@article {pmid41965837,
year = {2026},
author = {Munoz Briones, J and Ball, BK and Jena, S and Lescun, TB and Chan, DD and Brubaker, DK},
title = {Rumenomics: evaluation of rumen metabolites from healthy sheep identifies differentially produced metabolites across sex, age, and weight.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41965837},
issn = {2524-4671},
support = {DGE-1842166//National Science Foundation/ ; W911NF2110372//Defense Sciences Office, DARPA/ ; },
abstract = {BACKGROUND: The rumen harbors a diverse and dynamic microbiome vital in digesting vegetation into metabolic byproducts for energy and general biological function. Although previous studies have reported connections between the rumen and the overall health of the sheep, the exact biological process by which this occurs is not well understood. Therefore, our study aimed to quantify sheep rumen metabolites to determine if enriched biological pathways are differentiable across phenotypic features of sex, age, and weight.

RESULTS: We collected and quantified metabolites of rumen samples from sixteen sheep using liquid chromatography-tandem mass spectrometry. We performed a series of univariate and multivariate statistical analyses to interpret the rumen metabolomics data. To identify metabolic pathways associated with the phenotypic features of sex, weight, and age, we used MetaboAnalyst, which identified amino acid metabolism as a distinguishing factor. Among the pathways, phenylalanine metabolism emerged as a key pathway differentiating sheep based on sex and age. Additionally, phenylalanine, tyrosine, and tryptophan biosynthesis were exclusively associated with age. In univariate linear models, we also discovered that these amino acid and protein pathways were associated with weight by age-corrected effect. Finally, we identified arginine and proline biosynthesis as a pathway linked to metabolites with weight.

CONCLUSION: Our study identified differential pathways based on the sex, age, and weight features of sheep. Metabolites produced by the rumen may act as an indicator for sheep health and other ruminants. These findings encourage further investigation of the differentially produced metabolites to assess overall sheep health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00558-5.},
}

@article {pmid41968333,
year = {2026},
author = {Chen, C and He, J and Ma, Z and Na, W and Cao, Y and Li, B and He, Z and Yuan, H and Xiao, H and Wang, S and Liu, R and Yu, S and Kang, L},
title = {Sex differences in behaviors, neuronal activation, and gut-microbiota-metabolic axis in a repeated nitroglycerin-induced chronic migraine model.},
journal = {The journal of headache and pain},
volume = {27},
number = {1},
pages = {},
pmid = {41968333},
issn = {1129-2377},
support = {82201365//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Migraine is a debilitating primary headache disorder characterized by significant sex differences in epidemiology, clinical features, comorbidities, and treatment response, yet the underlying mechanisms remain obscure. This study aims to dissect the sex difference map in chronic migraine models and explore the underlying mechanisms driving these specific phenotypes.

METHODS: A mouse model of chronic migraine was established by intraperitoneal injection of nitroglycerin (NTG, 10 mg/kg, 5 times in 9 days). Both male and female mice were included. Mechanical withdrawal thresholds (MWTs) were measured to assess migraine-related hyperalgesia. Anxiety-like behaviors and acute malaise were evaluated using the Open Field Test (OFT), Elevated Plus Maze (EPM), and Light-Dark Box (LDB). Neuronal activation was mapped via c-Fos immunofluorescence. Medullary TNF-α levels were quantified by ELISA. 16S rRNA sequencing and targeted metabolomics characterized the gut microbiota composition and fecal metabolites, respectively.

RESULTS: Although male and female mice showed comparable responses in acute and chronic mechanical pain hyperalgesia, significant sex differences were observed in other migraine-like behaviors: only male mice exhibited significant acute-phase motor inhibition and anxiety-like behavior in the chronic phase. These phenotypic differences coincided with a male-restricted elevation of medullary TNF-α following NTG administration. In terms of regional brain activation, the AP stood out in males for its markedly elevated c-Fos cell. This sexual dimorphism extended to the gut-brain axis: while the female NTG group microbiome was enriched with g-Akkermansia, the male profile was dominated by g-Parabacteroides. Metabolomic profiling identified 29 differential metabolites (NTG vs. VEH) in males but only 3 in females. In males, these alterations were primarily enriched in the pentose and glucuronate interconversions and biosynthesis of unsaturated fatty acids pathways that are involved in neuropsychiatric disorders.

CONCLUSION: The NTG-induced chronic migraine model exhibits significant sexual dimorphism, with male mice showing greater sensitivity to acute discomfort and chronic emotional comorbidities. This exploratory study identifies the specific activation of the AP brain region, medullary neuroinflammation, and more severe disturbances in the gut microbiota-metabolic axis as potential contributors to this sex-dependent phenotype.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s10194-026-02360-9.},
}

@article {pmid42148582,
year = {2026},
author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L},
title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0346925},
doi = {10.1128/spectrum.03469-25},
pmid = {42148582},
issn = {2165-0497},
abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.},
}

@article {pmid42148717,
year = {2026},
author = {Lantz, AM and Collins, LB and Hirsch, EB and Staley, C and Nicol, MR},
title = {Prevotella bivia Influences Antiretroviral Pharmacokinetics and Viral Replication in an Ex Vivo Vaginal Tissue Model.},
journal = {Clinical and translational science},
volume = {19},
number = {6},
pages = {e70597},
pmid = {42148717},
issn = {1752-8062},
mesh = {Female ; Humans ; *Vagina/microbiology/virology/drug effects ; *Tenofovir/pharmacokinetics/pharmacology ; *Prevotella/physiology/drug effects ; *HIV Infections/virology/prevention & control/drug therapy ; *Virus Replication/drug effects ; *HIV-1/drug effects/physiology ; *Anti-HIV Agents/pharmacokinetics/pharmacology ; Microbiota/drug effects ; Bacteroidaceae Infections/microbiology ; Adenosine Triphosphate/metabolism ; },
abstract = {The vaginal microbiome plays a complex role in tenofovir's mucosal pharmacology. While the relative contribution of systemic versus local concentrations to PrEP PK/PD is an ongoing debate, the development of effective HIV prevention requires an understanding of events at the site of transmission. Our objective was to further understand the relationship between tenofovir mucosal pharmacology and non-optimal vaginal microbiota using the ex vivo vaginal tissue model. Vaginal and cervical explants were produced from cadaver tissue using a biopsy punch. Explants were incubated with Prevotella bivia (10[3]-10[5] colony forming units/ml) with and without tenofovir for 24 h. TFVdp and endogenous adenosine triphosphate (dATP) were quantified using liquid chromatography tandem mass spectroscopy. Explants were then challenged with 10[6] TCID50 the viral concentration where 50% of tissue cultures are infected, of HIVJR-CSF for 3 h. Explants were cultured on gel-foam rafts for 48 h then collected for HIV RNA quantification using RT-qPCR. TFVdp formation in vaginal tissue was approximately 76% lower in anaerobic conditions (p = 0.2) compared to aerobic. While dATP concentrations did not significantly differ between any Prevotella bivia concentrations and the Prevotella-free control, TFVdp and TFVdp:dATP ratio in vaginal tissue decreased as Prevotella bivia concentrations increased, although not statistically. Unexpectedly, tenofovir efficacy increased as Prevotella bivia concentrations increased. The ex vivo tissue model was successful in demonstrating the pharmacology of TFVdp is affected by Prevotella bivia. Viral replication was also affected by Prevotella bivia; therefore, further work is needed to fully understand effects on tenofovir pharmacodynamics.},
}

Female
Humans
*Vagina/microbiology/virology/drug effects
*Tenofovir/pharmacokinetics/pharmacology
*Prevotella/physiology/drug effects
*HIV Infections/virology/prevention & control/drug therapy
*Virus Replication/drug effects
*HIV-1/drug effects/physiology
*Anti-HIV Agents/pharmacokinetics/pharmacology
Microbiota/drug effects
Bacteroidaceae Infections/microbiology
Adenosine Triphosphate/metabolism

@article {pmid42148776,
year = {2026},
author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y},
title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0029226},
doi = {10.1128/msystems.00292-26},
pmid = {42148776},
issn = {2379-5077},
abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.

IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.},
}

@article {pmid42148824,
year = {2026},
author = {De Biasi, J and Giménez Bastida, JA and Krupa-Kozak, U},
title = {Biotics: The Food Ingredients Supporting the Intestinal Microbiota and Immune System in Psoriasis.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf252},
pmid = {42148824},
issn = {1753-4887},
support = {2022/45/B/NZ9/03004//National Science Centre, Poland, through project OPUS 23/ ; MICIU/AEI/10.13039/501100011033//National Science Centre, Poland, through project OPUS 23/ ; CNS2022-135253//the European Union NextGenerationEU/PRTR/ ; RyC2021-032111-I//the European Union NextGenerationEU/PRTR/ ; //MCIU/AEI/10.13039/501100011033/ ; PID2022-136915NA-I00//ERDF/EU/ ; },
abstract = {Psoriasis is a chronic immune-mediated inflammatory skin disease affecting 4 million new individuals worldwide each year. Although the etiology of psoriasis is not fully understood, genetic factors play a key role in conjunction with systemic inflammation and gut microbiota dysbiosis. Current methods of psoriasis treatment, while effective, may cause adverse reactions. Biotics (pre-, pro-, syn-, and postbiotics) are generally recognized as safe, have a good reputation, and have confirmed beneficial health effects. Considering the growing awareness of the impact of diet and lifestyle on health among individuals with psoriasis, the recognition of biotics as a potential source of health benefits with minimal constraints even during therapy has become more relevant. In this review, we highlight the therapeutic potential and beneficial effects of biotics in inflammatory skin diseases involving dysbiosis and screen the scientific data concerning recent randomized controlled trials that specifically assessed the use of biotics in psoriasis to understand the progress achieved to date. Most studies matching our screening criteria used lactic acid bacteria along with oligosaccharides as prebiotics. Probiotics have shown promising results in suppressing inflammatory pathways and alleviating the symptoms of psoriasis by modulating the gut microbiota. After several weeks of intervention, patients showed microbiome changes along with reduced levels of inflammatory biomarkers and psoriasis severity. Overall, biotics appear to be good candidates for improving the quality of life in patients with psoriasis; however, more randomized controlled trials with more rigid protocols and rigorously reported results are needed to properly assess their potential.},
}

@article {pmid42148825,
year = {2026},
author = {Lim, JJX and Morgan, NR and Bhuvanendran, S and Janarthanan, P and Radhakrishnan, AK},
title = {Effects of Fat-Soluble Vitamins on Gut Microbiome Composition: A Scoping Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag065},
pmid = {42148825},
issn = {1753-4887},
abstract = {As the gut microbiome emerges as a key player in human health, numerous studies have reported its close association with various diseases. Consequently, increasing attention has been given to exploring whether fat-soluble vitamins can modulate gut microbiome composition as a potential strategy to maintain microbial balance. This scoping review aimed to investigate whether interventions with fat-soluble vitamins (vitamins A, D, E, and K) could alter gut microbiome composition and, in turn, improve health outcomes. A total of 17 human studies and 47 animal studies were identified across 4 databases. Most studies reported that fat-soluble vitamins effectively altered gut microbiome composition; however, evidence linking these changes to consistent improvements in health outcomes remains limited. Overall, this review maps the potential link between vitamin-driven microbiome modulation and health benefits, while highlighting current research gaps to guide future investigations.},
}

@article {pmid42148838,
year = {2026},
author = {Kim, JH and Park, RY and Kim, ES and Kim, JH and Joo, BD and Yun, N and Koo, J and Kim, J and Kim, SH and Kim, J and Park, TG and Youn, SH and Kim, JH and Park, BS},
title = {Core Microbiota Drives Host-Specific Growth Enhancement: Evidence in a Harmful Algal Bloom Causing Dinoflagellate Prorocentrum lima.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c05294},
pmid = {42148838},
issn = {1520-5851},
abstract = {Bacterial microbiota influence algal growth and physiology, yet experimental validation in toxic benthic dinoflagellates remains limited. Here, we investigated the microbiota of six geographically distinct strains of the harmful benthic dinoflagellate Prorocentrum lima (P. lima) and identified core bacterial taxa shared across strains. Microbiota transplantation into an axenic P. lima strain revealed that donor consortia significantly enhanced early phase growth, increasing the specific growth rate by 61.1% compared to axenic controls. Coculture experiments with Marinobacter adhaerens (M. adhaerens), a core taxon isolated from P. lima, resulted in a significantly increased specific growth rate─up to 164.1% higher than the axenic control─while no such enhancement was observed in other tested microalgal species, indicating a host-specific interaction. Among several nutrient-limited conditions tested, this enhancement was uniquely observed under trace metal restriction. Genomic analysis and CAS assays revealed that M. adhaerens lacks canonical siderophore pathways but employs a noncanonical iron-acquisition strategy, which may contribute to enhanced iron availability under trace metal-limited conditions. These results provide experimental evidence that specific bacterial lineages closely associated with toxic dinoflagellates can promote their proliferation. Our findings highlight the ecological significance of dinoflagellate-associated core microbiota and offer new directions for microbiome-informed strategies in HAB monitoring and management.},
}

@article {pmid42149101,
year = {2026},
author = {Ambi, A},
title = {The Copper-Gut-Brain Axis: A Triple Inflammatory Pathway Driving Neuroinflammation in Alzheimer's Disease.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0375},
pmid = {42149101},
issn = {2152-5250},
abstract = {Serum copper increases progressively with normal aging, yet its downstream consequences for the gut microbiome and neuroinflammation remain unexplored. Gut microbiota dysbiosis and elevated lipopolysaccharide levels are established features of Alzheimer's disease, and growing evidence indicates that this dysbiosis drives neuroinflammatory disease progression. Yet the upstream trigger initiating this dysbiosis remains unknown. We propose that age-related copper dyshomeostasis serves as this missing trigger. The redox-active copper content of ceruloplasmin increases across the adult lifespan, and copper is selectively toxic to anaerobic bacteria, preferentially affecting butyrate-producing genera including Faecalibacterium, Roseburia, and Coprococcus while sparing copper-resistant species. This selective toxicity is supported by animal studies demonstrating copper-induced elimination of butyrate producers with reversible gut barrier damage and by Wilson's disease cohorts showing consistent depletion of butyrate-producing genera due to elevated copper levels. The resulting dysbiosis creates a triple inflammatory pathway: butyrate loss compromises gut barrier integrity and removes histone deacetylase-mediated suppression of neuroinflammation; the increase of Gram-negative bacteria elevates lipopolysaccharide translocation through the compromised barrier; and impaired blood-brain barrier integrity reduces amyloid-β clearance. These three insults trigger microglial activation through NF-κB signaling, creating a 'triple hit' on a single transcription factor that may explain the magnitude of neuroinflammatory effects observed in Alzheimer's disease. This mechanism explains the increased acetate/butyrate ratio recently identified as a biomarker distinguishing Alzheimer's-related from non-Alzheimer's cognitive impairment (AUC 0.951), since copper disrupts microbial metabolic cross-feeding networks that convert acetate to butyrate. We present specific, falsifiable predictions that can be tested in human cohorts and propose copper as a novel upstream therapeutic target for Alzheimer's disease prevention.},
}

@article {pmid42149113,
year = {2026},
author = {De Allende, CC and Salter, SJ and Brigg, SE and Boardman, M and Claassen-Weitz, S and Mwaikono, KS and Workman, L and Zar, HJ and Nicol, MP and Parkhill, J and Dube, FS},
title = {Characterization of Ornithobacterium hominis colonization dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42149113},
issn = {2057-5858},
mesh = {Humans ; *Nasopharynx/microbiology ; South Africa ; *Microbiota/genetics ; Phylogeny ; Female ; Cohort Studies ; Male ; RNA, Ribosomal, 16S/genetics ; Infant ; },
abstract = {Ornithobacterium hominis is a recently described Gram-negative bacterium that colonizes the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of O. hominis from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African O. hominis is more similar to Australian strains than those from Southeast Asia and that it may share genes with other members of the microbiome that are relevant for virulence, colonization and antibiotic resistance. Leveraging existing microbiome data from the cohort, O. hominis was found to be closely associated with bacterial co-colonizers that are rare in non-carrier individuals, including Suttonella, Rappaport, Helcococcus, Lwoffella, Moraxella and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain O. hominis. Individuals who have not yet acquired O. hominis have a higher abundance of Lwoffella lincolnii than individuals who never acquire O. hominis, suggesting that this could be a precursor state for successful colonization.},
}

Humans
*Nasopharynx/microbiology
South Africa
*Microbiota/genetics
Phylogeny
Female
Cohort Studies
Male
RNA, Ribosomal, 16S/genetics
Infant

@article {pmid42149451,
year = {2026},
author = {Edelkamp, J and Lousada, MB},
title = {In Situ Laser-Capture Microdissection for Detection of Components of the Hair Follicle and Scalp Microbiome.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3031},
number = {},
pages = {233-242},
pmid = {42149451},
issn = {1940-6029},
mesh = {*Hair Follicle/microbiology ; *Laser Capture Microdissection/methods ; *Microbiota/genetics ; Humans ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; },
abstract = {Laser-capture microdissection (LCM) enables the study of the hair follicle (HF) microbiome in relation to hair health and disease with high spatial resolution. It allows the precise excision of specific HF regions, each containing a unique and conserved microbiome, from full-length HFs encompassing all relevant HF compartments. With LCM, cross-contamination with microbiota from neighboring regions is minimized. Coupled with 16S rRNA gene or metagenomic shotgun sequencing, LCM offers great potential to assess region-specific microbiome changes, particularly in HF-associated disorders.},
}

*Hair Follicle/microbiology
*Laser Capture Microdissection/methods
*Microbiota/genetics
Humans
*Scalp/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods

@article {pmid42149452,
year = {2026},
author = {Edelkamp, J and Lousada, MB},
title = {Viable vs. Nonviable Microbiota Evaluation of the Hair Follicle and Scalp Microbiome.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3031},
number = {},
pages = {243-259},
pmid = {42149452},
issn = {1940-6029},
mesh = {Humans ; *Hair Follicle/microbiology ; *Microbiota/genetics ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; In Situ Hybridization, Fluorescence/methods ; Propidium/analogs & derivatives/chemistry ; Azides/chemistry ; Microbial Viability ; Real-Time Polymerase Chain Reaction/methods ; },
abstract = {Various hair follicle (HF)-associated disorders, such as acne vulgaris, hidradenitis suppurativa, and alopecia areata, are linked to dysbiosis, an imbalance between resident and pathogenic microbes. Characterization of the HF and skin microbiome employs techniques such as 16S rRNA gene sequencing and metagenomic shotgun sequencing, with the latter providing comprehensive taxonomic and functional insights. However, relic DNA from dead microbes and free environmental DNA can persist in samples, meaning that metagenomic data does not exclusively reflect living microbiota. For functional studies on HF dysbiosis or to assess potential therapeutic interventions, we describe here how propidium monoazide (PMA) treatment can be performed before (metagenomics) sequencing to distinguish viable microbial communities. Furthermore, we exemplify qPCR and (fluorescent) in situ hybridization (ISH) of two alternative viability screening methods for the HF and scalp microbiome.},
}

Humans
*Hair Follicle/microbiology
*Microbiota/genetics
*Scalp/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
In Situ Hybridization, Fluorescence/methods
Propidium/analogs & derivatives/chemistry
Azides/chemistry
Microbial Viability
Real-Time Polymerase Chain Reaction/methods

@article {pmid42149786,
year = {2026},
author = {Fluhr, JW and Bräutigam, MM and Proksch, E},
title = {Topical calcineurin inhibitors and the epidermal barrier in atopic dermatitis.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-20},
doi = {10.1159/000552559},
pmid = {42149786},
issn = {1421-9832},
abstract = {BACKGROUND: The topical calcineurin inhibitors [TCIs] pimecrolimus and tacrolimus, offer an effective non-steroidal option for treating atopic dermatitis [AD], particularly in sensitive skin areas and for long-term use. There are several studies published on the effect of calcineurin inhibitors on the skin barrier but a comprehensive review on this topic is still missing.

SUMMARY: This review summarizes current evidence on the impact of TCIs on epidermal barrier structure and function. Clinical studies in patients with AD show that TCIs improve transepidermal water loss [TEWL], enhance stratum corneum [SC] hydration, and promote normalization of structural proteins such as filaggrin and loricrin. Unlike topical corticosteroids [TCS], TCIs do not induce skin atrophy and may even reverse steroid-induced epidermal thinning. Additionally, TCIs partially preserve antimicrobial peptide [AMP] expression in lesional AD skin, which may help reduce Staphylococcus aureus colonization and support microbial diversity. Positive effects on lipid lamellar organization and natural moisturizing factor [NMF] levels further support barrier restoration. Animal data suggesting impaired lipid synthesis under TCI treatment contrast with consistent positive findings in clinical studies. Importantly, emerging evidence indicates that TCIs may improve the skin microbiome in AD.

