@article {pmid42083348,
year = {2026},
author = {Valentini, M and Valentini, GM and Akkawi, I and Zeppa, SD and Bartolacci, A and Pegreffi, F and Zmerly, H},
title = {The Interplay between Osteoarthritis and the Microbiome-joint Axis: A Systemic Perspective on Novel Therapeutic Targets.},
journal = {Current rheumatology reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115733971450825260423042902},
pmid = {42083348},
issn = {1875-6360},
abstract = {Osteoarthritis (OA) is a chronic and progressive joint disease involving the articular cartilage, synovium, subchondral bone, and ligaments, ultimately leading to pain, dysfunction, and, in advanced stages, joint destruction. Several factors contribute to the development and progression of OA, including genetic predisposition, biomechanical stress, metabolic imbalance, and chronic low-grade inflammation. Recently, a novel factor has emerged: the gut microbiome. Gut dysbiosis, defined as an alteration in gut microbiota homeostasis, can disrupt immune, metabolic, and inflammatory pathways, promoting systemic inflammation and accelerating degenerative changes in joint tissues. Conversely, restoration of a balanced gut microbiota may play a protective role and represent a promising avenue for innovative therapeutic strategies. The aim of this review is to analyse the relationship between gut dysbiosis and osteoarthritis, and to discuss potential therapeutic approaches targeting the microbiome to prevent disease progression.},
}

@article {pmid42083431,
year = {2026},
author = {Ebersole, JL and Kirakodu, SS and Gonzalez, OA},
title = {Transcriptomic analysis of gingival tissues in resolved experimental periodontal lesions of nonhuman primates.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70048},
pmid = {42083431},
issn = {1943-3670},
support = {P20GM103538/NH/NIH HHS/United States ; P40RR03640//Caribbean Primate Research Center/ ; //Microarray Core of the University of Kentucky/ ; },
abstract = {BACKGROUND: This study used a preclinical model of experimental periodontitis in nonhuman primates to evaluate the biological features of resolved periodontal lesions.

METHODS: Macaca mulatta (rhesus monkeys) were age-stratified into young [≤3 years (7-10-year-old humans)], adolescent/young adult [3-7 years (12-25-year-old)], adults [12-15 years (40-50-year-old)], and aged [17-23 years (60-80-year-old)]. The samples were also analyzed based on sex or matrilineal derivation. The gingival transcriptome was evaluated using microarray analyses on tissue biopsies from healthy tissues and at resolution (i.e., clinical improvement).

RESULTS: Resolution sites showed clinical improvement, as well as patterns of increased or decreased gene expression in resolution versus healthy tissues in all age groups. These differences represented a large array of adaptive immune genes that were elevated in resolution, with decreased metabolic, regulatory, structural, and transcription factor gene expression in the resolution samples. Many of these genes were common to all age groups or sex/matriline, thus suggesting some fundamental core profile of affected genes that discriminate healthy from lesion resolution tissues.

CONCLUSIONS: Irrespective of age, the biology of periodontal lesion resolution tissues is distinct from healthy tissues. Despite a robust inflammatory response to the ligature-induced microbiome changes during experimental periodontitis, younger individuals showed significantly less destructive disease and different transcriptome profiles that could reflect improved lesion resolution. While sex and matriline affected the gene expression patterns, these generally overlapped with the prominent genes identified for resolution versus health across age groups. Highly affected genes could be considered biomarkers for resolved tissues, linking clinical and biological resolution of periodontal lesions.},
}

@article {pmid42083540,
year = {2026},
author = {YuXuan, G and Iqbal, MK and Khan, B and Khan, H and Ud Din Shah, SS and Al-Hussain, F and Kiyani, MM and Bashir, S},
title = {The Gut-Brain Connection: Exploring the Connection Between the Gastrointestinal System and Parkinson's Disease.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273419693251206130059},
pmid = {42083540},
issn = {1996-3181},
abstract = {Parkinson's disease (PD) is a complex neurodegenerative disorder characterized by motor and non-motor symptoms. Recent studies indicate that the gut-brain axis contributes to both the initiation and progression of PD, a disorder that primarily affects the central nervous system. This article reviews current research on the interaction between the central nervous system and the gastrointestinal tract in PD. The vagus nerve, areas of the enteric nervous system (ENS), systemic inflammation, and the microbiome are all involved in this interaction. For example, recent studies have shown PD-related effects such as abnormal distribution of gut bacteria, increased gut barrier permeability, and α-synuclein transport from the gut to the brain. A comprehensive evaluation of motor and non-motor symptoms was conducted. Additionally, we explored drugs that specifically target the gastrointestinal system, the possible gastrointestinal symptoms of PD, and how these symptoms may serve as early indicators of the disease. Our article also discusses dietary modifications, probiotics, and fecal microbiota transplantation as potential treatments for PD. By reviewing clinical and basic scientific research as well as translational applications, this article highlights the relationship between the central nervous system and the digestive system in PD. A better understanding of this complex connection may lead to improved detection and treatment of this debilitating disease and offer new opportunities for prevention and therapy. Finally, this paper suggests directions for further research in this area.},
}

@article {pmid42083599,
year = {2026},
author = {Kozlova, AS and Zgoda, AV and Petushkova, NA and Bolochenkov, NA and Zgoda, VG and Salnitska, MA and Kazakov, DV and Lisitsa, AV},
title = {The Microbiomic Metaproteome of the Taiga Tick Ixodes persulcatus from the Tyumen Region.},
journal = {Acta naturae},
volume = {18},
number = {1},
pages = {55-63},
pmid = {42083599},
issn = {2075-8251},
abstract = {Metagenomic studies have revealed the taxonomic composition of the taiga tick (Ixodes persulca tus) microbiome, whereas metaproteomic data has provided information on the biochemically active fraction of the microbial community residing in the tick. The aim of this study was to characterize the biological pro cesses taking place within the microbiome of the taiga tick I. persulcatus using a metaproteomic approach. To expand the range of identifiable proteins, we used two trypsin concentrations in sample preparation for mass spectrometric analysis. The metaproteomes of unfed female and male ticks were analyzed, which ena bled identification of protein products encoded by 2,100 genes from microorganisms belonging to 203 bacteri al and fungal species. Increased abundance of proteins associated with Ascomycota fungi, particularly abun dant in females, were detected. Proteins from the pathogenic Rickettsia and Borrelia species were identified. These findings enable a transition from a taxonomic metagenomic description to a functional analysis of the microbial consortium role in the physiology of the vector tick, particularly given the identified microbiota differences related to the tick sex.},
}

@article {pmid42083728,
year = {2026},
author = {Gaskin, PS and Chami, PS},
title = {Low Weight Loss Response to Incretin Analogs: A Systematic Review.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70145},
doi = {10.1111/obr.70145},
pmid = {42083728},
issn = {1467-789X},
abstract = {The development of GLP-1 and GIP analogs has been a significant breakthrough in type 2 diabetes and obesity pharmacotherapy. However, individual responses to these medications can vary widely. This systematic review examines factors associated with low or no weight loss response to GLP-1 and GIP analogs. Key predictors of poor response include higher baseline body weight, BMI, HbA1c, and insulin resistance. Genetic factors, such as variants in the GLP1R gene, may also influence treatment outcomes. Metabolic health status, particularly glycemic control and insulin sensitivity, plays a crucial role in determining weight loss efficacy. Adherence to medication regimens is strongly associated with treatment success, with each additional month of treatment linked to greater weight loss. Lifestyle factors, including dietary habits and physical activity, can modulate responses to these medications. Emerging evidence suggests that gut microbiome composition may mediate weight loss outcomes. Demographic factors such as male sex and older age are associated with lower weight loss responses. Understanding these predictors is essential for optimizing treatment strategies, setting realistic expectations, and moving towards a precision medicine approach in obesity care. Further research is needed to validate these findings in diverse populations and develop practical tools for clinical decision-making.},
}

@article {pmid42083785,
year = {2026},
author = {Wu, Y and Liu, J and Ren, Y and Zou, C},
title = {Unravelling the Gut-Skin Axis in Chronic Urticaria: Dysbiosis, Metabolites and Immunological Mechanisms.},
journal = {Experimental dermatology},
volume = {35},
number = {5},
pages = {e70261},
doi = {10.1111/exd.70261},
pmid = {42083785},
issn = {1600-0625},
support = {2025C02080//the Key Research and Development Plan of Zhejiang Province/ ; WKJ-ZJ-2409//the National Health Commission Scientific Research Fund/ ; },
mesh = {Humans ; *Dysbiosis/immunology ; *Gastrointestinal Microbiome ; Animals ; *Chronic Urticaria/immunology/microbiology/metabolism ; *Skin/immunology/metabolism ; Mice ; Fatty Acids, Volatile/metabolism ; Mast Cells/immunology ; },
abstract = {Although the core pathophysiological pathways of chronic urticaria (CU) are increasingly understood, the upstream triggers and factors contributing to disease chronicity remain poorly understood. Emerging evidence suggests that gut microbiota dysbiosis represents a potentially modifiable upstream factor, which has been predominantly investigated in patients with chronic spontaneous urticaria (CSU). Multi-omics and Mendelian randomization studies have provided convergent evidence linking gut dysbiosis to systemic inflammation and mast cell instability. This is characterized primarily by the depletion of short-chain fatty acid (SCFA)-producing taxa (e.g., Faecalibacterium, Roseburia and Bifidobacterium) and the relative enrichment of pro-inflammatory Proteobacteria (particularly Enterobacteriaceae). Mechanistically, these alterations may lower the mast cell activation threshold and promote systemic immune dysregulation through specific metabolic shifts, such as the depletion of SCFAs and unsaturated fatty acids, and the translocation of endotoxins (e.g., lipopolysaccharide) due to compromised intestinal barrier function. In this review, we discuss how the use of Mendelian randomization (MR) and germ-free mouse models can advance the gut-urticaria axis (with a primary focus on CSU) from mere correlation to causation, while highlighting the crucial need to account for clinical confounders. Finally, we evaluate the clinical translational potential and associated challenges of microbiome-targeted interventions (e.g., probiotics, faecal microbiota transplantation) as novel adjuvant therapies.},
}

Humans
*Dysbiosis/immunology
*Gastrointestinal Microbiome
Animals
*Chronic Urticaria/immunology/microbiology/metabolism
*Skin/immunology/metabolism
Mice
Fatty Acids, Volatile/metabolism
Mast Cells/immunology

@article {pmid42083883,
year = {2026},
author = {Rutigliani, G and Cross, TL and de Jong, E and Glover, ES and Mendoza, ID and Adisa, M and Tomoo, K and Zhou, X and Mattes, RD},
title = {GLP-1 Receptor Agonists and Weight Loss: A Critical Review of Mechanisms.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70148},
doi = {10.1111/obr.70148},
pmid = {42083883},
issn = {1467-789X},
abstract = {GLP-1 receptor agonist medications have the potential to promote marked weight loss, but maximal and sustained benefit may be compromised by poor compliance and cessation of use. Development of next-generation medications that address current obstacles to effective use and development of effective adjunct treatments will benefit from better characterization of their mechanisms of action. This narrative review critically assesses eight purported mechanisms including modulation of appetite, chemosensory function, cravings/aversions, food noise, gastric emptying, the microbiome, incretin activity, and energy expenditure. Current evidence does not support a single dominant mechanism; a combination of subtle effects may underlie the efficacy of these medications. However, as experience with these medications and methods to assess their effects grows, it should be possible to better determine the relative importance of these and possibly other mechanisms.},
}

@article {pmid42083901,
year = {2026},
author = {Gago-Ferrero, P and Boehm, AB and Hsu-Kim, H and Li, XD and Gibson, JM and Vrijheid, M and Wang, B and Zimmerman, J},
title = {The Human Exposome: Integrating the Environment, Human Health, and Society for the Next 60 years.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c03080},
pmid = {42083901},
issn = {1520-5851},
abstract = {The exposome framework promises comprehensive characterization of chemical, physical, and biological exposures shaping human health, yet the measurement capacity now vastly outpaces interpretation and action. Here, we synthesize emerging frontiers that define the translation of exposome science into prevention: moving from "chemical dark matter" in high-resolution mass spectrometry toward functional exposomics; integrating the microbial exposome as both the target and modulator of exposures; deploying AI-enabled causal inference to bridge molecular precision with population-scale patterns; and embedding exposome evidence into proactive interventions, green chemistry, environmental redesign, and environmental justice frameworks. Progress over the next six decades will depend not only on measurement comprehensiveness but also on our capacity to shift from documenting environmental harm to designing healthier environments.},
}

@article {pmid42084201,
year = {2026},
author = {Ebihara, S and Kamada, N},
title = {The Oral-Gut Axis: Bidirectional Interactions Between Microbiome and Diseases.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70116},
pmid = {42084201},
issn = {1600-0765},
support = {DK108901/NH/NIH HHS/United States ; DK119219/NH/NIH HHS/United States ; CA288546/NH/NIH HHS/United States ; JP21gm6310023//Japan Agency for Medical Research and Development/ ; JP25gm4010030//Japan Agency for Medical Research and Development/ ; JP23H00404//Japan Society for the Promotion of Science/ ; },
abstract = {Increased colonization of typically oral microorganisms is frequently observed in the gut mucosa or lumen of individuals with gastrointestinal disorders, including patients with inflammatory bowel disease and colorectal cancer. Accumulating clinical and experimental evidence indicates that this phenomenon, known as "gut oralization," plays an important role in the pathogenesis of these diseases. Although several physiological barriers normally restrict the translocation and ectopic colonization of microorganisms from the oral cavity to the gut, certain oral pathobionts-often enriched in individuals with oral diseases such as periodontitis-have evolved specialized strategies to overcome these defenses. This review examines the bidirectional interactions through which bacterial traits, including unique adhesion systems and metabolic adaptations, support colonization and expansion within the gastrointestinal tract, as well as how disease-associated alterations in the gut environment and increased host vulnerability facilitate ectopic colonization by bacteria of oral origin. By integrating clinical and mechanistic evidence, this review highlights the potential of targeting the oral-gut microbial axis as a therapeutic approach for preventing and treating chronic gastrointestinal disorders.},
}

@article {pmid42084382,
year = {2026},
author = {Van Beeck, W and Lemos, MLP and Niesen, AM and Finnegan, P and Shih, TM and Ho, A and Rossow, HA and Marco, ML},
title = {Variations in cow milk and teat skin microbiota across the lactation cycle with intramammary cephalosporin use at dry-off.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0231225},
doi = {10.1128/aem.02312-25},
pmid = {42084382},
issn = {1098-5336},
abstract = {Cephalosporins and other broad-spectrum antibiotics are frequently administered prophylactically into the udder when dairy cows end their lactation cycle, termed dry-off, to reduce mastitis risk. However, the use of antibiotics on cows that do not have signs of infection may result in the selection of antibiotic-resistant microorganisms and negatively alter the udder microbiome. In this study, the effects of intramammary cephalosporin therapy with Cephapirin (CB) or Ceftiofur (CH) on milk and teat skin microbiota were examined for three dairies in California. Intramammary injections were given to healthy cows with high somatic cell counts (>200,000 cells/mL), indicative of infection. Samples were collected at dry-off (before treatment), 7 days later, and 55-75 days in milk (DIM) in the next lactation cycle. Dairy (milk: R[2] = 6.22, skin: R[2] = 7.56) and day of sampling (milk: R[2] = 4.74 and skin: R[2] = 3.77) had the highest impact on the milk and skin microbiota. CB or CH use was associated with a small but significant impact on milk microbiota beta-diversity (Bray-Curtis, P =0.003, R[2] = 1.4%), but no effect was observed on the skin. At one dairy (Dairy 3), milk from cows receiving CB and CH had reduced proportions of Staphylococcaceae at 55-75 DIM compared to untreated cows. Overall, antibiotic use did not result in large significant (beneficial or harmful) changes in bacterial diversity in milk or on the teat skin; instead, the microbiota differences were mainly influenced by the time and location of sampling.IMPORTANCEThe use of antibiotics in agriculture is under increasing scrutiny due to the rising spread of antimicrobial-resistant bacteria. Our study showed that common preventative antibiotic intramammary treatment of cows with cephalosporins at the end of their lactation (dry-off) had minimal effects on the milk and teat skin microbiota of asymptomatic cows with high somatic cell counts.},
}

@article {pmid42084394,
year = {2026},
author = {Liu, C and Ribeiro, MM and Yang, J and Li, L and Li, J and Chen, X and Wang, Y and Wang, L-L and Wang, B and Zhou, Y and Zhang, J and Jiang, J and Lin, J and Delbaje, E and Xu, J-F and Goldman, GH and Liang, S},
title = {Multi-omics profiling of fungal balls in chronic pulmonary aspergillosis patients reveals microbiome dynamics and metabolic adaptations.},
journal = {mBio},
volume = {},
number = {},
pages = {e0034826},
doi = {10.1128/mbio.00348-26},
pmid = {42084394},
issn = {2150-7511},
abstract = {Fungal balls (aspergillomas) are a debilitating complication of chronic pulmonary aspergillosis, but their functional biology as multi-kingdom ecosystems is poorly understood. Through integrated multi-omics analysis of 61 patient-derived fungal balls, we reveal their complex ecology. While Aspergillus fumigatus dominates the fungal niche (59% of patients), bacterial co-colonization is ubiquitous, primarily by Pseudomonas aeruginosa and Haemophilus influenzae. Metabolomics and metatranscriptomics unveil a structured division of labor and active warfare, including metabolic cross-feeding, competition for iron, and reciprocal antagonism via secondary metabolites, such as fumagillin and fumigaclavine C produced by A. fumigatus. Host metabolomics and transcriptomics revealed a potent but dysregulated human immune response, characterized by neutrophil activation and failed resolution. Our findings redefine aspergilloma not as a mere fungal aggregate, but as a resilient polymicrobial biofilm across kingdoms, in which synergistic and antagonistic inter-kingdom interactions drive pathogenesis and chronicity, suggesting new therapeutic strategies targeting the pathogenic consortium.IMPORTANCEChronic pulmonary aspergillosis (CPA) and its hallmark fungal balls (aspergillomas) represent a debilitating and difficult-to-treat respiratory disease, affecting millions worldwide. Here, we provide the first integrated multi-omics profile of surgically resected fungal balls from 61 CPA patients, revealing these structures not as mere fungal colonies, but as resilient, cross-kingdom biofilms teeming with bacterial co-colonizers, particularly Pseudomonas aeruginosa and Haemophilus influenzae. Our findings uncover a dynamic battlefield where fungi and bacteria engage in metabolic cross-feeding, chemical warfare, and competition for nutrients such as iron. We demonstrate that the host mounts a potent but dysregulated immune response characterized by chronic neutrophilic inflammation and failed resolution, driving tissue damage and disease persistence. Our data provide a foundation for novel therapeutic strategies aimed at disrupting microbial synergy, modulating host inflammation, and breaking the cycle of chronic infection, an approach that could significantly improve outcomes for patients with this refractory disease.},
}

@article {pmid42084439,
year = {2026},
author = {Wu, H and Han, Y and Wen, Z and Liu, WV and Tu, N and Yang, W and Li, J and Zha, Y},
title = {Higher Abundance of Genus Desulfovibrio May Underlie Resistance to Antipsychotic-Induced Weight Gain in Schizophrenia.},
journal = {Schizophrenia bulletin},
volume = {52},
number = {3},
pages = {},
pmid = {42084439},
issn = {1745-1701},
support = {JCZRQNB202600163//Natural Science Foundation of Hubei Province/ ; 2022YFC2009900//National Key R&D Program of China/ ; 2022YFC2009905//National Key R&D Program of China/ ; },
mesh = {Humans ; *Schizophrenia/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Antipsychotic Agents/adverse effects/pharmacology ; Male ; Female ; Adult ; *Weight Gain/drug effects ; *Obesity/microbiology/chemically induced ; *Desulfovibrio ; Middle Aged ; Young Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Obesity is prevalent among schizophrenia (SZ) patients receiving long-term antipsychotic treatment, yet a subset of patients remains lean or maintains a normal weight. While prior studies have linked the gut microbiome to antipsychotic-induced weight gain, its role in maintaining weight stability among non-obese SZ patients remains largely unexplored.

STUDY DESIGN: We recruited 177 participants for the discovery cohort, including chronically antipsychotic-treated SZ patients with or without obesity, as well as healthy controls (HCs) matched by weight status. Additionally, we enrolled 20 first-episode, drug-naïve SZ (FSZ) patients with normal weight to assess their weight changes during one year of antipsychotic treatment. Fecal 16S rRNA sequencing, combined with untargeted metabolomics, was conducted to characterize gut microbiota and metabolite profiles in non-obese SZ patients, and to investigate their association with antipsychotic-induced weight changes.

STUDY RESULTS: In total, 15 bacterial genera were identified. Among them, the genera Bacteroides, Dialister, and Pseudomonas exhibited the lowest abundance in non-obese SZ patients, whereas the genus Oscillospira showed the highest abundance. Notably, Desulfovibrio was more abundant in non-obese SZ patients and HCs than in their obese counterparts. This microbial profile was accompanied by enhanced tryptophan metabolism. In FSZ patients, higher baseline levels of Desulfovibrio were linked to less weight gain after 1 year of antipsychotic treatment. Moreover, Desulfovibrio abundance correlated positively with fecal indoleacetic acid levels and inversely with serum tryptophan concentrations.

