@article {pmid42221783,
year = {2026},
author = {Mingat, SX and Ehara, T and Izumi, H and Ejima, R and Mitsuyama, E and Nakamura, H and Miyaji, K and Xiao, JZ},
title = {Synbiotic effects of 2'-fucosyllactose and Bifidobacterium longum subsp. infantis M-63 in fermented human fecal communities.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1744839},
pmid = {42221783},
issn = {2296-861X},
abstract = {BACKGROUND/OBJECTIVES: Human milk oligosaccharides (HMOs) are the third most abundant solid component of human milk. HMOs are selectively utilized by infant-type human-residential bifidobacteria (HRB), resulting in the formation of a gut microbiota dominated by bifidobacteria and the production of health-beneficial metabolites, such as acetate and aromatic lactic acids (ALAs), in breastfed infants. HMOs play key roles in infant health by acting as prebiotics, preventing infections, and regulating the immune system. However, the prevalence of HMO-utilizing bifidobacteria in the gut microbiota of infants and young children varies greatly between countries and regions, with some infants and children containing none.

METHODS: We used a pH-controlled single-batch fermenter to model the human gut microbiota and evaluated whether HMOs provide infants or young children having or lacking bifidobacteria with HMO-utilizing ability with any physiological benefits. We conducted fecal fermentation with 2'-fucosyllactose (2'-FL), with or without supplementation with a probiotic HRB strain (Bifidobacterium longum subsp. infantis M-63).

RESULTS: 2'-FL alone did not significantly increase the relative abundance of bifidobacteria or the production of acetate and ALAs during fecal fermentation of infants and young children. Conversely, 2'-FL + M-63 significantly increased bifidobacteria and promoted acetate and ALA production in the fecal fermentation of both infants and young children.

CONCLUSION: Health benefits from 2'-FL may be restricted by inter-individual and age-dependent differences in gut microbiota response. Supplementation with a probiotic HRB with high HMO-utilizing ability could overcome this restriction. Our findings provide insights into the development of formulas for infants and young children.},
}

@article {pmid42221821,
year = {2026},
author = {Bischof, F and Krumbholz, P and Kleinau, G and Scheerer, P and Stäubert, C},
title = {Comparative analysis reveals molecular adaptation of mammalian HCA2 to microbial metabolites.},
journal = {iScience},
volume = {29},
number = {6},
pages = {116030},
pmid = {42221821},
issn = {2589-0042},
abstract = {Metabolite-sensing G protein-coupled receptors (GPCRs), such as hydroxycarboxylic acid receptor 2 (HCA2), translate endogenous and microbial signals into physiological responses, regulating metabolism and immunity, yet the extent of HCA2 functional diversification across mammals remain unclear. Here, comparative pharmacology, metabolomics, evolutionary analysis, and structural mapping of mammalian HCA2 orthologs reveal extensive functional diversification across mammals, especially in odd-toed ungulates. Notably, African rhinoceros HCA2 exhibits multiple HCA3-like substitutions, resulting in loss of responsiveness to HCA2 agonists and increased sensitivity to HCA3-specific ligands. Positive selection analyses and metabolomic profiling of fecal extracts implicate microbiome-derived metabolites, particularly phenylpropionic and trans-cinnamic acid, as potential drivers of this adaptive shift. Mutagenesis experiments identified key amino acid substitutions in extracellular and transmembrane regions that modulate ligand potency and efficacy. These findings demonstrate that mammalian HCA2 receptors have undergone lineage-specific molecular evolution shaped by host-microbe metabolic interactions, highlighting how ecological contexts drive receptor adaptation and functional diversification.},
}

@article {pmid42221840,
year = {2026},
author = {Ju, K and Shan, Y and Pan, L},
title = {Functional Recovery After Chemotherapy- and Radiotherapy-Induced Gastrointestinal Injury: Mechanisms, Clinical Assessment, and Management.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {610529},
pmid = {42221840},
issn = {1178-7074},
abstract = {Chemotherapy- and radiotherapy-induced gastrointestinal injury is a common complication of cancer treatment and may present with diarrhea, abdominal pain, urgency, bloating, rectal bleeding, and reduced oral intake. Although many cases improve after treatment completion, some patients develop persistent or late bowel dysfunction that impairs nutrition, treatment tolerance, daily functioning, and quality of life. Conventional terms such as toxicity, mucositis, and enteritis are clinically useful, but they do not fully capture the problem of incomplete functional recovery. We propose a practical recovery-oriented framework that operationalizes meaningful recovery across four interconnected domains: structural recovery, barrier recovery, clinical recovery, and patient-centered recovery. Using this framework, we summarize the acute-to-chronic clinical spectrum of luminal gastrointestinal injury, examine mechanisms of failed recovery, review clinical assessment and management, and discuss emerging strategies including biomarker-guided monitoring, microbiome-directed interventions, organoid-based platforms, and regenerative therapies. Current care remains largely supportive and symptom-centered. A recovery-oriented model may improve clinical decision-making by integrating symptom trajectory, nutritional status, treatment tolerance, patient-reported burden, and selected biological signals to better monitor and restore gastrointestinal function.},
}

@article {pmid42221959,
year = {2026},
author = {Wen, Y},
title = {Gut microbiota-derived tryptophan metabolites: molecular mechanisms, nutritional strategies and implications for swine health.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1807477},
pmid = {42221959},
issn = {2297-1769},
abstract = {Tryptophan, an essential amino acid, has nutritional value. Beyond that, it is an important signaling molecule that connects the gut microbiota with host physiology. While host-mediated pathways are well-characterized, the microbiota-driven indole pathway has emerged as a major modulator of host homeostasis. Commensal bacteria metabolize unabsorbed tryptophan into indole-3-propionic acid (IPA), indole-3-lactic acid (ILA) and other bioactive indole derivatives. These bioactive indole derivatives can act as ligands for aryl hydrocarbon receptor (AhR) and pregnane X receptor (PXR). This review makes a summary of the main tryptophan metabolic pathways. It also elucidates the molecular mechanisms by which microbial metabolites derived from tryptophan restore the integrity of the intestinal barrier, maintain immune homeostasis, and modulate host metabolism. Building on this, we discuss nutritional strategies, such as dietary patterns and probiotic interventions, and their potential to modulate tryptophan metabolism. Using pigs as a translational model, we summarize the potential applications of these metabolites in alleviating weaning stress and improving growth performance. This review focuses on tryptophan metabolism and provides a theoretical basis for microbiome interventions and precision nutrition strategies in swine production.},
}

@article {pmid42222135,
year = {2026},
author = {Gabriel, PO and Velasco-Cruz, C and Randall, JJ},
title = {Host genotype and environment shape rhizosphere and root microbiome composition of pecan rootstocks.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1778537},
pmid = {42222135},
issn = {2813-4338},
abstract = {The rhizosphere and root-associated microbiomes play a crucial role in nutrient acquisition, stress tolerance, and overall plant performance. However, little is known about how microbial communities assemble and shift across environments in pecan (Carya illinoinensis). In this study, we compared the bacterial and fungal community compositions in the roots and rhizosphere of four pecan clonal rootstocks (NMU03, NMU04, NMU05, and NMU155) cultivated under greenhouse conditions, as well as their subsets that were subsequently transplanted to the field. Amplicon sequencing of 16S rRNA and ITS regions revealed significant differences in microbial diversity and taxonomic composition across environments and genotypes. Bacterial assemblages in greenhouse roots were typically dominated by a few families (e.g., Burkholderiaceae, Rhodanobacteraceae, and unclassified taxa). In contrast, field samples exhibited broader taxonomic distributions, with families such as Xanthobacteraceae, Haliangiaceae, and Geminicoccaceae emerging as dominant members. Fungal OTU abundance was consistently higher than bacterial abundance across all genotypes, likely reflecting mutualistic associations with mycorrhizal fungi, such as those in the Elaphomycetaceae family. Interestingly, Aspergillaceae dominated greenhouse and field fungal communities, suggesting ecological adaptability and potential contributions to plant stress tolerance. Comparisons with earlier greenhouse studies revealed that while some signature core microbiome members were retained following transplantation from the greenhouse to the field, the abundance of others decreased, highlighting successional shifts in community structure driven by environmental transitions. Together, these findings demonstrate the dynamic, genotype and environment-specific structuring of pecan microbiomes and highlight the importance of microbiome-informed breeding strategies to improve plant-microbe associations under variable growth conditions among pecan breeders.},
}

@article {pmid42222136,
year = {2026},
author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC},
title = {Protist community sites and structure under two barn management systems at a commercial dairy.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1803341},
pmid = {42222136},
issn = {2813-4338},
abstract = {INTRODUCTION: Investigations into the location and load of protists in the environment arounddairies are scarce but are essential to maintaining the health of livestock.Moreover, the design of dairy barns has fluctuated over the decades to maximizecattle health and milk production without regard to influences on environmentalmicrobiomes. Beyond cost, the major emphasis of barn design is the managementof appropriate temperature and comfort for cattle. However, there havebeen no corresponding investigations into whether these design changes affect protist communities within barns.

METHODS: In this study, community shotgun metagenomic analysis was used to define the spatial composition and relative abundance of protist communities from 118 samples of manure, lagoons, troughs, and house and stable flies at a commercial dairy implementing two free-stall management systems: flow-through and cross-vent. Sequence reads were mapped to the CosmosID database. Viability was not assessed; therefore, results reflect DNA detection only not viability or disease occurrence.

RESULTS: The protist composition differed significantly between dairy components. Ecological findings showed that troughs and lagoons harbored high protist diversity, including the possible pathogen Neobalantidium coli and potential carriers Paramecium biaurelia and Acanthamoeba. Manure had the lowest protist diversity. Stable flies carried more protist taxa than house flies. Both fly species uniquely carried the non-pathogenic alveolate parasite Hammondia hammondi. The water mold plant pathogen Pseudoperonospora cubensis was identified in all sample types. Of the total relative abundance of protists, 2.10% were amoebas, 7.63% alveolate parasites, 62.71% water molds, 23.31% ciliates, 1.74% foraminifera, and 2.50% diatoms.