KEY MESSAGES: TCIs exert their beneficial effects on skin inflammation through selective T-cell modulation without disrupting keratinocyte differentiation or dermal matrix components. For this reason, the general indirect positive effects on skin barrier associated with reduction of skin inflammation is not counterbalanced by intrinsic barrier damaging mechanisms as observed with topical steroids. Further studies are needed to evaluate long-term effects on skin structure, microbiome stability, and their integration into biologic treatment algorithms.},
}

@article {pmid42149909,
year = {2026},
author = {Bonacolta, AM and Kravitz, T and Mozo, R and Baker, LJ and Heuer, RM and Grosell, M and Del Campo, J},
title = {Symbiotic bacteria may support calcium carbonate precipitation in the Gulf toadfish.},
journal = {PLoS biology},
volume = {24},
number = {5},
pages = {e3003764},
doi = {10.1371/journal.pbio.3003764},
pmid = {42149909},
issn = {1545-7885},
abstract = {Marine fish play a significant yet understudied role in the oceanic carbon cycle through the production of magnesium-rich calcium carbonate (CaCO3) precipitates known as ichthyocarbonates. These deposits form in the gut of marine teleost fish in response to salinity, serving as part of their osmoregulation strategy. Through this, marine fish may contribute as much as 9.04 Pg of CaCO3 per year in global new carbonate production, being equivalent to or potentially higher than the production by coccolithophores and pelagic foraminifera. Despite their ecological relevance, the biological mechanisms driving ichthyocarbonate precipitation remain to be fully resolved. Intriguingly, bacteria are consistently found in intimate association with ichthyocarbonate precipitates. Given the widespread capacity of prokaryotes to mediate CaCO3 precipitation, this association points to a previously unexplored microbial contribution to the process. To investigate the potential role of bacteria in ichthyocarbonate production, we subjected Gulf toadfish (Opsanus beta) to salinity treatments common to their native range and known to elicit changes in CaCO3 precipitation. To assess the respective contributions of the host and its microbiota to ichthyocarbonate formation in the gut, we characterized the microbiome across the toadfish gut and performed meta-transcriptomic analysis. Across the toadfish gut, we identify a high abundance of vibrios associated with ichthyocarbonates with the metabolic potential for CaCO3 precipitation. Specifically, we observe the expression of the transcriptional activator of urease (ureR) by Photobacterium damselae subsp. damselae, which can induce the precipitation of CaCO3 via the production of bicarbonate. We demonstrate that CaCO3 precipitation in marine fish may not solely be a host-driven process, but potentially the result of a functional symbiosis with gut-associated Vibrio bacteria. We hypothesize that just as photosymbionts enable corals to build reefs, fish hosts, along with their microbial partners, may synergistically contribute to oceanic carbonate production. This discovery, if confirmed, expands the role of symbiosis in marine biomineralization and underscores its broader influence on global biogeochemical cycles.},
}

@article {pmid42150103,
year = {2026},
author = {Moffatt, MF and Nishimura, T and Cox, MJ and Mcbrien, C and Burke, C and Cuthbertson, L and Lewis, K and Attanoos, R and Davies, GA and Chung, KF and Robertus, JL and Ish-Horowicz, J and O'Carroll, O and Bozeman, JM and Mcgowan, A and Hopkin, JM and Lathrop, GM and Riazalhosseini, Y and Cookson, WOC},
title = {Airway microbiome diversity, intra-mucosal bacteria, and spatial immunity in asthmatics and controls.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag232},
pmid = {42150103},
issn = {1535-4970},
abstract = {RATIONALE: Asthma is characterized by disruption of the thoracic airway mucosae and loss of microbial diversity. Spatial profiling of the mucosal transcriptome may systematically discover mechanisms for microbial influences on immunity.

OBJECTIVES: We investigated relationships between clinical measures, microbial communities, and the host mucosal transcriptome within different strata of bronchial biopsies in subjects with and without asthma.

METHODS: We bronchoscoped 65 adult asthmatics and 44 healthy controls, quantifying bacterial operational taxonomic units (OTUs) in bronchial brushings by 16S rRNA gene amplicon sequences. Biopsy histologic features were scored blind to diagnosis. Following 16S rRNA in situ hybridization of 44 biopsies, bacterial foci were scored in epithelium, basement membrane and stroma. Global human gene expression was quantified in epithelial and stromal compartments using Digital Spatial Profiling.

MEASUREMENTS AND MAIN RESULTS: Clinical asthma was independently predicted by basement membrane abnormalities (BaseMA), endobronchial bacterial diversity and circulating eosinophil counts, but not by specific OTU abundances. 16S rRNA staining revealed bacteria within epithelium and mucosa of all biopsies. Intra-mucosal bacteria (IMCBs) counts correlated negatively with spatially organized co-expression networks encoding antigen-specific immunity, neutrophil functions, and matrix activation, whereas BaseMA correlated positively with the adaptive immunity module. Eosinophil counts correlated with epithelial bacterial counts and senescence pathways. Clinical asthma was accompanied by upregulation of a Treg cell network.

CONCLUSIONS: Asthma and its related phenotypes are accompanied by complex mucosal events that extend beyond eosinophilic pathways. Components of diverse airway microbiota may modify immunity by beneficial interactions within the mucosa.},
}

@article {pmid42150350,
year = {2026},
author = {Guazzini, M and Marasco, R and Radović, S and Pellegrini, E and Vuerich, M and Lodovici, A and De Wittenau, GD and Paparelli, E and Magris, G and Zanin, L and Contin, M and De Luca, E and Daffonchio, D and Di Gaspero, G and Marroni, F},
title = {Variations in the root-soil system influence the grapevine holobiont by shaping plant physiology and root microbiome.},
journal = {The Science of the total environment},
volume = {1037},
number = {},
pages = {181874},
doi = {10.1016/j.scitotenv.2026.181874},
pmid = {42150350},
issn = {1879-1026},
abstract = {Soil-dwelling bacteria and fungi play a crucial role in plant health and productivity by engaging in complex interactions that shape and are shaped by soil physico-chemical properties. In this study, we employed a multi-omics approach to investigate how variations in soil composition affect the grapevine holobiont. Grape plantlets were grown in three distinct soil types, namely sand, peat, and peat-manure. To further assess how variation in soil and root conditions affects the holobiont's response, we included treatments involving soil autoclaving and root heat treatment across all soil types. We found that soil type significantly influences leaf multielement composition and concentration, while also shaping the bacterial and fungal communities associated with the plant rhizosphere. This shift led to changes in taxa involved in nitrogen fixation, biocontrol, and pathogenicity. Autoclaving soils consistently reduced bacterial diversity across all soil types, whereas fungal communities were less affected. In contrast, thermal treatment of roots had only a minor impact on microbial community composition but did induce transcriptional changes in the root and altered leaf macronutrient concentrations. Our findings indicate that differences in soil composition reshape the entire root-soil continuum, ultimately affecting plant physiology at multiple levels-from root function to leaf nutrient status. This highlights that the soil is not a passive growth medium but a key determinant of grape holobiont structure and function. These results reinforce the view that plant health and adaptation arise from integrated, dynamic interactions among the host, its associated microbiome, and the surrounding soil matrix.},
}

@article {pmid42150447,
year = {2026},
author = {Sharma, P and Iqbal, MZ and Chandra, R},
title = {The emerging insights on signaling molecule-mediated hyperaccumulation: Unlocking potential in metal-stressed plants with phytoremediation applications.},
journal = {Plant physiology and biochemistry : PPB},
volume = {235},
number = {},
pages = {111383},
doi = {10.1016/j.plaphy.2026.111383},
pmid = {42150447},
issn = {1873-2690},
abstract = {Phytoremediation, which involves plants and their associated microbiome, is a sustainable remediation strategy for removing, stabilizing, or degrading contaminants in the ecosystem. The technology revolves around hyperaccumulators that tolerate and remove contaminants through their physiological and molecular mechanisms that are facilitated by various signaling molecules [reactive oxygen species (ROS), phytohormones, calcium ions (Ca[2+]), nitric oxide (NO), and electrophysiological signals]. This review aims to define the phenomenon of phytoremediation, enumerate its types, and highlight its limitations, with an emphasis on the role of hyperaccumulator plants in environmental remediation. The major focus is on the signaling molecules-regulated molecular mechanisms of metal uptake, translocation, chelation, sequestration, and antioxidant defence. Remediation processes are optimized by regulatory networks resulting from phytohormonal cross-talk. The transgenic and CRISPR/Cas9 technologies can significantly improve the hyperaccumulator capacity through gene overexpression and gene editing of those encoding the biosynthesis of signaling molecules. The processes, phytostabilization, phytoextraction, and the microbial breakdown of organic pollutants by plants, have shown the most removal of contaminants in the in-situ experiments. The research gaps are the complexity of the pathway, the variability of the environment, and a detailed research plan, focusing on electrophysiology and the integration of Artificial intelligence/Machine learning. The concept of coupling microbial synergy, nanotechnology, and portable monitoring can accomplish the phytoremediation shift from the lab to the field. Signaling molecules can be utilized by hyperaccumulators to effectively address the global problem of contamination, thereby enabling the development of renewable and environmentally friendly solutions for the eco-restoration of contaminated sites.},
}

@article {pmid42150448,
year = {2026},
author = {Wang, L and Weng, W and Zhou, Z and Liang, B and Wang, S and Hu, X and Zhu, H and Wang, H and Sui, N},
title = {A regulatory network revealing spatial distribution differences of alkaloids, flavones, and carbohydrates in Fritillaria thunbergii bulbs by multi-omics analysis.},
journal = {Plant physiology and biochemistry : PPB},
volume = {235},
number = {},
pages = {111387},
doi = {10.1016/j.plaphy.2026.111387},
pmid = {42150448},
issn = {1873-2690},
abstract = {The secondary metabolites in the bulbs of Fritillaria species display distinct spatial distribution patterns, yet the underlying mechanisms remain unclear. In this study, bulbs of Fritillaria thunbergii were divided into inside (IS) and outside (OS) layers. Integrated physiological, transcriptomic, metabolomic, and microbiomic analyses were performed to elucidate the spatial regulation of alkaloids, flavonoids, and carbohydrates. The OS was significantly enriched in secondary metabolites, with total alkaloid, peimine, and total flavonoid contents being approximately 1.18-, 1.28-, and 1.24-fold higher, respectively, than those in the IS. In contrast, carbohydrates mainly accumulated in the IS, where sucrose and starch levels were 1.37- and 2.18-fold higher than those in the OS. Transcriptomic analysis revealed that carbohydrate enrichment in the IS was associated with the upregulation of sucrose synthase (SUS) and hexokinase (HK) genes, and the downregulation of β-amylase3 (BAM3) and invertase (INV). In the OS, genes related to steroidal alkaloid biosynthesis, including 3-hydroxy-3-methylglutaryl-CoA synthase (HMGCS), 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), and farnesyl-diphosphate farnesyltransferase 1 (FDFT1), as well as flavonoid biosynthesis genes phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), and cytochrome P450 monooxygenase CYP75B1 (CYP75B1), were upregulated. Moreover, bacterial taxa enriched in the OS, such as Actinomycetota and Ruminococcus, correlated positively with alkaloid accumulation, while the fungal genus Aspergillus was potentially associated with flavonoid regulation. Overall, the multi-omics insights provided here not only offer theoretical support for refined, region-specific processing of Zhejiang Fritillaria bulbs but also open new avenues to improve medicinal quality by manipulating host gene expression and microbial community composition.},
}

@article {pmid42150701,
year = {2026},
author = {Zhu, Z and Xu, H},
title = {Distinct microbiome signatures associated with wing polyphenism in the wing-dimorphic planthopper Nilaparvata lugens.},
journal = {Journal of insect physiology},
volume = {},
number = {},
pages = {104994},
doi = {10.1016/j.jinsphys.2026.104994},
pmid = {42150701},
issn = {1879-1611},
abstract = {Wing polyphenism is crucial for the ecological adaptation of the wing-dimorphic planthopper Nilaparvata lugens, yet its underlying association with symbiotic microbiota remains poorly understood. Here, we investigated three N. lugens strains (Field, HSD, and Lab) exhibiting stable but distinct macropterous-to-brachypterous ratios. 16S rRNA amplicon sequencing revealed that the composition and structure of the microbiota differed significantly not only among the diverse strains but also between distinct wing morphs within the same genetic background and living environment. Furthermore, functional predictions demonstrated that the relative abundance of aerobic bacteria and specific metabolic pathways, notably steroid hormone biosynthesis and linoleic acid metabolism, were positively correlated with the macropterous ratio. These findings suggest that wing morph determination in N. lugens is intimately associated with distinct microbiome configurations and host-microbe metabolic interactions, providing a novel microecological perspective on insect phenotypic plasticity. However, further experimental validations are required to determine whether these microbial shifts drive wing morph development or are a consequence of divergent host physiology.},
}

@article {pmid42150752,
year = {2026},
author = {Srinivasalu, VK and Subramaniam, N and Ibrahim, M and Das, M},
title = {Circulating Tumor DNA and Precision Biomarkers in Colorectal Cancer: Implications for Diagnosis, Monitoring, and Management of Advanced Disease.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70420},
pmid = {42150752},
issn = {1440-1746},
abstract = {Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide, with outcomes critically dependent on timely diagnosis, accurate risk stratification, and individualized treatment. Traditional markers such as CEA, KRAS/NRAS, BRAF, and MSI status, while foundational, are insufficient to address the full complexity of CRC biology. Over the past decade, a new generation of biomarkers has emerged spanning liquid biopsy, stool-based methylation, genomics, epigenomics, immune profiling, microbiome analysis, radiomics, patient-derived organoids, and multiomics integration-collectively redefining how CRC is detected, classified, and treated. This narrative review synthesizes evidence from 73 human studies published between 2010 and 2024, identified through structured searches of PubMed, Embase, Web of Science, and the Cochrane Library, and quality-assessed using QUADAS-2 and Newcastle-Ottawa tools. Circulating tumor DNA (ctDNA) emerged as the most clinically validated biomarker, demonstrating superior performance in minimal residual disease (MRD) detection, recurrence prediction, and real-time therapy monitoring. Stool DNA methylation assays showed strong sensitivity for early CRC and advanced adenoma detection. Genomic markers including BRAF V600E, POLE/POLD1, HER2, and KRAS G12C now directly inform targeted therapy selection, while immune biomarkers-MSI-H, TMB, and Immunoscore-guide immunotherapy decisions and stratify prognosis beyond TNM staging. Microbiome signatures, particularly Fusobacterium nucleatum and colibactin-producing Escherichia coli, were associated with chemo resistance and tumor progression. Radiomics and AI-driven imaging models provided noninvasive assessment of nodal involvement and neo-adjuvant therapy response. Patient-derived organoids demonstrated capacity to predict individual drug sensitivity, and multiomic integration enabled refined molecular subtyping. Despite this progress, widespread clinical adoption remains limited by assay variability, lack of prospective multicenter validation, and implementation barriers including cost and infrastructure. As these technologies mature, their integration into standardized, multidisciplinary workflows will be essential to translating biomarker innovation into improved patient outcomes across all stages of CRC care.},
}

@article {pmid42150759,
year = {2026},
author = {Evans, EM and Mayday, MY and Pearce, EM and Iwanaga, K and Ly, NP and Church, GD and Reyes, G and Simon, MR and Blum, J and Kim, H and Mu, J and Baez-Maidana, J and Auletta, JJ and Shaw, PJ and Kreml, EM and Martin, PL and Duncan, CN and Rowan, CM and Godder, K and Hurley, C and Cuvelier, GDE and Qayed, M and Abdel-Azim, H and Keating, AK and Fitzgerald, JC and Hanna, R and Killinger, JS and Hume, JR and Quigg, TC and Castillo, P and Satwani, P and Moore, TB and Dvorak, CC and Zinter, MS and , },
title = {Upper and Lower Respiratory Tract Compartmentalization in Pediatric Stem Cell Transplantation.},
journal = {American journal of respiratory cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrcmb/aanag106},
pmid = {42150759},
issn = {1535-4989},
abstract = {RATIONALE: Lung injury after hematopoietic stem cell transplantation (HCT) occurs due to infection, chemotherapy toxicity, and alloreactive inflammation. Analyses of bronchoalveolar lavage (BAL) fluid have revealed dominant pathobiologic signatures, but minimally-invasive diagnostics are needed.

OBJECTIVES: To determine whether microbiome and gene expression perturbations are shared along the respiratory tract or isolated to the alveoli in pediatric HCT patients with lung injury.

METHODS: We performed bulk RNA sequencing on 206 paired nasal and BAL samples from 160 HCT patients and 17 healthy controls enrolled at 28 children's hospitals (2016-2025). Microbial and human transcripts were compared using multivariable models accounting for age, sex, and paired sampling.

MEASUREMENTS AND MAIN RESULTS: HCT BAL and nasal transcriptomes differed across 13,698 genes, 48 cellular components, and network interactions linking inflammation, reactive oxygen species, and immunometabolism. Minimal BAL-nasal correlation was observed in gene expression levels (median ρ = 0.03, IQR -0.03 to 0.08) or fractional abundance of key cells such as neutrophils and CD8 + T-cells. BAL microbiomes harbored fewer commensal bacteria and more fungi and DNA viruses. BAL bacterial RNA was associated with diminished immune signaling whereas nasal bacterial RNA aligned with inflammatory gene expression. Further, only BAL microbial RNA was linked to transcriptional shifts in epithelial injury response, keratinization, and collagen deposition. Finally, BAL commensal microbiome depletion, epithelial injury, and immune dysregulation signatures were associated with death or prolonged mechanical ventilation, whereas nasal samples provided minimal prognostic information.

CONCLUSIONS: These data support alveolar compartmentalization in pediatric HCT and emphasize the ongoing need for minimally-invasive but informative diagnostics.},
}

@article {pmid42151055,
year = {2026},
author = {Dong, YH and Song, Y},
title = {[Exploring multidimensional environmental exposure and strategies for the co-prevention of multimorbidity in children and adolescents].},
journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi},
volume = {47},
number = {5},
pages = {791-798},
doi = {10.3760/cma.j.cn112338-20251118-00835},
pmid = {42151055},
issn = {0254-6450},
support = {2024YFC2707901, 2024YFC3308302//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Adolescent ; Child ; *Environmental Exposure/adverse effects/prevention & control ; *Multimorbidity ; Risk Factors ; Public Health ; },
abstract = {Multimorbidity in children and adolescents has become an increasingly prominent public health challenge, but the traditional single-etiology models cannot explain its complex phenotypic manifestations. This paper systematically summarizes the challenges and underlying mechanisms of the co-occurrence, multi-causal management, and co-prevention of multiple diseases associated with multidimensional environmental exposures in children and adolescents, showing that chemical (heavy metals, endocrine-disrupting chemicals, etc.), physical (PM2.5, noise, etc.), biological (microbiome, etc.), and socio-environmental factors (family stress, community resources, etc.) collectively form a mixed exposure network. These factors affect the health of multiple systems, including respiratory, metabolic, and neurodevelopmental systems, of children and adolescents through biological mechanisms such as epigenetic programming, immune-metabolic disruption, microbiome dysbiosis, and neuro-immune-endocrine network interactions, resulting in multi-disease co-occurrence. In addition, this paper introduces the co-occurrence of multiple diseases in children and adolescents in the context of "common exposure-common mechanism-common prevention" and suggests targeted intervention strategies, including risk factor identification, exposure source control and novel multidimensional environment management, to provide scientific evidence for building a co-prevention system for multiple childhood diseases and informing precision public health practices.},
}

Humans
Adolescent
Child
*Environmental Exposure/adverse effects/prevention & control
*Multimorbidity
Risk Factors
Public Health

@article {pmid42151161,
year = {2026},
author = {Wang, Y and Hou, Q and Lv, X and Liu, J and Wang, H and Zhao, Y and Tong, H and Liu, Y and Du, J and Yang, X and Wu, S and He, S and Yang, X},
title = {Inorganic nitrogen metabolic reprogramming of the gut microbiome drives fecal microbiota transplantation in ulcerative colitis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73290-y},
pmid = {42151161},
issn = {2041-1723},
support = {32172776//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Although fecal microbiota transplantation (FMT) shows promise for ulcerative colitis (UC), its clinical success appears to be contingent upon the degree of donor microbiota engraftment. Using an LD50-based ecological model, our study reveals that inorganic nitrogen utilization capacity (IN-uc) critically determines gut microbial assembly in high oxidative stress environments, which significantly influences microbial engraftment outcomes. Building on this mechanistic insight, we engineer a probiotic-metabolite consortia designed to synergistically increase IN-uc in the gut ecosystem. We find that PM-mix14 alleviates oxidative stress-mediated colonization barriers of donor microbiota by catalyzing the conversion of excess reactive nitrogen species through multi-step reactions, promotes L-glutamate biosynthesis and ATP production, thereby ensuring greater similarity in the structure and function of the recipient microbiota to those of the donor. In multiple male murine models of colitis, PM-mix14 supplementation during FMT significantly improves microbial engraftment fidelity, which is correlated with increased anti-inflammatory responses and attenuated colonic pathology. Network meta-analysis of multiple clinical datasets further substantiates the prognostic value of donor gut microbial IN-uc in UC remission. Our findings establish the gut microbial IN-uc as an ecological driver of microbiota engraftment and present a rationally designed microbial therapy that optimizes FMT efficacy through targeted metabolic reprogramming.},
}

