@article {pmid42832260,
year = {2026},
author = {Song, X and Jia, S and Chen, L and Cao, C and Chen, Z and Hang, L and Jiang, H and Chen, Z},
title = {Deep-sea Microbial Dataset of the Antarctic Ocean (dsMDAO): A high-resolution deep-sea microbial dataset of the Antarctic Ocean reveals potential for taxonomic and functional diversity.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
pmid = {42832260},
issn = {2057-5858},
mesh = {Antarctic Regions ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Archaea/genetics/classification/isolation & purification ; Metagenome ; Phylogeny ; *Microbiota/genetics ; Geologic Sediments/microbiology ; Oceans and Seas ; Metagenomics ; Biodiversity ; },
abstract = {Antarctic deep-sea ecosystems harboured unique and metabolically versatile micro-organisms that sustained key biogeochemical processes under extreme polar conditions. However, the genomic diversity and ecological functions of these sedimentary or deep-sea microbial communities remained largely unexplored. Here, we constructed a comprehensive deep-sea microbial dataset of the Antarctic Ocean (dsMDAO) by integrating three newly sequenced Prydz Bay sediment metagenomes with 22 publicly available datasets (9 seawater and 13 sediment samples), spanning water depths of ~300-3500 m. Genome binning yielded 186 metagenome-assembled genomes spanning 19 phyla, including 175 bacteria and 11 archaea, a substantial proportion of which represent previously uncharacterized species. Meanwhile, reads mapping with the available standard Kraken2 database (k2_standard) enabled the expansion of species richness of the dsMDAO database. Furthermore, functional annotation revealed diverse metabolic and ecological potentials, including carbon, nitrogen and sulphur cycling, as well as secondary metabolite biosynthesis, virulence-associated defence and cold-adaptation mechanisms. Sediment microbiomes exhibited higher phylogenetic and functional diversity, enriched in Thaumarchaeota and Chloroflexi, whereas seawater communities were dominated by Proteobacteria with more competitive biosynthetic and interaction potentials. Co-occurrence analyses further indicated complex and competitive networks in seawater versus modular and cooperative assemblages in sediments, reflecting distinct ecological strategies. Collectively, dsMDAO provides the first genome-resolved dataset of Antarctic deep-sea microbiota, revealing the hidden taxonomic and functional diversity that underpins ecosystem resilience in polar oceans. This resource lays a foundation for future ecological, evolutionary and biotechnological exploration of Antarctic microbial dark matter.},
}

Antarctic Regions
*Seawater/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
*Archaea/genetics/classification/isolation & purification
Metagenome
Phylogeny
*Microbiota/genetics
Geologic Sediments/microbiology
Oceans and Seas
Metagenomics
Biodiversity

@article {pmid42832270,
year = {2026},
author = {Almatrafi, R and Alqurainy, N and Hakami, M and Ajina, R and Alrabiah, S and Arafah, AM and Alotibi, RS and Aldriwesh, MG},
title = {Gut microbiome and healthy ageing: a systematic review of literature.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {10},
pages = {},
doi = {10.1099/mic.0.001779},
pmid = {42832270},
issn = {1465-2080},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Healthy Aging/physiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Aged ; Aging ; Centenarians ; Aged, 80 and over ; Longevity ; },
abstract = {The gut microbiome undergoes compositional and functional changes with ageing. However, microbial signatures specifically associated with healthy ageing, independent of age-related diseases, remain poorly defined. This systematic review aimed to identify compositional and functional features of the gut microbiome associated with healthy ageing. Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic search was conducted using PubMed, Web of Science and ScienceDirect for studies published up to January 2026. The search strategy focused on gut microbiome, ageing and healthy terms. Risk of bias was assessed using the Newcastle-Ottawa Scale. Gut microbiome composition was reviewed across five predefined age groups, while the functional pathways were reviewed for older adults and centenarians. The included studies represented several regions, including recognized longevity hotspots, although geographic representation remained limited. Most studies used 16S rRNA gene sequencing (n=24; 58.5%), followed by shotgun metagenomics (n=13; 31.7%), both (n=3; 7.4%) or metaproteomics (n=1; 2.4%). Enrichment of specific taxa such as Akkermansia, Alistipes and Parabacteroides was consistently reported in centenarians, alongside distinct patterns in older adults and long-lived individuals. Functional profiling suggested differences in pathways related to amino acid catabolism, vitamin biosynthesis and pathways potentially linked to immune modulation, inflammatory processes and gut barrier support. This review provides the first structured synthesis of gut microbiome signatures associated with healthy ageing across the lifespan, highlighting consistent functional traits and the need for a wider geographic representation in future research. It supports standardized, multi-omics framework to identify robust biomarkers and potential microbiome-based interventions for promoting healthy ageing.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Healthy Aging/physiology
*Bacteria/classification/genetics/isolation & purification
Metagenomics
RNA, Ribosomal, 16S/genetics
Aged
Aging
Centenarians
Aged, 80 and over
Longevity

@article {pmid42832303,
year = {2026},
author = {Bosch, P and Lackner, A and Dreo, B and Fessler, J and Moazedi-Fürst, F and Husic, R and Séneca, J and Haidmayer, A and Stadlbauer, V and Muralikrishnan, AS and Thiel, J and Stradner, M},
title = {Efficacy and safety of probiotic supplementation in psoriatic arthritis - a randomized controlled trial.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keag547},
pmid = {42832303},
issn = {1462-0332},
abstract = {OBJECTIVES: To evaluate the clinical efficacy and safety of a multispecies probiotic in patients with psoriatic arthritis (PsA) in moderate disease activity.

METHODS: In this single-centre, randomized, double-blind, placebo-controlled trial (RCT), 66 PsA patients with moderate disease activity (Psoriatic Arthritis Disease Activity Score [PASDAS] >3.2 to < 5.4) on stable immunomodulatory therapy were randomized 1:1 to receive either a multispecies (Lactobacillus, Bifidobacterium) probiotic or placebo for 12 weeks. The primary outcome was treatment response at week 12, defined as achieving low disease activity or remission (PASDAS ≤3.2) without treatment change. Secondary outcomes included gut permeability markers, immune cell and microbiome composition. Analyses were conducted per a modified intention-to-treat (only complete cases for primary outcome), with sensitivity analyses using multiple imputation, per-protocol datasets, and qPCR-based detection of the probiotic strains in stool (adherence).

RESULTS: Fifty-six participants were included in the main analysis. Thirteen (43%) participants in the probiotic group and 17 (65%) in the placebo group achieved the primary outcome (p = 0.167). The corresponding odds ratio was 0.4 (95% CI 0.13 to 1.18). Patient-reported pain and global assessment were the main PASDAS components improving over time, with no between-group differences. No differences were observed in secondary clinical outcomes, gut permeability markers (zonulin, calprotectin, alpha-1-antitrypsin), immune cell profiles, or stool microbiome composition between groups at week 12. No serious adverse events related to the study product were reported.

CONCLUSION: In this first RCT investigating probiotic supplementation in PsA, probiotic treatment did not show superiority over placebo in achieving treatment response, or altering gut microbiome, or permeability.},
}

@article {pmid42832344,
year = {2026},
author = {Simm, NM and Williams, GM and Fowler, S and Barlow, K and Carter, B and Talley, NJ and Keely, S and Duncanson, K and Hoedt, EC},
title = {Assessing diet-microbiome associations with linear models: variability across human studies.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2740905},
doi = {10.1080/19490976.2026.2740905},
pmid = {42832344},
issn = {1949-0984},
mesh = {Humans ; *Diet ; *Gastrointestinal Microbiome ; },
abstract = {Understanding and identifying relationships between dietary intake and the gastrointestinal microbiome can provide critical information for optimization of human health. However, methodological approaches largely differ and can impact research findings. Here we outline differences in reported diet-microbiome associations from a range of studies utilizing comparable statistical methods. From a subset of 25 studies using comparable methodology, only 3% of reported diet-microbe associations were common across more than one study. As such, we emphasize the inconsistencies of findings within the literature and wider implications of these differences.},
}

Humans
*Diet
*Gastrointestinal Microbiome

@article {pmid42832417,
year = {2026},
author = {L'Heureux, JE and Roelands, B and Wylie, L and Meeusen, R and Jones, AM and Vanhatalo, A},
title = {Oral microbiome signatures of ageing and cognitive function across distinct geographical cohorts.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0359559},
pmid = {42832417},
issn = {1932-6203},
mesh = {Humans ; *Cognition/physiology ; *Aging/physiology ; *Microbiota ; Female ; Aged ; Male ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; United Kingdom ; Adult ; Belgium ; Nitrates/blood/metabolism ; Middle Aged ; Cohort Studies ; Young Adult ; Nitrites/blood ; },
abstract = {Declining cognitive function in older adults may be linked to reduced nitric oxide (NO) bioavailability, which is supported by oral nitrate-reducing bacteria. Oral microbiome community structure varies geographically, complicating understanding of microbiome-cognition relationships across populations. This study aimed to identify consistent associations between the oral microbiome and cognitive function across two geographically distinct cohorts from the UK and Belgium, and to explore age-related differences in NO biomarkers, cognitive performance, and microbiome composition using 16S rRNA sequencing. Sixty healthy participants (15 young and 15 older adults per location) completed a cognitive test battery, blood pressure measurements, plasma and saliva collection for nitrate and nitrite analysis, and a tongue swab for oral microbiome assessment. Despite geographical differences in oral microbiome composition (PERMANOVA P = 0.04), age-related microbial shifts were consistent across geographic cohorts, including enrichment of Treponema and Tannerella in older adults. Nitrate-reducing taxa such as Haemophilus parainfluenzae and Neisseria flavescens were consistently associated with cognitive performance measures in both cohorts (P < 0.05). In the UK, higher plasma [nitrate] was associated with improved Digit Symbol Substitution Test (DSST) accuracy (β = 19.2, P < 0.01) and reaction times (β = -3444 ms, P < 0.05), but poorer Emotion Recognition Task (ERT) accuracy (β = -5.219, P < 0.05), while UK plasma [nitrite] was associated with slower Balloon Analog Risk Task (BART; β = 2277 ms, P < 0.001) and ERT (β = 8577 ms, P < 0.05) reaction times. In Belgium, saliva [nitrate] was associated with slower Visual Object Learning Test (VOLT) reaction times (β = 202 ms, P < 0.05), while in the UK, saliva [nitrite] correlated with slower BART (β = 111 ms, P < 0.05) and LOT (β = 1888 ms, P < 0.01). Overall, geography emerged as a major driver of oral microbiome variation, yet consistent age-related microbial and cognitive associations were preserved across populations. These findings emphasise the need to account for geographic context in microbiome-health research. A better understanding of oral microbial patterns may help inform future mechanistic or interventional studies to promote cognitive health in ageing.},
}

Humans
*Cognition/physiology
*Aging/physiology
*Microbiota
Female
Aged
Male
Saliva/microbiology
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
United Kingdom
Adult
Belgium
Nitrates/blood/metabolism
Middle Aged
Cohort Studies
Young Adult
Nitrites/blood

@article {pmid42832459,
year = {2026},
author = {Ajebli, M and Hebi, M and Ousaaid, D and Akdad, M and Mankour, Z and Khouya, T and Moukafih, B and El Kartouti, A and Eddouks, M},
title = {Apigenin and Hypertension: A Review of Natural Sources, Pharmacodynamic and Pharmacokinetic Evidence.},
journal = {Pharmacology},
volume = {},
number = {},
pages = {1},
doi = {10.1159/pha/aejag005},
pmid = {42832459},
issn = {1423-0313},
abstract = {PURPOSE: This review aimed to synthesize recent evidence on the pharmacological effects of APG in the management of hypertension.

METHODS: A comprehensive literature search was conducted using PubMed, Scopus, Web of Science, and Google Scholar.

RESULTS: Pharmacokinetic studies reveal that APG exhibits poor oral bioavailability due to low solubility and extensive metabolism yet demonstrates wide tissue distribution and neuroprotective potential. It interacts with drug-metabolizing enzymes and transporters, influencing the pharmacokinetics of co-administered agents while maintaining a favorable safety profile at dietary levels. Preclinical evidence shows that APG lowers blood pressure by promoting vasodilation through TRPV4/NO pathways, attenuating oxidative stress and inflammation, and regulating genetic signaling to prevent vascular and cardiac remodeling. Toxicity studies confirm safety up to 5000 mg/kg, while additional findings highlight its beneficial modulation of gut microbiota.

CONCLUSION: APG emerges as a promising supplementary compound for hypertension management, combining vascular, molecular, and microbiome-mediated mechanisms with a strong safety margin.},
}

@article {pmid42832478,
year = {2026},
author = {Calzada, D and Martín-López, L and Carnés, J},
title = {Genetic and microbiomics approaches allow the monitoring of the growth of Dermatophagoides pteronyssinus cultures and their environmental influences.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0359777},
pmid = {42832478},
issn = {1932-6203},
mesh = {Animals ; *Dermatophagoides pteronyssinus/growth & development/microbiology/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Dermatophagoides pteronyssinus is cultured in industrial facilities to produce allergen extracts for allergy diagnosis and therapeutic treatment. In these facilities, mite growth and production should be monitored, and exhaustive quality control is mandatory to harvest mites, reach optimal expansion, and avoid potential microbial contamination. In this study, we explored genetic approaches to monitor the growth of five independent D. pteronyssinus cultures. Microbiological studies were performed to characterise the evolution of microbial communities during culture. Finally, we designed a qRT-PCR application to quantify mite populations in the cultures. Our microbiome studies revealed the presence of non-pathogenic bacteria and the absence of Gram-negative bacteria. Despite the variability in microbiome genera at the beginning of the five cultures, the microbiome composition tended to be more homogeneous among the culture batches as mite growth progressed. Specifically, Staphylococcus sp., Virgibacillus sp., and Malassezia sp. appeared to be the most significant taxa involved in culture progression. In summary, we developed a specific method for quantifying and monitoring mite cultures, which could be used to establish an objective method for harvesting mites to manufacture standardised allergen extracts. Additionally, we provide a comprehensive description of the relationship between mites and their symbiotic microorganisms.},
}

Animals
*Dermatophagoides pteronyssinus/growth & development/microbiology/genetics
*Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid42832513,
year = {2026},
author = {Yuan, X and Arany, Á and Formanek, A and Moreau, Y and Lähdesmäki, H and Vatanen, T},
title = {LGTM: Gaussian process modulated neural topic modeling for longitudinal microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2741488},
doi = {10.1080/19490976.2026.2741488},
pmid = {42832513},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Models, Statistical ; Metagenome ; Normal Distribution ; },
abstract = {Longitudinal microbiome data are key to understanding the dynamics of microbial communities and their relationships with the host and environment. However, analysis of such data is challenging due to high dimensionality, compositionality, irregular sampling and temporal dependencies on external covariates. Existing analytical approaches typically address only subsets of these challenges, limiting their ability to yield biologically interpretable insights. We introduce LGTM, a probabilistic modeling framework that combines flexible non-linear longitudinal modeling with interpretable topic-based representations of the microbiome. LGTM simultaneously identifies microbial co-abundance patterns ("topics") and models how their proportions change over time and in relation to host and environmental covariates. Using multiple longitudinal human gut microbiome datasets, we demonstrate that LGTM identifies diverse microbial topics whose major patterns are reproducible across runs, while achieving competitive performance in imputation and forecasting tasks. A key strength of the framework is its interpretability: LGTM yields microbial topics with biologically interpretable taxonomic compositions and directly quantifies associations between covariates and microbial dynamics. LGTM is available at https://github.com/yuanx749/lgtm.},
}

Humans
*Gastrointestinal Microbiome
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification
Models, Statistical
Metagenome
Normal Distribution

@article {pmid42832545,
year = {2026},
author = {Souza, AK and Giroux, A and Zangirolamo, AF and Droher, RG and Bonato, FGC and Alfieri, A and Zamberlam, G and Seneda, MM and Costa, M},
title = {The impact of the estrous cycle on the vaginal microbiota of dairy cows.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0359551},
pmid = {42832545},
issn = {1932-6203},
mesh = {Animals ; Female ; Cattle ; *Vagina/microbiology ; *Estrous Cycle/physiology ; *Microbiota/genetics ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The present study investigated the vaginal microbiota of dairy cows throughout the estrous cycle and early gestation, under natural physiological conditions and without hormonal manipulation. Vaginal swabs were collected at estrus (D0), metestrus (D3), diestrus (D15), and Day 19 post-insemination (representing proestrus for non-pregnant cows or early gestation for pregnant cows). Pregnancy diagnosis was performed on day 31 post-insemination. Microbial characterization was performed using 16S rRNA gene sequencing, followed by analyses of alpha- and beta-diversity, community composition, and differential abundance. Overall, the vaginal microbiota exhibited high inter-individual variability and only subtle shifts across reproductive phases. Beta diversity analysis revealed modest but significant compositional rearrangements between estrus vs. proestrus (strictly within the non-pregnant cohort) and estrus vs. diestrus. Differential abundance testing identified two taxa enriched during pregnancy (Muribaculum and Hoministercoradaptatus), indicating potential microbial biomarkers associated with the gestational environment. These findings demonstrate that, in naturally cycling cows, physiological hormonal oscillations induce only mild microbial changes, whereas individual factors appear to play a dominant role in shaping the vaginal community. The work contributes to defining baseline microbial patterns in non-manipulated animals and highlights the importance of distinguishing natural variation from hormonally induced effects in reproductive microbiome research.},
}

Animals
Female
Cattle
*Vagina/microbiology
*Estrous Cycle/physiology
*Microbiota/genetics
Pregnancy
RNA, Ribosomal, 16S/genetics

@article {pmid42832647,
year = {2026},
author = {Hong, S and Kim, KW and Im, Y and Jang, J and Cheon, DH and Lee, EK and Han, YM and Park, JW and Lee, HJ and Park, H and Jo, SJ and Kim, D and Kang, HW and Im, JP and Kim, ES and Kim, JW and Kim, BG and Kim, JS and Koh, SJ},
title = {Enterotype-based stratification identifies clinically distinct microbial subtypes in inflammatory bowel disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag176},
pmid = {42832647},
issn = {1536-4844},
support = {//National Research Foundation of Korea/ ; RS-2023-00227939//Korean government (MSIT)/ ; NRF-2022R1F1A1076019//Korean government (MSIT)/ ; 26-2021-0060//Seoul National University Hospital Research Fund/ ; 04-2024-0370//Seoul National University Hospital Research Fund/ ; //Jeonbuk National University (2022)/ ; 2024-5//Korean Association for the Study of Intestinal Diseases/ ; 04-2025-0006//Seoul Metropolitan Government Seoul National University Boramae Medical Center/ ; },
abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) are heterogeneous disorders in which gut microbial dysbiosis may influence disease activity and clinical outcomes. However, it remains unclear whether microbiome-based stratification identifies clinically relevant IBD subtypes.

METHODS: We profiled the gut microbiome of a cohort comprising patients with IBD (n = 260), at-risk individuals (n = 166), and healthy control individuals (n = 57) using 16S rRNA gene amplicon sequencing. Unsupervised clustering was used to define gut microbial enterotypes. Associations with clinical characteristics and outcomes, including fecal calprotectin levels and medication step-up, were evaluated. Statistical and machine learning approaches were applied to identify enterotype-specific microbial signatures.

RESULTS: Four enterotypes were identified and labeled according to their most discriminative genera: Faecalibacterium and Blautia, Prevotella, Phocaeicola, and Bifidobacterium with reduced Faecalibacterium (Bif + Faec-low). Faecalibacterium and Blautia and Prevotella were enriched in healthy control individuals, Phocaeicola was enriched in at-risk individuals, and Bif + Faec-low was enriched in patients with IBD. The Bif + Faec-low enterotype was associated with lower body mass index, higher fecal calprotectin levels, and an increased risk of medication step-up (hazard ratio, 1.71; 95% confidence interval, 1.10-2.66). Microbial composition and network analyses identified distinct enterotype-specific taxa and hub genera, suggesting functional divergence among enterotypes.

CONCLUSIONS: Gut microbial enterotypes are associated with distinct clinical phenotypes and treatment escalation in IBD, and exhibit enterotype-specific microbial community structures and alterations across disease states. Enterotype-based stratification may provide a clinically relevant framework for assessing risk assessment and guiding personalized disease management.},
}

@article {pmid42832926,
year = {2026},
author = {Gu, QY and Wu, XH and Zhang, SY and Jiang, L and Song, LL and Li, XY and Sun, K and Zhang, W and Dai, CC},
title = {Root exudate-mediated interspecific interactions reshape the rhizosphere microbiome and promote the accumulation of bioactive compounds in Pinellia ternata.},
journal = {Microbiological research},
volume = {314},
number = {},
pages = {128746},
doi = {10.1016/j.micres.2026.128746},
pmid = {42832926},
issn = {1618-0623},
abstract = {Plant recognition and responses to neighbors are key mechanisms that regulate interspecific interactions. Although aboveground signaling via volatile organic compounds has received increasing attention, the role of soil-derived signals in belowground interactions remains poorly understood. In this study, a peanut (Arachis hypogaea L.)-Pinellia ternata (Thunb.) Makino intercropping system was used to investigate how root exudates regulate the recruitment of rhizosphere microbes to neighboring plants, with the aim of providing a theoretical basis for understanding how intercropping promotes plant growth. Intercropping with peanut significantly altered the rhizosphere microbial community structure of P. ternata and markedly enhanced the colonization of Sphingomonas spp. Inoculation experiments revealed that Sphingomonas sp. Y6 significantly increased both plant biomass and bioactive compounds of P. ternata. A belowground segregation experiment supported the role of root exudates as important mediators of interspecific interactions between peanut and P. ternata. Peanut-derived L-proline promoted the recruitment of Sphingomonas sp. Y6, increasing its rhizosphere colonization by 1.96-fold in the split-root experiment. Metabolomic profiling further indicated that exposure to peanut-derived signals was associated with increased accumulation of nucleoside compounds in P. ternata root exudates, which enhanced chemotaxis and biofilm formation by Sphingomonas sp. Y6. Overall, these findings identify a potentially important mechanism linking interspecific plant interactions, metabolite-mediated changes in root exudates, and rhizosphere microbial recruitment, ultimately contributing to increased bioactive compound accumulation in P. ternata, and provide new insights into optimizing plant-microbe interactions to enhance the accumulation of bioactive compounds in medicinal plants.},
}

@article {pmid42833212,
year = {2026},
author = {Vasquez, KS and Wong, DPGH and Kotaka, K and McKeithen-Mead, S and Pedro, MF and Brian Yu, F and Jain, S and Meng, X and Higginbottom, SK and DeFelice, BC and Neff, N and Bhatt, A and Tropini, C and Xavier, KB and Sonnenburg, JL and Good, BH and Huang, KC},
title = {Within-host evolution and transmission of a human gut symbiont across ecological scales.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.09.002},
pmid = {42833212},
issn = {1934-6069},
abstract = {Gut bacteria rapidly evolve in vivo, but their long-term success requires dispersal across hosts. Here, we quantify this interplay by tracking ∼70,000 genomically barcoded lineages of the commensal Bacteroides thetaiotaomicron (Bt) among co-housed mice. Adaptive mutations rapidly spread between hosts, overcoming colonization resistance imposed by resident Bt strains. Daily transmission rates varied >10-fold across hosts, but shared selection pressures drove predictable engraftment of specific lineages. Spatially resolved sampling within hosts revealed emergent preferences among adaptive lineages. The addition of a highly diverse community shifted the adaptive landscape without slowing the rate of evolution and reduced transmission while allowing specific mutants to engraft. Whole-genome sequencing uncovered diverse modes of adaptation involving complex carbohydrate metabolism. In vitro evolution across 29 carbon sources revealed variable overlap with in vivo selection pressures, potentially reflecting synergistic and antagonistic pleiotropies. These results illustrate how high-resolution lineage tracking enables quantification of commensal evolution across ecological scales.},
}

@article {pmid42833252,
year = {2026},
author = {van Vorstenbosch, R and Esenkova, EE and Jonkers, DMAE and Elizalde Vilalta, M and de Graaf, MCG and Keszthelyi, D and Pachen, D and van Schooten, FJJ and Mujagic, Z and Smolinska, A},
title = {Investigating the presence of microbiota-based phenotypes in Irritable Bowel Syndrome.},
journal = {Journal of breath research},
volume = {},
number = {},
pages = {},
doi = {10.1088/1752-7163/aeb043},
pmid = {42833252},
issn = {1752-7163},
abstract = {Irritable Bowel Syndrome (IBS) is heterogenous disorder of gut-brain interaction, with a key role for the dysregulated host-gut microbiota interplay. IBS subtyping is based only on symptoms of bowel habits, reflecting limited insight into underlying biological mechanisms. Aims: This study aimed to define microbiota-based IBS phenotypes and to compare these to traditional stool-based subtyping. Methods: The study utilised data from the Maastricht IBS cohort. Gut microbiota composition was analysed using shotgun metagenomic sequencing. Faecal volatile organic compounds (VOCs) were measured by gas chromatography mass spectrometry. Dietary intake and gastrointestinal and mental health symptoms were assessed using a food frequency questionnaire, the Dutch Healthy Diet-15 index, the Gastrointestinal Symptom Rating Scale, and Hospital Anxiety and Depression scores, respectively. Machine-learning approaches were applied to identify microbiota-based phenotypical clusters, which were compared with established Rome III subtypes, and associated with faecal VOCs, gastrointestinal symptom severity, diet and mental health. Results: 178 IBS patients and 134 healthy controls were included. Gut microbiota composition distinguished IBS patients from healthy controls with an AUCROC 0·8. This discriminatory profile was not associated with Rome III subtypes, while statistically significant associations were found with faecal VOCs profiles (i.e. R=0·67, p=4·46e-4) and symptom severity scores of abdominal pain (p=0·05), reflux (p=0·03), and diarrhoea (p=0·01) and depression (p<0·001). Dietary associations varied across clusters. Conclusion: These results suggest that gut microbiota profiling might provide a basis to define relevant IBS endotypes. Further exploration and validation efforts into this direction are needed using longitudinal studies to refine IBS patient stratification ultimately. .},
}