DISCUSSION: These results describe preliminary spatial overlaps and possible avenues of dissemination, providing a basis for assessing appropriate management systems and identifying protist reservoir sites within dairy operations.},
}

@article {pmid42222207,
year = {2026},
author = {Colussi-Pelaez, E},
title = {Histamine Intolerance Through a Functional Medicine Lens: A Systems-Based Review.},
journal = {Integrative medicine (Encinitas, Calif.)},
volume = {25},
number = {2},
pages = {86-88},
pmid = {42222207},
issn = {1546-993X},
}

@article {pmid42222260,
year = {2026},
author = {Alfaro-García, RG and Vargas-Mejía, P and Patiño-Conde, V and Rebollar, EA and Guerrero-Analco, JA and Vega-Arreguín, J and Reverchon, F and Méndez-Bravo, A},
title = {Phytophthora root rot induces compositional and functional changes in avocado rhizosphere bacterial communities.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag025},
pmid = {42222260},
issn = {2633-6685},
abstract = {Understanding how plant pathogens modulate the rhizosphere microbiota is essential to integrated disease management. Here, the compositional and functional shifts in the avocado rhizosphere bacteriome induced by Phytophthora cinnamomi were assessed to identify bacterial taxa enriched in the symptomatic condition and elucidate the microbial functions modulated by the infection. Metabarcoding and metatranscriptomics analyses revealed that Phytophthora root rot (PRR) induced compositional shifts in bacterial communities, leading to the enrichment of members of MND1, RB41, and Nitrospira. Functional analysis showed that this enrichment might be due to the release of nutrients following root rot, as carbohydrate metabolism was stimulated in rhizobacterial communities of infected trees. Moreover, the relative abundance of transcripts from genes associated with stress response and cell signaling increased in some of the most active genera in the rhizosphere of PRR-symptomatic trees, suggesting their potential to mitigate the adverse effects of infection. These findings highlight the need to combine compositional and functional microbiome data to differentiate between taxa attracted by nutrient release and those contributing to the plant defense. The interactions of beneficial bacterial taxa with the pathogen should be further studied, as they may constitute promising biocontrol agents.},
}

@article {pmid42222261,
year = {2026},
author = {Wassermann, B and Kögl, I and Gokul, JK and Wicaksono, WA and Schweitzer, M and Korsten, L and Berg, G},
title = {Diversity and selected functional traits of microbiota associated with traditional dried plant foods from South African informal markets.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag026},
pmid = {42222261},
issn = {2633-6685},
abstract = {Traditional plant-based products provide nutritional benefits and support cultural heritage; however, their sale in urban informal markets raises potential food safety considerations. We characterized the microbiota of five traditional dried plant products (baobab, masau, nyii, dinawa, and lude) obtained from three informal markets in South Africa (n = 51 samples) using 16S rRNA gene sequencing and quantitative real-time PCR; bacterial isolates (n = 87) were further evaluated using selected phenotypic assays. Bacterial abundance and composition varied across products and vendors. Baobab exhibited the highest microbial richness (1460 ASVs) but relatively low bacterial loads (10[6] 16S rRNA gene copies g[-1]), whereas dried leafy greens showed the lowest richness (470 ASVs) but the highest bacterial abundance (10[9] copies g[-1]). Across products, higher bacterial diversity correlated with genera such as Bifidobacterium and Prevotella, while higher bacterial abundance correlated with genera such as Salmonella, Vibrio, and Acinetobacter. Notably, health implications of detected taxa cannot be inferred from genus-level identification based on 16S rRNA gene sequencing. Phenotypic traits observed among selected isolates included growth in the presence of several antibiotics (particularly sulfadiazine and ampicillin), protease activity, and inhibition of indicator strains under laboratory conditions. Overall, traditional dried plant foods harbor diverse microbial communities shaped by plant characteristics and vendor-related practices, highlighting the importance of improved handling and drying practices.},
}

@article {pmid42222391,
year = {2026},
author = {Jiang, S and Du, Z and Wang, Y and Ma, H and Ma, Z and Wang, X},
title = {Dynamic changes and clinical significance of the gut microbiota and serum metabolites in breast cancer onset, progression and chemotherapy intervention.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1795317},
pmid = {42222391},
issn = {2234-943X},
abstract = {OBJECTIVE: Alterations of the gut microbiota and host metabolic reprogramming are closely associated with the development of breast cancer and the treatment response; however, integrated studies of the gut microbiota and metabolome spanning the transition from benign breast disease (BBD) to malignancy and the postchemotherapy phase remain limited. This study aims to systematically characterize the dynamic changes in the "gut microbiota-serum metabolome-breast tumor" axis from benign breast disease (BBD) to breast cancer (BC) and postchemotherapy breast cancer (PCBC) and to evaluate its potential value in diagnosis and disease monitoring.

METHODS: We enrolled 295 female participants, who were divided into a BBD group (n = 83), a BC group (n = 100), and a PCBC group (n = 88), and included 24 paired fecal samples from the same patients that were collected before and after chemotherapy. Fecal samples underwent 16S ribosomal RNA (rRNA) sequencing, while serum samples underwent an liquid chromatography-high-resolution mass spectrometry (LC-MS/MS) based nontargeted metabolomic analysis; we compared differences in gut microbiota diversity, taxonomic composition, and functional predictions across groups and screened for differentially abundant metabolites and enriched metabolic pathways. In a subset of patients with paired multiomics data (BBD n=19, BC n=31, and PCBC n=34), Spearman's correlation analysis, multiomics principle component analysis (PCA)/partial least squares-discriminant analysis (PLS-DA), and random forest models were employed to integrate the microbiota and metabolic features.

RESULTS: Cross-sectional remodeling of the gut microbiome structure occurred. The α diversity of the gut microbiota was similar across the three groups (BBD, BC, and PCBC); however, the β diversity analysis based on the weighted UniFrac distance revealed the significant separation of the microbial community structure among the three groups. At the taxonomic level, the BBD group was significantly enriched with beneficial commensal bacteria that produce short-chain fatty acids (e.g., Faecalibacterium and Roseburia); in contrast, the BC group shifted toward the enrichment of inflammation- or tumor-associated genera (e.g., Blautia, Fusobacterium, Sneathia, and Prevotella), while the PCBC group further accumulated various opportunistic pathogens (such as Phocaeicola, Sutterella, Enterococcus, and Chlamydia). As the disease progressed and chemotherapy was administered, the microbiome gradually shifted from a "metabolic protective" state to an "inflammatory/pathogenic" state. The characteristics of the dynamic remodeling of serum metabolomic profiles were identified. Nontargeted metabolomics revealed more than 3,000 metabolites, and the multivariate analysis indicated significant heterogeneity in the metabolomic profiles associated with malignant transformation and those measured before and after chemotherapy. In the BC group, energy, amino acid, and lipid metabolism were significantly disrupted, and widespread metabolite depletion was observed; however, in the postchemotherapy PCBC group, adaptive pathways such as estrogen, bile acid, and drug metabolism were activated, and persistent abnormalities in purine/nucleotide, carbon, and multiple amino acid metabolism were detected. Overall, the serum metabolic network underwent a dynamic remodeling process, transitioning from homeostasis to severe disruption and then to partial reconstruction following treatment. Among these changes, the differentially abundant metabolites torsemide, cortolone-3-glucuronide, and trimethylselenonium all had area under the curve (AUC) values greater than 0.75 in distinguishing between different disease stages and chemotherapy statuses, demonstrating their good potential as biomarkers. Interaction networks and multiomics predictive models of the "gut-metabolism-tumor" axis were established. Multiomics association networks revealed a systemic shift in gut-metabolism interaction patterns from a steady state characterized by "probiotic-energy/amino acid and polyphenol metabolism coupling" during the benign phase to a new steady state dominated by "proinflammatory/opportunistic pathogens-lipid reprogramming, exogenous metabolite metabolism, and oxidative stress." A multiomics classification model based on random forests demonstrated that the combined analysis of the gut microbiota and serum metabolite profiles exhibited exceptional efficacy in distinguishing between the BBD, BC, and PCBC groups. It identified a cluster of strongly associated features characterized by anaerobic gram-positive cocci, Lactobacillus-associated microbiota, and their paired metabolites, providing an important molecular fingerprint for clinical assessment.

CONCLUSIONS: This study integrates gut microbiome and serum metabolomic data to reveal that during the progression of benign breast lesions to breast cancer and throughout chemotherapy, the "gut microbiota-host metabolism-breast tumor" axis transforms from a state characterized by commensal depletion, the expansion of opportunistic pathogens, and reprogramming of energy/lipid metabolism to a persistent metabolic signature associated with drug metabolism and the activation of oxidative stress pathways. The integrated multiomics model helps characterize the biological differences across various stages of breast disease. The identified characteristic bacterial genera and metabolite combinations provide preliminary theoretical clues for the future exploration of microbiome-related mechanisms in breast cancer and for auxiliary assessments.},
}

@article {pmid42222592,
year = {2026},
author = {O'Shea, KM and Brooks, E and Polmear-Swendris, N and Slack, IF and Smith, JA and Gordon, A and Aquino, DM and Gern, JE and Khurana Hershey, GK and Johnson, CC and Wilkowski, J and Hines, J and Lukacs, NW and Schuler, CF and Baker, JR},
title = {The Michigan Sibling Immunity Birth Study (M-SIBS): Study design protocol for a unique food allergy birth cohort.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {5},
number = {4},
pages = {100721},
pmid = {42222592},
issn = {2772-8293},
abstract = {BACKGROUND: Food allergy is a rapidly escalating public health concern, yet the biologic pathways that link early-life exposures with disease onset remain poorly defined. No existing food-allergy birth cohort has yet paired criterion-standard oral food challenges with comprehensive, family-wide multiomics profiling.

OBJECTIVE: The Michigan Sibling Immunity Birth Study (M-SIBS) was established to elucidate early-life genetic and environmental interactions that drive disease. By enrolling entire families, including atopic siblings, the study leverages shared genetics, perinatal sampling, and household exposures to identify modifiable factors in food allergy development.

METHODS: M-SIBS is a prospective birth cohort at the University of Michigan that will enroll 1000 infants who have a first-degree relative with atopic disease. Mothers are recruited prenatally along with biologic fathers and siblings. Infants are then followed through 36 months of life. Extensive longitudinal phenotyping includes (1) serial skin prick and serum-specific IgE testing to the 9 most common food allergens at designated intervals; (2) standardized oral food challenges to confirm any positive result; (3) biospecimen collection at specified time points prebirth and postbirth; and (3) validated clinical, psychosocial, and environmental surveys administered longitudinally. It is designed to integrate genomic, epigenomic, transcriptomic, metabolomics, and microbiome data into a single multiomics framework across the family unit.

