@article {pmid42758536,
year = {2026},
author = {Gracia Alvira, JB and Migotti, S and Tian, X and Nolte, V and Schlötterer, C},
title = {Environmental temperature is a strong driver of subspecies competition in the Drosophila microbiome.},
journal = {eLife},
volume = {15},
number = {},
pages = {},
pmid = {42758536},
issn = {2050-084X},
support = {10.55776/W1225//Austrian Science Fund/ ; 10.55776/PAT7786824//Austrian Science Fund/ ; 10.55776/F91//Austrian Science Fund/ ; Achadapt/ERC_/European Research Council/International ; },
mesh = {Animals ; *Microbiota ; *Temperature ; *Drosophila/microbiology ; *Drosophila simulans/microbiology ; Symbiosis ; },
abstract = {Most microbiome research focuses on the taxonomic composition at the species level to understand the impact of environmental factors, but intraspecific diversity has largely been ignored. To address this significant knowledge gap, we took advantage of the simple, culturable microbiome of Drosophila. First, we documented that natural populations of D. simulans harbor three diverged clades of Lactiplantibacillus plantarum, a key nutritional symbiont. We studied the distinct ecological roles of these three clades by exposing flies with their native microbiome to two temperature regimes in the laboratory. Tracking the three clades within the complete Drosophila microbiome over a period of more than 10 years at two temperatures, we identified strikingly distinct dynamics in response to the selection regime. We confirmed the functional differentiation of the three clades using in vitro growth measurements and in vivo mono-association assays. Our results highlight that environmental selection operates at the subspecies level. Therefore, we conclude that the functional diversification of the microbiome can only be understood when intra- and interspecific diversity is considered.},
}

Animals
*Microbiota
*Temperature
*Drosophila/microbiology
*Drosophila simulans/microbiology
Symbiosis

@article {pmid42758655,
year = {2026},
author = {Ball, RAW and Mohammed, AD and Jolly, A and Johnson, K and Sklenicka, S and Kucherina, M and Peacock, T and Liu, E and Hogan, KM and Baird, M and Peña, MMO and Nagarkatti, P and Nagarkatti, M and Kubinak, JL},
title = {IgA deficiency reveals a microbiota-dependent pathway to gluten sensitivity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2724175},
doi = {10.1080/19490976.2026.2724175},
pmid = {42758655},
issn = {1949-0984},
mesh = {Animals ; *Glutens/adverse effects/immunology ; Mice ; Mice, Knockout ; *IgA Deficiency/microbiology/immunology ; *Gastrointestinal Microbiome ; Immunoglobulin A/genetics ; Intestinal Mucosa/pathology/immunology/microbiology ; Mice, Inbred C57BL ; Intestine, Small/pathology/immunology/microbiology ; Th17 Cells/immunology ; Diet, Gluten-Free ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Celiac Disease/microbiology/immunology ; Ileum/pathology/immunology/microbiology ; },
abstract = {Selective IgA deficiency (sIgAD) is the most common primary immunodeficiency and increases susceptibility to gluten-related enteropathies, but the underlying mechanisms of pathogenesis are unknown. Utilizing IgA[-/-] mice and wild-type controls, we investigated how dietary gluten shapes susceptibility to small intestinal inflammation. We found that IgA[-/-] mice developed gluten-induced villus blunting in the ileum and enhanced Th17 responses. Exposure to a gluten-free diet prevented villus blunting in IgA[-/-] mice. Dietary gluten promoted the expansion of Streptococcus and Desulfovibrio species, depletion of members of the order Lactobacillales, and shifts in microbial metabolic pathways related to lipid metabolism. Next, to determine if gluten sensitivity is microbiota-dependent, germ-free colonization experiments were performed using complete microbiota transfers or mono-colonization with a single Streptococcus species (Streptococcus lutetiensis), both of which were sufficient to recapitulate gluten-sensitive enteropathy. Our findings demonstrate that dietary gluten promotes small intestinal inflammation and mucosal remodeling in IgA-deficient mice through microbiota-dependent mechanisms. This work highlights a key role for sIgA in maintaining immune homeostasis at the diet-microbiota interface and reveals a novel microbial pathway underlying gluten sensitivity.},
}

Animals
*Glutens/adverse effects/immunology
Mice
Mice, Knockout
*IgA Deficiency/microbiology/immunology
*Gastrointestinal Microbiome
Immunoglobulin A/genetics
Intestinal Mucosa/pathology/immunology/microbiology
Mice, Inbred C57BL
Intestine, Small/pathology/immunology/microbiology
Th17 Cells/immunology
Diet, Gluten-Free
Bacteria/classification/genetics/isolation & purification/metabolism
*Celiac Disease/microbiology/immunology
Ileum/pathology/immunology/microbiology

@article {pmid42758711,
year = {2026},
author = {Emfietzoglou, M and Bantounou, MA and Osmani, S and Narimatsu, T and Baroutis, KG and Varsamidaki, A and Skondra, D and Papaconstantinou, D and Theodossiadis, P and Chatziralli, I and Miller, JW and Vavvas, DG},
title = {Shotgun metagenomic profiling of the fecal microbiome in Lamp2 knockout mice reveals limited genotype-associated differences under standard housing.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357009},
doi = {10.1371/journal.pone.0357009},
pmid = {42758711},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; Mice ; Male ; Mice, Knockout ; *Metagenomics/methods ; *Lysosomal-Associated Membrane Protein 2/genetics ; Genotype ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; Metagenome ; },
abstract = {BACKGROUND: Lysosomal pathways influence host-microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome-lysosome fusion, and pathogenic variants in LAMP2 cause Danon disease. Whether Lamp2 loss alters the gut microbiome in vivo has not been systematically evaluated using methods that profile both taxonomic composition and microbial functional potential, such as shotgun metagenomics.

METHODS: We performed shotgun metagenomic sequencing on 50 fecal samples from male Lamp2 knockout (Lamp2KO) mice and wild-type (WT) littermates sampled at 3, 6, 9, and 12 months under single-genotype cages or mixed-genotype cohousing. Two low-depth libraries (<3 × 105 classified genus-level reads) were excluded from primary inference (primary set: n = 48). We analyzed genus-level alpha diversity, beta diversity, and differential abundance using compositional, cage-aware mixed-effects models and cage-blocked permutation testing. We analyzed functional pathway profiles using copies-per-million abundances with centered-log-ratio transformation and mixed-effects modeling. We controlled multiple testing using the Benjamini-Hochberg false discovery rate.

RESULTS: In the primary set (48 samples from 27 cages), Lamp2KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray-Curtis distances). Primary mixed-effects models detected no genera with differential abundance after false discovery rate correction. Taxonomic profiles were broadly similar between genotypes and were dominated by Bacteroidota and Bacillota. Exploratory within-cage (paired) analyses identified consistent directional differences in a small set of genera, but these signals were not supported by the primary mixed-effects models. Functional pathway profiles were similar between genotypes; one pathway (dTDP-β-L-rhamnose biosynthesis) showed an exploratory association (FDR q < 0.10) within the 50 most abundant pathways.

CONCLUSIONS: In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with Lamp2 deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.},
}

Animals
*Feces/microbiology
Mice
Male
Mice, Knockout
*Metagenomics/methods
*Lysosomal-Associated Membrane Protein 2/genetics
Genotype
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
Metagenome

@article {pmid42758728,
year = {2026},
author = {Imrich, CN and Backman, LRF and Allworth, AP and Andorfer, MC and Paris, JC and Greeley, NM and Fu, B and Balskus, EP and Drennan, CL},
title = {The structural basis of malodorant skatole formation by the glycyl radical enzyme indoleacetate decarboxylase.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {38},
pages = {e2618341123},
doi = {10.1073/pnas.2618341123},
pmid = {42758728},
issn = {1091-6490},
support = {GM126982//HHS | NIH (NIH)/ ; T32ES007020//HHS | NIH (NIH)/ ; 1122374//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; 1144152//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; Gilliam//HHMI (HHMI)/ ; Gates Faculty Scholar Award (OPP1158186)//HHMI (HHMI)/ ; Waterman CHE-20380529//NSF (NSF)/ ; GM145910//HHS | NIH (NIH)/ ; Investigator//HHMI (HHMI)/ ; },
mesh = {*Carboxy-Lyases/metabolism/chemistry ; *Skatole/metabolism/chemistry ; Catalytic Domain ; Models, Molecular ; Cryoelectron Microscopy ; Decarboxylation ; *Bacterial Proteins/chemistry/metabolism ; },
abstract = {Glycyl radical enzymes (GREs) catalyze challenging chemical reactions using a posttranslationally installed glycyl radical cofactor. One such enzyme, indoleacetate decarboxylase (IAD), performs the radical-based decarboxylation of indole-3-acetate (I3A) to form the malodorant molecule skatole. In addition to being an odor nuisance, skatole is a human and livestock lung toxin, a suspected carcinogen, and a mosquito attractant, all of which impact human health, agriculture, food production, and wastewater treatment. Here, we use cryogenic electron microscopy to solve a 2.45-Å resolution structure of IAD from the gut bacterium Olsenella uli. We observe IAD in a homotetrameric form with the substrate I3A bound in all four protomers. The positioning of I3A in the active site is unexpected and is more consistent with a Kolbe-type decarboxylation mechanism, i.e., a decarboxylation initiated by a 1-electron oxidation of the carboxylate moiety rather than being initiated by hydrogen atom transfer (HAT). Previously, a high deuterium content in skatole from IAD assays in D2O was used to support a HAT mechanism over a Kolbe-type mechanism. However, we show here that deuterium content does not necessarily inform on mechanism as IAD can catalyze the exchange of skatole's 3'-methyl hydrogens postturnover. Structural comparisons show that both IAD and hydroxyphenylacetate decarboxylase display structural features that are not found in other characterized GREs, suggesting that they represent a distinct GRE-subclass. Collectively, these insights will inform IAD inhibitor design aimed at decreasing skatole production.},
}

*Carboxy-Lyases/metabolism/chemistry
*Skatole/metabolism/chemistry
Catalytic Domain
Models, Molecular
Cryoelectron Microscopy
Decarboxylation
*Bacterial Proteins/chemistry/metabolism

@article {pmid42758777,
year = {2026},
author = {Briard, M and Guillon, B and Venot, E and Grauso, M and Hennequet-Antier, C and Bruneau, A and Fenaille, F and Castelli, F and Thomas, M and Lezmi, G and Leite-de-Moraes, M and Adel-Patient, K and Saint-Criq, V},
title = {A microbiome-metabolome signature associated with pediatric severe asthma.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0358560},
doi = {10.1371/journal.pone.0358560},
pmid = {42758777},
issn = {1932-6203},
mesh = {Humans ; *Asthma/microbiology/metabolism ; *Microbiota ; *Metabolome ; Female ; Child ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Severity of Illness Index ; Case-Control Studies ; Adolescent ; },
abstract = {BACKGROUND: Severe asthma is a heterogeneous condition encompassing multiple phenotypes. Understanding lung-specific mechanisms in children with severe asthma may enable the development of more precise therapeutic strategies. We previously reported that immune components in bronchoalveolar lavages (BALs) differentiate children with severe asthma from non-asthmatic disease-controls and, frequent from non-frequent exacerbators, among children with severe asthma.

OBJECTIVE: To identify a local signature of severe asthma using complementary multi-omics analyses of BALs. A secondary objective was to evaluate whether bacterial taxa and metabolites discriminate severe asthma subtypes associated with distinct phenotypes or endotypes.

METHODS: BAL microbiome and metabolome were investigated in 20 children with severe asthma and 10 non-asthmatic children using 16S rRNA gene amplicon sequencing and liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS), respectively. Data were analysed separately and through integrative multi-omics approaches.

RESULTS: Compared with controls, BALs from children with severe asthma showed increased alpha-diversity, higher relative abundances of Actinobacteriota, Streptococcus, Moraxella, Corynebacterium, Tropheryma, and Treponema, and an altered polyamine pathway characterized by reduced arginine and increased spermine and spermidine levels. Integrated analyses revealed significant associations between Streptococcus and both spermine and spermidine. Independently, each dataset discriminated severe asthma phenotypes, notably exacerbation frequency and co-occurring atopic dermatitis. Unsupervised clustering of microbiome profiles identified four distinct clusters that may reflect severe asthma endotypes.

CONCLUSIONS: This study identifies a distinct airway microbiome-metabolome signature associated with pediatric severe asthma. Enrichment of specific bacterial taxa, particularly Streptococcus, together with altered polyamine metabolic pathway, highlights microbial-metabolic interactions potentially involved in disease pathophysiology. The ability of microbiome and metabolome profiles to independently and jointly discriminate clinical phenotypes underscores the relevance of multi-omics approaches for diagnosis and follow-up of severe asthma. Our findings support the importance of airway-level profiling to improve mechanistic understanding of severe asthma and inform on future targeted therapeutic strategies.},
}

Humans
*Asthma/microbiology/metabolism
*Microbiota
*Metabolome
Female
Child
Male
Bronchoalveolar Lavage Fluid/microbiology
RNA, Ribosomal, 16S/genetics
Multiomics
Severity of Illness Index
Case-Control Studies
Adolescent

@article {pmid42759240,
year = {2026},
author = {Xu, J and Song, Y and Wu, W and Zhou, H and Wu, Y and Li, C},
title = {The impact of maternal gestational diabetes mellitus on the microbiome of offspring: A systematic review.},
journal = {Journal of reproductive immunology},
volume = {178},
number = {},
pages = {104965},
doi = {10.1016/j.jri.2026.104965},
pmid = {42759240},
issn = {1872-7603},
abstract = {Gestational diabetes mellitus (GDM) adversely affects maternal and offspring health, and the early-life microbiome is implicated in developmental programming. This systematic review quantitatively evaluated the association between maternal GDM and alterations in the gut and oral microbiomes of offspring. We systematically searched PubMed, Web of Science, and Embase (up to August 2025) for eligible studies adopting high-throughput sequencing techniques. Random-effects meta-analysis was performed for alpha diversity metrics, while findings on beta diversity and microbial taxonomy were summarized narratively. Twenty-one studies were included. The meta-analysis revealed no statistically significant differences in gut microbial alpha diversity between infants exposed to maternal GDM and unexposed controls. Beta diversity exhibited substantial inter‑study heterogeneity, with no consistent shifts observed. In infants born to mothers with GDM, several microbial taxa including Gammaproteobacteria, Enterobacteriaceae, Micrococcaceae, Propionibacteriaceae, Rikenellaceae, Megasphaera, Staphylococcus, Collinsella, Rothia, Pelomonas, Veillonella, Shewanellaceae and Prevotella tended to decrease in abundance, whereas Escherichia tended to increase. Notably, no microbial taxon presented consistent abundance changes in three or more studies, and these repeated findings were based on limited evidence. Delivery mode appeared to have minimal influence on offspring gut alpha diversity. Collectively, maternal GDM may not be strongly linked to shifts in offspring gut or oral microbial alpha diversity. However, the consistent dysregulation of specific microbial taxa in GDM-exposed offspring may exert potential impacts on offspring immune and metabolic development. Further longitudinal multicenter investigations are warranted to elucidate the causal relationships and long-term health implications of GDM-induced microbial alterations in children.},
}

@article {pmid42759465,
year = {2026},
author = {Yang, W and Zhu, X and Zhang, J and Chen, Y and Liu, S and Si, T and Zhang, L},
title = {Silicon nanoparticles and jasmonic acid synergistically enhance cadmium phytoextraction by Sedum alfredii via coordinated metal acquisition and stress tolerance.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143556},
doi = {10.1016/j.jhazmat.2026.143556},
pmid = {42759465},
issn = {1873-3336},
abstract = {Cadmium (Cd) phytoextraction requires efficient metal acquisition and translocation without compromising plant growth and detoxification. We investigated the effects of silicon nanoparticles (Si-NPs) and jasmonic acid (JA), applied alone or together, on Cd phytoextraction by Sedum alfredii. The combined treatment increased shoot biomass and total Cd accumulation by 32.6% and 67.4%, respectively. Si-NPs-containing treatments increased rhizosphere available Cd by 5.4-5.9%, promoted Cd uptake and root-to-shoot translocation, and induced Cd- and Si-transport-related genes. JA strengthened antioxidant enzyme activities. The combined treatment further increased phytochelatin and glutathione levels by 152% and 48.7%, respectively, while reducing malondialdehyde by 38.5%. These responses indicate enhanced thiol-mediated detoxification and oxidative protection. Metabolomic and microbiome analyses further revealed compartment-specific responses. The rhizosphere was associated with Cd-mobilization-related metabolites and enrichment of potentially beneficial genera, including Polycyclovorans and Ramlibacter. In contrast, leaves showed enhanced sulfur-thiol metabolism, redox regulation, and secondary metabolism. Multiblock integration linked Cd phytoavailability and accumulation with detoxification and biomass production. Overall, Si-NPs and JA exhibited asymmetric functional complementarity, integrating enhanced Cd acquisition and transport with thiol-centered detoxification and growth maintenance. This accumulation-compatible tolerance strategy provides a mechanistic framework for improving assisted Cd phytoextraction by coordinating Cd flux with whole-plant detoxification capacity.},
}

@article {pmid42759480,
year = {2026},
author = {Hu, F and Liu, X and Zhang, Y and Tan, S and Wang, J and Xia, M and Lu, F and Zhang, Q},
title = {Polylactic acid microplastics enhance copper bioavailability and host-microbiome toxicity during black soldier fly bioconversion of food waste: Mechanisms and multi-level impacts.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143654},
doi = {10.1016/j.jhazmat.2026.143654},
pmid = {42759480},
issn = {1873-3336},
abstract = {Biodegradable microplastics are increasingly entering food waste (FW) streams, yet their effects on heavy metal behavior during black soldier fly larvae (BSFL) bioconversion remain unclear. This study investigated the combined effects of polylactic acid microplastics (PLA-MPs, 1% w/w) and Cu (100-300 mg/kg ww) in a BSFL-based FW conversion system. The 100-200 mg/kg treatments represented upper-range Cu exposure scenarios relevant to Cu-rich food residues. PLA-MPs increased Cu accumulation in larvae by 14-32% and shifted Cu toward more bioactive fractions in larvae and frass, indicating enhanced Cu mobility and bioavailability. Co-exposure intensified oxidative and detoxification responses, depleted glutathione, increased lipid peroxidation, and altered energy metabolism. Transcriptomic analysis indicated activation of xenobiotic metabolism, glutathione-related detoxification, and immune-associated pathways. PLA-MPs and Cu also reshaped gut and frass microbial communities, increased community stochasticity, suppressed dissolved organic matter humification, and reduced substrate stabilization and bioconversion performance. Partial least squares path modeling further linked Cu activation and migration, host physiological stress, and microbial dysbiosis to reduced bioconversion efficiency. Overall, PLA-MPs enhanced Cu bioavailability and amplified multi-level toxicity during BSFL-mediated FW treatment, highlighting potential risks to the safe valorization of contaminated organic waste.},
}

@article {pmid42759613,
year = {2026},
author = {Klingler, AM and Vidyant, S and Pyakurel, S and Viel, KCMF and Good, A and Rochman, Y and Brusilovsky, M and Caldwell, JM and Rothenberg, ME and Azouz, NP},
title = {Loss of kallikrein 5 expression exacerbates allergic skin inflammation including impairing filaggrin processing, promoting Th2 differentiation and inducing dysbiosis.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {100404},
doi = {10.1016/j.mucimm.2026.100404},
pmid = {42759613},
issn = {1935-3456},
abstract = {Atopic dermatitis (AD) is a chronic allergic skin disease with T helper 2 (Th2) cell predominance and epithelial barrier impairment. The serine protease kallikrein (KLK) 5 has an essential role in regulating keratinocyte desquamation and skin renewal. Increased expression and activity of KLK5 is sufficient to induce skin inflammatory responses including AD. We examined the consequences of Klk5 deficiency following exposures to the type 2-provoking agent calcipotriol in mice. Loss of KLK5 exacerbates a spectrum of AD-like responses including increased accumulation of skin eosinophils and langerhans cells, over-expression of an array of cytokines in the skin and exacerbated scratching behavior. Klk5[-/-] mice demonstrated microbiome dysbiosis with enriched actinobacteria and reduced firmicutes in the skin, alteration in skin metabolites involved in the acetyl-CoA pathway and decreased expression of mature filaggrin monomers. Cutaneous application of Cis-Urocanic acid (cUCA) attenuated inflammatory responses highlighting barrier dysfunction as primary mechanism. We reveal an unappreciated role for KLK5 in inhibiting type 2 responses, acting through its roles in filaggrin processing and modulation of the skin microbiome and metabolome. Though KLK5 overactivation is known to contribute to several inflammatory skin disorders, our findings demonstrate that complete loss of KLK5 is also pathogenic in AD-like responses in mice.},
}

@article {pmid42759845,
year = {2026},
author = {Glenn, E and Titus, C and Kasthuriarachchi, T and Burke, K and Chow, D and Lin, C and Liu, E and Zhang, H and Zhang, T and Li, Y},
title = {Maternal-offspring microbiome interface contributes to the impact of maternal use of central nervous system-active drugs on offspring neurodevelopment.},
journal = {Journal of pharmaceutical sciences},
volume = {},
number = {},
pages = {104509},
doi = {10.1016/j.xphs.2026.104509},
pmid = {42759845},
issn = {1520-6017},
abstract = {The prevalence of maternal central nervous system-active medication use has increased over the last two decades, raising questions regarding potential neurodevelopmental consequences for offspring. While most of these substances are known to cross the placenta and enter breast milk, their developmental impact remains unclear. This review synthesizes current evidence identifying the maternal-offspring microbiome interface as a possible conduit for neurodevelopmental programming. We examine how the maternal gut, placental, and breast milk microbiomes establish the foundation for the offspring's early microbial ecosystem, how drug-induced dysbiosis may disrupt these interactions, and how these may impact offspring neurodevelopment. However, isolating specific drug-induced microbial effects from the influence of underlying maternal psychiatric conditions and identifying specific microbial signatures that correlate with resilience or susceptibility in offspring remain a substantial challenge. Current literature relies heavily on preclinical models, highlighting an urgent need for longitudinal human studies to better inform risk-benefit analyses for maternal pharmacotherapy.},
}

@article {pmid42759892,
year = {2026},
author = {Halmi, MFA and Edinur, HA},
title = {Two decades of microbiome forensics: Bibliometric insights into publication trends, applications and methodological advancements.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107716},
doi = {10.1016/j.mimet.2026.107716},
pmid = {42759892},
issn = {1872-8359},
abstract = {Microbiome forensics focuses on complex microbial communities for use as unique identification methods for forensic inferences. They include individual identification, crime scene reconstruction, and estimation of post-mortem intervals. This study adopts a bibliometric approach to assess the global scientific output and knowledge structure of the microbiome forensics, applications and methodological advancement in microbiome forensics. A total of 220 documents spanning two decades (2005 to 2024) were retrieved from the Web of Science Core Collection using related keywords. Of the total number of scientific publications, 6306 citations were found, with an average of 28.66 citations per publication. The United States dominated this domain with the most publications, followed by China, Australia, England, and Germany. Although Michigan State University had the highest number of citations, but the works produced by the Centre National de la Recherche Scientifique in Paris, France, had the highest research impact. Research trend mapping of keyword co-occurrence revealed five major clusters of forensic microbiome research: i. post-mortem interval estimation, ii. human identification, iii. Body fluid identification, iv. geolocation and provenance, and v. computational methods. Subsequent analyses indicated that forensic microbiome research has evolved from the use of culture-based and polymerase chain reaction (PCR) amplification of 16S rRNA for microbial identification before 2017 to the application of next generation sequencing (NGS) coupled with machine learning and bioinformatics from 2018 onwards. The findings of this study may be used to strategically inform knowledge gaps and key areas for future investigations in this field. In addition, building partnerships between forensic societies is needed not only to effectively move the field forward through the development of standardised protocols and quality assurance but also in exchanging expertise with developing countries, where knowledge is urgently needed to resolve crime cases.},
}

@article {pmid42759909,
year = {2026},
author = {Hou, J and Li, Q and Li, Y and Liu, M and Xue, M and An, Y and Yao, Y and Xu, H},
title = {Intraspecific Rice Intercropping Reduces the Rhizosphere Resistome in Association with Organic Acid and low-ARG-burden Microbiota Enrichment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129180},
doi = {10.1016/j.envpol.2026.129180},
pmid = {42759909},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) in agricultural soils are an emerging environmental concern. However, sustainable strategies for reducing ARG in crop rhizospheres remain limited. Here, we investigated associations among rhizosphere metabolites, microbial communities, and ARG profiles in an intraspecific rice intercropping system. Compared with monoculture, intraspecific intercropping reduced the relative abundances of total ARGs and ARGs assigned to the Ranks I and II. Intercropping also altered rhizosphere metabolite profiles, with increased organic acid abundance, and was associated with convergent changes in microbial community composition. Nitrospirales, particularly Candidatus Sulfobium, was enriched under intercropping. MAGs assigned to this lineage contained relatively few annotated ARGs, which were predominantly classified as ARGs assigned to the Rank IV. Exogenous supplementation reproduced this field-associated pattern: citric acid treatment reduced total ARG and ARGs assigned to the Ranks I and II abundance and concurrently increased the relative abundance of Candidatus Sulfobium. These results support an association among rhizosphere organic acids, low-ARG-burden taxa, and reduced ARG abundance. Collectively, these findings highlight intraspecific rice intercropping as a low-input, source-control approach for cleaner rice production and ARG-risk mitigation.},
}

@article {pmid42760068,
year = {2026},
author = {Toufiq, R and Shahid, A and Zahra, R and Lankapalli, AK and Oduwo, J and Owinoh, EO and Aftab, S and Hassan, B and Thomson, K and Walsh, TR and Sands, K},
title = {Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e120775},
doi = {10.1136/bmjopen-2026-120775},
pmid = {42760068},
issn = {2044-6055},
mesh = {Humans ; Pakistan ; Female ; Infant ; Longitudinal Studies ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Breast Feeding/statistics & numerical data ; Anti-Bacterial Agents/therapeutic use ; Birth Cohort ; Adult ; Milk, Human/microbiology ; },
abstract = {PURPOSE: The Infant Gut Bacterial Study in Pakistan (INBUGS-P) was established to characterise the longitudinal development of the infant gut microbiome and resistome during the first year of life in a low- and middle-income country setting. The influence of early-life exposures, including mode of delivery, antibiotic use and infant feeding practices on gut bacterial diversity and antimicrobial resistance gene (ARG) profiles is being evaluated.