@article {pmid42833300,
year = {2026},
author = {Gan, C and Xiang, J and Liu, Y and Nie, S and Hu, Q and Yi, L and Liu, Y and Guo, X and Zou, J and Tang, Y and Cui, J and Xie, J},
title = {Nucleoside antitumor drugs: From molecular mechanisms and adaptive resistance to clinical translation.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {118501},
doi = {10.1016/j.bcp.2026.118501},
pmid = {42833300},
issn = {1873-2968},
abstract = {Nucleoside-based anticancer drugs are still needed to treat solid tumours and blood cancers, but due to systemic toxicity and the emergence of resistance, they have performed poorly in clinical practice. These agents inhibit deoxyribonucleic acid (DNA) synthesis, disrupt ribonucleic acid (RNA) metabolism, or deplete nucleotide pools in the past. However, a large number of studies have also found that the pharmacological effects of these agents include replication stress, epigenetic modification, viral mimicry and immunogenic cell death , as well as direct damage to nucleic acids. At the same time, resistance to nucleoside-based therapy is now known to be a system-level adaptation phenomenon. This resistance network includes impaired nucleoside transport, altered kinase-dependent activation, increased catabolism by enzymes such as cytidine deaminase (CDA) and sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), compensatory DNA damage repair, immune suppression, and microbiome-mediated drug inactivation in the tumour ecosystem. We will introduce the molecular mechanisms and multi-level resistance networks of nucleoside-type anticancer drugs in this paper, and based on the obtained results, put forward new therapeutic strategies. Particular emphasis is placed on phosphoramidate prodrug (ProTide) technology, multivalent oligonucleotide prodrugs, nanocarrier-mediated delivery and mechanism-guided combination therapy. We will also introduce the new applications of antibody-based delivery systems for tumour-selective delivery. According to the tumour's biology and drug-metabolism properties, delivery science and biomarker-guided therapy can be employed to convert nucleoside-based therapy into a form of personalised medicine that overcomes adaptive resistance.},
}

@article {pmid42833450,
year = {2026},
author = {Hao, H and Tong, Z and Wang, Q and Xiao, T and Zhang, Y and Yue, Y and Zhao, Z and Zhang, J and Chen, H},
title = {Flavonoid-associated microbial defense and Cellvibrio sp. C74 pretreatment collectively enhance straw degradation by Stropharia rugosoannulata.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136013},
doi = {10.1016/j.biortech.2026.136013},
pmid = {42833450},
issn = {1873-2976},
abstract = {Stropharia rugosoannulata efficiently utilizes straw in natural habitats, yet how it simultaneously defends against competing environmental microorganisms and degrades lignocellulose remains unclear. Here, transcriptomic, metabolomic, and microbiome analyses were integrated with flavonoid antibacterial assays and bacterial pretreatment experiments to characterize fungus-bacterium interactions during straw degradation. The flavonoid biosynthesis-related genes chi, fns, and fls were significantly upregulated during degradation, and the total flavonoid content reached 101.06 μg/g dry weight at the end of the process. Flavonoid accumulation was also significantly associated with specific bacterial taxa. At concentrations ≥ 25 μg/mL, both exogenous flavone and crude endogenous mycelial flavonoid extracts significantly inhibited Sphingomonas sp. S125, Cellvibrio sp. C74, and Sphingobacterium sp. S85, supporting a role for accumulated flavonoids in microbial defense. Conversely, pretreatment with Cellvibrio sp. C74 disrupted the straw surface and increased lignocellulolytic enzyme activities during subsequent fungal degradation, resulting in a 24.39 %-26.97 % increase in degradation efficiency relative to the sterilized-straw control. These findings extend the mechanistic understanding of straw degradation from fungal enzyme systems to fungus-bacterium interactions, revealing a dual mode of flavonoid-associated defense and Cellvibrio sp. C74-assisted degradation. Moreover, Cellvibrio sp. C74 represents a promising biological pretreatment agent for efficient straw bioconversion.},
}

@article {pmid42833452,
year = {2026},
author = {Julià, AL and Heintze, Q and Garcia, J and Gonzalez-Flo, E},
title = {Putative functional redundancy in cyanobacterial microbiomes allows stable bioplastic production despite shifts in dominant populations.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136012},
doi = {10.1016/j.biortech.2026.136012},
pmid = {42833452},
issn = {1873-2976},
abstract = {This study investigates whether a single initial cyanobacterial microbiome, originating from a mixed community, retains its capacity for polyhydroxybutyrate (PHB) production under non-sterile long-term operation when subjected to cultivation conditions that promote different dominant cyanobacterial populations. Distinct selective pressures were applied in two photobioreactors: one subjected to high pH (>10) and nutrient limitation, which favored the dominance of Synechococcus sp., and one operating under controlled pH (8.0-8.25) and sufficient nutrient supplementation, which promoted the enrichment of Synechocystis sp. Despite these shifts in cyanobacterial population dominance, the microbiome retained the capacity to accumulate PHB over 31 days, indicating functional stability and potential functional redundancy within mixed cyanobacterial consortia. Differences in productivity between photobioreactors, with the Synechocystis sp.-dominated culture achieving a maximum PHB content of 36 %dcw compared to 17 %dcw in the Synechococcus sp.-dominated culture, were more likely associated with the distinct operational conditions imposed rather than with the dominant cyanobacterial population, though the contribution of population composition cannot be fully excluded. Daily acetate addition (100 mg·L[-1]) proved to be an effective supplementation strategy for sustaining PHB accumulation in both systems. These findings suggest that bioplastic production can be maintained despite changes in cyanobacterial population dominance within a shared microbiome, consistent with putative functional redundancy, and that operational parameters may be more decisive than species dominance in determining PHB productivity.},
}

@article {pmid42833601,
year = {2026},
author = {Cheng, Q and Hong, L and Hui, C and Xu, L and Liu, Y and Wang, F and Wang, Q and Ma, J and Lin, H},
title = {Phycosphere microbiome remodeling and Brevundimonas partnership establishment enhance microalgal nonylphenol tolerance.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.10.006},
pmid = {42833601},
issn = {2090-1224},
abstract = {INTRODUCTION: Microalgae are vital primary producers in aquatic ecosystems yet increasingly threatened by nonylphenol (NP), a common endocrine disruptor. Current ecotoxicological assessments, however, largely rely on single-species models, overlooking the role of the phycosphere microbiome in host stress adaptation.

METHODS: Here, using the NP-tolerant microalgae Dictyosphaerium sp. as a model holobiont, we integrated multi-omics, axenic algae-bacteria co-culture, physiological, and metabolic analyses to unravel how associated microbes contribute to microalgal NP fitness.

RESULTS: Under environmentally relevant NP concentrations (10-900 µg/L), the holobiont sustained 20.3-91.3% higher biomass than axenic cultures. NP exposure reshaped the phycosphere community, enriching beneficial taxa. Among 16 bacterial isolates, Brevundimonas sp. D-1 exerted the strongest protective effect, boosting algal biomass by 39.9%. Mechanistically, D-1 significantly accelerated NP removal (P < 0.05), achieving a 28.8% increase within 4 days. Oxidative stress in NP-exposed algae was also markedly achieved, as reflected by 29.3% and 46.8% reductions in reactive oxygen species and malondialdehyde levels, respectively, alongside ultrastructural preservation and > 1.3-fold increases in photosynthetic pigment contents. Moreover, D-1 modulated extracellular polymeric substances, restraining their overproduction while enriching tyrosine- and tryptophan-like components to reinforce the interfacial barrier. Transcriptomic profiling further revealed downregulation of stress-defense genes (e.g., DNA repair and photoprotection) and restoration of growth-related pathways, including photosynthesis and energy metabolism.

CONCLUSION: Our findings establish a community-to-strain paradigm for phycosphere microbiome-mediated tolerance of microalgae to NP, deepen our understanding of inter-species cooperation, and provide a basis for designing tailored algae-bacteria consortia for bioremediation.},
}

@article {pmid42833737,
year = {2026},
author = {Fu, Y and Cannon, RD and Cheng, L and Li, KC and Ekambaram, M and Cooper, PR and Mei, ML},
title = {Smart peptide-based materials and their clinical application for caries management.},
journal = {Journal of the American Dental Association (1939)},
volume = {157},
number = {10},
pages = {1105-1117},
doi = {10.1016/j.adaj.2026.07.002},
pmid = {42833737},
issn = {1943-4723},
mesh = {Humans ; *Dental Caries/prevention & control/therapy/drug therapy ; Tooth Remineralization/methods ; Biofilms/drug effects ; *Peptides/therapeutic use ; *Antimicrobial Peptides/therapeutic use ; Biomimetic Materials/therapeutic use ; },
abstract = {BACKGROUND: Caries remains the most prevalent biofilm-mediated disease, requiring a shift toward minimally invasive, biologically driven management. Conventional therapies lack specificity and may disrupt microbial balance. Smart peptide-based materials provide a precision-guided strategy enabling the simultaneous targeting of cariogenic pathogens and promotion of biomimetic remineralization.

TYPES OF STUDIES REVIEWED: The authors examined the literature regarding the design principles, mechanisms of action, and translational potential of smart peptide-based anticaries systems, including antimicrobial, remineralizing, and environmentally responsive constructs, and clinical use in caries management.

RESULTS: Smart peptides are engineered to sense disease-associated cues such as acidic pH, specific cariogenic bacteria, or tooth-binding ability. Targeted antimicrobial peptides selectively inhibit cariogenic pathogens while preserving commensal microbiota. Remineralizing peptides guide biomimetic mineralization in early lesions. Multifunctional constructs that integrate these properties address both microbial dysbiosis and tissue demineralization. Although most systems remain preclinical, emerging in vivo and early clinical evidence support their feasibility and translational potential.

Smart peptide-based materials provide a precision-guided and minimally invasive approach for caries management. By means of integrating pathogen-targeted antimicrobial activity with biomimetic tissue repair and environmental responsiveness, these materials align closely with the principles of precision dentistry. Continued development and clinical validation may enable personalized, microbiome-sparing, and lesion-specific interventions in routine oral health care.},
}

Humans
*Dental Caries/prevention & control/therapy/drug therapy
Tooth Remineralization/methods
Biofilms/drug effects
*Peptides/therapeutic use
*Antimicrobial Peptides/therapeutic use
Biomimetic Materials/therapeutic use

@article {pmid42833816,
year = {2026},
author = {Das, R and Victor, C and Hatt, JK and Durán-Viseras, A and Konstantinidis, KT and Sinharoy, SS and Waller, L and Nalá, R and Levy, K and Freeman, MC and Jesser, KJ},
title = {Effect of diarrhea on early-life gut microbiome composition and subsequent infant growth in Beira, Mozambique: analysis of the PAASIM longitudinal birth cohort.},
journal = {The American journal of clinical nutrition},
volume = {124},
number = {4},
pages = {101464},
doi = {10.1016/j.ajcnut.2026.101464},
pmid = {42833816},
issn = {1938-3207},
mesh = {Humans ; Mozambique/epidemiology ; Infant ; Longitudinal Studies ; *Diarrhea/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Female ; Male ; Birth Cohort ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Child Development ; Infant, Newborn ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The first year of life is a critical period for gut microbiome maturation; however, the interplay between diarrheal burden, microbial development, and growth in high-burden settings remains poorly understood.

OBJECTIVES: We leveraged longitudinal data from the Pesquisa Sobre o Acesso à Água e a Saúde Infantil em Moçambique (PAASIM) longitudinal birth cohort study in Beira, Mozambique, to test whether diarrhea is associated with gut microbiome characteristics and whether microbiome profiles relate to infant growth.

METHODS: Stool samples collected at 3, 6, 9 (n ∼150 at each time point), and 12 (n = 536) mo underwent 16S rRNA gene sequencing, with microbial diversity and taxonomic composition analyzed alongside monthly caregiver-reported diarrhea and anthropometric measurements.

RESULTS: Alpha diversity increased across infancy, and beta diversity shifted significantly with age, consistent with the ongoing maturation of the microbiome. Cumulative period prevalence of diarrhea from birth to 12 mo was not associated with microbial diversity or community composition at 12 mo. Higher alpha diversity at 3 mo was positively associated with length-for-age z-scores (LAZ) at 12 mo [β coefficient: 1.49; 95% confidence interval (CI): 0.33, 2.67], whereas higher diversity at 6 mo was inversely associated with LAZ at 12 mo (β: -2.85; 95% CI: -4.25, -1.45), showing age-dependent relationships with later linear growth. At 12 mo, we observed small beta-diversity differences between wasted and nonwasted (permutational multivariate analysis of variance, PERMANOVA R[2] = 0.05, P = 0.012) and between stunted and nonstunted children (R[2] = 0.05, P = 0.014). An exploratory longitudinal analysis revealed a positive association between Finegoldia abundance and wasting at 12 mo (β = 1.66; 95% CI: 0.83, 2.48), which met multiple-testing thresholds [false discovery rate = 0.19].

CONCLUSIONS: These findings suggest that early microbial trajectories, independent of cumulative diarrheal burden, may be linked to growth outcomes, warranting further research to identify potential microbiome-targeted interventions in the first year of life, a pivotal window for promotion of healthy growth in resource-limited settings.},
}

Humans
Mozambique/epidemiology
Infant
Longitudinal Studies
*Diarrhea/microbiology/epidemiology
*Gastrointestinal Microbiome
Female
Male
Birth Cohort
Feces/microbiology
RNA, Ribosomal, 16S/genetics
*Child Development
Infant, Newborn
Bacteria/classification/genetics/isolation & purification

@article {pmid42833873,
year = {2026},
author = {Haque, M and Lesker, TR and Rolle-Kampczyk, U and Segers, A and De Vos, WM and Molinaro, A and Basavanapura, T and Chen, Y and Backhaus, M and Mohamed, MR and Jiang, L and Salih, Q and Candels, L and Henricsson, M and Bielecka, A and Lang, S and Tacke, F and Hengstler, JG and Schneider, CV and Demir, M and Strowig, T and von Bergen, M and Schneider, KM and Trautwein, C},
title = {Microbiota-host genetic interactions modulate MASLD risk in PNPLA3[I148M] carriers via ceramides and are reversible by targeted microbial interventions.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338178},
pmid = {42833873},
issn = {1468-3288},
abstract = {BACKGROUND: The factors that determine when genetic susceptibility to metabolic dysfunction-associated steatotic liver disease (MASLD) progresses to clinically significant liver injury remain incompletely understood.

OBJECTIVE: We investigated whether disruption of the intestinal host-microbiota interface acts as a contextual modifier that amplifies PNPLA3[I148M] -associated hepatic injury.

DESIGN: We used a dual-hit mouse model combining hepatic Pnpla3[I148M] -expression with Nlrp6-deficiency, a model of impaired intestinal mucosal homeostasis, under western-diet conditions. Multi-omics profiling, including metagenomics, metabolomics and transcriptomics, was integrated with analyses in human cohorts (Lifelines, Charité MASLD, Human Phenotype Project). Microbiota-dependent effects were examined using faecal microbiota transplantation (FMT), antibiotic-mediated depletion and targeted intervention with Akkermansia muciniphila or its membrane protein Amuc_1100.

RESULTS: In mice, the combination of Pnpla3[I148M] expression and impaired intestinal sensing synergistically exacerbated gut-barrier dysfunction and bacterial encroachment, accompanied by increased portal levels of microbiota-associated metabolites, including long-chain ceramides (Cer(d18:1/16:0), Cer(d18:1/18:0)) and bile acids. These changes were associated with hepatic mitochondrial stress and inflammatory responses. Human carriers with advanced MASLD displayed microbial and metabolic signatures consistent with increased gut-derived metabolic signalling. Restoration of eubiotic microbiota via FMT or Amuc_1100 treatment improved intestinal barrier integrity and attenuated hepatic lipid accumulation in experimental models.

CONCLUSION: These findings suggest that gut-derived signals resulting from a disrupted intestinal barrier may act as modifiers of PNPLA3[I148M] -clinical penetrance by amplifying downstream metabolic and inflammatory responses. By identifying these pathways linking environmental context to genetic susceptibility, this study highlights the host-microbiota interface as a potential target for strategies aimed at limiting MASLD progression in genetically at-risk individuals.},
}

@article {pmid42834054,
year = {2026},
author = {Wang, T and Ahmad, S and Santos de Lima Rosa, R and Binion, B and Fernandez-Materan, FV and Igbalaye, JO and Chung, D and Bushra, A and Perez, V and Biedak, MA and Tang, E and Barnick, B and Olukoya, D and Mbuvi, P and Dutta, D and Erdman, JW and Gaskins, HR and Yang, G and Irudayaraj, J and Bernardi, RC and Ridlon, JM},
title = {The urinary pathobiont Actinobaculum massiliense can generate androgens via the dirAB pathway.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42834054},
issn = {2041-1723},
support = {GM145920//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; CA287126//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; GM145965//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; MCB-2143787//National Science Foundation (NSF)/ ; },
mesh = {Humans ; Male ; *Androgens/biosynthesis/metabolism ; *Actinomycetaceae/metabolism/genetics/isolation & purification/enzymology ; Phylogeny ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {While overlooked during the Human Microbiome Project, characterizing the urinary microbiota in health and disease is a new frontier in microbiome science. Recent studies have associated differential abundance of bacterial taxa including Propionimicrobium lymphophilum and Actinobaculum/Actinotignum spp. with prostate cancer. In this study, we collected urine from subjects before prostate biopsy and applied a Human Sterolbiome Discovery High-throughput (HSDH) assay to identify culturable urinary bacteria with the ability to generate androgens. Application of the HSDH Assay to urine samples led to the isolation of eight P. lymphophilum strains positive for cortisol side-chain cleavage (steroid-17,20-desmolase), 17β-HSDH activity, or both. In addition, we isolated three strains of Actinobaculum massiliense that carry the DHEA isomerase reductase (dir) genes. The dirA gene encodes a multifunctional 3β/17β-hydroxysteroid dehydrogenase/Δ[4,5]-isomerase and the dirB gene encodes a 17β-hydroxysteroid dehydrogenase isoform. Structural prediction and molecular dynamics reveal probable catalytic mechanisms based on the shared catalytic triad but distinct binding-pocket geometries of DirA and DirB, which enabled predictions of their respective reactions. Phylogenetic analysis of DirA and DirB revealed homologs in urinary tract commensals and in bacteria associated with steroid degradation in aquatic and terrestrial environments. Taken together, the development of the HSDH Assay and the identification of the dir pathway genes provide the methodological foundation and provide the molecular basis for advancing our understanding of the role of urinary tract bacteria in host endocrine physiology.},
}

Humans
Male
*Androgens/biosynthesis/metabolism
*Actinomycetaceae/metabolism/genetics/isolation & purification/enzymology
Phylogeny
*Bacterial Proteins/metabolism/genetics

@article {pmid42834084,
year = {2026},
author = {Peñarete-Acosta, D and Noe, P and Kellogg, T and Li, S and Radolf, JD and Hyams, JS and Jalili, S},
title = {Microphysiological models of human gastrointestinal diseases.},
journal = {Nature biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {42834084},
issn = {2157-846X},
support = {P30CA034196//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Gastrointestinal (GI) diseases impose a growing global health burden, extending beyond localized pathology to disrupt systemic metabolism, immunity and cancer risk. Despite advances in conventional animal and cell models, critical mechanisms driving chronic inflammation, tumour initiation and host-microbiome dysregulation remain incompletely understood, limiting translational progress. Microphysiological systems, including organoids and organ-on-a-chip technologies, have transformed our ability to model human GI biology and pathology with increasing cellular, spatial and mechanical fidelity. Here we synthesize recent advances in organoid and organ-on-a-chip models of GI disease, highlighting their applications across inflammatory, infectious and neoplastic conditions throughout the GI tract. We integrate emerging engineering approaches with mechanistic and clinical insights, assessing how these systems advance disease modelling while identifying remaining gaps in complexity, translation and scalability. By bridging microengineering innovation with clinical gastroenterology, we outline how next-generation, human-relevant models can inform mechanistic discovery, guide targeted therapeutic development and support precision medicine in GI disease.},
}

@article {pmid42834089,
year = {2026},
author = {Jiang, J and Dai, DLY and Poulsen, CS and Tranæs, K and Wang, T and Petersen, C and Hoskinson, C and Moraes, TJ and Mandhane, PJ and Simons, E and Azad, MB and Subbarao, P and Chawes, B and Bønnelykke, K and Thorsen, J and Turvey, SE and Stokholm, J},
title = {Microbial-derived tryptophan metabolites in the infant gut associate with increased risk of asthma following cesarean section.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42834089},
issn = {2041-1723},
mesh = {Humans ; *Cesarean Section/adverse effects ; *Asthma/microbiology/etiology/metabolism/epidemiology ; *Tryptophan/metabolism ; Female ; Infant ; *Gastrointestinal Microbiome/physiology ; Feces/microbiology/chemistry ; Risk Factors ; Pregnancy ; Child, Preschool ; Male ; Birth Cohort ; Canada ; Metabolome ; },
abstract = {Delivery by cesarean section (CS) is a risk factor for childhood asthma and a strong determinant of the early-life gut microbiome. It has been reported that a CS-perturbed gut microbiome plays a mediating role in the association between CS and asthma risk. However, the underlying mechanisms remain unclear. Here, using deeply phenotyped participants in the Canadian birth cohort (CHILD), we characterized the CS microbial composition at 3 months and 1 year of age using machine learning models and described the perturbation using CS scores. The association between CS and the gut microbiota composition was more pronounced at 3 months (area under the curve (AUC) = 0.78) and attenuated at age 1 year (AUC = 0.60). An increased asthma risk at age 5 years was associated only with 1-year CS microbial scores (Odds ratio 1.41, P = 0.004; adjusted odds ratio 1.30, P = 0.034), consistent with our previous work. Extending this, we identified metabolic imbalances associated with 1-year CS microbial scores, marked by elevated tryptophan metabolites in the stool metabolome. These results replicate our previous findings about the mediating role of the 1-year CS microbial signature in the association between CS and asthma risk from the Danish COPSAC2010 cohort, and provide new insight into the underlying mechanism of host-microbe interaction following cesarean section.},
}

Humans
*Cesarean Section/adverse effects
*Asthma/microbiology/etiology/metabolism/epidemiology
*Tryptophan/metabolism
Female
Infant
*Gastrointestinal Microbiome/physiology
Feces/microbiology/chemistry
Risk Factors
Pregnancy
Child, Preschool
Male
Birth Cohort
Canada
Metabolome

@article {pmid42834167,
year = {2026},
author = {Hu, Y and Bode, J and Gómez-Pérez, D and Guerreiro, MA and Mari, A and Wang, K and Niemann, S and Mahmoudi, M and Kemen, A and Duran, P and Wacker, O and Straub, D and Nahnsen, S and Schwessinger, B and Roux, F and Alonso-Blanco, C and Ågren, J and Hacquard, S and Stukenbrock, EH and Kemen, E},
title = {Thiamine cross-feeding drives microbial coexistence in the leaf microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42834167},
issn = {2058-5276},
support = {2016-05435, 2020-04434//Vetenskapsrådet (Swedish Research Council)/ ; TRR356//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2124-390838134//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Microbiome homeostasis is crucial for host health and ecosystem function, yet the molecular and ecological mechanisms underlying community assembly and stability remain elusive. Here we uncover a conserved yeast-oomycete association that promotes their coexistence in the leaf microbiome. Using a continental-scale microbiome survey, we identified an asymmetric mutualistic interaction between two eukaryotic hub microbes: the yeast Dioszegia hungarica and the obligate oomycete Albugo laibachii. We show that Dioszegia facilitates Albugo colonization by supplying thiamine via a dedicated membrane permease, alleviating Albugo's auxotrophy. Genomic and transcriptomic analyses indicate that natural selection has acted on thiamine production in Dioszegia, shaping this metabolic complementation. In planta assays further suggest that Albugo presence supports Dioszegia persistence under glasshouse conditions. Our study illustrates how the evolution of nutrient cross-feeding mediates microbial coexistence and microbiome stability. Targeting microbial nutrient flows offers new strategies for engineering microbiomes and enhancing plant resilience in natural and agricultural systems.},
}

@article {pmid42834399,
year = {2026},
author = {Correa, F and Luise, D and Palumbo, F and Scicchitano, D and Rampelli, S and Molino, S and Panciroli, N and Candela, M and Garay-Mayol, B and Ávila-Gálvez, MÁ and González-Sarrías, A and Castagnetti, A and Trevisi, P},
title = {Chestnut-quebracho tannins shape the fecal metabolome of weaned pigs through microbiota-dependent urolithin production.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42834399},
issn = {1674-9782},
support = {n.818290//Horizon 2020 Framework Programme/ ; },
abstract = {BACKGROUND: Chestnut and quebracho tannins may support gut health in weaned piglets, but their efficacy likely depends on farm environment and microbial capacity to convert tannins into bioactive metabolites. This study evaluated the effects of a blend of chestnut-derived hydrolysable tannins and quebracho-derived condensed tannins on growth performance, diarrhea occurrence, gut metagenome, and fecal metabolome in piglets reared under two commercial farm conditions. A total of 160 weaned piglets (initial body weight 6.53 ± 0.13 kg) were assigned to a 2 × 2 factorial design comprising 2 weaning units (W1 and W2) and 2 dietary treatments (control diet or control diet + 2 g/kg tannin blend; 40 piglets per treatment × farm). The trial lasted 76 d, with weighings at T0 (entry into weaning, median 28 d), T1 (d 35), T2 (d 49), and T3 (d 76). Fecal scores and samples were collected at T1, T2, and T3 for shotgun metagenomics (155 samples per time point) and untargeted metabolomics, and targeted urolithin quantification was performed in tannin-treated piglets at T1 and T2.

RESULTS: Tannin supplementation did not affect overall growth performance throughout the weaning phase, but reduced diarrhea occurrence at T2 in W2 (P = 0.032). Species-level beta diversity was consistently affected by treatment across time points (R[2]= 0.01-0.03; P < 0.01), whereas alpha diversity was mainly farm-driven during the early post-weaning phase. Linear discriminant analysis effect size identified farm-dependent taxonomic markers, including Escherichia coli in control pigs from W1 at T1 and Megasphaera elsdenii, Faecalibacterium prausnitzii, and Lactobacillus amylovorus in tannin-treated pigs at later time points. Untargeted metabolomics revealed treatment-related fecal signatures, with isourolithin A and urolithin B among the most discriminant metabolites in treated pigs, especially in W2. Targeted analysis identified 3 urolithin metabotypes (metabotype B in 50.0% of samples), with higher isourolithin A, urolithin B, and urolithin A in W2 than W1 at T2 (P < 0.01). Network integration identified candidate cooperative microbial consortia associated with urolithin production, including Ellagibacter isourolithinifaciens; these co-abundance associations are correlative and remain to be functionally validated.