CONCLUSIONS: These findings suggest a potential protective role of genus Desulfovibrio against antipsychotic-induced weight gain, possibly through modulation of tryptophan metabolism.},
}

Humans
*Schizophrenia/drug therapy/microbiology
*Gastrointestinal Microbiome/drug effects
*Antipsychotic Agents/adverse effects/pharmacology
Male
Female
Adult
*Weight Gain/drug effects
*Obesity/microbiology/chemically induced
*Desulfovibrio
Middle Aged
Young Adult
Feces/microbiology

@article {pmid42084538,
year = {2026},
author = {Jongen, R and Gribben, PE and Erickson, KR and Marzinelli, EM},
title = {Ocean warming indirectly affects seagrass performance through effects on sediment microbial communities.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71195},
pmid = {42084538},
issn = {1469-8137},
support = {DP240100566//Australian Research Council/ ; LP200200220//Australian Research Council/ ; },
abstract = {Belowground microbes are increasingly recognised as mediators of plant responses to stress, but it remains unclear whether the thermal histories of marine plants and their associated belowground microbes influence plant performance under ocean warming. We conducted a common-garden field experiment at a long-term warmed site in Lake Macquarie (NSW, Australia, > 30 yr, 1-3°C warming), to test the effects of sediment origin (ambient vs warm-origin), plant origin (ambient vs warm-origin) and microbial disruption (intact vs disrupted rhizosphere and bulk sediment microbial communities) on seagrass (Zostera muelleri) performance. Both plant origins had lower aboveground biomass in intact warm-origin sediments, but warm-origin plants recovered when bulk sediment microbial communities were disrupted, indicating that warming-altered sediment microbial communities can suppress seagrass performance. Disrupted warm-origin sediments were enriched in sulphide-oxidising bacteria, which likely contributed to enhanced performance. In warm-origin sediments, rhizosphere bacterial communities were similar across plant origins, indicating that sediments shape rhizosphere bacterial assembly. Rhizosphere microbial disruption had no effect on plant performance. We show that ocean warming can shape sediment microbial communities in ways that suppress seagrass performance, suggesting that sediment microbial communities can override plant thermal history and act as hidden constraints on seagrass tolerance to warming.},
}

@article {pmid42084709,
year = {2026},
author = {Komal, A and Ilyas, D and Khan, MU and Rehman, MKU and Hassan, T and Ayub, H and Naqi, N and Ullah, N and Ilyas, U},
title = {Multi-modal therapeutic approaches to inflammatory bowel disease: plant-derived compounds, nanoparticle drug delivery systems, and gene-based interventions.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42084709},
issn = {1573-4978},
mesh = {Humans ; *Inflammatory Bowel Diseases/therapy/genetics/drug therapy ; *Nanoparticle Drug Delivery System/therapeutic use ; *Genetic Therapy/methods ; *Drug Delivery Systems/methods ; Nanoparticles ; Animals ; RNA, Small Interfering ; MicroRNAs/genetics ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder primarily affecting the gastrointestinal tract. The pathogenesis arises from complex interactions among genetic predisposition, immune dysregulation, and gut microbiota alterations. Recent advances in molecular biology, genomics, and microbiome research have identified novel therapeutic targets, enabling the development of innovative treatment strategies. Natural products derived from plants offer bioactive compounds with anti-inflammatory, antioxidant, and immunomodulatory properties, gaining attention for IBD symptom management. Conventional therapeutic management includes aminosalicylates, immunomodulators, corticosteroids, and biologics; however, 30-50% of patients show inadequate response, and oral drug delivery faces challenges due to gastrointestinal environmental heterogeneity. Recent years have witnessed substantial advances in nanoparticle-based drug delivery systems for IBD, offering improved targeting capabilities, enhanced therapeutic efficacy, and better tolerability through stimuli-responsive platforms (ROS-sensitive, pH-responsive) and active targeting strategies. Nanoparticle-mediated gene therapy, including siRNA, miRNA, and emerging CRISPR-based approaches, represents a paradigm-shifting strategy for modulating aberrant gene expression in IBD. This comprehensive review synthesizes the current understanding of IBD pathophysiology, evaluates both conventional and emerging therapeutic approaches, and provides critical analysis of advanced nanoparticle delivery systems and gene-based therapeutic strategies.},
}

Humans
*Inflammatory Bowel Diseases/therapy/genetics/drug therapy
*Nanoparticle Drug Delivery System/therapeutic use
*Genetic Therapy/methods
*Drug Delivery Systems/methods
Nanoparticles
Animals
RNA, Small Interfering
MicroRNAs/genetics

@article {pmid42084747,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {Harnessing the plant microbiome: innovation towards sustainable agriculture and ecological resilience.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42084747},
issn = {1572-9699},
mesh = {*Microbiota ; Soil Microbiology ; Climate Change ; *Crops, Agricultural/microbiology/growth & development ; *Agriculture/methods ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Plant Breeding ; },
abstract = {Assimilation of plant-microbiome synergism into contemporary sustainable approaches offers transformational prospective for augmenting crop production, and environment resilience. Efficient microbiome enhances nutrients acquisition, encouraging plant's growth, and mitigate diverse stressors. Synthetic microbial communities could be another strategy to augment crop yield by improving bioinoculants activity, regulating and reinstating microbial diversity. Long-term agricultural output depends on microbiome's intervened activities, such as nutrients acquisition, thereby lowering chemical fertilizers necessity. Microbes also contribute to climate change mitigation by endorsing soil carbon stowage and minimizing release of greenhouse gases via enhanced nutrients use efficacy. Developments in sustainable crop breeding and genomics have facilitated the recognition of plant traits and genetic loci that influence alliances of valuable microbes. Integration of plant-microbiome breeding tactics might lead to optimization of microbiome selection in plant varieties, thus improving yield and stress resilience. Such approaches will conserve biodiversity, restore ecosystem by nurturing functional microbiome population, supporting plant's diversity and soil health. Microbiome are also able to improve degraded soils recovery, plant's establishment, parallelly safeguarding ecosystem restoration. The integration of microbial technology in crops could enhance the nutritional value and safety of food while supporting environmental sustainability and human health. Understanding microbiome-plant-climate change interactions is critical for developing adaptive strategies that enhance resilience to environment and climate variability, ensure sustainable food systems, and promote ecological balance in a changing global environment.},
}

*Microbiota
Soil Microbiology
Climate Change
*Crops, Agricultural/microbiology/growth & development
*Agriculture/methods
*Plants/microbiology
Biodiversity
Ecosystem
Plant Breeding

@article {pmid42084764,
year = {2026},
author = {Joshi, G and Khannam, KS},
title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42084764},
issn = {1432-072X},
mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Biodegradation, Environmental ; },
abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.},
}

*Microbiota
*Biotechnology
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Biodegradation, Environmental

@article {pmid42084801,
year = {2026},
author = {Liu, G and Chen, K and Li, J and Zhang, K and Niu, G and Ding, Y and Lv, Y and Tian, Q and Cao, Z and Wang, H and Jia, J and Zhang, G and An, Y},
title = {Deciphering potential significances of biliary microbiome in cholelithiasis and cholangiocarcinoma.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42084801},
issn = {1572-9699},
support = {No. 25A330005//the Key Scientific Research Projects of Henan Higher Education Institutions/ ; No. 202510475073, 202510475143, 202510475139, XJ2025344, XJ2025363//the Innovation Project for College Students of Henan University/ ; No. 262102311042//the Program for Science and Technology Development in Henan Province/ ; },
mesh = {*Cholangiocarcinoma/microbiology ; *Cholelithiasis/microbiology ; Humans ; *Microbiota ; *Bile Duct Neoplasms/microbiology ; Bacteria/classification/genetics/isolation & purification ; Computational Biology ; *Biliary Tract/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: This study aims to investigate the role of biliary microbiota (defined as the microbial community colonizing the biliary tract, including the gallbladder, intrahepatic and extrahepatic bile ducts) in the pathogenesis of cholelithiasis (CHOL) and cholangiocarcinoma (CCA), with a focus on the associations between microbial communities and these biliary diseases.

METHODS: We conducted a comprehensive bioinformatics analysis using high-throughput sequencing data obtained from the Sequence Read Archive (SRA) database to characterize the composition of microbial communities in patients with CCA and CHOL. We performed operational taxonomic unit (OTU) clustering, statistical analyses and Mendelian randomization (MR) to elucidate the causal relationships between specific bacterial strains and disease outcomes.

RESULTS: Our findings revealed differences in the relative abundance of specific microbial taxa among research groups. The CCA + CHOL group exhibited a significant increase in the abundance of Fusobacteria, particularly Fusobacterium, compared to the Control or CCA group. This suggests a potential pathogenic role for these microorganisms in CHOL formation. Additionally, the CCA group demonstrated a higher diversity index, indicating that increased microbial diversity may contribute to the progression of the disease. MR analysis identified nominally significant statistical associations between specific bacterial strains. However, the presence of pleiotropy in some analyses necessitates caution when interpreting causal relationships.

CONCLUSION: Our study highlights the complex interplay between biliary microbiota and the pathogenesis of CHOL and CCA. Modulating biliary microbiota may represent a promising therapeutic strategy for managing these diseases. Future research should focus on the functional roles of specific taxa in bile metabolism and immune modulation, ultimately improving our understanding of biliary health and disease management.},
}

*Cholangiocarcinoma/microbiology
*Cholelithiasis/microbiology
Humans
*Microbiota
*Bile Duct Neoplasms/microbiology
Bacteria/classification/genetics/isolation & purification
Computational Biology
*Biliary Tract/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid42084812,
year = {2026},
author = {Ma, J and Tong, P and Yang, K and Jia, Y and Liu, Z and Zhao, M and Liu, J and Long, F},
title = {Lactiplantibacillus plantarum Mediated Tryptophan Metabolism to Alleviate Tropomyosin-induced Food Allergy.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42084812},
issn = {1867-1314},
support = {32472454//National Natural Science Fund/ ; YQK[2023]020//Guizhou Provincial Science and Technology Programme for Outstanding Young Talents in Science and Technology/ ; 2024NC-GJHX-04//Key Research and Development Projects of Shaanxi Province/ ; },
abstract = {Food allergy (FA) has become increasingly prevalent, affecting daily life. Probiotics alleviate FA by modulating immune-microbiome interactions. Nevertheless, the key metabolites and mechanisms by which L. plantarum alleviates FA remain unclear. In this study, L. plantarum demonstrated the ability to improve FA by modulating regulatory T/Th1/Th2 balance, modulating gut microbial composition, and regulating gut metabolites. Tropomyosin sensitization was associated with decreased levels of 5-hydroxyindole-3-acetic acid (5-HIAA) in cecum contents, a phenomenon also observed in the serum of FA mice and patients. In vitro experiments showed that tryptophan (Trp), tryptamine, tryptophol, kynurenine, 5-HIAA, and indole-3-acetamide inhibited RBL-2H3 cell degranulation; however, this inhibitory effect was attenuated by the aryl hydrocarbon receptor (AhR) antagonist CH223191. Moreover, in vivo results indicated that dietary supplementation with 5-HIAA or Trp downregulated IgE and cytokine levels in an AhR-dependent manner. This study provided evidence for the positive role of Trp metabolites in alleviating FA.},
}

@article {pmid42085218,
year = {2026},
author = {Wang, LL and Xie, Y and Shen, X and Xu, JF},
title = {Advances in understanding respiratory microbiome are reshaping the management of respiratory diseases.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag017},
pmid = {42085218},
issn = {1535-4970},
}

@article {pmid42085254,
year = {2026},
author = {Zissler, UM and Koczulla, AR},
title = {Lower Airway Dysbiosis Fuels NETosis in NTM Bronchiectasis: Rethinking the Microbiome-Host Axis.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag117},
pmid = {42085254},
issn = {1535-4970},
}

@article {pmid42085326,
year = {2026},
author = {Appuhami, IA and Bajracharya, S and Davis, DA and Bruce, TJ},
title = {Effects of probiotic dose on growth performance, health, and gut microbiota of Pacific white shrimp reared in biofloc conditions.},
journal = {Journal of aquatic animal health},
volume = {},
number = {},
pages = {},
doi = {10.1093/jahafs/vsag001},
pmid = {42085326},
issn = {1548-8667},
support = {58-6010-0-007//United States Department of Agriculture-Agricultural Research Service (USDA-ARS)/ ; ALA016-1-19143//USDA National Institute of Food and Agriculture Hatch/ ; ALA016-1-19102//USDA National Institute of Food and Agriculture Hatch/ ; },
abstract = {OBJECTIVE: This study evaluated the effect of commercial Bacillus spp. probiotics on growth performance, immunity, gut microbiota composition, and disease resistance to Vibrio parahaemolyticus in Pacific white shrimp Litopenaeus vannamei that were reared under biofloc conditions.

METHODS: A 56-d feeding trial was conducted in a static biofloc system with postlarval shrimp (1.00 ± 0.03 g). A total of 1,080 shrimp were randomly assigned to three groups: two treatment levels (recommended dose [PRO × 1] and a doubled dose [PRO × 2]) of a commercial probiotic blend, PRO4000X, alongside a control group (CTL; no probiotics). At the trial end point, hepatopancreas and gut samples were collected for gene expression. Gut samples were also obtained for gut microbiota analysis via 16S ribosomal RNA sequencing, and hemolymph samples were withdrawn to measure the total hemocyte count.

RESULTS: Probiotic applications did not significantly affect growth performance, including final biomass, mean weight, survival, and feed conversion ratio under the experimental conditions. The probiotic-treated shrimp exhibited enhanced survival during a V. parahaemolyticus (strain A3) challenge, with significantly lower mortality rates (P < 0.001; 42.5 ± 4.3% for PRO × 1 and 60 ± 6.5% for PRO × 2) relative to the CTL (100 ± 0.00%). Immune parameters, such as total hemocyte count, did not differ. Interestingly, the expression of the antioxidant gene sod (superoxide dismutase) in the shrimp gut was significantly downregulated in the PRO × 1 group relative to the control (P = 0.030), which suggests reduced oxidative stress under probiotic supplementation. The analysis of the gut microbiota revealed differences in alpha diversity, specifically in evenness and Shannon index, which were significantly higher in the PRO × 1 group. The analysis of the bacterial composition also revealed minor shifts in the dominant genera. Notably, Lysobacter was more abundant in the PRO × 1 group, which potentially reflects positive modulation of gut microbial communities in response to probiotic supplementation.

CONCLUSIONS: Overall, the application of PRO4000X probiotics significantly reduced the V. parahaemolyticus infection in the shrimp that were reared in biofloc water and supported the regulation of immunity and microbial communities in the gut. These findings indicate that probiotics potentially help to improve shrimp health when shrimp are cultured in biofloc systems.},
}

@article {pmid42085335,
year = {2026},
author = {Prentice, AM},
title = {Human Milk Bioactives in Breastfeeding: Understanding the Complex Biology of Mother-Child Interactions.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-3},
doi = {10.1159/000551893},
pmid = {42085335},
issn = {1421-9697},
}

@article {pmid42085336,
year = {2026},
author = {Mwaniki, M and Nabwera, HM},
title = {Transition from Breast Milk: When and How?.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000551169},
pmid = {42085336},
issn = {1421-9697},
abstract = {BACKGROUND: Breastfeeding is the cornerstone of infant and young child nutrition with implications for long-term health and well-being. However, despite having World Health Organization guidance on the transition from exclusive breastfeeding to complementary feeding, in practice it is often fraught with challenges. This review examines the biological and clinical foundations of breastfeeding, addresses the critical questions of when and how to introduce complementary foods and discusses the gaps that hinder optimal infant feeding practices across different geographies. Finally, it highlights the pivotal role of healthcare professionals in guiding safe and responsive feeding transitions.

SUMMARY: Human breast milk is an essential component of the factors that promote optimal child health, growth and neurodevelopment. Evidence supports exclusive breastfeeding for approximately 6 months. Readiness for complementary feeding should be judged by developmental cues rather than chronological age alone. Complementary feeding introduces new nutritional and immunological demands: texture progression supports oral-motor development, timely exposure to allergens may promote tolerance, and micronutrient status is critical. Global variation in infant feeding practices reflects socioeconomic, cultural, and structural barriers that often limit adherence to guidelines. When exclusive breastfeeding is not feasible despite an optimal healthcare provider and family, partial breastfeeding or formula feeding can support infant growth. However, such decisions ideally require guidance from healthcare providers, which may not be readily accessible to all mothers. Transitioning from exclusive breast milk should be viewed as a gradual layering of foods onto an existing nutritional foundation (often provided by breast milk) rather than abrupt weaning. For maternal and child health practitioners, the priority should be to provide person-centred care that is informed by the individual circumstances of the mother-infant dyad. This includes evidence-informed practical advice that is responsive to their needs, supporting exclusive breastfeeding whenever possible, while ensuring access to safe, nutritionally adequate and sustainable alternatives where needed. Aligning health systems, community support, and policy protections is essential to enable families globally to achieve optimal feeding practices.

KEY MESSAGES: Exclusive breastfeeding for about 6 months provides significant nutritional, immunological, and developmental benefits, but readiness for complementary feeding should be guided by developmental cues, not chronological age alone. Complementary feeding should emphasise iron-rich, diverse foods introduced with appropriate texture progression, alongside continued breastfeeding for sustained child health and growth. Implementation gaps persist globally largely due to unaddressed maternal challenges of navigating breastfeeding and the transition to complementary feeding. An interdisciplinary approach with mothers at the core is important in translating global guidelines into context-specific, practical guidance for families.},
}

@article {pmid42085795,
year = {2026},
author = {Kang, S and Han, X and Gao, J and Zhou, T and Yang, X and Zheng, F},
title = {Distribution patterns and driving mechanisms of antibiotic resistance genes and virulence factor genes under the urbanization gradient.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142270},
doi = {10.1016/j.jhazmat.2026.142270},
pmid = {42085795},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs), as emerging environmental contaminants, have become a global environmental health concern due to their distribution and dissemination across urbanization gradients. This study systematically investigated the diversity, abundance patterns, and driving mechanisms of 173 ARGs, 30 mobile genetic elements (MGEs), and 120 virulence factor genes (VFGs) along a typical urbanization gradient (urban, suburban, and ecological zones) using soil samples collected from Baoding city center to Baiyangdian Lake periphery. High-throughput sequencing and quantitative PCR analyses revealed that suburban areas exhibited significantly higher total relative abundance of ARGs compared to urban and ecological zones (p < 0.05), particularly for aminoglycoside-, fluoroquinolone-, Macrolide-Lincosamide-Streptogramin B-, and multidrug-resistance genes. Suburban soils also showed elevated levels of VFGs associated with Klebsiella pneumoniae, Salmonella enterica, and Escherichia coli (p < 0.05). Notably, significant associations between ARGs and VFGs were observed, with both demonstrating high loads in suburban areas, suggesting these transitional zones may serve as "incubators" for resistant pathogens. Correlation analyses suggest that both biotic (MGEs, microbial communities) and abiotic factors (urbanization, heavy metals, soil properties) may contribute to ARGs and VFGs dissemination, with MGEs appearing to play a central role. Structural equation modeling indicates that urbanization could influence ARGs and VFGs assembly, potentially by altering soil properties, heavy metals, and microbial communities. MGE-mediated horizontal transfer might facilitate ARGs spread, whereas heavy metals and specific microbial taxa may be associated with VFG distribution patterns. These findings provide critical scientific insights into the transmission dynamics of resistance genes during urbanization and offer strategic guidance for developing targeted environmental management policies to mitigate resistance dissemination.},
}

@article {pmid42085931,
year = {2026},
author = {Wang, Z and Wang, Y and Peters, BA and Post, WS and Brown, TT and Palella, FJ and Rinaldo, CR and Witt, MD and Gange, SJ and Kuniholm, MH and Sha, BE and Chichetto, NE and Clish, CB and Gerszten, RE and Hodis, HN and Sharma, A and Anastos, K and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB},
title = {Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV.},
journal = {EBioMedicine},
volume = {127},
number = {},
pages = {106281},
doi = {10.1016/j.ebiom.2026.106281},
pmid = {42085931},
issn = {2352-3964},
abstract = {BACKGROUND: How gut microbiota alterations may contribute to host inflammation and metabolomic profiles affecting atherosclerosis is not fully elucidated, especially in the context of HIV.

METHODS: We examined associations between gut microbial features (measured by shotgun metagenomics) and subclinical carotid atherosclerosis, as assessed by high-resolution B-mode ultrasound, in 359 men from the MACS/WIHS Combined Cohort Study. We measured 822 plasma metabolites using LC-MS/MS, and up to 2866 circulating proteins by the Olink Explore 3072/384 platform (with a primary focus on 617 proteins related to inflammation and immune function).

FINDINGS: Carotid artery plaque was detected in 115/359 men (32%). Adlercreutzia equolifaciens and Eubacterium sp3131 were associated with lower odds of plaque (OR [95% CI] = 0.57 [0.43, 0.77], 0.84 [0.76, 0.93], respectively), while Coprococcus sp13142 was associated with higher odds of plaque (OR [95% CI] = 1.14 [1.06, 1.23]). Results were consistent in men both with and without HIV. A. equolifaciens was positively correlated with HDL cholesterol and inversely correlated with systolic blood pressure. These plaque-associated microbial species were also associated with a range of circulating metabolites and inflammatory proteins. For example, A. equolifaciens positively correlated with the metabolites palmitoyl-EA and mesobilirubinogen, and inversely correlated with the pro-inflammatory chemokine CXCL9, the immune regulator CD160, and IL-24.

INTERPRETATION: We identified gut microbial features associated with carotid artery atherosclerosis, consistent across HIV status; these associations were partially explained by specific microbiota-related metabolites and inflammatory markers. If validated, these findings suggest gut microbiota-related targets for CVD prevention.

FUNDING: The study was funded by the National Heart, Lung, and Blood Institute (U01HL146204-04S1, K01HL169019).},
}

@article {pmid42086047,
year = {2026},
author = {Cai, C and Wang, A and Shao, Q and Zhang, J and Wang, Y and Hu, H and Yuan, K and Li, L and Wang, X and Fang, Q and Ma, Y},
title = {Cryo-EM structures of prevalent gut phage PD491P1 uncover extensive disulfide stabilization and distinct structural adaptations.},
journal = {Structure (London, England : 1993)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.str.2026.04.005},
pmid = {42086047},
issn = {1878-4186},
abstract = {Bacteriophages play crucial roles in modulating the human gut microbiome, yet structural characterization of prevalent gut phages remains limited. Here, we present high-resolution cryo-EM structures of Parabacteroides phage PD491P1, which is one of the most abundant bacteriophages in the human gut. The structures reveal its mature virion organization, including the capsid, head-to-tail interface, and tail tip regions. Strikingly, PD491P1 exhibits an exceptionally extensive disulfide bond network that covalently stabilizes nearly the entire virion. Unique structural features include an elaborate portal-adaptor-terminator interface and distinctive, upward-pointing and flexible tail fibers with multiple putative host recognition domains. These structural adaptations may enable phage PD491P1 to achieve survival and robust infection in the challenging gut environment. These findings expand our understanding of gut phage structural diversity, reveal mechanistic insights into phage stability and infection, and provide a foundation for future development of phage-based microbiome therapeutics.},
}

@article {pmid42086326,
year = {2026},
author = {Azulay, A and Gotesdyner, L and Aharoni-Frutkoff, Y and Focht, G and Talmor, Y and Borenstein, E and Plotkin, L and Orlanski-Meyer, E and Lev-Tzion, R and Ledder, O and Yogev, D and Assa, A and Broide, E and Yerushalmy-Feler, A and Kierkuś, J and Schwerd, T and Wine, E and Turner, D},
title = {Multi-omics-based machine learning model predicts response and guides treatment in Crohn disease: a case study in nutritional therapy.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag060},
pmid = {42086326},
issn = {1536-4844},
support = {//Leona M. and Harry B. Helmsley Charitable Trust/ ; },
abstract = {BACKGROUND: Biomarkers are needed to predict treatment response and guide therapeutic decisions in Crohn disease (CD). We aimed to develop and validate a multi-omics machine learning (ML) model to predict response to nutritional therapy in pediatric CD.

METHODS: Treatment-naive children with newly diagnosed CD who were initiating exclusive enteral nutrition (EEN) were prospectively enrolled in this study. Metabolomics and lipidomics were measured in the serum and stool, as well as the fecal microbiome. Following feature selection via minimum redundancy maximum relevance, random-forest models were constructed for single- and multi-omics and performances were evaluated. The models were externally validated in an independent prospective cohort of treatment-naive children and young adults with CD treated with EEN.

RESULTS: The discovery cohort consisted of 50 children (mean ± SD age 14.3 ± 2.7 years), of whom 34 (68%) responded to EEN. Combining complementary signals from host metabolism, gut microbiota, and lipid profiles from serum and stool in a multi-omics ML model yielded a model for predicting treatment response (training accuracy 94%; 95% CI, 82%-100%). Key predictive features included serum metabolites (2-hydroxyglutaric acid, Cer[d18:0/22:0], and HexCer[d18:1/d26:1]), fecal metabolites (3-methyladipic acid, DG[16:0 20:0], PC aa C42:2), and microbial taxa (family Bifidobacteriaceae and genus CAG-56). The validation cohort consisted of 21 patients of whom 12 (57%) responded to EEN. The multi-omics model performance achieved an area under the receiver operating characteristic curve (AUROC) of 0.81 (95% CI, 0.6-1.0). Clinical and endoscopic features did not improve the predictive ability of the model.

