@article {pmid42236792,
year = {2026},
author = {Wortmann, E and Groll, T and Strigli, A and Peuker, K and Volet, C and Arps, L and Bernier-Latmani, R and Zeissig, S and Steiger, K and Middelhoff, M and Clavel, T},
title = {Modulation of intestinal bile acids influences colonic mucosal responses.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42236792},
issn = {2045-2322},
abstract = {BACKGROUND: Elevated levels of secondary bile acids produced by the gut microbiome, in particular deoxycholic acid (DCA), influence epithelial cell proliferation and accelerate the development of colorectal cancer (CRC) under adverse dietary conditions, such as long-term, high fat intake. However, their effects on the intestinal epithelium have not been studied in detail.

AIM: To determine gut epithelial responses to bile acid modulation in vivo and in situ.

METHODS: We performed targeted colonization of gnotobiotic mice followed by single-cell RNA sequencing (scRNA-Seq) of colonic epithelial cells combined with immunostaining of human biopsies from: (i) an observational patient cohort with hyperproliferative polyps or cancer; (ii) an interventional study with bile acid-scavenging drugs.

RESULTS: Colonization of mice with a defined bacterial community including the 7α-dehydroxylating species Extibacter muris resulted in DCA production. ScRNA-Seq of colonic epithelial cells revealed increased cell density of bile acid-sensitive enterocytes but fewer stem cells, goblet cells, and transit amplifying cells in mice exposed to DCA. This was associated with increased expression of pyruvate dehydrogenase kinase (Pdk4) and decreased expression of mucin (Muc2). PDK expression was also increased in human hyperplastic polyps and adenomas, whilst MUC2 expression was reduced in adenomas and carcinomas compared to normal mucosa. In addition, treatment of ileostomy patients with chologenic diarrhea using bile acid sequestrants was associated with enhanced epithelial proliferation in colorectal biopsies.

CONCLUSION: This study provides insight into intestinal epithelial cell responses to bile acids and their potential clinical relevance.},
}

@article {pmid42236864,
year = {2026},
author = {Attri, K and Sharda, D and Tanwar, I and Gautam, P and Choudhury, D},
title = {Curcumin-stabilized silver nanoparticles target the Helicobacter pylori-tumor interface in gastric cancer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-54162-3},
pmid = {42236864},
issn = {2045-2322},
abstract = {Gastric cancer remains a major global health burden, ranking among the leading causes of cancer-related mortality worldwide. Chronic infection with Helicobacter pylori is a well-established etiological factor, promoting sustained gastric inflammation, epithelial transformation, and tumor progression through modulation of the gastric microenvironment. Therapeutic strategies that simultaneously target microbial virulence and tumor cell survival remain limited. In this study, we developed curcumin-stabilized silver nanoparticles (AgNPs) as a dual-functional nanoformulation designed to modulate the tumor-associated microbiome while exerting direct anti-cancer effects. The nanoparticles were chemically synthesized with a controlled diameter of 15 ± 2 nm, enabling enhanced surface reactivity and biological interaction. Antimicrobial evaluation revealed potent activity against H. pylori, with an IC50 of 3.86 µg/mL. Furthermore, AgNPs significantly inhibited urease activity-a critical virulence determinant for gastric colonization-achieving 80.46 ± 1.15% inhibition at 160 µg/mL. Broad-spectrum antibacterial efficacy was also observed against other tested strains, indicating potential for reshaping the tumor microbiome. Cytotoxicity assessment in AGS human gastric adenocarcinoma cells demonstrated substantial anti-proliferative activity, with 73.99 ± 2.13% reduction in cell viability. The integration of curcumin, a bioactive polyphenol with established anti-inflammatory and anti-neoplastic properties, with silver nanoparticles provides a synergistic platform targeting both microbial and tumor components of gastric carcinogenesis. Collectively, these findings highlight AgNPs as a promising microbiome-directed nanotherapeutic strategy for gastric cancer management, warranting further mechanistic and translational investigation.},
}

@article {pmid42236946,
year = {2026},
author = {Song, D and Duncan-Lowey, B and Khetrapal, V and Hamchand, R and Deng, T and Brown, H and Wu, A and Martin, AL and Bauer, KM and Zhao, Y and Nguyen, MT and Sonnert, ND and Leopold, SR and Wu, Q and Crawford, JM and Palm, NW},
title = {Commensal-derived acetylcholine enhances mucosal immune education.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42236946},
issn = {1476-4687},
abstract = {The microbiota produces thousands of potentially bioactive small molecules[1-3]. High-throughput bioactivity screens of in vitro commensal cultures have exposed microbiota metabolites that shape host physiology by activating diverse G-protein-coupled receptors (GPCRs)[4-7]. However, owing to technical limitations, the GPCRome-wide bioactivities of in vivo metabolomes, which result from complex diet-microorganism-host interactions, remain unclear. Here we used a multiplexed GPCR screening technology to assess GPCRome-wide bioactivities of 100 commensal strains grown in vivo in monoassociated germ-free mice or in vitro in bacterial culture medium. In vivo and in vitro commensal metabolomes exhibited distinct GPCR activation patterns due to (1) host-mediated metabolite degradation; (2) in vivo microbial metabolic reprogramming; and (3) biotransformation of dietary substrates. Notably, we found that multiple commensal strains produced acetylcholine (ACh) in vivo through the conversion of dietary choline, including select Bifidobacterium strains that dominate the microbiome in early life and a probiotic Pediococcus strain. Mechanistically, we identified and characterized the bacterial enzymes that mediate this biotransformation in Bifidobacterium breve and Pediococcus pentosaceus, and generated an isogenic mutant B. breve strain lacking ACh production. Mice colonized with ACh-producing B. breve exhibited enhanced intestinal immunoglobulin A (IgA) production, altered microbiota composition and increased resistance to enteric infection. These findings underscore the profound impacts of the in vivo environment on microbiota metabolism and reveal a diet-microbiome-host axis that strengthens mucosal immune defences and reinforces host-microbiota mutualism.},
}

@article {pmid42236978,
year = {2026},
author = {Le Bras, A},
title = {Microbiome clues to extreme longevity.},
journal = {Lab animal},
volume = {55},
number = {6},
pages = {197},
doi = {10.1038/s41684-026-01759-w},
pmid = {42236978},
issn = {1548-4475},
}

@article {pmid42237056,
year = {2026},
author = {Xing, Y and He, W and Chen, W and Gao, C and Zhang, M and Wu, Y and Qu, C and Dai, K and Huang, Q and Cai, P},
title = {Cadmium Stress Favours Biofilm Cooperation and Polysaccharide-Enriched Matrix Remodelling in Bacterial Consortia.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70347},
doi = {10.1111/1462-2920.70347},
pmid = {42237056},
issn = {1462-2920},
support = {42225706//National Natural Science Foundation of China/ ; 42407174//National Natural Science Foundation of China/ ; 460324005//Natural Science Foundation of Hubei Province of China/ ; BX20230139//China National Postdoctoral Program for Innovative Talents/ ; 202405AF140079//Science and Technology Talents and Platform Program (Workstation for Academicians and Experts)/ ; 2023AFA009//Innovative Research Group Project of Hubei Provincial Natural Science Foundation/ ; },
abstract = {Environmental stressors trigger complex adaptations in microbial communities, yet the associations between social network dynamics and metabolic strategies remain poorly understood, limiting our ability to design robust synthetic microbiomes. Here, we show that Cd stress was associated with structural simplification of soil bacterial co-occurrence networks, characterized by a 48.5% reduction in connectivity. In vitro assays further revealed a 93% increase in cooperative interactions within biofilms under Cd exposure. This shift in biofilm-associated cooperation coincided with altered physiological patterns, including a 45.9% increase in EPS synthesis and a 13.7% decrease in community CO2 emissions. Crucially, our analysis suggests that the intensity of cooperative interactions was associated with specific extracellular matrix allocation patterns. High-intensity cooperation was linked to a higher proportion of polysaccharide-rich matrices, which improved the stability and efficiency of Cd sequestration in vitro. Leveraging these interaction-informed patterns, we assembled a synthetic core consortium that modulated the rhizosphere microbiome in a proof-of-concept hydroponic system and reduced Cd accumulation in rice leaves by 52.9%. These findings support a conceptual framework in which biofilms may act as sites of social integration and altered extracellular matrix production, offering an interaction-informed basis for assembling stress-resilient microbiomes.},
}

@article {pmid42237178,
year = {2026},
author = {Zhang, Q and Khan, I and Lei, E and Chen, H and Tang, X and Ding, L and Hong, M},
title = {The gut-brain-gonad axis mediates salinity adaptation in an invasive turtle: causal evidence from microbiota transplantation and metabolite supplementation.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00583-4},
pmid = {42237178},
issn = {2524-4671},
abstract = {BACKGROUND: Preliminary studies have shown that salinity stress can impair the differentiation of spermatogonial stem cells (SSC) in red-eared slider (Trachemys scripta elegans) through the gut-brain-gonad axis, thereby affecting their reproductive ability. However, a direct causal link between salinity-induced gut microbiota alterations and reproductive suppression remains unclear. To test the hypothesis that gut microbiota and their metabolites mediate salinity adaptation by modulating the gut-brain-gonad axis, we conducted fecal microbiota transplantation (FMT) and metabolite supplementation experiments.

RESULTS: Results showed that the FMT group successfully recapitulated the donor's gut microbial profile and exhibited significant changes in intestinal metabolites. Both FMT and GABA supplementation mimicked the reproductive inhibitory phenotype observed under direct salinity stress: altered brain neurotransmitter levels (increased dopamine, decreased serotonin), downregulated expression of reproductive genes (e.g. GnRH1, FSHβ), and impaired SSC self-renewal and differentiation in testes, as evidenced by reduced marker gene expression (e.g. PLZF, Stra8) and disrupted testicular histology.

CONCLUSION: Our findings demonstrate that salinity stress reshapes the gut microbiota and metabolome. This leads to increased inhibitory signaling, notably via GABA, along the gut-brain-gonad axis. Ultimately, this signaling cascade suppresses reproductive function. This study provides novel mechanistic insights into the environmental adaptation strategies of an invasive species and highlights the potential of targeting the microbiome-metabolite axis for developing innovative, environmentally friendly biocontrol approaches against this invasive species.},
}

@article {pmid42237220,
year = {2026},
author = {Von, KY and Ab Majid, AH},
title = {16S rRNA gene amplicon data of midgut microbial diversity in German cockroach, Blattella germanica.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-026-01449-z},
pmid = {42237220},
issn = {2730-6844},
abstract = {OBJECTIVES: Blattella germanica, commonly known as German cockroach, is a globally prevalent household pest. The gut microbiota of B. germanica is influenced by multiple factors, yet their interactive effects remain poorly understood compared with other insect taxa. Midgut-specific microbial communities also remain understudied relative to whole gut or hindgut microbiota. In this study, 16S rRNA gene sequencing datasets were generated from midgut samples collected across varying life stages (adult and nymph), sexes (male and female), environmental origins (laboratory-reared and field-collected), and physiological states (fed and starved).

DATA DESCRIPTION: Genomic DNA was extracted using the HiYield Genomic DNA isolation kit and amplified targeting the V3-V4 hypervariable regions of the 16S rRNA gene using primer pair 338 F/806R. Raw sequences reads were subsequently analyzed using QIIME2 pipeline following quality control and host decontamination. Taxonomic classification consistently identified the bacterial families Lactobacillaceae, Desulfovibrionaceae, Lachnospiraceae, Dysgonomonadaceae, Christensenellaceae, and Rikenellaceae across all treatment groups. Diversity indices (Shannon, Simpson, and Chao1) showed similar trends across samples, indicating stable patterns of microbial diversity and richness. These datasets support the exploration of specific midgut-associated taxa as potential targets for biological control strategies against B. germanica.},
}

@article {pmid42237362,
year = {2026},
author = {Liu, S and Wang, S and Zhang, J and Tao, C and Ravanbakhsh, M and Xu, X and Wen, K and Xiang, D and Sheng, O and Shen, Z and Li, C and Li, R and Shen, Q and Kowalchuk, GA},
title = {Host-guided microbiome-metabolite interactions enable cross-kingdom SynComs for disease suppression.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02430-9},
pmid = {42237362},
issn = {2049-2618},
support = {KJYQ2025053//Fundamental Research Funds for the Central Universities/ ; KTTQ2025018//Fundamental Research Funds for the Central Universities/ ; 42477316//National Natural Science Foundation of China/ ; 2024YFD1401105//National key research and development program of China/ ; 322MS092//Hainan Provincial Natural Science Foundation of China/ ; NAUSY-CG-ZD-01//Achievement Transformation Fund project of Hainan Research Institute of Nanjing Agricultural University/ ; },
abstract = {BACKGROUND: The plant microbiome plays a crucial role in enhancing disease resistance, yet microbiome-based plant protection strategies remain limited by an incomplete understanding of how host selection, microbial interactions, and rhizosphere chemistry jointly shape pathogen suppression.

RESULTS: Here, we adopt a "learning from nature" approach to design synthetic microbial communities (SynComs) that recapitulate naturally evolved disease-suppressive interactions, using banana Fusarium wilt as a model system. High-throughput profiling revealed that both bacterial and fungal communities contribute to varietal resistance. Resistance-associated microbial taxa were identified and isolated to assemble bacterial, fungal, and cross-kingdom SynComs representative of resistant versus susceptible hosts. SynComs derived from resistant varieties suppressed pathogen growth more effectively than those from susceptible hosts, with cross-kingdom SynComs exhibiting the strongest effects. Cross-kingdom SynCom inoculation significantly reduced disease severity and restructured both the composition and functional potential of the rhizosphere microbiome. Integrative transcriptomic and metabolomic analyses revealed coordinated host metabolic reprogramming, characterized by increased accumulation of diverse metabolites, including alkaloids, amino acids, and flavonoids. Notably, supplementation with resistance-associated rhizosphere metabolites, such as stearic acid and shikimic acid, further enhanced disease suppression.

CONCLUSIONS: Together, our findings establish a mechanistic framework in which host-guided microbiome assembly and metabolite-mediated interactions jointly enable effective cross-kingdom SynComs for disease suppression, providing ecological principles for microbiome-based plant protection strategies. Video Abstract.},
}

@article {pmid42237386,
year = {2026},
author = {Chen, X and Feng, P and Zhang, J and Wu, J and Xie, Z and Huang, J and Yang, X and He, F and Chen, R},
title = {Multi-omics biomarkers in endometrial receptivity: from mechanisms to clinical translation.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08257-0},
pmid = {42237386},
issn = {1479-5876},
abstract = {BACKGROUND: Endometrial receptivity (ER) serves as a critical determinant for successful embryo implantation, yet its molecular complexity and limited clinical assessment methods pose significant challenges. Despite advancements in assisted reproductive technology (ART), recurrent implantation failure (RIF) linked to ER abnormalities persists, creating a need for precise, non-invasive diagnostics.

MAIN BODY: This review outlines ER research, from the biology of the window of implantation (WOI) to the roles of immune components and the microbiome in shaping the receptive microenvironment. Multi-omics integration reveals regulatory networks across transcriptomic, epigenomic, proteomic, and metabolomic levels, with uterine fluid biomarkers emerging as promising non-invasive candidates. The analysis further covers how chronic endometritis (CE), adenomyosis, and polycystic ovary syndrome (PCOS) impair ER: through mechanisms including inflammatory imbalance, microbial dysbiosis, abnormal extracellular matrix remodeling, and hormonal dysregulation. Commercial ER tests face limitations, including insufficient evidence and inconsistent results, which undermine their clinical reliability.

CONCLUSIONS: A significant translational gap remains between biomarker discovery and clinical application. Current challenges involve technical standardization and data integration, and poor model generalizability. Future progress requires combining multi-omics with artificial intelligence (AI) to establish standardized clinical pathways, advancing ER assessment into precision medicine, and improving global infertility management.},
}

@article {pmid42237409,
year = {2026},
author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X},
title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02433-6},
pmid = {42237409},
issn = {2049-2618},
support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; },
abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.

RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.

CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.},
}

@article {pmid42237424,
year = {2026},
author = {Yang, L and Chen, J},
title = {mPower: a real data-based power analysis tool for microbiome study design.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02427-4},
pmid = {42237424},
issn = {2049-2618},
support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; },
abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/. Video Abstract.},
}

@article {pmid42237550,
year = {2026},
author = {Boubaker, F and Sallem, O and Dridi, I and Chabbou, A},
title = {Clockwork symbiosis: The vital interplay of microbiota and human chronobiology.},
journal = {Chronobiology international},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/07420528.2026.2682478},
pmid = {42237550},
issn = {1525-6073},
abstract = {The human microbiota and host circadian system engage in a bidirectional dialogue with consequences for metabolism, immunity, and barrier physiology. This narrative review examines the microbiota-chronobiology interface across the gut and selected extra-intestinal niches and uses the term "clockwork symbiosis" as an organizing framework for this crosstalk. A structured, non-exhaustive search of PubMed, Scopus, Web of Science, Cochrane Library, and Embase was conducted for studies published between 2000 and 2024, with priority given to human evidence and mechanistic studies with clear translational relevance. The strongest evidence concerns the gut microbiota, for which both human and preclinical studies support diurnal variation in microbial composition, metabolite production, and host metabolic signaling. By contrast, evidence for vaginal, oral, skin, and respiratory microbiota remains comparatively limited and is best treated as emerging and largely hypothesis-generating. Across the literature, circadian disruption is associated with altered microbial rhythmicity and adverse metabolic or inflammatory phenotypes, but causality is often difficult to isolate from co-occurring changes in diet, sleep, stress, light exposure, medication use, and host disease state. Microbiota-derived metabolites, particularly short-chain fatty acids and bile-acid derivatives, provide plausible mechanistic links to peripheral clocks, although evidence for direct clinical manipulation remains preliminary. Overall, preserving host-microbiota temporal alignment appears biologically important, but clinical applications such as chrononutrition, timed biotics, and chronotherapy still require rigorous time-standardized human studies.},
}

@article {pmid42237575,
year = {2026},
author = {Tilves, C and Xiao, S and Tanaka, T and Differding, MK and Spira, AP and Ferrucci, L and Mueller, NT},
title = {Longitudinal associations of the gut microbiome with arterial stiffness in US adults: findings from the Baltimore Longitudinal Study of Aging.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwag119},
pmid = {42237575},
issn = {1476-6256},
abstract = {The gut microbiome affects arterial stiffness in experimental murine models; however, evidence in human longitudinal studies is lacking. In this study, we investigated longitudinal between-person (average) and within-person (change) associations of microbiome features with arterial stiffness. We assessed the fecal microbiome using whole genome metagenomic sequencing, and arterial stiffness using carotid-femoral pulse wave velocity (cfPWV). Our analytic sample consisted of 349 adults from the Baltimore Longitudinal Study of Aging, who contributed 915 visits between 2013-2019. Using linear mixed models, we found higher microbiome evenness and butyrate-producing bacteria were associated with lower cfPWV on average (between-person), but changes in diversity were not associated with changes in cfPWV (within-person). Several potentially pathogenic bacteria were positively associated with cfPWV, both between- and within-person. Butyrate-production pathways were inversely associated with cfPWV between-person and borderline within-person. Trimethylamine-production genes were positively associated with cfPWV between-person and borderline within-person. In addition, changes in other functional pathways including peptidoglycan biosynthesis and L-arginine biosynthesis were associated with changes in cfPWV. In conclusion, cfPWV was associated with both between-person and within-person differences in gut microbiome features, with strength and consistency depending on the feature. These results can inform which microbiome features to target in interventions to improve arterial stiffness.},
}

@article {pmid42237634,
year = {2026},
author = {Wang, N and Liu, X and Yan, Z and He, H and Wang, P and Ali, A and Wang, Z and Dong, H and Guo, J and Zhang, Y},
title = {Beauveria bassiana B094 as a dual-action biocontrol agent: Combining direct pathogenicity and endophytic colonization against Spodoptera exigua in sweet corn.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70306},
pmid = {42237634},
issn = {1744-7917},
support = {2024YFD1400300//National Key Research and Development Program of China/ ; CARS-02-26//China Agriculture Research System/ ; //The Science and Technology Innovation Project, the Chinese Academy of Agricultural Sciences/ ; },
abstract = {This study investigates the endophytic biocontrol potential of Beauveria bassiana strain B094 against Spodoptera exigua in sweet corn through laboratory, greenhouse and field assessments. Laboratory virulence screening identified B094 as pathogenic to S. exigua, inducing 99.8% mortality and exceeding 75% infection in 1st- and 3rd-instar larvae at 1 × 10[8] spores/mL. The LC50 for 3rd-instar larvae was 4.8 × 10[5] spores/mL. B094 established endophytic colonization in sweet corn varieties Zhetian 19 and Zaotiannuo 211 via seed inoculation. Colonization peaked at 7 d after emergence (DAE), with leaves exhibiting markedly higher frequency and density (91.1%, 1367 ± 95 CFU/g) than stems (40%, 353 ± 12 CFU/g) and roots (37.8%, 93 ± 9 CFU/g), then progressively declined to 24.3% in leaves and below 17.3% in stems and roots by 28 DAE. Feeding bioassay demonstrated that leaves from colonized plants at 14-21 DAE significantly increased larval mortality and disrupted development. Greenhouse and field trials confirmed efficacy, with inoculated plants exhibiting less foliar damage than controls and similar colonization patterns and biocontrol effects across varieties. Rhizosphere microbiome analysis revealed community shifts after B094 colonization. Bacterial genera often associated with plant growth promotion or biocontrol (e.g., Bacillus, Gemmatimonas), increased by 22.5% and 81.6%, whereas fungal genera commonly reported as plant pathogens (e.g., Gibberella and Fusarium), decreased by 87.7% and 78.1%, respectively. Our findings establish B. bassiana B094 as a dual-action biocontrol agent against S. exigua, combining direct pathogenicity with endophytic effects, supporting seed-treatment as an environmentally friendly strategy for sustainable pest management in sweet corn systems.},
}

@article {pmid42237711,
year = {2026},
author = {Oriquat, G and Al-Hasnaawei, S and Mousa, HM and Malathi H, and Singla, S and Sahoo, S and Arora, V and Chauhan, AS and Nourizadeh, M},
title = {Gut Microbiome-Sleep Crosstalk: Mechanistic Pathways, Dysbiosis Signatures, and Microbiome-Based Interventions.},
journal = {Brain and behavior},
volume = {16},
number = {6},
pages = {e71525},
doi = {10.1002/brb3.71525},
pmid = {42237711},
issn = {2162-3279},
abstract = {BACKGROUND: This review examines the bidirectional relationship between sleep regulation and the gut microbiome within the gut-brain axis, with particular attention to mechanistic pathways, disorder-associated dysbiosis patterns, and microbiome-targeted interventions in insomnia, obstructive sleep apnea, circadian disruption, and sleep loss-related states.

