@article {pmid41548440,
year = {2026},
author = {Hong, EH and Hyeong, J and Ahn, JH and Han, Y and Kim, S and Kim, SM and Yoo, HH and Jeong, H and Cho, HJ and Park, JH and Chang, SY and Ko, HJ},
title = {Limosilactobacillus reuteri alleviates psoriasis via aryl hydrocarbon receptor-mediated regulation of Interkeukin-17A.},
journal = {International immunopharmacology},
volume = {172},
number = {},
pages = {116194},
doi = {10.1016/j.intimp.2026.116194},
pmid = {41548440},
issn = {1878-1705},
abstract = {BACKGROUND: Psoriasis is a chronic immune-mediated skin disorder characterized by keratinocyte hyperproliferation and interleukin-17A-driven inflammation. Growing evidence highlights the contribution of microbiome-derived factors to cutaneous immune regulation. The study aimed to evaluate the therapeutic efficacy of heat-killed Limosilactobacillus reuteri NCHBL-005 in an imiquimod-induced psoriasis-like mouse model.

RESULTS: Both topical and oral administration of NCHBL-005 significantly alleviated clinical and histological features, including reduced epidermal thickness, improved Psoriasis Area and Severity Index scores, and diminished inflammatory cell infiltration. Mechanistically, NCHBL-005 suppressed interleukin-1 beta and interleukin-17A expression in psoriatic lesions and decreased interleukin-17A-positive RAR-related orphan receptor gamma t-positive T-cells while maintaining regulatory T-cell balance. These effects were retained in Toll-like receptor 2- and nucleotide-binding oligomerization domain-containing protein 2-deficient mice but abolished in aryl hydrocarbon receptor-deficient mice, underscoring the essential role of aryl hydrocarbon receptor signaling. NCHBL-005 directly attenuated inflammatory responses in keratinocytes by suppressing the expressions of interleukin-1 beta, interleukin-17A, and tumor necrosis factor-alpha, and by inhibiting nuclear factor kappa-light-chain-enhancer activation. Liquid chromatography-tandem mass spectrometry profiling identified indole-3-acetaldehyde, indole-3-carbinol, and indole-3-lactic acid as major aryl hydrocarbon receptor ligands derived from NCHBL-005. Among these, indole-3-acetaldehyde most effectively reproduced the therapeutic effects, reducing interleukin-17A-positive cells, epidermal hyperplasia, and nuclear factor kappa-light-chain-enhancer activation.

CONCLUSIONS: NCHBL-005 and its metabolite indole-3-acetaldehyde alleviate psoriatic inflammation through modulation of the aryl hydrocarbon receptor-interleukin-1 beta-interleukin-17A axis, thereby restoring skin immune homeostasis. This study highlights postbiotic intervention in the aryl hydrocarbon receptor-interleukin-1 beta-interleukin-17A axis as a promising therapeutic strategy for psoriasis.},
}

@article {pmid41548201,
year = {2026},
author = {Mirmozaffari, Y and Roca, C and Martin, WJ and Heetderks, KA and Van Dorsten, A and Cook, L and Benaim, EH and Wolfgang, MC and Kimple, AJ},
title = {Species-Level Characterization of the Nasal Microbiome in Various Disease States Utilizing Third-Generation Sequencing.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.70103},
pmid = {41548201},
issn = {2042-6984},
}

@article {pmid41547908,
year = {2026},
author = {Kim, YC and Won, SY and Jeong, BH},
title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-025-01699-2},
pmid = {41547908},
issn = {1297-9716},
support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; },
abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.},
}

@article {pmid41547903,
year = {2026},
author = {Hashmi, MA and Verma, S and Math, RGH and Muralidharan, S and Pranesh, G and Sahana, MP and Hariharan, N and N C, M and Kamath, V and Yaligod, V and Hiremath, SA and Jawali, A and Maddipati, T and Chandrasingh, S and Thomas, A and Mallnaik, N and Shanmuganand, VC and George, CE and Thomas, A and Ghosh, TS and Ramanathan, A},
title = {Integrative analysis of plasma small-molecule and gut-microbiome markers of sarcopenia in a pilot study within an Indian cohort.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35476-8},
pmid = {41547903},
issn = {2045-2322},
}

@article {pmid41547860,
year = {2026},
author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA},
title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {25},
pmid = {41547860},
issn = {2049-2618},
mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.

RESULTS: Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.

CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.},
}

Animals
Dogs/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41547850,
year = {2026},
author = {Naya-Català, F and Domingo-Bretón, R and Matias, RS and Calduch-Giner, JÀ and Belenguer, Á and Gomes, S and Guilhermino, L and Moroni, F and Valente, LMP and Pérez-Sánchez, J},
title = {Dietary rayon microfibers differentially reshape rearing water and host associated microbiomes of farmed European sea bass (Dicentrarchus labrax).},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00851-5},
pmid = {41547850},
issn = {2524-6372},
abstract = {BACKGROUND: Viscose-rayon microfibres (RFs) are cellulosic microfibres widely dispersed throughout aquatic environments. Whether ingested by or suspended in the surrounding environment, these microfibres may impact both wild and farmed animals. A previous study on European sea bass (Dicentrarchus labrax) showed that the increased presence of RFs in aquafeeds (CTRL-no RFs; RF1-0.001 g/kg; RF2-0.01 g/kg; RF3-0.1 g/kg) was linked to an exponential increase of RFs in water, intestine and skeletal muscle. This finding was associated to a fatty liver and tissue-specific transcriptional changes, depicting the up-regulation of hepatic lipogenic enzymes and intestinal/head kidney inflammatory markers. The aim of the present study was to extend this evaluation by investigating changes in associated microbial communities after the ingestion of RFs in the diet, employing a multi-layered approach for the integrative profiling of gut, skin, and environmental water microbiome using the Nanopore platform.

RESULTS: Amplicon-sequencing identified ~2800 taxa across water, skin and gut microbiomes. Gut and skin microbiomes were more similar to each other, but increasing RF exposure shifted the skin community toward the water microbiome. Moreover, RF induced the highest taxonomic variation in water (691 taxa), followed by skin (253) and gut (99), while microbial diversity Shannon and Simpson indexes declined from 4 down to 3.3 under RF2 and RF3 in a dose-dependent manner. Major exponents of this trend were the decrease of Synechococcus and Flavobacteriales in association with the increase of starch- and hydrocarbon-degrading taxa (Ardenticatenaceae and Gracilibacteria). In both gut and skin, bacterial richness decreased in fish fed low to intermediate RF doses, whereas RF3 fish resembled controls. Thus, compositional and discriminant analyses consistently grouped CTRL and RF3 samples, suggesting the existence of a dose threshold occurring in parallel with host counter-regulatory responses. Such feature was reflected by abundant skin-associated bacteria (Exiguobacterium and Planococcus) with at least the genetic potential to be linked to vitamin B6 biosynthesis and host-driven muscle regeneration markers, whereas predominant gut taxa with the same pattern (Microbacterium and Achromobacter) was associated with polysaccharide degradation and correlated with host gene inflammatory mechanisms.

CONCLUSIONS: This study revealed a concomitant dose-dependent and dose-threshold response among the bacterial communities composing the holobiont of European sea bass in response to dietary RFs ingestion, highlighting novel bacterial taxa and pathways through which microplastic exposure may differentially reshape rearing water and host-associated microbial communities.},
}

@article {pmid41547827,
year = {2026},
author = {Cavaliere, S and Fogolari, M and Iuliani, M and Foderaro, S and Cortellini, A and Simonetti, S and Mingo, EC and Calagna, S and Russano, M and Vincenzi, B and Tonini, G and Angeletti, S and Pantano, F},
title = {Salivary microbial signature highlighting actinomyces as a predictor of immune-checkpoint inhibitor monotherapy response in advanced non-small cell lung cancer.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07570-4},
pmid = {41547827},
issn = {1479-5876},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have improved survival in advanced non-small cell lung cancer (NSCLC), yet reliable biomarkers beyond programmed death-ligand 1 (PD-L1) expression remain limited. Increasing evidence links the gut microbiome to ICI activity, but the predictive value of the salivary microbiome is poorly defined.

METHODS: We prospectively analyzed baseline saliva from 71 stage IV NSCLC patients treated with anti-PD-1/PD-L1 (ICI) monotherapy. After quality control, 70 samples underwent 16 S rRNA gene sequencing of the V1-V3 region. Microbial diversity, differential abundance (LEfSe, Mann-Whitney/Kruskal-Wallis with false discovery rate correction) and survival associations (Kaplan-Meier; Cox proportional-hazards with LASSO-based variable selection and 1000-fold bootstrap validation) were examined. In this cohort, an exploratory genus-level cut-off was derived by receiver operating characteristic (ROC) analysis.

RESULTS: α-diversity and β-diversity did not differ between responders (progression-free survival (PFS) ≥ 12 months; n = 18) and non-responders (n = 52). Differential‑abundance profiling revealed a graded enrichment of the phylum Actinobacteria across all lower ranks, class Actinobacteria, order Actinomycetales, family Actinomycetaceae and genus Actinomyces,in non‑responders (LEfSe LDA > 3.5; p = 0.001 for each level; FDR ≤ 0.049). ROC analysis suggested an Actinomyces relative abundance of 11% (AUC = 0.768; sensitivity 0.94; specificity 0.44) as a data-driven threshold, classifying patients into low (≤ 11%, n = 46) and high (> 11%, n = 24) groups. High abundance was associated with shorter PFS (median 3 vs. 4 months; HR = 2.16, 95% CI 1.21-3.88, p = 0.009) and overall survival (OS) (median 5 vs. 9 months; HR = 2.61, 95% CI 1.48-4.61, p < 0.001) after multivariable adjustment for ECOG status, treatment line, corticosteroid and opioid use, smoking, histology and metastatic sites. Bootstrap validation supported model stability, with median bootstrap HRs of 2.56 (PFS) and 2.63 (OS), with narrow percentile CIs (PFS 1.57-4.49; OS 1.40-6.34) overlapping the original estimates.

CONCLUSIONS: In this exploratory cohort, salivary microbiome signature characterized by high Actinomyces abundance was independently associated with poorer ICI outcomes in NSCLC. Saliva profiling is non-invasive and, if validated in larger and independent cohorts, may complement tumour PD-L1 and clinical factors to refine patient stratification.},
}

@article {pmid41547778,
year = {2026},
author = {Park, SH and Park, SM and Suh, JW and Kim, JY and Sohn, JW and Yoon, YK},
title = {Clinical impact of altered gut microbiota and metabolite profiles on mortality in patients with candidemia: a prospective observational pilot cohort study.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12941-026-00850-x},
pmid = {41547778},
issn = {1476-0711},
abstract = {BACKGROUND: The gut microbiota plays an important role in defending against infectious diseases. However, data on the clinical implications of the microbiome profiles in patients with candidemia remain limited. In this study, we investigated the association between the intestinal microbiome and mortality in patients with candidemia.

METHODS: This prospective, observational, pilot cohort study enrolled adult patients with culture-confirmed candidemia. Fecal samples were collected within 5 days of diagnosis and analyzed using 16 S ribosomal RNA gene sequencing for microbiota profiling and gas chromatography-mass spectrometry for metabolomic analysis. Multivariate logistic regression was used to identify predictors of in-hospital mortality, defined as death during hospitalization.

RESULTS: Fifty-nine patients with candidemia were analyzed, and the in-hospital mortality rate was 40.7%. The median Shannon diversity index of the gut microbiota was significantly lower in non-survivors than that in survivors (P = 0.009). Linear discriminant analysis revealed 11 bacterial species that differed significantly between the two groups. Among the 111 fecal metabolites, only 3-isopropoxy-hexamethyl-tetrasiloxane differed significantly between the survivors and non-survivors (P = 0.007). Septic shock (adjusted odds ratio: 10.59; 95% confidence interval, 1.70-65.97), underlying malignancy (7.79 [1.41-43.10]), and Shannon diversity index (0.40 [0.19-0.84]) were significant predictors of in-hospital mortality.

CONCLUSIONS: Low gut bacterial diversity is independently associated with mortality in patients with candidemia. These preliminary findings warrant confirmation through larger, well-powered studies.},
}

@article {pmid41547669,
year = {2026},
author = {Isınıbılır, M and Doğan, O and Bilgin, R and Çalıcı, Z},
title = {Microbiome dynamics linked to Aurelia aurita during bloom and post-bloom periods in the Golden Horn Estuary: a snapshot via eDNA metabarcoding.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41547669},
issn = {1614-7499},
abstract = {Jellyfish blooms are significant events in marine ecosystems, profoundly impacting carbon and nutrient cycles. During these events, decomposing jellyfish release dissolved organic matter (DOM), which fuels bacterial growth and reshapes nutrient cycling. In this study, we employed an environmental DNA (eDNA) metabarcoding approach to capture bacterial communities associated with Aurelia aurita, and in different body parts, as well as its ambient surface water column during bloom (December 2022) and post-bloom (March 2023) periods in the Golden Horn Estuary, İstanbul, Türkiye. The results reveal distinct temporal and regional variations in bacterial diversity, highlighting the pivotal role of jellyfish blooms in reshaping bacterial communities.},
}

@article {pmid41547536,
year = {2026},
author = {Banik, M and Bashyal, S and Ahmed, KA and Banik, K and Dua, K and Choi, JP and Paudel, KR and Majumder, R},
title = {The Gut Microbiome of Australian Cats and Dogs: Dietary Influences, Health Impacts, and Emerging Research.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106566},
doi = {10.1016/j.tvjl.2026.106566},
pmid = {41547536},
issn = {1532-2971},
abstract = {The gut microbiome plays a pivotal role in the health, metabolism, and behaviour of companion animals, yet comprehensive syntheses of its composition and functional relevance in cats and dogs in Australia are overlooked and remain limited globally. This review synthesises current knowledge on the gut microbial communities inhabiting the gastrointestinal tracts of dog and cats, with a particular focus on taxonomic diversity, dietary modulation, and associations with disease states within Australian context. Core phyla including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria dominate the canine and feline gut, but marked interspecies and individual variability is shaped by factors such as feeding practices, living environment, obesity, and chronic disease. Recent studies have elucidated functional signatures linked to conditions ranging from the influence of microplastics to pet gut health, as well as gut-microbiome transmission between pets and their owners, highlighting this area as a promising field of investigation. In parallel, this review contextualizes the broader landscape of pet ownership in Australia, where nearly 70% of households own pets, and significant resources are devoted to nutrition, veterinary care, and preventive health. Emerging evidence also suggests bidirectional influences between pets and their human companions' microbiota, highlighting opportunities for integrated approaches. We identify critical knowledge gaps, including the need for region-specific microbial baselines, standardized methodologies, and controlled intervention trials targeting microbiome modulation and transmission. By consolidating advances across microbial ecology, veterinary medicine, and translational research, this review provides a foundation for future studies that aim to harness the diagnostic and therapeutic potential of the pet microbiome, thereby improving health outcomes for animals and humans alike.},
}

@article {pmid41547455,
year = {2026},
author = {Qu, Q and Gao, H and Gao, X and Li, P and Mou, Y and Kong, X and Tan, X},
title = {Dietary inulin mediates the molecular mechanism of intestinal metabolites to alleviate high salt diet-induced chronic kidney disease in mice.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110269},
doi = {10.1016/j.jnutbio.2026.110269},
pmid = {41547455},
issn = {1873-4847},
abstract = {It is recognized that excessive dietary salt intake is a critical factor contributing to chronic kidney disease (CKD). A high-salt diet (HSD) disrupts the balance of the gut microbiota, but the molecular mechanisms linking gut dysbiosis to target organ damage remain unclear. This study identified dietary prebiotic inulin (INU) as a potent regulator of the gut-short-chain fatty acid-kidney axis, capable of counteracting HSD-induced CKD. Sequencing analysis showed that INU selectively enriched Bifidobacterium and Faecalibaculum while downregulating Desulfovibrio. This microbiome shift restored intestinal tight junction proteins and reduced serum lipopolysaccharide (LPS) levels, thereby inhibiting TLR4/NF-κB-mediated renal inflammation. Notably, the effects of direct SCFA supplementation align with the renal protective effects of INU, confirming the critical role of the gut-kidney axis. Our study reveals INU as a dietary strategy that combats HSD-induced CKD via SCFAs produced by the microbiota, offering new insights into the gut-SCFAs-kidney axis as a therapeutic target.},
}

@article {pmid41547444,
year = {2026},
author = {Shan, Y and Huang, X and Han, X and Yang, Y and Zheng, M},
title = {3'-Sialyllactose ameliorates antibiotic-associated diarrhea by shaping unique gut microbiota and metabolite composition.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27362},
pmid = {41547444},
issn = {1525-3198},
abstract = {3'-Sialyllactose (3'-SL) is a naturally occurring prebiotic in milk, known to regulate intestinal microbiota and prevent diseases. However, the mechanisms through which 3'-SL alleviates antibiotic-associated diarrhea remain poorly understood. In this study, an antibiotic-associated diarrhea model was established through the co-administration of ampicillin and neomycin. The effects of 3'-SL supplementation on diarrhea phenotype, inflammation, intestinal permeability, and barrier function were examined in antibiotic-associated diarrhea-model mice. Moreover, gut microbiota composition, metabolite profiles, and their alterations were analyzed using genomic and metabolomic approaches. The results demonstrate that 3'-SL increased body weight and aquaporin (AQP) 3 and AQP4 levels but reduced diarrhea rate, cecal mass, and fecal water content in the model mice, indicating its therapeutic effect on diarrhea. Furthermore, 3'-SL reduced serum levels of IL-6, tumor necrosis factor (TNF)-α, and IL-1β, while increasing IL-10 levels in the mice. Moreover, 3'-SL reduced intestinal permeability by enhancing both the mechanical barrier (ZO-1 and occludin mRNA expression) and the chemical barrier (MUC2 mRNA and protein expression) in the mice. 16S rRNA analysis revealed that mice in the 3'-SL group exhibited greater abundances of Akkermansia, Bacteroides, and Dubosiella, along with a reduced relative abundance of the diarrhea-associated bacterium Alloprevotella. Furthermore, metabolomics analysis indicated that 3'-SL promoted enrichment of purine metabolism, pyrimidine metabolism, nucleotide metabolism, and the pentose phosphate pathway, which may be associated with diarrhea development, inflammation amelioration, and barrier regulation. In conclusion, our findings suggest that 3'-SL ameliorates antibiotic-associated diarrhea by modulating gut microbiota and metabolite profiles.},
}

@article {pmid41547433,
year = {2026},
author = {Engin, ED and Engin, AB and Engin, A},
title = {Bidirectional effect of intestinal microbiome and host in circadian rhythm disruption: Environmental factors and breast cancer development.},
journal = {Environmental toxicology and pharmacology},
volume = {},
number = {},
pages = {104939},
doi = {10.1016/j.etap.2026.104939},
pmid = {41547433},
issn = {1872-7077},
abstract = {Suppression of nocturnal circadian melatonin signaling amplitude, disruption of the host's circadian clock through diet or phase shifts, and imbalances in the gut microbiome are significant factors that increase the incidence of breast cancer. After host-derived mature microRNAs (miRNAs) are secreted from intestinal epithelial cells, they pass to the microbiota as faecal or exosomal miRNAs and modify the epigenetic profile of the microbiome. Subsequently, the profile of host miRNAs is altered by metabolites, which are derived from intestinal bacteria. Bidirectional epigenetic modulations of host and microbiota trigger the activation of oncogenic transcriptional pathways in extraintestinal tissues. However, the effect of the mutual epigenetic interactions between the gut microbiota and the host on the development of extraintestinal cancer is not clear. The aim of this review is to discuss the factors influencing bidirectional epigenetic regulation mechanisms between microbial dysbiosis and the host in breast cancer.},
}

@article {pmid41546966,
year = {2026},
author = {Buser-Young, J and Gardell, AM and Zalutskiy, V and Briggs, BR and Gawel, JE and Alaei, SR},
title = {Arsenic contamination drives homogenizing selection in freshwater lake periphyton.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181403},
doi = {10.1016/j.scitotenv.2026.181403},
pmid = {41546966},
issn = {1879-1026},
abstract = {Bacteria and other microbes are important contributors to arsenic biotransformation processes, which can alter the bioavailability and toxicity of arsenic within a contaminated environment. Multispecies biofilms, known as periphyton, have been identified as a significant site of arsenic bioaccumulation within shallow freshwater lakes impacted by legacy arsenic contamination. We hypothesized that prolonged arsenic exposure results in the formation of distinct prokaryotic communities within the periphyton and other environmental compartments in arsenic-contaminated lakes compared to uncontaminated lakes. We also predicted that the periphyton prokaryotic communities would be distinct from, but partially overlapping with, those found in the surrounding water column and nearby littoral sediment. To test these hypotheses, we determined the taxonomic composition and modeled the assembly processes that yielded the bacterial communities found within three environmental compartments (periphyton, littoral sediment, and water column) of three lakes that had been differentially impacted by legacy arsenic contamination. We identified unique microbiomes within these environmental compartments and observed a clear shift in microbial community composition within high arsenic-contaminated periphyton. Accumulation of arsenic (~400 ppm) in the periphyton correlated with non-random (deterministic) selection for prokaryotic taxa that are more related than expected by chance (homogenizing selection). We also identified key prokaryotic genera within the arsenic-contaminated periphyton that suggest prolonged arsenic contamination may shift iron and methane biogeochemical cycles, which may regulate arsenic accumulation and mobilization. Our results imply that legacy arsenic contamination, by altering bacterial community composition and metabolic potential at the base of the food web, may influence biogeochemical and nutrient cycles at a larger scale within a freshwater lake ecosystem.},
}

@article {pmid41546896,
year = {2026},
author = {He, X and Li, Z and Ji, D and Zhang, S and Shen, Z and Feng, C},
title = {Plastisphere as a unique metabolic hotspot in river water: Impact of plastic substrate biodegradability.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141168},
doi = {10.1016/j.jhazmat.2026.141168},
pmid = {41546896},
issn = {1873-3336},
abstract = {Microplastics in aquatic environments predominantly exist as carriers of plastispheres, yet the microbial community structures and co-occurrence patterns within submillimeter plastispheres (formed by approximately 100 μm plastic particles) remain poorly understood. The effects of plastic biodegradability on plastisphere microbiome assembly and function have also not been fully characterized. Hence, this study investigated the micro-ecological composition of submillimeter plastispheres in river water, focusing on plastic degradation and carbon-nitrogen biogeochemical cycling. Compared to surrounding water, these plastispheres create novel ecological niches that serve as microbial "metabolic hotspots," fostering complex, functionally interconnected networks with enhanced carbon and nitrogen metabolic potential through strong selective pressures. Plastispheres derived from biodegradable plastics create nutrient-rich environments that favor polymer-degrading taxa, promoting niche differentiation and more stable ecological networks. Higher biodegradability was associated with greater enrichment of genes encoding plastic-degrading enzymes and elevated potential for nitrogen fixation, denitrification, and methane production. In contrast, plastispheres from non-biodegradable plastics exhibited intensified interspecific competition and increased species diversity, while limited carbon availability and tight microbial interactions facilitated enrichment of methane oxidation genes. These findings highlight submillimeter plastispheres as potential hotspots for greenhouse gas emissions, providing new insights into the ecological risks of microplastics in aquatic environments.},
}