CONCLUSION: As a proof-of-concept, we showed that integrated multi-omics ML models can predict EEN response in pediatric CD patients, supporting their potential use in precision nutrition and personalized care strategies.},
}

@article {pmid42086392,
year = {2026},
author = {Fan, J and Ye, Y and Xia, W},
title = {Comment on: "Intratumoral microbiome composition and its role in tumor recurrence in primary liver cancer".},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.04.114},
pmid = {42086392},
issn = {0929-6646},
}

@article {pmid42086396,
year = {2026},
author = {Zhang, J and Yang, B and Martin, FM},
title = {Harnessing microbiomes to redefine medicinal plant agriculture.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.007},
pmid = {42086396},
issn = {1878-4380},
abstract = {Medicinal plants link agriculture, ecosystem health, and human therapeutics, with bioactive compound profiles providing a direct and economically meaningful readout of microbiome function. Although microbial inoculation can enhance pharmacologically relevant metabolites under controlled conditions, these effects are context dependent and rarely reproducible in the field. This efficacy gap reflects three ecological constraints: introduced microbes are excluded by resident communities, environmental variation overrides laboratory-optimised functions, and inoculants fail to persist without mutualistic feedback. Addressing these barriers requires shifting from disposable inputs to microbiome stewardship: rewilding beneficial communities, designing climate-adapted consortia, and managing soil as living infrastructure. Whether such stewardship produces measurably different bioactive profiles and therapeutic outcomes under field conditions remains the empirical question on which its One Health rationale ultimately depends.},
}

@article {pmid42086397,
year = {2026},
author = {Cheng, Y and Wang, Y and Luo, T and Guo, L},
title = {Challenges and future directions in AI-driven biomaterials for microbiome-associated oral infectious diseases: A systematic review.},
journal = {Dental materials : official publication of the Academy of Dental Materials},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dental.2026.04.025},
pmid = {42086397},
issn = {1879-0097},
abstract = {Oral biofilm-induced antimicrobial resistance is the core pathogenic mechanism of microbiome-associated oral infectious diseases (dental caries, periodontitis, peri-implantitis, and endodontic infection). Traditional therapies and biomaterials are limited by poor biofilm penetration, drug resistance induction, single functionality, and inadequate adaptation to dynamic oral microenvironmental changes (e.g., pH fluctuations, salivary rinsing, masticatory stimulation). Artificial intelligence (AI) has transformed the field by integrating materials science, microbiology, and stomatology data. Via machine learning, deep learning, and multi-physics simulation, AI optimizes biomaterial physicochemical properties, decodes microenvironmental signals, constructs precise sensing-response loops, and supports the full chain of material design, performance prediction, and action simulation, advancing treatment from empirical intervention to precision regulation. This systematic review retrieved literature from PubMed, Embase, and Web of Science (January 2016-January 2026) using keywords across three dimensions: AI, biomaterials, and oral microbiome. Following inclusion/exclusion criteria, 99 articles were included. It elaborates on five core mechanisms of AI-driven oral biomaterials (precise oral microbiome analysis, targeted material design/optimization, performance prediction/simulation, targeted delivery/intervention, effect evaluation/dynamic regulation), analyzes their applications in microbiome-targeted biomaterial research and development (R&D) and clinical practice for the four major oral infectious diseases, addresses technical bottlenecks (insufficient targeting specificity and precision of biomaterials, poor stability and durability in complex oral microenvironments, inadequate biofilm disruption capacity, and clinical translation obstacles), and proposes future directions (multimodal design to enhance targeting specificity, structural and component optimization to improve stability/durability, development of multi-mechanism synergistic biofilm disruption strategies, strengthening translational research for clinical application, and deep integration of AI in the full chain of biomaterial R&D). This work provides comprehensive theoretical and practical support for the R&D, optimization, and clinical translation of AI-driven microbiome-targeted oral biomaterials.},
}

@article {pmid42086572,
year = {2026},
author = {Gracie, R and Wiedenmann, J and Lam, P and Sweet, M and D'Angelo, C},
title = {Breakdown of microbial networks links nutrient stress and reef coral disease.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42086572},
issn = {2041-1723},
support = {522271101//Leverhulme Trust/ ; INSPIRE DTP//RCUK | Natural Environment Research Council (NERC)/ ; },
mesh = {Animals ; *Coral Reefs ; *Anthozoa/microbiology ; Nitrogen/metabolism/analysis ; *Microbiota/physiology ; Seawater/chemistry/microbiology ; Phosphorus/metabolism/analysis ; Cyanobacteria/isolation & purification/metabolism ; Symbiosis ; Stress, Physiological ; Nutrients/metabolism ; Ecosystem ; },
abstract = {Coral diseases are increasing in prevalence, accelerating the global decline of tropical reefs, which threatens over 25% of marine biodiversity and vital ecosystem services for human societies. While outbreaks are frequently linked to environmental change, including heat stress, sedimentation, and reduced water quality, the mechanisms by which such factors promote disease remain poorly understood. Here we show that nutrient stress, caused by skewed seawater nitrogen-to-phosphorus (N:P) stoichiometry, promotes the onset of Black Band Disease (BBD), a common and easily recognisable syndrome that affects corals around the globe. Using Turbinaria reniformis as a model system, controlled laboratory experiments demonstrate that skewed N:P ratios disrupt the functional integrity of coral-associated microbial networks while favouring opportunists that exploit dysfunctional host-symbiont interactions. Disease lesion-associated microbial mats are dominated by cyanobacteria and include sulphur-metabolising bacteria, hallmarks of natural BBD communities. Strikingly, similar cyanobacterial taxa are also detected in the visually healthy coral tissue ahead of the expanding lesions, suggesting an opportunistic recruitment of disease-associated members from the resident microbiome. Global analyses of BBD outbreaks reveal that over 88% occurred in regions with skewed N:P ratios, compared with only 16% that were linked to prior heat stress. Together, our findings identify nutrient-driven microbiome destabilisation as a key pathway to coral disease, reinforcing nutrient management as a major lever for reef conservation and restoration practice.},
}

Animals
*Coral Reefs
*Anthozoa/microbiology
Nitrogen/metabolism/analysis
*Microbiota/physiology
Seawater/chemistry/microbiology
Phosphorus/metabolism/analysis
Cyanobacteria/isolation & purification/metabolism
Symbiosis
Stress, Physiological
Nutrients/metabolism
Ecosystem

@article {pmid42086594,
year = {2026},
author = {Wang, K and Li, Y and Li, C and Kahiel, M and Nagaoka, K and Shen, D and Li, C},
title = {Lung microbiota-mediated biotransformation of mogroside preserves pulmonary barrier integrity and attenuates PM2.5-induced inflammation via NF-κB-Th17 modulations.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00992-y},
pmid = {42086594},
issn = {2055-5008},
support = {32372935, 32072781//National Natural Science Foundation of China/ ; KYLH2025004//Fundamental Research Funds for the Central Universities/ ; 2023YFD1300802-4//National Key Research and Development Program of China/ ; },
abstract = {PM2.5-induced lung injury challenges poultry health with limited treatments. Mogroside's unique therapeutic impact on pulmonary inflammation may involve modulating the lung microbiome, which influences immune function and respiratory health. We first demonstrated that mogroside (MG) supplementation improved growth performance and mitigated PM2.5-induced alveolar damage, inflammatory cytokine release, and Th17 differentiation (p < 0.05). MG increased the abundance of beneficial bacteria, particularly Lactobacillus (p < 0.01). Notably, MG IIE accumulated in lung tissues and bronchoalveolar lavage fluid (BALF). To further clarify the role of microbe-metabolite interactions, BALF from MG-treated broilers was transplanted. Only complete BALF containing both MG and microbiota significantly alleviated fibrosis (p < 0.05), reshaped lung microbial composition, and modulated metabolites such as taurine and lactic acid. Microbiome analysis identified Sphingomonas as a key taxon enriched in MG-BALF, strongly correlated with protective metabolites. In vitro assays confirmed that Sphingomonas degraded MG IIE into mogrol via β-glucosidase activity. Finally, a Calu-3-Jurkat T lymphocytes co-culture model revealed that MG IIE, particularly in combination with Sphingomonas metabolites, preserved barrier integrity, suppressed NF-κB phosphorylation, reduced ROS, and inhibited Th17-associated cytokine expression. Collectively, MG IIE and its Sphingomonas-mediated metabolites form a lung microbiota-metabolite-host axis that protects against PM2.5-induced pulmonary injury.},
}

@article {pmid42087172,
year = {2026},
author = {Chamberlin, ML and Spears, ML and Cooper, G and Miller, ZJ and Bothner, B and Walk, ST and Yeoman, CJ and Miles, MP},
title = {Impact of the gut microbiome on health impacts of Haskap berries: study protocol for a randomized control trial.},
journal = {Trials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13063-026-09759-4},
pmid = {42087172},
issn = {1745-6215},
support = {2024-67018-42493//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Haskap berries have great potential as a superfood due to high polyphenolic content which confers both anti-inflammatory and antioxidant activity. These health impacts are mitigated, at least in part, by the gut microbiome as most ingested polyphenols pass to the large intestine for microbial enzymatic action and conversion to secondary phenolic metabolites. These microbial actions mediate both the bioavailability and the bioefficacy of Haskap-derived phenolics. However, clinical intervention trials characterizing the impact of long-term Haskap consumption on human health and the interaction between Haskap-derived phenolics and the gut microbiome are limited. This study aims to determine the impact of Haskap consumption on gut microbiome composition, gut microbial and serum metabolites, and other health outcome metrics in a cohort of adults with both low and high risk of metabolic syndrome.

METHODS: This is a four-armed, randomized, triple-blind, placebo-controlled clinical trial conducted in a cohort of adults with both low and high risk of metabolic syndrome. A total of 120 participants (60 metabolically healthy, 60 metabolically unhealthy) will be randomized in a 1:1 ratio to consume a daily dose of either Haskap or placebo juice for 8 weeks. Outcome measures will be collected before and after the intervention period to determine the health impacts of Haskap in both groups. Primary outcome measures include fasting blood markers of glucose and lipid metabolism and inflammation, fat oxidation rates during submaximal exercise, 16S rRNA fecal microbial composition data, and mass spectrometry-acquired fecal and serum metabolomic data. Secondary outcome measures include anthropometric and sleep quality measures as well as acute and habitual dietary intake data.

DISCUSSION: Investigating how the gut microbiome influences the health benefits of consuming Haskap berries will help elucidate potential mechanisms of Haskap-induced metabolic health benefits and help inform the development of effective strategies to decrease metabolic disease risk through Haskap consumption.

TRIAL REGISTRATION: ClinicalTrials.gov NCT06546020. Registered on 1 August 2024.},
}

@article {pmid42087225,
year = {2026},
author = {Youn, HY and Park, S and Min, H and Ngoc, NB and Kim, YH and Cha, KH and Park, YT and Kwon, HY and Lee, CG and Kim, M},
title = {Micheliolide ameliorates colon cancer cachexia by modulating gut microbiota-immune signaling via Phocaeicola vulgatus enrichment.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02412-x},
pmid = {42087225},
issn = {2049-2618},
support = {26Z0001//Korea Institute of Science and Technology intramural research grant/ ; },
abstract = {BACKGROUND: Cancer cachexia profoundly impacts patient survival and quality of life. Current treatments fail to halt this trajectory, highlighting an urgent clinical need for host-directed therapies capable of uncoupling skeletal muscle wasting from tumor progression. This study investigated the therapeutic potential of micheliolide (MCL) across distinct tumor contexts.

METHODS: We employed immunocompetent murine models of colon cancer (CT26) and lung cancer (LLC) cachexia, pseudo-germ-free (pseudo-GF) mice, murine C2C12 myotubes, and primary human skeletal muscle cells. We evaluated MCL's impact on muscle wasting, systemic inflammation (splenic CD4[+] T cell phenotypes), gut microbiota composition, and short-chain fatty acid (SCFA) production. The direct effects of Phocaeicola vulgatus (P. vulgatus) administration were also assessed in the CT26 model.

RESULTS: MCL functions as a potent host-directed therapy, ameliorating muscle wasting in both models-particularly CT26-completely uncoupling muscle preservation from tumor cytotoxicity. In vitro, MCL directly prevented catabolism in both C2C12 and human primary myotubes. In vivo, MCL robustly rescued muscle mass and function. This was associated with the suppression of local muscle NF-κB hyperactivation and a marked reduction in the absolute counts of activated (CD25[+]) and exhaustion marker-expressing (PD-1[+], TIM-3[+]) splenic CD4[+] and CD8[+] T cells, resolving splenomegaly. Crucially, targeted microbiota depletion in pseudo-GF mice entirely abrogated these anti-cachectic benefits, establishing the gut microbiome as an indispensable mediator. MCL selectively enriched the beneficial bacterium P. vulgatus while differentially suppressing potential pathobionts like Enterococcus faecalis in CT26 and Streptococcus acidominimus in LLC. Microbial functional analysis indicated MCL increased the predicted potential for biotin biosynthesis in the CT26 model. Correlation analyses linked P. vulgatus abundance and increased SCFAs to reduced cachexia severity and modulated T cell profiles. Validating its functional significance, oral P. vulgatus administration significantly attenuated muscle wasting, increased cecal butyrate, and beneficially altered specific gut bacterial taxa in the CT26 model.

CONCLUSION: By therapeutically rewiring the gut-immune-muscle axis, MCL exerts pronounced and context-dependent anti-cachectic efficacy. Through dampening of systemic inflammation via T cell modulation, beneficial remodeling of the gut microbiota, and enhancement of predicted microbial biosynthesis pathways, MCL serves as a highly translational, host-directed intervention to mitigate cancer-induced systemic catabolism independent of tumor growth inhibition. Video Abstract.},
}

@article {pmid42087248,
year = {2026},
author = {Duan, Y and Ma, Z and Liu, Y and Jia, Y and Zhang, Z and Yang, C and Gong, X and Mao, Z and Li, C and Ma, F},
title = {MdUGT88F1 enhances plant resistance to Fusarium proliferatum f.sp. malus domestica MR5 via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02416-7},
pmid = {42087248},
issn = {2049-2618},
support = {32302476//National Natural Science Foundation of China/ ; U24A20414//National Natural Science Foundation of China/ ; NO.ts20190923//Taishan Scholar Funded Project/ ; CARS-27//Agriculture Research System of China/ ; 2023B02018//Xinjiang Key Research and Development Project/ ; },
abstract = {BACKGROUND: Apple replant disease (ARD) is a major threat to the sustainable development of China's apple industry. It is primarily caused by the accumulation of phloridzin and the pathogen Fusarium proliferatum f.sp. malus domestica MR5 (Fpmd MR5). MdUGT88F1-mediated phloridzin biosynthesis is known to enhance disease resistance, but its role in shaping the rhizosphere microbiome and conferring resistance against Fpmd MR5 remains unclear. In this study, we used wild-type (WT) and MdUGT88F1 transgenic apple lines to systematically investigate the mechanism by which MdUGT88F1 regulates the rhizosphere microbiome to mitigate ARD.

RESULTS: Compared with WT and MdUGT88F1-OE plants, MdUGT88F1-RNAi plants exhibited enhanced tolerance to ARD, as indicated by reduced disease severity, decreased abundance of Fpmd MR5 in the rhizosphere soil, and lower phloridzin content. Further greenhouse experiments demonstrated that the rhizosphere bacterial communities were triggered mainly by changes in community composition. Multi-omics joint analysis revealed that members of the family Bacillaceae with multiple plant growth-promoting traits were enriched in the MdUGT88F1-RNAi plant rhizosphere but only upon Fpmd MR5 invasion. MdUGT88F1-RNAi plants exhibited significantly higher exudation of D-tagatose, D-galactose, sucrose, 3-O-methyl-D-glucose, and maltitol. Interestingly, exogenous application of these compounds promoted the proliferation of Bacillus, enhancing plant resistance to Fpmd MR5. In vitro assays demonstrated that the recruited Bacillus significantly inhibited the hyphal growth and fumonisin B1 production of Fpmd MR5 and alleviated plant disease symptoms. We experimentally validated this observation by inoculating a synthetic microbial community (Bacillus velezensis, Bacillus mojavensis, Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus licheniformis) into replanted soil, which led to a significant reduction in pathogen Fusarium abundance and promoted plant growth.

CONCLUSION: Overall, these findings highlight that plant disease resistance is a complex trait driven by dynamic interactions among the host genetic background, rhizospheric microbial communities, and pathogens. Targeted modulation of the rhizospheric microbiome represents a potent "prebiotic" strategy. This approach can indirectly enhance plant disease resistance by fostering beneficial microbial activity in the rhizosphere. This study also provides a theoretical basis and practical solutions for the green control of ARD through prebiotics and synthetic microbial communities. Video Abstract.},
}

@article {pmid42087326,
year = {2026},
author = {Iida, A and Toyota, Y and Itagaki, T and Yawaka, Y and Hasebe, A},
title = {Oral and Gut Microbiota in Individuals With Autism Spectrum Disorder: A Pilot Case-Control Study.},
journal = {International journal of paediatric dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1111/ipd.70095},
pmid = {42087326},
issn = {1365-263X},
support = {20K18798//Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (JSPS KAKENHI)/ ; },
abstract = {BACKGROUND: Recent studies suggest that gut microbiota play important roles in individuals with autism spectrum disorder (ASD), potentially influencing the development and severity of the condition. Oral bacteria may be directly or indirectly involved in the biological and symptomatic aspects of ASD through their effect on gut microbiota.

AIM: This pilot study aimed to characterise compositional alterations in the oral and gut microbiota of individuals with ASD and to identify bacterial taxa in saliva and faeces that may serve as potential microbial indicators of ASD.

DESIGN: Salivary and faecal samples were collected from 10 individuals with ASD and 10 typically developing controls. The oral and gut microbiota were evaluated using 16S ribosomal RNA marker-gene sequencing.

RESULTS AND CONCLUSION: Distinct features of the oral and gut microbiota were identified that differed between individuals with ASD and typically developing controls. Based on linear discriminant analysis effect size, the relative abundances of the genera Neisseria were higher in the oral microbiota of the ASD groups, whereas the genera Faecalibacterium were enriched in the gut microbiota. These findings highlight the potential relevance of the oral-gut-brain axis in ASD. Additionally, non-invasive sampling of saliva and faeces may be utilised for early ASD screening.},
}

@article {pmid42087591,
year = {2026},
author = {Ebersole, JL and Kirakodu, SS and Zhang, X and Dawson, D and Miller, CS},
title = {Salivary Biological Responses to Nonsurgical Periodontal Treatment in Type 2 Diabetics.},
journal = {JDR clinical and translational research},
volume = {},
number = {},
pages = {23800844261437825},
doi = {10.1177/23800844261437825},
pmid = {42087591},
issn = {2380-0852},
abstract = {BACKGROUND: This investigation evaluated the predictive capacity of the oral microbiome and host salivary biomarkers on treatment outcomes for periodontitis in patients with type 2 diabetes mellitus (T2DM).

METHODS: Two patient cohorts were enrolled: T2DM without periodontitis (DWoP; n = 32) and T2DM with periodontitis (DWP; n = 29). Whole saliva was collected at baseline and 4 to 7 wk posttreatment (i.e., DWoP, supragingival prophylaxis; DWP, scaling and root planing). The oral microbiome (operational taxonomic units; OTUs) and targeted salivary biomarkers were assessed in pre- and posttreatment saliva.

RESULTS: Most OTUs (57%-68%) and salivary biomarkers (43%-55%) decreased after treatment in both groups. Supragingival prophylaxis in the DWoP patients altered a limited number of taxa (V. dispar, P. denticola, Rothia, Neisseria), showing substantial increases in the microbiome, whereas predominantly gram-negative OTUs decreased. In the DWP, decreases were observed following therapy for Bacillota, Bacteroidetes, and Proteobacteria, again representing primarily gram-negative taxa. Microbe-host response biomarker correlations increased posttherapy in DWoP and decreased in DWP samples. Importantly, poor response (PR) to therapy was independent of HbA1c levels but associated with higher pretreatment levels of multiple bacterial genera (i.e., Alloprevotella, Campylobacter, Corynebacterium, Fusobacterium, and Leptotrichia) and elevated levels of interleukin (IL)-1b, IL-6, matrix metalloprotease-8 (MMP-8), adiponectin, and resistin. After therapy, PR was characterized by increases in Lachnospiraceae, Prevotella, and a lack of effects on Leptotrichia, Alloprevotella, Porphyromonas, and Stomatobaculum.

CONCLUSIONS: Poor clinical response to therapy was characterized by (1) less microbiome diversity and elevated levels of specific bacteria and salivary analytes pretherapy and (2) posttherapy elevations in multiple taxa and sustained levels of IL-1b and MMP-8 in both groups of PR patients. These findings support that a panel of salivary features could enhance our prediction and earlier decisions on response to therapy at the biological level, thus opening the door for more precise patient-level management.Knowledge Transfer Statement:These findings contribute to a pathway for understanding oral health using biological measures as a standard for better decisions in oral health care. Specifically, microbiome and host response parameters provided important insights with predictive value and differential biological presentation related to response to therapy. While these measures do not dictate disease causation, they appear to reflect the periodontal environment, hallmarks of disease, and response to therapy.},
}

@article {pmid42087714,
year = {2026},
author = {Mautone Gomes, H and Kleber Silveira, A and Santos Froemming, L and Martins Silva, A and Campos Soares, M and Hansen, J and Carazza Kessler, FG and Bastos Mendes, L and da Rosa Paz, AH and Gasparotto, J and Gelain, DP and Fonseca Moreira, JC},
title = {In vivo methylmercury toxicity is exacerbated by polystyrene microplastic exposure, leading to colon barrier disruption, gut dysbiosis, and systemic oxidative imbalance.},
journal = {Journal of toxicology and environmental health. Part A},
volume = {},
number = {},
pages = {1-29},
doi = {10.1080/15287394.2026.2666544},
pmid = {42087714},
issn = {2381-3504},
abstract = {Methylmercury (MeHg) is a well-recognized toxicant, whereas microplastics (MP) are contaminants whose health effects continue to be explored. Evidence suggests that concomitant exposure to MeHg and polystyrene (PS) may enhance adverse outcomes in the gastrointestinal system. The aim of this study was to investigate the combined effects of MeHg and PS-MP on intestinal homeostasis, as well as systemic oxidative and inflammatory responses. A total of 64 rats with 30-days-old (n = 16 per group) were exposed to environmentally relevant doses of 0.5 mg/L MeHg and/or 0.2 mg/L PS-MP of 5 µm during 8 weeks. Co-exposure resulted in colon shortening, mucus depletion, and disruption of tight junction proteins, accompanied by macrophage infiltration and elevated pro-inflammatory cytokines. Structural and inflammatory changes were accompanied by gut dysbiosis, including altered microbial composition and reduced diversity indices. Biochemically, co-exposure amplified oxidative stress in the colon, with loss of free thiols and enhanced lipid peroxidation, while not markedly affecting glutathione-S-transferase activity. Systemically, combined treatment increased serum cytokines and induced genotoxicity. Although compensatory antioxidant responses were detected in blood, oxidative stress was evident in peripheral organs, particularly liver, kidneys, and heart. Taken together, these findings demonstrate that the intestine may be an early and sensitive target following co-exposure to MeHg and PS-MP, driving cytokine release into circulation and contributing to systemic injury. Our study provides novel in vivo evidence that combined PS-MP and MeHg exposure exacerbates some biological outcomes noted with individual contaminant exposure, indicating the importance of considering co-contamination scenarios in risk assessment of emerging pollutants.},
}

@article {pmid42087981,
year = {2026},
author = {Wang, Q and Zhou, K and Zhang, M and Dong, Y and Zhao, M},
title = {Association between dentition defects and Alzheimer's disease risk: a systematic review and meta-analysis.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1783171},
pmid = {42087981},
issn = {2673-4915},
abstract = {BACKGROUND: Alzheimer's Disease (AD) is the most common neurodegenerative disorder among the elderly, with a steadily rising prevalence that poses a significant global public health challenge. Recently, dentition defects (DD), such as tooth loss, have gained attention as potential risk factors influencing neurocognitive health. However, the relationship between DD and AD remains inconclusive, necessitating a systematic analysis to clarify this association.