CONCLUSIONS: Overall, chestnut-quebracho tannins were associated with a farm-dependent reduction in post-weaning diarrhea and modulated the gut ecosystem through microbiota-dependent polyphenol metabolism.},
}

@article {pmid42834458,
year = {2026},
author = {Liao, Y and Gui, Y and Li, T and Zhou, Q and Chen, X and Chen, Q},
title = {The Therapeutic Potential of Berberine in Treating Diabetes and Its Complications: Molecular Mechanisms and Future Perspectives.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-34},
doi = {10.1142/S0192415X26500795},
pmid = {42834458},
issn = {1793-6853},
abstract = {Diabetes mellitus (DM), a chronic metabolic disorder characterized by persistent hyperglycemia, poses a significant global health burden. Berberine (BBR), a natural isoquinoline alkaloid derived from medicinal plants such as Coptidis Rhizoma, has shown therapeutic promise for DM and its complications. Preclinical and clinical studies have revealed that BBR exerts multi-target effects, including remodeling the gut microbiome, promoting insulin secretion, ameliorating insulin resistance, and inhibiting hepatic gluconeogenesis. Its protective mechanisms against diabetic complications, such as nephropathy, cardiomyopathy, and retinopathy, involve modulating key pathways like AMPK/SIRT1, PI3K/Akt, and TGF-[Formula: see text]/Smad, which attenuate oxidative stress, inflammation, and fibrosis. Despite its low oral bioavailability, a wide array of formulation strategies, including polymer nanocarriers, lipid-based nanocarriers, mixed micelles, and absorption enhancer, have improved systemic exposure in preclinical models, although clinical translation remains limited. This review synthesizes evidence from the past decade spanning preclinical mechanisms, randomized controlled trials, pharmacokinetics and nanoformulation strategies, concluding that BBR is a promising candidate for complementary therapy, although the supporting clinical evidence remains limited. Further studies are warranted to clarify its mechanisms, and optimize its delivery. In particular, larger and longer-term trials, along with systematic pharmacokinetic-pharmacodynamic studies of BBR and its metabolites, are needed to confirm its efficacy and long-term safety.},
}

@article {pmid42834635,
year = {2026},
author = {Limaye, S and Bhide, P and Kale, A and Bokey, N},
title = {SCFA Alterations in IBS Subtypes: Systematic Evidence and Future Prospects for Biomarker-Based Diagnosis in India.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2605029},
doi = {10.4014/jmb.2605.05029},
pmid = {42834635},
issn = {1738-8872},
mesh = {Humans ; *Biomarkers/analysis ; *Irritable Bowel Syndrome/diagnosis/classification/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; Feces/chemistry/microbiology ; India ; Butyrates/analysis ; Propionates/analysis/metabolism ; Acetates/analysis ; Gastrointestinal Microbiome ; },
abstract = {Irritable bowel syndrome (IBS) is a chronic disorder of gut-brain interaction characterized by abdominal pain and altered bowel habits. Short-chain fatty acids (SCFAs), microbial metabolites of dietary fiber, play key roles in gut physiology and have been implicated in IBS pathogenesis. Propionate, acetate, and butyrate are of particular interest as potential biomarkers for diagnosis and subtype differentiation. A systematic search of PubMed, Web of Science, and Embase identified studies reporting fecal SCFA concentrations in IBS patients versus healthy controls (HCs). Adult cohorts diagnosed by Rome criteria, case-control or randomized designs, and sufficient SCFA data for effect size calculation were included. Data were harmonized to mean ± SD and analyzed; pooled standardized mean differences (SMDs) with 95% confidence intervals (CI) were calculated, with subgroup analyses for IBS-D and IBS-C. Methodological quality was assessed using the Newcastle-Ottawa Scale (NOS). Eleven studies met inclusion criteria. Across all IBS cohorts, propionate was significantly elevated compared to HCs, while acetate and butyrate showed no differences. In IBS-D, propionate was consistently higher. In IBS-C, total SCFAs were significantly reduced, with negligible heterogeneity. Acetate, propionate, and butyrate remained non-significant, with moderate to substantial heterogeneity. NOS assessment indicated that most studies were of good quality, with one rated moderate. This meta-analysis highlights propionate elevation as a biomarker for IBS, particularly IBS-D, and reduced total SCFAs as a distinct metabolic signature in IBS-C. Variability in individual metabolites reflects dietary and methodological influences. The absence of Indian cohorts limits generalizability; future studies integrating SCFA profiling with microbiome analysis in Indian populations are needed to validate biomarker utility and support precision management of IBS.},
}

Humans
*Biomarkers/analysis
*Irritable Bowel Syndrome/diagnosis/classification/metabolism
*Fatty Acids, Volatile/metabolism/analysis
Feces/chemistry/microbiology
India
Butyrates/analysis
Propionates/analysis/metabolism
Acetates/analysis
Gastrointestinal Microbiome

@article {pmid42834636,
year = {2026},
author = {Grover, M},
title = {Maternal circadian rhythm writes immune fate in offspring.},
journal = {Journal of biosciences},
volume = {51},
number = {36},
pages = {},
doi = {10.1007/s12038-026-00608-9},
pmid = {42834636},
issn = {0973-7138},
mesh = {Animals ; *Circadian Rhythm/genetics/immunology ; *Caenorhabditis elegans/immunology/genetics/microbiology ; *Caenorhabditis elegans Proteins/genetics/immunology ; Female ; Pseudomonas aeruginosa/pathogenicity/immunology ; },
abstract = {An organism's environment is rarely constant. Light, temperature, humidity, food availability, and microbial exposure often fluctuate rhythmically, creating daily patterns that organisms must anticipate and respond to (Paranjpe and Sharma 2005; van der Linden et al. 2010; Thaiss et al. 2014). The ability of biological systems to align physiology with such environmental cycles has fascinated biologists for decades, and circadian regulation is now known to influence diverse processes, including metabolism, behaviour, development, immunity, and stress responses (Fagiani et al. 2022; Poole and Kitchen 2022). Whether environmental rhythms experienced by the mother can influence offspring physiology has only begun to be explored (Yao et al. 2025). In a recent study, Lalsiamthara et al. (2026) provide compelling evidence that infection vulnerability in offspring can be shaped by maternal circadian rhythms. Using Caenorhabditis elegans, the authors first asked whether genetically similar animals differ in a measurable pre-infection state that anticipates later infection outcomes. They focused on irg-5, a PMK-1/p38 MAPK-regulated infection-response reporter (Peterson et al. 2019), and found that animals with high basal irg-5 expression before infection were more susceptible to subsequent Pseudomonas aeruginosa PA14 challenge. Importantly, this high-irg-5 state was not simply a sign of generally poor health, because these animals did not show obvious differences in baseline lifespan, feeding, movement, or pathogen avoidance. The study then asked whether this pre-infection state could be influenced by maternal circadian rhythms. Mothers were exposed to alternating 12 h light/20 C and 12 h dark/15 C cycles, mimicking daily fluctuations that worms may experience in nature. This entrainment did not increase irg-5 expression in the mothers themselves; instead, it rhythmically altered the proportion of offspring entering the high basal irg-5 state. The transgenerational effect of this state was further supported by the observation that high-irg-5 mothers produced more high-irg-5 offspring than low-irg-5 mothers. Consistent with clock-associated regulation, knockdown of nhr-23, a C. elegans homolog of mammalian ROR clock genes (Hiroki and Yoshitane 2024), disrupted this rhythmic oscillation. Together, these experiments connect maternal environmental timing, offspring immune-marker heterogeneity, and infection vulnerability in a single framework. These observations raise mechanistic and evolutionary questions. Mechanistically, what maternal cues are transmitted to offspring: metabolites, small RNAs, chromatin-associated states, or nutrients, and how do they influence basal immune state? Evolutionarily, why might mothers generate heterogeneous offspring states, especially when the high-irg-5 state increases susceptibility to PA14 in this study? One possibility is that this state is not universally maladaptive. Caenorhabditis elegans inhabits transient microbe-rich substrates such as rotting vegetation and compost, where temperature, humidity, food availability, and microbial communities can fluctuate with daily cycles (Schulenburg and Felix 2017). In such habitats, rhythmic cues are not merely background variables; they may act as reliable signals of changing risk. Temperature cycles can influence worm development, movement, and feeding, while also altering microbial growth and community composition (Felix and Braendle 2010). Light exposure may be indirect in soil or rotting-fruit microenvironments, but together with temperature it can serve as a proxy for day-night transitions (van der Linden et al. 2010). Maternal entrainment to these cues could therefore allow offspring physiology to be adjusted in anticipation of conditions that are likely, but not guaranteed, to follow. A state that is costly against one pathogen may be beneficial under other microbial, thermal, or nutritional conditions. Maternal generation of heterogeneous offspring states could therefore resemble bet-hedging, spreading risk across uncertain environments rather than optimizing all progeny for a single challenge. In a self-fertilizing organism with limited genetic diversity, such non-genetic heterogeneity could increase the chance that at least some individuals are appropriately tuned to future conditions. This idea could be tested further by asking whether natural genetic variation or microbiome context modifies intergenerational circadian immune heterogeneity in C. elegans. Such modifiers are plausible since, in mice, the gut microbiome can influence host circadian gene expression and metabolic rhythms (Thaiss et al. 2014), while in humans, genetic variation has well-established effects on circadian timing and behaviour (Kalmbach et al. 2017). Wild C. elegans isolates and defined natural microbiota (Dirksen et al. 2020) would therefore provide useful context to ask about the general nature and ecological sensitivity of this phenomenon. Beyond circadian regulation of intergenerational immune heterogeneity, the study also raises an important point about how basal immune markers should be interpreted. The irg-5 result is counterintuitive because irg-5 is an established PMK-1-regulated infection-response gene (Peterson et al. 2019), yet animals with high basal irg-5 expression were more susceptible to PA14. This does not mean that immune activation is generally harmful, or that irg-5 alone defines immune status. Instead, the same immune-marker expression may have different implications before and after infection: pathogen-induced expression may participate in defence, whereas high basal expression may mark altered intestinal homeostasis, metabolic imbalance, low-grade stress-pathway activity, or marker-specific transcriptional regulation. Mechanistically, prior ChIP data support binding of UNC-62 (MacNeil et al. 2015), a conserved MEIS/homeobox transcription factor (Van Nostrand et al. 2013), near the irg-5 promoter, and the present study shows that loss of UNC-62 increases basal irg-5 expression in mothers through PMK-1 and ELT-2. Thus, basal irg-5 heterogeneity appears to be a regulated transcriptional state shaped by UNC-62-dependent control. More broadly, this adds to an emerging view in C. elegans immunity that conserved developmental regulators can be redeployed in differentiated tissues to tune adult immune defence (Drury et al. 2023; Liu et al. 2024). The broader relevance of this work lies in connecting two ideas that are often considered separately: circadian regulation of immunity and maternal shaping of offspring physiology. Mammalian studies have shown that immune function is strongly time-of-day dependent, and that disruption of circadian rhythms can alter inflammatory responses and susceptibility to infection (Curtis et al. 2014; Poole and Kitchen 2022). Separately, the maternal environment, for example, nutritional state during pregnancy and lactation, can shape offspring metabolic, developmental, and behavioural physiology (Yao et al. 2025). Lalsiamthara et al. (2026) bring these themes together in a genetically tractable organism by showing that maternal circadian rhythms can shape infection-relevant heterogeneity in the next generation. Although the molecular details may be partly conserved and partly organism- or context-specific, the conceptual message is broad: before the pathogen arrives, vulnerability may already carry the imprint of time, ancestry, and environment.},
}

Animals
*Circadian Rhythm/genetics/immunology
*Caenorhabditis elegans/immunology/genetics/microbiology
*Caenorhabditis elegans Proteins/genetics/immunology
Female
Pseudomonas aeruginosa/pathogenicity/immunology

@article {pmid42834904,
year = {2026},
author = {Chulenbayeva, L and Rakhmankulova, A and Kamzayeva, N and Kozhakhmetov, S and Terzic, M and Bapayeva, G and Aimagambetova, G and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Ukybassova, T and Kushugulova, A},
title = {Cervicovaginal microbiome alterations across HPV infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1907605},
pmid = {42834904},
issn = {2235-2988},
mesh = {Humans ; Female ; *Microbiota ; *Papillomavirus Infections/virology/microbiology ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; *Human Papillomavirus Viruses/classification/genetics ; Cross-Sectional Studies ; Adult ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Dysbiosis ; Papillomaviridae/classification/genetics ; },
abstract = {INTRODUCTION: The cervicovaginal microbiome is a proposed modifier of HPV-associated cervical disease, yet its relationship with viral type heterogeneity, cytological grade, and community state type (CST) remains incompletely understood.

METHODS: This cross-sectional study characterized cervicovaginal microbiome composition and functional potential across HPV infection status, viral type categories (No HPV, HPV High Risk, HPV16, HPV18, HPV Other), cervical cytological grades, and CSTs in 311 non-pregnant women using whole-genome shotgun metagenomic sequencing, integrated diversity analyses, MaAsLin2 differential abundance testing, and HUMAnN 3.0 functional pathway profiling.

RESULTS: HPV-positive samples showed increased bacterial species richness, and a reciprocal Lactobacillus-to-Gardnerella dominance shift compared to HPV-negative samples. HPV Other showed the highest bacterial species richness and distinct taxonomic and predicted functional associations, including higher inferred abundance of siderophore- and lipopolysaccharide-biosynthesis pathways; however, overall species-level community composition did not differ significantly across HPV type groups. CST I and CST II exhibited compositional stability regardless of HPV status, while CST IV showed pronounced Lactobacillus depletion in HPV-positive women. LSIL was associated with lower Fannyhessea vaginae and Alloscardovia omnicolens abundance and higher Phocaeicola vulgatus abundance relative to NILM.

DISCUSSION: These findings indicate that oncogenic potential and dysbiosis severity are not aligned, and that CST type modifies HPV-microbiome interactions.},
}

Humans
Female
*Microbiota
*Papillomavirus Infections/virology/microbiology
*Vagina/microbiology/virology
*Cervix Uteri/microbiology/virology
*Human Papillomavirus Viruses/classification/genetics
Cross-Sectional Studies
Adult
Bacteria/classification/genetics/isolation & purification
Metagenomics
Dysbiosis
Papillomaviridae/classification/genetics

@article {pmid42834939,
year = {2026},
author = {Springer, A and Wagner, L and Koehler, S and Klinger, S and Wendt, M and Breves, G and Brüggemann, DA and Strube, C},
title = {Adult Ascaris suum roundworms and their antigens modulate the porcine intestinal microbiome and metabolome.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {10},
number = {},
pages = {100441},
pmid = {42834939},
issn = {2667-114X},
abstract = {The porcine roundworm, Ascaris suum, affects host intestinal physiology, microbiota composition and metabolic profiles. To better understand the mediators of these alterations, six pigs each were experimentally exposed to (i) 30 adult roundworms via gastric tube, or (ii) received injections into the duodenum of A. suum total excretory-secretory (ES) antigens, ES antigens secreted exclusively from the parasites' body surface (trans-cuticular ES), or cuticular somatic antigens, respectively. Six further pigs served as untreated controls. Microbiome composition in faeces, ingesta and mucosa samples from different intestinal compartments three days after transfer was studied by next-generation 16S rDNA sequencing. Metabolite profiles were assessed in ingesta and serum samples by nuclear magnetic resonance. Transfer of adult worms and their antigens significantly affected the caecal and colonic microbiome. Adult worm transfer also led to significantly increased levels of short-chain fatty acids (SCFAs) in the colon. Similarities between pigs exposed to adult A. suum and their antigens included increased relative abundance of operational taxonomic units (OTUs) representing potentially beneficial bacteria like Lactobacillus spp., Prevotella spp., and Eubacterium coprostanoligenes, while some opportunistic pathogens like Citrobacter spp. and Mucispirillum schaedleri were also increased. The net health effect during natural A. suum infections requires further study, but these preliminary findings warrant the hypothesis that low A. suum burdens might promote intestinal health. The results further indicate that certain microbial alterations are indeed mediated by A. suum antigens, although SCFA levels were unaffected in the antigen-treated groups, possibly due to the single application. Further investigations on chronically exposed animals are warranted, especially as porcine A. suum infections serve as a model for human ascariosis.},
}

@article {pmid42835196,
year = {2026},
author = {Liang, S and Ma, J and Zhang, H and Li, H and Zou, S and Li, D},
title = {Research on the spillover risk of antibiotic resistance gene from the gut microbiome of wild animal: A case study of the golden snub-nosed monkey.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117624},
pmid = {42835196},
issn = {2589-0042},
abstract = {Wild animals are "reservoirs" of antibiotic resistance genes (ARGs), and the interface of rivers between wild animals and humans is an ideal environment for spreading ARGs. In order to explore the risk of ARGs from wild animals to the human ecosystem through rivers, metagenomic sequencing was used to obtain the microbiome in the gut of golden snub-nosed monkeys (Rhinopithecus roxellana) and in the rivers. We performed collinearity analysis between the high-risk ARGs (Rank I ARGs) from golden snub-nosed monkeys and the metagenome-assembled genomes (MAGs) from river samples to assess the potential of river microorganisms to acquire Rank I ARGs. The number of collinear events between Rank I ARGs and MAGs in the WHD group (rivers within the disturbed monkey habitat) was five times higher than that in the WCK (rivers within the undisturbed monkey habitat) group. This implies a significant spillover risk of ARGs from wild animals to the human ecosystem via river interfaces, a risk that is further intensified by human disturbances. This research complemented the content that evaluated the spillover risk of ARGs from wild animals to humans.},
}

@article {pmid42835245,
year = {2026},
author = {Mujahid, W and Safdar, S and Aftab, A and Tabassum, S and Bakhtiar, SM},
title = {Integrative Metagenomic Analysis Reveals Human Gut Microbiome-Derived Candidate Non-invasive Biomarkers for Type II Diabetes Mellitus.},
journal = {Iranian journal of medical sciences},
volume = {51},
number = {9},
pages = {617-629},
pmid = {42835245},
issn = {1735-3688},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/diagnosis ; Biomarkers/analysis ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics/physiology ; Case-Control Studies ; Bacteroides/genetics ; Dysbiosis/diagnosis ; },
abstract = {BACKGROUND: Type II Diabetes Mellitus (T2DM) is increasingly associated with alterations in the gut microbiome, which influences host metabolism, inflammation, and insulin sensitivity. Metagenomic profiling has emerged as a promising non-invasive strategy for identifying disease-associated microbial signatures. However, distinguishing disease-specific biomarkers from general dysbiosis remains a major challenge. This study aimed to develop an integrative subtractive metagenomic framework to identify candidate disease-specific gut microbial biomarkers.

METHODS: This in silico case-control study used publicly available metagenomics datasets from healthy controls and individuals with T2DM. Assembly-based and read-based taxonomic profiling approaches were integrated. Differential abundance analysis using the Wilcoxon rank-sum test identified key microbial taxa significantly associated with T2DM.

RESULTS: Potential microbial biomarkers were identified as Bacteroides dorei, Bacteroides gracilis, Bacteroides stercoris, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Eggerthella lenta, Escherichia coli, Faecalibacterium prausnitzii, Parabacteroides distasonis, Ruminococcus torques, and Subdoligranulum. These taxa are involved in gut metabolic homeostasis and may serve as candidate non-invasive biomarkers for T2DM.

CONCLUSION: The results of this study advance understanding of microbiome-disease crosstalk and form the basis for further in vitro and in vivo validation and microbiome-targeted therapeutic approaches. Overall, this integrative metagenomic study supports alteration of microbial ecology in T2DM, validating the use of gut microbiome profiling as a diagnostic and therapeutic tool in metabolic disease research.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/diagnosis
Biomarkers/analysis
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics/physiology
Case-Control Studies
Bacteroides/genetics
Dysbiosis/diagnosis

@article {pmid42835332,
year = {2026},
author = {Wang, Z and Guo, M and Huang, Z and Cheng, J and Chen, Y and Lai, L and Xiao, J and Huang, W and Chen, Y},
title = {Metagenomic and metabolomic profiling of laterally spreading tumors identifies a microbiome with putative pro-tumorigenic features in high-grade intraepithelial neoplasia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844759},
pmid = {42835332},
issn = {1664-302X},
abstract = {INTRODUCTION: Laterally spreading tumors (LSTs) are pathologically classified into adenomas, including low-grade intraepithelial neoplasia (LGIN) and high-grade intraepithelial neoplasia (HGIN), and sessile serrated lesions (SSL). HGIN has a higher risk of progressing to colorectal cancer.

METHODS: This study compared the gut microbiome across these three pathological subtypes using fecal shotgun metagenomic sequencing and non-targeted metabolomics in 53 patients.

RESULTS: Overall community structure was similar among groups by Bray-Curtis NMDS and ANOSIM, although HGIN exhibited higher alpha diversity than SSL and enrichment of inflammation-associated and opportunistic taxa (e.g., Desulfovibrio, Bilophila, Helicobacter, Acinetobacter) alongside depletion of selected commensal taxa associated with mucosal homeostasis, including Bifidobacterium-, Lachnospiraceae-, and Ruminococcus-related species. Functionally, the HGIN-associated microbiome showed an expanded resistome and increased mobile genetic element-related potential, particularly in the HGIN versus LGIN comparison, with enrichment of beta-lactamase genes, MCR-family genes, and mobileOG features related to DNA transfer, recombination, transposition, plasmid maintenance, secretion, pilus-associated functions, and phage-linked mobility. In exploratory analyses, untargeted metabolomics suggested a bile- and lipid-rich metabolic pattern in HGIN, with nominal increases (P < 0.05; none significant after FDR correction) in lithocholyltaurine, LysoPE(P-16:0/0:0), tridecanoic acid and cortexolone. GSEA revealed nominal enrichment of unsaturated fatty acid biosynthesis, pyruvate metabolism, and propanoate metabolism. Exploratory species-metabolite correlations linked HGIN-enriched pathobionts with lipid/steroid-, bile-acid-, amino-acid-, and fatty-acid-related metabolites, while HGIN-depleted commensals were associated with amino-acid and organic-acid metabolic features.

DISCUSSION: Together, these findings identify microbial and metabolic features associated with high-grade histopathology within the LST spectrum, including FDR-supported microbial remodeling-pathobiont enrichment and expanded resistome and mobile genetic potential-accompanied by exploratory, nominally significant metabolomic alterations involving bile/lipid- and SCFA-related metabolites.},
}

@article {pmid42835356,
year = {2026},
author = {Xu, S and Fei, X and Lin, F and Wu, W and Zhuang, J and Mo, Q and Zhan, X and Fu, A},
title = {Gut virome orchestrates nitrogen partitioning between the host and microbiome.},
journal = {iMeta},
volume = {},
number = {},
pages = {e70177},
pmid = {42835356},
issn = {2770-596X},
abstract = {Dietary protein is essential for host growth and nitrogen homeostasis. How dietary protein shapes intestinal phage-bacteria interactions and influences the translation of dietary cues into host physiological outcomes remains poorly understood. We show that low-protein diet (LPD) substantially remodels the murine gut virome by altering phage-bacteria dynamics. Under LPD, nutritional stress suppresses bacterial phage release without altering the predicted proportion of lysogenic phages, leading to reduced free phage abundance and weaker bacterial lysis. Lysogenic phages carrying carbohydrate-related auxiliary metabolic genes (AMGs) may promote expansion of the bacterial host population while suppressing urease-mediated nitrogen recycling. High bacterial load coupled with low free phage availability creates a nitrogen trap that both sequesters host-accessible nitrogen and accelerates urea loss, thereby constraining host growth. Both the normal diet (ND) virome, defined by its high free phage abundance and lytic potential, and an equivalently sized LPD phage pool partially rescued nitrogen flow in mice fed a LPD. These results reveal a previously unrecognized gut "viral shunt," in which balanced phage-bacteria interactions redistribute nitrogen within the gut. Together, this study highlights the ecological significance of phage-bacteria interactions in host nutritional adaptation and suggests that targeted viral manipulation may offer a potential therapeutic strategy for protein-deficiency-related disorders.},
}

@article {pmid42835413,
year = {2026},
author = {Talebzadeh, S and Saris, PEJ},
title = {Targeted in vitro suppression of Parkinson's disease-associated Desulfovibrio by selective probiotic and potential probiotic strains.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1925465},
pmid = {42835413},
issn = {1664-302X},
abstract = {INRODUCTION: Emerging evidence links fecal Desulfovibrio (DSV) abundance with Parkinson's disease (PD) severity. While probiotics may relieve symptoms, their direct effects on DSV remain unexplored.

METHODS: This study evaluated the inhibitory potential of 32 probiotic and potential probiotic strains against three DSV strains isolated from three individual PD patients. Antimicrobial activity was quantified using agar well diffusion and microplate assays, and the operational minimum inhibitory con centration (MIC₉₀) was determined based on the total crude dry matter content of cell-free supernatants (CFS).

RESULTS: All tested lactic acid bacteria (LAB) strains, except Limosilactobacillus reuteri Hambi410, inhibited DSV. Quantitative micro assay results showed that Lacticaseibacillus rhamnosus LGG exhibited the highest inhibition (up to 44.82% ± 8.31%) after neutralization and catalase treatment. Among the eight tested Bifidobacterium strains, Bifidobacterium bifidum CUL-17 and Bifidobacterium longum E-96664 exhibited inhibitory effects comparable to those observed in LAB. The MIC₉₀ values revealed that Lactobacillus acidophilus Hambi1448 and Lactiplantibacillus plantarum E98 were the most potent, with MIC₉₀ values ranging from 25.2 to 29.8 mg/mL. Spearman's correlation confirmed a significant inverse relationship between initial pH and inhibition zones (p < 0.001). Crucially, analysis of covariance (ANCOVA) demonstrated that strain specific inhibitory variations remained highly significant (p < 0.005) after statistically controlling for the confounding effect of acidification, which is consistent with the involvement of non-acidic bioactive metabolites. Probiotic Bacillus strains showed no direct inhibition but are discussed for their role in alleviating PD-related constipation.

