@article {pmid41774319,
year = {2026},
author = {Pereira, EJ and de Souza, V and da Silva Braulio, C and de Jesus Santos, AF},
title = {Epiphytic bacteria from Tacinga inamoena (K. Schum.) N.P. Taylor & Stuppy improve plant growth in cucumber seedlings.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {4},
pages = {415-422},
pmid = {41774319},
issn = {1618-1905},
abstract = {The phyllosphere of host plants harbors microorganisms that represent a novel source of agricultural bioinputs. This unique microbiome opens a promising frontier for developing innovative agricultural alternatives. In this study, we evaluated the potential of Brevibacillus sp. UPT4 and Pantoea sp. SPM1, two epiphytic bacterial strains of Tacinga inamoena isolated from the Caatinga biome. In vitro assays exhibited plant growth-promoting traits, such as auxin production, nitrogen fixation, and tolerance to abiotic stresses. Under greenhouse conditions, cucumber plants inoculated with the strains and their consortium exhibited significant increases (p < 0.05) in shoot and root parameters, ranging from 13.58% to 194.86% when compared to the control treatment. Redundancy analysis (RDA) indicated that most of the variability observed in the biometric parameters is associated with the plant growth-promoting reported in this study. These results highlight the potential of epiphytic bacteria from semi-arid land as a promising candidate for the development of new bioinputs, offering an innovative tool for sustainable agriculture.},
}

@article {pmid41803694,
year = {2026},
author = {Sun, F and Lu, J and Qiu, J and Jiao, Y and Zhuang, J and Meng, B and Kwok, LY and Zhong, Z},
title = {Temporal dynamics and functional maturation of the infant gut microbiota during the first year of life.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41803694},
issn = {1471-2180},
support = {BR250107//the Inner Mongolia Agricultural University Young Faculty Research Capacity Enhancement Program/ ; NJYT24055//the Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {BACKGROUND: The infant gut microbiota undergoes structured, time-dependent succession during the first year of life, yet high-resolution longitudinal characterization remains limited. Here, full-length 16S rRNA gene sequencing was performed using PacBio long-read technology on 68 fecal samples from 12 exclusively breastfed infants in Hohhot, China, across six time points from birth to one year (7, 30, 60, 100, 200, and 360 days).

RESULTS: In this study, 68 fecal samples from 12 infants were analyzed. A total of 16 bacterial phyla, 192 genera and 251 species were annotated, with the dominant phyla being Firmicutes, Actinobacteriota and Proteobacteria; the dominant genera including Bifidobacterium, Streptococcus and Escherichia-Shigella; and the dominant species comprising Streptococcus_salivarius, Bifidobacterium_longum and Bifidobacterium_pseudocatenulatum. Alpha diversity generally increased by days 360, while community composition shifted from early Bifidobacterium dominance toward greater taxonomic and functional complexity. Permutational multivariate analysis of variance (PERMANOVA) revealed that host and environmental factors collectively explained 33.92% of community variation (P = 0.001). Six temporal colonization patterns were observed through MaAsLin2 analyses., including mid-term explosive and sustained increasing trajectories. Functional profiling using Tax4Fun2 revealed time-specific enrichment of metabolic pathways, including fatty acid biosynthesis, xenobiotic degradation, and autophagy regulation at day 360. The findings of this longitudinal study be interpreted considering its modest sample size (n = 68). Future studies with larger cohorts are needed to validate and generalize these observations.

CONCLUSIONS: These findings demonstrate that infant gut microbiota assembly follows a non-random, host-guided trajectory, with dietary transitions and microbial interactions driving structural and functional maturation, providing a high-resolution framework for understanding early-life microbiome development and its implications for infant health. However, due to the limited sample size, the relevant research results have certain limitations. In the future, it is necessary to expand the sample scale and conduct more convincing studies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04930-y.},
}

@article {pmid41803805,
year = {2026},
author = {Park, SY and Jung, MY and Nguyen, CD},
title = {Effect of biodegradable microneedle acupuncture for symptom relief moderate or milder atopic dermatitis: a study protocol for a multicenter, randomized, sham-controlled trial.},
journal = {BMC complementary medicine and therapies},
volume = {26},
number = {1},
pages = {},
pmid = {41803805},
issn = {2662-7671},
abstract = {BACKGROUND: Atopic dermatitis (AD) has no definitive cure; therefore, alternative treatments should be developed. We have demonstrated in preliminary clinical trials that Biodegradable Microneedle Acupuncture (BMA) treatment improves symptoms and is safe for mild to moderate AD.

AIMS: The study focused on evaluating the effectiveness and safety of a new medical device called BMA for AD, while also assessing its cost-effectiveness. It also explored the gut microbiome of patients with AD before and after BMA treatment.

METHODS: This multicenter, participant-assessor-blinded, sham-controlled trial will be conducted from January 10, 2025, to January 10, 2026. In total, 184 participants with AD (n = 92 per group) will be recruited. Participants will be assigned randomly to two equal-sized groups: the BMA and sham groups. Treatment will be administered three times per weekduring the 4-week intervention phase. The primary outcome measure will be the objective SCORing Atopic Dermatitis index. Secondary outcome measures will include the Eczema Area and Severity Index, Dermatology Life Quality Index, Patient-Oriented Eczema Measure, and pruritus Visual Analog Scale scores. Other outcome measures will include gut microbiome, economic and safety evaluations.

DISCUSSION: This study protocol will provide an important and thorough assessment of the effectiveness of BMA treatment in improving the symptoms of moderate or milder AD. In addition, we will evaluate the safety and costeffectiveness of BMA. We will also determine the link between AD and the microbiome. This clinical trial has been registered with the Korean Clinical Trial Registry (registration number: KCT0009870; date of registration: 25 October 2024).},
}

@article {pmid41803883,
year = {2026},
author = {Wei, Z and Xu, T and Gu, X and He, Q and Feng, Q and Li, M},
title = {Single-cell RNA-seq and in vitro study reveal Fusobacterium nucleatum impairs β-cell identity in type 2 diabetes via the NF-κB-CDKN1C axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41803883},
issn = {1479-5876},
abstract = {BACKGROUND: The pathogenesis of type 2 diabetes is characterized by insulin resistance and a progressive decline in β-cell function. A key driver of this dysfunction is the loss of β-cell identity, which reduces functional β-cell mass and leads to inadequate insulin secretion. Periodontal pathogens have been implicated in promoting insulin resistance; however, their role in the transformation of β-cell identity remains poorly understood. This study aims to investigate the impact of periodontal pathogen Fusobacterium nucleatum (F. nucleatum) on β-cell identity maintenance and the underlying molecular mechanisms.

METHOD: Single-cell RNA sequencing (scRNA-seq) data from human pancreatic islets of nondiabetic (ND), prediabetic (Pre-T2D), and type 2 diabetes (T2D) donors were analyzed to assess changes in β-cell proportion, differentiation trajectory, and associated molecular pathways. The Single-cell Analysis of Host-Microbiome Interactions (SAHMI) method was used to detect F. nucleatum sequences in pancreatic islets. Pearson correlation analysis identified key genes associated with the action of F. nucleatum, followed by in vitro validation using a co-culture model of F. nucleatum and MIN6 cells to elucidate the underlying mechanisms.

RESULTS: scRNA-seq analysis revealed a reduced proportion of β-cells and decreased expression of key β-cell identity-maintenance genes in the T2D group. The expression levels of transdifferentiation markers and β-cell disallowed genes were elevated, alongside a trend toward α-cell transdifferentiation. The NF-κB signaling pathway was significantly activated in the T2D group, accompanied by a significant increase in the SPP1 inflammatory signal, while the WNT pathway was markedly diminished. Integrated Pearson correlation and in vitro analyses identified the cell cycle regulator CDKN1C as a central mediator through which F. nucleatum promotes β-cell identity loss. Mechanistically, F. nucleatum activated the NF-κB pathway, leading to downregulation of CDKN1C expression and thereby promoting loss of β-cell identity, which played an important role in the progression of diabetes associated with periodontitis.

CONCLUSION: This study demonstrates that β-cells in T2D primarily undergo transdifferentiation towards α-cells, and the periodontal pathogen F. nucleatum promotes β-cell identity loss via NF-κB-mediated downregulation of CDKN1C.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07981-x.},
}

@article {pmid41917955,
year = {2026},
author = {Nazir, SM and Saied, SMM and Eskander, ME and Mansour, MM and Abdelrahman, H and Elbackly, RM and Elnawam, HM},
title = {Is apical periodontitis a matter of microbial diversity or time? A scoping review.},
journal = {Head & face medicine},
volume = {22},
number = {1},
pages = {},
pmid = {41917955},
issn = {1746-160X},
abstract = {BACKGROUND: The pathophysiology of apical periodontitis is complicated involving host immunological response, virulence factors, and a diverse microbiome. Understanding how microbial diversity influences lesion size is crucial for improving therapeutic strategies.

OBJECTIVE: This scoping review aimed to have an insight through literature to determine whether primary or secondary apical periodontitis lesions of different sizes are correlated with the quantity and diversity of microorganisms or the duration of the disease.

METHODS: The Joanna Briggs Institute (JBI) methodology for conducting scoping reviews was followed. A comprehensive electronic search was conducted through PubMed, Scopus, Web of Science, and Google Scholar to identify relevant studies published up to February 2025. In addition, handsearching was performed to identify additional studies that were not retrieved in the electronic search. Eligibility criteria of the screened papers included clinical studies performed in healthy patients with symptomatic or asymptomatic apical periodontitis where microbial analysis was performed. The EndNote Web reference manager (EndNote X9; Thomson Reuters) was used to ingest articles from various sources, categorize the references, and automatically eliminate duplicates.

RESULTS: Out of 4010 papers, 132 studies met the inclusion requirements and were added to the current review. Approximately half of the papers examined bacterial diversity in endodontic infections, while just a small percentage discussed lesion size and were identified as randomized clinical trials. Brazil, USA, Germany and China were found to have the highest frequency of published articles. Fusobacteria, Streptococcus, Enterococcus faecalis and Porphyromonas species were the most detected microorganisms responsible for apical pathosis regardless of lesion size, while other microbiomes were associated with large lesions only, such as Olsenella, Lactococcus lactus and HHV-6 with 3% each and HPV with 6.1%. Other microbiomes such as Candida albicans, Filifactor alocis, HSV1, Pyramidobacter piscolens and Phocaeicola abscessus were seen only associated with small sized lesions with 4.3% each.

CONCLUSIONS: Microbial diversity and microbial load seem to be a strong determinant of apical lesion size while lesion duration could not be adequately assessed due to cross-sectional study designs. Lesion size is an important variant to be recorded to give insight into microbial diversity and provide the basis for personalized targeted antimicrobial therapies in the future. This scoping review was registered in the open science framework; DOI: 10.17605/OSF.IO/DC95Z.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13005-026-00610-4.},
}

@article {pmid41981054,
year = {2026},
author = {Mansour, NY and Ismail, MF and Sayed, NH and El-Ansary, AR and Mohanad, M},
title = {Serum metabolomics identifies gut-derived uremic toxins and bile acid dysregulation associated with chronic kidney disease severity.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41981054},
issn = {2045-2322},
abstract = {UNLABELLED: Chronic kidney disease (CKD) affects more than 700 million people worldwide, however conventional biomarkers like creatinine cannot identify early-stage disease or accurately predict progression. In this study, untargeted and targeted metabolomic approaches were combined to identify novel biomarkers relevant for CKD staging and early detection in an underrepresented Egyptian population. Untargeted ultra-high-performance liquid chromatography–mass spectrometry analyses in both ionization modes were performed on serum samples of 50 CKD patients [25 early-stage CKD (eCKD), 25 end-stage kidney disease (ESKD)] and 20 controls. Differential metabolites were determined by univariate and multivariate analyses, coupled with pathway analysis and correlations with estimated glomerular filtration rate (eGFR). Five discriminating metabolites (p-hydroxyphenyllactic acid, indoxyl sulfate, xanthurenic acid, trimethylamine-N-oxide, and glycochenodeoxycholate) were subjected to targeted LC-MS/MS validation in an independent cohort (35 eCKD, 35 ESKD, 15 controls). Gut-derived uremic toxins, bile acid and tryptophan–kynurenine metabolic dysregulation were associated with CKD severity. p-hydroxyphenyllactic acid, xanthurenic acid, glutamyl-valine and indoxyl sulfate showed strong inverse correlations with eGFR (r = -0.75 to -0.85). A five-metabolite panel (indoxyl sulfate, p-hydroxyphenyllactic acid, trimethylamine-N-oxide, glycochenodeoxycholate, xanthurenic acid), demonstrated superior discriminatory performance compared with creatinine alone for distinguishing ESKD, especially indoxyl sulfate and p-hydroxyphenyllactic acid (AUC 0.847 and 0.828, respectively vs. 0.688). This first comprehensive metabolomics study in Egyptian CKD patients identifies alterations in gut microbiome–derived metabolites and bile acid metabolism associated with CKD severity. The multi-metabolite panel demonstrates potential for non-invasive discrimination between CKD stages and supports future longitudinal metabolomic studies aimed at improving CKD risk stratification and patient management.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44271-4.},
}

@article {pmid41982989,
year = {2026},
author = {Yoon, KN and Lee, HG and Yeom, SJ and Kim, SS and Park, JH and Song, BS and Yi, SW and Hur, TY and Eun, JB and Park, SH and Lee, JH and Kim, HB and Lee, JH and Kim, JK},
title = {Modulation of microbial community and metabolism through Lactiplantibacillus argentoratensis AGMB00912 supplementation in weaning piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {562-585},
pmid = {41982989},
issn = {2055-0391},
abstract = {Dietary supplementation effects with Lactiplantibacillus argentoratensis strain AGMB00912 (LA) on gut microbiota and metabolic functions of weaned piglets were investigated. Eight 25-day-old weaned piglets were evenly divided into a control group and an LA-supplemented group, with the LA group receiving 1.0 × 10[8] CFU/mL of LA daily for 10 days. Fecal samples taken on the 10[th] day were analyzed using 16S rRNA gene sequencing to assess microbial composition and metabolic function prediction. Supplementation with LA promoted a stable microbial environment by increasing the relative abundance of short-chain fatty acid-producing bacteria, including Faecalitalea, Catenibacterium, and Butyrivibrio, while reducing harmful genera like Treponema and Campylobacter. Administration of LA significantly influenced the metabolic activity of the microbial community, particularly by upregulating carbohydrate metabolism pathways, which enhanced the capacity for short-chain fatty acid production. This shift in microbial metabolism also extended to pathways involved in the biosynthesis of amino acids, lipids, cofactors, and vitamins, indicating an improved capacity for microbial-driven nutrient assimilation and utilization. Furthermore, LA supplementation promoted the biosynthesis of antimicrobial non-ribosomal peptides within the microbiome, crucial for inhibiting the growth of pathogenic microorganisms and maintaining microbial balance. The modulation of microbial metabolism is also predicted to reduce glycan degradation and increase peptidoglycan biosynthesis, contributing to enhanced gut barrier function and a more regulated immune response. These metabolic changes within the microbial community are predicted to stabilize the gut microbiota, providing enhanced disease resistance and supporting the overall health and growth of weaned piglets.},
}

@article {pmid41983000,
year = {2026},
author = {Lee, JY and Lim, C and Seo, YJ and Kyoung, H and Lee, S and Kim, Y and Shin, M and Song, M and Ryu, Y and Kim, JM},
title = {Multi-omics integrated approach reveals host-microbiome interactions in the adaptive mechanisms of weaning piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {603-628},
pmid = {41983000},
issn = {2055-0391},
abstract = {The weaning transition is a critical phase in piglet development, marked by physiological challenges that influence growth and health. Therefore, this study aims to investigate host-microbiome interactions during the weaning transition using a multi-omics integrated approach. Fecal samples were collected from piglets on the weaning day (W0), 7 days post-weaning (W7), and 14 days post-weaning (W14). Ileal microbiota, microbial-derived metabolites, and tissue samples (ileum, thymus, and mesenteric lymph nodes) were collected at W0 and W14. Fecal microbiota analysis revealed a more stable community at W14 than at W7, with increased presence of fiber-degrading bacteria, including Prevotella, Treponema, Muribaculaceae, and Lachnospiraceae. The ileal microbiota exhibited an adaptive pattern with increases in Lactobacillus, Clostridium_sensu stricto_1, and Enterobacteriaceae, optimized for solid feed digestion and gut stabilization. Morphological analysis of the ileum showed changes in villus architecture between W0 and W14, including increased crypt depth and villus area and decreased villus width, while villus height and goblet cell counts were numerically higher at W14. Transcriptomic profiling revealed the ileum as the primary site of molecular adaptation, with 506 differentially expressed genes (DEGs) involved in immune response pathways, including viral protein interactions with cytokine and cytokine receptor pathways and T cell receptor signaling. The thymus (158 DEGs) and mesenteric lymph nodes (30 DEGs) exhibited modulation of structural pathways linked to systemic immune development, indicating tissue-specific molecular adaptation. Integrated analysis of the host transcriptome and microbial-derived metabolites revealed upregulated glycerophospholipid and glutathione metabolic pathways in piglets 14 days post-weaning, consistent with modulation of membrane structure, barrier function, and antioxidant defense during gut adaptation. Overall, the multi-omics findings provide a comprehensive description of molecular changes associated with weaning adaptation and identify candidate targets for piglet health management during the weaning transition.},
}

@article {pmid41983002,
year = {2026},
author = {Jeong, JY and Kim, J and Kim, M and Kim, YB and Park, C and Song, J and Kim, DW and Kim, M and Park, NG},
title = {Effect of probiotics on growth performance, cytokine levels, and gut microbiome composition of broiler chickens for 7 and 35 days.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {586-602},
pmid = {41983002},
issn = {2055-0391},
abstract = {Through microbial fermentation, probiotics are essential for improving growth performance and gut health in broiler chickens. This study aimed to assess the effects of three additives on growth performance, cytokine levels, and cecal microbiota in broiler chickens. One-day-old Arbor Acres chicks (total 300) were randomized into four groups: (1) control: basal diet, (2) Bacillus subtilis (BS) + basal diet, (3) essential oil + basal diet, and (4) Bacillus velezensis + basal diet. All chickens were fed and watered ad libitum throughout the experiment. Feed intake and body weight were measured weekly. On days 7 and 35, cecal contents of one bird per replicate, based on average body weight, were collected and analyzed for microbiota using 16S rRNA gene amplicon sequencing. The BS group exhibited enhanced growth performance, including increased final body weight, average daily gain, and reduced feed conversion ratio compared to that of the other groups. On day 7, the BS group exhibited a higher abundance of Eisenbergiella (8.24%), and on day 35, there was an increased abundance of Firmicutes (99.63%) and Lachnoclostridium (1.4%). These results indicate that B. subtilis may be a promising probiotic for enhancing broiler health by modulating gut microbiota.},
}