CONCLUSIONS: M-SIBS integrates criterion-standard clinical diagnostics for food allergy with family-based multiomics to generate an unprecedented data set on the earliest drivers of food allergy.},
}

@article {pmid42222691,
year = {2026},
author = {L'Orphelin, JM and Morice, C and Gardères, J and Chopin, S and Lucas, C and Bouchet, C and Bailly-Caillé, B and Da Silva-Dias, V and Mourad, N and Jouandet, M and Akroun, J and Acher, A and Dompmartin, A and Parienti, JJ},
title = {Sensoriality of emollient creams: can sensory experience compromise blinding in trials?.},
journal = {Skin health and disease},
volume = {6},
number = {3},
pages = {250-258},
pmid = {42222691},
issn = {2690-442X},
abstract = {BACKGROUND: Regular application of emollients, particularly those that enhance the skin's acid mantle and promote ceramide production, can help restore skin barrier integrity, reduce inflammation and prevent disease flares. These emollients not only protect the skin, but also modulate on the skin microbiome, which has become a cornerstone in disease management. Sensory properties, such as texture, appearance and the sensation of freshness, are critical factors influencing patient perception, treatment adherence and product efficacy.

OBJECTIVES: To test, a controlled study involving 120 participants, the ability of consumers to recognize emollient creams based solely on sensory characteristics to ensure that sensory stimuli from emollients cannot be a source of unblinding in a clinical trial involving topical corticosteroids.

METHODS: We conducted a double-blind quantitative assessment in a controlled environment involving 120 healthy volunteers who were regular users of moisturizing creams, of whom 50% were classified as 'naïve' users and 50% as 'connoisseurs'. The creams under investigation (n = 4) were placed in identical bottles and evaluated in monadic sequence according to a Latin square experimental design.

RESULTS: There were no significant statistical differences in overall appearance, shine or transparency between the four emollients. Only 6% of consumers recognized Neutraderm, 8% La Roche-Posay, 6% Avene and 4% Uriage (i.e. figures below any recognition by chance). Overall, we report a satisfaction rate of almost 60% for the topicals used (from 45% up to 64%).

CONCLUSIONS: This finding supports the feasibility of conducting blinded clinical trials on the emollients used in this study as sensory cues are unlikely to compromise the blinding.},
}

@article {pmid42222730,
year = {2026},
author = {Rahim, M and Lawrence, B and Ganga, G},
title = {Indole-3-acetic acid production by endophytic consortia from red ginger lily (Alpinia purpurata (Vieill.) K. Schum) and its application in plant growth promotion.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {32},
number = {5},
pages = {1041-1053},
pmid = {42222730},
issn = {0971-5894},
abstract = {UNLABELLED: Indole-3-acetic acid (IAA) is a widely studied plant hormone, produced by plants and microorganisms like bacteria and fungi, which regulates plant growth and development. The current study was conducted to investigate the IAA production by endophytes isolated from Alpinia purpurata (Vieill.) K. Schum (red ginger lily), a medicinally and ornamentally important rhizomatous plant whose endophytic microbiome remains largely unexplored, particularly with respect to phytohormone production. This study assembled an effective IAA producing consortium, confirming IAA production by LC MS and evaluated its plant growth promotion potential by seed-germination assays, hydroponics, tissue culture, and field trials. A total of fifty morphologically distinct bacteria were obtained, whose IAA production ranged from 17.75 ± 0.02 to 257.35 ± 0.77 µg/mL. Three strains, Agrobacterium radiobacter, Pseudomonas psychrophila, and Lysinibacillus macroides, were used to form a microbial consortium that produced more IAA (320.77 ± 02 µg/mL) than the individual isolates. IAA was confirmed to be present in the sample at 0.442 µg/mL with a typical retention period by LC MS analysis. When compared to untreated controls, plant growth assessments showed improved rhizome yield (70.8%), shoot development (41.7%), leaf characteristics (45.6%), and seed germination (50%). This is the first study to report on IAA production by endophytic bacteria derived from Alpinia purpurata, resulting in the formation of a functionally compatible microbial consortium that produces biologically active IAA, validated by LC-MS/MS, and shown to promote germination and plant growth in tissue culture, hydroponic, and field environments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-026-01745-z.},
}

@article {pmid42222738,
year = {2026},
author = {Park, JH and Chung, J and Lee, HJ and Na, HS},
title = {Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2679807},
pmid = {42222738},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease driven by a dysbiotic subgingival microbiome. While 16S rRNA gene amplicon sequencing is widely used, whole-genome shotgun (WGS) metagenomics is increasingly applied for higher taxonomic and functional resolution.

OBJECTIVE: The aim of this study was to directly compare 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomic sequencing using matched subgingival plaque samples from patients with periodontitis.

METHODS: Subgingival plaque samples from 28 patients with periodontitis were analyzed using both 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomics. Taxonomic composition, microbial diversity, differential abundance and functional analysis were compared across platforms.

RESULTS: WGS generated markedly higher read counts than 16S rRNA gene amplicon but showed wide variability in non-human reads, whereas 16S rRNA gene amplicon yielded a consistent proportion of non-chimeric reads. High taxonomic overlap was observed at the phylum level but declined at higher taxonomic ranks. WGS preferentially detected taxa such as Actinomyces, Corynebacterium and Olsenella, while the 16S rRNA gene amplicon more frequently captured Saccharibacteria (TM7) and low-abundance taxa. Core genera, including Rothia, Neisseria and Cardiobacterium showed comparable abundance patterns across platforms. When patients were grouped depending on probing pocket depth (PPD), LEfSe analysis resulted in platform-specific enrichment patterns. Functional analyses revealed shared central pathways, such as pyruvate metabolism, while 16S-based PICRUSt2 emphasized reductive and degradative pathways and WGS-based HUMAnN highlighted oxidative and biosynthetic pathways. Notably, WGS-based functional profiles were strongly influenced by microbial read depth.

CONCLUSIONS: This comparative analysis demonstrates that 16S rRNA gene amplicon (V1-V2) sequencing and WGS both robustly capture core subgingival microbial signatures. While WGS provides higher species-level and functional resolution, the resolution was strongly constrained by microbial read depth in host-rich subgingival samples. These findings provide practical guidance for selecting appropriate sequencing strategies and optimizing sample preparation when designing WGS-based periodontal microbiome studies.},
}

@article {pmid42223229,
year = {2026},
author = {Miao, S and Liu, W and Li, Y and Gu, R and Wang, Y},
title = {Mapping the Research Landscape of Gut Microbiota in Autoimmune Eye Diseases: A Bibliometric Analysis and Knowledge Evolution Study.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/09273948.2025.2606819},
pmid = {42223229},
issn = {1744-5078},
abstract = {PURPOSE: This study aims to systematically analyze and map the research landscape of gut microbiota in autoimmune eye diseases through comprehensive bibliometric analysis.

METHODS: We retrieved 261 relevant publications from the Web of Science Core Collection (2010-2024) and analyzed them using CiteSpace, VOSviewer, and biblioshiny.

RESULTS: The results reveal three distinct developmental phases: initial exploration (2010-2015), emerging growth (2016-2020), and rapid expansion (2021-2024). International collaboration analysis identified the United States and China as leading contributors, with strong European research clusters. Core research themes centered on gut microbiota-host immune system interactions, inflammatory pathways, and disease-specific microbial signatures. Temporal analysis demonstrated evolution from fundamental studies to mechanistic investigations and therapeutic applications. Citation analysis identified landmark studies that established gut-eye axis mechanisms and pathogenic processes. Analysis of research hotspots revealed increasing focus on personalized medicine approaches, multi-omics integration, and microbiome-based therapeutics.

CONCLUSION: This study provides a comprehensive overview of the field, identifies research frontiers, and proposes future research directions, namely, methodological advancement, mechanistic understanding, and clinical translation.},
}

@article {pmid42223258,
year = {2026},
author = {Riedmuller, KC and Dyer, JE and Ottesen, EA},
title = {Large temperature excursions have modest impacts on community composition in the high diversity gut microbiome of omnivorous American cockroaches (Periplaneta americana).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0028826},
doi = {10.1128/spectrum.00288-26},
pmid = {42223258},
issn = {2165-0497},
abstract = {UNLABELLED: Microbial residents of ectothermic hosts are exposed to variations in temperature that have the potential to impact their physiology and the host-microbe symbiotic relationship. In this experimental warming study, laboratory populations of American cockroaches (Periplaneta americana) were kept at a baseline low room temperature of 20-22°C or a high temperature of 30°C, for 2 weeks. We quantified bacterial load and performed high-throughput 16S rRNA gene sequencing to assess the hindgut microbiome's response to a near 10°C shift in environmental temperature. We report modest impacts of temperature on cockroach gut microbiome composition. The high temperature treatment induced increases in the relative abundance of Proteobacteria and Euryarchaeota phyla, as well as the Lactobacillaceae and Enterococcaceae families. We also observed increased interindividual variability. There were no significant differences in the dominant Bacteroidota or Firmicutes phyla, and no significant losses or reductions in taxa, or bacterial load, respectively. This suggests that the gut community of American cockroaches is largely resilient to prolonged increases in temperature, and has implications for the cockroach to withstand the impacts of climate change.