METHODS: We critically synthesized evidence from both human and preclinical studies, focusing on microbial metabolites, neuroimmune and neuroendocrine signaling, circadian regulation, and intervention-based approaches. Rather than only summarizing individual studies, we aimed to distinguish associative human findings from mechanistic evidence derived mainly from animal models.

RESULTS: Current evidence supports a bidirectional link between sleep and the gut microbiome. Microbiota-derived metabolites, particularly short-chain fatty acids, tryptophan-related metabolites, and gamma-aminobutyric acid, appear to influence sleep homeostasis through effects on intestinal barrier integrity, inflammatory tone, stress-axis regulation, and central signaling pathways. Across sleep disorders, recurrent microbial patterns include reduced abundance of potentially beneficial taxa such as Bifidobacterium and Faecalibacterium and enrichment of pro-inflammatory or stress-associated taxa, although these signatures are not yet fully consistent across cohorts or disorders. In humans, most data remain observational and support association rather than causation, whereas stronger mechanistic support comes from experimental models of sleep deprivation, intermittent hypoxia, and microbiota transfer. Early intervention studies suggest that selected probiotics, prebiotics, dietary modulation, and related microbiome-directed strategies may improve sleep-related outcomes, but the magnitude and reproducibility of these effects remain uncertain.

CONCLUSION: The gut microbiome represents a promising mechanistic and therapeutic target in sleep medicine, but clinical translation is still constrained by heterogeneity in microbiome profiling, sleep phenotyping, intervention design, and strain-specific effects. Future work should prioritize longitudinal human studies, standardized outcome measures, and mechanistically informed trials capable of identifying clinically actionable and biologically credible microbiome signatures.},
}

@article {pmid42237734,
year = {2026},
author = {Kim, TH and Kim, SM and Kim, MH},
title = {Unveiling the Molecular Repertoire of Akkermansia muciniphila: From Mechanistic Insights to Precision Biotherapeutics.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604017},
doi = {10.4014/jmb.2604.04017},
pmid = {42237734},
issn = {1738-8872},
abstract = {The gut microbiota has been established as a cornerstone of host physiological homeostasis. Among its diverse members, Akkermansia muciniphila has gained significant prominence as a premier next-generation probiotic candidate, demonstrating broad efficacy in alleviating metabolic disorders, inflammatory bowel disease, and neurodegenerative conditions. While early research primarily focused on clinical correlations and population abundance, recent scientific paradigms have shifted toward elucidating the underlying molecular mechanisms and specific host-microbe interactions. This review provides a comprehensive synthesis of recent breakthroughs in identifying A. muciniphila-derived bioactive effectors, including structural components, secreted enzymes, and signaling peptides. We examine how these molecular postbiotics orchestrate host health by reinforcing intestinal barrier integrity, modulating systemic immune responses, and reprogramming the tumor microenvironment. By integrating these multifaceted modes of action into a unified framework, we evaluate the therapeutic potential of both live bacteria and cell-free derivatives. Furthermore, we address the critical challenges regarding strain-specific efficacy and ecological impacts, providing a strategic roadmap for the clinical translation of A. muciniphila into the next frontier of precision microbiome medicine.},
}

@article {pmid42237904,
year = {2026},
author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH},
title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01505},
pmid = {42237904},
issn = {1520-5851},
abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.},
}

@article {pmid42237944,
year = {2026},
author = {},
title = {Correction to: Quantitative genetics of microbiome-mediated traits.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpag092},
pmid = {42237944},
issn = {1558-5646},
}

@article {pmid42237982,
year = {2026},
author = {Utreja, S and Andreani, GA and Mahmood, S and Patel, MS and Buck, MJ and Rideout, TC},
title = {Dietary pulse prebiotic fibre intake in a rat obese pregnancy model alters maternal caecal microbiome and protects against steatosis in newly weaned offspring.},
journal = {Journal of nutritional science},
volume = {15},
number = {},
pages = {e37},
pmid = {42237982},
issn = {2048-6790},
abstract = {We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.},
}

@article {pmid42238109,
year = {2025},
author = {Sirko, J and Bor, B and He, X},
title = {Microbial dark matter and the future of dentistry.},
journal = {JADA foundational science},
volume = {4},
number = {},
pages = {100043},
pmid = {42238109},
issn = {2772-414X},
}

@article {pmid42238119,
year = {2025},
author = {Mark Welch, JL and Borisy, GG},
title = {Dental plaque: Who is in the neighborhood and why it matters.},
journal = {JADA foundational science},
volume = {4},
number = {},
pages = {100051},
pmid = {42238119},
issn = {2772-414X},
}

@article {pmid42238322,
year = {2026},
author = {Hao, Y and Chu, D and Li, H and Zheng, L and Liu, Y and Xi, Q and Liu, S},
title = {Functionalized polysaccharides for infection-resistant and regenerative therapies in gynecology.},
journal = {International journal of pharmaceutics: X},
volume = {11},
number = {},
pages = {100568},
pmid = {42238322},
issn = {2590-1567},
abstract = {Gynecological infections and implant-related complications, such as bacterial vaginosis (BV), pelvic inflammatory disease (PID), and endometritis, are exacerbated by biofilm-forming pathogens such as G. vaginalis, E. coli, and S. aureus, posing significant clinical challenges worldwide. These biofilms, resistant to antibiotics, contribute to chronic infections and device failures in gynecological implants. Rising antibiotic resistance underscores the need for innovative biomaterials. Chitosan, hyaluronic acid (HA) and alginate are three representative natural polysaccharides, showing broad application potential in antibacterial materials and tissue engineering due to their excellent biocompatibility, biodegradability and modifiable structures. In their natural forms, they exhibit a certain degree of anti-biofilm activity by inhibiting bacterial adhesion and disrupting bacterial membranes. Functional modification significantly enhances their antibacterial performance such as AMPs grafting, cross-linking, quaternization, and nanocomposites. This review explores the antibacterial mechanisms of natural polysaccharides in the vaginal microbiome and endometrial tissue, highlighting advances in functionalization with antimicrobial peptides, nanoparticles, and chemical modifications to enhance antibacterial efficacy. The toxicological effects of natural polysaccharide materials on gynecological tissues generally show the characteristics of mainly protective and restorative effects, rather than causing damage. Natural polysaccharides and their applications offer promising potential for infection-resistant, regenerative therapies in gynecology, promising safer and more effective interventions.},
}

@article {pmid42238443,
year = {2026},
author = {Bode, MR and Lydecker, AD and Robinson, GL and Roghmann, MC and Kalan, LR},
title = {Long-Term Daily Chlorhexidine Foot Cleansing Reduces Staphylococcal Burden on the Feet of People with Prior Diabetic Foot Complications.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.14.26352248},
pmid = {42238443},
abstract = {BACKGROUND: Individuals with diabetes remain at high risk for diabetic foot ulcers (DFUs) even after ulcer healing. Dysbiosis of the skin microbiome has been associated with ulcer formation. Topical chlorhexidine gluconate (CHG) is a broad-spectrum antiseptic commonly used to reduce microbial burden. In a prior randomized clinical trial comparing daily CHG foot treatment with soap-and-water treatment, no statistically significant reduction in new DFUs was observed, prompting evaluation of whether CHG produced durable changes in the skin microbiota.

OBJECTIVE: To compare changes in foot skin microbiota (including bacterial bioburden, diversity, and community composition) associated with daily CHG versus soap-and-water use over one year in people with diabetes and prior foot complications.

METHODS: In a single-center, double-blind, placebo-controlled randomized trial, 87 participants were randomized to daily CHG wipes or soap-and-water wipes for 12 months. Foot swabs were collected at baseline, 3 and 12 months, and 4 weeks post-treatment. Bacterial bioburden was quantified. Microbiota composition was assessed using 16S rRNA and ITS amplicon sequencing.

KEY RESULTS: CHG treatment significantly reduced bacterial bioburden, increased microbial diversity, and altered community composition, including sustained reductions in Staphylococcus abundance. Several microbiota changes persisted more than 4 weeks after treatment cessation. Soap⍰and⍰water treatment showed similar but smaller and largely nonsignificant trends.

CONCLUSIONS: Daily CHG use durably modifies foot skin microbiota in high-risk individuals with diabetes. However, this alone may be insufficient to prevent new foot complications, highlighting the need for additional interventions. These findings have implications for long-term CHG use in populations at risk for staphylococcal infections.

KEY POINTS: Long-term daily chlorhexidine foot cleansing in adults with diabetes reduces Staphylococcus abundance and overall bacterial burden more effectively than soap-and-water, with microbiota effects persisting for up to one month after treatment cessation, demonstrating durable pathogen suppression.},
}

@article {pmid42238447,
year = {2026},
author = {Chen, J and Li, A and Wu, W and Xu, W and Zhao, T and Starkweather, AR and Rodriguez, L and Chen, MH and Cong, XS},
title = {Gut microbiota signatures differentiate trajectory-defined response phenotypes and predict self-management outcomes in irritable bowel syndrome.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.18.26353470},
pmid = {42238447},
abstract = {BACKGROUND: Heterogeneity in symptom presentation and treatment response in irritable bowel syndrome (IBS) remains poorly understood. The gut microbiota may contribute to this variability, but its role in shaping symptom trajectories and responses to self-management interventions is unclear.

OBJECTIVE: To identify symptom trajectory phenotypes and determine whether gut microbiota composition and function distinguish these phenotypes and predict multidimensional responses to pain self-management interventions in young adults with IBS.

DESIGN: Ancillary data analysis from a randomized control trial (NCT03332537).

METHODS: Participants with longitudinal data (n = 62) were analyzed using longitudinal k-means clustering (KML) based on trajectories of measures in IBS quality of life (QOL), Brief Pain Inventory (BPI), and psychoneurological outcomes (anxiety, applied cognition, depression, fatigue, global health, positive affect, and sleep disturbance) over 12 weeks. Baseline differences between clusters were assessed with Wilcoxon rank-sum tests, and longitudinal changes were evaluated with linear mixed models. Gut microbiota composition and predicted functional pathways were compared between phenotypes. Bayesian Additive Regression Trees (BART) models were used to identify baseline microbial taxa and pathways predictive of longitudinal changes in QOL, BPI pain interference, and severity.

RESULTS: Two distinct trajectory-defined response phenotypes were identified: a Constrained Response Phenotype (Phenotype A, n = 35) and an Adaptive Multidomain Response Phenotype (Phenotype B, n = 27). At baseline, Phenotype B showed lower pain severity and interference, but higher levels of anxiety, depression, and fatigue compared to Phenotype A. Over 12 weeks, both phenotypes showed improvements in pain outcomes (all p < 0.05), but only Phenotype B demonstrated broad improvements across psychoneurological domains and QOL (all p < 0.05). Phenotype A exhibited more limited improvements and worsening in several psychoneurological domains. Gut microbiota functional pathways differed between phenotypes, including pathways related to xenobiotic degradation, amino acid metabolism, bile secretion, and immune-related processes (all raw p < 0.05), although these did not remain significant after multiple testing correction. Machine learning models identified distinct, phenotype-specific microbial predictors of intervention response. In Phenotype A, genera such as Alistipes and Sutterella were consistently identified across models, whereas in Phenotype B, predictors included Phascolarctobacterium , Collinsella , and Parabacteroides . Functional pathways also differed between phenotypes, suggesting distinct microbiome-linked mechanisms underlying symptom trajectories and responses to pain interventions.

CONCLUSIONS: Young adults with IBS exhibit distinct multidimensional response phenotypes that are associated with differential clinical and microbiome profiles. Baseline gut microbiota composition and functional capacity demonstrate phenotype-specific predictive signatures of treatment response, supporting a microbiome-informed framework for stratifying patients and advancing personalized self-management strategies in IBS.

WHAT IS KNOWN: □ Substantial heterogeneity exists in irritable bowel syndrome symptoms and treatment response, with variability across pain, psychological distress, and quality of life domains.□ Gut microbiota composition and function are linked to IBS pathophysiology, including associations with pain sensitivity, inflammation, and brain-gut signaling.□ Self-management interventions (e.g., mindfulness, behavioral strategies) can improve IBS symptoms, but responses are inconsistent and difficult to predict.

WHAT IS NEW HERE: □ Distinct longitudinal symptom trajectory phenotypes were identified, separating individuals with pain-predominant and limited psychoneurological improvement from those with lower pain and greater multidomain psychoneurological improvement.□ Gut microbiota composition and functional profiles varied between trajectory-defined clusters, indicating a biological foundation for differences in symptom patterns.□ Machine learning models showed that gut microbiota features predict pain severity, interference, quality of life, and their longitudinal changes, supporting microbiome-based stratification for self-management outcomes.},
}

@article {pmid42238882,
year = {2026},
author = {Skow, C and Ott, LC and Wannemuehler, MJ and Mellata, M},
title = {A defined microbiota mouse model for Salmonella Paratyphi A oral infection.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1824783},
pmid = {42238882},
issn = {1664-302X},
abstract = {INTRODUCTION: Salmonella Paratyphi A (SPtA) is an emerging pathogen that primarily infects humans and causes enteric fever, yet it has not received sufficient research attention. To facilitate further investigation, an appropriate animal model is necessary for testing SPtA infection.

METHODS: In this study, we utilized gnotobiotic mice harboring the altered Schaedler flora (ASF) from either C3H/HeN or 129S6/SvEv genetic backgrounds. These mice, subjected to various inflammatory conditions, were orally challenged with SPtA. The colonization and persistence of the pathogen were assessed in both intestinal and extraintestinal tissues, while also examining changes in gut microbiota, the expression of tight junction proteins, cytokines, and histopathological changes.

RESULTS: Our findings revealed that both the inflammatory state and the sex of the ASF mice significantly affected the colonization of SPtA. Notably, infection of the 129S6/SvEv IL10[-/-] mice with SPtA replicated key features observed in humans. This included the extraintestinal dissemination of SPtA, the inhibition of pro-inflammatory cytokines, and progressively worsening pathological changes over time following infection in IL10[-/-] ASF mice.

CONCLUSION: The results of this study suggest that ASF mice represent a suitable low-cost model for investigating the pathogenesis of SPtA infection. The presence of ASF creates an open niche for SPtA colonization, allowing for the retention of a defined microbiome. This enables researchers to study perturbations in the microbiome without the limitations inherent to an antibiotic-treated model alternative. Furthermore, the chronic inflammatory conditions associated with IL10[-/-] phenotype enable SPtA extraintestinal invasion and disease progress in the murine host, facilitating a functional model of SPtA pathogenesis.},
}

@article {pmid42238894,
year = {2026},
author = {Gilardini, F and Sabatucci, A and Cifani, C and Segura-Garcia, C and Pucci, M and Rania, M and D'Addario, C},
title = {Dysregulation of neurodevelopmental regulatory networks in Anorexia Nervosa: an integrated multi-layered omics analysis.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1761785},
pmid = {42238894},
issn = {2296-634X},
abstract = {Anorexia nervosa (AN) is a severe metabo-psychiatric disorder with the highest mortality rate among psychiatric conditions. Its characteristic onset during adolescence suggests that disrupted neurodevelopmental processes during critical periods may contribute to disease pathophysiology. In this exploratory study, we conducted an integrated multi-layered omics analysis to identify molecular alterations affecting neurodevelopmental pathways in individuals with AN. We employed three complementary approaches: DNA methylation sequencing via Reduced Representation Bisulfite Sequencing (RRBS), microRNA (miRNA) expression profiling using panel-based qPCR, and microbiome characterization through 16S rRNA sequencing in a sample of 38 patients with AN and 40 healthy controls. Analyses focused on molecular mechanisms involved in neurodevelopmental processes. RRBS analysis identified methylation differences in neurodevelopmentally relevant genes, particularly CACNA1C (voltage-gated calcium channel) and ZNHIT2 (transcription factor). miRNA profiling revealed extensive dysregulation, with 74 miRNAs showing altered levels in the AN pools. Network analysis highlighted that miR-135 family targets KCNN3 (SK3 channel involved in neuronal excitability), while miR-374b regulates IGFBP3 (IGF-1 signaling modulator). Microbiome analysis revealed that 42% of the AN group exhibited dramatic oral dysbiosis characterized by Proteobacteria dominance. Our findings demonstrate coordinated multi-level dysregulation of mechanisms governing neural circuit maturation during adolescence, supporting a neurodevelopmental framework for understanding AN. The convergence of molecular alterations on ion channels and growth factor signaling suggests systems-level perturbations in developmental regulatory mechanisms. The identified miRNAs represent potential biomarkers and therapeutic targets, while microbiome heterogeneity suggests distinct clinical subgroups. While exploratory in nature, this work provides novel insights into AN molecular architecture and generates testable hypotheses for future mechanistic studies incorporating individual-level data essential to validate these candidates and establish robust clinical correlations.},
}

@article {pmid42238975,
year = {2023},
author = {Ayyadurai, VAS and Deonikar, P and Stashenko, P},
title = {Molecular systems architecture of host-microbiome interactions in periodontitis.},
journal = {JADA foundational science},
volume = {2},
number = {},
pages = {100026},
pmid = {42238975},
issn = {2772-414X},
abstract = {OBJECTIVES: To develop a systems-level understanding of host-microbial interactions that lead to the pathogenesis of periodontitis. Such an understanding may identify therapeutic targets for developing efficacious treatments for periodontitis.

SEARCH STRATEGY: Three databases are searched for relevant peer-reviewed articles published from January 1980 through April 2022.

CITATION SOURCES: The citation sources include PubMed, MEDLINE, and Google Scholar.

STUDY SELECTION CRITERIA: The systems biology tool CytoSolve (CytoSolve) was used to perform the systematic review and to support the curation and development of the molecular systems architecture of periodontitis pathogenesis. Full-length articles that contained Medical Subject Headings key words relevant to periodontitis pathogenesis were selected for a comprehensive review.

DATA ELEMENTS INCLUDED: The molecular interactions across the 8 cell types-gingival epithelial, fibroblast, periodontal ligament, endothelial, keratinocyte, microbial, bone, and immune-of the periodontal microenvironment that leads to the pathogenesis of periodontitis are identified. These interactions are organized into 14 molecular systems involved in periodontitis.

OVERALL CONCLUSIONS: A molecular systems architecture is developed to provide a visual framework for comprehending the complexity of molecular interactions across the 8 cell types involved in periodontitis pathogenesis. The resulting architecture may be used for target identification and discovery of single and multicombination therapeutics to treat periodontitis more effectively.},
}

@article {pmid42239041,
year = {2026},
author = {Phandanouvong-Lozano, V and Pastore, L and Miller, G and Lin, KY and Wolf, AR},
title = {A bidirectional nanAKE locus enables sialic acid catabolism in gut microbiome member Hungatella hathewayi.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.18.725967},
pmid = {42239041},
issn = {2692-8205},
abstract = {UNLABELLED: Sialic acids are abundant components of host- and diet-derived glycans in the human gut and serve as important nutrients that shape microbial fitness and interspecies competition. Excess free sialic acids are also linked to inflammation and pathogen susceptibility. While well-studied gut bacteria such as E. coli and Bacteroides spp. catabolize sialic acids via the NanAKE or NanLE-RokA pathways, the metabolic capacity of many microbiome members remains undefined. To identify sialic acid catabolizing bacteria, we cultured fecal samples from healthy human donors. The gut anaerobe Hungatella hathewayi was selected under sialic acid-supplemented conditions. H. hathewayi is a poorly characterized gram-positive Lachnospiraceae associated with long-lived individuals and purine metabolism. Here we establish that H. hathewayi grows robustly on sialic acids as a sole carbon source using a pathway homologous to the canonical NanAKE system of E. coli , despite the species' phylogenetic distance. We functionally validated these orthologs through growth assays and heterologous complementation in E. coli knockout strains. Comparative analyses further showed that key catalytic residues in H. hathewayi NanA are conserved despite overall sequence divergence from E. coli . Additionally, we find that colocalized sialic acid transporters and regulatory proteins are not orthologous to E. coli proteins and instead are related to proteins from other gut anaerobes. Together, these findings expand our understanding of sialic acid utilization within the human gut microbiome. We identify H. hathewayi as an overlooked but capable sialic acid degrader that can contribute to modulation of gut sialic acid levels and related inflammation.