METHODS: This systematic review and meta-analysis was conducted in accordance with PRISMA guidelines. We searched PubMed, Embase, Web of Science, and Cochrane Library databases to identify relevant studies published between 1996 and 2022. Eligible studies assessing the relationship between DD and AD were included. A random-effects model was applied to estimate the pooled odds ratios (ORs) with 95% confidence intervals (CIs). Heterogeneity and publication bias were also assessed.

RESULTS: Fourteen studies were included, with sample sizes ranging from 52 to 156,450 participants. The meta-analysis revealed a significant association between DD and an increased risk of AD (OR=1.38, 95% CI: 1.09-1.74, P < 0.05). Heterogeneity among the studies was substantial (I² = 97%), reflecting considerable variability in study designs, populations, and exposure definitions. Sensitivity analysis and publication bias assessments indicated the reliability of the results despite high heterogeneity. Mechanistic analyses suggested that DD may elevate AD risk through pathways such as chronic inflammation, nutritional deficiencies, alterations in the oral microbiome, and reduced cognitive reserve.

CONCLUSIONS: DD are significantly associated with an increased risk of AD. Improving oral health may represent a modifiable factor warranting. However, further high-quality prospective studies are needed to validate these findings and explore the underlying mechanisms.},
}

@article {pmid42088008,
year = {2026},
author = {Sgarbossa, C and Forth, E and Squires, S and Groth, A and Farid, M and Gallant, K and Desai, D and Redfearn, W and Milev, R},
title = {Neurobiological effects of microbial treatments within psychiatry: a systematic review.},
journal = {Frontiers in psychiatry},
volume = {17},
number = {},
pages = {1745964},
pmid = {42088008},
issn = {1664-0640},
abstract = {OBJECTIVE: Though microbial interventions such as probiotics and fecal microbiota transplantation have had a growing body of evidence suggesting their efficacy in alleviating the symptoms of psychiatric illnesses, their exact mechanisms of action and impacts on the brain are still not fully characterized. The aim of this review is to compile and summarize the current literature regarding neurobiological changes associated with microbial interventions targeting psychiatric symptoms in healthy and psychiatric populations.

METHODS: A systematic search of four databases was conducted using key terms related to neuroimaging, microbial interventions, and psychiatric illnesses and/or symptoms. All results were then evaluated based on specific eligibility criteria.

RESULTS: 10 studies met eligibility criteria and were included in this systematic review. Three of the five healthy control studies and all five of the studies conducted within psychiatric populations, observed significant neurobiological changes associated with probiotic intervention either in areas with psychiatric relevance, in the direction of a healthier profile, or correlated with improved psychiatric and/or affective symptoms. The interventions used in these studies consisted of probiotics with bacterial species primarily from the lactobacillus and bifidobacterium genera, at doses ranging from 1-900 billion CFU, taken for durations ranging from 4 weeks to 6 months.

CONCLUSIONS: The findings from this review suggest that probiotic intervention may be associated with neurobiological changes, and that these changes could play a role in ameliorating psychiatric symptoms. More research is needed to replicate these findings, explore other psychiatric populations and microbial interventions, and fully elucidate the mechanisms driving these promising neurobiological and clinical changes.},
}

@article {pmid42088307,
year = {2026},
author = {Wen, S and Jayaweera, DT and Marzouka, GR and Dong, C},
title = {The role of microRNAs in cardiovascular disease associated with the consumption of ultra-processed foods: a comprehensive review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1790304},
pmid = {42088307},
issn = {2296-861X},
abstract = {Ultra-processed foods (UPFs) now dominate dietary intake in many countries and are consistently associated with higher risks of cardiovascular disease (CVD), including myocardial infarction, stroke, and heart failure. Beyond excess sodium, sugar, and unhealthy fats, UPFs may exert cardiovascular harm through food matrix disruption, processing-generated toxicants, additive exposure, and microbiome perturbation. These upstream insults converge on inflammatory, oxidative, and metabolic signaling pathways that regulate microRNAs (miRNAs), a class of small non-coding RNAs that orchestrate post-transcriptional gene expression across endothelial cells, vascular smooth muscle cells, macrophages, platelets, and metabolic tissues. In this review, we propose a unifying mechanistic framework in which UPF exposure reshapes both intracellular and extracellular vesicle (EV)-associated miRNA networks, thereby linking gut, liver, adipose tissue, and the vascular wall in a feed-forward cardiometabolic signaling loop. We synthesize evidence across epidemiology, experimental models, and human dietary intervention studies, while explicitly distinguishing established, emerging, and speculative mechanisms to avoid over-interpretation. We further discuss translational opportunities, including circulating miRNA/EV-miRNA biomarkers, nutritionally responsive miRNA signatures, and miRNA-targeted therapeutics. Together, this framework positions the UPF-miRNA/EV axis as a plausible molecular bridge between modern dietary exposure and atherosclerotic disease progression, and highlights priority areas for mechanistic validation and clinical translation.},
}

@article {pmid42088314,
year = {2026},
author = {Alsanie, SA},
title = {Probiotic-fortified functional foods: integrating nutrient delivery and gut health benefits.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1815558},
pmid = {42088314},
issn = {2296-861X},
abstract = {Foods fortified with probiotics are a fast-emerging field at the crossroads of food technology, nutritional biochemistry and microbiome science. The increased interest in the gut microbiota as a key controller of host metabolism, immunity and overall homeostasis has led to the creation of diets that provide key nutrients with live and beneficial microbes. Compared to the conventional dietary supplementation, there are improved microbe stability, bioavailability, and microbe-nutrient interactions of probiotic fortification of food matrices. This review is a summary of the literature on the impact of probiotics on the host immunological and metabolic signalling pathways, intestinal barrier functioning, and gut microbiota composition. The biological mechanisms of interaction of probiotics with the intestinal microenvironment are specifically focused on the production of short-chain fatty acids, expulsion of pathogens, the regulation of immune cells, and the communication of the gut-brain axis. New information that can be used to correlate the administration of probiotics with the improvement of gastrointestinal health, systemic inflammation, metabolic maintenance and neurobehavioral phenotypes is narratively synthesized based on available preclinical and clinical evidence. The opportunities of probiotic-enriched functional foods have been highlighted in this review as a strategic tool of disease prevention and health promotion in the context of the mechanistic knowledge in combination with translational health outcomes. The complexity in the interactions between microbial delivery systems and host physiology is the clue to the best efficacy, safety and the future innovation in the development of functional foods.},
}

@article {pmid42088498,
year = {2026},
author = {Bu, K and Scherzi, T and Cantor, A and Teng, AA and Pablo, JV and Shandling, AD and Randall, AZ and Davis, E and Jackson, C and Looney, RJ and Campo, JJ and Seppo, A and Järvinen, KM and Clemente, JC},
title = {Gut microbial IgA coating in infants with traditional farming lifestyle and urban infants with allergic outcomes.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1793302},
pmid = {42088498},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Infant ; *Immunoglobulin A/immunology ; Female ; Male ; Feces/microbiology ; *Hypersensitivity/immunology/epidemiology/microbiology ; Milk, Human/immunology ; Urban Population ; Agriculture ; Bacteria/immunology ; Life Style ; },
abstract = {BACKGROUND: The sharp increase in prevalence of atopic disease suggests a role for environmental factors, such as the microbiome. Here, we study the impact of immunoglobulin A (IgA) coating of gut bacteria in infancy on allergic outcomes in two distinct populations: (1) an urbanized cohort of Rochester infants (ROC) enriched for allergies (prevalence of 40%) and (2) infants from a traditional, agrarian Old Order Mennonite (OOM) community with a low prevalence of allergies (less than 2%).

METHODS: We performed immunoglobulin A sequencing (IgA-SEQ) on stool samples collected at an average of 6 months of life to assess gut microbiome IgA coating levels in 9 OOM and 21 ROC infants. Atopic outcomes were diagnosed throughout the first 2 years; 10 of the ROC infants were diagnosed with atopic dermatitis and/or food allergy, while none of the OOM infants were allergic. We also assessed human milk IgA-binding of taxa-derived protein antigens, as well as IgA binding to live bacterial cell cultures.

RESULTS: Gut microbiome composition was dominated by Bifidobacterium, followed by Ruminococcus, Enterobacteriaceae, and Blautia. Higher IgA coating of P. melaninogenica and Pasteurellaceae were associated with allergic outcomes and higher coating of R. gnavus was observed in non-allergic infants. IgA coating levels of Atopobium, Bifidobacterium, and Coprococcus were positively associated with infant age, and coating levels of Corynebacterium associated negatively with infant age. In non-allergic infants, IgA coating of Clostridium was decreased, while in allergic infants, IgA coating of Corynebacterium was decreased. Furthermore, breastfeeding was associated with higher levels of fecal IgA in infancy, and IgA-binding capacity to B. infantis, a keystone infant commensal, was subsequently assessed using in vitro experiments. Compared to the ROC cohort, milk from OOM mothers exhibited a higher level of IgA response to B. infantis and several other commensals. Surprisingly, IgA-binding to B. infantis was partially mediated by Fab-independent interactions through binding to glycosylated regions of immunoglobulins.

CONCLUSION: Differential gut microbial IgA coating may play a role in development of allergic diseases in infancy. Human milk from communities with low rates of allergic diseases exhibit higher IgA responses to infant commensals, including B. infantis.},
}

Humans
*Gastrointestinal Microbiome/immunology
Infant
*Immunoglobulin A/immunology
Female
Male
Feces/microbiology
*Hypersensitivity/immunology/epidemiology/microbiology
Milk, Human/immunology
Urban Population
Agriculture
Bacteria/immunology
Life Style

@article {pmid42088528,
year = {2026},
author = {Liu, H and Wang, D and Zhu, L and Li, T and Liu, B and Sun, J and Zuo, X and Chen, S and Liu, J and Xian, J and Feng, X and Zhang, C and Yang, W},
title = {Angelicin: A promising tricyclic aromatic agent for ulcerative colitis through cysteine-mediated proliferation of intestinal epithelial cells.},
journal = {Journal of pharmaceutical analysis},
volume = {16},
number = {5},
pages = {101435},
pmid = {42088528},
issn = {2214-0883},
abstract = {Angelicin (Ang), a natural tricyclic aromatic compound and quality marker derived from Fructus Psoraleae, exhibits significant anti-inflammatory efficacy. Fructus Psoraleae has long been utilized clinically for treating ulcerative colitis (UC). However, the specific role of Ang in UC remains poorly characterized. The present study aimed to elucidate the anti-UC effects of Ang and its underlying mechanisms. The anti-UC activity of Ang was evaluated using two UC models induced by dextran sulfate sodium (DSS) and 2,4,6-trinitrobenzenesulfonic acid (TNBS). Results demonstrated that Ang markedly inhibited the progression of UC. Microbial profiling indicated that the Ang-treated microbiome, particularly Lactobacillus murinus, provided protective effects against UC. Mechanistically, Ang facilitated proliferation of normal colonic epithelial cells, thus enhancing the intestinal mucosal barrier (IMB). Cysteine (Cys) played a crucial intermediary role by promoting glutathione (GSH) synthesis, maintaining redox homeostasis, and consequently facilitating cell proliferation. Additionally, increased Cys levels supported ribosomal biogenesis, enhancing protein translation and further stimulating cell proliferation. G-rich RNA sequence-binding factor 1 (GRSF1) was identified as a direct molecular target of Ang during ribosomal biogenesis. These findings indicated that Ang is a promising agent for promoting Cys-mediated cell proliferation, highlighting its role in maintaining redox homeostasis and protein translation. This study provides evidence supporting the future development of Ang as a therapeutic candidate for UC.},
}

@article {pmid42088583,
year = {2026},
author = {Zuo, S and Kurumi, H and Ogihara, R and Kanda, T and Isomoto, H},
title = {Gut microbiota-M cell co-culture in inflammatory bowel disease and its therapeutic potential in organoid platforms.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1778142},
pmid = {42088583},
issn = {1663-9812},
abstract = {Dysbiosis of the gut microbiota is a key driver in the onset and persistence of inflammatory bowel disease (IBD). However, the mechanisms by which microbes influence mucosal immunity via specific epithelial routes remain incompletely elucidated. Microfold (M) cells within follicle-associated epithelium serve as a critical "gateway" for luminal antigens and microbes to access the mucosal immune system. While essential for surveillance of commensal microbes, M cells could also be exploited by adherent-invasive strains and adverse environmental factors to amplify inflammation. Recent studies suggest that both in Crohn's disease and ulcerative colitis, M cell abundance and function are aberrantly regulated, linking microbial imbalance with heterogeneous mucosal inflammatory phenotypes. Traditional animal models and two-dimensional culture systems retain limited capacity to selectively manipulate M cells without perturbing systemic immunity, thereby constraining systematic studies of microbiota-M cell co-cultures. Advances in intestinal organoid technology now enable controlled induction of functionally mature M cells within three-dimensional epithelial structures, and have started to shed light on the roles of RANKL signaling, negative regulators, and microbe-associated factors in M cell differentiation and homeostasis. In this review, we focused on key evidence supporting microbiota-M cell interactions in IBD, discussed how M cell-enriched intestinal organoid models could be leveraged to dissect the impact of pathogenic microbes, candidate probiotics, dietary components, and existing therapies on these interactions as well as to evaluate the related potential and limitations for microbiome interventions and drug screening. Integrating gut microbial plasticity with M cell epithelial entry and organoid platforms promises to provide new experimental foundations and theoretical support for individualized microbiome-based therapies and targeted mucosal treatments in IBD.},
}

@article {pmid42088715,
year = {2025},
author = {Alfredo, K and Bedard, E and Buse, HY and Cazals, M and Francisco, P and Lee, J and Masters, S and Osann, E and Stillwell, A and Westerhoff, P and Bartrand, TA},
title = {Ten questions concerning water quality in building hot water systems.},
journal = {Building and environment},
volume = {275},
number = {},
pages = {},
pmid = {42088715},
issn = {0360-1323},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {Hot water systems - water heaters and connected downstream plumbing and fixtures - are at the center of the water-energy nexus. They are ubiquitous and deliver an essential service but are subject to water quality degradation and health risks, scalding risks, energy consumption and greenhouse gas production, and water wastage. While the focus of this paper is on water quality, hot water quality is intimately connected to hydraulics, system layout, water conservation, energy conservation, and user outcomes. Despite their importance, hot water systems are less studied than drinking water production and transmission systems. Better knowledge about hot water will help professionals who design, install, and operate the systems; system users to manage competing risks; and researchers to identify opportunities for innovation. The ten questions posed are focused on the United States. The questions were developed during a workshop that brought together experts in all aspects of hot water systems to identify and prioritize research and innovation opportunities for hot water systems. The questions are ordered to first provide a general description of hot water systems and the chemical and microbiological processes that occur within them, then to discuss the state-of-the-art in modeling and informatics (both critical given the wide diversity in hot water systems), next to explore user and usage aspects of systems and the importance of user-focused design, and finally to identify and prioritize hot water system research and innovation opportunities.},
}

@article {pmid42088993,
year = {2026},
author = {Ul Malook, S and Chen, X and Olukolu, BA and Occhialini, A and Lenaghan, SC and Neal Stewart, C and Chen, F},
title = {Microbial-type terpene synthases enable enhanced insect and fungal resistance in engineered plants.},
journal = {Biodesign research},
volume = {8},
number = {2},
pages = {100087},
pmid = {42088993},
issn = {2693-1257},
abstract = {A major challenge in crop improvement is enhancing resistance to diverse biotic stresses. Because terpenoids play key roles in chemical defense, an envisioned strategy is to introduce new terpene metabolic pathways into crops through engineering. Microbial-type terpene synthase-like (MTPSL) genes are widespread in nonseed plants but absent in seed plants. Here, we engineered terpene metabolism in Nicotiana benthamiana using MTPSL genes, enabling production of sesquiterpenes absent in flowering plants and enhanced resistance to pest insects and fungal pathogens. Two liverwort MTPSL genes, RlMTPSL3 and RlMTPSL4, which produce sesquiterpenes absent from flowering plants, were selected for metabolic engineering. In N. benthamiana, both genes generated sesquiterpenes consistent with their in vitro activities, and co-expression yielded combined profiles. Co-expression of RlMTPSL3 and RlMTPSL4, individually or together, with 3-hydroxy-3-methylglutaryl-CoA reductase, the rate-limiting enzyme in sesquiterpene pathway, substantially increased sesquiterpene production. Bioassays of engineered tissues with two defoliating herbivores beet armyworm (Spodoptera exigua) and Colorado potato beetle (Leptinotarsa decemlineata) showed growth suppression and up to 30% mortality. The gut microbiome of beet armyworm feeding on engineered tissues showed differences from those feeding on control tissues, suggesting a potential mechanism underlying reduced pest insect performance. Engineered sesquiterpenes were recovered from larval frass, indicating stability through digestion. Transformed leaves emitted elevated sesquiterpenes as volatiles that repelled beet armyworm. In addition, extracts of engineered tissues inhibited the growth of Fusarium oxysporum, a fungal pathogen, by ∼50%. Together, these results demonstrate that MTPSL-based engineering can introduce new sesquiterpenes into flowering plants, providing a promising strategy for broad-spectrum crop protection.},
}

@article {pmid42089012,
year = {2026},
author = {Anderson, KE and Copeland, DC and Mott, BM and Kortenkamp, OL and Erickson, RJ and Allen, NO and Maes, PW and Chao, N and Dalenberg, H and Spivak, M},
title = {A propolis-rich hive environment affects redox gene expression and gut microbiota at the individual and social level in honey bees.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag019},
pmid = {42089012},
issn = {2633-6685},
abstract = {The microbiome of the honey bee is associated with immunity, oxidative state, and disease susceptibility. Here we investigated the effects of increased colony-level propolis exposure on gut microbiota and host worker immune and redox gene expression. Sampling pre-marked adult worker bees at 9-days post emergence revealed significantly larger populations of core microbiota in worker guts from propolis-rich colonies, but little change in taxonomic composition or relative structure. We found an overall trend towards decreased expression of immune genes in propolis-rich colonies. The expressions of both pro-phenol oxidase and catalase were significantly reduced in the worker fat body suggesting that propolis-rich colonies better support host redox balance in individual workers. Increased propolis levels resulted in greater expression of superoxide dismutase from the worker fat body and social head glands, consistent with tissue-specific expression considered beneficial in model organisms and humans. Our results suggest that propolis-rich conditions and social head gland secretions contribute to total redox activity throughout the niche space of social immunity. Moreover, our results are consistent with a companion paper that sampled the same colonies and age cohorts, reporting drastic increases in beneficial native bacteria and reduced pathogen prevalence on the mouthparts, a primary marker of social immunity.},
}

@article {pmid42089017,
year = {2026},
author = {Taketani, RG and Clark, IM and Yau, PTO and Liu, L and Zhang, F and Bak, GR and Thompson, CMA and Bonnin, JM and Stewart, H and Malone, JG and Jones, S and Holden, N and Ryan, MJ and Mauchline, TH},
title = {Host plant selects bacterial rhizosphere microbiome function whereas community structure is determined by soil legacy.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag083},
pmid = {42089017},
issn = {2730-6151},
abstract = {The drivers between host plant, associated rhizosphere microbiome functions, and related plant health implications are complex and a field of continuous development. Furthermore, understanding of the interplay between soil, plant, and microbiome across different plant species and contrasting geographical areas is scarce. The United Kingdom (UK) Crop Microbiome Cryobank project, the world's first open crop/soil microbiome resource can fill this research gap. It utilizes contrasting UK soil types, with comprehensive environmental and agronomic metadata and has generated associated rhizosphere and bulk soil microbiome information for six crops (wheat, barley, oats, fava beans, oilseed rape, and sugar-beet) including a bacterial culture collection and 16S rRNA gene datasets. Here, using functional and taxonomic data from 24 000 bacterial cultures and 315 16S rRNA gene metabarcoded soil libraries, we show that geographical location and soil environment primarily influence the phylogeny of rhizosphere bacterial communities, whereas crop genotype is key in determining the function of associated rhizosphere microbiota. Sugar-beet and oilseed rape predominantly select for drought tolerant microbes, barley for Zn-solubilizing microbes and fava bean has a reduced selection of N-mineralizing microbes. These findings emphasize the need to consider the host plant's developmental requirements and edaphic factors for successful deployment of microbiome facilitated agriculture.},
}

@article {pmid42089091,
year = {2025},
author = {Frey, JS and Grogg, MW and Hoisington, AJ and Wong, BA and Mumy, KL and Mauzy, CA},
title = {In vivo lung microbiome alterations from burn pit emissions and/or sand inhalation exposures.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1693310},
pmid = {42089091},
issn = {2296-2565},
mesh = {Animals ; Rats, Sprague-Dawley ; Rats ; *Microbiota/drug effects ; *Lung/microbiology ; *Inhalation Exposure/adverse effects ; *Sand ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; RNA, Ribosomal, 16S ; Open Waste Burning ; },
abstract = {INTRODUCTION: In-theater inhalation exposure to burn pit emissions (BPEs) and sand has been linked to respiratory issues, prompting a study to identify molecular alterations and potential biomarkers related to exposure and outcomes.

METHODS: Using a complex in vivo exposure scenario to mimic in-theater inhalation exposures, Sprague-Dawley rats were exposed to clean air (Control), BPEs, Sand, or a combination of BPE + Sand via whole-body exposure chambers. After euthanasia, bronchoalveolar lavage fluid was collected at 4 days and 90 days post-exposure, and bacterial amplicon sequence variants were identified using genomic DNA extraction and 16S rRNA gene sequencing.

RESULTS: Both BPE and BPE + Sand exposures significantly altered the lung microbiome, demonstrating increased mean alpha diversity and the highest number of unique ASVs. These changes in the lung microbiome began as early as 4 days post-exposure and continued throughout 90 days post-exposure. BPE and BPE + Sand groups had increased levels of Bradyrhizobium and Methylobacterium and decreased levels of Pseudomonas compared to the Control and Sand groups. The genera most associated with the differences at 4 days post-exposure between the BPE vs. Control and BPE + Sand vs. Control groups were Corynebacterium, Geobacillus, Sphingomonas, and Streptococcus. Interestingly, the lung microbiome from the Sand or Control groups was not significantly altered based on alpha or beta diversity and shared the most abundant genera.