IMPORTANCE: Insects, as with most animals, often harbor microbial symbionts that play an essential role in host health and nutrition. As insects are ectotherms, these microbial symbionts are subject to the same temperature fluctuations as their hosts, potentially impacting host temperature responses. Here, we demonstrate that the American cockroach (Periplaneta americana) gut microbiome exhibits only modest changes following an ~10°C increase in environmental temperature. This contrasts with studies in other insects, whose microbiota were highly responsive to temperature variation. This work illustrates that the microbiota of insects may vary in their sensitivity to long-term temperature shifts, providing a more comprehensive understanding of potential variability in insect responses to climate change.},
}

@article {pmid42223272,
year = {2026},
author = {Borton, MA and Oliverio, AM and Narrowe, AB and Villa, JA and Rinke, C and Hoyt, DW and Liu, P and McGivern, BB and Bechtold, EK and Ellenbogen, JB and Daly, RA and Smith, GJ and Angle, JC and Flynn, RM and Freiburger, AP and Louie, KB and Stemple, B and Northen, TR and Henry, C and Miller, CS and Morin, TH and Bohrer, G and Wrighton, KC},
title = {Mapping the soil microbiome functions shaping wetland methane emissions.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0068025},
doi = {10.1128/msystems.00680-25},
pmid = {42223272},
issn = {2379-5077},
abstract = {Accounting for only 8% of Earth's land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.IMPORTANCESoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single-lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.},
}

@article {pmid42223530,
year = {2026},
author = {Pokharel, SK and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, DC},
title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag140},
pmid = {42223530},
issn = {1751-7370},
abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Time-lapse microscopy revealed that Archangium exhibited reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate) but maintained robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.},
}

@article {pmid42223629,
year = {2026},
author = {Bahar, A and Khazaei, M and Tahmasebi, H},
title = {The complex of gut microbial metabolites and sex hormones in Alzheimer's disease.},
journal = {Seminars in immunopathology},
volume = {48},
number = {1},
pages = {},
pmid = {42223629},
issn = {1863-2300},
mesh = {Humans ; *Alzheimer Disease/metabolism/etiology ; *Gonadal Steroid Hormones/metabolism ; *Gastrointestinal Microbiome ; Animals ; Disease Susceptibility ; Dysbiosis ; Blood-Brain Barrier/metabolism ; },
abstract = {Alzheimer's Disease (AD) is a progressive neurodegenerative disorder with a complex pathophysiological mechanism and a marked sex difference in prevalence and disease severity, with women being more affected and showing a more aggressive disease course. Recent studies indicate that a complex interplay among gut microbiota (GM), their metabolites, and sex hormones is a crucial factor in AD pathogenesis. In this review, we attempted to synthesize current studies to critically discuss the tripartite interplay among GM, sex hormones, and the brain in AD. Firstly, we discuss the role of the microbiota-gut-brain axis in AD pathogenesis with a focus on how gut dysbiosis contributes to neuroinflammation, disruption of the blood-brain barrier (BBB), and accumulation of pathological proteins. Then, we discuss the mechanistic roles of various GM-derived metabolites in AD pathogenesis, with a focus on the two-edged role of SCFAs and their derivatives, the neuroactive role of tryptophan and its derivatives, and the modulatory roles of bile acids and trimethylamine N-oxide. Finally, we discuss a novel concept, the "microgenderome," referring to the bidirectional interplay between sex hormones and GM, and how GM regulates sex hormone levels through unique enzymatic functions termed the "estrobolome" and a newly proposed "testobolome."},
}

Humans
*Alzheimer Disease/metabolism/etiology
*Gonadal Steroid Hormones/metabolism
*Gastrointestinal Microbiome
Animals
Disease Susceptibility
Dysbiosis
Blood-Brain Barrier/metabolism

@article {pmid42223784,
year = {2026},
author = {Moghaddam, NA and Mohabbat, A and Jigheh, MP and Mahboubi, A and Ravanlo, ZZ and Shanehbandi, D and Shokri, S and Baghi, HB},
title = {The interplay between HPV, vaginal microbiota and host immunity in cervical carcinogenesis.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-026-05169-9},
pmid = {42223784},
issn = {2730-6011},
abstract = {Cervical cancer (CC) remains a major global health challenge, largely driven by persistent infection with high-risk human papillomavirus (HPV) genotypes. Emerging evidence suggests that the interplay between HPV, the vaginal microbiota (VM), and host immune responses critically influences viral persistence and disease progression. In particular, dysbiotic VM marked by reduced Lactobacillus dominance and increased prevalence of anaerobic bacteria such as Gardnerella, Sneathia, Prevotella, and Atopobium-can impair HPV clearance, promote chronic inflammation, and facilitate progression from cervical intraepithelial neoplasia (CIN) to invasive carcinoma. Understanding these tripartite interactions offers opportunities for novel preventive and therapeutic strategies, including microbiome modulation, immunotherapy, and gene editing. This review highlights the potential of microbiome-targeted interventions to enhance immune responses against HPV and reduce the burden of CC, although the underlying causal mechanisms require further investigation in prospective studies.},
}

@article {pmid42223828,
year = {2026},
author = {J, G and Ranganathan, N and A S, V and Chopra, H},
title = {Targeting Type 2 and Non-type 2 Asthma: Emerging Biologics and Personalized Strategies.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42223828},
issn = {1534-6315},
mesh = {Humans ; *Asthma/immunology/drug therapy/therapy ; *Precision Medicine/methods ; *Biological Products/therapeutic use ; *Anti-Asthmatic Agents/therapeutic use ; Cytokines/antagonists & inhibitors ; Th2 Cells/immunology ; },
abstract = {PURPOSE OF REVIEW: Asthma continues to pose a serious global health issue affecting billions of people and causing significant morbidity. It is immunologically heterogeneous disease, classified as Type 2 (Th2/ILC2-mediated, eosinophilic) or Type 1 (Th1-mediated, neutrophilic, steroid-resistant) inflammation. This review aims to evaluates current biologic therapies, emerging strategies, and challenges in asthma management and highlights the challenges and future directions in personalized asthma management.

RECENT FINDINGS: Current biologics for Type 2 asthma like anti-IgE (omalizumab), anti-IL-5 (mepolizumab, reslizumab, benralizumab), anti-IL-4/IL-13 (dupilumab) and anti-TSLP (tezepelumab) were effectively controlling severe eosinophilic asthma. Emerging therapies for Type 1 and mixed phenotypes include anti-TNF-α agents, CXCR2 antagonists, IL-17 blockers, JAK-STAT inhibitors and microbiome-based approaches and upstream epithelial cytokine-targeting therapies such as anti-TSLP agents. Dual or broad-spectrum strategies, such as bispecific antibodies and endotype-guided biologic selection offer more targeted interventions. Despite these advances, challenges persist regarding high costs, limited accessibility, absence of robust biomarkers, and potential risks of immunosuppression. Biologics have transformed severe Type 2 asthma management, but effective treatments for Type 1 and steroid-resistant asthma remain limited. Future directions involve multi-omics, machine learning and gene therapy to optimize personalized therapy and develop inclusive strategies for the diverse inflammatory endotypes.},
}

Humans
*Asthma/immunology/drug therapy/therapy
*Precision Medicine/methods
*Biological Products/therapeutic use
*Anti-Asthmatic Agents/therapeutic use
Cytokines/antagonists & inhibitors
Th2 Cells/immunology

@article {pmid42223880,
year = {2026},
author = {Li, J and Liu, Y and Jia, L},
title = {The Role of Lacticaseibacillus Rhamnosus in Periodontitis Management: From Microecological Regulation to Clinical Application.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42223880},
issn = {1867-1314},
support = {82571088//the National Nature Science Foundation of China/ ; 82101009//the National Nature Science Foundation of China/ ; 2024-1-2141//Capital's Funds for Health Improvement and Research/ ; G202532300//Beijing High-Level Innovation and Entrepreneurship Talent Support Program young backbone talent projects/ ; L242122//Beijing Natural Science Foundation/ ; YSP20200904//Beijing Stomatological Hospital, Capital Medical University Young Scientist Program/ ; },
abstract = {Periodontitis is a chronic inflammatory disease caused by dysbiosis of the periodontal microbiome, threatening both oral and systemic health. Current prevention and treatment strategies for periodontitis mainly rely on mechanical therapy, with antibiotics used as supplements. However, limitations of mechanical therapy and increasing antibiotic resistance have prompted the exploration of new adjunctive strategies. Probiotic therapy, particularly Lacticaseibacillus rhamnosus (L. rhamnosus), formerly known as Lactobacillus rhamnosus, has emerged as a promising approach due to its ability to modulate periodontal microecology. L. rhamnosus exerts therapeutic effects by inhibiting pathogens, modulating immune responses, and promoting tissue repair. L. rhamnosus has been applied in various forms for the adjuvant treatment of periodontitis and numerous clinical trials have confirmed its safety and effectiveness, indicating broad potential for application. Nevertheless, current clinical studies still face challenges such as unclear strain-specific effects and a lack of standardized administration protocols. Future research should investigate the mechanisms of different strains and evaluate targeted interventions in diverse patient populations to advance the clinical use of probiotic therapies.},
}

@article {pmid42224056,
year = {2026},
author = {Paiva, BR and Schultz, J and Modolon, F and Brito, JS and Ribeiro-Alves, M and Rosado, AS and Cardozo, LFMF and Mafra, D},
title = {Intestinal microbiota profile and inflammation in patients undergoing hemodialysis: a comparison between the Southern and Southeastern regions of Brazil.},
journal = {Jornal brasileiro de nefrologia},
volume = {48},
number = {3},
pages = {e20250097},
pmid = {42224056},
issn = {2175-8239},
mesh = {Humans ; Male ; *Renal Dialysis ; Brazil ; Female ; *Inflammation/microbiology/blood/etiology ; Middle Aged ; *Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/therapy/microbiology/blood ; Feces/microbiology ; },
abstract = {INTRODUCTION: Exogenous lifestyle factors, such as different cultures, diets, and geo-graphic location, can alter the microbiota in patients with chronic kidney disease (CKD), which is closely related to inflammation. However, few studies have examined how these factors influence the composition of the microbiota. Thus, the objective of this study was to characterize and compare the intestinal microbiota profile and inflammation in CKD patients undergoing hemodialysis (HD) in the Southern and Southeastern regions of Brazil.

METHODS: Blood and stool samples were obtained from two groups of HD patients: one from the city of Blumenau (Southern region) and the other from the city of Rio de Janeiro (Southeastern region). Fecal DNA was extracted, and the V4 region of the bacterial 16S ribosomal RNA gene was sequenced. The fecal microbiome was analyzed using bioinformatic tools. Plasma concentrations of IL-6 and TNF-α were evaluated by ELISA.

RESULTS: Thirty patients were included in the study, with 14 individuals residing in the Southern region (group S) [50% male, 58 (13.5) years of age] and 16 individuals residing in the Southeastern region (group SE) [47.1% male, 57 (19) years of age]. The α- and β-diversity indices of the intestinal microbiota did not differ significantly between the groups. However, patients from the Southern region had higher plasma TNF-α (p = 0.008) and IL-6 (p = 0.003) levels than those from the Southeastern region.