@article {pmid41983140,
year = {2026},
author = {Liu, P and Cui, L and Peng, G and Han, X},
title = {Molecular insights into the role of vitamin D in atopic dermatitis: pathogenesis, diagnosis, and emerging therapies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1739412},
pmid = {41983140},
issn = {1664-3224},
mesh = {Humans ; *Vitamin D/metabolism/therapeutic use/analogs & derivatives ; *Dermatitis, Atopic/diagnosis/etiology/therapy/epidemiology/metabolism/immunology ; *Vitamin D Deficiency/immunology/epidemiology ; Skin/immunology/metabolism/pathology ; Animals ; Receptors, Calcitriol/metabolism ; Biomarkers ; Microbiota/immunology ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by skin barrier dysfunction, immune dysregulation, and microbial imbalance. Increasing evidence suggests that vitamin D, a secosteroid hormone with pleiotropic effects, plays a key role in modulating the pathogenesis of AD. This review provides a comprehensive overview of the molecular mechanisms through which vitamin D influences skin integrity and immune function, focusing on vitamin D receptor-mediated pathways, genetic and epigenetic modifiers, and the interplay with immune cells and microbiota. We also examine the epidemiological correlations between vitamin D deficiency and AD prevalence, diagnostic considerations including biomarkers and serum 25-hydroxyvitamin D evaluation, and therapeutic strategies involving systemic and topical vitamin D interventions. The review further discusses ongoing controversies regarding optimal dosing and evaluates the limitations of current clinical evidence. Finally, emerging research directions, such as vitamin D-microbiota-skin axis and personalized vitamin D therapy, are proposed as promising avenues for advancing AD management.},
}

Humans
*Vitamin D/metabolism/therapeutic use/analogs & derivatives
*Dermatitis, Atopic/diagnosis/etiology/therapy/epidemiology/metabolism/immunology
*Vitamin D Deficiency/immunology/epidemiology
Skin/immunology/metabolism/pathology
Animals
Receptors, Calcitriol/metabolism
Biomarkers
Microbiota/immunology

@article {pmid41983252,
year = {2026},
author = {O'Sullivan, TA and Nicholl, A},
title = {Exploring the dairy milk matrix beyond isolated nutrients-a narrative review.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/10408398.2026.2648097},
pmid = {41983252},
issn = {1549-7852},
abstract = {The concept of the food matrix considers individual components along with how they are structured, interact, and are modified during processing. There is increasing interest around the health effects of individual nutrients versus whole foods, creating a need to better understand how the matrix may influence health outcomes. This narrative review explores the dairy milk matrix and compares health effects with those of isolated components, with additional comparisons to plant-based milk alternatives. Comparative evidence suggests that while calcium from food and supplements generally has similar effects (depending on the form of the supplemental calcium), consumption of food-based sources such as milk may have fewer adverse effects associated with high-dose supplemental intake. Fermented milk products appear to offer additional health benefits compared with unfermented milk, likely due to bioactive compounds produced during fermentation. Structural and functional manipulation of milk proteins, such as whey and lactoferrin, can also modify matrix functionality; for example, appropriate processing conditions can preserve lactoferrin's iron-binding capacity, supporting iron transport and bioavailability. Compared with plant-based milks, which often require fortification and extensive processing, the dairy milk matrix is particularly effective at promoting nutrient absorption. Our findings highlight the importance of adopting a whole food perspective when considering milk in dietary recommendations and research.},
}

@article {pmid41983715,
year = {2026},
author = {Zhu, K and Zhao, J and Li, T and Zhang, S and Liu, C and Xu, Z and Lv, C and Zhang, G and Kang, Y and Huang, J},
title = {ROS-Responsive Hydrogel Delivering Bio-Nanoselenium for Targeted Therapy of UVB-Induced Skin Photodamage.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.6c00317},
pmid = {41983715},
issn = {1944-8252},
abstract = {Ultraviolet B (UVB) radiation is a major environmental factor that induces skin photodamage through oxidative stress and inflammation. To address this, we developed a reactive oxygen species (ROS)-responsive hydrogel, SeNPs@HPTA, for the intelligent delivery of biogenic selenium nanoparticles (BioSeNPs) synthesized by Bifidobacterium animalis. The hydrogel was fabricated by cross-linking phenylboronic acid-grafted hyaluronic acid (HA-PBA) with tannic acid (TA), forming dynamic boronic ester bonds that cleave under high ROS conditions to enable on-demand BioSeNPs release. Transcriptomic analysis revealed that B. lactis H15 efficiently reduces selenite (Se(IV)) to elemental SeNPs by upregulating ion transport and NADPH-regenerating pathways. In vitro, SeNPs@HPTA enhanced HaCaT cell viability, scavenged ROS, and promoted cell migration post-UVB irradiation. In vivo, topical application alleviated skin lesions, improved hydration, reduced epidermal hyperplasia, and suppressed collagen degradation. Mechanistically, the hydrogel conferred therapeutic effects by enhancing antioxidant defenses, inhibiting inflammation and attenuating ferroptosis via GPx4/Nrf2 activation. Critically, genetic knockdown of GPx4 abolished its therapeutic effects, establishing a strict dependence on this key selenoenzyme. The formulation exhibited an excellent biosafety profile. This study presents a microbiome-inspired, stimulus-responsive strategy for precise skin photodamage treatment. We anticipate this microbiome-inspired, intelligent delivery system will offer a powerful and precise strategy for treating oxidative stress-related dermatoses.},
}

@article {pmid41983734,
year = {2026},
author = {Andrade, C},
title = {Proton Pump Inhibitors and the Risk of Dementia.},
journal = {The Journal of clinical psychiatry},
volume = {87},
number = {2},
pages = {},
doi = {10.4088/JCP.26f16420},
pmid = {41983734},
issn = {1555-2101},
mesh = {Humans ; *Proton Pump Inhibitors/adverse effects ; *Dementia/chemically induced/epidemiology ; Risk Factors ; Cognitive Dysfunction/chemically induced ; Aged ; },
abstract = {Proton pump inhibitors (PPIs) are the most prescribed gastric acid suppressant drugs; the category includes omeprazole, esomeprazole, lansoprazole, dexlansoprazole, pantoprazole, and rabeprazole. In 2015, a study suggested that PPI use was associated with an increased risk of dementia. An early meta-analysis confirmed this concern, but the findings were inconsistent in subsequent meta-analyses. Also problematic is that these meta-analyses used questionable approaches, and their findings were characterized by very high heterogeneity. Notably, the high heterogeneity appeared to be driven by large studies with widely different outcomes. Nonetheless, one finding stands out in the body of research examined: older subjects who initiated and continued PPIs (implying chronic use) were at a significantly increased risk of dementia and mild cognitive impairment. Although there are causal and non-causal pathways that associate PPI use with dementia, for reasons that are explained in this article, a cause-effect relationship cannot at present be presumed; so, PPI use is best considered to be a marker of future dementia risk. However, because chronic use of PPIs has been associated with many adverse medical outcomes (eg, disturbances of the gut microbiome, orthopedic complications), and because some PPIs are associated with pharmacokinetic drug interactions (mainly inhibition of CYP2C19), it would be wise to limit the use of PPIs to the shortest duration necessary and to deprescribe PPIs when there does not appear to be need for their continuation.},
}

Humans
*Proton Pump Inhibitors/adverse effects
*Dementia/chemically induced/epidemiology
Risk Factors
Cognitive Dysfunction/chemically induced
Aged

@article {pmid41983840,
year = {2026},
author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K},
title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e299936},
doi = {10.1590/1519-6984.299936},
pmid = {41983840},
issn = {1678-4375},
mesh = {Animals ; Cattle/microbiology ; *Livestock/microbiology ; Camelus/microbiology ; Sheep/microbiology ; *Microbiota/genetics/physiology ; Chickens/microbiology ; Horses/microbiology ; },
abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.},
}

Animals
Cattle/microbiology
*Livestock/microbiology
Camelus/microbiology
Sheep/microbiology
*Microbiota/genetics/physiology
Chickens/microbiology
Horses/microbiology

@article {pmid41983959,
year = {2026},
author = {Li, C and Yang, J and Wang, X and Tan, C and Luo, Y and Jin, Z and Zhou, X and Zhang, G},
title = {Maternal Exposure to Bisphenol A Bis(diphenyl Phosphate) Induces Offspring Colitis through Disrupting the Gut Microbiome-Metabolite Axis.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11474},
pmid = {41983959},
issn = {1520-5851},
abstract = {Bisphenol-A bis(diphenyl phosphate) (BDP) has been detected in biological organisms, but its toxicological effects remain unclear. In this study of 4376 participants, the characteristic BDP metabolite diphenyl phosphate was associated with gastrointestinal diseases via a nonlinear dose-response relationship, and was identified as a risk factor (OR = 1.02; 95% CI: 1.01-1.04; P = 0.013). Pregnant rats received 50 mg/kg/day BDP during gestation (GD 14-20) or gestation plus lactation (GD 14-PND 35). Both regimens triggered colonic inflammation and gut microbiome dysbiosis in offspring. The combined exposure group showed more severe effects, including persistent histopathological damage, elevated Il-1β and Il-6, and reduced microbial diversity. LC-MS/MS and 16S rRNA sequencing were used to assess BDP distribution and gut microbiome alterations. BDP crossed the placental barrier. SourceTracker analysis confirmed maternal microbiome transmission as the primary source (>70%) of offspring gut microbiome, accompanied by Streptococcus enrichment and Bifidobacterium depletion. Metabolite-inflammation network analysis showed positive correlations of butyrate and negative correlations of propionate with proinflammatory cytokines (IL-1β, IL-6, and TNF-α), which were subsequently confirmed by in vitro experiments. These findings demonstrate a transgenerational mechanism whereby prenatal BDP exposure induces offspring colonic inflammation via the gut microbiome-metabolite axis, informing maternal-infant intervention strategies.},
}

@article {pmid41983965,
year = {2026},
author = {Nguyen, J and Nguyen, J and Chau, T and Murphy, R and Richardson, J and Evans, E and Tiller, G},
title = {The campus microbiome: insights into soil bacterial diversity from 16S V3-V4 rRNA amplicon sequencing.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0129325},
doi = {10.1128/mra.01293-25},
pmid = {41983965},
issn = {2576-098X},
abstract = {This study consisted of characterizing soil bacterial diversity via 16S V3-V4 amplicon sequencing on CCLA's campus, with a focus on analyzing samples collected near college dormitories. The data provides a sufficient starting point for us to characterize bacterial diversity both on and off campus in Northwest Louisiana.},
}

@article {pmid41984040,
year = {2026},
author = {Sordillo, A and Heldrich, J and Turcotte, R and Sheth, RU},
title = {A Postbiotic Positively Shifts the Canine Oral Microbiome.},
journal = {Journal of veterinary dentistry},
volume = {},
number = {},
pages = {8987564261439741},
doi = {10.1177/08987564261439741},
pmid = {41984040},
issn = {2470-4083},
abstract = {The oral microbiome is an important aspect of overall oral health in dogs. To investigate the ability of a postbiotic, canine oral health postbiotic (COHP), to support oral health, a double-blind, placebo-controlled study was conducted with a dirty tooth model to assess its ability to reduce volatile sulfur compound (VSC) producing microbes that cause halitosis and modulate canine oral microbiome composition. Ten client-owned dogs were randomly split into 2 groups. The groups received either the COHP or a placebo as a powder topper on food for 7 days. Oral microbiome samples were collected on day 0 and day 7 along with the buccal gingival margin. Hydrogen sulfide (H2S)-producing colonies were quantified by plating the oral microbiome samples and counting pigment-producing colonies. Additionally, oral microbiome samples were sequenced, and taxa abundance was quantified. A trend toward a reduction in H2S-producing colonies was observed in the COHP group (P = .06), but not in the placebo group (P = .9). Canine oral health postbiotic reduced the abundance of 9 times as many taxa as the placebo, including taxa that form biofilms and produce VSCs. The placebo reduced the abundance of only one taxon, which is not associated with biofilms or VSCs. The findings provide evidence for COHP's ability to promote a positive shift in the canine oral microbiome, and, together with previous results, provides evidence that it may broadly help to maintain canine oral health.},
}

@article {pmid41984077,
year = {2026},
author = {De Wilde, M and Maarsingh, B and de Monte, LGG and Dekinga, A and Bijleveld, AI and Kressin, H and Zomer, AL and Piersma, T},
title = {Molluscivorous red knots rapidly adjust to a plant diet.},
journal = {Biology open},
volume = {15},
number = {4},
pages = {},
doi = {10.1242/bio.062365},
pmid = {41984077},
issn = {2046-6390},
support = {NZ4543.24//Universiteit Utrecht/ ; //Koninklijk Nederlands Instituut voor Onderzoek der Zee/ ; },
mesh = {Animals ; *Diet ; Feces/chemistry ; *Adaptation, Physiological ; *Feeding Behavior ; },
abstract = {Dietary flexibility is key to adjusting to environmental change. In Mauritania, the seemingly obligatory molluscivorous red knots Calidris canutus were observed to eat seagrass rhizomes. To study the ability of knots to live on plant material, we performed a diet-change experiment on captive individuals. Two groups of five were fed protein-rich pellets for 13 weeks, then plant-based pellets for 6 weeks, then reversed back to protein-rich pellets for 4.5 weeks. During the first days following the shift to the plant diet, body mass declined by 14% before increasing and stabilizing to lower levels. Faecal colour changed from green (i.e. gall, suggesting starvation) to brown and was produced in larger quantities when the birds ate plant pellets. These experimental data prove that knots can indeed live on a plant-based diet, with the observed changes suggesting that adjustments of the digestive system, i.e. gut morphology and microbiome, take only a few days.},
}

Animals
*Diet
Feces/chemistry
*Adaptation, Physiological
*Feeding Behavior

@article {pmid41984345,
year = {2026},
author = {Brienza, M and Peña-Herrera, JM and Trotta, V and Chiron, S and Sauvêtre, A},
title = {Trichoderma harzianum enhances lettuce biomass and modulates plant-soil emerging contaminant dynamics under reclaimed wastewater irrigation.},
journal = {Biodegradation},
volume = {37},
number = {3},
pages = {},
pmid = {41984345},
issn = {1572-9729},
mesh = {*Lactuca/growth & development/metabolism/microbiology ; *Wastewater/chemistry ; Biodegradation, Environmental ; Agricultural Irrigation ; Biomass ; *Soil Pollutants/metabolism ; Plant Roots/metabolism/microbiology ; Soil/chemistry ; *Hypocreales ; Plant Leaves/metabolism ; Carbamazepine/metabolism ; Soil Microbiology ; Plant Growth Regulators/metabolism ; },
abstract = {The use of wastewater for irrigation in agricultural soils offers a sustainable means to reduce freshwater consumption and recycle nutrients, but also poses contamination risks associated with emerging pollutants. Furthermore, potentially toxic transformation products may form in soil and rhizosphere, and could subsequently be taken up by plants. Several products containing spores of symbiotic fungi are available and could serve as effective solutions to enhance the biodegradation of micropollutants in agricultural soils irrigated with treated wastewater. In this study, the effect of the fungus Trichoderma harzianum on the distribution of two emerging contaminants, carbamazepine and climbazole, and their main transformation products among soil and lettuce tissues was investigated under controlled conditions. Physiological effects were also investigated by quantifying phytohormones in roots and leaves. Inoculation with Trichoderma harzianum did not significantly affect the uptake of the parent compounds but increased the concentration of their transformation products in soil and reduced their levels in plant leaves after three weeks. The fungus enhanced plant biomass and altered certain phytohormones involved in defense mechanisms such as salicylic acid and microbiome recruitment in roots and soils. Findings of this study provide valuable insights that can be effectively applied to crop cultivation using reclaimed wastewater, leveraging readily available biological products for improved sustainable practices.},
}

*Lactuca/growth & development/metabolism/microbiology
*Wastewater/chemistry
Biodegradation, Environmental
Agricultural Irrigation
Biomass
*Soil Pollutants/metabolism
Plant Roots/metabolism/microbiology
Soil/chemistry
*Hypocreales
Plant Leaves/metabolism
Carbamazepine/metabolism
Soil Microbiology
Plant Growth Regulators/metabolism

@article {pmid41984779,
year = {2026},
author = {Sun, Z and Shi, M and Zheng, Y},
title = {Interpreting circulating microbiome-related metabolites in coronary heart disease.},
journal = {PLoS medicine},
volume = {23},
number = {4},
pages = {e1005056},
pmid = {41984779},
issn = {1549-1676},
mesh = {Humans ; Biomarkers/blood ; *Coronary Disease/microbiology/blood/metabolism/diagnosis ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Circulating microbiome-related metabolites have emerged as promising biomarkers for coronary heart disease. A recent multi-stage study in PLOS Medicine strengthens signal prioritization but highlights the persistent gap between association and causality.},
}

Humans
Biomarkers/blood
*Coronary Disease/microbiology/blood/metabolism/diagnosis
*Gastrointestinal Microbiome
*Microbiota

@article {pmid41984783,
year = {2026},
author = {Calderón-Romero, P and Valderrama, B and Bastiaanssen, TFS and Lillo, P and Thumala-Dockendorff, D and Clarke, G and Cryan, JF and Slachevsky, A and González-Billault, C and Court, FA},
title = {The neuroactive potential of the elderly human gut microbiome is associated with mental health status.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0343493},
pmid = {41984783},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; *Mental Health ; Cognition/physiology ; *Aging/psychology ; Aged, 80 and over ; Depression/microbiology ; Middle Aged ; Chile ; Cohort Studies ; },
abstract = {Ageing is usually associated with physiological decline, increased mental health issues, and cognitive. deterioration, alongside specific changes in the gut microbiome. However, the relationship between the neuroactive potential of the gut microbiome and mental health and cognition among the elderly remains less explored. This study examines a cohort of 153 older Chilean adults with cognitive complaints, assessing anthropometric data, mental health via five distinct tests, and gut microbiome composition through 16SV4 sequencing. Our findings reveal associations between anthropometric factors and depression scores in mental tests of participants with their gut microbiome composition. Notably, depression was associated with changes in the abundance of Lachnospiraceae Eubacterium xylanophilum group and Fusobacteriaceae Fusobacterium. Additionally, bacterial pathways involved in metabolising neuroactive compounds such as tryptophan, short-chain fatty acids, p-cresol, glutamate, and nitric oxide were associated with participant age, sex, and cognitive performance. Moreover, participants' sex was associated with the neuroactive potential of specific bacteria, suggesting a role of the gut microbiome in sex-related mental health differences in the elderly. Altogether, this study provides the first evidence from a South American cohort linking the inferred neuroactive potential of the gut microbiome to cognitive and psychological function in older adults with cognitive complaints, offering novel insights into microbiota-based mechanisms that may contribute to mental health and ageing.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Aged
*Mental Health
Cognition/physiology
*Aging/psychology
Aged, 80 and over
Depression/microbiology
Middle Aged
Chile
Cohort Studies

@article {pmid41984912,
year = {2026},
author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , },
title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e86058},
pmid = {41984912},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant, Newborn ; Female ; Infant ; Longitudinal Studies ; Prospective Studies ; Birth Cohort ; South Africa ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Observational Studies as Topic ; Rural Population ; Milk, Human/microbiology/chemistry ; Male ; Risk Factors ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.

OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.

METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.

RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.

CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Infant, Newborn
Female
Infant
Longitudinal Studies
Prospective Studies
Birth Cohort
South Africa
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Observational Studies as Topic
Rural Population
Milk, Human/microbiology/chemistry
Male
Risk Factors

@article {pmid41985067,
year = {2026},
author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR},
title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.},
journal = {Archives of insect biochemistry and physiology},
volume = {121},
number = {4},
pages = {e70159},
doi = {10.1002/arch.70159},
pmid = {41985067},
issn = {1520-6327},
support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science & Technology, New Delhi, India (INSPIRE-JRF)/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Microbiota ; Metagenomics ; *Culicidae/microbiology/growth & development ; *Metamorphosis, Biological ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.},
}

Animals
Larva/microbiology/growth & development
*Microbiota
Metagenomics
*Culicidae/microbiology/growth & development
*Metamorphosis, Biological
Bacteria/genetics/classification
Metagenome

@article {pmid41985313,
year = {2026},
author = {Khushbu, and Das, S and Debanth, N},
title = {From bench to gut: Translational horizons in probiotic nanoencapsulation for enhanced host-microbiome synergy.},
journal = {Biomaterials advances},
volume = {185},
number = {},
pages = {214871},
doi = {10.1016/j.bioadv.2026.214871},
pmid = {41985313},
issn = {2772-9508},
abstract = {Delivering viable probiotics to the gastrointestinal tract remains a challenge due to harsh physicochemical conditions and limited stability during processing and storage. Conventional microencapsulation techniques, such as spray drying, lyophilization, and emulsification, enhance survival but face scalability and efficiency constraints. Emerging nanostructured delivery platforms overcome these barriers by leveraging unique physicochemical properties of nanomaterials, including high surface area, enhanced solubility, and stimuli-responsive release. Functionalized nanocarriers enable site-specific adhesion, systemic delivery, and prolonged mucosal residence, thereby enhancing therapeutic precision and reducing off-target effects. This article highlights the potential of co-encapsulating probiotics with microbial metabolites, prebiotic carbohydrates, and polyphenolic compounds within biopolymeric matrices, which can significantly enhance translational applications and strengthen conventional probiotic nanoencapsulation strategies. This review consolidates current advancements in probiotic nanoencapsulation, emphasizing the design of multifunctional matrices that preserve microbial integrity, extend shelf life, and optimize host-microbiome interactions. By elucidating nanoparticle-probiotic interfacial dynamics, it lays the groundwork for next-generation probiotic therapeutics with improved efficacy and translational potential.},
}

@article {pmid41985330,
year = {2026},
author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K},
title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {198},
number = {},
pages = {119370},
doi = {10.1016/j.biopha.2026.119370},
pmid = {41985330},
issn = {1950-6007},
abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.

METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).

RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.

CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.},
}

@article {pmid41985576,
year = {2026},
author = {Weitekamp, CA and Watson, C and Hata, E and Hester, K and Kodavanti, UP and Lau, C and Lehmann, DM and Miller, CN and Shaffer, RM and Soliman, F and Powers, M and Branch, FM},
title = {A systematic literature inventory on the interaction between dietary factors and environmental chemical exposures for nervous system health outcomes.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {213},
number = {},
pages = {116096},
doi = {10.1016/j.fct.2026.116096},
pmid = {41985576},
issn = {1873-6351},
abstract = {Environmental health research from the last seven decades suggests that dietary factors can modify adverse health outcomes associated with chemical exposures. However, the interplay between diet, chemical exposures, and health is complex and remains poorly understood. Here, to survey the existing evidence and stimulate future research, we systematically identified and cataloged available literature on the interactions between chemical exposures and dietary factors for one health outcome category, neurotoxicity. The goal of this systematic literature inventory was to identify the relationship of dietary factors on chemical exposure mediated health outcomes related to central nervous system toxicity, given the importance of the microbiome-gut-brain axis in mediating these interactions. From an initial set of 32,529 references, we identified 80 epidemiological studies, 707 toxicological studies, and 175 in vitro studies that met inclusion criteria. Study design information was captured for the 80 epidemiological studies and for 113 toxicological studies that met additional scoping criteria. The most frequently studied chemical-diet interactions across the human and animal evidence streams were metals/metalloids and micronutrients. Knowledge gaps included dietary components known to be central to microbiome function, as well as adverse dietary modifiers compared to protective dietary factors. This systematic literature inventory is intended to support future research.},
}

@article {pmid41985591,
year = {2026},
author = {Ma, R and Wang, C},
title = {Microbiome analysis reveals the positive effects of exercise on the gut microbiota in horse.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108501},
doi = {10.1016/j.micpath.2026.108501},
pmid = {41985591},
issn = {1096-1208},
abstract = {Gut microbiota is vital to host health, involving many aspects including immunity, metabolism and digestion. Exercise is recognized as a significant factor influencing the gut microbiota. However, the effects of exercise on the gut microbiota in horses remain unclear. Here, this study aims to investigate the effects of exercise on the gut bacterial and fungal communities in the horses using 16S rDNA and ITS genes amplicon sequencing. Results indicated that exercise significantly increased the ACE, Chao1 and Shannon indices of the gut bacterial community, accompanied by significant alterations in the primary components of the gut bacterial community. Conversely, exercise did not affect the diversity and abundance of the gut fungal community. Although exercise did not change the dominant bacterial phyla and genera, it resulted in significant changes in the abundance of some bacteria and fungi. Bacterial taxonomic analysis revealed that exercise significantly increased the relative abundance of 8 phyla and 187 genera, while the relative abundance of three phyla and 197 genera decreased markedly. Moreover, exercise also resulted in a significant increase in the relative abundance of five phyla and 105 genera, whereas the relative abundance of two phyla and 82 genera decreased significantly in the gut fungal community. In summary, this study indicated that exercise can affect the composition and structure of gut microbiota. Moreover, this study also conveys an important message that exercise may exert health benefits to the host by affecting the gut microbiota. Future research could investigate the effects of various types and intensities of exercise on gut microbiota to optimize health management strategies.},
}

@article {pmid41985731,
year = {2026},
author = {Lee, E and Han, K and Mun, S},
title = {CST-Based Molecular Profiling of Vaginal Microbiota Validated by qRT-PCR and 16S Amplicon Sequencing.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2026.03.015},
pmid = {41985731},
issn = {1095-9130},
abstract = {The vaginal microbiome is commonly classified into five Community State Types (CSTs) based on the dominance and relative abundance of Lactobacillus species, which play a central role in maintaining vaginal homeostasis through the production of lactic acid and hydrogen peroxide. Disruption or depletion of Lactobacillus spp. Leads to elevated vaginal pH, thereby promoting the overgrowth of anaerobic bacteria associated with bacterial vaginosis (BV). Although next-generation sequencing (NGS)-based microbiome profiling has been widely used to characterize vaginal microbial communities, its routine clinical application remains limited by high cost, long turnaround time, and reduced suitability for rapid, species-specific quantification. In this study, we developed and validated species-specific quantitative real-time polymerase chain reaction (qRT-PCR) primer sets targeting four health-associated Lactobacillus species (Lactobacillus crispatus, Lactobacillus. gasseri, Lactobacillus. iners, and Lactobacillus. jensenii) and four BV-associated bacterial taxa (Atopobium vaginae, Clostridiales genomosp. BVAB1, Prevotella bivia, and Megasphaera type 1). Quantitative results obtained by qRT-PCR were systematically compared with relative abundance profiles derived from 16S rRNA gene V3-V4 sequencing, revealing a strong concordance between the two platforms in identifying key vaginal microbial signatures. Collectively, these findings demonstrate that qRT-PCR represents a rapid, cost-effective, and sensitive approach for targeted vaginal microbiome assessment and supports its potential utility as a molecular diagnostic tool for the precise detection of vaginal microbiota imbalance.},
}

@article {pmid41985795,
year = {2026},
author = {Shen, X and Gibson-Kueh, S and Nelson, SP and Poon, ZWJ and Terence, C and Vu, NT and Carrai, M and Awate, S and Vij, S and Tan, MR and Jerry, DR and Domingos, JA},
title = {Scale drop disease virus (SDDV) infection induces intestinal dysbiosis and secondary Vibrio expansion in Asian seabass (Lates calcarifer).},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111344},
doi = {10.1016/j.fsi.2026.111344},
pmid = {41985795},
issn = {1095-9947},
abstract = {Scale drop disease virus (SDDV) is a major viral pathogen causing high mortality in farmed Asian seabass (Lates calcarifer), yet its impacts on host-associated microbiota remain poorly understood. In this study, juvenile L. calcarifer were intraperitoneally challenged with 10[7] viral copies (0.1 ml SDDV), resulting in 94.2% cumulative mortality over a 24-day experimental period. A total of 36 intestinal content samples were collected at defined time points relative to challenge (dpc) from clinically healthy (H) and sick (S) fish, representing five stages: pre-infection baseline (H0 dpc), early infection (H6 dpc), peak mortality (H10 dpc and S10 dpc), declining mortality (S15 dpc) and recovery (H24 dpc). Histopathological examination revealed progressive intestinal pathology, characterised by multifocal vesicle formation and epithelial necrosis, consistent with SDDV-associated enteropathy. 16S rRNA gene sequencing demonstrated pronounced intestinal dysbiosis during infection, with a significant collapse of alpha diversity at peak mortality (10 dpc; Kruskal-Wallis test with Dunn's post-hoc comparisons, p < 0.05) where Chao1 decreased from 942 at baseline to 416 and Shannon from 4.3 to 1.9. At peak disease, the gut microbiome was overwhelmingly dominated by Vibrio (>80% relative abundance), suggesting secondary opportunistic expansion associated with virus-induced intestinal damage. Co-occurrence network analysis further revealed fragmentation of microbial interactions during peak infection, followed by partial restoration of network connectivity and re-emergence of taxa such as Photobacterium and Rhodobacteraceae during recovery from infection. Collectively, these findings demonstrated that SDDV infection induced severe intestinal pathology accompanied by dynamic restructuring of the gut microbiome in L. calcarifer, linking viral epithelial damage to destabilization of the intestinal microbial homeostasis and secondary Vibrio overgrowth. Distinct microbiome features, including reduced community diversity and Vibrio dominance at peak disease, as well as recovery-associated taxa in surviving fish, may represent potential microbial indicators of disease progression and intestinal recovery, providing a reference framework for future microbiome-informed health management strategies aimed at mitigating SDDV impacts in L. calcarifer aquaculture.},
}

@article {pmid41986005,
year = {2026},
author = {Ansari, A and Shete, O and Ghosh, TS},
title = {Artificial intelligence in microbial metagenomics.},
journal = {Progress in molecular biology and translational science},
volume = {221},
number = {},
pages = {255-276},
doi = {10.1016/bs.pmbts.2026.01.009},
pmid = {41986005},
issn = {1878-0814},
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; Microbiota/genetics ; Machine Learning ; },
abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.},
}

*Metagenomics/methods
*Artificial Intelligence
Humans
Microbiota/genetics
Machine Learning

@article {pmid41986382,
year = {2026},
author = {Dahmouni, S and Benabdelmoumene, D and Bengharbi, Z and Fodil, MK and Umar, KM and Qadi, WSM and Krache, F and Waqar, M and Tong, X and Han, R and Abu Bakar, ZH and Sarian, MN and Mediani, A and Jam, FA and Hamezah, HS},
title = {Postbiotics and paraprobiotics in food biochemistry mechanisms stability and nutritional applications.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00838-z},
pmid = {41986382},
issn = {2396-8370},
support = {DIP-2024-021//Universiti Kebangsaan Malaysia/ ; },
abstract = {Postbiotics, defined as preparations of inanimate microorganisms and their components that confer health benefits, are emerging as stable and safe alternatives to probiotics. This review summarizes recent advances in the biochemical composition, mechanisms of action, and applications of postbiotics and paraprobiotics in human and animal nutrition. It also highlights innovations in omics technologies, artificial intelligence, and sustainable production strategies that are shaping next-generation microbiome-based functional foods and therapeutic interventions.},
}

@article {pmid41986393,
year = {2026},
author = {Gimeno-Molina, B and Correia, GDS and Ng, S and Lee, YS and Bayar, E and Love, RL and Zhao, S and Mountain, KE and Teoh, TG and Brown, RG and David, AL and Lewis, HV and Terzidou, V and Botto, M and Kropf, P and MacIntyre, DA and Bennett, PR and Sykes, L},
title = {Complement and neutrophils are actively involved at the cervicovaginal interface in cases of adverse microbial composition, cervical shortening and spontaneous preterm birth.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00969-x},
pmid = {41986393},
issn = {2055-5008},
abstract = {Microbial-driven spontaneous preterm birth (sPTB) is linked to adverse vaginal microbiome and dysregulated immune responses, yet this knowledge has not translated into predictive tools or therapies. We sampled 186 high-risk pregnant women and assessed 14 complement proteins and the neutrophil immunophenotype at the cervicovaginal interface to expand potential targets. Alterations in classical and alternative complement pathway components were associated with bacterial community composition and preceded cervical shortening and sPTB. At 12[+0]-16[+6] weeks, women with Community State Type (CST) IV had significantly higher concentrations of C1q, C4, C4b, Factor B, D, C3b/iC3b, and Factor H, I than those with CST I. Women who later developed a short cervix and delivered preterm showed lower L. crispatus abundance and elevated complement activation. Neutrophils were the dominant local immune cell and exhibited enhanced activation relative to peripheral neutrophils, with altered expression of CD11b, CD62L, CD63 and CD66b. Cervical neutrophil CD63, CD66b, and CD88 differed between CST IV and CST I, though not by pregnancy outcome. Neutrophil abundance correlated with cytokines, complement proteins, and MMPs, suggesting roles in inflammation and tissue remodelling. These findings highlight a microbiota-driven complement-neutrophil axis present before cervical remodelling and sPTB, identifying potential complement-based predictors and therapeutic targets.},
}

@article {pmid41986507,
year = {2026},
author = {Venkidesh, BS and Acharya, M and Narasimhamurthy, RK and Murali, TS and Rao, BSS and Mumbrekar, KD},
title = {Multi-strain bacterial combination mitigates pelvic irradiation-induced gut damage by preserving gut integrity, inhibiting inflammation and apoptosis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47773-3},
pmid = {41986507},
issn = {2045-2322},
}

@article {pmid41986930,
year = {2026},
author = {Raghav, S and Frishman, WH},
title = {Childhood Obesity, Medications, and Surgeries.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000001230},
pmid = {41986930},
issn = {1538-4683},
abstract = {The obesity pandemic continues to increase in prevalence in children and adolescents, with its increase outpacing the rate of adult obesity; the human developmental index, body mass index, and family income all display associations to childhood obesity. There are numerous adverse complications of childhood obesity, including cardiovascular, endocrine, and gastrointestinal manifestations. Obesity is thought to be an interaction of several different factors, such as leptin, proopiomelanocortin, glucose uptake in adipocytes, melanocortin receptor 4, protein convertase 1/3, brain-derived neurotrophic factor, fat-mass and obesity-associated gene, melanocortin receptor 4, tumor necrosis factor, interleukin-6, and long noncoding RNA. Epigenetic regulation, the unique gut microbiome role in contributing to obesity, environmental factors, and the social context of a child can precipitation of childhood obesity. In this review, we hope to explore the different medications for obesity, orlistat, glucagon-like peptide-1 agonists, liraglutide, semaglutide, exenatide, setmelanotide, metreleptin, naltrexone, lorcaserin, phentermine, metformin, fluoxetine, lisdexamfetamine, and zonisamide, while also reviewing surgeries such as the Roux-en-Y gastric bypass, laparoscopic or vertical sleeve gastrectomy, and adjustable gastric banding.},
}

@article {pmid41986966,
year = {2026},
author = {Sourij, C and Müller, A and Al-Baghdadi, A and Aziz, F and Tripolt, NJ and Pferschy, PN and Andritz, E and Kojzar, H and Stadlbauer, V and Garcia, SL and Sourij, H},
title = {Safety and efficacy of intermittent fasting with or without exercise in people living with overweight or obesity and type 2 diabetes-The INTERFAST-3 study design.},
journal = {Diabetic medicine : a journal of the British Diabetic Association},
volume = {},
number = {},
pages = {e70328},
doi = {10.1111/dme.70328},
pmid = {41986966},
issn = {1464-5491},
support = {//Austrian Science Fund/ ; },
abstract = {AIMS: Lifestyle modification, including caloric restriction and exercise, is fundamental in the treatment of people living with overweight and type 2 diabetes mellitus (T2D). The overall aim of lifestyle intervention schemes is to reduce body weight and improve glycaemic control to reduce the future risk of diabetes-associated complications. The aim of this study is to determine whether intermittent energy restriction, exercise or their combination is best suited for reaching these targets in individuals with T2D not treated with insulin.

METHODS: This randomized, controlled, monocentric parallel-group trial is designed to investigate participants living with T2D, body mass index >27 kg/m[2], HbA1c ≥53 mmol/mol (≥7.0%) and ≤86 mmol/mol (≤10.0%) and without insulin therapy. Participants are equally and randomly allocated to one of four study groups: (1) intermittent energy restriction group, (2) exercise group, (3) combined intermittent energy restriction and exercise group and (4) control group. The intervention phase lasts 12 weeks, followed by a two-year follow-up phase. In addition to assessing body weight and glycaemic parameters, resting energy expenditure (REE) and body composition are measured. An oral glucose tolerance test is carried out at baseline and at the end of the intervention. Additionally, stool samples for microbiome analyses and individual-related outcomes are collected, and all participants are equipped with continuous glucose monitoring (CGM). The primary outcome measure is the change in bodyweight from baseline to day 84.

TRIAL REGISTRATION: The study was registered at DRKS (Deutsches Register Klinischer Studien-German Clinical Trial Register DRKS-ID: DRKS00032036)-Date of registration: 11.10.2023.},
}

@article {pmid41987215,
year = {2026},
author = {Yan, M and Firkins, J and Guo, J and Relling, A and Yu, Z},
title = {Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02422-9},
pmid = {41987215},
issn = {2049-2618},
abstract = {BACKGROUND: Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem.

RESULTS: To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways.