IMPORTANCE: Sialic acids play an important role in mammalian and microbial signalling. Excess free sialic acids increase susceptibility to gut pathogens and induce inflammation. Gut bacteria can both generate and consume free sialic acids, and these pathways are conserved across diverse bacteria. E. coli and B. fragilis consume sialic acids as a carbon source, decreasing free sialic acid levels. We identify H. hathewayi as another bacteria capable of sialic acid consumption and define the enzymes responsible. H. hathewayi is a prevalent member of the human gut microbiome, but it is not genetically tractable, limiting enzymatic characterization. H. hathewayi is enriched in the gut microbiomes of long-lived individuals and expected to be an important contributor to purine degradation to limit gout risk. Defining sialic acid catabolism in non-model species is essential to understanding the evolution and conservation of this pathway as well as how nutrient competition shapes gut microbiome composition.},
}

@article {pmid42239051,
year = {2026},
author = {Lalgudi, C and Kotaka, M and Yaffe, E and Lopez, JA and Yu, FB and Ng, K and Sonnenburg, JL and Good, BH and Huang, KC and Shi, H},
title = {Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.22.727306},
pmid = {42239051},
issn = {2692-8205},
abstract = {Recovery of the gut microbiome after antibiotic exposure is often incomplete and variable, and the processes underlying this variation remain unclear. We performed longitudinal shotgun metagenomic sequencing of 2876 daily fecal samples from replicated humanized and conventional mouse cohorts exposed to controlled antibiotic perturbations. Metagenomic profiling recapitulated ecological trajectories previously observed by 16S sequencing, while revealing extensive strain-level dynamics, including reproducible sweeps of standing variants and de novo mutations in antibiotic target sites and regulatory loci. We also identified genetic changes whose effects depended on community composition, competitive release, and perturbation history. Cross-housing experiments revealed bidirectional strain transfer, with antibiotic-induced niche clearance enabling replacement of resident strains. In parallel, phage dynamics were heterogeneous and clustered by cage. Together, these findings show that post-antibiotic microbiome recovery is a path-dependent process shaped by selection, transmission, and phage activity, producing divergent outcomes even among closely matched communities exposed to the same perturbations.},
}

@article {pmid42239183,
year = {2026},
author = {Cirolia, G and Gustafson, JT and Aswani, A and Wolf, A},
title = {Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.21.727052},
pmid = {42239183},
issn = {2692-8205},
abstract = {Microbiome-based machine learning classifiers show increasing promise for disease identification across gastrointestinal, metabolic, and immune-mediated conditions. Inflammatory bowel disease (IBD), a chronic immune-mediated disorder associated with disruption of the gut microbiome, has been a particularly successful application area. However, while many predictive models achieve high performance within individual datasets, their ability to generalize across independent populations and geographic contexts remains unclear. Here, we tested whether model class and training dataset composition influence model generalizability across geographically diverse evaluation studies. We compiled seven publicly available shotgun metagenomic studies spanning five geographic regions, comprising 697 individuals with IBD or healthy controls. We trained 246,986 model configurations across seven model classes and five distinct training dataset combinations and evaluated top-performing models on independent studies from the USA, Ireland, Germany, Israel and China. Extreme gradient boosting and random forest models showed the highest and most consistent performance across training datasets, a ranking that was maintained on independent evaluation studies. However, models trained on geographically diverse datasets did not outperform those trained on USA-only datasets. Instead, model performance was strongly dependent on the evaluation study itself, with consistent differences in achievable accuracy across studies. Despite most models achieving similar AUC scores, there was limited overlap in the key microbial species identified. Furthermore, even for the small set of disease predictive microbes shared between models, the direction of enrichment between IBD or healthy subjects often varied in opposing directions across study populations. These findings suggest that study-specific factors constrain generalization and may help explain the lack of consistent microbiome-based biomarkers for IBD.},
}

@article {pmid42239190,
year = {2026},
author = {Pietropaolo, J and El Khoury, S and Guo, L and McGee, M and Shapira, M},
title = {Attraction to secreted isoamyl alcohol as a signal for beneficial commensals.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.22.727293},
pmid = {42239190},
issn = {2692-8205},
abstract = {C. elegans, a bacterivore living in microbially-complex environments, harbors a characteristic community of gut bacteria that contribute to its health and fitness. What determines which environmental bacteria end up as commensals is largely unknown in C. elegans , as in other animals. Previous work found that gut Pantoea isolates supported rapid worm development and infection resistance, while environmental congenerics were inferior. Notably, worms were preferentially attracted to the more beneficial gut isolates. Using bioactivity-guided fractionation and gas chromatography-mass spectrometry analysis, we identified bacterially derived isoamyl alcohol (IAA) as a secreted volatile attractant underlying this preference. Screening of worm mutants implicated AWC sensory neuron-associated genes in preferential attraction to beneficial Pantoea and established a causal link between IAA sensing and colonization by beneficial strains. While IAA sensing was important for initial colonization, gut-associated Pantoea strains ultimately outcompeted environmental congenerics over time, indicating that microbiome assembly is shaped by two complementary processes: host behavioral preference for high-IAA producers and bacterial competitive fitness within the gut. While IAA is a product of leucine metabolism and may function as a nutritional cue, we found that it could also directly enhance host infection resistance, suggesting an additional role in modulating host physiology. Finally, knockout analysis identified a bacterial branched-chain amino acid aminotransferase homolog as important for IAA production. Together, these findings identify bacterial volatile sensing as an important and underexplored mechanism shaping microbiome composition and its contributions to host fitness.},
}

@article {pmid42239356,
year = {2026},
author = {Madamanchi, K and Gurrala, S and Watson, J and Melkani, GC},
title = {Microbiome Integrity Protects Against Glial-Mediated Tau and Amyloid Pathology Through Circadian and Autophagy Homeostasis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.726549},
pmid = {42239356},
issn = {2692-8205},
abstract = {Alzheimer disease referred as AD is characterized not only by tau and amyloid beta aggregation but also by systemic disruptions in circadian rhythms, metabolism, and gut-brain communication that exacerbate neuroinflammation and neurodegeneration. While glial cells play central roles in inflammatory signaling and proteostasis, the contribution of the gut microbiome to glia-driven AD pathology remains poorly understood. Here, we used Drosophila models with glial-specific expression of human tau and amyloid-associated transgenes to investigate how microbiome integrity influences disease progression. AD models exhibited significant shifts in gut microbial composition, particularly in Lactobacillus and Acetobacter species, suggesting an adaptive microbial response to pathological stress. Strikingly, microbiome depletion (axenic condition) markedly worsened behavioral and physiological outcomes, including disrupted sleep-circadian rhythms, impaired memory, and reduced locomotor function. These deficits were accompanied by amplified neuroinflammatory signaling, increased apoptotic gene expression, lipid dysregulation, and altered synaptic markers. Moreover, microbiome loss induced energy stress marked by elevated phospho-AMPK, yet failed to restore proteostasis, as evidenced by accumulation of ubiquitinated proteins and the autophagy adaptor Ref2p, indicating impaired autophagic flux. This dysfunction correlated with increased tau, phospho-tau, and Abeta42 accumulation. Together, our findings demonstrate that microbiome depletion exacerbates glial-mediated inflammation, disrupts circadian and metabolic homeostasis, impairs proteostasis, and accelerates cognitive and motor decline. This work highlights a previously underappreciated role of the gut microbiome in restraining glial dysfunction and mitigating AD like pathology, positioning microbial homeostasis as a critical modulator of neurodegenerative disease progression.},
}

@article {pmid42239363,
year = {2026},
author = {Yakar, N and Hasturk, H and Rivas, CA and Zimmerman, P and Guney, Z and Yilmaz, BT and Uzun, Y and Trackman, P and Kantarci, A},
title = {Estrogen Deprivation and Periodontitis Interact Across Multiple Tissues.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.15.725533},
pmid = {42239363},
issn = {2692-8205},
abstract = {UNLABELLED: The study investigated the interaction between estrogen deprivation and periodontitis, systemically, in the bone marrow, and locally in periodontal tissues using a mouse model.

METHODS: We used the ligature-induced periodontitis (LIP) model concurrently with ovariectomy-induced estrogen deprivation. Bone marrow was assessed for myeloid cell proportion by flow cytometry. The femur metaphysis was examined histologically and by micro-CT. Cytokine responses of CD11b [+] myeloid cells to lipopolysaccharide stimulation were investigated ex vivo across ovary-intact (Sham), ovariectomized (OVX), and estrogen-replaced (OVX+E2) mice with or without periodontitis. Estrogen-related alterations in periodontitis, including microbiome composition and transcriptomic changes in the gingiva and dentoalveolar complex, were investigated by 16S rRNA sequencing and bulk RNA sequencing, respectively.

RESULTS: Ovariectomy increased osteoblast-like and adipocyte-like cell numbers in femoral marrow, whereas LIP reduced both populations (p = 0.020 and p = 0.029, respectively). LIP increased the bone marrow CD45 [+] hematopoietic fraction in Sham mice. LPS-stimulated bone marrow CD11b [+] cells from OVX mice showed lower Tnfα, Ccl2 , and Il10 expression than Sham mice (p = 0.003, p = 0.005, and p = 0.001, respectively). OVX exacerbated LIP-associated alveolar bone loss, reducing BV/TV (p = 0.003) and increasing osteoclast numbers (p = 0.012). Neither OVX nor E2 replacement significantly altered ligature-associated microbial composition in 16S rRNA sequencing. Bulk RNA sequencing demonstrated estrogen-responsive transcriptomic changes in both the gingiva and dentoalveolar complex, including OVX-associated gene-expression changes that returned toward Sham levels in OVX+E2 mice. These included genes related to stromal regulation (Acan, Igfbp3, Erbb3) and immunity (Gp2, Spib, B2m).

CONCLUSION: Periodontitis and estrogen deprivation exert combined effects on the bone marrow niche. Estrogen deprivation modulates immune- and healing-related gene expression in the gingiva and remaining dentoalveolar tissues during periodontitis.},
}

@article {pmid42239394,
year = {2026},
author = {Almotah, K and Tran, U and Gilbert, H and Schweickart, RA and Fisher, RC and Bisikalo, Y and Ali, M and Buhaya, M and Cheng, M and Cruise, M and Chi, Z and Sarvestani, SK and Huang, EH and Wessely, O},
title = {Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.18.725891},
pmid = {42239394},
issn = {2692-8205},
abstract = {Ulcerative colitis is a chronic inflammatory bowel disease that can progress from dysplasia to cancer. Inflammatory responses are critical drivers in this process, typically triggered by epithelial lesions and the ensuing infiltration of microbiota into the interstitial layer. Here, we focus on the pro-inflammatory state of the interstitial fibroblasts, which promotes immune infiltration and augments disease progression. The study aims to provide a mechanistic link how fibroblasts of the colitis-associated microenvironment integrate inflammatory signals, microbial infiltration and cellular memory. To this end, we investigated a large number of primary colon fibroblasts obtained from normal, colitis and colon cancer samples using a range of in vitro approaches and an in vivo co-inoculation cancer model. mRNA sequencing analysis identified that the disease-associated fibroblasts are exhibit a cellular inflammatory status, which involves the injury-induced senescence pathway. Using CXCL8, a potent chemokine upregulated in colitis and cancer colon fibroblasts, as a paradigm, this inflammatory status is triggered by the activation of the NFκB signaling via immune-derived cytokines (TNFα, IL-1β), bacterial signals (LPS) and the microbiome itself using mycoplasma as a paradigm. Finally, iPSC reprogramming studies indicate that fibroblasts from ulcerative colitis retain an epigenetic memory that sustains elevated CXCL8 expression. Together, our findings demonstrate that the senescence associated secretory phenotype of colon fibroblasts is a robust indicator for inflammation-driven colon tumorigenesis.},
}

@article {pmid42239425,
year = {2026},
author = {Hasegawa, Y and Swain, O and Rajpal, U and France, M and Ncube, L and Mogno, I and Zierden, H and Ravel, J and Elovitz, MA},
title = {Exposure to Antibiotics Modifies the Immune Profiles of Bacterial Extracellular Vesicles from Common Vaginal Anaerobes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.21.726874},
pmid = {42239425},
issn = {2692-8205},
abstract = {BACKGROUND: The female lower reproductive tract harbors a complex microbiome that plays a critical role in reproductive health. A vaginal microbiome dominated by Lactobacillus crispatus (LC; Community State Type (CST) I) supports vaginal health, whereas a microbiome enriched with anaerobic species, such as Gardnerella vaginalis (GV) and Mobiluncus mulieris (MM) (CST IV) is linked to bacterial vaginosis (BV) and adverse outcomes, including sexually transmitted infections, infertility, and preterm birth. Although antibiotics such as metronidazole and clindamycin are commonly prescribed to treat BV, recurrence rates remain high, and the impact of these treatments on bacterial extracellular vesicles (bEVs), critical mediators of host-microbe interactions, is poorly understood.

RESULT: We investigated how antibiotic treatment at a dose below minimum inhibitory concentration alters the production and immunomodulatory function of bEVs derived from GV, MM, and LC. Using nanoparticle tracking analysis, cytokine profiling, and TLR pathway analyses, we found that antibiotic treatment significantly enhanced the inflammatory properties of bEVs in a species- and antibiotic-specific manner. Notably, bEVs from antibiotic-exposed GV and MM cultures induced elevated cytokine responses in epithelial and immune cells, primarily through TLR2 activation for GV bEVs, and through both TLR2 and TLR5 activation for MM bEVs. While LC bEVs are typically non-inflammatory, exposure to metronidazole, even at a lower dose than what is used clinically, rendered them immunostimulatory, suggesting a potential unintended proinflammatory consequence of treatment on beneficial microbes. We also detected bEVs in human vaginal swabs, including vaginolysin-positive bEVs, even in CST I microbiomes, indicating that low-abundance microbes, including pathogens, remain transcriptionally active.

CONCLUSIONS: These findings suggest that antibiotics not only reduce microbial load but also reshape bacterial communication via bEVs, potentially contributing to inflammation, epithelial barrier disruption, persistent dysbiosis, and recurrent infections. This work underscores the need for precision antimicrobial strategies that eliminate pathogens while preserving beneficial bacteria and their functional bEVs. Future therapies may benefit from considering the ecosystem-wide effects of antibiotics on the vaginal microbiome and its bEV-mediated signaling network.},
}

@article {pmid42239480,
year = {2026},
author = {Qian, J and Ghadermazi, P and Maret, S and Kemp, JF and Frank, D and Melanson, EL and Hendricks, AE and Krebs, N and Tang, M and Olm, MR},
title = {IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.19.726352},
pmid = {42239480},
issn = {2692-8205},
abstract = {BACKGROUND: IgA is the dominant antibody in the human gut and a key regulator of host-microbe interactions. Infants begin to produce IgA at around 6 months old and receive large quantities of IgA via human milk, but technical limitations have prevented species-level characterization of IgA binding in early life. This has left basic knowledge gaps about which species are targeted by IgA in infancy, and how modifiable lifestyle factors like breastfeeding and complementary feeding impact IgA targeting.

RESULTS: Here we adapt Metagenomic Immunoglobulin Sequencing (MIg-Seq) for low-biomass infant fecal samples and apply this optimized protocol to 32 longitudinal samples from 16 infants enrolled in the MINT trial, a four-arm randomized controlled trial comparing meat-based, dairy-based, plant-based, and reference complementary feeding patterns, with fecal sampling at 6 and 12 months (pre and post intervention). Infant IgA targeting mirrors adults at the phylum level, with both age groups showing significantly higher IgA targeting of Pseudomonadota and lower targeting of Bacteroidota relative to other phyla. During the substantial microbiome compositional shifts noted between 6 and 12 months, IgA targeting is significantly more stable than the microbiome itself. Among persistent colonizers, IgA targeting strengthens significantly from 6 to 12 months, with the most pronounced effect observed for Bifidobacterium , a finding robust across all dietary arms and feeding modes. The feeding arm to which infants were enrolled was not significantly associated with IgA binding, but several nutrient-specific associations were discovered. Animal-derived nutrients, particularly cholesterol, are strongly positively correlated with IgA targeting of Bifidobacterium longum , while plant-derived carotenoids are positively associated with IgA targeting of Flavonifractor plautii and Ruminococcus gnavus .

CONCLUSIONS: This study introduces an experimental and computational framework for species-level IgA profiling in the infant gut. The progressive strengthening of IgA targeting of Bifidobacterium and other beneficial persistent colonizers suggests a role for IgA in reinforcing beneficial microbes during infancy. The nutrient-specific dietary effects on IgA targeting reveal the immunological consequences of the complementary feeding period, and highlight a contrast between animal-versus plant-based diets. Together, these findings point to early nutritional interventions and IgA-based therapeutics as promising tools for promoting healthy immune-microbiome development.},
}

@article {pmid42239487,
year = {2026},
author = {Aldekhail, W and Al-Beltagi, M and Indrio, F and Al-Nemri, AM and Tomerak, A and Al Sawai, A and Al-Refaee, F and Al-Ghanem, G and Rozi, IH and Alallah, J and Khan, JM and Abouhazima, K and Al-Mannaei, K and El-Atawi, K and Sleiman, R and Miqdady, M},
title = {Infant gut microbiota following cesarean section in the Middle East: a multidisciplinary expert consensus based on a targeted narrative review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1809889},
pmid = {42239487},
issn = {2296-2360},
abstract = {BACKGROUND: Early-life dysbiosis associated with Cesarean section (C-section) delivery is increasingly recognized as a modifiable risk factor influencing short- and long-term health outcomes. This multidisciplinary expert consensus summarizes the clinical implications of C-section on infant gut microbiota. It proposes evidence-based strategies to mitigate these effects, with a focus on the critical window of the first 1,000 days of life.

METHODS: A multidisciplinary panel of 16 pediatricians, neonatologists, pediatric gastroenterologists, and nutrition experts conducted a targeted narrative review of the literature to inform a structured expert consensus process and participated in an online structured consensus process. Seventeen consensus statements were developed and validated through discussion, expert voting, and commentary, supported by a targeted review of current scientific evidence.

RESULTS: The expert panel reached consensus on the impact of C-section delivery on early microbiota composition and its clinical relevance, emphasizing that the rising prevalence of C-sections worldwide demands urgent attention. Experts unanimously emphasized the importance of exclusive breastfeeding as the primary strategy to support healthy microbiota development in infants born by cesarean section. When exclusive breastfeeding is not possible, evidence-based nutritional approaches, including selected prebiotics and probiotic strains with documented clinical efficacy, are recognized as promising alternatives for supporting microbial balance. Notably, the panel underscored that not all probiotics are equally effective and recommended shifting toward evidence-based strains shown to help restore gut dysbiosis in this population. Also, experts advocated for continuing microbiota-targeted support throughout the first 1,000 days of life, viewing this developmental window as a critical continuum rather than a limited early-life phase, while acknowledging the need for more long-term data. Additionally, education for healthcare professionals and parents about the long-term implications of C-section delivery was emphasized as a key enabler of the broader adoption of eubiosis-targeted strategies.

CONCLUSIONS: Optimizing microbial colonization in infants born by cesarean section requires a multifaceted approach that prioritizes breastfeeding, supports judicious use of evidence-based nutritional interventions when needed, and emphasizes education and continuity of care across early life. By aligning clinical practice with emerging microbiome science, early-life interventions may reduce dysbiosis-associated risks and improve long-term health outcomes.},
}

@article {pmid42239536,
year = {2026},
author = {Singh, P and Saravanan, A and Seitz, J and Alkarzon, N and Medugu, N},
title = {A one health perspective on the intestinal microbiome's role in COVID-19 outcomes and recovery.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1763844},
pmid = {42239536},
issn = {2235-2988},
abstract = {Emerging infectious diseases, particularly zoonotic ones, remain major global health concerns. The Coronavirus Disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), highlights the interconnectedness of human, animal, and environmental health within the One Health framework. The intestinal microbiome plays a central role in host immunity and systemic homeostasis, and its disruption has been linked to altered disease severity and recovery patterns in COVID-19. Evidence suggests that SARS-CoV-2 infection induces intestinal dysbiosis, modifies immune signaling, and affects the microbiota-gut-brain axis (MGBA), contributing to neuropsychiatric and metabolic complications. This review synthesizes current findings on the intestinal microbiome's role in COVID-19 pathophysiology and recovery, explores emerging therapeutic strategies including probiotics, prebiotics, and fecal microbiota transplantation, and emphasizes the importance of integrating microbiome research into pandemic preparedness through a One Health approach.},
}

@article {pmid42239539,
year = {2026},
author = {Jiang, X and Chen, B and Wang, Q and Liu, Y and Li, N and Zhang, L},
title = {Structural variation analysis suggests strain-level maternal-infant microbial transmission in early life.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1765801},
pmid = {42239539},
issn = {2235-2988},
abstract = {INTRODUCTION: Structural variations (SVs)-large, functionally consequential genomic alterations-serve as high-resolution markers for strain-level differentiation in the human microbiome, yet their relevance to vertical transmission of the maternal microbiota and early-life colonization remains unclear.

METHODS: Using metagenomic data from a 98-pair longitudinal mother-infant cohort and a 25-pair multi-niche cohort, we profiled microbial taxa, functions, and SVs, characterized variable SVs (vSVs), deletion SVs (dSVs), and transmitted SVs (tSVs), and evaluated the potential influence of delivery mode, feeding regimen, and maternal ecological niches.

RESULTS: We identified 5,578 SVs across 51 reference strains, with infants showing increasing SV diversity during the first year of life, and observed significantly greater SV similarity within mother-infant pairs than unrelated pairs. Abundance-based analysis identified 90 microbial species shared between mothers and infants. However, when incorporating SV-based tracking, only 14 strains showed patterns consistent with sustained maternal contribution across time points. Furthermore, exploratory subgroup analyses suggested that both delivery mode and feeding regimen may influence the vertical transmission patterns of maternal microbial strains and transmitted SVs. Functionally, tSVs were enriched in pathways linked to carbohydrate, amino acid, and lipid metabolism, as well as transport and environmental adaptation modules such as T4SS. Multi-niche analysis further suggested that the maternal gut showed the strongest inferred signal of SV-supported strain sharing with both the infant gut and oral microbiota.