PARTICIPANTS: A total of 107 mother-infant pairs were recruited at the Pakistan Institute of Medical Sciences between December 2023 and June 2024. Follow-up was conducted at 10 predefined timepoints from birth to 12 months, during which 921 infant stool samples, 158 maternal rectal swabs, 246 breast milk samples and 2171 environmental swabs were collected. Sociodemographic, clinical, cultural and biological data were collected at enrolment and at each follow-up visit using Research Electronic Data Capture.

FINDINGS TO DATE: Baseline characteristics of 98/107 mother-infant dyads are included in the analysis. The cohort reflects an urban low-income population: median household income was PKR 30,000 per month (approximately US$170 per capita per month). Caesarean section accounted for 55% (54/98) of deliveries; 13.0% of infants were late preterm, and 10.0% had low birth weight (<2500 g). Breastfeeding was the predominant feeding mode though only 24 infants were exclusively breastfed from birth to 6 months. Antibiotics were prescribed to almost all mothers following delivery, and 19 infants received antibiotics during follow-up, most commonly amikacin combined with ceftazidime.

FUTURE PLAN: Shotgun metagenomic sequencing of infant stool samples is underway to enable species-level and plasmid-level profiling of microbial communities and ARGs. Subject to funding, hybrid long- and short-read sequencing and extended follow-up to 24 months are planned.},
}

Humans
Pakistan
Female
Infant
Longitudinal Studies
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Breast Feeding/statistics & numerical data
Anti-Bacterial Agents/therapeutic use
Birth Cohort
Adult
Milk, Human/microbiology

@article {pmid42760112,
year = {2026},
author = {Dendooven, E and Genouw, E and Aerts, O},
title = {Smelly Pig Manure: A Hypothetical Explanation for Sodium Metabisulphite Contact Allergy Mimicking Atopic and Seborrheic Dermatitis.},
journal = {Contact dermatitis},
volume = {},
number = {},
pages = {},
doi = {10.1111/cod.70248},
pmid = {42760112},
issn = {1600-0536},
}

@article {pmid42760157,
year = {2026},
author = {Shin, HR and Kim, TY and Min, K and Park, UH and Oh, SW and Kim, JK},
title = {Epigenetic determinants of GLP-1 responsiveness: Integrating dietary modulation beyond genetics.},
journal = {Obesity research & clinical practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.orcp.2026.09.004},
pmid = {42760157},
issn = {1871-403X},
abstract = {Glucagon-like peptide-1 receptor (GLP-1R) agonists have become major therapeutic agents for obesity and type 2 diabetes, yet clinical responses vary substantially among individuals. Although genetic variation contributes to this heterogeneity, it does not fully explain differences in glycemic control, body weight reduction, or broader metabolic outcomes. This narrative review discusses diet-driven epigenetic regulation as a potential framework linking modifiable nutritional exposures to GLP-1 physiology and variability in GLP-1R agonist responsiveness. Endogenous GLP-1 biology and the pharmacological targeting of incretin signaling are first summarized, followed by genetic determinants of GLP-1 responsiveness and their limitations. Major diet-sensitive regulatory mechanisms are then examined, including one-carbon metabolism and DNA methylation, histone modification and chromatin remodeling, microbiome-derived metabolites, and RNA-mediated or epitranscriptomic regulation. These mechanisms may influence endogenous GLP-1 secretion and degradation, GLP-1R expression, β-cell functional capacity, and the broader metabolic or inflammatory context in which incretin signaling occurs. However, direct clinical evidence linking diet-induced epigenetic changes to GLP-1R agonist therapeutic response remains limited. Therefore, diet-epigenome interactions should be interpreted as plausible modifiers of GLP-1-related metabolic biology rather than established determinants of pharmacological efficacy. Future studies integrating dietary assessment, gut hormone profiling, microbiome analysis, epigenomic markers, and multidimensional therapeutic outcomes are needed to determine whether diet-sensitive molecular signatures can support precision nutrition strategies alongside GLP-1-based therapy.},
}

@article {pmid42760326,
year = {2026},
author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C},
title = {Publisher Correction: Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41588-026-02788-4},
pmid = {42760326},
issn = {1546-1718},
}

@article {pmid42760420,
year = {2026},
author = {Wang, Y and Nie, J and Lin, G and He, X and Zhou, H},
title = {Genetic and microbial regulation of NOD2 signaling in homeostasis and disease.},
journal = {MedScience},
volume = {},
number = {},
pages = {},
pmid = {42760420},
issn = {3091-4981},
abstract = {Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) is a key intracellular pattern recognition receptor that senses bacterial peptidoglycan-conserved motifs, and has long been implicated in initiating immune responses. Loss-of-function mutations in NOD2 have been identified as the strongest genetic risk factor for Crohn's disease (CD), a primary subtype of inflammatory bowel disease (IBD), underscoring its significance in the gut homeostasis. Recent advancements extend our understanding of NOD2, revealing how gut microbiota variation impacts NOD2 signaling and broadening its pathological significance far beyond CD. This review highlights the transition from focusing on genetic mutations in NOD2 to examining its dynamic regulation by the gut microbiome. This new perspective not only deepens our understanding of NOD2 in diverse health contexts, but also paves the way for innovative therapeutic strategies targeting the gut microbiota-NOD2 axis.},
}

@article {pmid42760588,
year = {2026},
author = {Abdelhamid, M and Padhi, P and Gifani, M and Beck, JS and Thomas, JP and Khadse, G and Kudela, C and Phillips, GJ and Kanthasamy, AG and Counts, SE},
title = {Bioengineered microbiotic levodopa therapy improves cognition and reduces pathology in a rat model of Alzheimer's disease.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70670},
pmid = {42760588},
issn = {1476-5381},
support = {R01AG060731//National Institutes of Health (NIH)/ ; U01AG074960//National Institutes of Health (NIH)/ ; //Johnny Isakson Endowed Chair, Coach Mark Rich Endowment/ ; //Georgia Research Alliance Eminent Scholar funds/ ; },
abstract = {BACKGROUND AND PURPOSE: Degeneration of the pontine noradrenergic and midbrain dopaminergic systems contributes to cognitive-behavioural disturbances during the prodromal stages of Alzheimer's disease (AD). We developed a genetically engineered, programmable probiotic Escherichia coli Nissle 1917 strain (EcN[rha] L-DOPA) capable of producing L-3,4-dihydroxyphenylalanine (L-DOPA) in a sustained and titratable manner, thus offering a novel gut-brain delivery mechanism to increase brain levels of noradrenaline and dopamine during the early stages of AD.

EXPERIMENTAL APPROACH: We replicated locus coeruleus (LC) projection system degeneration in AD by administering dopamine-β-hydroxylase IgG-saporin immunotoxin into the prefrontal cortex of 6-months-old Tg344-19 AD rats. The animals then received EcN[rha] L-DOPA/benserazide or placebo by daily gavage for 6 weeks. We assessed cognitive-behavioural function prior to postmortem assessments of amyloid-β plaque load, glial cell activation and neuronal and synaptic markers. Gut colonization, along with plasma and brain L-DOPA, dopamine, noradrenaline and metabolite levels, were also measured.

KEY RESULTS: EcN[rha] L-DOPA displayed stable gut colonization and resulted in sustained therapeutic levels of L-DOPA in plasma and brain, resulting in increased cortical and hippocampal noradrenaline levels. EcN[rha] L-DOPA reduced anxiety-like behaviour improved spatial and working memory. The treatment reduced forebrain Aβ plaque and MHC-II antigen-presenting microglial load. Additionally, EcN[rha] L-DOPA increased protein levels of the dendritic spine marker PSD95.

CONCLUSIONS AND IMPLICATIONS: This translational study suggests that EcN[rha] L-DOPA modifies AD by boosting brain catecholamine production, reducing Aβ accumulation and neuroinflammation, promoting synaptic health, and enhancing cognitive function. Collectively, these results highlight EcN[rha] L-DOPA as a promising preclinical engineered gut microbiome-based therapeutic strategy for early-stage AD.},
}

@article {pmid42760760,
year = {2026},
author = {Parmar, P and Couts, KL},
title = {Mucosal Melanoma: Clinical and Biological Implications of Anatomic Site.},
journal = {Pigment cell & melanoma research},
volume = {39},
number = {5},
pages = {e70120},
doi = {10.1111/pcmr.70120},
pmid = {42760760},
issn = {1755-148X},
mesh = {Humans ; *Melanoma/pathology/therapy/genetics/immunology ; *Mucous Membrane/pathology ; Animals ; Female ; },
abstract = {Mucosal melanoma is a rare and aggressive malignancy arising from anatomically distinct mucosal sites that share a common melanocytic origin but differ in their clinical presentation, biology, and management. Accumulating evidence indicates that the anatomic site of origin fundamentally shapes clinical presentation, immune and microbial microenvironments, molecular drivers, and therapeutic vulnerabilities. In this review, we integrate epidemiologic, clinical, genomic, immunologic, microbiome, and translational data to systematically compare mucosal melanomas arising from the sinonasal tract, oral cavity, anorectal region, and vulvovaginal tract. We highlight striking site-specific differences in patterns of presentation and metastasis, immune and microbiome composition, enrichment of actionable molecular alterations, and responses to therapies. We further discuss how current preclinical models often fail to account for this biologic diversity, limiting translational progress. Collectively, these data support viewing mucosal melanoma as a unified disease entity with clinically meaningful heterogeneity shaped by anatomic site of origin, with important implications for classification, clinical management, and trial design.},
}

Humans
*Melanoma/pathology/therapy/genetics/immunology
*Mucous Membrane/pathology
Animals
Female

@article {pmid42760956,
year = {2026},
author = {Dai, Q and Fang, C and Du, Y and Sun, H and Duan, Z},
title = {Psychobiotic, nutritional, and behavioral interventions targeting the microbiome-gut-brain axis in depression, anxiety, and stress: a scoping review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1856471},
pmid = {42760956},
issn = {2296-861X},
abstract = {Probiotics and psychobiotics are increasingly investigated as microbiome-gut-brain axis (MGBA)-targeted strategies for managing depression, anxiety, and stress-related symptoms, but human evidence remains fragmented across intervention types and biomarker domains. We conducted a scoping review of human intervention studies to map MGBA-targeted psychobiotic, nutritional, dietary, and behavioral interventions, with a specific focus on symptom-biomarker bridging evidence. Searches of major biomedical and multidisciplinary databases combined key terms for the microbiome/gut-brain axis, depression/anxiety/stress, probiotics/psychobiotics, dietary or behavioral interventions, and biomarker domains. The search yielded 1,390 records; 72 full-text reports were assessed; 32 original reports were retained after report-level adjudication; and, after study-family consolidation, 30 independent human studies were included in the study-level synthesis. Studies were classified as direct bridge, parallel evidence, or no bridge according to whether biomarker changes were statistically linked to emotional outcomes. Most included studies focused on probiotic or psychobiotic interventions, with fewer studies examining prebiotics, synbiotics, short-chain fatty acid approaches, dietary interventions, or mind-body/behavioral strategies. Across the 30 studies, 9 were classified as direct bridge, 18 as parallel evidence, and 3 as no bridge. The most frequently examined biomarker domains were gut microbiota, microbial metabolites, and inflammation/immune markers, with common specific readouts including BDNF, 5-HT/serotonin-related markers, IL-6, TNF-α/CRP, cortisol/CAR, and SCFA/metabolite measures. Overall, MGBA-related nutritional and psychobiotic interventions may contribute to mood-symptom management by modulating microbial, metabolic, immune, neuroendocrine, and neurotrophic pathways, but robust symptom-biomarker bridging evidence remains limited. Future trials should predefine bridge hypotheses, standardize core biomarker domains and sampling time points, and clearly distinguish primary trial reports from linked secondary publications.},
}

@article {pmid42761134,
year = {2026},
author = {Otero Ramírez, ID and Sánchez Trujillo, SM and Paz Narvaez, IE and Hoyos Concha, JL},
title = {Effect of a bioformulation with native Bacillus subtilis and Bacillus thuringiensis strains on the control of Fusarium oxysporum and the rhizosphere microbiome of strawberry (Fragaria × ananassa).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1932414},
doi = {10.3389/fmicb.2026.1932414},
pmid = {42761134},
issn = {1664-302X},
abstract = {INTRODUCTION: Strawberry (Fragaria × ananassa) is an economically important fruit crop whose production has increased substantially in recent years. However, its productivity is severely affected by a wide range of pathogens, including Fusarium oxysporum, the causal agent of wilt. Although chemical control remains widely used, biological strategies have gained increasing attention because of their environmental benefits and contribution to sustainable agriculture. The objective of this study was to evaluate the biocontrol potential of native bacterial bioformulations against F. oxysporum in strawberry under field conditions.

METHODS: Bacteria isolated from rhizosphere soil and root samples collected from eight producing farms in Cauca, Colombia, were screened for antagonistic activity, and the most effective isolates were identified by 16S rRNA gene sequencing. Bioformulations based on Bacillus subtilis UCBF11 and Bacillus thuringiensis UCBF2 were developed as microbial "bioinputs" and evaluated under open-field conditions in strawberry crops inoculated with F. oxysporum. Agronomic variables such as root growth and biomass, biomass promotion indexes, and the bioinput efficiency index were determined. Additionally, the effect of the treatments on the rhizosphere microbiota was analyzed using high-throughput sequencing of the 16S rRNA and ITS regions.

RESULTS AND DISCUSSION: A total of 350 isolates were obtained. B. subtilis UCBF11 and B. thuringiensis UCBF2 showed high antagonistic activity against F. oxysporum, with inhibition percentages of 79.72% and 84.95%, respectively. Field application of these bioinputs significantly increased root length and biomass compared to the control treatments, with B. subtilis UCBF11 showing the most outstanding performance. Metataxonomic analysis showed modifications in the structure of bacterial and fungal communities among treatments, and bioinput application was associated with a lower increase in the relative abundance of F. oxysporum. These results demonstrate the potential of B. subtilis UCBF11 and B. thuringiensis UCBF2 as biological control agents against F. oxysporum in strawberry crops.},
}

@article {pmid42761166,
year = {2026},
author = {Li, M and Zhao, X and Zhang, B and Cao, R and Wang, Z and Huang, Z and Cheng, C and Lu, S and Jiang, X},
title = {Gut microbiome-metabolome signatures of osteosarcopenia in fracture patients in China.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1863988},
doi = {10.3389/fendo.2026.1863988},
pmid = {42761166},
issn = {1664-2392},
mesh = {Humans ; Female ; Male ; Middle Aged ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Prospective Studies ; *Fractures, Bone/metabolism/microbiology/complications/epidemiology ; Aged ; China/epidemiology ; *Metabolome ; *Sarcopenia/microbiology/metabolism/epidemiology ; Multiomics ; Metabolomics ; Metagenomics ; },
abstract = {BACKGROUND: Osteosarcopenia, defined as the coexistence of low bone mass and sarcopenia, is a disabling musculoskeletal condition, yet its gut microbial and metabolic characteristics in clinical populations remain incompletely understood. Integrative multi-omics approaches may help clarify species-metabolite networks associated with this condition, particularly in fracture patients.

METHODS: In this single-center, prospective cross-sectional study, 69 fracture patients aged ≥50 years were classified into four phenotypes: Normal (n = 18), isolated low bone mass (Bone, n = 18), isolated sarcopenia (Muscle, n = 19), and osteosarcopenia (Both, n = 14). Fecal samples were analyzed using shotgun metagenomics and untargeted metabolomics, yielding paired multi-omics data for 52 participants.

RESULTS: The Bone group had the highest mean age (66.6 ± 9.46 years), whereas the mean ages of the other groups ranged from 60.6 to 61.8 years (overall p = 0.029), while sex, BMI, lifestyle factors, and comorbidities did not differ significantly. Neither α-diversity nor overall β-diversity showed marked differences across phenotypes, suggesting that broad community replacement was not observed. A multi-stage, multi-method strategy yielded a 17-species consensus feature set associated with differences among musculoskeletal phenotypes. Taxonomic patterns were consistent with a candidate fiber/short-chain fatty acid (SCFA)-associated module, whereas exploratory microbe-metabolite correlations suggested a candidate lipid/sterol-associated module. The latter included correlations linking Firmicutes bacterium CAG:24053_14 with putatively annotated cholesterol and N-acylethanolamines.

CONCLUSIONS: Osteosarcopenia in fracture patients was associated with unadjusted differences in selected gut microbial taxa and fecal metabolites within a broadly shared microbial community. These findings are hypothesis-generating and require validation in larger independent cohorts before clinical or biomarker application.},
}

Humans
Female
Male
Middle Aged
Cross-Sectional Studies
*Gastrointestinal Microbiome
Prospective Studies
*Fractures, Bone/metabolism/microbiology/complications/epidemiology
Aged
China/epidemiology
*Metabolome
*Sarcopenia/microbiology/metabolism/epidemiology
Multiomics
Metabolomics
Metagenomics

@article {pmid42761183,
year = {2026},
author = {Kim, J and Son, B and Yoo, W and Shin, H},
title = {Gut microbiome-immune-metabolic axis in fatigue: mechanistic insights and food science approaches.},
journal = {Food science and biotechnology},
volume = {35},
number = {12},
pages = {3449-3463},
doi = {10.1007/s10068-026-02282-x},
pmid = {42761183},
issn = {2092-6456},
abstract = {Fatigue is a heterogeneous symptom associated with lifestyle, infection, exercise, and chronic disease, but its biological links with the gut microbiome remain incompletely defined. This review summarizes clinical and mechanistic evidence connecting gut microbiome alterations with fatigue-related phenotypes, focusing on myalgic encephalomyelitis/chronic fatigue syndrome, post-acute COVID-19 syndrome, general adult fatigue, and exercise-induced fatigue. Evidence was interpreted according to fatigue-related phenotype, microbiome function, microbial metabolite, gut barrier marker, inflammatory response, and food-based intervention. Current studies suggest that reduced short-chain fatty acid production, impaired butyrate-producing capacity, gut barrier dysfunction, microbial translocation, low-grade inflammation, altered tryptophan metabolism, host energy imbalance, and gut-brain/gut-muscle axis signaling may contribute to fatigue-related physiological vulnerability. Food components/ingredients, including dietary fiber, fermented food, prebiotic, probiotic, postbiotic, polyphenol, and polysaccharide, may support microbiome-mediated recovery pathways. Further controlled, phenotype-specific, multi-omics intervention studies are required.},
}

@article {pmid42761216,
year = {2026},
author = {Corral-Jara, KF and Ramayo-Caldas, Y and Bernard, L and Martin, C and Tournayre, J and Morgavi, DP and Popova, M},
title = {Species-specific rumen microbial responses to dietary inhibition of methanogenesis in cows and goats.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852812},
doi = {10.3389/fmicb.2026.1852812},
pmid = {42761216},
issn = {1664-302X},
abstract = {INTRODUCTION: Methane, a greenhouse gas, is produced in the rumen microbiome of ruminants. Various nutritional strategies can reduce enteric methane (CH4) emissions from livestock, but it is unclear whether diet affects rumen microbiome similarly across ruminant species. The objective of this study was to determine whether cows and goats differ in their rumen microbial functional responses to dietary strategies based on starch and/or lipid supplementation, and whether these differences explain diet-associated variation in CH4 emissions under comparable experimental conditions.

METHODS: Experiments were conducted simultaneously, and both species received the same diet based on grassland hay and concentrate as the Control diet (CTL) or supplemented with corn oil and wheat starch (COS), marine algae powder (MAP) or hydrogenated palm oil (HPO). To identify biologically relevant features from the rumen microbial metatranscriptomes, we followed a five-step integrative statistical and network analysis pipeline, combining a network-based approach with clustering and supervised model fitting to associate differentially expressed genes and taxa with CH4 emissions in the rumen.

RESULTS: The COS diet lowered CH4 emissions in both cows and goats and altered their rumen microbiomes. However, the number of differentially expressed KEGG orthologs and differentially abundant OTUs identified in the COS vs CTL comparison was greater in cows than in goats. Moreover, clustering analysis revealed differences in network topology between ruminant species. In goats, CH4 emission reduction was strongly associated with genes involved in carbohydrate metabolism and methylotrophic and hydrogenotrophic pathways of methanogenesis; whereas in cows, hydrogenotrophic pathways were prominent. Additionally, sparse Partial Least Squares (sPLS) analysis identified species-specific discriminant microbial features.

DISCUSSION: Overall, these results show that host species modulates rumen microbial responses to diet and suggest that microbial interactions underlying CH₄ mitigation differ between cows and goats, although validation in independent studies involving larger sample sizes is required.},
}

@article {pmid42761239,
year = {2026},
author = {Matera, M and Besostri, A and Cavecchia, I and Illiceto, MT and Lenzi, MB and D'Ambrosio, T and Baldassarre, ME and Biagioli, V},
title = {Developmental ecology of the infant oral ecosystem: a framework for early childhood caries.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1956432},
doi = {10.3389/froh.2026.1956432},
pmid = {42761239},
issn = {2673-4842},
abstract = {BACKGROUND: Early childhood caries (ECC) has traditionally been regarded as a biofilm-mediated disease driven by sugar exposure and acidogenic microorganisms. However, this perspective primarily captures the final stage of a much longer biological process. We propose the Developmental Ecology of the Infant Oral Ecosystem as a conceptual framework in which ECC represents the clinical manifestation of a disrupted developmental ecology of the infant oral ecosystem, resulting from altered host-microbe-environment interactions that operate from the prenatal period through the first 1,000 days of life with maternal, nutritional, inflammatory, immune, metabolic, microbial, and environmental influences shaping early developmental trajectories.

METHODS: This narrative review synthesizes current evidence into an integrated developmental ecological framework encompassing maternal microbial transmission, infant oral microbiome assembly, breastfeeding, complementary feeding, dietary ecology, tooth eruption, biofilm maturation, and the oral-gut axis. These processes are interpreted within the One Health and Developmental Origins of Health and Disease (DOHaD) paradigms to provide a comprehensive ecological perspective on ECC development.