@article {pmid42151236,
year = {2026},
author = {Khalifa, AM and ElBaghdady, KZ and Hamed, MM and Mohammad, AS and Khaled, MA},
title = {Integrating spectral signatures and microbial profiling to differentiate diseased and healthy corals in the Red sea.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42151236},
issn = {2045-2322},
mesh = {Animals ; *Anthozoa/microbiology ; Indian Ocean ; Coral Reefs ; *Bacteria/classification/isolation & purification ; Microbiota ; },
abstract = {Coral reef ecosystems face increasing threats from microbial diseases, especially those induced by bacterial infections. Conventional diagnostic techniques often require invasive sampling, extended processing time and are limited in their spatial applicability. Spectral reflectance analysis offers a non-invasive means for detecting subtle physiological alterations associated with coral disease; however, its application in characterizing microbiological changes remains largely unexplored. This research aimed to differentiate healthy from diseased coral colonies by analyzing the spectral fingerprints of the disease and their associated bacterial communities, using hyperspectral data, microbial profiling, and multivariate statistical analysis. The bacterial species identified in healthy coral samples included Bacillus subtilis, Cytobacillus firmus, Bacillus amyloliquefaciens, and Bacillus sporothermodurans. In contrast, the bacteria associated with diseased coral samples were Vibrio pelagius and Vibrio fortis. Healthy corals demonstrate consistently lower reflectance across all bands in comparison to diseased corals. The reflectance of diseased Favia lacuna showed a notable increase when compared to healthy specimens, especially at wavelengths of 594 nm, 649 nm, and 702 nm. In contrast, Acropora humilis exhibited heightened peaks at wavelengths of 580 nm, 693 nm, and 702 nm. The analysis of the second derivative revealed that coral colonies affected by disease exhibited distinct negative peaks at wavelengths of 450-460 nm, 580-590 nm, and 700-800 nm. The identified peaks are likely associated with tissue thinning, skeletal exposure, or microbial biofilm accumulation rather than pigment absorption, given that this region is dominated by scattering effects. In contrast, healthy colonies exhibited stable characteristics at approximately 675 nm, indicating the presence of intact symbiotic chlorophyll and preserved physiological structure. The present study demonstrates that hyperspectral reflectance profiling of bacterially infected corals shows promising potential as a non-invasive approach for differentiating healthy and diseased coral microbiomes. The integration of spectral indicators with microbial community data provides preliminary insights into coral health assessment and may contribute to the development of improved strategies for disease detection and understanding coral-microbe interactions under environmental stress.},
}

Animals
*Anthozoa/microbiology
Indian Ocean
Coral Reefs
*Bacteria/classification/isolation & purification
Microbiota

@article {pmid42151282,
year = {2026},
author = {Visci, G and Notario, E and Defazio, G and Caratozzolo, MF and Cox, SN and Fosso, B and Marzano, M and Pesole, G},
title = {Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49725-3},
pmid = {42151282},
issn = {2045-2322},
support = {PNC0000002 - CUP: B53C22006420001//Ministero dell'Università e della Ricerca/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Università e della Ricerca/ ; H93C22000560003//Regione Puglia/ ; },
abstract = {Two culture-independent methods, amplicon-based sequencing and shotgun metagenomics, have significantly advanced the study of microbial communities. To date, short-read sequencing technologies have enabled high accuracy and deep coverage, while long-read sequencing approaches are increasingly being applied to improve genome assembly, despite challenges related to sequencing errors and nucleic acid input requirements. In this benchmark study, we compared the shotgun metagenomics approach across three sequencing technologies, Illumina (short reads), PacBio and Nanopore (long reads), using a 20-species commercial mock microbial community with even species representation. Specifically, we evaluated the effectiveness of the data generated by each platform in reconstructing genomes and identifying specific known taxa, as well as in understanding their functional potential, considering annotated genes, the length of predicted proteins and the number and types of inferred functions. Illumina sequencing provided high-throughput and high-quality data, but its limited read length precluded complete genome assembly. This affected the functional analysis, leading to an underestimation of coding and non-coding genes. Nanopore sequencing yielded the longest reads, resulting in more contiguous assemblies, although it was affected by higher error rates and the choice of assembly method. PacBio offered the best balance between read length and base accuracy, but with a lower number of reads. This affected genome coverage for certain taxa, influencing the quality of their assemblies, the completeness of MAGs (Metagenome Assembled Genomes), and the accuracy of functional annotation. Nevertheless, PacBio successfully retrieved MAGs for all mock community species, and the genome annotation was consistent with the reference. Evaluating the strengths and limitations of different NGS technologies and assembly strategies, this benchmark provides a practical framework for selecting the most suitable approach for optimizing data quality in microbiome genome characterization, according to study-specific goals.},
}

@article {pmid42151303,
year = {2026},
author = {de Tacca, LMA and Lima, RN and de Oliveira, MA and Pascoal, PV and Bambil, D and Rosinha, GMS and Signor, D and Freire, M and Rech, E},
title = {The soil microbiome of the Caatinga drylands in Brazil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50433-1},
pmid = {42151303},
issn = {2045-2322},
support = {20-122//Conrad Prebys Foundation/ ; },
abstract = {Drylands cover a significant portion of the Earth's surface and play a key role in maintaining global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. The Interplant differences suggested the influence of root exudates. Altogether, the metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.},
}

@article {pmid42151371,
year = {2026},
author = {Monsalves-Álvarez, M and Calderón-Romero, P and Hayes-Ortiz, T and Bobadilla, S and Sánchez, F and de Tudela, CP and Utreras-Mendoza, Y and Campos, C and Reyes, Á and Gómez, J and Zara, B and Sepúlveda, C and Troncoso, R and Correa-Burrows, P and Gonzales-Billault, C and Court, FA and Flores-Opazo, M and Valladares-Ide, D},
title = {Protein yogurt and whey protein produce comparable muscle gains, but divergent microbiome shifts during strength training in older adults.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51209-3},
pmid = {42151371},
issn = {2045-2322},
support = {FONDECYT 11230186//Agencia Nacional de Investigación y Desarrollo/ ; FONDECYT 1241959//Agencia Nacional de Investigación y Desarrollo/ ; ACT210006//Fund for Research Centers in Priority Areas/ ; 15150012//Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias/ ; FONDAP-15150012//Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias/ ; FB210008//Financiamiento Basal para Centros Científicos y Tecnológicos de Excelencia Centro Ciencia and Vida/ ; },
abstract = {Sarcopenia, the age-related decline in muscle mass and strength, affects the functional capacity of older adults. Strength training (ST) combined with adequate protein intake is a key element in reversing and improving functional capacity. Protein, especially Whey Protein isolates (WPI), is widely used to improve muscle mass. In contrast, high-protein products, such as protein yogurt (PY), may offer similar benefits for muscle health and drive additional effects on gut health, which is altered in older adults. For this, we aim to compare WP and PY supplementation during ST on body composition, strength, and gut microbiome in untrained older adults. Seventeen untrained adults (60-70 years) were randomized to either consume WP (25 g) or PY (24.5 g) along with an 8-week supervised ST program (3 sessions/week). Initial and final assessments included body composition (BIA), strength (10RM, isokinetic torque, handgrip), gait speed, resting metabolic rate, and gut microbiome (16 S rRNA sequencing). Data were analyzed using repeated-measures ANOVA and diversity metrics. Both groups increased skeletal muscle mass (WP: +0.47 kg; PY: +0.50 kg) and improved strength and gait speed (p < 0.01), with no between-group differences. Fat mass decreased only in WP (p = 0.02), while resting metabolic rate increased in PY (p = 0.03). Microbiome analysis revealed distinct shifts: WP increased the Firmicutes/Bacteroidota ratio and enriched Subdoligranulum, whereas PY enhanced alpha diversity and increased the abundance of Coprococcus. Functional pathway predictions indicated differential enrichment in metabolic and signaling processes. High-protein yogurt and whey protein similarly improve muscle mass, strength, and functional capacity during ST, while exerting distinct effects on gut microbiome composition. Yogurt represents a cost-effective alternative to whey protein and may confer additional gut health benefits.Trial registration: Clinicaltrials.gov identifier NCT06412302. Date of registration 06/05/2024.},
}

@article {pmid42151475,
year = {2026},
author = {Kobiałka, M and Świerczewski, D and Walczak, M and Pisarek-Pacek, A and Wóycicki, RK},
title = {Complementary Microscopic and Metabarcoding Studies Allow for a Better Understanding of the Symbiotic Microbiome of Leafhopper Species Iassus lanio (Hemiptera, Cicadellidae).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02790-7},
pmid = {42151475},
issn = {1432-184X},
support = {Sonata 17, project no. 2021/43/D/NZ8/02183//National Science Centre, Poland/ ; },
abstract = {Leafhoppers' microbiome patterns were shaped by deep co-evolutionary adaptation driven by dietary specialization. Their microbiome is dominated by obligate symbionts that supplement their nutrient-poor phloem-sap diet, as well as facultative symbionts, including both bacterial and fungal microorganisms. In this study, NGS metabarcoding techniques were performed, supplemented by confocal and electron microscopy, to thoroughly investigate the symbiotic system of the Auchenorrhyncha species Iassus lanio, a representative of the poorly studied leafhopper subfamily Iassinae. The obtained results include descriptions of the composition, distribution, and ultrastructure of microorganisms, as well as the phylogeny of ancient symbionts. Two obligate symbionts were found: the ancient Auchenorrhyncha symbiont Karelsulcia bacterium and the yeast-like symbiont Ophiocordyceps. Karelsulcia bacteria occur exclusively in specialized organs called bacteriomes, while fungal microorganisms inhabit mycetocytes within the fat body. Both symbionts are transmitted transovarially from mother to offspring. The presence of Wolbachia, Sodalis and Cardinium was detected. Sodalis and Cardinium were observed in the fat body. The ultrastructure of Cardinium showed a characteristic microtubule crest inside. The obtained phylogeny of Karelsulcia bacteria indicates Iassinae affinity with the Coelidiinae and Deltocephalinae subfamily symbionts. Taxonomic profiling revealed that both sequencing methods detected the same range of bacterial taxa, while ONT exhibited improved resolution for dominant species. Differential abundance analysis emphasized platform-specific biases. These studies highlight the complementary roles of different microscopy and metabarcoding techniques, demonstrating the complexity of symbiotic systems in leafhoppers and thereby improving our understanding of the host-symbiont relationship and expanding our knowledge of the structure and localization of insect microorganisms.},
}

@article {pmid42151682,
year = {2026},
author = {Blackburn, D and Rahman, B and Saroyia, AP and Parish, AJ and Driscoll, M and Szewczyk, NJ and Vanapalli, SA and Samuel, BS},
title = {Defining Microbiome Impact on Host Physiology During Spaceflight Using Caenorhabditis elegans.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3000},
number = {},
pages = {251-275},
pmid = {42151682},
issn = {1940-6029},
mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Space Flight ; *Microbiota ; Weightlessness ; *Host Microbial Interactions ; },
abstract = {Microbiome-integrated Caenorhabditis elegans cultivation methods enable investigation of host-microbiome interactions in the context of space-relevant stresses using three key innovations: introduction of live bacterial communities replacing chemically defined media, implementation of auxin-inducible degradation systems to prevent progeny production, and development of complementary hardware platforms. Polyethylene bags provide gas-permeable cultivation environments for large populations with complex microbiomes supporting downstream molecular analyses, while NemaCapsules with micropillar arrays and passive culturing chambers allow real-time phenotypic assessment through on-orbit imaging, transforming our ability to correlate molecular signatures with physiological outcomes in microgravity.},
}

Animals
*Caenorhabditis elegans/microbiology/physiology
*Space Flight
*Microbiota
Weightlessness
*Host Microbial Interactions

@article {pmid42151788,
year = {2026},
author = {Ahmed, B and Nazari, M and Elfermi, R and Kabir, AH and Hijri, M and Smith, DL},
title = {Effects of bacillin 20 on microbial community structure and cross-domain networks in the soybean root-rhizosphere interface.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05135-z},
pmid = {42151788},
issn = {1471-2180},
abstract = {BACKGROUND: Understanding how biostimulants modulate plant-associated microbiomes is critical for advancing sustainable agriculture. Here, we investigated the effects of Bacillus-derived bacillin 20 on the root and rhizosphere microbiomes of soybean (Glycine max) using amplicon-based profiling, community ecology, and network analysis.

RESULTS: Microbial community assembly was driven primarily by plant compartmentalization, with higher bacterial richness in the rhizosphere and stronger host filtering in root-associated microbiomes. PERMANOVA analysis indicated that compartment explained most of the variation in community structure, whereas bacillin 20 treatment had no statistically significant effect. Despite no meaningful shifts in alpha diversity, bacillin 20 was associated with subtle, non-significant compositional trends in specific taxa across treatments. Indicator species and core microbiome analyses revealed compartment-specific taxa with potential roles in nutrient cycling, stress tolerance, and plant growth promotion.

CONCLUSION: Bacillin 20 was associated with changes in cross-domain microbial co-occurrence patterns, including differences in network connectivity, particularly in the rhizosphere, where several fungal ASVs (e.g., ASV33, ASV5, ASV8, and ASV88) exhibited high centrality. These findings indicate that bacillin 20 is associated with changes in microbial interaction patterns while maintaining overall community diversity. Overall, treatment effects were minor relative to compartment-driven structuring of the microbiome. Together, our results suggest that microbiome-informed approaches, including the use of targeted biostimulants, may contribute to the management of plant-microbe interactions in agricultural systems. Future studies integrating multi-omics approaches will be required to elucidate the underlying mechanisms of these interactions.},
}

@article {pmid42151989,
year = {2026},
author = {Deng, R and Qian, J and Liu, Y and Bu, Q and Cao, T and Gao, M and Huang, Z},
title = {The dual role of the microbiome in chronic wound management.},
journal = {Cell communication and signaling : CCS},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12964-026-02937-6},
pmid = {42151989},
issn = {1478-811X},
support = {82405398//National Science Foundation of China/ ; LKZ2024015//The key project of elderly health research in Jiangsu Province/ ; },
abstract = {Chronic wounds are characterized by delayed healing driven by persistent dysbiosis of the wound microbiome. Distinct microbial communities, often organized as biofilms, dominate different chronic wound types and impair tissue repair through metabolic disruption, immune evasion, and sustained inflammation. Emerging evidence indicates that probiotics can modulate wound-associated microbiota by suppressing pathogenic colonization, reshaping local metabolic and immune responses, and promoting a pro-regenerative microenvironment, both locally and via the gut-skin axis. Recent advances in natural product-derived biomaterials provide new opportunities to enable probiotic-based interventions through controlled delivery and protection of microbial function. This review summarizes the dual role of the microbiome in chronic wound pathology and healing, evaluates the challenges and risks of probiotic therapies, and highlights microbiome-responsive materials as translational tools. We propose that targeted microbiome interventions should evolve through a closed-loop strategy integrating microbiome profiling, strengthened product and technology development, and adaptive clinical management to achieve precision wound care.},
}

@article {pmid42152157,
year = {2026},
author = {Kohl, KD and Anderson, R and Andreadis, C and Baiz, MD and Bodawatta, KH and Campos-Cerda, F and Chaves, JA and Clark, AB and Costantini, MS and Davidson, GL and Davies, CS and Dietz, MW and Florkowski, M and Hird, SM and Houtz, JL and Karasov, WH and Knutie, SA and Lim, HC and Mason, NA and Rowe, M and Rudzki, EN and San Juan, PA and Skeen, HR and Slevin, MC and Somers, S and West, AG and Worsley, SF and Videvall, E and Trevelline, BK},
title = {The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42152157},
issn = {2524-4671},
support = {2150473//Directorate for Biological Sciences/ ; },
abstract = {To holistically understand the biology of animals, we must unravel the complexities and specificities of host-microbe interactions across animal taxa. Birds represent enigmatic and scientifically compelling hosts in which to understand these interactions. Here, we present a brief summary of a series of conversations among avian microbiome researchers regarding methodological challenges facing the avian microbiome field, where most research to date has focused on bacterial communities of the gut. Collectively, we acknowledged a commonly shared but underreported issue facing the avian microbiome field: that of difficulty in obtaining high-quality and high-yield microbial DNA from avian fecal samples. We discuss some of the potential reasons underlying low DNA yields, such as inhibitory compounds and rapid DNA degradation, and provide recommendations for how researchers in the avian microbiome field might cope with these methodological challenges. Collective and dedicated efforts to address these challenges will be required for a robust understanding of host-microbe interactions in avian systems.},
}

@article {pmid42152656,
year = {2026},
author = {Qiu, WJ and Chen, Y and Ye, SY and Chen, L and Zhao, CF},
title = {Critical Role of Calcitonin Gene-related Peptide (CGRP) in the Microbiome-gut-brain Axis.},
journal = {Current protein & peptide science},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892037454118260504132328},
pmid = {42152656},
issn = {1875-5550},
abstract = {Calcitonin gene-related peptide (CGRP), a neuropeptide with α and β isoforms, is a pivotal regulator connecting the neural, immune, and gastrointestinal systems. This comprehensive analysis delineates the evidence-based mechanistic roles of CGRP within the microbiome-gut-brain axis, focusing on its bidirectional modulation of enteric and central nervous system pathways. Both α- and β-CGRP are widely expressed in sensory and enteric neurons, where they govern vasodilation, intestinal motility, secretion, and mucosal homeostasis. CGRP-mediated signaling integrates gut microbiota-derived cues with central neurocircuitry, influencing visceral sensitivity, immune activation, and behavioral states such as anxiety and satiety. Furthermore, CGRP interacts with major neurotransmitter systems-including serotonin (5-HT), histamine, dopamine, and glutamatethereby linking peripheral microbial activity to central pain and emotional processing. We discuss isoform-specific and receptor-level mechanisms (e.g., CLR/RAMP1) as evidence permits and highlight gaps in translating preclinical findings to human physiology. Although CGRP has significant roles in other systems, such as in metabolism and pancreatic function, these are beyond the scope of this review, which focuses specifically on the neuro-immune-gastrointestinal interface. Collectively, CGRP emerges as a critical neuroendocrine mediator in coordinating communication across the microbiota-gut-brain axis. A deeper understanding of its spatiotemporal dynamics and isoformspecific functions will be crucial for the development of targeted therapeutic strategies for CGRPrelated disorders affecting both neurological and gastrointestinal systems.},
}

@article {pmid42152808,
year = {2026},
author = {Smith, RW and Jarman, EH and Francis, S and Burgess, JB and Hayashiganati, K and Sharma, A and Sanchez Rangle, U and Singh, A and Green, A and Fox, PM},
title = {Antibiotic eluting collagen-based hydrogel improves wound healing in a biofilm challenged murine stented wound model.},
journal = {Journal of applied biomaterials & functional materials},
volume = {24},
number = {},
pages = {22808000261447657},
doi = {10.1177/22808000261447657},
pmid = {42152808},
issn = {2280-8000},
mesh = {Animals ; *Biofilms/drug effects ; *Wound Healing/drug effects ; Mice ; *Anti-Bacterial Agents/pharmacology/chemistry ; Pseudomonas aeruginosa/drug effects/physiology ; *Collagen/chemistry/pharmacology ; *Hydrogels/chemistry/pharmacology ; Disease Models, Animal ; Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; Male ; Gentamicins/pharmacology/chemistry ; *Pseudomonas Infections/drug therapy/pathology/microbiology ; Staphylococcal Infections/drug therapy/pathology ; },
abstract = {Biofilm-colonized chronic wounds are difficult to treat due to a constantly evolving microbiome. In this study, a cHG augmented with antibiotics was examined for the topical treatment of biofilm-challenged wounds in vivo. Two studies were performed in series using a murine stented wound model. Mice were divided into four groups: control (wound only), infection only (IO), infection + cHG (IcHG), and infection + cHG + antibiotics (IcHG + Abx). We first examined Pseudomonas aeruginosa biofilms treated with gentamicin, and then MRSA biofilms treated with clindamycin. Wound healing was assessed using photography, immunohistochemistry, and histology. Systemic symptoms were monitored with hematological laboratory tests. Pseudomonas aeruginosa infected wounds treated with cHG + Abx healed faster and were protected from bacteremia. In the MRSA infected mice, wound treatment significantly affected the outcome, explaining 5.56% of total variance (ANOVA: F(3, 366) = 17.38, p < 0.0001). Additionally, infected wounds treated with cHG + Abx demonstrated less inflammatory tissue and accelerated closure rate on day 8 (76.53% ± 7.43% vs 48.40% ± 4.95%, p < 0.0001) and day 14 (96.00% ± 3.07% vs 82.38% ± 8.24%, p = 0.003), as compared to the infection only wounds. cHG offers a biocompatible, topical option with dual functionality: antibiotic augmentation to target biofilm pathogens, and a collagen-rich dressing to accelerate wound healing.},
}