DISCUSSION: Together, these findings suggest that microbial SVs can serve as complementary markers for investigating maternal contribution and vertical transmission-related strain-level patterns in early-life microbiome development, providing new insights into microbial inheritance and early-life health trajectories.},
}

@article {pmid42239553,
year = {2026},
author = {Alharbi, ZM},
title = {Integrative Approaches to Gut Microbiota: Biomarkers, Dysbiosis, and Therapeutic Potential.},
journal = {Saudi medical journal},
volume = {47},
number = {5},
pages = {787-800},
pmid = {42239553},
issn = {1658-3175},
mesh = {*Gastrointestinal Microbiome/physiology ; Biomarkers/metabolism ; Autoimmune Diseases/etiology/microbiology ; Humans ; *Dysbiosis/complications/microbiology/therapy ; Brain-Gut Axis/physiology ; Immune System/physiology ; },
abstract = {The human gut contains bacteria, viruses, and archaea that influence health depending on age, diet, and location. An individual harbours about 150 bacterial species. An imbalance of these microorganisms, known as dysbiosis, can negatively impact health. Commensal bacteria maintain microbial homeostasis by building short chain fatty acids. The 2-way communication channel that connects the gut and the brain is referred to as the gut-brain axis. Dysbiosis of the gut leads to some autoimmune diseases. A decline of beneficial bacteria causes the progression of rheumatoid arthritis. Gut dysbiosis increases intestinal permeability, allowing toxins and cytokines to enter the bloodstream and damage neurons. Through interactions with the immune system, the gut microbiota plays a complex role in both health and disease, including contributing to the development of type 1 diabetes. This review stresses the need to integrate measures to identify microbial biomarkers and also metabolic and genetic interplay between the microbiome and health.},
}

*Gastrointestinal Microbiome/physiology
Biomarkers/metabolism
Autoimmune Diseases/etiology/microbiology
Humans
*Dysbiosis/complications/microbiology/therapy
Brain-Gut Axis/physiology
Immune System/physiology

@article {pmid42239568,
year = {2026},
author = {El-Mokaddem, OK and Elmasry, GF and Mahmoud, WR and Abdel Ghany, LMA},
title = {Bridging the gap in Alzheimer's therapy: strategic design and SAR evolution of coumarin-based hybrids as potent MTDLs.},
journal = {RSC advances},
volume = {16},
number = {32},
pages = {29631-29660},
pmid = {42239568},
issn = {2046-2069},
abstract = {Due to their multitargeting potential, coumarin-based hybrid molecules represent a new and valuable drug development strategy for the treatment of Alzheimer's disease (AD). This review summarizes recent advances in the design, synthesis, and evaluation of coumarin hybrids as multi-target-directed ligands (MTDLs) for AD. This review covers various coumarin hybrid classes, including those incorporating triazole, thiazole, quinoline, chalcone, and other pharmacophores, highlighting their diverse mechanisms of action, such as acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibition, amyloid-beta (Aβ) aggregation prevention, BACE-1 inhibition, MAO-B modulation, antioxidant activity, and metal ion chelation. Structure-activity relationship (SAR) studies have identified key structural features for optimal activity, including linker length, substitution patterns, and physicochemical properties influencing CNS penetration. Molecular docking and dynamics simulations reveal information about drug-target interactions and demonstrate the ability to engage multiple targets. Coumarin hybrids are already showing ecological in vivo efficacy in animal models, and also the desired safety window and metabolic stability make them potential clinical candidates. Future research directions include incorporating emerging therapeutic targets, advanced computational design, and a focus on the microbiome-gut-brain axis to develop more effective and disease-modifying AD therapeutics.},
}

@article {pmid42239715,
year = {2026},
author = {Yang, H and Zhang, N},
title = {Effects of omega-3 PUFA-enriched egg consumption on metabolic parameters in elderly adults with metabolic syndrome: study protocol for a randomized controlled trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1831128},
pmid = {42239715},
issn = {2296-861X},
abstract = {BACKGROUND: Metabolic syndrome (MetS) affects approximately one-third of community-dwelling older adults (≥65 years) and is characterized by concurrent dysregulation of glucose and lipid metabolism alongside chronic low-grade inflammation. Poor long-term adherence to conventional omega-3 supplementation has prompted interest in sustainable, food-based delivery systems. Omega-3 polyunsaturated fatty acid (PUFA)-enriched eggs-produced through dietary modification of hen feed to enhance eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content-represent a palatable and easily incorporated dietary vehicle for sustained intervention.

METHODS: This is a three-arm, parallel-group randomized controlled trial that will enroll 180 community-dwelling adults aged ≥ 65 years with MetS. Participants will be randomly allocated (1:1:1) to receive either omega-3 PUFA-enriched eggs, regular eggs, or no egg intervention (usual diet) for 12 weeks. Those assigned to the egg intervention groups will consume one boiled egg daily, five days per week. The control group will maintain their habitual dietary patterns without additional egg consumption. Biological samples (blood, urine, and stool) will be collected at baseline and weeks 4, 8, and 12. Plasma concentrations of omega-3 fatty acids, lipid metabolism indicators,inflammation and oxidative stress markers will be measured. Exploratory outcomes include comprehensive multi-omics profiling, encompassing metabolomics and gut microbiome will be tested.

RESULTS: The primary outcome will be the longitudinal changes in fasting triglycerides (TG) measured at Weeks 0, 4, 8, and 12, with comparisons between the omega-3 PUFA-enriched eggs group and the regular eggs control group. Secondary outcomes will include glucose levels, insulin concentrations, lipid profiles, as well as biomarkers of inflammation and oxidative stress. Integrative multi-omics analyses will be conducted to explore the pathways linking omega-3 PUFA-enriched eggs consumption to alterations in metabolomic features and gut microbiota.

CONCLUSIONS: This trial will aim to assess the efficacy, feasibility, and mechanisms of omega-3 PUFA-enriched eggs in elderly adults with MetS, so as to provide insights and evidence to support scalable community-based dietary interventions.

TRIAL REGISTRATION: The protocol has been registered on the website of Chinese Clinical Trial Registry. The Identifier code is ChiCTR2600120125. The Registry date is 10 March, 2026. Registry name is "Interventional Effect of ω-3 Polyunsaturated Fatty Acid-Fortified Eggs on Elderly Patients with Metabolic Syndrome." Registration URL is [https://www.chictr.org.cn/bin/userProject].},
}

@article {pmid42240192,
year = {2026},
author = {Wang, T and Fan, N and Cao, X and Wang, Z},
title = {Entire Journey of Foliar Applied Nanomaterials with Different Surfactants Modification on Tomato Leaves and Subsequent Modulation of Stress Resistance.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.6c06235},
pmid = {42240192},
issn = {1936-086X},
abstract = {Foliar application of nanomaterials (NMs) offers great potential for sustainable crop disease management. However, how the presence of surfactants alters the behavior of NMs on leaf surfaces and their subsequent modulation of disease resistance remains unclear. Here, surfactants were incorporated into NMs suspensions to enhance foliar adhesion and deposition, thereby suppressing early blight (Alternaria solani) in tomato. Nonionic surfactants (Tween-80 and Silwet L-77) significantly improved the foliar deposition and translocation of La10Si6O27 nanorods (NRs). The treatment combining La10Si6O27 NRs with Silwet L-77 (NRs + L77) achieved the highest efficacy, reducing disease severity by 70%, which is 19.99% higher than La10Si6O27 NRs alone treatment. Mechanistically, (1) NRs + L77 activated the antioxidant defense system, increasing superoxide dismutase and peroxidase activities by 21.22% and 140.10%, respectively, while decreasing malondialdehyde content by 28.72%; (2) NRs + L77 optimized the phyllosphere microbiome, enriching beneficial genera such as Bacillus, Pantoea, and Klebsiella and restoring microbial network complexity; and (3) NRs + L77 upregulated defense-related gene expression, activated phenylpropanoid and flavonoid metabolic pathways, and induced systemic acquired resistance. In addition, NRs + L77 exhibited favorable biosafety toward nontarget organisms. This study demonstrates the potential of surfactant-modified NMs in improving disease control efficiency and contributing to sustainable crop protection.},
}

@article {pmid42240277,
year = {2026},
author = {Liu, W and Wang, X and Zhang, Y and Liu, J and Li, M and Zhou, Q and Wang, L and Liu, S and Chen, W and Chu, ES and Lau, HC and Song, Q and Zhou, X and Gou, H and Zhang, JX and Tian, GB and Wang, L and Li, X and Peng, S and Wong, CC and Kuang, M and Xu, L and Yu, J},
title = {Gut pathobionts translocate into liver and reshape intrahepatic microbiome to facilitate hepatocellular carcinoma.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-25-1355},
pmid = {42240277},
issn = {2159-8290},
abstract = {The role of intrahepatic microbiome in hepatocellular carcinoma (HCC) remains elusive. Here, we profiled matched gut and intrahepatic microbiomes from HCC patients and healthy subjects. Compared to healthy subjects, we observed increased gut-liver microbiome similarity and a gut pathobionts-centred network in HCC, implying microbial transfer via gut-liver axis. Consistently, HCC stool transplantation to germ-free mice impaired gut barrier function and increased bacterial load in liver. Multi-site analysis of intrahepatic microbiome and host transcriptome revealed that gut pathobionts in tumor regions positively correlate with host cytokine expression and oncogenic pathways. Administration of HCC-enriched Bacteroides fragilis disrupted gut barrier in mice and led to live bacteria translocation to liver. Bacteroides fragilis exacerbated liver damage and promoted HCC development in mice. Mechanistically, Bacteroides fragilis surface protein Enolase interacts with and activates Vimentin on hepatocytes, triggering oncogenic cascades. Our findings provide insight into how gut pathobionts translocate to liver to promote hepatocarcinogenesis.},
}

@article {pmid42240365,
year = {2026},
author = {Chen, B and Su, Z and Sun, Y and Shao, Z and Yu, X and Jiang, X and Xue, X and Yu, L and Wang, L and Zhao, W and Feng, Y and Ning, K and Zhang, M and Cao, A and Zhang, L},
title = {Gut microbial culturomics identifies autism-associated Shigella and reveals species-level remodeling during fecal microbiota transplantation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0079726},
doi = {10.1128/spectrum.00797-26},
pmid = {42240365},
issn = {2165-0497},
abstract = {Autism spectrum disorder (ASD) has been repeatedly linked to gut microbiota alterations, yet mechanistic insight remains limited by the scarcity of ASD-specific cultured isolates. Here, we performed large-scale gut microbial culturomics on fecal samples from 41 children with ASD and 12 typically developing (TD) controls, generating 1,724 isolates across six phyla. Longitudinal culturomics profiling was further conducted in 17 ASD children undergoing a 9-week fecal microbiota transplantation (FMT) intervention. All isolates underwent 16S rRNA sequencing and non-redundant clustering to assess species-level diversity, ASD-TD differences, and microbial dynamics associated with clinical response. ASD children harbored a distinct culturable microbiota enriched for Shigella flexneri and Shigella boydii, whereas TD children were enriched in beneficial taxa, such as Bifidobacterium catenulatum subsp. and other health-associated species. Notably, 20 species isolated from ASD children and 20 from TD children were absent from major existing gut microbiota biobanks, thereby expanding the cultivable repertoire. Among FMT participants, clinical responders exhibited increased alpha diversity, progressive enrichment of TD-associated beneficial taxa, such as Bacteroides fragilis, Anaerostipes hadrus, Parabacteroides merdae, and Turicibacter sanguinis, and a marked reduction of ASD-associated Shigella flexneri and Shigella boydii, whereas non-responders showed minimal shifts. Acquisition of TD-enriched strains at week 9 was strongly correlated with clinical improvement, suggesting that species-level ecosystem remodeling may contribute to FMT efficacy. This work establishes one of the first ASD-focused gut microbial culturomics resources, identifies Shigella as a potential ASD-associated taxon, and provides foundational evidence and testable mechanistic hypotheses for future microbiome-based interventions in ASD.IMPORTANCEMost autism spectrum disorder (ASD) microbiome studies rely on sequencing, which identifies associations but lacks live strains needed for mechanistic tests. We cultured 1,724 isolates from ASD and typically developing (TD) children, providing an ASD-focused, strain-level resource. ASD samples showed a significantly higher prevalence of Shigella flexneri. Longitudinal profiling during fecal microbiota transplantation (FMT) showed that clinical responders gained TD-enriched taxa and lost Shigella spp., and these shifts correlated with symptom improvement. This resource enables functional assays and gnotobiotic studies with ASD-relevant strains and provides a foundation for rational microbiome-based interventions.},
}

@article {pmid42240375,
year = {2026},
author = {Wirth, VR and Xie, SYL and Russell, MM and Bu, S and Sugino, KY and Keller, SF and Zhang, L and Alaimo, K and Beavers, AW and Comstock, SS},
title = {Antimicrobial resistance genes and mobile genetic elements in compost amendments, soil, and the human gastrointestinal bacterial communities of gardeners during a single gardening season.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0088225},
doi = {10.1128/msphere.00882-25},
pmid = {42240375},
issn = {2379-5042},
abstract = {UNLABELLED: The purpose of this study was to assess the antimicrobial resistance gene (ARG) and mobile genetic element (MGE) gene presence and abundance in soil, dairy manure and plant mixed compost (DMP), plant-based compost (P), and gardeners who used DMP across three time points. Soil (n = 1), DMP (n = 1), P (n = 1), and participant (n = 11) stool samples were collected at three time points during the 2019 gardening season in the Lansing, MI, area. DNA was extracted from each sample and stored at -20°C until use. Quantitative real-time PCR was used to detect ARGs and MGEs in each sample. Alpha diversity was assessed using richness, Shannon, and inverse Simpson indices. Shapiro-Wilk tests were used to assess normality. Beta diversity was assessed using Sorensen and Bray-Curtis dissimilarity indices. We detected a diverse composition of ARGs and MGEs in soil, compost, and human stool samples. DMP and soil exhibited greater ARG richness than P compost. In human stool, ARG and MGE profiles showed inter-participant variability but remained largely consistent within individuals across the gardening season. Alpha and beta diversity metrics revealed no significant shifts in the overall human gut resistome diversity across the gardening season. However, MGE gene composition differed significantly between DMP compost and human stool samples. Although ARG and MGE were detected in the soil and compost samples, there was no change in the ARG and MGE composition of gardeners' gut resistomes over the gardening season. These findings suggest that short-term exposure to AMR-rich compost or soil may not substantially alter gut resistome structure in healthy adult populations.

IMPORTANCE: Antimicrobial resistance is a growing public health concern, and compost and soil can contain genes that help bacteria resist antibiotics or share resistance with other bacteria. Many gardeners use manure-based compost, but it is unclear whether short-term exposure affects antimicrobial resistance in bacteria residing within the human gut. In this study, we detected antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in soil, two types of compost, and stool from gardeners across the 2019 gardening season near Lansing, MI. We found that manure-based compost and soil contained more ARGs than plant-based compost, but gardeners' gut resistomes remained stable over time. These results suggest that short-term compost exposure through gardening may not substantially alter the gut resistome.},
}

@article {pmid42240627,
year = {2026},
author = {Corsello, A and Romano, A and Romano, C},
title = {Proton pump inhibitors in children: indications and safety.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/17474124.2026.2683678},
pmid = {42240627},
issn = {1747-4132},
abstract = {INTRODUCTION: Proton pump inhibitors (PPIs) are among the most frequently prescribed medications in pediatric practice. While highly effective in acid-mediated disorders, concerns regarding overuse, inappropriate indications, and potential adverse effects have emerged, particularly in infants and children with nonspecific symptoms.

AREAS COVERED: This review summarizes the current evidence on the indications, efficacy, and safety of PPIs in the pediatric population. A literature search was performed in PubMed/MEDLINE and Embase, supplemented by landmark earlier studies and current clinical practice guidelines. We discuss guideline recommendations and examine the role of PPIs across different clinical scenarios including gastroesophageal reflux disease, esophagitis, eosinophilic esophagitis and special populations. Particular attention is given to emerging data on adverse outcomes, including infections, microbiome alterations, and long-term safety concerns. Strategies for appropriate prescribing, deprescribing, and individualized patient management are also addressed.

EXPERT OPINION: PPIs remain overprescribed in pediatrics, often for indications lacking clear benefit. Future efforts should prioritize diagnostic precision, short-term therapeutic trials and systematic deprescribing strategies. A shift toward stewardship-based prescribing, combined with improved clinician education and use of objective diagnostic tools, is essential to optimize outcomes and minimize unnecessary exposure.},
}

@article {pmid42240700,
year = {2026},
author = {Ghorab, MA and Khalil, MS and El-Sayyad, GS and Nada, HG and Elfadil, D and El-Sherif, DM and Gaballah, MS and Elgarahy, AM and Abouelnasr, HS and Saleh, DM and Liu, M and Chen, S},
title = {Microbial degradation of organophosphorus pesticides: mechanisms, environmental impacts, and future perspectives.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42240700},
issn = {1573-0972},
support = {2024A04J6583//Guangzhou Basic and Applied Basic Research Project, China/ ; },
abstract = {The pervasive global dispersion of organophosphorus pesticides (OPs) as a primary insecticidal agent for enhanced agricultural productivity presents an enduring ecological and human health exigency. Unfettered field-scale applications result in the ubiquitous contamination of diverse ecosystems, precipitating deleterious effects extending from the disruption of soil microbiome homeostasis and attendant biogeochemical cycles to significant morbidity in non-target biota and human populations. The pronounced hazards associated with specific OPs, including methamidophos, methyl parathion, and parathion, categorized as highly hazardous by the World Health Organization (WHO) and consequently restricted in numerous countries - underscore the imperative for effective remediation strategies. This review critically examines the natural attenuation of OPs, accentuating the burgeoning field of bioremediation and biodegradation as environmentally sustainable and efficacious approaches for decontaminating affected niches. We provide a comprehensive synthesis of the current understanding of the remarkable metabolic versatility exhibited by a phylogenetically diverse consortium of fungal and bacterial genera, exemplified by genera such as Pseudomonas, Bacillus, Acinetobacter, and Aspergillus, capable of catabolizing a broad repertoire of OP compounds in both soil and aqueous matrices. Furthermore, this analysis elucidates the central role of specific microbial organophosphorus hydrolase genes (oph, opd, mph, hocA, and opaA) in the evolutionary adaptation of novel metabolic pathways and the expression of cognate hydrolase enzymes that catalyze the crucial initial steps in OP degradation. This focused synthesis highlights recent advances in deciphering the intricate molecular mechanisms governing microbial OP biodegradation and critically evaluates the potential of these biological systems as robust and scalable bioremediation interventions for the effective restoration of OP-contaminated water and soil environments.},
}

@article {pmid42240810,
year = {2026},
author = {Vitiello, A and Zovi, A},
title = {Early-onset colorectal cancer: epidemiology, risk factors, and implications for clinical practice.},
journal = {Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {42240810},
issn = {1699-3055},
abstract = {The incidence of colorectal cancer (CRC) in individuals under 50 years of age has increased steadily over the past two decades in several high-income countries, contrasting with declining rates in older populations following the implementation of screening programmes. This epidemiological shift represents an emerging challenge for clinical practice and public health systems. This clinical review aims to summarise current epidemiological evidence, risk factors, and biological characteristics of early-onset colorectal cancer, and to examine its implications for screening strategies and health policy. Although hereditary cancer syndromes account for a minority of cases, most earlyonset CRCs occur in individuals without a recognised genetic predisposition. Identified risk factors include obesity, unhealthy dietary patterns, physical inactivity, microbiome alterations, and early-life environmental exposures. Diagnostic delays are common, as symptoms such as rectal bleeding or changes in bowel habits are frequently attributed to benign conditions in younger adults, leading to presentation at more advanced stages. Growing epidemiological data and modelling studies support lowering the age of average-risk screening initiation to 45 years, a strategy already adopted in several countries. However, implementation requires careful consideration of healthcare capacity, cost-effectiveness, and equitable access. Early-onset colorectal cancer represents a significant and evolving public health concern. Enhanced clinical vigilance in symptomatic young adults, together with evidence-based adjustments to screening policies, will be essential to mitigate the increasing burden of disease in this population.},
}

@article {pmid42241172,
year = {2026},
author = {Chen, Q and Xu, Z and Zheng, T and Pang, H and He, Z},
title = {Association between lipid metabolism and lung adenocarcinoma: Evidence from Mendelian randomization and tissue microbiome analysis.},
journal = {Journal of cancer research and therapeutics},
volume = {22},
number = {2},
pages = {403-414},
pmid = {42241172},
issn = {1998-4138},
abstract = {BACKGROUND: Tissue-resident microbiota play an important role in lung cancer development. This study aimed to characterize the microbiota profile associated with fatty acid metabolism and related genes and examine its effect on treatment outcomes in lung cancer.

METHODS: Genome-wide association data on saturated fatty acid ratio, total cholesterol, and linoleic acid ratio were analyzed with lung adenocarcinoma as the outcome. Mendelian randomization (MR) and multivariable MR using significant single nucleotide polymorphisms assessed causal effects with sensitivity analyses. TCGA and GEO microbial data were explored via GSEA, STRING, and CIBERSORT, and Bacillus velezensis was validated in tumor tissue by quantitative polymerase chain reaction.

RESULTS: MR identified saturated fatty acids and total cholesterol as risk factors for lung adenocarcinoma (LUAD), while linoleic acid was protective. Microbial profiling showed distinct tumor versus adjacent tissue communities, with Bacillus velezensis enriched in LUAD. Its abundance was negatively associated with the cholesterol-response pathway (GOBP_CELLULAR_RESPONSE_TO_CHOLESTEROL). Twelve cholesterol-related genes were differentially expressed, and a derived risk model predicted poor prognosis. Among them, GPLD1 exhibited tumor-suppressor characteristics, with lower tumor expression linked to worse survival. GPLD1 is detectable in plasma (~2.8 mg/L) and reduced in lung cancer patients, supporting its potential as a noninvasive biomarker.