FINDINGS: The reviewed evidence supports a developmental-ecological interpretation in which interconnected early-life ecological processes shape microbial succession, oral ecosystem resilience, and susceptibility to dysbiosis. Rather than acting as the primary cause of disease, the cariogenic biofilm is interpreted within the proposed framework as the ecological endpoint of disrupted developmental trajectories that impair the establishment and maintenance of oral homeostasis.

CONCLUSIONS: Reframing ECC as a developmental ecological disorder complements established preventive approaches, including fluoride use, dietary sugar control, oral hygiene, and regular dental care, while highlighting the importance of maternal health, early-life nutritional ecology, and microbiome-informed preventive strategies aimed at preserving oral ecosystem resilience from the earliest stages of life. The proposed framework is intended to generate testable hypotheses for future longitudinal and interventional research.},
}

@article {pmid42761274,
year = {2026},
author = {Xie, C and Wu, J and Song, P and Xiao, X and An, X and Wu, H and Sun, Z},
title = {Early-stage intercropping modulates rhizosphere soil properties, microbiome composition, and photosynthetic physiology of Phellodendron chinense: a comparative analysis of five cultivation systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1882609},
doi = {10.3389/fpls.2026.1882609},
pmid = {42761274},
issn = {1664-462X},
abstract = {INTRODUCTION: Phellodendron chinense is an important medicinal plant in China. However, continuous monoculture has caused soil degradation and physiological constraints, which have become a key bottleneck limiting its sustainable production. Intercropping with companion plants is an effective approach to break this dilemma.

METHODS: We selected five representative cultivation systems commonly practiced of Phellodendron chinense and systematically measured their rhizosphere soil properties, microbial community composition, and leaf gas-exchange traits. The overarching goal was twofold: (i) to characterize the intercropping-induced variations in these three dimensions (soil properties, microbial communities, and photosynthetic physiology, and (ii) to elucidate the coupling relationships among these three dimensions.

RESULTS AND DISCUSSION: The results demonstrated that total nitrogen(N), total sodium(Na), and magnesium(Mg) contents in the T4 and T2 patterns were significantly higher than those in other patterns. The T2 and T4 patterns significantly enhanced microbial community α-diversity. In contrast, the T3 pattern caused significant soil acidification (pH 4.69) and elevated the relative abundance of the tolerant phylum Chloroflexi. T4 and T2 patterns significantly alleviated stomatal limitations in P. chinense, achieving optimal net photosynthetic rate(Pn) and stomatal conductance(Gs). Correlation analysis showed that Pn was significantly and positively correlated with soil P and Mg contents, while Gs was significantly and positively correlated with soil Na content, and N and Na were the critical factors affecting the structural variation of bacterial and fungal communities. Overall, this study demonstrates that intercropping promote soil nutrient accumulation enhances rhizosphere microbial diversity to facilitate the alleviation of photosynthetic physiological limitations. Intercropping P. chinense with bamboo or tea synergistically mitigates the host's photosynthetic physiological limitations through a belowground positive feedback pathway. These findings provide an important theoretical basis for the efficient and sustainable cultivation of this rare medicinal plant.},
}

@article {pmid42761306,
year = {2026},
author = {Kumar, R and Pakbin, B and Singh, MR and Muruganantham, B},
title = {Editorial: Unlocking the potential of the microbiome in cancer therapy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1950129},
doi = {10.3389/fmicb.2026.1950129},
pmid = {42761306},
issn = {1664-302X},
}

@article {pmid42761415,
year = {2026},
author = {Yu, M and Shi, X and Li, D and Li, Y and Sun, M},
title = {Spatial niches of the colorectal cancer microbiome: differences, interrelationships, and clinical implications of fecal, mucosal, and intratumoral microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1904188},
doi = {10.3389/fcimb.2026.1904188},
pmid = {42761415},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/diagnosis ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Intestinal Mucosa/microbiology ; *Microbiota ; Animals ; },
abstract = {Colorectal cancer (CRC) is one of the most common malignancies worldwide and a leading cause of cancer-related mortality. The gut microbiome has attracted growing attention because of its involvement in CRC initiation and progression, early detection, prognostic evaluation, and therapeutic response. However, CRC microbiome studies continue to face inconsistent findings and limited reproducibility, partly because of differences in specimen type. Directly comparing microbial signals from fecal, mucosal, and intratumoral samples may therefore bias mechanistic interpretation and mislead clinical translation. From a spatial-niche perspective, this review summarizes the distinct characteristics, formation mechanisms, interrelationships, and clinical implications of fecal, mucosal, and intratumoral microbiota during CRC progression. We further propose a "seed bank-colonizers-specialized populations" model to conceptualize the continuous but non-equivalent hierarchy among these niches. By providing a clearer spatially stratified framework, this review aims to help move CRC microbiome research beyond descriptive associations toward precision-oriented applications supported by mechanistic interpretability, reproducible evidence, and clinical translatability.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/diagnosis
*Feces/microbiology
*Gastrointestinal Microbiome
*Intestinal Mucosa/microbiology
*Microbiota
Animals

@article {pmid42761444,
year = {2026},
author = {Zou, Z and Liu, H and Hu, Y and Ge, X and Zhang, J and Li, X},
title = {Gut microbiota and microbiota-derived metabolites in radiation-induced injury: mechanisms and therapeutic opportunities.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1923929},
doi = {10.3389/fmicb.2026.1923929},
pmid = {42761444},
issn = {1664-302X},
abstract = {Radiation-induced injury is a complex pathological process involving DNA damage, oxidative stress, inflammatory amplification, epithelial barrier disruption, immune dysregulation, metabolic remodeling, and impaired tissue repair. Accumulating evidence indicates that the gut microbiota is not merely altered by irradiation but may also modify host radiation responses and tissue recovery; however, direct causal support remains confined to selected microbes, metabolites, and pathways, predominantly in preclinical models. Irradiation is frequently associated with reduced microbial diversity, depletion of selected commensals, expansion of opportunistic pathobionts, and altered microbial metabolic output; selected experimental studies further indicate that these changes can modify intestinal injury and host recovery. Conversely, defined microbes and metabolites have improved radiation outcomes in preclinical intervention models by supporting epithelial, immune, and metabolic homeostasis. In this review, we summarize current advances in understanding the gut microbiota-metabolite axis in radiation-induced injury. We first discuss radiation-induced gut dysbiosis and the major microbial metabolites involved, including short-chain fatty acids, tryptophan-derived metabolites, bile acids, lipid metabolites, polyamines, and other bioactive molecules. We then highlight the key mechanisms by which gut microbiota and microbial metabolites mitigate radiation injury, including suppression of oxidative stress, inhibition of inflammatory signaling, restoration of epithelial barrier integrity, promotion of intestinal stem cell-mediated regeneration, regulation of immune homeostasis, and modulation of lipid peroxidation-associated ferroptosis. Finally, we evaluate microbiota-targeted intervention strategies, including probiotics, prebiotics, postbiotics, fecal microbiota transplantation, antibiotic modulation, natural products, engineered probiotics, and nanomedicine-assisted delivery systems. Overall, the gut microbiota-metabolite axis represents a biologically plausible and increasingly testable target for radioprotection and mitigation, although its clinical utility remains to be established. Future studies should move beyond descriptive microbiome profiling toward causal, function-oriented, and multi-omics-driven investigations, with particular emphasis on the microbiota-lipid metabolism-ferroptosis axis and precision microbiome therapeutics. Carefully validated microbiota-targeted approaches may provide future opportunities to reduce normal-tissue toxicity and improve recovery without compromising tumor control.},
}

@article {pmid42761446,
year = {2026},
author = {Li, S and Wan, J and Liang, Z and Li, J and Jiang, H and Luo, L and Li, Y and Luo, S and Huang, H},
title = {Gypenosides ameliorate polycystic ovary syndrome via gut microbiota modulation: An integrated gut microbiome and ovarian transcriptome study.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117478},
doi = {10.1016/j.isci.2026.117478},
pmid = {42761446},
issn = {2589-0042},
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder with complex metabolic and reproductive manifestations. Gut microbiota dysbiosis has emerged as a key factor in PCOS, yet the causal role of microbiota-targeted interventions remains to be fully defined. In a letrozole-induced rat model, we show that gypenosides (GPs)-bioactive saponins from Gynostemma pentaphyllum-alleviate weight gain, hormonal imbalance, and estrous cycle disruption, alongside reducing systemic oxidative stress and inflammation. Integrated ovarian transcriptomics and gut microbiome 16S rRNA sequencing reveal that GPs modulate ovarian gene expression related to inflammation and cellular function while reshaping gut microbiota by enriching beneficial genera including Lactobacillus and Romboutsia. Fecal microbiota transplantation (FMT) establishes causality: PCOS-derived microbiota transfers disease traits to normal recipients, whereas GPs-conditioned microbiota alleviates PCOS phenotypes in recipients. These findings demonstrate that GPs act through a "gut microbiota-oxidative stress-ovary" axis, supporting GPs as a promising microbiota-targeted intervention for PCOS management.},
}

@article {pmid42761474,
year = {2026},
author = {Anand, S and Verma, A},
title = {Response to the Letter to the Editor Entitled "Promising Urinary Microbiome Signals in Congenital Anomalies of the Kidney and Urinary Tract, but not yet Ready for Clinical Risk Stratification".},
journal = {Kidney international reports},
volume = {11},
number = {10},
pages = {107022},
doi = {10.1016/j.ekir.2026.107022},
pmid = {42761474},
issn = {2468-0249},
}

@article {pmid42752812,
year = {2026},
author = {Colares, HC and Silva, TNL and Tarabal, VS and Meira, HGR and Cardoso, JF and Parreira, AG and da Silva, JA and da Silva, GR and de Magalhães, JT and Gonçalves, DB and Granjeiro, PA},
title = {Weissella paramesenteroides M4: Optimization of bioprocesses, antioxidant property, and a potentially probiotic strain with in vitro activity against Cutibacterium acnes.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42752812},
issn = {1874-9356},
abstract = {The skin microbiota is linked to conditions such as acne. As antibiotic resistance limits the effectiveness of conventional treatments, microbiome-based strategies are needed. This study aimed to optimize the biomass production of Weissella paramesenteroides M4, evaluate its antioxidant properties, and assess its efficacy in a topical gel formulation against Cutibacterium acnes. Growth dynamics were established, followed by biomass optimization using fractional factorial and central composite rotatable designs with deproteinized whey as a sustainable substrate. Optimization increased biomass production by 974% (reaching 8.7 × 10[10] CFU/mL, equivalent to 2.031 g/L dry weight under validated conditions); significant variables included yeast extract, peptone, and MnSO4. Antioxidant assays showed activities of 80% (intact cells) and 61% (lysed cells), with 82% relative growth under 1.0 mM H2O2 oxidative stress (estimated spectrophotometrically). Notably, W. paramesenteroides M4 selectively inhibited the pathogen C. acnes ATCC 6919 in vitro without affecting the commensal S. epidermidis ATCC 12,228 in vitro. A cosmetic gel containing the strain maintained antimicrobial efficacy and stability for 15 days at 4 °C. W. paramesenteroides M4 demonstrates high bioprocess efficiency, robust antioxidant potential, and selective in vitro antimicrobial activity. The formulated gel containing the candidate probiotic strain retained antimicrobial activity under refrigeration during storage and shows potential for innovative topical applications, providing a preliminary foundation for alternative acne management. This research provides a sustainable framework for high-yield probiotic production using industrial by-products and introduces a potentially probiotic lactic acid bacterium with selective in vitro activity, representing a promising candidate for alternative acne treatment, addressing a significant gap in current dermatological therapies.},
}

@article {pmid42753081,
year = {2026},
author = {Goyal, MK and Goyal, O and Sehgal, T and Vuthaluru, AR and Goyal, K and Sood, A},
title = {What is new in Rome V?: Redefining diagnostic criteria and clinical pathways in disorders of gut-brain interaction.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42753081},
issn = {0975-0711},
abstract = {The Rome-V criteria represent a major evolution in the conceptualization and clinical application of disorders of gut-brain interaction (DGBIs). Building upon the biologically grounded framework established in Rome IV, Rome V moves beyond rigid symptom-based definitions toward a multi-dimensional, clinically operational model that integrates symptom patterns, temporal characteristics, physiological testing and psycho-social context. A central advance is the transition from categorical classification to dimensional phenotyping, recognizing the continuum and overlap inherent to DGBIs. The recalibration of diagnostic thresholds, most notably the re-introduction of abdominal discomfort and the requirement for symptom intermittency in irritable bowel syndrome, restores diagnostic sensitivity while improving mechanistic specificity. Rome V further introduces Rome Clinical Criteria, addressing the substantial sub-diagnostic population and enabling earlier, context-driven diagnosis in routine practice. Across organ systems, diagnostic definitions are refined to align more closely with underlying pathophysiology and clinical decision-making. This is exemplified by the integration of physiological frameworks in esophageal disorders, temporal stratification in gastroduodenal syndromes, the redefinition of centrally mediated abdominal pain and the incorporation of motor-sensory phenotyping in anorectal disorders. In parallel, Rome V emphasizes harm reduction in biliary disorders and introduces greater continuity across pediatric and adult frameworks. Despite these advances, challenges remain, including the absence of validated biomarkers, variability in global applicability and the need for further validation of new constructs. Overall, Rome V represents a shift from static diagnostic criteria to dynamic clinical pathways, providing a robust platform for mechanism-informed and increasingly individualized care in DGBIs.},
}

@article {pmid42753220,
year = {2026},
author = {Garma, LD and Pernas, S and Vicente Baz, D and García Campelo, R and Terrasa, J and Nasarre, B and Vera García, R and Bermejo, B and González Santiago, S and Fullana, B and Rodríguez-Pérez, M and Fernandez Bruno, M and Reboredo Rendo, C and Perelló, A and Jiménez, D and Guerra, JA and Arrazubi, V and de la Cruz, S and Cejalvo, JM and Tebar, C and Núñez Berrueco, E and Hernández-Marín, B and Rogado, J and Olmos, PM and Arbaizar, LP and Villalba Oliva, MA and Madrid, Y and Sanz-Landaluze, J and Moreno-Martín, G and Morillas, A and Lopez-Alonso, A and Rodríguez-Patón, A and Colomer, R and Artés-Rodríguez, A and Quintela-Fandino, M},
title = {Longitudinal Clinical, Physiological, and Molecular Profiling of Female Patients With Metastatic Cancer: Protocol and Feasibility of a Multicenter High-Definition Oncology Study.},
journal = {JCO precision oncology},
volume = {10},
number = {9},
pages = {e2501185},
doi = {10.1200/PO-25-01185},
pmid = {42753220},
issn = {2473-4284},
mesh = {Humans ; Female ; Feasibility Studies ; Prospective Studies ; *Breast Neoplasms/pathology/genetics ; Neoplasm Metastasis ; Multicenter Studies as Topic ; Longitudinal Studies ; Middle Aged ; Adult ; *Lung Neoplasms/pathology/genetics ; *Colorectal Neoplasms/pathology/genetics ; Pilot Projects ; Aged ; },
abstract = {PURPOSE: A substantial proportion of patients receiving genomically matched therapies do not achieve clinical benefit, underscoring the influence of nongenetic factors on cancer outcomes. High-Definition Oncology (HDO) proposes integrating longitudinal, multimodal patient data-spanning clinical, molecular, physiological, and behavioral domains-to enable truly individualized cancer care. This manuscript describes the HDO study design, framework, and feasibility results in women with metastatic cancer.

METHODS: We initiated a prospective, multicenter observational study (HDO study; ClinicalTrials.gov identifier: NCT06590506) enrolling 300 female patients with newly diagnosed metastatic breast, lung, or colorectal cancer. Here, we report the study design, standardized workflows, prespecified feasibility criteria, and early internal pilot results. Eleven data modalities are collected longitudinally, including tumor and germline genomics, germline epigenomics, gut microbiome, blood and stool metabolomics and proteomics, exposome characterization, wearable-derived physiological monitoring, digital footprint assessment, medical imaging, and patient-reported outcomes. Standardized workflows govern clinical procedures, data acquisition, biospecimen processing, and quality control across all participating sites.

RESULTS: Feasibility was evaluated in the first 30 participants (10% of planned accrual). Patients completed 100% of scheduled clinical visits, 97.4% of planned plasma collections, 80.7% of stool samples, and all tumor biopsies. Wearable devices captured activity, heart rate, sleep, and blood oxygen saturation data during 95.0%, 84.2%, 90.6%, and 70.7% of total patient-days, respectively. Biospecimens met predefined quality control metrics across all molecular modalities. Engagement with mobile applications for pain and emotion reporting exceeded 80%.

CONCLUSION: The HDO study demonstrates the feasibility of comprehensive, longitudinal, multimodal data collection in women with metastatic cancer. This internal pilot establishes an integrated framework for future analyses aimed at characterizing disease trajectories, defining molecular and physiological determinants of outcomes, and developing patient-specific computational models.},
}

Humans
Female
Feasibility Studies
Prospective Studies
*Breast Neoplasms/pathology/genetics
Neoplasm Metastasis
Multicenter Studies as Topic
Longitudinal Studies
Middle Aged
Adult
*Lung Neoplasms/pathology/genetics
*Colorectal Neoplasms/pathology/genetics
Pilot Projects
Aged

@article {pmid42753230,
year = {2026},
author = {Zhang, Y and Giovannucci, EL},
title = {Ultra-processed Foods, Cancer, and Early-onset Cancer: A Comprehensive Review.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgag068},
pmid = {42753230},
issn = {1460-2180},
abstract = {The classification of foods according to their degree of processing, and particularly the concept of ultra-processed foods, is relatively new. Consumption of ultra-processed foods has increased markedly worldwide in recent decades. Their growing consumption has coincided with a rising global burden of cancer, including marked increases in several cancers diagnosed before age 50 years. In this comprehensive review, we summarize trends in ultra-processed food consumption and the sociodemographic, psychological, and behavioral characteristics associated with higher intake. We further review the epidemiological evidence linking ultra-processed foods with cancer incidence and mortality, with particular attention to the limited but emerging evidence relevant to early-onset cancer. Potential mechanisms linking ultra-processed foods to cancer include unfavorable nutrient displacement, changes in body composition and fat deposition, and increased exposure to additives, processing by-products, and other chemicals. These influences may converge on a range of biological pathways, including metabolic dysfunction, chronic inflammation, immune dysregulation, gut microbiome disruption, DNA damage and genomic instability, and epigenetic alterations. Substantial uncertainties remain, including heterogeneous exposure definitions and classification practices, limitations in dietary assessment and temporal exposure capture, residual confounding, and the complexity of putative biological mechanisms. We conclude by highlighting key research challenges and future directions, along with considerations related to policy, regulation, and industry practices.},
}

@article {pmid42753294,
year = {2026},
author = {Saleh, ZH and El Enbaawy, MI and Kamal, MA and Mahmoud, H and Hassan, M},
title = {Heat stress, respiratory dysbiosis, and poultry pathobiome: A comprehensive review of chronic respiratory disease in chickens.},
journal = {Veterinary microbiology},
volume = {322},
number = {},
pages = {111225},
doi = {10.1016/j.vetmic.2026.111225},
pmid = {42753294},
issn = {1873-2542},
abstract = {The poultry respiratory microbiome is increasingly recognized as a critical determinant of poultry health, mucosal immunity, and host resistance to opportunistic pathogens. Chronic Respiratory Disease (CRD) exerts a severe economic toll on the global broiler industry. While conventionally attributed to specific etiological agents such as Mycoplasma gallisepticum, disease progression is fundamentally tied to broad ecological dysbiosis within the respiratory tract. This comprehensive review synthesizes current knowledge on the functional roles and compositional dynamics of the poultry respiratory microbiome in both healthy and diseased states. Notably, we acknowledge the emerging threat of climate change, elucidating how heat stress physically and immunologically disrupts the respiratory mucosal microenvironment, acting as a primary catalyst for microbiome destabilization and CRD susceptibility. By shifting the paradigm from a single-pathogen model to a comprehensive pathobiome perspective, we detail the microbial shifts that characterize CRD. Furthermore, because investigating this low-biomass environment presents unique analytical challenges, we critically evaluate current technical methodologies. We address critical bottlenecks in sample collection, DNA extraction biases, and the comparative efficacy of 16S rRNA amplicon versus shotgun metagenomic sequencing. Ultimately, this synthesis provides a foundational framework for optimizing diagnostic methodologies and developing microbiome-targeted interventions -such as next-generation probiotics- to mitigate CRD in an era of escalating environmental stressors.},
}

@article {pmid42753435,
year = {2026},
author = {Xue, P and Huang, B and Wang, Y and Zhao, L and Mao, L},
title = {Environmental fate and risk of diverse oxygenated isomeric prothioconazole biotransformation products in soil.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143509},
doi = {10.1016/j.jhazmat.2026.143509},
pmid = {42753435},
issn = {1873-3336},
abstract = {Isomeric biotransformation products (TPs) of organic pesticides substantially expand structural diversity and may exhibit distinct environmental behaviors compared with their parent compounds. However, the formation mechanisms and ecological risks of such isomers (regioisomers) in soil remain poorly understood. In this study, the triazole fungicide prothioconazole (PTC) was incubated in agricultural soil, and 21 isomeric TPs were identified and classified into six structural groups using high-resolution mass spectrometry (HR-MS) based on diagnostic fragmentation patterns. These secondary oxygenated isomeric TPs were derived from three primary intermediates (PTC-desthio, PTC-dehydrated, and PTC-S-methyl) via site-selective oxygenation. Toxicity predictions indicated substantial variability among isomers, with certain hydroxylated derivatives exhibiting higher predicted ecotoxicity than others, challenging the assumption that biotransformation necessarily leads to detoxification. Metagenomic analysis showed that PTC exposure significantly altered the soil microbial community, enriching genes associated with xenobiotic degradation and central carbon metabolism. Notably, functional microbial shifts, particularly involving the genus Acinetobacter, were strongly associated with specific isomer profiles. These results suggest a potential link between microbial metabolic responses and the formation of structurally diverse isomeric TPs. The widespread occurrence of such isomers highlights that assessments based solely on parent compounds may underestimate the environmental fate and risks of PTC in agroecosystems.},
}

@article {pmid42753826,
year = {2026},
author = {Li, B and Li, X and Deng, Y and Luo, Y and Huang, Y and She, D and Li, H and Ji, S and Liu, G and Wang, Y and Zu, M and Kundu, SC and Zhang, P and Lv, P and Shi, X and Xiao, B},
title = {Ultrasound-driven plant lipid vesicles amplify oncolytic virotherapy in colorectal cancer.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {115368},
doi = {10.1016/j.jconrel.2026.115368},
pmid = {42753826},
issn = {1873-4995},
abstract = {Colorectal cancer (CRC) remains a highly aggressive malignancy, and its treatment with oncolytic virotherapy is hindered by multiple delivery barriers and delayed therapeutic kinetics. To address these challenges, we developed a plant lipid-based vesicular system (P-M@Ce6-OVs) co-encapsulating oncolytic viruses (OVs) and sonosensitizer chlorin e6 (Ce6), enabling ultrasound (US)-guided, spatiotemporally controlled delivery to deep colorectal tumors. Under US exposure, the system enhanced mucus infiltration, tumor penetration, and lysosomal escape, while activating sonodynamic therapy to rapidly induce tumor ablation and compensate delayed viral oncolysis. In CRC mouse models, rectal administration of P-M@Ce6-OVs with US exposure achieved a 10.3-fold reduction in tumor burden compared with the control (without treatment), markedly outperforming monotherapies. Importantly, combination with αPD-L1 not only suppressed primary CRC and re-challenged tumors mimicking metastatic relapse, but also induced durable systemic immune protection. This triple combination further potentiated systemic and mucosal antitumor immunity, restoring cytotoxic T-cell function and reinforcing humoral and gut-localized immune responses. Notably, this treatment reshaped gut microbiota by enriching nucleoside-metabolizing bacteria (e.g., Lactobacillus taiwanensis) and altering microbial metabolic profiles, including the pathways related to pyrimidine catabolism and arachidonic acid oxidation. These microbiota and metabolic changes were associated with immune remodeling and tumor suppression. Collectively, this platform integrated US-enabled delivery, sonodynamic activation, and microbiome remodeling to synergistically suppress CRC and re-challenged tumor progression, amplifying virotherapy and antitumor immunity.},
}

@article {pmid42753985,
year = {2026},
author = {Sun, Y and Phipatanakul, W and Lai, PS},
title = {Reframing the asthma microbiome: Multikingdom, multisite, and multiomic perspectives.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.08.026},
pmid = {42753985},
issn = {1097-6825},
abstract = {The field of asthma microbiome research has shifted rapidly in recent years. Advances in sequencing technology have led to an increased ability to characterize multikingdom microbial species and integration with host -omics profiling to enhance future translational applications. Traditional bacteria-centric, cross-sectional studies are giving way to mechanistic frameworks that incorporate fungi, viruses, and host-immune interactions. In this state-of-the-art review of emerging concepts in microbiome asthma research, we first propose a structured framework to consider microbiome studies across 5 major domains-microbial kingdom, site of sampling, integration with host -omics, clinical outcome domain, and translational relevance-in order to synthesize recent high-impact human microbiome studies in asthma. We highlight emerging evidence that fungal and viral communities contribute independently to asthma risk and that human microbial communities are linked to distinct inflammatory and immune pathways shaped by host genetic susceptibility.},
}

@article {pmid42753987,
year = {2026},
author = {Benech, N and Guarino-Vignon, P and McLellan, P and Campidelli, C and Sergeant, M and Joubert, F and Truong, S and Barbier, P and Sandoz, E and Ruffié, P and Sedda, D and Delmeule, A and Pradat, P and Landman, C and Bourrier, A and Marchand, L and Alric, L and Scanzi, J and Cassir, N and Dureault, A and Piet, E and Gallet, S and Botelho-Nevers, E and Roussel-Gaillard, T and Cuerq, C and Ader, F and Guillet, M and Rolhion, N and Grill, JP and Lamaziere, A and Chatel, JM and Pechine, S and Langella, P and Sokol, H},
title = {Faecalibacterium prausnitzii EXL01 Strain for the prevention of multiple-recurrent Clostridioides difficile Infection.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.09.002},
pmid = {42753987},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Recurrent Clostridioides difficile infection (rCDI) results from persistent microbiome dysfunction and impaired colonization resistance. Although fecal microbiota transplantation (FMT) is effective, defined and scalable alternatives are needed. We evaluated whether a single commensal strain could restore key microbiome functions and prevent recurrence.