CONCLUSION: Although HD patients with CKD residing in the Southern and Southeastern regions present similar intestinal microbial patterns, patients from the Southern region had higher concentrations of inflammatory markers.},
}

Humans
Male
*Renal Dialysis
Brazil
Female
*Inflammation/microbiology/blood/etiology
Middle Aged
*Gastrointestinal Microbiome
*Renal Insufficiency, Chronic/therapy/microbiology/blood
Feces/microbiology

@article {pmid42224283,
year = {2026},
author = {Correale, J and Marrodan, M and Piedrabuena, MA and Soman, K and Farez, MF and Baranzini, SE},
title = {Microbiome-derived metabolites from vitamin B2 and B9 pathways modulate MAIT cells from multiple sclerosis patients.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585261447695},
doi = {10.1177/13524585261447695},
pmid = {42224283},
issn = {1477-0970},
abstract = {BACKGROUND: Mucosal-associated invariant T (MAIT) cells recognize microbial vitamin B2 and B9 metabolites via MR1 and have been implicated in multiple sclerosis (MS). How patient-specific gut microbiota shape human MAIT-cell pathogenicity at the clonal level remains unknown.

MATERIAL AND METHODS: We generated 62 MAIT-cell clones from relapsing-remitting multiple sclerosis (RRMS) patients and 50 from healthy controls (HCs). Clones were stimulated with riboflavin- or folate-pathway metabolites, paraformaldehyde-fixed patient-matched gut bacterial isolates, or interleukin (IL)-12/IL-18. Activation markers, cytokine secretion, cytotoxicity, and competitive MR1-ligand inhibition were assessed. Intestinal permeability was evaluated using I-FABP, LBP, GLP-2, and fecal α-1-antitrypsin.

RESULTS: MS-derived MAIT clones showed markedly enhanced activation, increased interferon-gamma (IFN-γ), IL-17, and granulocyte-macrophage colony-stimulating factor (GM-CSF) secretion, and greater cytotoxicity compared with HCs when stimulated with riboflavin-producing taxa isolated from the same patients. Importantly, several responses diverged from predictions based on murine models and genomic inference, including mixed cytokine profiles and graded competitive inhibition by folate-derived ligands. These findings highlight species-specific differences in MR1 ligand handling and MAIT-cell activation. Activation required uptake of intact bacteria and acid-dependent MR1 loading. MS patients exhibited significant intestinal barrier dysfunction, linking dysbiosis to systemic MAIT-cell hyperactivation.

CONCLUSION: At clonal resolution, this study demonstrates that patient-specific microbial metabolism, MR1-ligand competition, and epithelial barrier disruption cooperate to amplify MAIT-cell pathogenicity in MS, revealing human-specific mechanisms not predicted by animal models.},
}

@article {pmid42224874,
year = {2026},
author = {Kenzi, M and Benbernou, M and Khelifa, H and Tbahriti, HF},
title = {Machine learning-based prediction of antibiotic resistance gene distribution in agricultural soils under different climate change scenarios.},
journal = {The Science of the total environment},
volume = {1042},
number = {},
pages = {181905},
doi = {10.1016/j.scitotenv.2026.181905},
pmid = {42224874},
issn = {1879-1026},
abstract = {Antibiotic resistance genes (ARGs) in agricultural soils represent a major public health concern, as climate change is believed to augment their dissemination and abundance. Understanding the impact of future climate change scenarios on ARG abundance is essential to implement predictive and proactive One Health strategies. In this study, a total of 2301 soil samples from 67 countries across six continents were compiled from three global metagenome databases, namely NCBI SRA, MG-RAST, and JGI IMG/M. Six machine learning models, namely LightGBM, XGBoost, Random Forest, Support Vector Machines, Deep Neural Networks, and Logistic Regression, were used to predict ARG distribution patterns in agricultural soils, and their performance was evaluated using stratified 10-fold cross-validation with metrics such as AUC-ROC, precision, recall, F1 score, and Matthews Correlation Coefficient. WorldClim 2.1 and CMIP6 models were used to project ARG distribution under three Representative Concentration Pathway scenarios, namely RCP 2.6, RCP 4.5, and RCP 8.5, for the years 2050 and 2070. The LightGBM model achieved the best predictive performance, with an AUC-ROC of 0.957 (95% CI: 0.951-0.963), substantially higher than that of the other models, while the Deep Neural Networks model achieved an AUC-ROC of 0.891. The LightGBM model demonstrated high stability across cross-validation folds, with minimal fold-to-fold variance, defined as the standard deviation of AUC-ROC scores across the 10 folds (SD = 0.008). SHAP feature importance analysis identified soil temperature, pH, and organic carbon content as the top three factors influencing ARG relative abundance, with SHAP values of 0.342, 0.287, and 0.251, respectively. Annual precipitation and soil moisture level were also identified as significant contributors to ARG distribution. SHAP dependency plots revealed critical thresholds for ARG relative abundance, with a sharp increase observed independently when soil temperature exceeds 18 °C and when soil pH drops below 6.5. Furthermore, a non-linear accelerating increase in ARG abundance risk was observed as climate change intensity worsened across scenarios. Projections for future climate change scenarios indicate a potential 34.7% increase in high-risk ARG zones by the year 2070, with the largest changes expected in South Asia, Sub-Saharan Africa, and Mediterranean regions. Paired t-tests revealed significant differences in performance among all models (p < 0.001). These findings demonstrate that gradient-boosting methods such as LightGBM outperform deep learning approaches for ARG prediction from soil microbiome data, offering higher accuracy and interpretability. As climate change is projected to increase ARG risks in a non-linear manner, the development of climate-adaptive agricultural practices and global surveillance systems is urgent. This framework provides actionable risk-mapping tools to support precision farming and region-specific policy interventions within the One Health approach.},
}

@article {pmid42224947,
year = {2026},
author = {Alake, SE and Ice, JA and Orphan, J and Adedigba, P and Islam, P and Hatter, B and Lu, P and Perez, L and Olawale, F and Butcher, JT and Knotts, TA and Wozniak, KL and Lin, D and Chowanadisai, W and Smith, BJ and Lucas, EA},
title = {Pinto bean supplementation prevents vascular dysfunction by modulating the gut microbiome in an interleukin-10-dependent manner in mice fed an atherogenic diet.},
journal = {Nutrition research (New York, N.Y.)},
volume = {151},
number = {},
pages = {120-133},
doi = {10.1016/j.nutres.2026.05.001},
pmid = {42224947},
issn = {1879-0739},
abstract = {The risk of cardiovascular disease increases under gut inflammatory conditions, but the underlying mechanism remains unclear. Pinto bean (PB) consumption reportedly increases the ileal expression of the anti-inflammatory cytokine interleukin (IL)-10. We investigated the effects of PB supplementation on inflammatory signature and vascular endothelial function in mice. We hypothesize that the effect of PB is mainly mediated by IL-10. Eight-week-old female mice from a C57BL/6 J background were randomized to groups in a 2 × 3 design, with genotype (Il10[+]/[+], WT or Il10[-]/[-], KO) and diets (AIN-93 M [CON] diet, atherogenic diet with 36.5% fat kcal and 1% cholesterol [Ath], or Ath diet + 5% PB, wt/wt [Ath+PB]) as factors. Gut microbiota composition, fecal short-chain fatty acids (SCFAs), ileal T-cell populations, inflammatory markers, and vascular endothelial function were examined. In WT mice, PB supplementation preserved gut microbial diversity and maintained fecal butyrate concentrations compared with atherogenic diet alone (P< .05), while sustaining the relative abundance of SCFA-producing taxa (Alistipes, Roseburia). These microbial changes were accompanied by an increased proportion of ileal regulatory T cells (P < .001) and preserved acetylcholine-induced, endothelium-dependent vasodilation (P < .05). In contrast, IL-10 KO mice exhibited impaired endothelial function and reduced microbial diversity irrespective of diet, and PB supplementation did not significantly improve vascular or immune outcomes. Overall, PB supplementation was associated with preserved vascular endothelial function and favorable microbiota and immune profiles in WT but not IL-10-deficient mice, suggesting these dietary benefits require intact IL-10 signaling.},
}

@article {pmid42224959,
year = {2026},
author = {Das, R and Baldi, A and Pasricha, SR and Thompson, LM and Díaz-Artiga, A and Grajeda, LM and McCracken, JP and Jesser, K and Waller, L and Freeman, MC and Clasen, T and Sinharoy, SS},
title = {Upper respiratory microbiome composition and associations with air pollution and infant respiratory health: a longitudinal study in Guatemala.},
journal = {International journal of hygiene and environmental health},
volume = {276},
number = {},
pages = {114843},
doi = {10.1016/j.ijheh.2026.114843},
pmid = {42224959},
issn = {1618-131X},
abstract = {The early-life composition and maturation of the upper respiratory microbiome, and their associations with environmental exposures and respiratory health, remain poorly characterized. We collected nasopharyngeal (NP) and oropharyngeal (OP) samples (n = 257) from a cohort of 114 Guatemalan infants at birth and six months between February and August 2019. We analyzed their NP and OP microbiomes using 16S rRNA gene sequencing and examined associations with air pollution and respiratory outcomes during the first year of life. Results show that NP and OP microbiomes exhibited distinct developmental trajectories, with NP diversity declining and OP diversity increasing by six months, accompanied by age-related compositional restructuring. Taxonomic succession was anatomically site-specific; NP communities matured toward lower alpha diversity with facultative dominance, whereas OP communities showed anaerobic enrichment and rising alpha diversity, yielding stable, differentiated airway communities. Neither alpha nor beta diversity was consistently associated with WHO IMCI (Integrated Management of Childhood Illness) pneumonia (both severe and non-severe), cough, or hypoxemia, except for higher NP alpha diversity at birth, which predicted increased odds of fast breathing episodes (Shannon: adjusted OR = 4.81, 95% CI: 1.80, 7.46 & inverse Simpson: aOR = 1.20, 95% CI: 1.04, 1.43). Higher NP Bacteroidota relative abundance at birth was associated with lower odds of subsequent WHO IMCI pneumonia (aOR: 0.003, 95% CI 0.001-0.02; FDR = 0.10). Higher personal PM2.5 exposure at 3 months was associated with differential NP microbiome composition at 6 months, including lower Firmicutes abundance (β = -0.53; 95% CI: -0.82, -0.25; FDR = 0.17) and higher Prevotella abundance (β = 3.21; 95% CI: 1.90, 4.51; FDR = 0.08), consistent with PM2.5 acting as an ecological stressor that may predispose to airway dysbiosis. These findings reveal coordinated but site-specific patterns of microbial maturation in early infancy and suggest that predictable age-related shifts in community composition, together with both environmental exposures, shape upper airway microbial communities with implications for respiratory health.},
}