CONCLUSION: Our findings suggest a causal link between the components of a high-fat diet and LUAD by identifying key genes and microbial communities. Moreover, GPLD1 represents a promising biomarker for the early diagnosis and prognosis of this patient population.},
}

@article {pmid42241374,
year = {2026},
author = {Scionti, K and Schoissengeier, V and Vaclavkova, I and Fleiss, H and Cuparencu, C and Olsen, A and Jilani, H and Lucassen, DA and de Zoete, E and Feskens, E and Boshuizen, HC and Vingerhoeds, MH and Ummels, M and Haider, S and Winzer, E and Wakolbinger, M and Crevenna, R and Jordakieva, G and Hasenöhrl, T and Wolzt, M and Wallner, M and Riederer, M and Ressler, M and Fuchs-Neuhold, B and Höfler, C and Aufschnaiter, AL and Wrzesińska, MA and Binder-Olibrowska, KW and Ptaszyński, P and Rakoczy, J and Dros, C and Lammers-van der Holst, H and Kramer, A and Maier, B and Matullat, I and Papantoniou, K and Wagner, KH},
title = {Investigating the risk of obesity in European night shift workers: a study protocol for cross-sectional and mechanistic studies in the SHIFT2HEALTH Project.},
journal = {Obesity facts},
volume = {},
number = {},
pages = {1-25},
doi = {10.1159/000552231},
pmid = {42241374},
issn = {1662-4033},
abstract = {Introduction Approximately one in five workers in Europe is engaged in shift work. Studies reveal that night shift work leads to an increased risk of overweight, obesity and related diseases. Yet, the biological and behavioural mechanisms underlying these associations are not fully understood. The cross-sectional and mechanistic studies within the European SHIFT2HEALTH project aim to investigate biological, behavioural and psychosocial key risk factors responsible for the association between night work and obesity across five European countries. Methods A multi-centric cross-sectional study is designed to unravel obesogenic risk factors, eating habits and sleep patterns in night shift workers and day workers from the health- and various industrial sectors. Recruitment takes place in Austria, Denmark, Germany, Poland, and the Netherlands, aiming at 500 night shift workers and 500 day workers. Anthropometric measurements, sensory perception and food preference tests are performed, alongside extensive questionnaires. In addition, biological samples (blood, hair, urine, faeces) are collected for biomarker measurements of inflammation, oxidative stress, glycaemic and lipaemic parameters, for microbiome and metabolomics analyses and chronotype assessment. In a nested mechanistic study, night shift workers (N=200) recruited in Austria and in the Netherlands, additionally collect urine samples from all voids over 24 hours during a day shift and a night shift, as well as dried blood spots and tongue swabs at four time points and undergo continuous sleep, activity and light exposure monitoring through actigraphy. The association between night shift work and its metrics with levels of pre-obesity biomarkers will be evaluated in crude and multivariable-adjusted regression models, adjusting for potential confounders. Stratified analyses by age, gender, sector and chronotype will be conducted. Conclusion In the cross-sectional and mechanistic studies of the SHIFT2HEALTH project, biological, behavioural and psychosocial factors of night shift workers will be compared with those of day workers across sectors. The outcomes of these studies will serve as a basis for future intervention studies and, together, will contribute to the development of strategies to prevent and reduce overweight and obesity with the aim to improve the health and wellbeing of night shift workers. Trial registration: clinicaltrials.gov, ID: NCT06288568.},
}

@article {pmid42241759,
year = {2026},
author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Robinson, K and Hauck, R},
title = {Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations[1].},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107151},
doi = {10.1016/j.psj.2026.107151},
pmid = {42241759},
issn = {1525-3171},
abstract = {This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.},
}

@article {pmid42241765,
year = {2026},
author = {Xiong, X and Sun, H and Hu, Z and Tian, Y and Zeng, T and Lu, L and Shi, F and Li, Y},
title = {Influence of age on eggshell quality in ducks: An analysis based on calcium metabolism, gut microbiota, and uterine transcriptome.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107182},
doi = {10.1016/j.psj.2026.107182},
pmid = {42241765},
issn = {1525-3171},
abstract = {Our current project aims to elucidate the impact of advancing date on eggshell quality in Shanma ducks and its underlying mechanisms. A total of 60 healthy Shanma ducks from the youth group (160 days old) and the elderly group (560 days old) were selected to evaluate eggshell physicochemical properties, serum calcium and phosphorus metabolism, gut microbiota, and uterine tissue transcriptomic expressions. Results demonstrated that the elderly group exhibited significantly reduced eggshell thickness and strength, with ultrastructural analysis revealing uneven calcium deposition and a thinner effective layer compared to the youth group. Elderly ducks showed decreased serum levels of 25-hydroxyvitamin D3, alongside elevated parathyroid hormone and bone remodeling markers (TRAP-5b, BAP), suggesting disrupted calcium metabolism. Histological observation identified duodenal villus atrophy, humeral matrix erosion, and uterine interstitial edema in elderly ducks. Gut microbiome analysis indicated reduced microbial diversity and simplified community structure in elderly ducks, with Helicobacter and Lactobacillus becoming dominant genera, and significant downregulation of mineral absorption-related functional pathways. Uterine transcriptomics identified 607 differentially expressed genes, significantly enriched in pathways such as calcium signaling and steroid hormone biosynthesis. Correlation network analysis further revealed that eggshell strength was closely associated with bone resorption markers, Helicobacter abundance, and the expression of multiple calcium metabolism-related genes (e.g., KCNS2, GABRA1, FOXF1, ATP1B1). Notably, the positive correlation between eggshell strength and SMAD9 observed in the youth group was absent in the elderly group. In conclusion, the age-related decline in eggshell quality results from the combined effects of calcium metabolism imbalance, enhanced bone remodeling, gut microbial dysbiosis, and uterine functional disruption, providing multi-omics insights into the decline of avian reproductive performance with age.},
}

@article {pmid41974789,
year = {2026},
author = {Jia, Z and Zhu, LF and Wang, L and Zhang, J and Liu, S and Tian, F and Yi, Y and Wang, J and Tang, J and Gong, J},
title = {Phosphorus application, nutrient absorption, and endophytic root bacterial communities in maize grown in phosphorus-deficient rocky arid soils, China.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41974789},
issn = {2045-2322},
support = {Qiankehechengguo[2022] zhongdian 010//Major Scientific and Technological Special Project of Guizhou Province/ ; Qianjiaoji [2023] No.004//Science and Technology Research Project of Guizhou Provincial Department of Education/ ; QKHZC[2021]YB459//Science and Technology Support Project of Guizhou Province/ ; },
abstract = {Phosphorus deficiency is one of the major constraints for crop growth in Karst rocky desertification regions. Different phosphorus treatments have become important strategies for enhancing agricultural productivity; however, the effects of phosphorus fertilization on nutrient allocation and root endophytic microbiome at different growth stages under field conditions remain inadequately explored. Therefore, this study implemented four phosphorus application treatments in a field-based maize cultivation system: P0 (0 kg ha[-1]), P1 (75 kg ha[-1]), P2 (150 kg ha[-1]), and P3 (225 kg ha[-1]). Nutrient distribution and root endophytic microbial community dynamics were analyzed at the jointing and milk-ripening stages. The results demonstrated that: (1) With increasing phosphorus application, the total nitrogen (TN) and total phosphorus (TP) in roots and leaves at the jointing, silking, and milk-ripening stages exhibited a pattern of “low phosphorus treatment enhancing TP content, while high phosphorus treatment suppressing TP uptake.” Total potassium (TK) content showed a decreasing trend, with the highest nutrient uptake observed at the phosphorus application rate of 150 kg ha[-1]. (2) Analysis of the root bacterial community revealed a decline in bacterial diversity with increasing phosphorus levels, but the abundance of Proteobacteria and Actinobacteria were significantly enhanced. (3) Correlation analysis indicated that low phosphorus treatment (P0) induced microbial community restructuring, high phosphorus treatment (P3) promoted the proliferation of functional taxa such as Pseudomonadaceae, while medium phosphorus treatment (P2) showed the most significant correlation between microbial community structure and phosphorus availability. This study provides valuable scientific insights for optimizing phosphorus fertilization in maize production in karst regions.},
}

@article {pmid42010688,
year = {2026},
author = {Yadav, RK and Zhang, Y and Lv, Y and Liu, S and Yang, J and Wang, Y and Gang, X},
title = {Mechanisms of weight recurrence after bariatric surgery.},
journal = {Nutrition & metabolism},
volume = {23},
number = {1},
pages = {},
pmid = {42010688},
issn = {1743-7075},
support = {YDZJ202402042CXJD, YDZJ202401410ZYTS, 82272993, 2022-CXM-06, 81972372//Science and Technology Department, and National Natural Science Fund, Jilin Province, China/ ; },
abstract = {UNLABELLED: Obesity is a major health concern in today’s growing population, significantly raising the risk of disease and death. Bariatric surgery is the most effective treatment for obesity and its related conditions. However, weight recurrence remains a common issue post-surgery. This study aims to understand the mechanisms of Weight recurrence after Bariatric surgery, other than anatomic surgery failure. Weight recurrence may result from various factors, including genetic predisposition, psychological and behavioral influences, neuroendocrine changes, alterations in the gut microbiome, bile acid signaling, and post-surgery hypoglycemia. Prevention and management strategies include lifestyle modifications, mental health support, pharmacotherapy, and, in some cases, revision surgery. This study explores the controversial hormonal changes involved in weight recurrence, as well as the roles of gut microbiota, bile acid signaling, and genetic factors. Additionally, the study highlights several preventable factors that are crucial for maintaining long-term weight loss and minimizing weight recurrence after bariatric surgery. By gaining insight into these hormonal changes and other contributing factors, we can implement effective preventive measures and medical treatments to enhance long-term weight loss success and improve patients’ quality of life. Nonetheless, further research is needed to fully understand the contributions of bile acid signaling and gut microbiota in the process.

GRAPHICAL ABSTRACT: [Image: see text]},
}

@article {pmid42228350,
year = {2026},
author = {Wang, M and AlQahtani, A and Liu, L and Ran, L and Liu, C and Liang, Y and Yu, J and Wu, Y and Guan, Q},
title = {Microalgae Oil Improves Hepatic Lipid Metabolism in A High-Fat Diet-Induced Mouse Model.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {231},
pages = {},
doi = {10.3791/71168},
pmid = {42228350},
issn = {1940-087X},
mesh = {Animals ; Mice ; Diet, High-Fat/adverse effects ; *Liver/metabolism/drug effects ; *Lipid Metabolism/drug effects ; *Microalgae/chemistry ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Docosahexaenoic Acids/pharmacology/administration & dosage ; },
abstract = {Metabolically, dysfunctional steatotic liver disease is a prevalent metabolic disorder associated with gut microbiota dysbiosis and hepatic lipid imbalance. In this study, a high-fat diet-induced mouse model was established to evaluate the effects of supplementation with DHA-rich microalgae oil. Mice (n = 4 per group) were fed a high-fat diet for 8 weeks and received daily oral administration of microalgae oil, probiotics, or the combination of DHA-rich microalgae oil and probiotics. Metabolic parameters, gut microbiota composition (16S rRNA sequencing), microbial functional pathways, and hepatic metabolomic profiles were assessed. The results showed that DHA-rich microalgae oil improved lipid homeostasis, as indicated by reduced serum LDL-c and hepatic triglyceride levels and increased high-density lipoprotein (HDL-c), and was associated with alleviation of liver injury and oxidative stress. Microbiome analysis revealed selective changes in gut microbial composition, including enrichment of Lactobacillus and Bifidobacterium and reduction of high-fat diet-associated taxa such as Clostridium and Ruminococcus. Functional profiling indicated alterations in microbial metabolic pathways, including the L-methionine salvage cycle and phenylethylamine degradation. Integrated microbiome-metabolome analysis further identified associations between microbial taxa and hepatic metabolites involved in fatty acid metabolism, bile acid turnover, and amino acid pathways. These findings indicate that DHA-rich microalgae oil supplementation is associated with improvements in hepatic lipid metabolism and gut microbiota composition in this model, without implying a direct causal mechanism.},
}

Animals
Mice
Diet, High-Fat/adverse effects
*Liver/metabolism/drug effects
*Lipid Metabolism/drug effects
*Microalgae/chemistry
Male
Mice, Inbred C57BL
Disease Models, Animal
Docosahexaenoic Acids/pharmacology/administration & dosage

@article {pmid42228448,
year = {2026},
author = {Brandt, E and Koivisto, A and Pereira, P and Mustanoja, E and Auvinen, P and Saari, T and Rusanen, M and Leinonen, V and Scheperjans, F and Kärkkäinen, V},
title = {Early Gut Microbiome Alterations in Mild Cognitive Impairment Reflect Changes in Alzheimer Disease.},
journal = {Alzheimer disease and associated disorders},
volume = {},
number = {},
pages = {},
doi = {10.1097/WAD.0000000000000732},
pmid = {42228448},
issn = {1546-4156},
abstract = {INTRODUCTION: Alterations in the gut-brain axis have been increasingly linked to neurodegenerative diseases, including Alzheimer disease (AD). It remains unclear whether these microbiome changes are already present during early cognitive decline. We examined whether gut microbiome alterations characteristic of AD are detectable in mild cognitive impairment (MCI) and whether these changes follow a similar pattern across the cognitive continuum.

METHODS: This case-control study included 78 participants: 37 cognitively healthy controls, 20 individuals with MCI, and 21 individuals with prodromal or mild AD. Cognitive performance was assessed using the CERAD neuropsychological battery, and disease severity was assessed using the Clinical Dementia Rating. Dietary data were collected, and fecal samples were analyzed using 16S rRNA gene amplicon sequencing.

RESULTS: We identified 16 bacterial genera associated with cognitive status. Genera such as Lacticaseibacillus, Raoultella, and Buttiauxella were reduced in AD, with similar decreases already evident in MCI. In contrast, Anaerovorax and an unclassified Comamonadaceae genus were increased in AD. Several alterations showed a consistent trend from normal cognition through MCI to AD.

DISCUSSION: Gut microbiome alterations characteristic of AD appear already present in early cognitive decline and follow a similar pattern in MCI. These findings support the potential of microbiome profiles as early, noninvasive biomarkers of AD.},
}

@article {pmid42228521,
year = {2026},
author = {Csorba, AB and Fora, CG and Balog, A},
title = {Diversity analyses of corn leaf aphid Rhopalosiphum maidis (Hemiptera: Aphididae) endosymbiotic microbiome and soil microbiome-preliminary results.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {3},
pages = {},
pmid = {42228521},
issn = {1536-2442},
support = {PN-III-P4-PCE-2021-0543//UEFISCDI Romania/ ; //Faculty of Engineering and Applied Technologies/ ; //University of Life Sciences/ ; //Timișoara/ ; },
mesh = {Animals ; *Aphids/microbiology ; *Microbiota ; *Symbiosis ; *Soil Microbiology ; Zea mays ; Europe ; Bacteria/classification/genetics ; },
abstract = {The corn leaf aphid, Rhopalosiphum maidis Fitch (Hemiptera: Aphididae), microbial symbiont and 9 soil-type microbial diversities were genetically analyzed along a gradient of maize management systems that includes 3 different crop control strategies from 3 climatic regions. The central point of interest was to assess whether any similarity could be detected between the corn leaf aphid's rapid distribution increase throughout mainland Europe and variation in its endosymbiont microbiome diversity. According to the results, it was detected that the bacterial community differs between regions. The obligate symbiont Buchnera aphidicola dominated across all climate regions, while facultative symbionts such as Serratia symbiotica and Wolbachia varied in relative abundance under different temperature conditions. Fewer effects of soil types were detected. Our study comprises analyses about a pest aphid and its associated symbiont community in relation to ambient temperature conditions, and as such, we believe it may well help in the development of new control strategies.},
}

Animals
*Aphids/microbiology
*Microbiota
*Symbiosis
*Soil Microbiology
Zea mays
Europe
Bacteria/classification/genetics

@article {pmid42228562,
year = {2026},
author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N},
title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.},
journal = {Cell reports},
volume = {45},
number = {6},
pages = {117478},
doi = {10.1016/j.celrep.2026.117478},
pmid = {42228562},
issn = {2211-1247},
abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.},
}

@article {pmid42228606,
year = {2026},
author = {Waghmode, S and Viswanathan, R and Koligudde, V and Umare, P and Lavania, M},
title = {Microbial shifts in early life: the pediatric gut microbiome and its role in health and disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2681763},
pmid = {42228606},
issn = {1949-0984},
abstract = {This review explores the pivotal role of the pediatric gut microbiome in shaping early-life development and influencing susceptibility to disease, emphasizing its impact on immune, metabolic, and neurodevelopmental processes. The neonatal period represents a critical window for host-microbiome interactions, beginning at birth when intestinal barrier function is still developing and immune responses remain immature. During this formative stage, rapid microbial colonization and ecological succession are influenced by delivery mode, infant feeding practices, antibiotic exposure, and environmental factors. Beyond bacterial populations, the early-life gut virome composed of bacteriophages and eukaryotic viruses evolves dynamically and contributes to microbial community structure, gene exchange, and immune system maturation. Microbially derived signals and metabolites support the development of mucosal integrity, immune programming, and host microbe equilibrium, with long-term implications for systemic immune function. Breastfeeding fosters the establishment of microbial communities and metabolic profiles associated with immune tolerance, whereas formula feeding and early-life antibiotic use may disrupt normal microbiome development. Alterations in early microbial trajectories have been associated with heightened risk of pediatric conditions, including allergic diseases, obesity, inflammatory bowel disease, and neurodevelopmental disorders. The review further evaluates emerging microbiome-directed strategies, such as probiotics, prebiotics, and fecal microbiota transplantation, considering both their therapeutic promise and current challenges. Collectively, current evidence underscores the early-life gut microbiome as a central determinant of host development and a compelling target for disease prevention strategies.},
}

@article {pmid42228693,
year = {2026},
author = {Marquez Rosales, S and Amitabh, P and Olmstead, EM and Avey, EPR and Wall, ES and Ortiz de Ora, L and Wiles, TJ and Parthasarathy, R},
title = {Imaging the impact of rotifer consumption on bacterial behaviors in the zebrafish gut.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0349516},
pmid = {42228693},
issn = {1932-6203},
mesh = {Animals ; *Zebrafish/microbiology ; *Vibrio/physiology ; Larva/microbiology ; *Rotifera/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Enterobacter/physiology ; *Intestines/microbiology ; Microscopy, Fluorescence ; },
abstract = {The gut microbiota influence many aspects of their host's health and physiology including the digestion of food, and food intake in turn influences the composition of the gut microbiome. However, the ways in which food can alter the behavior of intestinal bacteria remain largely unknown, due in large part to the difficulty of assessing behavior in situ. Larval zebrafish provide a model for addressing this gap because of their optical transparency and their ability to be prepared germ-free and then associated with specific microbial species. Using light sheet fluorescence microscopy to visualize bacteria inside the intestines of live zebrafish larvae, we examine the properties of two commensal strains with markedly different physical characteristics. One is a zebrafish-commensal Enterobacter species that forms large aggregates in unfed larvae, and the other is a pathobiont Vibrio species, capable of damaging intestinal tissue, that is motile and planktonic. We use recently developed ultraviolet irradiation methods to dramatically lower the microbial content in rotifers, a common live food for larval fish, thereby enabling the assessment of feeding effects independent of the introduction of new microbes. Following host consumption of rotifers, Enterobacter clusters disintegrate into motile individuals. Vibrio remains planktonic in fed larvae but decreases the activity of its Type VI Secretion System, as revealed by a fluorescent fusion protein comprising one of the secretion apparatus proteins and green fluorescent protein, leading to a strong decrease in damage to host tissue. Our results reveal that feeding can have major impacts on bacterial behavior that should be considered in models of normal gut microbiome dynamics as well as pathogenesis.},
}

Animals
*Zebrafish/microbiology
*Vibrio/physiology
Larva/microbiology
*Rotifera/microbiology/physiology
*Gastrointestinal Microbiome/physiology
*Enterobacter/physiology
*Intestines/microbiology
Microscopy, Fluorescence

@article {pmid42228750,
year = {2026},
author = {Qiu, C and Wang, H and Liu, R},
title = {Associations between body composition and gut microbiota in female college students with and without dance training.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350639},
pmid = {42228750},
issn = {1932-6203},
mesh = {Humans ; Female ; *Body Composition/physiology ; Students ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Dancing ; Young Adult ; Universities ; Feces/microbiology ; Adiposity ; Electric Impedance ; Adult ; },
abstract = {Physical activity has been associated with gut microbiota variation and body composition phenotypes, but evidence in female dance students remains limited. This study compared body composition profiles and gut microbiota characteristics between female university students majoring in dance and those from non-dance majors. Seventy students were included (n = 35 per group). Body composition was assessed using bioelectrical impedance analysis (InBody 970), and fecal samples were analyzed by 16S rRNA gene sequencing. Dance students exhibited significantly lower adiposity related parameters and central fat accumulation indices, including PBF, BFM, FMI, VFA, VFL, WC, WHR, WHtR, ABSI, and conicity index (P < 0.001), while showing higher SMM/WT, TBW/WT, and lower limb lean mass distribution (P < 0.001). No significant differences were observed in FFM, SMM, or SMI (P > 0.05). Gut microbiota composition differed between groups, with differential taxa observed across multiple taxonomic levels. Notably, Faecalibacterium and Lachnospiraceae_ND3007_group showed negative correlations with adiposity related indices and positive correlations with muscle and hydration related parameters, whereas Peptoniphilus, Ezakiella, and Fenollaria were positively correlated with adiposity related indices. In addition, Fusobacterium and Escherichia Shigella were positively associated with central adiposity measures. These findings indicate that female dance students exhibit distinct body composition profiles, while microbiome-related differences and associations appear modest and exploratory, warranting further validation in larger and well-controlled studies.},
}

Humans
Female
*Body Composition/physiology
Students
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Dancing
Young Adult
Universities
Feces/microbiology
Adiposity
Electric Impedance
Adult