CONCLUSION: These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.},
}

@article {pmid41987241,
year = {2026},
author = {Zhong, Y and Peng, Y and Zhang, S and Wen, L and Liu, G and Xu, B and Liang, Y and Huang, H and He, J and Feng, Y and Zeng, J and Liang, J},
title = {An integrated microbiome-drug interaction and bioinformatics approach identifies active deglycosylated and glycosidic chain metabolites of Platycodin D targeting PTPN2/HIF1A in acute lung injury.},
journal = {Biology direct},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13062-026-00779-3},
pmid = {41987241},
issn = {1745-6150},
}

@article {pmid41987825,
year = {2026},
author = {Haque, S and Ponton, F and Allen, AP and Gamage, HKAH and Encinas-Viso, F and Paulsen, IT and Dudaniec, RY},
title = {Environment and Pollen Diversity Differentially Affect the Gut Microbiomes of Introduced Honeybees and Bumblebees.},
journal = {Evolutionary applications},
volume = {19},
number = {4},
pages = {e70234},
pmid = {41987825},
issn = {1752-4571},
abstract = {Invasive species may exhibit shifts in their gut microbiome in response to novel environments and diet, but this may differ across host species and their time since colonisation. We investigate if site environmental variables and foraged pollen resources differentially shape the gut microbiomes of two bee species with contrasting introduction histories: The European honeybee, Apis mellifera (introduced 1831), and the recently invasive bumblebee, Bombus terrestris (invaded 1992). Using landscape-scale metabarcoding across the island state of Tasmania in Australia, we characterised gut bacteria (16S rRNA) and corbicular pollen diversity (ITS2) for each species. Gut bacterial composition was significantly associated with mean annual temperature for A. mellifera and with mean annual precipitation and percentage of pasture for B. terrestris. In B. terrestris, the core and facultative gut microbial diversity and richness showed associations with precipitation, foraged pollen diversity, wind velocity and temperature. Foraged pollen diversity of native plants more strongly predicted the facultative gut microbiome across species. Overall, the gut microbiome of B. terrestris showed a stronger response to abiotic and biotic predictors compared to A. mellifera. Our findings advance understanding of how environmental and dietary factors shape pollinator gut microbiomes at landscape scales, with implications for pollinator health and survival.},
}

@article {pmid41987827,
year = {2026},
author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR},
title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag036},
pmid = {41987827},
issn = {2730-6151},
abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.},
}

@article {pmid41987828,
year = {2026},
author = {Martino, ME and Gallo, M and Nai, I and Quagliariello, A and Rovere, GD and Babbucci, M and Monticelli, G and Graziano, M and Franch, R and Racaku, M and Cardazzo, B and Milan, M and Peruzza, L and Bargelloni, L},
title = {Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag059},
pmid = {41987828},
issn = {2730-6151},
abstract = {In the context of rapidly accelerating global warming, the rising frequency of heatwaves is driving large-scale ecological shifts, profoundly affecting organismal physiology and ecosystem functioning. Thermal tolerance is a key determinant of species resilience. Evidence from diverse model systems indicates that this tolerance can be enhanced through thermal priming, a pre-adaptive process in which organisms are exposed to sublethal heat stress. Beyond intrinsic host factors, the adaptive potential of host-associated microbiomes is increasingly recognised as a critical role in shaping organismal thermal resilience. However, the extent to which microbiomes alone can enhance host thermal tolerance remains largely unknown. Here, we used the Manila clam (Ruditapes philippinarum), one of the most widely farmed bivalves, as a model system to test whether thermal pre-adaptation of the microbiome is sufficient to improve host thermal tolerance. Clams were thermally primed, their microbiota isolated, and subsequently transplanted into non-acclimated individuals, which were then exposed to simulated heatwave conditions. By integrating microbial community profiling, host physiological measurements, and transcriptomic analyses, we demonstrate that transplantation of a microbiome from animals previously exposed to heat stress is sufficient to enhance host resilience during subsequent heat stress. This effect arises from adaptive shifts in microbiome composition that promote energy conservation and survival through elevated antioxidant activity and a broad downregulation of host transcriptional pathways, placing the host in an energy-efficient, stress-mitigating state. Our findings provide novel insights into holobiont-level adaptive mechanisms to stress adaptation and hold practical potential for developing microbiome-based interventions to enhance thermal tolerance in aquaculture systems.},
}

@article {pmid41987880,
year = {2026},
author = {Cipriano, GL and Grimaldi, A and Marra, A and Quartarone, A and Maresca, G},
title = {Gut microbiota and cognitive decline: a scoping review of microbial mechanisms and adaptive responses in dementia.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1782720},
pmid = {41987880},
issn = {1663-4365},
abstract = {Dementia is a progressive disease that results in a loss of mental capacity. Some of the most affected cognitive skills are memory, orientation, and language. These skills are also associated with behavioral shifts such as increased agitation and apathy, worsening the affected person's quality of life. The most common type of dementia is Alzheimer's disease, and it is especially concerning in older adults. Alzheimer's is characterized by the formation of beta-amyloid plaques and neurofibrillary tangles that are made of hyperphosphorylated tau proteins. These plaques and tangles lead to inflammation in the central nervous system, damage to the connections between neurons, and overall degeneration of the nervous system. Newer studies have started to identify the gut microbiome and the gut-brain axis as components critical to the progression of neurodegenerative diseases. Dysbiosis, which is characterized by an imbalance or loss of microbial diversity in the gut, has been attributed to the worsening of neurodegenerative diseases. The gut microbiome has been shown to have a large impact on the brain and how it responds neurochemically. An imbalance in the gut microbiome has also been shown to lead a person to emotional and cognitive dysfunction. It has been shown that in dementia patients, there is also an associated intestinal dysbiosis and increased inflammation systemically and within the brain. Certain gut bacteria stimulate the production of pro- inflammatory cytokines and neuroinflammation, which is a defining characteristic of diseases associated with dementia. This review is focused on three main aspects in which dysbiosis is related to cognitive decline.},
}

@article {pmid41987902,
year = {2026},
author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S},
title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1729497},
pmid = {41987902},
issn = {2235-2988},
mesh = {*Diarrhea/microbiology/prevention & control ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Cross-Sectional Studies ; *Probiotics/therapeutic use ; Feces/microbiology ; Pilot Projects ; Female ; Prognosis ; Male ; High-Throughput Nucleotide Sequencing ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Prospective Studies ; Biomarkers/analysis ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.

HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.

AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.

METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.

RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.

CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.},
}

*Diarrhea/microbiology/prevention & control
*Gastrointestinal Microbiome/genetics
Humans
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Cross-Sectional Studies
*Probiotics/therapeutic use
Feces/microbiology
Pilot Projects
Female
Prognosis
Male
High-Throughput Nucleotide Sequencing
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Prospective Studies
Biomarkers/analysis
DNA, Bacterial/genetics

@article {pmid41987918,
year = {2026},
author = {Wang, Y and Ni, M and Zheng, A and Peng, Y and Liu, J and Xiong, Q and Wang, X and Savkovic, V and Kang, S},
title = {A stage-based framework to interpret regulatory T cell biology after heart transplantation.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1777360},
pmid = {41987918},
issn = {2297-055X},
abstract = {Regulatory T cells play a pivotal role in immune responses following heart transplantation, influencing the entire post-transplant process. This article examines Treg dynamics in a stage-specific framework and their clinical implications. In the early phase (0-30 days), dominated by injury-related sterile inflammation, Treg recruitment affects local inflammation resolution and tissue repair, potentially altering risks of early immune injury and rejection. The intermediate phase (1-6 months) features high acute cellular rejection risk with ongoing immunosuppression adjustments; Treg quantity, phenotype, and suppressive function are closely associated with the regulation of anti-donor immune responses. In the late phase (>6 months), chronic low-grade inflammation and progressive vascular remodeling predominate, where Tregs suppress persistent immune attacks but may promote fibrosis via repair pathways, exhibiting bidirectional effects. This article highlights Treg detection limitations, including FOXP3 specificity, epigenetic stability, and blood-graft discrepancies. Future directions encompass multimarker monitoring, dynamic risk models, Treg cell therapy, and interventions like cytokine/microbiome modulation to achieve precise immunoregulation, reduce rejection, minimize complications, and improve long-term graft survival.},
}

@article {pmid41988036,
year = {2026},
author = {Alzahrani, SS},
title = {Gut microbiome-epigenetic crosstalk in obesity and type 2 diabetes: mechanisms, evidence, and translational opportunities.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1805937},
pmid = {41988036},
issn = {1664-302X},
abstract = {Obesity and type 2 diabetes mellitus are closely linked metabolic disorders in which gut microbial alterations interact with host epigenetic regulation to influence inflammation, insulin sensitivity, and energy homeostasis. This review examines the gut microbiome-epigenetics interface in these conditions by integrating mechanistic evidence with a Scopus-based bibliometric analysis of publications from 2016 to 2025, thereby providing both disease-focused synthesis and field-level context. Bibliometric mapping identified 1,153 documents from 515 sources authored by 5,445 researchers, with a marked annual growth rate of 27.79%, indicating rapid expansion of this interdisciplinary area. Mechanistically, current evidence converges on three major epigenetic domains: DNA methylation, histone modifications, and non-coding RNA regulation. Microbiota-derived metabolites, particularly short-chain fatty acids, folate-related methyl donors, and other bioactive compounds, influence enzymes such as DNA methyltransferases and histone deacetylases, as well as downstream chromatin marks and microRNA networks relevant to metabolic dysfunction. In obesity and type 2 diabetes, recurrent findings include reduced abundance of butyrate-producing taxa and enrichment of pro-inflammatory or endotoxin-associated bacteria, although these patterns remain heterogeneous across populations, study designs, and analytical methods. Accordingly, the review emphasizes that phylum-level or taxa-level associations should be interpreted cautiously and that causality remains incompletely resolved. A key contribution of this review is the combined evaluation of mechanistic pathways, context-dependent microbial signatures, and translational limitations within a single framework. Overall, microbiome-targeted interventions remain promising but insufficiently validated, and progress toward clinical application will require longitudinal, multi-omics, and interventional studies that directly link specific taxa, metabolites, and epigenetic modifications.},
}

@article {pmid41988038,
year = {2026},
author = {Qin, H and Gong, H and Wang, X and Liu, Y and Song, W and Li, Z and Xiang, H},
title = {Rhizosphere microbial patterns and climatic correlates of phenotypic variation in Rosa roxburghii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762588},
pmid = {41988038},
issn = {1664-302X},
abstract = {Plant phenotypic variation represents an important expression of diversity among populations and their responses to heterogeneous environments. However, the factors associated with such variation remain incompletely characterized. In this study, we examined eight phenotypic traits of Rosa roxburghii across environmentally heterogeneous sites and characterized rhizosphere bacterial and fungal communities using 16S rRNA and ITS high-throughput sequencing. Marker taxa were identified, and statistical analyses were applied to explore associations between microbial patterns, climatic context, and phenotypic traits. Our results revealed significant differences among populations in fruit length, fruit width, and stem diameter. Microbial community analyses indicated inter-population divergence in both bacterial and fungal communities, with fungi showing relatively stronger compositional differentiation. Using complementary analytical approaches (LEfSe, LASSO, and sPLS-DA), we identified a consensus set of 12 marker taxa, including six bacterial and six fungal genera. Correlation analyses suggested that fungal markers exhibited broader associations with phenotypic traits than bacterial markers, and regression analyses indicated that fungal markers were statistically associated with variation in fruit size. Stem diameter showed associations with both climatic variables and microbial markers. Overall, phenotypic variation in R. roxburghii was associated with patterns in rhizosphere microbial communities and climatic context, highlighting complex relationships that warrant further investigation. This study contributes descriptive insights into plant-microbe and environment-phenotype associations and provides a foundation for future work aimed at elucidating underlying mechanisms.},
}

@article {pmid41988103,
year = {2025},
author = {Cheng, C and Ma, H and Zhong, Y and Uhlemann, AC and Feng, X and Hu, J},
title = {BIOMARKER DETECTION FOR DISEASE CLASSIFICATION IN LONGITUDINAL MICROBIOME DATA.},
journal = {The annals of applied statistics},
volume = {19},
number = {2},
pages = {943-966},
pmid = {41988103},
issn = {1932-6157},
support = {P30 CA013696/CA/NCI NIH HHS/United States ; R01 AI143886/AI/NIAID NIH HHS/United States ; },
abstract = {The microbiome has been found to have a close relationship with human health. Advancements in sequencing technologies have enabled in-depth studies of microbial communities and their associations with various diseases. When analyzing microbiome data, it is common to perform compositional scale normalization to ensure statistical validity. This requires special treatment to address the unique characteristics of microbiome data. Furthermore, biomedical studies often involve repeated measurements of microbial samples, which adds complexity to the data analysis. In this paper we focus on a liver transplant microbiome study. The main objective is to investigate the association between the colonization status of multidrug-resistant bacteria (MDRB) and the longitudinal microbial abundance profile. To accomplish this, we employ a regularized functional logistic regression model in our analysis. Specifically, we utilize the log-contrast model with a low-rank approximation to handle the compositional covariates and nonconvex penalties to select the important components in the covariate space. We propose an efficient estimation algorithm and establish the oracle property of the estimator. We name this new development as Functional Compositional data Quadratic Method (FCQM). We demonstrate the promise of the proposed method with extensive simulation studies and the liver transplant application.},
}

@article {pmid41988382,
year = {2026},
author = {Dong, H and Cao, H and Gong, Y and Zhao, Z and Wang, K and Zhang, X and Zhang, F},
title = {Chronic kidney disease as an active driver of digestive tract tumors: mechanistic insights and emerging management strategies.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1797181},
pmid = {41988382},
issn = {2296-634X},
abstract = {Digestive tract tumors (DTT), particularly gastric cancer (GC) and colorectal cancer (CRC), remain among the leading causes of cancer-related morbidity and mortality worldwide. Accumulating epidemiological evidence indicates that patients with chronic kidney disease (CKD) exhibit a significantly increased risk of developing gastrointestinal malignancies and experience worse clinical outcomes. However, the biological mechanisms underlying this association have not been comprehensively synthesized. In this review, we integrate clinical and experimental evidence to delineate how CKD functions as a systemic pro-tumorigenic condition rather than a passive comorbidity. We highlight three interrelated mechanistic axes linking CKD to DTT: (i) persistent systemic inflammation and oxidative stress, (ii) metabolic and endocrine dysregulation driven by uremic toxin accumulation, vitamin D deficiency, and mineral imbalance, and (iii) immune perturbations associated with dialysis modalities and post-transplant immunosuppression. These processes converge to disrupt gastrointestinal barrier integrity, reshape the gut microbiota, impair antitumor immune surveillance, and promote malignant transformation and tumor progression. Importantly, we discuss how CKD-specific interventions, including dialysis strategies, kidney transplantation, dietary management, and modulation of gut microbiota, may further modify gastrointestinal cancer risk. Finally, we propose CKD-oriented preventive and screening strategies for GC and CRC, emphasizing the need for risk stratification based on renal function, proteinuria, and metabolic profiles. By framing CKD as an active driver of gastrointestinal carcinogenesis, this review provides a novel integrative framework that synthesizes interconnected mechanistic pathways and explicitly links them to CKD-specific clinical management strategies, a translational perspective that informs early detection, prevention, and integrated care of DTT in patients with CKD.},
}

@article {pmid41988384,
year = {2026},
author = {Zhang, C and Tang, X and Chen, S and Akanyibah, FA and Mao, F},
title = {The role of extracellular vesicles in the transport and regulation of novel inflammatory mediators in IBD and its associated CRC.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1760517},
pmid = {41988384},
issn = {2296-634X},
abstract = {Inflammatory bowel disease (IBD), comprising ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammation of the gut characterized by an imbalance in the intestinal microbiome and ecology. IBD raises the risk of developing colorectal cancer (CRC). CRC is one of the most commonly diagnosed cancers in the world, with high incidence rates. Extracellular vesicles (EVs) play a crucial role in intercellular communication and are vital for maintaining intestinal homeostasis. Recent research highlights novel inflammatory mediators, such as specialized pro-resolving mediators (SPMs), damage-associated molecular patterns (DAMPs), alarmins, non-coding RNAs (ncRNAs), and metabolic intermediates, as crucial in the pathophysiology of IBD and CRC. These novel inflammatory mediators are transported by EVs, influencing the pathogenesis of IBD and associated CRC. Therefore, this article examines the role of novel inflammatory mediators transported by EVs in the pathogenesis of IBD and related CRC, as well as the interaction between EVs and the tumor microenvironment. We also review new research on EV use as a diagnostic indicator and on the potential of EVs, such as mesenchymal stem cell-derived EVs (MSC-EVs), as therapeutic delivery channels for cancer treatment targeting unique inflammatory mediators.},
}

@article {pmid41988471,
year = {2026},
author = {Gonzalez, AM and Townsend, JR and Sapp, PA and Edwards, C and Kirby, TO and Wright, J and Lamendella, R and Esposito, R},
title = {Effect of AG1[®] supplementation on nutritional adequacy and gut microbial composition in trained adults.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1783951},
pmid = {41988471},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary supplements that combine vitamins, minerals, phytonutrients, prebiotics, and probiotics have gained popularity among health-oriented consumers seeking convenient ways to fill nutritional gaps and support gut health.

METHODS: This randomized, double-blind, placebo-controlled crossover study examined the effects of two weeks of the nutritional supplement (AG1[®]) on gut microbial composition, nutritional adequacy, and tolerability. Twenty resistance-trained men (n = 10; 26.4 ± 6.5 y) and women (n = 10; 26.9 ± 5.3 y) supplemented daily with either AG1[®] or placebo (PL) for 14 days. Following a 2-week washout, participants crossed over to the other condition. Participants provided stool samples for gut microbial composition analysis, completed the Digestion-associated Quality of Life Questionnaire (DQLQ), and completed a 24-h dietary intake assessment at the beginning and end of each 14-day supplementation period. Outcomes were analyzed using repeated-measures and multivariate statistical approaches for dietary intake, gut microbiota, metabolomics, and questionnaire data.

RESULTS: AG1[®] did not produce large, global shifts in microbial alpha or beta diversity, supplementation was associated with selective enrichment of key bacterial taxa commonly linked to gut health, including Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, and Bifidobacterium animalis. AG1[®] supplementation significantly improved nutritional adequacy by increasing the total number of micronutrient Estimated Average Requirements (EARs) met compared to placebo (2.8; p = 0.0011), with no significant differences in digestive quality of life between groups (p = 0.777). Vitamins A, C, and E were the most common nutrient gaps filled by AG1 supplementation.