METHODS: We assessed Faecalibacterium prausnitzii EXL01 in a murine CDI model and a multicenter, open-label single-arm phase I trial including adults with ≥3 CDI episodes. Following vancomycin preconditioning, patients received oral EXL01 for 8 weeks with 8-week follow-up. Primary endpoint was safety. Secondary endpoints included recurrence at week 8. Longitudinal stool samples underwent shotgun metagenomics and metabolomics. Outcomes were benchmarked against matched FMT cohorts. Additional in vitro and murine studies of EXL01 were performed.

RESULTS: In mice, EXL01 reduced C. difficile burden and intestinal inflammation in an antibiotic-disrupted murine model. Six patients were treated; no treatment-related serious adverse events occurred. Five of six patients (83.3%) remained recurrence-free at week 8, comparable to matched FMT cohorts. EXL01 was detectable in stool up to 8 weeks post-treatment. Multi-omics analyses showed that EXL01 engraftment was correlated with restoration of bile acid metabolism, including reduced primary bile acids and increased secondary bile acids, and increased short-chain fatty acid production, particularly butyrate, despite limited taxonomic recovery. EXL01 selectively deconjugated bile acids in vitro.

CONCLUSIONS: A single, well-characterized bacterial strain was associated with restoration of key microbiome functions and low recurrence rates in high-risk rCDI. These findings support precision microbiome therapeutics targeting ecosystem function rather than taxonomic complexity. Controlled trials are ongoing. (clinicaltrials.gov; NCT06306014).},
}

@article {pmid42754090,
year = {2026},
author = {Zuccaro, V and Asperges, E and Bruno, R},
title = {Beyond eradication: a microbiome approach to the management of bacterial vaginosis during pregnancy.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.09.003},
pmid = {42754090},
issn = {1469-0691},
}

@article {pmid42754113,
year = {2026},
author = {Tang, X and Guo, Y and Liu, Y and Wu, Z and Zhang, H and Li, S and Yang, Y and Yao, W and Cai, B and Ge, J},
title = {Organic phosphorus activation by functional bacterial consortium promotes lead immobilization in contaminated soil.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135850},
doi = {10.1016/j.biortech.2026.135850},
pmid = {42754113},
issn = {1873-2976},
abstract = {Microbial remediation of lead (Pb)-contaminated soil through phosphate-mediated stabilization is often hindered by limited microbial stress tolerance and phosphorus availability. To address these limitations, directional enrichment, microcosm experiments, high-throughput sequencing, and functional gene microarray analysis were combined to develop a composite functional consortium with Pb tolerance and phosphate-solubilizing capacity. The results revealed that the co-enrichment strategy produced a composite functional consortium with strong Pb resistance and high capacities for inorganic phosphorus solubilization and organic phosphorus mineralization. After inoculation, soil acid phosphatase and phytase activities significantly increased, thereby promoting organic phosphorus activation and Pb immobilization. Moreover, Pb leachability, mobility, and bioaccessibility decreased by 50%, 67%, and 55%, respectively, relative to their corresponding initial values on day 0. Functional gene microarray analysis revealed a significant decrease in pbrT abundance and enrichment of genes associated with the czc efflux system, cadA, and mobile genetic elements. This pattern suggests a potential shift in microbial Pb resistance strategies from intracellular uptake to extracellular efflux. Partial least squares path modeling further revealed distinct but complementary association patterns among microbial guilds. Specifically, passivators were mainly associated with phosphorus-mediated Pb stabilization, while tolerators were more closely linked to Pb-stress adaptation and extracellular polymeric substance-mediated Pb binding. These findings provide a theoretical basis for microbiome-based remediation of heavy metal-contaminated soils using native organic phosphorus pools.},
}

@article {pmid42754150,
year = {2026},
author = {Nilsson, JK and Walker, SVM and Prescott, SL and Ireland, DJ and Perrella, SL and Palmer, DJ},
title = {Infant formula introduced within 24 hours of birth increases egg allergy risk.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2026.08.040},
pmid = {42754150},
issn = {2213-2201},
abstract = {BACKGROUND: Breast secretions of colostrum precede milk production in the first few days after birth, providing nutrition and playing a critical role in shaping the newborn's gut microbiome and immune system development. Infants fed commercial milk formula in the first few days consume less colostrum, and previous studies have found an associated increased risk of food allergy.

OBJECTIVE: To determine the risk of food allergen sensitization and IgE-mediated food allergy development in infants who received any formula during their first 3 days of life.

METHODS: In a high-risk (defined by family history) cohort of 563 infants, born at 37 weeks' gestation or later, early-life infant feeding practices data were prospectively collected. At age 1 year, infant IgE-mediated food allergy, food allergen sensitization, and medically diagnosed eczema were assessed.

RESULTS: In their first 3 postnatal days, 36.8% (207 of 563) of infants received formula, with 21.8% (123 of 563) of infants receiving formula within 24 hours of birth. Overall, 3.4% of infants developed egg allergy, despite timely egg introduction in the infant diet at age 6 months. There was an increased risk of egg allergy (adjusted odds ratio, 3.62; 95% CI, 1.29-10.16; P = .014) and egg sensitization (adjusted odds ratio, 2.50; 95% CI, 1.09-5.74; P = .031) following formula introduction within 24 hours of birth. No associations were found with other food allergies or sensitization, but there were only a few cases.

CONCLUSIONS: Along with timely infant diet food allergen introduction, avoiding formula supplementation especially within 24 hours of birth is another potential food allergy prevention strategy that warrants further investigation in randomized trials.},
}

@article {pmid42754202,
year = {2026},
author = {Zhu, H and Jia, L and Li, C and Shi, H and Xu, M and Fan, W and Yang, J},
title = {Rhizosphere microbiome-mediated aluminum detoxification in acidic soils: From microbial mechanisms to microecology-based management.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129188},
doi = {10.1016/j.envpol.2026.129188},
pmid = {42754202},
issn = {1873-6424},
abstract = {Aluminum (Al) toxicity in acidic soils severely constrains global crop production. Classical mechanisms of plant Al tolerance, established primarily in sterile laboratory systems, have centered on organic acid secretion. However, such mechanisms do not capture the critical contributions of rhizosphere microorganisms under field conditions. This review synthesizes current advances in microbe-mediated Al detoxification, aiming to reinterpret classical tolerance mechanisms from a microbial perspective and explore strategies for translating these insights into sustainable field applications. Microorganisms alleviate Al stress through direct mechanisms including proton buffering, adsorption, precipitation, and metabolic cross-feeding, as well as indirect mechanisms such as improving phosphorus nutrition, remodeling root cell wall architecture via brassinosteroid signaling, and activating systemic plant defenses. Fungi further contribute through hyphal filtration and cross-kingdom cooperation. Revisiting classical tolerance mechanisms in a microbial context reveals that organic acid exudation, cell wall binding, and stress signaling function as integrated plant-microbe processes. Recent methodological advances in multi-omics, synthetic microbial community (SynCom) construction, and in situ visualization now enable mechanistic validation. Nevertheless, field application remains constrained by poor inoculant colonization, necessitating a shift from single strains to functionally complementary consortia. Future progress will require integrating plant genotype-microbiome interactions into breeding programs and developing closed-loop strategies that couple mechanistic discovery with field deployment. Critically, such strategies must be evaluated not only for short-term yield gains but also for their capacity to restore soil health, enhance ecosystem multifunctionality, and maintain functional resilience under climate-induced environmental stresses, thereby ensuring sustainable agriculture on acidic soils.},
}

@article {pmid42754330,
year = {2026},
author = {Na, SI and Kim, J and Kim, SY and Park, J and Cho, YJ},
title = {SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.71150/jm.2606011},
pmid = {42754330},
issn = {1976-3794},
abstract = {Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.},
}

@article {pmid42754368,
year = {2026},
author = {Khan, SA and Hegelmaier, T and Wegner, F and Höllerhage, M and Peters, M and Duscha, A and Desel, C and Haghikia, A and Klietz, M},
title = {Gut microbiome dysbiosis, short-chain fatty acid depletion and implications for neuroinflammation in atypical parkinsonian syndromes - a systematic review of patient cohorts.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X261485793},
doi = {10.1177/1877718X261485793},
pmid = {42754368},
issn = {1877-718X},
abstract = {IntroductionAtypical parkinsonian syndromes (APS) such as progressive supranuclear palsy (PSP), multiple system atrophy (MSA) and corticobasal syndrome (CBS) pose a major clinical challenge due to their progressive disease course, reduced life expectancy and resistance to dopaminergic therapy. The gut microbiome has gained increasing attention as a potential contributor to APS etiology and progression.AimThe literature analysis aims to systematically evaluate alterations in the gut microbiome in APS, their correlation with clinical symptoms and their potential diagnostic and therapeutic relevance.Material and methodsPubMed and Web of Science were searched separately for ''progressive supranuclear palsy'', ''multiple system atrophy'' and ''corticobasal syndrome'', each combined with "gut microbiome" AND "human". Inclusion criteria were ≥ 10 subjects per group, clinically confirmed APS and gut microbiome analysis in a case-control, cross-sectional, longitudinal or randomized controlled trial study design. 7 studies met the inclusion criteria (1 PSP, 1 PSP/MSA, 5 MSA). No studies with CBS patients could be included.ResultsThe gut microbiome is altered in APS compared to healthy controls, with several alterations correlating with clinical symptoms in individual studies. A reduction of short-chain fatty acid (SCFA) producing bacteria and an enrichment of pro-inflammatory taxa were observed, alongside impaired markers of intestinal barrier integrity.Discussion and conclusionAPS are associated with dysbiosis that correlates with clinical symptoms, although causality remains to be established. Generalizability is limited due to the lack of geographic heterogeneity in the included studies. Longitudinal studies with larger cohorts are required to identify robust microbial markers and therapeutic potential.},
}

@article {pmid42754660,
year = {2026},
author = {Plazzo, AP and Filz, V and Prothiwa, M and Lambrecht, R and Delgado, ME and Fleming, JR and Duschek, J and Pilgram, E and Friedrich, J and Eisenring, R and Kurtz, L and Stemmer, K and Stenman, LK and Amaya Garcia, F and Unterlass, M and Mayans, O and Böttcher, T and Brunner, T},
title = {Microbiome-host communication via vaccenic acid modulates LRH-1/NR5A2 activity and ameliorates metabolic liver disease.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42754660},
issn = {1757-4684},
support = {BR 3369/4-2//Deutsche Forschungsgemeinschaft (DFG)/ ; },
abstract = {Interactions between microbiota and the host can profoundly affect human health. In particular, microbiota-derived metabolites influence liver physiology and contribute to the development of metabolic diseases, yet the molecular mechanisms underlying microbiome-host communication remain incompletely understood. Here, we identify bacterial lipids as modulators of the nuclear receptor Liver Receptor Homolog-1 (LRH-1/NR5A2), a regulator of hepatic metabolism. Lipid extracts from multiple bacterial species, including the probiotic Bifidobacterium animalis subsp. lactis B420[TM], activated LRH-1, leading to the identification of the long-chain fatty acid vaccenic acid (VA) as a previously unrecognized endogenous LRH-1 ligand. VA directly bound the LRH-1 ligand-binding domain and stimulated receptor-dependent transcriptional activity. In high-fat diet-induced obese and hyperglycemic mice, VA-mediated LRH-1 activation improved glucose homeostasis and attenuated metabolic liver disease. Transcriptomic analyses revealed suppression of hepatic de novo lipogenesis as a principle downstream response to LRH-1 activation. Together, these findings establish a microbiota-LRH-1 signaling axis that links bacterial lipid metabolism to host metabolic regulation, identify VA as a functional LRH-1 agonist, and provide a mechanistic rationale for targeting LRH-1 in metabolic liver disease.},
}

@article {pmid42754709,
year = {2026},
author = {Selten, G and Lamouche, F and Gómez-Repollés, A and López, JL and Zhang, XM and Smart, C and Blahovska, Z and Zarate Camargo, G and Kelly, S and de Jonge, R and Radutoiu, S},
title = {Functional capacities drive recruitment of bacteria into plant root microbiota.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42754709},
issn = {2058-5276},
support = {OPP11772165//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; NNF24SA0096909//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF24SA0096909//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 024.004.14//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
abstract = {Root-associated microbiomes are shaped by the plant, yet vary across environments and hosts, challenging prediction and engineering. Here, to uncover principles of bacterial selection at the root-soil interface, we applied a systems-level approach using reconstitution studies with communities of isolates from Arabidopsis, barley and Lotus grown in soil. Functional divergence among the microbiota of the host plants reflected distinct strategies: in Arabidopsis and barley, recruitment was primarily shaped by inoculum, while Lotus root environment favoured fewer, functionally diverse isolates, akin to a 'Swiss army knife' strategy. Despite taxonomic variability, root microbiomes encoded overlapping functions. Across major taxa, isolates with broad but distinct functional repertoires within their families were consistently more abundant. Using a genome-to-function framework that is function centric, taxonomically inclusive and host-context aware, we identified 266 functions enriched across all root microbiomes. This functional backbone emerged as a core signature of plant-associated bacteria, providing a solid foundation for microbiome engineering in agriculture.},
}

@article {pmid42754770,
year = {2026},
author = {Petri, RM and Ricci, S and Jelinski, M and Hund, A},
title = {Observational study of the microbiome of perforated abomasal ulcers in unweaned beef calves in Canada.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42754770},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Abomasum/microbiology/pathology ; *Cattle Diseases/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *Stomach Ulcer/veterinary/microbiology ; Canada ; Bacteria/classification/genetics/isolation & purification ; Male ; *Microbiota ; },
abstract = {In western Canada, perforating abomasal ulcers (AU) are generally diagnosed postmortem in beef calves up to 2 months of age. Certain microbes have been associated with AU, but the evidence is circumstantial. Thus, analyzing the abomasal microbiome in calves with and without AU may provide insight into the etiology of the disease. Using 16S rRNA gene sequencing, abomasal tissues from Western Canadian beef calves, with (n = 27) and without AU (n = 17), were analyzed for microbial diversity. No significant differences were seen between microbiomes of AU and CON calves despite numerical differences in abundance. Therefore, a subsample of 18 tissues (12 AU, 6 CON) were analyzed using untargeted metagenomic sequencing for determination of phylogeny, and the presence of antimicrobial resistance genes (ARGs). Staphylococcaceae (1.5%), Campylobacteraceae (1.4%) and Enterobacteriaceae (1.4%) were seen across all samples. Differential abundance analysis revealed Streptomyces spp. REN17 to be less abundant in AU calves, suggesting a potential association between Streptomyces spp. and calf gut health. An ARG associated with polymyxin resistance was found to be differentially abundant in calves with a history of antimicrobial therapy. Although differences were observed in the predicted metabolic functions among groups, none reached statistical significance. In our study, no consistent microbial signature associated with AU was identified, despite the differential abundance of individual taxon, nor did prior antimicrobial therapy associate to the growth of specific microbiota. To better understand the potential role of the abomasal microbiota in AU etiology and the impact of early life interventions in beef calves, a larger sample size is needed.},
}

Animals
Cattle
*Abomasum/microbiology/pathology
*Cattle Diseases/microbiology
RNA, Ribosomal, 16S/analysis/genetics
*Stomach Ulcer/veterinary/microbiology
Canada
Bacteria/classification/genetics/isolation & purification
Male
*Microbiota

@article {pmid42754802,
year = {2026},
author = {Silva de Avó Freixo, H and Miot, HA and Ogawa, MM and de Castro Martins, IM and Leite E Silva, VR and Andreo Filho, N and Lopes, PS and Filho, RM and Bagatin, E},
title = {Urban Exposome and Skin Microbiome in Atopic Dermatitis: A Comparative Study Between Two Brazilian Municipalities.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42754802},
issn = {2193-8210},
support = {Vichy Exposome Grant 2022//Fondation L'Oréal/ ; },
abstract = {INTRODUCTION: Atopic dermatitis (AD) is thought to arise from the interplay of skin barrier dysfunction, type 2 immune dysregulation, and cutaneous dysbiosis, the last of these characterized by reduced bacterial diversity and predominance of Staphylococcus aureus. The urban exposome, including air pollution and reduced environmental microbial diversity, may modulate this dysbiosis. We hypothesized that patients with AD residing in a metropolitan area with a higher pollutant burden would show greater skin dysbiosis, reflected by a higher relative abundance of S. aureus, than patients residing in a municipality with a lower pollutant load and greater environmental biodiversity.

METHODS: This cross-sectional, comparative study enrolled ten children (6-12 years) and ten adults (20-31 years) with active AD, without specific treatment in the preceding 30 days, residing in the metropolitan region of São Paulo or in Botucatu, an interior municipality of São Paulo State, Brazil. Skin swabs were collected from eczematous lesions and characterized by 16S ribosomal RNA (rRNA) gene (V3-V4) sequencing. Alpha and beta diversity and the relative abundance of S. aureus, S. epidermidis, and S. hominis were compared between municipalities and age groups using generalized linear models, Bray-Curtis dissimilarity, principal coordinates analysis (PCoA), and permutational multivariate analysis of variance (PERMANOVA).

RESULTS: The sample (n = 20) had a predominance of male sex (60%) and moderate AD severity (75%). A total of 658 taxa were identified. Alpha diversity did not differ by municipality or age group, and PERMANOVA revealed no global difference in bacterial community composition (p > 0.1). However, participants residing in the metropolitan municipality showed a significantly higher relative abundance of S. aureus and higher proportions of S. aureus relative to total bacteria and to other staphylococci than those residing in the interior municipality.

CONCLUSION: Despite similar overall microbial diversity, patients with AD living in a metropolitan municipality showed selective enrichment of S. aureus compared with those in a less polluted interior municipality. These exploratory findings generate the hypothesis that the urban exposome contributes to cutaneous dysbiosis in AD and warrant confirmation in larger studies with objective exposure measurement.},
}

@article {pmid42754908,
year = {2026},
author = {Kaufhold, G and Bartolomaeus, TUP and Schütte, K and Schütte, T and Kamboj, S and Löber, U and Rahn, G and McParland, V and Braun, L and Markó, L and Mammadli, M and Krannich, A and Bahr, LS and Gutmann, F and Paul, F and Ducarmon, QR and Zeller, G and Mesnage, R and Wilck, N and Zernecke, A and Oefner, PJ and Gronwald, W and Müller, DN and Forslund-Startceva, SK and Bähring, S and Bartolomaeus, H and Siebert, N},
title = {Machine learning identifies microbiome and clinical predictors of sustained weight loss following prolonged fasting.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42754908},
issn = {1756-994X},
mesh = {Humans ; *Fasting ; Female ; *Machine Learning ; Male ; Adult ; *Weight Loss ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology/chemistry ; Body Mass Index ; Metabolome ; Body Composition ; Multiomics ; *Microbiota ; Predictive Learning Models ; Intermittent Fasting ; },
abstract = {BACKGROUND: Prolonged fasting may improve metabolic health, but controlled data in healthy adults with longer follow-up and multi-omics profiling are limited. We investigated the immediate and 12-week follow-up effects of a 5-day fasting intervention on body composition, gut microbiome, and circulating and fecal metabolites, and assessed whether baseline characteristics predict individual weight-loss response.

METHODS: In a randomized, waitlist-controlled trial, 38 healthy adults completed a 5-day fasting intervention with 12-week follow-up (LEANER study). Outcomes included body mass index and body composition, gut microbiome composition, and plasma and fecal metabolites. Changes over time and between groups were evaluated using regression-based models and paired non-parametric tests, as appropriate. Additionally, permutation-based multivariate testing was performed on microbiome and metabolome data. Twelve-week body weight response was predicted using data-driven machine learning with cross-validation, followed by external validation in three independent cohorts undergoing prolonged fasting protocols.

RESULTS: Fasting reduced body mass index acutely, predominantly driven by loss of fat mass, and these improvements partially persisted at 12 weeks. Fasting induced marked shifts in gut microbiome composition and in plasma and fecal metabolites. Post-fasting and longer-term changes in microbial diversity were associated with baseline microbiome diversity. A model combining baseline microbiome and clinical variables predicted body mass index response at 12 weeks; prominent predictors included an unclassified Faecalibacterium species, Oscillibacter sp. 50_27, low-density lipoprotein cholesterol, and systolic blood pressure. The model generalized to three independent cohorts, including individuals with metabolic syndrome, patients with multiple sclerosis exposed to repeated fasting, and healthy volunteers fasting for 6-12 days.

CONCLUSIONS: In healthy adults, a 5-day prolonged fasting intervention produces robust short-term metabolic changes with partial persistence and consistent remodeling of the gut microbiome and metabolite profiles. Baseline microbiome and clinical characteristics can help stratify expected longer-term responses, supporting the development of individualized fasting-based interventions.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT04452916. Prospectively registered on June 29, 2020.},
}

Humans
*Fasting
Female
*Machine Learning
Male
Adult
*Weight Loss
*Gastrointestinal Microbiome
Middle Aged
Feces/microbiology/chemistry
Body Mass Index
Metabolome
Body Composition
Multiomics
*Microbiota
Predictive Learning Models
Intermittent Fasting

@article {pmid42754913,
year = {2026},
author = {Bajiya, RK and Agabi, R and García, JO and Torreno, VP and Armengaud, J and Grenga, L},
title = {From functional annotation to functional meaning in microbiome research.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42754913},
issn = {2524-6372},
support = {23002679//Région Occitanie Pyrénées-Méditerranée/ ; FoodMap//ANSES - CEA/ ; 101225682//Marie Skłodowska-Curie Actions Doctoral Networks programme/ ; 101225682//Marie Skłodowska-Curie Actions Doctoral Networks programme/ ; ANR-24-CE15-7400-01//Agence Nationale de la Recherche/ ; },
abstract = {Microbiome research has moved from cataloging community composition to asking what these communities do, but "function" is often used to describe fundamentally different levels of evidence. Functional claims may refer to functional capacity (what is encoded), functional realization (what molecular functions are actively engaged under specific conditions), or functional impact (the resulting consequences for hosts, microbial communities, or ecosystems). In this Perspective, we examine how functional annotations in microbiome research generate biological meaning and why current approaches support different kinds of inference. We propose a framework that distinguishes three levels of functional inference: capacity, realization, and impact. Homology-based, domain-centric, pathway-based, machine learning-driven, and multi-omics approaches each contribute differently to these levels, but none alone captures microbiome function in full. We argue that microbiome function should be interpreted as a hierarchy of inferences rather than a single property. Recognizing this distinction should improve how functional findings are interpreted, reported, and compared across microbiome studies. Accordingly, functional studies should explicitly state whether their conclusions concern capacity, realization, or impact, thereby clarifying the evidential basis of functional claims and improving their interpretation and comparison across microbiome studies.},
}

@article {pmid42755070,
year = {2026},
author = {Zhang, R and Niu, CE and Shi, HN and An, XJ and Li, Q and Geng, ZG and Zhang, JX and Xu, ZF and Yue, YJ},
title = {Comparative analysis of four compound stomachs development, fermentation dynamics, and microbiome structure in Hu sheep and its crossbred combinations.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.260416},
pmid = {42755070},
issn = {2765-0189},
abstract = {OBJECTIVE: This study was conducted to investigate the differences in fermentation parameters, epithelial development, and microbial composition across the four stomach compartments between Hu sheep and its crossbreds.