@article {pmid41546711,
year = {2026},
author = {Ye, L and Du, J and Huang, L and Zhao, M and Tan, F and Zhang, X and Chen, X and Xu, Q and Liu, C and Lin, Y and Zhao, X and Liu, C and Chen, L},
title = {Stability of the skin microbiome during short-term in situ and in vitro conditions: Foundational support for the potential to trace skin sites and identify individuals.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {41546711},
issn = {1437-1596},
abstract = {As the largest human organ, the skin frequently interacts with the environment and retains abundant microbial information, making it a crucial source of forensic biological evidence. However, the temporal dynamics of microbial communities between in situ and in vitro samples, as well as the traceability of in vitro samples back to their donors based on corresponding in situ samples, remain unverified through longitudinal sampling and dynamic tracking. A total of 15 young adult volunteers participated in the study, during which skin microbiome samples were collected from their palms and cheeks. A short-term exposure experiment was designed, with a duration of between 0 and 72 hours. Fresh samples were collected at corresponding timepoints, in a synchronised manner. In this study, we utilised a combination of 16S rRNA gene (V3-V4 regions) sequencing and machine learning algorithms to analyse the environmental exposure effects on microbial community structure and their forensic applicability. The results indicated that the relative abundance of dominant genera remained largely stable, regardless of exposure status, with no significant temporal variations observed in the short term. Although individual lifestyles exerted an influence on microbiome composition, they did not affect significant alterations to the overall community architecture. The random forest model attained an accuracy of 91.33% in skin site identification, while the individual differentiation accuracy attained 97.33% when integrating palm and cheek data. These results indicate that the skin microbiome exhibits considerable structural stability under both in situ and in vitro conditions during short-term exposure and maintains high host specificity and site-specific characteristics.},
}

@article {pmid41546695,
year = {2026},
author = {Zhang, T and Liu, H and Huang, Z and He, Z and Fan, Y and Liu, F and Su, E and Ming, Y and Zhu, W and Wang, C and Yu, X and Niu, M and Wu, K and Sun, X and Yang, Y and He, Z and Yan, Q},
title = {Microbially Driven Organic Carbon Degradation and Nutrient Cycling during Macroalgal Decomposition.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09758},
pmid = {41546695},
issn = {1520-5851},
abstract = {The release of labile organic carbon (OC) and nutrients during seasonal macroalgal blooms can undermine blue carbon sequestration in coastal ecosystems. Although marine microorganisms mediate OC degradation during macroalgal decay, the underlying mechanisms remain poorly defined. This study employed an integrated multiomics approach (amplicon sequencing, metagenomics, and metatranscriptomics) to investigate microbial regulation of OC degradation and coupled nutrient cycling in coastal sediments with and without decomposing Sargassaceae. Total carbon in sediments increased by over 33% in the Sargassaceae area. Microbial α-diversity in the Sargassaceae area decreased significantly (p < 0.05), while processes linked to OC degradation, carbohydrate metabolism, nitrate (NO3[-]) reduction, inorganic phosphorus utilization, and sulfur metabolism were significantly upregulated (p < 0.05). Accordingly, gene expression and extracellular hydrolase activities targeting key biopolymers (i.e., cellulose, hemicellulose, starch, and chitin) were significantly upregulated (p < 0.05) in the area with Sargassaceae. Metabolism reconstruction of metagenome-assembled genomes identified Vibrio, Pseudoalteromonas, Alteromonas, and Exiguobacterium_A as primary OC degraders, with genomic capacities enriched in NO3[-] reduction and assimilatory sulfate reduction. Key environmental drivers─including the C/N ratio, dissolved organic carbon, total dissolved nitrogen (DON), and NO3[-]─shaped microbial metabolic activities during macroalgal decomposition. Our finding demonstrates that microbially driven OC degradation is a pivotal process coupled with nutrients cycling, advancing the mechanistic understanding of microbial carbon processing and its biogeochemical linkages during macroalgal decomposition in coastal ecosystems.},
}

@article {pmid41546639,
year = {2026},
author = {Sun, J and He, Y and Chen, R and Li, Z and Li, X and Han, X and Li, Y and Tang, Z and Hu, L},
title = {PTEN/PI3K/AKT Axis Mediates Aflatoxin B1-Induced Intestinal Injury via Dual Regulation of Apoptosis and Necroptosis in Jejunal Epithelial Cells.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15463},
pmid = {41546639},
issn = {1520-5118},
abstract = {Aflatoxin B1 (AFB1), the most toxic and widely distributed aflatoxin, poses considerable health hazards to both animals and humans. Following oral intake, the gastrointestinal tract is the primary site of contact. Our study shows that AFB1 exposure markedly alters the gut microbiota composition, mainly by reducing the population of beneficial bacteria. It also increases PTEN expression and suppresses the downstream PI3K/AKT signaling pathway both in jejunal and IPEC-J2 cells, promoting apoptosis and necroptosis. In addition, AFB1 impaired intestinal barrier function by decreasing expression of ZO-1 and Occludin. Notably, the PTEN-specific inhibitor VO-Ohpic can effectively alleviate the above changes induced by AFB1, confirming PTEN's key role. Our study has first elucidated the mechanism by which AFB1 induces intestinal damage through disrupting gut microbiota structure and the "PTEN/PI3K/AKT─epithelial barrier" axis, providing new targets and theoretical basis for the prevention and treatment of AFB1 poisoning.},
}

@article {pmid41546540,
year = {2026},
author = {Thelen, AC and Korten, NM and Blischke, L and Voelz, C and Beyer, C and Seitz, J and Trinh, S},
title = {Faecal Microbiota Transplantation in Anorexia Nervosa: A Systematic Review of Methodologies, Outcomes, and Challenges With Recommendations for Future Studies.},
journal = {European eating disorders review : the journal of the Eating Disorders Association},
volume = {},
number = {},
pages = {},
doi = {10.1002/erv.70080},
pmid = {41546540},
issn = {1099-0968},
support = {//Doktor Robert Pfleger-Stiftung/ ; START (101/23)//RWTH Aachen University/ ; START (16/22)//RWTH Aachen University/ ; },
abstract = {OBJECTIVE: Anorexia nervosa (AN) is a severe psychiatric disorder displaying an altered gut microbiome. Faecal microbiome transplantation (FMT) has emerged as a powerful research tool and potential treatment option in AN due to the microbiome-gut-brain axis. Current studies are limited and reveal variable FMT protocols. This leads to heterogeneous outcomes and complicates drawing definitive conclusions from existing literature. This review aims to compile and assess the different protocols and develop recommendations on ideal donors, handling of faeces, recipients, duration/frequency of FMT, and measuring transfer success for future FMT studies regarding AN.

METHODS: We systematically screened three databases (Pubmed, Embase, Web of Science), identifying 13 studies, including two human case reports, one human study protocol, and 10 animal studies.

RESULTS: While all studies demonstrated microbial alterations in the recipients, not all animal studies successfully induced an AN/underweight phenotype, suggesting that precise coordination of study protocol components to allow further refinement is essential.

CONCLUSION: Researchers should prioritise clear, comprehensive, and transparent documentation to ensure the interpretability and reproducibility of FMT procedures. Detailed reporting will enable more meaningful comparisons across studies, deepen our understanding of the microbiome's role in AN, and help identify methodological factors that influence outcomes. Ultimately, completeness of documentation in FMT studies in AN has substantial potential to support future clinical applications and improve patient care.},
}

@article {pmid41546396,
year = {2026},
author = {Xiao, Y and Chen, X and Liao, J and Wang, J and Lu, L and Chen, H and Niu, C and Wang, M},
title = {Dismantling the Necroptotic Engine: An Oral Theranostic Nanosponge for Ulcerative Colitis.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e16297},
doi = {10.1002/adma.202516297},
pmid = {41546396},
issn = {1521-4095},
support = {82400615//National Natural Science Foundation of China/ ; 82502030//National Natural Science Foundation of China/ ; 2024JJ4095//Hunan Province Outstanding Youth Fund/ ; 2022JJ40818//Hunan Provincial Natural Science Foundation of China/ ; 2025JJ60833//Hunan Provincial Natural Science Foundation of China/ ; 2025JJ70023//Hunan Provincial Natural Science Foundation of China/ ; 2024-63//Social Investment Project of Zhuzhou City in 2024/ ; },
abstract = {Ulcerative Colitis (UC) treatments often lack target specificity and have significant side effects. A key pathological driver is the excessive necroptosis of intestinal epithelial cells (IECs), which disrupts the gut barrier. To address this, we designed an intelligent oral theranostic nanoplatform, CurN@I, to dismantle the necroptosis-inflammation axis. CurN@I consists of a barium sulfate (BaSO4) core for computed tomography (CT) imaging, encapsulated within a pH-responsive silk protein nanosponge. This scaffold is co-loaded with a necroptosis inhibitor (Necrostatin-1s, Nec-1s) and an antioxidant (demethoxycurcumin, DMC). The nanostructure is condensed in the acidic stomach but swells at the neutral pH of the inflamed intestine for localized drug release. Its negative surface charge facilitates durable electrostatic adhesion to the inflamed mucosa. In murine UC models, oral CurN@I significantly outperformed first-line clinical drugs. Mechanistic analysis showed it inhibits IEC necroptosis, alleviates oxidative stress, promotes barrier regeneration, and reshapes the gut microbiome. This work presents a non-invasive, targeted oral strategy that integrates diagnosis with multi-faceted therapy to restore intestinal homeostasis, demonstrating strong potential for clinical translation.},
}

@article {pmid41546197,
year = {2026},
author = {Jian, L and Lin, Y and Zhao, Y and Wang, C and Li, Z and Li, Z},
title = {Low-dose undecanone from Stenotrophomonas maltophilia suppresses Astragalus root rot and shapes the rhizosphere bacterial microbiome.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70554},
pmid = {41546197},
issn = {1526-4998},
support = {42277317//National Natural Science Foundation of China/ ; 2025QCY-KXJ-035//Shaanxi Province Technology Innovation Guidance Project/ ; },
abstract = {BACKGROUND: Astragalus membranaceus var. mongholicus is an important Chinese herbal medicine. Root rot in Astragalus caused by Fusarium oxysporum is a destructive soil-borne disease. Biocontrol agents are currently regarded as an ecofriendly strategies for controlling root rot; however, the inherent complexity of natural environments often prevents beneficial bacteria from establishing long-term residence in the plant rhizosphere. Therefore, more effective methods against pathogenic fungi are urgently needed to safeguard both the yield and quality of Astragalus, and harnessing microorganism-derived volatile organic compounds (VOCs) is a promising strategy.

RESULTS: We isolated the bacterium Stenotrophomonas maltophilia strain B45 from the Astragalus rhizosphere that exhibited effective control of root rot. The ability of strain B45 to produce antibiotics and VOCs was determined to elucidate the possible mechanisms by which B45 inhibits pathogenic fungi. The results showed that the VOCs emitted by B45 significantly inhibited both mycelial growth and conidial germination in pathogenic fungi. Among the selected VOCs, 2-undecanone demonstrated the strongest antifungal activity and caused severe structural damage to fungal cell walls. Pot experiments confirmed that 2-undecanone fumigation markedly alleviated root rot symptoms in Astragalus. Furthermore, 2-undecanone exhibited broad-spectrum antimicrobial activity with a significantly strong inhibitory effect on both fungi and bacteria. This selective pressure led to substantial shifts in the rhizosphere microbiome composition of Astragalus. Notably, fumigation with low concentrations of 2-undecanone increased the complexity of bacterial co-occurrence networks and enriched beneficial genera, including Rhizobium, Bradyrhizobium, Sphingomonas and Lysobacter.

CONCLUSION: Our results indicate that low concentrations of 2-undecanone did not compromise the disease-suppressive capacity of the rhizosphere microbial community, and support the potential application of microbial VOCs as ecofriendly strategies for managing soil-borne diseases in agriculture. © 2026 Society of Chemical Industry.},
}

@article {pmid41546147,
year = {2026},
author = {Cho, YT and Chu, CY},
title = {Distinct Gut Microbiome Signatures of Complete Responders to Omalizumab in Chronic Spontaneous Urticaria.},
journal = {Experimental dermatology},
volume = {35},
number = {1},
pages = {e70208},
doi = {10.1111/exd.70208},
pmid = {41546147},
issn = {1600-0625},
support = {MOST 109-2314-B-002-052-MY3//The Ministry of Science and Technology of Taiwan/ ; 108-CGN12//National Taiwan University Hospital/ ; //Novartis Taiwan Co. Ltd/ ; },
mesh = {Humans ; *Omalizumab/therapeutic use ; *Gastrointestinal Microbiome ; *Chronic Urticaria/drug therapy/microbiology/blood ; Female ; Male ; Adult ; Middle Aged ; *Anti-Allergic Agents/therapeutic use ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; Interleukin-17/blood ; },
abstract = {The gut microbiota composition of patients with chronic spontaneous urticaria (CSU) has been shown to be different from that of healthy controls. However, whether the gut microbiome is different between CSU patients with different treatment responses to omalizumab is seldom examined and is largely unknown. Antihistamine-refractory CSU patients were enrolled to receive three injections of omalizumab. The patients were divided into two groups based on their treatment responses to omalizumab determined using the weekly urticarial activity score. Demographic data, blood samples and faecal specimens were collected before, during and after omalizumab treatment. Faecal specimens underwent bacterial 16S ribosomal RNA sequencing to determine the gut bacterial microbiome. Serum biomarkers were examined using enzyme-linked immunosorbent assay. Fourteen patients were enrolled and were divided into two groups: complete responders (CRs) and non-complete responders (NCRs). At baseline, the α-diversity indices of the CR group were higher than those of the NCR group. The bacterial microbiota composition was different between the groups, but these differences became less obvious after omalizumab treatment. At baseline, the genera Bacteroides, Lactobacillus, Prevotella_9, Butyricimonas, Dialister, Megasphaera and Ruminococcaceae_UCG-002 were more abundant in the CR group. In addition, the changes in the IL-33 and IL-17 levels after omalizumab treatment were correlated with the changes in the relative abundances of Dialister (r = 0.929, p = 0.003) and Ruminococcaceae-UCG-002 (r = -0.828, p = 0.022), respectively. In conclusion, the CR patients' distinct and characteristic gut bacterial microbiota profile before treatment may contribute to their better responses to omalizumab.},
}

Humans
*Omalizumab/therapeutic use
*Gastrointestinal Microbiome
*Chronic Urticaria/drug therapy/microbiology/blood
Female
Male
Adult
Middle Aged
*Anti-Allergic Agents/therapeutic use
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Treatment Outcome
Interleukin-17/blood

@article {pmid41546121,
year = {2026},
author = {Dib, EY and Attieh, P and Karam, K and Al Akel, L and Al Sayed, L and Charafeddine, T and Al Akel, L and Khoury, S and Khalek, WA},
title = {Blastocystis hominis infection inducing gut microbiome dysbiosis and aggravating Parkinson's disease symptoms: a case report.},
journal = {Journal of medical case reports},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13256-025-05763-5},
pmid = {41546121},
issn = {1752-1947},
abstract = {BACKGROUND: Blastocystis hominis infection in patients with Parkinson's disease may exacerbate gut microbiota dysbiosis, potentially worsening neurological symptoms; however, such associations remain speculative without microbiome data. Targeted interventions to restore gut microbial balance could mitigate disease progression and improve patient outcomes.

CASE PRESENTATION: An 86-year-old Caucasian male presented to the emergency department with severe watery diarrhea, up to six episodes per day, of 1 month duration. The patient's diarrhea was nonbloody and nonmucoid. He denied fever, nausea, vomiting, abdominal pain, bloating, loss of appetite, or anal itching. There was no history of weight loss, fatigue, or systemic symptoms. A stool sample was examined microscopically using normal saline, revealing Blastocystis hominis cysts (the burden was not quantified) and a rare white blood cell count. The sample was concentrated using acetylacetate and ether. Additional tests, including Clostridioides difficile and other common infectious pathogens, were ruled out in our patient to address alternative infectious etiologies.The patient was started on intravenous ciprofloxacin and metronidazole, resulting in an improvement in diarrhea consistency and frequency until the resolution of symptoms within 4 days of initiating intravenous therapy. The patient also reported mild improvement in his Parkinson's disease symptoms by the end of hospitalization, though objective neurologic post-treatment scoring (eg. Unified Parkinson's Disease Rating Scale) was not performed.

CONCLUSION: This case highlights the need to consider parasitic infections in patients with Parkinson's disease presenting with chronic diarrhea. While we hypothesize that B. hominis infection may transiently worsen Parkinson's disease symptoms through inflammatory or microbiota-mediated pathways, this remains speculative in the absence of microbiome sequencing or objective neurologic evaluation. Further studies integrating clinical, microbiological, and microbiome analyses are warranted.},
}

@article {pmid41545888,
year = {2026},
author = {Wang, J and Zhang, Z and Chen, Y and Zhou, X and Xiang, J and Yang, C and Rodionov, DA and Osterman, AL and Qiu, Q and Deng, Y and Liu, Y and Wang, C and Shang, X and Huang, L and Sun, C and Guo, J and Yang, Z and Zhai, L and Bian, Z and Lyu, A and Han, L and Jia, W and Fang, X and Zhang, L},
title = {Exploring differences in the human gut microbiome between Han Chinese and non-Chinese populations.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03932-3},
pmid = {41545888},
issn = {1474-760X},
support = {No. SZ2024KF22//State Key Laboratory of Dampness Syndrome of Chinese Medicine/ ; No. 82004234//National Natural Science Foundation of China/ ; No. 2020B1111100005//Science and Technology Planning Project of Guangdong Province, China/ ; No. C2004-23Y//Young Collaborative Research grant/ ; No. 11221026//HMRF grant/ ; RCMS/24-25/03//HKBU RCMS/ ; },
abstract = {BACKGROUND: The human gut microbiota exhibits significant diversity across populations, influenced by factors such as geography, diet, and lifestyle, particularly between the Han Chinese and non-Chinese populations. While previous studies have predominantly focused on the taxonomic abundance of the gut microbiome, the impact of single nucleotide polymorphisms (SNPs) in driving population-specific differences remains largely underexplored.

RESULTS: In this study, we systematically investigated gut microbial differences between the Han Chinese and non-Chinese populations using the Human Gut Microbiome Reference Genome Catalog (HGMRGC). We observed geography was the primary driver of microbial variation of abundance and SNPs. We identified 689 population-specific genome clusters from the Collinsella genus with functional differences in carbohydrate utilization and 108 species exhibiting distinct prevalence related to vitamin biosynthesis, antibiotic resistance, and carbohydrate metabolism. Beta diversity analysis highlighted significant inter-population differences in both microbial abundance and SNPs, while alpha diversity analysis revealed that non-Chinese populations exhibited higher diversity in microbial abundance, and Han Chinese populations displayed greater diversity in SNPs.

