@article {pmid41531549,
year = {2026},
author = {Barnea, ER and Nazareth, A and Purandare, CN and Pinheiro-Borovac, A and Carluccio, RD and Purandare, NC and McAuliffe, FM and , },
title = {Optimizing Maternal Microbiome: Role in Improved Conception and Pregnancy Outcome.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70014},
doi = {10.1002/rmb2.70014},
pmid = {41531549},
issn = {1445-5781},
abstract = {PURPOSE: To evaluate the role of optimizing the maternal microbiome in improving pregnancy outcomes, focusing on preconception and early gestation, and to propose practical diagnostic and preventive strategies, particularly in low- and middle-income countries (LMIC).

METHODS: A comprehensive review of peer-reviewed literature was conducted, analyzing the impact of vaginal, endometrial, gastrointestinal, urinary, and oral microbiomes on fertility and pregnancy. Key factors included microbial dysbiosis, sexually transmitted infections (STIs), and lifestyle interventions. Diagnostic approaches (cultures, gene sequencing) and preventive measures (nutrition, probiotics, vaccinations) were assessed for efficacy in optimizing the microbiome.

RESULTS: An optimized microbiome, particularly with Lactobacillus crispatus dominance, enhances fertility and reduces pregnancy complications like miscarriage, preterm birth, and congenital infections. Dysbiosis, linked to obesity, antibiotic overuse, and poor nutrition, increases STI susceptibility and pregnancy risks. Preconception screening and targeted treatments (e.g., antibiotics for STIs, probiotics) improve outcomes. Nutritional interventions, including Mediterranean diets and supplements, support microbial health. LMIC face challenges due to limited access to care and nutrition, exacerbating adverse outcomes to be addressed.

CONCLUSIONS: Preconception microbiome optimization through diagnostics, lifestyle changes, and targeted therapies significantly improves pregnancy outcomes. Simple, cost-effective measures are critical also in LMIC to prevent and reduce maternal and fetal morbidity and mortality.},
}

@article {pmid41531391,
year = {2026},
author = {Liang, J and Li, S and Dai, Y and Pi, Z and Liu, J and Li, P and Sun, W and Jiang, T and Xu, T and Yu, P},
title = {Integrating Transcriptomics and Gut Microbiota Analysis Reveals the Anti-Osteoporotic Mechanisms of Wine and Oil Co-Processed Epimedium.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {2},
pages = {e71319},
doi = {10.1096/fj.202501534RR},
pmid = {41531391},
issn = {1530-6860},
support = {20230204034YY//Jilin Provincial Scientific and Technological Development Program (Jilin Scientific and Technological Development Program)/ ; 2024128//Administration of Traditional Chinese Medicine of Jilin Province/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Epimedium/chemistry ; Female ; *Osteoporosis/drug therapy/metabolism/microbiology ; *Transcriptome/drug effects ; Ovariectomy ; *Wine ; *Drugs, Chinese Herbal/pharmacology ; STAT3 Transcription Factor/metabolism ; Mice, Inbred C57BL ; Gene Expression Profiling ; },
abstract = {Wine- and suet oil co-processed Epimedium (WSOEP) is a traditional Chinese herbal preparation produced by processing raw Epimedium with wine and suet oil as adjuvants. Although WSOEP has been used clinically for the treatment of osteoporosis, its precise therapeutic indications and underlying molecular mechanisms remain incompletely defined. This study integrates transcriptomic profiling with gut microbiota analysis to systematically elucidate the anti-osteoporotic efficacy of WSOEP and its mechanistic basis. In a mice model of osteoporosis induced by bilateral ovariectomy (OVX), WSOEP administration significantly attenuated bone loss and improved multiple key bone parameters compared to the Mod group. Mechanistically, WSOEP treatment markedly downregulated SRC protein expression while simultaneously upregulating both total STAT3 and p-STAT3, indicating restoration of the dysregulated SRC/STAT3 signaling axis. Furthermore, WSOEP effectively modulated gut microbial homeostasis by enriching beneficial taxa, including Bacilli, Verrucomicrobiae, and Bacteroidales, while suppressing potentially detrimental lineages such as Proteobacteria, Clostridia, and Akkermansia. This is the first study to demonstrate that WSOEP exerts robust protective effects against OVX-induced osteoporosis through dual modulation of the SRC/STAT3 pathway and the gut microbiome. These findings not only position WSOEP as a promising candidate for osteoporosis therapy but also offer a novel paradigm for multi-component herbal interventions targeting the gut-bone axis in metabolic bone diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Epimedium/chemistry
Female
*Osteoporosis/drug therapy/metabolism/microbiology
*Transcriptome/drug effects
Ovariectomy
*Wine
*Drugs, Chinese Herbal/pharmacology
STAT3 Transcription Factor/metabolism
Mice, Inbred C57BL
Gene Expression Profiling

@article {pmid41531341,
year = {2026},
author = {Mellor, D and McArdle, P and Spiro, A and Stanner, S and Marsland, N and Kudzin, S and Twenefour, D},
title = {Summary of the Development of a Joint Position Statement on Low and No-Calorie Sweeteners (LNCS) From the British Dietetic Association (BDA), British Nutrition Foundation (BNF) and Diabetes UK.},
journal = {Nutrition bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1111/nbu.70044},
pmid = {41531341},
issn = {1467-3010},
abstract = {Low and no-sugar sweeteners (LCNS) are used in the food supply, notably within the beverage industry in many countries, where sugar reduction is a key public health concern. In the UK, following the announcement and implementation of the Soft Drinks Industry Levy (SDIL), nearly 9 out of 10 soft drinks contain < 5 g sugar per 100 mL, most of which now contain LNCS. In 2023, the World Health Organisation (WHO) issued a guideline with a conditional recommendation advising that LNCS should not be used as 'a means of achieving weight control or reducing the risk of non-communicable disease' (NCDs). This recommendation potentially conflicted with existing recommendations from several authoritative sources at the time, including the Diabetes UK position statement published in 2018 (developed in collaboration with the British Dietetic Association, BDA and the British Nutrition Foundation, BNF), as well as information on the NHS website, which suggests that LCNS can be helpful in reducing sugar intake. More recently, a working group comprising the BDA, BNF and Diabetes UK produced an updated insight document. This review included a re-evaluation of the WHO's systematic review and meta-analysis, alongside the Scientific Advisory Committee on Nutrition (SACN) statement on the guideline. The narrative review outlines the relationship between LNCS and a range of public health outcomes, including weight management, dental health, cardiovascular disease, type 2 diabetes (T2D), cancer and related risk markers such as appetite and gut microbiome composition. The insights document also considered the safety of LNCS and their impact on overall dietary quality. The insight document informed a subsequent joint position statement from the three organisations, highlighting research gaps and providing practical guidance for healthcare professionals to support individuals living with obesity and diabetes in reducing sugar intake. It also includes recommendations for policymakers and identifies actions for the food industry. The Position Statement emphasises that, while LNCS may not directly promote weight loss or reduce disease risk, they can serve as a useful tool for reducing sugar intake at both individual and population levels, at least acting as a 'stepping stone' from sugar-sweetened foods and unsweetened food and beverages.},
}

@article {pmid41530974,
year = {2026},
author = {Xu, XY and Wang, CL and Xu, JY and Dong, CJ and Tan, C and He, YX and Hu, HW and Shu, K and Dai, CC and Chen, ZH and Sun, K},
title = {Seed-microbiome interactions: Mechanistic insights and utilization toward seed performance for sustainable agriculture.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101716},
doi = {10.1016/j.xplc.2026.101716},
pmid = {41530974},
issn = {2590-3462},
abstract = {Global climate change poses increasing threats to seed production and thus food security. The seed microbiome plays an essential role in regulating the whole seed life cycle. Specific seed endophytes and spermosphere microorganisms orchestrate the maintenance and termination of dormancy towards the synchronization of germination plasticity to meet agricultural demands. In this review, we summarize recent advances by linking seed-microbiome interactions with seed processes. We review the sources of seed microbiomes and their physiological regulation on dormancy and germination in response to environmental changes with a focus on phytohormone crosstalk. We also discuss the molecular mechanisms by which seed-microbe interactions affect seed destiny. Finally, we explore emerging precision applications of microbiomes in the seed industry by integrating cutting-edge technologies such as microbial seed coatings and artificial intelligence (AI) in seed science and technology. In conclusion, harnessing microbiome-based strategies to manipulate seed life cycle holds immense promise for sustainable food production in a changing global climate.},
}

@article {pmid41530889,
year = {2026},
author = {Bonacolta, AM and Keeling, PJ},
title = {Modern microbialites harbor an undescribed diversity of chromerid algae.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00852-4},
pmid = {41530889},
issn = {2524-6372},
support = {GBMF9201//Gordon and Betty Moore Foundation/ ; },
abstract = {BACKGROUND: Chromerid algae are the closest photosynthetic relatives of apicomplexan parasites. While chromerids have been central to understanding the evolutionary transition from free-living algae to parasitism within Apicomplexa, their ecology remains poorly understood. Although often considered coral-associated symbionts, emerging evidence suggests this link is incidental and that chromerids may be more broadly associated with calcium carbonate environments, including microbialites. These microbial structures represent modern analogues of ancient reef-like ecosystems but are difficult to study due to their rarity and protected status as world heritage sites. Prokaryotic members of the microbialite microbiome have been studied at length, while the microeukaryotes associated with these environments have gone mostly ignored. To further investigate the link between microbialites and chromerid algae, we re-analyzed previously published microbialite sequencing data with the aim of investigating chromerid diversity and distribution.

RESULTS: Through a novel plastid-focused metagenomic binning workflow combined with re-analysis of rRNA metabarcoding data, we reveal that chromerid algae are consistent associates of microbialites across diverse marine and freshwater environments worldwide. Most notably, we report the first recovery of plastid genomes from microbialite-associated chromerids: a complete Vitrella brassicaformis plastid genome and a second, partial plastid genome from a previously undescribed Chromera-related lineage in Highborne Cay thrombolites. This partial plastid genome contained photosystem genes, confirming this novel Chromera-related lineage as a photosynthetic chromerid. These findings not only expand the known ecological and biogeographic range of chromerids but also provide evidence for their overlooked diversity.

CONCLUSIONS: Our analyses prove that this overlooked algal lineage is not found exclusively associated with corals, but instead occurs across a wide range of microbialite habitats, including those found in freshwater. By extending their known distribution beyond coral hosts and the marine environment, our results not only highlight the diversity and ecological range of the most recently discovered algal lineage but also broaden our understanding of the ancestral lifestyles that may have preceded apicomplexan evolution. This research underscores the value of targeted mining of public sequencing datasets to address specific ecological questions, particularly in rare or hard-to-access environments such as microbialites.},
}

@article {pmid41530845,
year = {2026},
author = {Liu, CM and Erikstrup, LT and Edslev, SM and Park, DE and Salazar, JE and Aziz, M and Rendboe, AK and Pham, T and Dinh, KM and Roach, K and Onos, A and Sung, E and Weber, NO and Andersen, PS and Ullum, H and Skov, R and Hungate, BA and Stegger, M and Erikstrup, C and Price, LB},
title = {Composition and dynamics of the adult nasal microbiome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02250-3},
pmid = {41530845},
issn = {2049-2618},
abstract = {BACKGROUND: The nasal microbiome, a dynamic assemblage of commensals and opportunistic pathogens, is crucial to human health.

RESULTS: Using cross-sectional data from 1,608 adults and longitudinal sampling of 149 individuals over 8-22 months, we identified nine nasal community state types (CSTs), defined by bacterial density and indicator taxa, with varying stability and transition patterns. Core taxa such as Staphylococcus epidermidis and Cutibacterium acnes were highly stable, while opportunistic pathogens like Staphylococcus aureus and Moraxella catarrhalis had shorter residence times. Interactions between Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum/propinquum were linked to reduced S. aureus colonization. Host factors, including age and biological sex, significantly shaped microbiome dynamics: men exhibited higher bacterial densities and pathogen colonization, while women showed more stable commensal-dominated CSTs. Aging was associated with shifts in CST frequencies, with declining S. aureus and increasing Enterobacterales.

CONCLUSIONS: These findings reveal potential strategies by modulating nasal microbiome dynamics to reduce pathogen colonization and improve health. Video Abstract.},
}

@article {pmid41530829,
year = {2026},
author = {Yan, D and Yu, Y and Liang, C and Cui, Z and Shi, L and Li, G and Ren, C},
title = {Intratumoral microbiome: the double-edged sword in remodeling cancer immunotherapy.},
journal = {Molecular cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12943-025-02566-6},
pmid = {41530829},
issn = {1476-4598},
support = {82172345//National Natural Science Foundation of China/ ; BK20221281//Natural Science Foundation of Jiangsu Province/ ; SBJC22003//Crosscooperation project of Subei Peoples' Hospital of Jiangsu Province/ ; },
abstract = {Emerging evidence reveals that intratumoral microbial (ITM) communities within the tumor immune microenvironment (TIME) critically influence tumor progression and immunotherapy response. Studies have shown that resident bacteria within tumors, such as Sphingobacterium multivorum, regulate the secretion of chemokines like CCL20 and CXCL8, promoting the infiltration of regulatory T cells (Tregs) and inhibiting the function of cytotoxic T cells (CD8[+] T cells)-thereby weakening the efficacy of immune checkpoint inhibitors. Additionally, microbial metabolites may serve as potential biomarkers for predicting sensitivity to immunotherapy. Concurrently, engineered bacteria (e.g., oncolytic mineralizing bacteria) demonstrate significant antitumor effects by activating innate immunity and enhancing antitumor-specific immune responses, providing new strategies to overcome immunotherapy resistance. These findings highlight the dual role of ITM in tumor immune evasion and immunotherapy sensitivity, laying an important theoretical foundation for developing novel immunotherapy strategies targeting tumoral microbiota metabolism.},
}

@article {pmid41530817,
year = {2026},
author = {Li, R and Liao, X and Fu, X and Li, X and Liao, X and Cen, S and Zeng, J and Huang, L and Chi, H and Zou, Y},
title = {Microbiota-driven tryptophan metabolism and AhR triggered intestinal stem cell differentiation: mechanisms of huangqin decoction in ulcerative colitis repair.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {33},
pmid = {41530817},
issn = {1749-8546},
support = {2022A1515140011//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A1515010012//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 20231800936162//Dongguan Science and Technology of Social Development Program/ ; 20221800905632//Dongguan Science and Technology of Social Development Program/ ; },
abstract = {BACKGROUND: Promoting intestinal barrier repair and epithelial regeneration is a core therapeutic objective in managing ulcerative colitis (UC). Intestinal stem cell (ISC) differentiation is pivotal in sustaining epithelial renewal and mucosal homeostasis. Huangqin decoction (HQD), a classical herbal formulation comprising Scutellaria baicalensis, Ziziphus jujuba, Paeonia lactiflora, and Glycyrrhiza uralensis, is clinically used for inflammatory bowel disease. Nevertheless, how HQD precisely regulates ISC differentiation to promote UC repair remains unclear.

PURPOSE: This research sought to assess whether HQD ameliorates UC by concurrently modulating the gut microbiome, tryptophan metabolism, aryl hydrocarbon receptor (AhR) activation, and ISC differentiation.

METHODS: Mice developed colitis after drinking water with a 3.5% (w/v) concentration of dextran sulfate sodium. We evaluated HQD effects on colon length, weight trajectory, disease activity index score, histological damage, and colonic inflammatory mediator abundance. Metagenomic sequencing resolved microbiota restructuring, while UPLC-MS/MS quantified fecal tryptophan metabolites such as indole derivatives. AhR pathway activity (AhR, CYP1A1), its downstream cytokine IL-22, and ISC fate were mapped by combining immunofluorescence, ELISA, Western blot, and RT-qPCR, probing Lgr5 for stem-cell identity and MUC2, LYZ, and ChgA for lineage-specific differentiation. The involvement of AhR and gut microbiota was investigated using AhR inhibitors and broad-spectrum antibiotics.

RESULTS: High-dose HQD significantly alleviated colitis symptoms, reduced colon damage, and corrected gut dysbiosis. HQD increased the abundance of related bacteria that elevated colonic levels of indole-3-propionic acid, indole-3-acetamide, and tryptamine, acting as AhR ligands that upregulate AhR and its downstream targets CYP1A1 and IL-22. Crucially, HQD promoted a shift in expression from the ISC marker Lgr5 toward differentiation markers MUC2, LYZ, and ChgA, indicating enhanced ISC differentiation and improved barrier function. These effects were effectively blocked by AhR inhibition or antibiotic treatment.

CONCLUSION: HQD restores intestinal mucosal integrity and attenuates colonic inflammation by modulating gut microbiota composition, increasing microbial tryptophan metabolites with AhR-agonist activity, activating the AhR signaling pathway, and promoting ISC differentiation into functional epithelial cells. This work reveals a novel "microbiota-tryptophan metabolism-AhR-ISC differentiation" axis underlying HQD's therapeutic efficacy in UC.},
}

@article {pmid41530663,
year = {2026},
author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX},
title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {40},
pmid = {41530663},
issn = {1471-2164},
support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
}

@article {pmid41530658,
year = {2026},
author = {Kaloterakis, N and Braun-Kiewnick, A and Rashtbari, M and Giongo, A and Babin, D and Zamberlan, PM and Razavi, BS and Smalla, K and Reichel, R and Brüggemann, N},
title = {Bacillus seed coating mitigates early growth reduction in successive winter wheat without altering rhizosphere bacterial and archaeal communities.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08128-2},
pmid = {41530658},
issn = {1471-2229},
abstract = {The soil legacy of successively grown winter wheat (WW) often leads to lower plant growth and yield. In this study, we assessed the effect of Bacillus pumilus seed inoculation on the early growth of successively grown WW. We conducted an outdoor experiment using newly designed temperature-regulated rhizotrons. WW was grown in soil from two rotational positions, i.e., first WW after oilseed rape (W1) and second WW after oilseed rape (W2), until the end of tillering. We measured several plant and soil biochemical parameters. In addition, amplicons of the 16S rRNA gene were sequenced to account for bacterial and archaeal community shifts in the rhizosphere, and functional genes involved in the nitrogen cycle were quantified to estimate possible changes in N cycling due to B. pumilus inoculation. B. pumilus seed coating significantly compensated for the early growth reduction of W2, and this effect was primarily linked to changes in root plasticity with a higher root length density and a smaller specific root length in inoculated W2 compared with non-inoculated W2. There was a higher LAP activity in the rhizosphere of inoculated W2 plants than in the rhizosphere of non-inoculated W2 plants and this was followed by a reduction in soil NO3[-], most probably due to an enhanced plant N uptake capacity. This was also shown in the increased potassium content of the inoculated W2 plants compared with their non-inoculated counterparts. B. pumilus seed coating did not influence the bacterial and archaeal alpha and beta diversity, but differential abundance analysis identified differences in the relative abundance of certain taxa between non-inoculated and inoculated W2. While B. pumilus seed coating significantly improved root growth and nutrient uptake in W2, this was not accompanied by a higher absolute abundance of bacterial or archaeal genes involved in N-cycling. Our study suggests that certain plant-beneficial microbes can reverse the negative plant-soil feedback in successive WW rotations and provides strong evidence of B. pumilus seed coating to promote WW productivity under such rotations.},
}

@article {pmid41530607,
year = {2026},
author = {Miller, CB and Bader, GA and Kay, CL},
title = {Fecal Microbiota Transplantation in 2025: Two Steps Forward, One Step Back.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {5},
pmid = {41530607},
issn = {1534-312X},
mesh = {*Fecal Microbiota Transplantation/trends/methods ; Humans ; *Irritable Bowel Syndrome/therapy ; *Clostridium Infections/therapy ; *Inflammatory Bowel Diseases/therapy ; },
abstract = {PURPOSE OF REVIEW: This review summarizes the history and current landscape of fecal microbiota transplantation (FMT), with an emphasis on use of the therapy for Clostridioides difficile infection (CDI), inflammatory bowel disease (IBD), and irritable bowel syndrome (IBS). We clarify indications, evidence, and current recommendations for FMT-highlighting major advances and minor setbacks that have led to the state of FMT in 2025.