DISCUSSION: These findings demonstrate that specific probiotics can target PD-derived DSV, offering a novel strategy for microbiome-based PD management.},
}

@article {pmid42835440,
year = {2026},
author = {Timilsina, M and Chundru, D and Harris, A and Ghanem, M},
title = {Impact of Avibacterium paragallinarum infection on the upper respiratory tract microbiome of chickens.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1911133},
pmid = {42835440},
issn = {2297-1769},
abstract = {Avibacterium paragallinarum, the causative agent of infectious coryza, causes infection in the upper respiratory tract (URT) of chickens, leading to substantial economic losses. While respiratory pathogens are known to disrupt host-associated microbiomes, A. paragallinarum's impact on the chicken URT microbiome remains poorly understood. This study characterized microbiome changes in chicken URT following A. paragallinarum infection and examined whether different field strains induced distinct alterations. Four field strains were used to challenge separate groups of four-week-old specific-pathogen-free chickens, with one uninfected control group. Choanal swabs were collected at multiple time points post-challenge, pooled by group, and subjected to 16S rRNA V3-V4 amplicon sequencing. Microbial composition and diversity were characterized and compared among groups. Because of the limited biological replicates, statistical analyses and associated p-values were interpreted as exploratory. The URT microbiome was initially dominated by Firmicutes, followed by Proteobacteria, with the latter showing an increasing trend during infection. Infected group exhibited lower microbial richness compared to the noninfected based on the Chao1 index (p = 0.03175) and observed ASVs (p = 0.03372), with richness reaching the lowest level at 4 days post-inoculation (dpi) and returning to baseline by 9 dpi. Microbial community composition differed between infected and noninfected groups based on unweighted UniFrac distances (p = 0.027, PERMDISP ns). No differences in microbial diversity measures were observed among the individual strain groups. The findings suggest that A. paragallinarum infection is associated with transient yet notable alterations in microbial richness and community composition in URT, even in absence of overt clinical signs.},
}

@article {pmid42835511,
year = {2026},
author = {Cuadros, J and Tapia-Perdomo, V and Nieto, C and Rincón-Orozco, B and Duque, JE},
title = {Ecological origin and natural Trypanosoma cruzi infection are associated with reconfiguration of the Rhodnius pallescens midgut microbiome.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {10},
number = {},
pages = {100442},
pmid = {42835511},
issn = {2667-114X},
abstract = {The intrusion of the secondary vector Rhodnius pallescens into urban and peri-urban environments in Colombia poses an emerging risk for Chagas disease transmission, compounded by rising insecticide resistance. Developing novel control strategies requires the identification of stable gut symbionts; however, high-resolution microbial profiles for urban-intruding vector populations remain poorly defined. To characterize the intestinal microbiome and identify candidate taxa for paratransgenesis, we generated high-resolution taxonomic composition and predicted functional profiles using 16S rRNA amplicon sequencing of individually processed midgut tissues from laboratory-reared and wild-caught adult R. pallescens with and without Trypanosoma cruzi infection collected in the Bucaramanga metropolitan area, Andean region, Santander, Colombia. Beta diversity analyses revealed that ecological origin and infection status significantly drive microbial restructuring (PERMANOVA P = 0.001). The transition from a sylvatic to a laboratory environment induced a severe taxonomic contraction dominated by the genus Dickeya (79.19% relative abundance). From these wild-type insects, non-infected populations maintained a balanced, functionally redundant midgut community featuring Dickeya (46.82%), Williamsia (20.6%), and Corynebacterium (16.76%). On the other hand, natural T. cruzi colonization was associated with a marked taxonomic reorganization in wild vectors, characterized by the marked expansion of Actinobacteriota, specifically Williamsia (51.22%) and Nocardia (29.99%), alongside an enrichment of predicted pathways for oxidative stress management. Therefore, we hypothesize that ecological origin and T. cruzi infection are primary determinants of microbial structure in R. pallescens. In naturally infected insects, we identify the genus Williamsia as a priority candidate for future studies aimed at evaluating its stability, cultivability, functional role, and potential use in paratransgenic strategies.},
}

@article {pmid42835678,
year = {2026},
author = {Jin, T and Lv, Y and Jiang, S and Jia, Y},
title = {Beyond antibiotics: collateral damage to the gut microbiome during cancer therapy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1955949},
pmid = {42835678},
issn = {1664-302X},
abstract = {Antibiotics are major drivers of microbiome disruption in oncology, but they do not fully explain the ecological changes observed during cytotoxic treatment. The central question of this Mini Review is when chemotherapy-associated microbiome change should be interpreted as transient compositional variation and when it constitutes a loss of ecosystem function with potential clinical consequences. We use collateral microbiome injury as a conceptual framework, rather than a formally established clinical diagnosis, to describe treatment-associated loss of microbial load, function, spatial organization, colonization resistance, or recovery capacity that is not required for antitumor activity. Three questions organize the review: which changes are directly attributable to a defined chemotherapeutic agent; which arise from the broader oncology exposome, including mucosal injury, antibiotics, nutritional disturbance, hospitalization, and supportive medications; and which ecological mechanisms are inferred from non-chemotherapy models. The evidence is therefore classified as direct chemotherapy evidence, oncology-exposome evidence, or general ecological evidence. Agent-specific studies support microbial transformation of irinotecan and fluoropyrimidines, whereas longitudinal leukemia studies more often capture composite treatment episodes. Across these settings, depletion of obligate anaerobe functions, altered nutrient and redox conditions, pathobiont domination, oral-to-gut niche coalescence, and impaired recovery may weaken colonization resistance. However, the strongest persistent-disruption and infection data arise from intensive hematologic treatment and should not be generalized uncritically to conventional solid-tumor chemotherapy. We propose operational criteria, multidimensional recovery metrics, and evidence-stratified translational priorities for moving from descriptive dysbiosis toward testable, microbiome-sparing supportive care.},
}

@article {pmid42835739,
year = {2026},
author = {Liang, S and Jia, G and Chen, H and Zhou, C and Peng, W and Liu, S and Ai, C and Zhang, Y and Ding, G},
title = {Differential effects of yeast derivatives on pepper productivity, stress resilience, and soil microbial communities.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21604},
pmid = {42835739},
issn = {2167-8359},
mesh = {*Capsicum/growth & development/microbiology ; *Soil Microbiology ; *Stress, Physiological ; Rhizosphere ; *Yeasts/chemistry ; Fertilizers ; Biomass ; Nitrogen/metabolism ; },
abstract = {The excessive application of chemical fertilizers is a prevalent issue in modern agriculture, as it increases production costs, undermines economic returns, and degrades soil health. In this study, the effects of two compositionally distinct yeast derivatives, namely Yeast Glycoside Type I (YD1) and Water-Soluble Yeast Glycoside (YD2), on the growth, nutrient use efficiency, low-temperature (LT) stress tolerance, and rhizosphere microbial communities of pepper (Capsicum annuum L.) were investigated. The yeast derivatives (YD) were characterized using scanning electron microscopy (SEM) and biochemical analysis, which revealed distinct profiles: YD2 contained higher nitrogen (11.89%), isindole-3-acetic acid (IAA), and 1-Aminocyclopropane-1-carboxylic acid (ACC), whereas YD1 was enriched in cytokinins (isopentenyl adenine, iP; trans-zeatin, tZ). Under normal temperature (NT) conditions, application of YD2 at concentrations of 1% significantly enhanced pepper yield, shoot biomass, and nitrogen/potassium use efficiency, whereas YD1 exerted minimal effects. However, under low-temperature (LT) stress, applications of YD1 and YD2 did not significantly increase yield. Despite this, YD2 maintained root activity, mitigated chlorophyll degradation, and increased the activities of antioxidant enzymes under LT stress. Both YD altered rhizosphere bacterial community structure under NT conditions (PC1: 42.09%, p = 0.007); however, this effect was attenuated under LT stress (PC1: 24.85%, p = 0.003). Specifically, YD1 was associated with an increased relative abundance of Microscillaceae (NT) and Thiobacillus (LT), while YD2 was linked to an increase in Kaiserbacteria (NT) and Armatimonadales (LT). These findings suggest that the two YDs, particularly YD2, can influence pepper productivity and stress resilience through associations with improved nutrient uptake, physiological adjustments, and shifts in the rhizosphere microbiome. This pot-based study provides insights into the potential of tailored yeast derivatives as biostimulants, offering a basis for developing more sustainable agricultural practices.},
}

*Capsicum/growth & development/microbiology
*Soil Microbiology
*Stress, Physiological
Rhizosphere
*Yeasts/chemistry
Fertilizers
Biomass
Nitrogen/metabolism

@article {pmid42835748,
year = {2026},
author = {Shao, M and Liu, L and Wang, Q and Shen, X and Zhang, W},
title = {Digital intelligence-enabled tumor microbiome research: from mechanistic dissection to clinical translation.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1972980},
pmid = {42835748},
issn = {2234-943X},
abstract = {Tumor-associated microbiomes are integral components of the tumor microenvironment, modulating tumorigenesis and progression through immune and metabolic pathways. Microbiome data are high-dimensional, sparse, and compositional, which limits conventional analytical approaches. Digital intelligence-an umbrella term encompassing artificial intelligence (AI), machine learning (ML), big-data analytics, and multi-omics integration-has emerged as a powerful paradigm for tumor microbiome research. In this review, we delineate the applications of digital intelligence across the full pipeline: intelligent preprocessing of sequencing data, multi-modal data integration, inference of microbe-host interactions, construction of diagnostic and prognostic models, and discovery of immunotherapy biomarkers. We explicitly distinguish computational association from experimental mechanistic validation and clinical utility, and we critically appraise methodological limitations, including overfitting, data leakage, batch effects, and the scarcity of external prospective validation. Microbiome-related biomarkers are framed as prognostic, predictive, or dynamic, and we caution against equating retrospective performance with clinical value. Finally, we discuss current challenges-data standardization, model interpretability, and ethical privacy-and future directions, including spatial and single-cell microbiomics, FMT-based interventions, and prospectively validated clinical translation.},
}

@article {pmid42835761,
year = {2026},
author = {Chen, F and Zhang, C and Yao, G and Meng, R and Fan, P and Chen, L and Ou, Y and Jin, Y},
title = {Deciphering the gut microbiota's role in infection risk: Mendelian randomization analysis of microbial taxa and infectious outcomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821422},
pmid = {42835761},
issn = {1664-302X},
abstract = {BACKGROUND: Observational studies have linked the gut microbiota (GM) to infectious diseases, but confounding, reverse causation, and disease-related microbiome changes limit causal interpretation. We combined Mendelian randomization (MR) with focused experimental analyses to investigate microbiota-infection relationships.

METHODS: Two-sample MR evaluated genetically predicted microbial taxa across 75 infectious outcomes. Inverse-variance weighted (IVW) estimates were used as the primary analysis, with weighted-median and MR-Egger estimates as complementary methods. Benjamini-Hochberg false discovery rate (FDR) and Bonferroni corrections were applied across all IVW tests. Instrument strength, Cochran's Q, MR-Egger intercepts, leave-one-out analysis, MR-PRESSO, and Steiger directionality testing were used to assess robustness. Exploratory association patterns were used to prioritize a Coriobacteriia-related respiratory signal for experimental investigation using Collinsella aerofaciens cell-free supernatant and A549 epithelial cells.

RESULTS: Among 15,728 IVW tests, 659 associations had nominal P < 0.05. After global correction, three taxonomically related associations with urinary tract infection (UTI) remained significant. Higher genetically predicted abundance of genus Bifidobacterium was associated with lower UTI risk (odds ratio [OR] 0.29, 95% confidence interval [CI] 0.17-0.49; FDR-adjusted P = 0.029), while order Bifidobacteriales and family Bifidobacteriaceae showed similar estimates (both OR 0.25, 95% CI 0.14-0.45) and met the Bonferroni threshold. Sensitivity analyses showed no significant heterogeneity or MR-PRESSO-detected outliers, and leave-one-out and Steiger analyses were supportive, although MR-Egger intercepts suggested possible directional pleiotropy. Exploratory analyses identified clustering between Coriobacteriia-lineage taxa and respiratory outcomes. C. aerofaciens cell-free supernatant altered 993 genes and enriched inflammatory pathways in A549 cells. qPCR supported increased CSF2, CXCL8, and CCL20 expression, while ELISA detected IL-8 and MIP-3α but not quantifiable GM-CSF. Untargeted metabolomics identified 201 differential metabolites between bacterial supernatant samples and matched BHI controls.

CONCLUSION: The corrected Bifidobacterium-related UTI association was the principal MR finding, while the broader analysis identified exploratory microbiota-infection patterns. The C. aerofaciens model linked extracellular metabolic remodeling during bacterial growth with epithelial transcriptional and inflammatory responses, providing focused directions for further investigation.},
}

@article {pmid42835783,
year = {2026},
author = {Nichols, HL and Dhokiya, V and Hoque, AF and Heinz, E and Hughes, GL and Coon, KL},
title = {Transplant of cryopreserved mosquito gut microbiota reveals strain-specific patterns of microbial acquisition and assembly.},
journal = {ISME host microbe},
volume = {1},
number = {1},
pages = {aazag010},
pmid = {42835783},
issn = {2978-8285},
abstract = {Mosquitoes are important vectors of human pathogens, and their gut microbiome influences traits such as survival, fecundity, pathogen resistance, insecticide resistance, and vector competence. Manipulating this microbiome offers a promising strategy for reducing mosquito-borne disease. While 16S rRNA gene amplicon sequencing has revealed global patterns of gut microbial diversity, the factors driving these patterns remain poorly understood. Here, we used a community-transplantation approach that allows the collection, cryopreservation, and transfer of whole adult microbial communities into axenic (germ-free) mosquitoes to investigate the determinants of microbiome assembly and host-microbe interactions. Using reciprocal transplants between Aedes aegypti Liverpool strains maintained in isolation for nearly 50 years at the University of Wisconsin-Madison (UW) and the Liverpool School of Tropical Medicine (LSTM), we found striking strain-specific responses: UW mosquitoes exhibited altered bacterial composition and developmental defects, whereas LSTM mosquitoes did not. Transplant fidelity depended on donor community composition and recipient genotype, and we observed conserved assembly patterns across the mosquito life cycle. These results reveal how host genetics and microbial community structure interact to shape microbiome assembly and support the development of microbiome-based vector control strategies.},
}

@article {pmid42836017,
year = {2026},
author = {Agrimbau Vázquez, J and Boggio Marzet, C and Peralta, R and Taussig, R and Lopez, P and Viale, D and Alonso, C and Curtti, T and Perez Gagni, ML and Cassará, ML and Urrutia, L and Bustamante, JP},
title = {Altered gut microbial functional landscape in children with pediatric inflammatory multisystem syndrome following SARS-CoV-2 infection: an exploratory metagenomic study.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1881538},
pmid = {42836017},
issn = {2296-2360},
abstract = {BACKGROUND: Pediatric Inflammatory Multisystem Syndrome (PIMS), also known as MIS-C (Multisystem inflammatory syndrome in children), is a severe post-infectious inflammatory condition associated with SARS-CoV-2 in children. While coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, primarily affects the respiratory system, growing evidence highlights gastrointestinal involvement and the relevance of the gut-lung axis in systemic inflammation. However, the taxonomic and, particularly, the functional landscape of the gut microbiome in children with PIMS remains insufficiently characterized.

METHODS: This exploratory study analyzed fecal samples from pediatric patients diagnosed with PIMS and age-matched clinically healthy controls using shotgun metagenomic sequencing. Taxonomic profiling was performed with MetaPhlAn4, and functional and metabolic pathway analyses were conducted using HUMAnN3. Alpha and beta diversity metrics were assessed, and differential abundance analyses were applied to identify microbial taxa and putative functional pathways associated with PIMS.

RESULTS: 12 pediatric patients diagnosed with PIMS and 11 age-matched clinically healthy controls were included. Alpha diversity indices did not differ significantly between groups, although consistently lower mean values were observed in children with PIMS. In contrast, beta diversity analysis demonstrated a significant separation in microbial community composition between patients with PIMS and controls (PERMANOVA, p = 0.01). Children with PIMS exhibited increased relative abundance of Prevotella copri clade C, Duodenibacillus massiliensis, Phascolarctobacterium succinatutens, and Enterocloster bolteae, alongside a relative reduction of several commensal taxa. Putative functional profiling revealed significant differences in enzyme-coding genes and metabolic pathways, including increased metagenomic abundance of aconitate hydratase and other functions potentially relevant to inflammatory and immunomodulatory processes in the PIMS group.

CONCLUSION: These findings suggest an association between gut microbiota unbalance, potential microbial functional alterations, and PIMS, supporting the need for further investigation of the gut microbiome in post-COVID-19 systemic inflammation in pediatric populations. Given the exploratory nature of this study, these observations require validation in larger, longitudinal cohorts before microbial biomarkers or therapeutic implications can be established.},
}

@article {pmid42836028,
year = {2026},
author = {Emmanuel Shittu, O and Ge, J and Babalola, OO},
title = {Metagenomic Tools as Predictive Approaches to Decipher Soil and Rhizosphere Microbial Communities and Their Functions for Sustainable Agriculture.},
journal = {International journal of genomics},
volume = {2026},
number = {},
pages = {3098615},
pmid = {42836028},
issn = {2314-4378},
abstract = {The increasing demand for resilient and sustainable food production necessitates a comprehensive understanding of rhizosphere microbial communities and their functional roles in enhancing plant health, nutrient acquisition, stress resilience, and crop productivity, thereby supporting food security and sustainable agriculture. However, soil microbiomes are composed of complex and unculturable communities of beneficial microorganisms that drive critical ecosystem functions, which traditional culture methods cannot capture. This limits the understanding of their roles and impacts on plant health and agricultural sustainability. Metagenomic tools have emerged as transformative approaches for characterizing microbial diversity in soil. Therefore, this review presents an overview of how metagenomic techniques can be harnessed to predict microbial community structures and their associated functional potentials, ultimately contributing to the development of resilient farming strategies. Next-generation sequencing and bioinformatics enable metagenomics to analyze microbial genetic material in soil and rhizospheres. This study provides insights into microbial diversity and profiles of key functional genes linked to nutrient availability and soil functions. We discuss the use of metagenomics tools to predict soil health and microbial functions for sustainable agroecosystems, emphasizing predictive models that help farmers optimize yields and minimize environmental impact. This review explores how metagenomics tools in agriculture can serve as a predictive model to transform our understanding of soil-microbe interactions. This advancement can facilitate the formulation of novel, more resilient, productive, and sustainable agricultural systems.},
}

@article {pmid42836099,
year = {2026},
author = {Kruthika, K and Aishwarya, MU and Vaishnavi, K and Shetty, KP and Divyadharshini, J},
title = {Electronic cigarette use and periodontal tissue damage: a scoping review and an evidence-informed conceptual framework.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1956724},
pmid = {42836099},
issn = {2673-4915},
abstract = {BACKGROUND: Electronic cigarette (e-cigarette) use has increased worldwide and is often promoted as a safer alternative to conventional smoking. However, its effects on periodontal health remain incompletely understood because of heterogeneous findings. This scoping review aimed to synthesize evidence comparing periodontal health among electronic cigarette users, conventional cigarette smokers, and non-smokers and to develop an evidence-informed conceptual framework illustrating potential biological and clinical pathways linking electronic cigarette use to periodontal tissue changes.

METHODS: A scoping review was conducted according to PRISMA-ScR. PubMed, Embase, Scopus, and Google Scholar were searched for studies published between January 2015 and March 2025. Eligible studies comparing periodontal clinical outcomes and inflammatory biomarkers among electronic cigarette users, conventional smokers, and/or non-smokers were narratively synthesized, and an evidence-informed conceptual framework was developed.

RESULTS: Of 379 records identified, 10 studies met the eligibility criteria. Conventional cigarette smokers generally demonstrated greater periodontal destruction than electronic cigarette users. Electronic cigarette users frequently demonstrated intermediate periodontal findings, including increased probing depth, clinical attachment loss, plaque accumulation, and alterations in bleeding on probing and inflammatory biomarkers; however, findings varied across studies. Potential pathways involving oxidative stress, immune dysregulation, vascular alterations, impaired wound healing, and oral microbiome alterations were identified.

CONCLUSIONS: The available evidence suggests that electronic cigarette use may be associated with adverse periodontal changes compared with non-smoking, although findings are heterogeneous. The proposed evidence-informed conceptual framework integrates potential biological and clinical pathways and may guide future mechanistic, longitudinal, and multicenter research and periodontal risk assessment.},
}

@article {pmid42836172,
year = {2026},
author = {Raab, M and Behr, JH and Vasileiadis, S and Neumann, G and Smalla, K and Grosch, R and Geistlinger, J and Rozhon, W and Babin, D and Kampouris, ID},
title = {Positive effects of reduced tillage intensity on soil organic matter are linked to shifts of K-/r-strategists in soil bacterial community composition.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag251},
pmid = {42836172},
issn = {2730-6151},
abstract = {Compared to conventional ploughing, reduced tillage intensity (e.g. cultivator tillage) benefits soil organic matter (SOM) accumulation, which has been attributed to lower disruption of soil aggregates under reduced tillage intensity. While soil microorganisms have been known to contribute to SOM accumulation, the contribution of microbial processes to SOM content has been overlooked, with the underlying mechanisms remaining unclear. We here estimated how cultivator tillage shifts soil bacterial community composition toward slower-growing K-strategists, in contrast to faster-growing r-strategists, by analyzing previously generated data from a long-term field trial in loess chernozem soil. We annotated the 16S rRNA genes from the whole amplicon sequence variant dataset through sequence alignment and identified publicly available genomes phylogenetically related to them with at least 97% sequence identity. Next, we computationally inferred traits such as growth rate, genome size, and the number of carbohydrate catabolism-related genes. These traits were strongly associated with positive responders to cultivator or mouldboard-plough tillage in the bulk soil bacterial communities. Moreover, mouldboard-plough tillage showed a lower ratio of slower- to faster-growing bacterial taxa compared to cultivator tillage in the bulk soil. While this relationship was absent in rhizosphere bacterial communities, these communities showed an overall lower ratio of slower- to faster-growing bacterial taxa than the bulk soil bacterial communities. Moreover, this ratio was negatively correlated with SOM only under mouldboard-plough tillage in bulk soil bacterial communities. Overall, our results indicate that tillage intensity influences the relationship of bacterial K-/r-strategists with SOM.},
}

@article {pmid42836222,
year = {2026},
author = {Bickel, S and Abdelfattah, A and Tack, AJM and Wicaksono, WA and Berg, G},
title = {Associations among soil microbial and plant richness across global terrestrial biomes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag266},
pmid = {42836222},
issn = {2730-6151},
abstract = {Soil microbiomes play a crucial role in terrestrial ecosystems by influencing plant diversity and ecosystem functions, yet global patterns linking soil microbial and plant species richness remain unclear. Here we employed machine learning models integrating environmental variables to map global richness patterns of plants, bacteria, and fungi across terrestrial biomes and examined their associations. We found distinct biogeographical distributions and high diversity regions: plant richness peaked in tropical forests, soil bacterial richness was highest toward arid and transitional zones, and soil fungal richness was prominent in tundra and boreal forests. Notably, plant richness correlated positively with microbial richness and strongly with fungal endophyte richness, supporting the concept that diversity fosters further diversity. These findings reveal complex cross-kingdom interactions shaping terrestrial biodiversity and underscore the importance of integrated conservation strategies that consider multiple organismal groups and their environmental drivers.},
}

@article {pmid42836268,
year = {2026},
author = {Baptista, LSM and Santos, MKR and Soratto, TAT and Wagner, G and Hauptli, L and Trevizan, L and Pinto, CFD and Pires, PGS and Feksa, L and Moraes, PO},
title = {Short-term changes in photographed dental calculus coverage and pooled supragingival microbiota after baked dental treats containing a pomegranate-propolis blend or sodium hexametaphosphate in dogs.},
journal = {The Journal of small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1111/jsap.70207},
pmid = {42836268},
issn = {1748-5827},
support = {25/2025//FAPESC/ ; },
abstract = {OBJECTIVES: To compare short-term changes in the photographed percentage of visible tooth surface covered by pre-existing dental calculus among dogs receiving additive-free baked treats, sodium hexametaphosphate-containing treats or pomegranate-propolis-containing treats, and to describe pooled supragingival bacterial profiles before and after the intervention. A fixed-side brushing procedure was additionally explored from day 9 onward.

MATERIALS AND METHODS: Twelve adult dogs (four per group) were enrolled in a 19-day exploratory pilot study and randomly allocated to one of three treatment groups: additive-free baked dental treats, baked dental treats containing 0.6% sodium hexametaphosphate or baked dental treats containing a 0.6% pomegranate-propolis blend. Dogs received two treats daily throughout the study. A fixed-side tooth-brushing protocol was applied from day 9 onwards, with the right dental arch brushed daily and the left arch left unbrushed for within-dog comparison. Photographed dental calculus coverage was assessed at predefined time points using standardised image analysis. Pooled supragingival bacterial profiles were descriptively characterised at baseline and day 19 by 16S rRNA gene sequencing.

RESULTS: Photographed dental calculus coverage declined in all treatment groups over the 19-day study. The largest mean descriptive reduction was observed in dogs receiving baked dental treats containing the pomegranate-propolis blend, followed by sodium hexametaphosphate and additive-free baked dental treats. A greater descriptive reduction in photographed dental calculus coverage was observed on the brushed right dental arch after day 9. Exploratory analysis of pooled supragingival bacterial profiles showed descriptive differences in the relative abundance of bacterial taxa between baseline and day 19.