Animals
*Biofilms/drug effects
*Wound Healing/drug effects
Mice
*Anti-Bacterial Agents/pharmacology/chemistry
Pseudomonas aeruginosa/drug effects/physiology
*Collagen/chemistry/pharmacology
*Hydrogels/chemistry/pharmacology
Disease Models, Animal
Methicillin-Resistant Staphylococcus aureus/drug effects/physiology
Male
Gentamicins/pharmacology/chemistry
*Pseudomonas Infections/drug therapy/pathology/microbiology
Staphylococcal Infections/drug therapy/pathology

@article {pmid42152835,
year = {2026},
author = {Misra, S and Motiwala, ZY and Puniyani, A and Kumar, S and Nair, D and Poddar, B and Nadeem, F and Idhrees, M},
title = {The association between gut microbiome and aortic aneurysm: a review article.},
journal = {Indian journal of thoracic and cardiovascular surgery},
volume = {42},
number = {6},
pages = {754-764},
pmid = {42152835},
issn = {0970-9134},
abstract = {Aortic aneurysm is influenced by traditional risk factors such as atherosclerosis, hypertension, and diabetes. Latest evidence states that the gut microbiome may play a crucial role in its pathogenesis. This review aims to explore the relationship between the gut microbiome and aortic aneurysm. We conducted a comprehensive literature review using PubMed, Embase, and Google Scholar to understand the association between aortic aneurysm and the gut microbiome. Relevant studies were evaluated and critically analyzed to narratively summarize existing knowledge and highlight research gaps. The analysis revealed that gut dysbiosis affects systemic inflammation and immune response. This in turn contributes to the degeneration of the vessel wall and aneurysm development. Bacterial metabolites, such as short-chain fatty acids (SCFAs), were found to influence inflammatory pathways, while microbial translocation exacerbates oxidative stress. Understanding the gut microbiome-aortic aneurysm axis can lead to the development of innovative prevention and therapeutic strategies focused on aortic aneurysm formation.},
}

@article {pmid42152993,
year = {2026},
author = {Bogatyrenko, E and Dunkai, T and Kim, A},
title = {Correction: Core Bacterial Microbiome in Wild Sea Cucumbers (Apostichopus japonicus) from the Sea of Japan.},
journal = {Indian journal of microbiology},
volume = {66},
number = {2},
pages = {476},
doi = {10.1007/s12088-025-01497-6},
pmid = {42152993},
issn = {0046-8991},
abstract = {[This corrects the article DOI: 10.1007/s12088-025-01493-w.].},
}

@article {pmid42071306,
year = {2026},
author = {Zhong, C and Chen, K and Lin, S and Huang, Y},
title = {Obesity-Related Cognitive Impairment: An Update Overview of Mechanisms and Treatments.},
journal = {Expert reviews in molecular medicine},
volume = {28},
number = {},
pages = {e19},
doi = {10.1017/erm.2026.10049},
pmid = {42071306},
issn = {1462-3994},
support = {NSFC 82200871//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Obesity/complications/therapy/metabolism ; *Cognitive Dysfunction/etiology/therapy/metabolism ; Animals ; Gastrointestinal Microbiome ; Brain/metabolism ; Insulin Resistance ; },
abstract = {BACKGROUND: Lifestyle changes and unhealthy eating habits have led to a sharp rise in obesity rates worldwide. Obesity is closely associated with a range of complications, including cognitive impairment and dementia. Accumulating evidence indicates that obesity negatively affects cognitive function and may increase the risk of neurodegenerative diseases. Conversely, cognitive dysfunction may further contribute to the development and progression of obesity. With growing attention in this field, obesity-related cognitive impairment has emerged as an important research focus at the intersection of metabolic and neurological disorders.

METHODS: This article reviews the potential mechanisms underlying obesity-related cognitive impairment and summarizes emerging therapeutic strategies.

RESULTS: The development and progression of obesity-related cognitive impairment involve multiple mechanisms, including insulin resistance, systemic and central inflammation, immune dysregulation, microcirculatory alterations and changes in neurotransmitters and synaptic plasticity. Recent studies have focused on the adipose tissue-brain axis and the microbiota-gut-brain axis, in particular, the targeted effects of extracellular vesicles released from adipose tissue and microbiota on the brain.

CONCLUSIONS: This article systematically reviews the mechanisms underlying obesity-related cognitive impairment and presents novel therapeutic strategies.},
}

Humans
*Obesity/complications/therapy/metabolism
*Cognitive Dysfunction/etiology/therapy/metabolism
Animals
Gastrointestinal Microbiome
Brain/metabolism
Insulin Resistance

@article {pmid42091223,
year = {2026},
author = {Tagoe, J and Ojha, B and Horne, S and Prüß, B},
title = {Azospirillum brasilense and tomato exudate or cytidine increase phytopathogen resistance and modulate phyllosphere/rhizosphere.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-14},
doi = {10.1139/cjm-2026-0032},
pmid = {42091223},
issn = {1480-3275},
mesh = {*Solanum lycopersicum/microbiology/chemistry/metabolism ; *Azospirillum brasilense/physiology/genetics ; *Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Pseudomonas syringae/pathogenicity ; *Disease Resistance ; *Plant Exudates/pharmacology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {Tomatoes are an important crop worldwide and phytopathogens can cause devastating losses. This study describes a treatment, consisting of Azospirillum brasilense Sp7 and either tomato seedling exudate or the exudate compound cytidine. The combination of A. brasilense Sp7 with cytidine showed a remarkable reduction of 83.4% in disease severity of tomatoes challenged with Pseudomonas syringae pv. tomato DC3000. Replacing cytidine with exudate was less effective at 71%, but the reduction in disease severity was still larger than by A. brasilense Sp7 alone at 55%. This reduction in disease severity was not paralleled by a decrease in P. syringae in leaf homogenates. Cytidine caused a 6.7 fold increase in A. brasilense Sp7 16S rDNA in root homogenates. In phyllosphere and rhizosphere, treatments modulated the microbial composition. In the phyllosphere, specific associations between treatment groups and bacterial orders could be computed. In the rhizosphere, principal component analysis revealed that variation along PC1 was dominated by the presence or absence of A. brasilense. Intriguingly, the inoculant caused an increase in the abundance of other Azospirillales species.},
}

*Solanum lycopersicum/microbiology/chemistry/metabolism
*Azospirillum brasilense/physiology/genetics
*Rhizosphere
*Plant Diseases/microbiology/prevention & control
Plant Leaves/microbiology
Plant Roots/microbiology
Pseudomonas syringae/pathogenicity
*Disease Resistance
*Plant Exudates/pharmacology
RNA, Ribosomal, 16S/genetics
Soil Microbiology

@article {pmid42144148,
year = {2026},
author = {Ullah, H and Huang, S and Pei, Q and Gui, P and Shi, H and Hu, X},
title = {A review on the system-level bioactivity of polysaccharides along the structure-target-microbiome axis.},
journal = {International journal of biological macromolecules},
volume = {367},
number = {},
pages = {152569},
doi = {10.1016/j.ijbiomac.2026.152569},
pmid = {42144148},
issn = {1879-0003},
abstract = {Polysaccharides are structurally diverse biological macromolecules whose functional properties extend beyond simple structure-activity relationships. This review synthesizes current literature on bioactive polysaccharides from fungal, plant, algal, marine, and microbial sources, spanning foundational studies to recent advances up to 2026, with emphasis on structural glycobiology, host-microbe interactions, and translational glycoscience. We propose the Structure-Target-Microbiome (STM) axis as a mechanistic framework in which polysaccharide bioactivity arises from the integrated interplay of molecular architecture, host receptor engagement, and microbiome-mediated biotransformation. Unlike conventional structure-activity models that correlate individual structural features with single endpoints, the STM axis integrates structural determinants (monosaccharide composition, glycosidic linkages, branching, molecular weight, and chemical modifications), microbial carbohydrate-active enzymes, metabolite production, and host physiological responses into a systems-level perspective. Accumulating evidence indicates that major polysaccharide classes, including β-glucans, pectins, hemicelluloses, arabinogalactans, sulfated marine polysaccharides, and microbial exopolysaccharides, exert biological effects through both direct host signaling and microbiota-dependent metabolic conversion. However, the literature also reveals substantial inconsistency, with many polysaccharides showing weak, absent, or context-dependent activity influenced by structural heterogeneity, purity, dosage, microbial composition, and experimental variability. Limited fermentability and inter-individual microbiome differences further contribute to divergent outcomes across experimental models. Current limitations include incomplete structural characterization, batch-to-batch variability, contamination in crude extracts, and poor reproducibility across in vitro and in vivo systems, all of which restrict translational confidence. Overall, polysaccharide bioactivity is best understood as an emergent property of structure-host-microbiome interactions rather than molecular structure alone. Future advances require standardized structural annotation, harmonized experimental protocols, microbiome-informed study design, and clinical validation to enable predictive and translational applications in functional foods and biomedicine.},
}

@article {pmid42144491,
year = {2026},
author = {Voorhees, PJ and Ponek, RM and Liu, JD and Lai, SK},
title = {A Droplet Digital PCR Assay for Quantification of Bacteriophage Viral Vector Titer and Purity.},
journal = {Annals of biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {42144491},
issn = {1573-9686},
support = {2013-39274//David and Lucile Packard Foundation/ ; R21AI185808//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/ ; DK007737-30/DK/NIDDK NIH HHS/United States ; },
abstract = {PURPOSE: Bacteriophage (phage)-based vectors offer considerable promise as tools for tuning the microbiome with molecular and genetic precision. However, standardized methods to rigorously characterize phage vectors remain lacking. Here, we present an optimized digital droplet PCR (ddPCR)-based assay for quantifying both the purity and potency of phage vector preparations.

METHODS: We utilized central composite design to develop a ddPCR assay capable of quantifying the number of phage vector capsids packed with the phage vector genome or packed with the transgenic DNA of interest. This assay targets 2 unique DNA barcodes, designed to be biologically inert and maximally orthogonal to existing DNA sequences.

RESULTS: Through stringent optimization, we were able to achieve assay conditions that enable a dynamic range of nearly 3 orders of magnitude and correct for systemic error in the assay. We then show that biological activity assays consistently underestimate transgene-packed vector titers, leading to overestimation of true transduction efficiency, particularly when contamination by genome-packed vectors is high. We further demonstrate how this approach facilitates optimization of vector production conditions and substantially improves the precision and reproducibility of phage vector transduction.

CONCLUSION: Compared to assays of biological activity, this optimized ddPCR assay has improved accuracy and, through design of experiments optimization, high precision (CVs = 5.5 ± 1.3% and 4.5 ± 1.0% for the genome and transgene barcodes, respectively). This assay can be broadly adopted to characterize and quality control vector preparations for various applications.},
}

@article {pmid42144716,
year = {2026},
author = {Shen, Y and Li, Y and Zheng, R and Xia, C and Gundel, PE and Nan, Z and Duan, T},
title = {Arbuscular Mycorrhizal Fungi Dominate Over Maternally Inherited Epichloë Endophytes in Controlling Rhizosphere Processes and Pathogen Resistance.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70613},
pmid = {42144716},
issn = {1365-3040},
support = {32071879//National Science Foundation of China/ ; CARS-22 Green Manure//China Modern Agriculture Research System/ ; },
abstract = {Plant-microbe symbioses form a multi-layered system integrating vertically transmitted Epichloë endophytes, arbuscular mycorrhizal fungi (AMF), and the rhizosphere microbiome, with implications for nutrient acquisition and pathogen resistance. Epichloë endophytes are maternally inherited and may exert priority effects that influence subsequent associations with AMF and root microorganisms, ultimately shaping defensive pathways. Here, we manipulated symbiosis of perennial ryegrass (Lolium perenne) with Epichloë sp. LpTG-3 strain AR37 and the AM fungus Acaulospora delicata to examine exudate metabolites and the recruited rhizosphere microbiome in relation to host responses to the pathogen Bipolaris sorokiniana. Dual symbiosis with Epichloë and AMF increased host growth and pathogen resistance through enhanced nutrient uptake, elevated defensive enzyme activities in leaves and rhizosphere, and reduced malondialdehyde concentrations. It also recruited potentially beneficial microorganisms and enriched metabolites negatively associated with disease severity; notably, the metabolite Acetamide 1, which accumulated under dual symbiosis, strongly inhibited the pathogen in vitro. Significant correlations among metabolites, rhizosphere microbial communities, and rhizosphere soil properties revealed coordinated belowground responses under the synergistic regulation of AMF and Epichloë that reduced disease severity. Although both symbionts enhanced host performance, AMF played a stronger role than maternally inherited Epichloë in shaping the rhizosphere processes driving growth and pathogen resistance.},
}

@article {pmid42144903,
year = {2026},
author = {de Assis, MR and Guimarães, I},
title = {Cholinergic anti-inflammatory pathway and vagus nerve stimulation in rheumatoid arthritis.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000001170},
pmid = {42144903},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: To integrate mechanistic and clinical evidence on vagal regulation of immunity via the cholinergic anti-inflammatory pathway, linking neural and inflammatory signaling in rheumatoid arthritis (RA). It highlights how reduced vagal tone contributes to disease onset and progression and frames neuromodulation as a rationale for adjunctive therapeutic strategies.

RECENT FINDINGS: Preclinical and clinical data demonstrate that vagal efferent activity modulates immune responses through noradrenergic circuits and activation of α7-nicotinic-acetylcholine-receptors on immune cells, inhibiting NF-κB nuclear translocation and reducing pro-inflammatory cytokines. This neuroimmune axis interacts with the hypothalamic-pituitary-adrenal axis and the microbiome, supporting an integrated model of inflammation. Vagus nerve stimulation (VNS) has been associated with reductions in inflammatory markers and clinically meaningful improvements in patients with RA. Implantable VNS has demonstrated efficacy and has received regulatory approval for moderate-to-severe RA refractory to disease-modifying antirheumatic drugs; however, the available evidence remains limited and requires confirmation in larger and more diverse populations. Noninvasive approaches show favorable safety profiles but heterogeneous efficacy and currently lack regulatory approval for immune-mediated diseases.

SUMMARY: VNS represents a promising adjunct to conventional immunosuppressive therapy for RA. Further well-designed trials are needed to standardize stimulation protocols, and define optimal strategies for clinical implementation.},
}

@article {pmid42144927,
year = {2026},
author = {Fraser, DR and Mason, RS},
title = {Microbial biosynthesis of vitamin D2.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-21},
doi = {10.1017/S0029665126103073},
pmid = {42144927},
issn = {1475-2719},
abstract = {In the early history of vitamin D research most of the studies on its chemistry and function were performed with vitamin D2 which was readily obtained by UV irradiation of ergosterol from yeast. Yet, in the physiological economy of vitamin D for most vertebrates, including humans, fish and especially for birds, vitamin D3 produced in skin by solar irradiation of 7-dehydrocholesterol, is the natural form of vitamin D. Vitamin D2, as a dietary supplement, while of comparable potency to vitamin D3 in most mammals, has been found in nature only when ergosterol in fungi is inadvertently exposed to solar UV radiation. Nevertheless, some herbivorous animals, horses and elephants, seem to maintain adequate vitamin D status with vitamin D2 rather than vitamin D3. The source of that vitamin D2 has been assumed to be the traces derived from ergosterol in endophytic fungi exposed to the sun on grass being consumed. However, outdoor grazing sheep in winter maintained adequate vitamin D status with vitamin D2, yet no vitamin D2 could be detected on the grass they were consuming. Bovine rumen contents, fermenting in an artificial rumen, had an increase in vitamin D2 concentration, particularly when cellulose fibre was added as a fermentation substrate. Furthermore, mice being raised from weaning on a vitamin D-free diet had vitamin D2 in their colon contents. This review examines anaerobic microbial production of vitamin D2 in the alimentary tract, in the dark, and describes a natural function for vitamin D2 in microorganisms and potentially for gut health.},
}

@article {pmid42145141,
year = {2026},
author = {Sreekumaran, S and V K, P and M N, A and Premnath, M and P S, S and P R, P and Mathew, J and E K, R},
title = {Comparative Human-Poultry Fecal Resistome Profiling from Broiler Farms Reveals Diverse Antimicrobial Resistance Genes.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {15353141261449964},
doi = {10.1177/15353141261449964},
pmid = {42145141},
issn = {1556-7125},
abstract = {Indiscriminate use of over-the-counter antibiotics has led to the rapid emergence of resistant genes in bacteria, with the ultimate crisis to global health. One of the prominent sectors with the antimicrobial resistance (AMR) concern is the farm animals that exist in close contact with humans where the environmental conditions are favorable for the rapid dissemination of pathogenic organisms and resistance genes. Hence, to understand the threat with environmental AMR, a detailed molecular insight is very important. In this study, fecal samples from both poultry and associated humans were studied by metagenomics analysis. From the results, a primary understanding on the microbial diversity difference could be generated from the selected samples. Here, the poultry samples were identified to have more microbial diversity. At the same time, several pathogens were found to be shared commonly between the hosts. Upon detailed examination, several AMR genes were also observed to be common between the poultry and human samples. The results of the study are highly relevant in light of the "One Health" concept where an integrated approach is targeted.},
}

@article {pmid42145228,
year = {2026},
author = {Lischka, J and Weghuber, D and Dinan, TG and Le Roux, CW and Schellekens, H},
title = {Optimizing Adherence and Outcomes: Potential Strategies to Enhance the Effectiveness of nutrient-stimulated hormone therapies.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-27},
doi = {10.1017/S0029665126103036},
pmid = {42145228},
issn = {1475-2719},
abstract = {Nutrient-stimulated hormone therapies (NuSH) therapies, a key class within obesity management medications, have reshaped obesity and type 2 diabetes care, producing substantial weight loss, improved glycaemic control, and significant cardiometabolic benefits in adults and adolescents. Yet outcomes vary widely, and NuSH therapy-induced changes in appetite, eating behaviour, and gastrointestinal function can compromise nutrient intake, lean mass preservation, and long-term adherence. This review synthesises evidence across nutrition, behavioural science, microbiota research, and metabolic-bariatric surgery (MBS) to outline supportive strategies that optimise clinical outcomes with NuSHs.Preclinical studies consistently show that NuSH therapies shift gut microbiota toward "lean-associated" profiles, while emerging human findings suggest that baseline microbial signatures may contribute to variability in response and tolerability. However, evidence in humans remains limited, heterogeneous, and underpowered. Across age groups, structured nutritional and behavioural support remains essential to ensure nutrient adequacy, manage side effects, strengthen adherence, and guide sustainable lifestyle change.Key research priorities include defining behavioural and microbial contributors of treatment response and adherence, evaluating microbiota-targeted adjuncts, and developing scalable, multidisciplinary care models for both adult and paediatric populations. NuSH therapies are powerful tools, but their long-term success depends on integrated, personalised nutrition and behavioural care, with growing opportunity for microbiome-informed approaches.},
}

@article {pmid42145481,
year = {2026},
author = {Godoy-Vitorino, F and Méndez-Lázaro, P and Bolaños-Rosero, B and Baerga-Ortiz, A and Torres-Rodríguez, P and Sosa, MA and Vázquez, M and Rivera-Rivera, NL and Cardona-Cordero, N and Colón-López, V and Ortiz, AP},
title = {Environmental exposures, microbiome dynamics and chronic disease risk in climate-vulnerable regions: interdisciplinary perspectives from Puerto Rico.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1807779},
pmid = {42145481},
issn = {2296-2565},
mesh = {Humans ; Puerto Rico/epidemiology ; *Microbiota ; *Environmental Exposure/adverse effects ; Chronic Disease/epidemiology ; *Air Pollution/adverse effects ; *Vulnerable Populations ; },
abstract = {Environmental factors such as air pollution, weather events, and ambient toxins are major contributors to human disease, with disproportionate impacts on vulnerable populations. In Puerto Rico, chronic exposure to air pollution and ecological disruption poses significant public health risks, particularly for cancer and other chronic conditions. These risks are unevenly distributed, disproportionately affecting children and older adults, groups central to community resilience yet highly susceptible to pollution-related health effects. This perspective review synthesizes emerging evidence linking chronic air pollution and environmental exposures to cancer, respiratory and cardiovascular disease, and microbiome alterations that may mediate long-term health trajectories. Drawing on interdisciplinary efforts from the Caribbean Cancer Research Center on Environmental and Natural Hazards, the Center for the Promotion of Cancer Health Equity, the Caribbean Collaborative Action Network, a NOAA CAP/RISA Team, and the Puerto Rico Center for Microbiome Sciences, this paper examines how environmental exposures shape health disparities. We highlight studies demonstrating that fungal spores, particulate matter, and chemical pollutants disrupt microbiome balance, immune regulation, and metabolic pathways, thereby increasing disease risk in early life and aging populations. The review also considers social determinants of health, spatial inequities, infrastructure vulnerabilities, and policy frameworks that influence exposure and resilience. By integrating environmental epidemiology, microbiome research, and public health policy, this synthesis underscores the urgency of planetary health-informed prevention, surveillance, and management strategies to mitigate pollution-related disease burdens, reduce inequities, and strengthen health in climate-sensitive regions globally.},
}