RECENT FINDINGS: After decades of steady progress, the U.S. Food and Drug Administration (FDA) approved the first FMT-based therapies: fecal microbiota, live-jslm and fecal microbiota spores, live-brpk-in 2022 and 2023, respectively. The 2024 American Gastroenterological Association (AGA) Practice Guideline on Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases made specific recommendations for conventional FMT and these FDA-approved therapies for multiple CDI presentations, as well as for IBD and IBS. Conventional FMT remains an option for CDI; however, OpenBiome's halt of shipped, frozen FMT preparations on December 31, 2024, has made access more challenging in 2025. Although first reported almost seventy years ago, extensive efforts over the last two decades have placed FMT in routine algorithms for many patients with CDI. While understanding of the intestinal microbiome's role in other gastrointestinal conditions is expanding, and FMT may modulate these pathways, additional evidence is needed before FMT becomes routine outside CDI.},
}

*Fecal Microbiota Transplantation/trends/methods
Humans
*Irritable Bowel Syndrome/therapy
*Clostridium Infections/therapy
*Inflammatory Bowel Diseases/therapy

@article {pmid41530574,
year = {2026},
author = {Deng, YH and Liu, Q and Luo, XQ},
title = {The gut-kidney axis in pediatric acute kidney injury: a review of pathophysiological mechanisms and therapeutic frontiers.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {41530574},
issn = {1432-198X},
support = {2024JJ6595//Natural Science Foundation of Hunan Province/ ; },
abstract = {Acute kidney injury (AKI) is a frequent and severe condition in hospitalized children, leading to significant morbidity, mortality, and long-term risk of chronic kidney disease. This review explores the gut-kidney axis, a concept describing the bidirectional relationship between the gut microbiome and kidney function, as a critical driver of pediatric AKI. In critically ill children, interventions such as broad-spectrum antibiotics and necessary nutritional support strategies (e.g., parenteral nutrition or fasting) can cause profound gut microbial imbalance (dysbiosis). This dysbiosis initiates a deleterious feedback loop, exacerbating kidney injury. Key mechanisms include the disruption of the intestinal barrier (leaky gut), which allows bacterial endotoxins to enter the bloodstream, triggering renal inflammation via Toll-like receptor 4 signaling. Concurrently, the dysbiotic gut increases production of directly nephrotoxic gut-derived uremic toxins, such as indoxyl sulfate and p-cresyl sulfate, while failing to produce protective anti-inflammatory metabolites like short-chain fatty acids. While therapies targeting the microbiome, such as probiotics, prebiotics, and fecal microbiota transplantation, are theoretically promising, their clinical use in pediatric AKI is unsupported by evidence and carries substantial risks, particularly iatrogenic infection. A significant knowledge gap exists due to a relative lack of pediatric-specific clinical research. The conclusion emphasizes an urgent need for longitudinal, multi-omics studies in children to understand this axis, identify functional biomarkers, and develop safe, targeted therapies to improve outcomes.},
}

@article {pmid41530533,
year = {2026},
author = {Ning, J and Zhao, Y and Lu, G and Wei, L},
title = {Melatonin Alleviated Cadmium Induced Microbiota-Gut-Brain Disorder in Adult Zebrafish: Insights from Transcriptomic and Microbiome Analysis.},
journal = {Biological trace element research},
volume = {},
number = {},
pages = {},
pmid = {41530533},
issn = {1559-0720},
support = {KYQD(ZR)21138//Scientific Research Start-up Fund of Hainan University/ ; },
abstract = {Cadmium (Cd), a toxic metal, poses significant threats to ecological and human health due to its neurotoxic and gut toxicity effects. However, the mechanisms by which Cd disrupts brain-gut axis interactions remain unclear, and strategies to mitigate these effects are limited. Melatonin (MT), known for its anti-inflammatory and antioxidant properties, has shown promise in counteracting heavy metal toxicity. This study investigated the protective mechanisms of MT against Cd-induced toxicity in adult zebrafish using histopathological analysis, 16 S rRNA sequencing, RNA-sequencing, and qRT-PCR. Results showed that MT significantly alleviated Cd-induced structural damage in brain spongiosa and restored intestinal villi integrity. 16 S rRNA sequencing revealed that MT reduced pathogenic bacteria and increased beneficial bacteria in the gut microbiota. Transcriptomic analysis identified 31 differentially expressed genes (DEGs) in brain, KEGG enrichment analysis showed these DEGs are associated with neurodegenerative diseases pathways. Concurrently, 8 DEGs in gut were linked to oxidative phosphorylation signaling pathways. Correlation analysis showed pathogenic Legionella and Aeromonas were positively correlated with htr2b, il21r.2, il2rb, il21r.2, cyp46a1.3 cyp2ad3, cyp46a1.3 in brain, Candidatus_Protochlamydia was positively correlated with il7r, drd3 in gut, those are down regulated DEGs, whereas beneficial Acinetobacter and Achromobacter were positively correlated with cyp2 × 8 in gut, this is up regulated DEG. These suggests that Legionella, Candidatus_Protochlamydia, Achromobacter and Acinetobacter may be key bacterial that mediate the MT reduction in neurotoxicity and immunotoxicity induced by Cd. These findings highlight MT's potential to mitigate Cd-induced toxicity by modulating the gut microbiota, offering therapeutic insights for reducing Cd toxicity risks in aquaculture.},
}

@article {pmid41530470,
year = {2026},
author = {El-Sayed, ASA and Mohamed, NZ and Safan, S and Yassin, MA and Shaban, L and Shindia, AA and Shad Ali, G and Sitohy, MZ},
title = {Retraction Note: Restoring the Taxol biosynthetic machinery of Aspergillus terreus by Podocarpus gracilior Pilger microbiome, with retrieving the ribosome biogenesis proteins of WD40 superfamily.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1752},
doi = {10.1038/s41598-026-35501-w},
pmid = {41530470},
issn = {2045-2322},
}

@article {pmid41530275,
year = {2026},
author = {Wöber, D and Wernicke, M and Cerqueira, F and Wechselberger, K and Hansel-Hohl, K and Manhalter, S and Molin, EM},
title = {Intestinal microbiome interactions influence Metarhizium-based biocontrol efficacy against the sugar beet weevil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36038-8},
pmid = {41530275},
issn = {2045-2322},
abstract = {The sugar beet weevil is considered one of the most economically important insect pests in sugar beet cultivation. A promising biological control strategy involves the natural interaction between entomopathogenic fungi and arthropods. The successful application of M. brunneum as part of integrated biological control strategies against the sugar beet weevil has already been demonstrated resulting in lethal mycosis. However, the efficacy of this strain is affected by multiple factors. The intestinal microbiome of insects harbours beneficial microbes that possess various functions, such as defence mechanisms against insect-pathogens. Thus, investigating intestinal microbial interactions in combination with Metarhizium-application could reveal microbes that modulate susceptibility to pathogens. This study investigated whether intestinal microbial interactions influence mycosis caused by M. brunneum and M. robertsii. We analysed the intestinal microbiome of both treated and untreated sugar beet weevils, distinguishing between mycotic and non-mycotic individuals at the time of death. Notably, Pantoea and Enterobacter were significantly associated with mycotic individuals and may act as a potential antagonist to Metarhizium. In contrast, healthy individuals harboured diverse microbial communities that may provide a protective barrier against entomopathogens. However, the intestinal microbiome of non-mycotic specimens also comprised genera with presumed insecticidal properties, including Serratia, Penicillium and Cladosporium. The last two were also observed in the intestines of male individuals, which were generally at a higher risk of mortality. Further investigation is needed to confirm their insecticidal potential in the sugar beet weevil. A combined application could improve the efficacy of Metarhizium-based biocontrol, contributing to more sustainable pest management strategies.},
}

@article {pmid41530269,
year = {2026},
author = {Ludyga, S and Pedrini, L and Sarbach, L and Topyürek, B and Köhler, H and Furlano, R and Légeret, C},
title = {A comparative study of cognitive function among children with coeliac disease and healthy controls.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34500-7},
pmid = {41530269},
issn = {2045-2322},
abstract = {Coeliac disease (CD) is an immune-mediated systemic disorder triggered by gluten in genetically predisposed patients. The only available treatment is a strict life long gluten-free diet (GFD), which has been linked to a reduced quality of life (QOL) and causes alterations in the gastrointestinal microbiome. Abnormal compositions of the microbiome are now recognized as factors in the pathogenesis of neuropsychological disorders via gut-brain-axis. The aim of this study was to assess the QOL and the mental performance of children and teenagers with CD and compare it to healthy controls (HC). Children between the ages of 6 and 18 years with CD and age-and-sex-matched healthy controls (HC) filled in a questionnaire to assess QOL and performed the Flanker task, a standardized test to assess cognitive performance. A total of 444 children (210 CD patients and 234 HC) were included in the study. CD patients reported feeling statistically significantly more comfortable at school (p = 0.02) and being less exposed to bullying (p = 0.01); otherwise, no difference in QOL and sleep pattern was found compared to HC. The analysis of Flanker task revealed no difference in accuracy (HC: mean 0.97, CI 0.96-0.97; CD patients: mean 0.96, CI 0.96-0.97; p = 0.79), but there was a difference in reaction time (HC: mean 495.4 ms, CI 476.34-514.46; CD patients: mean 514.03, CI 493.68-534.39; p = 0.19). Children with CD in Switzerland have the same QOL as HC. There was a statistically non-significant difference in reaction time, therefore this study suggests that a GFD is not associated with impaired cognitive function.},
}

@article {pmid41530203,
year = {2026},
author = {Huang, X and Xu, B and Lei, Y and Qin, H and Zheng, J and Xu, Y and Zhao, D and Su, J and Li, J and Zhao, J},
title = {Bacillus velezensis mitigates deoxynivalenol-induced intestinal inflammation and liver injury via modulating the gut microbiota.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00707-9},
pmid = {41530203},
issn = {2396-8370},
abstract = {Deoxynivalenol (DON), a prevalent mycotoxin in food and feed, induces gastrointestinal and liver damage. The potential probiotic Bacillus velezensis may mitigate DON toxicity, though its precise mechanisms remain unknown. Our study demonstrates that B. velezensis WMCC10514 effectively survives and degrades DON within simulated gastrointestinal fluid. Fluorescently labeled WMC10514-GFP colonized murine intestines and persisted in simulated intestinal fluid (SIF), confirming its colonization capacity. In vivo, WMCC10514 alleviated DON-induced anorexia, restored murine growth, and reduced liver injury. Furthermore, the strain elevated ZO-1 and Occludin expression, enhanced intestinal barrier integrity and reduced DON accumulation in host tissues. Integrated transcriptomic and microbiome analyses revealed that the strain suppressed TLR4/NF-κB pathway activation in the intestine and liver, increased Lactobacillus abundance, restored SCFAs level, and modulated liver energy metabolism. These findings elucidate B. velezensis's role in mitigating mycotoxin toxicity through gut microbiota-driven regulation of the gut-liver axis.},
}

@article {pmid41530166,
year = {2026},
author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG},
title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68255-6},
pmid = {41530166},
issn = {2041-1723},
support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.},
}

@article {pmid41530018,
year = {2026},
author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW},
title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.12.011},
pmid = {41530018},
issn = {1873-5010},
abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.

METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).

RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.

CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.},
}

@article {pmid41530012,
year = {2026},
author = {Lechien, JR},
title = {Emerging Microbiome Findings in Laryngopharyngeal Reflux Disease: A Scoping Review.},
journal = {Journal of voice : official journal of the Voice Foundation},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jvoice.2025.12.023},
pmid = {41530012},
issn = {1873-4588},
abstract = {OBJECTIVE: To review the current literature linking laryngopharyngeal reflux disease (LPRD) with microbiome impairments.

METHODS: Two independent investigators conducted a systematic literature search for studies reporting microbiome findings in LPRD patients through PubMed, Scopus, and Cochrane Library databases. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and the Population, Intervention, Comparison, Outcome, Timing, and Setting (PICOTS) framework were followed. A methodological bias analysis was conducted with the Tool to Assess the Risk of Bias in Cohort Studies.

RESULTS: Of the 585 identified papers, eight studies met the inclusion criteria, including 245 patients with suspected or confirmed LPRD. Two studies using objective diagnostic approaches confirmed that LPRD is associated with significantly reduced alpha and beta diversities compared to controls. Streptococcus and Actinomyces emerged as key taxa consistently differentiating LPRD patients from controls across multiple studies. However, significant methodological heterogeneity was observed in LPRD diagnosis, microbiome assessment methods, and control group definitions.

CONCLUSION: Preliminary literature suggests that patients with suspected or confirmed LPRD exhibit salivary microbiome alterations characterized by reduced diversity and selective microbial shifts. Future high-quality methodological studies are needed to elucidate the mechanistic relationship and clinical consequences of LPRD-related dysbiosis.},
}

@article {pmid41529744,
year = {2026},
author = {Li, J and Tang, G and Xie, Z and Yang, L and Zhou, Z and Guo, K},
title = {Identification of oral microbial biomarkers for prediabetes in young adults: A two-stage population-based study.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113101},
doi = {10.1016/j.diabres.2026.113101},
pmid = {41529744},
issn = {1872-8227},
abstract = {AIM: This study aims to identify oral microbial signatures associated with prediabetes in young adults and to investigate potential oral risk factors for early-onset diabetes, as well as to pinpoint targets for monitoring and intervention.

METHODS: The study involved a large cross-sectional analysis of 3,142 participants from two independent cohorts. The discovery cohort consisted of 334 prediabetes cases and 1,266 controls, while the validation cohort had 325 prediabetes cases and 1,217 controls. We compared the basic and clinical characteristics of the different groups. Additionally, 16S rRNA gene sequencing was conducted on oral rinse samples.

RESULTS: Prediabetes-enriched taxa comprised Bacteroidetes, Prevotella_7, and Veillonella. In contrast, normoglycemic controls showed a higher presence of Firmicutes and Streptococcus. The combined models, constructed from indicators identified by LASSO regression, including BMI, HOMA-IR, and specific microbiota (Prevotella_7 or Veillonella), demonstrated discriminatory performance. In the discovery set, the AUC values were 0.761 and 0.758, respectively, whereas in the validation set, the AUC values were 0.693 and 0.696, respectively.

CONCLUSION: Reproducible alterations and enrichment of Prevotella_7 and Veillonella are linked to prediabetes in young adults. Furthermore, the combined interaction between specific bacterial genera and core clinical indicators may be crucial in the development of prediabetes in young individuals.},
}

@article {pmid41529362,
year = {2026},
author = {Le, VV and Taj, M and Esterhuizen, M and Kim, YJ and Jung, MY and Lee, SA},
title = {Shape-driven toxicity of polystyrene microplastics: Impacts on physiology and gut microbiota in Daphnia magna.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119218},
doi = {10.1016/j.marpolbul.2026.119218},
pmid = {41529362},
issn = {1879-3363},
abstract = {Microplastic pollution has emerged as a global issue that poses serious risks to aquatic ecosystems. Although Daphnia spp. are widely used as model organisms to study the effects of microplastics on their fitness, their microbiome response remains largely unexplored. This study investigated the effects of ground polystyrene microplastics (G-PS; fragments below the EC10 value) and commercial polystyrene microplastics (C-PS; beads below the EC10 value) on the physio-biochemical responses and gut microbiota of Daphnia magna. The toxicity of polystyrene microplastics to D. magna was shape-dependent, with G-PS being more toxic than C-PS. Exposure to G-PS and C-PS triggered Reactive oxygen species (ROS) production in D. magna. Although G-PS increased the abundance of both harmful (Fusobacterium) and beneficial bacteria (Blautia and Subdoligranulum) in the gut microbiota of Daphnia, C-PS only increased the abundance of beneficial bacteria (Lactobacillus, Ligilactobacillus, and Aerococcus), which may mitigate the toxicity of microplastics. Functional predictions based on amplicon sequencing suggested that altered microbiota may support the growth of D. magna by modulating associated metabolic pathways. D. magna exposed to G-PS exhibited a significantly higher abundance of gut microbiota pathways and enzymes associated with the detoxification of harmful compounds than those exposed to C-PS. This suggests that the higher toxicity of G-PS requires a stronger adaptive response from the gut microbiota. Overall, these findings highlight microplastic shape as a key factor influencing toxicity in D. magna and its associated microbiota.},
}

@article {pmid41529347,
year = {2026},
author = {Singh, S and Bajaj, A and Manickam, N},
title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181331},
doi = {10.1016/j.scitotenv.2025.181331},
pmid = {41529347},
issn = {1879-1026},
abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).},
}

@article {pmid41529345,
year = {2026},
author = {Chinthalapudi, DPM and Narayana, NK and Nekkalapudi, L and Sinha, N and Shanmugam, SG},
title = {Soil microbial diversity, stability, and function are enhanced by cover cropping: A machine learning-based pooled analysis of Mississippi agroecosystems.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181365},
doi = {10.1016/j.scitotenv.2026.181365},
pmid = {41529345},
issn = {1879-1026},
abstract = {Cover cropping has emerged as a pivotal strategy to enhance soil health and microbiome functionality across diverse agroecosystems. However, the extent to which cover crops reshape microbial diversity, composition, functional capacity, and ecological stability remains insufficiently understood, particularly within heterogenous environments like Mississippi. In this study, we conducted a comprehensive pooled analysis of 473 soil samples collected from multiple independent cover crop trials (2020-2024) across diverse cropping systems and edaphic contexts in Mississippi. Amplicon sequencing (16S rRNA and ITS2) coupled with machine learning, co-occurrence network modeling, and functional prediction tools were employed to evaluate microbial community responses to cover cropping. Results revealed that cover crops significantly elevated bacterial and fungal α-diversity, altered community composition, and enriched taxa associated with nitrogen fixation, organic matter turnover, and pathogen suppression. Notably, Proteobacteria, Acidobacteriota, and Chloroflexi were more abundant under cover cropping, whereas Firmicutes and Actinobacteriota dominated control plots. Fungal communities under cover cropping exhibited higher relative abundance of Rozellomycota and Chytridiomycota, indicating enhanced saprotrophic and decomposition potential. Functional predictions showed increased cellular and environmental processing functions in cover-cropped soils, alongside a marked reduction in KEGG pathways linked to human diseases and pathotroph dominance. Co-occurrence network analysis indicated increased connectivity, modularity, and robustness under cover cropping, suggested enhanced microbial interaction strength and ecological stability. Sloan's neutral model fitting and increased migration rates further revealed that stochastic processes played a greater role in microbial assembly under cover cropping. Random Forest model identified Bradyrhizobium, Bryobacter, and Solirubrobacter as top bacterial biomarkers enriched in cover-cropped soils, while Talaromyces, Purpureocillium, and Clonostachys were the most predictive fungal genera, known for their biocontrol and nutrient cycling roles. These findings underscore the ecological potential of cover crops to enhance soil microbial networks and sustainability within Mississippi production systems, while insights may inform similar humid, subtropical agroecosystems elsewhere.},
}

@article {pmid41528771,
year = {2026},
author = {Wittle, L and Ocius, KL and Chordia, MD and van Wagoner, C and Bullock, TNJ and Pires, MM},
title = {Identification and Evaluation of Benzimidazole- Agonists of Innate Immune Receptor NOD2.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00737},
pmid = {41528771},
issn = {2373-8227},
abstract = {Emerging evidence has demonstrated the importance of pattern recognition receptors (PRRs), including the nucleotide-binding and oligomerization domain receptor 2 (NOD2), in human health and disease states. NOD2 activation has shown promise with aiding malnutrition recovery, lessening irritable bowel disease (IBD) symptoms, and increasing the efficacy of cancer immunotherapy. Currently, most NOD2 agonists are derivatives or analogs of the endogenous agonist derived from bacterial peptidoglycan, muramyl dipeptide (MDP). These MDP-based agonists can suffer from low oral bioavailability and cause significant adverse side effects. With the goal of broadly improving NOD2 therapeutic interventions, we sought to discover a small molecule capable of activating NOD2 by screening a library of total 1917 FDA approved drugs in a phenotypic assay. We identified a class of compounds, benzimidazoles, that act as NOD2 agonists, with the most potent member of this class being nocodazole. Nocodazole activates NOD2 with nanomolar potency and causes the release of cytokines canonically associated with MDP-induced NOD2 activation, suggesting its potential to elicit similar therapeutic immune effects as MDP and potentially offer improved pharmacological properties.},
}

@article {pmid41528651,
year = {2026},
author = {He, YQ and Xue, WQ and Diao, H and Zhan, JY and Ji, MF and Yang, DW and Zhao, Y and Deng, CM and Wu, ZY and Zhou, T and Liao, Y and Zheng, MQ and Zhang, WL and Jia, YJ and Yuan, LL and Luo, LT and Li, DH and Wang, TM and Tong, XT and Du, Y and Tang, LL and Huang, JW and Huang, CL and Zhao, ZY and Wu, YX and Cao, LJ and Dong, SQ and Wang, F and Jiang, CT and Xiao, RW and Zhang, WB and Chen, XY and Wang, QL and Liu, QY and Zhao, YZ and Tang, CL and Ma, L and Zheng, XH and Zhang, PF and Li, XZ and Zhang, SD and Hu, YZ and Yu, X and Wu, BH and Li, FG and Wu, JH and Deng, BS and Liang, XJ and Jia, WH},
title = {Guangdong Biobank Cohort (GDBC) study.},
journal = {European journal of epidemiology},
volume = {},
number = {},
pages = {},
pmid = {41528651},
issn = {1573-7284},
support = {2023ZD0501000//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2016YFC1302700//National Key Research and Development Program of China/ ; 82473703//National Natural Science Foundation of China/ ; 82273705//National Natural Science Foundation of China/ ; 82373656//National Natural Science Foundation of China/ ; 82404339//National Natural Science Foundation of China/ ; 2024A04J00693//Science and Technology Planning Project of Guangzhou, China/ ; 2024A04J4560//Science and Technology Planning Project of Guangzhou, China/ ; YSTTGDPMAA202502//Young Science and Technology Talent Support Program of Guangdong Precision Medicine Application Association/ ; 24qnpy292//Sun Yat-sen University/ ; 24ykqb002//Sun Yat-sen University/ ; YTP-SYSUCC-0081//Young Talents Program of Sun Yat-sen University Cancer Center/ ; YTP-SYSUCC-0076//Young Talents Program of Sun Yat-sen University Cancer Center/ ; CIRP-SYSUCC-0017//Cancer Innovative Research Program of Sun Yat-sen University Cancer Center/ ; },
abstract = {The global rise of non-communicable diseases (NCDs) presents an urgent public health challenge, particularly in regions undergoing rapid economic and demographic transitions. Guangdong Province, China's most populous and economically advanced region, is experiencing a substantial and accelerating burden of NCDs. However, large-scale, population-based cohorts from this region remain scarce, limiting insights into region-specific disease determinants and prevention strategies. The Guangdong Biobank Cohort (GDBC) was established in 2017, enrolling 35,081 participants aged 40-84 years from urban and rural areas of Zhongshan City in the Pearl River Delta. At baseline, comprehensive data on 346 variables-including lifestyle, environmental exposures, medical histories, physical examinations, and laboratory profiles-were collected via a cloud-based member management information system (MMIS), alongside blood and saliva samples for biobanking. A sub-cohort underwent genome-wide genotyping (N = 2,530) and oral microbiome profiling via 16 S rRNA sequencing (N = 2,049). During dynamic follow-up, 44.2% (N = 15,499) completed Phase I resurvey with repeated measurements and updated biospecimens. Disease outcomes, including hypertension, diabetes, and cancer, were ascertained through active surveillance and regional registry linkage until December 2023. Baseline prevalence of hypertension, diabetes, and cancer was 25.3%, 8.0%, and 3.6%, respectively. Over follow-up, 1,767 hypertension cases, 814 diabetes cases, and 558 cancers were recorded, yielding crude incidence rates of 1,804.6, 649.7, and 423.1 per 100,000 person-years, respectively. The GDBC provides a comprehensive, dynamically updated resource to dissect gene-microbiome-environment interactions and develop precision prevention strategies to inform public health policies.},
}

@article {pmid41528513,
year = {2026},
author = {Muhammad, A and Sun, C and Shao, Y},
title = {Ecological and functional dynamics of gut microbiota in the model insect, silkworm Bombyx mori.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {39},
pmid = {41528513},
issn = {1573-0972},
support = {32250410276//National Natural Science Foundation of China/ ; SKLRI-ORP202401//State Key Laboratory of Resource Insects/ ; CARS-18//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Bombyx/microbiology ; Probiotics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Symbiosis ; Antimicrobial Peptides/metabolism ; Host Microbial Interactions ; },
abstract = {The silkworm (Bombyx mori) has emerged as a powerful invertebrate model for gut microbiome research due to its simple yet representative gut microbiota, cost-effective rearing, and established germ-free systems. This review synthesizes current knowledge on the ecological drivers and functional roles of silkworm gut microbiota, emphasizing its interaction with host health, environmental adaptation, and biotechnological applications. The microbial community of silkworms is highly plastic, shaped by various intrinsic (developmental stage, sex) and extrinsic (diet, environmental conditions) factors. Key microbial taxa, including Enterococcus, Bacillus, Acinetobacter, Pseudomonas, and Staphylococcus, form a dynamic core community with demonstrated probiotic attributes. These microbes contribute to nutrient metabolism (such as cellulose digestion and amino acid synthesis), immune modulation (through the production of antimicrobial peptides), and detoxification (by degrading xenobiotics). Meanwhile, their dysbiosis correlates with reduced growth, silk yield, and pathogen resistance. Notably, several gut symbionts produce or stimulate natural antimicrobial proteins, including bacteriocins (such as enterococcin LX) and host-derived antimicrobial peptides, which exhibit activity against microbial pathogens. Understanding these microbial associations is crucial for developing microbe-based probiotic formulations, antimicrobial therapies, and enzyme-driven bioprocesses to enhance sericultural productivity and sustainability. Despite progress, significant gaps remain in our understanding of host-microbe coevolution, immune-microbiota crosstalk, and the genetic basis of microbial resilience. Future research integrating multi-omics approaches and gnotobiotic models will unravel mechanistic insights, enabling targeted manipulation of the silkworm microbiota for agricultural, environmental, and medical innovations.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Bombyx/microbiology
Probiotics
Bacteria/classification/genetics/metabolism/isolation & purification
Symbiosis
Antimicrobial Peptides/metabolism
Host Microbial Interactions