DISCUSSION: These data indicate that BPE exposure significantly alter the lung microbiome, whereas sand inhalation exposures alone did not seem to cause significant changes, nor did they provide an additive effect when combined with BPE. While the sub-chronic exposure study design led to more subtle molecular alterations in the lung tissue than expected, BPE exposures resulted in distinct and significant microbiome compositional changes in the lung. The observed population shift provided a signature specific to the type of inhalation exposure. Further efforts could lead to an understanding of the role of individual lung microbiomes in inhalation exposure risks and outcomes.},
}

Animals
Rats, Sprague-Dawley
Rats
*Microbiota/drug effects
*Lung/microbiology
*Inhalation Exposure/adverse effects
*Sand
Male
Bronchoalveolar Lavage Fluid/microbiology
RNA, Ribosomal, 16S
Open Waste Burning

@article {pmid42089105,
year = {2026},
author = {Michalska-Madej, J and Janik-Superson, K and Zając, B and Krupiński, M and Smith, C and Seweryn, M and Ibáñez, A},
title = {Universes within universes: microbiome diversity associated with different body parts of the sand lizard (Lacerta agilis).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21061},
pmid = {42089105},
issn = {2167-8359},
mesh = {Animals ; *Lizards/microbiology ; *Microbiota/genetics ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Cloaca/microbiology ; Skin/microbiology ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {The bodies of animals host millions of microbial communities collectively known as the microbiome. The microbiome plays a crucial role in various processes related to the host's health and well-being. Although our understanding of the microbiome's importance to host functioning is growing rapidly, many aspects remain poorly understood. One such aspect is the role of the microbiome in chemical communication. To address this question, we used the sand lizard (Lacerta agilis), a reptile with well-developed chemosensory abilities and commonly distributed in Central Europe. Our first goal was to characterize the bacterial microbiome associated with different body parts potentially involved in chemical signalling (e.g., femoral glands, cloaca, and skin). Additionally, we examined sex-related differences in the microbiome that could be connected to intraspecific communication. Over two years, a total of 274 samples were collected. Amplicon sequencing of the 16S rRNA V3-V4 region revealed significant variation in microbial diversity across body parts, with the skin hosting the most diverse and balanced communities. In contrast, the cloaca and femoral glands contained less diverse but more specialised assemblages. No differences in microbial diversity between sexes were observed, but the year of sampling was an important factor, suggesting a highly dynamic microbiome in sand lizards. There was minimal overlap in the number of unique operational taxonomic units (OTUs) between body parts, indicating a small core microbiome (∼1% of shared taxa). Sex differences in tissue-specific bacteria were more pronounced in the cloaca, supporting the idea that the cloacal microbiome is highly specialised. Our findings suggest that microbial communities vary significantly among body parts, with strong tissue specificity, indicating that each region provides a distinct ecological niche. This study offers promising directions for future research into how host-associated microbiomes could influence chemical communication in vertebrates.},
}

Animals
*Lizards/microbiology
*Microbiota/genetics
Male
Female
RNA, Ribosomal, 16S/genetics
Cloaca/microbiology
Skin/microbiology
*Bacteria/genetics/classification/isolation & purification

@article {pmid42089249,
year = {2026},
author = {Barrett, TC and Zheng, Q and , and Thompson, A and Di Guglielmo, MD},
title = {Infant fecal microbiome dysbiosis varies by feeding type in setting of severe bronchiolitis.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70435},
pmid = {42089249},
issn = {1536-4801},
support = {U54-GM104941 (PI: Hicks) and the State of Delaware//Institutional Development Award (IDeA) from the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH)/ ; P20GM103446 (PI: Duncan)//IDeA from the NIH NIGMS/ ; //Nemours Fellowship Research Award/ ; },
}

@article {pmid42089362,
year = {2026},
author = {Southward, T and Zhuang, Y and Tam, A and Minsky, H and Ferri, J and Michel, J and Wu, S and Wu, X and Larman, T and Housseau, F and White, JR and Sears, CL and Queen, J},
title = {Enterotoxigenic Bacteroides fragilis induces host genotype-specific colonic epithelial and immune responses in mice.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag247},
pmid = {42089362},
issn = {1537-6613},
abstract = {BACKGROUND: Colorectal cancer pathogenesis involves complex interactions between multiple risk factors including somatic mutations and microbial dysbiosis. A number of individual microbiota members have been implicated in colorectal cancer, including enterotoxigenic strains of Bacteroides fragilis (ETBF). ETBF promotes inflammation in mouse models, which has been mechanistically linked to colon tumorigenesis. We hypothesized that ETBF would promote distinct patterns of colonic damage and inflammation in mice expressing different oncogenic mutations.

METHODS: Mice expressing mutations in the Apc tumor suppressor gene or the BRAF or Kras oncogenes were colonized with ETBF to induce acute colitis. Seven days after colonization, tissues and stools were collected to assess for colonization, epithelial damage, and local and systemic immune responses.

RESULTS: Despite uniform colonization of ETBF across all genotypes and some common features of colitis across groups, Apc, BRAF, and Kras mutations were associated with distinct patterns of colonic epithelial cell injury and goblet cell loss in response to ETBF. RNA sequencing analysis revealed varied transcriptional profiles based on mouse genotype and colon region. Flow cytometry of intra-epithelial leukocytes revealed differential recruitment of myeloid cells based on oncogenic mutation. In particular, mutant BRAF expression was uniquely associated with more systemic inflammation, resistance to goblet cell loss, an interferon-gamma gene signature, and recruitment of a macrophage-like polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) population in the midproximal colon.

CONCLUSIONS: ETBF promotes acute colitis in mice expressing different oncogenic mutations, but with distinct patterns of colonic epithelial cell damage and inflammation dependent on host oncogene context.},
}

@article {pmid42089668,
year = {2026},
author = {Lee, JH and Jung, GS and Kim, K and Park, H and Park, Y and Lee, I and Lee, MJ and Lee, J-H and Choi, YS and Cho, S},
title = {Microbiome in women with endometriosis and the in vitro effects of Lactobacillus reuteri on human endometrium.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0368925},
doi = {10.1128/spectrum.03689-25},
pmid = {42089668},
issn = {2165-0497},
abstract = {UNLABELLED: Endometriosis (EMS) is a chronic inflammatory disorder affecting ~10% of reproductive-age women, with increasing evidence implicating the microbiome in its pathogenesis through immunomodulation and estrogen metabolism. This study investigated microbiome composition in the vagina, endometrium, and peritoneal fluid (PF) of women with and without EMS and further assessed the effects of Lactobacillus reuteri (L. reuteri) on endometrial (EM) cells in vitro. Samples from 41 patients were analyzed using 16S rRNA gene sequencing, targeting the V3-V4 regions. Western blotting, ELISA, and LC-MS/MS were employed to evaluate protein expression and estrogen metabolism during EM-L. reuteri co-culture with or without estradiol-17-glucuronide (E2G). Microbiome analysis revealed no significant differences in alpha or beta diversity between EMS and controls across all compartments. However, LEfSe analysis identified several taxa with differential abundance, with L. reuteri consistently altered in both vagina and EM. Across the menstrual cycle, EM and vaginal microbiomes were stable, whereas PF microbiota showed phase-dependent variation involving 60 genera and 76 species. In vitro, L. reuteri alone did not alter endometriosis-related proteins, but in the presence of E2G, it reduced BAX/Bcl-2 ratios and increased p-NF-κB, suggesting anti-apoptotic and pro-inflammatory shifts. Progesterone receptor α/β expression decreased, while estrogen receptor levels remained unchanged. L. reuteri increased β-glucuronidase activity but did not enhance E2G-to-estradiol conversion. These findings highlight L. reuteri as a potentially important species in EMS, with in vitro evidence suggesting survival-promoting effects under estrogenic conditions. Further research should explore multi-species interactions and hormonal contexts to clarify microbial contributions to EMS pathogenesis.

IMPORTANCE: Although Lactobacillus reuteri appeared more abundant in the vagina and endometrium of controls, suggesting a protective role, in vitro findings paradoxically indicated anti-apoptotic and pro-inflammatory effects under estrogenic conditions, underscoring the need for further investigation of multi-species microbial interactions and hormonal contexts in endometriosis pathogenesis.},
}

@article {pmid42089950,
year = {2026},
author = {Robinson, JM and Robinson, K and Barrable, A},
title = {Viewing ourselves as nature: Holobiont literacy influences nature connectedness.},
journal = {Ambio},
volume = {},
number = {},
pages = {},
pmid = {42089950},
issn = {1654-7209},
abstract = {The human holobiont concept-humans as symbiotic assemblages of a host and trillions of microbes-offers a compelling lens for understanding human-nature relationships. This study examined whether: (a) prior holobiont knowledge correlates with nature connectedness, (b) exposure to holobiont information influences nature connectedness and (c) people feel more or less connected to microbes than to other natural entities. Using a randomised, blinded online survey (n = 190), participants were assigned to a holobiont treatment group (n = 91) receiving multimedia information or a control group (n = 99) receiving neutral content. Nature connectedness was measured before and after exposure. Results showed that prior holobiont knowledge was associated with higher nature connectedness, and, strikingly, that exposure to holobiont information significantly increased nature connectedness scores. No differences were found across nature types. These findings suggest that framing humans as holobionts may strengthen psychological connections to nature, with implications for environmental psychology, education and well-being.},
}

@article {pmid42090006,
year = {2026},
author = {Ray, SS and Goyal, N and Bhattacharyya, M and Arora, S and Bahukhandi, KD and Mahapatra, DM},
title = {Assessing soil microbiome alterations in agricultural land exposed to pesticides through amplicon-based sequencing.},
journal = {Biodegradation},
volume = {37},
number = {3},
pages = {},
pmid = {42090006},
issn = {1572-9729},
support = {SEED Grant-2021//University of Petroleum and Energy Studies/ ; },
mesh = {*Soil Microbiology ; *Pesticides/toxicity ; *Microbiota/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Soil Pollutants ; *Bacteria/genetics/classification/drug effects ; Soil/chemistry ; Biodegradation, Environmental ; Phylogeny ; India ; },
abstract = {The degradation of soil health due to intensive pesticide application has emerged as a critical global challenge, undermining ecological sustainability and agricultural productivity. In regions of high agronomic activity such as Dehradun, India, unsustainable practices including monocropping and excessive agrochemical inputs have been implicated in the decline of soil fertility and microbial diversity. This study employs 16S rRNA gene (V3-V4) amplicon-based sequencing to characterize shifts in bacterial community structure for agricultural farming and non-farming soils. Complementary physicochemical analyses revealed significant associations between soil health parameters and microbial community dynamics. Taxonomic profiling revealed distinct microbial signatures in pesticide-contaminated soils, with a notable enrichment of the phyla Proteobacteria, Acidobacteria, Firmicutes, and Actinobacteria. Dominant genera such as Bacillus sp., Chungangia sp., and Streptomyces sp. were identified, indicating their potential functional roles in biogeochemical cycling and adaptive resilience under chemical stress. Functional prediction using PICRUSt2 highlighted key microbial pathways associated with amino acid synthesis, fatty acid synthesis, degradation of aromatic compound, and other essential biochemical processes. These findings highlight the ecological significance of microbial communities in maintaining soil functionality and offer insights into the development of sustainable land management strategies in pesticide-impacted agroecosystems.},
}

*Soil Microbiology
*Pesticides/toxicity
*Microbiota/drug effects/genetics
RNA, Ribosomal, 16S/genetics
Agriculture
*Soil Pollutants
*Bacteria/genetics/classification/drug effects
Soil/chemistry
Biodegradation, Environmental
Phylogeny
India

@article {pmid42090015,
year = {2026},
author = {Arora, PK and Ali, M and Singh, AP and Dubey, VK and Srivastava, A and Garg, SK},
title = {Exploring the oral microbiome: from traditional techniques to advanced omics and databases.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42090015},
issn = {1572-9699},
mesh = {*Mouth/microbiology ; Humans ; *Microbiota ; Bacteria/genetics/classification/isolation & purification ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Proteomics/methods ; },
abstract = {The oral microbiome comprises analysis of microbes within the oral cavity. Omics, molecular, and bioinformatic methods have significant functions in examining the diversity, composition, and function of the oral microbiome. Molecular techniques, especially 16S and 18S rRNA sequencing, have transformed the study of the oral microbiome. Analysis by 16S rRNA gene sequences of the oral sample creates a broad portrait of the species composition of the oral microbiome and both existing and new species of bacteria. It is instrumental in detecting bacterial pathogens at specific levels, specifically those involved with dental caries, periodontal disease, and oral malignancy. Paralleling the above, analysis by 18S rRNA gene sequencing elicits information related to the composition of fungal as well as protist members within the oral microbiome that plays significant roles for oral health. It can detect oral cavity parasitic infections, which may lead to oral health conditions. Omics tools are general terms for the use of high-throughput approaches to study on a large scale a variety of biological molecules. Applying these technologies to the oral microbiome allows researchers to determine the genetic, transcriptomic, proteomic, and metabolomic profiles of microbes in the oral cavity. These tools help to obtain an overall picture of the oral microbiome, such as its composition, function, and interactions. There are several databases offering useful information on the oral microbiome. These databases store curated information regarding microbial communities in the oral cavity, which aid researchers in the exploration of oral microbiome diversity, composition, and functional characteristics. Some of the examples include Human Oral Microbiome Database (HOMD) and Oral Microbiome Database (OMD). In minireview, we have provided an overview of a variety of molecular and omics tools and databases utilized in the exploration of the oral microbiome.},
}

*Mouth/microbiology
Humans
*Microbiota
Bacteria/genetics/classification/isolation & purification
Computational Biology/methods
RNA, Ribosomal, 16S/genetics
Proteomics/methods

@article {pmid42090122,
year = {2026},
author = {Mikkelsen, E and Amabebe, E and Olmos-Ortiz, A and Hamburg-Shields, E and Prewit, EB and Shynlova, O and Gibbons, DL and Mesiano, S and Taggart, MJ},
title = {The Pathophysiology of Spontaneous Preterm Birth: Emerging Mechanisms Reviewed by the Preterm Birth International Collaborative.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {42090122},
issn = {1933-7205},
abstract = {Around 10% of global births are preterm (before 37 weeks of gestation), posing a significant challenge to maternal and neonatal health. Preterm infants face an increased risk of mortality and long-term health complications, impacting their survival and development across all life stages. Despite decades (~ 80 years) of research, effective methods to predict and prevent idiopathic or spontaneous preterm birth remain limited. Therefore, a deeper understanding of the pathophysiology of spontaneous preterm birth is warranted. This review explores some aspects of recent progress in unravelling the complex pathophysiology of both normal and preterm human birth. We present parturition as an inflammatory event, triggered by stressors affecting the uterine reproductive tissues (myometrium, decidua, and cervix), and involving multiple endocrine and paracrine pathways. These pathways, along with signals from fetal membrane senescence and the vaginal microbiome, contribute to labor induction. Proposed perspectives in parturition research include using mathematical modeling and machine learning (artificial intelligence) to map pregnancy trajectories and identify patient phenotypes associated with preterm birth risk. Additionally, incorporating preterm birth history into routine life course medical surveillance for affected individuals and their offspring is recommended. Finally, increased investment and prioritization from national funding bodies, along with greater support for international collaborations, are essential to identify the causes of preterm birth across multiple populations and develop new, effective treatments.},
}

@article {pmid42090226,
year = {2026},
author = {Constable, S and Minazadeh, Y and Buchanan, LB and Ssemunywa, H and Galiwango, RM and Kaul, R and Prodger, JL},
title = {Anaerobe-Driven Inflammation and Epithelial Barrier Disruption in Genital HIV Acquisition.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {5},
pages = {e70251},
doi = {10.1111/aji.70251},
pmid = {42090226},
issn = {1600-0897},
support = {//Canada Institutes of Health Research/ ; //Ontario Graduate Scholarship/ ; //Engineering Health Equity Fellowship/ ; //Frugal Biomedical Innovations Program at Western University/ ; CRC-2020-00175//Canada Research Chairs Program/ ; //Canada Graduate Scholarship (SC)/ ; },
mesh = {Humans ; *HIV Infections/immunology/microbiology/transmission ; Female ; Male ; *Vagina/microbiology/immunology ; *Bacteria, Anaerobic/immunology ; *Penis/microbiology/immunology ; *Inflammation/immunology/microbiology ; Microbiota/immunology ; *Urethra/microbiology/immunology ; *Dysbiosis/immunology ; *Mucous Membrane/microbiology/immunology ; },
abstract = {BACKGROUND: Genital microbiome dysbiosis is an important risk factor for the sexual acquisition of human immunodeficiency virus (HIV) in both the male and female genital tracts. The vaginal, penile and urethral mucosae are distinct microenvironments with characteristic microbiome compositions. However, all three sites can be colonised by a group of strictly anaerobic bacteria that are strongly associated with mucosal inflammation and HIV risk. Our understanding of the relationship between genital anaerobes and HIV acquisition has largely focused on mucosal target cell density and activation. Yet, genital anaerobes disrupt epithelial barrier integrity, a crucial component of mucosal defence.

OBJECTIVE: To comprehensively evaluate the influence of genital anaerobes on epithelial barrier integrity in the context of HIV acquisition, across the penile, vaginal, and urethral mucosae.

RESULTS: Within the vaginal microbiome, anaerobes have been studied extensively in the context of bacterial vaginosis and several mechanisms of mucosal barrier disruption, including mucus degradation, epithelial cell damage and junction protein cleavage, have been identified and linked to HIV risk. The effects of these same bacteria are less defined in the context of the penile and urethral epithelia, despite their prevalence and association with HIV acquisition.

CONCLUSIONS: Further investigation of genital anaerobe-mediated barrier disruption in both sexes is needed to elucidate shared and site-specific mechanisms influencing HIV transmission. This knowledge is essential to understanding HIV risk and developing effective prevention strategies.},
}

Humans
*HIV Infections/immunology/microbiology/transmission
Female
Male
*Vagina/microbiology/immunology
*Bacteria, Anaerobic/immunology
*Penis/microbiology/immunology
*Inflammation/immunology/microbiology
Microbiota/immunology
*Urethra/microbiology/immunology
*Dysbiosis/immunology
*Mucous Membrane/microbiology/immunology

@article {pmid42090264,
year = {2026},
author = {Dubinkina, V and Smith, BJ and Zhao, C and Pino, C and Pollard, KS},
title = {Linkage of nucleotide and functional diversity varies across gut bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {19},
pages = {e2521012123},
doi = {10.1073/pnas.2521012123},
pmid = {42090264},
issn = {1091-6490},
support = {R01HL160862//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; //San Simeon fund/ ; //Chan Zuckerberg Biohub/ ; predoctoral fellowship//NSF (NSF)/ ; PHY-2309135//NSF (NSF)/ ; 2919.02//Gordon and Betty Moore Foundation (GBMF)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Polymorphism, Single Nucleotide ; *Bacteria/genetics/classification ; Genome, Bacterial ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Linkage ; Genetic Variation ; },
abstract = {Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome collection to characterize patterns of intraspecific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.},
}

*Gastrointestinal Microbiome/genetics
Humans
Polymorphism, Single Nucleotide
*Bacteria/genetics/classification
Genome, Bacterial
Evolution, Molecular
Gene Transfer, Horizontal
*Genetic Linkage
Genetic Variation

@article {pmid42090359,
year = {2026},
author = {Cui, S and Zhou, L and Zhu, N and Hu, K and Wang, F and Huang, X and Kong, F and Jin, D and Xiao, H and Liu, Y},
title = {Grass-Livestock-Fruit System Enhances Grape Health and Productivity by Regulating Leaf and Fruit Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17775},
pmid = {42090359},
issn = {1520-5118},
abstract = {The crop-livestock system is a sustainable agricultural model. Plant microbiomes play essential roles in host fitness and functionality. Here, the responses and functional roles of microorganisms in leaves and fruits were systematically investigated. Endophytic communities remained stable and predominantly beneficial, while epiphytic microorganisms responded more strongly to grass planting and sheep grazing. Grass planting increased the alpha diversity of epiphytic bacteria on leaves, while grazing enhanced the alpha diversity of epiphytic fungi, though both treatments reduced epiphytic bacterial richness on fruits. Grazing enriched potentially beneficial taxa, suppressed potential pathogens, and enhanced the bacterial metabolic potential and symbiotic fungal guilds. Correlations between microbial community variation and grape growth, health, and yield were stronger in leaves than in fruits, more pronounced for epiphytic than endophytic, and greater for bacteria than for fungi. Management simplified fruit and endophytic networks while increasing leaf epiphytic complexity. These findings reveal that microbiome-mediated mechanisms underpin the ecological benefits of integrated management.},
}

@article {pmid42090363,
year = {2026},
author = {Satterthwaite, EV and Ruiz, TD and Patin, NV and Alksne, MN and Thomas, L and Dinasquet, J and Lampe, RH and Chan, KG and Patrick, NA and Allen, AE and Baumann-Pickering, S and Semmens, BX},
title = {Microbial and small zooplankton communities predict density of baleen whales in the southern California Current Ecosystem.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0334209},
doi = {10.1371/journal.pone.0334209},
pmid = {42090363},
issn = {1932-6203},
mesh = {Animals ; California ; *Ecosystem ; *Zooplankton/genetics ; *Balaenoptera/microbiology ; RNA, Ribosomal, 16S/genetics ; Population Density ; *Whales/microbiology ; *Microbiota ; Population Dynamics ; },
abstract = {Understanding the distribution and abundance of marine mammals is important for assessing population dynamics and evaluating the impacts of human activities on these species. Here, we assessed the capability of microbial and small plankton communities to predict the density of Balaenopteridae whales in the Southern California Current Ecosystem in each season from 2014 to 2020 using data from the California Cooperative Oceanic Fisheries Investigations (CalCOFI). Densities of Balaenopteridae whales were estimated from visual line transect surveys for three target species - blue (Balaenoptera musculus), fin (Balaenoptera physalus), and humpback (Megaptera novaeangliae) whales - and microbial and small plankton communities were examined in concurrent water samples via metabarcoding of the 16S and 18S rRNA genes. Planktonic communities specific to each target whale species appeared as strong statistical predictors of whale estimated density, explaining 81-99% of variability and predicting density estimates to within ~1 individual per 1000 km2. Our approach improved out-of-sample root mean square prediction error by up to 65% compared with simple alternative methods. Specific planktonic communities observed indicate that some predictor taxa may be ecologically associated with whales as parasites, as skin and respiratory microbiome species, or through the food chain of whale prey. However, further studies are needed to understand how these organisms function collectively as a community and interact with the "ecological habitat" that supports whales. Our results suggest that using planktonic communities to quantify the potential ecological habitat of larger organisms, like baleen whales, can enhance predictive models and may inform hypotheses about the ecological relationships between whales and the biological communities with which they co-occur.},
}

Animals
California
*Ecosystem
*Zooplankton/genetics
*Balaenoptera/microbiology
RNA, Ribosomal, 16S/genetics
Population Density
*Whales/microbiology
*Microbiota
Population Dynamics