CLINICAL SIGNIFICANCE: In this 19-day exploratory study, photographed dental calculus coverage declined in dogs receiving all three baked-treat formulations. The largest mean descriptive reduction occurred in the pomegranate-propolis group, followed by the sodium hexametaphosphate and additive-free groups. Because the study included four dogs per treatment, no group without a baked treat, a fixed right-side brushing protocol and pooled microbiome samples without biological replication, these findings should be interpreted as preliminary. Larger randomised studies beginning after standardised dental prophylaxis and using individual microbiome samples are required to determine preventive efficacy and clinical relevance.},
}

@article {pmid42836313,
year = {2026},
author = {Baindara, P and Paul, D and Mondal, SK and Dinata, R and Chakraborty, S and Kumari, S and Mandal, SM},
title = {FAs and their metabolites as antibacterial agents: mechanisms, food applications, and translational opportunities.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo03064e},
pmid = {42836313},
issn = {2042-650X},
abstract = {Antimicrobial resistance and the demand for effective food-preservation strategies have increased interest in fatty acids (FAs) and their derivatives as potential antibacterial agents. FAs can affect bacterial membranes, cellular energetics, biofilm-associated phenotypes, and, in some organisms, specific metabolic pathways. However, these effects vary considerably with FA structure, concentration, ionization state, pH, formulation, bacterial species, and assay conditions. Additionally, microbiota-derived short-chain FAs may also contribute to host defense by influencing epithelial integrity, immune signalling, microbiome composition, and colonization resistance. Still, researchers should distinguish these indirect effects from direct bacterial killing. Evidence from laboratory media cannot necessarily predict performance in complex foods, where proteins, lipids, processing conditions, oxidation, and sensory limitations can alter antibacterial activity. Next, monoglycerides, conjugates, and delivery systems may improve stability or availability, although their efficacy, safety, and regulatory status require formulation-specific evaluation. This review critically examines direct antibacterial activity, host- and microbiome-mediated effects, food-matrix applications, resistance-related considerations, and emerging formulation approaches. Current evidence supports the potential of selected FAs in defined applications, while emphasizing the need for standardized assays, appropriate food-matrix validation, and stronger animal and human evidence.},
}

@article {pmid42836349,
year = {2026},
author = {Zou, H and Yu, J and Li, H and Xu, J and An, M and Tian, L and Ma, Y},
title = {Microbial insights into the survival adaptation of the endemic orchid Corybas fanjingshanensis in a "sky island" habitat.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0371925},
doi = {10.1128/spectrum.03719-25},
pmid = {42836349},
issn = {2165-0497},
abstract = {Understanding the microbiological basis of species adaptation is crucial for effective conservation. This study investigates the endangered, narrow-endemic orchid Corybas fanjingshanensis and its symbiotic moss substrate in a "sky island" habitat, using high-throughput sequencing to analyze microbial communities and their potential roles in host survival. Results reveal significant divergence between endophytic and environmental microbiomes. Endophytic bacterial diversity was lower, but dominance was higher than in the moss substrate. We identified 65 core bacterial and 18 core fungal genera, predominantly enriched in nutrient acquisition and stress tolerance functions. Five key bacterial taxa, including Vicinamibacteraceae and Mucilaginibacter, were highlighted as potential conservation targets. The C. fanjingshanensis-moss symbiotic network exhibited strong positive interactions and high modularity, forming tight functional clusters likely enhancing environmental stress resistance. While bacterial functional genes remained stable across communities, fungal nutritional strategies were influenced by environmental heterogeneity. We propose conservation measures, including microbial transplantation to rebuild host-microbe symbioses, selective amplification of core taxa, and a holistic framework integrating habitat integrity with long-term microbial monitoring. This study offers insights into the survival strategies of narrow-endemic plants and advances microbiome-based orchid conservation, shifting the paradigm from habitat simulation to microbial network restoration.IMPORTANCEUsing Corybas fanjingshanensis, a critically endangered species with an extremely limited distribution, as the research subject, high-throughput sequencing technology was employed to investigate its survival adaptations from a microbial perspective within the unique "sky island" habitat. The findings provide a reference for microbiome-based conservation of endangered narrow-endemic species and offer insights into plant habitat reconstruction.},
}

@article {pmid42836409,
year = {2026},
author = {Yin, C and Zhang, M and Zhang, S and Ren, T and Ding, L and Wang, P and You, Q},
title = {Tanshinone IIA Ameliorates Sleep Deprivation-Induced Cognitive Impairment: Involvement of Gut Microbiota and the TLR4/NF-κB Signaling Pathway.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-30},
doi = {10.1142/S0192415X26500801},
pmid = {42836409},
issn = {1793-6853},
abstract = {Previous studies have indicated that Salvia miltiorrhiza Bunge (Danshen, DS) improves sleep deprivation (SD)-induced cognitive deficits, suggesting that tanshinone IIA (Tan IIA) may be a key pharmacodynamic substance. However, the mechanism behind this remains unclear. This study aims to evaluate the protective effects of Tan IIA on learning and memory abilities in SD model rats and to explore its potential mechanisms related to gut microbiota. The Morris water maze (MWM) test was used to assess cognitive function, while Hematoxylin and Eosin (H&E) staining, Nissl staining, immunofluorescence, and Alcian blue-periodic acid Schiff (AB-PAS) staining were employed to examine histopathology and barrier proteins. Enzyme-linked immunosorbent assay (ELISA), Western blot, and 16S rRNA microbiome sequencing were used to explore the mechanism of Tan IIA in the SD rat model. Tan IIA significantly protected cognitive function in SD model rats, rescued the BBB function (ZO-1 and Occludin), reduced hippocampal inflammation and neuronal death, and alleviated hippocampal microglial inflammatory activation and Aβ42 deposition. Additionally, Tan IIA treatment markedly reduced systemic inflammation (serum TNF-α, IL-1β, and IL-6), intestinal inflammation, and intestinal barrier disruption (MUC-2, ZO-1, and Occludin). 16S rRNA microbiome sequencing indicated that the therapeutic effects of Tan IIA were associated with gut microbiota regulation, reducing lipopolysaccharide (LPS) production and leakage, thereby modulating abnormal expression of the TLR4/NF-κB signaling pathways and the abnormal expression of downstream inflammatory cytokines (TNF-α, IL-1β, IL-6) and enzymes (iNOS and COX2). In conclusion, Tan IIA protects cognitive function in SD rats through anti-inflammatory mechanisms, in part by reshaping the gut microbiota and modulating the TLR4/NF-κB signaling pathway, providing a theoretical basis for the clinical application of Tan IIA in the prevention and treatment of SD-related cognitive impairment.},
}

@article {pmid42836419,
year = {2026},
author = {Chai, Y and Ma, G and Zhao, W and Song, J and Chen, Z and Luo, H and Xiao, X and Tang, X},
title = {Seminal Microbiota and Pregnancy Outcomes: Mechanistic Insights, Clinical Implications, and Future Directions.},
journal = {Andrology},
volume = {},
number = {},
pages = {},
doi = {10.1111/andr.70401},
pmid = {42836419},
issn = {2047-2927},
abstract = {BACKGROUND: Seminal fluid contains a low-biomass microbial community that may influence male reproductive health and pregnancy outcomes, but its biological and clinical significance remains uncertain.

OBJECTIVES: To critically synthesise evidence linking seminal microbiota with sperm quality, reproductive tract inflammation, natural conception, and assisted reproductive technology outcomes, and to evaluate proposed mechanisms and clinical implications.

MATERIALS AND METHODS: This review integrates human observational studies with relevant in vitro, animal, and female reproductive tract evidence, with particular attention to 16S rRNA gene sequencing, low-biomass contamination, and methodological heterogeneity.

RESULTS: Genus-enriched and compositionally distinct seminal profiles have been reported, but no reproducible community types have been established across populations. Lactobacillus-enriched profiles are associated with favourable semen parameters in some cohorts, whereas infection-associated or opportunistic taxa are more often linked to impaired semen characteristics. Proposed pathways include immune activation, oxidative stress, spermmicrobe interactions, and guttestis signalling.

DISCUSSION: Evidence remains predominantly observational and heterogeneous, with limited direct mechanistic validation and sparse longitudinal data.

CONCLUSION: Standardised, contamination-aware studies with independent validation are needed. Current evidence does not support routine seminal microbiome testing or microbiota-directed interventions in infertility care.},
}

@article {pmid42836554,
year = {2026},
author = {Bhetwal, A and Stenlund, E and Svärd, SG},
title = {Pathogenicity and virulence of Giardia intestinalis.},
journal = {Virulence},
volume = {},
number = {},
pages = {2745308},
doi = {10.1080/21505594.2026.2745308},
pmid = {42836554},
issn = {2150-5608},
abstract = {Giardiasis, caused by Giardia intestinalis, is a prevalent intestinal protozoan infection worldwide. Clinical manifestations are variable, and many infections remain asymptomatic. Disease pathogenesis is multifactorial, involving brush border enzyme deficiency, apoptosis, dysbiosis and increased intestinal permeability. Advances in genomics, genetic tools, and model systems have substantially improved our understanding of the parasite's virulence mechanisms. Giardia exhibits considerable genetic diversity, with distinct assemblages associated with differences in parasite biology. Attachment is mediated by the ventral disk, while the parasite's eight flagella contribute to motility and intestinal persistence. Antigenic variation of cysteine-rich surface proteins enables immune evasion and promotes chronic infection but the level of inflammation is low. The parasite releases a variety of proteins and extracellular vesicles containing proteins and small RNAs that play important roles in host-cell interactions and modulation of the gut microbiome. This review describes areas that need further research to connect pathogenesis to specific virulence mechanisms.},
}

@article {pmid42836610,
year = {2026},
author = {Ruth, N and Shakya, M and Lewis, CD and Erickson, CE and Dolinski, A and Jankowski, M and Fair, JM and Owen, JC and Bartlow, AW},
title = {Mallard super-shedders of avian influenza exhibit distinct cloacal microbial abundance profiles.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0208926},
doi = {10.1128/spectrum.02089-26},
pmid = {42836610},
issn = {2165-0497},
abstract = {In many infectious disease systems, a small fraction of hosts accounts for a disproportionate share of transmission, but the biological basis of this heterogeneity remains poorly resolved. In avian influenza, mallards show substantial variation in viral shedding, raising the possibility that only a subset of individuals contributes strongly to environmental contamination and onward spread. To examine whether host microbiome structure is associated with this variation, we experimentally infected wild, captive mallards with low-pathogenic avian influenza virus. We characterized cloacal microbiomes across control, low-shedding, and high-shedding birds using shotgun metagenomic sequencing combined with read-based taxonomic profiling and co-assembled metagenome-assembled genome (MAG) reconstruction. Although infected and uninfected birds were highly similar in species presence-absence, abundance-based analyses showed clear differences in shared taxa, particularly in high-shedding birds relative to controls. Differentially abundant taxa were dominated by taxa that belonged to groups that include host-associated opportunists, consistent with compositional imbalance rather than complete community restructuring. The phylum Pseudomonadota, especially the families Enterobacteriaceae and Moraxellaceae, is well represented. Together, these findings suggest that avian influenza infection is associated with shifts in the abundance of cloacal bacterial taxa rather than broad changes in species membership and that microbiome structure is associated with heterogeneity in shedding in a key wildlife reservoir.IMPORTANCEA small fraction of infected hosts often accounts for a disproportionate share of pathogen shedding, but the biological factors underlying this variation remain poorly understood. In experimentally infected mallards, a key wildlife reservoir for avian influenza A viruses, we found that high viral shedding was associated with shifts in the abundance of cloacal bacterial taxa rather than broad changes in microbial species membership. These results suggest that host-associated microbiome structure may be linked to shedding heterogeneity and could help explain why some individuals contribute more strongly to environmental contamination and onward transmission.},
}

@article {pmid42623301,
year = {2026},
author = {Pareek, S and Wright, RD and Ballarò, R and Xue, C and Bartelli, TF and Chandra, V and Li, L and Ortiz, J and Lam, T and Patel, H and Lee, J and Shrestha, P and Savage, H and Le Roux, O and Liu, H and Vallejo-Schmidt, T and De Maleki, R and Putluri, V and Putluri, N and Petrosino, JF and Burks, JK and Gomez, JA and Guarnerio, J and Katz, MHG and Ngo-Huang, A and Prakash, LR and Parker, NH and Petzel, MQB and Tan, L and Baydogan, S and McAllister, F and Schadler, KL},
title = {Exercise Modulates Microbial Metabolites and Induces Stromal Remodeling in Pancreatic Cancer.},
journal = {Cancer research},
volume = {},
number = {},
pages = {OF1-OF17},
pmid = {42623301},
issn = {1538-7445},
support = {P30 CA125123/CA/NCI NIH HHS/United States ; R01 CA282786/CA/NCI NIH HHS/United States ; R21 CA218732/CA/NCI NIH HHS/United States ; R37 CA237384/CA/NCI NIH HHS/United States ; },
abstract = {UNLABELLED: Exercise induces a variety of changes in the tumor microenvironment, with beneficial effects in several tumor types. However, a better understanding of the clinical effects of exercise and mediating mechanisms is needed to maximize the utility of exercise for patients. In this study, we analyzed tumors from patients with pancreatic ductal adenocarcinoma (PDAC) in the PancFit trial and identified an exercise-induced reduction in cells expressing α-smooth muscle actin (αSMA). Interrogation of changes in tumor stromal composition with exercise in a murine PDAC model revealed a microbially influenced reduction in αSMA+ cells and Il6-expressing inflammatory cancer-associated fibroblasts (iCAF). Cholic acid, a microbial bile acid, was increased in both patients and murine models with exercise, as a potential mediator of exercise-induced reduction in iCAFs. Consistent with these findings, patients that exercised more also exhibited fewer iCAFs and lower tumor IL6 expression, supporting a stromal remodeling effect of physical activity. In summary, this study demonstrates that the antitumor effect of exercise includes stromal remodeling, which is affected by microbial metabolites.

SIGNIFICANCE: Exercise-induced changes in cancer associated fibroblasts vary with microbiome composition, which may explain the heterogeneity in tumor responses to exercise and could guide future exercise trials in cancer patients.},
}

@article {pmid42828327,
year = {2026},
author = {Moody, ZK and Joseph, AT and Gill, R and Persaud, R and Gurreri, A and Manikkuttiyil, C and Ahmed, A and Golakoti, S and Villamil, S and Ghotra, R and Scripa, I},
title = {Exploring the Effect of Nutrition on Fetal Development in Pregnant Patients With Inflammatory Gut Diseases: A Scoping Review.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e115649},
pmid = {42828327},
issn = {2168-8184},
abstract = {Inflammatory gut diseases (IGDs) are increasing in prevalence and pose unique challenges during pregnancy. Poorly controlled IGDs in pregnant women are linked to adverse fetal outcomes such as low birth weight, preterm birth, and impaired gut microbiome development. Nutritional deficiencies, particularly in magnesium, folate, and vitamin B12, exacerbate these risks due to both inadequate intake and malabsorption. This scoping review aimed to evaluate the role of nutrition in fetal development among pregnant women with IGDs, highlighting dietary strategies that may enhance maternal gastrointestinal health and optimize fetal outcomes. This study was designed as a scoping review to examine the relationship between IGDs, pregnancy, and nutrition. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping review (PRISMA-ScR) guidelines, a search was conducted for peer-reviewed literature using the databases Embase, Web of Science, Ovid MEDLINE, and CINAHL. The search was restricted to studies published in English within the last ten years and that focused on pregnant or postpartum patients and fetuses in the context of nutrition and IGDs. The search strategy used predefined terms in multiple combinations with Boolean operators: "inflammatory bowel disease", "pregnancy", "fetus development", "nutritional deficiency", "diet restriction", and "vitamin supplementation". The search identified 1,589 records, of which 728 remained after duplicate removal. Following title and abstract screening, 103 full-text reports were sought for retrieval, 98 were assessed for eligibility, and five studies met the final inclusion criteria. The included studies suggest that multidisciplinary antenatal care, maintenance of disease remission, and attention to maternal nutritional status may support favorable maternal and neonatal outcomes. However, the available evidence is limited, consists primarily of observational studies, and no included study directly evaluated nutritional interventions and fetal outcomes. Research on fetal outcomes remains limited and warrants future investigations exploring long-term fetal outcomes, the impact of maternal nutritional deficiencies, and dietary interventions to improve treatment protocols. Advancements in this research can ultimately improve maternal and neonatal outcomes in IGD-affected pregnancies.},
}

@article {pmid42828346,
year = {2026},
author = {Zamfirescu, M and Chirila, SI and Gurgas, L and Gheorghe, E and Hangan, T},
title = {Ultraviolet Radiation and the Skin Microbiome: Dose-Dependent Effects and Consequences for Epidermal Barrier Integrity.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {630891},
pmid = {42828346},
issn = {1178-7015},
abstract = {The skin microbiome is continuously exposed to solar ultraviolet radiation (UVR), but the magnitude, direction and clinical meaning of the associated microbial changes remain uncertain. This narrative review critically evaluates evidence from controlled human, environmental, phototherapy, animal and in vitro studies linking UVA/UVB exposure to changes in skin microbial composition or function and to epidermal barrier outcomes. The available evidence indicates that UVA and UVB can alter community composition within minutes to days. However, these effects vary according to dose, wavelength, body site, host and sampling time, and may partly recover. The evidence does not support a universal pattern of decreased Cutibacterium acnes and increased Staphylococcus aureus. Dose is central to this relationship: repeated very-low or suberythemal exposure can induce antimicrobial peptides and adaptive responses, whereas single high exposures are more likely to cause inflammation, barrier injury and immunosuppression. Microbiome-dependent mechanisms include changes in tryptophan metabolites and AhR signaling, short-chain fatty acids, extracellular DNA and modulation of cytokine responses. Evidence from phototherapy studies shows that microbial remodeling can accompany clinical improvement, while sunscreen studies suggest that some formulations preserve microbial features without measurably disrupting dominant resident taxa. Because the available studies differ substantially in exposure, site, platform and endpoint, quantitative pooling is not currently defensible. Numerical results are therefore summarized in a structured evidence table Broad-spectrum photoprotection remains foundational. Microbiome-compatible formulations and microbial or metabolite adjuncts are promising but still require randomized, dose-resolved, multi-omic clinical validation.},
}

@article {pmid42828397,
year = {2026},
author = {Cai, P and Zhao, F and Zhao, Z and Zhang, X and Wu, C},
title = {Synthetic microbial communities for plant growth promotion and soil-borne disease suppression: design principles, mechanisms, and translational challenges.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1942488},
pmid = {42828397},
issn = {1664-302X},
abstract = {Declining soil health and soil-borne diseases threaten sustainable crop production, while single-strain inoculants often perform inconsistently in the field due to poor establishment, limited persistence, and narrow functional capacity within resident microbiomes. Synthetic microbial communities (SynComs), assembled from defined and functionally characterized microorganisms, offer a tractable strategy to improve plant growth and suppress disease through complementary and redundant functions. This review critically examines recent advances in plant-associated SynComs, emphasizing rational design over empirical strain mixing. We compare construction strategies based on core microbiome mining, trait-based screening, microbial interaction networks, host and niche adaptation, and multi-omics- or model-guided assembly. Available available evidence suggests that no single SynCom construction strategy is universally superior; rather, robust design requires an integrated, context-specific approach combining host- or core-microbiome-guided candidate selection, trait validation, interaction-informed assembly, and model-guided optimization. We synthesize direct and plant-mediated mechanisms, including nutrient mobilization, phytohormone modulation, stress alleviation, niche pre-emption, resource competition, antibiosis, rhizosphere restructuring, and immune priming. Evidence from representative crop-pathogen systems is evaluated based on mechanistic support, community stability, and validation under non-sterile greenhouse and field conditions. Major barriers to deployment include context-dependent efficacy, instability of community composition and function, formulation and delivery constraints, quality control, ecological safety, and regulatory uncertainty. We propose a design-to-deployment framework linking community assembly with ecological validation, formulation engineering, and multi-environment testing, providing a plant-centered roadmap for developing reliable SynCom-based biofertilizers as well as biocontrol products.},
}

@article {pmid42828409,
year = {2026},
author = {Song, Y and Xing, Y and Liu, Y and Zhang, X},
title = {Forensic applications of the skin microbiome: a structured narrative review of donor association, contact inference, and crime-scene reconstruction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1947173},
pmid = {42828409},
issn = {1664-302X},
abstract = {BACKGROUND: Skin-associated microbial communities are individualized, anatomically structured, temporally dynamic, and readily transferred to contacted surfaces. These properties have generated interest in the skin microbiome as complementary forensic evidence when conventional human DNA or fingerprint evidence is limited.

METHODS: We conducted a structured narrative review guided by the Scale for the Assessment of Narrative Review Articles (SANRA). PubMed/MEDLINE was searched from database inception through 2 August 2026, and reference lists of eligible studies and recent reviews were examined. Peer-reviewed studies were evaluated for relevance to skin microbial individuality, temporal stability, touch transfer, donor or source inference, postmortem interval estimation, analytical standardization, and legal or ethical interpretation. Evidence was synthesized according to study realism, analytical resolution, validation design, and proximity to forensic casework.

RESULTS: The biological basis for forensic use is supported by reproducible inter-individual and body-site variation, including persistent strain- and gene-level features. Controlled studies show that skin-associated communities can be recovered from touched objects and clothing and can support donor differentiation, particularly when targeted markers, microbial single-nucleotide polymorphisms, or metagenomic features are used. Nevertheless, performance estimates are strongly affected by cohort size, body site, substrate, time since deposition, environmental background, contamination, and machine-learning design. Evidence for body-site and biological-trace source inference is promising, whereas postmortem interval estimation, chronological contact reconstruction, and spatial trajectory inference remain exploratory.

CONCLUSION: Skin microbiome profiling should currently be regarded as a source of investigative intelligence and potentially complementary evidence rather than a replacement for human DNA profiling. Translation into practice requires harmonized protocols, realistic multicenter validation, open and representative reference datasets, explicit error-rate reporting, likelihood-based interpretation, and proportionate ethical and legal safeguards.},
}

@article {pmid42828627,
year = {2026},
author = {Alabi, A and Ngwese, MM and Essone, PN and Mbouna, AV and Kabwende, AL and Lotola-Mougeni, F and Mahmoudou, S and Kokou, K and Esen, M and Lell, B and Adegnika, AA and Ramharter, M and Grobusch, MP and Ley, RE and Kremsner, PG and Agnandji, ST},
title = {Gut resilience and clinical homeostasis following administration of neomycin and albendazole in soil-transmitted helminth-infected adults living in Lambaréné, Gabon.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42828627},
issn = {1439-0973},
abstract = {PURPOSE: Gut resilience and systemic homeostasis are interrelated dynamic functions. A gut that fails to regulate intestinal barrier integrity, metabolite production, and immune regulation will lead to systemic pathogenic invasion and susceptibility to infections. Gut resilience withstands stressors that can induce gut failure, and even when disturbances occur, it quickly restores its composition and functions. There is a paucity of data on the microbiome of people living in low- and middle-income settings. We therefore assessed the local and systemic conditions of gut resilience following neomycin treatment in individuals with intestinal soil-transmitted helminth infections.

METHODS: A randomised, placebo-controlled, participant-blinded study was conducted in adults up to 40 years with known soil-transmitted helminth infections (STH) living in Lambaréné, Gabon. Participants were randomly assigned to the intervention or placebo groups. The intervention group received neomycin 2000 mg per os (p.o) three times daily for 10 days and fluconazole 150 mg p.o once weekly for two weeks. On day 90, all study participants were treated with 400 mg of albendazole for three days. Outcome measures included egg counts of Ascaris lumbricoides, Necator americanus and Trichuris trichiura, a dual marker of gut barrier permeability and metabolite production (FABP2), incidence of adverse events, and assessment of pathogen proliferation.

RESULTS: Thirty-eight participants were enrolled and followed up for 180 days. At the gut level, the intestinal STH egg counts decreased on day 7 after neomycin administration. From day 14 onward, intestinal STH egg counts began to increase, reaching the initial counts by day 90. There was no difference in FABP2 marker concentration between the two groups. Adverse events occurred more frequently in the intervention group, most commonly side effects of neomycin and fluconazole. There was no pathogen proliferation.

CONCLUSION: Broad-spectrum antibiotic-induced changes in laying of STH helminth eggs in STH-infected adults, which occurred at the peak of the drug concentration observed in the blood, corresponding to a high availability in the gut. These changes support that the antibiotic-induced changes were transient and did not induce occurrence of clinical peripheral changes. The local resilience of the gut translated into peripheral-maintained homeostasis.