CONCLUSIONS: This study offers a comprehensive analysis of gut microbial differences between Han Chinese and non-Chinese populations, highlighting the profound influence of population-specific traits on microbial diversity and function. We also provide a comprehensive human gut microbial reference genome catalog, with a particular focus on the Han Chinese population, laying a foundation for future research on gut microbiota genomic variations.},
}

@article {pmid41545845,
year = {2026},
author = {Li, X and Weiland, JE and Ohkura, M and Luster, DG and Kong, P and Hong, C},
title = {Metabarcoding-based characterization of the boxwood root-zone soil microbiome.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-08094-1},
pmid = {41545845},
issn = {1471-2229},
support = {2072-22000-046-000-D//USDA-NIFA the Agricultural Research Initiative/ ; 0500-00059-001-000-D//USDA ARS Floriculture and Nursery Research Initiative/ ; 0500-00059-001-000-D//USDA ARS Floriculture and Nursery Research Initiative/ ; 2020-51181-32135//USDA-NIFA SCRI/ ; },
}

@article {pmid41545707,
year = {2026},
author = {Řezáč, T and Vrba, R and Stašek, M and Špička, P and Klos, D and Zbořil, P},
title = {The impact of preoperative oropharyngeal microflora, decontamination, and postoperative nosocomial and opportunistic infections on the occurrence of respiratory complications in patients undergoing esophagectomy for esophageal cancer after chemoradiotherapy. A single-center cohort.},
journal = {Langenbeck's archives of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00423-026-03966-y},
pmid = {41545707},
issn = {1435-2451},
}

@article {pmid41545429,
year = {2026},
author = {Maharaj, SD and Nkuna, R and Matambo, TS},
title = {Shotgun metagenomic and physicochemical profiling of municipal wastewater treatment plants using activated sludge and trickling filters.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35157-6},
pmid = {41545429},
issn = {2045-2322},
abstract = {In this study, which aimed to evaluate wastewater treatment and provide data to support improved wastewater treatment plant (WWTP) design, operation and ongoing monitoring strategies, mixed liquor, return activated sludge, primary effluent and secondary effluents of two WWTPs (n = 15) and five of the industries they service (n = 15) in Emfuleni municipality, Gauteng Province, South Africa, were characterised following a 5-month monitoring study. Following physical and chemical analysis, the parameters, including the Chemical Oxygen Demand (COD), were higher than local limits (75 mg/L) for both WWTPs and extremely high for the abattoir industry (13400 mg/L). In particular, high ammonia levels were recorded in both WWTPs. Following Illumina high-throughput sequencing and analysis using the Whole Metagenome Sequencing Assembly-based (WGSA2) pipeline on the Nephele platform, Bacteria was the dominant domain in the WWTPs. The dominant phyla were Proteobacteria (87.7%), followed by Firmicutes (8.25%), Actinobacteria (2.71%) and Bacteroidetes (0.68%). Aeromonas (39.86%) was the most dominant genus, with Acinetobacter (9.29%), Pseudomonas (6.78%), Bacillus (5.99%), and Thauera following (4.78%). Total Suspended Solids (TSS), pH, Total Dissolved Solids (TDS), and DO have influenced the diversity and distribution of the microbiome. Krona charts elucidated the xenobiotics degradation and metabolism distribution potential of the microbiome of each sampled site. This study reiterates the need for constant monitoring of WWTPs due to the high pollution parameters recorded from the WWTP effluent. The metagenomic data generated in this study provides insight into the diversity and functionality of the microbiome present in WWTPs of different process configurations which can inform existing WWTP configurations and future designs.},
}

@article {pmid41545383,
year = {2026},
author = {Wang, X and Liu, Y and Jiang, C and Huang, Z and Yan, H and Wong, SH and Johnson, CH and Zhang, J and Ge, Y and Zhang, F and Zhang, J and Lai, R and Gao, P and Zhang, X and Shen, X},
title = {TidyMass2: advancing LC-MS untargeted metabolomics through metabolite origin inference and metabolic feature-based functional module analysis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68464-7},
pmid = {41545383},
issn = {2041-1723},
support = {025402-00001//Ministry of Education - Singapore (MOE)/ ; },
abstract = {Untargeted metabolomics provides a direct window into biochemical activities but faces critical challenges in determining metabolite origins and interpreting unannotated metabolic features. Here, we present TidyMass2, an enhanced computational framework for Liquid Chromatography-Mass Spectrometry (LC-MS) untargeted metabolomics that addresses these limitations. TidyMass2 introduces three major innovations compared to its predecessor, TidyMass: (1) a comprehensive metabolite origin inference capability that traces metabolites to human, microbial, dietary, pharmaceutical, and environmental sources through integration of 11 metabolite databases containing 532,488 metabolites with source information; (2) a metabolic feature-based functional module analysis approach that bypasses the annotation bottleneck by leveraging metabolic network topology to extract biological insights from unannotated metabolic features; and (3) a graphical interface that makes advanced metabolomics analyses accessible to researchers without programming expertise. Applied to longitudinal urine metabolomics data from human pregnancy, TidyMass2 identified diverse metabolites originating from human, microbiome, and environment, and uncovered 27 dysregulated metabolic modules. It increased the proportion of biologically interpretable metabolic features from 5.8% to 58.8%, revealing coordinated changes in steroid hormone biosynthesis, carbohydrate metabolism, and amino acid processing. By expanding biological interpretation beyond MS[2] spectra-based annotated metabolites, TidyMass2 enables more comprehensive metabolic phenotyping while upholding open-source principles of reproducibility, traceability, and transparency.},
}

@article {pmid41545381,
year = {2026},
author = {Flörl, L and Schönenberger, P and Rienth, M and Bokulich, NA},
title = {Grape expectations: disentangling environmental drivers of microbiome establishment in winegrowing ecosystems.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00915-x},
pmid = {41545381},
issn = {2055-5008},
support = {310030_204275//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {Microbial communities play a central role in viticulture, influencing wine characteristics (a concept termed microbial terroir). Yet, the individual factors shaping these microbiomes remain poorly understood. We conducted a multi-year, large-scale survey of Swiss vineyards (95 sites, 680 samples), longitudinally sampling 12 sites (within 2.46 km and identical cultivar and rootstock) over three years. Using 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing, untargeted metabolomics (GC-MS, LC-MS/MS), environmental monitoring, and sensory data, we disentangled environmental factors associated with community assembly and fermentation dynamics. Topography and climate collectively structured microbiomes but affected soil- and plant-associated communities differently. Berry-associated fungi showed the strongest site-specific signature, enabling machine-learning predictions of microclimatic variation. Climatic factors and berry chemistry selectively favor fermentative yeasts, which are each linked to distinct metabolite and aroma profiles. Plant stress metabolites were further associated with microbial and metabolite composition. Our integrative approach thereby fundamentally advances our understanding of microbial biogeography and terroir in viticulture.},
}

@article {pmid41545378,
year = {2026},
author = {Kaan, AM and Duijster, DD and Ujcic-Voortman, JK and Haring, LV and Volgenant, CMC and Zaura, E},
title = {Oral health assessment in a prospective birth cohort study.},
journal = {BDJ open},
volume = {12},
number = {1},
pages = {10},
pmid = {41545378},
issn = {2056-807X},
abstract = {BACKGROUND: Robust oral health data collection in birth cohort studies is needed to understand the oral microbiome in relation to oral and general health.

OBJECTIVE: The aim of this paper is to describe the collection of oral health data in toddlers participating in a birth cohort focussing on microbiome development. Hereby, we aim to support the interpretation of variance in microbiome data.

METHODS: The Amsterdam Infant Microbiome Study (AIMS, n = ~500) is a longitudinal prospective birth cohort assessing microbiota, general health status, demographics, (oral) health behaviour and dietary behaviour in children from birth up to three years. The Oral Health Study (OHS) is a sub-study of AIMS, assessing the oral health of children and their mothers. From the mothers, data on periodontal health (clinical attachment loss, gingival bleeding), oral hygiene (dental plaque, calculus) and dental caries (DMFS) is collected. In children, data on caries prevalence (ICDAS) and infection (pufa), oral hygiene (dental plaque, calculus), Obstructive Sleep Apnoea (OSA), oromuscular function, and bitter taste sensitivity are collected.

RESULTS: Enrolment in OHS started in October 2022 and is planned to continue up to December 2028. In October 2024, 64 mother-child pairs were enroled in the study.

CONCLUSIONS: Data collection is expected to be completed by January 2028. Results will be shared at international conferences and via peer-reviewed publications.},
}

@article {pmid41545153,
year = {2026},
author = {Luo, Y and Ding, H and Mao, X and Kang, Z and Li, B and Zhou, Y},
title = {Mechanistic insights into rhizosphere microbiome assembly in Pinus tabuliformis: The role of cross-kingdom interactions and soil salinity gradients.},
journal = {Fungal biology},
volume = {130},
number = {1},
pages = {101695},
doi = {10.1016/j.funbio.2025.101695},
pmid = {41545153},
issn = {1878-6146},
mesh = {*Pinus/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Soil/chemistry ; Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Salinity ; *Microbiota ; Plant Roots/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Soil salinization caused by desertification and drought severely limits agricultural and forestry development. The rhizosphere core microbiome plays a vital role in helping host plants cope with environmental stress. However, in saline-alkali soils, it remains unclear how bacterial and fungal communities in the rhizosphere of Pinus tabuliformis interact and collectively respond to environmental factors to influence the plant. This study aims to identify the composition and functional potential of the core bacterial and fungal microbiota in the rhizosphere of P. tabuliformis in saline environments, as well as their interactions with environmental factors, thus providing a theoretical basis for utilizing core rhizosphere microbial resources. We performed high-throughput sequencing of root samples from P. tabuliformis at four locations. We analyzed the community structure and functional profiles of bacteria and fungi and their relationships with soil physicochemical properties. The environmental factors most influencing the number of core bacterial species were organic matter (OM), Na[+], and total potassium (TK). Meanwhile, total phosphorus (TP) was the most influential soil factor for core fungal species. Correlation analysis showed that TN, TP, and pH significantly affected both bacterial and fungal community variation (P < 0.05). Co-occurrence network analysis indicated complex cross-kingdom interactions between core bacterial and fungal taxa. Functional predictions suggested that bacterial communities exhibit both potential pathogenicity and stress resistance, while fungal communities are more saprotrophic and sensitive to environmental changes. Microbial communities at the SYH site displayed a "high pathogenicity-low resistance" profile, contrasting with those at the MC site. Correlation network analysis further uncovered complex mutualistic and competitive relationships among core bacterial and fungal genera. This study demonstrates that P. tabuliformis rhizosphere bacterial and fungal communities respond collaboratively to salinity stress through functional complementarity, such as bacterial enrichment in stress resistance and fungal dominance in saprotrophy. These findings may offer new insights into enhancing the adaptability of P. tabuliformis and improving sandy land ecosystems by targeted management of the soil microbiome.},
}

*Pinus/microbiology
*Rhizosphere
*Soil Microbiology
*Soil/chemistry
Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Salinity
*Microbiota
Plant Roots/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid41544734,
year = {2026},
author = {Ge, J and Gao, L and Yu, L},
title = {Intratumoral microbiota: distribution, mechanisms, and therapeutic implications.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105128},
doi = {10.1016/j.critrevonc.2026.105128},
pmid = {41544734},
issn = {1879-0461},
abstract = {Recent studies have increasingly highlighted the presence of microbiota within tumors and their substantial impact on tumor initiation, progression, and treatment efficacy. Intratumoral microbiota modulate tumor progression via multiple mechanisms, such as regulation of cancer cell proliferation, manipulation of immune microenvironment, and induction of the DNA damage. Notably, the distinct bacterial profiles associated with each tumor type can, in turn, promote or suppress tumor growth. Given the various mechanisms through which intratumoral microbiota influence tumor progression, a deeper understanding of their composition and functional roles in tumor dynamics is critical for the development of targeted therapies. In this review, we summarize current understanding and future perspectives of the bacterial lineages associated with different tumor types, discuss the mechanisms through which the intratumoral microbiome modulates tumor progression, and highlight emerging therapeutic strategies targeting intratumoral bacteria, including sonodynamic therapy (SDT), chemotherapy, immunotherapy, and oncolytic bacterial approaches.},
}

@article {pmid41544718,
year = {2026},
author = {Alexandre-Gouabau, MC and Moyon, T and Douarec, C and Moulazem, Y and Croyal, M and Gourdel, M and Roze, JC and Simon, L and Boscher, C and Billard, H and David-Sochard, A and Rezé, S and Misery, B and Bizec, BL and Guillou, S and Antignac, JP and Boquien, CY and Vigneau, E and Mahieu, B and Cano-Sancho, G},
title = {An Exploration of the Breast Milk Nutriome, Exposome and Microbiome and their Links to Early Growth in Preterm Infants.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110268},
doi = {10.1016/j.jnutbio.2026.110268},
pmid = {41544718},
issn = {1873-4847},
abstract = {BACKGROUND: Breastfeeding promotes improved growth and development in preterm infants, yet the mechanisms underlying these benefits remain unclear.

OBJECTIVE: This study explored the interplay of breast-milk nutritional, microbiological, and environmental chemical exposure on early preterm infant growth.

METHODS: In the prospective LACTACOL-cohort, growth was assessed in 137 exclusively breastfed preterm infants (including 40 twins) using Z-scores of discharge weight and fat-free mass (FFM, by air-displacement plethysmography). Breast-milk samples were analyzed for their nutriome (targeted and untargeted metabolomic and lipidomic profiling), exposome (targeting persistent organic pollutants, POPs), and microbiome (16s rRNA-sequencing). Correlation analysis and sequential random forest modelling were applied to integrate multi-omics datasets and identify determinants of discharge weight Z-score (36 observations) and FFM (21 observations).

RESULTS: The nutriome emerged as the primary contributor to the postnatal growth in preterm infants. Choline-containing lipids (sphingolipids, phosphatidylcholines and their plasmalogen forms), positively contributed to weight Z-score. Sphingomyelin enriched in nervonic acid supported positively FFM Z-score, whereas oxylipins had a negative effect. The exposome exhibited complex effects: the dioxin-like compound 1,2,3,7,8-PeCDD negatively impacted weight, while the polychlorinated biphenyl 123 positively influenced both weight and lean mass gains. Brominated flame retardants were associated with a lower FFM Z-score. Although the microbiome showed an overall minor impact, it varied with POPs and postnatal growth terciles, highlighting the co-dependencies between milk components.

CONCLUSIONS: This integrative hypothesis-generating pilot study provides novel evidence on the richness of breast-milk composition and the interplay of nutriome, exposome, microbiome in breast-milk and their joint influence on postnatal growth in preterm infants.

CLINICAL TRIAL REGISTRY: LACTACOL, ClinicalTrials.gov ID NCT NCT01493063 https://clinicaltrials.gov/study/NCT01493063.},
}

@article {pmid41544710,
year = {2026},
author = {Shivakoti, R and Laughton, B and Mandell, J and Barrios-Tascon, A and Rajendran, R and Glashoff, R and Bode, L and Aldrovandi, G and Kuhn, L},
title = {Limited evidence of benefits from clinical trials of human-identical milk oligosaccharides for infants.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100593},
doi = {10.1016/j.advnut.2026.100593},
pmid = {41544710},
issn = {2156-5376},
abstract = {Human milk oligosaccharides (HMOs) are complex carbohydrates unique to human milk and a wealth of observational and mechanistic studies indicate that HMOs are key to infant health by supporting gut microbiota and immune development. This review synthesizes evidence from randomized clinical trials evaluating whether supplementation with human-identical milk oligosaccharides (HiMOs), i.e. synthetic HMOs, in infants and young children improves health outcomes. We identified 12 randomized clinical trials: 8 in healthy infants, three in special populations of infants and one in young children. We selected only trials with a randomized, parallel group design; most of the included trials also had an observational human milk fed control group. The most widely evaluated HiMO was 2' fucosyllactose (2'FL) used alone or in combination with other HiMOs. In some trials, other bioactive components were included in the control and/or intervention formula groups complicating interpretation. All trials in healthy infants confirmed the non-inferiority of HiMO supplemented formula on growth and tolerability relative to control formula. Results were mixed with respect to reductions in morbidity and all studies were under-powered for more severe morbidity outcomes. Stool microbiota and biomarkers of inflammation and gut function generally shifted in a direction closer to human milk fed infants with HiMO intervention. Some growth improvements were noted in association with HiMO intervention in preterm infants and in infants with severe acute malnutrition. HiMO supplementation may be a promising intervention to improve child health, but due to the heterogeneity and limitations of the clinical trials that have been undertaken, many questions remain about the nature of the benefits and the specific populations who might benefit.},
}

@article {pmid41544689,
year = {2026},
author = {Ruan, W and Huang, M and Li, X and Peng, Z and Wei, Y and Mai, Z and Pan, M and Deng, J and Chen, X and Zhang, H and Meng, X and Zhang, J},
title = {Regulated cell death in COPD: Modulators, crosstalk mechanisms, and therapeutic opportunities.},
journal = {European journal of pharmacology},
volume = {1015},
number = {},
pages = {178557},
doi = {10.1016/j.ejphar.2026.178557},
pmid = {41544689},
issn = {1879-0712},
abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory airway disorder, with emerging evidence highlighting the central role of regulated cell death (RCD) in its pathogenesis. However, the regulatory mechanisms, crosstalk between different RCD pathways, and their role in intercellular communication remain poorly understood. This review examines major forms of RCD (apoptosis, necroptosis, ferroptosis, pyroptosis, NETosis, and PANoptosis) in COPD, exploring their regulation, crosstalk, role in intercellular signaling, and potential as therapeutic targets. Mechanistically, RCD is regulated through membrane receptors, epigenetic modifications, and post-translational processes. Endoplasmic reticulum (ER) stress, reactive oxygen species, and autophagy serve as common nodes across multiple RCD types. Excessive ER stress triggers apoptosis, while impaired autophagy promotes oxidative stress, cellular senescence, and inflammation. Conversely, excessive autophagy-including mitophagy, ferritinophagy, lysosomal autophagy, ER-phagy, and chaperone-mediated autophagy-can induce apoptosis, necroptosis, and ferroptosis. Regarding inter-pathway crosstalk and RCD-mediated intercellular communication: reduced macrophage apoptosis exacerbates epithelial inflammation and apoptosis; macrophage inflammation or ferroptosis can further promote epithelial ferroptosis or inflammatory responses. Ferroptosis in airway epithelial cells aggravates their own pyroptosis, and pyroptotic epithelial cells secrete exosomes that induce macrophage pyroptosis. NETotic neutrophils release extracellular DNA, driving inflammation in airway epithelia. Therapeutically, current exploratory strategies target these death pathways through diverse approaches, including existing pharmaceuticals, hormones, phytochemicals, recombinant proteins and nucleic acids, stem cell and regenerative therapies, and modulation of the airway microbiome. Deciphering the RCD network in COPD not only enhances our understanding of disease heterogeneity but also paves the way for developing precision therapeutics.},
}

@article {pmid41544466,
year = {2026},
author = {Li, B and Li, Y and Wang, B and Wang, Y and Liu, W and Xu, X and Liu, M and Zhang, X and Xiu, R},
title = {Modulation of gut microbiota by the herbal formulation Intestinal Flora Balance rescues pancreatic and intestinal microvascular dysfunction to alleviate type 2 diabetes mellitus.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157828},
doi = {10.1016/j.phymed.2026.157828},
pmid = {41544466},
issn = {1618-095X},
abstract = {BACKGROUND: The potential for microbial modulation to serve as both a therapeutic and prophylactic strategy against type 2 diabetes mellitus (T2DM)-induced microvasculopathy remains underexplored. We therefore compared the efficacy of the gut-centric herbal formulation Intestinal Flora Balance (IFB, BNFF™), when used for therapeutic reversal, synergistic rescue, or prophylactic protection.

METHODS: A murine T2DM model was used to compare three arms, IFB monotherapy, IFB-metformin combination therapy, and IFB pretreatment administered prior to disease induction. Pancreatic and intestinal microcirculation was quantified using in vivo laser Doppler and fiber optic probes. Fecal microbiota composition was analyzed via 16S rRNA gene sequencing.

RESULTS: As a therapeutic agent, IFB monotherapy effectively lowered blood glucose and restored microvascular function by reversing diabetic gut dysbiosis. Combination with metformin, while not further improving glycemia, acted synergistically to provide superior rescue of pancreatic microcirculation, indicating complementary modes of action. Prophylactic administration of IFB conferred protection, preserving microbial homeostasis and significantly attenuating the onset of both hyperglycemia and microvascular damage. IFB enhanced the richness and diversity of the intestinal microbiome in T2DM mice and restored the Bacteroidetes/Firmicutes ratio.

CONCLUSIONS: By demonstrating that IFB ecologically restores the microbiome, in contrast to metformin's pharmacological modulation, our study provides a new framework for its use as a prophylactic, a restorative monotherapy, or a synergistic partner to build microcirculatory resilience.},
}

@article {pmid41544465,
year = {2026},
author = {Zhang, WJ and Wang, J and Liao, MY and Li, CL and Liao, XX and Su, WW},
title = {Gut microbiome-metabolomics integration explores the adjunctive effect of Naoxintong capsule on atorvastatin in ameliorating hyperlipidemia: A randomized controlled pilot study.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157799},
doi = {10.1016/j.phymed.2026.157799},
pmid = {41544465},
issn = {1618-095X},
abstract = {BACKGROUND: Naoxintong Capsule (NXT), a prescribed traditional Chinese medicine (TCM), has been widely used in combination with Western medicine to treat patients with atherosclerotic cardiovascular diseases. The purpose of this study was to preliminarily investigate the effects and mechanisms of the addition of NXT to statin therapy in patients with hyperlipidemia.

METHODS: Thirty-two hyperlipidemia patients were randomly divided into two groups, which received atorvastatin and NXT plus atorvastatin treatment for 12 weeks respectively. The primary outcome was the change of lipid metabolism. Other outcomes included changes in inflammation, endothelial function, liver function and myocardial enzyme. Microbiome and metabonomics analysis were conducted to explore the potential mechanism of the effect of the addition of NXT to atorvastatin.

RESULTS: Compared to atorvastatin monotherapy, the combination therapy demonstrated an 11.3% greater reduction in LDL-C level (2.65 vs. 2.99 mmol/l, p = 0.027), a 24.7% increase in HDL-C level (1.06 vs. 0.85 mmol/l, p = 0.011) and an 18.8% greater reduction in TG (1.77 vs. 2.18 mmol/l, p = 0.011). Systemic anti-inflammatory benefits were evidenced by an 11.8% reduction in IL-6 (69.13 vs. 78.39 ng/l, p < 0.001) and a 10.4% decrease in TNF-α (90.16 vs. 100.63 ng/l, p = 0.030). Additionally, myocardial injury biomarkers showed marked improvement, with a 19.3% decrease in LDH (193.60 vs. 239.96 U/l, p < 0.001) and a 26.2% reduction in CK-MB (31.69 vs. 42.90 U/l, p < 0.001). Some key bacteria of Streptococcus_salivarius, Veillonella_parvula, Streptococcus_thermophilus, Anaerobutyricum_hallii and Ruminococcus_sp_5_1_39BFAA were discovered to be related to the enhanced effect of NXT to atorvastatin via the correlation analysis. Several metabolic pathways, such as citrate cycle, ether lipid metabolism, propanoate metabolism, and glutathione metabolism were uncovered to be closely involved in the outcome of NXT combination treatment.