@article {pmid42090386,
year = {2026},
author = {Pelland, ZJ and Zafar, A and Ay, AA and Belanger, KD},
title = {Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0345651},
doi = {10.1371/journal.pone.0345651},
pmid = {42090386},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Football/injuries ; Male ; Young Adult ; *Brain Concussion/microbiology ; Athletes ; Adult ; },
abstract = {Non-concussive head impacts (NHIs) are a significant health concern among at-risk groups, including athletes and military personnel. NHIs are hits to the head or head acceleration events (HAEs) that do not generate clinically detectable symptoms and are unlikely to meet diagnostic criteria for mild traumatic brain injury (mTBI). The composition of the gut microbiota influences many aspects of health and wellness and can be altered by TBIs and by brain-related diseases and disorders; however, microbiome alterations have not previously been linked to NHIs. We investigated whether NHIs in a cohort of American football players correlate with acute and long-term changes in the gut microbiome. This study monitored head impact exposure, gut microbiome composition, and a breadth of clinical and behavioral factors in a cohort of collegiate American football players across a competition season. Both short- and long-term changes in the microbiome were analyzed for correlation with head impact events and mathematical modeling was used to examine the contribution of NHIs and other clinical factors to these changes. We observe that NHI exposure correlates with changes in microbial diversity and composition three days following a head impact event. Furthermore, the athletes' gut microbiomes change significantly across the season, with evidence from mixed-effects modeling indicating that the cumulative effects of NHIs contribute to this change. Our results provide strong evidence for a link between NHIs and changes in the diversity and composition of the gut microbiome. The outcomes of this study emphasize the importance of careful monitoring of head impacts, including those that do not generate clinical symptoms.},
}

Humans
*Gastrointestinal Microbiome
*Football/injuries
Male
Young Adult
*Brain Concussion/microbiology
Athletes
Adult

@article {pmid42090556,
year = {2026},
author = {},
title = {Correction to: Exploring the role of normalization and feature selection in microbiome disease classification pipelines.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
doi = {10.1093/gigascience/giag050},
pmid = {42090556},
issn = {2047-217X},
}

@article {pmid41857155,
year = {2026},
author = {Wang, Z and Tan, W and Zhang, P and Xiong, H and Zhu, L and Cui, J and Li, L and Guo, C and He, L and Huang, J and Wei, H and Liu, H},
title = {Potential subtype-specific alterations in gut microbiota and branched-chain amino acid metabolism in hydrogen- and methane-predominant small intestinal bacterial overgrowth.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41857155},
issn = {2045-2322},
abstract = {We aimed to investigate the clinical, microbiome, and metabolomic characteristics of hydrogen (H2)- and methane (CH4)-predominant small intestinal bacterial overgrowth (SIBO) subtypes. We retrospectively enrolled adults who underwent standardized lactulose hydrogen–methane breath testing between February 2021 and July 2025. Participants were categorized as Normal, H2–SIBO, CH4–SIBO, or mixed H2/CH4–SIBO. Clinical characteristics were compared using Kruskal–Wallis tests and chi-square tests. Multivariable logistic regression was used to identify factors independently associated with each SIBO subtype. Expiratory gas profiles (AUC, peak, and mean values) were quantified, and correlations with age and body mass index (BMI) were assessed using Spearman analysis. In a subset of participants, stool samples underwent 16S rRNA gene sequencing and untargeted metabolomic profiling, followed by integrative analyses of microbiota composition, diversity, and metabolic signatures across SIBO subtypes. Among 503 participants, higher serum albumin levels were independently associated with H2–SIBO, whereas higher fasting glucose was independently associated with CH4–SIBO. Breath-test profiling indicated that methane parameters, rather than hydrogen, better differentiated SIBO subtypes, and total (H2 + CH4) gas output was modestly correlated with age but not BMI. In the exploratory multi-omics subset, fecal microbiota composition and metabolomic signatures differed by subtype; LEfSe identified Bacteroidaceae as a CH4-SIBO signature and Alcaligenaceae/Acidaminococcaceae as H2–SIBO signatures. Differential metabolites were enriched in pathways related to branched-chain amino acid biosynthesis, lipid metabolism, and mineral absorption. H2- and CH4-predominant SIBO subtypes exhibit distinct clinical correlates and stool microbiome–metabolome profiles. Methane exhalation appears more informative for differentiating subtypes, and age is modestly associated with total expiratory gas volumes. These findings support potential subtype-specific host–microbe metabolic interactions, although the multi-omics results should be interpreted as exploratory.},
}

@article {pmid42078608,
year = {2026},
author = {Ullah, T and Khan, AM and Mustafa, A and Fatima, M},
title = {Gut microbiome dysbiosis as a trigger for area postrema syndrome exacerbation in AQP4+ NMOSD with HBV co-exposure.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {5},
pages = {3002-3003},
pmid = {42078608},
issn = {2049-0801},
}

@article {pmid42078675,
year = {2026},
author = {Yang, X and Dong, LL and Jin, XX and Liu, XJ and Gao, M and Fang, J},
title = {Composition and Diversity Characteristics of Gut Microbiota during the Development of Telchinia issoria (Lepidoptera: Nymphalidae).},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73596},
pmid = {42078675},
issn = {2045-7758},
abstract = {Ramie (Boehmeria nivea) was a traditional economic crop of high commercial value, whose cultivation was threatened by the leaf-feeding pest Telchinia issoria. This study investigated how the gut microbiota of T. issoria shifted across its larval, pupal, and adult stages using 16S rRNA amplicon sequencing. We found that Pseudomonadota and Bacillota dominated across all stages, with stage-specific enrichments of key genera: Burkholderia-Caballeronia-Paraburkholderia in early larvae, Acinetobacter and Culicoidibacter in mid-instars, Serratia in late larvae, Enterococcus in pupae, and Pseudomonas in adults. Alpha diversity exhibited a U-shaped pattern during larval development, decreasing initially before rising again, with the lowest overall diversity observed in the pupal stage. Beta diversity confirmed distinct community structures in pupae and adults. Functionally, as predicted by PICRUSt2 based on 16S rRNA gene sequencing data, carbohydrate metabolism was enriched in pupae, whereas pathways associated with amino acid, cofactor, and vitamin metabolism were significantly decreased relative to other developmental stages. Correlation analysis suggested that elevated temperature may contribute to the decreased diversity observed in this study, which warranted further verification under controlled temperature gradients. This work establishes a foundational understanding of stage-specific microbial symbiosis in T. issoria and offers insights for future research into lepidopteran gut microbial ecology and potential biocontrol applications.},
}

@article {pmid42078837,
year = {2026},
author = {Pang, Y and Wang, Y and Deng, Q and Wang, X and Wang, J and Xue, W},
title = {Integrative transcriptomic and microbiome analyses reveal thermal adaptation mechanisms in green and red color morphs of Myzus persicae (Hemiptera: Aphididae).},
journal = {Frontiers in insect science},
volume = {6},
number = {},
pages = {1780864},
pmid = {42078837},
issn = {2673-8600},
abstract = {Under global warming, the frequency and severity of agricultural pest outbreaks have intensified, posing serious threats to agriculture. The green peach aphid (Myzus persicae (Hemiptera: Aphididae)), an important agricultural pest, exhibits green and red color morphs and differentiated thermal tolerance, yet the underlying molecular mechanisms remain unclear. In this study, based on transcriptome and 16S rDNA amplicon sequencing, we analyzed the gene expression patterns and microbial community dynamics of green and red morphs of M. persicae under high-temperature stresses (30 °C and 35 °C) and across different exposure durations, comparing their similarities and differences in heat-response processes. Principal component analysis of transcriptomic data indicated that temperature had a greater influence on the physiological responses of M. persicae than body color, with a more pronounced effect observed at 35 °C. Differential gene expression analysis revealed overlap in temperature-responsive genes but different response patterns between the two morphs, suggesting activation of divergent molecular response mechanisms. Genes encoding heat shock proteins, detoxification-related enzymes, ribosomal protein family and so on were significantly up-regulated under high temperature, with a more pronounced induction in the green morph, indicating morph-specific regulatory strategies in response to thermal stress. Moreover, 16S rDNA sequencing revealed that the primary symbiont Buchnera displayed different relative abundance trends in the green and red morphs, remaining relatively stable in the red morph but declining markedly in the green morph under heat stress, potentially associated with their variation in thermal tolerance. Collectively, this study elucidates the molecular responses and microbe-mediated regulatory mechanisms underlying thermal tolerance in green and red morphs of M. persicae, providing novel insights into the thermal adaptation of aphids and a theoretical basis for developing pest management strategies under global warming.},
}

@article {pmid42078866,
year = {2026},
author = {Ghura, S and Jmii, H and Griffith, J and Schaeffer, AJ and Klumpp, DJ},
title = {Gut Microbiome-Driven Microglial Activation Links Dysbiosis to Pain in Interstitial Cystitis/Bladder Pain Syndrome.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9087060/v1},
pmid = {42078866},
issn = {2693-5015},
abstract = {Background Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating condition of chronic pelvic pain associated with urinary frequency and comorbid anxiety and depression. Recent studies in IC/BPS patients and rodent models implicate fecal dysbiosis and increased systemic exposure to endotoxin. These changes potentially elicit innate immune responses via the activation of microglial cells in the central nervous system, key mediators of pain. Microglial ablation and inactivation have previously been associated with analgesia in preclinical studies, underscoring the role of microglia in IC/BPS pain. Here, we investigated whether IC/BPS-associated fecal microbiota differentially activate microglia and whether activation correlates with patient symptoms. Methods Microbiome-microglia interactions were assessed using three complementary in vitro culture models: BV2 cells, enriched primary microglia (~ 95% microglia), and mixed glial cultures (microglia and astrocytes). Microglial cultures were exposed to heat-killed, stool-derived microbiota, and the pro-inflammatory cytokines tumor necrosis factor-α (TNF-α), RANTES/CCL5, and interleukin-6 (IL-6) were quantified by ELISA. Cytokine levels were evaluated for patients and controls and correlated with patient-reported genitourinary pain index (GUPI) scores. Results In all culture models, microglia exhibited significantly increased proinflammatory responses to fecal microbiota of IC/BPS patients relative to controls. Mixed glial cultures, incorporating astrocyte-microglia interactions, exhibited the most robust cytokine responses. Cytokine levels positively correlated with GUPI pain scores. Conclusions Together, these findings further support a role for gut dysbiosis in IC/BPS symptoms and suggest microglial activation and glial-glial interactions as a contributing mechanism. Understanding gut-brain axis interactions in IC/BPS will thus enable development of novel microbiome-based therapies for treating IC/BPS patients.},
}

@article {pmid42079003,
year = {2026},
author = {Comerford, KB},
title = {The impacts of ready-to-eat-cereals and cereal fibers on gut health, body weight, and cardiometabolic health.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1717345},
pmid = {42079003},
issn = {2296-861X},
abstract = {Ready-to-eat breakfast cereals are a major source of dietary fiber, and their intake is associated with better diet quality and reduced incidence of chronic disease. However, dietary fiber intake remains significantly lower than recommended levels, particularly in North America. This fiber gap is one of the most important issues facing public health nutrition and deserves continued attention. This extensive analysis summarizes the body of research from the last decade on whole grain/high-fiber breakfast cereals, cereal fibers, and/or selected fiber sources commonly found in, or added to, breakfast cereals (e.g., wheat bran, psyllium). The primary health outcomes of interest for this review are digestive function, gut microbial effects, satiety signaling, body weight management, cardiovascular disease and blood glucose control. The evidence indicates that the fiber amount, fiber type, processing techniques, and numerous associated nutrients and phytochemicals in ready-to-eat breakfast cereals are all critical factors impacting health outcomes. Therefore, in addition to dietary guidance on total daily intake levels, guidance targeting specific health outcomes should also emphasize the unique mechanisms of action (e.g., gel-forming, digestion slowing, fecal-bulking, laxative, toxin binding, prebiotic) for the predominant types of fibers in ready-to-eat cereals and other fiber-rich foods. In particular, a growing body of research indicates that wheat bran, the predominant source of fiber in the U.S. and Canada, contains a novel array of fibers and phytonutrients that support bowel function and influence gut microbiota composition, and may help lower the risk for cardiometabolic disease. Notably, the research shows that individuals with low-cereal fiber consumption are most likely to benefit from an increase in their daily intake. While there is still much to discover regarding the mechanistic effects of different types of cereal fibers, continued encouragement to increase daily consumption of wheat fiber-rich foods, including ready-to-eat cereals, could help to close the fiber gap and reduce the incidence of multiple diet-related chronic diseases.},
}

@article {pmid42079098,
year = {2026},
author = {Wucher, BR and Pardo-De la Hoz, CJ and Stamper, I and Sharma, S and Kaune, D and Bendale, P and Peled, J and Xavier, JB},
title = {Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.20.716137},
pmid = {42079098},
issn = {2692-8205},
abstract = {The gut microbiota contains trillions of bacteria essential to health, but also harbors potential pathogens. The phylum Pseudomonadota, which includes Escherichia coli , Klebsiella pneumoniae , and Pseudomonas aeruginosa , typically composes <1% of the microbiota but causes disproportionate numbers of gut-borne bloodstream infections. Identifying the ecological dependencies that enable Pseudomonadota to cause gut-borne disease is important for human health. Here, we studied microbiota dynamics in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) to find that microbiota compositions permissive to Pseudomonadota had, following antibiotic prophylaxis, high levels of Bacteroides- a major reservoir of polysaccharide utilization loci (PULs). We tested the causality of this clinical association in a mouse co-colonization model and discovered that Bacteroides fragilis promotes Pseudomonas gut colonization and survival to ciprofloxacin, a drug commonly used as prophylactic in allo-HCT. In vitro experiments revealed a general mechanism by which diverse Pseudomonadota species depend on Bacteroides polysaccharide breakdown to grow better, form more biofilm, and survive ciprofloxacin treatment under anaerobic conditions, a type of ecological dependency termed metabiosis . Guided by this insight, we used metagenomics to identify the PUL-encoded functions underlying the metabiotic potential of a patient's microbiota and establish a link to gut-derived Gram-negative bacteremia in allo-HCT. Together, our findings translate mechanistically based microbiome ecology into a clinically actionable framework for early risk stratification and intervention.},
}

@article {pmid42079116,
year = {2026},
author = {Bar, O and Murthy, M and Cosgrove, K and Saidi, Y and El-Arar, W and Goldenberg, M and Sauvage, G and Bergerat, A and Cooley Demidkina, B and Laliberte, K and Xu, J and Pierson, G and Kwon, DS and Niles, J and Yassour, M and Mitchell, CM},
title = {An Observational Study of the Impact of Systemic B-cell Depletion on Cervicovaginal Mucosal Environment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.718227},
pmid = {42079116},
issn = {2692-8205},
abstract = {IMPORTANCE: Emerging data show that B-cell depleting chemotherapies, which are increasingly used to treat autoimmune disorders and multiple sclerosis, can be associated with mucosal side effects such as inflammatory vaginitis.

OBJECTIVE: Evaluate the impact of rituximab treatment on vaginal mucosal immune markers, endocervical immune cell populations and vaginal microbiome.

DESIGN: Cross-sectional observational study conducted between 2022 - 2024.

SETTING: Academic medical center, Boston Massachusetts.

PARTICIPANTS: We enrolled women aged >18 years who were either 1) receiving rituximab for autoimmune renal disease or were 2) healthy controls.

EXPOSURE: Treatment with rituximab, an anti CD20 monoclonal antibody.

MAIN OUTCOME AND MEASURE: We compared endocervical immune cell populations, vaginal fluid immune markers, vaginal fluid immunoglobulins and vaginal microbiome composition between individuals being treated with rituximab and healthy controls.

RESULTS: We enrolled 26 women treated with rituximab for autoimmune renal disease and 26 healthy controls. Median circulating and endocervical B-cell and plasma cell proportions were significantly lower in treated participants compared to controls. Median vaginal fluid IgA concentrations were significantly lower in participants treated with rituximab, while ILE, IgM, IgG1, IgG2, IgG3 and IgG4 were not different between groups. Total T cell frequencies were similar between groups, but the proportion of activated T cells (CD4+CD38+HLADR+) was significantly lower in people treated with rituximab. Concentrations of IL10, IL13, IL17, IL21, IL23, IL4, ITAC and TNFa were elevated in vaginal fluid from the rituximab group, while IL-8 was lower. A CST-IV-C, low- Lactobacillus pattern of vaginal microbiota was more common in the rituximab group.

CONCLUSIONS AND RELEVANCE: Systemic B-cell depletion is associated with reduced vaginal fluid IgA, a more diverse microbiome composition, and increases in many vaginal fluid immune markers compared to healthy controls. The reduction in vaginal fluid IgA may provide opportunities for vaginal bacteria to induce inflammation.

KEY POINTS: Question: How does circulating B-cell depletion impact the vaginal microenvironment?Findings: In this cross-sectional study of 52 women, B cell and plasma cell proportions were significantly lower in both blood and vaginal mucosa among rituximab-treated participants compared to healthy controls. Vaginal IgA concentrations, but not other immunoglobulins, were significantly lower in rituximab treated participants. In treated participants, vaginal cytokine concentrations were elevated, and microbiome composition shifted toward non- Lactobacillus -dominant communities. In six people with inflammatory vaginitis, both circulating and endocervical B cells were lowest in people with the most severe symptoms. Meaning: Systemic B cell depletion is associated with alterations in vaginal mucosal immune markers and microbiome composition which increase local inflammation.},
}

@article {pmid42079144,
year = {2026},
author = {Nkera-Gutabara, C and Olubayo, LAI and Oduaran, OO and Kisiangani, I and Khoza, S and Gama, K and Maritze, M and Mabunda, C and Keya, D and Adetunji, KE and Tollman, S and Micklesfield, LK and Mohamed, SF and Gómez-Olivé, FX and Tluway, F and Ramsay, M and Bhatt, AS and Hazelhurst, S and Maghini, DG and , },
title = {Participant engagement and feedback in microbiome projects: a case of AWI-Gen 2.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.20.718838},
pmid = {42079144},
issn = {2692-8205},
abstract = {UNLABELLED: Returning individualized microbiome results in ways that are ethical, comprehensible, and useful remains under-explored in African settings. We nested a multi-site, mixed-methods study within the AWI-Gen Wave 2 gut microbiome sub-study of 1,801 women aged 42 - 86 years to engage the participants and provide feedback. All (1,001) participants from Agincourt and Soweto (South Africa) and Nairobi (Kenya) were invited to feedback meetings: 496 from Agincourt, 87 from Soweto, and 195 from Nairobi responded. Engagement strategies were tailored by site (small-group and home-based sessions, visual metaphors, Foldscopes, and local-language delivery). Using semi-structured discussions and structured observations analysed thematically in MAXQDA under COREQ, five cross-cutting themes emerged: (1) understanding of microbiome reports, (2) emotional responses to feedback, (3) perceived health relevance, (4) trust in research institutions, and (5) suggestions for improving engagement. Culturally grounded explanations and local-language facilitation enhanced comprehension and perceived relevance; English-heavy sessions were associated with more confusion. Most participants expressed satisfaction and described planned or enacted dietary and lifestyle changes, while frustration centred on long delays between sampling and feedback. Trust increased with transparency and individualized return of results but was often conditional on minimizing burdensome procedures such as repeat blood sampling (phlebotomy) and ensuring timely feedback. Engagement was feasible and low-cost (approximately USD 29-59 per participant) with site-specific resource needs. Limitations included constrained generalizability beyond the three study sites. Returning individualized microbiome findings in community settings in Africa is acceptable, feasible, and can motivate health-promoting behaviours when delivered promptly and in culturally and linguistically appropriate ways.

IMPORTANCE: Microbiome studies rarely return individualized results in low-resource settings due to concerns about appropriate feedback and associated costs. This gap risks eroding trust and diminishing research impact. In three African communities, tailored feedback on gut microbiome profiles was provided to 778 women. By documenting a costed, multi-site engagement model and the themes influencing acceptance and actionability, this work offers a practical framework for ethically returning complex -omics results at scale in underrepresented populations - advancing scientific equity and strengthening community trust in microbiome research.},
}

@article {pmid42079178,
year = {2026},
author = {Zhang, S and Buttimer, C and Trepka, KR and Lam, KN and Hernandez, LAR and Soto-Perez, P and Noecker, C and Canigiula, P and Ortega, EF and Lee, J and Ramirez, L and Partipilo, G and Lawrence, HB and Bottacini, F and Draper, LA and Ross, RP and Coffey, A and Shkoporov, A and Hill, C and Turnbaugh, PJ},
title = {Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.24.720693},
pmid = {42079178},
issn = {2692-8205},
abstract = {Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage ΦKL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta , during in vitro growth. However, ΦKL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that ΦKL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.},
}

@article {pmid42079212,
year = {2026},
author = {Mills, T and Vinzelj, JM and Cook, ER and Mills, E and Rurik, AJ and Dallas, JW and Walker, DM and Stone, PA and Siler, CD and Elshahed, MS and Youssef, NH},
title = {Exploring the diversity and community structure of the Testudines fecal mycobiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.22.720109},
pmid = {42079212},
issn = {2692-8205},
abstract = {UNLABELLED: Most gut microbiome studies have focused on bacteria, leaving a knowledge gap regarding gut associated fungi. We assessed fungal diversity in the gastrointestinal tract of the reptilian order Testudines (turtles and tortoises) using samples from 6 families, 19 genera, and 27 species. A highly diverse community affiliated with 17 phyla and 157 orders was encountered, with four phyla (Neocallimastigomycota, Chytridiomycota, Ascomycota, and Basidiomycota) representing 89.13% of the community. Neocallimastigomycota was identified in host families Testudinidae (land tortoises), Chelidae , Chelydridae , Emydidae , Geoemydidae , and Kinosternidae , with higher relative abundances in Testudinidae (40.18±37.97%) compared to all other families combined (2.71±4.04%). Neocallimastigomycota sequences were mostly affiliated with orders Testudinimycetales in the host family Testudinidae and Neocallimastigales in other host families. Chytridiomycota was identified in all host families, but was more ubiquitous and abundant in Kinosternidiae (45.17±34.12%), and exhibited a high level of variability across samples. Dikarya communities were highly diverse, with 108 orders identified, and, similar to Chytridiomoycota, exhibited a highly stochastic distribution pattern. Representatives of multiple yet-uncultured phyla (Candidatus "Algovoracomycota", "Sedimentomastigomycota", "Tartumycota" and "Cantoromastigomycota") were identified, as well as eight novel orders in Chytridiomycota and Rozellomycota. Deterministic selection shaped community assembly in the host family Testudinidae , while the process was more stochastic in other host families. Distinct community structure was driven by differences in abundance and identity of the Neocallimastigomycota when comparing Testudinidae to. Our results describe a diverse and dynamic fungal community, shaped by the co-occurrence of autochthonous (resident) and transient (allochthonous) members of the gut microbiome.