@article {pmid42228922,
year = {2026},
author = {Poveda, J and Silva, D and Sousa, B and Romão, IR and Carmo Gomes, JD and Soares, C and Fidalgo, F and Duarte, I and Vilchez, JI},
title = {Endophytic seed microorganisms in legumes: Natural bioinoculants for sustainable agriculture.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag261},
pmid = {42228922},
issn = {1460-2431},
abstract = {As global food demand rises against the backdrop of environmental and health concerns from intensive agrochemical use, there is an urgent need for sustainable crop-management strategies. In this perspective, seed-borne endophytic microbes, including bacteria and fungi, in legumes offer a naturally inherited bioinoculant system. This review integrates 35 Scopus and Web of Science studies to examine the occurrence, transmission dynamics, and functional diversity of endophytes within seeds of key legume species. Seed endophytes contribute to plant development and productivity through multiple mechanisms: atmospheric nitrogen fixation; solubilization of phosphorus and potassium; synthesis of siderophores and indole-3-acetic acid; and modulation of rhizosphere microbial communities, collectively enhancing germination rate, biomass accumulation, and yield. Under abiotic stress conditions, such as drought, nutrient deficiency, or contaminant exposure (metals and pesticides), such beneficial microbes promote root architecture remodeling, exopolysaccharide secretion, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, thereby improving stress resilience. In biotic contexts, certain bacterial endophytes may contribute to biocontrol through antibiotic production, while fungal inoculants have been reported to synthesize alkaloids that can deter herbivores. By elucidating the multifaceted roles of legume seed endophytes, this review underscores their potential as a turnkey, eco-friendly bioinoculants, paving the way for greener agricultural practices without compromising crop performance.},
}

@article {pmid42229136,
year = {2026},
author = {Delgado, N and Fernández, KG and Zambrano-Alegría, C and Espinosa, ZYD and Ramos-Cabrera, E},
title = {Physiological and microbial alterations induced by pesticides in agricultural systems: A bioassay- and 16S rRNA-based approach.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142560},
doi = {10.1016/j.jhazmat.2026.142560},
pmid = {42229136},
issn = {1873-3336},
abstract = {The extensive use of pesticides in agricultural production systems has increased interest in understanding their potential impacts on soil environmental dynamics. This study evaluates the effects of pesticide application on Lactuca sativa L. and soil microbiota. An initial field survey identified the main active ingredients commercial pesticides, followed by bioassays assessing germination and early development of Lactuca sativa, as well as soil microbial structure through physiological assessments and metagenomic analyses based on 16S rRNA gene sequencing, during a three-week soil experiment. Thirty active ingredients were identified in 92 agricultural products. Chlorpyrifos was identified as one of the most commercialized insecticides, where insecticides represented 69% of marketed phytosanitary products, mainly organophosphates (18%) and pyrethroids (21%), despite its hazardous classification and ban in several countries. Germination assays showed a hormetic response at low dose (2200 mg/L), reaching 70% germination compared with 51% in the control, while the germination index decreased to 75% at the recommended dose (4400 mg/L). Statistical analyses revealed inhibition of hypocotyl elongation (p = 0.001) and cotyledon development (p = 0.029). Soil microbiome analysis showed that high chlorpyrifos concentrations reduced microbial richness and diversity, while beta diversity analyses explained 99% of the variance among treatments. Proteobacteria, Burkholderiales, and Sphingomonadales increased under pesticide exposure, indicating microbial adaptation and biodegradation potential. Functional prediction using PICRUSt2 revealed enrichment of genes K03381, K00446, K01048, and K01560 associated with potential organophosphate degradation pathways. These findings demonstrate that chlorpyrifos induces ecological and seedling alterations even at agronomically recommended concentrations. highlighting the need to strengthen sustainable pesticide management and environmental monitoring strategies.},
}

@article {pmid42229147,
year = {2026},
author = {Zhao, M and Zhou, J and Yang, W and Li, R and Wang, J and Peng, Y and He, Y and Zhou, H and Ye, Q},
title = {Differential Associations of Human Herpesviruses With Oral Bacteria and Periodontitis Severity: A Cross-Sectional Analysis.},
journal = {International dental journal},
volume = {76},
number = {4},
pages = {109650},
doi = {10.1016/j.identj.2026.109650},
pmid = {42229147},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: The polymicrobial synergy and dysbiosis model is increasingly recognized as a key pathogenic factor in periodontitis. Human herpesviruses (HHVs), including EBV, HCMV, and HSV-1, have been linked to periodontitis development. However, current research lacks sufficient evidence to clarify the correlation between HHVs, periodontitis progression, and periodontal microbiota. This study aimed to investigate the association between HHVs in gingival crevicular fluid (GCF) and periodontitis severity, as well as the correlation patterns between viruses and periodontal microbiota.

METHODS: A total of 339 subjects (64 healthy controls, 275 periodontitis patients) were stratified according to the 2018 periodontitis classification criteria. Viral loads were quantified by quantitative real-time PCR (qPCR), and microbial communities were analysed via high-throughput 16S rRNA sequencing.

RESULTS: HCMV and EBV loads were significantly positively correlated with clinical parameters including probing depth (PD), clinical attachment loss (CAL), and bleeding on probing (BOP) (all P < .001), and their infection status was closely associated with periodontitis staging. HSV-1 showed no significant association with any periodontal indicators (P > .05). In the EBV/HCMV coinfection group, 92.9% of patients were classified as stage II-IV periodontitis, suggesting potential combined viral associations with disease severity. Microbiome analysis revealed significantly higher microbial diversity in the HCMV-H compared to the HCMV-L. HCMV load was positively correlated with known pathogens such as Porphyromonas gingivalis and Tannerella forsythia, as well as novel associated bacteria (eg, Schwartzia succinivorans, Peptostreptococcus stomatis). Functional prediction showed significant enrichment of microbial metabolic pathways in HCMV-H patients, including Helicobacter pylori infection and isoquinoline alkaloid biosynthesis.

CONCLUSION: HCMV is strongly associated with periodontitis severity and bacterial dysbiosis, while EBV acts as an independent risk factor correlated with periodontitis severity. In contrast, HSV-1 shows no significant association with periodontitis severity. This study provides new evidence for the polymicrobial pathogenesis of periodontitis and highlights virus-bacteria associations as potential therapeutic targets, although further longitudinal studies are needed to establish causality.},
}

@article {pmid42229215,
year = {2026},
author = {Alharthy, OM and Alshegaihi, RM and Fayad, E and Binjawhar, DN and Alshaharni, MO and Alqurashi, M and Alhelaify, SS and Peijnenburg, W},
title = {Oxalic acid enhances wheat (Triticum aestivum L.) resilience to combined abiotic stresses through integrated physiological and rhizospheric microbial modulation.},
journal = {Plant physiology and biochemistry : PPB},
volume = {236},
number = {},
pages = {111432},
doi = {10.1016/j.plaphy.2026.111432},
pmid = {42229215},
issn = {1873-2690},
abstract = {Soil contamination and abiotic stress have become serious global problem due to rapid development of social economy. Oxalic acid (OA), an important organic acid and fertilizer component, has been found effective in enhancing plant tolerance against various abiotic stresses. For this purpose, we have designed the current experiment to explore the contribution of OA in mediating growth and eco-physiology by alleviating abiotic stresses, in wheat (Triticum aestivum L.). Seedlings of T. aestivum were subjected to the different abiotic stresses including drought, salinity, heat, and cold stress, and were supplemented with exogenous OA at 5 mM. Results from the present study revealed that the abiotic stresses induced a substantial decrease in shoot length, root length, number of leaves, leaf area, shoot fresh weight, root fresh weight, shoot dry weight, root dry weight, chlorophyll-a, chlorophyll-b, total chlorophyll, carotenoid content, net photosynthesis, stomatal conductance, transpiration rate, soluble sugar, reducing sugar, non-reducing sugar contents, calcium (Ca[2+]), magnesium (Mg[2+]), iron (Fe[2+]), and phosphorus (P) contents, microbial diversity, richness, and evenness in T. aestivum plants. In contrast, abiotic stresses in the soil significantly (P < 0.05) increased phenolic content, malondialdehyde (MDA), hydrogen peroxide (H2O2), health risk indices, bioaccumulation factors. Although, the activities of enzymatic antioxidants such as superoxide dismutase, peroxidase, catalase, ascorbate peroxidase in the T. aestivum plants and non-enzymatic such as phenolic, flavonoid, ascorbic acid, and anthocyanin contents were increased with the exposure of abiotic stresses. The application of OA significantly improved photosynthetic efficiency, microbial diversity, richness, and evenness, while reducing health risk indices, bioaccumulation factors, MDA, and H2O2 contents under stress conditions. Proteomic and transcriptomic profiling further supported the regulatory role of OA in modulating stress-responsive signaling pathways and enhancing stress tolerance in T. aestivum plants. Increased antioxidant enzyme activities in OA-treated plants appeared to play a crucial role in scavenging stress-induced reactive oxygen species. Research findings, therefore, suggested that OA application can ameliorate abiotic stresses toxicity in T. aestivum seedlings and resulted in improved plant growth and composition under abiotic stresses.},
}

@article {pmid42229603,
year = {2026},
author = {Wang, J and Cao, S and Li, X and Zhou, Z and Du, R},
title = {Extracellular polymeric substances Govern granule size differentiation and microbial assembly in denitratation-Anammox systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135040},
doi = {10.1016/j.biortech.2026.135040},
pmid = {42229603},
issn = {1873-2976},
abstract = {The Complete Ammonium and Nitrate Removal via Denitratation-Anammox over Nitrite (CANDAN) is a promising low-carbon strategy for sustainable nitrogen removal; however, the mechanistic linkage between extracellular polymeric substances (EPS), aggregation behavior, granule size differentiation, and microbial assembly remains unclear. Here, size-fractionated granules from a CANDAN reactor were systematically investigated to establish a multi-scale framework linking EPS structural properties to aggregation-driven granule organization and microbiome assembly. Medium-sized granules (0.5-1.0 mm) exhibited the highest aggregation capacity (74.5%) and fastest aggregation kinetics, indicating a cohesive and dynamically stable matrix. This aggregation advantage was closely associated with optimized functional performance, including high specific anammox activity (8.76 ± 1.36mg N g[-1] VSS h[-1]), the highest nitrate reduction and nitrite production rates, and a high nitrite transformation ratio (90.1%), reflecting efficient pathway coupling in CANDAN systems. EPS analyses revealed that aggregation and stability were governed primarily by structural organization rather than bulk EPS content. Medium-sized granules were characterized by a lower protein-to-polysaccharide ratio, enriched hydrophobic functional groups, and β-sheet-dominated protein conformations, which collectively enhanced intercellular cohesion and stabilized the EPS matrix. This structurally optimized aggregation regime further shaped microbial assembly, promoting the enrichment and coordination of Candidatus Brocadia and Thauera. Overall, this study identifies aggregation capacity as a key mechanistic driver linking EPS structural properties to granule size differentiation and microbial assembly, highlighting granule size as a mesoscale regulator bridging physicochemical structure and ecological function.},
}

@article {pmid42229782,
year = {2026},
author = {Nieboer, M and Rosenow, C and Koch, J and Barlow, J and Sanchez-Sotelo, J and O'Driscoll, S and Morrey, M},
title = {Morrey Award 2025: Cell Count and Differential of Aspirated Fluid in the Diagnosis of Periprosthetic Joint Infection of Total Elbow Arthroplasty.},
journal = {Journal of shoulder and elbow surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jse.2026.05.018},
pmid = {42229782},
issn = {1532-6500},
abstract = {BACKGROUND: Periprosthetic joint infection (PJI) is a common method of failure following total elbow arthroplasty (TEA). Diagnosis is often guided by synovial fluid leukocyte counts and neutrophil percentages. While cutoff values have been defined for hip and knee arthroplasty PJI, the elbow has a different microbiome and a higher rate of PJI. Currently, there are no data to guide determination of PJI following TEA. The purpose of this study was to identify cutoff values of synovial fluid leukocyte counts, neutrophil percentage, erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) to aid in detection of periprosthetic total elbow infection.

METHODS: We identified 135 TEA undergoing revision surgery that had preoperative aspiration of the synovial fluid at a single institution. Receiver operating characteristic (ROC) curves were utilized to determine the optimal cutoff points for synovial fluid leukocyte count, the neutrophil differential, the ESR and the CRP. Sensitivity, specificity, negative predictive value and positive predictive value were determined. Patients were determined to be infected when they had a positive intraoperative culture or gross purulence at the time of reoperation.

RESULTS: 35 elbows were found to be infected and 100 were determined to be aseptic. The infected elbow group had a higher mean fluid leukocyte count (8100 vs. 687 cells/μL, p <0.01), higher neutrophil differential (63% vs. 18%, p<0.01), higher ESR (32 vs. 15mm/1h, p<0.01) and higher CRP (15 vs. 5mg/L, p<0.01) than the aseptic cohort. Based on the ROC curves the optimal cutoff values were a leukocyte count of 1300 cells/μL (sensitivity 88%, specificity 75%), neutrophil differential of 70% (sensitivity 71%, specificity 92%), ESR >13 (sensitivity 76%, specificity 67%) and CRP >7 (sensitivity 73%, specificity 83%). When both the leukocyte count and neutrophil differential were below the cutoff values, the negative predictive value was 96%. When both the neutrophil differential and ESR were above the cutoff values the positive predictive value was 95%.

DISCUSSION: This study identifies optimal synovial fluid and inflammatory marker cutoff values to help clinicians determine the presence of a TEA PJI prior to revision surgery. The optimal cutoff values were a leukocyte count >1300 cells/μL, neutrophil differential >70%, ESR >13 and CRP >7.},
}

@article {pmid42229820,
year = {2026},
author = {Lee, DH and Kim, DY and Joung, HC and Kim, H and Jeon, Y and Lee, S and Shin, CH and Lee, YS and Bang, JY and Lee, EJ and Cha, SY and Bae, SH and Lee, HW},
title = {Probiotic-driven gut-liver redox crosstalk modulates hepatic Nrf2 signaling pathway and attenuates metabolic dysfunction-associated steatohepatitis.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2026.05.338},
pmid = {42229820},
issn = {1873-4596},
abstract = {Metabolic dysfunction-associated steatohepatitis (MASH) is a chronic liver disease characterized by persistent inflammation, oxidative stress, and progressive fibrosis. There is currently no effective pharmacological therapy for MASH. We investigated whether two defined probiotic bacteria strains, Lactobacillus delbrueckii subsp. lactis (L. lactis) CKDB001 and Lactiplantibacillus plantarum (L. plantarum) Q180, attenuate MASH pathology in association with modulation of gut-liver redox signaling. Using diet-induced preventive and therapeutic mouse models of MASH, we show that oral administration of these strains significantly improves hepatic steatosis, robustly attenuates fibrosis, and reduces inflammatory and oxidative stress markers. Probiotic treatment was associated with increased intestinal glutathione availability, and was accompanied by activation of hepatic nuclear factor erythroid 2-related factor 2 (Nrf2) signaling and upregulation of canonical antioxidant enzymes, consistent with improved hepatic redox homeostasis and reduced hepatocellular injury. Microbiome profiling revealed successful intestinal persistence of the administered strains and enrichment of other bacterial taxa associated with gut barrier integrity and metabolic resilience, including Akkermansia muciniphila, Parabacteroides goldsteinii, and Mediterraneibacter butyricigenes. Functional prediction analysis further suggested enhancement of microbial glutathione metabolism pathways, supporting a potential role for microbiota-driven redox modulation in host protection. Therapeutic efficacy was maintained after disease establishment and under conditions recapitulating features of a lean MASH-like phenotype, highlighting obesity-independent mechanisms of action. Collectively, our findings support a probiotic-driven association between intestinal glutathione dynamics and hepatic Nrf2 activation within the gut-liver axis, providing a mechanistically informed and translationally relevant framework for MASH intervention.},
}

@article {pmid42229856,
year = {2026},
author = {Rittmann, M and Wu, G and Zhao, L and Green, TJ and Hanselman, EC and Green, R and Lam, YY and Miller, JW},
title = {Associations Between Biomarkers of Vitamin B12 Status and Gut Microbial Guilds in a Cohort of Australian Adults.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101622},
doi = {10.1016/j.tjnut.2026.101622},
pmid = {42229856},
issn = {1541-6100},
abstract = {BACKGROUND: Vitamin B12 is an essential nutrient required for hematological and neurological function. Human gut microbes either synthesize B12 or utilize B12 consumed by hosts. Consequently, variation in gut microbiota may influence B12 status in humans.

OBJECTIVE: The goal was to assess associations between gut microbiota and serum B12 and a functional biomarker of B12 status, methylmalonic acid (MMA).

METHODS: In 90 adults (44 males/46 females; 20-75y) living in Sydney, Australia, 16S rRNA gene V3-V4 amplicon sequencing was used to profile gut microbiota at the amplicon sequence variant (ASV) level. B12 was measured by automated chemiluminescence and MMA by HPLC-tandem-mass spectrometry. Associations between tertiles of B12 and MMA and microbial alpha and beta diversity and overall microbiota composition were assessed. Microbial guilds were identified via co-abundance analysis on ASVs. Multivariate linear regression and random forest regression were used to assess the associations between guilds and the B12 biomarkers, controlling for age, sex, body mass index, and fiber intake.

RESULTS: Mean serum B12 and MMA were 389±177 pmol/L and 210±80 nmol/L, respectively. Gut microbial diversity and richness was significantly associated with B12 tertiles (Shannon index: p=0.010; Faith's phylogenetic diversity: p=0.048; ASV number: p=0.022). No associations were observed between B12 tertiles and beta diversity or between MMA tertiles and alpha or beta diversity. Thirty guilds were identified, with 2 guilds and age included in the final model predictive of B12 (p=0.03), and 3 different guilds and no covariates included in the final model predictive of MMA (p=0.003).

CONCLUSIONS: These results indicate that different guilds are predictive of serum B12 versus serum MMA. This suggests that some of the variance in serum MMA in adults is not specific to B12 status, which has ramifications for interpreting MMA as a marker of B12 status.},
}

@article {pmid42229880,
year = {2026},
author = {Zhang, L and Sun, W and Wang, X and Zhang, Z and Chen, H},
title = {Therapeutic-Dose Enrofloxacin Immersion Induces Intestinal Immunostimulation and Microbiota Dysbiosis in Juvenile Black Seabream Acanthopagrus schlegelii.},
journal = {Journal of applied toxicology : JAT},
volume = {},
number = {},
pages = {},
doi = {10.1002/jat.70260},
pmid = {42229880},
issn = {1099-1263},
support = {2024YFD2401803//National Key Research and Development Program of China/ ; 326MS0356//Hainan Provincial Natural Science Foundation of China/ ; 426MS0365//Hainan Provincial Natural Science Foundation of China/ ; 2024RC12//Central Public-interest Scientific Institution Basal Research Fund，South China Sea Fisheries Research Institute，CAFS/ ; 2023TD06//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
abstract = {Enrofloxacin (ENR) is a commonly identified veterinary pharmaceutical in global aquaculture products, and short-term therapeutic applications of ENR at recommended doses may exert adverse effects on farmed fish. The present investigation evaluated the toxicological impacts of ENR on intestinal detoxification capacity, immune response, and microbial community dynamics of commercially significant Acanthopagrus schlegelii. Short-term treatment of ENR at the clinically recommended dose (5 mg/L) showed little modulation on expression levels of key detoxification enzymes, while 10 mg/L ENR (over-therapeutic concentration) induced significantly elevated Phase I/II biotransformation enzymes in treated fish. Interestingly, 5 mg/L ENR (decontaminated for 72 h) triggered immunostimulation effects via significantly promoting inflammatory cytokines and lysozyme gene expression. In addition, persistent suppression of the diversity and richness of gut microbial communities was observed following immersion in 5 and 10 mg/L ENR. ENR exposure triggered restructuring of intestinal microbial composition of black seabream, characterized by a reduction in beneficial microbiota and an expansion of opportunistic and antibiotic-resistant bacteria, which may contribute to the observed immune perturbation and long-term health risks. In summary, our findings raise concerns about the safe use of ENR in aquaculture, suggesting that current practices may pose long-term health risks to marine farmed fish.},
}

@article {pmid42230118,
year = {2026},
author = {Zhong, ZW and Lu, YQ and Duan, Y and Ma, J and Liu, N},
title = {Fusobacterium nucleatum in cancer: from bystander to driver.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-338000},
pmid = {42230118},
issn = {1468-3288},
abstract = {The human microbiota comprises a diverse and extensive community of microorganisms that participate in intricate interactions with the host, several of which are increasingly acknowledged as key modulators of health and disease. Among these, Fusobacterium nucleatum (Fn), an oral commensal bacterium, has emerged as a significant oncobacterium implicated in tumour progression. The Fn genus comprises distinct subspecies, clades and strains, exhibiting marked phylogenetic and physiological heterogeneity. Consequently, pinpointing the true functional modulators within this complex community and elucidating their mechanisms in various physio-pathological states remains a critical yet challenging endeavour. Moreover, the complete mechanism underlying Fn's function across different spatial locations and physiological states remains to be fully elucidated. This review details the genetic and phenotypic heterogeneity among Fn subspecies, which underlies their differential characteristics and niche adaptation. We further delineate key effectors of Fn, such as adhesins, metabolites and exoproteins, which collectively facilitate host cell invasion, immune evasion and chemoresistance induction. We explore the translational potential of Fn, underscoring its utility as a diagnostic biomarker and a promising target for novel therapeutic strategies.},
}

@article {pmid42230119,
year = {2026},
author = {Alexander, JL and Mullish, BH and Thomas, L and Weersma, RK and Sokol, H and Roberts, LA and Edwards, LA and Emmanuel, A and Gerasimidis, K and Hall, LJ and Iqbal, TH and Kinross, JM and McIlroy, J and Monaghan, TM and Sergaki, C and Shawcross, DL and Stewart, CJ and Lamb, CA and Williams, HRT and Hansen, R and Hold, G},
title = {Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338252},
pmid = {42230119},
issn = {1468-3288},
abstract = {At around 10 years ago, at the time of the first publication by the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology, recognition of the gut microbiome's importance in health and disease was transitioning from fringe interest towards major global pursuit. A decade on, we appraise the considerable progress made in the field, while acknowledging ongoing challenges. Earlier human work characterising the 16S rRNA gene amplicon signature of particular conditions in small cohorts has been superseded by larger, multicentre studies with extensive metadata. Studies increasingly employ shotgun metagenomics and other 'omic' techniques-coupled with refined bioinformatic tools and disease models-to better characterise perturbation in gut microbiome functionality. The arrival of 'gold standard' pipelines for microbiome analysis and increased mechanistic validation of signals are key developments towards more clinically-translatable outcomes. Novel clinical areas where the gut microbiome has relevance have emerged, including early life and the efficacy of certain treatments (including immune checkpoint inhibitors and vaccination). Enthusiasm for 'microbiome diagnostics and treatments' has grown, but barriers to widespread adoption remain. Faecal microbiota transplant (FMT) is established for treating recurrent Clostridioides difficile infection, with donor-derived 'next generation' FMT products licensed for this condition in certain countries. Beyond FMT, other microbial therapeutic techniques-including nutritional, bacteriophage and probiotic therapies-show promise, but have not fulfilled their high expectations yet. Gut microbiome research is now well-established and shows significant translational potential; the future focus will be translational work to drive its utility in clinical diagnostics, prognostics and therapeutics.},
}