@article {pmid41528365,
year = {2026},
author = {Johnsen Stefani, L and Wohlgemuth, S and Schütte, L and Halbgebauer, R and Bergmann, CB and Huber-Lang, M and Wohlgemuth, L},
title = {Macrophages on demand: How tissue trauma shapes their role.},
journal = {European journal of trauma and emergency surgery : official publication of the European Trauma Society},
volume = {52},
number = {1},
pages = {17},
pmid = {41528365},
issn = {1863-9941},
mesh = {Humans ; *Macrophages/immunology/physiology ; *Wounds and Injuries/immunology ; *Wound Healing/immunology ; *Inflammation/immunology ; Regeneration/immunology ; },
abstract = {Macrophages, renowned for their plasticity, are central to both the immune response and tissue repair following physical trauma. This review delineates how tissue trauma dynamically modulates macrophage function across organs, highlighting their dichotomous roles in promoting inflammation versus regeneration. After injury, macrophages shift along a continuum from pro-inflammatory to pro-regenerative states, influenced by local and systemic cues, injury type, and microenvironmental factors, including damage-associated molecular patterns, and cytokines leading to pronounced organ-specific differences. The temporal and spatial dynamics of macrophage recruitment - from resident pools or via monocyte influx - dictate not only healing outcomes but also the risk of organ dysfunction and chronic inflammation. Emerging immunomodulatory strategies, encompassing stem cell therapies, pharmacological phenotype modulation, and microbiome-targeted approaches, underscore the clinical potential of precise macrophage-targeted interventions. Understanding macrophage adaptability post-trauma is crucial for devising organ- and context-specific therapies to optimize tissue repair and minimize adverse outcomes.},
}

Humans
*Macrophages/immunology/physiology
*Wounds and Injuries/immunology
*Wound Healing/immunology
*Inflammation/immunology
Regeneration/immunology

@article {pmid41528150,
year = {2026},
author = {Guo, M and Xia, Z and He, X and Wan, S and Wang, Y and Fan, S and Pérez-Moreno, J and Yang, Z and Yang, C and Liu, D and Yu, F},
title = {High-throughput sequencing reveals endophytic bacterial differentiation of common truffles (Tuber spp.) in China: diversity, biogeographical patterns, and fungal health implications.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0186625},
doi = {10.1128/spectrum.01866-25},
pmid = {41528150},
issn = {2165-0497},
abstract = {UNLABELLED: As valuable hypogeous fungi, truffles depend on fruiting-body-associated microorganisms for lifecycle functions like growth and nutrient cycling. This study sampled fruiting bodies of 10 Tuber species from 16 sites across six major truffle-producing provinces in China, characterizing endophytic bacterial communities via high-throughput sequencing and multivariate analysis. Proteobacteria dominated the endophytic bacteria, with Bradyrhizobium as the prevalent genus. Significant genus-level compositional differences occurred across provenances and species: Bradyrhizobium reached 99.80% relative abundance in Tuber sinense from Mengzi, Yunnan, versus 7.90% in Tuber shii from Dali (12.6-fold difference). Shannon diversity indices (n = 48) revealed striking species- and altitude-related variations (P < 0.001): Tuber lijiangense (5.111) and T. shii (5.091) had the highest diversity, while T. sinense (1.336) had the lowest (3.8-fold gap). Subtropical Dali samples exhibited a sevenfold higher diversity compared to those from the Mengzi region, which is geographically closer to the tropics. Non-metric scaling and principal coordinates analysis identified environmental factors (soil, climate) and host species as primary drivers, with species effects potentially overriding environment. Five core taxa (all Rhizobiales) suggested nitrogen-fixing roles, while Variovorax (via linear discriminant analysis effect size) emerged as an external-disturbance-sensitive opportunist. This study clarifies endophytic bacterial variation patterns and drivers, identifies key taxa, and informs truffle ecological interactions, providing a scientific basis for sustainable resource management and conservation.

IMPORTANCE: This study underscores the critical importance of truffle endophytic bacteria in mediating fungal health and ecological resilience, addressing a major knowledge gap in hypogeous fungal microbiome research. By integrating high-throughput sequencing across 10 Tuber species in China, we reveal how bacterial communities (dominated by Bradyrhizobium) shape biogeographical patterns and functional roles like nitrogen fixation. These findings advance understanding of microbe-fungal symbioses, with direct applications for sustainable truffle cultivation (e.g., microbial inoculants) and climate-resilient management-aligning perfectly with AEM's focus on applied microbial ecology and biotechnological relevance.},
}

@article {pmid41528122,
year = {2026},
author = {McMurray-Jones, A and Spann, K and Yarlagadda, PKDV and Fernando, J and Roberts, LW},
title = {Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41528122},
issn = {2057-5858},
mesh = {*Intensive Care Units ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Humans ; Queensland ; *Environmental Monitoring/methods ; Drug Resistance, Bacterial/genetics ; Microbiota/genetics ; Metagenomics/methods ; Cross Infection/microbiology ; },
abstract = {The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.},
}

*Intensive Care Units
*Bacteria/genetics/isolation & purification/classification/drug effects
Humans
Queensland
*Environmental Monitoring/methods
Drug Resistance, Bacterial/genetics
Microbiota/genetics
Metagenomics/methods
Cross Infection/microbiology

@article {pmid41527932,
year = {2026},
author = {Connell, E and Le Gall, G and McArthur, S and Lang, L and Breeze, B and Liaquat, M and Pontifex, MG and Sami, S and Pourtau, L and Gaudout, D and Müller, M and Vauzour, D},
title = {A novel Mediterranean diet-inspired supplement reduces hippocampal amyloid deposits and microglial activation through the modulation of the microbiota gut-brain axis in 5xFAD mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2614030},
doi = {10.1080/19490976.2026.2614030},
pmid = {41527932},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Microglia/drug effects/metabolism ; *Hippocampus/metabolism/drug effects/pathology ; Mice ; Male ; *Diet, Mediterranean ; Mice, Transgenic ; *Alzheimer Disease/metabolism/diet therapy/microbiology ; Female ; *Dietary Supplements ; Disease Models, Animal ; Amyloid beta-Peptides/metabolism ; Humans ; Brain-Gut Axis ; Brain/metabolism ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is projected to increase in prevalence, heightening the need for strategies to alleviate its neuropathological burden. The bioactive constituents of a Mediterranean-style diet are well-recognised for their neuroprotective properties. Due to their capacity to alter the gut microbiome composition, these benefits may involve modulation of the microbiota-gut-brain axis. In this study, we investigated whether a novel supplement enriched with key Mediterranean diet-derived bioactives (Neurosyn240) could reduce amyloid deposition and microglial activation in 5xFAD mice, a transgenic model of AD, through microbiota-mediated mechanisms.

METHODS: Male and female 5xFAD transgenic mice (n = 16 per sex) were randomly assigned to receive either a standard control diet or a diet supplemented with Neurosyn240 for 12 weeks. Employing a multi-omics approach, gut microbiota composition was profiled using 16S rRNA ampliconsequencing, serum metabolites were quantified via targeted metabolomics, and hippocampal gene expression was analysed through qPCR and RNA sequencing. Neuropathological markers, including amyloid-β deposition and microglial activation, were evaluated using immunofluorescence staining. Statistical analyses were performed using two-way ANOVA to examine the main effects of diet and sex and their interaction.

RESULTS: Neurosyn240 significantly shifted the gut microbiome composition, which was associated with increased circulatory serotonin levels and decreased kynurenine and bile acids (TCA, HDCA, TDCA, CDCA and LCA) concentrations. In the brain, Neurosyn240 consumption led to a significant reduction in hippocampal amyloid deposits and Iba-1 positive microglia (p<0.05), which were associated with decreased LCA and increased serotonin, respectively. Hippocampal RNA sequencing further highlighted the upregulation of genes involved in promoting amyloid beta clearance mechanisms.

CONCLUSIONS: Together, these findings highlight novel neuroprotective effects of Neurosyn240 in modulating metabolite-mediated pathways of the microbiota-gut-brain axis, accentuating its therapeutic potential against AD progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Microglia/drug effects/metabolism
*Hippocampus/metabolism/drug effects/pathology
Mice
Male
*Diet, Mediterranean
Mice, Transgenic
*Alzheimer Disease/metabolism/diet therapy/microbiology
Female
*Dietary Supplements
Disease Models, Animal
Amyloid beta-Peptides/metabolism
Humans
Brain-Gut Axis
Brain/metabolism

@article {pmid41527485,
year = {2026},
author = {Cheng, Q and Nolz, J and Karr, T and Dorn, N and Readhead, B and Krajmalnik-Brown, R and Mastroeni, D},
title = {Gut proteome and microbiome alterations: Analysis of transverse colon samples from pathologically confirmed Alzheimer's disease patients.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e71021},
doi = {10.1002/alz.71021},
pmid = {41527485},
issn = {1552-5279},
support = {U24 NS072026/NS/NINDS NIH HHS/United States ; P30AG19610//the National Institute on Aging/ ; P30AG072980//the National Institute on Aging/ ; 211002//the Arizona Department of Health Services/ ; 4001//the Arizona Biomedical Research Commission/ ; 0011//the Arizona Biomedical Research Commission/ ; 05-901//the Arizona Biomedical Research Commission/ ; and 1001//the Arizona Biomedical Research Commission/ ; //the Michael J. Fox Foundation for Parkinson's Research/ ; //Arizona Alzheimer's Consortium/ ; //Biodesign Center for Health Through Microbiomes/ ; },
mesh = {Humans ; *Alzheimer Disease/pathology/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Proteome/metabolism ; Female ; Male ; *Colon/microbiology/metabolism/pathology ; Aged ; Proteomics ; Aged, 80 and over ; Amyloid beta-Peptides/metabolism ; },
abstract = {INTRODUCTION: Alzheimer's disease (AD) has been regarded as a brain-first disorder. Emerging evidence suggests that the gut may influence central nervous system pathology, but the mechanisms remain unclear.

METHODS: We conducted a proteomic and microbial analysis of transverse colon samples from clinically and pathologically confirmed AD and control cases.

RESULTS: In the AD gut samples, antimicrobial humoral response and oxidative stress response were downregulated, while catabolic processes and insulin signaling were upregulated. Several complement (e.g., C5) and synaptic (e.g., synaptophysin) proteins were downregulated. Amyloid beta 42 was detected at higher levels. Christensenellaceae, Desulfovibrio, and Candida tropicalis amplicon sequence variants were higher in abundance, while Streptococcus, Lachnospiraceae, Blautia, and Nakaseomyces were lower. In general, bacterial composition correlated with AD clinical variables such as plaque and tangle burden.

DISCUSSION: These findings underscore the gut's possible involvement in AD pathogenesis and provide new insights into potential biomarkers and therapeutic targets.

HIGHLIGHTS: This study provides the first in-depth analysis of the proteome and microbiome in AD transverse colon tissues. Multiple immune and oxidative stress response pathways were downregulated in AD, while metabolic pathways were upregulated. Synaptic protein, complement protein, and Aβ42 levels were significantly different between AD and controls. Transverse colon microbial composition was associated with AD clinical variables.},
}

Humans
*Alzheimer Disease/pathology/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
*Proteome/metabolism
Female
Male
*Colon/microbiology/metabolism/pathology
Aged
Proteomics
Aged, 80 and over
Amyloid beta-Peptides/metabolism

@article {pmid41527479,
year = {2026},
author = {Zhang, T and Yu, Y and Bu, F and Li, J and Zhou, M and Lin, L and Zheng, L and Cheng, Y},
title = {Biodegradation of polypropylene by yellow mealworm (Tenebrio molitor) larvae: response of gut microbiome and metabolome to plastic polymers.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70223},
pmid = {41527479},
issn = {1744-7917},
support = {No. 2024J08148//Natural Science Foundation of Fujian Province/ ; No.MEEST-2023-05//MNR Key Laboratory of Eco-Environmental Science and Technology, China/ ; No.2021N040//Science and Technology Plan Project of Quanzhou City/ ; No.JAT220031//Education and Research Foundation of the Ministry of Education of Fujian Province for Young Teachers/ ; },
abstract = {The widespread use and improper disposal of polypropylene (PP) facemasks have resulted in persistent environmental pollution, posing urgent challenges for waste management. This study added bran-PP mixture, which increased the survival rate, consumption rate and removal rate of Tenebrio molitor feeding solely on PP. The average consumption of the larvae fed with the edible bran-PP mixture was 61.54% higher than those fed only PP. The removal rates were 39.26% and 36.14%, respectively. Fourier-transform infrared spectroscopy, thermal gravimetric analysis, gel permeation chromatography, and nuclear magnetic resonance confirmed the production of oxygenated compounds in the larval gut, indicating partial oxidation and degradation of PP masks within the intestinal tract. HT-GPC analysis revealed significant reductions in molecular weight parameters, with the number-average (Mn), weight-average (Mw), and Z-average (Mz) molecular weights decreasing by 51.07%, 33.60%, and 32.99%, respectively. High-throughput 16S rRNA sequencing revealed that feeding on PP enhanced gut microbiota richness and diversity. The bran-PP mixture group exhibited significantly higher relative abundances of Enterobacter and Spiroplasma, whereas the bran group was dominated by Lactobacillus. PICRUSt functional predictions indicated upregulation of plastic degradation-associated oxidases (alkane 1-monooxygenase, cyclohexanone monooxygenase) and hydrolases (chitinase, carboxylesterase) in larvae fed PP or bran-PP diets. Metabolomic profiling revealed significant enrichment in pathways related to histidine, glycerophospholipid, choline and steroid hormone metabolism in PP-fed larvae. These findings demonstrate that PP can be biodegraded in T. molitor larvae through gut microbe-mediated depolymerization involving a diverse microbial community.},
}

@article {pmid41527353,
year = {2026},
author = {Lu, Y and Zhang, CQ and Xu, XM and Zhu, WB and Hu, CY and Gong, T and Meng, YH},
title = {Novel Methylenetransferase from Human Gut Strain L. longoviformis Initiates Sesamin Conversion and Its Catalytic Mechanism.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13970},
pmid = {41527353},
issn = {1520-5118},
abstract = {Gut microbiota governs lignan bioactivation, yet the specific enzymes involved remain poorly characterized. Here, we identified a novel sesamin methylenetransferase from Lactonifactor longoviformis, LacAMT, that catalyzes the methylenedioxy bridge cleavage of sesamin (SESA) into catechol metabolites, with Km and kcat values of 1.203 mM and 0.83 min[-1]. LacAMT homologues are rare in human gut microbes, mainly in the Lachnospiraceae and Clostridiaceae families. Structural and mutational analyses revealed that LacAMT employs a unique catalytic mechanism distinct from those of typical GcvT methyltransferases and hepatic P450s. LacAMT cleaves SESA's methylenedioxy bridge and transfers the methylene group to tetrahydrofolate through Y218 and H222, acting as an acid-base pair. Moreover, enhanced substrate binding with Y218 likely facilitates proton transfer, resulting in 3.33-fold and 2.12-fold increases in catalytic efficiency for W107E and V94A, respectively. These findings elucidate how the human gut microbiome activates plant secondary metabolites, advancing our understanding of the interplay among the diet, gut microbiota, and human health.},
}

@article {pmid41527254,
year = {2026},
author = {London, RE},
title = {Microbiome-generated antifolates.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70252},
pmid = {41527254},
issn = {1873-3468},
support = {ZIA ES050111/ES/NIEHS NIH HHS/United States ; },
abstract = {The folate biosynthesis activity of the human microbiome provides reduced folate metabolites that are readily absorbed from the gastrointestinal (GI) tract. The bacterial folate biosynthesis enzyme dihydropteroate synthase (DHPS), which adds p-aminobenzoate (pABA) to an activated pterin precursor, is an important antibiotic target. Both the broad-spectrum p-aminobenzenesulfonamide antibiotics, and the drug p-aminosalicylate (PAS, 2-hydroxy-pABA) with high selectivity for Mycobacterium tuberculosis, are competitive DHPS substrates. The adducts formed from these drugs, DHP-sulfonamides (sulfapterins) and 2'-hydroxyfolate metabolites, respectively, have been reported to exhibit antifolate activity in studies of microorganisms. The presence of these DHP-adducts and their effects on the host organism are largely undetermined; however, their close structural relationship to dihydrofolate (DHF) suggests that they are likely to mediate some side effects reported for these antibiotics. Naturally occurring pABA analogs that probably function similar to DHPS-targeted antibiotics have been identified in carrots and bacteria. Impact statement pABA analogs represent an important class of antibiotics, that are converted into dihydrofolate analogs by organisms present in the human microbiome. These analogs may mediate reported side-effects associated with these antibiotics. Several naturally occurring pABA mimics have been identified that are likely to exhibit antibiotic activity.},
}

@article {pmid41527156,
year = {2026},
author = {Buffoni, M and Kerkvliet, JJ and Enting, H and Kers, JG and Rogers, M and Visser, JAGM and Paganelli, FL and Willems, RJL and Schürch, AC},
title = {Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {3},
pmid = {41527156},
issn = {2524-4671},
abstract = {BACKGROUND: Coccidiosis is a parasitic infection in the gut of livestock that poses a significant health challenge in poultry farming, underscoring the important role of intervention and prevention strategies in the poultry industry. The use of anticoccidial drugs raises concerns about antimicrobial resistance (AMR) due to their antimicrobial properties and the ability of bacteria to evolve resistance to these drugs. Whether anticoccidial drug resistance could extend beyond coccidiostats, leading to cross-resistance and co-selection against other antimicrobial resistance genes (ARGs), is currently under discussion. Also, it is not well understood to what extent coccidiosis reduction strategies may enable the emergence of ARGs in farm environments and transmission of ARGs to other environments through bacterial clonal transfer or horizontal transmission via mobile genetic elements (MGEs) like plasmids or transposons.

RESULTS: In this study, we used metagenomic sequencing of caecal and faecal dropping samples from broiler chickens to investigate how two anticoccidial prevention strategies (vaccination and coccidiostat drugs) influence bacterial taxonomic composition and ARG profiles. We also explored the mobile resistome, ARGs located on mobile genetic elements (MGEs) such as plasmids, which are capable of disseminating, investigating ARGs identifying with the potential to disseminate within and beyond farm settings. Our exploratory findings in bacterial composition, as well as resistome composition with 21 differentially abundant ARGs, illustrating the potential impact of anticoccidial strategies on the chicken gut microbiome and resistome. We also identified 14 plasmid fragments containing ARGs in faecal dropping samples, highlighting mobile ARGs potentially able to disseminate to other environments, including humans.

CONCLUSIONS: Our findings demonstrate the impact of anticoccidial strategies on the chicken gut microbiome and resistome with potential consequences for the dissemination of ARGs.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00497-7.},
}

@article {pmid41527141,
year = {2026},
author = {Liu, YY and Xia, F and Yimuran, R and Nuermamaiti, A and Yang, Y and Zhou, JT},
title = {Assessing whether rectal swabs reflect appendiceal microbiota profiles in acute appendicitis: a 16S rRNA-based comparative study.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00794-1},
pmid = {41527141},
issn = {1757-4749},
support = {2023D01A93//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {BACKGROUND: Acute appendicitis is associated with characteristic changes in the intestinal microbiota, but direct sampling of appendiceal contents is invasive and cannot be performed in healthy controls. We therefore evaluated whether rectal swabs could partially capture appendiceal microbiome signatures in adults with acute appendicitis.

METHODS: In a prospective cross-sectional study, we enrolled adults with acute appendicitis and healthy volunteers between October 2023 and December 2024. Four types of samples were collected: feces from healthy controls (HC), appendiceal luminal contents from patients with acute appendicitis (AC), intraoperative rectal swabs from patients with acute appendicitis (RS), and initial postoperative feces from patients with acute appendicitis (IF; first stool within 24 h after surgery). 16 S rRNA gene (V3-V4) sequencing was performed, and reads were processed with QIIME2. Alpha and beta diversity, differential taxonomic composition, and PICRUSt2-based functional predictions were compared across matrices. Genus-level and functional concordance between paired AC-RS samples was assessed.

RESULTS: After quality control, 64 AC, 34 RS, 24 IF, and 29 HC samples were included. Phylogenetic diversity (PD whole-tree) was higher in AC and RS than HC, with AC also higher than RS; IF showed lower PD than AC. Bray-Curtis principal coordinate analysis showed AC forming a distinct cluster separated from HC and RS along PC1, whereas IF overlapped with HC and RS. AC, RS, and IF were enriched for Escherichia/Shigella and Fusobacterium and depleted in butyrate-producing genera such as Faecalibacterium compared with HC. In the 21 paired AC-RS cases, genus-level relative abundances and several predicted functional pathways showed concordance, indicating that RS captured many but not all appendiceal dysbiosis features.

CONCLUSIONS: Our findings suggest that intraoperative rectal swabs may partially reflect appendiceal microbiome alterations at the genus and pathway levels and may serve as a minimally invasive adjunct for microbiome profiling in acute appendicitis. However, these associations are inferred from 16 S amplicon data in a modestly sized, antibiotic-exposed cohort and should be validated using shotgun metagenomics in larger, clinically stratified populations.},
}

@article {pmid41527126,
year = {2026},
author = {Zhu, H and Li, M and Lu, C and Wang, J and Ouyang, K and Zhang, J and Li, X and Chen, WH and Xiao, M},
title = {Efficacy of very low calorie diet in the intervention of obesity and the changes in oral microbiota: a prospective cohort study.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07087-w},
pmid = {41527126},
issn = {1479-5876},
support = {No.82274352//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Very Low Calorie Diet (VLCD) is a stringent caloric restriction regimen used in the short-term management of obese patients, which can effectively reduce body weight and blood glucose levels. This prospective study aimed to evaluate the short-term impacts of a VLCD on body composition, metabolic parameters, and oral microbiota in obese adults, exploring its therapeutic potential for metabolic dysfunction and inflammation-related comorbidities.