CONCLUSION: Taken together, our study demonstrates that the addition of NXT to atorvastatin could enhance the therapeutic effect against hyperlipidemia, which might be related to the composition alterations of gut microbiota and changes in plasma metabolite abundances. This study provides a novel perspective for understanding the mechanism of NXT in the combination treatment of hyperlipidemia in clinic. (Trial registration No. ChiCTR2500097533).},
}

@article {pmid41544456,
year = {2026},
author = {Szewc, AM and Nicholson, AC and Livingston, K and Hopper, C and McQuiston, JR},
title = {Design, validation and evaluation of a triplex real time qualitative PCR assay targeting zoonotic Capnocytophaga species in EDTA whole blood and plasma simulated clinical specimens.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {4},
pages = {117268},
doi = {10.1016/j.diagmicrobio.2026.117268},
pmid = {41544456},
issn = {1879-0070},
abstract = {Found in the oral microbiome of cats and dogs, bacteria from the genus Capnocytophaga occasionally infect humans and can cause serious disease or death if not identified and treated promptly. Described here is a real-time triplex qualitative PCR assay designed using gene targets (rplV and secY) identified as diagnostically relevant by analysis of genomes from the Capnocytophaga species. The assay was evaluated on simulated EDTA whole blood samples/plasma and is effective at detecting down to 10 copies per microliter (10000 copies per mL, 4 log/mL) for whole blood samples (rplV /secY), and 1 copy per microliter (1000 copies per mL, 3 log mL) (rplV) and 0.5 copy per microliter (500 copies per mL, 2.69 log mL) (secY) for plasma samples. Analytical sensitivity, specificity, and reproducibility were established in plasmid-spiked simulated EDTA whole blood and plasma specimens, and clinical performance in Capnocytophaga-positive patient samples remains to be determined.},
}

@article {pmid41544443,
year = {2026},
author = {Yang, W and Zhao, Y and Liu, X and Cai, Y and Dai, Y and Zhang, H and Chen, Y and Chen, F and Liu, F and Sun, C and Yang, N and Yan, W},
title = {Multi-omics reveals co-regulation of hepatic bile acid metabolism in laying hens by host genetics and the cecal Anaerostipes.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106388},
doi = {10.1016/j.psj.2026.106388},
pmid = {41544443},
issn = {1525-3171},
abstract = {Bile acids (BA) are central regulators of lipid metabolism and key signaling molecules within the gut-liver axis. Dysregulation of BA is implicated in fatty liver hemorrhagic syndrome (FLHS), a prevalent metabolic disorder in laying hens characterized by hepatic lipid accumulation, hemorrhage, reduced egg production, and increased mortality. However, the mechanisms governing BA regulation in poultry remain poorly understood. Here, we integrated multi-omics analyses to dissect how host genetics and gut microbiota interact to modulate hepatic total bile acids (HTBA) levels. A total of 686 hens at 90 weeks of age were profiled for HTBA, free fatty acids (FFA), triglycerides (TG), and total cholesterol (TC). We integrated single-nucleotide polymorphism (SNP)-based genome-wide association studies (GWAS), liver transcriptomics, 16S rRNA profiling across different intestinal segments, and cecal metabolomics, followed by Mendelian randomization (MR) to infer causality between gut microbes and HTBA. HTBA displayed a nonlinear association with FLHS severity-lower HTBA corresponded to higher disease risk, whereas increasing HTBA aligned with reduced risk. GWAS identified 11 SNPs associated with HTBA, including a signal at 2,435,887 bp on chromosome 6 that replicated across Mixed Linear Model (MLM) and FarmCPU models and was annotated to GRID1. The hepatic expression of GRID1 showed a significant positive correlation with HTBA levels. In addition, The liver transcriptome revealed a significant downregulation in the expression of the COL4A3 and ENSGALG000005008 genes in the high HTBA group compared to the low HTBA group. These findings provide new insights into the genetic background underlying bile acid metabolism in chickens, Transcriptome analysis contrasting high- versus low-HTBA groups yielded 893 differentially expressed genes enriched for bile-acid transporters and related signaling pathways. Microbiome analyses highlighted eight genera associated with HTBA; notably, cecal Anaerostipes exhibited a strong positive causal effect on HTBA in MR (β = 9.39, P = 1.4 × 10[-10]) and coincided with metabolomic shifts in the cecum (Dehydrocholic acid and other secondary bile acids, amino acids, and lipids were elevated; while aromatic amines decreased). Collectively, these findings indicate that hepatic bile-acid metabolism in laying hens is jointly shaped by host genetics and the gut microbiota. Maintaining an appropriate HTBA range appears essential for hepatic lipid homeostasis, providing a mechanistic basis for genetic or nutritional interventions targeting bile-acid pathways to mitigate FLHS.},
}

@article {pmid41544441,
year = {2026},
author = {Ren, J and He, Q and Shang, H and Lu, T and Xiong, X},
title = {Host genetic and environmental determinants of chicken gut microbiota: A review.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106432},
doi = {10.1016/j.psj.2026.106432},
pmid = {41544441},
issn = {1525-3171},
abstract = {The gut microbiota is a diverse and abundant microbial community in animals; it plays a key role in nutrient absorption and immune defense and is an important factor affecting chicken health and growth performance. Understanding the composition of chicken gut microbiota and its influencing factors can provide a theoretical foundation for maintaining the diversity and microecological balance of beneficial microbial communities in the chicken intestinal tract. This review aimed to explore the recent advancements in understanding the non-genetic e.g. environmental and host genetic factors that influence the chicken gut microbiome, focusing on the gut microbial composition including host genetic kinship, heritability, microbial quantitative loci, and candidate genes. Studies on host genetic factors have identified several genes associated with gut microbial composition including lipid droplet associated hydrolase (LDAH) and apolipoprotein B (APOB) associated with Staphylococcus; TOX high mobility group box family member 2 (TOX2) significant locus linked to Veillonella, and reelin (RELN), lumican (LUM), and S-phase cyclin A associated protein in the ER (SCAPER) associated with intestinal microbial abundance. These factors are involved in host growth, development, and immune system regulation, collectively indicating that host genes play a significant role in regulating chicken gut microbiota. Furthermore, a comprehensive exploration of both non-genetic and host genetic factors could provide a solid foundation and practical strategies for improving chicken health and production performance by regulating the gut microbiota.},
}

@article {pmid41544344,
year = {2026},
author = {Nepal, G and Yang, D and Ojha, R and Tu, Z},
title = {Association between dairy consumption and Parkinson's disease: A systematic review and meta-analysis.},
journal = {Public health},
volume = {252},
number = {},
pages = {106143},
doi = {10.1016/j.puhe.2026.106143},
pmid = {41544344},
issn = {1476-5616},
abstract = {OBJECTIVES: Parkinson's disease (PD) is a progressive neurodegenerative disorder with no cure and rising global prevalence. Genetic, environmental, and dietary factors may influence risk. Dairy intake, may influence risk through gut microbiome changes and alpha-synuclein spread along the gut-brain axis, though epidemiological evidence is mixed. This meta-analysis examines the association between dairy consumption and PD risk in observational studies.

STUDY DESIGN: This study is a systematic review and meta-analysis of published literature.

METHODS: PubMed and EMBASE were searched for original, peer-reviewed observational studies examining dairy intake and PD risk. Pooled risk estimates were calculated using fixed- or random-effects models depending on heterogeneity (I[2] threshold: 50 %). Subgroup analyses by dairy type and sex were conducted. This study adhered to PRISMA guidelines.

RESULTS: Nine studies (eight cohort, one case-control) comprising diverse populations from the U.S., Europe, and Asia were included. A total of 15 results from 9 observational studies were analyzed. The combined cohort studies encompassed 634,327 participants with 4285 incident PD cases, while the case-control studies included 617 individuals (368 controls and 249 PD cases). High total dairy intake was significantly associated with increased PD risk (RR = 1.211; 95 % CI: 1.071-1.37; p = 0.002), with a stronger effect in males (RR = 1.282) than females (RR = 1.019). Milk consumption was also associated with increased PD risk (RR = 1.13; 95 % CI: 1.079-1.20; p < 0.001), with consistent sex-specific results. No significant associations were found for yogurt/fermented milk, cheese, butter, or ice cream.

CONCLUSIONS: Higher consumption of total dairy and plain milk is associated with an increased risk of developing PD. Further studies involving diverse populations and ethnicities should explore this association, stratified by genetic and sporadic forms of PD.},
}

@article {pmid41544313,
year = {2026},
author = {Burckhardt-Bravo, V and Funes-Ferrada, R and Valenzuela, F},
title = {Update on novel acne treatments: a narrative review focused on microbiome modulation and non-pharmacological approaches.},
journal = {Anais brasileiros de dermatologia},
volume = {101},
number = {1},
pages = {501249},
doi = {10.1016/j.abd.2025.501249},
pmid = {41544313},
issn = {1806-4841},
abstract = {Acne vulgaris is a chronic inflammatory condition with multifactorial pathogenesis. Despite the availability of numerous treatment options, there remains a need for safe, well-tolerated, and microbiome-preserving therapies. This narrative review explores recent advances in non-pharmacological acne treatments, focusing on various microbiome modulation strategies. It highlights emerging therapeutic modalities and their potential impact on clinical practice. Key findings from recent studies are summarized, providing insights for future research and practical applications in dermatology.},
}

@article {pmid41544076,
year = {2026},
author = {Tanaka, Y and Mizushima, D and Izawa, Y and Matsumura, T and Yonekawa, C and Kato, H and Mato, T},
title = {Bacterial community associated with the surface and inside of centipede forcipules: Identification and characterization.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0341165},
pmid = {41544076},
issn = {1932-6203},
mesh = {Animals ; *Arthropods/microbiology ; *Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Japan ; Phylogeny ; Bites and Stings/microbiology ; },
abstract = {BACKGROUND: In tropical to subtropical regions, centipede bites may prompt medical attention, with manifestations largely reflecting venom-related discomfort, although infections, including rare fatal necrotizing soft tissue infection (NSTI), have been reported. However, no reports are available on the commensal bacteria on centipede forcipules.

OBJECTIVES: This study aimed to investigate bacterial species residing on and in centipede forcipules and their potential role in post-bite infections.

METHODS: Nine Scolopendra mutilans, three Scolopendra japonica, and two Bothropolys rugosus were collected from three regions in Japan. The bacterial composition of their forcipules was analyzed using 16S ribosomal ribonucleic acid gene sequencing and microbiome analysis.

FINDINGS: A diverse bacterial community was observed on the centipede forcipules. Among the NSTI-associated genera examined (Escherichia, Staphylococcus, and Streptococcus), only Staphylococcus was identified as a minor population.

CONCLUSION: This study provides the first evidence that some bacteria found on centipede forcipules have been previously isolated from centipede bite infections. The risk of infection from bacteria on centipede forcipules during a centipede bite appears low. However, the presence of diverse bacterial species emphasizes the importance of thoroughly cleaning centipede bite wounds to prevent secondary infection.},
}

Animals
*Arthropods/microbiology
*Bacteria/genetics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
*Microbiota
Japan
Phylogeny
Bites and Stings/microbiology

@article {pmid41543784,
year = {2026},
author = {Chen, X and Ke, Y and Huang, X and Chen, J and Chen, J and Chen, Z},
title = {Immunotherapy in clear cell renal cell carcinoma: current Status, novel Strategies, and future perspectives.},
journal = {Clinical and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10238-025-02031-0},
pmid = {41543784},
issn = {1591-9528},
abstract = {Clear cell renal cell carcinoma (ccRCC) remains a major clinical challenge, with high rates of recurrence and limited long-term survival despite surgical resection and VEGF-targeted therapy. Immune checkpoint inhibitors (ICIs)-targeting PD-1, PD-L1, and CTLA-4-have revolutionized first-line systemic treatment, particularly in combination with VEGF tyrosine kinase inhibitors or as dual ICI regimens. However, primary and acquired resistance, immune-related adverse events (irAEs), and heterogeneous treatment responses limit the durability of benefit in many patients. This review aims to address a central question: how can immunotherapy for ccRCC evolve from incremental survival extension to durable, potentially curative control? We highlight emerging strategies-including next-generation checkpoint inhibitors (LAG-3, TIM-3, TIGIT), bispecific T cell engagers, cytokine-based agents, CAR-T and TCR-T therapies, and cancer vaccines-designed to enhance and sustain anti-tumor immunity. In parallel, we examine the role of multi-omic and spatial biomarkers, such as PBRM1 mutations, interferon-γ signatures, single-cell spatial atlases, and gut microbiome profiles, in refining patient selection and predicting therapeutic outcomes. This review uniquely integrates mechanistic insights with translational advances, providing a forward-looking synthesis of precision immunotherapy in ccRCC. We also emphasize rational combination strategies, biomarker-guided personalization, and irAE management as key priorities to overcome resistance and improve long-term outcomes.},
}

@article {pmid41543665,
year = {2026},
author = {Fu, C and Tang, W and Lu, J and Lu, X and Huang, Y and Huang, Q and Zhao, J and Mo, L and Feng, Y and Hu, X and Tang, Y and Yi, S and Wei, H and Huang, H and Li, Q and Tan, J},
title = {Complexity of the respiratory microbiome in pediatric hMPV hospitalizations: a tNGS-based study linking microbial co-detection to severe clinical outcomes.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41543665},
issn = {1439-0973},
support = {S2024082//Guangxi Medical and Health Appropriate Technology Development and Promotion Application Project/ ; },
abstract = {OBJECTIVE: Human metapneumovirus (hMPV) is a significant contributor to pediatric respiratory hospitalizations. This study aimed to delineate the epidemiological patterns, clinical characteristics, and outcomes in a large cohort of hospitalized children with hMPV infection.

METHODS: From April 2021 to November 2023, 5,021 children with acute respiratory infections were enrolled at a tertiary care center. Respiratory samples underwent targeted next-generation sequencing (tNGS) for comprehensive microbial detection. Clinical, laboratory, and imaging data were analyzed to compare disease severity between cases with single hMPV detection and those with multiple microbial detections.

RESULTS: hMPV was detected in 12.5% (629/5,021) of cases. Strikingly, 94.8% (596/629) of these cases had co-detection of additional respiratory microbes, predominantly in hMPV-bacteria-virus (212/596) and hMPV-bacteria (123/596) combinations. Commonly co-detected agents included Haemophilus influenzae (40.8%, 257/629) and Mycoplasma pneumoniae (23.1%, 145/629). Cases with multiple microbial detections were associated with elevated serum amyloid A (median 26.4 vs. 5.9 mg/L, P = 0.018), prolonged hospitalization (6.0 vs. 5.0 days, P = 0.003), and higher costs (¥8,237.5 vs. ¥3,906.5, P < 0.001). Among the 629 hMPV-positive cases, 309 (49.1%) required respiratory support. Pulmonary consolidation and hypoxemia were the most common respiratory complications, while gastrointestinal dysfunction and myocardial damage were the primary non-respiratory complications. The median hospital stay was 6 days. Of these, 34 cases (5.4%) required intensive care unit (ICU) admission, and two cases (0.3%) resulted in mortality. These severe outcomes occurred exclusively in cases where multiple microbes were detected.

CONCLUSION: The respiratory microbiome in children hospitalized with hMPV is overwhelmingly complex, with frequent co-detection of multiple microbes (94.8%), which is associated with significant clinical burdens, including prolonged hospitalization, increased need for respiratory support, and higher treatment costs. tNGS, with its ability to simultaneously identify multiple microbes, shows potential diagnostic value in uncovering this complexity and could be promising for guiding clinical management and antibiotic stewardship.},
}

@article {pmid41543527,
year = {2026},
author = {Ibiwoye, DO and Dahunsi, SO},
title = {Amplicon sequence data from the gut microbiota of broiler chickens fed black soldier fly (Hermetia illucens) larvae-based diets.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0123025},
doi = {10.1128/mra.01230-25},
pmid = {41543527},
issn = {2576-098X},
abstract = {This manuscript describes 16S Ribosomal rRNA gene amplicon sequences from gut samples of broiler chickens fed diets containing 0%, 25%, 50%, and 100% black soldier fly larvae. The data set includes raw reads, amplicon sequence variants, and taxonomic assignments supporting microbiome analysis under insect-based feeding regimes.},
}

@article {pmid41543481,
year = {2026},
author = {Tanabe, G and Mack, DR and Stintzi, A},
title = {Complete genomes of Phascolarctobacterium faecium isolates obtained from pediatric mucosal-luminal interface aspirate samples.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0078925},
doi = {10.1128/mra.00789-25},
pmid = {41543481},
issn = {2576-098X},
abstract = {The bacterium Phascolarctobacterium faecium frequently colonizes the human gut and has been reported to have reduced abundance in people with Crohn's disease. Here, we report the complete genome sequences of two P. faecium strains isolated from mucosal-luminal interface samples taken from pediatric participants with/without Crohn's disease.},
}

@article {pmid41543328,
year = {2026},
author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L},
title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70375},
doi = {10.1002/mnfr.70375},
pmid = {41543328},
issn = {1613-4133},
support = {2023BCF01028//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Male ; *Lactiplantibacillus plantarum/physiology ; *Probiotics/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice, Inbred C57BL ; *Liver Diseases, Alcoholic/therapy/microbiology ; Liver/metabolism ; Mice ; Dysbiosis ; NF-E2-Related Factor 2/metabolism/genetics ; Oxidative Stress ; Bile Acids and Salts/metabolism ; Disease Models, Animal ; },
abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.},
}

Animals
Male
*Lactiplantibacillus plantarum/physiology
*Probiotics/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects/physiology
Mice, Inbred C57BL
*Liver Diseases, Alcoholic/therapy/microbiology
Liver/metabolism
Mice
Dysbiosis
NF-E2-Related Factor 2/metabolism/genetics
Oxidative Stress
Bile Acids and Salts/metabolism
Disease Models, Animal

@article {pmid41543291,
year = {2026},
author = {Khan, MT and Mohanty, S and Devi, S and Sharma, S and Tripathi, P},
title = {Dietary Flavonoid, Gut Microbiota, and Intestinal Diseases: A Review With Bibliometric Trends and Research Insights.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70368},
doi = {10.1002/mnfr.70368},
pmid = {41543291},
issn = {1613-4133},
support = {OLP-19//CSIR-Indian Institute of Toxicology Research/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Flavonoids/pharmacology ; *Diet ; Dysbiosis ; Animals ; *Intestinal Diseases/microbiology ; },
abstract = {Flavonoids are one of the bioactive compounds among polyphenols that are found in fruits and vegetables. The flavonoids mostly get metabolized in the alimentary canal, and their interaction with the gut microbiome becomes inevitable. The gut microbiota continuously interacts with dietary flavonoids and catabolizes them into more minor metabolites directly associated with the host health. The gut microbiota is resilient and highly dependent on environmental entities, such as xenobiotics, antibiotics, and diet patterns. Any abrupt alterations in these exogenous entities cause gut dysbiosis, resulting in different abnormalities and disorders. The flavonoids alter the proportion of Firmicutes to Bacteroidetes in the gut, and those bacteria play a decisive role in the host physiology. This review draws attention to how flavonoids ameliorate gut dysbiosis and inflammation. Additionally, the biomarkers and cell signaling before and after the onset of gut dysbiosis have been discussed. Ultimately, we emphasize how flavonoid-mediated gut microbiome ameliorates intestinal-related metabolic conditions such as obesity, Crohn's disease (CD), and intestinal ulcerative colitis (IUC). In the future, further studies on the clinical level and model-based studies will warrant the use of flavonoids as better therapeutics and understanding of host health correlated with the microbiome.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Flavonoids/pharmacology
*Diet
Dysbiosis
Animals
*Intestinal Diseases/microbiology

@article {pmid41543287,
year = {2026},
author = {Ji, X and Wang, Y and Li, L and Yang, H and Ma, Z and Wang, C and Zhao, Y and Ding, Y and Xia, Y},
title = {Oxidative Balance Score, Genetic Predictors of the Gut Microbiome, and the Risk of Metabolic-Associated Fatty Liver Disease: A Cohort Study.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70372},
doi = {10.1002/mnfr.70372},
pmid = {41543287},
issn = {1613-4133},
support = {XLYC2203168//Liaoning Revitalization Talents Program/ ; LJKMZ20221149//Scientific Research Project of the Liaoning Province Education Department/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Oxidative Stress ; Prospective Studies ; Risk Factors ; Aged ; *Fatty Liver/genetics/microbiology/epidemiology ; Cohort Studies ; Genetic Predisposition to Disease ; Adult ; Proportional Hazards Models ; *Non-alcoholic Fatty Liver Disease/microbiology/genetics ; Life Style ; Diet ; },
abstract = {The oxidative balance score (OBS) integrates dietary and lifestyle factors to reflect oxidative stress. OBS has been associated with metabolic dysfunction-associated steatotic liver disease (MASLD), but the modifying roles of genetic predisposition and gut microbiota remain unclear. This study evaluated the prospective association between OBS and MASLD and potential modification by genetic and microbial factors. We analyzed 182 601 UK Biobank participants free of MASLD at baseline. OBS was calculated from 16 dietary and 4 lifestyle components. Incident MASLD cases were identified from hospital and death records. Cox proportional hazards models estimated hazard ratios (HRs) and 95% confidence intervals (CIs). During a median 10.5 years of follow-up, 1500 participants developed MASLD. Compared with the lowest OBS quartile, adjusted HRs (95% CIs) were 0.82 (0.71-0.94), 0.71 (0.61-0.83), and 0.68 (0.58-0.81) for the second, third, and fourth quartiles (p-trend < 0.001). MASLD genetic risk score (GRS) and microbial GRSs for Ruminococcus torques and Sutterella were associated with MASLD risk but did not modify the OBS-MASLD association (all p-interaction > 0.05). Higher OBS was associated with lower MASLD risk, independent of genetic and microbial GRSs. These findings provide prospective association evidence that may inform future intervention studies.},
}

Humans
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
*Oxidative Stress
Prospective Studies
Risk Factors
Aged
*Fatty Liver/genetics/microbiology/epidemiology
Cohort Studies
Genetic Predisposition to Disease
Adult
Proportional Hazards Models
*Non-alcoholic Fatty Liver Disease/microbiology/genetics
Life Style
Diet

@article {pmid41543263,
year = {2026},
author = {Baral, B and Parajuli, M and Pinilla, J and Muniz, J and Baral, B and Cançado, GGL},
title = {Safety and efficacy of oral microbiome therapy for the treatment of recurrent Clostridioides difficile infection: a systematic review and meta-analysis of randomized controlled trials.},
journal = {Scandinavian journal of gastroenterology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/00365521.2026.2616310},
pmid = {41543263},
issn = {1502-7708},
abstract = {INTRODUCTION: This systematic review and meta-analysis aimed to assess the safety and efficacy of oral microbiome therapy (OMT) for the treatment of recurrent Clostridioides difficile infection (CDI).

METHODS: A comprehensive search was performed in PubMed, Cochrane library, Scopus and Embase. All randomized controlled trials (RCTs) meeting predefined inclusion criteria were included. Statistical analysis was performed using R software.

RESULTS: Three RCTs comprising 469 patients were analyzed, of whom 250 (53%) received OMT and 219 (47%) received placebo. OMT significantly reduced CDI recurrence at week 8 compared to placebo (risk ratio [RR] 0.57; 95% confidence interval [CI] 0.33-0.99; p = 0.04). In exploratory efficacy analyses, no significant differences in recurrence were observed between groups when stratified by prior fidaxomicin use (RR 0.36; 95% CI 0.03-4.01; p = 0.40) or vancomycin use (RR 0.68; 95% CI 0.30-1.55; p = 0.35). Similarly, Firmicutes engraftment at week 1 (mean difference [MD] 41.78; 95% CI -10.55 to 94.11; p = 0.12) and week 8 (MD 34.06; 95% CI -2.49 to 70.61; p = 0.07) did not show statistically significant between-group differences. Safety outcomes and adverse events were comparable between OMT and placebo.

CONCLUSION: OMT seems to reduce CDI recurrence at week 8 compared with placebo while demonstrating a comparable safety profile, supporting its role as an effective, well-tolerated therapy for recurrent CDI. New studies are necessary to confirm these findings.