IMPORTANCE: Fungi are known to inhabit the gastrointestinal tract (GIT) of humans and mammals. However, information on the fungal community in the GIT of reptiles is relatively sparse. We investigated the diversity and community structure of fungi in the reptilian order Testudines. We conducted a culture-independent diversity survey on fecal samples obtained from 27 different host species. We identify representatives of 17 fungal phyla. As well, we demonstrate that the anaerobic gut fungi (phylum Neocallimastigomycota) are not restricted to the family Testudinidae (land tortoises) as previously suggested, but could successfully colonize and inhabit all other testudines families, including those exhibiting a predominantly omnivorous or carnivorous lifestyles. In addition, we expand on the known fungal diversity by identifying additional representatives of multiple recently described yet-uncultured phyla, and describe multiple novel orders and classes within existing phyla. Collectively, this effort adds to the growing body of knowledge of mycobiomes in underexplored animal hosts.},
}

@article {pmid42079297,
year = {2026},
author = {Cornman-Homonoff, J and Rajendran, KM and Kolandaivelu, S and Coon, SD and Kupec, JT and Wang, L and Hu, G and Jala, VR and Sandle, GI and Rajendran, VM},
title = {Dietary Sodium Restriction Reprograms Gut Microbial Fermentation and Reduces Host Energy Harvest.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.20.719706},
pmid = {42079297},
issn = {2692-8205},
abstract = {Diet is a major determinant of gut microbiome structure and function, yet the role of dietary electrolytes-particularly sodium-remains poorly defined. Here, we identify dietary sodium availability as a key regulator of gut microbial fermentation and host energy harvest. Using a controlled sodium-sufficient versus sodium-deprived dietary intervention in rats, we integrated shotgun metagenomic sequencing, functional pathway analysis, targeted short-chain fatty acid (SCFA) quantification, and host physiological phenotyping. Sodium deprivation induced a coordinated restructuring of the gut microbiome, characterized by depletion of classical saccharolytic Firmicutes, including multiple Lactobacillus species, and enrichment of stress-tolerant, metabolically flexible taxa. Functional profiling revealed a shift away from growth-associated metabolic programs toward stress-adaptive and nutrient-scavenging pathways. Consistent with these changes, fecal concentrations of key SCFAs-including acetate, butyrate, hexanoate, and valerate-were significantly reduced, indicating impaired microbial fermentative capacity. These microbiome-level alterations translated into measurable host phenotypes, including reduced cecal mass and attenuated weight gain, consistent with decreased microbial energy harvest. Together, these findings establish a functional link between luminal sodium availability, microbial metabolic efficiency, and host energy balance, extending the framework of diet-microbiome interactions beyond macronutrients to include dietary electrolytes. This work identifies sodium as a previously underappreciated ecological constraint shaping gut microbial metabolism and suggests that modulation of dietary sodium intake may influence host metabolic outcomes through microbiome-mediated mechanisms.},
}

@article {pmid42079325,
year = {2026},
author = {Akif, A and Munami, JW and Das, R and Shawon, NJ},
title = {Dietary Polyphenols in Non-Communicable Chronic Diseases: Neuro-Enteric Mechanisms, Multi-Omics Biomarkers and Translational Opportunities.},
journal = {Food science & nutrition},
volume = {14},
number = {},
pages = {e71856},
pmid = {42079325},
issn = {2048-7177},
abstract = {Polyphenols from plant foods (tea, cocoa, berries, grapes, and extra-virgin olive oil) modulate oxidative stress, inflammation, vascular function, and the gut microbiome-axes central to non-communicable chronic diseases (NCCDs) that involve the brain and enteric nervous system (ENS). Recent randomized trials and longitudinal studies report modest but reproducible benefits on cognitive domains and vascular/endothelial function with berry/grape extracts, matcha/green tea, and high-polyphenol extra-virgin olive oil; effects appear stronger in older adults or those with metabolic risk. Complementary evidence in irritable bowel syndrome (IBS)-a prototypical gut-brain disorder-suggests polyphenol-based combinations (often with probiotics/fiber) can improve quality of life and inflammatory markers, supporting enteric-central crosstalk. Emerging genetics (Mendelian randomization) and multi-omics readouts strengthen causal inferences for tea polyphenols in neurodegeneration-adjacent outcomes and outline mechanistic mediators (endothelial/BBB function, cytokine tone, microbiome-derived metabolites). Key gaps remain: heterogeneous formulations/doses, limited head-to-head trials, sparse target engagement biomarkers, and uncertain durability after discontinuation. We synthesize clinical and mechanistic advances, propose a standardized biomarker set (neurocognitive, endothelial, immune, and microbiome-metabolome), and outline designs for mechanism-anchored RCTs that integrate ENS endpoints with brain outcomes to translate associative signals into precision nutrition strategies for NCCDs.},
}

@article {pmid42079427,
year = {2026},
author = {Xolalpa-Aroche, A and Contreras-Peruyero, H and Delgado-Suárez, EJ and Hernández-Mena, DI and Moguel-Chin, WI and Rivero-Cruz, JF and Velarde, RA and Ortiz-Vázquez, E and Rivero-Cruz, BE and Lovaco-Flores, JA and Rodríguez Orduña, L and Licona-Cassani, C and Barona-Gómez, F and Sélem-Mojica, N},
title = {Genome-resolved metagenomics reveals a phylogenetically cohesive Acetilactobacillus-like species complex dominating stingless bee pot honey.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag063},
pmid = {42079427},
issn = {2730-6151},
abstract = {Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing [Formula: see text]81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI [Formula: see text], interclade ANI [Formula: see text]), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.},
}

@article {pmid42079428,
year = {2026},
author = {Griggs, RG and Mills, DA and Bokulich, NA},
title = {Spatial heterogeneity and microbial terroir: balancing dispersal limitation and cultivar as drivers of microbial diversity in viticulture.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag074},
pmid = {42079428},
issn = {2730-6151},
abstract = {The microbial communities inhabiting grapevines and wines exhibit spatiotemporal patterns linked to region, climate, and cultivar. However, the degree of spatial heterogeneity within and between vineyards and its relationship to cultivar-associated biodiversity selection has not been studied previously. We combined high-density sampling of grapevine microbiota (N = 230) with spatial modeling and satellite imagery in two experiments: (i) two monoclonal Chardonnay vineyards to examine spatial heterogeneity in a genetically homogenous population and (ii) three old-vine vineyards interplanted with mixed cultivars to investigate the relative effects of spatial distance and cultivar on the microbiota. Contrary to expectations based on monoclonal vineyards, cultivar effects were not apparent in mixed-cultivar vineyards. Instead, we demonstrate extensive spatial variation in the bacterial and fungal communities inhabiting individual grapevines and vineyards, and that community similarity is correlated with spatial distance within and between vineyards. This suggests that dispersal limitation may play an important role in shaping grapevine microbiota, as well as cumulative diversity within the vineyard ecosystem (gamma diversity), with implications for both plant health and wine quality. Spatial models may identify abnormalities in microbial communities, such as contaminant sources within vineyards, and future studies examining microbiota in agricultural settings should account for spatial variation within the study design, e.g. by sufficiently dense spatial sampling or collection of aggregate samples (e.g. grape musts) to avoid undersampling bias. Overall, this study adds to the complicated story of microbial biogeography associated with winegrowing and wine quality (microbial 'terroir'), highlighting the roles of dispersal and potential microclimate effects in agricultural settings.},
}

@article {pmid42079429,
year = {2026},
author = {Christensen, R and Wang, YHD and Arnoldini, M and Cremer, J},
title = {Abundance-weighted pathway mapping demonstrates family-level structure of butyrate and propionate production across the human gut microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag075},
pmid = {42079429},
issn = {2730-6151},
abstract = {Fermentation products released by bacteria in the large intestine, such as butyrate and propionate, play central roles in host physiology and health. While the metabolic pathways producing these short-chain fatty acids (SCFAs) are well-characterized, less is known about their relative prevalence across hosts and gut conditions. Here, we introduce a genome-resolved, abundance-weighted bioinformatics framework that integrates pathway-based gene identification with extensive literature validation to systematically quantify the potential for butyrate and propionate production across bacterial species and human gut microbiomes. By comparing pathway predictions against over 700 experimentally characterized strains, we demonstrate high concordance with reported metabolic phenotypes, validating our approach beyond prior purely computational studies. Weighted by species abundance across ~18 000 metagenomic samples, we find that dominant gut taxa disproportionately drive SCFA production, with butyrate pathways enriched in Bacillota and propionate pathways in Bacteroidota. This abundance-weighted analysis reveals that pathway presence is well conserved at the family level, highlighting the ecological relevance of dominant taxa for community-level fermentation potential. Our results further show pronounced inter-individual variation and associations with age, birthing method, and inflammatory bowel disease, emphasizing how shifts in microbiota composition influence SCFA availability. By combining pathway-level resolution, abundance-weighted inference, and literature-based validation, our framework provides a robust, scalable approach to link microbial functional potential with host-relevant outcomes.},
}

@article {pmid42079430,
year = {2026},
author = {Scott, WT and Nataya, ED and Belzer, C and Schaap, PJ},
title = {Metabolic modeling unveils potential probiotic roles of Flavonifractor plautii in reshaping the Western gut microbiota landscape.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag077},
pmid = {42079430},
issn = {2730-6151},
abstract = {Flavonifractor plautii, a prevalent gut commensal, uniquely combines flavonoid degradation with the capacity to produce health-promoting short-chain fatty acids (SCFAs), notably butyrate and propionate. However, its metabolic pathways, ecological roles, and health impacts remain poorly characterized. To explore its probiotic potential and ecological functions, we developed a genome-scale metabolic model, iFP655, using automated reconstruction, deep-learning-based gap-filling, thermodynamic constraints, and transcriptomics. The iFP655 model substantially improved the predictions of growth rates and SCFA profiles compared to previous models. Simulations identified acetyl-CoA pathways as the preferred route for butyrate production, whereas the energetically costly lysine pathway remained inactive despite robust gene expression. Propionate synthesis occurred primarily via the methylmalonyl-CoA pathway. Community metabolic modeling with representative species of a Western minimal gut microbiota highlighted F. plautii's contributions to enhanced SCFA production, especially butyrate, amino acid metabolism, and syntrophic interactions driven by dietary substrates. Our findings indicate that diet-driven syntrophy significantly shapes microbial community structure and function, underscoring the ecological importance of F. plautii in gut microbial interactions and highlighting its potential as a probiotic candidate to beneficially modulate gut microbiota through dietary interventions.},
}

@article {pmid42079440,
year = {2026},
author = {Yang, L and Luo, R and Zhou, W and Yin, P and Feng, Y and Zhang, Y},
title = {Recent advances in noncanonical inhibition mechanisms of anti-CRISPR proteins.},
journal = {mLife},
volume = {5},
number = {2},
pages = {133-147},
pmid = {42079440},
issn = {2770-100X},
abstract = {The CRISPR-Cas system constitutes an adaptive immune mechanism in prokaryotes that defends against mobile genetic elements. Within the perpetual co-evolutionary arms race between bacteria and their viral predators, bacteriophages encode anti-CRISPR (Acr) proteins that use sophisticated molecular strategies to sabotage CRISPR-Cas function. While canonical Acr proteins rely on steric blockade of Cas effectors, recent discoveries reveal unprecedented noncanonical mechanisms spanning CRISPR immunity stages. This review synthesizes recent mechanistic advances in this field since 2023, highlighting the expansion of noncanonical inhibition mechanisms beyond type I to include types II, V, and VI, as well as novel Acr interventions targeting multiple functional stages, such as spacer acquisition, translation-coupled inhibition, complex assembly/disassembly, and R-loop DNA binding. Structural insights demonstrate how Acr proteins achieve substoichiometric inhibition via conformational hijacking, catalytic repurposing, and molecular mimicry. Forged by the intense selective pressure of the phage-host conflict, these molecular innovations represent both remarkable evolutionary adaptations and versatile precision tools. They enable spatiotemporal control of CRISPR technologies, from engineered off-switches to diagnostic reset mechanisms, while posing critical challenges for therapeutic safety and microbiome management.},
}

@article {pmid42079634,
year = {2026},
author = {Li, L and Cai, F and Liu, S and Peng, P and Liang, J and Liu, Z and Xu, H and Mo, W and Qin, J and Tang, S and Ruan, H and Zhang, J and Liang, C and Liu, S and Qin, M and Qin, R and Luo, F and Xiong, G and Yang, C and Geng, Y and Zou, J and Huang, J},
title = {Worldwide research trends on the Helicobacter pylori-gut microbiome nexus: a bibliometric analysis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1794021},
pmid = {42079634},
issn = {1664-3224},
mesh = {Humans ; *Helicobacter pylori/immunology ; *Gastrointestinal Microbiome/immunology ; *Helicobacter Infections/microbiology/immunology ; Bibliometrics ; Dysbiosis/microbiology ; *Biomedical Research/trends ; },
abstract = {INTRODUCTION: The impact of Helicobacter pylori (H. pylori) on the gastrointestinal tract ecosystem has been widely investigated beyond the stomach. Researchers have made considerable progress in understanding the relationship between H. pylori infection, gut microbiome dysbiosis, and systemic effects in recent years. This study aimed to explore the prospects and developing trends in the field of the H. pylori-gut microbiome nexus from a bibliometric perspective.

METHODS: Articles were collected from the Web of Science Core Collection, Scopus, and PubMed (2000-2025) and analyzed using bibliometrix, VOSviewer, and CiteSpace. Analysis of 1,592 publications reveals a distinct three-phase evolutionary structure in the field.

RESULTS AND DISCUSSION: Geographically led by China and the USA, the research focus has undergone a paradigm shift: evolving from an initial "infection and eradication" phase, through a transitional "dysbiosis and ecological intervention" phase, to the current "tumor-immunity axis" hotspot. Recent high-strength citation bursts for terms like "Fusobacterium nucleatum" and "immunity" underscore this transformation, indicating that academic attention has moved beyond local gastric pathogen control to understanding H. pylori's systemic role in modulating tumor microenvironments and therapeutic responses. This bibliometric analysis maps the field's rapid growth trajectory, highlighting its value for guiding future precision oncology and microecological strategies.},
}

Humans
*Helicobacter pylori/immunology
*Gastrointestinal Microbiome/immunology
*Helicobacter Infections/microbiology/immunology
Bibliometrics
Dysbiosis/microbiology
*Biomedical Research/trends

@article {pmid42079661,
year = {2026},
author = {Yu, J and Zhuang, WW and Lei, B and Shan, RY and Wang, XM and Qu, P and Hannig, M and Liu, Y},
title = {The oral-vascular axis: immune mechanisms linking periodontal dysbiosis to systemic vascular pathology.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1793621},
pmid = {42079661},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology ; *Periodontitis/immunology/microbiology ; Animals ; *Atherosclerosis/immunology ; *Mouth/immunology/microbiology ; *Cardiovascular Diseases/immunology ; },
abstract = {Periodontitis is among the most prevalent chronic inflammatory diseases worldwide and may affect vascular health beyond the oral cavity. Framed within the concept of an oral-vascular axis, this review synthesizes clinical and mechanistic evidence linking periodontal disease with atherosclerotic cardiovascular disease (ASCVD). Epidemiological studies and meta analyses consistently associate periodontitis with higher risks of coronary heart disease (CHD), stroke, and cardiovascular mortality, with modest but reproducible effect sizes that persist after adjustment for traditional risk factors. However, heterogeneous study designs and residual confounding preclude definitive causal inference. Interventional evidence is currently dominated by surrogate endpoints, and event-level cardiovascular benefit from periodontal therapy remains unproven. Mechanistically, chronic periodontal inflammation may influence endothelial function and atherogenesis through interlocking pathways that can be viewed as a spatiotemporal, dual-regulatory network of immunity and metabolism: local dysbiosis and barrier disruption increase systemic access to microbial ligands and vesicular cargo, while systemic immune activation interacts with metabolic remodeling to shape inflammatory set-points and vascular susceptibility. Microbe-derived and host-microbe co-metabolites may further modulate redox balance, inflammatory tone, and vascular homeostasis within this network. We highlight limitations of existing interventional trials, methodological challenges in microbiome- and genetics-based causal inference, and priorities for translational research. Clinically, the oral-vascular axis motivates interdisciplinary exchange and research-facing collaboration that integrates oral health assessment with immune and vascular phenotyping, while recognizing that cardiovascular benefit from periodontal interventions remains investigational and requires event-driven validation.},
}

Humans
*Dysbiosis/immunology
*Periodontitis/immunology/microbiology
Animals
*Atherosclerosis/immunology
*Mouth/immunology/microbiology
*Cardiovascular Diseases/immunology

@article {pmid42079714,
year = {2026},
author = {Guima, SES and Bischain, B and Morais Gama, LC and Faria, AC and Lourenço, T and Bueno, DF and Heller, D and Passos-Bueno, MR and Setubal, JC},
title = {The oral maternal microbiome plays a role in the development of cleft lip and palate condition in children.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21128},
pmid = {42079714},
issn = {2167-8359},
mesh = {Humans ; *Cleft Lip/microbiology ; *Cleft Palate/microbiology ; Female ; *Microbiota ; Male ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Infant ; Mothers ; Adult ; Case-Control Studies ; },
abstract = {Non-syndromic cleft lip or palate (NS-CL/P) is an oral birth defect with complex aetiology. We compared the microbial diversity and composition of the oral microbiome of mothers of babies with NS-CL/P (CLP group) and mothers of babies without NS-CL/P (control group). Oral microbiome composition was determined by sequencing the V3-V4 regions of the 16S rRNA gene. CLP and control groups had overall similar microbial compositions, but significant differences were observed. The most significant microbial genus related to these differences was Cutibacterium, which was more abundant in the CLP group. Based on the literature, we hypothesize that a member of the Cutibacterium genus present in the oral microbiota may have a role in inflammation processes that could be related to NS-CL/P development. We found additional differences in terms of differential abundance when subsetting the dataset for mothers with a male child; in this case, depletion of Limosilactobacillus and an unknown taxon, in the CLP group, was a significant result. We conclude that the maternal oral microbiome likely plays a role in the development of the NS-CL/P condition.},
}

Humans
*Cleft Lip/microbiology
*Cleft Palate/microbiology
Female
*Microbiota
Male
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Infant
Mothers
Adult
Case-Control Studies

@article {pmid42079748,
year = {2026},
author = {Zheng, L and Jia, T and Li, Y and Zhang, Z and Su, H and Zhang, R},
title = {The interplay between gastrointestinal dysfunction and gut microbiota dynamics in sepsis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1761536},
pmid = {42079748},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sepsis/microbiology/physiopathology/complications/immunology ; *Dysbiosis/microbiology ; Animals ; *Gastrointestinal Diseases/microbiology ; *Gastrointestinal Tract/microbiology/physiopathology ; Intestinal Mucosa/microbiology ; Multiple Organ Failure ; },
abstract = {Sepsis frequently involves early gastrointestinal dysfunction, in which intestinal barrier breakdown and microbiota dysbiosis amplify systemic inflammation and contribute to multi-organ failure. Emerging evidence indicates that the gut is not merely a bystander in sepsis but an active driver of pathogenic cascades through epithelial injury, mucosal immune dysregulation, ischemia-reperfusion stress, and impaired motility, collectively promoting microbial translocation and immune deviation. In parallel, sepsis is associated with profound remodeling of the gut microbiome, characterized by reduced commensal diversity, expansion of pathobionts, and functional shifts in key microbial metabolites, including short-chain fatty acids, bile acids, and tryptophan-derived products, which further compromise mucosal integrity and host immune tone. This narrative review synthesizes experimental, translational, and clinical findings to elucidate the bidirectional interaction gut barrier-microbiota interplay in sepsis and to summarize mechanistic links across epithelial, immune, and metabolic signaling pathways, including gut-liver and gut-brain axes relevant to sepsis-associated organ dysfunction. dysfunctional microbial community leads to systemic immune deviation, multi-organ dysfunction and sepsis-associated encephalopathy, a common and severe neurological complication of sepsis. We also discuss emerging therapeutic strategies targeting the gut-microbiota axis-such as early enteral nutrition, prebiotics/postbiotics, defined microbial consortia, fecal microbiota transplantation, and metabolite-based supplementation-and evaluate their potential and limitations in septic populations. Finally, we highlight key challenges, including unresolved causality, inter-individual variability, context-dependent responses, and safety concerns, underscoring the need for longitudinal multi-omic profiling, host-microbiome phenotyping, and mechanism-informed interventional trials to enable precision microbiome-based approaches for sepsis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Sepsis/microbiology/physiopathology/complications/immunology
*Dysbiosis/microbiology
Animals
*Gastrointestinal Diseases/microbiology
*Gastrointestinal Tract/microbiology/physiopathology
Intestinal Mucosa/microbiology
Multiple Organ Failure

@article {pmid42079749,
year = {2026},
author = {Pi, H and Lin, H and Zhou, J and Liu, H and Liang, S and Zhu, R and Li, D and Lu, X and Yang, M and Chen, H and Li, Y},
title = {Targeted next-generation sequencing analysis of pathogens and microecology in pediatric lower respiratory tract infections identifies risk factors for severe community-acquired pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1796357},
pmid = {42079749},
issn = {2235-2988},
mesh = {Humans ; *Community-Acquired Infections/microbiology/epidemiology ; Female ; Male ; Retrospective Studies ; Child, Preschool ; Risk Factors ; *High-Throughput Nucleotide Sequencing ; Child ; *Respiratory Tract Infections/microbiology/epidemiology ; Infant ; Severity of Illness Index ; *Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; *Pneumonia/microbiology ; Mycoplasma pneumoniae/genetics/isolation & purification ; Haemophilus influenzae/genetics/isolation & purification ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Traditional diagnostic methods have inherent limitations in the comprehensive assessment of the etiological spectrum and microecological characteristics of pediatric lower respiratory tract infections (LRTIs), particularly community-acquired pneumonia (CAP). Against this backdrop, the present study seeks to delineate the pathogen profile of children with LRTIs via targeted next-generation sequencing (tNGS), and further explore the associations between clinical manifestations, upper respiratory microbiome signatures and disease severity in pediatric CAP cases.

METHODS: A retrospective, single-center study was conducted on 2299 children with suspected lower respiratory tract infections. Throat swab samples from all patients underwent tNGS for pathogen detection. For 1845 CAP patients (293 SCAP, 1552 non-severe CAP [nsCAP]), clinical data and tNGS results were analyzed. Statistical comparisons, correlation analyses, and multivariate logistic regression were performed to identify factors associated with SCAP. Microbial diversity (Shannon/Simpson indices) and relative abundance of detected species were also analyzed.

RESULTS: Mycoplasma pneumoniae was the dominant atypical pathogen, with an outbreak peaking in July 2024. M. pneumoniae detection rate (35.8% vs. 8.9%, P<0.001) and relative abundance (RA) were significantly higher in SCAP than nsCAP patients and correlated positively with severity markers. Multivariate analysis identified M. pneumoniae positivity, older age, female sex, circulatory and metabolic diseases as independent risk factors for SCAP. In M. pneumoniae-negative patients, pathogens like Streptococcus pneumoniae and Haemophilus influenzae were more common in nsCAP. Upper respiratory microbial diversity was lower in SCAP patients. Increased RA of specific commensals like Schaalia odontolytica was a protective factor, while increased abundance of Stenotrophomonas maltophilia was a risk factor for SCAP. Compared to bronchoalveolar lavage fluid (BALF), throat swab tNGS showed high agreement for M. pneumoniae but higher detection of potential colonizers like H. influenzae.