METHODS: This prospective study was conducted on the basis of a cohort of overweight/obese individuals at Affiliated Hospital of Hubei University of Chinese Medicine. Patient eligibility for inclusion in this study was determined by the adoption of a complete short-term VLCD therapy following their entry into the cohort. The study aimed to explore the improvements in body composition, blood glucose, blood lipids, and inflammatory markers post-VLCD intervention, as well as the safety of the treatment. Additionally, it analyzed the changes in the microbiota of the upper gastrointestinal tract, specifically the oral coating. The study was concluded on December 31, 2023.

RESULTS: In the per-protocol cohort (n = 101), the VLCD intervention induced rapid, clinically meaningful reductions in body weight, body fat mass(BFM), body mass index (BMI), and visceral fat area(VFA). Skeletal muscle mass(SMM) decreased modestly. Metabolic parameters improved significantly, with decreases in fasting blood glucose (FBG), fasting insulin (FIns), and homeostasis model assessment of insulin resistance (HOMA-IR). Lipid profiles showed transient increases in low-density lipoprotein cholesterol (LDL-C) and total cholesterol (CHOL) at day 5, normalizing by two-week follow-up, alongside reduced triglycerides (TG). Systemic inflammation markers declined after resuming normal diet, including alanine aminotransferase (ALT) and high-sensitivity C-reactive protein (hs-CRP); uric acid (UA) peaked transiently during the VLCD before falling below baseline. Tongue-coating microbiota exhibited increased Shannon diversity and shifted community structure, with 12 reduced species associated with 19 systemic diseases.

CONCLUSIONS: The VLCD intervention shows significant short-term benefits in weight loss and body fat reduction. Furthermore, it shows potential for reducing the risk of chronic diseases by modulating systemic inflammation and altering the oral microbiome. Further studies are warranted to assess long-term efficacy and sustainability.

TRIAL REGISTRATION: Chinese Clinical Trail Registry (No. ChiCTR2200063126, date of registration: 31 August 2022), https://www.chictr.org.cn/hvshowproject.html?id=188695&v=1.2.},
}

@article {pmid41527105,
year = {2026},
author = {Pang, T and Wang, C and Jiao, G and Fan, X and Huang, D and Long, Z and Xiao, M and Sun, L and Chen, W and Zhang, F},
title = {Therapeutic potential of Sheng-Xian-Tang in doxorubicin-induced chronic heart failure by regulation of phenylalanine metabolism disruption.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {29},
pmid = {41527105},
issn = {1749-8546},
support = {2022YFC3501700//National Key Research and Development Program of China/ ; 82274059//National Natural Science Foundation of China/ ; SL-33//Naval Military Medical University Far East Talent Project/ ; NO. CPA-Z05-ZC-2024-003//Talent Project established by Chinese Pharmaceutical Association Hospital Pharmacy department/ ; },
abstract = {BACKGROUND: Sheng-Xian-Tang (SXT), a traditional Chinese medicine, ameliorates doxorubicin (DOX)-induced chronic heart failure (CHF), yet its molecular mechanisms remain elusive.

OBJECTIVE: To elucidate SXT's cardioprotective mechanisms against DOX-induced CHF.

METHODS: In vivo, cardioprotection was evaluated via echocardiography, oxidative stress assays, and histopathology. Integrated metabolomic and 16S rRNA sequencing identified metabolic disruptions. Serum pharmacochemistry analysis identified hepatic bioactive compounds targeting phenylalanine hydroxylase (PAH). Molecular docking, CETSA, SPR, and enzyme activity assay validated neomangiferin-PAH interactions.

RESULTS: SXT dose-dependently improved DOX-induced cardiac dysfunction in rats. Metabolomic and microbiome analyses confirmed phenylalanine metabolic disorder in the CHF rats. DOX exposure elevated phenylalanine levels in plasma, urine, and heart, reducing hepatic PAH expression and function while inducing ectopic phenylalanine catabolism in the heart. Phenylalanine administration exacerbated the cardiac abnormalities, whereas SXT effectively prevented attenuated DOX-induced cardiac toxicity. CETSA and SPR revealed a strong binding of neomangiferin to PAH, stabilizing its interaction with cofactor BH4 and preventing DOX-induced PAH inhibition.

CONCLUSIONS: SXT mitigated DOX-induced CHF through hepatic PAH modulation. Neomangiferin could enhance PAH stability via competitive binding. Targeting PAH-phenylalanine metabolism emerged as a novel therapeutic strategy for DOX-induced cardiac dysfunction.},
}

@article {pmid41526999,
year = {2026},
author = {Xu, L and Zhu, S and Sun, HZ and Yan, Y and Wang, X and Li, X and Bu, D},
title = {Intracellular microbial signals in the gastrointestinal tract of dairy cattle.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02319-z},
pmid = {41526999},
issn = {2049-2618},
support = {ZR2025MS327//Natural Science Foundation of Shandong Province/ ; ZR2024QC105//Natural Science Foundation of Shandong Province/ ; 25-1-1-251-zyyd-jch//Qingdao Natural Science Foundation/ ; 32102553//National Natural Science Foundation of China/ ; LR23C170001//Natural Science Foundation of Zhejiang Province/ ; },
abstract = {BACKGROUND: The presence of intracellular microbiota in epithelial cells of gastrointestinal tracts (GITs) of dairy cows, as well as their associations with rumen development, remains unclear.

RESULTS: Using a single-cell analysis of host-microbiome interactions (SAHMI) within a single-cell atlas derived from ten GITs tissue types collected from new-born (NB) and adult (AD) cows, we found that 20.5% of the single-cell RNA sequencing reads aligned to reference microbial genomes after filtering low-quality single cells and doublets. Comparative analysis revealed that abomasum tissue exhibited the highest proportion of cells detected microbial signals, with Paneth cells possessing the most genes classified as both marker genes and those related to microbial signals. In the NB rumen, Basal cells demonstrated the greatest overlap between differentially expressed genes in AD vs. NB comparison and the microbial signal-related genes. Notably, these microbiota-associated genes, which are mainly linked to Aliiroseovarius crassostreae, Enterobacter sp. T2, and Enzebya pacifica, are implicated in nucleotide excision repair mechanisms, including DNA replication and the cell cycle. Furthermore, bacterial fluorescence in situ hybridization (FISH) analysis indicated that these three microbial species were partially localized within the cytoplasm and nucleus of rumen epithelial cells in NB cattle.

CONCLUSIONS: These findings provide substantial evidence supporting the existence of an intracellular microbiome within the GITs of dairy cattle and highlight their potential relationships with rumen development. This research enhances our understanding of the crosstalk between hosts and microbiome during the maturation of ruminants. Video Abstract.},
}

@article {pmid41526953,
year = {2026},
author = {Quijia-Pillajo, J and Naik, S and Chapin, LJ and Owen, JS and Jones, ML},
title = {Calcium phosphate-solubilizing bacteria promote growth and alleviate phosphorus deficiency in French marigold with minimal impact on the rhizosphere microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00844-w},
pmid = {41526953},
issn = {2524-6372},
support = {2021-09976//NIFA Agriculture and Food Research Initiative - Foundational Knowledge of Agricultural Production Systems/ ; },
abstract = {BACKGROUND: Plant roots are surrounded by communities of microbes that influence plant growth, development, and disease resistance. In soilless culture, microbial diversity in root-associated communities primarily originates from the substrate, irrigation water, and applied microbial inoculants. Phosphate solubilizing bacteria (PSB) capable of mobilizing phosphate from insoluble Ca3(PO4)2 were identified from a greenhouse rhizobacteria collection. Plant growth promoting efficacy was investigated at different substrate pH. The influence of the inoculum composition on plant growth responses to the bacteria was also evaluated. Finally, we analyzed the impact of PSB inoculation on microbiome composition and function.

RESULTS: From 1044 isolates in the rhizobacteria collection, 14 solubilized more than 25% of the phosphorus provided in vitro. Only eight bacterial strains resulted in growth promotion benefits in planta when inoculated as a substrate drench onto marigolds grown in a peat-based substrate (pH 7.0) and fertilized with insoluble Ca3(PO4)2. In a follow up experiment, two newly identified (Pantoea sp. C2G6 and Enterobacter soli C4A1) and three previously identified PSB (Pantoea trifolii C2B11, Pantoea formicae C8D10, and Bacillus velezensis) that have demonstrated superior phosphate-mineral solubilization were evaluated. The PSB were tested at a substrate pH of 6.0 and 6.5 using water, 1% glucose, 2% Micromate, or 0.1X Luria-Bertani (LB) broth as inoculant supplements. All five bacteria promoted growth and improved plant health at both pH levels. A greater benefit to marigold growth and health was observed in plants growing at pH 6.5. C2B11, C8D10, C2G6, and B. velezensis treatment resulted in a significant increase in shoot P content. Microbiome diversity and community structure exhibited no significant alterations in response to PSB treatment. Genes enriched in PSB treated rhizospheres were mostly related to colonization, competition, and biofertilization traits.

CONCLUSIONS: PSB isolated from the rhizosphere of floriculture crops grown in soilless substrates promoted growth and enhanced health of marigolds grown under P limitation. They also enhanced growth under optimal or slightly basic pH, but their efficacy was not improved by the inoculant supplements evaluated in this experiment. The native microbial community in peat-based soilless substrate was resilient to PSB inoculation.},
}

@article {pmid41526937,
year = {2026},
author = {Arı, M and Erdogan, MA and Erbaş, O},
title = {Mitigative effects of Otilonium Bromide on methotrexate-induced hepatic damage in rats.},
journal = {BMC research notes},
volume = {19},
number = {1},
pages = {15},
pmid = {41526937},
issn = {1756-0500},
abstract = {OBJECTIVE: Hepatotoxicity is a significant adverse effect associated with long-term methotrexate (MTX) treatment, limiting its clinical utility. This study aimed to comprehensively evaluate the potential hepatoprotective effects of Otilonium Bromide (OB) against MTX-induced liver injury in an experimental rat model by integrating biochemical, molecular, and histopathological assessments.

RESULTS: MTX administration resulted in significant structural and functional liver damage, as evidenced by elevated biochemical markers, alanine aminotransferase (ALT), transforming growth factor-beta (TGF-β), NOD-like receptor family pyrin domain-containing 3 (NLRP3), platelet-derived growth factor (PDGF), malondialdehyde (MDA) and worsened histopathological scores, including increased hepatocyte necrosis, fibrosis, and cellular infiltration. Treatment with OB significantly reduced these biochemical markers and improved histopathological changes compared to the MTX + saline group. Otilonium Bromide demonstrated hepatoprotective effects in the rat model of MTX-induced liver injury, likely through its anti-inflammatory and antifibrotic properties. These effects may be mediated by modulation of oxidative stress and the intestinal microbiome. Further studies are needed to explore its clinical applicability.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13104-025-07585-6.},
}

@article {pmid41526934,
year = {2026},
author = {Fallahzadeh, A and Mahmoodi, T and Kwon, S and Liu, M and Nolan, A},
title = {Multi-omics of oxidative stress and particulate matter exposure: a systematic review.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-025-03487-0},
pmid = {41526934},
issn = {1465-993X},
support = {U01 -OH012069; -OH011855; -OH011300//Centers for Disease Control and Prevention Foundation/ ; UL1TR001445; KL2TR001446/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Exposure to particulate matter (PM) is a significant public health concern associated with respiratory, cardiovascular, and metabolic diseases. Oxidative stress is a key biological mechanism mediating the harmful effects of PM exposure. However, a comprehensive review of relating PM exposure to omics layers of oxidative stress has been lacking. We aimed to systematically review the current evidence on the associations between PM exposure and the multi-omics signatures of oxidative stress.

METHODS: We conducted a systematic review of studies published between January 2021 and March 2024 in PubMed and Web of Science, following a registered protocol (PROSPERO ID: CRD42024617742). Eligible studies assessed the impact of PM exposure on oxidative stress-related omics in adult human populations. Data on exposure assessment, study characteristics, and omics outcomes were extracted, and the risk of bias was evaluated using the Newcastle-Ottawa Scale and Cochrane's.

RESULTS: Seventy-seven studies were included. PM exposure was consistently associated with oxidative stress markers across multiple omics platforms. Studies on the analytes showed that PM was associated with an increase in oxidative markers. Metabolomics studies revealed alterations in pro-oxidant metabolites (e.g., eicosanoids, ceramides) and disruptions in antioxidant pathways (e.g., glutathione, vitamin C, and E metabolism). PM exposure was also linked to changes in energy metabolism, fatty acid oxidation, and detoxification pathways. Genomics studies reported differential methylation in genes involved in oxidative stress and inflammation. Microbiome studies suggest that PM exposure alters the composition of gut and nasal microbiota, favoring a pro-oxidative profile. However, some studies reported no significant associations, highlighting heterogeneity in findings.

CONCLUSION: Our systematic review demonstrates that PM exposure affects multiple molecular pathways related to oxidative stress across diverse omics platforms. These findings highlight the complex responses to PM, underscoring the need for integrative multi-omics approaches to fully understand the health impacts of air pollution.},
}

@article {pmid41526899,
year = {2026},
author = {Jia, K and Chen, Y and Dai, D and Xie, Y and Peng, H and Cao, Y and Zou, H and Qiu, C and Tan, Y and Zhang, X and Lu, Z and Yin, X and Peng, Z and Li, J and Shen, L},
title = {Impact of Helicobacter pylori infection on gut and intratumoral microbiome and its association with immunotherapy response in gastrointestinal cancer.},
journal = {BMC medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12916-025-04575-0},
pmid = {41526899},
issn = {1741-7015},
support = {823B2069//National Natural Science Foundation of China/ ; 82203881//National Natural Science Foundation of China/ ; U22A20327//National Natural Science Foundation of China/ ; 7222021//Beijing Natural Science Foundation/ ; QMS20201102//Beijing Hospitals Authority Youth Programme/ ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection is associated with enhanced efficacy of immunotherapy in gastric cancer (GC). However, the mechanisms underlying this enhancement are not fully understood.

METHODS: We recruited 218 GC patients, 134 esophageal squamous cell carcinoma (ESCC) patients, and 86 dMMR/MSI-H colorectal cancer (CC) patients and collected their stool and tumor samples to analyze the gut and intratumoral microbiome. We assessed microbial diversity and composition and correlated these findings with clinical outcomes to evaluate the relationship between H. pylori status, microbiome alterations, and immunotherapy efficacy.

RESULTS: H. pylori-positive patients showed higher alpha diversity and unique microbial signatures, which were associated with increased immune-related progression-free survival (irPFS) and overall survival (irOS). In addition, we found that the abundance of 45 gut microbiome species was significantly different between the two groups. The gut microbiome of the H. pylori-positive GC group was enriched with species such as Clostridium leptum, Oscillibacter sp. ER4, and Ruminococcus bromii, which were associated with improved treatment response. However, they predicted poor prognosis in patients with esophageal squamous cell carcinoma and colorectal cancer patients with dMMR/MSI-H. Microbial co-occurrence network revealed significantly distinct interaction patterns among the groups. In addition, we found enhanced L-arginine biosynthesis in the gut microbiome of H. pylori-positive GC. In terms of intratumoral bacteria, we identified two genera, Streptococcus and Granulicatella, that were mutually exclusive with H. pylori infection in GC. Enhanced L-lysine fermentation to acetate and butanoate was observed among intratumoral bacteria, suggesting potential metabolic shifts in the tumor microenvironment. Incorporating H. pylori infection status into the microbiome-based prediction model further improved the accuracy of predicting immunotherapy outcomes in GC.

CONCLUSION: These findings suggest that H. pylori had significant effects on the structure and functional activity of gut and intratumoral microbiome, some of which may affect the efficacy of immunotherapy. The clinical value of H. pylori infection status should be considered when establishing a prediction model for immunotherapy efficacy based on gut microbiome.},
}

@article {pmid41526636,
year = {2026},
author = {Neff, HA and Yıldız-Altay, Ü and Salam, N and Ward, DV and Shepard, D and Ramirez-Ortiz, ZG and Richmond, JM},
title = {Gut dysbiosis in a murine model of cutaneous lupus erythematosus correlates with antigen-specific T cells and antigen-presenting cells in skin.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34741-6},
pmid = {41526636},
issn = {2045-2322},
support = {Mechanisms & Targets Award//Lupus Research Alliance/ ; Mechanisms & Targets Award//Lupus Research Alliance/ ; },
abstract = {The commensal organisms constituting the human microbiome are increasingly appreciated to fortify epithelial barriers and modulate host immunity. Dysbiosis of both single strains and communities can contribute to inflammatory conditions. Here, we sought to characterize potential dysbiosis in our inducible mouse model of cutaneous lupus erythematosus (CLE). We hypothesized that gut dysbiosis would occur based on several studies that found lower Firmicutes/Bacteroidetes (F/B) ratios and decreased diversity in systemic lupus erythematosus (SLE) cohorts compared to healthy counterparts, a mouse study that identified Ro60 commensal orthologs that can trigger onset of lupus-like disease, and a study of CLE that identified outgrowth of Staphylococcus aureus in the skin. Using whole genome shotgun sequencing, we identified differences in pre- and post-irradiation cohorts, particularly an increase in Duncaniella, a decrease in Prevotella, and a reduction in alpha diversity following irradiation. Baseline alterations in CLE mice gut bacteria compared to littermate controls were also extant, including trends toward increased Parabacterides distasonis and Bacteroides acidifaciens in CLE mice. Importantly, we noted an increase in Phocaeicola sartorii in CLE mice compared to littermate controls post-disease induction. We examined the mycobiome in our mice and noted a reduction of Colletotrichum tofieldiae specifically in CLE mice post-disease induction, and a trend towards increased Periglandula ipomoeae. Last, we correlated abundance of genera and species with flow cytometry data obtained from the skin, lymph node and spleen, and identified specific strains that correlated with presence of antigen-specific T cells and different antigen presenting cell populations. Thus, our model exhibits similar changes to other models of lupus-like disease, and our data identify potential novel strains/species that could be modified for CLE and/or SLE treatment such as through generation of probiotics or specific antimicrobial agents.},
}

@article {pmid41526566,
year = {2026},
author = {Swarte, JC and Zhang, S and Bakker, SJL and Björk, JR and Weersma, RK},
title = {The gut microbiome in solid-organ and haematopoietic-stem-cell transplantation.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41526566},
issn = {1740-1534},
abstract = {Solid-organ transplantation (for example, kidney or liver) and haematopoietic-stem-cell transplantation have revolutionized treatment of end-stage organ failure and haematological malignancies. However, long-term outcomes are often undermined by complications such as allograft rejection, graft-versus-host disease in haematopoietic-stem-cell recipients, opportunistic infections, adverse effects of drugs and decreased quality of life. Emerging evidence now highlights the gut microbiome and its metabolites (such as short-chain fatty acids) as a potentially modifiable factor influencing transplantation outcomes. Transplantation recipients frequently exhibit gut dysbiosis, which has been linked to graft function, risk of infection (for example, vulnerability to multidrug-resistant bacteria), immune-mediated complications and patient survival. Furthermore, pharmacomicrobiomics studies indicate that microorganisms can metabolize immunosuppressive drugs into less active forms (such as the conversion of the immunosuppressive drug tacrolimus into less active or toxic forms through keto-reduction, glucuronidation or deconjugation) or can activate prodrugs (such as the conversion of mycophenolate mofetil into mycophenolic acid), thereby modulating drug efficacy and safety. Here, we discuss how the intestinal ecosystem is altered and persistently shaped by transplantation-related factors and immunosuppression and how these changes correlate with clinical outcomes. We provide a perspective on leveraging microbiome insights, through biomarkers or microbiome-targeted interventions, to improve outcomes in solid-organ and stem-cell transplantation.},
}

@article {pmid41526497,
year = {2026},
author = {Iktilat, K and Levin, G and Isacson, M and Turjeman, S and Tzemah-Shahar, R and Gamliel, G and Louzoun, Y and Koren, O and Agmon, M},
title = {Integrating gut microbiota and violence exposure metrics to classify psychological distress in middle-aged adults.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-025-01319-2},
pmid = {41526497},
issn = {2730-664X},
abstract = {BACKGROUND: Exposure to violence and psychological distress are positively correlated across populations. Microbiota-gut-brain crosstalk research supports that the microbiota is affected by environmental stressors and may influence mental state. Accordingly, we explored how the microbiota relates to exposure to violence and distress in midlife, a pivotal yet underexplored period. This life stage is marked by emerging vulnerability to chronic stress and mental health decline yet offers opportunities for early identification and intervention.

METHODS: We characterized the fecal microbiota of a previosly snowball-recruited Israeli-Muslim cohort (n = 305, 40-65 yrs) exposed to ongoing and increasing violence (during adulthood) and examined correlations with subjective reports of exposure to violence and psychological distress. We then used machine learning to leverage microbiota profiles and exposure to violence, classifying individuals into high- and low-distress categories.

RESULTS: We identify unique microbial signatures associated with increasing exposure to violence and distress. Some associated bacteria were previously identified in the literature, while others were not yet described in the context of the gut-brain axis. Microbial profiles associated with violence and distress are largely non-overlapping, yet we are able to classify participants into high- and low distress categories using a combination of microbiota and violence variables. This combined model outperforms those using only microbiota or demographics, but its classification accuracy remains modest (with a median area-under-the-curve of 0.595 (IQR 0.045).