METHODS: Forty-eight approximately 3-month-old male lambs, assigned to three genetic groups (HH:♂Hu×♀Hu, n=16; DH:♂Poll Dorset×♀Hu, n=16; SH:♂Southdown×♀Hu, n=16), were raised under uniform nutritional and management conditions for 95 days. Feed intake was determined daily and body weight were measured every 20 days. At the end of the trial, six sheep per group close to the average weight were slaughtered. Samples of digesta and tissue from the four stomachs were collected. Fermentation parameters, epithelial development, and microbial community structure were analyzed.

RESULTS: Compared with the HH group (acetate: 25.8, 21.8, and 6.36 mmol/kg; propionate: 6.8, 5.60, and 3.65 mmol/kg; butyrate: 3.66, 3.19, and 1.38 mmol/kg), the DH group exhibited significantly higher acetate concentrations (45.3, 33.7, and 12.9 mmol/kg), propionate (14.3, 11.1, and 5.94 mmol/kg), and butyrate (12.9, 6.69, and 4.52 mmol/kg) in the rumen, reticulum, and omasum, respectively (p<0.05), indicating enhanced fermentation capacity, a significantly thicker rumen mucosal epithelium (p<0.05) suggesting a greater capacity for VFA absorption. Taxonomic analysis showed that Firmicutes and Bacteroidota were the predominant phyla in four stomachs. Differential analysis identified that the DH group had significantly enriched taxa associated with fiber degradation (e.g., Fibrobacterota, Spirochaetota) in the forestomachs. Conversely, the rumen of HH group was enriched with Anaerolineae, associated with complex plant fiber degradation. PICRUSt2 functional prediction indicated that differentially microbes in the DH group were primarily linked to the biosynthesis of lysine and arginine, whereas those in the HH group were enriched in degradation pathways such as amino acid degradation.

CONCLUSION: The DH group markedly elevated VFA production by modulating the forestomach microbial structure. Combined with adaptive improvements in rumen epithelial, this effect potentially enhanced energy utilization and growth performance.},
}

@article {pmid42755168,
year = {2026},
author = {Jassey, VEJ and Lafont Rapnouil, T and Le Geay, M and Walcker, R and Gandois, L and Barret, M and Fanin, N and Robroek, BJM and Lauga, B and Andrews, LO and Greuza, AB and Bakker, MR and Bertrand, G and Birkwald, T and Borges, PAV and Branfireun, B and Brearley, FQ and Brousseau, C and Bu, ZJ and Carrias, JF and Coffinet, S and Corbarra, B and Dias, EMF and Dorrepaal, E and Francez, AJ and Fu, Y and Gabriel, M and Gabriel, R and Gerin, S and Gilbert, D and Gogo, S and Granath, G and Gray, E and Heffernan, L and Heger, TJ and Juutinen, S and Kardol, P and Karofeld, E and Klimkowska, A and Küttim, M and Küttim, L and Kuuri-Riutta, O and Lacourse, T and Lamentowicz, M and Le Roux, G and Lindo, Z and Mackenzie, R and Marcisz, K and Mazei, YA and Mazei, NG and Mendes, CMF and Mitchell, EAD and Mora-Gomez, J and Müller, R and Pouliot, K and Purre, AH and Quaiser, A and Río, BR and Rober, AR and Rochefort, L and Rodríguez, AC and Sannel, ABK and Seemann, F and Servière, L and Strack, M and Swindles, GT and Talbot, J and Tsyganov, AN and Tuittila, ES and Tveit, AT and Väliranta, MM and Wyatt, KH and Ylänne, H and Yu, Z and Zarov, EA and Hamard, S},
title = {Tipping Points in Bacterial Richness Amplify Extracellular Enzyme Activities in Northern Peatlands.},
journal = {Global change biology},
volume = {32},
number = {9},
pages = {e71099},
doi = {10.1111/gcb.71099},
pmid = {42755168},
issn = {1365-2486},
support = {ANR-17-CE01-0007//Agence Nationale de la Recherche/ ; ANR-23-ERCC-0001-01//Agence Nationale de la Recherche/ ; ANR-24-CE02-6475//Agence Nationale de la Recherche/ ; },
mesh = {*Soil Microbiology ; *Bacteria/enzymology/classification ; *Biodiversity ; *Wetlands ; Sphagnopsida/microbiology ; Carbon Cycle ; Carbon/metabolism ; *Microbiota ; },
abstract = {Bacterial communities are vital to northern peatlands' carbon and nutrient cycling, one of the Earth's largest terrestrial carbon stores. However, their diversity and ecological roles at broad geographic scales remain partially understood, limiting our ability to predict their response to global change. Here, we combine a trans-Holarctic survey across 171 Sphagnum-dominated peatlands (SDPs) with a continental-scale reciprocal transplantation experiment to quantify how bacterial diversity shapes carbon and nutrient cycling across bioclimatic gradients. We show that bacterial diversity and composition differ markedly among peatland bioclimatic regions and are primarily structured by the universal abiotic drivers of northern ecosystems: minimum temperature, snow cover, and soil water content. Ecological models further revealed that deterministic processes accounted for approximately 80% of bacterial community assembly, highlighting the strong influence of environmental filtering. Biodiversity-Ecosystem Function analyses identified bacterial richness as a key driver of carbon and nutrient cycling. Using moving-window structural equation models, we identified a critical bacterial richness threshold, below which extracellular enzyme activities increased by ~60%. This transition coincided with stronger environmental filtering and shifts towards bacterial communities with a greater predicted potential for extracellular nutrient acquisition and heterotrophic metabolism. Together, these findings demonstrate that bacterial richness underpins peatland biogeochemical functioning and suggest that biodiversity loss may accelerate carbon turnover, weakening the capacity of northern peatlands to retain carbon. As climate change threatens this unique microbiome, safeguarding bacterial diversity will be critical for maintaining ecosystem resilience and the stability of this globally important carbon sink.},
}

*Soil Microbiology
*Bacteria/enzymology/classification
*Biodiversity
*Wetlands
Sphagnopsida/microbiology
Carbon Cycle
Carbon/metabolism
*Microbiota

@article {pmid42755253,
year = {2026},
author = {Gupta, KH and Israni, AK and Onyeaghala, G},
title = {Gut microbial metabolism of immunosuppressive drugs: from metagenomic associations to functional enzyme biomarkers.},
journal = {Current opinion in organ transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOT.0000000000001314},
pmid = {42755253},
issn = {1531-7013},
abstract = {PURPOSE OF REVIEW: Inter-individual variability in immunosuppressant exposure remains a major challenge in transplantation. Pharmacogenomics and host-related factors contribute to this variability, with increasing evidence suggesting that the gut microbiome is also an important determinant of drug metabolism. This review summarizes recent advances in microbiome-mediated metabolism of immunosuppressive drugs like tacrolimus and mycophenolate and highlights emerging functional approaches to identify clinically relevant microbial enzymes.

RECENT FINDINGS: Microbial β-glucuronidases contribute to the enterohepatic recirculation of mycophenolic acid by deconjugating mycophenolic acid glucuronide, influencing systemic exposure and gastrointestinal toxicity. In parallel, gut bacteria such as Faecalibacterium prausnitzii can directly metabolize tacrolimus into less active metabolites, potentially contributing to variability in drug exposure and dose requirements. Recent studies further demonstrate that metaproteomic and enzyme activity-based approaches provide greater functional resolution than metagenomics alone for identifying microbiome-associated drug metabolism pathways.

SUMMARY: Current evidence supports a significant role for the gut microbiome in immunosuppressant pharmacokinetics and functional microbial enzymes represent promising biomarkers of immunosuppressant disposition. Moving beyond gene-level associations toward the functional characterization of microbial enzymes through the integration of metaproteomics, metabolomics, and enzyme activity assays with pharmacokinetic modeling may facilitate development of microbiome-based biomarkers and microbiome-guided precision dosing strategies in transplantation. Future integration of microbiome-derived functional data into therapeutic drug monitoring and pharmacokinetic models may improve individualized immunosuppressive therapy and transplant outcomes.},
}

@article {pmid42755267,
year = {2026},
author = {Sampath, V and Lee, K and Kim, SJ and Kim, IH},
title = {Partial Replacement of Molasses with Monosodium Glutamate-Condensed Molasses Soluble enhance growth performance by maintaining gut health in finishing pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag298},
pmid = {42755267},
issn = {1525-3163},
abstract = {A 10-week growth trial was conducted using three groups of 70 finishing pigs [210 head (Landrace × Yorkshire × (Duroc) with initial BW 53.92 ± 2.24 kg] to determine the effect of Monosodium Glutamate-Condensed Molasses Soluble (MSG-CMS) as a replacement for molasses on growth performance, nutrient digestibility, blood profiles, fecal microbiome composition, and meat quality in finishing pigs. For this, the pens of pigs (5 pigs/pen- 3 ♀and 2 ♂) were randomly allocated into 1 of 3 treatment groups in a completely randomized design with 14 replications/treatment. The dietary treatments were: TRT1, 4% Molasses; TRT2, 2% Molasses + 2% MSG-CMS; TRT3, 4% MSG-CMS. The test diets were fed in two phases: Phase 1, from week 0-5 and Phase 2, from week 5-10. Pigs fed the diet containing 4% MSG-CMS showed higher (P < 0.05) average daily gain and average daily feed intake during phases 1, 2, and the overall period compared with other treatments. However, final BW, gain-to-feed ratio, nutrient digestibility, backfat thickness, and lean meat percentage were not affected by dietary treatments. At week 10, pigs that received 4% MSG-CMS exhibited significantly higher (P < 0.05) blood insulin concentration, whereas no differences were detected in meat quality or carcass characteristics. Also, no differences were observed in alpha diversity indices among treatment groups. However, beta diversity analysis using unweighted UniFrac and Bray-Curtis PCoA demonstrated partial separation of microbial communities, with TRT3 showing a clearer clustering pattern. At the phylum level, TRT3 exhibited higher abundances of Firmicutes and Bacteroidota and a lower abundance of Proteobacteria. At the genus level, Prevotella and Lactobacillus were more abundant in TRT1, whereas Clostridium sensu stricto 1 was reduced in TRT3. LefSe analysis revealed enrichment of several fiber- and fermentation-associated taxa in TRT3, including unclassified Selenomonadaceae, Muribaculaceae, Treponema, and unclassified Ruminococcaceae. In summary, complete replacement of molasses with 4% MSG-CMS improved growth performance, without adversely affecting nutrient digestibility, gut microbial diversity, meat quality, or carcass characteristics, suggesting that MSG-CMS could serve as a potential alternative feed ingredient for improving the growth performance of finishing pigs.},
}

@article {pmid42755378,
year = {2026},
author = {Yuan, X and Li, N and Zhu, S and Zuo, T},
title = {Bacteriophages in humans: From discovery and mechanisms to therapeutic promise in combating disease.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {42755378},
issn = {2542-5641},
abstract = {Since the discovery of bacteriophages over a century ago, bacteriophages have evolved from fundamental biological models into promising therapeutic agents, especially in the era of antimicrobial resistance and in the treatment of human diseases. This article systematically reviews the key milestones in phage research and application at both international and Chinese fronts. It examines the evolving understanding of phage-bacterium interactions, which provides the development of targeted phage-based biocontrol and therapeutic strategies. Particular emphasis is placed on recent advances linking phages to human diseases, including their potential roles in gut microbiota modulation and chronic disease contexts. Despite promise, substantial challenges remain. The article concludes by discussing critical future directions, emphasizing the need for identifying key microbial targets in diseases, integrating phage therapy with emerging technologies to accelerate clinical translation, and exploring dietary phage interventions for disease prevention.},
}

@article {pmid42755487,
year = {2026},
author = {Hu, Y and Teng, C and Zhang, D},
title = {Global trends and emerging frontiers in cancer immunotherapy and gut microbiota-derived metabolites: a bibliometric analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1876450},
pmid = {42755487},
issn = {2235-2988},
mesh = {Humans ; *Bibliometrics ; *Immunotherapy/trends/methods ; *Neoplasms/therapy/immunology ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {OBJECTIVES: Cancer immunotherapy has achieved remarkable clinical success; however, therapeutic resistance remains a major challenge. Increasing evidence suggests that gut microbiota-derived metabolites play a critical role in modulating host immune responses and influencing treatment outcomes. This study aimed to systematically characterize the global research landscape and identify emerging trends in this field using bibliometric approaches.

METHODS: Publications were retrieved from the Web of Science Core Collection (WoSCC) and Scopus databases based on predefined search strategies. Only English-language articles and reviews were included. Bibliographic records were integrated and deduplicated using the bibliometrix R package. Descriptive analyses were performed to evaluate publication outputs, countries, institutions, authors, and journals. CiteSpace was used for reference burst detection, and VOSviewer was applied to construct keyword co-occurrence networks.

RESULTS: A total of 2,979 publications from 1973 to March 2026 were included, comprising 1,593 reviews and 1,386 original articles. China contributed the largest number of publications (1,121; 37.63%), followed by the United States (499; 16.75%). Notably, the United States exhibited the highest H-index and centrality, indicating its leading role in global research impact and collaboration networks. Sichuan University was the most productive institution (115 publications), with six of the top ten institutions located in China. Laurence Zitvogel (28 publications) and Guido Kroemer (22 publications) were the leading authors in this field. Frontiers in Immunology published the highest number of relevant articles (277). Keyword and temporal analyses indicated a shift from descriptive microbiome profiling toward mechanism-oriented and translational research. Recent hotspots include "immunomodulation", "the gut-liver axis", "intratumoral microbiota", and "microbial metabolites".

CONCLUSIONS: Microbial metabolites have emerged as key functional mediators shaping responses to cancer immunotherapy, reflecting a shift from microbiome composition toward metabolite-centered mechanisms. This field is undergoing a transition from descriptive profiling to mechanism-oriented and translational research. These findings provide important insights for developing microbiota-targeted strategies to enhance the efficacy of cancer immunotherapy.},
}

Humans
*Bibliometrics
*Immunotherapy/trends/methods
*Neoplasms/therapy/immunology
*Gastrointestinal Microbiome
Animals

@article {pmid42755519,
year = {2026},
author = {Schröttner, P and Harb, H},
title = {Editorial: Reviews in bacteria and host.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1961702},
doi = {10.3389/fcimb.2026.1961702},
pmid = {42755519},
issn = {2235-2988},
}

@article {pmid42755542,
year = {2026},
author = {Eom, JH and Cho, MY and Kim, JW and Kim, Y and No, J and Hwang, J and Kim, S and Lee, D and Baek, H and Kim, BK and Kim, YY and Her, SB and Ko, DY and Hwang, I and Kim, HS},
title = {Absolute quantification by mouthwash testing screens severe periodontitis and tracks species-specific microbial response to periodontal therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1917870},
pmid = {42755542},
issn = {2235-2988},
mesh = {Humans ; *Mouthwashes ; Porphyromonas gingivalis/isolation & purification/genetics ; *Periodontitis/microbiology/therapy/diagnosis ; Retrospective Studies ; Treponema denticola/isolation & purification/genetics ; *Bacterial Load/methods ; Fusobacterium nucleatum/isolation & purification/genetics ; Cross-Sectional Studies ; Tannerella forsythia/isolation & purification/genetics ; Real-Time Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Prevotella intermedia/isolation & purification/genetics ; Prospective Studies ; *Bacteria/isolation & purification/genetics/classification ; Multiplex Polymerase Chain Reaction/methods ; Female ; },
abstract = {BACKGROUND: Non-invasive molecular tools that can both screen for severe periodontitis and quantify treatment-associated pathogen changes remain an unmet need. We evaluated a non-invasive multiplex quantitative polymerase chain reaction (qPCR) mouthwash panel providing absolute colony-forming-unit (CFU) quantification of five periodontal pathogens (Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, Fusobacterium nucleatum), and asked whether a single test can both screen for severe disease and track each patient's species-level treatment response.

METHODS: Treatment-response monitoring was assessed in a real-world retrospective cohort (349 patients, 703 visits; 235 paired pre/post-treatment samples) using paired Wilcoxon signed-rank tests and Jonckheere-Terpstra trend tests across baseline stage. Screening performance was independently evaluated in a prospective cross-sectional cohort (n=87; 31 healthy, 56 Stage III/IV) with leave-one-out cross-validation (LOOCV) and a pre-specified sensitivity analysis.

RESULTS: For screening, LOOCV AUC was 0.96 for P. gingivalis and 0.97 for the combined panel, preserved under inclusion of antibiotic- and treatment-exposed subjects. Beyond screening, the panel resolved each patient's species-level response to non-surgical therapy: all five species decreased significantly, with median within-patient reductions of -0.37 to -0.72 log10 CFU (paired Wilcoxon, all p<0.001) and reduction magnitude scaling with baseline severity. This response was strongly species-specific and clinically informative at the individual level: In the implant-bearing high-baseline-burden subgroup, post-treatment F. nucleatum reached or fell below the Healthy reference median in 61% of evaluable patients, whereas P. gingivalis reached it in only 5% and remained approximately 500-fold above the Healthy reference at the median final visit, identifying residual keystone-pathogen burden not captured by clinical or radiographic assessment.

CONCLUSION: In this two-cohort evaluation, a single non-invasive mouthwash qPCR test provided two linked clinical outputs: high-accuracy screening for severe periodontitis and quantitative individual-level tracking of species-specific microbial response to therapy. These findings are preliminary, derive from a single-center screening cohort and a retrospective monitoring cohort, and require external validation before clinical deployment. By placing pathogen loads on the same absolute CFU scale, the assay supports both cross-sectional disease detection and longitudinal residual-burden monitoring as an adjunct to the 2018 AAP/EFP framework. Clinical Research Information Service (CRIS) registration: KCT0011511 (https://cris.nih.go.kr).},
}

Humans
*Mouthwashes
Porphyromonas gingivalis/isolation & purification/genetics
*Periodontitis/microbiology/therapy/diagnosis
Retrospective Studies
Treponema denticola/isolation & purification/genetics
*Bacterial Load/methods
Fusobacterium nucleatum/isolation & purification/genetics
Cross-Sectional Studies
Tannerella forsythia/isolation & purification/genetics
Real-Time Polymerase Chain Reaction/methods
Sensitivity and Specificity
Prevotella intermedia/isolation & purification/genetics
Prospective Studies
*Bacteria/isolation & purification/genetics/classification
Multiplex Polymerase Chain Reaction/methods
Female

@article {pmid42755618,
year = {2026},
author = {Li, L and Luo, Y and Liu, S and Liang, C and Ruan, H and Peng, P and Huang, Z},
title = {Genome-resolved gut metagenomics identifies an Escherichia coli-Collinsella signature associated with Wagner 4 gangrenous diabetic foot ulcers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1893357},
pmid = {42755618},
issn = {1664-3224},
mesh = {Humans ; *Escherichia coli/genetics ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Gastrointestinal Microbiome/genetics ; *Actinobacteria/genetics ; Metagenome ; Male ; Female ; Feces/microbiology ; },
abstract = {Diabetic foot ulcers (DFU) are a major complication of type 2 diabetes mellitus, but whether the gut microbiome captures systemic microbial features associated with advanced ulcer severity remains unclear. We performed shotgun metagenomic sequencing of stool samples from 43 patients with type 2 diabetes mellitus and active DFU, comparing Wagner grades 1-3 (n = 30) with Wagner 4 gangrenous disease (n = 13). De novo assembly and binning recovered 440 dereplicated metagenome-assembled genomes (MAGs) meeting medium-quality or high-completeness/low-contamination thresholds. Community-level diversity and dominant-taxon composition did not separate Wagner 4 from Wagner 1-3, indicating that advanced disease was not reflected by broad ecological restructuring. Feature-level analysis instead identified a genome-resolved MAG profile. To prioritize robust candidates, we combined two complementary approaches: random forest (RF) stability selection, which identified 24 MAGs with reproducibly high classification importance across resampled folds, and covariate-adjusted MaAsLin2 differential-abundance testing. Intersecting the results of both approaches prioritized three MAGs supported by each method: one Escherichia coli MAG enriched in Wagner 4 and two Collinsella MAGs depleted in Wagner 4. This three-MAG signature (out-of-bag AUC = 0.703) retained much of the discriminatory information captured by the broader 24-MAG RF classifier, with concordant, opposing abundance directions across classifier interpretation, differential-abundance testing, and per-MAG abundance distributions. Functional annotation further separated the Wagner 4-enriched Escherichia coli from the Collinsella MAGs. The Escherichia coli MAG carried antibiotic-resistance and virulence-factor signals and encoded respiratory metabolic capacity, whereas the two Collinsella MAGs lacked detectable resistance and virulence hits and showed metabolically compact profiles. Exploratory clinical association analysis linked the E. coli-Collinsella abundance score to longer DFU duration, consistent with a gut microbial correlate of chronic or advanced disease burden. These findings support longitudinal gut metagenomic validation to determine whether this signal tracks DFU progression, treatment response, or recovery.},
}

Humans
*Escherichia coli/genetics
*Diabetic Foot/microbiology
*Metagenomics/methods
*Diabetes Mellitus, Type 2/complications/microbiology
*Gastrointestinal Microbiome/genetics
*Actinobacteria/genetics
Metagenome
Male
Female
Feces/microbiology

@article {pmid42755640,
year = {2026},
author = {Speeckaert, MM and Delanghe, JR},
title = {Editorial: Community series in gut feelings: investigating the link between microbiota and kidney disease progression, volume II.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1915260},
pmid = {42755640},
issn = {1664-3224},
}

@article {pmid42755725,
year = {2026},
author = {Sharma, I and Barman, R and Kashyap, S and Patowary, A and Parasar, BJ and Jyoti, P and Agarwala, N},
title = {Global meta-analysis of drought associated rice rhizosphere microbiome data and soil application of selected bacteria reveals potential of Pantoea dispersa for drought stress alleviation in rice plants.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1904089},
pmid = {42755725},
issn = {1664-462X},
abstract = {INTRODUCTION: Drought stress poses a significant threat to global rice productivity, jeopardizing crop yield and food security, particularly in water-limited agroecosystems. The application of plant-associated microbes to enhance drought resilience in crops has gained considerable attention in recent years. However, systematic investigation on changes in rice rhizosphere microbial diversity under drought stress remains limited. This study aimed to identify drought-responsive bacterial taxa and evaluate selected rice rhizosphere bacteria for their potential to enhance drought tolerance in rice.

METHODS: A meta-analysis of 16S rRNA amplicon sequencing datasets from rice drought-associated studies was conducted to identify drought-responsive bacterial taxa. Based on the findings of meta-analysis and previous literature, five pre-isolated rice rhizospheric bacterial strains belonging to the genera Streptomyces, Burkholderia, Pantoea, Pseudomonas, and Variovorax were selected and characterized for key plant growth-promoting traits and osmotic stress tolerance using 25% of PEG. The selected isolates were subsequently evaluated for their potential to enhance drought tolerance in two Indian rice varieties, CR Dhan 802 (drought-tolerant) and Ranjit (drought-susceptible) under pot conditions.