@article {pmid42230163,
year = {2026},
author = {Chang, X and MacIsaac, HJ and Chorus, I and Bullerjahn, GS and Kurmayer, R and Ahn, CY and Kong, X and Wilhelm, SW and Wood, SA and Tang, X and Paerl, HW and Hilt, S and Jeppesen, E and Hamilton, DP and Nakano, SI and Visser, P and Huisman, J and Wang, H and Song, L and Mckay, RM and Qin, B and Sitoki, L and Xu, R},
title = {Scanning the horizon for harmful cyanobacterial blooms.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2026.04.012},
pmid = {42230163},
issn = {1872-8383},
abstract = {Harmful cyanobacterial blooms are increasing worldwide, threatening freshwater ecosystems, animal health, and human well-being. To guide research needed for effective prediction, prevention, and management, we identify four priorities: understanding eco-evolutionary and phylogeographic drivers that promote toxigenic cyanobacterial genotypes; resolving molecular and environmental controls on cellular cyanotoxin biosynthesis; integrating microbiome science with multiomics and epidemiology to assess associated health risks beyond cyanotoxins; and quantifying ecosystem-scale bottom-up and top-down controls in understudied settings, particularly tropical and benthic habitats. New research tools for addressing these priorities enable elucidating the mechanistic basis for anticipating cyanobacterial blooms and provide the understanding needed for their control in a rapidly changing world.},
}

@article {pmid42230169,
year = {2026},
author = {Octoman, A and Arrieta, MC},
title = {Early-life gut fungi as modulators of metabolic development.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2026.05.003},
pmid = {42230169},
issn = {1879-3061},
abstract = {Early life is a critical window during which microbes shape immune maturation, nutrient handling, and long-term metabolic health. Although fungi represent a minor proportion of the gut microbiome, emerging evidence suggests they exert a disproportionate influence. In this review, we synthesize current gut mycobiome knowledge during pregnancy and infancy, including ecological assembly, maternal and environmental sources, and links to early metabolic phenotypes. Recent studies on human cohorts and gnotobiotic mice demonstrate that specific fungal species can causally alter adiposity, adipose immune architecture, and bacterial function. We also highlight major knowledge gaps, including questions around true colonization, fungal activity, strain-level transmission, and the molecular basis of fungal-bacterial-host interactions. These findings position the early-life mycobiome as a promising frontier for discovery in metabolic development.},
}

@article {pmid42230260,
year = {2026},
author = {Cabezas-Cruz, A and Piloto-Sardiñas, E and Obregón, D},
title = {Host-vector microbiome similarity predicts immune-mediated disturbance and vector competence.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.05.010},
pmid = {42230260},
issn = {1471-5007},
abstract = {Vector-borne disease transmission is highly heterogeneous, yet existing models emphasize climate, host density, and pathogen load. We propose that host-vector microbiome similarity represents a previously unrecognized ecological axis in transmission biology. During blood feeding, vectors ingest host-derived immune effectors shaped by the host microbiota. When immune targeting depends on shared microbial features, microbiome similarity predicts the magnitude of immune-mediated disturbance within the vector gut, altering colonization resistance and influencing pathogen establishment. These effects are context-dependent and may enhance or suppress transmission. This framework generates testable predictions linking microbiome similarity, immune-mediated disturbance, and vector competence across systems. Incorporating microbiome similarity into transmission models may help explain heterogeneity and improve ecological understanding and intervention strategies.},
}

@article {pmid42230654,
year = {2026},
author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F},
title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01029-0},
pmid = {42230654},
issn = {2055-5008},
abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.},
}

@article {pmid42230678,
year = {2026},
author = {David, H and Balu, P and Vasudevan, S and Narayanan, VHB and Solomon, AP and Ramyadevi, D},
title = {Thermoresponsive carbohydrate polymer mucoadhesive gel for synergistic delivery of acarbose and fluconazole against Candida biofilms.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52764-5},
pmid = {42230678},
issn = {2045-2322},
abstract = {The emerging threat of drug-resistant Candida albicans, especially in recurrent vulvovaginal candidiasis (VVC) biofilms, has revealed weaknesses in existing monotherapeutic antifungal treatments. In this study, we investigated the antifungal activity of a new dual-drug in situ mucoadhesive gel system containing acarbose (AC), a pseudo-oligosaccharide sugar and FDA-approved α-glucosidase inhibitor, together with fluconazole (FLC). Although AC showed mild antifungal activity by itself, when combined with FLC, it dramatically potentiated fungicidal activity, disrupted biofilms, blocked morphogenetic switching, and arrested post-treatment hyphal regrowth. In checkerboard assays and time-kill kinetics, AC-FLC combination was highly synergistic against Candida spp., including clinical isolates, with > 2-log10 decrease in CFU/mL. The thermosensitive gel (PCH16), formulated using poloxamer 407 along with the carbohydrate-based polymers chitosan and HPMC, exhibited sustained drug release, favorable rheological properties, and strong mucoadhesion suitable for vaginal delivery. Notably, the formulation retained Lactobacillus species viability, suggesting microbiome compatibility. These results affirm the promise of repurposing acarbose as a novel, non-traditional antifungal adjuvant that, in co-administration with FLC in vaginal gel, represents an encouraging, localized, and microbiota-conserving therapy for treating recurrent and resistant VVC.},
}

@article {pmid42230679,
year = {2026},
author = {Giorgini, G and Leblanc, N and Muller, C and Dumais, E and Labbé-Blondeau, MN and Thibodeau, A and Flamand, N and Di Marzo, V and Silvestri, C},
title = {Seal and fish oils partially counteract inflammation and modulate endocannabinoidome lipid and oxylipin alterations in DSS-induced colitis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-54447-7},
pmid = {42230679},
issn = {2045-2322},
support = {IT19175//Mitacs/ ; },
abstract = {Colitis is associated with endocannabinoidome (eCBome) and gut microbiome alterations, both of which are influenced by the diet, and thus may be modulated through nutritional components as potential therapeutic targets for colitis. We assessed the effects of n-3 polyunsaturated fatty acid (PUFA)-rich fish (FO) and seal (SO) oils in the dextran sodium sulphate (DSS) colitis mouse model. Mice were assessed for effects on inflammation, intestinal permeability, anxiety-like behaviour, gut microbiota composition and colon, blood and brain eCBome mediator levels. While neither FO or SO counteracted DSS-induced loss of weight, SO mitigated the increase in intestinal permeability and was more efficacious at reducing inflammation markers (Il1b, Il6, Tnfa and Arg1) than FO. DSS-induced changes in the bacterial community were not altered by FO or SO, which however mitigated alterations in the abundance of the Family XII UCG01 genera. DSS altered several eCBome and oxylipin bioactive lipid levels in a tissue-specific manner. FO and/or SO counteracted some of these changes, especially by increasing the levels of those lipids derived from n-3 PUFAs, many of which have anti-inflammatory activities. Interestingly, the novel eicosapentaenoic acid-derived eCBome mediator 2-eicosapentaenoyl glycerol was a top defining lipid of both FO and SO groups in all tissues. These data point to FO and, particularly SO, as potentially beneficial treatments of colitis through alterations in the eCBome, which is dysregulated in colitis.},
}

@article {pmid42230754,
year = {2026},
author = {Bethlehem, L and Bartu, L and Marke, G and Mar, P and Feldman, S and Eggers, J and Ruprecht, C and Britton, GJ and Aggarwala, V and Bongers, G and Li, Z and Yang, N and Hohmann, EL and Mogno, I and Faith, JJ and Grinspan, A},
title = {15-strain live biotherapeutic product or same donor fecal microbiota transplant for recurrent Clostridioides difficile infection: a randomized phase 1b trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {42230754},
issn = {1546-170X},
abstract = {Fecal microbiota transplant (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) but has undefined composition and poor scalability. In vitro manufactured live biotherapeutic products (LBPs) enable both scalability and defined strain composition but with higher manufacturing complexity, resulting in few LBP clinical trials. Here we show how an accessible platform to produce human-grade LBPs could accelerate LBP development. We provide regulatory documentation and manufacturing protocols to facilitate translating microbiome advances to human trials. With this platform, we conducted the first direct comparison of the same bacterial strains from donor-sourced FMT compared to an in vitro manufactured 15-strain LBP drug product, MTC01, for the treatment of rCDI. In a phase 1b randomized controlled trial, 18 of 20 screened patients met eligibility and were randomized equally to one of four arms: low-dose FMT (n = 4), high-dose FMT (n = 5), low-dose MTC01 (n = 4) or high-dose MTC01 (n = 5), with a 5:1 female:male ratio. The primary outcome of safety was met with 10 adverse events across eight patients, evenly spread across MTC01 (five events) and FMT (five events) recipients and no treatment-related adverse events across all four groups. For secondary outcomes of efficacy and engraftment, rCDI was prevented 8 weeks after dosing in seven out of nine LBP patients, similar to eight out of nine FMT patients. Strain engraftment was high and durable for both FMT and MTC01 with a dose effect for the LBP. ClinicalTrials.gov: NCT05911997 .},
}

@article {pmid42230943,
year = {2026},
author = {González-Llera, L and Santos-Durán, GN and Vences, A and Buján, N and Balado, M and Barreiro-Iglesias, A},
title = {Spontaneous axon regeneration is preserved despite gut microbiota disruption after spinal cord injury in larval lampreys.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-56243-9},
pmid = {42230943},
issn = {2045-2322},
support = {PID2023-147266NB-I00//Agencia Estatal de Investigación/ ; },
abstract = {Spinal cord injuries (SCIs) often result in permanent disabilities in humans. One major reason for the lack of recovery is the inability of adult mammalian descending neurons to regenerate their axons after injury. In contrast, several fish species, such as the sea lamprey, exhibit spontaneous axon regeneration and successful functional recovery following a complete SCI. Recent studies have shown that a SCI in rodents and humans induces gut microbiome dysbiosis, which can impair recovery. Therefore, our goal was to examine how the microbiome changes after SCI in a regenerating animal model (the larval sea lamprey) and whether these changes influence the spontaneous regeneration of descending neuropeptidergic (cholecystokinergic) axons. Our data show that a complete SCI triggers an initial shift (5 weeks post-injury) in gut microbial communities in larval lampreys, characterized by an expansion of Legionellaceae family members. However, a treatment with broad-spectrum antibiotic gentamicin during the first 5 weeks post-injury, which profoundly altered the gut microbiome (eliminating Legionellaceae and promoting Bradyrhizobiaceae expansion), did not affect the spontaneous regeneration of descending cholecystokinergic axons at 10 weeks post-injury. This finding indicates that broad gentamicin-induced disruption of the gut microbiota does not detectably impair spontaneous regeneration of descending cholecystokinergic axons in larval lampreys.},
}

@article {pmid42230971,
year = {2026},
author = {Lin, TY and Hung, SC and Abe, T},
title = {An oral tyrosine challenge test for functional phenotyping of microbiota-derived phenyl sulfate production.},
journal = {npj metabolic health and disease},
volume = {4},
number = {1},
pages = {},
pmid = {42230971},
issn = {2948-2828},
support = {112-2314-B-303-009 -MY3, 114-2314-B-303-004//National Science and Technology Council, Taiwan/ ; 113-2314-B-303-012, 114-2314-B-303-017-MY3//National Science and Technology Council, Taiwan/ ; TCRD-TPE-114-01//Taipei Tzu Chi Hospital, Taiwan/ ; TCRD-TPE-114-02, TCMF-CP 111-02//Taipei Tzu Chi Hospital, Taiwan/ ; },
abstract = {Phenyl sulfate (PS), a gut microbiota-derived metabolite implicated in the pathogenesis of diabetic kidney disease, is generated through microbial conversion of dietary tyrosine to phenol, followed by hepatic sulfation via SULT1A1. We developed an oral tyrosine challenge test (OTyCT) to phenotype individual PS-producing capacity. Forty-eight healthy adults underwent a standardized tyrosine load with serial plasma PS levels measured over 48 h using LC-MS. OTyCT revealed substantial interindividual variability of PS production independent of baseline PS levels, highlighting marked heterogeneity in host-microbiome metabolic interactions. Sixteen participants in the highest tertile of the incremental area under the curve of PS were defined as high-PS producers. High PS producers exhibited distinct gut microbial signatures despite comparable abundances of known phenol-biosynthetic genes and host SULT1A1 genotypes. These findings suggest that susceptibility to PS-related complications may vary according to gut microbial profiles, supporting OTyCT as a practical tool for metabolic phenotyping and microbiome-informed precision nutrition. Clinical Trial registry name and registration number: Identification of P-Cresyl Sulfate Producer Phenotype by Oral Tyrosine Challenge Test: Interactions Among Diet, Gut Microbiota, and Host Genome, NCT04204174.},
}

@article {pmid42231021,
year = {2026},
author = {Lagomarsino, VN and Robinson, A and Mitchell, PE and Jiang, M and Hutchinson, LE and Sekela, JJ and Caron, P and Gehris, MK and Navas, KI and Duarte-Silva, M and Netherland, M and Hasan, NA and Guillemette, C and Redinbo, MR and Rao, M},
title = {Microbial reactivation of host androgens directs enteric neuronal regulation of gut motility.},
journal = {Nature neuroscience},
volume = {},
number = {},
pages = {},
pmid = {42231021},
issn = {1546-1726},
support = {R01DK130836//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01DK135707//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R03DK125636//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01GM135218//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM152079//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {The coordinated transit of intestinal contents is crucial for digestion and host defense, and is regulated by cross-talk between neural circuits, the muscular gut wall and luminal factors. Here we show that androgen signaling to Nos1[+] enteric neurons and Scn10a[+] spinal afferent neurons is required for normal intestinal transit in mice and is microbiome dependent. Microbial depletion with antibiotics abolished androgen receptor expression in enteric neurons, diminished serum testosterone and caused dysmotility. Androgens were necessary for antibiotics to affect transit and partly sufficient to rescue dysmotility. Nos1 neurons upregulate androgen receptor upon puberty in parallel with shifts in fecal bacterial beta-glucuronidase (GUS) enzymes that can deconjugate steroid glucuronides in mice and humans. Intracolonic administration of a GUS enzyme found to metabolize androgen glucuronides was sufficient to restore neuronal androgen signaling in microbe-depleted mice. Thus, gut microbial reactivation of host-excreted androgens via GUS enzymes represents a dynamic microbe-host interaction that is essential for peripheral nervous system function in homeostasis.},
}

@article {pmid42231156,
year = {2026},
author = {Yang, Q and Liang, Y and Liu, J and Jia, R and Li, J and Yan, Z},
title = {Fecal microbiota transplantation from Hezuo pigs alleviates intestinal inflammatory injury in Clostridium perfringens type C-infected piglets via modulation gut microbiota and intestinal barrier.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05169-3},
pmid = {42231156},
issn = {1471-2180},
support = {23JRRA1422//Natural Science Foundation of Gansu Province/ ; 32460845//National Natural Science Foundation of China/ ; GSARS10//Pig Industry in Gansu Agriculture Research System/ ; 2023-QN-135//Lanzhou Youth Science and Technology Talent Innovation Project/ ; },
abstract = {Clostridium perfringens type C (CpC)-induced piglet diarrhea is a major challenge in the swine industry. This study aimed to investigate the protective effects of fecal microbiota transplantation (FMT) from Hezuo pigs against intestinal injury in Duroc×Landrace×Yorkshire (DLY) suckling piglets infected with CpC. Piglets were divided into two groups, including CpC-challenged control group and FMT-treatment group, which received fecal suspension from Hezuo pigs prior to infection. Morphological, immunological, microbiomic, and metabolomic analyses were conducted after post-infection. The results demonstrated that FMT significantly alleviated jejunal damage, leading to a significant increase in jejunal villus height and a significant decrease in crypt depth (P < 0.01). The intervention elevated the number of goblet cells (P < 0.05) and upregulated the expression of tight junction protein genes Occludin, ZO-1, Claudin-1 and the anti-inflammatory cytokine IL-10, while significantly reducing the levels of pro-inflammatory cytokines TNF-α and IL-6 (P < 0.05). FMT enriched beneficial genera such as Akkermansia, Rothia, Peptococcus, and Proteocatella, and increased the levels of the sphingolipid metabolite ceramide (d18:1/18:0). Correlation analysis further indicated that these microbiota alterations were positively associated with intestinal barrier repair and anti-inflammatory activity, and were strongly correlated with ceramide (d18:1/18:0) levels. In conclusion, FMT mitigates CpC-induced intestinal injury by modulating the gut microbiota and metabolome, thereby enhancing intestinal barrier integrity and regulating inflammatory responses. This study provides theoretical support and practical insights for the application of FMT as a promising microbiome-based strategy to control CpC-associated intestinal diseases in piglets.},
}

@article {pmid42231158,
year = {2026},
author = {Kuang, Z and Zhan, Q and Tu, J and Li, A and Guo, W and Zheng, R and Jiang, H and Xu, B},
title = {Microbiome and metabolome patterns centered on cancer cachexia link skeletal muscle and adipose tissue depletion to clinical outcomes in locally advanced rectal cancer.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05171-9},
pmid = {42231158},
issn = {1471-2180},
abstract = {BACKGROUND: Cancer cachexia is a multifactorial syndrome characterized by involuntary weight loss and tissue wasting; it was associated with adverse survival outcomes in patients with locally advanced rectal cancer (LARC). However, its biological basis and links to the gut microbiome, circulating metabolites, and body composition in LARC remain unclear.

METHODS: We conducted a retrospective cohort study of 198 LARC patients, including 30 with cachexia. Gut microbial profiles were characterized using 16S rRNA sequencing with predictive functional inference. Serum metabolites were analyzed via orthogonal partial least squares-discriminant analysis (OPLS-DA) and validated by ROC analysis. Associations among microbial taxa, metabolites, body composition, and clinical indices were assessed using correlation analyses. Survival outcomes were evaluated by Kaplan-Meier curves and multivariate Cox regression models, with subgroup and sensitivity analyses performed to validate the robustness of findings.

RESULTS: Cachectic patients exhibited marked reductions in BMI, circulating triglycerides and cholesterol, as well as visceral and subcutaneous adipose tissue (VAT and SAT) and skeletal muscle area (SMA) (all P < 0.05). Microbial α- and β-diversity were comparable between groups, yet cachexia was associated with selective enrichment of Peptostreptococcaceae, Erysipelotrichaceae, Veillonella, and Fusobacterium, alongside depletion of Faecalibacterium, Roseburia, and Prevotella. Notably, UBA1819 (Ruminococcaceae) was enriched in cachectic patients and inversely correlated with Faecalibacterium, hemoglobin, and albumin, suggesting intra-family functional divergence. Specific cachexia-enriched taxa, including Veillonella and Erysipelotrichaceae, were inversely associated with SMA and VAT, whereas butyrate-producing genera showed positive correlations with muscle preservation. Functional predictions highlighted enrichment of N-acetylneuraminate degradation in cachexia versus TCA cycle pathways in non-cachectic patients. High abundance of Peptostreptococcaceae and Erysipelotrichaceae was associated with poorer overall survival. Metabolomic profiling identified lithocholic acid, cortisone, 3,5,9-trihydroxyergost-7-en-6-one, and 5,6-DHET as cachexia-associated metabolites (AUC 0.65-0.78), which formed cross-domain correlations with microbial taxa and host tissue measures.

CONCLUSION: Our findings reveal a coordinated linkage between the gut microbiome, metabolome, and host body composition in LARC cachexia. Specifically, selective microbial remodeling and metabolite perturbations are closely coupled with skeletal muscle and adipose tissue depletion and adverse survival. These results provide a conceptual foundation for future mechanistic and translational studies exploring the host-microbiome-metabolic interactions in cancer cachexia.},
}

@article {pmid42231385,
year = {2026},
author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N},
title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.},
journal = {Nutrition journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12937-026-01343-5},
pmid = {42231385},
issn = {1475-2891},
support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; },
abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.

METHODS: A total of 102 male Han participants was randomized to curcumin (812 mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.

RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P = 0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P < 0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P < 0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P < 0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.

CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.

TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.},
}

@article {pmid42231413,
year = {2026},
author = {Chuang, YC and Collman, RG and Ruan, SY and Chien, YC and Huang, YS and Hsu, CC and Wang, JT and Zou, HB and Chang, SC},
title = {Gut microbiome features associated with vancomycin-resistant Enterococcus acquisition in intensive care unit patients.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12941-026-00871-6},
pmid = {42231413},
issn = {1476-0711},
support = {110-2918-I-002-001//National Science and Technology Council/ ; 110-S4901//National Taiwan University Hospital/ ; },
abstract = {BACKGROUND: Vancomycin-resistant Enterococcus (VRE) infection poses a significant healthcare burden in intensive care units (ICUs), and is preceded by gut colonization. The gut microbiome may influence susceptibility to VRE, but its role in ICU patients remains incompletely defined.

METHODS: We conducted a prospective study of patients admitted to a medical ICU from 2019 to 2021. Stool samples were collected for bacterial 16 S rRNA gene sequencing, anal swabs were screened for VRE by culture, and bile acids were measured in initial stool samples.