CONCLUSIONS: This research sheds light on the microbiota-gut-brain axis, highlighting that psychological distress and exposure to violence are differentially associated with microbiota composition in midlife. These cross-sectional findings, together with moderate classification into distress classes based on the microbiome, suggest that holistic, context-aware approaches would benefit proactive mental health interventions.},
}

@article {pmid41526493,
year = {2026},
author = {Smith, DR and Haq, S and Niu, M and Malla, S and Saha, R and Peer, A and Bianco, P and Romanova, S and Samuelson, DR and Knoell, DL},
title = {ZIP8 loss impairs macrophage-mediated phagolysosomal removal of bacteria and is overcome by butyrate supplementation.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09504-8},
pmid = {41526493},
issn = {2399-3642},
support = {5R35GM143009//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Zinc deficiency impacts billions of people and contributes significantly to the increased incidence of community-acquired pneumonia worldwide. Myeloid cells require the zinc transporter ZIP8 for proper host defense. Previously, we observed that infection with S.pneumoniae in myeloid-specific Zip8 knockout mice (Zip8KO) results in increased bacterial burden and mortality despite increased recruitment of macrophages into the lung. Here, we reveal that the lungs of infected Zip8KO mice generate a unique population of dysfunctional macrophages with defects in phagolysosomal function and cell survival. In particular, Zip8KO bone marrow-derived macrophages have increased bacterial accumulation due to deficits in lysosomal number and function via defective mTORC1/TFEB signaling. Knowing that labile Zn cannot enter the cytosol through ZIP8 and that ZIP8 loss impairs butanoate synthesis by the gut microbiome, both previously reported by our group, we reveal an alternative treatment strategy via extended oral phenylbutyrate supplementation. Despite ongoing ZIP8-mediated impairment of lung host defense, phenylbutyrate restored macrophage-mediated bacterial clearance and improved host outcomes. Given the high incidence of diet-induced Zn deficiency and the rs13107325 ZIP8 defective variant allele in humans, future investigations that foster preventive, patient-centered treatment strategies that counter immune dysfunction due to Zn dyshomeostasis are warranted.},
}

@article {pmid41526416,
year = {2026},
author = {Hasan, R and Shaikh, MTM and Rawat, S and Singh, V and Tamang, R and Choudhury, S},
title = {Intratumoral microbiome signatures in a North Central Indian colorectal cancer cohort: identification of novel prognostic biomarkers and functional pathways.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1815},
pmid = {41526416},
issn = {2045-2322},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/mortality ; India/epidemiology ; Female ; Male ; Middle Aged ; Prognosis ; *Biomarkers, Tumor/genetics ; RNA, Ribosomal, 16S/genetics ; Aged ; *Gastrointestinal Microbiome ; Adult ; Cohort Studies ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {Colorectal cancer (CRC) remains a major global health burden, with emerging evidence implicating gut and oral microbiome dysbiosis in its pathogenesis. This comparative observational study aimed to investigate intratumoral microbial signatures in early-onset CRC (EOCRC) and their association with clinical outcomes. In fact, till date there is no comprehensive study yet that directly compares the microbiome of EOCRC patients in North Central India to other EOCRC groups globally. We analysed 50 matched tumor and adjacent normal tissues (obtained from the same patient) using 16S rRNA amplicon sequencing. Taxonomic and functional analyses were conducted using DESeq2, LEfSe, and KEGG pathway prediction (via PICRUSt2). Our findings revealed distinct intratumoral enrichment of oral pathobionts such as Leptotrichia buccalis and Filifactor alocis, which showed significant correlation with mortality risk. Caldilinea aerophila was detected for the first time in human tumor tissue and was strongly associated with advanced TNM stages (p = 0.01; 83% specificity) in North Central Indian population. LEfSe analysis identified an overrepresentation of Actinomycetales. KEGG pathway analysis revealed enrichment of MAPK signaling, styrene, and aminobenzoate degradation pathways. Depletion of Lactobacillus plantarum and presence of dietary-linked microbes suggest microbial modulation by lifestyle. These findings highlight novel microbial biomarkers and immune-related pathways with potential prognostic implications in this regional CRC cohort.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/mortality
India/epidemiology
Female
Male
Middle Aged
Prognosis
*Biomarkers, Tumor/genetics
RNA, Ribosomal, 16S/genetics
Aged
*Gastrointestinal Microbiome
Adult
Cohort Studies
*Microbiota
Bacteria/genetics/classification

@article {pmid41526369,
year = {2026},
author = {Fu, W and Sun, C and Sun, B and Li, P and Ding, X and Guo, Q and Yuan, J and Lai, H},
title = {Flavonoid-mediated bacterial spermidine biosynthesis enhances vitamin accumulation in tomato fruits.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68244-9},
pmid = {41526369},
issn = {2041-1723},
abstract = {Rhizosphere microbes benefit plant growth and health. How plant-microbe interactions regulate fruit quality remains poorly understood. Here, we elucidate the multi-level modulation of vitamin accumulation in tomato by flavonoid-mediated crosstalk between host plants and rhizosphere microbes. SlMYB12-overexpressing plants with up-regulated flavonoid biosynthesis accumulate higher levels of vitamins C and B6 in fruits compared to wild-type plants grown in natural soil. Flavonoid-mediated improvement of fruit quality depends on the presence of soil microbiomes and relates to rhizosphere enrichment of key taxa (e.g. Lysobacter). Multi-omics analyses reveal that flavonoids attract Lysobacter soli by stimulating its twitching motility and spermidine biosynthesis, which in turn boosts vitamin accumulation in fruits across tomato cultivars and soil types. RpoN acts as a dual regulator in L. soli that is responsive to flavonoids, controlling bacterial motility and spermidine production. Our study provides insight into flavonoid-mediated rhizosphere signalling and underscores plant-microbiome orchestration for improved tomato fruit quality.},
}

@article {pmid41526362,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R},
title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00905-5},
pmid = {41526362},
issn = {2055-5008},
abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.},
}

@article {pmid41526019,
year = {2026},
author = {Donaubauer, AJ and Frey, B and Agaimy, A and Lange, F and Mogge, L and Fietkau, R and Iro, H and Munoz, LE and Weber, M and Kesting, M and Gaipl, US and Haderlein, M and Müller, S},
title = {Definition of predictive and prognostic immune biomarkers for salivary gland cancer from the intratumoural and systemic immune status: detailed protocol of the prospective, observatory ImmoGlandula study.},
journal = {BMJ open},
volume = {16},
number = {1},
pages = {e100021},
doi = {10.1136/bmjopen-2025-100021},
pmid = {41526019},
issn = {2044-6055},
mesh = {Humans ; *Salivary Gland Neoplasms/immunology/therapy/pathology ; Prospective Studies ; Prognosis ; *Biomarkers, Tumor/immunology ; Immunotherapy ; Observational Studies as Topic ; Female ; },
abstract = {INTRODUCTION: Salivary gland carcinomas (SGC) are rare tumours. The term SGC is not more than an umbrella for a variety of histogenetically, morphologically and biologically distinct entities. Accordingly, SGCs have not been sufficiently investigated to date. Their rarity makes it difficult to reach high patient numbers for individual entities in clinical studies, leading to pooling patients with different histological subtypes to attain sufficient participants. The different histological subtypes of SGC differ significantly in their clinicopathological features, such as their grading, their occurrence and their outcome. SGCs are usually stratified into low-grade, intermediate-grade or high-grade tumours. In most kinds of SGC, specific targetable molecular markers are lacking. The inclusion of immunotherapy (IT), however, might improve the outcome of patients suffering from high-grade SGCs. In order to integrate IT as a therapeutic option for SGC and to facilitate therapeutic decisions based on tumour (immune) biology, predictive and prognostic immunological biomarkers are indispensable.

METHODS AND ANALYSIS: In this prospective study, 500 patients will be enrolled, who are distributed in three arms. The observational cohort includes patients with malignant salivary gland tumours, whereas patients with benign tumours of a salivary gland are grouped in the control group 1. In the control cohort, 2 patients do not have a salivary gland tumour but have a planned functional surgery of the nose or ear or a maxillofacial surgery. The local immune status from the tumour tissue and the microbiome will be sampled before treatment. In addition, the systemic immune status from peripheral blood will be analysed before and after surgery and after the adjuvant and definitive chemoradiotherapy, if applicable. Clinical baseline characteristics and outcome parameters will additionally be collected. Data mining and modelling approaches will finally be applied to identify interactions of local and systemic immune parameters and to define predictive and prognostic immune signatures based on the evaluated immune markers.

ETHICS AND DISSEMINATION: Approval from the institutional review board of the Friedrich-Alexander-Universität Erlangen-Nürnberg was granted in September 2023 (application number 23-292-B). The results will be disseminated to the scientific audience and the general public via presentations at conferences and publication in peer-reviewed journals.

TRIAL REGISTRATION NUMBER: NCT06047236.},
}

Humans
*Salivary Gland Neoplasms/immunology/therapy/pathology
Prospective Studies
Prognosis
*Biomarkers, Tumor/immunology
Immunotherapy
Observational Studies as Topic
Female

@article {pmid41525802,
year = {2026},
author = {Cheng, C and Xu, S and Liu, Z and Zhang, H and Yang, Y and Zhang, Y and Ge, E and Xu, J and Zhu, Q and Li, X and Yu, B and Liu, M and Guo, Y},
title = {Microbial community differences between healthy and Ustilago-infected oats.},
journal = {Genomics},
volume = {},
number = {},
pages = {111202},
doi = {10.1016/j.ygeno.2026.111202},
pmid = {41525802},
issn = {1089-8646},
abstract = {Ustilago, a pathogenic fungus, poses a serious threat to oat growth and yield. However, the species composition, abundance, and distribution of microbial communities in Ustilago-infected oats remain poorly characterized. In this study, we conducted 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing and biochemical assays to compare microbial profiles and physiological traits between healthy (n = 60) and Ustilago-infected oats (n = 60). Our analyses revealed higher bacterial diversity in healthy oats, particularly in the spikes and stems. Significant shifts in microbial community structure were observed across all tissues in diseased plants. While the microbiome of healthy oats predominantly comprised beneficial bacteria, including Exiguobacterium indicum, infected plants were largely colonized by pathogens, including Ustilago hordei, Pyrenophora chaetomioides, and Curtobacterium flaccumfaciens pv. flaccumfaciens, suggesting the occurrence of disease-driven microbial restructuring. Functional predictions indicated that enriched pathways were primarily associated with metabolism, followed by genetic information processing and environmental signal transduction. Malondialdehyde content was significantly lower in most healthy oat tissues compared to Ustilago-infected oats, whereas the activities of the antioxidant enzymes superoxide dismutase and peroxidase were markedly higher. These results implied that Ustilago infection induced severe oxidative damage to membrane systems, likely compromising the plant's ability to scavenge superoxide ions and hydrogen peroxide, thereby reducing overall plant health.},
}

@article {pmid41525776,
year = {2026},
author = {, and Proctor, LM},
title = {Integrating microbiomes into One Health: insights from the 2025 One Health World Microbiome Partnership Summit.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101319},
doi = {10.1016/j.lanmic.2025.101319},
pmid = {41525776},
issn = {2666-5247},
}

@article {pmid41525625,
year = {2026},
author = {Weng, Q and Hu, M and Peng, G and Lu, W and Wang, H and Zhu, J},
title = {Variational Bayesian Multi-Output Gaussian Process Regression for Metabolic Profiles Prediction with Microbiome Data.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2026.3653067},
pmid = {41525625},
issn = {2998-4165},
abstract = {Understanding the pivotal role of the human microbiome in health necessitates accurate metabolite prediction, which is crucial for unraveling the intricate interplay between the gut microbiome and human health. This study introduces an innovative approach, Variational Bayesian Multi-Output Gaussian Process Regression (VBMOGPR), to address the challenges posed by the complex, high-dimensional nature of microbiome data. VBMOGPR predicts microbial metabolites, quantifies the model confidence, and incorporates uncertainty estimates. Employing a Bayesian framework with Automatic Relevance Determination (ARD) for feature selection enhances interpretability and performance. Comparative analysis across 14 datasets within a meta-database demonstrated the superiority of VBMOGPR, marking a significant advancement in metabolite prediction and its implications for microbiome impact on human health. In addition, we confirmed that VBMOGPR could tap the potential microbial metabolic association.},
}

@article {pmid41525344,
year = {2026},
author = {van der Ploeg, GR and White, FTG and Jakobsen, RR and Westerhuis, JA and Heintz-Buschart, A and Smilde, AK},
title = {ACMTF-R: Supervised multi-omics data integration uncovering shared and distinct outcome-associated variation.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0339650},
pmid = {41525344},
issn = {1932-6203},
mesh = {Female ; Humans ; Pregnancy ; Algorithms ; Metabolomics/methods ; Milk, Human/microbiology/metabolism ; *Multiomics ; Feces/microbiology ; Infant ; },
abstract = {The rapid growth of high-dimensional biological data has necessitated advanced data fusion techniques to integrate and interpret complex multi-omics and longitudinal datasets. Shared and unshared structure across such datasets can be identified in an unsupervised manner with Advanced Coupled Matrix and Tensor Factorization (ACMTF), but this cannot be related to an outcome. Conversely, N-way Partial Least Squares (NPLS) is supervised and captures outcome-associated variation but cannot identify shared and unshared structure. To bridge the gap between data exploration and prediction, we introduce ACMTF-Regression (ACMTF-R), an extension of ACMTF that incorporates a regression step, allowing for the simultaneous decomposition of multi-way data while explicitly capturing variation associated with a dependent variable. We present a detailed mathematical formulation of ACMTF-R, including its optimisation algorithm and implementation. Through extensive simulations, we systematically evaluate its ability to recover a small [Formula: see text]-related component shared between multiple blocks, its robustness to noise, and the impact of the tuning parameter ([Formula: see text]) which controls the balance between data exploration and outcome prediction. Our results demonstrate that ACMTF-R can robustly identify the [Formula: see text]-related component, correctly identifying outcome-associated shared and distinct variation, distinguishing it from existing approaches such as NPLS and ACMTF. The development of ACMTF-R was motivated by a real-world dataset investigating how maternal pre-pregnancy BMI affects the human milk microbiome, human milk metabolome, and infant faecal microbiome. Emerging evidence suggests that inter-generational transfer of maternal obesity may affect multiple omics layers, highlighting the need to identify outcome-associated variation. The applicability of ACMTF-R is therefore validated by applying it to this multi-omics dataset. ACMTF-R successfully identifies novel mother-infant relationships associated with maternal pre-pregnancy BMI, underscoring its utility in multi-omics research. Our findings establish ACMTF-R as a versatile tool for multi-way data fusion, offering new insights into complex biological systems by integrating common, local, and distinct variation in the context of a dependent variable.},
}

Female
Humans
Pregnancy
Algorithms
Metabolomics/methods
Milk, Human/microbiology/metabolism
*Multiomics
Feces/microbiology
Infant

@article {pmid41525336,
year = {2026},
author = {Li, X and Smart, CE and Millard, K and Bell, KJ},
title = {Nutrition and healthy lifestyles for children and adolescents with early-stage type 1 diabetes.},
journal = {Hormone research in paediatrics},
volume = {},
number = {},
pages = {1-20},
doi = {10.1159/000550434},
pmid = {41525336},
issn = {1663-2826},
abstract = {Increasingly children and adolescents are being identified in early-stage type 1 diabetes (T1D), defined as two or more islet autoantibodies without hyperglycemia (above diagnostic threshold) or reliance on intensive insulin therapy. They require clinical monitoring and care. Healthy lifestyle education is recommended in guidelines, however evidence synthesis to inform clinical practice is lacking. Therefore, this review summarizes current evidence on nutrition, lifestyle to delay progression to stage 3 T1D; and proposes lifestyle strategies for children and adolescents with early-stage T1D. Specifically, we suggest a key focus on reducing beta-cell stress, promoting a healthy gut microbiome and establishing healthy lifestyles and relationships with food, prior to the introduction of intensive insulin therapy. As secondary prevention of T1D is an emerging research area and randomized controlled trials are scarce, evidence has been largely drawn from prospective cohort studies and routine clinical care for stage 3 T1D. A balanced and varied diet, limiting intake of foods containing high amounts of saturated fat and added sugar, and moderate levels of physical activity, are likely beneficial for overall health in children and adolescents with early-stage T1D. Low glycemic index (GI) diets may be protective against progression to stage 3 T1D.},
}

@article {pmid41525322,
year = {2026},
author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI},
title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013883},
doi = {10.1371/journal.pcbi.1013883},
pmid = {41525322},
issn = {1553-7358},
abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.},
}

@article {pmid41525151,
year = {2026},
author = {Walsh, SK and Armet, AM and Nikolaeva, DD and Mota, JF and Lucey, AJ and Oliero, M and Walter, J},
title = {Optimizing Dietary Fiber Intake: Strategies for Human Nutrition and Food Science.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-052824-044842},
pmid = {41525151},
issn = {1941-1421},
abstract = {Adequate dietary fiber intake from plant foods is critical for the prevention of noncommunicable chronic diseases (NCDs). However, across industrialized nations, consumption remains insufficient to meet established intake recommendations. This gap provides a strong rationale to include functional fibers into processed foods or use them as supplements, although their effectiveness in reducing NCD risk is inconclusive . In this review, we examine current nutritional strategies to optimize fiber intake, spanning whole-plant foods, processed foods made or enriched with fiber-containing ingredients, and fiber supplements. We examine the structure and physicochemical properties of the fiber types represented in these strategies and explore the mechanisms by which they influence the gut microbiome and NCD risk markers. Drawing on evidence from human intervention studies, we critically assess the strengths and limitations of each strategy to improve health outcomes and propose a framework for the effective and systematic integration of fiber into nutrition and food science.},
}

@article {pmid41525137,
year = {2026},
author = {Jackson, SA and Hrab, P and Zdouc, MM and Clarke, DJ and Dobson, ADW},
title = {New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41525137},
issn = {2057-5858},
mesh = {*Porifera/microbiology ; Animals ; *Metagenome ; *Microbiota/genetics ; Secondary Metabolism/genetics ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Multigene Family ; Genome, Bacterial ; Sequence Analysis, DNA ; },
abstract = {Marine sponges are found in all of the world's oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 bacterial phyla have been observed to be associated with sponges, and thousands of unique natural products have been extracted from sponges or their microbial symbionts. However, sponges from the deep sea and their associated microbial communities are relatively understudied, largely due to sampling-associated difficulties. Secondary metabolism biosynthetic gene clusters are phylogenetically distinct and hold the potential to produce novel chemistry with potential pharmacological or industrial utility. In order to gain further insights into the microbiome of the deep-sea sponge Inflatella pellicula, the metagenome of this sponge, sampled from a depth of 2,900 m, was sequenced. A large fraction of the sequence reads appeared to be 'biological dark matter' and could not be taxonomically classified. Further, unlike similar studies from different marine ecosystems, relatively few metagenome-assembled genomes (MAGs) could be assembled, and relatively few secondary metabolism biosynthetic gene clusters were identified. The identified clusters were, however, very dissimilar to known characterized clusters, but some shared similarities with clusters annotated in MAGs assembled from sponge metagenomes from disparate geographic locations. Therefore, renewed efforts to cultivate the hosts of these gene clusters may yield valuable small-molecule natural products.},
}

*Porifera/microbiology
Animals
*Metagenome
*Microbiota/genetics
Secondary Metabolism/genetics
Phylogeny
*Bacteria/genetics/classification/metabolism/isolation & purification
Multigene Family
Genome, Bacterial
Sequence Analysis, DNA

@article {pmid41525049,
year = {2026},
author = {Nishu, and Verma, K and Noor, SA and Mathur, V},
title = {Aboveground insect herbivory shapes plant-soil feedback and ecosystem resilience.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {41525049},
issn = {2676-8607},
abstract = {The interaction between plants and their surrounding soil ecosystems is complex, with plant-soil feedback acting as legacy effects from previous plants, influencing subsequent plant growth and insect interactions. Recent studies have shown that experiments focusing on individual factors in isolation do not accurately predict the outcomes of these complex interactions. Aboveground herbivores impact the development of root exudates and their surrounding microbiome, suggesting that herbivory indirectly shapes belowground biotic communities. Such impact of insect herbivory on plant-soil feedback is a crucial area of ecological research. Most studies focus on root-associated organisms and their influence on foliar herbivorous insects, and little attention has been given to the reverse interaction-how foliar herbivory affects the soil environment and PSF. This study explores the bidirectional influence of herbivory and PSF, revealing that aboveground insect herbivory can significantly alter plant-soil feedback mechanisms, influencing not only plant performance but also the broader community structure. A holistic approach that integrates soil microbial complexity with insect herbivory is needed to better predict community-level outcomes and enhance plant protection strategies. Our study thus highlighted the need for a community-based perspective when studying interactions among plants, insects and soil microorganisms.},
}

@article {pmid41525005,
year = {2026},
author = {Mir, PA and Kumar, N and Bhutia, GT and Chaudhary, P and Kaur, G and Gupta, SK},
title = {The aging gut-glia-immune axis in alzheimer's disease: microbiome-derived mediators of neuroinflammation and therapeutic innovation.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41525005},
issn = {2509-2723},
abstract = {Alzheimer's disease (AD), the most common cause of dementia in the aging population, is marked by amyloid-beta (Aβ) plaques, tau tangles, and progressive neuronal degeneration, placing heavy clinical and socioeconomic burdens on healthcare worldwide. Aging remains the strongest risk factor, with chronic low-grade inflammation, oxidative stress, mitochondrial dysfunction, and impaired proteostasis creating a vulnerable brain environment that accelerates AD onset and progression. Recent evidence highlights the gut-glia-immune axis as a critical pathway linking age-related microbiome changes to glial dysfunction. Microbial metabolites, such as short-chain fatty acids and tryptophan derivatives, regulate microglial maturation, astrocytic activity, and neuroimmune signaling. However, age-associated dysbiosis disrupts glial homeostasis, amplifies neuroinflammation, and impairs amyloid clearance, thereby worsening neurodegeneration. Preclinical models including germ-free mice and fecal microbiota transplantation along with clinical studies of elderly AD patients, provide compelling evidence of microbiome-driven modulation of disease. From a therapeutic perspective, microbiome-targeted interventions including probiotics, prebiotics, synbiotics, and microbiota-directed small molecules offer promising strategies to restore glial balance, reduce inflammation, and protect cognitive function. This review highlights the therapeutic potential of probiotics, synbiotics, and fecal microbiota transplantation for mitigating neuroinflammation and cognitive decline in Alzheimer's disease. However, given the multifactorial nature of neurodegenerative disorders, these strategies are unlikely to be universally effective and must be tailored to individual patient profiles.},
}

@article {pmid41524878,
year = {2026},
author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M},
title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
pmid = {41524878},
issn = {1534-4681},
abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.

PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.

RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.

CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.},
}

@article {pmid41461908,
year = {2025},
author = {, and Alberts, T and Albritton, CF and Alcazar, R and Aljabri, Z and Alvarez, M and Aradhey, A and Ayalew, M and Azizian, N and Balayah, Y and Ball, DD and Barragan, E and Beshoar, C and Best, L and Biggane, E and Biggane, J and Blick, J and Blosser, M and Brown, AK and Campbell, MC and Canizares, Z and Chanhuhwa, FN and Chen, Y and Chin, DR and Chowdhury, K and Collins, T and Compton, B and Da Silva, J and Davis, NR and DeCaro, N and Delgadillo, F and Deng, Y and Duncan, J and Egwu, AC and Ekalle, GD and Elnawam, N and Enke, R and Ewhe, N and Ferrel, MA and Fierst, J and Freymiller, G and Fuller, K and Fulton-Wright, L and Gaysinskaya, V and Gill, T and Gillespie, E and Gonzalez Moreno, P and Goodwin, S and Graham, N and Graham, ME and Graves, JL and Grob, E and Gutierrez, R and Hager, A and Hakim, ST and Harris, A and Hoffman, AM and Hoffmann, T and Horton, AM and Hughes, A and Humphries, EM and Ikechi-Konkwo, JS and Ishtiaq, A and Jackson, R and James, JR and James, K and Jamison, SA and Jimenez, A and Johnson, R and Kauffman, A and Kaur, H and Kc, K and Keeton, A and Kelly, OE and Kerr, J and Kucher, N and Kuehu, DL and Larson, WA and Lee, J and Lee, A and Leek, JT and Lemaic, D and Liburd, LE and Lopez, AF and Mahmanzar, M and Mamae, K and Manjikian, R and Marone, M and Marquez, K and Martinson, A and Mavruk Eskipehlivan, S and Medrano, A and Melendrez-Vallard, M and Meller, R and Méndez, LB and Mendez Gonzalez, MP and Mesquita, N and Miller, CM and Mohd-Ibrahim, I and Mortensen, P and Mosher, S and Muja, A and Nasrin, N and Nasu, M and Nguyen, MH and Nguyen, BT and Nishiguchi, M and O'Connor, LM and Okie, D and Olowookorun, T and Ostrovsky, A and Ozuna, K and Pandey, A and Patel, SB and Paul, G and Pawar, S and Pearson, A and Petrik, D and Platero, J and Pontino, C and Pratap, AP and Pratap, S and Qin, Y and Rai, SK and Ray, N and Repesh, E and Rhinehardt, K and Roche, B and Rodriguez, A and Roy, S and Roy, S and Sawa, A and Schatz, MC and Sen, SK and Serikawa, R and Smith, T and Smith, L and Sniezek, J and Stewart, RD and Suarez-Martinez, EB and Taganna, J and Tan, FJ and Tsotakos, N and Udolisa, N and Ulbricht, K and Veo, T and Vessio, J and Walker, L and Wang, O and Wang, Q and Wappel, R and Wesby, K and Whitford, M and Wild, N and Xie, X and Yang, H and York, S and Zirkle, L},
title = {Unearthing soil biodiversity through collaborative genomic research and education.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {41461908},
issn = {1546-1718},
support = {2011934//National Science Foundation (NSF)/ ; U24 HG013013/HG/NHGRI NIH HHS/United States ; 75N92022P00232//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5T34GM151403//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 2221924//National Science Foundation (NSF)/ ; 1839895//National Science Foundation (NSF)/ ; 2000157//National Science Foundation (NSF)/ ; U24HG013013//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 75N92023P00302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The BioDIGS project is a nationwide initiative involving students, researchers and educators across more than 40 research and teaching institutions. Participants lead sample collection, computational analysis and results interpretation to understand the relationships between the soil microbiome, environment and health.},
}

@article {pmid40045571,
year = {2026},
author = {Kim, DS and Kim, EH and Kim, JY and Kim, DH and Choi, YJ and Jeong, J and Sung, YH and Woo, DC and Kim, CJ and Lee, JC and Yun, M and Jeong, JY and Rho, JK},
title = {The Profile of Gut Microbiota in Carcinogenesis Driven by Mutant EGFR in Non-Small Cell Lung Cancer.},
journal = {Cancer research and treatment},
volume = {58},
number = {1},
pages = {115-127},
doi = {10.4143/crt.2024.1177},
pmid = {40045571},
issn = {2005-9256},
support = {2022IP0029//Asan Institute for Life Science/ ; RS-2023-00261982//Korea Health Industry Development Institute/Republic of Korea ; HR21C0198//Ministry of Health and Welfare/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; ErbB Receptors/genetics ; *Lung Neoplasms/genetics/pathology/microbiology ; Humans ; Mice ; *Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology ; Mutation ; *Carcinogenesis/genetics ; Mice, Transgenic ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Feces/microbiology ; Female ; },
abstract = {PURPOSE: Accumulating evidence has clarified that gut dysbiosis is involved in lung cancer development and progression. Although the relationship between tumors and gut microbiota has been extensively studied using clinical samples, no studies have examined the association between mutant epidermal growth factor receptor (EGFR)-induced lung carcinogenesis and dysbiosis in gut microbiota. Therefore, we investigated the gut microbiota profiles in stool samples from human lung-specific conditional EGFR-mutant transgenic mice during lung tumor carcinogenesis.

MATERIALS AND METHODS: Stool samples were collected before tamoxifen treatment (V1) and at each time point following mutant EGFR expression in lung tissue (V2) and lung tumor appearance (V3). Fecal 16S rRNA taxonomy was analyzed to assess microbial diversity, composition, and dynamic changes at each time point.

RESULTS: We found that microbiota richness and diversity were significantly elevated when tumors developed and grew in the lung. Phylogenetic analysis of the microbial community revealed that Lachnospiraceae, Ruminococcaceae, Porphyromonadaceae, Rhodospirillaceae, Odoribacteraceae, and Desulfovibrionaceae showed a significant increase at the V3 stage compared to the V1 stage at the family level. In contrast, Lactobacillaceae, Bacteroidaceae, Muribaculaceae, Coriobacteriaceae, and Rikenellaceae significantly decreased at the V3 stage compared to the V1 stage. Furthermore, Lactobacillus species, also known as short chain fatty acid-producing bacteria, were relatively abundant at the V1 stage but were depleted with the occurrence of lung tumors at the V3 stage.

CONCLUSION: Changes in gut microbiota, such as Lactobacillus species, may be a predictive factor for the emergence and progression of tumors in an animal model of lung adenocarcinoma induced by mutant EGFR.},
}

*Gastrointestinal Microbiome/genetics
Animals
ErbB Receptors/genetics
*Lung Neoplasms/genetics/pathology/microbiology
Humans
Mice
*Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology
Mutation
*Carcinogenesis/genetics
Mice, Transgenic
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny
Feces/microbiology
Female

@article {pmid41524843,
year = {2026},
author = {Haysom-McDowell, A and Paudel, KR and Mehndiratta, S and Singh, M and Malik, MZ and Kokkinis, S and Pakan, PD and Williams, FE and Singh, SK and Dua, K and De Rubis, G},
title = {Fisetin-loaded Nanoemulsion and Fecal Microbiome Extract Enhance In Vitro Inhibition of Non-Small Cell Lung Cancer Progression.},
journal = {Cell biochemistry and biophysics},
volume = {},
number = {},
pages = {},
pmid = {41524843},
issn = {1559-0283},
}

@article {pmid41524809,
year = {2026},
author = {Singh, G and Aran, KR},
title = {Rethinking on bile acid-brain axis: decoding neurotoxic and neuroprotective landscape in aging and Alzheimer's disease.},
journal = {Biogerontology},
volume = {27},
number = {1},
pages = {37},
pmid = {41524809},
issn = {1573-6768},
mesh = {Humans ; *Alzheimer Disease/metabolism/drug therapy/pathology ; *Bile Acids and Salts/metabolism ; *Aging/metabolism ; *Brain/metabolism/pathology ; Animals ; Gastrointestinal Microbiome ; Neuroprotective Agents ; Neuroprotection ; },
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative condition in which aging serves as the predominant risk factor. Emerging research underscores the importance of bile acids (BAs), traditionally recognized for their role in digestion, as key signaling mediators involved in both systemic metabolism and neural communication. Disruption of bile acid (BA) metabolism during aging arises from altered hepatic synthesis, gut microbial imbalance, and defective receptor signaling. These changes have been implicated in several neurodegenerative processes, including Aβ accumulation, tau protein abnormalities, mitochondrial impairment, and disturbances in immune regulation. Aging induces a shift in BA composition toward more cytotoxic species, contributing to blood-brain barrier disruption and enhanced neuronal damage. Multi-omics analyses have identified distinct BA signatures in plasma and cerebrospinal fluid of individuals with mild cognitive impairment and AD. These alterations show strong correlations with brain atrophy and progressive cognitive decline. Experimental and early clinical findings suggest potential neuroprotective effects of hydrophilic BAs such as ursodeoxycholic acid and tauroursodeoxycholic acid, along with therapeutic opportunities through modulation of BA receptors and microbiome-driven BA regulation. In the current era of AD research, the gut-liver-brain BA axis emerges as a novel mechanistic framework linking systemic metabolic aging to neurodegeneration. This review examines the molecular pathways through which BA dysregulation influences aging and AD, emphasizing its therapeutic relevance and supporting the development of biomarker-based and precision medicine approaches for neurodegenerative disorders.},
}

Humans
*Alzheimer Disease/metabolism/drug therapy/pathology
*Bile Acids and Salts/metabolism
*Aging/metabolism
*Brain/metabolism/pathology
Animals
Gastrointestinal Microbiome
Neuroprotective Agents
Neuroprotection

@article {pmid41524665,
year = {2026},
author = {Pibaque, P and Porporato, G and Cescutti, S and Cruz-Flores, A and Busche, T and Winker, A and Rapp, TM and Bergkamp, P and Doneva, A and Chakarov, N},
title = {Domination Versus Sisterhoods in the Blood Microbiota of Migrating Birds: Patterns of Within- and Between-Individual Blood Parasite Diversity Revealed Through Metabarcoding.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70056},
pmid = {41524665},
issn = {1749-4877},
abstract = {Avian blood parasites of the genera Plasmodium, Haemoproteus, and Leucocytozoon are typically identified through Sanger sequencing of a partial cytochrome b fragment, the MalAvi barcoding region. This approach limits the detection of mixed infections and the relative frequencies of co-infecting parasites. In contrast, next-generation sequencing (NGS) can resolve these problems but has been underused for haemosporidian lineage identification in samples from the wild. We used an improved PCR protocol and sequencing with Illumina MiSeq to determine haemosporidian assemblages in wild birds captured at a migration stopover site in Bulgaria, Europe. From 406 samples obtained from 52 bird species, we detected 81 haemosporidian lineages in 131 infected samples from 32 species (32% prevalence). On average, individuals were infected with 2.4 lineages, with 59 birds infected by a single lineage, and 21 birds infected with 5-9 lineages. A subset of samples was Illumina- and Sanger-sequenced in parallel, finding mixed infections in 72 samples and 8× higher detection rate of mixed and co-infections through high-throughput sequencing. Both methods identified the same dominant (co-infecting) lineage (91%). Metabarcoding identified common mixed infections of sister lineage groups ("sisterhoods") known for prevalent lineages and morphospecies, including Plasmodium relictum p_SGS1, Haemoproteus motacillae h_YWT2, and Haemoproteus parabelopolskyi h_SYAT01. Some other lineages appeared consistently more dominant. Our study shows that in some host communities, metabarcoding can reveal a great diversity of mixed infections. This opens new horizons to the study of assemblages of haemosporidian parasites, their interactions within individual hosts, and co-evolution with other members of the blood microbiome and the hosts.},
}

@article {pmid41524491,
year = {2026},
author = {},
title = {Correction to "The Microbiome in Hidradenitis Suppurativa Tunnels: A Systematic Review".},
journal = {International journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ijd.70241},
pmid = {41524491},
issn = {1365-4632},
}

@article {pmid41524460,
year = {2026},
author = {Li, X and Yang, M and Jones, DL and Du, X and Liu, J and Guo, X and Tang, Z},
title = {Rhizosphere Metabolites and Microbial Communities Shape Lettuce Responses to Oxytetracycline Stress.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c10653},
pmid = {41524460},
issn = {1520-5118},
abstract = {Oxytetracycline (OTC), a persistent antibiotic frequently detected in agricultural soils, can influence plant growth and rhizosphere ecology. Using lettuce (Lactuca sativa L.) as a model, this study compared the effects of OTC under hydroponic and soil cultivation systems and integrated physiological, metabolomic, and microbiome analyses. Hydroponic exposure consistently inhibited growth, whereas soil culture showed a biphasic, dose-dependent pattern─low OTC doses stimulated growth while high doses suppressed it. In soil systems, OTC exposure reprogrammed rhizosphere metabolites and reshaped microbial networks, enriching taxa associated with OTC degradation and plant growth promotion (Chryseolinea, Nitrospira, Devosia, Haliangium). Structural equation modeling indicated that rhizosphere diversity and metabolite profiles mediate plant biomass responses. These findings reveal that rhizosphere metabolite-microbe networks play a key role in modulating plant hormetic responses to antibiotic stress, providing mechanistic insight into antibiotic-plant-microbe interactions in agroecosystems.},
}

@article {pmid41524424,
year = {2026},
author = {Grundmann, CO and Tomo, CJ and Hershelman, JL and Wolfe, BE and Sanchez, LM},
title = {Spatial metabolomics reveals the role of penicillic acid in cheese-rind microbiome disruption by a spoilage fungus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0130525},
doi = {10.1128/msystems.01305-25},
pmid = {41524424},
issn = {2379-5077},
abstract = {Microbial interactions in cheese rinds influence community structure, food safety, and product quality. But the chemical mechanisms that mediate microbial interactions in cheeses and other fermented foods are generally not known. Here, we investigate how the spoilage mold Aspergillus westerdijkiae chemically inhibits beneficial cheese-rind bacteria using a combination of omics technologies. In cheese-rind community and co-culture experiments, A. westerdijkiae strongly inhibited most cheese-rind community members. In co-culture with Staphylococcus equorum, A. westerdijkiae strongly affected bacterial gene expression, including upregulation of a putative bceAB gene cluster that is associated with resistance to antimicrobial compounds in other bacteria. Mass spectrometry imaging revealed spatially localized production of secondary metabolites, including penicillic acid and ochratoxin B at the fungal-bacterial interface with Brachybacterium alimentarium. Integration of liquid chromatography-tandem mass spectrometry and genome annotations confirmed the presence of additional bioactive metabolites, such as notoamides and circumdatins. Fungal metabolic responses varied by bacterial partner, suggesting species-specific chemical strategies. Notably, penicillic acid levels increased 2.5-fold during interaction with B. alimentarium, and experiments with purified penicillic acid showed inhibition in a dose-dependent manner against this rind bacterium. These findings show that A. westerdijkiae deploys a context-dependent suite of mycotoxins and other metabolites, disrupting microbial community assembly in cheese rinds.IMPORTANCEThis study identifies the chemical mechanisms underlying the negative impacts of Aspergillus westerdijkiae on cheese-rind development, revealing how specialized metabolites like penicillic acid and ochratoxin B influence rind bacterial communities. By integrating biosynthetic gene cluster analyses with mass spectrometry, we demonstrate how chemical communication shapes microbial interactions, with possible implications for food safety and cheese quality. Understanding these interactions is essential for assessing the risks of fungal-driven spoilage and mycotoxin production in cheese-rind maturation. Beyond cheese, these findings contribute to broader microbiome ecology, emphasizing how secondary metabolites mediate microbial competition in natural and fermented food environments.},
}

@article {pmid41524423,
year = {2026},
author = {Benedict, EE and Agee, W and Hink, T and Parrish, KL and Reske, KA and Peacock, K and Bosserman, RE and Valencia, A and Saluja, A and Ovchiyan, E and Arter, O and Jolani, K and Dubberke, ER and Dantas, G and Kwon, JH},
title = {Community-associated quinolone-resistant and extended-spectrum beta-lactamase-producing Escherichia coli isolates are similar to clinical infection isolates by sequence type and resistome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0159125},
doi = {10.1128/msystems.01591-25},
pmid = {41524423},
issn = {2379-5077},
abstract = {Escherichia coli is a public health threat capable of causing multiple types of infection, carrying a variety of antimicrobial resistance genes (ARGs), and disseminating ARGs to other microbes. Since ARG-carrying E. coli can exist as a commensal gut microbe, intestinal E. coli in community-associated (CA) members presents an under-appreciated reservoir of ARGs. We cultured 75 CA E. coli isolates from stool of 64 patients lacking inpatient healthcare exposures >24 hours in the previous 12 weeks. Remnant stool submitted to the Barnes-Jewish Hospital (BJH) microbiology laboratory for Clostridioides difficile testing was plated to MacConkey agar with ciprofloxacin and extended-spectrum beta-lactamase (ESBL) Chrome Agar to isolate resistant E. coli colonies, which were whole-genome sequenced. Isolates were compared to ESBL E. coli genomes published by Mahmud et al. (B. Mahmud, M. A. Wallace, K. A. Reske, K. Alvarado, et al., mSystems 7:e00519-22, 2022, https://doi.org/10.1128/msystems.00519-22), which were collected from bloodstream and urinary tract infections. We identified ESBL genes and quinolone resistance elements in E. coli isolates from all patients, 32 (50%) of whom had no recent antibiotic exposure. Sequence type (ST) 131 isolates carried more quinolone resistance elements but fewer ESBL genes than other STs. Eleven patients carried two distinct E. coli lineages simultaneously. CA ESBL E. coli displayed a lower diversity of beta-lactamase genes but similar rates of antibiotic resistance genes compared to ESBL E. coli reported by Mahmud et al. (https://doi.org/10.1128/msystems.00519-22). Carriage of resistance elements without recent antimicrobial exposure suggests the presence of circulating, resistant E. coli. Our results show the continually evolving resistance profile of CA E. coli, demonstrating the importance of characterizing antimicrobial resistance in the community.IMPORTANCEAntimicrobial-resistant Escherichia coli presents a substantial threat to public health, limiting treatment options and potentially horizontally transferring its resistance to other members of the gut microbiome. Resistance to quinolones and beta-lactams, specifically, hinders treatment of urinary tract and gastrointestinal infections, both commonly caused by E. coli. Tracking successful lineages, such as ST131, within the healthcare setting can inform clinicians about resistance patterns among their patients, but this work shows that other STs present an even higher antimicrobial resistance burden than ST131. In addition to monitoring multiple lineages of antimicrobial-resistant E. coli, it is necessary to identify and understand community-associated carriage of this organism, as evidenced by the increasing prevalence of community-associated ESBL E. coli carriage and our specific results showing similar resistance burdens within the clinic and community. This work presents insight into antimicrobial-resistant E. coli among those without significant healthcare exposures, providing important community-focused surveillance that is currently lacking.},
}

@article {pmid41524397,
year = {2026},
author = {Kozik, AJ},
title = {Out of the box: toward new frameworks for understanding human microbiomes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0100024},
doi = {10.1128/msphere.01000-24},
pmid = {41524397},
issn = {2379-5042},
abstract = {The study of the human microbiome (mirroring broader practice across biomedical science), has historically defaulted to the use of simplified, socially constructed "boxes," such as racial and ethnic labels, that fail to accurately capture human variation and fundamentally misdirect the search for mechanisms to explain differences in health outcomes. Five years ago, I proposed a "frameshift," a fundamental conceptual shift away from relying on these categories and toward a more nuanced, careful approach to the complexity of human variation. Moving "out of the box" means tackling the difficult but essential work of analyzing microbial variation through a systems lens, connecting large-scale ecosocial drivers to individual mechanisms and outcomes. In this Full Circle review, I discuss rapid progress in the field toward this new framework and argue that by adopting transdisciplinary methods, we can generate more accurate, actionable, and equitable solutions for human health.},
}

@article {pmid41524293,
year = {2026},
author = {Sassun, R and Brucchi, F and Sileo, A and Vignati, B and Crippa, J and Achilli, P and Maggioni, D and Spinelli, A and Montroni, I and Hawkins, AT and Mari, G},
title = {Recurrent left-sided diverticulitis after surgery: A systematic review and single arm meta-analysis.},
journal = {Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland},
volume = {28},
number = {1},
pages = {e70368},
doi = {10.1111/codi.70368},
pmid = {41524293},
issn = {1463-1318},
mesh = {Humans ; Recurrence ; *Diverticulitis, Colonic/surgery ; Elective Surgical Procedures/adverse effects/statistics & numerical data ; Male ; Female ; *Colectomy/adverse effects ; Middle Aged ; *Postoperative Complications/etiology ; Aged ; Surgical Stomas/statistics & numerical data ; },
abstract = {INTRODUCTION: Recurrent diverticulitis after resection remains a key concern despite advances in minimally invasive surgery. These recurrences may result from incomplete resection of the diseased segment, unrecognized synchronous diverticulosis or ongoing alterations in colonic motility and microbiome composition. This systematic review and single-arm meta-analysis aimed to estimate long-term recurrence and stoma rates following elective surgery for left-sided diverticulitis.

METHODS: Following PRISMA guidelines and PROSPERO registration, PubMed, Cochrane and Scopus databases were searched (2000-2025) for studies reporting recurrence after elective resection. Single-arm meta-analysis of proportions was performed using random-effects models. Quality was assessed using the JBI Checklist, while subgroup and sensitivity analyses explored heterogeneity. A comparative meta-analysis with medical treatment was not performed due to selection bias, crossover and lack of standardized non-operative protocols.

RESULTS: Twenty-four studies (7,525 patients; mean follow-up 53 months) were included. Pooled recurrence rate was 6.2% (95% CI: 4.8-8.0%; I[2] = 80.6%), with no difference between RCTs (6.3%) and observational studies (6.1%) or complicated vs. uncomplicated disease. Stoma rate (16 studies, 6,400 patients) was 17.1% (95% CI: 8.4-31.9%; I[2] = 99.3%), significantly higher in complicated (31.0%) than uncomplicated (5.5%) cases (p = 0.009) and significantly lower post-2020 (8.0% vs. 31.2%; p = 0.003). Quality was high in 92% of studies, while sensitivity analyses confirmed robustness.