TRIAL REGISTRATION: The study was registered at the Pan African Clinical Trial Registry (https//pactr.samrc.ac.za/) database with identification numberPACTR201707002361207.},
}

@article {pmid42828629,
year = {2026},
author = {Alkhanafsa, M and Wafi, J and Deek, S},
title = {Oral tebipenem pivoxil for complicated urinary tract infections: evidence, potential role in IV-to-oral transition, and antimicrobial stewardship.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42828629},
issn = {1439-0973},
abstract = {Complicated urinary tract infections (cUTIs), including pyelonephritis, are increasingly challenging when resistant Enterobacterales eliminate conventional oral treatment options. Tebipenem pivoxil (UTEBZI), approved by the US Food and Drug Administration in June 2026, is the first oral carbapenem approved in the United States for selected adults with cUTI. This review evaluates its pharmacology, microbiological activity, efficacy, safety, and potential role in intravenous (IV)-to-oral treatment and antimicrobial stewardship METHODS: A structured narrative review of PubMed/MEDLINE, regulatory documents, clinical-trial reports, guidelines, pharmacokinetic/pharmacodynamic studies, microbiological studies, and relevant oral step-down literature was conducted through 12 August 2026. Priority was given to randomized phase 3 trials, FDA prescribing information, and IDSA guidance RESULTS: ADAPT-PO and PIVOT-PO demonstrated noninferiority of complete oral tebipenem regimens to IV ertapenem and IV imipenem-cilastatin, respectively, with high clinical cure rates. Tebipenem retains activity against many ESBL- and AmpC-producing Enterobacterales but lacks reliable activity against major carbapenemases. Neither phase 3 trial randomized clinically improving patients after initial IV therapy; therefore, direct randomized evidence for a formal tebipenem step-down strategy is lacking. Important uncertainties include limited bacteremia data, every-six-hour adherence, optimal post-IV duration, cost-effectiveness, microbiome effects, and resistance selection CONCLUSION: Tebipenem is an important culture-directed oral option for selected adults with cUTI when narrower effective oral agents are unavailable. Its most defensible early role is replacement of otherwise necessary continued IV carbapenem therapy in carefully selected patients, with source control, susceptibility confirmation, renal doseadjustment, safety screening, duration planning, and stewardship oversight. Dedicated switch, bacteremia, implementation, and resistance-surveillance studies remain needed.},
}

@article {pmid42828642,
year = {2026},
author = {Balabat, MTJ and Loquero, EJ and Amer, NB and Coñado, JC and Cabolbol, HJB and Romarate, RA and Mabuhay-Omar, J and Watanabe, K and Chien, MF and Bacosa, HP},
title = {Urban Road Dust as a Microbial Hotspot: Spatial Variation of Bacterial Communities and Metal Associations in the Philippines.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42828642},
issn = {1573-0972},
mesh = {*Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Philippines ; *Dust/analysis ; Cities ; *Metals/analysis ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics ; Environmental Monitoring ; Phylogeny ; Soil Microbiology ; },
abstract = {Urban road dust is a reservoir and transport medium for diverse microorganisms, yet its bacterial communities in tropical environments remain poorly understood. This study examined the spatial variation of road dust bacterial communities across three Philippine metropolitan areas: Metro Manila, Metro Cebu, and Metro Cagayan de Oro, spanning the country's three principal island groups. Dust from nine sites was analyzed using 16 S rRNA gene metabarcoding (V3-V4), with community composition, diversity, predicted functional potential (PICRUSt2), and metal associations evaluated; contamination was assessed using pollution indices (PLI, degree of contamination, and ecological risk). Proteobacteria and Actinobacteria dominated all sites, and a small core of genera: Paracoccus, Acinetobacter, Kocuria, and Deinococcus, was consistently detected. Alpha diversity did not differ among cities (Kruskal-Wallis, p > 0.05), whereas community composition did (PERMANOVA: R[2] = 0.466, p = 0.004), with distinct metropolitan clustering. This decoupling indicates that local conditions shape which taxa dominate rather than overall diversity, consistent with environmental filtering of a shared regional pool. Alkanindiges reached its highest relative abundance at Metro Cebu's commercial core. In Metro Cagayan de Oro, Paracoccus increased toward the most trace-metal-laden site (D3) and correlated positively with cobalt and nickel; with elevated predicted denitrification in this area, this points to a possible pollution-responsive signal. Metro Cagayan de Oro also showed a pronounced higher relative abundance of Chloroflexi, marking it as a distinctive, transitional urban environment. Pollution indices indicated baseline-to-moderate contamination across the sampled roadsides. Predicted function paralleled taxonomy (R[2] = 0.467). These findings establish a baseline for tropical road-dust microbiota and support integrating microbial assessment into urban environmental monitoring.},
}

*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Philippines
*Dust/analysis
Cities
*Metals/analysis
*Microbiota
Biodiversity
DNA, Bacterial/genetics
Environmental Monitoring
Phylogeny
Soil Microbiology

@article {pmid42828644,
year = {2026},
author = {Kaur, M and Mishra, AK},
title = {Next-generation probiotics and microbiome-based therapeutics highlighting Akkermansia muciniphila and Amuc_1100.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42828644},
issn = {1573-0972},
mesh = {*Probiotics/therapeutic use/pharmacology ; Humans ; *Gastrointestinal Microbiome ; Animals ; Akkermansia ; Verrucomicrobia ; *Bacterial Proteins ; Intestinal Mucosa/microbiology ; },
abstract = {The gut microbiota is pivotal in regulating host metabolism, immune signaling, and the integrity of the mucosal barrier, thus serving as a critical factor in various metabolic, inflammatory, and gastrointestinal disorders. Traditional probiotics, primarily comprising Lacticaseibacillus and Bifidobacterium species, have been utilized to enhance gut health; however, the strain-dependent effects and variable clinical outcomes associated with these probiotics have prompted increased interest in next-generation probiotics (NGPs). Akkermansia muciniphila, a commensal organism that degrades mucin and resides at the mucosal interface, has emerged as a prominent NGP owing to its ability to reinforce epithelial integrity, modulate immune responses, and foster metabolic homeostasis. Of particular significance is its surface protein, Amuc_1100, which acts as a parabiotic molecule. This protein engages host pattern-recognition pathways, bolsters tight-junction proteins, and alleviates low-grade inflammation. In contrast to live bacterial formulations, purified Amuc_1100 presents advantages concerning stability, safety, and regulatory compliance. This review aims to synthesize contemporary insights into gut microbiome functionality while comparing traditional probiotics with next-generation alternatives. Additionally, it delineates the therapeutic potential of A. muciniphila and Amuc_1100. The discussion further encompasses clinical advancements, regulatory frameworks, and formulation considerations that are propelling the shift towards mechanism-based microbiome therapeutics.},
}

*Probiotics/therapeutic use/pharmacology
Humans
*Gastrointestinal Microbiome
Animals
Akkermansia
Verrucomicrobia
*Bacterial Proteins
Intestinal Mucosa/microbiology

@article {pmid42828686,
year = {2026},
author = {Kazarina, A and Vaškevica, A and Senkāne, DE and Zayakin, P and Hušča, S and Vīksne, K and Pirsko, V and Sokolovska, L and Sergejeva, N and Nakurte, I and Pastare, L and Ruhl, S},
title = {Salivary microbiome responses to chlorhexidine and Coriandrum sativum essential oil mouthwashes in patients with periodontitis in a randomized 2-week clinical trial.},
journal = {Clinical oral investigations},
volume = {30},
number = {10},
pages = {},
pmid = {42828686},
issn = {1436-3771},
mesh = {Humans ; *Mouthwashes/pharmacology ; *Saliva/microbiology ; *Chlorhexidine/pharmacology ; *Microbiota/drug effects ; *Oils, Volatile/pharmacology ; Female ; Male ; *Periodontitis/drug therapy/microbiology ; *Coriandrum/chemistry ; Adult ; Middle Aged ; Porphyromonas gingivalis/drug effects ; },
abstract = {OBJECTIVES: To compare the short-term salivary microbiome effects of a Coriandrum sativum essential oil (CSEO) mouthwash, chlorhexidine (CHX) as a benchmark comparator, and water in patients with periodontitis.

MATERIALS AND METHODS: In this randomized three-arm trial, participants with periodontitis rinsed twice daily for 14 days with water, CSEO, or 0.12% CHX. Preclinical anti-Porphyromonas gingivalis and fibroblast cytotoxicity assays informed CSEO concentration selection. Shotgun metagenomic sequencing was performed on 54 saliva libraries, two per participant, from 27 participants sampled at baseline and week 2 (H2O n = 9, CSEO n = 8, CHX n = 10). Alpha diversity, within-subject Bray-Curtis change, and differential abundance were analysed longitudinally.

RESULTS: Both active agents inhibited P. gingivalis in vitro, with CHX showing greater potency. In the clinical trial, no statistically detectable difference between CSEO and water was observed for the primary species-level Bray-Curtis outcome (q = 0.413), alpha diversity (all q ≥ 0.259), or differential abundance. CHX showed greater species-level Bray-Curtis change than water (q = 0.020), lower species-level Simpson diversity (q = 0.014), and broad taxonomic restructuring.

CONCLUSIONS: Under the tested formulation and exposure conditions, CSEO did not produce a statistically detectable group-level salivary microbiome shift relative to water. CHX provided a benchmark for broad ecological perturbation. The CSEO null finding does not exclude modest or heterogeneous effects in a larger cohort.

CLINICAL RELEVANCE: No clinical benefit can be inferred from the absence of a detectable CSEO-associated microbiome shift. Larger studies integrating clinical, inflammatory, and direct functional outcomes are needed.

TRIAL REGISTRATION: ISRCTN79156900, retrospectively registered on 11 May 2026.},
}

Humans
*Mouthwashes/pharmacology
*Saliva/microbiology
*Chlorhexidine/pharmacology
*Microbiota/drug effects
*Oils, Volatile/pharmacology
Female
Male
*Periodontitis/drug therapy/microbiology
*Coriandrum/chemistry
Adult
Middle Aged
Porphyromonas gingivalis/drug effects

@article {pmid42828720,
year = {2026},
author = {Naveed, M and Yang, T and Togliatti, O and Joe, B and Hill, JW},
title = {Gut dysbiosis, blood pressure regulation, and cardiometabolic risk in polyendocrine metabolic ovarian syndrome (PMOS).},
journal = {Reviews in endocrine & metabolic disorders},
volume = {},
number = {},
pages = {},
pmid = {42828720},
issn = {1573-2606},
abstract = {Polyendocrine metabolic ovarian syndrome (PMOS), formerly known as polycystic ovary syndrome (PCOS), is a common endocrine-metabolic disorder associated with increased hypertension and cardiometabolic risk. Gut dysbiosis is also frequently reported in affected women, raising the question of whether microbiome-linked pathways contribute to blood pressure elevation or vascular risk in this syndrome. To evaluate and synthesize the available evidence linking gut dysbiosis, gut microbial function, and microbiome-related mechanisms to hypertension, blood pressure regulation, and cardiovascular risk in women with PMOS, we conducted a narrative review of the literature in PubMed, Scopus, Web of Science, Google Scholar, and citation tracking. Search terms included PCOS, PMOS, gut microbiota, gut dysbiosis, hypertension, blood pressure, cardiovascular risk, microbial metabolites, bile acids, intestinal permeability, inflammation, renin-angiotensin signaling, renal sodium handling, and autonomic regulation. Human studies, animal models, interventional studies, and mechanistic investigations relevant to PMOS and hypertension were reviewed according to predefined inclusion and exclusion criteria. Eligible publications were preclinical studies, human studies, English language, adult females, and peer-reviewed original or review articles. Clarifying whether gut dysbiosis contributes to hypertension in PMOS may improve understanding of the mechanisms underlying cardiometabolic risk in affected women and inform the development of microbiome-targeted diagnostic and therapeutic strategies. Achieving this goal will require well-phenotyped clinical studies integrating PMOS, blood pressure and vascular assessments with functional microbiome analyses.},
}

@article {pmid42828814,
year = {2026},
author = {Shah, AM and Li, Z and Chen, L and Zhao, Y and Jiang, J and Ma, Y and Wang, W},
title = {Dietary date (Phoenix dactylifera) modulates antioxidant defenses, immune function, and cecal microbiota to improve performance in Muscovy ducks.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107852},
doi = {10.1016/j.psj.2026.107852},
pmid = {42828814},
issn = {1525-3171},
abstract = {Phytogenic feed additives from agro-industrial byproducts are increasingly explored as antibiotic alternatives in poultry, yet their efficacy in Muscovy ducks remains poorly documented. This study investigated the effects of dietary date (Phoenix dactylifera) fruit supplementation at 0% (control), 5% (D1), and 10% (D2) on growth performance, blood biochemistry, antioxidant status, immune function, meat quality, intestinal morphology, and cecal microbiota in Muscovy ducks over a 42-day feeding trial. Date fruit supplementation dose-dependently improved final body weight, average daily gain, and feed conversion ratio (p < 0.05) without affecting feed intake. Serum antioxidant capacity was markedly enhanced, with elevated T-SOD, GSH-Px, and T-AOC alongside reduced MDA in both treated groups (p < 0.05). Immunologically, date significantly increased IgA and IgG while decreasing TNF-α and IL-6 (p < 0.05). Intestinal histomorphometry revealed improved ileal villus height, width, and crypt depth (p < 0.05). Cecal microbiome analysis showed increased alpha diversity, phylum-level shifts favoring Bacillota and Actinomycetota, and genus-level enrichments correlated with enhanced performance and immunity. Meat quality remained largely unaffected, with only reduced leg muscle redness. Correlation analyses linked specific beneficial genera to improved antioxidant and immune indices. Collectively, these findings provide the first systematic evidence that 10% whole date fruit inclusion is a safe, effective functional additive for Muscovy ducks, enhancing productivity through antioxidant, immunomodulatory, and microbiome-modulating mechanisms and offering a sustainable nutritional strategy to reduce reliance on synthetic additives in duck production systems.},
}

@article {pmid42829048,
year = {2026},
author = {Hashem, MA and Kayesh, MEH and Kohara, M and Tsukiyama-Kohara, K},
title = {Combining antiviral therapy with cancer treatment in HBV-associated HCC: A translational approach.},
journal = {Virus research},
volume = {373},
number = {},
pages = {199812},
doi = {10.1016/j.virusres.2026.199812},
pmid = {42829048},
issn = {1872-7492},
abstract = {Hepatitis B virus (HBV) infection remains a major global health concern and is a leading cause of hepatocellular carcinoma (HCC). Despite advances in antiviral therapy and cancer treatment, HBV-related HCC (HBV-HCC) continues to pose significant challenges due to its complex pathogenesis involving chronic inflammation, viral persistence, and liver fibrosis. Current antiviral therapies reduce viral load and liver inflammation but often fail to eliminate integrated viral DNA or prevent carcinogenesis. On the other hand, cancer therapies such as surgery, ablation, immunotherapy, and targeted therapy have limited success when used in isolation, especially in patients with active HBV replication. This review examines the emerging concept of combining antiviral and anticancer strategies to improve clinical outcomes in HBV-HCC. We discuss the molecular mechanisms linking HBV infection to HCC, the role of antiviral therapy in reducing recurrence post-HCC treatment, and the impact of HBV reactivation during cancer therapy. In addition, we explore emerging biomarkers for early detection and prognosis, the therapeutic implications of HBV DNA integration, and the potential of gene-editing technologies targeting viral reservoirs. We further review the influence of HBV-induced immune dysregulation on immunotherapy outcomes, the relevance of host-microbiome interactions in liver carcinogenesis, and the utility of precision medicine approaches in guiding treatment. We highlight recent translational studies, clinical trials, and future directions that support a dual-modality approach, aiming for long-term remission and improved survival in patients with HBV-HCC.},
}

@article {pmid42829191,
year = {2026},
author = {Schaefer, HR and Frankenfeld, CL and Wikoff, D},
title = {Low- and No-Calorie Sweeteners Lack Shared Target Organs or Modes of Action Required for Cumulative Risk Assessment.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {116424},
doi = {10.1016/j.fct.2026.116424},
pmid = {42829191},
issn = {1873-6351},
abstract = {BACKGROUND AND OBJECTIVE: The safety of individual low- and no-calorie sweeteners (LNCS) has been well established over decades, yet interest has grown in potential combined effects from concurrent exposure. This study evaluated (a) whether existing cumulative risk assessment (CRA) frameworks are appropriate for LNCS and (b) their applicability to aspartame, saccharin, sucralose, acesulfame-K, steviol glycosides, and cyclamate.

METHODS: Regulatory CRA guidance and safety evaluations for each LNCS were reviewed. Toxicological data from repeat-dose and reproductive/developmental studies were synthesized by organ system and effect thresholds. A structured review of human microbiome studies was also conducted. Evidence was assessed for shared structure, target organ toxicity, and mode of action relevant to CRA frameworks.

RESULTS: Existing frameworks rely on grouping chemicals with shared structure or mode of action; however, LNCS lack common structural features, toxicological profiles, and target organ effects. Kidney findings observed at high doses were inconsistent, species-specific, and considered toxicologically insignificant. Microbiome effects were variable, sweetener-specific, and not indicative of cumulative impact.

CONCLUSIONS: LNCS do not exhibit properties necessary for cumulative assessment under established CRA methods. Evidence supports no cumulative effects at typical intake levels, reinforcing the adequacy of individual acceptable daily intakes (ADIs) for safety evaluation.},
}

@article {pmid42829202,
year = {2026},
author = {Zhang, J and Jiang, X and Lin, Z and Li, H and Jiang, S},
title = {Clinical Landscape of Microbiome Modulators in Gynecological Tumor Treatment: From Pre-Clinical to Clinical Trials.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {101043},
doi = {10.1016/j.bj.2026.101043},
pmid = {42829202},
issn = {2320-2890},
abstract = {Intestinal microbiota dysbiosis is linked to gynecological tumors (endometrial, ovarian, cervical cancers), and microbiome modulators show therapeutic potential by regulating gut microbiota. This Perspective analyzes the field from pre-clinical to clinical stages. Pre-clinically, a Web of Science bibliometric analysis (2010-2025, 114 articles, 86 reviews) revealed focus on "epithelial ovarian cancer," "estrogen," and "mechanism," with key studies by Baker et al. (2017, gut microbiota-estrogen-endometrial cancer link) and Kopustinskiene et al. (2020, flavonoids' anti-tumor effect via gut flora). Clinically, 4 INFORMA-database trials (2 closed, 1 completed, 1 planning) targeted ovarian/endometrial cancer (no cervical cancer trials), using live microorganisms/faecal modulators mainly for immuno-oncology therapy; bacteriophages (e.g., M13) also emerged as potential modulators. Challenges include unclear optimal combination therapies, lack of cervical cancer trials, and limited modulator types. This analysis offers a field overview and future research directions. The intestinal microbiota constitutes a complex ecological community that influences the normal physiological and pathological processes of distal organs through its metabolic activities. Previous research has demonstrated that dysbiosis of the intestinal microbiota can contribute to the development of endometrial cancer, ovarian cancer, and cervical cancer [1-3]. Microbiome modulators enhance host health by regulating the intestinal microbiota and hold potential as therapeutic agents for gynecological tumors [4]. Consequently, it is imperative to analyze the landscape of clinical trials investigating the efficacy of microbiome modulators in the treatment of gynecological tumors.},
}

@article {pmid42829336,
year = {2026},
author = {Merecz, K and Jarząbek, J and Fichna, J},
title = {Recent developments in the role of oxidative stress in pathogenesis and treatment of inflammatory bowel diseases.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2026.2744666},
pmid = {42829336},
issn = {1747-4132},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a chronic and relapsing disorder of the gastrointestinal tract. Its prevalence has risen rapidly, and nowadays it is a global health concern. Currently available medications reduce inflammation and alleviate the symptoms, but do not cure the disease. Recent findings suggest that dysregulated redox homeostasis may contribute to IBD progression, positioning oxidative stress as one of the primary mechanisms driving inflammation.

AREAS COVERED: Data for this review were identified through a comprehensive search of PubMed and Google Scholar for the period from February 2013 to September 2026. This review aims to describe recent approaches focused on oxidative stress and IBD, including the use of oxidative stress biomarkers, treatment options employing neutrophils and nanoparticles, the emerging role of the Nrf2 signaling pathway, ferroptosis suppression, and oxidative stress-related changes in the microbiome. Furthermore, inflammaging and dietary interventions are discussed in the context of oxidative stress, as they modulate redox homeostasis and influence inflammatory pathways.

EXPERT OPINION: A better understanding of the interplay between ROS, inflammation, microbiome, and dietary interventions may provide valuable insights into mechanisms underlying IBD pathology, while targeting these pathways may facilitate the development of novel, adjunctive therapeutic approaches in IBD management.},
}

@article {pmid42829422,
year = {2026},
author = {Xie, SS and Hu, J and Zhou, W and Ge, XL and Luo, YY and Liu, ZG},
title = {Microbiome signatures and mechanistic pathways in pediatric obesity: from early-life risk to precision interventions.},
journal = {World journal of pediatrics : WJP},
volume = {},
number = {},
pages = {},
pmid = {42829422},
issn = {1867-0687},
support = {82470544//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The gut microbiota is increasingly recognized as a modulator of metabolic health in children, influencing nutrient absorption, immune tone, epithelial barrier function, and energy homeostasis. This review summarizes current evidence on microbial signatures and mechanistic pathways associated with pediatric obesity and evaluates microbiota-targeted strategies for prevention and intervention.

DATA SOURCES: Relevant studies published between January 2000 and February 2026 were identified through searches of PubMed, Embase, and Web of Science using keywords related to pediatric obesity, gut microbiota, microbial metabolites, and microbiota-based interventions. Human studies and mechanistic animal models examining host-microbe metabolic interactions were included.

RESULTS: Pediatric obesity is associated with shifts in gut microbial composition, although taxonomic findings are heterogeneous across studies and should not be interpreted as universal biomarkers. Relatively consistent patterns include reduced Bifidobacterium and Akkermansia muciniphila, whereas associations involving Faecalibacterium, Blautia, and lactobacilli are context-, species-, and strain-dependent. Functional alterations include changes in short-chain fatty acid production, bile acid signaling, microbial branched-chain and aromatic amino acid metabolism, and endotoxin-related inflammatory pathways. The enrichment of Gram-negative taxa such as Enterobacteriaceae may contribute to impaired epithelial barrier integrity, lipopolysaccharide translocation, toll-like receptor 4 signaling, chronic low-grade inflammation, and insulin resistance. Early-life exposures, including cesarean delivery, formula feeding, and antibiotic use, are repeatedly associated with altered microbial succession and later obesity risk, although causality remains incompletely defined. Interventional studies indicate that dietary fiber enrichment and selected probiotic strains can improve microbial and metabolic outcomes in some settings, but efficacy remains strain-specific and clinically heterogeneous.

CONCLUSIONS: Microbial and metabolic signatures are associated with pediatric obesity, converging on pathways of energy harvest, epithelial barrier dysfunction, inflammation, and disrupted host-microbe signaling. Integrative multi-omic and longitudinal studies are required to establish causality and guide the development of personalized, microbiota-based interventions for obesity prevention and treatment in children.},
}

@article {pmid42829460,
year = {2026},
author = {Salman, A and Salman, MA and Abdallah, A and Elewa, A and Marwan, A},
title = {Microbiology and antimicrobial resistance in biliary tract infections including acute and post-ERCP cholangitis: a systematic review and meta-analysis.},
journal = {Annals of Saudi medicine},
volume = {46},
number = {5},
pages = {388-403},
pmid = {42829460},
issn = {0975-4466},
mesh = {Humans ; *Cholangitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Bile/microbiology ; *Cholangiopancreatography, Endoscopic Retrograde/adverse effects ; *Biliary Tract Diseases/microbiology ; Acute Disease ; },
abstract = {BACKGROUND: Organisms cultured from bile in biliary tract infection, and their resistance, vary widely between settings, and pooled estimates to guide empirical therapy are lacking.

OBJECTIVE: Estimate bile-culture yield, organism distribution, and resistance.

DESIGN: Systematic review and random-effects meta-analysis of PubMed and reference lists.

SETTING: Reports spanned nine countries across Asia, Europe, Africa, and North America.

METHODS: We extracted ductal-bile culture data from observational studies published from 2015 to 2025 of biliary infection/cholangitis; noninfectious, gall bladder-only, microbiome-only, and nonextractable reports were excluded. DerSimonian-Laird models, subgroup analysis, and JBI appraisal were used.

MAIN OUTCOME MEASURE: Culture yield; secondary organism proportions and resistance.

SAMPLE SIZE: 5147 patients (97% retrospective; 3% prospective); organisms: 35 267 observations.

RESULTS: Yield was 77.3% (95% CI, 67.8-84.6); Gram-negative organisms 69.8% (65.6-73.7), E. coli, 27.4% (23.5-31.7), K. pneumoniae, 14.1% (12.3-16.2).

HETEROGENEITY: I[2]=86.0%-97.7%; all P<.001.

RISK OF BIAS: Fourteen reports were low risk, two moderate; exclusions minimally changed estimates.

CONCLUSION: Bile-culture yield was high and Gram-negative organisms, particularly E. coli and K. pneumoniae, predominated, but estimates were highly heterogeneous and resistance could not be pooled; culture-directed therapy guided by local antibiograms is therefore preferable to a universal empirical regimen.

LIMITATIONS: PubMed-only/open-access search, retrospective designs, inconsistent definitions, one dominant dataset.

REGISTRATION: Retrospectively registered on OSF (89wqs; DOI: 10.17605/OSF.IO/89WQS).},
}

Humans
*Cholangitis/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial
Bile/microbiology
*Cholangiopancreatography, Endoscopic Retrograde/adverse effects
*Biliary Tract Diseases/microbiology
Acute Disease

@article {pmid42829701,
year = {2026},
author = {Métris, KL and Métris, J},
title = {Fungus above us: exploring the atmospheric mycobiome by aircraft.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21746},
pmid = {42829701},
issn = {2167-8359},
mesh = {*Fungi/classification/isolation & purification/genetics ; *Air Microbiology ; *Aircraft ; *Mycobiome ; *Atmosphere ; Seasons ; Biodiversity ; Ecosystem ; Environmental Monitoring/methods ; },
abstract = {Fungi play a key role in ecosystems, influencing the global bioaerosol budget and pollution dynamics even when metabolically inactive. Despite this, diversity and transport of fungi in the atmosphere are not well explored. This study shows that the atmosphere contains diverse fungi with varied ecological classifications and recruitment patterns reflecting underlying terrestrial habitats. Abundant genera include Neoascochyta, Cladosporium, Alternaria, Coniothyrium, Penicillium, Hymenochaetopsis, Lachnum, and Fonsecazyma. The atmospheric mycobiome is dominated by decomposers and pathogens; over 40% of the sampled airborne fungi are putative plant or animal pathogens. Using aircraft surveys from 2022 to 2023 in distinct seasons alongside comprehensive environmental datasets, airborne fungal diversity was found to decline with altitude and increasing vegetation productivity. Patterns of diversity in atmospheric fungal communities are shaped by vegetation productivity and meteorology. Remote sensing and meteorological data provide valuable insight into this diversity and reinforce the role of local or regional phenology as an important determinant of atmospheric biodiversity. Additionally, the proportional composition of functional guilds in the atmosphere shifts with vegetation productivity and surface winds, suggesting that seasonal transport dynamics may contribute to shaping assembly of the atmospheric mycobiome. This work demonstrates how integrated genomic and environmental datasets acquired by aircraft and satellite data could be leveraged in future to clarify aerobiology questions and contribute to a unified view of fungal ecology.},
}

*Fungi/classification/isolation & purification/genetics
*Air Microbiology
*Aircraft
*Mycobiome
*Atmosphere
Seasons
Biodiversity
Ecosystem
Environmental Monitoring/methods

@article {pmid42830139,
year = {2026},
author = {Hayashi-Okamura, Y and Shintani, T and Obayashi, N and Morihara, N and Oki, Y and Yoshimoto, T and Ando, T and Suzuki, M and Kataoka, N and Yasuda, G and Kobayashi, Y and Miyata, R and Kajiya, M},
title = {Age-related shifts in the salivary microbiome linked to cariogenic changes: A cross-sectional study.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {107091},
doi = {10.1016/j.jdent.2026.107091},
pmid = {42830139},
issn = {1879-176X},
abstract = {INTRODUCTION: Although the prevalence of dental caries in older individuals is increasing, there are limited reports on the dental health of this population. In this cross-sectional study, we compared caries risk assessed using saliva and microbiome components between older and younger individuals.