RESULTS: Based on meta-analysis of 16S amplicon datasets and literature review bacterial isolates possessing drought tolerance and plant growth-promoting traits, were selected for the pot experiments. Soil inoculation with selected bacterial strains showed that the treatment groups Pantoea dispersa NA-08, Burkholderia cepacia NA-07, and Consortium-I (S. jiujiangensis NA-06, B. cepacia NA-07 and P. dispersa NA-08) alleviated drought stress in both the rice varieties. Furthermore, these treatment groups showed significant enhancement in plant anti-oxidative and soil enzymatic activities. However, the treatments with Streptomyces jiujiangensis NA-06 and Variovorax guangxiensis NA-16 exhibited growth promotion in rice plants, but no significant alleviation of drought stress was observed.

CONCLUSION: The isolate P. dispersa NA-08 showed the higher potential for enhancing rice drought tolerance in pot experiments and might serve as a promising isolate for evaluation under field conditions.},
}

@article {pmid42755786,
year = {2026},
author = {Xiang, X and Zhai, X and Lei, Y and Feng, J and Wang, Q},
title = {The effectiveness of the intervention model based on cognitive behavioral therapy in reducing risky sexual behaviors among MSM.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1870879},
pmid = {42755786},
issn = {2296-2565},
mesh = {Humans ; *Cognitive Behavioral Therapy/methods ; Male ; *Homosexuality, Male/psychology ; *Risk-Taking ; Adult ; *Sexual Behavior/psychology ; *Unsafe Sex/prevention & control ; },
abstract = {METHODS: Based on CBT theory and the Internet, we established an intervention model targeting high-risk sexual behavior patterns in MSM. We then conducted a randomized controlled trial (n = 50) to assess the impact of the CBT-based intervention on high-risk sexual behaviors and gut microbiota changes in this population.

RESULTS: Prior to the implementation of the intervention, 44% of the participants engaged in high-risk behaviors despite having better cognitive levels. However, preliminary findings from post-intervention investigations indicate that intervention measures based on CBT demonstrate greater efficacy compared to traditional methods. After intervention with CBT, the incidence of unprotected anal intercourse in the intervention group was significantly reduced compared to the control group (p = 0.016). Some bacterial taxa (e.g., Bifidobacterium longum and Prevotella) showed potential associations with behavioral changes following CBT; however, these microbiome-related findings are exploratory and hypothesis-generating, not conclusive.

CONCLUSION: The high-risk sexual behaviors of MSM increase health risks. However, the method of intervention through the CBT courses can effectively correct the deviation between the cognition and practice. In this process, changes in gut microbiota were observed to be potentially associated with behavioral changes, but these associations are preliminary and warrant further investigation in confirmatory studies.},
}

Humans
*Cognitive Behavioral Therapy/methods
Male
*Homosexuality, Male/psychology
*Risk-Taking
Adult
*Sexual Behavior/psychology
*Unsafe Sex/prevention & control

@article {pmid42755803,
year = {2026},
author = {Marjanović, M and Maletin, N and Kukić, B and Nikolić, I and Petrović, N and Radić, J and Đurić, A and Knezević, M and Dejanović, B and Ćalić, V},
title = {Gut microbiome-mediated primary and acquired resistance to immune checkpoint inhibitors in MSI-H/dMMR colorectal cancer: mechanisms, biomarkers, and therapeutic implications-a narrative review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1907957},
pmid = {42755803},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/drug therapy/genetics/immunology/microbiology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/immunology ; *Drug Resistance, Neoplasm ; Microsatellite Instability ; Tumor Microenvironment/immunology ; DNA Mismatch Repair ; Animals ; Biomarkers, Tumor ; },
abstract = {INTRODUCTION: Immune checkpoint inhibitors (ICIs) have transformed the management of microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) colorectal cancer (CRC). However, a substantial proportion of patients exhibit primary resistance or eventually develop acquired resistance, highlighting the need for a better understanding of the biological mechanisms influencing therapeutic response. Increasing evidence suggests that the gut microbiome-immune axis is an important regulator of antitumor immunity through complex interactions among microbial communities, microbial metabolites, host immunity, and the tumor microenvironment.

MAIN BODY: This narrative review summarizes current evidence regarding the role of the gut microbiome-immune axis in mediating primary and acquired resistance to immune checkpoint inhibition in MSI-H/dMMR CRC. We discuss the physiological interactions that maintain immune homeostasis and review the functional mechanisms through which alterations in microbial metabolic pathways, including short-chain fatty acids, bile acids, tryptophan-derived metabolites, inosine, and polyamines, may influence antitumor immune responses. We further examine microbial composition and functional biomarkers associated with immune checkpoint inhibitor response, together with emerging therapeutic strategies aimed at modulating the gut microbiome-immune axis, including dietary interventions, prebiotics, probiotics, selective antimicrobial approaches, fecal microbiota transplantation, live biotherapeutic products, and next-generation precision microbiome engineering. Finally, we discuss current translational challenges and future research priorities required for successful clinical implementation.

CONCLUSION: The gut microbiome-immune axis represents a promising area of investigation for understanding resistance to immune checkpoint inhibition in MSI-H/dMMR CRC. While growing evidence supports its biological relevance, much of the current knowledge remains preclinical or is derived from early-phase clinical studies. Future progress will depend on mechanistic investigation, longitudinal multi-omic microbiome profiling, standardized methodologies, prospective biomarker validation, and the rational development of microbiome-directed therapeutic strategies to support precision immuno-oncology.},
}

Humans
*Colorectal Neoplasms/drug therapy/genetics/immunology/microbiology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/immunology
*Drug Resistance, Neoplasm
Microsatellite Instability
Tumor Microenvironment/immunology
DNA Mismatch Repair
Animals
Biomarkers, Tumor

@article {pmid42755879,
year = {2026},
author = {Juhász, Á and Wazzani, Y and Tavaszi-Sárosi, S and Patonay, K and Olasz, F and Posta, K},
title = {Rhizosphere bacterial and fungal community structure varies among field-grown Mentha spicata accession plots with different essential oil profiles.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1939529},
pmid = {42755879},
issn = {1664-302X},
abstract = {INTRODUCTION: Aromatic plants produce diverse secondary metabolites, yet how within-species phytochemical variation relates to rhizosphere bacterial and fungal communities remains poorly resolved. Mentha spicata displays substantial essential oil (EO) compositional variation, providing a field system to examine rhizosphere microbiome structuring among accession plots.

METHODS: Five vegetatively propagated M. spicata accessions representing three operational EO-based groups (L-carvone group, Piperitenone oxide group, and Dihydrocarvone group) were examined under open-field conditions at full flowering. Each accession was grown in a single field plot, from which three spatially separated rhizosphere soil samples were collected; managed inter-row bulk soil was included as a contextual control. Soil physicochemical properties, aerial-tissue EO composition, and bacterial 16S ribosomal RNA gene and fungal ITS amplicon profiles were characterized. Bray-Curtis ordination, permutational multivariate analysis of variance, and distance-based redundancy analysis were used to assess community differences and associations with soil properties and accession-level EO profiles.

RESULTS: Bacterial communities were dominated by Actinomycetota, Pseudomonadota, Chloroflexota, Acidobacteriota and Bacillota, whereas fungal communities were dominated by Ascomycota, followed by Mortierellomycota and Basidiomycota. Fungal taxonomic profiles varied more strongly among groups, with J14 showing the highest Ascomycota proportion and Basidiomycota being most abundant in J7 and J11. Alpha-diversity differences were limited and, for bacteria, mainly reflected lower diversity in bulk soil. After excluding bulk soil, grouping by accession plot remained significant for bacteria (R[2] = 0.6619, p = 0.0001) and fungi (R[2] = 0.5060, p = 0.0001), with bacterial communities showing more compact structuring. Soil-based constrained models were significant for both microbial groups. pH and nitrate + nitrite nitrogen were significantly associated with bacterial and fungal community composition, while humus content was additionally significant for fungi. In contrast, accession-level models based on aerial-tissue EO gradients were not significant for bacteria (p = 0.342) or fungi (p = 0.317).

DISCUSSION: Field-grown M. spicata accession plots with contrasting aerial-tissue EO profiles harbored differentiated rhizosphere bacterial and fungal communities, and community variation was significantly associated with local soil properties. A statistically supported relationship with aerial-tissue EO composition was not detected, and these profiles are best regarded as accession-level chemical descriptors rather than direct rhizosphere drivers.},
}

@article {pmid42755889,
year = {2026},
author = {Yin, S and Jing, C and Dai, C and Zhou, X and Ai, J and Sun, H},
title = {Microbiome-metabolome interaction reveals rhizosphere ecological, bioactive, and antioxidant responses of Paeonia lactiflora Pall. to intercropping and harvest timing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1934798},
pmid = {42755889},
issn = {1664-302X},
abstract = {Paeonia lactiflora Pall. (P. lactiflora) is a medicinal plant with considerable economic value. During its growth, root secondary metabolism and rhizosphere microbes interact closely; however, no systematic study has examined microbiome and metabolome dynamics under different planting systems and harvest times. To address this, we employed amplicon sequencing for microbial diversity and untargeted metabolomics for metabolite profiling. The datasets were then integrated, and correlation analysis was performed. We measured paeoniflorin by high-performance liquid chromatography (HPLC), total phenolic content by the Folin-Ciocalteu method, total flavonoid content by the NaNO2-Al(NO3)3 method, and antioxidant activity by DPPH, ABTS, hydroxyl radical scavenging, and FRAP assays. The results revealed that Proteobacteria was the most abundant phylum in the bacterial community, and among classified genera, Subgroup_2 exhibited the highest relative abundance. In the fungal community, Ascomycota dominated at the phylum level, while Coniosporium was the most abundant genus. Metabolomic analysis revealed clear separation among sample groups by principal component analysis. Four pairwise comparisons identified differential metabolites predominantly classified as lipids, phenylpropanoids, and polyketides. Functional enrichment analysis indicated that these differences were mainly associated with metabolic pathways, particularly amino acid metabolism, secondary metabolite biosynthesis, and ABC transporters. Furthermore, monoculture with late-stage harvest (CS-4) represented the optimal strategy for maximizing medicinal quality. Under intercropping, mid-stage harvest (TZ-2/TZ-3), with adjustments based on annual climatic conditions, is recommended to balance quality and ecological benefits. Collectively, these findings reveal differences in P. lactiflora across planting systems and harvest periods, providing a theoretical basis for the optimization of cultivation strategies.},
}

@article {pmid42755905,
year = {2026},
author = {Beyzaei, Z and Weiskirchen, R},
title = {Microplastics in food production systems: Sources, exposure pathways, and gastrointestinal health effects.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101557},
pmid = {42755905},
issn = {2665-9271},
abstract = {Microplastics (MPs) and nanoplastics (NPs) have become ubiquitous contaminants in food production systems, raising increasing concerns regarding their potential effects on gastrointestinal and systemic health. This review summarizes current evidence on the occurrence, sources, and biological effects of MPs/NPs within food production chains and their implications for the human gut. Experimental in vitro studies demonstrate that MPs/NPs can induce oxidative stress, inflammation, genotoxicity, metabolic dysregulation, and epithelial barrier dysfunction, while in vivo animal studies show disruption of gut homeostasis, microbiota alterations, systemic translocation, and hepatic, metabolic, and immune disturbances. Co-exposure to environmental pollutants and food-associated chemicals may further enhance toxicity through synergistic mechanisms. Although human evidence remains limited, MPs have been detected in human tissues, including the liver, indicating the possibility of systemic exposure. Emerging evidence also suggests complex interactions between MPs/NPs and the gut microbiome, although the clinical significance of these findings remains uncertain. Therefore, current knowledge is derived predominantly from experimental models, and substantial uncertainties remain regarding human exposure levels, dose-response relationships, and long-term health consequences. Further well-designed human studies and standardized exposure assessment methods are essential to clarify the health risks associated with dietary MPs/NPs.},
}

@article {pmid42755932,
year = {2026},
author = {Pascual, J and Martínez-Blanch, JF and Amaro, C and Roig, FJ},
title = {Editorial: Advances in immunity and microbiome: exploring key interactions and innovations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1933468},
doi = {10.3389/fimmu.2026.1933468},
pmid = {42755932},
issn = {1664-3224},
}

@article {pmid42755999,
year = {2026},
author = {Feole, B and Grouzdev, D and Pales Espinosa, E and Cacot, G and Allam, B},
title = {Sampling method influences hemolymph bacterial communities in the eastern oyster, Crassostrea virginica.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1862013},
pmid = {42755999},
issn = {1664-302X},
abstract = {As the microbiome becomes increasingly recognized for its role in driving animal health and disease, accurate characterization of microbial community composition is essential. With this research comes the critical need for standardized sampling methods along with an understanding of the biases inherent to these methods. In oysters, hemolymph is a valuable system for microbiome research due to its diverse physiological functions, role as an indicator of health, and ease of collection. Unfortunately, much of the current literature regarding oyster hemolymph microbiome composition is opaque in its description of tissue collection methods. When these methods are clearly described, investigators often collect hemolymph via a needle inserted into the adductor muscle through a notch cut in the shell. However, due to the needle's movement through soft tissues and mucous membranes exposed to the surrounding seawater, this notch method carries significant risk of sample contamination. An alternative hemolymph sampling method, hereafter referred to as the hole method, minimizes this potential contamination as the needle is inserted through a hole drilled in the shell directly above the adductor muscle, circumventing other soft tissues. Here, we tested whether notch and hole hemolymph collection methods produce different 16S rRNA bacterial community profiles in C. virginica. To compare these two sampling methods and evaluate the potential method-specific biases, particularly biases that may result from tissue contamination, oysters had hemolymph collected through both a notch and hole while alternating method order. Following taxonomic classification and differential abundance analysis of the resultant 16S rRNA sequences, the presence of disproportionate Vibrio spp. enrichment in notch-associated samples was evident. Notch-collected samples yielded significantly higher 16S rRNA gene copy numbers (p = 0.037) and a 16-fold higher relative abundance of Vibrio spp. compared to hole-collected samples (52.6% vs. 3.2%, p adj = 0.006) despite no significant change in absolute counts of the dominant genus Poseidonibacter. Overall, this analysis demonstrates both the potential of the hole sampling method and the need for microbiome researchers to account for biases in bacterial community composition associated with their chosen sampling method.},
}

@article {pmid42756118,
year = {2026},
author = {Xiong, S and Yao, R},
title = {Klebsiella pneumoniae in inflammatory bowel disease and rectal cancer: from gut inflammation to a potential driver of carcinogenesis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1948813},
pmid = {42756118},
issn = {1664-302X},
abstract = {The gut microbiota is a critical modulator of intestinal inflammation and colorectal cancer (CRC), yet the specific microbial drivers that bridge inflammatory bowel disease (IBD) to rectal carcinogenesis remain poorly defined. Klebsiella pneumoniae (K. pneumoniae) has recently emerged as a compelling candidate at this nexus; however, several critical questions remain unresolved: (i) whether K. pneumoniae colonization is a cause or a consequence of rectal carcinogenesis; (ii) how strain level heterogeneity determines pathogenic versus commensal outcomes; and (iii) which rectal microenvironmental factors selectively amplify its carcinogenic potential. Moreover, the potential utility of persistent colonization with carcinogenic K. pneumoniae strains as a predictive biomarker and target for chemoprevention warrants further investigation. This review systematically addresses these questions by integrating findings from microbial ecology, virulence factor biology, host immunology, and oncogenic signaling. We dissect the dual role of K. pneumoniae along the inflammation cancer axis, focusing on its capacity to promote T helper 17 (Th17) driven inflammation, disrupt the epithelial barrier, and directly alkylate host DNA via colibactin-like genotoxins. We propose a mechanistic framework in which chronic K. pneumoniae colonization acts as a bridge between IBD activity and rectal tumorigenesis, and we critically evaluate the potential of phage therapy, virulence inhibitors, and microbiome-based biomarkers to intercept this process. Finally, we highlight key knowledge gaps and outline future directions required to establish causality and translate these insights into clinical strategies for IBD associated rectal cancer prevention.},
}

@article {pmid42756159,
year = {2026},
author = {Jiang, P and Zhou, M and Liao, Y and Du, W and Liu, M},
title = {Associations of the gut mycobiome and its cross-kingdom interactions with estrus return in post-weaning sows revealed by metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1892244},
pmid = {42756159},
issn = {1664-302X},
abstract = {Post-weaning estrus return is a critical determinant of reproductive efficiency in the swine industry. While the gut microbiome, particularly bacteria, has been significantly associated with estrus return in sows, the role of the gut mycobiome and its cross-kingdom interactions with bacteria in this context remains largely unexplored. Here, we employed fecal metagenomics to characterize the gut mycobiome in 85 sows and investigated its association with post-weaning estrus return. A total of 22 fungal species were significantly associated with estrus return. Normal-return sows were characterized by increased abundance of Arxiozyma slooffiae (formerly Kazachstania slooffiae) and decreased abundances of Malassezia pachydermatis and Alternaria rosae. Moreover, we uncovered cross-kingdom interactions between fungi and bacteria associated with estrus return, where Arxiozyma slooffiae showed a positive correlation with Prevotella spp. enriched in normal-return sows. These interactions were predicted to involve the exchange of metabolites, including Fe[2+], thiamine, and nicotinate. Fungal biomarkers demonstrated good discriminatory power for distinguishing normal-return and non-return sows (AUC = 0.906), and the combination with bacterial biomarkers further enhanced the performance (AUC = 0.947). Integrated multi-omics analysis revealed extensive associations between gut fungi and hormones and hormone-related compounds, as well as microbial functional pathways. Notably, Arxiozyma slooffiae was positively correlated with phytoestrogens (including daidzein and genistein) and the steroid hormone biosynthesis pathway but negatively correlated with testosterone. Collectively, these findings provide comprehensive insights into the role of the gut mycobiome and its cross-kingdom interactions in sow reproductive performance.},
}

@article {pmid42756188,
year = {2026},
author = {Kang, JI and Park, CI and Seo, JH and Kang, CS and Kim, YK and Kim, SJ},
title = {Pre-treatment serum extracellular vesicle-enriched microbiome profiles and SSRI treatment response in obsessive-compulsive disorder: a prospective naturalistic cohort study.},
journal = {Frontiers in psychiatry},
volume = {17},
number = {},
pages = {1913728},
pmid = {42756188},
issn = {1664-0640},
abstract = {OBJECTIVE: The microbiome is emerging as an important component of brain-body communication and may influence treatment outcomes in psychiatric disorders. This naturalistic cohort study prospectively evaluated whether baseline microbiome abundance and composition of circulating bacterial extracellular vesicles (EVs) are associated with subsequent response to selective serotonin reuptake inhibitors (SSRIs) in patients with obsessive-compulsive disorder (OCD).

METHODS: Thirty-two drug-naïve or medication-free patients with OCD were enrolled and assessed at baseline and at 12 weeks following the initiation of SSRI pharmacotherapy. Serum EV microbiome profiling was performed at baseline, before any pharmacological treatment was commenced, ensuring that all biological measurements reflect a pharmacologically unconfounded pre-treatment state. Good responders were defined as patients with a 35% or greater reduction in the Yale-Brown Obsessive-Compulsive Scale score at 12 weeks, while poor responders were defined as those with less than a 35% reduction. Baseline microbiome abundance and composition of circulating bacterial EVs in serum were compared between these groups.

RESULTS: Of the 32 participants, 29 completed the 12-week study. Based on the treatment response at 12 weeks, the OCD group was classified into 15 good responders (5 females) and 14 poor responders (7 females). The two groups did not differ significantly in age, sex, age of onset, baseline Y-BOCS or MADRS scores, or medication type. No significant differences in alpha or beta diversity were observed between the groups. Taxonomic analysis of pre-treatment serum EV profiles revealed a nominally higher relative abundance of the genus Acinetobacter in patients who subsequently showed poor response compared to good responders. However, this association did not remain statistically significant after correction for multiple comparisons, age adjustment, or compositionally-aware reanalysis.

CONCLUSION: These results provide no statistically defensible evidence of a taxon-level microbiome difference between response groups, and the nominal Acinetobacter finding should not be regarded as a validated biomarker. Global diversity measures also did not distinguish the response groups. These findings are hypothesis-generating and support the feasibility of pre-treatment serum EV-associated bacterial profiling in OCD. Larger, adequately powered studies incorporating compositionally appropriate statistical methods and rigorous contamination-control procedures are warranted to determine whether reproducible microbiome-treatment response associations exist.},
}

@article {pmid42756190,
year = {2026},
author = {Liu, S and Feng, S and Yuan, Z and Mei, Z and Yin, J and Chen, L and Zhang, Y},
title = {The effects of maternal dietary fiber and short-chain fatty acids on the health of offspring: a mini review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1867014},
pmid = {42756190},
issn = {2296-861X},
abstract = {Maternal nutrition during pregnancy is a critical determinant of offspring long-term health. Dietary fiber has emerged as a key modifiable factor. Through gut microbial fermentation, fiber is converted into short-chain fatty acids (SCFAs), primarily acetate, propionate, and butyrate. This mini review synthesizes current evidence from molecular, animal, and human studies on the role of maternal SCFAs in programming offspring metabolic and immune health. Mechanistically, SCFAs act via two complementary pathways: activation of G protein-coupled receptors (GPCRs) and inhibition of histone deacetylases, leading to rapid signaling and long-term epigenetic regulation. Animal studies demonstrate that maternal fiber deprivation impairs offspring glucose metabolism, promotes low-grade inflammation and obesity, and compromises immune tolerance, whereas fiber or short-chain fatty acid (SCFA) supplementation confers protective effects. Human observational studies support these findings, showing associations between maternal SCFA levels and favorable neonatal metabolic profiles, neurodevelopmental outcomes, and reduced obesity risk, although randomized controlled trials remain limited. Key translational challenges include inter-species differences, individual microbiome variability, and optimal intervention timing. Despite these uncertainties, promoting adequate and diverse dietary fiber intake during pregnancy represents a safe, low-cost, and scalable public health strategy to improve intergenerational health outcomes.},
}

@article {pmid42756193,
year = {2026},
author = {Nguyen, ADD and Kern, R and Dombrovski, T and LaFramboise, T},
title = {The circulating metatranscriptome in acute myeloid leukemia patients: an RNA-seq reanalysis.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1903806},
pmid = {42756193},
issn = {2813-4338},
abstract = {The human microbiome comprises the collection of microbiota residing on or within human tissues. It is now well-established that microbial composition impacts an individual's health. In the cancer realm, the vast majority of microbiome studies have been focused either on the gut, or at the site of solid tumors. Few studies have assessed microbial content at the site of hematological malignancies - blood and bone marrow. Here we characterize the circulating metatranscriptome (i.e. the bacterial and viral RNA in circulation) of 411 patients with acute myeloid leukemia (AML). We find that the circulating metatranscriptome in AML differs substantially from that of healthy controls, and high metatranscriptome loads are associated with antibacterial host response. We observe that specific bacterial genera are associated with response to anti-cancer therapy and disease history, and are tied to host gene expression signatures of heme metabolism. Overall, our study represents an inferred landscape of circulating microbial RNA in AML and suggests potential for its use as a biomarker.},
}

@article {pmid42756390,
year = {2026},
author = {Osawa, R and Inoue, J and Fukuda, I and Shirai, Y and Kodama, Y},
title = {Function-based personalization of dietary fiber selection enhances gut microbial fermentation: a proof-of-concept crossover trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1907988},
pmid = {42756390},
issn = {2296-861X},
abstract = {UNLABELLED: Text Responses to dietary fiber supplementation vary markedly among individuals, yet no validated platform exists to prospectively identify optimal fiber types based on individual gut microbiome function. Here we present My Dietary Fiber Finder (MyDFF), an ex vivo functional screening platform that predicts optimal dietary fibers for individual gut microbiomes through direct fermentation profiling. For each participant, the dietary fiber with the highest saccharification index (SI) was designated M-PDF, and that with the lowest SI was designated L-PDF. In a crossover trial involving eight healthy Japanese adults (72 longitudinal observations, each participant serving as their own control), the pre-specified per-participant analysis (Dunnett's test) showed that M-PDF significantly increased fecal volatile fatty acid (VFA; acetate + propionate + butyrate) concentrations over baseline in two of eight participants and total short-chain fatty acid (SCFA) concentrations in one, whereas the non-personalized fiber (L-PDF) did so in none. Post hoc group-level analysis confirmed a significant increase over baseline for M-PDF (total VFA and total SCFA, both p < 0.01) but not for L-PDF, and in a within-participant comparison M-PDF exceeded L-PDF in seven of eight participants (mean difference = 32.4 μmol/g; 95% CI: 8.7-56.1; p = 0.014; Cohen's d = 1.14). However, the magnitude of the pre-intervention saccharification-index differential between the two fibers did not significantly correlate with the magnitude of the in vivo VFA response differential across participants (Pearson r = 0.082, p = 0.85), indicating that the assay did not quantitatively predict response magnitude. Exploratory 16S rRNA gene sequencing analysis showed no significant cohort-level shift in overall gut microbial community composition during either intervention phase. In four separate validation donors, individual fermentation profiles remained relatively stable over the observed 3-9-month follow-up. These proof-of-concept findings support the potential of function-based framework for personalized prebiotic design and motivate larger validation studies.