Humans
Puerto Rico/epidemiology
*Microbiota
*Environmental Exposure/adverse effects
Chronic Disease/epidemiology
*Air Pollution/adverse effects
*Vulnerable Populations

@article {pmid42145567,
year = {2026},
author = {Silva, FA and da Silva, RT and Harcourt, N and Biggs, E and Magnani, M},
title = {Indigenous microbiology: Why Indigenous knowledge matters in microbial science.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag024},
pmid = {42145567},
issn = {2633-6685},
abstract = {Indigenous knowledge has long engaged with microorganisms through relationships with environment, food, and health, yet these understandings remain marginal in mainstream microbiology. In this article, we argue that Indigenous microbiology offers a broader framework for microbial science by placing microorganisms within ecological, cultural, and ecosystem-specific relationships. This perspective is relevant to current challenges in sustainable agriculture, food security, and antimicrobial resistance. Drawing on examples from environmental management, traditional fermented foods, and therapeutic practices, we show that Indigenous knowledge can deepen microbiome research and contribute to developing healthy and sustainable strategies. Indigenous microbiology should not be treated as an informal add-on to existing science, but as a valuable framework for asking better questions about microbial life and its role in human and environmental wellbeing.},
}

@article {pmid42145603,
year = {2026},
author = {Waltmann, A and Puerto-Meredith, SM and Chinkhumba, J and Mzembe, E and Kayange, M and Carroll, I and Roach, J and Mathanga, DP and Gutman, JR and Juliano, JJ},
title = {Beyond malaria prevention: sulfadoxine-pyrimethamine treatment in pregnancy selectively remodels the maternal gut microbiome to increase gestational weight gain and improve birthweight.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.03.26352319},
pmid = {42145603},
abstract = {Intermittent preventive treatment in pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP), an antifolate drug with antimalarial and antibiotic activity, reproducibly improves birthweight across sub-Saharan Africa and the Western Pacific. This clinical protection is independent of SP's original malaria indication: it is not diminished by widespread antimalarial resistance or reduced transmission, and SP outperforms more potent non-antibiotic antimalarials (e.g., dihydroartemisinin-piperaquine, DP) for fetal growth. The biological mechanism is unexplained. We previously showed that gestational weight gain (GWG) is a significant component of this mechanism and mediates two-thirds of SP's overall birthweight benefit (NCT03009526). In the first longitudinal characterization of antifolate antibiotic effects on the pregnant gut microbiome, we show that ∼45% of SP's GWG advantage over DP is explained by gut microbial changes consistent with its pharmacology. Microbiome-mediated GWG coincided with 126g higher birthweight in SP but not DP recipients (95%CI 22.6-229.3g; p=0.019). Relative to DP, SP suppressed gastrointestinal pathobionts and enriched anaerobic commensals with recognized roles in mucosal immunity and host metabolism, a microbiome-sparing pattern distinct from conventional antibiotic-associated dysbiosis.},
}

@article {pmid42145647,
year = {2026},
author = {Xing, J and Xu, Z and Zhang, Y and Zhang, H and Zheng, L and Zhang, M and Guo, W and Liu, J and Pan, Y and Zhang, J and Jie, Z and Baele, G and Li, C and D'Souza, A and Zhao, J and Li, J and Chen, T and Wu, H},
title = {Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.06.26352545},
pmid = {42145647},
abstract = {Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.},
}

@article {pmid42145753,
year = {2026},
author = {Wu, Y and Yan, H and Li, P and Liu, Y and Leng, J and Cui, Y and Lv, X and Pang, L and Zang, N},
title = {Bridging the gaps: the gut-lung axis and microbial metabolites in the pathogenesis and treatment of pulmonary fibrosis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1817835},
pmid = {42145753},
issn = {2296-858X},
abstract = {Pulmonary fibrosis (PF) is a chronic interstitial lung disease characterized by structural damage to the lung parenchyma, excessive deposition of extracellular matrix (ECM), and irreversible decline in lung function. Current pharmacological treatments cannot effectively reverse fibrosis, highlighting an urgent need for novel therapeutic targets. Recently, the gut-lung axis and its bidirectional communication have received increasing attention for their roles in PF progression. Metabolites derived from gut microbiota, including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, lipopolysaccharides (LPS), and trimethylamine N-oxide, regulate immune responses, modulate signaling pathways, influence epigenetic modifications, and maintain intestinal barrier integrity, thereby exerting bidirectional effects on PF. Protective metabolites primarily inhibit fibroblast activation and collagen deposition, whereas pathological metabolites promote fibrosis by inducing inflammatory responses and oxidative stress. Potential therapeutic strategies targeting the gut-lung axis include fecal microbiota transplantation (FMT), probiotic and dietary interventions, and Traditional Chinese Medicine (TCM). However, clinical applications face challenges such as donor standardization, immunological safety, and consistency of therapeutic efficacy. Critical limitations remain, including reliance on acute-injury animal models that inadequately represent the chronic, irreversible nature of human PF. Translating findings across distinct PF subtypes requires caution, as their genetic architectures, immune landscapes, and microbiome interactions may differ considerably. Additionally, the causal relationship between microbial dysbiosis and fibrosis remains unclear, and clinical translation currently lacks stratified intervention strategies based on biomarkers. Future research should prioritize large-scale longitudinal cohort studies, integrated multi-omics analyses, organoid models, and gut-lung chip platforms to identify key effector molecules and therapeutic targets, ultimately facilitating precise clinical interventions targeting the gut-lung axis.},
}

@article {pmid42145889,
year = {2026},
author = {McGrath, AH and Steinberg, PD and Kjelleberg, S and Marzinelli, EM},
title = {Effects of Extreme Rainfall on a Dominant Seaweed Are Mitigated by Its Microbiota.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73644},
pmid = {42145889},
issn = {2045-7758},
abstract = {Extreme weather events are becoming more intense and frequent, driving unprecedented ecological changes globally. The effects of such extreme events can be particularly profound if they affect the performance of habitat-forming organisms (trees, corals, kelp). Further, the emergence of the "holobiont" concept in biology suggests that these impacts can occur directly on the habitat-forming "host" and/or via disruption of their associated microbiota. Following a one-in-100 year rainfall event along the coast of Sydney, Australia, we examined the effects of rainfall (in the field) and lowered salinity (in the lab) on the performance and reproductive output of a dominant, habitat-forming intertidal seaweed, Hormosira banksii. We then examined the ability of surface-associated microbes to mitigate host responses to extreme rainfall via microbial manipulations in the field. Extreme rainfall and reduced salinity (< 25 ppt) negatively affected host reproductive output. Manipulative field experiments using a combination of antimicrobial treatments applied once (pulse) or regularly (press) showed that disruption of Hormosira's microbiota after extreme rainfall affected host photosynthesis and, more importantly, inhibited the post-event recovery of host reproductive output. Press disruption of the host-microbiota prevented recovery of normal (control) levels of reproductive output and photosynthesis for over 4 months. These experiments demonstrate that host-associated microbiota can play a significant role in mediating responses of habitat-forming seaweeds to extreme weather events, with consequences for key components of fitness. Given the increased frequency of flooding and storm events experienced by many systems, the microbiome may provide a key role in influencing habitat resilience to stress.},
}

@article {pmid42145945,
year = {2026},
author = {O'Sullivan, E and Solano, O and Oliveira, JS and Johnson, AJ and Dhital, S and S Pillai, PK and Dias, F and Ubbink, J and Lin, AW and Teigen, L},
title = {The food matrix as a confounder in diet‒microbiome studies: methodological challenges and research gaps.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2671724},
pmid = {42145945},
issn = {2993-3935},
abstract = {Interactions of structural and physicochemical properties of food (e.g. texture, viscosity, and solubility), known as the food matrix, are primary drivers of host digestive kinetics. While the impact of matrix-driven variability on nutrient bioaccessibility, glycemic response, and caloric absorption is well documented, these dynamics are often overlooked in diet-microbiome research. Adequately modeling the spatiotemporal availability of microbial substrate is essential to understanding how dietary patterns impact the microbiome throughout the gastrointestinal tract. This narrative review 1) synthesizes current evidence on how food processing and structure affect human digestion and absorption of macronutrients; 2) illustrates how host digestive kinetics impact forms and quantity of substrate delivered and available to the gut microbiota; and 3) identifies challenges and knowledge gaps in current diet-microbiome research regarding food structure. The challenges and knowledge gaps discussed here call for in vivo models that can better model microbial substrate availability throughout the gastrointestinal tract to improve our understanding of diet-microbiome interactions.},
}

@article {pmid42146050,
year = {2026},
author = {Huang, X and Yang, X and Yu, Y and Huang, J and Tao, W and Yu, R},
title = {Bibliometric analysis of human microbiota-associated animal model (2005-2025).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1777297},
pmid = {42146050},
issn = {1664-302X},
abstract = {BACKGROUND: The research on human microbiota-associated (HMA) animal models is an important tool for studying the human microbiome and holds great potential for elucidating disease mechanisms and microbe-based therapeutic interactions. However, a systematic bibliometric assessment of this field has been limited.

METHODS: This study employed bibliometric methods, retrieving relevant publications published between 2005 and 2025 from the Web of Science Core Collection, Scopus, and PubMed, and visualizing the data with VOSviewer and CiteSpace.

RESULTS: The analysis revealed a continuous upward trend in the number of publications on this topic. The United States and its research institutions contributed the most and maintained close collaborations with multiple countries. The majority of the articles appeared in journals such as Gut Microbes, Microbiome, and Proceedings of the National Academy of Sciences of the United States of America (PNAS). Keyword and highly-cited reference analyses focused on the application of these models in investigating disease mechanisms and therapeutic exploration, particularly for metabolic, gastrointestinal, oncological, and neurodegenerative diseases. In addition, the impact of modeling factors such as diet and host genetics on the models has also attracted attention.

CONCLUSION: HMA animal models have become a core platform linking clinical and basic microbiology research, demonstrating unique advantages in recapitulating disease-associated microbial features and phenotypes. Nevertheless, because these models are essential for testing causal links between microbiota and disease, methodological standardization and procedural refinement are needed to enhance reproducibility and clinical applicability.},
}

@article {pmid42146054,
year = {2026},
author = {Li, X and Yu, X and Zhong, Y and Zhou, G and Zou, Y},
title = {Microecological modulators-new perspectives for treating sex hormone disorders.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1795152},
pmid = {42146054},
issn = {1664-302X},
abstract = {Sex hormone related disorders, characterized by complex etiology and long-term health risks, pose a significant challenge to global health. Hormone-based therapies are often accompanied by adverse effects and fail to address the underlying pathophysiological mechanisms. The "gut microbiota-sex hormone axis" maintains endocrine homeostasis through diverse pathways, including enzymatic reactions, immune modulation, metabolic regulation, and the microbiome-gut-brain axis. Dysregulation of this axis has been identified as a critical factor in the pathogenesis of sex hormone-related disorders. Probiotics have emerged as a promising adjunctive therapeutic strategy by targeting this axis. Preclinical and clinical studies have demonstrated that specific probiotic strains ameliorate hormonal imbalances, attenuate inflammation, and optimize metabolic parameters, showing positive efficacy in sex hormone-related disorders. This review systematically elaborates the regulatory mechanisms of this bidirectional axis and highlights the application of probiotics and its regulatory roles as targeted interventions in related disorders.},
}

@article {pmid42146064,
year = {2026},
author = {Sin, J and Choi, D and Hwang, I and Kim, S and Bunch, H and Kim, H and Chung, DK},
title = {Culture supernatants from human-derived commensal bacteria alleviate DNCB-induced atopic dermatitis through modulation of inflammatory and barrier-associated pathways.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1813592},
pmid = {42146064},
issn = {1664-302X},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by immune dysregulation, impaired epidermal barrier function, and recurrent episodes of itching and inflammation. Emerging evidence suggests that skin-resident microbiota influence host immune responses and may modulate AD pathogenesis. Here, we investigated the anti-inflammatory, barrier-restoring, and neuro-supportive effects of culture supernatants (CSs) derived from skin-resident bacteria.

METHODS: Human keratinocytes (HaCaT) stimulated with tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ) were treated with CSs from various isolates. For in vivo evaluation, a 2,4-dinitrochlorobenzene (DNCB)-induced AD-like mouse model was utilized, receiving topical applications of the CSs. Furthermore, differentiated SH-SY5Y neuronal cells were treated with keratinocyte- or fibroblast-conditioned media, prepared after stimulation with bacterial CSs, to evaluate their neurotrophic potential.

RESULTS: CSs from Brachybacterium paraconglomeratum and Brevibacterium casei significantly suppressed interleukin-6 (IL-6) and C-C motif chemokine ligand 17 (CCL17) while restoring filaggrin expression. In keratinocytes and human dermal fibroblasts, these CSs increased brain-derived neurotrophic factor (BDNF) expression. In the DNCB-induced AD-like mouse model, topical application of B. paraconglomeratum and B. casei CSs reduced epidermal hyperplasia and immune cell infiltration, downregulated tyrosine hydroxylase (TH), and restored cutaneous BDNF, glial cell line-derived neurotrophic factor (GDNF), and filaggrin (FLG) expression. In differentiated SH-SY5Y neuronal cells, the conditioned media treatments markedly upregulated BDNF, GDNF, and nerve growth factor (NGF). Mechanistically, CS treatment inhibited p38 MAPK and JAK-STAT signaling.

DISCUSSION: Collectively, these findings demonstrate that specific skin-derived bacterial metabolites exert coordinated anti-inflammatory, barrier-reinforcing, and neurotrophic activities, thereby promoting associated changes in neurotrophic markers. Such microbial products may serve as promising biologic candidates for managing atopic dermatitis.},
}

@article {pmid42146065,
year = {2026},
author = {Orwa, P and Kuhl-Nagel, T and Meinhold-Ernst, R and Jehle, JA and Mwirichia, R and Linkies, A},
title = {Linking microbiome structure to functional analysis identifies resilient Pseudarthrobacter, Pseudomonas, and Streptomyces antagonists of Phytophthora infestans in tomato.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1810932},
pmid = {42146065},
issn = {1664-302X},
abstract = {INTRODUCTION: Late blight, caused by Phytophthora infestans, remains one of the most destructive tomato diseases, driving the need for sustainable measures to reduce intensive fungicide use. Plant-associated microbial communities offer a promising but still underexplored source of biological control agents. Moreover, links between community-level microbiome patterns and functionally effective antagonists remain poorly resolved.

METHODS: In this study, we combine culture-dependent isolation, functional profiling of lytic enzymes and siderophores, with 16S rRNA Illumina-based microbiome analysis to identify ecologically relevant bacterial antagonists of P. infestans in tomato. Healthy and P. infestans-challenged tomato plants cultivated in soils from two organic tomato farms in the Rhine-Main region of Germany were analyzed.

RESULTS: Of the 594 bacterial isolates from tomato rhizosphere and phyllosphere, 84 inhibited P. infestans, and 63 of these suppressed Alternaria solani in vitro. Functional screening identified 28 isolates with broad-spectrum antagonistic potential, predominantly affiliated with the genera Pseudomonas, Bacillus, Streptomyces, Paenibacillus, and Pseudarthrobacter, characterized by broad siderophore and taxon-specific lytic enzyme activities. In planta assays identified Pseudarthrobacter sp._Pb177 as a novel and most effective antagonist of P. infestans, alongside effective Streptomyces and Pseudomonas isolates. Amplicon-based microbiome analyses of different tomato compartments under both healthy and P. infestans-challenged conditions revealed soil origin as the primary driver of bacterial community assembly, particularly in the rhizosphere and phyllosphere. Disease-associated shifts were limited to specific soil-compartment combinations (rhizosphere soil B). Key rhizosphere bacterial taxa (Acinetobacter and Chryseobacterium) remained largely stable across plant health states. Instead, disease effects are confined to shifts among rare or conditionally detected ASVs. Mapping cultured isolates to amplicon sequence variants demonstrated that most antagonists corresponded to low-abundance members of the tomato microbiome (including Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, Streptomyces, etc.), with their distribution shaped primarily by soil and plant compartment rather than disease.

DISCUSSION: These findings indicate that effective biocontrol candidates are defined less by abundance than by their resilience and function within plant-associated microbial communities. By linking microbial community profiling with functional screening and in planta assays, this study outlines a microbiome-informed approach for identifying bacterial antagonists of P. infestans and supports an ecologically grounded framework for managing tomato late blight.},
}

@article {pmid42146066,
year = {2026},
author = {Matsushima, Y and Himi, E and Kitashima, M and Ogura, K and Kotani, S and Hino, A and Inoue, K and Hosoya, H},
title = {A defined synthetic algal medium enables lettuce-free culturing of unfed Paramecium bursaria while preserving host-associated microbiome composition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821058},
pmid = {42146066},
issn = {1664-302X},
abstract = {Paramecium bursaria is widely cultured using undefined plant-based infusions such as lettuce extract, yet the variable composition of these media remains a major obstacle to experimental reproducibility and microbiome research. Here, we tested whether a chemically defined synthetic algal medium (AF-6) can replace conventional lettuce infusion while maintaining host physiology and associated microbial communities. An unfed clonal strain of P. bursaria, established in 2023 and capable of growth without external nutrient supplementation, proliferated comparably in AF-6 and lettuce media. To confirm that these results were not specific to unfed conditions, we additionally examined a publicly maintained algae-fed strain (NIES-2891), which exhibited similar growth patterns across both media. Cell size, compression-induced extension, and symbiotic algal abundance showed no significant differences between culture conditions. rbcL metataxonomic analysis revealed that Chlorella variabilis was the sole algal endosymbiont detected in all samples. Furthermore, 16S rRNA gene sequencing demonstrated that host-associated bacterial community composition remained largely conserved after replacement of lettuce infusion with AF-6 within each strain, although clear differences were observed between strains. Together, these findings establish an "unfed strain + defined algal medium" framework as a reproducible experimental platform for investigating tripartite interactions among ciliate hosts, symbiotic algae, and associated bacteria.},
}

@article {pmid42146070,
year = {2026},
author = {Chen, C and Shi, Y and Zheng, M and Han, S and Zhang, J and Sun, Z and Yue, Z},
title = {Consecutive monoculture of sweet potato reduces yield due to deteriorated soil health and disrupted nutrient cycling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1747390},
pmid = {42146070},
issn = {1664-302X},
abstract = {Sweet potato (Ipomoea batatas L.) is a staple food with many promising health benefits. However, obstacles associated with continuous cropping are common in modern intensive sweet potato production, partially due to imbalances in the soil microbiome. This research investigates the succession of the soil microbiome and its impacts following 1, 3, and 5 years of consecutive sweet potato monoculture. The results showed significantly higher diversity and homogeneity in bacteria than in fungi. Although a large proportion of operational taxonomic units (OTUs) were shared, richness analysis indicated a significant decrease in the total number of OTUs for both bacteria and fungi, especially in the fifth year. At the phylum level, Firmicutes and Parcubacteria significantly decreased, while Cryptomycota significantly increased (p < 0.05). Further analysis of the prokaryotic community using BugBase and the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database showed significant changes in many phenotypes and functions. In particular, alterations in human pathogens and Cyanobacteria, as well as differences in carbon metabolism and nitrogen conversion in soils, were revealed for the first time. It was also observed that the contents of soil organic matter (OM), total carbon (TC), and total nitrogen (TN) had a linear correlation with the abundance of Cyanobacteria. However, yield was positively correlated with soil pH but negatively correlated with disease incidence. Taken together, in addition to the distinct succession of the microbial community structure, the study indicates that consecutive monoculture of sweet potato has a significant impact on the health status of soil and nutrient cycling.},
}

@article {pmid42146094,
year = {2026},
author = {Krupa-Kotara, K and León-Guereño, P and Rozmiarek, M},
title = {Editorial: Women's health in an interdisciplinary dimension - determinants of nutritional disorders: Volume II.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1844748},
doi = {10.3389/fnut.2026.1844748},
pmid = {42146094},
issn = {2296-861X},
}

@article {pmid42146321,
year = {2026},
author = {Leyshon, C and Leyshon, M and Esmene, S and Leyshon, M and Clabburn, O},
title = {The Challenges Facing VCFSEs in Integrated Care Systems: A Qualitative Case Study of a Unitary Authority in England.},
journal = {International journal of integrated care},
volume = {26},
number = {2},
pages = {9},
pmid = {42146321},
issn = {1568-4156},
abstract = {INTRODUCTION: Integrated Care Systems (ICSs) in England seek ever-closer collaborative relationships between health and social care providers, local authorities, and the Voluntary, Community, Faith and Social Enterprise (VCFSE) sector to deliver public services in place. However, ICSs present significant challenges for VCFSEs.

METHODS: In-depth qualitative case study of VCFSEs in an ICS contiguous with a Unitary Authority in England.