METHODS: Between February 2022 and September 2025, 229 younger people (12-35 years) and 111 older people (≥50 years) underwent caries risk testing and oral bacterial count measurement using stimulated saliva at the Oral Examination Center of Hiroshima University Hospital. Caries risk was assessed using salivary secretion volume, salivary pH, buffering capacity, and cultures of Mutans streptococci (MS), Lactobacillus, and Candida species. The DMFT index and plaque control record were obtained from medical records. Bacterial DNA was extracted from a randomly selected subset of 30 younger-group samples and 58 older-group samples. The diversity and composition of the microbiome were analyzed by 16S rRNA sequencing. Data were compared between the two groups using univariate and multivariate analyses.

RESULTS: MS levels and salivary buffering capacity were significantly higher in the older group compared to the younger group (p < 0.05). Microbial diversity was lower in the older group. Prevotellaceae and Actinomycetota were among the most prevalent bacteria in the older group. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed elevated expression of genes involved in anaerobic metabolism and glucose metabolism in the older group compared to the younger group.

CONCLUSION: These findings suggest that age-related ecological shifts in the oral microbiome may increase the risk of dental caries.},
}

@article {pmid42830277,
year = {2026},
author = {Feng, T and Shang, J and Ma, Y and Li, J and Qin, Y and Zhang, J and Cheng, S and Zhang, G and Xie, H},
title = {Metagenomic analysis of rhizosphere soil microbiota in wild and cultivated Notopterygium incisum, an umbelliferae medicinal herb.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42830277},
issn = {1471-2180},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Metagenomics/methods ; *Apiaceae/microbiology/growth & development ; *Plants, Medicinal/microbiology/growth & development ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Notopterygium incisum is not only a traditional Chinese medicine but also an endemic herb. Artificial domestication and large-scale cultivation are crucial for resolving the crisis of wild resources and the supply-demand imbalance of N. incisum, yet current techniques have failed to stably provide the herb medicine in good quality. Metagenomic analyses revealed significant differences in the rhizomicrobiota between wild and cultivated N. incisum, particularly in microbial composition, gene functions, and community assembly. The rhizomicrobiota of the wild N. incisum from 3 different sites with an altitude drop over 1400 m had a similar composition when being compared with the cultivated samples. The wild N. incisum had higher abundances of beneficial microbes, particularly Hyphomicrobiales (Rhizobiales) (21.27% on average). In contrast, the rhizosphere microbial communities of the cultivated N. incisum showed a high prevalence of functional genes involved in the pathways of DNA repair and recombination proteins, replication and repair, peptidases and inhibitors, DNA replication proteins, and transfer RNA biogenesis. The co-occurrence networks analysis indicated that the stability of the wild samples' network remained significantly more robust when nodes were proportionally removed, as the wild samples' network had approximately the same positive and negative links while the cultivated samples' network had nearly all positive links and many fewer connectors. This is related to the conclusion that wild N. incisum exhibits superior efficacy, as reported in previous studies. Additionally, it can be observed from the sampling images that the root surface of wild N. incisum has more pronounced tiny protrusions, which may be associated with rhizobial attachment, thereby enhancing the nitrogen fixation process. Importantly, the observed shifts in rhizosphere microbial communities, particularly the enrichment of beneficial rhizobia in wild plants, are closely linked to enhanced accumulation of bioactive secondary metabolites such as coumarins and volatile oils. These microbiome-driven differences are likely associated with the superior medicinal quality of wild N. incisum compared to cultivated counterparts, highlighting the pivotal role of rhizosphere microbes in shaping therapeutic efficacy.},
}

*Rhizosphere
*Soil Microbiology
*Metagenomics/methods
*Apiaceae/microbiology/growth & development
*Plants, Medicinal/microbiology/growth & development
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification

@article {pmid42830393,
year = {2026},
author = {Gao, YY and Xu, JJ and Wu, YX and Xu, HM and Wang, GZ and Zhou, GB},
title = {Air pollution and early-onset lung cancer: from environmental carcinogenesis to early intervention strategies.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgag070},
pmid = {42830393},
issn = {1460-2180},
abstract = {Air pollution remains a global public health challenge, with nearly the global population (99%) breathing air that exceeds World Health Organization (WHO) guideline limits-annual means of 5 μg/m3 for PM2.5 and 15 μg/m3 for PM10. Both household and ambient air pollution are classified as Group 1 carcinogens and contain hazardous components, including polycyclic aromatic hydrocarbons (PAHs), heavy metals, and volatile organic compounds. Exposure contributes to a broad spectrum of systemic diseases and is responsible for more than 14% of global lung cancer deaths, while also elevating risks for breast, gastrointestinal, and brain cancers. Mechanistically, air pollutants drive early lung carcinogenesis through intrinsic genomic instability, manifesting as DNA damage, telomere dysfunction, mitochondrial impairment, and specific mutational signatures, alongside epigenetic dysregulation. Concurrently, they foster a tumor-promoting niche via chronic inflammation mediated by CXCL13 and IL-1β and facilitate early immune evasion through activation of the PD-L1 and CD47-SIRPα axes. In addition, air pollution disrupts the respiratory-gut microbiome, reducing microbial diversity and promoting pathogenic enrichment. A range of early biomarkers-including genomic, epigenomic, inflammatory, and microbiome profiles-have been validated for preventive interventions, with multi-marker combinations demonstrating improved efficacy. Multiple chemopreventive targets have also been identified to counteract oxidative stress, inflammation, and immune evasion. Looking ahead, research priorities should include exploring gene-environment interactions, clinically validating biomarkers and therapeutic targets, translating basic discoveries into clinical practice, and developing precision prevention strategies for high-risk populations. Ultimately, integrating biomarker-guided early detection with multi-target chemoprevention will be essential to reducing the global burden of air pollution-induced early-onset lung cancer.},
}

@article {pmid42830658,
year = {2026},
author = {AlRamadneh, TN and Jyothi-S, R and Priyadarshini-Nayak, P and Nanda, A and Al-Hasnaawei, S and Bhatt, A and Singh-Chauhan, A and Singla, S and Mishra, MK},
title = {The Microbiome in Glioblastoma: Mechanisms, Tumor-Immune Interactions, and Translational Perspectives.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70431},
doi = {10.1002/mbo3.70431},
pmid = {42830658},
issn = {2045-8827},
mesh = {Humans ; *Glioblastoma/immunology/microbiology ; Animals ; *Brain Neoplasms/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Microbiota ; Translational Research, Biomedical ; },
abstract = {Despite multimodal treatment, glioblastoma (GBM) remains difficult to control because of diffuse invasion, tumor heterogeneity, immune dysfunction, and frequent recurrence. Increasing attention has focused on whether intestinal microbial communities and their products can modify systemic and central nervous system processes relevant to GBM. This narrative review critically evaluates current evidence linking microbial communities, microbial metabolites, tumor-associated microbial signals, and host immune responses with GBM biology and clinical translation. PubMed, Scopus, Web of Science, and Google Scholar were searched for English-language studies published from January 2019 through August 2026, with earlier foundational studies included when necessary. Human cohorts, tumor-tissue studies, glioma models, microbiota-transfer experiments, and mechanistic investigations were considered. Preclinical evidence supports several plausible pathways, including changes in short-chain fatty acid availability, microglial and macrophage states, blood-brain barrier regulation, systemic immunity, and tryptophan-related signaling. However, many relevant metabolites may originate from microbial, host, immune, or tumor sources. Human studies remain limited and vulnerable to confounding, reverse causation, treatment effects, and geographic variation. Bacterial nucleic acids and bacteria-associated HLA-bound peptides have been detected in brain tumors, but these findings do not establish viable colonization or a gut origin. Low microbial biomass also necessitates rigorous contamination control and orthogonal validation. Microbial influences are biologically plausible modifiers of GBM rather than established drivers. Clinical translation requires longitudinal human studies, source-resolved analyzes, standardized low-biomass methods, mechanistic validation, and independent replication. No microbiome-based biomarker or microbiome-directed therapy is currently validated for routine GBM care or patient stratification in clinical practice.},
}

Humans
*Glioblastoma/immunology/microbiology
Animals
*Brain Neoplasms/microbiology/immunology
*Gastrointestinal Microbiome/immunology
*Microbiota
Translational Research, Biomedical

@article {pmid42830770,
year = {2026},
author = {Gopinath, D and Selvakumar, B and Sekar, P and Mohammed, MM and Li, Z},
title = {Metabolic effects of periodontal pathogens Fusobacterium nucleatum and Porphyromonas gingivalis in colorectal cancer cells.},
journal = {Journal of Taibah University Medical Sciences},
volume = {21},
number = {5},
pages = {998-1006},
pmid = {42830770},
issn = {1658-3612},
abstract = {BACKGROUND: Periodontal pathogens are increasingly recognized as key regulators of cancer biology. However, their roles in modulating metabolism-related gene expression in colorectal cancer remain poorly understood.

METHODS: Human colorectal cancer (HCT)116 cells were exposed to Fusobacterium nucleatum and Porphyromonas gingivalis for 6 h and 24 h. Expression levels of genes involved in lipid metabolism (ACAT1 and PLD2), amino acid metabolism (PAH), polyamine synthesis (SMS), kynurenine pathway (KYNU), and detoxification (ALDH2) were evaluated using quantitative real-time PCR (qPCR). The expression profiles of these genes were also compared between colorectal tumor and normal tissues using The Cancer Genome Atlas (TCGA) RNA-seq data.

RESULTS: F. nucleatum and P. gingivalis induced distinct, time-dependent metabolic changes in HCT116 cells. At 6 h, F. nucleatum upregulated KYNU, PLD2, and ACAT1 , whereas P. gingivalis broadly suppressed SMS, PAH, KYNU, ACAT1, and ALDH2. At 24 h, F. nucleatum and P. gingivalis maintained predominantly suppressive effects on KYNU, SMS, and PAH. mRNA expression analysis indicated the downregulation of ACAT1 and ALDH2, and upregulation of KYNU, PLD2, PAH, and SMS in colorectal cancer, and partial overlap with F. nucleatum-induced changes.

CONCLUSION: The distinct impacts of the two bacterial species demonstrated the complexity of colorectal cancer host-microbiome interactions. These findings suggest that microbial species may influence tumor biology through different metabolic processes, leading to diverse rather than uniform metabolic changes in colorectal cancer cells.},
}

@article {pmid42830840,
year = {2026},
author = {Rizvi, M and Mufarji, AA and Shizawi, NA and Jabri, ZA and Haque, OI and Haider, M and Sami, H and Malehi, AA and Mohammad, R and Masters, K and Khan, F and Mamari, AA and Bahlani, SA and Mohamed, O and Stepanskyi, D and Khan, M and Shaukat, A and Gautam, A and M Luthfee, N and Malhotra, S and Agarwal, J and Gur, R and Siddiqui, AH and Devi, S and Thakuria, B and Princess, I and Gupta, A and Sultan, A and Jitendranath, A and G S, B and Kalita, JB and Jain, M and Singh, NP and Mohapatra, S and Farooq, S and Jankhwala, MS and Devi, VRY and Sen, M and Al-Hattali, H and Al-Ghussaini, HS and Ghafari, MSHA and Jardani, AA},
title = {Public perceptions on antibiotic use and resistance: a social media-based multicountry survey during WAAW 2022.},
journal = {IJID regions},
volume = {21},
number = {},
pages = {100975},
pmid = {42830840},
issn = {2772-7076},
abstract = {OBJECTIVES: This study aimed to assess the global public's knowledge, attitudes, and practices concerning antibiotic use and antimicrobial resistance (AMR) during World Antimicrobial Awareness Week 2022 because public engagement is crucial in promoting responsible antibiotic use.

METHODS: A validated trilingual questionnaire (Cronbach α 0.78) created in Google Forms was disseminated via the social media platforms of the Diagnostic and Antimicrobial Stewardship to Protect Antibiotics study group, yielding 766 responses from 30 countries. The survey explored the respondents' sociodemographic data, antibiotic knowledge, AMR awareness, and behavioral intentions in common clinical scenarios. Statistical analysis evaluated knowledge, attitudes, and practices scores by education level, academic background, and geographic region.

RESULTS: Respondents were predominantly from Asia and Africa. Higher education levels overall and a science background in particular were strongly associated with higher knowledge and more positive attitudes (P < 0.001). However, only 38% knew that antibiotics treat bacterial infections. Over half expected antibiotics for cold or flu symptoms; 31% would question why doctors were not prescribing them, and 18.5% would seek a second opinion. Awareness of the impact of antibiotics on the gut microbiome and fetal health was linked to reduced antibiotic-seeking behavior.

CONCLUSION: The findings primarily reflect engagement from the Middle East and the Indian subcontinent. The critical gaps in the public's understanding of appropriate antibiotic use support the need for school- and university-based AMR curricula, greater community engagement, and strategic use of digital platforms to foster responsible antibiotic practices.},
}

@article {pmid42831109,
year = {2026},
author = {Luo, H and Zhao, C and Yu, S and Zhou, C and Wei, D and Lin, W and Wang, X and Gong, Z and Xie, K},
title = {Ecological assembly of activated sludge microbiomes under contrasting process configurations and influent regimes.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1912780},
pmid = {42831109},
issn = {2296-4185},
abstract = {Activated sludge microbial communities are central to pollutant removal and operational stability in petrochemical wastewater treatment plants (PWWTPs). However, in full-scale systems, the relative associations of process configuration and influent composition with microbial community organization and treatment performance remain difficult to disentangle. This study investigated four full-scale PWWTPs in Northeast China, including three oxic systems and one anoxic/oxic system receiving different proportions of petrochemical, mixed industrial, and domestic wastewater inputs. We combined 16S rRNA gene sequencing, phylogenetic bin-based null model analysis (iCAMP), and partial least squares path modeling (PLS-PM) to evaluate microbial community structure, inferred assembly patterns, and their associations with influent characteristics, effluent quality, and chemical oxygen demand (COD) removal. The oxic systems showed higher alpha diversity than the anoxic/oxic system, although this comparison was potentially influenced by differences in influent composition and site-specific operational conditions. Community composition differed among influent types, with Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota showing contrasting enrichment patterns. iCAMP indicated a predominance of stochastic assembly patterns in the oxic systems and deterministic assembly in the anoxic/oxic system. Core zOTUs, including members of Rhodocyclaceae, Pseudomonadaceae, and Candidatus Berkiella, were associated with COD and nitrogen removal, supporting their potential as ecological indicators of treatment performance. Within the PLS-PM, influent characteristics showed stronger direct statistical associations with COD removal than process configuration, whereas process-related associations were represented mainly by indirect paths through microbial community composition. These findings highlight the joint influence of influent composition and process configuration on activated sludge microbial communities and treatment performance while providing an ecological basis for future microbiome-informed monitoring and process diagnosis in PWWTPs.},
}

@article {pmid42831379,
year = {2026},
author = {Huang, S and Tang, Y and Wang, Z and Li, D},
title = {Biofilm-associated microbial risks in a mega water diversion project: distribution of putative pathogen-associated taxa and concrete biocorrosion potential in the Middle Route canal of the South-to-North water diversion project.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/08927014.2026.2742367},
pmid = {42831379},
issn = {1029-2454},
abstract = {The ecological assembly of putative pathogen-associated taxa and the biogeochemical potential related to concrete biocorrosion have rarely been examined within an integrated framework in large freshwater diversion systems. We conducted quarterly biofilm sampling at eight stations along the Middle Route canal of the South-to-North Water Diversion Project, and combined 16S rRNA gene amplicon sequencing with shotgun metagenomics to characterize longitudinal and seasonal microbial patterns. Taxonomy-based screening identified 279 putative pathogen-associated ASVs with a mean relative abundance of 3.40%, primarily affiliated with Bacillus and Brevundimonas. Their relative abundance was lowest in the middle reaches, where higher flow velocity and dissolved oxygen may reduce biofilm-associated retention. Total nitrogen accounted for the largest individual contribution among the measured environmental variables (6.13%), whereas normalized stochasticity ratios indicated that stochastic processes predominated in overall community assembly. Metagenomic analysis further revealed spatially structured nitrogen- and sulfur-cycling potential, including biocorrosion-associated taxa such as Thiobacillus and Desulfovibrio, with several related functional pathways showing comparatively higher abundances in upstream biofilms. These findings establish an integrated ecological framework in which stochastic assembly, nutrient-associated selection, and hydrodynamic modulation jointly shape biofilm-associated microbial risks. The study provides critical insights for safeguarding both water-quality monitoring and century-scale infrastructure performance in mega water diversion systems.},
}

@article {pmid42831621,
year = {2026},
author = {Espinoza, JL and Phillips, AJ and Dupont, CL},
title = {Leviathan: fast, memory-efficient, and scalable taxonomic and pathway profiling for (pan)genome-resolved metagenomics and metatranscriptomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0097026},
doi = {10.1128/msystems.00970-26},
pmid = {42831621},
issn = {2379-5077},
abstract = {Functional profiling of meta-omics is essential for understanding microbial communities, yet support for custom genome-resolved reference databases is limited. We introduce Leviathan for integrated taxonomic and functional profiling at both genome and pangenome resolution. Leviathan combines Sylph for ultrafast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA space against (pan)genome-resolved gene catalogs, producing dual metrics per (pan)genome: pathway abundance and graph-based pathway coverage. Benchmarking alignment backends on synthetic metagenomes, we show that DNA-space pseudo-alignments retain competitive (pan)genome-level classification performance compared to traditional alignment, reducing resource requirements, while translated searches in protein space lose classification resolution from ambiguous mapping events. Leviathan's utility is demonstrated through two case studies: a marine plastisphere metagenomics data set analyzing metabolic shifts between early and mature biofilm communities, and a dental caries metatranscriptomics data set where co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.IMPORTANCEUnderstanding what microbes can do, not just which ones are present, is central to translating microbiome research into actionable insight. Existing functional profiling tools either rely on fixed reference databases or require complex multi-step pipelines when applied to custom genome collections, and none natively compute per-(pan)genome pathway abundance and graph-based pathway completeness in a single workflow. This limits the ability for researchers to directly compare functional profiles to tangential analyses on their specific genome catalogs. Leviathan addresses this gap with integrated taxonomic and functional profiling against user-defined (pan)genome-resolved references using pseudo-alignment, achieving competitive classification accuracy, with lower resource requirements compared to current methods. Native pangenome support enables routine quantification of metabolic potential and transcriptional activity at both genome and pangenome resolution, revealing functional variation across related strains that single-genome or community-level analyses obscure.},
}

@article {pmid42831644,
year = {2026},
author = {Beck, CW and Younge, SN and Gerardo, NM and Blumer, LS},
title = {Implementation and continuation in a network CURE: insights from the Bean Beetle Microbiome Project.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0022226},
doi = {10.1128/jmbe.00222-26},
pmid = {42831644},
issn = {1935-7877},
abstract = {The positive impact of course-based undergraduate research experiences (CUREs) on student outcomes is widely acknowledged. Yet, barriers to initial and then continued implementation of CUREs limit their use. In this Perspective, we expand on previous research on why faculty do (or do not) implement CUREs by exploring patterns and reasons for CURE implementation and continuation in the context of a network CURE that provided intensive faculty professional development, and curricular and financial resources. The compatibility of the CURE to existing curricula, the complexity of the CURE from the perspective of both instructors and students, and changes in faculty positions or the courses they were teaching were the biggest barriers to both initial and continued implementation. In contrast, in-person, hands-on faculty professional development, and flexibility in the duration of implementation were the biggest facilitators of implementation and continuation. We propose the following recommendations to encourage even broader implementation and continuation of CUREs: (i) in-person hands-on faculty development workshops, (ii) implementation flexibility, allowing for either full-semester or half-semester implementations or modular activities with core modules and then a selection of add-ons, (iii) maximize learning-teaching innovation compatibility with already existing courses and curriculum by focusing on foundational skills and knowledge, (iv) implement CUREs in core courses with multiple sections and instructors to increase implementation success and foster systemic change, and (v) give faculty resources and support to lead students in a CURE for which the faculty are not experts, and the outcome is unknown.},
}

@article {pmid42831655,
year = {2026},
author = {Fulcher, JA and Newman, KP and Pham, BT and Li, F and Cho, GD and Elliott, J and Tobin, NH and Shoptaw, S and Gorbach, PM and Aldrovandi, GM},
title = {Comparison of oral and gut microbiome highlights the role of oral bacteria in systemic inflammation in HIV.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0038426},
doi = {10.1128/msphere.00384-26},
pmid = {42831655},
issn = {2379-5042},
abstract = {UNLABELLED: Chronic HIV-1 infection is associated with increased inflammation-related comorbidities, despite effective viral suppression with antiretroviral therapy. While the role of the gut microbiome in inflammation is well studied, the contribution of the oral microbiome remains less clear. This study investigates the relationship between the oral and gut microbiomes in driving systemic inflammation in persons with HIV. This cross-sectional study utilized archived samples from 198 participants (99 with HIV and 99 without HIV). Oral and gut microbiome composition was analyzed via 16S rRNA sequencing, and systemic inflammatory biomarkers were measured using multiplex assays. Bacterial inflammatory potential was assessed through in vitro co-culture and epithelial barrier permeability assays. The oral microbiome in HIV was characterized by increased Veillonella, Capnocytophaga, and Megasphaera, and several decreased genera including Fusobacterium. Using permutational multivariate analysis of variance, we found that the oral microbiome was a significant driver of cytokine variation in HIV compared to the gut microbiome and identified specific associations with oral Veillonella and Megasphaera. We found no differences in anti-Veillonella parvula serum IgG by HIV status, but IgG titers did correlate with microbial translocation markers sCD14 and LBP in HIV. In vitro studies demonstrated that Veillonella parvula increased oral epithelial barrier permeability and induced monocyte activation. These studies suggest that the oral microbiome, particularly Veillonella parvula, may contribute to systemic inflammation in HIV through mechanisms involving epithelial barrier disruption, oral translocation, and monocyte activation.

IMPORTANCE: In HIV, persistent inflammation contributes to the elevated risk of cardiovascular disease, metabolic disorders, and other non-AIDS comorbidities. Alterations in the gut microbiome and resultant microbial translocation are contributors to this ongoing inflammation. Most microbiome research has focused on the gut compartment, though there is increasing appreciation for the role of the oral microbiome in chronic inflammatory diseases. Few studies have systematically compared the oral and gut compartments in HIV-associated inflammation. In this study, we identify Veillonella parvula as a plausible oral driver of epithelial barrier disruption and immune activation, expanding current understanding of microbial contributors to persistent inflammation in HIV.},
}

@article {pmid42831995,
year = {2026},
author = {Biswas, A and Ghosh, B and Kumari, P and Rangra, A and Chowdhury, KR and Kumar, A},
title = {Pharmacomicrobiomics-driven targeted drug delivery for precision microbiome modulation.},
journal = {Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences},
volume = {34},
number = {2},
pages = {},
pmid = {42831995},
issn = {2008-2231},
mesh = {Humans ; *Drug Delivery Systems/methods ; *Microbiota ; Probiotics/administration & dosage ; Precision Medicine/methods ; Multiomics ; Prebiotics ; Animals ; },
abstract = {BACKGROUND: The human microbiome can actively influence how drugs are handled and processed in our body. More knowledge of host-microbiome-drug interactions has shifted drug delivery from current approaches to precision therapeutics.

OBJECTIVES: The review is to evaluate various targeted strategies and mechanisms of drug delivery systems (DDS) driven by pharmacomicrobiomics. Moreover, the pharmacomicrobiomics-based DDS will also be discussed in terms of their therapeutic applications, translation, and new technologies for microbiome precision.

METHODS: Assessment on the latest development on microbiome-drug interactions and microbiome-based drug delivery strategies, including microbial enzyme activated prodrugs, nano- and micro-particle systems, probiotics, prebiotics, postbiotics, bacteriophages, genetically modified microorganisms, smart materials, and niche-selective delivery systems. The researchers also investigated clinical evidence, security, regulatory issues, Pharmacoeconomics and new emerging multi-omics and AI based strategies.

RESULTS: Microbiome-targeted DDS enable localized drug activation, site-specific delivery, and reduced systemic exposure. Enzyme-responsive systems achieved up to a 3-fold increase in local drug concentration, while SER-109 (VOWST) reduced CDI recurrence to 12% versus 40% with placebo at 8 weeks. FMT combined with pembrolizumab achieved objective responses in 40% (6/15) of previously non-responsive melanoma patients. Engineered microbial therapeutics, including SYNB1618 and AG013, further demonstrate the growing translational potential of programmable microbiome-based therapies.

CONCLUSION: Pharmacymicrobiomics-driven drug delivery systems (DDS) represent an innovative approach to precision therapeutics utilizing microbes. However, challenges such as individual microbiome variability, unvalidated biomarkers, safety concerns, intricate regulatory hurdles, and inconsistent translational outcomes from preclinical studies persist. A comprehensive integration of omics data and interdisciplinary collaboration is essential to enhance the predictability of microbiome therapies. Future efforts should focus on microbiome profiling, validating mechanism-based biomarkers, scalable manufacturing, and conducting clinical studies to define patient selection, ensure therapeutic consistency, and confirm long-term benefits.},
}

Humans
*Drug Delivery Systems/methods
*Microbiota
Probiotics/administration & dosage
Precision Medicine/methods
Multiomics
Prebiotics
Animals

@article {pmid42832042,
year = {2026},
author = {Cihan, E and Campbell, PM and Wu, Y and Ledder, RG and Summers, AM and Augustine, T and Knight, CG and McBain, AJ},
title = {Taxon-specific oral mycobiome differences and bacterial-fungal associations in kidney transplant recipients and donors.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag247},
pmid = {42832042},
issn = {1365-2672},
abstract = {AIMS: This study characterised the pre-transplant salivary mycobiome of kidney transplant recipients and living donors and investigated cross-kingdom associations with the bacteriome.