CONCLUSIONS: Surgical resection achieves durable control with low recurrence and stoma rates. Research priorities include standardized definitions of recurrence, assessing long-term QOL and exploring microbiome influences to refine patient selection and minimize residual risk.},
}

Humans
Recurrence
*Diverticulitis, Colonic/surgery
Elective Surgical Procedures/adverse effects/statistics & numerical data
Male
Female
*Colectomy/adverse effects
Middle Aged
*Postoperative Complications/etiology
Aged
Surgical Stomas/statistics & numerical data

@article {pmid41524247,
year = {2026},
author = {Mir, HD and Giorgini, G and Santos-García, I and Dumais, E and Rodríguez-Cueto, C and de Lago, E and Silvestri, C and Flamand, N and Fernández-Ruiz, J and Di Marzo, V},
title = {Defining the Intestinal eCBome and Oxylipin Signaling Systems in a TDP-43 Mouse Model of Frontotemporal Dementia.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {2},
pages = {e71306},
pmid = {41524247},
issn = {1530-6860},
support = {RTI-2018-098885-B-100//Federación Española de Enfermedades Raras (FEDER)/ ; PID2021-128906OB-I00//Federación Española de Enfermedades Raras (FEDER)/ ; //Canada Excellence Research Chairs, Government of Canada (CERC)/ ; CFREF-2014-00001//UL|Sentinelle Nord, Université Laval (Sentinel North)/ ; },
mesh = {Animals ; Mice ; *Endocannabinoids/metabolism ; Disease Models, Animal ; *Oxylipins/metabolism ; Gastrointestinal Microbiome ; *Frontotemporal Dementia/metabolism/genetics/pathology ; *Signal Transduction ; *DNA-Binding Proteins/genetics/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Transgenic ; },
abstract = {Frontotemporal dementia (FTD) is a group of early onset and progressive disorders, characterized by degeneration in the frontal and temporal lobes, and subsequent deterioration in cognition, personality, social behavior, and language, with aggregates of the RNA-binding protein TDP-43 being present in ~45% of the cases. We reported alterations of the endocannabinoidome (eCBome) in the brain of a TDP-43 mouse model of FTD. Here we investigated the small intestinal eCBome, oxylipins, and, preliminarily, the gut microbiome. The duodenum, jejunum, and ileum of TDP-43 overexpressing versus wildtype mice were investigated. Lipid mediators were measured by HPLC-MS/MS, and mRNA expression of genes involved in eCBome mediator action and metabolism, or intestinal permeability and inflammation, was analyzed by qPCR. Intestinal content microbiota composition and fecal short-chain fatty acids were studied by 16S DNA sequencing and GC-FID, respectively. Alterations were observed in TDP-43 mice for polyunsaturated fatty acids, N-acyl-ethanolamines, and oxylipins in the duodenum and the jejunum, and for oxylipins and 2-monoacylglycerols in the ileum. Regarding the receptors, mRNA expression of Cnr1 and Gpr119 was increased in the ileum, and that of Pparg in the duodenum, where Gpr55 was instead down-regulated. Regarding the enzymes, Faah and Napepld expression was increased in the ileum. Preliminary gut microbiota data suggest increases of Paraprevotella and Monoglobus in the feces, of DNF00809 in the ileum, and of Butyricicoccus, Candidatus_Arthromitus, and Oscillospira in the cecum, where Paraprevotella, Mucispirillum, and Akkermansia were instead decreased. Fecal acetic, butyric, and isobutyric acid were reduced. We suggest the existence of lipid signal-mediated gut-brain interactions in FTD.},
}

Animals
Mice
*Endocannabinoids/metabolism
Disease Models, Animal
*Oxylipins/metabolism
Gastrointestinal Microbiome
*Frontotemporal Dementia/metabolism/genetics/pathology
*Signal Transduction
*DNA-Binding Proteins/genetics/metabolism
Male
Mice, Inbred C57BL
Mice, Transgenic

@article {pmid41524133,
year = {2026},
author = {Santos, YR and Andréo-Filho, N and Lopes, PS and Leite-Silva, VR},
title = {A review of skin microbiome and new challenges to cosmetic microbiome-friendly formulations.},
journal = {International journal of cosmetic science},
volume = {},
number = {},
pages = {},
doi = {10.1111/ics.70073},
pmid = {41524133},
issn = {1468-2494},
abstract = {Human skin is a complex ecosystem that hosts diverse species of microorganisms. Unbalanced conditions caused by intrinsic and/or extrinsic factors can lead to dysbiosis, presenting symptoms, such as dryness, high transepidermal water loss, reduced barrier protection, premature ageing, and in severe cases, inflammatory dermatoses. Strategies to maintain the skin microbiome balance are becoming increasingly suggested, with prebiotic, probiotic, or postbiotic ingredients promoting the diversity and relative abundance of important microorganisms. Topical products directly influence this balance, both traditional ingredients and specific active ingredients. The concentration and combination of these ingredients, as well as the pH of the final product, are extrinsic characteristics that can affect homeostatic skin condition. Focused on repairing or preserving the skin microbiota, microbiome-friendly cosmetics are gaining prominence in the cosmetics industry, with a focus on reducing or replacing ingredients with adverse effects on skin microbiota or adding positive compounds for the microbiota. This review approaches the main characteristics of the skin microbiome, in symbiosis and dysbiosis, elucidates strategies for skin microbiota rebalance, and addresses the challenges of developing microbiome-friendly products through studies of the interaction between skin microbiome and substantial classes of cosmetic ingredients, such as surfactants, lipophilic compounds, preservatives, fragrances, vitamins, and UV filters. The presented findings elucidate the relationship between the host, the skin microbiome, and the use of cosmetics, which could serve as a tool for the development of microbiome-friendly cosmetics. Given the growing popularity of this topic, we also highlight the need for further research focused on the dynamics between the skin microbiome and cosmetic ingredients.},
}

@article {pmid41524110,
year = {2026},
author = {Ogawa, M and Isobe, Y and Uchino, H and Hirayama, M and Kato, T and Negishi, K and Arita, M},
title = {The Microbiome Modulates Corneal Wound Healing via the Induction of Cholesterol Sulfotransferase Pathway.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {2},
pages = {e71429},
pmid = {41524110},
issn = {1530-6860},
support = {JPMJER2101//MEXT, Japan Science and Technology Agency (JST)/ ; 22zf0127007//Japan Agency for Medical Research and Development (AMED)/ ; 21ae0121036//Japan Agency for Medical Research and Development (AMED)/ ; 22KJ3143//MEXT, Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Animals ; *Sulfotransferases/metabolism/genetics ; Mice ; *Wound Healing/physiology/drug effects ; Mice, Knockout ; Humans ; *Microbiota/physiology ; Mice, Inbred C57BL ; *Corneal Injuries/microbiology/metabolism/pathology/drug therapy ; Cholesterol Esters/metabolism ; *Cornea/metabolism/microbiology ; Anti-Bacterial Agents/pharmacology ; Cholesterol/metabolism ; Male ; },
abstract = {The ocular surface is in direct contact with the external environment and is susceptible to injury from dust, dryness, or other foreign objects. Once corneal injury occurs, a local inflammatory response is triggered, followed by effective repair of the epithelial layer. In this study, we demonstrated that antibiotic treatment delayed corneal wound healing in mice. LC-MS/MS-based untargeted lipidomics and qPCR analyses revealed that the levels of cholesterol sulfate (CS) and the CS-synthesizing enzyme SULT2B1 were significantly upregulated by antibiotic treatment, and SULT2B1 knockout mice exhibited accelerated corneal wound healing along with increased recruitment of neutrophils and eosinophils. Topical application of CS delayed corneal wound healing. In vitro scratch assays revealed that CS delayed the wound healing of human corneal epithelial cells, potentially by inhibiting the DOCK2-Rac pathway. These results highlight the role of commensal bacteria in controlling corneal wound healing via the cholesterol-sulfotransferase pathway.},
}

Animals
*Sulfotransferases/metabolism/genetics
Mice
*Wound Healing/physiology/drug effects
Mice, Knockout
Humans
*Microbiota/physiology
Mice, Inbred C57BL
*Corneal Injuries/microbiology/metabolism/pathology/drug therapy
Cholesterol Esters/metabolism
*Cornea/metabolism/microbiology
Anti-Bacterial Agents/pharmacology
Cholesterol/metabolism
Male

@article {pmid41523970,
year = {2025},
author = {Xu, C and Kong, L and Mou, T and Tang, A and Hu, S and Lai, J},
title = {Vitamin B12 and Affective Disorders: A Focus on the Gut-Brain Axis.},
journal = {Alpha psychiatry},
volume = {26},
number = {6},
pages = {49138},
pmid = {41523970},
issn = {2757-8038},
abstract = {Accumulating evidence highlights the role of Vitamin B12 (VitB12) in the pathophysiology of affective disorders. However, its influence on brain function and the underlying mechanisms remain incompletely understood. In humans, VitB12 is obtained solely from dietary sources, primarily animal-based foods. VitB12 deficiency leads to the accumulation of homocysteine, a known contributor to emotional and behavioral dysregulation. VitB12 plays a critical role in maintaining neuron stability, synapsis plasticity, and regulating neuroinflammation by modulating key bioactive factors. These processes help to alleviate hippocampal damage, mitigate blood-brain barrier disruption, reduce oxidative stress, and enhance both structural and functional connectivity-collectively contributing to resilience against affective disorders. VitB12 from both diet and microbial sources is essential to gut homeostasis. Within the gut lumen, it stabilizes gut microbial communities, promotes short-chain fatty acid (SCFA) production, and supports neurotransmitter metabolism (e.g., serotonin and dopamine) via its role in S-adenosyl-l-methionine biosynthesis. Crucially, VitB12, gut microbiota, SCFAs, intestinal mucosa, and vagal nerve signaling interact synergistically within the gut-brain axis (GBA) to maintain gut microenvironment stability, protect the gut-blood barrier, and suppress neuroinflammatory cascades, eventually reducing the susceptibility to affective disorders. This review synthesizes current evidence on the involvement of VitB12 in the GBA, its association with mood regulation, and its potential as a nutritional adjunct in managing affective disorders. By elucidating this integrative mechanism, we provide new insights into targeting the GBA to improve clinical outcomes in affective disorders.},
}

@article {pmid41523930,
year = {2025},
author = {Kanaya, A and Luković, E and Emala, C and Mikami, M},
title = {Effects of chronic allergic lung inflammation on gut microbiota and depression-like behavior in mice.},
journal = {Exploration of asthma & allergy},
volume = {3},
number = {},
pages = {},
pmid = {41523930},
issn = {2837-5076},
support = {K08 HL143052/HL/NHLBI NIH HHS/United States ; },
abstract = {AIM: Emerging epidemiological studies have reported a link between allergic diseases, including asthma, and depression. Evidently, the gut microbiota is involved in the pathogenesis of asthma and depression. Therefore, we investigated whether allergic lung inflammation in mice causes gut microbial dysbiosis, via the gut-brain axis, which is potentially associated with depression.

METHODS: Wild-type C57BL/6J female mice were sensitized with intranasal house dust mite (HDM) antigen or phosphate-buffered saline (PBS) for 6 weeks to induce chronic allergic lung inflammation. Sucrose preference tests were performed for assessing depression. Fecal samples were collected, and 16S ribosomal RNA gene sequencing was performed to detect differences in gut microbiota composition between the HDM and PBS groups. The distance calculation, clustering of operational taxonomic units, rarefaction analysis, and estimator calculation (α- and β-diversity) were performed.

RESULTS: There was a significant difference in β-diversity (Bray-Curtis dissimilarity, F-statistics = 6.16, p = 0.001) of the gut microbiota between HDM and PBS groups. However, there was no difference in the α-diversity. We observed multiple differentially abundant bacteria in the HDM and PBS groups. The order class Clostridia (p = 0.0036) and genus Faecalibaculum (p = 0.028) were more abundant in the HDM group, whereas the phylum Firmicutes (p = 0.037) and genera Dubosiella (p = 0.00024) and Turicibacter (p = 0.037) were more abundant in the PBS group. Notably, the relative abundance of some bacteria was correlated with the sucrose preference test results.

CONCLUSIONS: Six weeks of intranasal HDM administration to mimic the chronic status of lung inflammation in asthma changed the gut microbiome in mice and was associated with depression-like behavioral changes.},
}

@article {pmid41523773,
year = {2025},
author = {Martín Giménez, VM and García Menéndez, S and Sanz, RL and Schiavone, M and Ferder, L and Inserra, F and Manucha, W},
title = {Potential role of nanopharmacology in reducing neuroinflammation associated with hypertension and metabolic disorders.},
journal = {World journal of experimental medicine},
volume = {15},
number = {3},
pages = {106743},
pmid = {41523773},
issn = {2220-315X},
abstract = {Hypertension disrupts cerebral blood flow, leading to endothelial dysfunction, breakdown of the blood-brain barrier (BBB), and inflammatory cell infiltration. This cascade triggers glial cell activation, increases oxidative stress, and causes pro-inflammatory cytokine release, creating a neurotoxic environment. In this context, we explore the intricate connection between hypertension, neuroinflammation, and neurodegeneration, as well as how hypertension interacts with other metabolic disorders, such as obesity and diabetes, to further worsen neuroinflammation. Additionally, we discuss the role of the renin-angiotensin-aldosterone system, the impact of the microbiome, and the potential contribution of chronic infections in exacerbating neuroinflammation. It is essential to emphasize the potential of nanotechnology to transform therapeutic approaches. Nanoparticle-based drug delivery systems can enhance the bioavailability and selectivity of antihypertensive drugs, antioxidants, and neuroprotective compounds, enabling targeted delivery across the BBB. By combining effective blood pressure management with nanotechnology-enabled therapies that modulate inflammation, oxidative stress, and protein aggregation, we can explore new avenues for preventing and treating hypertension and metabolic disorder-associated neurodegenerative conditions. Ultimately, hypertension significantly contributes to neuroinflammation and neurodegeneration by promoting neuronal cell death, primarily through impaired cerebral blood flow and disruption of the BBB. The interaction of hypertension with metabolic disorders exacerbates these effects. However, advancements in our understanding and new technologies reveal promising nanopharmacological approaches for targeted drug delivery to the brain, thereby improving treatment outcomes, enhancing adherence, and reducing side effects.},
}

@article {pmid41523758,
year = {2025},
author = {Khan, AS and Kamthan, M and Ali, A},
title = {Understanding the intricate interactions between microbiota and host.},
journal = {World journal of experimental medicine},
volume = {15},
number = {3},
pages = {101277},
pmid = {41523758},
issn = {2220-315X},
abstract = {The review examines the intricate relationship between the microbiota and its host, highlighting how these microbial communities influence various physiological functions beyond simple coexistence. The microbiota plays a crucial role in regulating the immune system, metabolism, and overall health. We explore the diverse microbial populations inhabiting different body regions and their essential contributions to maintaining balance within the host. Recent research has uncovered molecular mechanisms that govern microbiota-host interactions, offering new insights into how these microbes support health and, conversely, how imbalances known as dysbiosis can increase susceptibility to diseases. While much attention has been given to the gut microbiota, this review also explores the influence of microbes in other parts of the body, including their effects on various organs and tissues. Additionally, we discuss emerging evidence on the gut-brain axis, illustrating how the microbiota can impact brain function and behavior. Understanding this connection could open new possibilities for treating neurological and psychological disorders. Finally, we evaluate microbiota-based therapies such as probiotics and fecal microbiota transplantation, emphasizing the importance of personalized approaches. By integrating findings from multiple disciplines, this review provides a comprehensive perspective on the microbiota's vital role in human health and its potential as a therapeutic target.},
}

@article {pmid41523692,
year = {2026},
author = {Nosal, BM and Aksenov, A and Andersen, C and Lee, EC and Zhou, Y and Chun, OK},
title = {The gut-bone axis: potential influence of anthocyanins and implications for postmenopausal osteoporosis.},
journal = {Food science and biotechnology},
volume = {35},
number = {1},
pages = {13-25},
pmid = {41523692},
issn = {2092-6456},
abstract = {With the aging population worldwide and increased life expectancy, the risk of postmenopausal osteoporosis (PMO) is an increased public health concern. Current treatments for PMO have declined in use over the past decade which has led to an increased focus on finding dietary agents that possess antioxidant and anti-inflammatory properties for prophylaxis and treatment of osteoporosis. Anthocyanins (ACNs) have been shown to exert therapeutic effects in chronic diseases due to their antioxidant and anti-inflammatory properties. ACNs are also thought to be involved in modulating the gut microbiome owing to their prebiotic properties. The gut microbiome has been implicated as a potential target for osteoporosis prevention and treatment since it can modulate immune and endocrine systems, which influence bone metabolism. This review summarizes findings related to ACNs' influence on the gut-bone axis, with a focus on the immune and endocrine systems and potential implications for PMO prevention.},
}

@article {pmid41523651,
year = {2026},
author = {Sitohang, IBS and Legiawati, L and Widaty, S and Nilasari, H and Agustin, T and Chairunnisa, S and Manurung, THP},
title = {Comparative Profile of Microbiome in Normal Skin and Acne Vulgaris Skin Patients.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {1-7},
pmid = {41523651},
issn = {1178-7015},
abstract = {INTRODUCTION: Changes in the skin microbiome are associated with acne vulgaris (AV), a condition characterized by comedones, papules, and pustules. While some bacteria have been studied, many others remain unexplored, highlighting the need to understand the microbiome differences between acne-prone and normal skin. This study aimed to compare skin microbiome profiles between AV patients and healthy individuals and to explore associations with microbial diversity and specific bacterial populations involved in AV pathogenesis.

METHODS: A total of 144 participants were recruited, comprising 36 AV patients and 108 healthy controls. Skin samples were collected from the left cheek after standardized preconditioning. DNA was extracted using the DNeasy PowerSoil Kit™, and the V3-V4 region of 16S rRNA was amplified and sequenced. Microbial diversity was assessed by the Shannon index, and correlations with sebum levels were analyzed.

RESULTS: The results revealed significant differences in microbial diversity, with AV patients exhibiting a markedly lower Shannon index compared to controls, indicating decreased microbial diversity and potential dysbiosis. While the relative abundance of Cutibacterium acnes, a bacterium commonly associated with AV, showed no significant differences between the two groups, the prevalence of Staphylococcus epidermidis was notably higher in AV patients. This suggests that S. epidermidis may play a complex role in the inflammatory processes associated with AV. Moreover, the study identified a negative correlation between microbial diversity and sebum levels, suggesting that increased sebum production may favor the growth of S. epidermidis, potentially exacerbating the condition.

CONCLUSION: These findings highlight the interaction between host factors and microbial composition. This study emphasizes the role of skin microbiome dysbiosis in acne vulgaris and provides insights for future microbiome-based therapeutic strategies. Further research is needed to clarify microbial mechanisms and potential interventions targeting the microbiome in the management of acne vulgaris.},
}

@article {pmid41523287,
year = {2026},
author = {Fang, S and Wang, S and Liu, Y and Zhu, C and Wang, S and Xu, F},
title = {Clinical Safety and Tolerability of Bifidobacterium bifidum BBi32: An 8-Week Randomized, Double-Blind, Placebo-Controlled Trial With Genomic and In Vitro Corroboration.},
journal = {Food science & nutrition},
volume = {14},
number = {1},
pages = {e71420},
pmid = {41523287},
issn = {2048-7177},
abstract = {Bifidobacterium bifidum BBi32, isolated from a healthy infant, underwent a multi-tiered safety assessment to evaluate its genetic features, in vitro properties, and effects on gut microbiota and host biomarkers. Whole-genome sequencing (WGS) and functional annotation were performed alongside in vitro assays assessing acid and bile tolerance, mucin degradation, hemolysis, Caco-2 cytotoxicity, and antibiotic susceptibility. Acute oral toxicity was tested in mice. A randomized, double-blind, placebo-controlled clinical trial (n = 40, 8 weeks) evaluated tolerability and exploratory endpoints, including hematology, liver and renal function, LL-37 levels, gastrointestinal symptom scores, and 16S rRNA-based microbiome profiling. The BBi32 genome comprised a 2.2 Mbp circular chromosome with 99.99% average nucleotide identity to the type strain, no plasmids, and no acquired antimicrobial resistance or virulence genes. Functional categories were enriched for ABC transporters, purine metabolism, and defense mechanisms. BBi32 demonstrated tolerance to acid and bile, lacked mucin-degrading, or hemolytic activity, showed no cytotoxicity to Caco-2 cells, and was susceptible to most antibiotics. Acute toxicity test yielded an LD50 > 2 × 10[10] CFU/kg with no adverse effects. In the clinical trial, daily BBi32 administration (3 × 10[10] CFU) was well tolerated, with no hematological or hepatic abnormalities. Compared with placebo, BBi32 reduced uric acid, urea, and creatinine levels, increased LL-37, and improved gastrointestinal symptom scores. Microbiome analysis revealed higher alpha diversity, distinct community clustering, enrichment of Romboutsia, and predicted functional shifts toward amino acid biosynthesis and peptidase activity. Genomic, in vitro, toxicological, and clinical data collectively indicate that BBi32 meets key safety criteria and favorably modulates host and microbiome biomarkers, supporting its probiotic potential.},
}

@article {pmid41523278,
year = {2026},
author = {Ji, G and Li, C and Yao, Z and Li, Z and Yang, B and Hu, L and Yu, H and Jiang, T and Wang, S and Wang, H},
title = {Therapeutic Potential of Irpex lacteus Polysaccharides in Lupus Nephritis: Insights From Gut Microbiota and Metabolomics Analysis in MRL/Lpr Mice.},
journal = {Food science & nutrition},
volume = {14},
number = {1},
pages = {e71446},
pmid = {41523278},
issn = {2048-7177},
abstract = {Polysaccharides from Irpex lacteus (PCP) were evaluated for their therapeutic effects on lupus nephritis (LN) in MRL/lpr mice. After 8-week interventions with low- and high-dose PCP, we systematically evaluated the therapeutic efficacy by measuring the levels of autoantibodies, the expression of inflammatory cytokines, and renal function-related parameters. Finally, 16S rDNA gut microbiome sequencing with metabolomics analysis was used to explore the pharmacological mechanism of PCP intervention in LN. PCP could reverse the phenotype of MRL/lpr mice, reduce autoantibody levels, alleviate inflammatory responses, and improve renal function. Gut microbiome analysis found that PCP can improve gut microbiota composition and abundance of two phyla (Firmicutes, Bacteroidota) and five genera (Lachnospiraceae NK4A136 group, Alistipes, Butyricicoccus, Bacteroides, Lactobacillus), which play an important role in the process of PCP intervention on metabolism in MRL/lpr mice. UHPLC-MS untargeted metabolomics showed that PCP significantly affects multiple key differential metabolites, including Linoleic acid, L-Phenylalanine, L-Tyrosine, and 56 other metabolites. These metabolites are primarily involved in metabolic pathways such as tryptophan metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, tyrosine metabolism, linoleic acid metabolism, and arachidonic acid metabolism. Correlation analysis between gut microbiota and differential metabolites reveals a close relationship, suggesting that gut microbiota promoting host metabolism may be one of the mechanisms by which PCP treats LN. PCP alleviates LN by modulating the "microbiota-metabolism axis," reducing autoantibodies, inflammation, and renal damage, while reshaping gut microbiota and regulating key metabolic pathways.},
}

@article {pmid41523242,
year = {2025},
author = {Qi, W and Tian, L and Li, Z and Xu, J and Wang, T},
title = {Pathogen spectrum and management strategies for opportunistic infections in lung cancer in the immunotherapy era: recent advances from fungi to mycobacteria.},
journal = {American journal of cancer research},
volume = {15},
number = {12},
pages = {5140-5167},
pmid = {41523242},
issn = {2156-6976},
abstract = {Lung cancer is one of the most common cancers and the leading cause of cancer death worldwide. Opportunistic infections (OI) are increasingly recognized in this population due to disease-related immune dysfunction and treatment-induced immunosuppression. Compared with the chemotherapy era, the use of immune checkpoint inhibitors and targeted agents has shifted the OI profile. Pneumocystis jirovecii pneumonia (PJP) and invasive pulmonary aspergillosis (IPA) are reported more often in older adults and patients with lymphopenia, while tuberculosis (TB) and nontuberculous mycobacteria (NTM) cluster in those with structural lung disease (e.g., bronchiectasis, cavities) and prolonged immunosuppression. High-risk features include absolute lymphocyte count <500/µL, corticosteroids ≥20 mg prednisone-equivalent for ≥4 weeks, airway obstruction, prior TB, chronic obstructive pulmonary disease/interstitial lung disease (ILD), and recent broad-spectrum antibiotics. Diagnosis should integrate high-resolution computed tomography (HRCT) patterns (e.g., diffuse ground-glass for PJP; nodules with halo sign for IPA), microbiology [bronchoalveolar lavage fluid (BALF) culture/microscopy, galactomannan (GM)/β-D-glucan (BDG)], and metagenomic next-generation sequencing, interpreted against host factors and treatment timeline, while carefully distinguishing immune-related pneumonitis and TKI-associated ILD. Prophylaxis with TMP-SMX is recommended for high-risk patients; voriconazole (or isavuconazole) is first-line for IPA with attention to drug-drug interactions; TB/NTM regimens require coordination with anticancer therapy, especially where rifamycins interact with TKIs. Vaccination (influenza, pneumococcus, zoster) and antimicrobial stewardship are essential. Future work should validate risk scores prospectively and clarify microbiome-immunotherapy-infection relationships.},
}