REGISTRATION: The study protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) under registration number CRD420251022230.},
}

@article {pmid41543249,
year = {2026},
author = {Beals, DG and Carper, DL and Hochanadel, LH and Jawdy, SS and Klingeman, DM and Piatkowski, BT and Weston, DJ and Doktycz, MJ and Pelletier, DA},
title = {Genomic signatures in Variovorax enabling colonization of the Populus endosphere.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160525},
doi = {10.1128/msystems.01605-25},
pmid = {41543249},
issn = {2379-5077},
abstract = {Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.IMPORTANCEPlants often depend on diverse microbial partners to support their growth, resilience, and adaptation to changing environments. Among these microbes, some bacteria inhabit the rhizosphere (the narrow zone around roots where microbes interact with the plant) while others are able to enter and persist within root tissues. The traits that distinguish these two lifestyles remain poorly understood. In this study, we examined a group of related Variovorax strains from poplar tree root microbiomes to ask why some rhizosphere-associated strains also become successful endosphere colonizers. We found that strains appear to succeed through different strategies: some may benefit from rapid growth on plant-derived carbon sources, while others may rely on stress tolerance or fine-tuned regulation. These results suggest that there is no single path from the rhizosphere into the root interior, but rather multiple strategies shaped by the host environment. Understanding this diversity can inform efforts to design resilient plant-microbe communities.},
}

@article {pmid41543226,
year = {2026},
author = {Xu, Z and Hu, J and Luo, H and Qi, X and Liu, R and Liu, Y and Zheng, Y and Li, H and Wu, B},
title = {Association between dental flossing frequency and oral microbiome in U.S. adults.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2614826},
doi = {10.1080/07853890.2026.2614826},
pmid = {41543226},
issn = {1365-2060},
mesh = {Humans ; Middle Aged ; Male ; Adult ; Female ; Cross-Sectional Studies ; *Microbiota/genetics ; United States/epidemiology ; Aged ; *Mouth/microbiology ; *Dental Devices, Home Care/statistics & numerical data ; RNA, Ribosomal, 16S/genetics ; Nutrition Surveys ; Phylogeny ; },
abstract = {BACKGROUND: The oral microbiome is vital for health, yet population-based evidence on how self-reported flossing relates to microbial communities remains limited. This study examined the association between self-reported dental flossing frequency and oral microbiome diversity in a nationally representative sample of U.S. adults.

METHODS: This cross-sectional analysis included 4,772 adults aged 30-69 from NHANES 2009-2012. Flossing frequency was categorized as non-users (0 days/week), some flossing (1-6 days/week), and daily users (7 days/week). Oral microbiome composition was profiled using 16S rRNA sequencing. α-diversity was calculated using Observed amplicon sequence variants (ASVs), Shannon, Inverse Simpson, and Faith's Phylogenetic Diversity (PD); β-diversity using Bray-Curtis and UniFrac distances. Survey-weighted linear regression and PERMANOVA were used with covariate adjustment.

RESULTS: Participants included, non-users (32%), some flossing (38%), and daily users (30%). A dose-response relationship was observed between flossing frequency and reduced microbial richness and phylogenetic diversity. Compared with non-users, daily users exhibited significantly lower richness (Observed ASVs: β = -11.46, 95% CI: -15.62 to -7.29) and phylogenetic diversity (Faith's PD: β = -0.88, 95% CI: -1.20 to -0.56). Daily flossing was associated with a modest reduction in Shannon diversity, with no significant association for the Inverse Simpson index. Inverse associations were more pronounced among younger and lower-income adults, but not among current smokers. β-diversity differed significantly across groups, although effect sizes were minimal (Bray-Curtis R[2] = 0.059%; unweighted UniFrac R[2] = 0.090%).

CONCLUSIONS: Frequent flossing was associated with reduced microbial richness and phylogenetic diversity, potentially indicating a favorable shift toward a healthier microbial community.},
}

Humans
Middle Aged
Male
Adult
Female
Cross-Sectional Studies
*Microbiota/genetics
United States/epidemiology
Aged
*Mouth/microbiology
*Dental Devices, Home Care/statistics & numerical data
RNA, Ribosomal, 16S/genetics
Nutrition Surveys
Phylogeny

@article {pmid41543131,
year = {2026},
author = {Chesneau, G and Noel, A and Bréard, D and Boulanger, A and Briand, M and Bonneau, S and Brin, C and Saux, MF and Liu, Y and Hendrickson, A and Nielsen, T and Sarniguet, A and Guilet, D and Arkin, A and Lui, L and Barret, M},
title = {Lactuchelins represent lipopeptide siderophores produced by Pseudomonas lactucae that inhibit Xanthomonas campestris.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag003},
pmid = {41543131},
issn = {1751-7370},
abstract = {The seed is a habitat with limited resources and space. Although it is widely accepted that microbial competition is a key driver of the assembly of seed-associated microbial communities, the underlying mechanisms of this competition are not well understood. The initial objective of this work was to assess the importance of contact-independent microbial competition between the phytopathogenic bacterium Xanthomonas campestris pv. campestris 8004 (Xcc8004) and 30 strains representative of the bacterial populations most commonly associated with radish (Raphanus sativus) seeds. We identified Pseudomonas lactucae CFBP 13502 as a potent inhibitor of Xcc8004, mediated by exometabolites, specifically induced by certain seed-borne strains. Transcriptomic analysis linked this inducible activity to the upregulation of a gene cluster encoding a lipopeptide siderophore. Targeted gene deletion in P. lactucae CFBP 13502 confirmed that this cluster is essential for antagonism against Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, strongly supporting iron chelation as the underlying mechanism. Through comparative metabolomics, we elucidated the structure of a family of lipopeptide siderophores, produced by P. lactucae CFBP 13502, which we named lactuchelins. Our findings provide molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.},
}

@article {pmid41543055,
year = {2025},
author = {Kozin, SV and Sigareva, AS and Moiseev, AV and Kozlova, EA and Rubailo, AD and Kravtsov, AA},
title = {[Drinking with increased deuterium content affects the gut microbiome and the antioxidant status of the organism].},
journal = {Voprosy pitaniia},
volume = {94},
number = {6},
pages = {15-27},
doi = {10.33029/0042-8833-2025-94-6-15-27},
pmid = {41543055},
issn = {0042-8833},
support = {state registration number 125011700394-5//The study was conducted within the framework of the State Task of the Southern Scientific Center of the Russian Academy of Sciences for 2025/ ; },
mesh = {Animals ; Male ; Rats ; *Deuterium/pharmacology ; Rats, Wistar ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome/drug effects ; Brain/metabolism ; *Drinking ; *Oxidative Stress/drug effects ; },
abstract = {UNLABELLED: As preparations for a manned mission to Mars are currently underway, it is crucial to understand the impact of a drinking ration with a deuterium level corresponding to those found in Martian glaciers on mammals. The objective of the research was to study the dynamics of deuterium levels in laboratory animals and changes in oxidative processes following daily consumption of a drinking ration with a deuterium concentration of 6704‰.

MATERIAL AND METHODS: The experiments were conducted on male Wistar rats, which had an initial body weight 270-300 g. The response of laboratory animals to increased deuterium level was studied using 60 Wistar rats. The animals were divided into two groups (30 rats each): Group 1 consumed a drinking ration with a deuterium concentration corresponding to the natural level (-37‰); Group 2 consumed a drinking ration containing 6704‰ deuterium. Five animals were removed from the experiment on days 5, 8, 11, 16, 21 and 31. Fecal, blood and brain samples were collected during these procedures. The stress-protective activity of the drinking ration with a modified isotopic composition was studied using 3 groups of rats (7 rats each). The «Control, -37‰» group consumed water with a deuterium concentration of -37‰. Animals of the «Stress, -37‰» and "Stress, 6704‰" groups consumed water with a deuterium concentration of -37 ‰ and 6704‰, respectively, for 38 days while simulating immobilization stress (4 hours) for 3 days, starting from the 33rd day. Deuterium level in water and blood serum was determined on a NMR spectrometer (Bruker Avance NEO 700 MHz). A DELTA V Advantage isotope mass spectrometer was used to assess deuterium level in lyophilized cerebral cortex. The activity of free radical processes was assessed by the intensity of chemiluminescence of blood plasma and cerebral cortex supernatant. Catalase activity in the cerebral cortex was measured by spectrophotometry, and gene expression levels were determined using realtime polymerase chain reaction (PCR). The proportion of dominant bacterial phyla in the intestinal microbiome was assessed using polymerase chain reaction with phylum-specific primers to 16s rRNA.

RESULTS: Consuming water w ith a deuterium concentration of 6704‰ for 31 days increased its concentration in rat blood plasma from -25±4 to 4425±103 ‰, while in brain tissue, deuterium content increased from -127±7 to 667±32‰. As deuterium accumulated in the body, catalase activity increased (2.2-5.3 fold from the 8th to the 31st day, p<0.05) and the expression of several genes involved in antioxidant protection (Cat, Gclc, Nrf2) changed. Fluctuations in the composition of the intestinal microbiome were observed, especially on the 5th and 8th days of the experiment. These fluctuations resulted in a decrease in Bacteroides by 13 and 22%, respectively, and an increase in Firmicutes by 12 and 16%, respectively. These effects are the result of adaptive responses to stress caused by increased deuterium concentrations in the body's internal environment. The decrease in the intensity of oxidative stress in rat brain and blood after immobilization stress is due to the prolonged intake of water with a deuterium level of 6704‰ and the development of a cross-adaptation effect.

CONCLUSION: It has been established that increased deuterium levels in the body fluids and tissues of laboratory animals trigger a stress response, activating mechanisms for adaptation to new conditions. This results in activation of the antioxidant system, which enhances the body's protective properties during immobilization stress.},
}

Animals
Male
Rats
*Deuterium/pharmacology
Rats, Wistar
*Antioxidants/metabolism
*Gastrointestinal Microbiome/drug effects
Brain/metabolism
*Drinking
*Oxidative Stress/drug effects

@article {pmid41543052,
year = {2026},
author = {Pérez Pérez, M and King, J and Lawson, PA and Stubbendieck, RM},
title = {Rothia similimucilaginosa sp. nov., isolated from the human nasal cavity.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {1},
pages = {},
pmid = {41543052},
issn = {1466-5034},
mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; Bacterial Typing Techniques ; Humans ; Fatty Acids/analysis/chemistry ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Nucleic Acid Hybridization ; Base Composition ; *Nasal Cavity/microbiology ; *Micrococcaceae/classification/isolation & purification/genetics ; Wisconsin ; Child ; },
abstract = {Four strains of a Gram-stain-positive, coccoid, catalase-positive, non-motile bacterium were recovered from nasal lavage samples collected from children in Wisconsin during the Spring of 2008. These strains, designated RSM42[T], RSM292, RSM386 and RSM407, were subjected to a comprehensive biochemical and polyphasic taxonomic investigation. Despite the novel bacterium sharing 99.6% 16S rRNA gene sequence identity with Rothia mucilaginosa 5762/67[T], BLAST+ average nucleotide identity, MUMmer3 average nucleotide identity and digital DNA-DNA hybridization values of 91.3%, 91.9% and 43.1%, respectively, were below the cut-off values routinely used for species demarcation. Consistent with these findings, phylogenetic and pangenomic comparisons indicated that RSM42[T], RSM292, RSM386 and RSM407 form a separate lineage within the genus Rothia. Strain RSM42[T] is further distinguished from R. mucilaginosa 5762/67[T] by its unique ability among Rothia species to use fructose-6-phosphate as a sole carbon source. RSM42[T] also exhibits an enzyme activity profile consistent with R. mucilaginosa, as it is positive for valine arylamidase and negative for C4 esterase, β-glucosidase, pyrazinamidase and trypsin, a combination not observed in other Rothia species. The major fatty acids were anteiso-C15:0 (44.2%) and iso-C16:0 (14.4%), and the moderate fatty acids were anteiso-C13:0 (2.3%), iso-C14:0 (6.0%), C14:0 (2.3%), iso-C15:0 (5.9%), C15:0 (1.9%), C16:0 (9.3%) and anteiso-C17:0 (9.5%). The major polar lipids were aminoglycolipid and diphosphatidylglycerol. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, these isolates represent a novel species within the genus Rothia, closely related to R. mucilaginosa, for which the name Rothia similimucilaginosa sp. nov. is proposed. The type strain is RSM42[T] (=ATCC TSD-447[T]=DSM 118581[T]).},
}

*Phylogeny
RNA, Ribosomal, 16S/genetics
Bacterial Typing Techniques
Humans
Fatty Acids/analysis/chemistry
DNA, Bacterial/genetics
Sequence Analysis, DNA
Nucleic Acid Hybridization
Base Composition
*Nasal Cavity/microbiology
*Micrococcaceae/classification/isolation & purification/genetics
Wisconsin
Child

@article {pmid41542943,
year = {2026},
author = {Broderick, C and Poulsen, CS and Hjelmsø, MH and Marrs, T and Radulovic, S and Logan, K and Li, X and Wu, Z and Sørensen, SJ and Ezzamouri, B and Alexander, H and Fyhrquist, N and Alenius, H and Bhattacharyya, M and Neumann, AU and Lack, G and Perkin, M and Bønnelykke, K and Stokholm, J and Flohr, C},
title = {Associations between early-life exposures and the infant skin microbiome.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf524},
pmid = {41542943},
issn = {1365-2133},
abstract = {BACKGROUND: Factors influencing the early-life skin microbiome, and the association with atopic dermatitis (AD), are relatively unexplored.

OBJECTIVE: To evaluate associations with the infant skin microbiome during the first year of life.

METHODS: 3-month-old infants from the Enquiring About Tolerance (EAT) birth cohort were examined for AD at enrolment, 1 and 3 years of age. Parent-completed questionnaires, trans-epidermal water loss (TEWL), and filaggrin mutation status were evaluated. Bacterial swabs were collected from the elbow crease and volar forearm in 148 infants at 3 months and 1 year of age, and the microbiome composition was characterized using 16S rRNA gene sequencing (V3-V4 region).

RESULTS: Shannon diversity was significantly higher at the forearm compared to the elbow. Staphylococcus, Acinetobacter, and Streptococcus were the most abundant genera across time and body-site. Microbiome community composition was primarily associated with body-site and age (p≤0.001, both). Other significant associations were found with ethnicity (p=0.009), filaggrin status (p≤0.001), urban-vs-rural residence (p=0.005), older siblings (p=0.041), bath product usage at 3 months (p=0.011), but not with pets (p=0.159), systemic antibiotics (p=0.27) nor with bathing frequency (p=0.109). The microbiome was associated with elevated TEWL (3-months p=0.004, 1-year p≤0.001) and with concurrent AD (3-months p=0.027, 1-year p≤0.001). Streptococcus parasanguinis was significantly less abundant in non-lesional skin of infants with AD at 3 months.

CONCLUSION: In addition to age and body-site, the infant skin microbiome is associated with heritable factors, the home environment, hygiene practices, and with the presence of AD.},
}

@article {pmid41542784,
year = {2026},
author = {Junger, PC and Kavagutti, VS and Deutschmann, IM and Gazulla, CR and Huber, P and Menezes, M and Paranhos, R and Amado, AM and Ferrera, I and Rigonato, J and Chaffron, S and Gasol, JM and Logares, R and Sarmento, H},
title = {Ecological Processes Shaping Marine Microbial Assemblages Diverge Between Equatorial and Temperate Time-Series.},
journal = {Molecular ecology},
volume = {35},
number = {2},
pages = {e70241},
pmid = {41542784},
issn = {1365-294X},
support = {2014/13139-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2017/26786-1//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2020/02517-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 474759/2013-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ)/ ; 303906/2021-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ)/ ; 313784/2023-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ)/ ; PVE400313-2014-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ)/ ; 3213/2020-83//Fundação de Apoio Institucional ao Desenvolvimento Científico e Tecnológico (FAI/UFSCar)/ ; 862923//Horizon 2020 Framework Programme/ ; FP7-ENV-2012-308392//European Commission/ ; PID2019-105775RB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PID2022-136281NB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CEX2024-001494-S//Ministerio de Ciencia, Innovación y Universidades/ ; 117/14//Agencia Santafesina de Ciencia, Tecnología e Innovación/ ; BJT013/2012//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Mediterranean Sea ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Seawater/microbiology ; Atlantic Ocean ; *Microbiota/genetics ; Ecosystem ; Biodiversity ; Seasons ; Bacteria/genetics/classification ; Temperature ; },
abstract = {Marine microbial communities are structured by a complex interplay of deterministic and stochastic processes, yet how these vary across latitudes remains poorly understood. Most long-term microbial observatories are restricted to temperate regions, limiting our ability to assess latitudinal contrasts in microbial dynamics. Here, we compare coastal microbial communities from two contrasting marine time-series stations using standardised molecular protocols: a new tropical site in the Equatorial Atlantic (EAMO, 6° S) and a well-studied temperate site in the Mediterranean Sea (BBMO, 41° N). Monthly 16S and 18S rRNA gene sequencing of two size-fractions (0.22-3 μm and > 3 μm) over 41 months (from April 2013 to August 2016) revealed marked differences in taxonomic composition, temporal variability and ecological assembly processes. Temperate communities exhibited strong seasonal turnover, higher beta-diversity and tighter coupling with environmental variables such as temperature and daylength. In contrast, tropical communities were compositionally more stable and more governed by biotic factors and stochastic processes such as historical contingency and ecological drift. These patterns were consistent across taxonomic domains and size-fractions, though selection was generally stronger in prokaryotes and the smallest size-fraction. Co-occurrence networks at the temperate site were more densely connected and environmentally responsive compared to tropical networks, where stochastic processes and putative biological interactions gain prominence. This study highlights the importance of integrating observatories from underrepresented latitudes into global microbial monitoring efforts, particularly as climate change alters the amplitude and frequency of environmental drivers across the ocean.},
}

Mediterranean Sea
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 18S/genetics
*Seawater/microbiology
Atlantic Ocean
*Microbiota/genetics
Ecosystem
Biodiversity
Seasons
Bacteria/genetics/classification
Temperature

@article {pmid41542760,
year = {2026},
author = {Balamurugan, J and Adeyeye, SAO},
title = {Artificial Intelligence in Nutrigenomics: A Critical Review on Functional Food Insights and Personalized Nutrition Pathways.},
journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association},
volume = {39},
number = {1},
pages = {e70200},
doi = {10.1111/jhn.70200},
pmid = {41542760},
issn = {1365-277X},
mesh = {*Nutrigenomics/methods ; Humans ; *Artificial Intelligence ; *Precision Medicine/methods ; *Functional Food ; Diet ; },
abstract = {BACKGROUND: This review critically evaluates the applications of artificial intelligence in nutrigenomics, focusing on its role in interpreting functional food-gene interactions, supporting personalized nutrition strategies, and enabling evidence-based dietary interventions for improved health outcomes.

METHODS: A systematic literature search was conducted using PubMed, Scopus, Web of Science, and Google Scholar to identify studies published between 2010 and 2025 addressing AI applications in nutrigenomics and functional foods. Search terms included "artificial intelligence," "nutrigenomics," "personalized nutrition," and "functional foods." Retrieved records were screened for relevance, methodological rigor, and thematic alignment. Following title, abstract, and full-text screening based on predefined inclusion criteria, 176 articles were assessed in detail, and 142 studies were included in the qualitative synthesis. Data were extracted and synthesized to identify key trends, methodological approaches, research gaps.

RESULTS: Artificial intelligence (AI) is increasingly transforming nutrigenomics by enabling personalized dietary recommendations based on genetic, metabolic, and lifestyle data. Machine learning and deep learning approaches facilitate the identification of complex gene-diet interactions, thereby improving the prediction of metabolic and disease-related outcomes. AI-based models support biomarker discovery, genotype-informed dietary guidance, and real-time monitoring through wearable and glucose-monitoring technologies, contributing to improved management of obesity, diabetes, and cardiovascular disorders. These tools enhance understanding of individual variability in dietary response and support precision nutrition strategies.

CONCLUSION: Despite challenges related to algorithmic bias, data privacy, and ethical governance, AI-driven nutrigenomics offers significant potential to advance personalized nutrition. Continued methodological refinement and responsible implementation are crucial for translating these innovations into clinically meaningful and equitable health applications.},
}

*Nutrigenomics/methods
Humans
*Artificial Intelligence
*Precision Medicine/methods
*Functional Food
Diet

@article {pmid41542635,
year = {2026},
author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA},
title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.08.698441},
pmid = {41542635},
issn = {2692-8205},
abstract = {UNLABELLED: Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS carriage in the vaginal tract is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D paired with vaginal GBS colonization to investigate the impact of diabetes on glucose availability, bacterial composition of the vaginal microbiome, and vaginal cytokine profiles at baseline and in response to GBS. We observed that, despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal defining compositional characteristics with decreased Mammaliicoccus being the only significant taxonomic difference. Vaginal cytokine profiling revealed consistently depressed cytokine signaling in diabetic mice, beginning with KC at baseline and expanding to an array of eight pro-inflammatory cytokines post-GBS infection. Pairing cytokine observations with GBS colonization outcomes revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS vaginal colonization. Supplementation with intravaginal rIL-1α was sufficient to resolve GBS burden differences between diabetic mice and non-diabetic controls, confirming that deficient vaginal cytokine responses contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention in the susceptible diabetic population.

IMPORTANCE: People with T2D are more susceptible to microbial infections, but there is limited understanding of the mechanisms that drive this vulnerability. One possibility is that T2D enhances colonization of opportunistic pathogens, like GBS, in mucosal reservoirs as a precursor to infection. In this study, we used a diabetic mouse model to test whether diabetes alters the vaginal mucosa to promote GBS colonization. We found that increased vaginal GBS colonization in diabetic mice was not linked to tissue glucose availability or changes to the vaginal microbiome, but instead was associated with impaired vaginal immune responses. These findings provide a foundation for translational approaches to reduce GBS persistence and dissemination in at-risk individuals.},
}

@article {pmid41542584,
year = {2026},
author = {Montgomery, TL and Nelson, EA and Downs, LA and Heney, ER and Lee, MFJ and Martino, C and McDonald, D and Rahman, G and Knight, R and Krementsov, DN},
title = {Integrated multi-omics analysis identifies microbial and metabolic signatures and drivers of CNS autoimmunity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.08.698420},
pmid = {41542584},
issn = {2692-8205},
abstract = {UNLABELLED: Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) driven by genetic and environmental determinants. The gut microbiome of people with MS (pwMS) is distinct and influences disease through immunomodulatory metabolite production. Circulating metabolites are altered in pwMS, but identifying microbial-metabolic drivers remains challenging. We previously showed that colonization by the gut commensal Limosilactobacillus reuteri (L. reuteri) exacerbates disease in the experimental autoimmune encephalomyelitis (EAE) model of MS, in a tryptophan-dependent manner. Here, we integrated microbiomic and metabolomic datasets from a longitudinal EAE study utilizing high and low tryptophan diets in mice colonized or not with L. reuteri . Gut microbiome dynamics under short- and long-term alterations in tryptophan bioavailability, were affected by diet, microbiome context, or disease. During short-term dietary intervention, L. reuteri colonization exerted a greater impact on microbiome composition than tryptophan bioavailability. With longer dietary exposure and EAE progression, high dietary tryptophan and L. reuteri colonization synergized to elicit profound microbiota changes, including alterations in Lachnospiraceae, Blautia , and Akkermansia . Integration of metabolomic and microbiomic datasets using joint Robust Aitchison PCA revealed clusters of associated metabolites and microbiota enriched for functional pathways, including bile acid and tryptophan metabolism. Metabolites outperformed microbiota in predicting EAE severity, identifying p-cresols and indoles as top disease-associated metabolites. Treatment with p-cresol or 3-indoleglyoxylic acid exacerbated EAE, enhanced proinflammatory T cell responses, and increased cerebellar pathology. These data demonstrate that dietary responses are shaped by gut microbiome composition and that integrated microbiomic-metabolomic analyses can identify drivers of disease worsening in MS.