CONCLUSIONS: During the study period, M. pneumoniae was a key driver of SCAP in children. Beyond single-pathogen detection, decreased upper respiratory microbial diversity and shifts in colonizing bacteria abundances were associated with pneumonia severity, offering a new ecological perspective. Throat swab tNGS is valuable for pathogen screening. The associations between upper respiratory microbial features and severity highlight a potential ecological dimension of pneumonia pathogenesis.},
}

Humans
*Community-Acquired Infections/microbiology/epidemiology
Female
Male
Retrospective Studies
Child, Preschool
Risk Factors
*High-Throughput Nucleotide Sequencing
Child
*Respiratory Tract Infections/microbiology/epidemiology
Infant
Severity of Illness Index
*Bacteria/genetics/classification/isolation & purification
Microbiota/genetics
*Pneumonia/microbiology
Mycoplasma pneumoniae/genetics/isolation & purification
Haemophilus influenzae/genetics/isolation & purification
Community-Acquired Pneumonia

@article {pmid42080299,
year = {2026},
author = {Li, Z and Ren, M and Hu, A and Meng, F and Wang, J},
title = {Depth Stratification Shapes Viral Diversity, Interactions, and Metabolic Potential in a Deep Freshwater Lake.},
journal = {Molecular ecology},
volume = {35},
number = {9},
pages = {e70367},
doi = {10.1111/mec.70367},
pmid = {42080299},
issn = {1365-294X},
support = {U24A20578//National Natural Science Foundation of China/ ; 42507557//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; BK20240111//Basic Research Program of Jiangsu Province/ ; },
mesh = {*Lakes/virology/microbiology ; *Viruses/genetics/classification ; Metagenomics ; Fresh Water/virology ; Microbiota/genetics ; Ecosystem ; Geologic Sediments/virology ; Biodiversity ; Metagenome ; },
abstract = {Deep freshwater lakes exhibit distinct microbial community stratification across depth gradients, which plays important roles in biogeochemical cycling and ecosystem stability. As crucial regulators of microbiome composition and function, viruses may play key ecological roles in these stratified systems, yet their distribution patterns and ecological significance in deep-lake surface sediments remain poorly understood. Here, we assessed viral community dynamics and functional potential across the entire water depth gradient (0-155 m) of Fuxian Lake using metagenomics from 44 surface sediment samples. A total of 11,523 viral OTUs were recovered, with only 18% annotated to the family level and approximately 93% classified as putatively lytic. Viral communities showed systematic depth-related shifts across multiple dimensions. Specifically, alpha diversity, community turnover, and stochastic assembly processes increased significantly with water depth, accompanied by enhanced lytic virus dominance and larger genome sizes. Predicted virus-host association networks transitioned from highly connected and generalized at shallow depths to increasingly sparse and specialized at greater depths. Virus-encoded auxiliary metabolic genes showed significantly increasing abundance with water depth, along with functional shifts from host defense to enhanced biosynthesis and energy metabolism, especially regarding carbon fixation and organic matter degradation. Collectively, these results highlight the importance of water depth gradients in structuring viral communities within surface sediments and expand our understanding of viral ecological functions in deep lake ecosystems.},
}

*Lakes/virology/microbiology
*Viruses/genetics/classification
Metagenomics
Fresh Water/virology
Microbiota/genetics
Ecosystem
Geologic Sediments/virology
Biodiversity
Metagenome

@article {pmid42080579,
year = {2026},
author = {Sidi Mabrouk, A and Depelteau, JS and Foini, C and Kempff, A and Jonker, S and Brenzinger, S and Limpens, R and Majrouh, M and Meijer, AH and Briegel, A},
title = {ICP1 bacteriophage treatment antagonizes colonization of the zebrafish larval intestine by Vibrio cholerae.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0356525},
doi = {10.1128/spectrum.03565-25},
pmid = {42080579},
issn = {2165-0497},
abstract = {UNLABELLED: Outbreaks of cholera pose a major threat to human health. Currently, antibiotics are the most effective treatment against the causative agent, the bacterium Vibrio cholerae. However, the use of antibiotics eventually leads to the emergence of resistant strains, which necessitates the need for alternative approaches. The use of bacteriophages to target the infection by antibiotic-resistant bacteria is one promising alternative. While clearance of Vibrio cholerae with the use of phages has been performed on several animal models, none of these models are naturalistic hosts of V. cholerae. Therefore, we set out to investigate the interaction between V. cholerae and bacteriophage ICP1 both in vitro and in vivo in a naturalistic host, the zebrafish model, Danio rerio. To study the interplay between host, bacteria, and phages, we used a combination of light and ultrastructural imaging techniques, including confocal fluorescence microscopy, serial block face scanning electron microscopy (EM) imaging, and cryogenic EM, which allowed us to investigate both the colonization process by V. cholerae and clearance by the ICP1 bacteriophage. In addition, we determined the effects of the microbiome on this treatment by using germ-free, conventionalized, and monoassociated zebrafish larvae as a host. Independent of the presence and composition of microbiomes used here, V. cholerae efficiently colonized the larval intestine. Finally, we demonstrate significant in vivo clearance of V. cholerae N16961-dsRED by ICP1, underscoring the role of phage-bacteria dynamics in shaping pathogen colonization within the zebrafish larval host.

IMPORTANCE: Cholera remains a life-threatening disease that causes recurring outbreaks and significant mortality, particularly in developing and conflict-affected regions. As antimicrobial resistance continues to rise, there is an urgent need to better understand the ecological and microbial dynamics that govern Vibrio cholerae colonization and persistence. This research investigates how V. cholerae interacts with bacteriophages, the host environment, and the resident microbiota within a natural vertebrate host, offering new insights into the factors that influence pathogen clearance and shaping of the gut ecosystem during infection. The powerful combination of serial block-face scanning and cryogenic electron microscopy, fluorescence microscopy, and traditional colony/plaque counting methods revealed previously unobserved aspects of the interplay between host, pathogen, phages, and selected microsymbionts, highlighting phage-driven clearance of V. cholerae during colonization.},
}

@article {pmid42081026,
year = {2026},
author = {Zomorodimanesh, S and Razavi, SH and Zomorodimanesh, P},
title = {Exploring the Role of Probiotics in the Prevention and Treatment of Gastrointestinal Cancer.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42081026},
issn = {1867-1314},
abstract = {Probiotics, live microorganisms with health-promoting properties, play a vital role in modulating the gut microbiota and enhancing immune responses. Their potential for regulating key signaling pathways, including NF-κB, PI3K/AKT, and Wnt/β-Catenin, suggests promise in cancer prevention as they can mitigate inflammation, strengthen intestinal barriers, and influence cytokine production, offering multiple therapeutic benefits. This review highlights the mechanisms by which probiotics may contribute to gastrointestinal cancer prevention and treatment, discussing their capacity to regulate inflammatory cytokines, enhance epithelial integrity, and balance gut microbiota. Evidence from preclinical and a growing number of clinical studies is summarized. Additionally, challenges such as strain specificity, dose optimization, and safety evaluations are analyzed alongside potential integration into conventional cancer therapies. Current data indicate that probiotics hold potential as complementary agents in oncology, possibly capable of inhibiting tumor growth, enhancing immune surveillance, and improving the efficacy of existing treatments. Future research should prioritize robust, long-term clinical trials and molecular studies to optimize their application in cancer management.},
}

@article {pmid42081130,
year = {2026},
author = {Bak, NK and Østergaard, SK and Schacksen, PS and Nielsen, JL and Rohde, PD and Kristensen, TN},
title = {Host genetics and diet jointly shape the microbiome of Drosophila melanogaster but do not predict lifespan or age-related traits.},
journal = {Biogerontology},
volume = {27},
number = {3},
pages = {},
pmid = {42081130},
issn = {1573-6768},
support = {DFF-2032-00205A//Danmarks Frie Forskningsfond/ ; },
mesh = {Animals ; *Drosophila melanogaster/microbiology/genetics/physiology ; *Longevity/genetics ; *Microbiota/genetics ; *Diet ; *Aging/genetics ; Genetic Variation ; Male ; Female ; },
abstract = {The microbiome is a key determinant of organismal health, yet inter-individual variability and heterogeneous responses to environmental conditions complicates the understanding of its effects on hosts. Here, we present a comprehensive analysis using the Drosophila Genetic Reference Panel (DGRP) to investigate how the interplay between host genetic variation and diet influences microbiome composition, and to assess whether microbiome features in young flies can be used to predict lifespan and age-related traits. Our findings show that adult flies reared on a nutritionally rich control diet exhibited higher microbial richness but lower evenness compared to those on a nutritionally poor restricted diet. Principal component analysis (PCA) highlighted substantial diversity among lines reared on the same diet, and this variation was evidenced by high heritability estimates for all measured α-diversity metrics, including Unique OTU counts, Shannon and Simpson indices, as well as the relative abundances of genera and species with relative abundances exceeding 1%. These results underscore the critical roles of both environmental factors and genetic variation in shaping microbiome composition under different dietary conditions. Moreover, we identified widespread genotype-by-diet interactions, suggesting that the genetic regulation of the microbiome is highly complex. Finally, we found that the microbiome features of young flies including diversity indices, taxonomic abundances, or ordination scores cannot predict age-associated phenotypes (lifespan, locomotor activity, dry weight, and heat knockdown time). Our findings offer valuable insights into the genetic architecture that governs microbiome composition, dietary responses, and aging in Drosophila melanogaster.},
}

Animals
*Drosophila melanogaster/microbiology/genetics/physiology
*Longevity/genetics
*Microbiota/genetics
*Diet
*Aging/genetics
Genetic Variation
Male
Female

@article {pmid42081188,
year = {2026},
author = {Pollock, J and Liu, R and Rwenji, E and Orobi, E and Udayakumar, S and Huibner, S and Kung'u, M and Kabuti, R and Babu, H and , and Irungu, E and Ngurukiri, P and Muthoga, P and Adhiambo, W and Weiss, HA and Seeley, J and Abramsky, T and Kimani, J and Beattie, TS and Kaul, R},
title = {Assessing the Impact of Female Genital Mutilation/Cutting on Genital Inflammation and Microbiota Among Kenyan Female Sex Workers.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {5},
pages = {e70250},
pmid = {42081188},
issn = {1600-0897},
support = {MR/R023182/1//Medical Research Council (MRC) and the UK Department of International Development (DFID)/ ; //EDCTP2 supported by the European Union/ ; PJT-156123//Canadian Institute of Health Research (CIHR)/ ; PJT-180629//Canadian Institute of Health Research (CIHR)/ ; },
mesh = {Humans ; Female ; Kenya/epidemiology ; *Sex Workers ; Adult ; *Microbiota/immunology ; *Circumcision, Female/adverse effects ; *HIV Infections/epidemiology/immunology ; *Inflammation/immunology ; Young Adult ; Cytokines/metabolism ; *Vagina/microbiology/immunology ; *Genitalia, Female/microbiology/immunology ; },
abstract = {PROBLEM: Female genital mutilation/cutting (FGM/C) is harmful to physical, mental, and reproductive health, though the effect of this practice on a woman's HIV susceptibility is poorly understood. Despite the known associations of FGM/C with short-term vaginal epithelial damage, neither genital inflammation nor the genital microbiome have been explored in women who have undergone FGM/C. In this study we compare the genital immune milieu and microbiome among female sex workers (FSWs) by FGM/C status, hypothesizing that these biological factors are dysregulated in women who have undergone FGM/C, heightening their risk of HIV acquisition.

METHOD OF STUDY: 1003 FSWs in Nairobi, Kenya, were enrolled in the Maisha Fiti study and visited a study clinic up to three times from June 2019 to March 2021. Participants self-reported any previous exposure to FGM/C as well as other relevant sociodemographic factors. Levels of proinflammatory cytokines and soluble E-cadherin (sE-cad), a biomarker of epithelial barrier disruption, were measured by multiplex immunoassay using self-collected cervicovaginal secretion samples provided by HIV-uninfected participants. Genital inflammation was defined using a composite score of inflammatory cytokines previously associated with HIV acquisition. The presence of inflammation was compared longitudinally between groups using mixed models to control for potential confounders including age, bacterial vaginosis (BV) status as defined by Nugent score, and others. Vaginal bacterial abundance, Shannon diversity, and total levels of key vaginal bacteria were measured by qPCR and compared by FGM/C status in an exploratory analysis.

RESULTS: 44 of 1003 (4%) participants had undergone Type I or II FGM/C. These participants were older (p < 0.001) and more likely to test positive for herpes simplex virus-2 (HSV-2; p = 0.04), and less likely to have completed primary education (p = 0.03). Among HIV-uninfected participants, there was no evidence that genital inflammation was associated with FGM/C status after controlling for potential confounders (aOR = 0.70; 95% CI: 0.31-1.59; p = 0.40). There was no evidence of a difference in BV prevalence (p > 0.99), total bacterial abundance (p = 0.96), or Shannon diversity (p = 0.15) by FGM/C status.

CONCLUSIONS: Type I or II FGM/C was not associated with genital inflammation or microbial dysregulation in the long-term among HIV-negative FSWs in this cohort. This may be due to the duration elapsed since FGM/C occurred or the lowered mucosal immune activation previously observed in FSWs.},
}

Humans
Female
Kenya/epidemiology
*Sex Workers
Adult
*Microbiota/immunology
*Circumcision, Female/adverse effects
*HIV Infections/epidemiology/immunology
*Inflammation/immunology
Young Adult
Cytokines/metabolism
*Vagina/microbiology/immunology
*Genitalia, Female/microbiology/immunology

@article {pmid42081950,
year = {2026},
author = {Garvey, MI and Moran, RA and Wilkinson, MAC and Sanches Ferreira, AD and Gardiner, A and Holden, E and McNally, A},
title = {What grows in the sink splash zone.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2026.04.010},
pmid = {42081950},
issn = {1532-2939},
abstract = {BACKGROUND: The hospital sink drain microbiome can harbour opportunistic pathogens and antimicrobial resistance genes. Patients may be exposed to waterborne pathogens via water outlets and sink drains. We have previously shown water from a clinical hand wash basin can splash up to two metres away from the sink/tap. Here we wanted to identify which organisms could be cultured from environmental sampling within the splash zone.

METHODS: Queen Elizabeth Hospital Birmingham (QEHB) is a large UK tertiary centre. We placed an SAS Super 180 air sampler within the splash zone at approximately one metre distance of a tap on a clinical hand wash basin in the critical care unit and undertook sampling both with and without the tap running. All Gram-negative organisms were cultured and any carbapenemase producing Enterobacterales (CPE) isolated were sequenced.

RESULTS: Environmental sampling undertaken when the tap was running yielded a variety of organisms, with Gram-negative isolates including Citrobacter freundii, Enterobacter kobei, Enterobacter cloacae, Enterobacter asburiae, Pseudomonas aeruginosa and Sphingobacterium multivorum. Amongst these, we identified one CPE, C. freundii isolate QE-SINK-CF1, which carried a plasmid bearing the blaKPC-2 gene. Structural variants of this plasmid have been involved in clinical infections at QEHB. Control sampling without the tap running yielded no Gram-negative organisms.

CONCLUSIONS: Here we show a variety of Gram-negative microorganisms, including CPE, can be cultured from within the 2-metre sink splash zone. This latest work provides further evidence healthcare settings should consider splash zones and waterborne pathogen transmission risk.},
}

@article {pmid42082045,
year = {2026},
author = {Zhang, Y and Wang, Y and Yang, Q and Yang, L and Yang, X and Zhao, X and Zhao, S},
title = {Unveiling the interactions of 8:2 fluorotelomer sulfonic acid (8:2 FTSA) with the earthworm-microbe symbiosis in soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {400},
number = {},
pages = {128247},
doi = {10.1016/j.envpol.2026.128247},
pmid = {42082045},
issn = {1873-6424},
abstract = {8:2 fluorotelomer sulfonic acid (8:2 FTSA), an important per- and polyfluoroalkyl substance (PFAS) found in aqueous film-forming foams (AFFFs), is frequently detected in soil. However, the interactions of 8:2 FTSA with soil-terrestrial invertebrate systems are poorly understood. This study investigated the biotransformation, toxicity, microbiome shifts, and microbial degradation of 8:2 FTSA in a soil-earthworm system through in vivo, in vitro, and multi-omics analyses. Earthworms efficiently accumulated 8:2 FTSA and biotransformed it into 11 distinct PFAS via α/β-oxidation mediated by metabolic enzymes, with trifluoroacetic acid (TFA) as the predominant metabolite. 8:2 FTSA induced significant oxidative stress, activated metabolic detoxification, and caused potential neurotoxic effects in earthworms. Furthermore, 8:2 FTSA exposure disrupted the microbial communities in the earthworm-soil system, with greater sensitivity observed in communities on the earthworm skin and in the soil compared to those in the gut. Predicted functional profiling further suggested that the gut microbiota may have greater potential for xenobiotic transformation, whereas the skin microbiota exhibited a host-dependent and low-activity phenotype. Raoultella ornithinolytica, isolated from earthworm gut and skin, transformed over 68% of 8:2 FTSA in 6 days via α/β-oxidation. Our findings advance the understanding of 8:2 FTSA interactions with the soil-earthworm system and provide a critical foundation for assessing its ecological risk in terrestrial environments.},
}

@article {pmid42082125,
year = {2026},
author = {Marzec-Grządziel, A and Borsuk, G},
title = {Between Host and Parasite: The Microbiome of Varroa destructor and Its Relationship with Honey Bees.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105617},
doi = {10.1016/j.dci.2026.105617},
pmid = {42082125},
issn = {1879-0089},
abstract = {The study of the microbiome of the mite Varroa destructor is crucial for understanding parasite-host interactions and their potential health implications for honey bees (Apis mellifera). The aim of this research was to characterize the microbial diversity of Varroa destructor populations collected from the body surface of honey bees and compare it with microbiome of Apis mellifera. DNA isolation was performed using standard methods, followed by next-generation sequencing (NGS) of the V3-V4 region of the 16S rRNA gene. The obtained bioinformatic data underwent taxonomic analysis, enabling the identification of dominant bacterial genera present in the Varroa and Apis mellifera microbiome. Results revealed significant microbial diversity, with dominance primarily by bacteria belonging to the families Acetobacteraceae, Morganellaceae, and Segniliparaceae. The identified bacteria may play a critical role in the pathogenicity of Varroa destructor, directly or indirectly affecting the health and condition of bees. These findings provide new insights into potential therapeutic and preventive targets for protecting bee colonies against the detrimental effects of Varroa mites.},
}

@article {pmid42082515,
year = {2026},
author = {Geng, Y and Zhang, J and Hu, Y and Tong, Q and Ye, Z and Yu, J and Tu, J and Wang, N and Zhang, HY and Liu, S and Jiang, Q and Yan, X and Wang, Y and Feng, Z},
title = {A manually curated pig gut microbiome dataset for precision feeding.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07238-8},
pmid = {42082515},
issn = {2052-4463},
support = {203-61022300002//the National Digital Animal Husbandry (Pig) Innovation Center Project/ ; },
abstract = {The gut microbiome of pigs is a complex microbial ecosystem critical to host health and agricultural productivity. While amplicon sequencing studies have expanded our understanding of this community, a lack of standardized data and metadata often hinders comparative analysis and data reuse. To address this challenge, we present the Pig Gut Microbiome Dataset (PGMD, version 1.0), a comprehensive resource developed through the systematic selection of publications, extensive manual curation of associated metadata, and standardized reprocessing of raw amplicon sequencing data. This initial release integrates 202 publications (encompassing 207 16S rRNA gene sequencing data BioProjects), comprising 12,336 samples, collected from 22 countries. The dataset encompasses 52 host species and 3,028 taxonomic groups. Samples are systematically categorized by research topics and host phenotypes, enabling users to explore microbial community composition, identify differentially abundant taxa across experimental conditions and phenotypes, investigate six core phenotype-associated microbial clades, and determine dominant taxa across four key growth stages. PGMD significantly enhances the standardization and integration of pig gut microbiome data, serving as a valuable resource for research towards precision feeding and improved animal health. All data in the dataset are hosted and available in figshare https://doi.org/10.6084/m9.figshare.25911745.v1.},
}

@article {pmid42082522,
year = {2026},
author = {Motger-Albertí, A and Gallardo-Nuell, L and Rosell-Díaz, M and Stefoglo, M and Pons, J and Garre-Olmo, J and Pérez-Brocal, V and Moya, A and Puig, J and Ramos, R and Mayneris-Perxachs, J and Fernández-Real, JM},
title = {Sex-specific microbial and tryptophan signatures of depression implicate archaeal methanogens and indole-3-acetic acid only in women.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00983-z},
pmid = {42082522},
issn = {2055-5008},
support = {PI20/01090//Instituto de Salud Carlos III/ ; PI15/01934//Instituto de Salud Carlos III/ ; CNS2023-144218//Ministerio de Ciencia, Innovación y Universidades/ ; 2021 SGR 01263//Generalitat de Catalunya/ ; },
abstract = {Sex differences in mental health are often overlooked, yet gut microbiota-host metabolite interactions may contribute to sexual dimorphism in depression. In a population-based cohort, we investigated sex-specific links among plasma tryptophan metabolites, depressive symptoms (PHQ-9), and the gut microbiome, controlling for smoking, diet, alcohol, and physical activity. Women (N = 419) exhibited higher plasma indole-3-acetic acid (IAA) and picolinic acid (PA) concentrations, but lower trigonelline (TRIG) than men (N = 383). Machine learning models with SHAP explanations revealed that IAA and TRIG were positively associated, whereas PA was negatively associated with depression severity in women, whereas only kynurenic acid (KA) was inversely associated in men. In women, depression severity strongly correlated with methanogenic archaea, including Methanobrevibacter smithii, and microbial methane-production pathways. Methanobrevibacter and specifically M. smithii were negatively linked to genes for tryptophan, PA, and KA biosynthesis, but positively to genes for IAA and nicotinate/nicotinamide metabolism. Most microbial species associated with depression severity in women were predicted to produce IAA. These findings reveal pronounced sex-specific microbiome-metabolite interactions, highlighting potentially distinct microbial mechanisms shaping depression in men and women.},
}

@article {pmid42082767,
year = {2026},
author = {Lebeer, S and Goormachtig, S},
title = {Practical lessons from microbiome citizen-science projects.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42082767},
issn = {2058-5276},
support = {852600//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049022N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; S006424N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; VR 2016 2312 Doc.1521/4//Vlaams Instituut voor Biotechnologie (Flanders Institute for Biotechnology)/ ; },
}

@article {pmid42082772,
year = {2026},
author = {Alshareedah, I and Brunner, JD and Chain, PSG and Kumar, A},
title = {Significance and challenges in dissecting cancer-bacteriome interactions.},
journal = {BJC reports},
volume = {4},
number = {1},
pages = {},
pmid = {42082772},
issn = {2731-9377},
support = {20251143PRD1//Los Alamos National Laboratory/ ; },
abstract = {Cancer is the leading cause of death around the world. While some types of cancer have become manageable due to advancements in medicine, most cancers still lack available cures and treatments. Recent studies have shown that changes in the human microbiome, especially in the bacteriome, are associated with some cancers. Certain bacterial strains have been reported to promote the initiation and progression of cancer in humans. Other studies have used sequencing to observe changes in the bacteriome of healthy and cancer patients. However, studies that investigate the interactions between cancer cells and the complex bacteriome as a whole remain scarce. This is due to the absence of experimental methods to study the interactions between cancer cells and complex bacterial populations, which has delayed the progress in identifying cancer-causing and cancer-inhibiting bacteria, and in understanding the bacterial interactions and their influence on host cells. Here, we review approaches to studying cancer cell interactions with complex bacteriomes and suggest possible routes to overcome this problem, highlighting the need for interdisciplinary studies that may help advance this field. We speculate that a good understanding of cancer-bacteriome interactions may open the door to new lines of holistic bacteriotherapy for cancer that is otherwise unavailable.},
}

@article {pmid42083021,
year = {2026},
author = {Han, Y and Cui, J and Huang, X and Guo, P and Yang, S},
title = {Microbial inoculants with straw mediate degradation-level-specific changes in soil carbon cycling genes and microbial community.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00898-4},
pmid = {42083021},
issn = {2524-6372},
support = {2022YFD1500600//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood.

RESULTS: Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera (Sphingomonas, Bradyrhizobium) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus (Chaetomium) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding α-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils.

CONCLUSIONS: Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1-5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.},
}