METHODS AND RESULTS: Mycobiome profiling was performed using ITS sequencing of donor and recipient samples, while paired bacteriome data were obtained from our previous study. No significant differences in fungal or bacterial alpha diversity or beta diversity were detected between recipients and donors, indicating an absence of broad community-level separation. Malassezia and Candida were the dominant fungal genera in both groups. Differential abundance analyses using ANCOM-BC2 and DESeq2 consistently identified lower Malassezia abundance in recipients, alongside predominantly lower abundance of several bacterial taxa. Cross-kingdom network analysis showed low Jaccard similarity in highly central taxa between donors and recipients, despite no significant differences in global network properties. This pattern persisted across most sample-size-matched subsamples.

CONCLUSIONS: These findings suggest that oral microbiome differences between kidney transplant recipients and donors are more apparent in specific taxonomic changes, particularly the reduction in Malassezia, and in the relative organisation of central community members than in broad shifts in overall microbial composition.},
}

@article {pmid42828250,
year = {2026},
author = {Snelling, TJ and Johnson, CA and Warren, HE and Taylor-Pickard, J and Huntington, JA and Sinclair, LA},
title = {Correction: Modulation of the rumen microbiome and metabolism in dairy cows by altering the concentrate feeding pattern and the inclusion of Saccharomyces cerevisiae yeast.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1965017},
doi = {10.3389/frmbi.2026.1965017},
pmid = {42828250},
issn = {2813-4338},
abstract = {[This corrects the article DOI: 10.3389/frmbi.2026.1884444.].},
}

@article {pmid42828283,
year = {2026},
author = {Doshier, J and Anderson, B and Yang, F and Stewart, SD and Calapa, KA and Cooper, R and Wilson-Robles, H and Embree, M and Khanna, C},
title = {Correction: Pilot study evaluating tolerability and changes in fecal microbiota associated with novel probiotic administration to dogs with diarrhea.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1981863},
doi = {10.3389/fvets.2026.1981863},
pmid = {42828283},
issn = {2297-1769},
abstract = {[This corrects the article DOI: 10.3389/fvets.2025.1720932.].},
}

@article {pmid42828306,
year = {2026},
author = {Wayah, SB and Arakawa, K and Philip, K},
title = {From predicted bacteriocins to ecological function.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100662},
pmid = {42828306},
issn = {2666-5174},
abstract = {Genome and metagenome mining have uncovered large repertoires of predicted bacteriocin loci, but ecological interpretation has lagged behind discovery. This review uses bacteriocins as a focused model for a broader problem in antimicrobial gene prediction: sequence identifies encoded potential, but it does not establish expression, product deployment, target engagement, or community-level consequence. We distinguish four forms of bacteriocin "silence": transcriptional silence, where loci are not detectably expressed under tested conditions; conditional silence, where expression or activity emerges only under specific environmental or social cues; phenotypic silence, where expression or product formation does not yield detectable activity in routine assays; and ecological silence, where activity is observed but its consequences for coexistence, exclusion, colonization, or community assembly remain unresolved. We also clarify how this framework extends previous reviews of bacteriocin diversity and microbiome-shaping roles by providing an inference-centered taxonomy that separates encoded potential from demonstrated ecological function. Finally, we propose a function-first roadmap for bacteriocin research, including condition-resolved transcriptomics and proteomics, promoter and cue-dissection experiments, expanded target panels, spatially structured assays, defined consortia and microcosms, producer/non-producer comparisons, and explicit tests of resistance, immunity, and fitness consequences. Treating predicted bacteriocin loci as hypotheses rather than conclusions will improve how the field moves from gene catalogs to causal ecological understanding.},
}

@article {pmid42828326,
year = {2026},
author = {Kinyua, WN and Munyiri, SW and Wagacha, JM and Mwaura, MN and Njage, PMK},
title = {Agroecological drivers of aflatoxin contamination in maize-based systems: a review.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1802402},
pmid = {42828326},
issn = {1664-462X},
abstract = {Aflatoxin contamination of maize remains a global food safety and public health challenge, particularly because it is a dietary staple food and feed ingredient produced across diverse agroecological zones. Although numerous mitigation strategies have been developed, contamination levels remain variable. This reflects complex interactions among climate, soil properties, crop management practices, plant physiological stress and rhizosphere microbial communities. This review synthesizes evidence on key agroecological drivers of aflatoxin contamination in maize, highlighting climate variability, soil properties, crop and nutrient management, cropping systems, and rhizosphere microbial communities as primary determinants. We examine how these factors influence Aspergillus population dynamics, microbial interactions and aflatoxin biosynthesis across contrasting production environments. Evidence synthesized in this review indicates that inconsistent outcomes of existing management including biological control strategies largely arise from insufficient consideration of soil-plant-microbe interactions and spatial heterogeneity. We identify climatic stress, soil properties and crop management strategies as the dominant determinants of aflatoxin risk, acting through biological mediators such as plant physiological status, rhizosphere microbial communities and fungal population. The review argues that effective and scalable aflatoxin mitigation requires integrated, context-specific and systems-based approaches. We conclude that incorporating agroecological heterogeneity into research design, predictive models and management frameworks is essential for improving risk prediction and developing aflatoxin control strategies in maize-based cropping systems.},
}

@article {pmid42824926,
year = {2026},
author = {Zhao, N and Leng, Z and Li, Q and Wei, S and Li, M and Zhang, Y and Wang, C},
title = {Renal tissue microbiota and metabolite profiling reveal dysregulated signatures in diabetic kidney disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1898177},
pmid = {42824926},
issn = {1664-302X},
abstract = {INTRODUCTION: Diabetic kidney disease (DKD) has become the main cause of end-stage renal disease in China. Mounting evidence links microecological disorders to DKD progression. However, the composition and the functional characteristics of the renal microecology in DKD patients remain poorly defined. This study characterized renal tissue microbiota and metabolite profiles in DKD patients, aiming to provide insights for novel diagnostic strategies for DKD.

METHODS: Renal tissue microbiome was analyzed in 42 DKD patients and 10 controls via 16S ribosomal DNA sequencing. Renal metabolomics was performed in 20 DKD patients and 10 controls using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Spearman correlation analysis clarified associations of clinical parameters with renal microbiome and metabolites. Biomarkers were identified by multi-omics integration.

RESULTS: IHC, IF and TEM reveals the presence of bacteria in both glomeruli and renal tubules. A significant separation in microbial community composition was observed between DKD patients and controls (p < 0.05). The relative abundance of Acidobacteriota, Acinetobacter and Afipia genus were significantly elevated in DKD group, whereas Ralstonia genus was decreased. Notably, the genus Acinetobacter demonstrated a significant negative correlation with the eGFR, while Afipia genus exhibited a significant positive correlation with blood glucose levels. Renal microbiota resembled urinary microbiota more closely than gut microbiota. Metabolomic analysis revealed significant difference in renal tissue metabolites between DKD patients and healthy controls. Lactate, hypoxanthine and phosphorylcholine were significantly positively correlated with the eGFR. Comprehensive multivariate analyses identified the genus Ralstonia as a crucial biomarker associated with renal fibrotic injury in DKD, consistent across urinary and gut microbiomes. Decreased serum levels of stearylcarnitine (Car18:0), oleylcarnitine (Car18:1) and tryptophan were closely associated with renal injury, whereas decreased urinary serine and tyramine levels reflected the change of renal metabolites in DKD.

CONCLUSION: Our finding confirms the existence of microbiota within renal tissue and demonstrates that its structure and composition are significantly altered in DKD. These disruptions in renal microecology are closely associated with the progression of DKD. Multi-omics analysis further identified a panel of candidate markers for evaluation of DKDs.},
}

@article {pmid42825108,
year = {2026},
author = {Knoll, RL and Rossow, V and Rössler, J and Hilbert, K and Jarquín-Díaz, VH and Bartolomaeus, TUP and Nitsche, O and Essex, M and Löber, U and Meng, C and Kleigrewe, K and Gehring, S and Forslund-Startceva, SK and Poplawska, K},
title = {A longitudinal multi-omic dataset of pediatric cystic fibrosis patients receiving lumacaftor/ivacaftor therapy: clinical, microbiome, inflammatory and metabolomic measurements collected over 24 months.},
journal = {Data in brief},
volume = {69},
number = {},
pages = {113237},
pmid = {42825108},
issn = {2352-3409},
abstract = {This article describes a longitudinal multiomic dataset generated within a prospective phase IV pilot study of eight children with cystic fibrosis homozygous for the F508del mutation who initiated lumacaftor/ivacaftor therapy. Participants were followed for up to 24 months with repeated collection of clinical metadata, anthropometric measurements, sweat chloride concentrations, lung function assessments, inflammatory markers, conventional microbiology results, stool samples, respiratory samples, and serum metabolomics. The resulting dataset links host phenotypes, microbiome composition, inflammatory parameters, and metabolomic measurements across multiple body sites and time points. Microbiome data were generated from stool, sputum and throat swab samples using 16S rRNA gene sequencing, while serum metabolomics was assessed using untargeted mass spectrometry. The dataset is publicly available through SRA, MassIVE and GitHub repositories and may support future studies of longitudinal host-microbiome interactions, biomarker discovery, methodological benchmarking and comparative analyses across CFTR modulator eras.},
}

@article {pmid42825194,
year = {2026},
author = {Prasad, SS and Singh, A and Ramteke, P and Veres, C and Büchner, R and Vágvölgyi, C},
title = {Symbiotic interactions of plant microbiota in alleviating stress: a review.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1892395},
pmid = {42825194},
issn = {1664-462X},
abstract = {Plants continuously encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Because they are sessile, plants cannot escape these unfavorable conditions and therefore rely on a diverse array of morpho-physiological, biochemical, and molecular adaptations to survive. Among these adaptive strategies, symbiotic associations with beneficial microorganisms have emerged as a crucial mechanism for enhancing stress tolerance. These plant-microbe interactions are mediated by intricate chemical signaling networks that regulate nutrient exchange, defense responses, and stress adaptation. Despite their immense potential for sustainable agriculture, the large-scale application of beneficial microbes remains limited owing to poor microbial establishment under field conditions and an incomplete understanding of the complex mechanisms governing plant-microbe mutualism. Deciphering these interactions is particularly challenging because they are highly dynamic and involve continuous communication between plants and diverse microbial communities. Recent advances in omics technologies, synthetic biology, and nanotechnology provide unprecedented opportunities to unravel these complex relationships at the molecular and systems levels. This review summarizes plant adaptive strategies under biotic and abiotic stresses, examines the role of microbial symbiosis in stress alleviation, and highlights emerging approaches, including multi-omics integration, synthetic microbial consortia, engineered quorum-sensing circuits, holobiont-level analyses, and nanoparticle-mediated modulation of the rhizosphere microbiome, for understanding and engineering beneficial plant-microbe interactions. Collectively, these advances offer new insights into symbiotic crosstalk and provide a foundation for developing resilient and sustainable agricultural systems.},
}

@article {pmid42825217,
year = {2026},
author = {Zhu, Y and Zhang, J and Wei, Y and Zhou, S and Qin, X},
title = {Biochar application alters soil properties and microbial gene profiles in a continuous cassava cropping system.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21731},
pmid = {42825217},
issn = {2167-8359},
mesh = {*Manihot/growth & development ; *Soil Microbiology ; Rhizosphere ; *Charcoal/pharmacology ; *Soil/chemistry ; Nitrogen/metabolism ; Metagenome ; *Microbiota/genetics ; Nitrogen Cycle ; },
abstract = {Continuous cassava cropping can lead to soil degradation and disturbances in soil microbial functions, threatening the sustainability of cassava production systems. To address these challenges, this study examined the effects of biochar on soil physicochemical properties and microbial functional profiles in a continuous cassava cropping system. Two biochar application rates (0 and 3 Mg ha[-1]) were applied, and metagenomic sequencing was conducted to evaluate microbial community composition and functional genes related to carbon and nitrogen cycling in rhizosphere and bulk soils. The results demonstrated that biochar was associated with higher soil pH, soil organic matter, and available nutrient content, with a stronger effect in rhizosphere soil. Biochar application altered the genetic potential of microbial communities, particularly in the rhizosphere soil. In terms of functional categories, biochar was related to higher gene abundances in "homologous recombination" and "DNA replication" categories (Kyoto Encyclopedia of Genes and Genomes (KEGG) database), as well as the "replication, recombination, and repair" category (evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database) in rhizosphere soil. Biochar also affected the abundance of carbon cycling genes, particularly in the rhizosphere. The abundance of the aerobic respiration-related gene coxA was increased, while the abundance of the anaerobic fermentation gene L-lactate dehydrogenase (LDH) was decreased. Additionally, in rhizosphere soil, biochar significantly increased the abundance of norB (denitrification), GDH2 (nitrogen mineralization), and nifD (nitrogen fixation), while decreasing the abundance of genes involved in nitrogen assimilation (gltB), assimilatory nitrate reduction (nirA), nitrogen mineralization (cynS), and nitrogen uptake (nrtA, nasF, cynA, nrtC, and nasD). Together, these results suggest that biochar application may enhance nutrient availability and reshape microbial functional potential primarily in the cassava rhizosphere, providing field evidence for biochar use in continuous cassava cropping.},
}

*Manihot/growth & development
*Soil Microbiology
Rhizosphere
*Charcoal/pharmacology
*Soil/chemistry
Nitrogen/metabolism
Metagenome
*Microbiota/genetics
Nitrogen Cycle

@article {pmid42825219,
year = {2026},
author = {Sabourin, KR and Mugisha, J and Marshall, VA and Miley, WJ and Chen, T and Billodeaux, J and Whitby, D and Rochford, R and Newton, R},
title = {The association between the oral microbiome and oral Kaposi's sarcoma-associated herpesvirus (KSHV) shedding is modified by age and HIV status in a rural Ugandan cohort.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2737698},
pmid = {42825219},
issn = {2000-2297},
abstract = {BACKGROUND: Kaposi's sarcoma-associated herpesvirus (KSHV) spreads through saliva. KSHV shedding is intermittent, suggesting individual-level factors affect reactivation.

OBJECTIVE: Identify associations between oral microbiome and KSHV shedding.

DESIGN: Oral mouthwash samples from 67 KSHV-seropositive participants (ages 4-78) were tested for KSHV DNA by qPCR and microbiome composition via 16S rRNA V4 region sequencing (Illumina MiSeq, Earth Microbiome Project protocols). Samples were selected on age, self-reported HIV status, and KSHV shedding. Alpha and beta diversity and relative abundances at species, genus and phylum levels were compared by KSHV shedding status. Analyses of KSHV shedding and the oral microbiome were stratified by HIV status (n = 49 adults only) and by age (n = 37 without HIV only, children <18 vs adults ≥18).

RESULTS: Neither alpha nor beta diversity differed by KSHV shedding status. Shedders had higher differential abundance of Prevotella multisaccharivorax, Bifidobacterium dentium, B. moukalabense and Bifidobacterium genus and lower Absconditabacteria G-1 bacterium HMT-875. Whether stratified by HIV and KSHV shedding or by age and KSHV shedding, alpha and beta diversity and several taxa at species, genus and phylum levels differed significantly.

CONCLUSIONS: Differences in oral microbiome were associated with KSHV shedding and possibly modified by age and HIV status. Future research should consider the multifactorial nature of the oral environment and KSHV reactivation.},
}

@article {pmid42825245,
year = {2026},
author = {Jia, M and Yang, R and Xu, Y and Wu, Z and Lu, J and Li, Z and Yan, Q and Fan, G and Gui, Y},
title = {Oral microbiome-metabolome axis links glycerophospholipid dysregulation to Alzheimer's disease.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2732297},
pmid = {42825245},
issn = {2000-2297},
abstract = {INTRODUCTION: This study aimed to evaluate the feasibility of using tongue biofilm as a non-invasive, patient-friendly, and cost-effective biomarker source for identifying early microbial and metabolic disturbances associated with Alzheimer's disease (AD).

MATERIALS AND METHODS: A total of 62 outpatients were enrolled (31 with AD and 31 cognitively normal controls). Tongue biofilm samples were analyzed using 16S rRNA sequencing and untargeted metabolomics via UPLC-Q/TOF-MS. Additionally, cerebrospinal fluid (CSF) samples from 36 individuals (18 per group) were examined under identical untargeted metabolomics processing protocols to validate the metabolomic findings.

RESULTS AND DISCUSSION: Microbiome analysis revealed an increased relative abundance of Proteobacteria in the AD group, while Firmicutes and Bacteroidetes were enriched in controls. Metabolomic profiling identified 88 significantly different metabolites between groups, 64 of which achieved area under the curve (AUC) values > 0.90 in the ROC analysis. Glycerophospholipid metabolism has emerged as a key dysregulated pathway in AD, a finding further corroborated by CSF metabolomic analysis. Tongue biofilm represents a non-invasive, cost-effective, and accessible biomarker source, offering potential for AD diagnosis and research when coupled with microbiome and metabolomic analyses. Moreover, the role of glycerophospholipid metabolism in AD pathogenesis warrants further investigation.},
}

@article {pmid42825323,
year = {2026},
author = {Cheong, P and Mangan, C and Clarke, ED and Stanford, J and Cairns, MJ and Collins, CE and Marques, FZ and Snelson, M},
title = {Personalized Nutrition for Hypertension: Current Evidence and Future Directions.},
journal = {Circulation. Genomic and precision medicine},
volume = {},
number = {},
pages = {e005566},
doi = {10.1161/CIRCGEN.125.005566},
pmid = {42825323},
issn = {2574-8300},
abstract = {Hypertension is a leading risk factor for cardiovascular disease, with lifestyle interventions, particularly diet, playing a pivotal role in its management. Recent advancements in personalized nutrition that tailor dietary recommendations based on an individual's unique biology (eg, genetics, microbiome) and lifestyle factors can potentially improve blood pressure control. Indeed, emerging evidence suggests that personalized nutrition can result in more effective and sustained blood pressure reductions than general dietary guidelines. This review explores the current evidence supporting personalized nutrition as a novel strategy for managing hypertension, while leveraging established approaches for controlling glycemia. We evaluate studies integrating genetic markers and genomics, gut microbiome profiles, and metabolic phenotypes to design personalized dietary interventions to reduce blood pressure. Specifically, we discuss how nutritional factors, including sodium and fiber intake and diets such as the Dietary Approaches to Stop Hypertension, interact with an individual's genetic predisposition and gut microbiota composition to influence blood pressure outcomes. However, challenges remain in translation to clinical practice, including the need for larger, long-term trials in real-world settings, accessibility of advanced dietary assessments, considerations of patient adherence, and equity. We highlight the potential of personalized nutrition to refine hypertension treatment and call for further research to optimize its implementation at the public health and clinical practice levels. Particularly in low- and middle-income countries, where hypertension prevalence is higher, cost is an important consideration for successful implementation. However, some personalized treatments focusing on diet are cost-effective and should be prioritized. Ultimately, a personalized nutrition approach may offer a powerful tool for mitigating the global burden of hypertension through targeted, individualized dietary strategies.},
}

@article {pmid42825349,
year = {2026},
author = {Wang, J and Liao, Z and Liu, M and Wang, Y and Cui, Y and Chen, H and Zeng, F and Zhu, Z},
title = {Novel insights into the role of the renal interstitial microenvironment in Randall's plaque formation (Review).},
journal = {International journal of molecular medicine},
volume = {58},
number = {5},
pages = {},
doi = {10.3892/ijmm.2026.6004},
pmid = {42825349},
issn = {1791-244X},
mesh = {Humans ; Animals ; *Cellular Microenvironment ; Calcium Oxalate/metabolism ; *Kidney Medulla/pathology/metabolism ; *Kidney Calculi/pathology/metabolism ; *Kidney/pathology/metabolism ; Durapatite/metabolism ; },
abstract = {Randall's plaque (RP) consists of subepithelial hydroxyapatite (HAP) deposits within renal papillae and provides a well‑established attachment substrate for a subset of idiopathic calcium oxalate (CaOx) kidney stones. However, RP has traditionally been viewed as a passive mineral surface onto which crystals accrete, with comparatively less focus on the cellular and molecular events that build the plaque itself. The renal papillary interstitium has been indicated as a dynamic microenvironment that undergoes molecular remodeling during plaque‑associated mineralization. The present review aimed to organize the current evidence regarding interconnected processes that may overlap in vivo rather than occur in a fixed sequence. Physicochemical conditions in the inner medullary interstitium favor HAP nucleation and provide the foundation for plaque formation. Epithelial injury responses, regulated cell death, osteogenic‑like fibroblasts and immune remodeling may contribute to the development of a pro‑calcific microenvironment; however, the spatial relationship, temporal order and plaque specificity of these processes remain incompletely defined. Macrophage polarization may influence whether local crystal‑associated inflammation and mineralization are amplified or reduced. As interstitial HAP deposits enlarge and become exposed through focal disruption of the renal papillary epithelium, these deposits can interact with pelvic urine and support CaOx nucleation and overgrowth. Systemic metabolic abnormalities and urinary or gut microbiome alterations are associated with stone disease and may modify the papillary microenvironment; however, direct evidence that they alter human RP burden is lacking to date. Of note, available animal and cell models demonstrate selected aspects of mineralization or crystal injury but do not reproduce the chronic, progressive interstitial HAP plaque observed in humans. In conclusion, considering RP as an interstitial microenvironmental disorder may help identify potential biomarkers of early papillary remodeling and generate potential therapeutic strategies for stone prevention in the future.},
}

Humans
Animals
*Cellular Microenvironment
Calcium Oxalate/metabolism
*Kidney Medulla/pathology/metabolism
*Kidney Calculi/pathology/metabolism
*Kidney/pathology/metabolism
Durapatite/metabolism

@article {pmid42825360,
year = {2026},
author = {Lu, F and Macpherson, CW and Haj-Husein, I and Klein, MS and Iskandar, MM and Kubow, S},
title = {Metabolomic signatures of probiotic secretomes reveal strain-specific biofunctional potential: insights from Lacticaseibacillus rhamnosus R0011 and Bifidobacterium longum R0175.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo05684e},
pmid = {42825360},
issn = {2042-650X},
abstract = {Probiotic secretomes are cell-free byproducts of bacterial growth, which contain bioactive metabolites. These metabolites have antioxidant and anti-inflammatory effects and mediate the host-microbe and microbe-microbe interactions. However, the metabolomic profiles of probiotic secretomes are strain-specific and have not been fully investigated. Untargeted metabolomic analysis was used to characterise the metabolomic profiles of Lacticaseibacillus rhamnosus R0011 (R11) secretome (LR) and Bifidobacterium longum R0175 (R175) secretome (BL). LR and BL had distinct metabolomic profiles. LR exhibits a greater relative abundance of branched-chain hydroxy and aromatic lactic acids, mannitol/sorbitol, mevalonate and flavin mononucleotide. BL is characterized by higher relative abundance of indolelactate, γ-glutamylamino acid, niacin-related metabolites, and organic acids in the citric acid cycle. This study is the first to reveal distinct metabolomic signatures of two widely used probiotic species, providing new insights into their strain-specific roles in host health and microbiome modulation.},
}

@article {pmid42825575,
year = {2026},
author = {Abeysinghe, G and Nagy, E and Wagner, T and Parunandi, S and Santos, J and Bagavathiannan, M and Antony-Babu, S},
title = {A hyphal release-capture soil microcosm for recovering hyphosphere bacterial communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0109626},
doi = {10.1128/msystems.01096-26},
pmid = {42825575},
issn = {2379-5077},
abstract = {Fungal hyphae form spatially confined interfaces in soil that mediate close associations with bacteria, collectively referred to as the hyphosphere. Despite its recognized ecological importance, experimental access to hyphosphere-associated microbial communities under realistic soil and plant-associated conditions has remained limited. Here, we present a soil-mimetic microcosm that enables controlled recovery of hyphosphere bacterial communities embedded within plant-associated soil. The system integrates field-derived soil, a native soil microbial inoculum, living cotton seedlings, and a spatially constrained fungal inoculum housed within sterile cell-strainer assemblies, permitting hyphal extension into soil while preserving a recoverable fungal-soil boundary. Using the soil-borne plant pathogen Fusarium oxysporum f. sp. vasinfectum as a model filamentous fungus, we show that the microcosm enables reproducible recovery of hypha-associated soil microaggregates containing physically attached bacterial cells. Full-length 16S rRNA profiling revealed pronounced reductions in bacterial richness and evenness in hyphosphere samples relative to bulk and rhizosphere soils (Shannon diversity, Kruskal-Wallis H = 15.25, P = 0.0016, with genus richness declining by 87% in bulk soil and 24% in rhizosphere soil contexts), consistent with recruitment of a restricted subset of the surrounding microbiota. Ordination analyses demonstrated clear compositional separation between soil and hyphosphere compartments (PERMANOVA F = 7.14, R[2] = 0.572, P = 0.001), with hyphosphere communities of bulk and rhizosphere origin converging to similar composition despite differing starting soils (R[2] = 0.128, P = 0.307). Phylogenetic turnover analyses (βNTI) indicated phylogenetic structuring (exceeding the +2 threshold), whereas taxonomic analyses identified a conserved set of bacterial genera consistently associated with hyphae, alongside compartment-specific taxa influenced by soil and plant context. Together, these findings establish the novel hyphal release-and-capture microcosm as a reproducible, ecologically grounded platform for studying hyphosphere-associated bacterial communities in plant-associated soils.IMPORTANCESoil fungi recruit distinct bacterial communities along their hyphae, forming a specialized microhabitat known as the hyphosphere. Despite its ecological importance, studying hyphosphere-associated bacteria under realistic plant-soil conditions has remained experimentally difficult. Here, we present a soil-mimetic hyphal release-capture microcosm that enables controlled reconstruction and recovery of bacterial communities assembled along fungal hyphae in intact plant-associated soils. Using the cotton wilt pathogen Fusarium oxysporum f. sp. vasinfectum, we show that fungal hyphae reproducibly recruit reduced and compositionally distinct bacterial assemblages from surrounding soils through strong deterministic selection. Because this pathogen is a regulated quarantine organism for which field inoculation is restricted, this system provides a tractable experimental platform for studying hyphosphere assembly under controlled yet ecologically relevant conditions. This approach provides new opportunities to investigate fungal-bacterial interactions, microbial community assembly, and plant-associated soil microbiomes at spatially resolved hyphal interfaces.},
}