IMPORTANCE: MS is a multifactorial disease influenced not only by genetics but also by environmental factors, potentially including diet and the composition of the gut microbiome. We show that interactions between diet and commensal gut microbiota profoundly impact levels of immunomodulatory systemic metabolites, including several that are associated with disease in pwMS. Importantly, we demonstrate that individual gut microbiota produced metabolites are sufficient to worsen disease in a mouse model of MS. Integration of gut microbiome and blood metabolite datasets combined with subsequent predictive modeling, may bolster biomarker identification and the capacity to predict disease severity in pwMS, as compared to performance of individual datasets alone. These findings highlight metabolites as key mediators linking diet and the gut microbiota to neuroinflammation. Importantly, this work suggests that targeting microbial metabolites or modifying diet-microbiome interactions may represent new strategies to reduce disease activity in MS and related autoimmune disorders.},
}

@article {pmid41542572,
year = {2026},
author = {Hayes, AMR and Klug, ME and Sharma, M and Kao, AE and Sun, S and Lopez Gonzalez, EDJ and Zhu, H and Dent, JC and Clark, RJ and Sell, DR and Nelson, D and Monnier, VM and Tsan, L and Rea, JJ and Ahuja, A and Tanios, N and Gianatiempo, I and Shanmugam, MV and Park, Y and Yu, KB and Hsiao, EY and Schier, LA and Fodor, AA and Woodruff, TM and Shuck, SC and Gati, C and Herring, BE and Coughlan, MT and Kanoski, SE},
title = {Consumption of processed foods impairs memory function through dietary advanced glycation end-products.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.07.698065},
pmid = {41542572},
issn = {2692-8205},
abstract = {Consumption of processed foods is associated with dementia, obesity, and other negative health outcomes. Sustained heat treatment, a common food processing approach to enhance flavor, induces the chemical Maillard reaction that promotes the formation of dietary advanced glycation end-products (AGEs). The neurocognitive impacts of consuming dietary AGEs are poorly understood. Here we modeled an AGE-rich diet through heat treatment fed to rats during adolescence, a critical period of neural development, to mechanistically evaluate the long-term impact of early life dietary AGEs on behavioral and neural processes. Consuming the AGE-rich diet impaired hippocampal-dependent memory function and altered the gut microbiome without inducing obesity or nonspecific behavioral deficits. AGE-induced memory deficits were coupled with impaired hippocampal glutamatergic synaptic neurotransmission and altered expression in the synapse-pruning complement system. Hippocampal synaptic deficits likely result from direct AGE-complement interactions, as our extended studies reveal competitive antagonist action of AGEs on complement receptors. Memory impairments were prevented by administration of the AGE-inhibitor, alagebrium, and by supplementation with an AGE-inhibiting bacterial taxon, Lactococcus lactis , which was depleted in the heat-treated diet. These findings reveal a functional connection between early life dietary AGEs, the microbiome, and memory impairments, thus illuminating mechanisms through which food processing negatively impacts neurocognition.},
}

@article {pmid41542410,
year = {2026},
author = {Xiao, S and Wang, M and Martin, TG and Scott, B and Fang, X and Liu, X and Yang, Y and Fu, S and Truong, SD and Gugel, JF and Maas, GL and Mullen, MP and Hill, JH and Li, VL and Markhard, AL and Zhao, M and Qi, W and Reghupaty, SC and Zhao, M and Spaas, J and Wei, W and Moholdt, T and Hawley, JA and Voldstedlund, CT and Richter, EA and Chen, X and Svensson, KJ and Bernstein, D and Leinwand, LA and Xu, Y and Long, JZ},
title = {Python metabolomics uncovers a conserved postprandial metabolite and gut-brain feeding pathway.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.09.698526},
pmid = {41542410},
issn = {2692-8205},
abstract = {Most mammals consume small and frequent meals. By contrast, pythons are ambush predators that exhibit extreme feeding and fasting patterns and provide a unique model for uncovering molecular mediators of the postprandial response [1-3] . Using untargeted metabolomics, here we show that circulating levels of the metabolite para -tyramine-O-sulfate (pTOS) are increased >1,000-fold in pythons after a single meal. In pythons, pTOS production occurs in a microbiome-dependent manner via sequential decarboxylation and sulfation of dietary tyrosine. In both pythons and mice, pTOS administration activates a neural population in the ventromedial hypothalamus (VMH). In mice, these VMH neurons are required for the anorexigenic effects of pTOS. Chronic administration of pTOS to diet-induced obese male mice suppresses food intake and body weight. pTOS is also present in human blood, where its levels are increased after a meal. Together, these data uncover a conserved postprandial anorexigenic metabolite that links nutrient intake to energy balance.},
}

@article {pmid41542073,
year = {2025},
author = {Kapoor, S and Mehta, P and Patial, V and Pandey, R and Padwad, YS},
title = {Phloretin-induced modulation in gut microbiome, mitigates colonic inflammation and alleviates colitis-associated colorectal cancer in mice.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {2730-2746},
pmid = {41542073},
issn = {2001-0370},
abstract = {Colitis associated colorectal cancer (CAC) is the fourth common cancer known to cause significant mortalities worldwide. Phloretin is a dihydrochalcone naturally found in apple, pear and strawberry. It exhibited different biological activities, namely anti-inflammatory, anticancer and anti-microbial. In the present study, the role of phloretin towards alleviating colonic inflammation and regulating gut microbiota was explored. The treatment of phloretin led to the reduction in the intestinal inflammation and maintained colon length-weight ratio by decreasing the total number of tumor nodules. We registered reduction in the colonic inflammatory cytokines levels namely TNFα, IL1β, IFNγ, and IL6 as well as expression of HSP90, Cox2, and Src found decreased. Results highlighted the restoration in the levels of tight junction proteins and the expression of Muc2 and Muc3. Further, role of phloretin in inducing apoptosis of tumor cells and the deregulation β-catenin pathway was studied. The histopathological analysis revealed normal colonic structure by decreasing leukocyte infiltration, as well as, circumvention in the reduction of the numbers of goblet cell, crypt abscess and ulceration in phloretin and 5-ASA (5-aminosalicylic acid) treated animals, compared to the diseased group. Metagenomic analysis of the gut microbiome in CAC mice revealed that phloretin significantly increased the abundance of Lactobacillus species, which exert probiotic effects and inhibit synchronous colon tumor growth by modulating β-catenin signaling. The increased abundance of L. reuteri and L. murinus was associated with regulated cellular proliferation, reduced TNF-α production, and decreased expression of COX-2, cyclin D1, and Bcl-2. In conclusion, the results obtained signify the nutraceutical potential of phloretin in restoring the intestinal barrier, maintaining the beneficial gut microbial population, and amelioration of CAC in mice.},
}

@article {pmid41542055,
year = {2026},
author = {Schluter, J and Maan, H and Jogia, W and Duan, C and Matheis, F and Nishimoto, E and Zhang, C and Sullivan, A},
title = {Sugar ABC transporter repertoires predict ecological dynamics in gut microbiome communities.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8380132/v1},
pmid = {41542055},
issn = {2693-5015},
abstract = {The gut microbiome plays a central role in human health, but modern diets and lifestyles alter its composition. Increased sugar consumption is a hallmark of modern diets, yet its impact on the microbiome remains poorly understood. Here, we combine comparative genomics, experiments, and longitudinal human diet-microbiome records to show that the response of the microbiome to dietary sugars is explained by the carriage of sugar ABC (ATP-binding cassette) transporters. Bacteria encoding these transporters exhibit enhanced growth and consistently outcompete others in both monocultures and complex consortia across contexts. Targeted deletion of sugar transporter genes in Escherichia coli, a model gut pathobiont of the expanded Oligo-Mouse-Microbiota (OMM15) consortium, reveals that a specific sugar ABC transporter gene is required to compete, and invade this community. In gnotobiotic mice colonized with the OMM15 consortium, dietary sugar supplementation selectively increases the expansion of sugar ABC transporter-positive bacteria, including E. coli. Paired human diet-microbiome data reveal that intake of dietary sugars significantly correlates with the expansion of sugar ABC transporter-positive genera. Taken together, our work identifies a genomic predictor of microbiome responses to dietary sugars and suggests ways to anticipate major shifts in the abundances of important gut bacteria.},
}

@article {pmid41542043,
year = {2026},
author = {Johnson, E and Bañuelos, P and Comrie, J and Richter, A and Le, H and Thompson, S},
title = {Characterization of dietary choline uptake by the gut microbiome reveals choline assimilating microbes and influences on host choline metabolism.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8491198/v1},
pmid = {41542043},
issn = {2693-5015},
abstract = {Choline is an essential nutrient with diverse roles in host metabolism; however, the current understanding of its microbial fate is largely restricted to trimethylamine production. Here, we apply the BioOrthogonal-labeling, Sorting, Sequencing, and mass Spectrometry (BOSSS) workflow to map dietary choline-specific gut microbial interactions. Using an alkyne-modified choline analog (propargylcholine) in mice, we fluorescently label and flow-sort choline-assimilating gut bacteria, identifying a varied set of taxa enriched in probiotic species, including Limosilactobacillus reuteri (L. reuteri). In vitro studies confirm that L. reuter i assimilates choline and converts it to long chain fatty acylcholines. Metabolomic and transcriptomic profiling revealed that L. reuteri colonization, with a choline sufficient diet, selectively elevates serum choline and increases lysophosphatidylcholine production, findings corroborated by transcriptomic evidence of upregulated hepatic genes involved in lipid metabolism. These findings uncover a new metabolic fate for dietary choline, expand the known repertoire of microbiome-derived lipids, and illustrate how specific host-microbe-diet interactions can influence host status.},
}

@article {pmid41541710,
year = {2026},
author = {Yang, RZ and Lin, S and Huang, LT and Weng, J and Liu, QM and Chen, HS and Ruan, N and Zeng, K},
title = {Effect of Targeted Probiotics on Anesthesia-Induced Sleep Disturbances via Modulating the Gut Microbiome and Metabolites.},
journal = {Food science & nutrition},
volume = {14},
number = {1},
pages = {e71447},
pmid = {41541710},
issn = {2048-7177},
abstract = {Post-operative/post-anesthesia sleep disturbances are a major concern to patients, impacting recovery and overall well-being. Probiotics may offer potential benefits for sleep promotion by modulating microbial diversity and abundance. This study aimed to investigate the effect of targeted probiotic treatment on anesthesia-induced sleep disturbances and its impact on the microbiota and metabolites in the gut and lungs. Eight-week-old male SD rats received a continuous inhalation of isoflurane, combined with oral yogurt treatment without or containing probiotic Lactobacillus and Bifidobacteria. Rats underwent electrode implantation and 7 days of polysomnography. 16S rRNA sequencing and untargeted metabolomic analysis from fecal and BALF samples were used to investigate the changes in the gut and lung microbiota and their metabolites. Isoflurane exposure led to sleep disturbances associated with a significant reduction in Lactobacillus and Bifidobacteria in the gut. Targeted probiotic supplementation improved post-anesthesia sleep quality (NREM sleep time on day 1: Yogurt+ISO group 597.25 ± 100.15 vs. Probiotic+ISO group 772.77 ± 29.36 min, p = 0.002), increased the abundance of beneficial gut bacteria, and reduced wake-related metabolites in both the gut and lungs. Correlation analysis revealed significant negative correlations between the abundance of beneficial gut flora and wake-related metabolites (all p < 0.05). The present study first indicated that targeted probiotic treatment alleviated post-anesthesia sleep disturbances by modulating both the gut and lung microbiota and their metabolites. These findings suggest that peri-anesthesia probiotic treatment may be a viable strategy for improving sleep disturbances, although further clinical research into the underlying mechanisms is needed.},
}

@article {pmid41541603,
year = {2026},
author = {Cheung, SLY and Kenway, LC},
title = {Pathophysiological Mechanisms and Nonpharmacological Interventions in Irritable Bowel Syndrome: Current Insights and Future Directions.},
journal = {Journal of nutrition and metabolism},
volume = {2026},
number = {},
pages = {4520019},
pmid = {41541603},
issn = {2090-0724},
abstract = {Irritable bowel syndrome, diagnosed using the ROME IV diagnostic criteria, is one of the most common dysfunctional disorders of the gastrointestinal system with a high global prevalence. Although symptom presentation is diverse, symptoms primarily manifest as abdominal pain, bloating, and alterations to bowel habits, negatively impacting quality of life but without an associated increase in mortality risk. Disruptions to the gut-brain axis, the bidirectional communication system between the central nervous system and the enteric nervous system, are hypothesised to be at the core of irritable bowel syndrome. Dysfunction may also be associated with stress and anxiety, as well as dietary factors, among other aspects related to physical and social environment, genetic predisposition and medical history. Patients with irritable bowel syndrome have also demonstrated increased vulnerability to neurotransmitter imbalances, with abnormalities associated with changes in gastrointestinal motility, low-grade inflammation and visceral pain. Moreover, chronic stress and anxiety may significantly exacerbate symptoms through the upregulation of cortisol secretion, disrupting the gut microbiome and elevating visceral sensitivity. While the gut microbiome maintains the integrity of the gut-brain axis and intestinal barrier, decreases in its diversity heighten susceptibility to intestinal inflammation. Although there is currently no known cure for irritable bowel syndrome, research supports stress management and behavioural therapies, a low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet, and probiotic supplementation as key interventions to alleviate symptoms. Additionally, faecal microbiota transplantation emerges as a promising intervention that addresses some of the limitations in current interventions. This literature review explores the pathophysiological mechanisms relating to irritable bowel syndrome, with insight into current interventions and future directions to directly address the underlying factors driving symptomology.},
}

@article {pmid41541500,
year = {2025},
author = {Broedlow, CA and Swanson, E and Cherenack, EM and Basting, C and Nogueira, NF and France, M and Yue, P and Chakrawarti, A and Salazar, A and Acosta, L and Raccamarich, P and Gale, M and Ravel, J and Fein, LA and Holm, J and Alcaide, ML and Klatt, NR},
title = {Common cervicovaginal sequencing methods result in discordant molecular diagnoses of bacterial vaginosis and reveal strain level effects of Gardnerella vaginalis.},
journal = {npj women's health},
volume = {3},
number = {},
pages = {},
pmid = {41541500},
issn = {2948-1716},
support = {P30 AI073961/AI/NIAID NIH HHS/United States ; R01 AI138718/AI/NIAID NIH HHS/United States ; },
abstract = {Bacterial vaginosis (BV) is associated with HIV transmission and pre-term birth, yet the etiology of BV remains unknown. Our analysis addressed that knowledge gap by comparing diagnostic techniques and using Bayesian inference to find species-specific associations with clinical indicators. We also assessed the effect of sequencing methodology on the results of molecular BV profiling. We observed significant differences in microbial diversity within BV-associated CSTs based on clinical diagnosis. CST assignments were substantially influenced by sequencing methodology, with concordance between methods as low as 59% for metatranscriptomic and metataxonomic-based CST assignment. We also found that Gardnerella has a strain-dependent association with individual Amsel's criteria, and that Dialister micraerophilus and Parvimonas micra are positively associated with Amsel's criteria while Lactobacillus is negatively associated. These results highlight the challenge of characterizing a condition without a single etiological agent, reinforcing the need for more granular diagnoses and treatments that are sensitive to BV variability.},
}

@article {pmid41541221,
year = {2026},
author = {Cai, Z and Wang, M and Xian, Z and Hu, Y and Pan, Y and Feng, X and Sun, B and Deng, M and Li, Y and Liu, G and Hu, W and Liu, D and Guo, Y},
title = {Effects of inactivated Lactobacillus acidophilus on growth performance, blood parameters, fecal fermentation and microbiota in neonatal Holstein calves.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {24},
number = {},
pages = {1-16},
pmid = {41541221},
issn = {2405-6383},
abstract = {Inactivated probiotics can exhibit beneficial properties similar to live probiotics while offering greater stability and safety. However, the understanding of how inactivated probiotics affect the growth, health, and gut microbiota of neonatal calves is still limited. This study investigated the effect of inactivated Lactobacillus acidophilus (ILA, ≥1 × 10[8] CFU equivalents/mL) on growth performance, blood parameters, and fecal fermentation and microbiota of neonatal dairy calves. Forty female Holstein calves (37.92 ± 2.04 kg; 2.45 ± 0.96 d) were randomly assigned to a basal diet supplemented with 0 (CK), 2, 4, or 6 mL/d of ILA (ILA2, ILA4, and ILA6) until 54 d of age. The results showed that while ILA supplementation did not affect body weight or feed efficiency, it linearly increased structural growth indices (body length and heart girth) at both 30 and 54 d of age (P < 0.05). Crucially, ILA significantly reduced fecal scores (P < 0.001) and diarrhea incidence (P = 0.019), particularly in the ILA4 group. Serum analysis revealed that ILA elevated the levels of immunoglobulins A, G, and M (P < 0.001), as well as total protein, globulin, glucose, and superoxide dismutase (P < 0.05), indicating improved immune status and metabolic health. Furthermore, ILA modulated fecal fermentation, inducing a quadratic response in acetic acid (P = 0.005) and total volatile fatty acids (P = 0.010). Microbiome analysis indicated linear increases in Firmicutes, Proteobacteria, and the genus Faecalibacterium, coupled with linear decreases in Bacteroidota, Spirochaetota, and Rikenellaceae_RC9_gut_group (P < 0.05). This ILA-induced microbial shift enriched functional pathways associated with transport, transcription, replication, and butanoate metabolism compared with the CK group (P < 0.05). Spearman correlation analysis identified significant correlations between fecal microbiota composition and host growth, metabolism, and health. Collectively, the beneficial effects of ILA on structural growth, diarrhea reduction, fecal fermentation, and metabolic health in calves are closely related to dynamic changes in fecal microbiota. These beneficial effects may stem from ILA's ability to modulate the composition, diversity, and function of the gut microbiota. This study offers a scientific basis for the application of ILA in calf production.},
}

@article {pmid41541069,
year = {2025},
author = {Jafari-Nakhjavanlou, A and Irajian, P and Zahedi Bialvaei, A},
title = {Potential mechanisms linking bacterial factors to the development and progression of multiple sclerosis.},
journal = {Infectious medicine},
volume = {4},
number = {4},
pages = {100219},
pmid = {41541069},
issn = {2772-431X},
abstract = {Multiple sclerosis (MS) is a chronic neurodegenerative and autoimmune disease of the central nervous system (CNS). While the exact etiology remains unclear, emerging evidence suggests that bacterial toxins play significant roles in MS pathogenesis and progression. We aimed to review mechanisms by which bacterial toxins influence MS development, focusing on molecular mimicry, epitope spreading, bystander activation, and blood-brain barrier (BBB) disruption. Specific toxins, including Clostridium perfringens epsilon toxin, Staphylococcus aureus superantigens, and Chlamydia pneumoniae heat shock proteins, demonstrate distinct pathogenic mechanisms in promoting CNS inflammation. Crucially, several toxins disrupt BBB integrity, making it easier for immune cells and cytokines that promote inflammation to enter the CNS and exacerbate neural inflammation. Furthermore, through molecular mimicry and epitope dissemination, bacterial antigens can initiate cross-reacting immune responses that may lead to autoimmune attacks on myelin. This review highlights the complex interplay between bacterial toxins, immune modulation, and genetic susceptibility in MS. Understanding these toxin-mediated pathways reveals the complex interplay between the microbiome and MS pathogenesis, potentially leading to novel therapeutic interventions targeting bacterial contributions to autoimmune neurodegeneration.},
}

@article {pmid41540767,
year = {2026},
author = {Yoo, E and Uchida, AM},
title = {Response to: An Overview of Predictive Biomarkers and Detection Approaches for Immunotherapy Response in GI Malignancies.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70242},
pmid = {41540767},
issn = {1440-1746},
}

@article {pmid41540666,
year = {2026},
author = {Munyaneza, V and Zhang, W and Haider, S and Ren, L and Song, H and Yi, B and Wang, C and Shi, L and Xu, F and Kant, S and Ding, G},
title = {Soil Microorganisms as Drivers of Pollutant Degradation, Metal Detoxification, and Sustainable Agriculture.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13543},
pmid = {41540666},
issn = {1520-5118},
abstract = {Soil microorganisms are essential drivers of ecosystem functioning and mediate pollutant degradation, metal detoxification, and nutrient cycling. This review aims to synthesize recent mechanistic advances in understanding how microbes degrade organic contaminants, transform or immobilize metals, mitigate toxic effects on plants through chelation, redox reactions, sequestration, and support soil structure and fertility. Microbial consortia and rhizosphere-associated taxa accelerate pollutant breakdown, reduce metal toxicity, and enhance plant resilience in acidic or contaminated soils. Integration of microbial processes with amendments such as biochar and organic matter further improve remediation efficiency and sustainability. Key insights reveal that microbial signaling networks, biofilm formation, and plant-microbe interactions are critical for maintaining the ecosystem stability under stress. These findings underscore the potential of microbial driven strategies to restore degraded soils, minimize reliance on chemical inputs, and promote sustainable agricultural practices, although field-scale persistence and ecological interactions warrant further research.},
}

@article {pmid41540554,
year = {2026},
author = {Busby, PE and Apigo, A and Sirova, D and Pérez-Pazos, E and Gervers, KA and Neat, A and Romero-Jiménez, MJ and Anderegg, LDL and Taylor, G},
title = {Do stomatal traits modulate leaf microbiome assembly?.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70914},
pmid = {41540554},
issn = {1469-8137},
support = {2022-67013- 37437//National Institute of Food and Agriculture/ ; 2020-67013-31797//National Institute of Food and Agriculture/ ; 2209329//Directorate for Biological Sciences/ ; 2319568//Division of Emerging Frontiers/ ; 2146552//Division of Integrative Organismal Systems/ ; CZ.02.01.01/00/22_010/0003414//Ministry of Education, Youth and Sports: MSCA Fellowship/ ; },
abstract = {Elucidating the factors controlling plant microbiome assembly is a major research goal in plant biology given a growing awareness of microbial community contributions to host plant health and fitness. While stomata have long been recognized to influence pathogen colonization, less is known about whether or how stomatal traits regulate diverse communities of nonpathogenic microbes that make up the majority of the leaf microbiome. In this Viewpoint, we propose that stomata are a primary filter by which plants influence the assembly of leaf-associated microbial communities. We discuss three nonmutually exclusive hypotheses for how stomatal traits influence leaf microbes, including preliminary support for each based on published studies of foliar fungi and bacteria. The stomatal density hypothesis argues that a greater density of pores increases the rate of microbial entry into the leaf, while the stomatal function hypothesis posits that the duration and speed of stomatal opening and closing regulate microbial access into the leaf. The stomatal covariation hypothesis recognizes that many other leaf traits covary with stomatal traits and thus could contribute to observed relationships between stomatal traits and leaf microbiome structure. Finally, we propose research priorities to improve our understanding of stomatal control over leaf microbiome assembly.},
}

@article {pmid41540478,
year = {2026},
author = {Premathilaka, C and Godakumara, K and Peffers, MJ and Clarke, EJ and Dorbek-Sundström, E and Orro, T and Kodithuwakku, S and Fazeli, A},
title = {Cryptosporidium spp. infection drives distinct alterations in the faecal extracellular vesicles metaproteome of calves.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {8},
pmid = {41540478},
issn = {1674-9782},
support = {857418 "COMBIVET"//Horizon 2020/ ; 101079349 "OH-Boost"//Horizon 2020/ ; P17019VLKM//Eesti Maaülikool/ ; },
abstract = {BACKGROUND: The gut is primarily responsible for digestion and nutrient absorption, plays essential roles in immune regulation and metabolic balance, and is supported by a diverse microbiome essential for digestion, absorption, and defence from pathogens. Understanding gut physiology and pathophysiology in pre-weaned calves is essential, as infections like cryptosporidiosis can lead to gut dysbiosis, impair growth, and negatively affect long-term productivity. Faeces are considered easily accessible biological specimens that can be used to monitor gastrointestinal disorders. The methods employed in this study aimed to investigate the potential use of faecal extracellular vesicles (fEVs) as a non-invasive tool for assessing gut health and infections in calves. Particularly, considering Cryptosporidiosis as a model for gut infectious disease.