RESULTS: We enrolled 108 patients. Thirty-four patients were VRE + on initial screen and remained so (VRE+/+) while 74 were initially negative, of whom 23 acquired VRE (VRE-/+) and 51 remained negative (VRE-/-). There was no difference in alpha-diversity initially between VRE-/- and VRE-/+ groups, whereas VRE+/+ patients had significantly lower alpha-diversity (P < 0.001). VRE-/+ patients had a significantly more rapid decrease in alpha-diversity than VRE-/- patients (P = 0.04). Beta-diversity of initial stool differed among groups (P = 0.001), driven mainly by VRE+/+ patients. A lower Bacteroides/Enterococcus ratio (P = 0.049) and low Clostridium scindens abundance (P = 0.031) were associated with VRE acquisition. Initial stool from VRE-/- patients had a higher combined concentration of deoxycholic acid and lithocholic acid than that of VRE-/+ patients (P = 0.034).

CONCLUSIONS: VRE acquisition in the ICU was associated with an initial gut microbiome characterized by lower Bacteroides/Enterococcus ratios, lower C. scindens abundance, and lower deoxycholic and lithocholic acid concentrations. Our findings are consistent with a possible role of these microbiome features in colonization resistance, as suggested by in vitro and animal models. However, given the single-center design, these associations should be considered hypothesis-generating and require validation before clinical application.},
}

@article {pmid42231422,
year = {2026},
author = {Maruyama, H and Sato, K and Sakai, K and Yasui, H and Okada, R and Xinheng, L and Umeda, K and Rahman, S and Nguyen, VS and Hibi, H},
title = {Near infrared photo-bacterialflora modulation technology realized controlling periodontitis: modulation of disease-associated dysbiosis in oral microbiota using near infrared photo-antibacterial targeting therapy (NIR-PAT[2]).},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42231422},
issn = {1479-5876},
support = {25K22916//JSPS/ ; 25K03451//JSPS/ ; 18K15923//JSPS/ ; CREST JPMJCR19H2//Japan Science and Technology Corporation/ ; JPMJFR2017,FOREST//Japan Science and Technology Corporation/ ; Research Grant from The Chemo-Sero-Therapeutic Research Institute//The Chemo-Sero-Therapeutic Research Institute/ ; },
abstract = {BACKGROUND: Periodontitis is a complex polymicrobial disease driven by synergistic interactions within a dysbiotic oral community. Within this network, Porphyromonas gingivalis acts as a keystone pathogen that orchestrates the pathogenic transformation of the microbiota. Current broad-spectrum antimicrobials often disrupt the entire microbial ecosystem and release immunogenic lipopolysaccharides (LPS). We aimed to develop a targeted approach, Near-Infrared Photo-Antibacterial Targeting Therapy (NIR-PAT[2]), using an antibody-photosensitizer conjugate (IgY-IR700) to reduce P. gingivalis load within this polymicrobial complex and modulate the community profile.

METHODS: We evaluated the binding and bactericidal mechanism of NIR-PAT[2] in vitro compared to antimicrobial photodynamic therapy (aPDT), using scanning electron microscopy (SEM) and endotoxin assays. In vivo, a ligature-induced periodontitis mouse model was used to assess therapeutic effects on alveolar bone resorption and microbiome community structure (16 S rRNA sequencing).

RESULTS: In vitro, NIR-PAT[2] eliminated P. gingivalis without affecting human cells. SEM analysis revealed a distinct mechanism: unlike aPDT, which caused bacterial disintegration, NIR-PAT[2] induced lethal transmembrane perforations while maintaining structural integrity. In parallel, endotoxin assays demonstrated that NIR-PAT[2] treatment significantly suppressed LPS release compared to aPDT. In vivo, NIR-PAT[2] treatment significantly inhibited alveolar bone resorption. Crucially, microbiome analysis demonstrated that NIR-PAT[2] did not merely eliminate the environment but induced a compositional shift toward a health-associated profile. By suppressing Porphyromonas, the treatment facilitated the partial restoration of commensal genera such as Streptococcus, disrupting the dysbiotic network.

CONCLUSIONS: This study suggests that NIR-PAT[2] functions as a "Near-Infrared Photo-Bacterialflora Modulation (NIR-PBAM)" technology. By targeting a keystone pathogen within the polymicrobial community, NIR-PBAM offers a strategy to partially restore microbial balance while presenting a potential advantage in limiting LPS release, thus overcoming the ecological disruption caused by conventional broad-spectrum antimicrobials.},
}

@article {pmid42231509,
year = {2026},
author = {Sarhan, MS and Samadelli, M and Zink, A and Maixner, F},
title = {The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42231509},
issn = {2049-2618},
support = {FESR1078-MummyLabs//European Regional Development Fund/ ; },
abstract = {BACKGROUND: The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.

RESULTS: By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.

CONCLUSIONS: Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.},
}

@article {pmid42231528,
year = {2026},
author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA},
title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2679516},
doi = {10.1080/19490976.2026.2679516},
pmid = {42231528},
issn = {1949-0984},
abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.},
}

@article {pmid42231914,
year = {2026},
author = {Lv, Y and Li, J and Xu, Z and Zhang, Y and Li, W and Kan, X and Dai, S and Lin, Y and Xu, X and Chen, W},
title = {Engineered skin commensal nanogels mitigate psoriasiform inflammation through dual regulation of cutaneous flora and host immunity.},
journal = {Materials today. Bio},
volume = {38},
number = {},
pages = {103267},
pmid = {42231914},
issn = {2590-0064},
abstract = {Psoriasis is a chronic inflammatory skin disorder characterized by immune dysregulation and alterations in the cutaneous microbiota. Current microbiome-targeted therapeutic strategies predominantly involve the topical delivery of live probiotics using hydrogel platforms. However, these approaches are hindered by limitations such as poor bacterial viability, transient colonization, and unresolved safety concerns, while often failing to address systemic immune dysfunction. To overcome these challenges, we developed nanogels derived from Staphylococcus epidermidis lysates via EDC/NHS crosslinking. The optimized formulation exhibited a uniform hydrodynamic diameter of 98.3 ± 30.2 nm and remained stable for up to 5 days without significant protein degradation. Leveraging their sub-100 nm size, these nanogels enabled multiple therapeutic mechanisms. First, they penetrated the epidermal barrier through psoriatic scales and were internalized by target cells, leading to suppressed keratinocyte hyperproliferation and reduced local inflammation. Second, they trafficked systemically via the cutaneous microvasculature, resulting in decreased activation of splenic dendritic cells (CD11c + CD80[+]) and normalization of the CD4+/CD8+ T-lymphocyte ratio. Concurrently, residual nanogels retained on the skin surface selectively inhibited the proliferation of Staphylococcus aureus while promoting the enrichment of commensal Staphylococcus species, thereby restoring microbial homeostasis and reinforcing barrier integrity. This strategy addresses key limitations of conventional live biotherapeutics by leveraging the enhanced biocompatibility of bacterial components and the multifunctional advantages of nanoscale delivery. It offers a synergistic and safe approach for effective psoriasis management.},
}

@article {pmid42231929,
year = {2026},
author = {Mejía-Granados, DM and Kawasaki de Araújo, T and Malan-Müller, S and Oliveira Ribeiro de Aguiar Araújo, PA and Braz Dos Santos, LH and Yasuda, CL and Koutsodontis Machado Alvim, M and Carvalho, BS and Cendes, F and Lopes-Cendes, I},
title = {Intestinal microbial community assessment in patients with different forms of epilepsy and autoimmune encephalitis: An exploratory study.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2679348},
pmid = {42231929},
issn = {2993-3935},
abstract = {Despite the availability of antiseizure medications (ASMs), approximately one-third of patients with epilepsy remain refractory to treatment. Evidence suggests that the gut microbiota modulates central nervous system function through neuroimmune and metabolic pathways. We characterized the fecal microbiome of patients with epilepsy and autoimmune encephalitis (AE) using 16S rRNA sequencing. Ninety-six participants from a tertiary hospital in Brazil were included: mesial temporal lobe epilepsy (MTLE; n = 38), genetic generalized epilepsy (GGE; n = 11), AE (n = 10), and healthy controls (n = 37). Microbial community composition differed between treatment-responsive and refractory patients. Compared with responsive individuals (n = 16), refractory patients (n = 43) showed lower relative abundances of Agathobaculum, Bacteroides, Bilophila, and Coprobacter, and higher abundance of Guopingia. Dietary fiber intake was negatively associated with Enterocloster and Frisingicoccus. Riboflavin (vitamin B2) and niacin (vitamin B3) were positively associated with Schaalia and Hominimerdicola, respectively. Functional predictions indicated that valproic acid use and treatment responsiveness were associated with increased microbial potential for GABA synthesis and tryptophan degradation, and reduced potential for dopamine and histamine degradation. These findings link the gut microbiome to epilepsy subtype and treatment response.},
}

@article {pmid42232188,
year = {2026},
author = {Shree Kumari, GR and Vaithilingam, M},
title = {Exploring the probiotic landscape in understanding postbiotics from indigenous bacteria isolated from the stool samples of a tribal population at Mulluvadi village, Tamil Nadu, India.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1817531},
pmid = {42232188},
issn = {1663-9812},
abstract = {BACKGROUND: Urbanisation has been associated with a decline in the diversity of the gut microbiome that could potentially limit access to functionally robust probiotic strains. In contrast, traditional tribal populations represent underexplored reservoirs of diverse microbiota with unique metabolic capabilities. In this study, isolated and functionally characterised culturable probiotic bacteria from the gut microbiomes of individuals from the Mulluvadi tribal community (Tamil Nadu, India), with a focus on their inferred postbiotic-producing potential.

METHODS: A total of 112 microbial isolates were obtained from the stool samples of 25 healthy individuals, from which 13 representative bacterial strains were shortlisted by sequential screening based on phenotypic and functional criteria. These isolates were evaluated for tolerance to gastrointestinal stress conditions (pH, bile salts, NaCl, and temperature), cell surface hydrophobicity, auto-aggregation, safety attributes, and functional properties, including antibacterial activity, exopolysaccharide production, protease activity, biofilm formation, and short-chain fatty acid (SCFA) production.

RESULTS: The 13 isolates, mainly comprising Lactiplantibacillus plantarum and Lacticaseibacillus rhamnosus, exhibited >70% survival under simulated gastric and biliary conditions, high levels of hydrophobicity (60%-80%), strong inhibition of pathogens (12-25 mm), significant production of SCFAs, high levels of protease activity (15-20 mm clearance), and marked membrane stabilising effects of human red blood cells (65%-82%). All isolates were non-haemolytic, negative for DNase production, and displayed safety profiles consistent with those of probiotics. In particular, L. plantarum and Heyndrickxia coagulans were identified as the most functionally potent strains.

CONCLUSION: Probiotic isolates from the gut microbiomes of a tribal population show remarkable postbiotic-producing capacity and potential functional relevance. These strains are promising candidates for further investigations toward the development of postbiotic-based functional formulations; however, their efficacies must be first established in animal and clinical trials and validated through additional in vivo and clinical studies for gut dysbiosis and other related disorders.},
}

@article {pmid42232211,
year = {2026},
author = {Cheng, Z and Gao, L and Luo, D and Bi, C and Chen, Q and Chen, X},
title = {A prospective cohort study exploring salivary microbial predictors of white spot lesions during fixed orthodontic treatment.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2679805},
pmid = {42232211},
issn = {2000-2297},
abstract = {INTRODUCTION: White spot lesions (WSLs) are a common adverse outcome of fixed orthodontic treatment, prompting the search for salivary microbial predictors for early risk identification.

MATERIALS AND METHODS: Sixty-four patients undergoing fixed metal self-ligating orthodontic treatment were categorized into WSL and non-WSL groups based on lesion development after 12 months. Clinical indices (DI-S, CI-S, OHI-S, GI) and unstimulated whole saliva samples were collected at baseline and after 12 months. The salivary microbiome was analyzed using 16S rRNA gene sequencing.

RESULTS: The prevalence of WSLs was 54.7% at the patient level. Clinical indices did not differ significantly between groups. Although overall microbial community structure was similar at baseline, several taxa were enriched in patients who later developed WSLs, including Actinomyces, Rothia and Granulicatella. After 12 months, the WSL group showed reduced phylogenetic diversity and a microbial profile enriched in acidogenic and anaerobic taxa. Functional prediction indicated increased carbohydrate metabolism and fermentative pathways in WSL patients.

CONCLUSIONS: WSL development during fixed orthodontic treatment was associated with baseline salivary microbial differences and treatment-related ecological shifts. Salivary microbiome profiling may help identify patients at higher risk and support early risk stratification and preventive strategies in orthodontic care.},
}

@article {pmid42232608,
year = {2026},
author = {Lopes, M and Vila Nova, C and Oliveira, RC and Schmitt, F and Mendes, F and Martins, D},
title = {Microbiome and Response to Therapy in Triple Negative Breast Cancer: A Systematic Review.},
journal = {Oncology research},
volume = {34},
number = {6},
pages = {4},
pmid = {42232608},
issn = {1555-3906},
abstract = {Objectives: Triple-negative breast cancer (TNBC) accounts for approximately 15% of all invasive breast cancers and is characterized by aggressive behavior, limited therapeutic options, and poor clinical outcomes. Due to the absence of hormone receptors and HER2 expression, systemic treatment relies predominantly on chemotherapy, which is associated with high rates of early recurrence and mortality. Emerging evidence suggests that alterations in the microbiome can contribute to TNBC progression and influence therapeutic response, particularly affecting the efficacy of chemotherapy and immunotherapy through immune-mediated mechanisms; however, its role in TNBC remains incompletely understood. This systematic review aims to explore the role of the microbiome in TNBC. It specifically aims to understand if the microbiome influences complete pathological response in TNBC. Methods: This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A comprehensive literature search was performed in PubMed and Cochrane databases. Fourteen eligible studies were included, encompassing preclinical and clinical evidence. Results: The findings indicate that both gut and tumor-associated microbiota significantly influence therapeutic response in TNBC, especially in the context of neoadjuvant chemotherapy (NACT) and immune checkpoint blockade (ICB). Higher microbial diversity and the presence of specific commensal taxa were consistently associated with enhanced antitumor immune activation, increased immune cell infiltration, and improved treatment efficacy. Conversely, antibiotic-induced dysbiosis was linked to reduced pCR rates and poorer clinical outcomes. Microbiome-modulating interventions demonstrated potential in restoring eubiosis and enhancing therapeutic responsiveness. Conclusions: Overall, the available evidence supports the microbiome as a promising biomarker and therapeutic target for optimizing treatment strategies and improving outcomes in TNBC.},
}

@article {pmid42232902,
year = {2026},
author = {Lachnit, T},
title = {Nutrient-rich environments drive microbiome restructuring and mucus shedding in a coastal cnidarian.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1792133},
pmid = {42232902},
issn = {1664-302X},
abstract = {INTRODUCTION: Anthropogenic nutrient enrichment is increasing in coastal ecosystems, yet its effects on host-microbe interactions and animal fitness remain insufficiently understood. This study investigates how elevated dissolved nutrient availability and differing nutrient compositions influence microbiome structure and host responses in the sea anemone Nematostella vectensis.

METHODS: We experimentally enriched seawater with either a complex organic nutrient source or a protein-rich substrate. We then assessed resulting changes in microbiome composition, host behavior (including mucus shedding), and population growth.

RESULTS: Nutrient enrichment caused substantial restructuring of the host-associated microbiome, characterized by reduced diversity and increased dominance of fast-growing bacterial taxa. Community composition differed depending on nutrient type. Enriched conditions also triggered increased ectodermal mucus shedding, which physically removed surface-associated microbes. Copiotrophic taxa that proliferated under nutrient enrichment were disproportionately represented in shed mucus relative to whole polyps, suggesting spatial structuring of microbial associations with host surfaces. While this response limited microbial overgrowth, it imposed significant physiological costs, leading to reduced or negative population growth.

DISCUSSION: These findings demonstrate that nutrient enrichment alters host-associated microbiomes and identify mucus shedding as a host-mediated mechanism for microbial regulation. Although effective, this response carries substantial fitness costs, highlighting a trade-off between microbial control and host performance. This study provides mechanistic insight into how eutrophication may drive microbiome restructuring and impact host physiology in coastal cnidarians.},
}

@article {pmid42232906,
year = {2026},
author = {Jin, Y and Zhu, J and Liao, D and Jin, X},
title = {From "spleen governing muscle" to gut microbiota: mechanisms of sarcopenic obesity in perimenopausal women.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1817839},
pmid = {42232906},
issn = {1664-302X},
abstract = {BACKGROUND: Sarcopenic obesity (SO) in perimenopausal women-characterized by the paradoxical coexistence of skeletal muscle loss and visceral adiposity-represents a complex metabolic challenge that conventional estrogen replacement therapies have failed to fully address. Emerging evidence from traditional Chinese medicine (TCM) suggests that the "spleen governing muscle" theory may offer a unique lens through which to understand this condition, with the gut microbiota serving as a critical mechanistic link between spleen deficiency and musculoskeletal deterioration.

OBJECTIVE: To systematically review the mechanisms linking spleen deficiency, gut microbiota dysbiosis, and sarcopenic obesity risk in perimenopausal women, integrating TCM theory with modern biomedical evidence.

METHODS: We synthesized findings from clinical observational studies, randomized controlled trials (RCTs), and mechanistic investigations examining the "spleen-gut-muscle" axis, with particular attention to studies employing 16S rRNA sequencing, metabolomics, and multi-omics approaches.

RESULTS: Spleen deficiency-manifesting as impaired transformation and transportation of nutrients-correlates with characteristic alterations in gut microbiota composition, including reduced diversity, elevated Firmicutes/Bacteroidetes ratios, and depletion of short-chain fatty acid (SCFA)-producing taxa. These microbial changes propagate systemic inflammation through lipopolysaccharide (LPS)-TLR4 signaling, activate muscle protein degradation via MuRF1 upregulation, and compromise insulin sensitivity through diminished GLP-1 secretion. Notably, TCM interventions-including herbal formulations (Sijunzi decoction, Buzhong Yiqi decoction), acupuncture, moxibustion, catgut embedding, and tuina massage-demonstrate potential to restore microbial homeostasis, increase SCFA production, and improve muscle mass and function. However, the evidence quality remains modest, with methodological limitations including inadequate blinding, small sample sizes, and short follow-up durations.

CONCLUSION: The "spleen-gut-muscle" axis represents a promising therapeutic target for perimenopausal sarcopenic obesity, bridging TCM theory with modern microbiome science. Nevertheless, current evidence is predominantly associative rather than causally definitive, derived largely from small-scale trials and preclinical models. Rigorous, large-scale RCTs with standardized TCM protocols, multi-omics endpoints, and extended follow-up are essential to establish efficacy and safety before microbiota-based TCM interventions can be recommended as adjunctive or standalone therapies.},
}

@article {pmid42232910,
year = {2026},
author = {Oskolkov, N},
title = {Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1603339},
pmid = {42232910},
issn = {1664-302X},
abstract = {Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.},
}

@article {pmid42232978,
year = {2026},
author = {Indolfi, C and Klain, A and Dinardo, G and Colosimo, S and Ferrara, S and Grella, C and Galdiero, M and De Filippis, A and Fiore, V and Miraglia Del Giudice, M},
title = {Association between Staphylococcus aureus colonization and clinical improvement in pediatric atopic dermatitis treated with dupilumab: a pilot study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1836967},
pmid = {42232978},
issn = {2296-858X},
abstract = {BACKGROUND: Moderate-to-severe atopic dermatitis (AD) in children is characterized by impaired skin barrier function, type 2 inflammation, and frequent Staphylococcus aureus colonization, contributing to disease severity and risk of superinfection. Dupilumab, an anti-IL-4/IL-13 receptor monoclonal antibody, improves clinical outcomes in pediatric AD, but longitudinal data on culture-based skin and nasal microbial changes remain limited.

OBJECTIVE: To assess dupilumab efficacy in children with moderate-to-severe AD unresponsive to conventional therapy and to describe skin and nasal microbial colonization patterns at the 12-month time point compared with moderate AD receiving conventional topical therapy and healthy controls.

METHODS: Prospective observational study. Children aged 6-16 years were enrolled in three groups: (a) moderate-to-severe AD starting dupilumab (assessments at baseline, 3, 6, and 12 months); (b) moderate AD receiving conventional topical therapy not eligible for biologic therapy; and (c) age-matched healthy controls. Outcomes included Eczema Area and Severity Index (EASI), Children's Dermatology Life Quality Index (C-DLQI), and Peak Pruritus Numerical Rating Scale (NRS). At 12 months, nasal and skin e-Swabs were cultured; isolates were identified by MALDI-TOF with antimicrobial susceptibility testing. Longitudinal changes were analyzed using the Friedman test (p < 0.05).

RESULTS: Ten dupilumab-treated children (mean age 13 years; 60% males) showed rapid and sustained improvement in C-DLQI (median 13.5 to 3 at 3 months; 3.5 at 12 months), EASI (24.5 to 5.65 at 3 months, 1.2 at 12 months), and pruritus (NRS 10 to 4.5 at 3 months; 5.5 at 12 months). No adverse events or discontinuations occurred. At 12 months, nasal S. aureus colonization was detected in 2/10 dupilumab-treated patients versus 4/10 moderate AD receiving conventional topical therapy and 1/10 controls; skin S. aureus was absent in dupilumab-treated patients but present in 8/10 children with moderate atopic dermatitis receiving conventional topical therapy and 0/10 controls.

CONCLUSION: Dupilumab provides sustained clinical benefit and, in this cross-sectional assessment of a small pilot cohort, is associated with lower S. aureus colonization and the presence of commensal staphylococci in pediatric atopic dermatitis.},
}

@article {pmid42233016,
year = {2026},
author = {Di Simone, N and Barnea, ER and Mueller, M},
title = {Editorial: Community series in the immunological role of the maternal microbiome in pregnancy, Volume II.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1872195},
doi = {10.3389/fimmu.2026.1872195},
pmid = {42233016},
issn = {1664-3224},
}