CONCLUSIONS: Two weeks of AG1[®] supplementation improved micronutrient adequacy in healthy resistance-trained adults by reducing nutrient gaps. Supplementation also selectively enriched key beneficial gut microbial taxa and putative microbial functional without inducing major disruptions to overall community structure. Importantly, AG1[®] was well tolerated and did not negatively impact digestion-associated quality of life.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier: NCT06521424.},
}

@article {pmid41988516,
year = {2026},
author = {Liang, Y and Chen, H and Ren, G and Jiang, G},
title = {Research progress on the role and therapeutic applications of traditional Chinese medicine in radiation enteropathy.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1747735},
pmid = {41988516},
issn = {1663-9812},
abstract = {Radiation enteropathy (RE) is a debilitating complication following radiotherapy, with currently limited treatment options. Multi-target intervention strategies such as Traditional Chinese Medicine (TCM) botanical formulas and acupuncture have been investigated as potential complementary approaches for its management. This review systematically synthesizes the evidence on TCM botanical formulas (e.g., Modified Baitouweng Decoction, Xihuang Pill, TJ-14) and acupuncture for the treatment of RE. Existing studies suggest multiple mechanisms of action, including anti-inflammatory and antioxidant effects, regulation of apoptosis and proliferation, restoration of intestinal barrier integrity, and modulation of gut microbiota. Clinical studies have reported improvements in symptoms and reductions in inflammatory markers, while preclinical models have demonstrated protective effects against radiation-induced intestinal injury. However, the current body of evidence is generally constrained by methodological limitations. Many clinical studies have small sample sizes and lack rigorous designs (e.g., absence of randomized controls), while mechanistic research often provides limited causal inference and relies on models with questionable clinical relevance, resulting in a significant translational gap. Based on this appraisal, we critically evaluate the limitations of existing research and propose future directions. These include: (i) employing CRISPR-based microbiome editing to investigate causal mechanisms; (ii) developing pharmacokinetic-pharmacodynamic (PK-PD) models for dose individualization; and (iii) utilizing innovative trial designs such as Bayesian adaptive trials to bridge the gap between empirical practice and evidence-based medicine. Rigorous further investigation is essential to define the role of these TCM interventions within the integrative treatment strategy for RE.},
}

@article {pmid41988525,
year = {2026},
author = {Kong, L and Wang, C},
title = {A machine learning model integrating gut microbiota biomarkers for predicting neurological recovery after cerebral hypoxia-ischemia: a single-center study augmented with public data.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1756017},
pmid = {41988525},
issn = {1663-9812},
abstract = {OBJECTIVE: To evaluate the predictive value of gut microbiota biomarkers for neurological recovery after cerebral hypoxia-ischemia and to develop a clinically oriented, validated machine learning (ML) for early outcome prediction.

METHODS: In this single-center cohort study, 772 patients (2022-2024) were stratified according to 1-year neurological outcomes into favorable (n = 538) and poor recovery (n = 234) groups, gut microbiota composition, microbial metabolites, systemic inflammatory and oxidative stress markers, and selected gene expression profiles were assessed using blood and fecal samples. Microbial profiling was assessed via 16S rRNA sequencing and whole-genome sequencing. LASSO regression, random forest (RF), and neural networks models were constructed and evaluated using internal validation strategies and augmented with publicly available datasets.

RESULTS: Patients with favorable neurological recovery exhibited significantly higher levels of short-chain fatty acids, increased superoxide dismutase activity, and upregulated neuroprotective gene expression, along with reduced pro-inflammatory cytokines and harmful metabolites (all P < 0.001). Microbiota analysis demonstrated enrichment of beneficial taxa (e.g., Bifidobacterium longum) and depletion of pro-inflammatory species (e.g., Clostridium difficile). Across ML approaches, IL-6 consistently emerged as a key predictive feature, with RF confirmed its prelative importance. The neural network model showed stable predictive performance across validation analyses, indicating robustness for high-dimensional biomarker integration.

CONCLUSION: Gut microbiota-associated biomarkers, when combined with systemic inflammatory indicators such as IL-6, enable robust early prediction of neurological recovery following cerebral hypoxia-ischemia. ML-based integration of multi-modal biomarkers may facilitate clinically applicable prognostic assessment, while also providing a foundation for future investigations into microbiota-targeted interventions.},
}

@article {pmid41988834,
year = {2026},
author = {Taléns-Visconti, R and Diez-Sales, O and Nácher, A},
title = {Cosmetic Interventions for Skin Microbiome Modulation: Current Strategies and Future Directions.},
journal = {Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)},
volume = {32},
number = {4},
pages = {e70352},
pmid = {41988834},
issn = {1600-0846},
mesh = {Humans ; *Microbiota/drug effects/physiology ; *Skin/microbiology/drug effects ; *Cosmetics/pharmacology ; Dysbiosis ; Probiotics ; Prebiotics ; Skin Microbiome ; },
abstract = {BACKGROUND: Human skin harbors a highly diverse and dynamic microbiome that maintains barrier function and homeostasis, while endogenous/exogenous factors and cosmetic products modulate microbial balance. Dysbiosis contributes to inflammatory diseases like atopic dermatitis and acne; however, evidence for microbiome-targeted cosmetics remains preliminary. This article critically examines the impact of cosmetic products on the skin microbiota, distinguishing between potentially harmful formulations and those specifically developed to preserve microbial balance, collectively termed "microbiome-friendly" cosmetics.

MATERIALS AND METHODS: This narrative review synthesizes clinical, microbiological, and mechanistic studies on the skin microbiome's composition, endogenous/exogenous determinants, dysbiosis in skin diseases, and the impact of conventional and microbiome‑targeted cosmetics. Databases were searched up to January 2026 for peer‑reviewed studies, with emphasis on human clinical trials and systematic analyses.

RESULTS: Most conventional cosmetics do not induce major dysbiosis in healthy skin when properly formulated. For advanced formulations, including ingredients such as probiotics, prebiotics, postbiotics, and paraprobiotics, early clinical and microbiological studies report promising benefits without compromising microbial diversity. However, evidence is limited by heterogeneous designs, small sample sizes, and the lack of standardized criteria for "microbiome‑friendly" claims.

CONCLUSIONS: The evidence indicates that informed cosmetic selection and use of skincare products support microbiome balance as a complementary skin health strategy as may be key for both preventative and therapeutic strategies in managing skin disorders, just as allowing a dynamic understanding of the skin microbiome to improve human health.},
}

Humans
*Microbiota/drug effects/physiology
*Skin/microbiology/drug effects
*Cosmetics/pharmacology
Dysbiosis
Probiotics
Prebiotics
Skin Microbiome

@article {pmid41989100,
year = {2026},
author = {Yang, J and Du, H and Tao, F and Ashraf, MA and Gao, X and Huang, X and Zhu, K and Li, G and Zheng, J and Bonfante, P and Cardinale, F and Liu, J},
title = {Rhizosphere microbial shifts drive amygdalin detoxification and jasmonate-mediated alleviation of peach autotoxicity.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag095},
pmid = {41989100},
issn = {1751-7370},
abstract = {Plant-associated microbes play essential roles in maintaining plant health and modulating responses to environmental stresses. Autotoxicity from allelopathic compounds is a major constraint on perennial crop production, yet the potential for plants to recruit microbiota to counteract such toxicity remains understudied. Our research combined field sampling from a multi-replant peach system, multi-omics, pot, and hydroponic experiments to elucidate plant-microbe interactions that alleviate amygdalin-induced autotoxicity. Metabolomic analysis of peach orchard soils showed that amygdalin accumulated progressively in the rhizosphere with longer continuous cultivation. Exogenous amygdalin inhibited plant growth, with stronger suppression observed in sterilized soil, suggesting a protective role of soil microbes. Amygdalin application altered rhizobacterial community structure and enriched several taxa, including Burkholderia-Caballeronia-Paraburkholderia and Sinomonas. In vitro assays confirmed that amygdalin serves as a selective substrate for these enriched bacteria. We further found that three strains isolated from the amygdalin-stressed peach rhizosphere significantly alleviated autotoxic inhibition, and their co-inoculation showed the greatest enhancement of plant performance. Metabolomic and transcriptomic analyses revealed activation of plant jasmonic acid (JA) pathway. Its involvement was confirmed by the alleviation of amygdalin-induced stress upon exogenous JA application and by the attenuation of microbiota-mediated stress relief upon JA pathway inhibition. Our study reveals a critical mechanism by which host plants enrich specialized microbes that can alleviate autotoxicity by direct amygdalin degradation, activation of the JA pathway, and modulation of redox homeostasis in peach. These findings provide new insights into plant-microbe interactions in perennial systems and highlight the potential of microbiome-informed microbial interventions for mitigating replant disease.},
}

@article {pmid41989132,
year = {2026},
author = {Parhi, P and Banerjee, A and Thatoi, H},
title = {The role of gut microbiome in chemoresistance property development in colorectal cancer tissue and its novel therapeutic strategies.},
journal = {Journal of chemotherapy (Florence, Italy)},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/1120009X.2026.2653339},
pmid = {41989132},
issn = {1973-9478},
abstract = {Colorectal cancer remains the second contributor to cancer-related mortality worldwide. Despite various advances in chemotherapeutic approaches, chemoresistance still poses a significant risk, hampering the effectiveness of the treatment. Recent researches have explored the crucial role of dysbiotic gut microbiota in the progression of CRC. Specific dysbiosed gut microbiota plays a key role in enhancing chemoresistance in CRC patients through different mechanisms by metabolizing drugs, and modulating the immune system, creating a barrier between CRC tissue and chemotherapeutic drugs. Various microbial genes have been linked to chemoresistance that code for different enzymes, resulting in the degradation of chemotherapeutic drugs, thus reducing drug's efficiency and identifying these genes can provide insight into various resistance pathways. Therefore, identifying the microbial signature for predetection of chemoresistance in patient, prevention of colonizing chemoresistance inducing bacteria and interventions like modification of gut flora for enhancing the effectiveness of chemotherapeutics is essential to overcome these challenges.},
}

@article {pmid41989202,
year = {2026},
author = {Mankel, D and Maierhaba, Y and Momjian, C and Calabrese, F and Duhamel, S and Marlow, J},
title = {Dual-BONCAT reveals distinct subpopulations of anabolically active cells.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0239125},
doi = {10.1128/aem.02391-25},
pmid = {41989202},
issn = {1098-5336},
abstract = {Bio-orthogonal non-canonical amino acid tagging (BONCAT) has emerged as a prominent molecular technique that enables microbial ecologists to visualize and identify metabolically active cells in cultures and complex microbial communities. To date, researchers have used just one non-canonical amino acid (ncAA) in a given experiment; here, we validate a novel approach using two different ncAAs in a single experiment. This advancement facilitates the detection of differentially active subpopulations within the same experimental context, thereby reducing the uncertainty and variability associated with parallel treatments and providing precise spatial information about organisms that are active under distinct conditions or at different times. We show that both ncAAs can be taken up by E. coli cultures and by constituents of the Little Sippewissett Salt Marsh microbiome, resulting in fluorescence signals that are significantly higher than background and ncAA-free control experiments, as well as differential labeling patterns reflective of distinct subpopulations. As a proof of concept, we implemented this "dual-BONCAT" approach in salt marsh sediments, adding one ncAA during daytime hours and the other at night. Subpopulations of cells that were anabolically active during the day and/or night were distinguishable by both fluorescence microscopy and by fluorescence-activated cell sorting. Subsequent high-throughput 16S rRNA gene amplicon sequencing of active subpopulations revealed that Methylobacterium, potentially feeding on plant exudate carbon, was preferentially active during the day, while sulfur-cycling taxa dominated the night-active population. Dual-BONCAT offers an important advancement in multiplexing substrate analog probing techniques, providing a more realistic understanding of metabolic activity under distinct environmental conditions.IMPORTANCEMicrobial communities are complex and dynamic, with different groups of microbes active under distinct conditions. Bio-orthogonal non-canonical amino acid tagging (BONCAT) uses synthetic amino acids to tag newly made proteins, allowing researchers to see and identify the active subset of a community. While BONCAT studies to date have used a single synthetic amino acid to evaluate cell activity in a single experimental context, here, we introduce a new approach, "dual-BONCAT," using two synthetic amino acids to track differential responses to changing conditions. After validating the approach with E. coli, we deployed it in a salt marsh sediment community, finding that organisms potentially feeding on plant root sugars were more active during the day, while microbes likely metabolizing sulfur were more active at night. We believe dual-BONCAT will prove useful in many studies, as it illuminates microbial community responses to changing conditions, which has important implications for ecosystem dynamics.},
}

@article {pmid41989380,
year = {2026},
author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M},
title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659400},
doi = {10.1080/19490976.2026.2659400},
pmid = {41989380},
issn = {1949-0984},
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology ; Child ; Male ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; *Diet ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology
Child
Male
*Gastrointestinal Microbiome
Female
Feces/microbiology
*Diet
Bacteria/classification/genetics/isolation & purification

@article {pmid41989563,
year = {2026},
author = {Saini, V and Verma, A and Kumari, S and Chaudhary, S and Mishra, A and Kumar, A and Jha, HC},
title = {The gut microbiome axis: how Lactobacillus-fermented soymilk orchestrates health.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {41989563},
issn = {1432-072X},
support = {2103365//PMRF (IN)/ ; IITI/CRDT/2022-23/05//CRDT-IIT Indore/ ; ANRF/PAIR/2025/000018/PAIR-A(G)//Anusandhan National Research Foundation (IN)/ ; },
}

@article {pmid41989595,
year = {2026},
author = {Walker, MR and Schwarzfischer, M and Scharl, M},
title = {The cancer-microbiome axis: Mechanisms and emerging therapeutic strategies.},
journal = {Seminars in immunopathology},
volume = {48},
number = {1},
pages = {},
pmid = {41989595},
issn = {1863-2300},
}

@article {pmid41990128,
year = {2026},
author = {Giagnoni, L and Deb, S and Tondello, A and De Noni, M and Borella, M and Stevanato, P and Cecchinato, A and Squartini, A and Spanu, C},
title = {The legacy of raw milk storage temperature is associated with cheese microbiome composition, notwithstanding pasteurization and starter addition.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag046},
pmid = {41990128},
issn = {1574-6968},
abstract = {Using DNA metabarcoding, we assessed the relative impact of two variables: (a) raw milk storage temperature and (b) cheese maturation duration, on a semi-fresh cheese bacteriome composition under authentic factory-scale industrial conditions. The study is compared to a prior literature report run at a high-quality milk facility, whilst in the present case, milk from an average-quality farm, better reflecting typical local standards, was used. We tested three milk storage temperatures (4 °C, 7 °C, 9 °C) and sampled cheese at six maturation stages (0, 10, 25, 30, 45, and 60 days). Results showed that raw milk storage temperature was the variable most strongly associated with microbial community composition across the sampled stages, exceeding the variation associated with maturation time. Even the pasteurization step and the addition of a Streptococcus thermophilus starter culture did not erase the microbial 'memory' of initial milk conditions. Interestingly, the cheese bacterial community shaping associated with different milk tank temperatures was moreover compositionally uncoupled from the dominant taxonomical pattern of the starting milk. Additionally, the study provided insights into balancing milk quality and storage temperatures to prevent spoilage by psychrotrophic pseudomonads. Under the conditions tested here, the findings suggest that the 4°C storage benchmark may warrant re-evaluation.},
}

@article {pmid41990265,
year = {2026},
author = {Liang, CL and Chen, Y and Lu, C and Liu, H and Qin, F and Dai, S and Qiu, F and Chen, H and Lu, W and Bromberg, JS and Dai, Z},
title = {High Humidity Exacerbates Psoriasiform Skin Disease Relapse by Increasing Tissue-Resident Memory T Cells via Altering Skin Microbiota.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04061},
doi = {10.1002/advs.202504061},
pmid = {41990265},
issn = {2198-3844},
support = {82104867//National Natural Science Foundation of China/ ; 82004377//National Natural Science Foundation of China/ ; 2023B1212060063//Science and Technology Planning Project of Guangzhou/ ; 2025A03J1082//Science and Technology Planning Project of Guangzhou/ ; 2022A1515011704//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A1515010807//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A1515010295//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2026A1515012112//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
abstract = {Psoriasis recurrence remains a common and difficult medical problem, while environmental humidity appears to have an impact on psoriasis morbidity. However, it remains unknown whether and how high humidity impacts psoriasis relapse. Using unique mouse models of psoriasis relapse, we found that high humidity exposure exacerbated psoriasis recurrence by increasing skin-resident memory CD8[+] T (TRM) cells through a mechanism depending on its upregulation of IL-15Rα on keratinocytes. Keratinocyte-specific knockout of IL-15Rα or administrating soluble sIL-15Rα to block IL-15 abrogated these effects. Moreover, the effects of high humidity on psoriasis relapse, IL-15Rα expression and skin TRM cell formation were attributed to cutaneous Staphylococcus nepalensis since its recolonization or its specific metabolite, asymmetric dimethylarginine (ADMA), upregulated IL-15Rα expression on keratinocytes, increased skin CD8[+] TRM cells and worsened psoriasis relapse. However, treatment with mupirocin, an antibiotic, alleviated recurrent psoriasis. In vitro experiments showed that culture supernatant of Staphylococcus nepalensis upregulated IL-15Rα expression on keratinocytes, while IL-15Rα-expressing keratinocytes promoted formation of CD8[+] TRM phenotypes. Finally, high humidity also aggravated psoriatic skin lesions in humanized mice. Thus, our findings enhanced a new understanding of how climatic factors govern psoriasis recurrence and unveiled a role for IL-15Rα-expressing keratinocytes in skin CD8[+] TRM formation and psoriasis relapse.},
}

@article {pmid41990601,
year = {2026},
author = {Kholif, AE and Olafadehan, OA and Anele, UY},
title = {Tannins in ruminant feeding: effects of tannin type and dosage on rumen fermentation, production performance, health, and sustainability.},
journal = {Research in veterinary science},
volume = {206},
number = {},
pages = {106181},
doi = {10.1016/j.rvsc.2026.106181},
pmid = {41990601},
issn = {1532-2661},
abstract = {Tannins are plant-derived polyphenolic compounds of variable molecular weights that have attracted considerable attention as natural feed additives in ruminant nutrition. Their ability to modulate rumen microbial ecology, improve nutrient utilization, mitigate enteric methane (CH4) emissions, and promote animal health has positioned them as potential tools for improved, sustainable ruminant production systems. This review critically evaluates and synthesizes published evidence on the effects of tannins on rumen fermentation dynamics, nutrient digestibility, hematological and biochemical parameters, production performance, and overall health status of ruminants. A systematic literature search was conducted using Scopus, Web of Science, ScienceDirect, Google Scholar, and PubMed, targeting peer-reviewed English-language studies published between January 2000 and September 2025. Search terms were organized using Boolean operators across tannin chemistry and type, ruminant species, and production-, environmental-, or health-related outcomes. Studies were included if they reported in vitro or in vivo responses of ruminants to tannins, while non-ruminant studies, conference abstracts, and non-English publications were excluded to ensure comprehensive comparability. Collectively, available evidence indicates that hydrolyzable tannins generally exert more consistent positive effects on feed intake, nutrient digestibility, and CH4 mitigation than condensed tannins, although responses remain highly dependent on tannin source, chemical structure, diet composition, dietary inclusion level, and the extent of animal adaptation. Low to moderate inclusion levels (generally <3% of dietary dry matter [DM]) were associated with neutral to beneficial effects on feed intake, rumen fermentation characteristics, nitrogen utilization, and animal performance. In contrast, higher rates (>5% of dietary DM) frequently impair digestibility, depress feed intake, compromise nitrogen efficiency, and reduce productive performance, indicating dose-dependent responses. Besides nutritional modulation, other ancillary benefits of tannins include reduced internal parasite burden and decreased incidence of ruminal bloat. Positive changes in hematological and biochemical indices further suggest potential improvements in physiological response and health status at moderate levels, although high rates may induce adverse metabolic alterations. In summary, tannins represent a promising nutritional strategy for improving the sustainability of ruminant production systems; however, their successful application depends on careful selection of tannin type, strategic dosage optimization, and feeding strategy. Future research should prioritize defining optimal inclusion thresholds, elucidating rumen microbiome adaptation mechanisms at the molecular level, and assessing long-term production and health outcomes under practical production conditions.},
}