@article {pmid42225162,
year = {2026},
author = {Wu, G and Wang, Z and Tsigkou, K and Vrieze, J and Angelidaki, I},
title = {A stress-response-recovery framework integrating microbial life-history strategies for stressed anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135055},
doi = {10.1016/j.biortech.2026.135055},
pmid = {42225162},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a mature biotechnology; however, its operational stability remains constrained by the limited predictability of microbial responses to environmental stress. In this review, stressed AD systems are defined as microbial ecosystems in which one or more environmental stressors disrupt microbial functioning, reduce microbial growth and survival, and drive deterministic and/or stochastic shifts in the AD microbiome, thus impacting process performance. For stressed AD, this review proposes a unifying stress-response-recovery framework integrating microbial life-history strategies. Specifically, stress acts as an ecological filter that suppresses stress-sensitive microorganisms while selecting stress-tolerant ones. During the response phase, system resilience can be achieved through multiple forms of microbial plasticity, including spatial reorganization (e.g., granulation), metabolic rerouting (e.g., shifts from acetoclastic methanogenesis to syntrophic acetate oxidation), and alternative electron-transfer pathways such as direct interspecies electron transfer. Importantly, recovery does not necessarily ensure a return to the original community structure; instead, it is governed by functional redundancy, microbial memory, and ecological hysteresis, often resulting in alternative stable states with reconfigured metabolic networks while preserving methane production. Collectively, these insights provide complementary ecologically informed management strategies, highlighting the potential of strategy-based monitoring, microbiome engineering, and targeted interventions to enhance system resilience. By integrating ecological theory with engineering practice, this review advances the understanding of AD stress and provides a framework for designing more robust and adaptable anaerobic systems.},
}

@article {pmid42225178,
year = {2026},
author = {Wilczynski, W and Musiałowski, M},
title = {Chronic effects of the organoarsenicals adamsite and triphenylarsine on the intestinal microbiota of Danio rerio.},
journal = {Environmental toxicology and pharmacology},
volume = {},
number = {},
pages = {105051},
doi = {10.1016/j.etap.2026.105051},
pmid = {42225178},
issn = {1872-7077},
abstract = {Organoarsenicals, including the chemical warfare-related adamsite and triphenylarsine (TPA), are contaminants of emerging concern in aquatic environments. While the chronic effects of these compounds on zebrafish (Danio rerio) survival, growth, and other toxicological endpoints have been characterized, the role of gut microbiota in host responses remains unclear. Here, we investigated the effects of 28-day sublethal exposure to adamsite (0.05, 0.15, 0.20, 0.25μg/L) and TPA (0.73, 0.17, 1.88, 3.00, 4.80μg/L) on the intestinal microbiota of zebrafish. Microbiota composition and predicted function were assessed using 16S rDNA sequencing and PICRUSt2. Adamsite caused concentration-dependent microbial diversity loss and substantial shifts in community composition, as well as predicted function, consistent with its high toxicity. In contrast, TPA induced only minor changes, with microbial diversity maintained and functional potential retained, reflecting the comparatively lower toxicity. These findings highlight the gut microbiota as a responsive target of organoarsenical toxicity, supporting microbiome-aware ecotoxicological risk assessment.},
}

@article {pmid42225253,
year = {2026},
author = {Singh, L and Bhullar, G and Shaik, S and Ganesh, V and Kesani, H and Rai, M},
title = {Gut Feeling: Microbiota as a Hidden Regulator of Hypertension.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101623},
doi = {10.1016/j.tjnut.2026.101623},
pmid = {42225253},
issn = {1541-6100},
abstract = {Emerging evidence identifies the gut microbiota as a key regulator of blood pressure through its role in metabolizing dietary substrates into bioactive compounds that influence vascular, immune, and neurohumoral pathways. This review synthesizes recent mechanistic, preclinical, and clinical evidence linking gut microbial dysbiosis to hypertension, with particular emphasis on nutrition-dependent microbial metabolism and its translational implications. Experimental studies demonstrate that depletion of short-chain fatty acid (SCFA)-producing bacteria and enrichment of pro-inflammatory and trimethylamine-producing taxa contribute to endothelial dysfunction, immune activation, and renin-angiotensin-aldosterone system dysregulation. Fecal microbiota transplantation (FMT) and germ-free animal models provide causal evidence that hypertensive microbiota can directly elevate blood pressure. Human multi-omics and metabolomic studies further show that microbial functional capacity and metabolite production, rather than taxonomic composition alone, are strongly associated with hypertensive phenotypes and therapeutic responsiveness. Importantly, dietary interventions, including high-fiber diets, resistant starch, and the Dietary Approaches to Stop Hypertension (DASH) diet, modulate microbial composition and enhance SCFA production, providing a mechanistic basis for their antihypertensive effects. Microbiota-drug interactions have also emerged as a novel determinant of antihypertensive treatment efficacy. Collectively, these findings support a metabolite-centered framework in which diet-microbiota interactions influence blood pressure regulation. Targeting the gut microbiota through nutritional and microbiome-based strategies represents a promising adjunctive approach for hypertension prevention and personalized management. However, large-scale longitudinal and interventional human studies are needed to establish causality and optimize microbiota-targeted therapies.},
}

@article {pmid42225474,
year = {2026},
author = {Bao, W and Li, G and Ding, Y and Wang, Y},
title = {Harnessing the gut microbiome for MASLD management: opportunities and challenges.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2026.05.017},
pmid = {42225474},
issn = {2095-9281},
}

@article {pmid42226086,
year = {2026},
author = {Ravi, SSN and Pipinos, A and Insley, N and Kaur, C and Kan, J and Heller, W and H Smith, A and Zinati, G and Richie, J and Bais, H},
title = {Exploring the role of ergothioneine and mycorrhizal fungi in shaping the wheat soil microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00913-8},
pmid = {42226086},
issn = {2524-6372},
abstract = {BACKGROUND: The association between plants and soil microbes is critical for both soil and plant health. Introducing beneficial microbial inoculants, such as arbuscular mycorrhizal fungi (AMF), can enhance the uptake of nutrients and compounds in plants including ergothioneine (ERGO), a well-known antioxidant and anti-inflammatory compound that humans must obtain through diet. However, little is known about how ERGO and inoculated AMF influence ERGO uptake in plants or affect soil microbiome composition, including bacteria, archaea, and fungi. This study investigates the interaction between soil-applied ERGO and AMF inoculation in plant-microbe symbioses to assess (1) whether these treatments increase ERGO content in the staple crop wheat (Triticum aestivum), and (2) how they alter soil microbiome structure.

RESULTS: Combined treatment with ERGO and AMF significantly increased wheat (Triticum aestivum) biomass and ERGO accumulation in roots and shoots. This co-treatment also led to higher bacterial diversity in rhizosphere. PERMANOVA analysis confirmed that both AMF and AMF/ERGO treatments significantly influenced microbiome composition, particularly bacterial communities. Indicator species analysis showed enrichment of Thioalkalivibrio, Chlorobi bacterium, Planctomycetes (Planctomycete A-2) and Candida subhashi, Paecilomyces zollerniae under ERGO and AMF/ERGO treatments.

CONCLUSIONS: Overall, the data show that plants can readily take up ERGO from the soil, with or without AMF, and that both ERGO and AMF amendments reshape soil microbiome communities. These findings highlight the broader role of ERGO and AMF in connecting soil microbiome to plant and human nutrition, a link that warrants further investigation.},
}

@article {pmid42226305,
year = {2026},
author = {Grundler, F and Ducarmon, QR and Holley, A and Knufinke, M and Strathmeyer, S and Heelemann, S and Geyer, R and Martínez-Téllez, B and MacArthur, MR and Zeller, G and Wilhelmi de Toledo, F and Mesnage, R},
title = {Health benefits of a five-day at-home modified fasting program: a randomised controlled trial.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42226305},
issn = {1756-994X},
support = {ALTF 1030-2022//EMBO postdoctoral fellowship/ ; RYC2022-036473-I//MCIN/AEI/10.13039/501100011033/ ; },
mesh = {Humans ; Female ; *Fasting ; Adult ; Male ; Blood Pressure ; Weight Loss ; Metabolomics ; Middle Aged ; Biomarkers ; },
abstract = {BACKGROUND: Fasting is one of the most cost-effective methods to improve cardiometabolic health. We tested a 5-day hypocaloric (~ 600 kcal/day) and ketogenic, modified fasting program (MFP) in a two-arm randomised controlled trial, where sixty-four healthy subjects were randomised to MFP or control group.

METHODS: We randomly assigned 64 participants to a group receiving the MFP or to a group of participants who were told to continue with their usual eating behaviour and lifestyle (control group). The changes in blood pressure and body weight were considered as primary endpoints. Secondary outcomes included ketosis, glucose and lipid metabolism, inflammatory markers, antioxidant capacity and well-being. Biological pathways and metabolic processes were explored with nuclear magnetic resonance blood metabolomics and gut metagenomics analyses. Outcomes were assessed at baseline, end of the MFP, after food reintroduction, and one month later.

RESULTS: MFP participants (n = 32) experienced weight loss compared to controls (- 0.52 ± 0.03 kg vs. - 0.03 ± 0.02 kg, p < 0.001). Changes in blood pressure caused by the MFP were non-significant at the end of the fasting period. However, blood pressure was significantly reduced following food reintroduction (systolic: -0.56 ± 0.12 mmHg vs. - 0.16 ± 0.12 mmHg, p < 0.05 and diastolic: -0.36 ± 0.08 mmHg vs. - 0.01 ± 0.08 mmHg, p < 0.01). Serum biochemistry showed the MFP reduced glucose levels and coagulation factors. The MFP also significantly increased physical well-being. Blood metabolomics revealed a significant decrease in chronic inflammation markers. Shotgun metagenomics of the gut microbiome showed significant changes in relative abundance of 11 bacterial species and in the genomic repertoire of 52 carbohydrate-active enzymes (CAZymes), reflecting an increase in families metabolising host-derived glycan substrates. None of these differences in gut microbiome and blood metabolome were shown to be statistically different from the control group one month after the intervention. Comparing MFP effects with a previous cohort's 5-day prolonged fasting showed similar metabolic changes.

CONCLUSIONS: This MFP is safe and transiently improves cardiometabolic health and physical well-being in healthy individuals.