RESULTS AND DISCUSSION: i) the role of the 'microbiome' of smallest VCFSE in the ICS is unclear; ii) current commissioning models work against the effective participation of VCFSEs in ICSs; iii) short-term and under-funded contracts threaten VCFSEs; iv) substitution and appropriation represent tangible threats to VCFSEs through increased demand and bureaucratisation; v) the degree to which ICS support a vibrant, heterogeneous, and sustainable VCFSE sector depends on 'system maturity'.

CONCLUSIONS: Integration is a process, not an event. The evolving landscape of service design presents both opportunities and challenges for VCFSEs, requiring careful management to harness strategic advantages while addressing operational risks.},
}

@article {pmid42146396,
year = {2026},
author = {Mitchener, MM and Anderson, CM and Veleba, M and Teo, K and Roch, M and Chen, R and Yuan, Y and Han, I and Dziergowska, A and Pethe, K and Begley, TJ and Kline, KA and Dedon, PC},
title = {Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State in Enterococcus faecalis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.07.723122},
pmid = {42146396},
issn = {2692-8205},
abstract = {UNLABELLED: Enterococcus faecalis is a Gram-positive commensal bacterium of the human gut microbiome and an opportunistic pathogen responsible for many hospital-acquired infections. Despite the clinical importance of E. faecalis , how gene and protein expression are coordinated with growth remains poorly defined. Here, we profiled transcript, protein, and tRNA pool dynamics across distinct phases of E. faecalis growth. Differences in protein abundance and corresponding mRNA levels suggested growth phase-dependent posttranscriptional regulation. Growth-associated genes exhibited biased synonymous codon usage, with ribosomal and glycolytic proteins enriched in low-abundance codons read by queuosine-modifiable tRNAs. Analysis of tRNA modification and tRNA isoacceptor abundance revealed growth phase-dependent changes, particularly in anticodon stem loop modifications that influence synonymous codon translation. Changes in queuosine levels preceded shifts in ribosomal proteins, suggesting a contribution to codon-biased translation. Collectively, these findings reveal growth phase-associated remodeling of the E. faecalis tRNA pool and support a model in which queuosine-dependent translational reprogramming shapes protein expression during bacterial growth.

IMPORTANCE: Enterococcus faecalis is a common cause of hospital-acquired infections. Despite its clinical importance, a comprehensive understanding of the organism's physiology and adaptation to environmental changes remains incomplete. Here, we characterized protein, transcript, and tRNA dynamics across bacterial growth phases, uncovering a role for post-transcriptional regulation marked by tRNA reprogramming and biased synonymous codon usage. These findings enhance our understanding of E. faecalis growth and support a model of translational reprogramming therein.},
}

@article {pmid42146479,
year = {2026},
author = {Haran, V and Wang, J and Morimoto, M and Wong, WM and Rouyer, LSF and McDonald, JG and Meeks, JP},
title = {Bile acid chemosensation in mammals supports species and gut microbiome evaluation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.30.721772},
pmid = {42146479},
issn = {2692-8205},
abstract = {UNLABELLED: The rodent accessory olfactory system (AOS) detects chemosignals emitted by conspecifics and other species to support beneficial behaviors. Peripheral vomeronasal sensory neurons (VSNs), the AOS' chemical sensors, detect fecal bile acids in patterns that have unknown significance to the animal. We used a combination of mass spectrometry and VSN calcium imaging to investigate the AOS' capacity to use bile acid information to discriminate between fecal samples from captive reptiles and mice with varying gut microbiome states. Mass spectrometry analysis revealed bile acid patterns that distinguished biologically relevant samples from one another, representing theoretical discrimination axes. We measured VSN response patterns to bile acid stimuli aligned with theoretical discrimination axes. We found that VSNs perform stimulus "whitening" via an inverse relationship between natural bile acid abundance and population response magnitude. VSNs showed maximum sensitivity to taurine-conjugated bile acids, which have high theoretical discriminatory value, but were found at low natural abundance levels. Individual taurine-conjugated bile acids drove threat assessment behavior when added to familiar mouse fecal extracts, suggesting high behavioral significance. Finally, we analyzed the degree to which the AOS utilizes the theoretical information about species, diet, and gut microbiome status from bile acids. We found that VSN tuning patterns align with theoretical axes for discriminating reptilian predators from vegetarians, and between mice with different gut microbiome states. VSN tuning was especially well-aligned with the information available about conspecific gut microbiome status. These results show that AOS bile acid chemosensation supports discrimination of multiple biologically relevant states.

SHORT ABSTRACT: The rodent accessory olfactory system (AOS) detects fecal bile acids via combinatorial codes with unknown biological significance. We investigated whether AOS bile acid chemosensation supports species and gut microbiome evaluation using mass spectrometry, calcium imaging in vomeronasal sensory neurons (VSNs), and analytical modeling. Bile acid excretion patterns theoretically supported discrimination of reptilian predators from vegetarians, and germ-free mice from conventionally raised counterparts. VSNs demonstrated stimulus "whitening" via an inverse relationship between natural bile acid abundance and population response magnitude. VSNs had highest sensitivity to taurine-conjugated bile acids, a novel class of chemosignals that elicited behavioral aversion. VSN tuning aligned with ideal discrimination axes, which was especially strong for gut microbiome-associated bile acid abundance patterns. These results show that AOS bile acid chemosensation supports discrimination of multiple biologically relevant states.},
}

@article {pmid42146481,
year = {2026},
author = {Jensen, O and Hanson, L and Hénault, M and Haskins, BE and Trujillo, E and Brown, C and Brunetti, T and McCabe, M and Russo, BC and Heasley, L and Ost, KS},
title = {A Candida glabrata adhesin-like effector drives fitness and immunogenicity in the gut.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.04.722752},
pmid = {42146481},
issn = {2692-8205},
abstract = {Candida glabrata is a leading cause of invasive candidiasis. The gut serves as its primary reservoir, yet factors governing colonization and pathogenic potential remain poorly defined. Here, we identify immunoglobulin A (IgA) as a key regulator of C. glabrata within the intestinal microbiome. We found that C. glabrata induces an IgA response in a strain-specific manner. Comparative transcriptional and proteomic analyses of IgA-inducing and non-inducing strains identified a putative adhesin, Awp11, whose expression correlated with IgA induction. Awp11 is directly targeted by IgA and is required for inducing C. glabrata -specific IgA and Th17 responses in vivo. Functionally, Awp11 promotes colonization of a complex intestinal microbiome, and intestinal IgA limits this advantage. In most strains, AWP11 transcription is dynamic and limited by IgA in the gut. This identifies Awp11 as a key determinant of strain-dependent immunogenicity and gut colonization that C. glabrata may dynamically regulate to balance colonization and immune evasion.},
}

@article {pmid42146533,
year = {2026},
author = {Steininger, HM and Iglesias-Aguirre, CE and Panzer, AR and Durack, J and McKean, M and Cabana, MD and Diamond, S and Lynch, SV},
title = {Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential of Bacteroides cellulosilyticus.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.28.721144},
pmid = {42146533},
issn = {2692-8205},
abstract = {Childhood atopic disease is linked to delayed gut microbiome development and metabolic dysfunction, however microbial drivers remain unclear. To explore microbial correlates of asthma risk during a time of active gut microbiome development, we analyzed stool from 6-month-old infants at high asthma risk (HR) or healthy controls (HC), using Genome-resolved metagenomics (HR=7; HC=12) and untargeted metabolomics (HR=11; HC=15). We recovered 82 bacterial species-level metagenomic-assembled genomes (MAGs). Global Taxonomic composition did not differ by asthma risk. Anticipating that key differences might associate with specific genomes, a machine-learning approach pinpointed Bacteroides cellulosilyticus, Hungatella effluvii, and Enterocloster aldenensis as linked with asthma risk status. All three species were more abundant in HC infants and the B. cellulosilyticus genome was enriched for carbohydrate metabolism genes relative to other MAGs. Metabolomic profiling revealed variance associated with asthma risk (PERMANOVA, R2=0.069, p=0.016). HR fecal metabolomes were enriched in simple sugars, whereas HC contained more nitrogenous compounds. Integrative genome-metabolic modeling of compounds that significantly differentiate asthma-risk groups revealed risk-dependent interactions with community-encoded metabolic potential (CEP), for arabinose and agmatine, whose fecal concentrations are linked with B. cellulosilyticus and H. effluvii functional traits respectively. These findings suggest that microbial-influenced metabolic differences associate with asthma risk at 6 months, with B. cellulosilyticus and H. effluvii emerging as candidate bacteria influencing this observed metabolic remodeling.},
}

@article {pmid42146538,
year = {2026},
author = {Yengo, CK and Liu, X and Langley, RJ and Avila, F and Sagar, M and Ochsenbauer, C and Bensing, BA and Hioe, CE},
title = {HIV-1 interactions with sialic acid-binding bacterial lectins promote virus infectivity in vitro and mucosal transmission in humanized mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.05.722898},
pmid = {42146538},
issn = {2692-8205},
abstract = {UNLABELLED: Most HIV-1 transmission occurs at mucosal surfaces, which are colonized by the host microbiota. However, interactions between HIV and bacteria or bacterial products derived from the human microbiome are poorly characterized, and their biological consequences are largely unexplored. Here, we evaluated the effects of sialic acid-binding lectins expressed by bacterial species ubiquitous in the human microbiota on HIV-1 infectivity using viruses produced in 293T cells and human primary cells. We demonstrated that these bacterial lectins enhanced HIV-1 infectivity in a sialoglycan-dependent manner. Specifically, Siglec-like binding region lectins (SLBR-N, SLBR-H, and SLBR-B) from Streptococcus gordonii and Staphylococcal superantigen-like lectins (SSL3, SSL4, and SSL11) from Staphylococcus aureus increased HIV-1 infectivity to varying extents, depending on lectin type and virus strain. Among these lectins, SLBR-N exhibited the greatest potency, corresponding with its superior ability to bind virions and promote virus-cell attachment. This enhancing activity was observed for direct infection of TZM-bl reporter cells and primary CD4+ T cells, as well as trans-infection in the presence or absence of the mannose-binding host lectin DC-SIGN. Importantly, these findings were corroborated in vivo using humanized mice, in which pre-exposure to SLBR-N promoted rectal HIV-1 transmission and increased viral burdens in plasma and splenic cells. Collectively, the data show sialoglycan-binding bacterial lectins as microbial factors that can enhance HIV-1 transmission at mucosal surfaces, highlighting a potential direct role for the microbiota in modulating HIV-1 acquisition risk.

AUTHOR SUMMARY: HIV is commonly transmitted from one person to another across mucosal surfaces, such as those lining the genital and rectal tracts, which are densely populated by bacteria that make up the human microbiota. Yet, surprisingly little is known about how these bacteria and the molecules they produce influence HIV infection. In this study, we investigated a group of bacterial proteins known as sialic acid-binding lectins that are expressed by common members of the human microbiome: Siglec-like binding region lectins from Streptococcus gordonii and superantigen-like lectins from Staphylococcus aureus . Using multiple HIV strains and several types of target cells, we demonstrate that lectin binding to HIV can increase virus attachment to target cells and thereby enhance infection, although the magnitude of this effect varies among lectins and virus strains. Lectin binding also facilitates HIV spread from cell to cell and promotes mucosal HIV infection in a humanized mouse model, resulting in a higher viral burden in the blood and tissues. These findings identify bacterial lectins as important factors that can influence HIV infection and implicate a potential role for the human microbiota in determining susceptibility to HIV infection.},
}

@article {pmid42146631,
year = {2025},
author = {Madaan, T and Nieman, ML and Rakheja, T and Siddiqui, N and Gherardini, D and Sertorio, M and Kamble, NS and Thomas, SC and Hartman, A and Koch, SE and Knipper, L and Marino, VA and Sadayappan, S and Lorenz, JN and Konhilas, JP and Kotagiri, N},
title = {Modulating Cardiac-Gut Microbiome Interaction Post-Myocardial Infarction with Engineered Bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.10.664025},
pmid = {42146631},
issn = {2692-8205},
abstract = {The gut microbiome plays a critical role in the pathophysiology of acute myocardial infarction (MI). MI events significantly impact intestinal integrity which results in leakage of bacterial products into the systemic circulation. We demonstrate that MI not only compromises intestinal integrity, leading to systemic leakage of bacterial products like LPS, but also results in the translocation and colonization of live, intact gut bacteria in the MI heart - a novel aspect of the heart-gut axis. Our initial findings with natural murine gut microbiome were substantiated using orally administered E. coli Nissle 1917 (EcN), as a tracer bacterium. Furthermore, we engineered EcN to express the microbial anti-inflammatory molecule (MAM) derived from the probiotic Faecalibacterium prausnitzii . Treatment with this engineered strain, EcN-MAM, led to significantly improved survival and cardiac function in MI mice. This was attributed to enhanced gut barrier integrity, resulting in reduced systemic bacterial permeation and subsequent inflammation. These findings shed light on a previously unrecognized dimension of the heart-gut axis and highlight the potential of microbiome-based interventions in MI management.},
}

@article {pmid42146777,
year = {2026},
author = {Mikulikova, I and Lepkova, Z and Bandouchova, H and Blahova, J and Papezikova, I and Novotna, H and Toulova, I and Kobelkova, K and Odehnalova, K and Postulkova, E and Radojicic, M and Mares, J and Mudronova, D and Palikova, M},
title = {The effect of Lactiplantibacillus plantarum probiotic supplement on rainbow trout challenged with Aeromonas salmonicida.},
journal = {Veterinarni medicina},
volume = {71},
number = {4},
pages = {156-168},
pmid = {42146777},
issn = {0375-8427},
abstract = {Two probiotic (Lactiplantibacillus plantarum) supplementation strategies (continuous and cyclic) were evaluated for their ability to enhance resistance of rainbow trout (Oncorhynchus mykiss) to Aeromonas salmonicida infection. Neither of these strategies improved post-challenge survival. Instead, cyclic administration resulted in a significantly higher mortality rate (73%) compared with continuous supplementation (52%) and the control group (46%). One week post-challenge, most haematological, plasma biochemical, and immune parameters showed no significant difference between treatments, though fish receiving cyclic supplementation did exhibit a reduced lymphocyte count. However, three weeks post-challenge, this same group showed a significant decrease in total phagocyte number and in the proportion of phagocytes within white blood cells. IgM concentrations were significantly lower in both probiotic-supplemented groups than in the control group. In the cyclic group, reductions in interleukin-10 and elevations in total protein levels were also observed. Microbiome analysis of gut content three weeks post-challenge revealed a marked decline in microbial diversity in both probiotic-treated groups. These findings indicate that, under the experimental conditions, probiotic supplementation did not provide protection against A. salmonicida infection and that cyclic administration may disrupt immune homeostasis and intestinal microbial stability, ultimately compromising host resilience.},
}

@article {pmid42146906,
year = {2026},
author = {Orletskaia, VA and Olekhnovich, EI},
title = {Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0065},
pmid = {42146906},
issn = {2001-0370},
abstract = {Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multicancer cohorts, with melanoma (72.7%, n = 456) and other cancer types collectively accounting for 27.3% (n = 171), including gastrointestinal, non-small-cell lung, breast, ovarian, and other types. Our catalog comprises 3,816 operational genomic units and reveals the key ecological determinants of immune checkpoint inhibitor response. Clinical benefit was associated with gut ecosystems dominated by prevalent, autochthonous taxa. Indeed, the population frequency of a taxon was a positive predictor of its favorable outcome association. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism, including specialized mucin degradation and amino acid biosynthesis. In contrast, nonresponse was characterized by enrichment of low-prevalence, exogenous oral and food-derived bacteria and enriched for replication-associated pathways. Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas nonresponse represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and functional coherence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes.},
}

@article {pmid42147140,
year = {2026},
author = {Vincent, SA and Devlin, PF},
title = {Fungicides disrupt total and endophytic phyllosphere bacterial communities but a salicylic acid hyperimmune mutant shows microbiome resilience.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag102},
pmid = {42147140},
issn = {2730-6151},
abstract = {Stable colonization of plants by beneficial microbes enhances disease resistance, nutrient uptake, and stress tolerance. Disruption of these communities often reduces plant fitness. The phyllosphere microbiome is especially vulnerable to agrochemicals. In this study we examined how synthetic fungicides affect the phyllosphere bacterial community of Arabidopsis thaliana. Application of several widely-used fungicides led to a pronounced decrease in bacterial diversity and depletion of beneficial taxa in both surface and internal leaf microbial communities. Moreover, these microbial responses were influenced by the host plant's genetic background. We previously showed that the phyllosphere microbiomes of plants exhibiting heightened salicylic acid-driven immune responses are enriched in xenobiotic degradation traits. We, therefore, examined whether the disrupted phyllosphere of one such line, the fhy3 far1 mutant, is buffered against fungicide-induced dysbiosis. The fhy3 far1 mutant showed reduced fungicide-induced microbiome disruption in both surface and endophytic microbiomes across both systemic and contact fungicides, supporting the hypothesis that innate plant immunity may help buffer against collateral damage from chemical treatments. Our identification of fungicide-resilient microbial taxa holds promise for the development of next-generation biostimulant products and, additionally, our findings raise the possibility that salicylic acid-mediated immunity could be strategically leveraged as a complementary tool alongside traditional fungicides.},
}

@article {pmid42147160,
year = {2026},
author = {Turnbaugh, P and Zhang, S and Buttimer, C and Trepka, K and Lam, K and Hernandez, LR and Noecker, C and Soto-Perez, P and Canigiula, P and Ortega, E and Lee, J and Ramirez, L and Partipilo, G and Lawrence, H and Bottacini, F and Shkoporov, A and Draper, L and Ross, RP and Coffey, A and Hill, C},
title = {Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9488777/v1},
pmid = {42147160},
issn = {2693-5015},
abstract = {Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage ΦKL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta , during in vitro growth. However, ΦKL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that ΦKL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.},
}

@article {pmid42147173,
year = {2026},
author = {Ng, J and Trannguyen, J and Wilkinson, R and Conard, F and Fehrenback, S and Ebersole, B and Ghosh, D and Apewokin, S},
title = {Conditioning chemotherapy exposure is associated with epigenetic modifications in Clostridioides difficile isolates from stem cell transplant recipients.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8865869/v1},
pmid = {42147173},
issn = {2693-5015},
abstract = {Clostridioides difficile is a highly methylated organism within the gut microbiome that is responsible for Clostridioides difficile infection (CDI), a common disease that is mediated by toxins production from the bacterium. C. difficile infection is ten times more common in chemotherapy patients than the average patient, but the reasons for this disparity are unclear. Conditioning chemotherapy (CC), an integral part of cancer treatments, has the ability to induce methylation changes in many cell types. We posit that CC induces methylation changes within C. difficile that may promote toxin production and consequently CDI. To test our hypothesis, we sought to identify the epigenetic changes, particularly methylation changes, within C. difficile isolates before and after chemotherapy and within isolates that express toxin and isolates that do not. After stool sampling, we isolated C. difficile by culture then sequenced and created a hybrid assembly of each isolate using nanopore long read sequencing and Illumina short read sequencing. Bioinformatics tools such as Dorado and Samtools were used to basecall and determine methylation states, while Unicycler was used for genome assembly. Methylartist was then used for data visualization. Genome-wide methylation profiling revealed distinct epigenetic signatures in Clostridioides difficile associated with toxin expression and chemotherapy exposure. Whole-genome 6mA analysis demonstrated significant differences between toxin-positive and toxin-negative isolates, with prominent methylation changes in tcdA and tcdE , while selected sporulation genes were unmethylated in toxin-negative strains. Chemotherapy was associated with a significant shift in global 6mA methylation patterns. Targeted 5mC analysis of the pathogenicity locus revealed reduced methylation around tcdB and across multiple toxin genes following chemotherapy, whereas sporulation genes remained unaffected. These findings suggest chemotherapy-associated epigenetic remodeling of toxin-associated loci in C. difficile .},
}

@article {pmid42147178,
year = {2026},
author = {Gough, E and Basu, S and Brubaker, J and DeNeraing, B and Sack, D and Bourgeois, AL and Walker, R and Harro, CD and Chakraborty, S},
title = {Influence of Gut Microbiota on Immune Responses and Protection in Volunteers Receiving the Live Attenuated Oral ETEC Vaccine ACE257 followed by Virulent ETEC H10407 Challenge.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9284363/v1},
pmid = {42147178},
issn = {2693-5015},
abstract = {Enterotoxigenic Escherichia coli (ETEC) remains a major cause of diarrheal morbidity with no licensed vaccines. Role of gut microbiota in vaccine immunogenicity and protection was investigated using 16S rRNA sequencing from the stool samples of 27 volunteers receiving two doses of the live attenuated oral ETEC vaccine ACE527 followed by virulent ETEC H10407 challenge. Systemic and mucosal IgG and IgA responses to heat-labile toxin-B (LTB) and colonization-factor-antigen-I (CFA/I) were quantified by ELISA in serum and antibody-in-lymphocyte-supernatant (ALS). Microbiome α-diversity, β-diversity, and taxa-immune associations were evaluated using regression models, MiRKAT, and relaxed LASSO. Vaccination increased (~ 25-30%) Eubacterium_brachy_group, Family_XIII_AD3011 and Actinomyces. Higher α-diversity (inverse-Simpson) was associated with reduced ALS anti-LTB and CFA/I IgA responses, whereas β-diversity correlated with increased serum anti-CFA/I IgA. Members of Anaerovoraceae, Peptostreptococcaceae, Oscillospiraceae, and Veillonellaceae enhanced immune responses and protection against severe diarrhea and ETEC colonization, while Ruminococcaceae, Sutterellaceae, Coriobacteria, Clostridia, and Actinobacteria showed antagonistic associations.},
}