@article {pmid41990662,
year = {2026},
author = {Wen, X and Fu, Y and Xiang, L and Liao, M and Harindintwali, JD and Wang, Y and He, C and Gao, Z and Jiang, J and Jiang, X and Wang, F},
title = {Rhizosphere reprogramming by integrated bio‑organic fertilizer and seed coating mitigates atrazine phytotoxicity in soybeans.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142058},
doi = {10.1016/j.jhazmat.2026.142058},
pmid = {41990662},
issn = {1873-3336},
abstract = {The widespread use of atrazine in maize fields poses a persistent threat to subsequent soybean production due to its soil persistence and phytotoxicity. Here, we present an integrated field strategy by synergistically combining a vermicompost-based bio-organic fertilizer with a targeted seed coating, both delivering the efficient atrazine‑degrading Paenarthrobacter sp. AT5. This synergy thereby provides a dual guarantee of precise rhizosphere colonization and a conducive soil environment for atrazine degradation. The combined treatment significantly reduced atrazine concentrations in roots, stems, and leaves by 38.8%, 23.2%, and 35.5%, respectively, while elevating hydroxyatrazine to 8.2-31.0 times the levels in the atrazine-only treatment. Soil atrazine residues decreased while hydroxyatrazine accumulated, particularly in the rhizosphere. Microbiome analyses revealed that the combined treatment enriched key bacterial genera, including Flavobacterium and Bacillus, potentially harboring atrazine-degrading capabilities, and increased the abundance of the functional gene trzN. In parallel, it restored deterministic community assembly processes and re-established cooperative interactions within the rhizosphere bacterial network. Together, these findings elucidate the mechanistic basis by which synergistic inoculation mitigates atrazine phytotoxicity under field conditions and highlight a scalable, microbiome-based strategy for sustaining soybean productivity in herbicide-impacted agroecosystems.},
}

@article {pmid41990710,
year = {2026},
author = {Moeckli, B and Rocha, M and Wassmer, CH and El Hajji, S and Collet, TH and Lacotte, S and Toso, C},
title = {Maternal obesity and the intergenerational risk of cancer: Epidemiologic evidence and mechanistic insights.},
journal = {Cancer epidemiology},
volume = {102},
number = {},
pages = {103079},
doi = {10.1016/j.canep.2026.103079},
pmid = {41990710},
issn = {1877-783X},
abstract = {Over recent decades, the prevalence of obesity has markedly surged. While excess maternal weight is a well-established risk factor for adverse pregnancy outcomes, growing evidence suggests that maternal obesity may also increase the long-term risk of cancer in offspring. This comprehensive review synthesizes epidemiological and experimental data linking maternal obesity to heightened cancer susceptibility in the next generation. Observational studies demonstrate increased risks of childhood leukemia and colorectal cancer in offspring of obese mothers, whereas preclinical models support associations with breast, liver, colon, and pancreatic cancers. Mechanistically, maternal obesity induces epigenetic reprogramming, immune dysregulation, and vertical transmission of a dysbiotic gut microbiota, which may lead to persistent alterations in metabolic and inflammatory signaling pathways in offspring, thereby promoting a pro-tumorigenic environment and potentially increasing cancer susceptibility. Given the global burden of obesity, this intergenerational risk has critical public health implications. Lifestyle modifications, weight-loss interventions, and targeted approaches such as probiotic supplementation may offer promising strategies to mitigate cancer risk in offspring, but require scientific confirmation in further studies. Future research should prioritize mechanistic dissection of exposure windows, identification of predictive biomarkers, and the development of effective, scalable preventive therapies.},
}

@article {pmid41990750,
year = {2026},
author = {Gonzalez Pastor, B and Shkoporov, AN and Hill, C},
title = {Not just passengers: Phages as agents of genetic exchange in fecal microbiota transplantation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.017},
pmid = {41990750},
issn = {1934-6069},
abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection and is increasingly being explored for other microbiota-associated diseases. However, general research has largely focused on bacterial engraftment, overlooking the contribution of the gut virome. In this perspective, we highlight phage-mediated horizontal gene transfer (HGT) as a potentially influential process occurring following FMT. Donor-derived phages may potentially influence community structure, engraft in resident bacteria, and modulate microbial functions or host physiology. In addition, temperate phages are well-equipped to mobilize bacterial genes, such as metabolic functions, stress-response traits, and antibiotic resistance determinants, raising the possibility that gene flow could well contribute to FMT outcomes. We propose a conceptual model in which phages act as bidirectional mediators of adaptation, not only accompanying bacterial communities but also influencing gut ecosystems in subtle, yet potentially consequential, ways.},
}

@article {pmid41990911,
year = {2026},
author = {Espín-Sánchez, D and Russo, L and Diambra, L and Mannino, MC and Scorsetti, AC and Huarte-Bonnet, C and Pedrini, N},
title = {Host transcriptional and microbiome metatranscriptomic changes in soybean plants carrying the insect-pathogenic fungus Beauveria bassiana as an endophyte.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108629},
doi = {10.1016/j.jip.2026.108629},
pmid = {41990911},
issn = {1096-0805},
abstract = {Entomopathogenic fungi, such as Beauveria bassiana, have been naturally isolated from various plant species and have also been introduced as endophytes to enhance plant health and resilience. These fungal endophytes are often associated with improved plant defense against insect pest herbivory. This study aimed to assess the endophytic capacity of B. bassiana ARSEF 2860 in soybean plants and to investigate the associated changes in gene expression and leaf microbiome activity one-week post-inoculation. The results showed that B. bassiana successfully colonized the leaves, stems, and roots of soybean plants and induced gene expression changes in both the host leaves and their associated microbiome. In the soybean leaves, the fungal endophyte down-regulated genes related to responses to far-red light and the abscisic acid pathway, while up-regulating genes involved in photosynthesis, lipid and carbohydrate biosynthesis, and stress response. Additionally, plant inoculation with B. bassiana was associated with a reduction in total microbiome transcript abundance. This shift was characterized by a relative decrease in reads mapping to potentially pathogenic bacteria, alongside a relative increase in transcripts from bacteria commonly associated with beneficial functions. Total fungal reads were also lower in B. bassiana-colonized plants compared to control samples, with plant-pathogenic fungal reads being reduced. These findings highlight the role of entomopathogenic fungal endophytes to promote plant growth by potentially enhancing photosynthesis and strengthening plant defense mechanisms. The shift in the microbial activity highlights the capacity of endophytes to modulate plant-associated microbiota towards communities that may enhance health and resilience.},
}

@article {pmid41991203,
year = {2026},
author = {Sefer, AP and Aydiner, EK},
title = {From bench to bedside: advances in standardized oral immunotherapy and early predictors of persistent cow's milk allergy in children.},
journal = {Allergologia et immunopathologia},
volume = {54},
number = {S Pt 1},
pages = {18-27},
pmid = {41991203},
issn = {1578-1267},
support = {//None./ ; },
mesh = {Humans ; *Milk Hypersensitivity/therapy/immunology/diagnosis ; *Desensitization, Immunologic/methods/standards ; Child ; Animals ; *Allergens/immunology/administration & dosage ; Administration, Oral ; Immunoglobulin E/immunology ; Cattle ; },
abstract = {Immunoglobulin E (IgE)-mediated cow's milk allergy (CMA) remains the most prevalent pediatric food allergy and a major cause of early-life anaphylaxis, with a substantial proportion of children developing persistent disease despite traditional avoidance-based management. Oral immunotherapy (OIT) has emerged as a proactive strategy that modulates the allergic immune response through controlled and sustained allergen exposure, shifting immunity from T-helper (Th) 2-dominant pathways toward a more regulatory and tolerogenic profile. Current evidence from randomized trials and real-world cohorts demonstrates that cow's milk oral immunotherapy (CM-OIT) achieves desensitization in most treated children, reduces accidental reaction risk, and improves quality of life, although sustained unresponsiveness remains variable and protocol-dependent. Marked heterogeneity exists across protocols regarding dosing, antigen formulation, maintenance targets, and escalation speed, reflecting differing therapeutic philosophies rather than standardized practice. Safety concerns, including dose-related reactions and rare cases of eosinophilic esophagitis, underscore the need for careful patient selection, optimization of comorbid atopic diseases, and shared decision-making. Advances in precision immunology, including component-resolved diagnostics, epitope mapping, basophil activation testing, and emerging transcriptomic and microbiome signatures, now enable the earlier identification of children at high risk of persistent CMA who may benefit most from OIT, while low-risk phenotypes can be safely observed. Adjunctive biologic therapy, particularly anti-IgE agents, has improved tolerability and expanded eligibility in high-risk patients. This review synthesizes current evidence on efficacy, safety, biomarkers, protocols, and adjunctive strategies, emphasizing a personalized, risk-adapted approach to CM-OIT and outlining future directions toward standardized formulations, biomarker-guided stratification, and integrated biologic-assisted immunomodulation.},
}

Humans
*Milk Hypersensitivity/therapy/immunology/diagnosis
*Desensitization, Immunologic/methods/standards
Child
Animals
*Allergens/immunology/administration & dosage
Administration, Oral
Immunoglobulin E/immunology
Cattle

@article {pmid41991444,
year = {2026},
author = {Simpson, RC and Cutler, HB and James, DE and Masson, SWC},
title = {The gut microbiome as an effector of metabolic disease gene variants.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2026.03.011},
pmid = {41991444},
issn = {0168-9525},
abstract = {Here, we discuss emerging studies that have identified overlap in the genetic drivers of the gut microbiome and metabolic disease, and we evaluate the possibility that some genes affecting host metabolic function do so by first manipulating the microbiome.},
}

@article {pmid41991448,
year = {2026},
author = {Diab, E and Thome, NU and Elsayed, SS and Raaijmakers, JM and van Wezel, GP},
title = {Chemical dialogues at the crossroads of host-bacteria interactions.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.013},
pmid = {41991448},
issn = {1878-4380},
abstract = {Microbiomes are now recognised as the second genome of eukaryotes, providing diverse life-support functions for their hosts. The impact of microbiome members on the growth and health of their hosts is determined by chemical cues from the host that modulate microbial physiology, virulence, and the biosynthesis of specialised metabolites. In this review, we provide a cross-kingdom comparison of the role of human and plant molecules in regulating bacterial gene expression. We highlight specific feedback loops and discuss common mechanisms of bidirectional cueing in human- and plant-associated bacteria. Despite the different taxonomies of human- and plant-associated bacteria, we find striking functional similarities in the chemical dialogues at the crossroads of host-bacteria interactions.},
}

@article {pmid41991462,
year = {2026},
author = {Zang, Y and Guo, Z and Ledesma-Amaro, R and Xin, Y and Wu, Y and Gu, Z and Zhang, L},
title = {Engineering Bacillus subtilis as a sustainable platform for the production of functional bile acids.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.03.021},
pmid = {41991462},
issn = {1879-3096},
abstract = {Bile acids and their derivatives are key regulators of host metabolism, immunity, and microbiome interactions, with growing therapeutic potential. Conventional production methods of bile acids relying on animal extraction or chemical synthesis are inefficient, costly, and environmentally unfriendly. Microbial synthesis offers a sustainable alternative but is limited by the absence of genetic tools for native anaerobic producers. Here, we reconstructed the bile acid 7α-dehydroxylation pathway in Bacillus subtilis, a safe and tractable host. We characterized the key Bai enzymes and performed comprehensive analyses of the bile acids generated through in vitro assays and whole-cell catalysis. Multiple intermediates and end products, including cholyl-CoA, 3-oxo-cholic acid, 3-oxo-4,5-6,7-didehydro-deoxycholic acid, 3-oxo-4,5-dehydro-deoxycholic acid, 3-oxo-deoxycholic acid, and deoxycholic acid, were identified. This work establishes a functional heterologous platform for bile acid biosynthesis, enabling sustainable production and future applications in therapeutics and microbiome engineering.},
}

@article {pmid41991481,
year = {2026},
author = {Pyrzanowska, KI and Smith, EN and Ramalingam, C and Greig, M and Gandhi, RA and Heyes, S and Sanger, D and Smith, T and Partridge, DG and Stafford, GP},
title = {A Survey of the Microbiome, Culturome and ARG Profile of a Cohort of Chronic Diabetic Foot Lesions.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {134},
number = {4},
pages = {e70203},
doi = {10.1111/apm.70203},
pmid = {41991481},
issn = {1600-0463},
support = {BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NIHR203321//NIHR Sheffield Biomedical Research Centre/ ; },
mesh = {*Diabetic Foot/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Aged ; Female ; *Bacteria/isolation & purification/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Cohort Studies ; Drug Resistance, Bacterial ; Adult ; },
abstract = {This study aimed to analyse the microbiome of chronic infected diabetic foot ulcers (DFUs) using parallel methods: traditional culture (the culturome), 16S rRNA gene sequencing (the microbiome) as well as the Antibiotic Resistance Gene (ARG) profile of isolated strains. Swab samples were collected in parallel from affected ulcers. The microbiome sequencing results identified that all patients had a polymicrobial flora with the five most frequent genus level OTUs as Escherichia, Staphylococcus, Streptococcus, Pseudomonas and the anaerobe Anaerococcus. Microbiological culture from the same swabs identified multiple species in all but two patient samples and revealed the most common isolates as CoNS Staphylococcus (17%), Enterococcus faecalis (14.3%), Corynebacterium spp. (10.7%), Anaerococcus spp. (7%), Staphylococcus aureus (8%) and Pseudomonas aeruginosa (6%). Enteric pathogens such as Klebsiella spp. were also frequently isolated. Attempts to revive anaerobes were largely unsuccessful, identifying a limitation in clinical microbiology storage protocols. Genome sequencing of 55 isolates revealed a high number of ARGs relating to β-lactams and tetracyclines, indicating multi-drug-resistant organisms (MDROs). This was confirmed by phenotypic antimicrobial susceptibility data that included several highly resistant Gram-negative bacteria. Overall, our data add to the picture of DFU microbiome as complex and displaying high levels of anti-microbial resistance (AMR).},
}

*Diabetic Foot/microbiology
Humans
*Microbiota
RNA, Ribosomal, 16S/genetics
Middle Aged
Male
Aged
Female
*Bacteria/isolation & purification/genetics/classification/drug effects
Anti-Bacterial Agents/pharmacology
Cohort Studies
Drug Resistance, Bacterial
Adult

@article {pmid41991624,
year = {2026},
author = {Garg, PM and Malhotra, A},
title = {Emerging role of non-coding RNAs as biomarkers and therapeutic targets in preterm infants with necrotizing enterocolitis.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41991624},
issn = {1530-0447},
abstract = {Necrotizing enterocolitis (NEC) is a leading cause of morbidity and mortality in preterm infants, marked by intestinal necrosis, inflammation, hemorrhage, and impaired repair. Despite advances in neonatal care, early diagnostics and targeted therapies remain limited. Emerging evidence shows that non-coding RNAs (ncRNAs), including microRNAs, long ncRNAs, and tRNA-derived fragments, regulate key inflammatory, cell-death, angiogenic, and immune pathways in NEC. Distinct ncRNA signatures correlate with histopathology, and plasma-derived exosomal ncRNAs show promise as early biomarkers. Human milk exosomal microRNAs exhibit protective effects, while ncRNA-microbiome interactions may influence disease susceptibility. Larger studies using high-throughput sequencing are needed to advance biomarker-driven precision care.},
}

@article {pmid41991647,
year = {2026},
author = {Liu, CC and Grencewicz, D and Chakravarthy, K and Li, L and Liepold, R and Wolf, M and Marcho, LM and Sangwan, N and Tzeng, A and Hoyd, R and Jhawar, SR and Grobmyer, SR and Al-Hilli, Z and Sciallis, AP and Spakowicz, D and Ni, Y and Eng, C},
title = {Breast tumor microbiome regulates anti-tumor immunity and T cell-associated metabolites.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48719-5},
pmid = {41991647},
issn = {2045-2322},
support = {K01AG070310/AG/NIA NIH HHS/United States ; Innovator Award (1046611)//American Lung Association/ ; Research Scholar Award (RSG-23-1023205)//American Cancer Society/ ; P30CA016058//National Institutes of Health, United States/ ; 8UL1TR000090-05/TR/NCATS NIH HHS/United States ; GRAYFDN1908CE//Gray Foundation/ ; },
}

@article {pmid41991788,
year = {2026},
author = {Imran, H and Nouha, F and Wael, T and Haroun, BA and Wissal, M and Thouraya, BH and Darine, T},
title = {Mesorhizobium inoculation and Water-nitrogen regimes enhance Potato-chickpea intercropping performance and Rhizosphere microbiome diversity.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41991788},
issn = {1573-0972},
}

@article {pmid41991820,
year = {2026},
author = {Akuaka, GO and Haris, H and Zarkasi, KZ and Furusawa, G and Lau, NS and Madukpe, VN},
title = {Quantifying the contribution of the rare biosphere and functional potential to the compacted clay baseliner of sanitary landfill.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41991820},
issn = {1573-0972},
}

@article {pmid41991911,
year = {2026},
author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q},
title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71929-4},
pmid = {41991911},
issn = {2041-1723},
support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.},
}

@article {pmid41992000,
year = {2026},
author = {Schneider, SM and Fan, C and Wang, Y and Jenq, RR and Watowich, SS},
title = {Microbiota and immune-related adverse events in cancer immunotherapy.},
journal = {Nature reviews. Cancer},
volume = {},
number = {},
pages = {},
pmid = {41992000},
issn = {1474-1768},
abstract = {In response to treatment with immune checkpoint inhibitors (ICIs), patients with cancer can develop immune-related adverse events (irAEs), which are off-target toxicities affecting non-tumour tissues. Development of an irAE can require cessation of ICI treatment and cause additional morbidities, unrelated to cancer. Although the mechanisms that drive irAEs remain largely unknown, thus limiting treatment strategies, emerging evidence implicates tissue microbiomes, particularly in the gastrointestinal tract, lung and skin, as potential mediators. Here we review evidence that supports roles for the microbiome in irAEs. We focus on ICI colitis, a common irAE that has strong association with the gut microbiome. We examine clinical and preclinical studies that shed light on the immune and microbial drivers of ICI colitis and discuss current experimental treatments. By summarizing recent findings, we aim to encourage research into therapies that reduce irAE risk and severity while preserving anti-tumour efficacy of ICI treatment.},
}

