest that paraprobiotics may modulate microbiota composition and oxidative stress in both intestinal and brain tissues, and may attenuate dopaminergic neurodegeneration in an experimental model of PD.},
}

@article {pmid42106160,
year = {2026},
author = {Wang, Y and Liu, J and Verbeke, K and Retamal, NG and Akkerman, R and de Vos, P},
title = {Dietary fiber and GLP-1 receptor agonists in obesity management: converging mechanisms, interactions, and strategies for durable weight control.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100647},
doi = {10.1016/j.advnut.2026.100647},
pmid = {42106160},
issn = {2156-5376},
abstract = {Glucagon-like peptide-1 receptor agonists (GLP-1RAs) have transformed the management of obesity by producing substantial and durable weight loss. However, gastrointestinal adverse effects, including nausea, vomiting, and constipation, are a common, dose-dependent, and frequent cause of discontinuation. Furthermore, weight regain is typical after drug withdrawal, reflecting the chronic and relapsing nature of obesity. Long-term adherence is essential but often constrained by high cost, injection burden, and patient preference. Moreover, the consequences of chronic GLP-1 receptor activation on gut physiology, microbiota composition, and immune tolerance remain incompletely defined. In parallel, dietary fibers offer a physiological means of engaging the same gut-brain axis through microbial fermentation and the stimulation of endogenous GLP-1. Fibers deliver broad benefits as they strengthen gut barrier function, enrich short chain fatty acid, and recalibrate immunity toward an anti-inflammatory state. Nevertheless, weight loss with fiber alone is typically more modest than with GLP-1RAs and depends on the type, dose, and duration of use. Tolerability can be limited by bloating or gas, particularly if intake is increased too rapidly. This review critically examines the convergence and divergence between GLP-1RAs and dietary fibers. We discuss their mechanistic overlaps in appetite control, metabolism and immune modulation, and highlight potential interactions, such as altered fermentation dynamics during pharmacological slowing of gastric emptying and the potential for GLP-1R desensitization. We explore opportunities for fibers to mitigate GLP-1RA-related adverse effects, support bowel regularity, and stabilize the microbiota during treatment or after discontinuation. A pragmatic framework is raised to place dietary fiber and lifestyle measures as the foundation of care, reserves GLP-1RA therapy for highest-risk individuals, and plans for fiber supplements once pharmacotherapy is reduced. Well-designed trials that combine GLP-1RAs with well-characterized fibers, include microbiome end points, and assess long-term outcomes are needed to optimize efficacy and reduce dependence on costly pharmacotherapy.},
}