CLINICAL TRIAL REGISTRATION: This trial was prospectively registered at ClinicalTrials.gov (NCT05821660) on 6 April 2023 prior to the start of patient recruitment.},
}

Humans
Female
*Fasting
Adult
Male
Blood Pressure
Weight Loss
Metabolomics
Middle Aged
Biomarkers

@article {pmid42226423,
year = {2026},
author = {Xu, Q and Zhang, X and Tian, H and Yang, X and Zhang, J and Li, H and Ma, Z and Zhang, D and Huang, K and Zhang, Y and Zhao, Y and Li, X and Zhao, L and Cheng, J and Xu, D and Li, F and Weng, X and Wu, W and Wang, W},
title = {Integrating rumen microbiome and host metabolome to investigate feed conversion ratio across different fattening stages in Hu sheep.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.260317},
pmid = {42226423},
issn = {2765-0189},
abstract = {OBJECTIVE: Feed conversion ratio (FCR) is a crucial economic trait in animal breeding and management and is also of great significance for environmental sustainability. This study aimed to investigate the potential regulatory mechanisms of FCR in sheep by integrating rumen microbiota and host metabolome through multi-omics analysis.

METHODS: FCR data were collected from 127 male Hu sheep. Extreme individuals were selected for rumen metagenomic and serum metabolomic analyses to identify key factors driving FCR across early and late fattening stages.

RESULTS: Bacteroides, Prevotella, and other genera were identified as dominant taxa in the rumen across both stages, suggesting their involvement in FCR regulation. Notably, Nocardia tengcongensis differed significantly between the highest FCR values (HF) and lowest FCR values (LF) groups at different stages, indicating its potential as a predictive biomarker of feed efficiency. Functional analysis revealed that the pentose phosphate pathway (M00004) and lysine biosynthesis via the succinyl-DAP pathway (M00016) were enriched in the LF group, whereas the methanogenesis pathway (M00357) was significantly enriched in the HF group, indicating increased methane production. Thirteen metabolites consistently differed between HF and LF across fattening stages and may serve as predictive biomarkers. In addition, the abundance of Prevotella and Bacteroides increased over time and showed significant correlations with key metabolites.

CONCLUSION: These findings suggest strong interactions between rumen microbiota and host metabolites that may collectively influence FCR, providing new insights into microbial and metabolic regulation of feed efficiency and a theoretical basis for optimizing feeding strategies in sheep.},
}

@article {pmid42226511,
year = {2026},
author = {Schindler, JC and Pillai, GV and Raffay, TM and Viswanath, SE and Seth, P},
title = {Computational Quantification of Peristalsis in Preclinical Mouse Models Using Smartphone Videography.},
journal = {Neurogastroenterology and motility},
volume = {38},
number = {6},
pages = {e70353},
doi = {10.1111/nmo.70353},
pmid = {42226511},
issn = {1365-2982},
support = {1R01CA280981-01A1/CA/NCI NIH HHS/United States ; 1U01CA294415-01A1/CA/NCI NIH HHS/United States ; 1R01NR019585-01A1/NR/NINR NIH HHS/United States ; 1R01EB037526-01/EB/NIBIB NIH HHS/United States ; 1I01BX006439-01//Veterans Affairs Biomedical Laboratory Research and Development Service/ ; //Northeast Ohio Renal Research Innovation Award/ ; F30-ES03527/NH/NIH HHS/United States ; T32-GM007250/NH/NIH HHS/United States ; T32-GM152319/NH/NIH HHS/United States ; R01-HL172894/HL/NHLBI NIH HHS/United States ; R01-DK128347/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Peristalsis/physiology/drug effects ; Mice ; *Smartphone ; *Video Recording/methods ; Gastrointestinal Motility/physiology ; Gastrointestinal Transit/physiology ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/physiology ; },
abstract = {BACKGROUND: A number of diseases and medical interventions affect gastrointestinal motility. However, quantitative methods for measuring effects on peristalsis in live animals are uncommon, cumbersome, and lack standardization.

METHODS: Here we present a new computational method for quantifying gut peristalsis in preclinical mouse models that requires only a video taken using a mobile phone camera. Our analytical pipeline processes the videographic data to track motion as it correlates to gastrointestinal transit.

RESULTS: This method is compatible with different mouse models (such as conventionally housed and germ-free), gut microbiome compositions, and can further be used to screen the impact of drugs on gut motility, which we demonstrate using methacholine as an example. Quantitative peristalsis measurements after methacholine treatment of conventionally housed and germ-free mice with or without reconstitution of their gut microbiomes demonstrate that our analytical method can detect and quantify changes in peristalsis driven not only by endogenous acetylcholine signaling but also by colonic anatomy and the microbiome.

CONCLUSION: We envision that our computational tool will find uses in preclinical drug or mouse model screenings and forms the cornerstone to expand this methodology to other non-gastrointestinal applications.},
}

Animals
*Peristalsis/physiology/drug effects
Mice
*Smartphone
*Video Recording/methods
Gastrointestinal Motility/physiology
Gastrointestinal Transit/physiology
Mice, Inbred C57BL
Gastrointestinal Microbiome/physiology

@article {pmid42226580,
year = {2026},
author = {Ahmed, MT and Majumdar, S and Noman, AA and Alam, MJ and Alam, MJ},
title = {Identification of Key Microbial Signatures Associated With Breast Cancer: Machine Learning-Based Approaches Using Gut Microbiome Data.},
journal = {Cancer medicine},
volume = {15},
number = {6},
pages = {e72008},
doi = {10.1002/cam4.72008},
pmid = {42226580},
issn = {2045-7634},
mesh = {Humans ; Female ; *Breast Neoplasms/microbiology ; *Machine Learning ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Predictive Learning Models ; *Bacteria/genetics/classification ; Middle Aged ; Case-Control Studies ; Random Forest ; },
abstract = {BACKGROUND: Breast cancer (BC) is one of the most common types of cancer incidence and mortality rates among women all over the world. Limitations in existing diagnostic methods, especially in low- and middle-income countries, require novel, noninvasive biomarkers. A complex and modifiable ecosystem, the gut microbiome has become a potential origin of such biomarkers because it has a systemic influence on host immunity, metabolism, and regulation of hormones. This study explores the gut microbiome alterations associated with BC and evaluates machine learning (ML) models to predict disease status based on 16S rRNA gene sequencing data of Ghanaian cohort (520 BC patients, 442 healthy controls).

RESULTS: Following high-quality sequence processing with QIIME2 and DADA2, alpha and beta diversity analyses showed a lower microbial richness and different community structures in BC patients (PERMANOVA, p = 0.001). Random Forest-based feature selection was used to find the top 20 discriminative genera, which were used to train 10 supervised ML algorithms. Ensemble models, particularly Random Forest, achieved the highest performance in predictive models (mean across 100 folds: AUC = 0.78, accuracy = 0.70), indicating strong discriminative potential. The results of SHAP analysis provided clear pictures of how specific microbes influence BC risk. We identified several risk-associated genera, notably Bacteroides, Lachnoclostridium, Parasutterella, and Tannerellaceae, whereas Coprococcus, Romboutsia, Ruminococcus, and Prevotella were associated with lower BC risk.

CONCLUSION: This study reveals a clear shift in the gut microbiome community structure among BC patients. We identified specific bacterial genera that act as either elevated or decreased disease risk. These findings not only highlight the power of machine learning models for noninvasive risk prediction but also provide a foundation for novel microbiome-based diagnostic strategies.},
}

Humans
Female
*Breast Neoplasms/microbiology
*Machine Learning
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
Predictive Learning Models
*Bacteria/genetics/classification
Middle Aged
Case-Control Studies
Random Forest

@article {pmid42226885,
year = {2026},
author = {Wang, S and Wikle, CK and Micheas, AC and Welch, JLM and Starr, JR and Lee, KH},
title = {Inference for Stationary Log-Gaussian Cox Point Processes using Bayesian Deep Learning: Application to Human Oral Microbiome Image Data.},
journal = {Spatial statistics},
volume = {73},
number = {},
pages = {},
pmid = {42226885},
issn = {2211-6753},
support = {R01 GM126257/GM/NIGMS NIH HHS/United States ; R21 DE026872/DE/NIDCR NIH HHS/United States ; },
abstract = {It is common in nature to see aggregation of objects in space. Exploring the mechanism associated with the locations of such clustered observations can be essential to understanding the phenomenon, such as the source of spatial heterogeneity, or comparison to other event generating processes in the same domain. Log-Gaussian Cox processes (LGCPs) represent an important class of models for quantifying aggregation in a spatial point pattern. However, implementing likelihood-based Bayesian inference for such models presents many computational challenges, particularly in high dimensions. In this paper, we propose a novel likelihood-free inference approach for LGCPs using the recently developed BayesFlow approach, in which invertible neural networks are employed to approximate the posterior distribution of parameters of interest. BayesFlow is a neural simulation-based method based on "amortized" posterior estimation. That is, after an initial training procedure, fast feed-forward operations allow rapid posterior inference for any data within the same model family. Comprehensive numerical studies validate the reliability of the framework and show that BayesFlow achieves substantial computational gain in repeated application, especially for two-dimensional LGCPs. We demonstrate the utility and robustness of the method by applying it to two distinct oral microbial biofilm images.},
}

@article {pmid42226891,
year = {2026},
author = {Gong, Q and Ding, K and Lou, W and Wang, J and Bian, G},
title = {Associations Between Social Jetlag and Gut Microbiome Profiles in Adolescents.},
journal = {Nature and science of sleep},
volume = {18},
number = {},
pages = {603131},
pmid = {42226891},
issn = {1179-1608},
abstract = {BACKGROUND: The microbiota-gut-brain axis plays a vital role in health, with growing evidence linking SJL to the gut microbiome. In this study, the relationship between self-reported SJL and gut microbiome composition is evaluated in an adolescent population.

METHODS: A total of 120 healthy adolescents (69 females, 51 males; mean age 12.69±0.65 years) were included. We investigated the associations of self-reported SJL with gut microbial α-diversity, the Firmicutes/Bacteroidetes (F/B) ratio, specific bacterial taxa, and functional gene diversity.

RESULTS: Participants had an average SJL of 0.87±0.73 h, with 25.0% experiencing SJL ≥2 h/d. Although continuous SJL was negatively correlated with α-diversity at the family level (Shannon and Simpson indices, all P<0.05), no significant differences were found between the SJL <2 and ≥2 h/d groups. Several taxa across multiple taxonomic levels (e.g. Bacteroidia and Bacteroidales) were associated with SJL (P<0.05). Differential abundance was observed for multiple families and genera between these two SJL groups. After FDR correction (q≤0.05), only the glutamate dehydrogenase gene gdh_K00262 was significantly enriched in the high SJL group (q=0.05).