@article {pmid41992021,
year = {2026},
author = {Chioccioli, S and Meriggi, N and Monroy, MM and Renzi, S and Cerasuolo, B and Caderni, G and De Filippo, C},
title = {Combination of a pesco vegetarian diet with non-steroidal anti-inflammatory drugs reduces colorectal cancer risk and modulates gut microbiota in PIRC rats.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48074-5},
pmid = {41992021},
issn = {2045-2322},
abstract = {Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide, with genetic predispositions such as Familial Adenomatous Polyposis (FAP) contributing significantly to early-onset disease. This study investigated the synergic chemopreventive potential of two non-steroidal anti-inflammatory drugs (NSAIDs), acetylsalicylic acid (ASA) and sulindac (SU), in combination with a pesco-vegetarian diet (PVD), using Apc-mutated PIRC rats, a well-established model of CRC. Animals were treated over three months with two doses of ASA (800 and 1600 ppm) or a single low dose of SU (80 ppm), and tumour burden and gut microbiota composition were assessed. Results confirmed the robust protective effect of the PVD diet in reducing the intestinal tumorigenesis, particularly in the colon, independent of pharmacological treatment. ASA treatment, especially at the higher dose, significantly reduced tumour incidence in both dietary groups, with additive effects seen in combination with PVD, while SU did not show a significant protective effect. Microbiota analysis revealed distinct shifts in bacterial composition associated with both dietary and pharmacological interventions. Notably, taxa such as Roseburia and Colidextribacter, previously linked to intestinal homeostasis and anti-inflammatory activity, were modulated by ASA and diet, suggesting a microbiome-mediated chemoprevention although mechanistic effect still need to be understood. These findings underscore the independent and complementary roles of diet and pharmacological interventions in CRC prevention and highlight the gut microbiota as a promising target for future personalised preventive strategies.},
}

@article {pmid41992275,
year = {2026},
author = {Won, S and Hong, J and Kim, H and Lee, J and Ko, YC and Yang, B and Kim, SH and Koh, SS and Park, J and Guak, GO and Lee, GI and Choi, Y and Lee, SH and Kang, G and Cho, S and Kim, H},
title = {Mycobacterium tuberculosis infection disrupts gut and respiratory microbial communities and networks with incomplete restoration after two months of treatment.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00834-4},
pmid = {41992275},
issn = {1757-4749},
support = {2022-ER2004-01//Korea National Institute of Health/ ; },
}

@article {pmid41992364,
year = {2026},
author = {Cummins, C and Sutton, W and McLeod, T and Dallas, JW and Ghotbi, M and Vargas-Gastélum, L and Alexander, NR and Rurik, AJ and McGinnity, D and Reinsch, SD and Sandonato, P and Arbour, J and Freake, M and Ashley, A and Ternes, W and Culp, E and Spatafora, J and McPhail, K and Stajich, JE and Hardman, R and Walker, DM},
title = {Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis).},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41992364},
issn = {2524-4671},
support = {EF-2125067//National Science Foundation/ ; EF-2125066//National Science Foundation/ ; EF-2125065//National Science Foundation/ ; },
}

@article {pmid41794765,
year = {2026},
author = {Wu, G and Zhang, J and Yan, S and Liu, N and Chen, W and Wu, F and Wang, Z and Zhang, J and Yang, Y and Deng, Y and Qiu, X and Liu, J and Shi, L and Cui, X and Wan, R and Li, X and Han, Y and Yang, G},
title = {Circadian rhythms and microbiota: molecular crosstalk and its implications for health and disease.},
journal = {Biology direct},
volume = {21},
number = {1},
pages = {},
pmid = {41794765},
issn = {1745-6150},
abstract = {UNLABELLED: Circadian rhythms, evolutionarily conserved 24-hour oscillations, exert precise regulatory control over microbial communities across host niches including the gastrointestinal tract, oral cavity, urinary bladder, and skin. This bidirectional interplay is critical to host physiology: host circadian clocks shape the composition and functional rhythms of resident microbiota, while microbiota-derived signals reciprocally modulate circadian entrainment and tissue-specific rhythmicity. Circadian disruption from shift work, irregular feeding, light pollution, or sleep deprivation trigger microbial dysbiosis and circadian misalignment, contributing to metabolic diseases, gastrointestinal disorders, neuropsychiatric conditions, cardiovascular diseases, and dermatological or reproductive disorders. Mechanistically, this crosstalk is mediated by rhythmic hormonal secretion, microbial metabolites, epigenetic regulation, and immune signaling. Therapeutic strategies such as time-restricted feeding, probiotics, melatonin, and polyphenol-rich diets show promise in restoring temporal homeostasis. This review synthesizes current evidence on circadian-microbiota interplay, elucidates its roles in physiology and disease, and highlights translational opportunities for chrono-microbiome-based interventions to optimize host health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13062-026-00748-w.},
}

@article {pmid41929220,
year = {2026},
author = {Pedreros, MB and Irigoyen, MF and Simoes-Barbosa, A and Riestra, AM and de Miguel, N},
title = {Chemotaxis and selective interactions of Trichomonas vaginalis with the vaginal bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41929220},
issn = {2692-8205},
abstract = {Trichomonas vaginalis is an extracellular parasite that inhabits the human genital tract, yet little is known about how it senses and responds to the complex vaginal microbial ecosystem. Here, we show that T. vaginalis exhibits chemotactic behavior on semisolid surfaces, forming multicellular assemblies that coordinate collective migration. Parasite colonies display both positive and negative chemotactic responses, indicating the ability to detect and react to diffusible signals. Different parasite strains display marked mutual avoidance between neighboring colonies, highlighting specific recognition mechanisms. Furthermore, we show that T. vaginalis is strongly attracted to acidic environments, revealing a niche-adapted pH taxis. Given that vaginal bacteria critically shape local pH, we examined parasite responses to representative members of the vaginal microbiota. T. vaginalis exhibited preferential chemotactic migration toward Lactobacillus gasseri, a hallmark species of eubiotic community state types (CSTs), over Gardnerella vaginalis, which is associated with dysbiotic CST-IV communities, while showing no detectable attraction to Escherichia coli. This selective migration correlated with a robust chemotactic response to lactic acid, a major metabolite produced by lactobacilli. Additionally, when the parasite is co-cultured with the equal number of L. gasseri and G. vaginalis, T. vaginalis exhibits a clear preferential binding to L. gasseri, as demonstrated by flow cytometry and fluorescent microscopy. We show that co-culture of T. vaginalis with either L. gasseri or G. vaginalis results in enhanced parasite growth only in the presence of L. gasseri. Collectively, these findings reveal pH taxis; bacteria-directed migration and preferential association with Lactobacillus as previously underappreciated behavioral traits of T. vaginalis. Such behaviors may destabilize protective microbial communities and drive the transition toward a CST-IV-type dysbiotic state which is frequently associated with trichomoniasis.},
}

@article {pmid41979573,
year = {2026},
author = {Serrage, HJ and Farrar, MD and McBain, AJ and Pennock, J and O'Neill, C},
title = {Skin Staphylococcus species differentially modulate keratinocyte cytokine secretion in response to UVB.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0154925},
doi = {10.1128/aem.01549-25},
pmid = {41979573},
issn = {1098-5336},
abstract = {Skin acts as the body's first line of defense against environmental insults including ultraviolet radiation (UVR) from sunlight and engages in a dynamic dialog with the resident skin microbiota, increasingly recognized for its role in shaping and educating the immune responses of the skin in both health and disease. However, how or indeed if the resident skin microbiota mediates inflammatory responses to sunlight remains unclear. To address this, we investigated the effects of five abundant members of the skin microbiota on cytokine secretion in human primary keratinocytes exposed to a single dose of UVB. Co-culture of primary keratinocytes with a defined five-species skin commensal community resulted in a broad increase in the secretion of innate immune mediators including interleukin-6 (IL-6), independent of UVB exposure. In the absence of UVB, Staphylococcus epidermidis was the dominant species, followed by Staphylococcus hominis within the five-species community. UVB induced a marked shift in community composition, characterized by increased proliferation of S. hominis and reduced S. epidermidis abundance, as confirmed by species-specific growth curve analyses. Assessment of species-specific effects using mono-associated host cells revealed S. epidermidis as the predominant contributor to the enhancement of immune mediator secretion. Without the presence of additional community members, UVB amplified S. epidermidis-induced cytokine secretion. However, co-culture of S. epidermidis with S. hominis attenuated the heightened inflammatory response to UVB typically associated with S. epidermidis, likely due to the reduced abundance of S. epidermidis following UVB exposure. These findings suggest that the resident skin microbiota may contribute to our inflammatory response to sunlight.IMPORTANCEThis study reveals that the skin microbiome may play a role in shaping inflammatory responses to UVB exposure. It provides evidence of organisms capable of both amplifying and mitigating inflammatory responses to UVB, highlighting the importance of microbial composition in photoprotection. These findings suggest individual responses to sunlight may be influenced not only by skin type but also by specific microbes present on the skin.},
}

@article {pmid41979582,
year = {2026},
author = {Smółka, L and Strugała, M and Kursa, K and Pomianowski, B and Blady, K and Bratek, K},
title = {The impact of the gut microbiome on the development of atherosclerosis and peripheral arterial disease: A narrative review.},
journal = {Przeglad epidemiologiczny},
volume = {79},
number = {4},
pages = {580-594},
doi = {10.32394/pe/214773},
pmid = {41979582},
issn = {0033-2100},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology ; *Peripheral Arterial Disease/microbiology ; *Dysbiosis ; },
abstract = {Atherosclerosis is a chronic, progressive process affecting medium and large arteries, while peripheral artery disease (PAD) represents one of its clinical manifestations in the limb arteries. Although classical risk factors such as poor diet, hypertension, diabetes, and smoking are well established, increasing evidence indicates that the gut microbiome is an important and modifiable contributor to vascular pathophysiology. This paper reviews current knowledge on the role of the gut microbiome in the initiation and progression of atherosclerosis and PAD, with emphasis on bacterial metabolites, proinflammatory mechanisms, and potential therapeutic interventions. Gut dysbiosis-an imbalance in the intestinal microbial community-has been associated with increased cardiovascular risk. Patients with vascular diseases show higher levels of pro-atherogenic taxa, including Enterobacteriaceae, Streptococcus spp., Lachnoclostridium, and Family XI, alongside a reduction of beneficial short-chain fatty acid (SCFA)-producing bacteria such as Roseburia, Faecalibacterium, Coprococcus2, and Ruminococcaceae. Two key microbial metabolites influence vascular health. Trimethylamine N-oxide (TMAO), formed from choline and L-carnitine via microbial and hepatic metabolism, promotes endothelial dysfunction, inflammation, and platelet reactivity, thereby accelerating atherosclerosis. Conversely, SCFAs-acetate, propionate, and butyrate-exert anti-inflammatory effects, improve insulin sensitivity, and enhance nitric oxide synthesis, resulting in vascular protection. Therapeutic strategies targeting the gut microbiota show promising potential. These include the use of probiotics and prebiotics (notably Lactobacillus rhamnosus GG), adherence to a Mediterranean diet, and fecal microbiota transplantation (FMT), all aimed at restoring eubiosis and a favorable intestinal metabolic profile. In summary, the gut microbiome appears to be a key modulator of the pathogenesis of atherosclerosis and PAD. Targeted modulation of gut microbial composition and activity may emerge as an innovative and effective strategy for the prevention and treatment of cardiovascular diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Atherosclerosis/microbiology
*Peripheral Arterial Disease/microbiology
*Dysbiosis

@article {pmid41979594,
year = {2026},
author = {Ager, EO and Nickodem, CA and Brown, J and Jendza, J and Neeno-Eckwall, E and Schuldes, M and Dittoe, DK and Hite, JL},
title = {Diet-vaccine interactions: SQM Iron and Salmonella vaccination shape poultry gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0012726},
doi = {10.1128/aem.00127-26},
pmid = {41979594},
issn = {1098-5336},
abstract = {UNLABELLED: Vaccines to prevent Salmonella are rapidly gaining traction in the poultry industry. Yet how these interventions interact with other management strategies to influence the broader gut microbial community, rather than Salmonella per se, remains poorly understood. Understanding these effects is critical because shifts in the microbiome can alter nutrient metabolism, immune function, and pathogen dynamics in ways that could either enhance or suppress management strategies aimed at improving bird health and food safety. Here, we examine how a live-attenuated Salmonella vaccine (AviPro Megan Vac 1) and iron supplementation, two widely adapted management strategies, individually and jointly shape the cecal microbiome of broiler chickens. Specifically, we compare standard iron supplements (FeSO4) with a polysaccharide-complexed iron supplement (SQM Iron) which uses a complexation process that "hides" iron from Salmonella via time- and tissue-specific release of this critical nutrient. Using 16S rRNA gene sequencing, we found that while overall microbial diversity was unchanged, both interventions induced reproducible shifts in community composition, including enrichment of taxa linked to fermentation and short-chain fatty acid production. Vaccination alone promoted Bacillota genera associated with gut homeostasis, whereas iron supplementation altered competitive dynamics by reducing Streptococcus and favoring several rare taxa. Strikingly, combining these treatments suppressed several beneficial fermentative genera, and Staphylococcus was markedly increased, revealing nonadditive effects. These findings illuminate the potential of integrated strategies, combining immune stimulation with precision micronutrient supplementation, to improve poultry health and food safety. However, these results also underscore the intricate microbial trade-offs that must be carefully navigated to avoid unintended consequences in modern production systems.

IMPORTANCE: Globally, non-typhoidal Salmonella (NTS) is a persistent food safety challenge and pre-harvest control is an industry priority. While Salmonella vaccines are rapidly gaining adoption, their interactions with other common management practices such as nutritional strategies remain unclear. Iron metabolism is particularly important, as it influences host immunity, pathogen colonization, and shapes the gut microbiome. This study investigates how live-attenuated Salmonella vaccine (AviPro Megan Vac 1) and iron-based nutritional management interact to shape the cecal microbiota of broiler chickens. Specifically, we focus on SQM Iron, with a complexation process that enables time- and tissue-specific release of this critical nutrient. Our findings indicate that targeted combinations of immune stimulation and micronutrient supplementation can selectively remodel the poultry gut microbiome, with potential implications for nutrient utilization, microbial metabolism, and integrated, non-antibiotic approaches to reduce Salmonella burden while supporting flock health.},
}

@article {pmid41979614,
year = {2026},
author = {Ibrahim, MN},
title = {The Immune Cost: How Virtual Life Becomes a Modifiable Risk Factor for Immune Dysregulation.},
journal = {Clinical laboratory},
volume = {72},
number = {4},
pages = {},
doi = {10.7754/Clin.Lab.2025.250624},
pmid = {41979614},
issn = {1433-6510},
mesh = {Humans ; Risk Factors ; *Stress, Psychological/immunology ; Gastrointestinal Microbiome/immunology ; *Immune System/immunology ; },
abstract = {BACKGROUND: The emergence of technology-based lifestyles has led to what may be called "virtual isolation," as people spend more and more time in front of screens and less and less time in the world. Though the psychological consequences of this isolation are broadly appreciated, the biological impact of such isolation, especially on the immune system, has not been well-studied.

METHODS: This letter synthesizes interdisciplinary research in neuroendocrinology, psychoneuroimmunology, and microbiome science to explore the biological implications of digital isolation on immune system regulation.

RESULTS: Long-term digital immersion has been linked to higher levels of the stress hormone cortisol, disrupted sleep and reduced oxytocin signaling - all which disarray both innate and adaptive immune function. The lack of social bonding in the real world limits the sharing of microbes and gut microbiome diversity, making immune homeostasis even worse. Digital addiction is also associated with raised inflammatory indicators and increased sus-ceptibility to infections and immune dysregulation.

CONCLUSIONS: The virtual bubble is nice, psychologically, but carries an insidious and deepening challenge to the integrity of the immune system. Tackling digital over exposure is essential to restore immunological balance, particularly in a post-pandemic society prone to stress-driven immunosuppression.},
}

Humans
Risk Factors
*Stress, Psychological/immunology
Gastrointestinal Microbiome/immunology
*Immune System/immunology

@article {pmid41979934,
year = {2026},
author = {Mertz, L},
title = {Suite of Ingestible Devices Opens Window to the Gut Nervous System, Microbiome.},
journal = {IEEE pulse},
volume = {17},
number = {1},
pages = {26-32},
doi = {10.1109/MPULS.2026.3659238},
pmid = {41979934},
issn = {2154-2317},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Optogenetics ; Animals ; *Gastrointestinal Tract/innervation ; },
abstract = {Ingestible capsules reveal gut neural signaling and microbiome dynamics through sensing and optogenetics.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Optogenetics
Animals
*Gastrointestinal Tract/innervation

@article {pmid41980076,
year = {2026},
author = {Liu, J and Zhang, J and Hu, S and Jiang, M and Lin, X and He, P and Peng, C},
title = {Endogenous Mechanisms of Selenium-Induced Antagonism against Cadmium Toxicity in Crops: Integration and Reconstruction of a Multilevel Defense Network.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17688},
pmid = {41980076},
issn = {1520-5118},
abstract = {Selenium (Se) orchestrates a multilevel endogenous defense network in crops against cadmium (Cd) toxicity. This network operates from rhizosphere immobilization (e.g., Cd-Se complexes, microbiome interactions, iron plaque, and root exudates) and subcellular sequestration via transporter regulation (e.g., OsNramp5, OsHMA3) to antioxidant enhancement and selenoprotein activation. Critically, Se acts as a signaling initiator, engaging pathways (e.g., GATA3-COMT1-melatonin) to systemically reprogram stress responses. This review highlights that Se's antagonistic efficacy is form-, dose-, and genotype-dependent, providing a mechanistic basis for precision agronomic strategies. Future efforts must bridge laboratory findings to field applications by elucidating molecular switches and developing integrated predictive technologies.},
}