@article {pmid42147179,
year = {2026},
author = {Belger, C and Wirbel, J and Maghini, D and Carstens, N and van Coller, A and Beasley, JC and Melzheimer, J and Berkman, AY and Strauss, WM and Hetem, RS and Hazelhurst, S},
title = {The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9092464/v1},
pmid = {42147179},
issn = {2693-5015},
abstract = {Background: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking. Results: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism-critical for processing the lions' high-purine diet-with nearly complete pathways for degrading adenine and guanine to urea. Conclusions: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.},
}

@article {pmid42147183,
year = {2026},
author = {Topacio, TM and Maltz, MR and Lo, DD and Zaza, M and Porter, WC and Freund, L and Lyew, A and Cocker, D and Biddle, T and Yisrael, K and Castillo, DD and Dingilian, H and Drover, RW and Botthoff, J and Aronson, E},
title = {Chronic exposure to Salton Sea aerosols elicits pulmonary inflammation and shifts in murine lung and fecal microbiome diversity.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9569949/v1},
pmid = {42147183},
issn = {2693-5015},
abstract = {Lung disease is rampant around the Salton Sea, California's largest inland lake and a major source of airborne particulates. To examine root causes of pulmonary disease, we investigated the exposure impacts of spatiotemporal variation in aerosols collected near the Salton Sea on lung and fecal microbiomes. We collected dust during the summer and fall at three different sites around the Salton Sea from 2020 to 2022. Dust was filtered to remove microbial cells and aerosolized for 7-day chronic murine exposures within controlled environmental chambers, after which mouse lung and fecal samples were used for 16S rRNA V3-V4 amplicon sequencing. We verified that chronic exposure to aerosols elicits neutrophilic pulmonary inflammation, particularly in mice exposed to collections from the Wister site near the Salton Sea. We found that spatiotemporal variation drove variation in lung microbiome composition in mice exposed to aerosols from 2022. The lung microbiomes of Salton Sea aerosol-exposed mice were found to increase in alpha-diversity and richness, while simultaneously decreasing in evenness. In contrast, the fecal microbiomes of aerosol-exposed mice decreased in diversity and richness. Our findings suggest that chronic exposure to aerosols from Wister, a site immediately Southeast of the Salton Sea, triggers a systemic stress response in mice characterized by high pulmonary neutrophil recruitment, increased lung microbiome diversity, and decreased fecal microbiome diversity. Back trajectory analyses for aerosol surface type frequencies revealed higher contributions from the Salton Sea in 2020 and 2022 collections from Wister. These findings suggest that chronic exposure to Salton Sea aerosols have impacts on host pulmonary and systemic health, as emphasized by significant but opposing effects on lung and fecal microbiome diversity. Furthermore, these findings demonstrate the variable capacity of environmental aerosol exposure to elicit health consequences relative to seasonal weather events.},
}

@article {pmid42147187,
year = {2026},
author = {Caspi, R and Zhang, A and Horai, R and Jittayasothorn, Y and Badger, J and Wu, Z and Shi, G and Gupta, A and Arunkumar, S and Murphy, C and Nagarajan, V and McCulloch, J and Kodati, S and Sen, H and Lee, JW and Jacobs, J and Xu, X and Mattapallil, M and Peng, Z and Xu, B and Palmer, R and Majdalani, N and Honda, K and O'hUigin, C},
title = {Gut microbial interaction networks control autoimmunity to neuroretina.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9528424/v1},
pmid = {42147187},
issn = {2693-5015},
abstract = {The gut microbiome influences the development of immune-mediated inflammatory diseases, including autoimmune uveitis, a sight-threatening ocular inflammation driven by retina-specific T cells1. Using a model of spontaneous autoimmune uveitis (sEAU) we showed that gut commensals provide immune stimuli that trigger disease2. Here we report that uveitis-promoting microbes are present in human gut flora and that colonization of germ-free (GF) mice with commensals from healthy human donors was sufficient to provoke disease. Severity of sEAU correlated with expansion of Akkermansia and contraction of short-chain fatty acid (SCFA)-producing Firmicutes, followed by decreased SCFA levels and a dominant gut Th1 effector response. Mechanistic gain-of-function experiments, enriching GF sEAU mice with Akkermansia, reproduced these microbiome, metabolite and immune phenotype shifts, and exacerbated disease, suggesting that Akkermansia promotes autoimmunity by outcompeting SCFA-producers and enhancing Th1-type responses. An inverse correlation between Akkermansia (Verrucomicrobia) and Firmicutes was also present in patients with uveitis, multiple sclerosis and Crohn's disease. These findings reveal a stereotypic gut microbial interaction network that regulates systemic immune balance, and may represent an ecologically conserved mechanism through which the gut microbiome modulates autoimmune and inflammatory diseases.},
}

@article {pmid42147198,
year = {2026},
author = {Lewis, K and Patil, P and Liang, HW and Astley, E and Taher, R and Lee, MH and Norment, D and Iinishi, A and Gupta, N and Sobolevskaia, K and Chen, E and Nawab, A and Adzre, J and Moss, C and Hawkins, B and Bourgeois, J and Caimano, M and Brissette, C and Hu, L},
title = {A deformylase inhibitor expands therapeutic options for Lyme disease.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9335039/v1},
pmid = {42147198},
issn = {2693-5015},
abstract = {Lyme disease incidence continues to rise globally. This vector-borne infection remains a major public health burden. Broad-spectrum doxycycline and ceftriaxone disrupt the gut microbiome, drive resistance in commensals, and offer suboptimal efficacy against neuroborreliosis. Here we show that forazemin, previously known as BB-83698, is an orally bioavailable peptide deformylase inhibitor with potent and selective bactericidal activity against spirochaetes, including diverse Borrelia species. Targeting the deformylation of nascent peptides, forazemin halted protein synthesis, thereby killing the spirochaetes. In murine models of Lyme borreliosis and neuroborreliosis, short oral dosing regimens cleared infection, and forazemin was more effective than doxycycline in tick-bite prophylaxis. Forazemin preserved microbiome diversity and spared beneficial gut symbionts. These findings support forazemin as a candidate for the treatment and prevention of Lyme disease.},
}

@article {pmid42147301,
year = {2026},
author = {Barbosa, MC and Pellegrinetti, TA and da Cunha, ICM and da Silva, AVR and Marcandalli Boleta, EH and Losovoi, LA and Mendes, R and Tsai, SM and Mendes, LW},
title = {Genotype-dependent stability and specialization of arbuscular mycorrhizal fungal communities under drought in common bean.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1786322},
pmid = {42147301},
issn = {1664-462X},
abstract = {Arbuscular mycorrhizal fungi (AMF) represent a key biological strategy for enhancing agricultural resilience under extreme climatic events such as drought. However, how AMF interact with drought-tolerant plant genotypes to sustain performance under water limitation remains poorly understood. Here, we used high-throughput DNA sequencing to investigate AMF communities associated with drought-tolerant (BAT477 and SEA5) and drought-susceptible (IAC-Milênio and IAC-80SH) common bean genotypes, integrating taxonomic, structural, and functional perspectives under contrasting water regimes. We hypothesized that drought tolerance is not simply linked to AMF presence, but rather to the ability of host genotypes to structure and stabilize their mycorrhizal communities under stress. Our results reveal genotype-specific responses to drought, with distinct community restructuring dynamics observed across individual genotypes. Drought-tolerant genotypes maintained or increased AMF relative abundance, diversity, and functional integrity under drought, whereas susceptible genotypes displayed opposing changes in the community's structure. Although most genotypes displayed high dissimilarity in AMF community structure between control and drought conditions, tolerant genotypes reorganized their communities through increase in the relative abundance of key ASVs, whereas susceptible genotypes experienced substantial reductions in abundance, diversity, and specialist ASVs. Niche occupancy and functional guild analyses further showed that AMF communities in tolerant genotypes were dominated by specialist and symbiotrophic ASVs, whereas susceptible genotypes shifted toward rare and functionally reduced assemblages. At the plant level, AMF community stability was positively associated with root biomass and negatively associated with foliar nutrient, indicating a tight coupling between mycorrhizal community structure, host nutritional status, and growth. Collectively, our findings indicate that drought tolerance in common bean emerges, at least in part, from a cooperative host-microbiome strategy in which the host actively regulates the structure and functional stability of AMF communities under water stress. These results advance our understanding of plant-mycorrhizal interactions in drought adaptation and highlight the potential of integrating mycorrhizal functionality into plant breeding strategies aimed at developing climate-resilient crops.},
}

@article {pmid42147430,
year = {2026},
author = {Liu, D and Chen, Y and Pan, J and He, Z and Zhou, Y and Dai, G and Dai, X and Lin, Z and Zhao, P and Lu, H and Zheng, M},
title = {Effect of modified Zengye decoction on age-related constipation via modulation of the host-microbial metabolic axis.},
journal = {Gastroenterology report},
volume = {14},
number = {},
pages = {goag031},
pmid = {42147430},
issn = {2052-0034},
abstract = {BACKGROUND: Constipation is a common digestive disorder in the elderly caused by weakened intestinal peristalsis and reduced mucus secretion that significantly impacts quality of life. Current treatments typically provide only temporary symptomatic relief and may lead to dependence and adverse effects.

METHODS: This study investigated the therapeutic effects of a modified traditional Chinese formula, modified Zengye decoction (MZD) on age-related constipation by modulating the gut microbiome and metabolomics. Aged constipated rats were gavage-fed with or without MZD. After detection of the indicators related to the disease, the microbial and metabolic profiles were generated for all the fecal samples by using 16S rRNA gene sequencing and [1]H nuclear magnetic resonance ([1]H NMR) spectroscopy, respectively.

RESULTS: MZD effectively alleviated constipation symptoms in aged mice by enhancing the intestinal peristalsis and antioxidant capacity. Gut microbiome analysis revealed that MZD significantly altered the abundance of Firmicutes, Bacteroidetes, and Actinobacteria. Specifically, the abundance of beneficial bacteria such as Corynebacterium, Roseburia, and Clostridium increased by 6-fold, 4-fold, and 3-fold, respectively. These changes in microbial composition enhanced the production of short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate. Additionally, MZD significantly increased the expression of Mucin 2 protein and the moisture content of the small intestine, while decreasing pro-inflammatory cytokines such as tumor necrosis factor-alpha, interleukin-1 beta, and interleukin-6, and increasing anti-inflammatory interleukin-10, which may be attributed to the elevated levels of SCFAs.

CONCLUSIONS: By effectively regulating the gut microbiome and SCFA metabolism, MZD demonstrated significant anti-inflammatory and mucus-secretion-promoting effects, showing therapeutic potential for age-related constipation, enteritis, and other inflammation-related intestinal diseases.},
}

@article {pmid42147745,
year = {2026},
author = {Li, W and Jiang, J and Zhou, J and Li, P and Duan, X},
title = {Gut Microbiota Metabolite, Trimethylamine N-Oxide, Aggravates Cognitive Impairment in Cerebral Ischemia-Reperfusion Injury.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {594053},
pmid = {42147745},
issn = {1178-7074},
abstract = {PURPOSE: Cerebral ischemia-reperfusion injury (CIRI) causes neuronal inflammation, oxidative stress, and cognitive impairment. We hypothesized that gut microbiota dysbiosis exacerbates post-ischemic cognitive deficits, with trimethylamine N-oxide (TMAO) acting as a potential mediator.

METHODS: In the primary experiment, mice received an antibiotic cocktail for 28 days to induce gut dysbiosis prior to bilateral common carotid artery occlusion (BCCAO), a model of CIRI (n = 12 per group). Gut microbial composition was analyzed using 16S rRNA sequencing, and cognitive function was assessed with the Morris water maze. Functional enrichment analyses (Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups) and microbiota-metabolite database mapping were used to identify candidate metabolites. In a separate validation cohort (n = 6 per group), TMAO (6.5 mg/day) was administered intraperitoneally for 7 days before BCCAO.

RESULTS: Antibiotic treatment markedly altered microbial diversity and composition, characterized by an expansion of Proteobacteria and a reduction in Lactobacillus. Bioinformatic analyses identified TMAO, a metabolite associated with Proteobacteria/Enterobacteria, as a potential mediator. Mice with antibiotic-induced dysbiosis subjected to CIRI exhibited impaired spatial memory, as indicated by fewer platform crossings and reduced time spent in the target quadrant. Similarly, TMAO pretreatment reproduced these cognitive deficits in BCCAO mice.

CONCLUSION: Antibiotic-induced gut dysbiosis appears to exacerbate CIRI-related cognitive impairment, at least in part through elevated TMAO levels. These findings highlight a potential microbiota-metabolite axis as a target for therapeutic intervention.},
}

@article {pmid42147973,
year = {2026},
author = {Wardi, M and Amin, AB and El Belghiti, I and Lemkhente, Z and Belmouden, A},
title = {Importance of human microbiome: an update.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1787662},
pmid = {42147973},
issn = {2813-4338},
abstract = {Millions of microorganisms-including bacteria, viruses, fungi, archaea, and protists-reside on and within the human body, collectively forming the human microbiota. This complex and dynamic community plays a crucial role in modulating physiological processes, particularly the development and regulation of the immune system. Modern behaviors such as frequent washing, excessive hygiene, and widespread use of antimicrobial agents can disrupt the natural composition and functional balance of the microbiota, leading to altered immune responses and increased susceptibility to disease. In this review, we focus primarily on the bacterial component of the human microbiome. While we acknowledge the importance of viruses, fungi, archaea, and protists, these components are beyond the scope of the current review. We highlight recent advances in bacterial microbiome research that are reshaping our understanding of host-microbe interactions, immune modulation, and the health consequences of microbiota dysbiosis.},
}

@article {pmid42148043,
year = {2026},
author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS},
title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.},
journal = {Environmental health perspectives},
volume = {134},
number = {1},
pages = {75-90},
doi = {10.1021/EHP.6c00064},
pmid = {42148043},
issn = {1552-9924},
mesh = {Humans ; Uganda ; Female ; *Gastrointestinal Microbiome ; *Air Pollution, Indoor/statistics & numerical data/adverse effects ; Adult ; *Virome ; Middle Aged ; },
abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.},
}

Humans
Uganda
Female
*Gastrointestinal Microbiome
*Air Pollution, Indoor/statistics & numerical data/adverse effects
Adult
*Virome
Middle Aged

@article {pmid42148231,
year = {2026},
author = {Niu, Y and Li, Y and Zhou, X and Kong, W and Zhou, B and Hu, X and Guo, J},
title = {Geraniol alleviates benzo[a]pyrene-induced neurotoxicity by regulating the NLRP3/Caspase-1 pathway and gut microbiome in mice.},
journal = {Food science and biotechnology},
volume = {35},
number = {7},
pages = {1905-1918},
pmid = {42148231},
issn = {2092-6456},
abstract = {Benzo[a]pyrene (BaP) exposure has been associated with an increased risk of neurotoxicity, including learning and memory impairment. As an antioxidant and a potential prebiotic, geraniol is speculated the potential preventive agent against neurotoxicity. This study aims to reveal the neuroprotection of geraniol on BaP-induced neurotoxicity. The results indicate geraniol increases immunofluorescence intensity of PSD-95, and decreases the immunofluorescence intensity of Iba-1 and GFAP, as well as the level of inflammatory cytokines, and pyroptosis biomarkers. Geraniol also up-regulates the expression of tight junction proteins markedly. In addition, lipopolysaccharide (LPS), might originate from intestinal flora and closely correlated with inflammation and pyroptosis, varies in brain and serum between each group. It is summarized that the underlying mechanism of neuroprotection effect of geraniol might be located on improving intestinal physical barrier function, decreasing LPS releasing, down-regulating pyroptosis and inflammatory response, thereby alleviating neurotoxicity induced by BaP in mice model.},
}

@article {pmid42148333,
year = {2026},
author = {Szalus, K and Sakowicz-Burkiewicz, M and Pawełczyk, T and Nowicki, RJ and Trzeciak, M},
title = {The mRNA levels of COL1A1, COL2A1, COL3A1 and COL4A1 in non-lesional and lesional skin of atopic dermatitis patients.},
journal = {Postepy dermatologii i alergologii},
volume = {43},
number = {1},
pages = {94-100},
pmid = {42148333},
issn = {1642-395X},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is a complex, multifactorial inflammatory disease. The multifaceted aetiology and pathophysiology consist of different elements, including genetic and immunological disorders, skin barrier defects, microbiome dysbiosis and environmental interactions. To date, little has been known about the genes involved in the relationship between extracellular matrix (ECM) expression and the pathogenesis of atopic dermatitis.

AIM: The aim of our study was to examine the mRNA transcript levels of genes encoding collagen type I, II, III and IV in the skin of atopic dermatitis patients vs. controls and to search for associations with subjective clinical symptoms and disease severity.

MATERIAL AND METHODS: A total of 18 subjects participated in the study. Nine biopsies were taken from lesions, nine from non-lesional AD skin and nine from healthy volunteers. The mRNA levels of COL1A1, COL2A1, COL3A1 and COL4A1 were determined using real-time RT-PCR. AD severity was evaluated by calculating the SCORAD score and measuring the pruritus intensity using the Visual Analogue Scale (VAS).

RESULTS: A significant increase in the mRNA levels of COL3A1 in the study group compared to the control group was associated with an increase in the intensity of clinically reported symptoms as assessed by the SCORAD and the itching scale VAS (p = 0.0293). In addition, there was a statistically significant difference in the mRNA levels of the COL3A1 gene and the mRNA levels of the COL4A1 gene between subjects in the lesional and non-lesional skin of the study group. The transcript level of mRNA COL3A1 was statistically higher in lesional skin than in non-lesional skin among subjects with AD than in healthy volunteers. Conversely, mRNA COL4A1 expression was significantly higher in non-lesional skin than in lesional skin among AD subjects; however, there was no statistical difference between AD subjects and healthy volunteers.

CONCLUSIONS: Our results suggest a role for collagen mRNA levels in AD pathogenesis. Further studies are needed to assess its role as a new potential biomarker, as a predictive element for assessing the intensity of AD or as a new target for AD therapy in the era of personalized medicine. The question to be answered is the importance of remodelling processes in AD.},
}

@article {pmid42148336,
year = {2026},
author = {Kalicka, M and Biadasiewicz, M and Tekielak, A and Frątczak, A and Bergler-Czop, B},
title = {The role of the skin microbiome in modulating rosacea.},
journal = {Postepy dermatologii i alergologii},
volume = {43},
number = {1},
pages = {1-6},
pmid = {42148336},
issn = {1642-395X},
abstract = {INTRODUCTION: The skin microbiome is a contributing factor in the pathogenesis of rosacea, and disturbances in its composition may play a pivotal role in the development of the disease.

METHODS: A review of the literature in PubMed and Embase databases from inception to February 2025 to identify 13 scientific studies on the influence of the skin microbiome on the modulation of the course of rosacea.

RESULTS: Rosacea patients consistently exhibit microbial dysbiosis, which is characterized by an increased bacterial diversity, particularly involving pro-inflammatory taxa such as Staphylococcus epidermidis, Corynebacterium, and Streptococcus.