RESULTS: The analysis using a hybrid reference-based metaproteomic approach revealed that the proteomic profiles of fEVs significantly differed from that of faecal crude (FC) suspensions. Both sample types contained microbial and host proteins, which are important for maintaining gut defence and microbial homeostasis. However, Cryptosporidium spp. infection significantly shifted the fEV proteome, reducing both host and microbial proteins involved in gut defence. It also reduced proteins from microbes that are important for maintaining microbial homeostasis, while increasing stress-related proteins. Further, lyophilisation of fEVs significantly altered the protein profiles.

CONCLUSION: These findings underscore that fEVs contain host and microbial proteins that are a valuable resource for studying gut physiology, pathophysiology, host-microbe-pathogen interactions, and microbiome dynamics. Changes in the proteomic profile of fEVs during Cryptosporidium spp. infection demonstrates the pathogen's ability to manipulate host immune defences and microbiome composition for its survival and replication. Overall, these findings support the utility of fEV proteomics as a non-invasive platform for biomarker discovery and advancing research in gastrointestinal health and disease in livestock.},
}

@article {pmid41541076,
year = {2023},
author = {Nwafor, DC and Brichacek, AL and Rallo, MS and Bidwai, N and Marsh, RA},
title = {Subarachnoid hemorrhage: New insights on pathogenesis.},
journal = {Frontiers in stroke},
volume = {2},
number = {},
pages = {1110506},
pmid = {41541076},
issn = {2813-3056},
abstract = {Subarachnoid hemorrhage (SAH) is a type of hemorrhagic stroke characterized by high morbidity and mortality. Saccular intracranial aneurysms account for most cases of SAH. While the role of hemodynamic stress and inflammation have been extensively studied in SAH, little is known about the role of the microbiome in SAH despite recent studies uncovering new insights on the effects of microbiome alteration in ischemic stroke. This review presents the current knowledge around the role of the microbiome in intracranial aneurysm formation and rupture. We also highlight the influence of diet on intracranial aneurysm formation and provide evidence that corroborates the targeting of inflammatory pathways as a potential strategy to curb SAH-associated neurological dysfunction.},
}

@article {pmid41540332,
year = {2026},
author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L},
title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04699-6},
pmid = {41540332},
issn = {1471-2180},
abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.},
}

@article {pmid41540252,
year = {2026},
author = {Jo, Y and Joshi, NR and Chellappa, K},
title = {The microbiome at the centre of NAD[+] supplementation.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {41540252},
issn = {2522-5812},
}

@article {pmid41540124,
year = {2026},
author = {Nickols, WA and Kuntz, T and Shen, J and Maharjan, S and Mallick, H and Franzosa, EA and Thompson, KN and Nearing, JT and Huttenhower, C},
title = {MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41540124},
issn = {1548-7105},
support = {U19AI110820//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32GM135117//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Microbial community analysis typically involves determining which microbial features are associated with properties such as environmental or health phenotypes. This task is impeded by data characteristics, including sparsity (technical or biological) and compositionality. Here we introduce MaAsLin 3 (microbiome multivariable associations with linear models) to simultaneously identify both abundance and prevalence relationships in microbiome studies with modern, potentially complex designs. MaAsLin 3 can newly account for compositionality either experimentally (for example, quantitative PCR or spike-ins) or computationally, and it expands the range of testable biological hypotheses and covariate types. On a variety of synthetic and real datasets, MaAsLin 3 outperformed state-of-the-art differential abundance methods, and when applied to the Inflammatory Bowel Disease Multi-omics Database, MaAsLin 3 corroborated previously reported associations, identifying 77% with feature prevalence rather than abundance. In summary, MaAsLin 3 enables researchers to identify microbiome associations more accurately and specifically, especially in complex datasets.},
}

@article {pmid41539935,
year = {2026},
author = {Vizon, C and Hochart, C and Galand, PE and Nugues, MM},
title = {Impacts of Nearby Algae on Recruitment Success and Early Microbiome Development of the Coral Acropora cytherea.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70241},
doi = {10.1111/1462-2920.70241},
pmid = {41539935},
issn = {1462-2920},
support = {ANR-18-CE02-0009-01//Agence Nationale de la Recherche/ ; },
mesh = {*Anthozoa/microbiology/growth & development ; Animals ; *Microbiota ; Coral Reefs ; *Bacteria/classification/genetics/isolation & purification ; Larva/microbiology/growth & development ; Symbiosis ; *Dinoflagellida/physiology ; Ecosystem ; },
abstract = {The persistence of coral reefs is dependent on the arrival and settlement of coral larvae followed by their post-settlement growth and survival. Despite evidence showing that benthic algae have variable effects on corals, it is still unclear how benthic communities of the coral nursery habitat impact the early development of the coral microbiome and if these impacts relate to the survival and growth of newly settled corals. Here, we tested whether the survival and growth of Acropora cytherea recruits are impacted by surrounding algae, and whether specific algae influence their associated bacterial and Symbiodiniaceae communities. A 6-month survey of coral larvae experimentally settled near different algae showed that crustose coralline algae enhanced recruit survival. However, despite variation in their microbiome, the presence of different algae did not impact the coral microbial community composition. The recruit microbiome was colonised by bacteria shared among all benthic substrates rather than bacteria unique to specific algae. Furthermore, the microbiome of coral larvae was different from that of the recruits. We conclude that the microbiome of corals in their early life stages is structured by host ontogeny rather than by their surrounding benthos, but that the surrounding benthos contributes to the transfer of opportunistic bacteria.},
}

*Anthozoa/microbiology/growth & development
Animals
*Microbiota
Coral Reefs
*Bacteria/classification/genetics/isolation & purification
Larva/microbiology/growth & development
Symbiosis
*Dinoflagellida/physiology
Ecosystem

@article {pmid41539801,
year = {2026},
author = {Zhang, X and Zang, X and Zhuang, J and Cheng, Y and Qin, Y and Jiang, J and Liang, Y and Song, Y and Liu, Y},
title = {Construction of a synthetic microbial community model for the predicting of characteristic aromas in Penglai Cabernet Sauvignon wines.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118162},
doi = {10.1016/j.foodres.2025.118162},
pmid = {41539801},
issn = {1873-7145},
mesh = {*Wine/analysis/microbiology ; Fermentation ; Saccharomyces cerevisiae/metabolism/genetics ; *Odorants/analysis ; *Vitis/microbiology ; *Microbiota ; Food Microbiology ; *Microbial Consortia ; Volatile Organic Compounds/analysis ; },
abstract = {To address the challenge of achieving targeted flavor formation in traditional fermented foods by overcoming the unpredictability of spontaneous fermentation, this study introduces a novel approach using Chinese Penglai Cabernet Sauvignon wines as a model system. First, the study identified and selected a collection of core functional microbial strains, including key Saccharomyces cerevisiae genotypes and non-Saccharomyces, from the indigenous spontaneous fermentation microbiome. By reconstituting them into a defined synthetic microbial community, we successfully developed a mathematical model that quantitatively correlates microbial community structure with characteristic aroma compounds. This model enables the accurate prediction and targeted shaping of desired aroma profiles through the rational design of starter cultures. This work provides a methodological framework that moves beyond the descriptive analysis of spontaneous fermentations towards the engineering of synthetic microbial consortia for targeted wine style. The core microbial resources and the predictive model presented here offer a concrete strategy for enhancing regional typicity and quality consistency in Penglai Cabernet Sauvignon production.},
}

*Wine/analysis/microbiology
Fermentation
Saccharomyces cerevisiae/metabolism/genetics
*Odorants/analysis
*Vitis/microbiology
*Microbiota
Food Microbiology
*Microbial Consortia
Volatile Organic Compounds/analysis

@article {pmid41539791,
year = {2026},
author = {Liu, P and Gao, C and Li, S and Wu, D and Zhang, Z and Chen, W and Li, W and Shao, F and Wang, HD and Yang, Y},
title = {A novel Fucose-specific lectin from Morchella esculenta modulates gut-liver Axis to alleviate non-alcoholic fatty liver disease.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118106},
doi = {10.1016/j.foodres.2025.118106},
pmid = {41539791},
issn = {1873-7145},
mesh = {*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Diet, High-Fat/adverse effects ; *Lectins/pharmacology/chemistry/isolation & purification ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Male ; *Fucose/metabolism ; Lipid Metabolism/drug effects ; Disease Models, Animal ; },
abstract = {Morchella esculenta is an underexplored source of lectins with diverse bioactivities. In this study, a novel fucose-specific lectin (MEP5) was isolated from M. esculenta, with a molecular weight of 33.12 kDa and a characteristic carbohydrate-recognition domain. Structural analysis revealed that MEP5 predominantly consists of random coils and extended strands, with α-helix as a minor component. In a high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD) mouse model, MEP5 treatment significantly ameliorated NAFLD by normalizing lipid profiles (TG, TC, LDL-C, HDLC), repairing adipose tissue morphology, and reducing hepatic lipid accumulation. Mechanistically, MEP5 exerted hepatoprotective effects through transcriptional modulation of key lipid metabolic regulators (PPARα, SREBP-1, Fasn, Hmgcr, G6pc1, UCP-1, CD36, ABCA1, PRDM16). Network pharmacology and experimental validation indicated that MEP5 alleviated hepatic steatosis by inhibiting the MAPK signaling pathway. Additionally, integrated metabolomic and 16S rRNA sequencing analyses identified alterations in the gut microbiome, with enrichment of Duncaniella, CAG-485, and UBA3282, and depletion of Desulfovibrio-R, which were linked to MEP5's protective effects. This study highlights the potential of M. esculenta lectins as a therapeutic tool, advancing our understanding of gut-liver interactions and metabolic regulation.},
}

*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism
Animals
*Gastrointestinal Microbiome/drug effects
Mice
Diet, High-Fat/adverse effects
*Lectins/pharmacology/chemistry/isolation & purification
*Liver/metabolism/drug effects
Mice, Inbred C57BL
Male
*Fucose/metabolism
Lipid Metabolism/drug effects
Disease Models, Animal

@article {pmid41539761,
year = {2026},
author = {Long, M and Wang, H and Zhang, F and Ran, Y and Li, Y and Luo, J and Chen, Z and Tian, Z and Tan, S and Liu, X},
title = {Nanogel-encapsulated Rosa roxburghii Tratt fruit polyphenols ameliorated ulcerative colitis by regulating gut microbiota and PI3K/Akt and NF-κB pathways.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118149},
doi = {10.1016/j.foodres.2025.118149},
pmid = {41539761},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; *Polyphenols/pharmacology/chemistry ; Proto-Oncogene Proteins c-akt/metabolism ; *Fruit/chemistry ; Signal Transduction/drug effects ; *Rosa/chemistry ; Phosphatidylinositol 3-Kinases/metabolism ; Nanogels/chemistry ; Male ; Mice ; Anti-Inflammatory Agents/pharmacology ; Oxidative Stress/drug effects ; Mice, Inbred C57BL ; Antioxidants/pharmacology ; },
abstract = {Rosa roxburghii Tratt fruit polyphenols (RP) possess antioxidant, anti-inflammatory, and immunomodulatory properties, showing potential for ulcerative colitis (UC) treatment. However, their efficacy is limited by bioavailability and targeting efficiency. To address this, RP were encapsulated into acylated chitosan-crosslinked carboxymethyl konjac glucomannan (ACs-CKGM) nanogel (RPNG). Experimental results demonstrated that RPNG significantly enhanced intestinal barrier function by upregulating tight junction proteins (ZO-1, Occludin and Claudin-3) and mucus secretion (MUC2). It effectively mitigated oxidative stress by restoring antioxidant enzymes (SOD, GSH-Px and CAT) while reducing MPO, COX-2 and iNOS activation. Through integrated ELISA, western blot, and transcriptomic analyses, we emonstrated that RPNG specifically inhibited PI3K/Akt/mTOR and NF-κB signaling pathways, decreasing inflammatory cytokines (e.g., TNF-α, IL-6) while increasing anti-inflammatory mediators (e.g., IL-10). Gut microbiome analysis showed RPNG reversed DSS-induced dysbiosis by enriching beneficial bacteria (e.g., Muribaculum sp.) and suppressing pathogens (e.g., Escherichia coli). These findings highlight RPNG as a novel targeted strategy for UC management, supported by multi-omics mechanistic insights.},
}

*Gastrointestinal Microbiome/drug effects
*Colitis, Ulcerative/drug therapy/microbiology
Animals
NF-kappa B/metabolism
*Polyphenols/pharmacology/chemistry
Proto-Oncogene Proteins c-akt/metabolism
*Fruit/chemistry
Signal Transduction/drug effects
*Rosa/chemistry
Phosphatidylinositol 3-Kinases/metabolism
Nanogels/chemistry
Male
Mice
Anti-Inflammatory Agents/pharmacology
Oxidative Stress/drug effects
Mice, Inbred C57BL
Antioxidants/pharmacology

@article {pmid41539751,
year = {2026},
author = {Zhou, M and Xia, C and Jing, B and Duan, J and Li, H and Che, H},
title = {Sepia pharaonis ink derived melanin ameliorated high-fat diet induced lipid dysmetabolism: Insights from microbiome and hepatic transcription.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118086},
doi = {10.1016/j.foodres.2025.118086},
pmid = {41539751},
issn = {1873-7145},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Liver/metabolism/drug effects ; *Melanins/pharmacology ; *Lipid Metabolism/drug effects ; Male ; *Sepia/chemistry ; Mice ; Mice, Inbred C57BL ; },
abstract = {Sepia pharaonis ink melanin (MSI) is a natural eumelanin-rich compound with anti-inflammatory activities and gut microbiota-regulating effects. However, its impact on lipid dysmetabolism triggered by high-fat diet (HFD) remains unclear. This study sought to investigate the improvement and the underlying mechanisms of MSI on lipid metabolism through biochemical indicators, liver transcriptomics, and intestinal microbiota analyses. The results demonstrated that MSI administration obviously reduced weight gain and fat accumulation, and reduced anomalous lipid levels in liver and serum. Liver transcriptome analysis suggested that MSI mainly affected PPARα signaling pathway and fatty acid degradation to enhance lipid metabolism. Furthermore, MSI lowered hepatic and intestinal inflammation, and boosted the levels of ZO-1 and occludin in a dose-dependent manner. Concurrently, 16S rRNA sequencing of gut microbiota showed that MSI treatment decreased the Firmicutes/Bacteroidetes ratio and increased dominant bacterial of Muribaculum, Alistipes and Odoribacter. Collectively, these findings suggested that MSI alleviated HFD-induced lipid accumulation by modulating inflammation, intestinal barrier function and gut microbiota. This comprehensive study offered a basis for the development and utilization of MSI in tackling lipid dysmetabolism.},
}

Animals
*Diet, High-Fat/adverse effects
*Gastrointestinal Microbiome/drug effects
*Liver/metabolism/drug effects
*Melanins/pharmacology
*Lipid Metabolism/drug effects
Male
*Sepia/chemistry
Mice
Mice, Inbred C57BL

@article {pmid41539628,
year = {2026},
author = {Peng, Y and Liu, H and Xing, T and Zhen, F and Wu, D and Sun, Y},
title = {Instability mechanisms of overloaded anaerobic digestion: Insights from volatile fatty acid metabolism.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {134006},
doi = {10.1016/j.biortech.2026.134006},
pmid = {41539628},
issn = {1873-2976},
abstract = {To clarify the mechanisms driving process instability under overload stress, a long-term semi-continuous overload instability simulation experiment was conducted. High-throughput sequencing and metagenomics were used to determine the response of the process parameters, community composition, and volatile fatty acid (VFA)-related metabolic functional genes to the organic loading rate (OLR). When the OLR increased to 12.5 kg VS/m[3]/d, the methane yield remained low at 226.40 ± 10.78 mL CH4/g VS. Further increasing the OLR to 20 kg VS/m[3]/d completely destabilized the reactor, resulting in a final methane yield as low as 0.29 mL CH4/g VS, a hydrogen partial pressure as high as 357.37 Pa, and concentrations of butyrate, propionate, and acetate of 4328.49 ± 538.18, 1036.13 ± 75.48, and 9939.67 ± 427.68 mg/L, respectively. Organic overload stress caused reactor instability mainly by blocking VFA metabolism. When the OLR was ≥ 11 kg VS/m[3]/d, the relative abundances of key genes (aceE, buk, ptb, atoD) in the butyrate and propionate metabolic pathways decreased, resulting in the accumulation of butyrate and propionate. Despite a shift in syntrophic acetate oxidation metabolism from the methyl to the carbonyl branch under overload, the latter's recovery was insufficient to compensate for the severe impairment of the methyl branch, ultimately leading to acetate accumulation. VFA accumulation caused severe inhibition of acetogens and some methanogens, while hydrolytic and acidogenic bacteria dominated the microbiome (relative abundance: 94.18 %). As a result, the microbial metabolic balance was broken. Our results provide new insights into the mechanisms driving process instability under overload stress.},
}

@article {pmid41539609,
year = {2026},
author = {Yang, D and Ren, D and Zhang, Y and Hao, Y and Yue, Y and Li, Q and Fan, Q and Sun, C and Cui, M and Zhang, M},
title = {The Gut Microbiota Dysbiosis in Geriatric Multimorbidity: Pharmacotherapeutic Implications, Pathophysiological Mechanisms, and Precision Modulation Strategies.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103023},
doi = {10.1016/j.arr.2026.103023},
pmid = {41539609},
issn = {1872-9649},
abstract = {Aging around the world is accelerating. With that comes the intersection of geriatric multimorbidity and polypharmacy, creating a large uncertainty about the pharmacological efficacy and therapeutic consequences of medications used when multiple concurrent health issues exist. The gut microbiota coordinates the way drugs work through multiple pathways: through the way drugs are metabolised, the way they maintain immune homeostasis, and the way they regulate the epithelial barrier. For these reasons, the gut microbiota is becoming an important therapeutic target for optimizing precision medicine strategies in treating patients with geriatric multimorbidities. In this narrative review, we systematically synthesize the evidence regarding how gut dysbiosis leads to decreased efficacy of multi-drug regimens through the interplay between metabolism, immune response, and barrier function in aging patients with multimorbidities, and we evaluate targeted interventions. Furthermore, we demonstrate that current interventions (e.g., probiotics, prebiotics, fecal microbiota transplants (FMT), phage therapy, and dietary modulation) have unique benefits but are limited by inter-individual variability, safety concerns, and a lack of proven long-term efficacy. Thus, many areas of microbiota-drug interactions in older adults with multimorbidity should be explored through future research. Key areas to address are: the establishment of large, multicenter longitudinal cohorts of older adults with multimorbidity that would allow for repeated collection of microbiota profiles, medication use, and health outcomes to identify the evolving interaction between multimorbidity, microbiota, and polypharmacy; the urgent need for standardized and integrated databases of microbiome-drug interactions that harmonize data formats, provide metabolic annotations and medication identifiers in order to support reproducible cross-study validation; and the further validation and application of artificial intelligence (AI) and machine learning (ML) in clinical trials. High-dimensional data collected from cohorts and databases will enable the development of predictive algorithms to identify individual drug responses and how effective microbiota-targeted interventions will be; these algorithms must then be prospectively validated. Ultimately, these initiatives are necessary to move toward the personalized management of microbiota-drug interactions in older adults with multimorbidity, providing greater safety of polypharmacy and promoting healthy aging.},
}

@article {pmid41539598,
year = {2026},
author = {Wei, S and Li, W and Ran, S and Zhang, J and Zhang, Z and Yang, Z and Tian, F and Chen, L and Hu, P and Yuan, J and Lin, H},
title = {Multi-organ metabolic dysregulation and cecal microbiota alterations following black carbon exposure.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.027},
pmid = {41539598},
issn = {2090-1224},
abstract = {BACKGROUND: Black carbon (BC) has been linked to adverse health outcomes, yet underlying mechanisms remain unclear. Integrating metabolomic and metagenomic data across tissues may clarify BC-induced biological pathways.

METHODS: We performed human epidemiology and mice experimental approaches. We included 248,288 participants with annual BC exposure estimates and plasma metabolomic profiles. Elastic net regression identified BC-associated metabolites. Male C57BL/6J mice were exposed to filtered air or BC (1 mg/m[3], 1 h/day, 5 days/week, 12 weeks). Multi-tissue metabolomics and cecal contents microbiota sequencing were conducted, with histology and gene expression measurements.