@article {pmid41980084,
year = {2026},
author = {Aragón, M and Spyridis, H and Mostard, P and Reichelt, M and Gershenzon, J and Dicke, M and Kloth, KJ},
title = {Jasmonic and Salicylic Acid Pathways Shape the Rhizosphere Microbiome, affecting Aphid Herbivory and Soil-Mediated Insect-Plant Interactions in a density-dependent manner.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcag048},
pmid = {41980084},
issn = {1471-9053},
abstract = {Aboveground induction of plant defense pathways can shape root-associated microbial communities. However, whether these changes are pathway-specific and how they affect plant growth and resistance remains unclear. We evaluated how induction of the Jasmonic Acid (JA) and Salicylic Acid (SA) defense pathways shapes the root microbiome of Brassica oleracea, and whether these soil-mediated shifts affect plant growth and resistance to herbivory in a subsequent generation using a plant-soil feedback (PSF) approach. In the conditioning phase, defense pathways were induced either through foliar application of methyl jasmonate (MeJA) and SA solutions, or through herbivory by caterpillars (JA) and aphids (SA). Both pathways led to distinct shifts in microbial communities, with bacterial and fungal composition varying by pathway identity and induction method. JA induction resulted in more differentially abundant ASVs than SA, particularly with Proteobacteria depletion. Conversely, Planctomycetota (bacteria) and Mortierellomycota (fungi) were enriched under both pathways, suggesting that these represent general stress-responsive groups. In the feedback phase, JA- and SA-conditioned soils had no effect on resistance under high aphid pressure, whereas under low aphid density, plants grown in SA-conditioned soil exhibited reduced phloem feeding and lower aphid population development. Together, our results indicate that benefits provided by the defense-shaped root microbiome depend on pest pressure intensity and arise from overall community shifts rather than specific taxa enrichment. Our findings underscore the complex interactions between plant-defense pathways, rhizosphere microbes, and herbivores.},
}

@article {pmid41980215,
year = {2026},
author = {Zhang, L and Dove, A and Du, J and Yang, D and Su, Q and Huang, X and Wang, J and Yue, J},
title = {The Lung-Brain Axis in Cognitive Impairment and Dementia: Mechanisms and Therapeutic Prospects.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0095},
pmid = {41980215},
issn = {2152-5250},
abstract = {The lung-brain axis has been recognized as a critical interface linking lung health to cognitive disorders, including cognitive impairment, Alzheimer's disease, and dementia. Epidemiological and clinical evidence shows a close association between compromised lung health-including chronic obstructive pulmonary disease (COPD), asthma, obstructive sleep apnea (OSA), and pulmonary infections-and cognitive impairment and dementia. Potential mechanisms include established factors (systemic inflammation and immune crosstalk, hypoxic injury, and air-pollutant-induced neurotoxicity) and exploratory mechanisms (lung microbiome dysregulation). Notably, lung-centric strategies targeting the lung-brain axis involve repurposing pulmonary medications, intervening in shared mechanisms, and employing non-pharmacological strategies. Furthermore, realizing this promise will require future randomized controlled trials (RCTs) to develop comprehensive management strategies and alleviate the global burden of cognitive impairment and dementia.},
}

@article {pmid41980217,
year = {2026},
author = {Yagi, M and Mizukoshi, R and Ito, K and Isogai, N and Funao, H and Fujita, R},
title = {Microbiome-Linked Metabolic Architecture of Accelerated Biological Aging in Humans.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0237},
pmid = {41980217},
issn = {2152-5250},
abstract = {Biological aging is a major determinant of frailty, functional decline, and vulnerability to age-related diseases; however, its upstream metabolic and inflammatory signatures remain incompletely understood. We investigated biological aging using an integrated multi-omics approach in a clinically enriched human cohort. In this prospective study, 120 patients with adult spinal deformity (ASD) and 480 age- and sex-matched healthy controls were included for comparison of PhenoAge. Within the ASD cohort, high-resolution plasma metabolomics and targeted proteomics were performed to characterize metabolic and inflammatory correlates of biological aging. A composite trimethylamine N-oxide (TMAO) Pathway Index (TPI) was constructed using standardized methylamine-related metabolites. Biological age was significantly elevated in ASD compared with matched controls. Within the ASD cohort, metabolomic profiling revealed enrichment of methylamine-related and glycation-associated metabolites among the strongest correlations of PhenoAge. The TPI showed a strong, age-independent, near-linear association with PhenoAge. In sensitivity analyses adjusted for age, sex, BMI, smoking status, and eGFR, this association remained significant (β = 2.92, 95% CI 0.74-5.10, p = 0.009). Targeted proteomic analyses showed that tumor necrosis factor-α was selectively associated with both PhenoAge and the TPI, whereas associations with interleukin-1β, interleukin-6, and adiponectin were limited. Higher PhenoAge was also associated with reduced physical performance, increased frailty, and impaired health-related quality of life. These findings support an exploratory, hypothesis-generating framework in which methylamine-related metabolism and chronic inflammatory signaling are associated with biological aging in ASD. Because of the cross-sectional design, these results should be interpreted as associative rather than causal.},
}

@article {pmid41980282,
year = {2026},
author = {Sun, W and Wang, Y and Bao, J and Tong, Z and Zhang, J and Huang, M and Chen, H},
title = {Environmental concentration of chlorantraniliprole induces dysbiosis of gut microbiota and metabolism in crayfish (Procambarus clarkii).},
journal = {Ecotoxicology and environmental safety},
volume = {316},
number = {},
pages = {120139},
doi = {10.1016/j.ecoenv.2026.120139},
pmid = {41980282},
issn = {1090-2414},
abstract = {The widespread application of chlorantraniliprole (CAP) in rice-crayfish co-culture systems poses a potential threat to the health of the non-target crustacean Procambarus clarkii. However, the sub-chronic effects of environmentally relevant concentrations of CAP on intestinal health remain poorly understood. In this study, we conducted a 14-day exposure experiment at two environmentally realistic CAP doses (0.05 and 0.5 mg/L) to investigate its effects using an integrated approach combining histopathology, biochemical assays, 16S rRNA gene sequencing, and untargeted metabolomics. Our results demonstrated that CAP exposure induced dose-dependent intestinal damage, ranging from villi degeneration to severe enterocyte dissolution and cytoplasmic vacuolation. This structural compromise was accompanied by significant CAP accumulation and oxidative stress, as evidenced by the suppression of antioxidant enzymes (SOD, CAT) and the depletion of GSH, along with increased lipid peroxidation (MDA). Furthermore, CAP exposure caused significant gut microbiota dysbiosis, characterized by an increased Firmicutes/Proteobacteria ratio, reduced alpha diversity, and taxon-specific, dose-dependent shifts in genus abundance. Metabolomic analysis revealed substantial reprogramming of the host-associated metabolome, with the high-dose group exhibiting a distinct profile and a stronger disruption in amino acid metabolism pathways. Crucially, Mantel test analysis revealed a dose-dependent intensification of the microbiota-metabolite correlation, indicating that the dysbiotic gut microbiome actively mediated the host's metabolic dysfunction under high-level CAP exposure. Our findings provide a comprehensive perspective on the intestinal toxicity of CAP in crayfish, highlighting the gut microbiome as a key mediator of pesticide-induced metabolic dysregulation.},
}

@article {pmid41980294,
year = {2026},
author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Glucose metabolism's impact on Blastocystis presence in the human gut.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106647},
doi = {10.1016/j.clnu.2026.106647},
pmid = {41980294},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.

METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.

RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.

CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.},
}

@article {pmid41980384,
year = {2026},
author = {Ye, W and Yan, Y and Dai, J and Wang, P and Jiang, H and Yao, W and Zheng, W},
title = {Subacute dimethylated monothioarsenate (DMMTA) exposure induces hepatotoxicity and disrupts the gut microbiota-bile acid-liver axis: A multi-omics study in mice.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142031},
doi = {10.1016/j.jhazmat.2026.142031},
pmid = {41980384},
issn = {1873-3336},
abstract = {Dimethylated monothioarsenate (DMMTA), an emerging thiolated organic arsenical frequently detected in rice, exhibits in vitro cytotoxicity comparable to trivalent inorganic arsenic. However, its in vivo hepatotoxicity and underlying mechanisms remain largely unknown. Here, a 28-day subacute DMMTA exposure study was conducted in C57BL/6 mice, integrating hepatic transcriptomics, targeted bile acid metabolomics and 16S rRNA microbiome profiling to elucidate DMMTA-induced perturbations along the gut-liver axis. Phenotypically, DMMTA induced an atypical hepatotoxicity characterized by paradoxical liver atrophy coexisting with severe steatosis, alongside inflammatory infiltration and a non-monotonic elevation of liver ALT activity. Mechanistically, DMMTA critically impaired hepatic detoxification and redox homeostasis, evidenced by the inhibited nuclear translocation of Nrf2 and the concerted suppression of downstream xenobiotic-metabolizing genes (e.g., Gsts, Ugts). Targeted metabolomics revealed a profound disruption of enterohepatic circulation, marked by a 29% reduction in the primary to secondary bile acid ratio and 6.0-fold increase in toxic accumulation of 6,7-diketo LCA. Concurrently, microbiome profiling identified a highly selective dysbiosis driven by the massive expansion of Negativibacillus (71.1-fold) and the depletion of Blautia (20.3-fold). Multi-omics integration (Procrustes, M[2] < 0.46, P < 0.05) robustly linked these microbiota shifts to the accumulation of hepatotoxic secondary bile acids. Collectively, this study challenges the traditional "low toxicity" paradigm of organic arsenicals and highlights the gut-liver axis as a central mediator of DMMTA hepatotoxicity, providing vital mechanistic evidence to refine environmental risk assessment for rice-based diets.},
}

@article {pmid41980702,
year = {2026},
author = {Chlebicz, M and Reese, TA},
title = {The Trouble with "Clean" Mice: How Infection History Alters Host Immune Responses.},
journal = {Annual review of virology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-virology-092623-094931},
pmid = {41980702},
issn = {2327-0578},
abstract = {Laboratory mice are widely used in biomedical research due to their low cost, genetic tractability, and ease of manipulation. To reduce experimental variability, they are typically housed under specific pathogen-free (SPF) conditions that limit microbial exposure. While this approach minimizes confounding infections, it also creates an immunological environment that differs markedly from that of humans, reducing the translational relevance of mouse immune studies. This limitation has driven the development of alternative models known as "dirty" or microbially experienced (ME) mice. Despite methodological differences, ME models demonstrate that lifelong microbial exposure profoundly shapes immune development. Although immune maturation in these mice is often attributed to microbiome changes, persistent exposure to endemic rodent viruses and other pathogens also may drive sustained immune activation. Here, we review the immune implications of the various ME models and highlight the critical role the virome plays in aligning mouse immune responses more closely with those of humans. Through harnessing microbial experience as a complementary tool to traditional SPF housing conditions and germ-free models, researchers can more faithfully model a mature, pathogen-shaped immune system.},
}

@article {pmid41980780,
year = {2026},
author = {Dai, DLY and Manus, MB and Hoskinson, C and Jiang, J and Sbihi, H and Miliku, K and Campisi, SC and Korczak, DJ and Duan, Q and Moraes, TJ and Mandhane, PJ and Finlay, BB and Simons, E and Lishman, H and Patrick, DM and Subbarao, P and Azad, MB and Chawes, B and Bønnelykke, K and Sørensen, SJ and Thorsen, J and Stokholm, J and Petersen, C and Turvey, SE},
title = {Breastfeeding may lessen socioeconomic disparities in child health through differences in the infant gut microbiome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102755},
doi = {10.1016/j.xcrm.2026.102755},
pmid = {41980780},
issn = {2666-3791},
abstract = {Lower familial socioeconomic status (SES) is linked to increased childhood disease risk. Since SES has no inherent biological basis, identifying how it becomes physiologically embedded is essential for equitable intervention. Using data from the Canadian CHILD birth cohort (n = 2,752) with replication in the Danish Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010) cohort (n = 681), we analyze modifiable pathways linking SES to child health and find that the infant gut microbiota plays a key mediating role. Breastfeeding is associated with a stabilized infant microbiota, buffering against environmental impacts and reducing health risks in lower SES contexts. The presence of Bifidobacterium infantis, enriched through breastfeeding, is linked to protection against adverse outcomes from SES. Together, these results suggest that improving breastfeeding rates and restoring breastfeeding-enriched microbes, like B. infantis, may help buffer early biological impacts of social inequality and support healthier trajectories for children growing up in industrialized settings.},
}

@article {pmid41980904,
year = {2026},
author = {Bebelman, S and Artuyants, A and Nijmeijer, B and Fitzgerald, S and Henry, C and Blenkiron, C},
title = {Evaluating Sequencing Strategies for Endometrial Microbiome Profiling in Endometrial Cancer: A Comparative Study of Short- and Long-Read 16S rRNA Approaches.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {9},
number = {4},
pages = {e70540},
pmid = {41980904},
issn = {2573-8348},
support = {//Cancer Research Trust New Zealand/ ; //Cancer Society of New Zealand/ ; //Maurice and Phyllis Paykel Trust/ ; },
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/pathology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; New Zealand ; *Endometrium/microbiology/pathology ; Middle Aged ; Pilot Projects ; *High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/isolation & purification ; *Bacteria/genetics/isolation & purification/classification ; Aged ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Endometrial cancer (EC) is the most common gynaecological malignancy globally, with rising incidence and notable disparities in outcomes. In New Zealand, EC rates have increased significantly, particularly among Māori and Pacific women, who face higher risks of advanced disease and poorer outcomes. Microbial dysbiosis has been implicated in EC pathogenesis, but characterising the uterine microbiome is challenging due to low microbial biomass and high contamination risk.

AIMS: This study aimed to pilot a protocol that could inform the preparation of a larger cohort trial. Short-read Illumina MiSeq and long-read Oxford Nanopore Technologies (ONT) 16S rRNA gene sequencing were investigated to profile the uterine microbiome in people with EC.

METHODS AND RESULTS: Uterine and vaginal swabs were analysed to assess platform performance in terms of DNA recovery, sequencing success, diversity metrics, and taxonomic resolution. The impact of sample freezing or immediate lysis prior to DNA extraction was also evaluated. ONT sequencing provided enhanced species-level resolution and improved detection of low-abundance taxa but showed variable performance in low-yield samples. Freezing prior to cell DNA extraction modestly increased bacterial 16S copy numbers and improved community consistency. Contamination was a problem across both platforms, particularly in low-biomass samples, but can be minimised during data analysis.

CONCLUSION: This study provides practical guidance for sequencing platform selection and sample handling in uterine microbiome research. Our findings support future efforts to elucidate microbial contributions to EC pathogenesis and highlight the importance of rigorous contamination control. Importantly, this is the first presentation of a New Zealand cohort and contributes valuable data from an underrepresented population and informs future research in diverse clinical settings.},
}

Humans
Female
*Endometrial Neoplasms/microbiology/pathology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
New Zealand
*Endometrium/microbiology/pathology
Middle Aged
Pilot Projects
*High-Throughput Nucleotide Sequencing/methods
DNA, Bacterial/genetics/isolation & purification
*Bacteria/genetics/isolation & purification/classification
Aged
Dysbiosis/microbiology

@article {pmid41980940,
year = {2026},
author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z},
title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00986-w},
pmid = {41980940},
issn = {2055-5008},
support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.},
}

@article {pmid41980958,
year = {2026},
author = {Kim, NH and Oh, J and Lee, JH and Lee, S and Jung, ES and Suh, DH and Kang, HJ and Kim, B and Kim, HS and Jung, HR and Kim, H and Yun, INR and Ji, Y and Cho, SY and Lee, SW},
title = {A colon mimetic screening approach reveals Lactobacillus fermentum as a microbiome-based therapy for COPD.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00978-w},
pmid = {41980958},
issn = {2055-5008},
support = {RS-2024-00439165//Korean Health Industry Development Institute/ ; RS-2023-NR077159//National Research Foundation of Korea/ ; 2024ER080601//National Institute of Health research project/ ; },
abstract = {Chronic obstructive pulmonary disease (COPD) remains a major health burden with few effective therapies, particularly for emphysema. The gut-lung axis and microbial metabolites, such as short-chain fatty acids (SCFAs), have emerged as modulators of lung inflammation. We investigated the therapeutic effects of Lactobacillus fermentum HEM20792 (LF), identified through a colon mimetic personalized pharmaceutical meta-analytical screening (PMAS) platform using fecal samples from severe COPD patients. LF and Lactobacillus sakei HEM20224 (LS) were orally administered to smoke-exposed mice, followed by lung function testing, histopathology, RNA sequencing, single-cell transcriptomics, and fecal microbiome/SCFAs analyses. LF attenuated emphysematous changes, improved compliance, and reduced macrophage and IL-17+ lymphocyte infiltration. Single-cell analysis showed restoration of alveolar macrophages and reduction of pathogenic C1q[+] macrophages, while transcriptomics revealed normalization of NF-κB and arachidonic acid pathways and attenuation of IL-17- and SPP1-associated signaling. LF also increased fecal SCFAs levels. These findings provide preclinical evidence for LF as a promising microbiome-based therapeutic candidate for COPD.},
}

@article {pmid41980965,
year = {2026},
author = {Arp, G and Levy, S and Jiang, AK and Dufault-Thompson, K and Zhong, A and Grant, M and Li, Y and Jiang, X and Hall, B},
title = {SpiR is a gut microbial enzyme that drives cholesterol conversion.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41980965},
issn = {2041-1723},
support = {R35-GM155208//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Cholesterol/metabolism ; Humans ; Phylogeny ; *Eubacterium/enzymology/genetics ; *Bacterial Proteins/metabolism/genetics ; Oxidation-Reduction ; },
abstract = {The gut microbiota contributes to cholesterol homeostasis by converting cholesterol into coprostanol, a non-absorbable sterol excreted in the feces. However, the enzymes mediating this process remain poorly defined. Here, we identify spiR, a steroid Δ[5-4] isomerase/3-keto reductase from Eubacterium coprostanoligenes that catalyzes the initial oxidation of cholesterol to cholestenone, a requisite step in coprostanol production. We confirm that SpiR oxidizes both cholesterol and pregnenolone, and stereospecifically reduces 3-keto-steroids to 3β-hydroxylated forms. We show that SpiR preferentially binds to cholesterol over related steroids and functions as an NAD(H)-dependent homodimer. Through phylogenetic analysis, we show that spiR clusters with known Δ[5-4] isomerases and is restricted to an uncultured clade within Acutalibacteraceae, where it frequently co-occurs with species encoding ismA, a gene previously implicated in cholesterol conversion. We analyze a multi-omic dataset from three human cohorts and find that spiR homologs were strongly enriched in individuals exhibiting cholesterol conversion. We also show that spiR homologs have a greater predictive power for cholesterol conversion than ismA homologs, establishing them as superior markers of microbial cholesterol metabolism. Our findings refine the enzymatic model of cholesterol metabolism in the gut and establish spiR as a critical biomarker and mechanistic driver for microbiome-mediated cholesterol reduction.},
}

*Gastrointestinal Microbiome/physiology
*Cholesterol/metabolism
Humans
Phylogeny
*Eubacterium/enzymology/genetics
*Bacterial Proteins/metabolism/genetics
Oxidation-Reduction

@article {pmid41981035,
year = {2026},
author = {Faber, Q and Baker, CCM and West, JR and Doherty, SJ and Ernakovich, JG and Barbato, RA},
title = {Antimicrobial resistance varies with warming in active layer soil and permafrost.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46295-2},
pmid = {41981035},
issn = {2045-2322},
support = {PE 0602144A Program "Defense Resiliency Platform Against Extreme Cold Weather"//United States Department of Defense/ ; },
}