CONCLUSIONS: It seems there is growing evidence to suggest a link between the skin microbiome and the development of rosacea. This link involves changes in bacterial composition, interactions with the immune system, and the induction of inflammation. However, therapeutic implications remain largely speculative.},
}

@article {pmid42148465,
year = {2026},
author = {Chang, J and Bhuvanagiri, GM and Dulkanchainun, M and Wang, C},
title = {Osteoporosis and Periodontitis: Two-Way Epidemiological and Mechanistic Evidence.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70125},
pmid = {42148465},
issn = {1600-0765},
support = {R01 DE029200/DE/NIDCR NIH HHS/United States ; },
abstract = {Osteoporosis and periodontitis are highly prevalent, chronic inflammatory diseases that constitute a major global health burden. Strong epidemiological evidence shows an association between the two diseases, in which osteoporosis patients have an increased risk of periodontitis, specifically in postmenopausal women. Osteoporosis and periodontitis are linked by bidirectional relationships through shared inflammatory and bone-resorptive pathways. Such a connection is explained by shared osteo-immunologic pathways, particularly as highlighted by recent breakthrough findings in the field. In this review, we comprehensively examined the seven links between osteoporosis and periodontitis across microbial translocation, systemic meta-inflammation, maladaptive myelopoiesis, immune cell trafficking, masticatory dysfunction-diet interactions, underlying vulnerabilities, and functional alterations of the oral microbiome, drawing on current biological findings and clinical evidence. This bidirectional relationship underscores the importance of integrated medical and dental screening and management strategies to improve patient outcomes for both conditions.},
}

@article {pmid42148573,
year = {2026},
author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC},
title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0411725},
doi = {10.1128/spectrum.04117-25},
pmid = {42148573},
issn = {2165-0497},
abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.},
}

@article {pmid42148579,
year = {2026},
author = {Liu, M and Zhang, W and Zhang, J and Lv, N and Wu, X and Alalawy, AI and Zhao, W and Bao, H and Wu, J},
title = {Multi-site microbiomes' response to chronic obstructive pulmonary disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0000726},
doi = {10.1128/spectrum.00007-26},
pmid = {42148579},
issn = {2165-0497},
abstract = {This study aimed to evaluate changes in the oral, nasal, pulmonary, and gut microbiota in patients with chronic obstructive pulmonary disease (COPD) and to explore their interrelationships compared with the healthy group. This study included 33 COPD patients and 29 healthy individuals. A total of 162 oral, nasal, sputum, and fecal samples were obtained. The microbiota was determined using full-length 16S rRNA gene sequencing on the PacBio platform. Alpha diversity was significantly reduced in sputum and fecal samples of COPD patients, while oral and nasal microbiota showed no significant differences. Beta diversity revealed substantial overlap between oral and sputum microbiota in both groups, while nasal and fecal communities were clearly distinct. Linear discriminant analysis effect size analysis identified Haemophilus parahaemolyticus as a sputum biomarker. Source tracking confirmed that the majority of lung microbiota originated from the oral cavity. Interleukin-6 was inversely correlated with short-chain fatty acids (SCFAs)-producing microbiota in fecal samples, suggesting that depletion of these bacteria may contribute to systemic inflammation. Co-occurrence network analysis revealed that the sputum microbial network in COPD patients exhibited reduced robustness and lacked prominent hub nodes. Lung microbiota largely originates from the oral cavity but is changed in COPD. The lung microbiome is still more sensitive and accurate than the oral, nasal, and fecal microbiomes for COPD diagnosis. Fragmented networks in COPD indicate reduced community resilience.IMPORTANCELung and gut microbial diversity is significantly reduced in COPD patients. Oral microbiota is the primary source of lung microbes, but poorly predicts COPD status. Haemophilus parahaemolyticus was identified as a novel sputum biomarker in COPD. The bacterial network in COPD lungs is fragmented, lacking the resilience seen in healthy individuals.},
}

@article {pmid42148581,
year = {2026},
author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S},
title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0377525},
doi = {10.1128/spectrum.03775-25},
pmid = {42148581},
issn = {2165-0497},
abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.},
}

@article {pmid42136740,
year = {2026},
author = {Chen, Y and Li, J and Sun, Y and Yue, X and Tian, XH and Liu, F and Wang, DY and Shen, J},
title = {Biofilm-targeted liposomal curcumin delivery system for anti-caries therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1808450},
pmid = {42136740},
issn = {2235-2988},
mesh = {*Biofilms/drug effects ; *Liposomes/chemistry ; *Dental Caries/drug therapy/microbiology ; Animals ; *Curcumin/administration & dosage/pharmacology ; Streptococcus mutans/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Drug Delivery Systems ; Rats ; Hydrogen-Ion Concentration ; Humans ; Disease Models, Animal ; },
abstract = {INTRODUCTION: Dental caries, driven by acidogenic biofilms, remains a major global health challenge. Current chemical treatments, such as chlorhexidine and fluoride, can disrupt oral microbial homeostasis and cause adverse effects, including tooth discoloration, dentin hypersensitivity, and taste disturbances. Curcumin, a natural photosensitizer, exhibits antibacterial activity and favorable biocompatibility, however, its clinical application is limited by poor stability, low aqueous solubility, and restricted biofilm penetration. There is an urgent need to develop innovative therapeutic strategies to enhance curcumin transport into acidic cariogenic biofilms.

METHODS: We developed a pH-responsive liposomal delivery system (Cur/DCPA-H2O) engineered to penetrate acidic cariogenic biofilms and enhance curcumin transport. The physicochemical characterization of Cur/DCPA-H2O was performed using a UV-1800 spectrophotometer, transmission electron microscopy (TEM), and dynamic light scattering (DLS). Biocompatibility was assessed by Cell Counting Kit-8 (CCK-8) assays, hemolysis tests, and Live/Dead cell staining. The antibacterial efficacy in vitro and ex vivo was evaluated using colony-forming unit (CFU) counting, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and crystal violet (CV) staining. An in vivo caries model was established to assess the therapeutic efficacy of Cur/DCPA-H2O, using micro-computed tomography (micro-CT), Keyes' scoring, and 16S rRNA sequencing.

RESULTS: The liposomes exploit charge reversal to interact with representative caries-associated bacteria (Streptococcus mutans and the early colonizer Streptococcus sanguinis), enabling deep biofilm penetration. Upon light irradiation, Cur/DCPA-H2O was observed to generate reactive oxygen species (ROS), which may contribute to partial disruption of the biofilm matrix and reduced bacterial viability in vitro. In a rat caries model, treatment with Cur/DCPA-H2O under light irradiation reduced caries severity and decreased lesion depth by approximately 50%. It also shifted the oral microbiome composition toward a less dysbiotic profile, as confirmed by 16S rRNA sequencing.

DISCUSSION: This study demonstrates that a biofilm-targeted, pH responsive liposomal curcumin delivery system may provide a safe and effective strategy for caries prevention, highlighting the potential of natural therapeutics to modulate pathogenic biofilms with limited impact on the overall microbial community.},
}

*Biofilms/drug effects
*Liposomes/chemistry
*Dental Caries/drug therapy/microbiology
Animals
*Curcumin/administration & dosage/pharmacology
Streptococcus mutans/drug effects
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Drug Delivery Systems
Rats
Hydrogen-Ion Concentration
Humans
Disease Models, Animal

@article {pmid42136780,
year = {2026},
author = {Ahmed, SH and Islam, ZS and Zaidi, SM and Khalid, T},
title = {Surgical Solution of C-Section Associated Surgical Site Infection in LMICs: A Narrative Review.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {411AASC},
pages = {S122-S129},
pmid = {42136780},
issn = {1682-024X},
abstract = {Cesarean section (CS) is a life-saving procedure worldwide, accompanied by a substantial burden of surgical site infections (SSIs), with the most significant impact felt in low- and middle-income countries (LMICs). This review consolidates current knowledge on the surgical management of post-cesarean infections, highlighting the vaginal microbiome as a key source of infection and the physiological immunosuppression in the postpartum period. We describe the categories of deep and organ-space SSIs that require operative management, from wound debridement to laparoscopic drainage and laparotomy. The analysis also assesses proven preventive measures, such as dual-agent antibiotic prophylaxis, advanced closure techniques, and structured care bundles. It includes a standardized, context-sensitive checklist designed for LMICs, which combines pre, intra, and postoperative measures to prevent and manage SSIs, with the aim to reduce maternal morbidity and mortality in resource-limited settings.},
}

@article {pmid42136862,
year = {2026},
author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M},
title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1805596},
pmid = {42136862},
issn = {2296-858X},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.

OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.

METHODS: Skin samples were collected from 12 AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).

RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p = 0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p = 0.042) and between moderate and severe groups (p = 0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.

CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.},
}

@article {pmid42136892,
year = {2026},
author = {Hu, CY and Pai, AH and Wang, YW and Lu, PC and Wu, HM and Huang, HY},
title = {Endobiota-Estrobolome Profiles in Reproductive-Aged Women With Ovarian Endometriosis.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70061},
pmid = {42136892},
issn = {1445-5781},
abstract = {PURPOSE: This case-control study investigated whether ovarian endometriosis is associated with altered estrogen metabolism and gut or urogenital microbiota by analyzing enzyme activity, bacterial composition, and variations of estrogen metabolites in fecal, vaginal, and urinary samples.

METHODS: Thirty-eight reproductive-aged women were enrolled, including 24 with pathologically confirmed ovarian endometriosis and 14 controls. Stool, urine, and vaginal samples were collected preoperatively. Gut β-glucuronidase and β-glucosidase activities were measured, estrogen and 14 metabolites were quantified using liquid chromatography-mass spectrometry, and gut and vaginal microbiota were analyzed by 16S rRNA gene sequencing. Microbial composition, diversity, and abundance were compared between groups.

RESULTS: Gut β-glucuronidase activity and overall microbial diversity were comparable between groups; however, the control group showed a higher prevalence of the genus Rothia, whereas several genera, including Megamonas and [Eubacterium] coprostanoligenes_group, were enriched in the ovarian endometriosis group. In contrast, vaginal samples from patients with ovarian endometriosis demonstrated significantly reduced bacterial abundance and diversity, accompanied by lower levels of 4-methoxyestrone, 2-methoxyestrone, and 2-hydroxyestrone-3-methyl ether.

CONCLUSIONS: Although overt dysbiosis was not observed, specific microbial shifts and altered estrogen metabolites may reflect disturbances in estrogen metabolism and urogenital-gastrointestinal microbiota in ovarian endometriosis.},
}

@article {pmid42136931,
year = {2026},
author = {Mweetwa, MN and Ahsan, K and Louis-Auguste, J and Besa, E and Posma, JM and McNulty, NP and Barratt, MJ and Gordon, JI and Kelly, P},
title = {Erratum: Intestinal microbiome changes in response to amino acid and micronutrient supplementation: secondary analysis of the AMAZE trial - CORRIGENDUM.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e6},
doi = {10.1017/gmb.2026.10025},
pmid = {42136931},
issn = {2632-2897},
abstract = {[This corrects the article DOI: 10.1017/gmb.2025.10011.].},
}

@article {pmid42137127,
year = {2025},
author = {Ahmadi, N and Hossein Tehrani, MJ and Alamdary, A and Moukhah, R and Mardani, R and Shahali, M},
title = {Gut microbiome dysbiosis and inflammatory markers in severe COVID-19: links to atherosclerosis and potential therapeutic insights.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {110-120},
pmid = {42137127},
issn = {2008-2258},
abstract = {BACKGROUND: COVID-19 is implicated in the exacerbation of atherosclerosis, potentially leading to its clinical manifestations. The aim of this study was to evaluate serum biomarkers, including albumin (ALB), C-reactive protein (CRP), ferritin (FERR), CD16, CD18, NLRP3, interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α), in patients with COVID-19. In addition, assessment of microbiome profiles may provide insights into disease severity and gastrointestinal health.

METHOD: In this case-control study, serum samples were collected from 90 individuals: 30 patients with COVID-19 admitted to the intensive care unit, 30 hospitalized patients with COVID-19, and 30 healthy individuals. Concentrations of ALB, CRP, FERR, NLRP3, CD16, CD18, IL-6, and TNF-α were measured. Quantitative PCR (qPCR) was used to assess microbial diversity in stool samples.

RESULT: No significant age difference was noted between the patient (55.40 ± 10.34 years) and the control groups (58.34 ± 11.71 years). Substantial increases in CRP, CD-18, CD-16, IL-6, Alb, and TNF-α (P < 0.001) were observed in severe cases compared to non-severe cases. Microbiome analysis indicated a 40% decrease in Roseburia and a 35% reduction in Faecalibacterium in ICU patients.

CONCLUSION: Evaluating these biomarkers provides critical insights into atherosclerosis susceptibility in COVID-19 patients and reveals meaningful relationships among COVID-19, atherosclerosis, and gastrointestinal health.},
}

@article {pmid42137129,
year = {2025},
author = {Tavanaeian, S and Feizabadi, MM and Falsafi, S and Asadzadeh Aghdaei, H},
title = {Machine learning and microbiome analysis for early detection of pancreatic cancer.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {76-84},
pmid = {42137129},
issn = {2008-2258},
abstract = {AIM: To develop machine learning (ML) models integrating clinical and microbial predictors for early pancreatic cancer (PC) detection.

BACKGROUND: Pancreatic cancer is a leading cause of cancer-related mortality, with a 5-year survival rate of ~12%. Limited biomarkers and non-specific risk factors hinder early diagnosis. Emerging evidence links oral and gut microbiota, such as Fusobacterium nucleatum and Roseburia species, to PC risk, offering potential for non-invasive biomarkers.

METHODS: We analyzed a retrospective cohort of 40 participants (20 PC cases, 20 controls). Clinical (e.g., age, WBC) and microbial (e.g., Fusobacterium nucleatum, Roseburia-to-Fusobacterium ratio [RI/FN]) predictors were evaluated using five ML classifiers (logistic regression, SVM, random forest, naïve Bayes, neural network) under Leave-Group-Out Cross-Validation (LGOCV; 80/20 split, 200 repetitions). Elastic-net regularization and stability selection identified key predictors. Performance metrics included AUC, sensitivity, specificity, PPV, NPV, and accuracy. Nomograms were developed for clinical utility.

RESULTS: Age (AUC 97.4%) and microbial markers (e.g., RI/FN ratio, AUC 100%) showed excellent discrimination. Multivariable models using age and RI/FN achieved excellent performance (AUC 98-100%). Nomograms provided interpretable risk estimates.

CONCLUSIONS: Integrating clinical and microbial predictors with ML offers a promising approach for non-invasive PC detection. The RI/FN ratio and age are robust biomarkers that warrant further validation in larger cohorts. However, the small sample size limits generalizability and warrants validation in larger cohorts.},
}

@article {pmid42137133,
year = {2025},
author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K},
title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {85-96},
pmid = {42137133},
issn = {2008-2258},
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).

METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.

RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.

CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.},
}

@article {pmid42137389,
year = {2026},
author = {El Halabi, L and AlBayeh, A and Khoury, A and Katrib, M and Nasr, J and Al-Obaidi, A},
title = {Vitamins and Cancer Risk: A Comprehensive Review of Epidemiologic and Clinical Evidence.},
journal = {Kansas journal of medicine},
volume = {19},
number = {Suppl 1},
pages = {12},
doi = {10.17161/kjm.vol19.25377},
pmid = {42137389},
issn = {1948-2035},
abstract = {INTRODUCTION: Vitamin supplementation nearly is universal among patients with cancer, yet the scientific landscape is far more complex. Across decades of research, vitamins have demonstrated profound biological effects ranging from immune activation and ferroptosis modulation to paradoxical tumor promotion.

OBJECTIVE: This scoping review maps the breadth of compelling and controversial evidence surrounding vitamins A, D, E, K, C, and the B-complex in cancer prevention, treatment response, and toxicity.

METHODS: Guided by PRISMA-ScR domains, we synthesized mechanistic studies, epidemiologic cohorts, randomized trials, and therapeutic investigations addressing vitamins in the oncology context. Eligibility focused on sources examining cancer risk, progression, treatment interactions, or toxicity.

RESULTS: Several vitamins exhibit striking anticancer mechanisms: vitamin K2 triggers autophagy-driven leukemia cell death; pharmacologic vitamin C selectively kills KRAS- and BRAF-mutated colorectal cancer cells; niacin reshapes the tumor immune microenvironment; and vitamin D enhances microbiome-dependent antitumor immunity. Yet the review also identifies potential harms, including beta-carotene increasing lung cancer risk in smokers, vitamin E raising prostate cancer risk, and antioxidant supplementation potentially weakening the oxidative mechanisms essential for chemotherapy and radiotherapy efficacy. Dose-response patterns frequently are U-shaped, with both deficiency and excess linked to greater risk. High-dose intravenous vitamin C, vitamin D repletion during immunotherapy, and vitamin-targeted nanoparticles emerge as promising but unproven therapeutic strategies.

CONCLUSIONS: Across vitamins, benefits appear highly context-dependent. Routine supplementation is unsupported, while targeted correction of true deficiencies remains essential. This rapidly evolving field demands individualized decision-making and rigorously designed trials to define when vitamins act as allies, and when they become adversaries, in cancer care.},
}

@article {pmid42137425,
year = {2026},
author = {Miki, T and Ito, M and Haneda, T and Okada, N and Kim, YG},
title = {Infection strategies of SalmonellaTyphimurium for gut-lumen colonization: Overcoming host defenses, exploiting host responses, and adapting to the enteric niche.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2671472},
pmid = {42137425},
issn = {2993-3935},
abstract = {Diarrheal disease is a leading cause of child morbidity and mortality globally, largely resulting from contaminated food and water and exposure to enteric pathogens. Salmonella enterica serovar Typhimurium (STm) is an enteropathogenic bacterium that infects the gastrointestinal tract using diverse strategies that are still being elucidated. Meanwhile, the gut comprises a complex ecosystem known as the microbiome, which is densely inhabited by microbial communities. The microbiome confers colonization resistance against enteropathogenic bacteria, whereas STm can overcome these defenses to establish infection. Here, we review STm infection strategies in the gut, with a particular focus on evidence from mouse models. Understanding STm virulence mechanism and adaptation strategies may inform the development of targeted interventions to prevent and treat gastrointestinal infection.},
}

@article {pmid42137495,
year = {2026},
author = {Sekito, T and Hirakawa, H and Sadahira, T},
title = {Unraveling the vaginal microbiota-based etiology of recurrent cystitis: the potential role of Lactobacillus vaginal suppositories.},
journal = {Therapeutic advances in urology},
volume = {18},
number = {},
pages = {17562872261448600},
pmid = {42137495},
issn = {1756-2872},
abstract = {Recurrent cystitis is a common problem in women that substantially impairs quality of life and contributes to increasing healthcare costs. Traditionally regarded as an ascending infection originating from the gut, recurrent cystitis is now increasingly understood as a disorder rooted in vaginal dysbiosis, with the vagina acting as a key reservoir for uropathogenic Escherichia coli. Loss of a Lactobacillus-dominant vaginal microbiota and overgrowth of enteric and anaerobic bacteria are strongly associated with recurrent cystitis, particularly in postmenopausal women. Lactobacillus species promote vaginal health by producing lactic acid, maintaining a low pH, generating antimicrobial compounds, inhibiting pathogen adhesion, and modulating mucosal immune responses. At the same time, long-term antimicrobial prophylaxis, although effective in reducing recurrences, is limited by adverse effects and the promotion of antimicrobial resistance. These concerns have driven interest in strategies that restore the protective vaginal ecosystem rather than relying on repeated antimicrobial exposure. This narrative review summarizes current concepts linking vaginal dysbiosis to recurrent cystitis, highlights the protective role of Lactobacillus, and synthesizes clinical data on Lactobacillus vaginal suppositories, particularly Lactobacillus crispatus (L. crispatus)-based preparations, as a targeted, non-antimicrobial prophylactic option. Across pilot, phase II, and randomized trials, Lactobacillus vaginal therapy has demonstrated a generally favorable safety and tolerability profile, with preliminary evidence suggesting a potential to reduce recurrent cystitis episodes while restoring a Lactobacillus-dominant vaginal microbiota. However, larger, standardized studies are still needed. Collectively, these findings provide a rationale for investigating Lactobacillus vaginal suppositories as a microbiome-informed, non-antimicrobial strategy for the long-term prevention of recurrent cystitis, particularly in postmenopausal and other high-risk women, and highlight the importance of further research to define the role of vaginal microbiota-directed therapies in future recurrent cystitis management.},
}

@article {pmid42137543,
year = {2026},
author = {Zhang, K and Zomer, H and Potkamp, G and Salles, JF and Tieleman, BI and Dietz, MW},
title = {Seasonal Dynamics of the Gut Microbiome in Urban Feral Pigeons Are Associated With Environmental Conditions, Not With Diet Shifts.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73682},
pmid = {42137543},
issn = {2045-7758},
abstract = {Gut microbiomes play a crucial role in host physiology and seasonal adaptation. While seasonal shifts in avian gut microbiota are often attributed to seasonal diet variation, environmental factors may be equally or more important, particularly in urban ecosystems. This study aimed to determine whether seasonal variation in the gut microbiome of free-living feral pigeons (Columba livia f. domestica) inhabiting urban environments is associated with seasonal changes in diet and environmental conditions. We captured feral pigeons at three locations in Groningen, the Netherlands, during winter (January-February 2019) and summer (July-August 2019). Cloacal swabs and fecal samples were collected to assess gut microbiota via 16S rRNA sequencing and diet via DNA metabarcoding, respectively. Microbial diversity and composition showed significant seasonal variation and location effects. At Vismarkt, one of the three urban sampling sites within the city of Groningen, Firmicutes were more abundant in summer than in winter, while Actinobacteria were more abundant in winter. Dominant genera also varied seasonally, with Lactobacillus more abundant in summer. In contrast, the diet composition was dominated by Poaceae (grasses), Fabaceae (legumes), and Asteraceae (daisies) across all seasons and locations, with no detectable differences between locations or seasons. Distance-based redundancy analysis indicated that temperature was significantly associated with microbiome composition, whereas diet as measured here showed no detectable association. This suggests that seasonal microbiome variation in urban feral pigeons may be related to seasonal environmental conditions even without detectable dietary shifts, consistent with the idea that seasonal environmental conditions can contribute to microbiome seasonality in birds.},
}