RESULTS: In humans, long-term BC exposure significantly altered plasma metabolites, notably increasing saturated fatty acids (β = 0.048), while decreasing docosahexaenoic acid (β = -0.002). Amino acid metabolism was broadly disrupted, involving elevated valine (β = 0.011) and reduced glutamine (β = -0.006). In mice, metabolomic profiling showed organ-specific shifts, including increased glutathione and cortisol in the liver (2.88-fold and 2.06-fold), increased PC(16:0/18:1(9Z)) in the heart (3.22-fold), elevated anandamide and arachidonic acid in the kidney (2.35-fold and 1.48-fold), and decreased multiple fatty acids and lysophospholipids across organs. Cecal microbiota exhibited reduced alpha-diversity (Shannon: 3.67 vs. 4.50, P < 0.05) and taxonomic shifts, including an increased abundance of g_Akkermansia and decrease in g_Bacteroides. Multi-omics integration revealed significant microbiota-metabolome correlations in the cecum and plasma (Mantel r = 0.276, P = 0.012). Histological examination confirmed organ injuries, notably lung inflammation, cardiac edema, and neuronal condensation. Gene expression analysis showed increased Il-6 in the lung (5.35-fold, P = 0.047), increased Mb in the heart (5.18-fold, P = 0.010), and increased Igfbp7 in the kidney (3.03-fold, P = 0.001), while Tjp1 expression in cecum was reduced (0.42-fold, P = 0.004).

CONCLUSIONS: Our findings suggest that BC exposure may alter systemic metabolism and gut microbiota, potentially contributing to tissue injury and inflammation. The gut-organ axis could be a target for mitigating BC-related health effects.},
}

@article {pmid41539591,
year = {2026},
author = {Pravin, V and Vellapandian, C and Naveen Kumar, V},
title = {The oral-gut-brain axis in periodontitis: microbial signaling in systemic and neuroinflammatory disease.},
journal = {Brain research},
volume = {},
number = {},
pages = {150168},
doi = {10.1016/j.brainres.2026.150168},
pmid = {41539591},
issn = {1872-6240},
abstract = {Periodontitis, a chronic inflammatory disease of the oral cavity, has been identified as a modifiable risk factor of the development of systemic and neurological disorders via a complicated interplay of microbiological, immunological, and neural interactions. Periodontal pathogens breach local immune homeostasis, are translocated to the gut and brain, and trigger a cascade of immune deregulation, leaky gut, and blood-brain barrier, thereby forming a tri-directional communication network that links local oral inflammation to systemic and neurovascular conditions. This review synthesizes existing evidence on how oral dysbiosis, can spread to the gut and trigger systemic inflammation, leading to neuroinflammation and neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. Mechanistically, the OGB axis acts through various processes, such as hematogenous spread, retrograde axonal transport, immune cell trafficking (Trojan horse mechanism), and extracellular vesicle-based signaling corresponding to the causes of neuroinflammation, microglial activation, and the pathology of tau and amyloid. The diagnostic and therapeutic implications of the OGB axis provide new pathways toward early intervention with precision medicine, microbiome remodeling, immune-based therapy, and neuroprotective approaches. Emerging technologies, including AI-based diagnostics and biosensing technologies, offers noninvasive tools to track host-microbial interactions and inflammatory biomarkers. This integrative view underscores the central importance of oral health in systemic homeostasis and the development of neurodegenerative conditions, necessitating collaborative approaches between dentistry, neurology, and immunology to cooperate to deliver efficacy in disease elimination and mitigation.},
}

@article {pmid41539578,
year = {2026},
author = {Chehadeh, C and Nakatsuji, T and Gallo, RL},
title = {Staphylococcus aureus in Atopic Dermatitis: How a common bacterium exploits and drives disease.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.12.1009},
pmid = {41539578},
issn = {1097-6825},
abstract = {The role of Staphylococcus aureus (S. aureus) in atopic dermatitis (AD) has been extensively studied. Although its role in the pathophysiology of AD was previously controversial, current evidence now shows that it is a major factor promoting the disease and is responsible for significant morbidity. Its influence in AD stems from widespread exposure since S. aureus is common on healthy skin and is frequently part of the normal human skin microbiome. In AD, S. aureus and the closely related S. epidermidis gain a selective growth advantage over most other members of the skin microbiome due to a complex relationship involving the skin's innate immune system, other members of the microbiome, and skin barrier properties. Disruption in the functioning of those components or changes in their interactions leads to dysbiosis, skin barrier damage, and the progression of skin disease. This review summarizes research findings on these relationships and highlights the interactions and factors that promote S. aureus survival on skin and its participation in the pathogenesis of AD.},
}

@article {pmid41539526,
year = {2026},
author = {Uddin, G and Song, J and Lu, Z and Chaofie, Z and Sajjad, W and Li, P and Fan, Q},
title = {Microbial Taxonomic and Functional Responses to Heavy Metal Gradients in Mining-Impacted Stream Sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123778},
doi = {10.1016/j.envres.2026.123778},
pmid = {41539526},
issn = {1096-0953},
abstract = {Legacy heavy metal pollution from historical mining restructures sediment microbial composition and function directly impacting contaminant fate and ecosystem health. The Dongdagou stream (Baiyin, China) possesses a pronounced geochemical gradient caused by long-term discharge of potentially toxic metals including Cd, Cu, Pb, and Zn. We employed this natural gradient to characterize microbial taxonomic and functional responses to metal stress. Sediment samples from four zones along the contamination gradient were analyzed for geochemistry, metal concentrations, and microbial composition (bacteria, archaea, and fungi) via high-throughput amplicon sequencing, with functional potential inferred using PICRUSt2. We found that microbial community structure and function were primarily shaped by metal concentration, with db-RDA explaining 18.1%, 12.4%, and 12.9% of the variance for bacteria, archaea, and fungi, respectively. Cadmium was identified as the strongest individual predictor for both bacterial (r[2] = 0.50, p = 0.001) and fungal (r[2] = 0.38, p = 0.001) communities. Bacterial diversity increased significantly downstream as contamination declined, with Shannon diversity increasing from 5.17 in the Source Zone to 6.28 in the Distal Zone (Tukey's multiple comparison test, p < 0.05). Upstream sediments were dominated by metal-tolerant taxa such as Sulfurifustis (17.4%) and Acidithiobacillus (5.0%), while downstream taxa shifted to heterotrophic genera like Gallionella (4.8%) with diverse metabolic capabilities. Despite cadmium being a key predictor, archaeal and fungal communities demonstrated greater compositional stability than bacteria, as shown by their lower beta-dispersion (ANOSIM R = 0.3152 and 0.5762, respectively, compared to 0.7222 for bacteria), indicating potential functional redundancy. Metagenomic predictions revealed a significant enrichment of genes for metal detoxification, anaerobic respiration, and oxidative stress response in polluted zones. These findings establish that microbial communities are both sensitive bioindicators and key mediators of contaminant dynamics, providing a framework for using microbial signatures to assess sediment health and monitor remediation efficacy.},
}

@article {pmid41539436,
year = {2026},
author = {Berube, LT and Wang, C and Curran, M and Pompeii, ML and Hu, L and Barua, S and Li, H and St-Jules, DE and Schoenthaler, A and Segal, E and Bergman, M and Popp, CJ},
title = {Personalized dietary feedback mediates the association of dietary self-monitoring adherence and weight loss: a post-hoc analysis of the Personal Diet Study.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101364},
doi = {10.1016/j.tjnut.2026.101364},
pmid = {41539436},
issn = {1541-6100},
abstract = {BACKGROUND: Dietary self-monitoring is central to effective personalized nutrition, providing critical data to inform tailored feedback and support behavior change.

OBJECTIVE: To examine the impact of dietary self-monitoring adherence and the indirect effect of personalized scores to predict postprandial glycemic response (PPGR) on weight loss.

METHODS: Post-hoc analysis of the Personal Diet Study that investigated the impact of a machine algorithm-based diet that integrates clinical and microbiome features (Personalized) compared to a standard, low-fat diet (Standardized) on weight loss. All participants received behavioral counseling and were encouraged to self-monitor dietary intake via a smartphone app. Personalized received algorithm-based scores (1 to 5) on predicted PPGR to foods logged (PPGR score; 1-2 indicating optimal; 3-5 suboptimal). Dietary self-monitoring adherence was the percentage of days logging ≥50% of target calories, classified as high or low. PPGR score quality was calculated by the proportion of optimal predicted PPGR scores per day; defined as "high-PPGR quality" days when this exceeded the group average. Mediation analysis assessed whether PPGR quality mediated the relationship between dietary self-monitoring adherence and weight loss.

RESULTS: Participants with high self-monitoring adherence lost an average of 4.2% of their baseline weight, compared to 1.9% among those with low adherence (p=0.016). High self-monitoring adherence was associated with a greater likelihood of achieving ≥5% weight loss (aOR=3.67, 95% CI: 1.63-8.50). Within Personalized, high PPGR quality mediated 53.4% of the total effect of self-monitoring adherence on weight loss (p<0.001).

CONCLUSION: Consistent self-monitoring coupled with personalized feedback may significantly enhance weight loss in a precision nutrition approach.

CLINICAL TRIAL REGISTRATION: NCT03336411.},
}

@article {pmid41539328,
year = {2026},
author = {Meduri, GU and Lannini, S and Smit, JM},
title = {Limitations in the Design of Critical Care Studies and Suggestions for Future Research Directions.},
journal = {Seminars in respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2762-8278},
pmid = {41539328},
issn = {1098-9048},
abstract = {Glucocorticoid (GC) therapy has been a cornerstone of critical care; however, its full potential has been constrained by fixed-dose regimens and trial designs that predate current insights into the dynamic, phase-specific functions of glucocorticoid receptor α (GRα). This study shifts focus from mechanistic pathways to the clinical implications of phase-adaptive care, emphasizing how GC therapy can be optimized through individualized, response-guided strategies tailored to illness trajectory and biological variability. Rather than reiterating GRα's mechanistic role, which is discussed in Chapter 3, this work highlights its practical relevance in therapeutic decision-making across the three sequential phases of critical illness: priming, modulatory, and restorative. In this clinically oriented framework, phase-specific treatment adjustments are informed by real-time changes in systemic stress markers, immune dynamics, and metabolic indicators. Earlier randomized controlled trials were instrumental in establishing safety but often failed to account for evolving physiological demands or receptor variability, contributing to inconsistent outcomes. To bridge this translational gap, this study proposes the integration of response-guided protocols utilizing accessible clinical biomarkers-such as C-reactive protein, interleukin-6, D-dimer, and lactate-allowing for adaptive dosing and tapering strategies aligned with patient-specific recovery patterns. Moving beyond pharmacologic dosing, the study outlines adjunctive clinical strategies-including targeted micronutrient supplementation and microbiome-supportive therapies-not as theoretical possibilities but as practical co-interventions that can be incorporated into intensive care unit protocols. Furthermore, it explores how artificial intelligence-enabled clinical decision systems and adaptive trial designs can operationalize precision care by dynamically stratifying patients and tailoring interventions to shifting biological profiles. Together, these applied strategies support a transition from static treatment paradigms to a precision medicine model in critical care-one that aligns GC therapy with individualized recovery trajectories, maximizes therapeutic responsiveness, and reduces treatment-related risks through multimodal, phase-responsive interventions.},
}

@article {pmid41539295,
year = {2026},
author = {Zhang, H and Liao, C},
title = {Illuminating the functional dark matter of the gut microbiome.},
journal = {Cell host & microbe},
volume = {34},
number = {1},
pages = {12-14},
doi = {10.1016/j.chom.2025.12.004},
pmid = {41539295},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/genetics/enzymology ; Bacterial Proteins/metabolism/chemistry ; Bacteriophages ; Host Microbial Interactions ; },
abstract = {In this issue of Cell Host & Microbe, Liu et al. provide a roadmap for decoding the gut microbiome's functional dark matter through a structural atlas of gut phage and bacterial proteins, validating structure-guided functions from endolysins to microbial-host isozymes, and developing an alignment-free method for detecting bacteria-human remote homologs.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Bacteria/genetics/enzymology
Bacterial Proteins/metabolism/chemistry
Bacteriophages
Host Microbial Interactions

@article {pmid41539238,
year = {2026},
author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K},
title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106371},
doi = {10.1016/j.psj.2026.106371},
pmid = {41539238},
issn = {1525-3171},
abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.},
}

@article {pmid41539110,
year = {2026},
author = {Shrivastav, K and Pandey, M and Gor, H and Nema, V},
title = {Gut virome plays an extended role with bacteriome in neurological health and disease.},
journal = {Journal of the neurological sciences},
volume = {481},
number = {},
pages = {125754},
doi = {10.1016/j.jns.2026.125754},
pmid = {41539110},
issn = {1878-5883},
abstract = {The gut-brain axis (GBA) is a complex two-way communication system that links the gastrointestinal tract and the central nervous system (CNS) through neural, immune, hormonal, and microbial pathways. The microbiota-gut-brain axis (MGBA), a more specific concept, focuses on how gut microorganisms, including bacteria, viruses, and other microbes, modulate this communication and influence neurological health. This comprehensive review examines the intricate mechanisms through which gut microorganisms modulate neural function and contribute to neurological health and disease pathogenesis. The gut microbiota, comprising bacteria, viruses, fungi, and bacteriophages, produces essential neuroactive compounds including neurotransmitters- Gamma-Aminobutyric Acid (GABA), serotonin (5-HT), dopamine (DA), short-chain fatty acids (SCFAs), and metabolites that directly influence brain physiology through vagal, hormonal, and immunological pathways. Dysbiosis of the gut microbiota has been implicated in various neurological disorders, including Alzheimer's disease, Parkinson's disease, autism spectrum disorders, and schizophrenia. In healthy conditions, beneficial bacterial strains such as Lactobacillus species synthesize GABA and regulate mood, while SCFA-producing bacteria like Fecalibacterium prausnitzii maintain blood-brain barrier integrity and exert neuroprotective effects. Conversely, pathological states demonstrate altered microbial compositions, reduced bacterial diversity, and compromised production of beneficial metabolites. Emerging evidence highlights the previously underexplored role of the gut virome, particularly bacteriophages, in regulating bacterial populations and influencing neurodevelopment. Viral dysbiosis correlates with cognitive impairment and neurodegenerative processes through modulation of bacterial metabolism and inflammatory responses. Understanding these complex host-microbiome-virome interactions provides novel therapeutic opportunities for neurological disorders through targeted interventions including probiotics, fecal microbiota transplantation, and phage-based therapies, representing a paradigm shift toward microbiome-centered approaches in neurological medicine.},
}

@article {pmid41539094,
year = {2026},
author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z},
title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157804},
doi = {10.1016/j.phymed.2026.157804},
pmid = {41539094},
issn = {1618-095X},
abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.

PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.

METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.

RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.

CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.},
}

@article {pmid41537815,
year = {2025},
author = {Aoki, LR and Graham, OJ and Yoshioka, RM and Maher, R and Alma, L and Hofmann, EE and Burge, CA and Harvell, D and Groner, ML},
title = {Wasting disease of a marine foundation species links community interactions to disease dynamics.},
journal = {Biology letters},
volume = {21},
number = {12},
pages = {},
doi = {10.1098/rsbl.2025.0579},
pmid = {41537815},
issn = {1744-957X},
support = {//National Science Foundation/ ; //William Calver Postdoctoral Fellowship/ ; },
mesh = {*Zosteraceae/microbiology/parasitology/physiology ; *Ecosystem ; Animals ; Climate Change ; Microbiota ; *Plant Diseases/parasitology ; },
abstract = {Infectious disease plays a key role in shaping marine communities, including in seagrass meadows, which form biodiverse coastal habitats. Eelgrass (Zostera marina) is the most widespread seagrass species and is susceptible to seagrass wasting disease, caused by the protist Labyrinthula zosterae. As a foundation species, eelgrass strongly influences ecosystem structure, function and services; recent work has begun to explore the links between critical community interactions and seagrass wasting disease. Here, we highlight recent advances about how the eelgrass community regulates and responds to seagrass wasting disease, from the microbiome to herbivores and filter feeders. We further show how efforts to model seagrass wasting disease progression can build on prior efforts to predict eelgrass growth and productivity and can inform our understanding of ecosystem health, resilience and vulnerability. As climate change alters environmental conditions, potentially favouring the wasting disease pathogen, efforts to integrate community interactions with disease ecology will be critical to forecast ecosystem dynamics and to develop effective coastal management strategies. We offer guidance on addressing major knowledge gaps in the study of eelgrass wasting disease in order to deepen both ecological theory and applied practices and identify how an integrated marine-disease-community ecology can inform a broader, cross-cutting understanding of disease.},
}

*Zosteraceae/microbiology/parasitology/physiology
*Ecosystem
Animals
Climate Change
Microbiota
*Plant Diseases/parasitology

@article {pmid41538371,
year = {2026},
author = {Alves, G and Hamaneh, MB and Ogurtsov, AY and Yu, YK},
title = {Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach.},
journal = {Journal of the American Society for Mass Spectrometry},
volume = {},
number = {},
pages = {},
doi = {10.1021/jasms.5c00332},
pmid = {41538371},
issn = {1879-1123},
abstract = {Microbiome communities are found across diverse environments and play critical roles in both ecosystem function and human health. Mass-spectrometry-based metaproteomics provides a powerful means for directly identifying and quantifying microbial proteins. However, its application is hindered by the shared peptide problem, where peptides map to multiple proteins across taxa, complicating taxon-protein quantification. To address this challenge, we extend a previously published modified expectation-maximization algorithm that incorporates taxonomic biomass constraints into the Microorganism Classification and Identification (MiCId) workflow. This enhanced expectation-maximization algorithm is used to quantify taxon-protein pairs derived from clusters of identified taxon-protein pairs, thereby enabling more accurate quantification and representation of taxonomic-level proteomes. The performance of the approach is evaluated using synthetic datasets consisting of simple mixtures with known relative species abundances, a more complex 24-species synthetic dataset, and a clinical human stool microbiome dataset. It is shown that, in simple synthetic datasets, fold changes computed for species-protein pairs closely match the expected values and are consistent with those obtained from MaxQuant. Using the 24-species synthetic dataset, we show that the algorithm accurately redistributes peptide extracted ion count among taxon-protein pairs that share peptides. Finally, analyzing the clinical stool microbiome dataset, we demonstrate that MiCId's results are accurate and consistent with previously reported findings. These results demonstrate the robustness of MiCId's algorithm for quantifying taxon-protein pairs in complex microbial communities. By resolving the shared peptide problem, the method enables accurate representation of taxonomic-level proteomes, thereby advancing the application of metaproteomics in microbiome research.},
}

@article {pmid41538368,
year = {2026},
author = {Dame-Teixeira, N and Melo, JLMA and Parolo, CCF},
title = {Caries Microbiome: time to move from blame to balance.},
journal = {Caries research},
volume = {},
number = {},
pages = {1-23},
doi = {10.1159/000550472},
pmid = {41538368},
issn = {1421-976X},
abstract = {BACKGROUND: Advances in next-generation sequencing(NGS) and multi-omics approaches reinforced the concept of functional diversity within biofilm communities, revealing roles beyond bacterial taxonomy and highlighting metabolic and ecological mechanisms operating at the individual level rather than within isolated caries lesions. Moving toward new clinical solutions will require broader perspectives; to this end, we propose key directions to advance the translational potential of caries microbiome research. We present a perspective that connects ecological theory, molecular evidence, and clinical implications through three central topics: (I)microbial composition, (II)microbial function, and (III)individual-level characteristics.

SUMMARY: From a compositional perspective, caries microbiome research should move beyond the search for bacterial culprits and instead consider the broader microbial ecosystem, including low-abundance and non-bacterial members (such as archaea). Within this framework, microbial taxa and functions should not be viewed as inherently "good" or "bad," but rather as context-dependent components of a dynamic ecosystem shaped by sustained environmental pressures. Functionally, the recurrent enrichment of pathways related to carbohydrate metabolism, sugar transport, and acid production likely reflects microbial adaptation to persistent sugar exposure rather than intrinsic virulence traits. This perspective suggests that progress in caries research depends on moving beyond disease-centered models toward understanding how microbial stability preserves oral health. At the individual level, individuals with previous caries experience may retain disease-associated microbial or functional signatures during remission, a phenomenon referred to here as a microbiological dysbiosis scar. This ecological memory may help explain why past caries experience remains one of the strongest predictors of future lesions and highlights the importance of incorporating individual history into the design and interpretation of caries microbiome studies. Integrating detailed clinical metadata with advanced bioinformatic approaches, including artificial intelligence, will be essential for establishing meaningful biological links.

KEY MESSAGES: Progress in caries microbiome research depends on refining study design across microbial composition, functional, and individual levels. Strengthening the resilience of the oral microbiome rather than eliminating specific pathogens or the microbiome should be the central goal of caries microbiology. Moving from blame to balance is not merely semantic; it represents a fundamental shift in how we study, prevent, and manage dental caries.},
}

@article {pmid41537975,
year = {2026},
author = {Sless, T and Chau, K and Nguyen, P and Rehan, S},
title = {Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2062},
pages = {},
doi = {10.1098/rspb.2025.1823},
pmid = {41537975},
issn = {1471-2954},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Bees/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/analysis ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; DNA Barcoding, Taxonomic ; },
abstract = {Recent years have seen a rapidly growing interest in the study of microbiomes to understand the health and well-being of host animals. Within bees, much of this work has focused on managed species of agricultural importance, such as honeybees and bumblebees. However, unmanaged wild bees are also vital to both agricultural and natural systems, and studying their microbial associates is essential to understanding the impacts of microbiomes on bee health. We used metabarcoding based on 16S rRNA and internal transcribed spacer region (ITS1) loci to identify bacterial and fungal associates of adult bees from 16 species, 10 genera and 5 families, representing a diverse sampling of wild bees common to eastern North America. Overall, Apilactobacillus was the largest component of bacterial communities, while fungal communities were dominated by Cladosporium. Alpha diversity of both bacteria and fungi differed significantly across genera and species, while beta diversity varied at all taxonomic levels. Additionally, we conducted a broad phylogenetic comparison of bacterial communities across bees using previously published 16S rRNA datasets and contrasted these findings with functional traits across the bee tree of life. Several bacterial taxa showed evidence of strong phylogenetic signal in prevalence, while the presence of corbiculae was more strongly associated with bacterial community composition than sociality or nesting habit. This study provides expanded insights into the microbial associates of wild bees, as well as the broadest investigation to date into patterns of phylogenetic conservation in bacterial communities across a total of 42 species representing the five most diverse bee families.},
}

Animals
Bees/microbiology
Phylogeny
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics/analysis
*Microbiota
*Fungi/classification/genetics/isolation & purification
DNA Barcoding, Taxonomic