@article {pmid41523241,
year = {2025},
author = {Wang, Y and Sun, W and Li, H and Xu, F and Cui, W},
title = {Decoding the metastatic nexus: how chronic stress reprograms neuroendocrine-metabolic-microbiome circuits to fuel tumor metastasis.},
journal = {American journal of cancer research},
volume = {15},
number = {12},
pages = {5058-5083},
pmid = {41523241},
issn = {2156-6976},
abstract = {Metastasis, the leading cause of death in patients with solid tumors, involves the spread of cancer cells to distant organs. While genetic and environmental factors contribute, chronic stress is a crucial factor in metastatic progression by disrupting neuroendocrine, immune, metabolic, and microbial homeostasis. This review synthesizes evidence linking chronic stress to tumor metastasis through three pathways: (1) direct effects on tumor cell metabolism, (2) remodeling of the tumor microenvironment, and (3) dysregulation of the gut microbiota. Describe how activation of the hypothalamic-pituitary-adrenal axis and sympathetic nervous system influence epithelial-mesenchymal transition, immune evasion, and angiogenesis via β-adrenergic and glucocorticoid receptor signaling. Explore how microbial metabolites and barrier dysfunction influence immune and neuroendocrine circuits, creating a pro-metastatic loop. Finally, we highlight therapeutic strategies, including psychological interventions and pharmacologic approaches, to alleviate chronic stress. This review proposes a mechanistic framework linking neuroendocrine signaling, metabolic reprogramming, and the microbiome-immune axis.},
}

@article {pmid41523132,
year = {2025},
author = {Arita, R},
title = {Targeted therapies for meibomian gland dysfunction - The role of antibiotics in meibomian gland dysfunction management.},
journal = {Taiwan journal of ophthalmology},
volume = {15},
number = {4},
pages = {516-525},
pmid = {41523132},
issn = {2211-5072},
abstract = {Meibomian gland dysfunction (MGD) is a leading cause of evaporative dry eye, significantly impairing the quality of life. Bacterial proliferation and inflammation play central roles in the pathogenesis of MGD, creating a vicious cycle of gland obstruction and ocular surface instability. Antibiotics, particularly tetracyclines (e.g. doxycycline and minocycline), and macrolides (e.g. azithromycin and erythromycin), are widely used as adjunctive therapy for moderate-to-severe or refractory MGD. This review conducted a comprehensive literature search of PubMed, focusing on original peer-reviewed articles published in English that reported on the efficacy and/or safety of oral or topical antibiotics for MGD or blepharitis. Eligible studies were identified using the specific search terms, screened by title and abstract, and selected based on predefined inclusion and exclusion criteria. Relevant data were extracted and synthesized, with an emphasis on randomized controlled trials and comparative studies. The review indicates that both oral and topical antibiotics improve subjective symptoms, tear film stability, ocular surface staining, meibum quality, and lid margin abnormalities in the short term. Oral azithromycin may be at least as effective as doxycycline, with a shorter treatment course and fewer adverse events, while topical azithromycin offers similar or superior efficacy to systemic regimens with reduced systemic exposure. However, benefits are usually limited to active treatment periods, and optimal dosing and duration remain uncertain. Long-term efficacy, safety, risk of resistance, and effects on the ocular microbiome require further investigation. Antibiotics should be used judiciously as part of a comprehensive, individualized management strategy for MGD.},
}

@article {pmid41523060,
year = {2025},
author = {Agrawal, R and Shah, M and Srivastava, V and Naik, SR and Patel, NR and Dwivedy, S and Mehta, M and Patel, BJ and Makkad, RS},
title = {An In vitro Study of the Isolation of Candidal Strains in Patients at Increased Risk of Oral Squamous Cell Carcinoma.},
journal = {Journal of pharmacy & bioallied sciences},
volume = {17},
number = {Suppl 4},
pages = {S2870-S2872},
pmid = {41523060},
issn = {0976-4879},
abstract = {BACKGROUND: OSCC stands as a prominent oral malignancy that develops because of lifestyle behavior and microbial activity. The pathogenesis of OSCC receives attention through modern research since Candida species reportedly contribute to the development of OSCC through inflammatory responses and nitrosamine generation and epithelial tissue malformation.

MATERIALS AND METHODS: Sixty subjects participated in this in vitro study, which was separated into two distinct groups: Group A with 30 patients who had high OSCC risk oral lesions (leukoplakia and erythroplakia) and Group B which included 30 healthy subjects. A laboratory research involved collecting samples through swabs from saliva and mucosa, which were subsequently cultured on Sabouraud Dextrose Agar (SDA) alongside CHROMagar for fungal detection. The researchers identified isolated colonies by checking their ability to form germ tubes combined with carbohydrate assimilation tests.

RESULTS: Out of the 30 Group A samples, 80% (24/30) demonstrated candidal growth where Candida albicans constituted 70.8% of strains and Candida tropicalis made up 16.7% alongside Candida glabrata counting for 12.5%. The overall candidal growth among participants in Group B was limited to 30% (9/30) as C. albicans constituted 88.9%, whereas C. glabrata accounted for 11.1%. The incidence of candidal colonization proved markedly higher among the high-risk group compared to controls according to statistical analysis (P = 0.002).

CONCLUSION: The numbers of Candida species, particularly C. albicans, rise substantially within the oral environments of patients dealing with potentially malignant disorders. The obtained data support the possibility that oral cancer development may be related to candidal colonization, thus demanding additional studies on this association.},
}

@article {pmid41523026,
year = {2025},
author = {Sahu, M and Agarwal, G and Jain, G and Saad, T and Qureshi, MA and Mishra, S},
title = {Determination of Gut Microbiome Patterns Associated with Developing Active Tuberculosis in a Case-Control Study.},
journal = {Journal of pharmacy & bioallied sciences},
volume = {17},
number = {Suppl 4},
pages = {S3069-S3071},
pmid = {41523026},
issn = {0976-4879},
abstract = {BACKGROUND: The gut microbiome plays a critical role in modulating systemic immunity and may influence susceptibility to infectious diseases, such as tuberculosis (TB). This study aimed to compare gut microbial profiles between individuals with active pulmonary TB and healthy controls to identify potential microbial signatures associated with disease development.

METHODS: A hospital-based case-control study was conducted with 90 participants: 45 treatment-naïve TB patients and 45 healthy controls. Stool samples were collected and analyzed using 16S rRNA sequencing. Microbial diversity was assessed using the Shannon index, and relative abundances of key bacterial phyla were compared. Statistical analysis included Mann-Whitney U tests and LEfSe for differential taxa identification.

RESULTS: TB patients showed significantly lower alpha diversity (Shannon index: 2.91 ± 0.37) compared to controls (3.81 ± 0.28, P < 0.001). The relative abundance of Proteobacteria was significantly higher in TB cases, while Firmicutes and Bacteroidetes were more abundant in controls. These findings indicate a pro-inflammatory gut microbiota shift in active TB.

CONCLUSION: Active tuberculosis is associated with gut microbial dysbiosis, marked by reduced diversity and altered bacterial composition. These microbial signatures could aid in early diagnosis and serve as future targets for microbiome-based interventions.},
}

@article {pmid41522762,
year = {2025},
author = {Yang, H and Liu, X and Yuan, D and Li, H and Mu, X},
title = {A prognostic nomogram for colorectal cancer: integrating blood microbiome and clinical factors.},
journal = {Journal of gastrointestinal oncology},
volume = {16},
number = {6},
pages = {2651-2663},
pmid = {41522762},
issn = {2078-6891},
abstract = {BACKGROUND: The microbiota is pivotal in colorectal cancer (CRC), yet the prognostic value of the blood microbiome and its utility in clinical prediction models remain poorly explored. This study aims to develop a blood microbiome-associated prognostic score (MAPS) that integrates blood microbiome data with clinical factors to improve the accuracy of CRC prognosis prediction and enhance our understanding of the tumor microenvironment (TME).

METHODS: We analyzed whole-genome and transcriptomic sequencing data of CRC patients from The Cancer Genome Atlas (TCGA). A MAPS was developed from blood microbiome data using the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm. A nomogram integrating MAPS and key clinical factors was constructed to predict overall survival (OS). Its predictive accuracy was validated via time-dependent receiver operating characteristic (ROC) analysis, yielding area under the curve (AUC) values for 1-, 3-, and 5-year OS. Underlying mechanisms were investigated through gene set enrichment analysis (GSEA) and immune cell infiltration estimation from matched RNA sequencing (RNA-seq) data.

RESULTS: The MAPS, comprising seven key blood microbes, was an independent prognostic factor. The integrative nomogram demonstrated robust predictive performance, with AUCs of 0.800, 0.805, and 0.755 for predicting 1-, 3-, and 5-year OS, respectively. Mechanistically, the high-MAPS subgroup exhibited enriched pro-tumorigenic pathways (e.g., inflammatory response, hypoxia) and an immunosuppressive TME characterized by increased Treg cell infiltration. We further identified S100A8 and PROK2 as potential therapeutic targets.

CONCLUSIONS: Our study delivers a validated prognostic nomogram based on the blood microbiome and elucidates its link to an immunosuppressive TME, highlighting its dual utility in patient stratification and target discovery.},
}

@article {pmid41522496,
year = {2026},
author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S},
title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20566},
pmid = {41522496},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Onions/microbiology/growth & development/physiology ; *Soil Microbiology ; Fertilizers ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.},
}

*Rhizosphere
*Onions/microbiology/growth & development/physiology
*Soil Microbiology
Fertilizers
*Microbiota
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification

@article {pmid41522492,
year = {2026},
author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R},
title = {Cross-sectional comparative shotgun metagenomic analysis of the subgingival resistome in healthy subjects and patients with periodontitis from four countries.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2610588},
pmid = {41522492},
issn = {2000-2297},
abstract = {BACKGROUND: The oral cavity is a known reservoir of antibiotic resistance genes (ARGs), but little is known about their subgingival distribution across health states and regions.

OBJECTIVE: This study aimed to characterize and compare the subgingival resistome and mobile genetic elements (MGEs) in healthy subjects (HS) and periodontitis patients (PP) from Belgium, Chile, Peru and Spain.

DESIGN: Subgingival samples pooled from the deepest site of each quadrant of 40 HS and 40 PP were analyzed via shotgun metagenomic sequencing. After human DNA depletion, the microbial composition was assessed with MetaPhlAn 4.0; ARGs were identified using MEGAHIT and AMRFinderPlus; and MGEs with MGEfinder.

RESULTS: ARG richness was significantly higher in PP (mean 3.98) than in HS (2.15). PP from Peru showed more ARGs than HS from Chile and Spain. In total, 28 ARGs were found, conferring resistance to eight antibiotic classes. β-lactam, tetracycline and aminoglycoside resistance were more abundant in PP. Macrolide resistance was lower in Chilean samples than in Peruvian and Spanish ones. Additionally, 99 MGE-associated genes were detected, with 16 differing by diagnosis and 78 by country.

CONCLUSIONS: Subgingival resistome profiles vary significantly by periodontal status and geography, underscoring the influence of clinical and regional factors on antimicrobial resistance in the oral microbiome.},
}

@article {pmid41522487,
year = {2026},
author = {Al Qassab, M and Chaarani, N and Hamou, A and Harb, R and Jradi, A and Zeineddine, M and Ghadieh, HE and Khattar, ZA and Azar, S and Kanaan, A and Harb, F},
title = {The Gut Microbiota-Insulin Resistance Axis: Mechanisms, Clinical Implications, and Therapeutic Potential.},
journal = {FASEB bioAdvances},
volume = {8},
number = {1},
pages = {e70080},
pmid = {41522487},
issn = {2573-9832},
abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in regulating host metabolism and contributing to the development of insulin resistance (IR). Gut dysbiosis alters the production of critical metabolites, including short-chain fatty acids (SCFAs), bile acids, indole derivatives, and trimethylamine N-oxide (TMAO), which influence intestinal barrier integrity, inflammatory pathways, and glucose homeostasis. Recent clinical and translational studies indicate that SCFAs can improve fasting insulin and HOMA-IR, although the magnitude of benefit varies substantially across individuals, highlighting ongoing controversy surrounding their metabolic effects. Altered microbial regulation of bile-acid metabolism has also been implicated in impaired lipid and glucose signaling, reinforcing the relevance of FXR- and TGR5-mediated pathways in IR. Elevated TMAO levels have further been associated with adverse metabolic outcomes, though debate persists regarding its causal role versus its function as a diet-dependent biomarker. Microbiota-targeted strategies, including dietary fiber, probiotics, and fecal microbiota transplantation (FMT), show potential to modulate these metabolic pathways, yet clinical results remain inconsistent. This narrative review synthesizes recent mechanistic discoveries and clinical findings on microbiota-derived metabolites in IR, highlights key controversies, and outlines future priorities for translating microbiome science into effective and personalized interventions for metabolic disease prevention and management.},
}

@article {pmid41522466,
year = {2026},
author = {Jain, V},
title = {Gut microbiome in biliary atresia.},
journal = {World journal of pediatric surgery},
volume = {9},
number = {1},
pages = {e001068},
pmid = {41522466},
issn = {2516-5410},
abstract = {Biliary atresia (BA) is a progressive cholangiopathy of infancy and the leading cause of pediatric liver transplantation. Despite surgical intervention with the Kasai portoenterostomy, long-term outcomes remain poor, with many patients progressing to cirrhosis. Emerging evidence implicates the gut microbiota-a dynamic ecosystem crucial to immune development and liver homeostasis-in BA pathogenesis and clinical progression. This review synthesizes current literature on gut microbiota composition in BA before and after the Kasai procedure, highlighting consistent patterns of dysbiosis, including pathobiont expansion and depletion of beneficial microbes such as Bifidobacterium. The review explores associations between microbial profiles and clinical outcomes-highlighting potential mechanisms involving bile acid metabolism, microbial translocation, and immune modulation. Further understanding of gut-liver-microbiota interactions in BA may inform microbiome-targeted therapies to improve native liver survival.},
}

@article {pmid41522445,
year = {2025},
author = {Glazunova, E and Molodtsova, P and Grabarnik, I and Kurnosov, A and Bikaeva, I and Shipulin, G and Zlobovskaya, O},
title = {Healthy human gut microbiome: Towards standardized research.},
journal = {AIMS microbiology},
volume = {11},
number = {4},
pages = {786-820},
pmid = {41522445},
issn = {2471-1888},
abstract = {OBJECTIVE: An increasing number of international researchers are focusing on the taxonomic composition of fecal microbiota and its correlation with disorders. Thousands of researchers compare conditionally healthy cohorts to those with specific diseases to identify potential markers. However, clinical application requires assessing the feasibility of synthesizing these findings and establishing reference intervals for normal gut flora, at least at higher taxonomic levels.

DESIGN: This study involves a systematic review and meta-analysis of human gut microbiota research based on 16S rRNA gene next-generation sequencing (NGS). Relevant research was sourced following the PRISMA guidelines. Descriptive statistics, linear regression analysis by weighted least squares method, Mann-Whitney test, and Benjamini-Hochberg procedure adjustments were employed. The study has been registered with PROSPERO (CRD42023431467).

RESULTS: Of the 4,346 studies initially identified, 86 publications involving 20,748 unique participants met the quality criteria and were included in the analysis of the impact of fecal sample preparation on taxonomic composition. The phylotype composition, in relation to preprocessing methods and cohort locations, are presented as relative abundances (%): Bacillota (median 49.5-59.6%), Bacteroidota (28.0-33.4%), Pseudomonadota (3.4-5.9%), Actinomycetota (2.3-3.7%), Verrucomicrobiota (0.5-1.0%), Fusobacteriota (maximum 4.6%), and Euryarchaeota (maximum 2.11%). The content of 27 key family-level representatives was also evaluated. The well-known hypothesis regarding the influence of the homogenization stage on taxonomic composition was examined using generalized results.

CONCLUSION: While supported by a strong theoretical basis and evidence from individual practical cases, none of the phyla showed a statistically significant association and consistent relationship with sample preparation or cohort location when generalizing across studies after the two exceptionally large cohorts exclusion, both originating from a single research group. These findings underscore the need for strict methodological standardization in microbiome studies. Key features of the 16S NGS process accounting for these results are outlined, along with proposed optimizations for microbiome research.},
}

@article {pmid41522435,
year = {2025},
author = {Zalila-Kolsi, I},
title = {Engineered bacteria as living therapeutics: Next-generation precision tools for health, industry, environment, and agriculture.},
journal = {AIMS microbiology},
volume = {11},
number = {4},
pages = {946-962},
pmid = {41522435},
issn = {2471-1888},
abstract = {Synthetic biology has revolutionized precision medicine by enabling the development of engineered bacteria as living therapeutics, dynamic biological systems capable of sensing, responding to, and functioning within complex physiological environments. These microbial platforms offer unprecedented adaptability, allowing for real-time detection of disease signals and targeted therapeutic delivery. This review explores recent innovations in microbial engineering across medical, industrial, environmental, and agricultural domains. Key advances include CRISPR-Cas systems, synthetic gene circuits, and modular plasmid architectures that provide fine-tuned control over microbial behavior and therapeutic output. The integration of computational modeling and machine learning has further accelerated design, optimization, and scalability. Despite these breakthroughs, challenges persist in maintaining genetic stability, ensuring biosafety, and achieving reproducibility in clinical and industrial settings. Ethical and regulatory frameworks are evolving to address dual-use concerns, public perception, and global policy disparities. Looking forward, the convergence of synthetic biology with nanotechnology, materials science, and personalized medicine is paving the way for intelligent, responsive, and sustainable solutions to global health and environmental challenges. Engineered bacteria are poised to become transformative tools not only in disease treatment but also in diagnostics, biomanufacturing, pollution mitigation, and sustainable agriculture.},
}

@article {pmid41522308,
year = {2025},
author = {Henry, GD and Diaz, N and Phillips, CD and Lentz, AC and Perito, P and Natale, R and Bennett, N and Stuart, AR and Henry, CJ and Chung, PH},
title = {Methods and early findings from a study comparing next-generation sequencing versus traditional cultures for penile implants concerning for low-grade infection.},
journal = {Translational andrology and urology},
volume = {14},
number = {12},
pages = {3945-3951},
pmid = {41522308},
issn = {2223-4691},
abstract = {Microbial culture is the current standard of care to choose therapeutic antibiotics for infection occurring with inflatable penile prostheses (IPPs). However, next-generation sequencing (NGS) of DNA has proven beneficial for analysis of biofilm composition and relative abundance of specific microorganisms. The main goal of this study is to evaluate whether NGS compared to microbial culture can better guide the management and antibiotic selection and device survival rates. We hypothesize that identifying microbial composition with NGS, as compared with traditional culture, will lead to better therapeutic strategies resulting in improved patient outcomes and device survival. In this present manuscript, we describe the overall study methodology and analyze device survival rates, classify clinical presentations of IPP infections, and determine infected implant microbial composition and antibiotic resistance among an early patient cohort. These early results included 18- to 80-year-old consecutive male patients who received antimicrobial treatment without surgical replacement for at least 7 days since identification of infected IPPs. Subjects were randomized into two analytic arms: traditional culture and NGS. Throughout the study, investigators and patients completed questionnaires to provide data for comparison. To date, of the 9 patients enrolled in the study, 6 eventually underwent device removal due to worsening infection within 7 days of initiating empiric antibiotic treatment. Six patients were seen in a clinic setting, while 3 were seen in the hospital/emergency department: 7 implants were primary, while 2 were secondary. All subjects received a Coloplast IPP but had differing reservoirs and reservoir locations. In cases where penile shaft tenderness was present, the implanted IPP was more often removed within 7 days. In contrast, when no tenderness was reported, the device remained viable for at least 10 days. As of this report, 11 active sites have participated in the study, with ongoing patient enrollment aimed at reaching sufficient sample sizes for statistical comparison. Penile shaft tenderness was a common presentation among patients whose early antibiotic treatment for IPP infection failed. Recruitment of additional patients to this prospective, randomized controlled trial will help to identify favorable presentations of IPP infection. Additional data will allow comparison of implantation outcomes between NGS and traditional culture.},
}

@article {pmid41521788,
year = {2026},
author = {Hernandez-Rovira, B and Villamaria, E and Oh, J and Ozarslan, B and Wyles, S},
title = {Topical Carboxytherapy Modulates the Skin Microbiome Following CO2 Laser Resurfacing: A Pilot Study.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {1},
pages = {e70668},
doi = {10.1111/jocd.70668},
pmid = {41521788},
issn = {1473-2165},
support = {//Lumisque Skincare, LLC/ ; },
}

@article {pmid41521690,
year = {2026},
author = {Bailey, AM and Hofseth, LJ},
title = {Microplastics in Early Onset Carcinogenesis.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgaf093},
pmid = {41521690},
issn = {1460-2180},
abstract = {Plastics have become integral to modern life, but their persistence has generated vast quantities of microplastics (MPs, <5 mm) and nanoplastics (NPs, <1 µm) that now contaminate food, water, air, and human tissues. Although not yet classified as carcinogens by the International Agency for Research on Cancer, accumulating experimental and epidemiologic evidence raises concern that MPs may contribute to cancer development. Global plastic production has risen from 2 megatons in 1950 to more than 450 megatons annually in 2022, leaving behind pervasive waste that fragments into MPs and NPs. These particles act as xenobiotics, carrying toxic additives and adsorbed pollutants, provoking oxidative stress, chronic inflammation, DNA damage, and microbiome disruption; all processes central to carcinogenesis. MPs have been detected in human cancers, and animal studies show tissue accumulation, fibrosis, and genomic instability following exposure. Importantly, the proliferation of plastics parallels a global rise in early-onset cancers (diagnosed before age 50), suggesting a possible, though unproven, temporal association. Individuals born after the 1950s plastic boom have experienced continuous MP exposure beginning in utero, potentially predisposing them to carcinogenic pathways later in life. In this review, we integrate human biomonitoring data, experimental findings, and clinical observations to evaluate the emerging hypothesis that chronic MP exposure contributes to cancer risk. While causality has not been established, the biological plausibility and mounting evidence underscore the urgent need for mechanistic and epidemiologic studies to clarify the role of MPs and NPs in cancer development. It also underscores an urgent need for research into causal pathways and preventive mechanisms.},
}