CLINICAL TRIAL REGISTRATION: https://jrct.niph.go.jp, identifier jRCTs051220163.},
}

@article {pmid42756392,
year = {2026},
author = {Chen, Z and Du, Y and Li, H and Wen, X and Chen, L and Wang, W and Wu, P},
title = {Amended engineered soil promotes coordinated soil-plant-microbiome responses during early-stage slope restoration.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1918442},
pmid = {42756392},
issn = {2296-4185},
abstract = {Amended Engineered Soil (AES), a functional substrate incorporating biomass-derived straw fiber, has been applied for the ecological restoration of degraded slopes. However, how AES affects the coordinated responses of substrate structure, root development, and rhizosphere microbiome assembly during early-stage restoration remains unclear. In this study, AES and Conventional Engineered Soil (CES) were compared during a 90-day slope restoration experiment using Lolium perenne as the target species. Compared with CES, AES substantially improved substrate moisture and nutrient conditions, with water content increasing from approximately 10.4%-16.6% and available phosphorus increasing more than fivefold. AES also promoted the formation of large water-stable aggregates, indicating improved structural stability of the reconstructed substrate. These changes were accompanied by marked improvements in vegetation establishment, including a 18.4% increase in plant height, more than 40% increase in dry biomass, and a pronounced increase in root length. Root tensile strength was also enhanced, suggesting greater belowground reinforcement. AES significantly increased bacterial richness and Shannon diversity, whereas the fungal response was mainly reflected in increased richness rather than diversity. Correlation analysis further showed close associations among substrate nutrient conditions, plant growth, root reinforcement, and microbial diversity. These findings suggest that AES promotes early-stage slope restoration through the coordinated improvement of substrate quality, vegetation establishment, root development, and rhizosphere microbial communities, while providing a sustainable pathway for biomass resource utilization.},
}

@article {pmid42756418,
year = {2026},
author = {Soufla, A and Fragoulis, GE and Iliopoulos, A},
title = {Diagnostic Pitfall: Prolonged COVID-19 Presenting as Organising Pneumonia in a Rituximab-Treated Patient with Rheumatoid Arthritis.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {3},
pages = {619-621},
pmid = {42756418},
issn = {2529-198X},
abstract = {Rituximab (RTX)-induced B-cell depletion is associated with prolonged SARS-CoV-2 infection. We describe a case of persistent COVID-19 in a patient with rheumatoid arthritis (RA) initially misdiagnosed as cryptogenic organising pneumonia (COP), highlighting the diagnostic and management challenges in RTX-treated patients. Retreatment with a second 5-day course of nirmatrelvir/ritonavir led to rapid clinical improvement and complete radiological resolution. Persistent SARS-CoV-2 infection should be considered in RTX-treated patients with non-resolving pulmonary infiltrates, particularly when corticosteroid therapy is ineffective.},
}

@article {pmid42756631,
year = {2026},
author = {Theiopoulou, DC and Vassilopoulos, D and Mavragani, CP and Bertsias, G},
title = {The Gut Microbiota in Rheumatoid Arthritis: Evaluation of Microbial Profiles, Disease Activity, Biomarkers, and Treatment Response.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {3},
pages = {469-480},
pmid = {42756631},
issn = {2529-198X},
abstract = {OBJECTIVES: Rheumatoid arthritis (RA) is a chronic autoimmune disease with complex etiopathogenesis, and variable clinical course. The human gastrointestinal (GI) tract is a dynamic ecosystem in which micro-organisms influence metabolism, immune signalling, and pathogen resistance. Understanding these interactions is key to exploring the microbiota's role in RA. This review examines how intestinal and oral microbiota differ in RA patients and influence disease activity and treatment response.

METHOD: A literature search was conducted using PubMed, from inception until January 3, 2025. Studies were selected based on the inclusion of original research involving human subjects diagnosed with RA. Exclusion criteria comprised reviews, case reports, animal studies, and studies with insufficient data. Of the 329 records identified, 72 were included in this review.

RESULTS: Most studies have implicated changes in bacterial composition involving specific phyla in RA-associated dysbiosis. The imbalance is primarily driven by alterations in the phyla Bacillota, Pseudomonadota, and Bacteroidota, with Bacillota and Pseudomonadota accounting for 70% of increased taxa, and Bacillota and Bacteroidota for 83% of decreased intestinal taxa. Other findings include reduced α-diversity in seronegative patients and associations between decreased Prevotella taxa and higher disease activity, inflammation biomarkers, and autoantibodies. Smaller studies have also reported elevated serum zonulin-a marker of intestinal permeability-in RF-positive patients.

CONCLUSION: This review highlights key bacterial phyla linked to RA and emphasises the potential of probing gut micro-biota-immune system interactions to improve diagnosis and treatment.},
}

@article {pmid42756659,
year = {2026},
author = {Abdelmaksoud, A and Igoe, A and AbdAlnaeem, MA and Toraih, EA and Roller, BA and Kaelber, KL and Kaelber, DC},
title = {Increased Risk of Gout among Patients with Trisomy 21: Insights from a Population-Based Study of over 30,000 Patients with Trisomy 21.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {3},
pages = {590-597},
pmid = {42756659},
issn = {2529-198X},
abstract = {BACKGROUND: Primary trisomy 21 is associated with an elevated incidence of conditions such as cardiac anomalies, hypothyroidism, type 1 diabetes mellitus, and auditory impairments. However, the potential association between trisomy 21 and gout remains insufficiently studied, with existing evidence largely limited to case reports. This study aimed to determine the prevalence of gout among individuals with trisomy 21 and compare it with those without trisomy 21 to evaluate a potential association and examine demographic factors influencing gout risk.

METHODS: This retrospective analysis utilised electronic health records from the US Collaborative Network within the TriNetX clinical research platform, representing over 100 million patients. We identified 30,171 individuals with trisomy 21 and compared them with 3,502,718 non-trisomy 21 controls using propensity score matching. Gout prevalence and relative risk (RR) with 95% confidence intervals (CI) were assessed between groups.

FINDINGS: Patients with trisomy 21 exhibited higher gout prevalence than controls (2.90% vs 1.05%, p < 0.0001). The relative risk of gout was 2.76 in individuals with trisomy 21 compared with controls (95% CI 2.43-3.14). Increased risk persisted across age, sex, and racial groups.

INTERPRETATION: These findings demonstrate an association between trisomy 21 and increased risk of gout. Further research is needed to understand the underlying mechanisms and inform targeted screening and management strategies in this population.},
}

@article {pmid42756774,
year = {2026},
author = {Huang, Z and Dai, Z and Liu, Q},
title = {Efficacy and safety of fecal microbiota transplantation for chronic constipation: a systematic review and meta-analysis integrating pre-post and single-arm evidence.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1900353},
pmid = {42756774},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic constipation is a common functional gastrointestinal disorder with a global prevalence of 12%-17%. Conventional treatments have limited efficacy for refractory cases, with high recurrence and side effects. Fecal microbiota transplantation (FMT) offers a novel strategy by restoring gut microecological balance, yet its efficacy requires systematic evaluation. This meta-analysis evaluated FMT efficacy and safety through an innovative "three-in-one" framework.

METHODS: We systematically searched CENTRAL, PubMed, Embase, and CNKI for RCTs, single-arm studies, and cohort studies. The framework comprised: (1) RCT random-effects meta-analysis; (2) single-arm proportional meta-analysis with Freeman-Tukey transformation; (3) pre-post paired sensitivity analysis (r = 0.5, with sensitivity tests at r = 0.3, 0.7, 0.9). Publication bias was assessed via Egger, Harbord, trim-and-fill, and fail-safe N tests.

RESULTS: 12 RCTs (n = 1040), 16 single-arm studies (n = 403), and 4 cohort studies (n = 422) were included. After trim-and-fill adjustment for publication bias, FMT was associated with a clinical total response rate of RR = 1.21 (95% CI: 1.10-1.33). The unadjusted pooled estimate was RR = 1.36 (95% CI: 1.21-1.52, P < 0.001); however, the Harbord test indicated potential publication bias (P = 0.003), necessitating this correction. Wexner score improved (MD = -2.08, 95% CI: -3.35 to -0.81, P = 0.003). Among the 16 single-arm studies, 8 (n = 249) reported remission/improvement rates, showing a remission rate of 51.7% (95% CI: 40.3%-62.9%) and paired pre-post improvements in BSFS, Wexner, and PAC-QOL; these within-group changes cannot establish causal efficacy. During follow-up periods of up to 24 weeks, no serious adverse events were reported; long-term safety data are lacking.

CONCLUSION: Current evidence suggests FMT is a promising therapeutic option for chronic constipation, with an adjusted clinical total response rate of RR = 1.21 (95% CI: 1.10-1.33) after correction for publication bias. While FMT was associated with improvements in symptom scores, quality of life, and intestinal function, the evidence quality is limited by publication bias, high heterogeneity, and high risk of bias in all included RCTs. More high-quality, sham-controlled RCTs are needed to validate these findings.

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD420261394673, identifier: CRD420261394673.},
}

@article {pmid42756821,
year = {2026},
author = {Xie, F and He, X and Chen, W and Li, J and Lin, S and Bao, Q and Li, W and Cheng, J and Ma, Y and Wu, Z and Li, H},
title = {Integrative multi-omics analysis prioritizes compartment-specific candidate targets of gut microbiota metabolites in diabetic kidney disease.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1925910},
pmid = {42756821},
issn = {1664-3224},
mesh = {*Diabetic Nephropathies/metabolism/microbiology/genetics ; Humans ; Multiomics ; *Gastrointestinal Microbiome ; Molecular Docking Simulation ; Gene Expression Profiling ; *Metabolome ; Gene Regulatory Networks ; },
abstract = {OBJECTIVE: The gut-kidney axis has emerged as a critical area of investigation. However, the compartment-specific regulatory mechanisms of gut microbiota metabolites within the glomerular and tubulointerstitial regions of diabetic kidney disease (DKD) remain incompletely understood.

METHODS: The gutMGene, SEA, STP, GEO, Nephroseq v5, and KIT databases were interrogated. Multi-omics and experimental approaches were applied, involving differential expression analysis, Weighted Gene Co-expression Network Analysis (WGCNA), machine learning, Mendelian randomization (MR), Gene Set Enrichment Analysis (GSEA), immune infiltration, gene set variation analysis (GSVA), clinical correlation, single-cell profiling, molecular docking, molecular dynamics simulation, CCK-8 assay, and RT-qPCR. The "Microbiota-Substrate-Metabolite-Target" (M-S-M-T) network was constructed for each compartment.

RESULTS: Machine learning identified six glomerular (IGFBP6, PLA2G4A, CTSK, HTR2B, PDGFRA, MMP7) and five tubulointerstitial (CA2, HSD11B2, NQO2, MMP7, CYP24A1) core genes. Mendelian randomization, single-cell profiling, and clinical cohorts provided supportive genetic and clinical evidence linking these genes to the estimated glomerular filtration rate (eGFR) and to DKD. Immune infiltration analysis and GSVA indicated a higher estimated proportion of M2 macrophages and a shift of the estimated mast cell composition from activated to resting states in both compartments, which correlated with core gene expression. Via the "M-S-M-T" network, drug-likeness and toxicity screening, caffeic acid and naringenin chalcone were prioritized as shared candidate metabolites. Molecular docking and molecular dynamics simulations suggested favorable in silico binding to HTR2B and MMP7. Both metabolites attenuated high glucose (HG)-induced core gene dysregulation in HK-2 cells and podocytes.

CONCLUSION: This study proposed a compartment-specific "M-S-M-T" regulatory network in the DKD glomerulus and tubulointerstitium. The shared metabolites caffeic acid and naringenin chalcone, which targeted HTR2B and MMP7, produced a preliminary protective transcriptional response in vitro. These findings are hypothesis-generating and require validation in real-world microbiome, metabolomic and in vivo studies before any therapeutic inference can be drawn.},
}

*Diabetic Nephropathies/metabolism/microbiology/genetics
Humans
Multiomics
*Gastrointestinal Microbiome
Molecular Docking Simulation
Gene Expression Profiling
*Metabolome
Gene Regulatory Networks

@article {pmid42756843,
year = {2026},
author = {Baune, BT},
title = {Pharmaco-multiomics in major depressive disorder: a narrative review and proposed translational framework for difficult-to-treat and treatment-resistant depression.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1934360},
pmid = {42756843},
issn = {1663-9812},
abstract = {BACKGROUND: Antidepressant prescribing in major depressive disorder (MDD) remains dominated by sequential trial and error, particularly when illness becomes difficult to treat (DTD) or meets conventional treatment-resistant depression (TRD) criteria.

OBJECTIVE: This narrative review evaluates pharmacogenomics (PGx), therapeutic drug monitoring (TDM), metabolomics/lipidomics, immune-inflammatory markers, proteomics, transcriptomics, epigenomics, microbiomics, and multi-omics machine learning according to their capacity to improve defined pharmacological decisions.

METHODS: Evidence was identified through structured PubMed/MEDLINE searches updated to 29 July 2026, targeted searches of ClinicalTrials.gov and the WHO International Clinical Trials Registry Platform, and backward and forward citation searching. The review was restricted to adult MDD and used author-assigned categories that distinguish prognostic, predictive, pharmacokinetic, and treatment-emergent monitoring markers and differentiate discovery, independent replication, external validation, and clinical utility. The article is a narrative Review, not a PRISMA systematic review; study selection, extraction, and translational classification were performed by one author without formal study-level risk-of-bias grading.

RESULTS: Most evidence derives from general adult MDD rather than prospectively defined DTD/TRD cohorts. Drug-specific, guideline-supported PGx and indication-specific TDM are the most clinically proximal molecular tools, but their value is bounded and depends on medication history, inhibitors and inducers, adherence, organ function, assay coverage, and phenoconversion. Commercial combinatorial PGx trials show small and sometimes nonpersistent clinical effects. Metabolomic, inflammatory, proteomic, transcriptomic, epigenomic, microbiomic, and integrated machine-learning studies identify plausible mechanisms and candidate predictors, but the majority remain discovery-stage or internally validated. Positive subgroup signals, including C-reactive protein-defined differential response, are counterbalanced by null prospective trials and inconsistent thresholds.

CONCLUSION: Current clinical application should remain limited to systematic medication and interaction review, drug-specific guideline-supported PGx, and indication-specific TDM. Dynamic omics layers should be treated as investigational until locked models are externally validated and prospective biomarker-guided strategies demonstrate incremental decision value, clinical benefit, feasibility, equity, and cost-effectiveness. The review proposes a future-state architecture and staged evidence-to-implementation framework for DTD/TRD.},
}

@article {pmid42756900,
year = {2026},
author = {Cheng, Y and Zhao, H and Lin, L and Chen, Y and Lin, H},
title = {Gut microbiota-host adaptive immune interactions in type 2 diabetes mellitus: mechanisms, disease progression, and microbiota-based therapeutic strategies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1934029},
pmid = {42756900},
issn = {1664-302X},
abstract = {Type 2 diabetes mellitus (T2DM) is a prevalent metabolic disorder whose development and progression are influenced not only by genetic susceptibility, obesity, and lifestyle-related factors but also by gut microbiota dysbiosis, chronic low-grade inflammation, and disruption of immunometabolic homeostasis. The gut microbiota regulates adaptive immune responses through diverse signals, including microbial structural components, metabolites, extracellular vesicles, and other secreted molecules. These microbial-derived signals modulate antigen presentation, T-cell differentiation, B-cell function, and IgA-mediated mucosal immunity, thereby influencing adaptive immune populations such as Th1 cells, Th17 cells, CD8[+] T cells, and regulatory T cells (Tregs). Conversely, the adaptive immune system can reshape microbial composition and functional outputs by regulating intestinal barrier integrity, mucosal immune homeostasis, and ecological niche stability, forming a dynamic and bidirectional gut microbiota-adaptive immunity interaction network. This reciprocal interaction persists throughout the progression from metabolic risk accumulation and insulin resistance to T2DM onset and diabetic complications, contributing to chronic low-grade inflammation, impaired insulin signaling, and pancreatic β-cell dysfunction. Unlike previous reviews that have primarily focused on gut microbiota dysbiosis, microbial metabolites, or innate immune regulation, this review highlights the bidirectional interactions between the gut microbiota and adaptive immunity as a central framework. We systematically summarize the underlying molecular mechanisms, dynamic disease evolution, and advances in microbiota-targeted therapeutic strategies. In recent years, dietary modulation, probiotics, prebiotics, synbiotics, postbiotics, fecal microbiota transplantation, and engineered microbiome-based therapies have emerged as potential approaches targeting the microbiota-immune axis. Among these strategies, dietary interventions and certain microbiota-based supplements have obtained preliminary clinical support, whereas fecal microbiota transplantation, engineered bacteria, and phage-based therapies remain under active investigation. However, clinical translation of microbiome-targeted therapies is still challenged by interindividual microbiota heterogeneity, insufficient standardization of interventions, uncertain long-term safety, and limited causal evidence. Future efforts should integrate microbial composition, functional metabolic profiles, adaptive immune signatures, and host metabolic states to achieve precise patient stratification and facilitate the development of personalized microbiome-based interventions. This review provides a conceptual framework for understanding immunometabolic mechanisms in T2DM and offers new perspectives for precision therapeutic strategies.},
}

@article {pmid42756901,
year = {2026},
author = {Salahi, A and El-Ghany, WAA},
title = {Gut microbial signatures in poultry under low-protein diets and lysine restriction: implications for precision nutrition.},
journal = {Veterinary and animal science},
volume = {34},
number = {},
pages = {100848},
pmid = {42756901},
issn = {2451-943X},
abstract = {Three key signatures - microbial, nutritional, and epigenetic - are pivotal in nutrigenomics, mediating poultry responses to nutritional signals, such as low-protein diets (LPDs) and lysine restriction (LR). These multidimensional signatures - encompassing bacterial, archaeal, and fungal taxonomy, functional genes, and metabolomic profiles (short-chain fatty acids; SCFAs) - orchestrate host metabolism, immunity, and feed conversion ratio (FCR). This PRISMA-ScR scoping review synthesizes multi-omics evidence showing that LPDs shift cecal fermentation toward saccharolytic pathways, enriching butyrate-producing taxa (Ruminococcaceae, Lachnospiraceae) while suppressing Proteobacteria and toxic proteolytic metabolites (ammonia, branched-chain fatty acids). LR elevates Actinobacteria/Synergistetes, triggers microbial nitrogen limitation, and reconfigures SCFA profiles through cross-feeding, thereby activating host nutrient sensors (mTOR downregulation, GCN2 upregulation) to prioritize immunity and FCR gains. Methanogenic archaea (Methanobrevibacter) fine-tune hydrogen economies, although diet-induced changes require deeper exploration. Key signatures forecast performance, featuring optimized Firmicutes/Bacteroidetes ratios and ureolytic genes (gdhA/glnA) as markers of protein resilience and profiles for breed-specific responses. SCFAs drive epigenetics (HDAC suppression, histone acetylation) and immunometabolism (Treg expansion, NF-κB dampening), bridging microbiome to host benefits via gut-liver interplay. Emerging applications span next-generation probiotics (NGPs) and live biotherapeutic products (LBPs), tailored from signature consortia (L. reuteri + B. velezensis) or archaeal agents, to sustain diet-induced states in antibiotic-free regimens. Major gaps persist in causal multi-omics validation, breed-specific responses, standardized baselines, and archaeal contributions. Integrating LPD/LR with tailored NGPs/LBPs promises precision nutrition strategies that enhance nitrogen utilization, reduce emissions, and improve welfare. Gnotobiotic, FMT, and AI trials are essential for translating microbial signatures into scalable flock-level precision management.},
}

@article {pmid42756918,
year = {2026},
author = {Davies, JT and Gely, Y and Yeramilli, V and Martin, C},
title = {Maternal and perinatal risk factors for necrotizing enterocolitis.},
journal = {World journal of pediatric surgery},
volume = {9},
number = {5},
pages = {e001205},
pmid = {42756918},
issn = {2516-5410},
abstract = {Necrotizing enterocolitis (NEC) remains among the most devastating complications of prematurity, carrying significant mortality and lifelong morbidity despite decades of mechanistic and translational research. Although NEC is classically framed as an inflammatory disease of intestinal immaturity, driven by microbial dysbiosis and exaggerated immune signaling, this model does not fully explain the uneven distribution of disease burden across infants, hospitals and communities. In this review, we reframe NEC within a broader maternal-perinatal systems context grounded in the Developmental Origins of Health and Disease (DOHaD) framework. This review synthesizes evidence linking maternal psychosocial stress to activation of the hypothalamic-pituitary-adrenal axis. This alters placental signaling and disrupts fetal gut development and microbiome establishment. This is further compounded by paternal stress-related epigenetic mechanisms, suboptimal maternal nutrition, poor metabolic health and environmental pollutants that disproportionately affect socioeconomically disadvantaged neighborhoods. These prenatal influences intersect with postnatal modifiers within neonatal intensive care units and health systems. Social and structural determinants of health further affect prenatal exposures and the delivery of neonatal care. This framework does not replace traditional pathogenesis models of NEC but rather contextualizes them within broader developmental and health systems. This perspective may help identify earlier targets for prevention while supporting more equitable and multidisciplinary approaches to reducing the burden of NEC.},
}

@article {pmid42757129,
year = {2026},
author = {Fan, K and Xu, Z and Sun, K and Chu, H},
title = {Optimizing rhizosphere metabolic circular economy toward sustainable ecosystems.},
journal = {Sustainable microbiology},
volume = {3},
number = {3},
pages = {qvag037},
pmid = {42757129},
issn = {2755-1970},
abstract = {The rhizosphere metabolic circular economy (RMCE) governs the exchange, reuse, and reconfiguration of metabolites at the root-soil interface. Building on traditional binary plant-microbe models, this perspective advances an expanded RMCE framework by integrating three additional interdependent dimensions that explain how rhizosphere metabolic processes persist over time, organize across space, and recover under environmental stress. First, the live-dead plant-microbe continuum enables metabolic persistence by incorporating microbial necromass and root residues into long-term carbon sequestration and nutrient regeneration. Second, spatial organization across rhizosphere microzones optimizes microscale metabolic interactions through niche heterogeneity. Third, adaptive restoration dynamically re-establishes disrupted metabolic networks through coordinated plant-microbiome stress responses. We further outline scenario-based management strategies to translate the RMCE insights into practical solutions, which necessitates multiple approaches targeting root exudate quality, microbial necromass dynamics, rhizosphere spatial architecture, and cross-kingdom signaling. Together, these advances redefine RMCE as a dynamically regulated, spatially structured, and ecologically complex system, providing a more comprehensive basis for its optimization in sustainable ecosystems.},
}

@article {pmid42757169,
year = {2026},
author = {Guhanraj, R},
title = {Targeting cancer hallmarks with microbiome-derived bacteriocins and postbiotics: molecular mechanisms and translational opportunities in oncology.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1899156},
pmid = {42757169},
issn = {2234-943X},
abstract = {BACKGROUND: The human microbiome is an abundant reservoir of bioactive molecules with considerable therapeutic potential in oncology. Among these microbial products, bacteriocins and other postbiotic metabolites have emerged as promising anticancer agents due to their diverse biological activities and ability to modulate multiple cancer-related pathways. Growing evidence suggests that microbiome-derived compounds may provide novel opportunities for the development of safer and more targeted cancer therapeutics.

OBJECTIVES: This review aims to comprehensively evaluate the current knowledge on bacteriocins and postbiotic metabolites as anticancer agents, highlighting their sources, structural and functional properties, mechanisms of action, computational-assisted discovery approaches, nanotechnology-based delivery systems, and challenges associated with clinical translation.

METHODS: A critical analysis of the available literature was conducted to summarize the biological characteristics of bacteriocin-producing microorganisms, the classification and mechanisms of bacteriocins, and the anticancer activities of major postbiotic metabolites. Recent advances in molecular docking, molecular dynamics simulations, systems biology, artificial intelligence, and nanotechnology-based drug delivery platforms were also examined to assess their contributions to therapeutic development.

RESULTS: Bacteriocins exhibit anticancer effects through multiple mechanisms, including disruption of cancer cell membranes, induction of apoptosis, regulation of oxidative stress, inhibition of cell proliferation, suppression of angiogenesis and metastasis, epigenetic modulation, and enhancement of antitumor immune responses. In addition, postbiotic metabolites such as short-chain fatty acids, indole derivatives, reuterin, and microbial exopolysaccharides contribute to tumour suppression and modulation of host-microbe interactions. Computational approaches have accelerated the identification and optimization of bacteriocin-derived therapeutic candidates, while nanotechnology-based delivery systems have improved their stability, bioavailability, and tumour-targeting capabilities. Nevertheless, challenges including limited clinical evidence, non-standardized experimental methodologies, poor pharmacokinetic properties, manufacturing constraints, and regulatory barriers remain significant obstacles to clinical implementation.

CONCLUSION: Bacteriocins and postbiotic metabolites represent a versatile and promising class of microbiome-derived anticancer agents with substantial potential for precision oncology. The integration of microbiome science, synthetic biology, computational drug discovery, and advanced drug delivery technologies is expected to facilitate the translation of these natural compounds into clinically effective cancer therapeutics. Future research should focus on mechanistic validation, large-scale production, pharmacological optimization, and well-designed clinical studies to accelerate their development and therapeutic application.},
}

@article {pmid42757275,
year = {2026},
author = {Li, S and Wang, S and Ren, Y and Yan, J},
title = {Chemotherapy-Induced Remodeling of the Gut Microbiota-Inflammation Axis: Implications for the Course of Bipolar Disorder.},
journal = {Journal of multidisciplinary healthcare},
volume = {19},
number = {},
pages = {637471},
pmid = {42757275},
issn = {1178-2390},
abstract = {There is growing evidence that bipolar disorder, BD and cancer share several biological features, including immune dysregulation, gut microbiota alterations, and chronic inflammation. Chemotherapy remains a mainstay of cancer treatment but can substantially alter the gut microbial ecosystem, impair intestinal barrier integrity, and contribute to systemic inflammation. However, little research has been done on whether these changes brought on by chemotherapy affect how BD develops clinically. This review summarizes the mechanisms through which chemotherapy may modify the gut microbiota-inflammation axis, along with how these changes may impact BD via the microbiota-gut-brain axis. We discuss how intestinal barrier failure, microbial metabolite production, microbial composition, and inflammatory signaling pathways-such as the LPS-TLR4/NF-κB axis and NLRP3 inflammasome activation-are affected by chemotherapeutic drugs. We also investigate the role of gut-derived inflammatory responses in neuroinflammation, dysregulation of the hypothalamic-pituitary-adrenal,HPA axis, impaired neuroplasticity, neurotransmitter imbalance, and cognitive dysfunction, all of which may contribute to mood instability, treatment resistance, and neuroprogression in BD. We also evaluate developing microbiome-targeted therapies, such as probiotics, fecal microbiota transplantation, and dietary modification, and explore the possible therapeutic consequences of chemotherapy-induced microbiota remodeling for patients with concomitant cancer and BD. Taken together, the available evidence supports the possibility that chemotherapy-induced modification of the gut microbiota-inflammation axis may contribute to the clinical course of BD. This integrated mechanistic paradigm offers a potential platform for future translational research and the creation of tailored treatment approaches for patients with comorbid cancer and BD, despite the lack of direct clinical proof. This narrative review summarizes the current evidence linking chemotherapy-induced gut dysbiosis and inflammatory responses to the clinical course of bipolar disorder and discusses their potential implications for integrated therapeutic strategies.},
}

@article {pmid42757563,
year = {2026},
author = {Bravo, M and Herrera Díaz, LD and Bravo Santillana, C and Martín Terroso, R and Simón, I and Cerrato, R},
title = {Postbiotic Intervention Improves Bowel Function and Promotes Systemic Health in Institutionalized Older Adults.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {18},
pages = {e70610},
doi = {10.1002/mnfr.70610},
pmid = {42757563},
issn = {1613-4133},
mesh = {Humans ; Aged ; Male ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects ; Female ; Aged, 80 and over ; Inflammation ; *Probiotics ; Dysbiosis ; },
abstract = {Postbiotic interventions represent a promising strategy to modulate gut health, but clinical evidence in older adults is limited. This study aimed to evaluate the effects of a postbiotic supplement consisting of inactivated bacterial cells on bowel function, systemic inflammation, and gut microbiota composition in institutionalized older adults. In this randomized, double-blind intervention study, 48 older adults received either postbiotic or placebo for 8 weeks. Daily assessment of gastrointestinal manifestations, bowel movements, and laxative use were collected, alongside pre- and post-intervention hematological and clinical biochemical assessments. Postbiotic supplementation improved bowel regularity, reduced diarrheal episodes, and decreased laxative reliance, effects that paralleled reductions in systemic inflammatory markers and improvements in red blood cell parameters. These clinical and hematological changes were accompanied by a more favorable gut microbiota profile, characterized by an increase in bacterial groups associated with anti-inflammatory effects in the postbiotic group and of taxa linked to dysbiosis in the placebo group. Our findings suggest that postbiotic supplementation in institutionalized older adults promotes beneficial shifts in gut microbiota, which are associated with reduced systemic low-grade inflammation and consequent improvements in bowel function and inflammation-related anemia, indicating an integrated microbiota-mediated mechanism supporting gut and systemic health.},
}

Humans
Aged
Male
Double-Blind Method
*Gastrointestinal Microbiome/drug effects
Female
Aged, 80 and over
Inflammation
*Probiotics
Dysbiosis

@article {pmid42757589,
year = {2026},
author = {Austin, G and Ferguson, JJA and Eslick, S and Garg, ML and Martins, R},
title = {Plant-based diets, cognitive function, and Alzheimer's disease.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo01946c},
pmid = {42757589},
issn = {2042-650X},
abstract = {Background: Alzheimer's disease (AD) represents 60-70% of global dementia cases, with up to 45% attributed to modifiable risk factors. Plant-based diets (PBDs) are increasingly recognised for their potential benefits on the gut microbiome, cardiometabolic risk factors and prevention of neurodegenerative disorders. This narrative review synthesises PBDs association with cognitive decline and AD risk. Methods: This review aims to summarise evidence from observational and interventional studies examining vegan, vegetarian, pesco-vegetarian, semi-vegetarian dietary patterns, and PBD indices in relation to cognitive function, incident dementia, AD biomarkers, and neuroimaging outcomes. Results: Long-term observational studies suggest greater adherence to vegan, vegetarian and healthy PBD indexs are associated with lower risk of cognitive decline and dementia, while higher intake of red and processed meat is linked to increased risk. Pesco-vegetarian dietary patterns and higher fish intake appear to confer benefits in memory tests and reduced risk of all-cause dementia, although research is limited. Mechanistically, PBDs are rich in unsaturated fats, fibre, polyphenols and low in saturated fats, which contribute to improving lipid profiles, glycaemic control, endothelial function, and favourable gut-derived metabolites, thereby reducing cardiometabolic burden that is known to accelerate early-stage AD pathophysiology. However, nutritional considerations, including potential deficiencies in vitamin B12 and long-chain omega-3 fatty acids, require consideration when following a PBD. Conclusions: Current evidence suggests PBDs may support cognitive health and reduce the risk of dementia including AD through vascular and metabolic pathways, though long-term interventional studies incorporating biomarkers and neuroimaging are needed to clarify effects and optimise dietary recommendations for AD prevention.},
}

@article {pmid42757781,
year = {2026},
author = {Jappe, U and Risha, MA and Agache, I and Bachert, C and Bröker, B and Castagnoli, R and Gadermaier, G and Goodman, RE and Guemari, A and Hilger, C and Jacquet, A and Kespohl, S and Klimek, L and Kuehn, A and Lidholm, J and Mahler, V and Ollert, M and Platts-Mills, TA and Raulf, M and Schmid-Grendelmeier, P and Schmiedeke, F and van Hage, M and Vitte, J and Zakzuk, J and Pomés, A},
title = {IgE-Binding Bacterial Components Not Yet Documented in the Allergen Databases and Their Allergenic Mechanisms: An EAACI Position Paper.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70510},
pmid = {42757781},
issn = {1398-9995},
support = {40605//European Academy of Allergy and Clinical Immunology/ ; },
abstract = {Among bacteria that are associated with the development and/or exacerbation of allergic/atopic diseases, several have been described to produce IgE-binding components. However, only one bacterial protein, Bac s 1, is currently listed in the official database of the World Health Organization/International Union of Immunological Societies (WHO/IUIS) Allergen Nomenclature Sub-Committee. The aim of this position paper was to identify potential bacterial allergens and their reported clinical relevance in the published literature and consider candidates for the Allergen Nomenclature database. PubMed and the WHO/IUIS Allergen Nomenclature database were searched up to October 2025. Consensus was obtained during task force meetings and by a written commentary process. Sixty-six IgE-binding components in 20 different species of bacteria were found, most associated with clinical symptoms. Allergen candidates include staphylococcal superantigens, bacterial enzymes, and components from two Chlamydia species, some of which are potential marker allergens for disease severity. The results point to long-neglected evidence of "bacterial allergy" that in certain cases may be induced by unconventional mechanisms. Diseases that are currently considered non-allergic might be re-classified as allergic if these IgE-binding components are recognized as allergens and used for diagnosis in the future.},
}

@article {pmid42757843,
year = {2026},
author = {Taillandier, P and Clément, K and Le Roy, T},
title = {Complete genome sequence of Subdoligranulum sp. strain DSM 23681 isolated from the cecum of a broiler chicken.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0061926},
doi = {10.1128/mra.00619-26},
pmid = {42757843},
issn = {2576-098X},
abstract = {We report the complete genome sequence of strain ic1395 (DSM 23681), an anaerobe previously isolated from the cecum of a broiler chicken and affiliated with the Subdoligranulum genus. Its average nucleotide identity with the closest species with standing in nomenclature indicates that this strain represents a divergent and distinct lineage.},
}

@article {pmid42758012,
year = {2026},
author = {Liu, JCW and Gorbovskaya, I and Zhang, AY and Hahn, MK and De Palma, G and Müller, DJ},
title = {Investigation of the Gut Microbiome in Treatment-Resistant Schizophrenia Compared to Healthy Controls: A Cross-Sectional Pilot Study: Étude du microbiome intestinal chez les patients atteints de schizophrénie résistante au traitement par rapport aux témoins sains : étude pilote transversale.},
journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
volume = {},
number = {},
pages = {7067437261487782},
doi = {10.1177/07067437261487782},
pmid = {42758012},
issn = {1497-0015},
abstract = {BackgroundSchizophrenia (SCZ) is a debilitating disorder affecting approximately 1% of the Canadian population and remains a major contributor to disease burden and disability. Up to one-third of individuals with SCZ are affected by treatment-resistant SCZ (TRS). Clozapine remains the most effective treatment for TRS. However, its use is limited by serious metabolic and immune-related side effects. The gut microbiome may be a potential contributor to both SCZ pathology and antipsychotic-induced side effects, though studies examining this in the clozapine-treated TRS population remain limited.MethodsThis cross-sectional case-control study compared the gut microbiome composition of 25 TRS patients receiving long-term clozapine treatment to 25 healthy controls (HCs) matched for age, sex, body mass index, and smoking status. Participants provided fecal samples and completed assessments of psychiatric symptoms, eating behaviors, dietary intake, and metabolic measures. Fecal microbiome composition and predicted function were assessed using 16S rRNA gene sequencing (v3 region).ResultsIndividuals with TRS being treated with clozapine presented with a distinct microbiome in comparison to HC, including reduced microbial diversity. Taxonomic analyses revealed reduced relative abundance of Firmicutes, while elevated relative abundance of Eggerthella spp., Mucispirillum spp., and unclassified species within the order SHA-98 (class Clostridia). Exploratory analyses also identified nominal associations between select microbial features and clinical measures, including Positive and Negative Syndrome Scale (PANSS) scores and gastrointestinal symptoms. Predicted functional pathway analysis suggested alterations in microbial metabolic potential consistent with a metabolically stressed, pro-inflammatory microbiome.ConclusionsIndividuals with clozapine-treated TRS demonstrate differences in gut microbiome composition compared to HC and are predicted to have some functional consequences relating to metabolic potential. These findings remain exploratory but contribute to a limited but growing body of literature in this clinically relevant population and provide a basis for longitudinal studies with appropriate comparator groups to better characterize these relationships and assess their clinical relevance.},
}

@article {pmid42758297,
year = {2026},
author = {Xu, H and Zhong, T and Li, J},
title = {The link of oral microbiome diversity to stroke risk: Evidence from the National Cohort Study in the United States.},
journal = {The International journal of neuroscience},
volume = {},
number = {},
pages = {1-35},
doi = {10.1080/00207454.2026.2736054},
pmid = {42758297},
issn = {1563-5279},
abstract = {OBJECTIVE: To assess whether oral microbiome diversity and periodontal health are independently associated with stroke prevalence in a U.S. adult cohort, with implications for risk stratification in physical medicine and rehabilitation.

METHODS: We analyzed cross-sectional data from 4,438 adults in the National Health and Nutrition Examination Survey (NHANES) 2009-2012, using survey-weighted logistic regression to evaluate associations between stroke and oral microbiome β-diversity (unweighted UniFrac), α-diversity (Shannon, Simpson), and clinical periodontal measures (probing depth, clinical attachment loss, and tooth count), adjusting for age, sex, race/ethnicity, education, income, smoking, alcohol consumption, body mass index, and diabetes.

RESULTS: In crude models, each 1-mm increase in mean probing depth was associated with higher stroke odds (odds ratio [OR] = 1.89, 95% confidence interval [CI] = 1.39-2.56), as was each 1-mm increase in clinical attachment loss (OR = 1.50, 95% CI = 1.32-1.71); each additional tooth was associated with lower odds (OR = 0.91, 95% CI = 0.88-0.94). After stepwise adjustment, attachment loss (OR = 1.23, 95% CI = 1.04-1.46; P = 0.017) and tooth count (OR = 0.96, 95% CI = 0.92-0.99; P = 0.024) remained significant, whereas probing depth did not (OR = 1.30, 95% CI = 0.90-1.88; P = 0.156). A threshold effect was observed at approximately 1.46 mm for probing depth. β-Diversity clusters did not differ in stroke prevalence after adjustment (global P = 0.61), and neither α-diversity index was significant in the stepwise- or fully-adjusted models (Shannon fully-adjusted OR = 1.29, 95% CI = 0.97-1.72; P = 0.081). Periodontal associations were consistent across sex and age strata; the non-significant findings in younger participants were attributable to limited statistical power.

CONCLUSION: Clinical periodontal measures, particularly attachment loss and tooth count, were associated with stroke prevalence independently of traditional cardiovascular risk factors, whereas oral microbiome diversity indices were not. These measures may serve as readily accessible markers for refining stroke risk assessment. The cross-sectional design precludes causal inference, and findings require validation in prospective cohorts with adjudicated stroke outcomes and metagenomic profiling before clinical translation. Nevertheless, these results support integrating oral health assessment into routine stroke risk evaluation and highlight periodontal inflammation as a potentially modifiable contributor to cerebrovascular disease.},
}

@article {pmid42758428,
year = {2026},
author = {Kwiatkowska, M and Walczak, Ł and Twarowski, B and Pawłaszek, M and Rokosz-Mierzwa, J and Lejman, M},
title = {The Impact of Cancer Treatment On Oral Structures and the Facial Part of the Skull - Implications for Prosthetic Treatment and Oncological Risk.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42758428},
issn = {1534-6269},
mesh = {Humans ; Osseointegration ; *Dental Implants/adverse effects ; *Neoplasms/therapy ; *Skull/pathology/drug effects ; *Mouth/microbiology/drug effects/pathology ; },
abstract = {PURPOSE OF REVIEW: This study aims to identify complications and difficulties in oncology patients undergoing dental implant osseointegration, considering the impact of treatment on the microarchitecture of the craniofacial region, the oral cavity microbiome, and oral cavity inflammation.

RECENT FINDINGS: Surgical resection, radiotherapy, chemotherapy, and targeted therapies significantly affect the condition of bones, mucous membranes, and soft tissues, and consequently the possibilities and limitations of prosthetic rehabilitation. Chemotherapy significantly affects calcium and phosphorus metabolism. It has been observed that there is an increased risk of fractures, as well as changes in their microarchitecture, and a reduction in the resorption of biomaterials after transplantation has been observed, impairing bone repair in critical defects. These changes may also affect the processes of osteogenesis and osteoclastogenesis and lead to osteoblast cell apoptosis. The impact of therapy on the oral microbiota, as well as on increased inflammation and oxidative stress in the oral cavity, is also significant. These changes can lead to difficulties in implant osteointegration, as well as opportunistic infections, which reduce the patient's prognosis for implant acceptance. Complications after implantation in oncology patients may include inflammation of the mucosa around the implant and inflammation of the tissues around the implant, soft tissue ulceration, marginal bone loss, and partial loss of osseointegration. Due to the complexity of the processes occurring in the oral cavity of oncology patients, prosthetic treatment planning should be interdisciplinary and involve an oncologist, surgeon, prosthodontist, and conservative dentist.},
}

Humans
Osseointegration
*Dental Implants/adverse effects
*Neoplasms/therapy
*Skull/pathology/drug effects
*Mouth/microbiology/drug effects/pathology

@article {pmid42758523,
year = {2026},
author = {Lan, G and Li, X and Lu, Z and Zhang, Y and Feng, F and Liu, J and Wu, W and Liu, J and Zhou, Y and Gu, J and Ma, R and Qi, D},
title = {Gut Microbiome Functional Reprogramming Reflects Divergent Social Strategies in a Wild Primate.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70185},
pmid = {42758523},
issn = {1749-4877},
support = {2025JZG01//Foundation for Non-Invasive Research on Golden Snub-Nosed Monkeys in Baihe Nature Reserve/ ; CAZG2025C13//Chengdu Research Base of Giant Panda Breeding/ ; 32570615//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a critical interface between host physiology and environmental challenges, yet its role in mediating behavioral strategies in socially complex mammals remains unclear. Using metagenomic sequencing of wild golden snub-nosed monkeys (Rhinopithecus roxellana), we investigated how social status (one-male unit [OMU] leaders vs. all-male unit [AMU] individuals) and seasonal variation (winter-spring [WS] and summer-autumn [SA]) shape gut microbial structure and function. We found that seasonal shifts drive primary microbial restructuring, but social status exerts a strong influence, particularly during the SA mating season. OMU leaders maintained stable microbial communities enriched in energy conservation and cellular maintenance pathways including methane metabolism and peptidoglycan biosynthesis. In contrast, AMU individuals exhibited highly plastic microbiomes potentially suited for competition, with enhanced functions in environmental sensing (e.g., flagellar assembly and two-component systems) and nitrogen metabolism. AMU gut microbiomes also showed reduced diversity in SA, indicating specialization for competitive readiness. These results demonstrate that the gut microbiome is functionally compartmentalized by social status, providing distinct metabolic toolkits that align with divergent behavioral strategies-investment in unit fitness for OMU leaders versus risk-taking for AMU individuals. Our study reveals the gut microbiome is closely associated with social adaptation in primate societies, serving as a dynamic indicator of divergent behavioral strategies.},
}

@article {pmid42523320,
year = {2026},
author = {Morabbi, SM and Bhowmik, N and Sutherland, S and Wylie, EA and Decker, RS and Daerwish, AA and Pérez, MP and Pascual, E and Lutter, EI and Philmus, B and Stubbendieck, RM},
title = {Differential Metabolite Production Underlies Disruption of the Cystic Fibrosis Airway Microbiota by Pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42523320},
issn = {2692-8205},
abstract = {Cystic fibrosis (CF) is a multisystem disease characterized by the accumulation of mucus in the airways that promotes pathogen colonization, leading to respiratory exacerbations, lung failure, and death. Culture-independent approaches have revealed that the CF airway harbors a complex microbiota, including opportunistic pathogens and bacteria that colonize the oropharynx. Here, we reanalyzed 5,260 16S rRNA gene microbiota datasets to infer ecological associations between members of the CF microbiota. We determined that pathogens are more likely to proliferate and dominate when present, while oropharyngeal bacteria are more likely to form persistent communities. Further, we found higher diversity and increasing numbers of inferred interactions were positively associated with lung function. In contrast, pathogens were negatively associated both with each other and with oropharyngeal bacteria, suggesting that they may disrupt the microbiota. To validate these predictions, we cultured 1,597 bacterial isolates from 96 people with CF and performed 12,542 coculture assays against eight representative CF pathogenic and oropharyngeal bacteria. 23% of these interactions resulted in growth inhibition. While Pseudomonas isolates were, on average, the most inhibitory, we observed variable activity among isolates. We then confirmed that Pseudomonas aeruginosa isolates, even those from the same donor and timepoint, exhibited significant differences in their metabolome and bioactivity profiles that correlated with acquisition of mutations. Together, our results suggest that pathogens may disrupt the CF microbiota and bloom in part through differential metabolite production. Furthermore, these data highlight that characterizing multiple isolates is necessary to capture the full landscape of chemically mediated interactions within microbial communities.},
}

@article {pmid42538473,
year = {2026},
author = {Voolstra, CR and Hermann, RJ and Stibor, H and Keller, A and Becks, L},
title = {Timescale mismatch: redefining ecological opportunity for evolution in the Anthropocene.},
journal = {The EMBO journal},
volume = {45},
number = {18},
pages = {6359-6366},
pmid = {42538473},
issn = {1460-2075},
support = {9196//Gordon and Betty Moore Foundation (GBMF)/ ; CAP-2024-1692//CORDAP/ ; },
abstract = {The Anthropocene is defined by unprecedented biodiversity loss, but also by a profound mismatch of timescales: environmental change unfolds orders of magnitude faster than response times for most ecological and evolutionary processes. Rapid perturbations create transient ecological opportunities, yet these windows are often too brief for diversification to manifest. The central challenge to understanding biodiversity change in the Anthropocene is not whether ecological opportunity—the availability of novel resources or niches that relax competition—arises, but whether it persists long enough for evolution to act. Microbiome-mediated as well as behavioral and physiological plasticity can buffer organisms against short-term instability and enable swift niche shifts, but such flexibility is reversible, typically non-heritable, and fragile under sustained disturbance. Without enduring selection or sufficient genetic variation, flexibility cannot substitute for evolution. The classical framework of ecological opportunity—conceived for stable environments and gradual change—is therefore inadequate. Diversification, i.e., the rebuilding of biodiversity in the Anthropocene, demands a time-scale integrated framework that unites evolutionary, ecological, and microbiome dynamics to pinpoint when fleeting opportunities can be stabilized for lasting diversification.},
}

@article {pmid42747964,
year = {2026},
author = {Chudhary, A and Wang, X},
title = {Molecular mimicry and functional convergence of bacterial proteins in host-microbe interactions.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117983},
doi = {10.1016/j.celrep.2026.117983},
pmid = {42747964},
issn = {2211-1247},
abstract = {Bacterial proteins modulate host immunity through diverse molecular strategies that are often broadly described as molecular mimicry. However, inconsistent terminology has obscured distinctions between genuine host-like interactions and other forms of host-directed immune modulation. We propose an operational framework that classifies bacterial proteins into four mechanistic categories: molecular mimicry, mimic-like behavior, functional convergence, and pathway interference. The framework prioritizes explicit criteria, including host-target engagement, interaction-interface similarity, functional equivalence, predominant molecular mechanism, and strength of supporting evidence, rather than immune outcome alone. Representative bacterial effectors are discussed alongside their evolutionary origins, computational prediction, experimental validation, and emerging technologies for mechanistic investigation. By separating evolutionary processes from molecular action and applying evidence-based classification criteria, this review clarifies ambiguous terminology and provides a consistent conceptual foundation for interpreting bacterial immune modulation. The framework may also guide future mechanistic studies, comparative analyses, and translational research across diverse pathogenic and commensal host-microbe interaction systems.},
}