CONCLUSION: SJL is associated with shifts in functionally relevant gut taxa, rather than a global ecological restructuring, in adolescents. Future work is needed to decipher the mechanisms of this microbiome-SJL interaction and its health significance.},
}

@article {pmid42227044,
year = {2026},
author = {Singh, VK and Gupta, P and Jain, SK and Matreja, PS},
title = {The gut-brain axis in Alzheimer's and Parkinson's diseases: a systematic review of microbiota-derived biomarkers and novel therapeutic approaches.},
journal = {Journal of clinical and experimental neuropsychology},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/13803395.2026.2673084},
pmid = {42227044},
issn = {1744-411X},
abstract = {BACKGROUND: The altered gut microbiota substantially impacts the onset and progression of Alzheimer's disease (AD) and Parkinson's disease (PD), the two most widely studied neurodegenerative conditions. Microbiome-derived metabolites have been increasingly associated with disease onset, progression, and therapeutic targets in neurodegenerative disorders. Exploring the diagnostic and therapeutic implications of gut microbiome-derived biomarkers is critical to advancing our understanding and management of neurodegeneration.

METHODOLOGY: We systematically reviewed both clinical and preclinical studies published from 2010 to 2025. Studies examining gut microbiota composition, microbial-derived metabolites, or therapeutic interventions targeting the gut microbiome were included. Identification of gut microbiome alterations, discovery of microbial or metabolite-based biomarkers, association with disease onset or progression, and/or therapeutic effects on cognitive, neurological, or inflammatory outcomes were evaluated.

RESULT: Short-chain fatty acids(SCFAs) such as butyrate and acetate were found to be noninvasive biomarkers in patients with Alzheimer's disease (AD), mild cognitive impairment (MCI), and Parkinson's disease (PD). Lower SCFA levels correlated with cognitive decline. Diagnostic accuracy improved when SCFA combinations were used, with AUCs ranging from 0.75 to 0.87. Trimethylamine N-oxide(TMAO) levels showed inconsistent associations, with both elevated and reduced levels linked to disease risk. Therapeutic approaches targeting gut microbiota, including probiotics, prebiotics, dietary changes, and fecal microbiota transplantation, demonstrated cognitive benefits and modulation of gut-brain signaling pathways.

CONCLUSION: Overall, gut-derived biomarkers offer a promising avenue for early diagnosis and novel therapeutic approaches in AD and PD, while acknowledging that evidence in other neurodegenerative diseases remains limited through modulation of the gut-brain axis.},
}

@article {pmid42227074,
year = {2026},
author = {Akinsuyi, OS and Ojeda, A and Xhumari, J and Ruggles, JV and Santos de Freitas, A and Roesch, LFW},
title = {Host transcriptional signatures associated with microbial sequence signals reveal age-related decline in intestinal homeostasis.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/17460913.2026.2682676},
pmid = {42227074},
issn = {1746-0921},
abstract = {AIMS: To characterize age-associated alterations in intestinal barrier homeostasis by integrating host transcriptomic profiles and mucosa-associated microbial sequence signals recovered from human colonic biopsy RNA-seq datasets.

MATERIALS AND METHODS: We performed an integrative host-microbiome metatranscriptomic analysis of human colonic biopsies from adults aged 20 to >70 years (n = 238). RNA-seq libraries from four public datasets were analyzed using DESeq2, GSEA, Ingenuity Pathway Analysis (IPA), and SAHMI for differential expression, pathway enrichment, and microbial profiling.

RESULTS: Aging was associated with progressive transcriptional remodeling of the intestinal barrier. Key epithelial genes regulating differentiation (GATA5), extracellular matrix (ECM) turnover (MMP9, ADAMTS4), and lipid metabolism (FABP6, LRP2, LPA) showed age-dependent dysregulation, accompanied by elevated chemokine and cytokine signaling (CXCL1, CCL19, IL17A, IL22). Pathway analyses identified enrichment of IL-17 and ECM-cytokine signaling, consistent with chronic inflammatory activation. Parallel microbial profiling revealed a shift from butyrate-producing commensals (Faecalibacterium, Roseburia, Bifidobacterium) toward mucolytic and pro-inflammatory taxa (Ruminococcus torques, Acidaminococcus intestini, Bacteroides ovatus).

CONCLUSIONS: This study supports a continuum model of immune, structural, and microbial remodeling associated with aging. The findings highlight mucosal host-microbe interactions as potential therapeutic targets for preserving epithelial resilience and promoting healthy aging.},
}

@article {pmid42227124,
year = {2026},
author = {Akimova, NI and Alekseeva, MG and Bekker, OB and Danilenko, VN},
title = {[Toxin-Antitoxin Systems: Formation of Genetic Networks of Human Microbiome Bacteria and Prospects for Application].},
journal = {Molekuliarnaia biologiia},
volume = {60},
number = {2},
pages = {248-265},
doi = {10.7868/S3034555326020049},
pmid = {42227124},
issn = {0026-8984},
abstract = {Toxin-antitoxin systems are modules consisting of genes that encode a stable toxin and a labile antitoxin. These systems are found in the genomes of most bacteria and archaea species. At present, eight types of toxin-antitoxin systems are distinguished. They perform a variety of functions in bacterial cells, the most important of which is adaptation to environmental stress. This review focuses on various types of toxin- antitoxin systems, their functions, and the mechanisms regulating interactions between the main components. These systems are described in detail for Bifidobacterium bifidum, Bifidobacterium longum, Lacticaseibacillus rhamnosus, and Mycobacterium tuberculosis. Furthermore, promising applications of toxin-antitoxin systems in biotechnology and infectious disease therapy are described.},
}

@article {pmid42227171,
year = {2026},
author = {Rodriguez-Cisneros, C and Agashe, A and Chaudhury, R and Daniel, K and Hewedy, OA and Maric, A and Hartman, S},
title = {Anticipate, acclimate, recuperate and remember: How spatiotemporal signal integration controls flooding stress resilience in plants.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag262},
pmid = {42227171},
issn = {1460-2431},
abstract = {Flooding is a major abiotic stress that restricts terrestrial plant growth and survival. A plant tissue's ability to avoid or sustain critical oxygen deprivation (hypoxia) and subsequent re-oxygenation damage is vital for its survival. Submergence triggers rapid ethylene and hypoxia signalling that in turn control acclimation responses, promoting plant resilience. Interestingly, an extensive range of additional environmental and internal factors were shown to influence these canonical signalling pathways associated with flooding acclimation and tolerance. Here, we discuss how such integrative ethylene- and hypoxia-dependent signalling enables plants to anticipate and prepare for potential flooding-induced hypoxia stress, fine-tune acclimation according to the environmental and internal metabolic context, and effectively orchestrate re-oxygenation responses. Furthermore, plants naturally experience environmental stress manifold throughout their lives, which may lead to long-term morphological adaptations and the encoding of stress memory to promote survival against sequential stressors.},
}

@article {pmid42227223,
year = {2026},
author = {Pérez-Ortega, S and Ortiz-Álvarez, R and Wierzchos, J and Blázquez, M and Gérault, A and de Los Ríos, A},
title = {Exploring the lichenization continuum through the marine tripartite symbiosis of Collemopsidium pelvetiae.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e70210},
doi = {10.1002/ajb2.70210},
pmid = {42227223},
issn = {1537-2197},
abstract = {PREMISE: Symbioses between lichen-forming fungi and brown algae (phaeophytes) are extremely rare. We investigated the interactions between the marine fungus Collemopsidium pelvetiae and its two photosynthetic partners, the brown alga Pelvetia canaliculata and a cyanobacterial symbiont to address questions on symbiosis biology, lichenization, and the diversity of fungal-photosynthetic associations in marine environments.

METHODS: We combined light microscopy, fluorescence microscope in structural illumination microscopy mode (SIM), and transmission electron microscopy (TEM) to characterize thallus architecture, symbiont interfaces, and ultrastructural interactions. Amplicon-based 16S rRNA sequencing profiled cyanobacteria and heterotrophic bacteria from two regions (northern Spain and Brittany, France).

RESULTS: Collemopsidium pelvetiae had distinct interactions with its two photosynthetic partners and with heterotrophic bacteria. Interactions with Pelvetia canaliculata were restricted to the region beneath the perithecia, where hyphae penetrated the outer amorphous cell-wall layer, without any evident host defense response. In contrast, the interaction with cyanobacteria involved the formation of intracellular haustoria, which ultimately lead to the death of the cyanobionts, suggesting a controlled parasitic relationship or a transitional stage toward lichenization. Unexpectedly, C. pelvetiae also produced haustorium-like projections into heterotrophic bacterial cells, a structure not previously reported in lichen symbioses. Microbiome analysis identified Pleurocapsa as the most likely cyanobiont genus associated with C. pelvetiae and revealed consistent heterotrophic bacterial communities, suggesting a species-specific assemblage.

CONCLUSIONS: This marine tripartite symbiosis involves distinct interaction modes, challenging strict lichen definitions. We propose that lichen symbioses form a multidimensional continuum of strategies rather than a single mutualistic model.},
}

@article {pmid42227270,
year = {2026},
author = {Medeiros, MJ and Schoville, S and Price, DK and Yew, JY},
title = {Microbiome Structure of Endemic Hawaiian Drosophila Is Shaped More by Habitat Than Host Identity.},
journal = {Molecular ecology},
volume = {35},
number = {11},
pages = {e70417},
doi = {10.1111/mec.70417},
pmid = {42227270},
issn = {1365-294X},
support = {2025669//National Science Foundation/ ; P20GM125508/NH/NIH HHS/United States ; P20GM139753/NH/NIH HHS/United States ; 19CON-95452//Hawai'i Community Foundation/ ; },
mesh = {Animals ; Hawaii ; *Drosophila/microbiology/genetics ; *Ecosystem ; *Microbiota/genetics ; Phylogeny ; Fungi/classification/genetics ; Bacteria/classification/genetics ; },
abstract = {The Hawaiian Drosophila radiation exemplifies rapid adaptation and species diversification. Many factors have been attributed to these phenomena, including allopatry, sexual selection, and ecological specialization. In recent years, the microbiome has come to the forefront as an important driver of adaptation that is capable of facilitating host survivorship, enhancing resilience to local environmental challenges, and enabling the use of different dietary resources. To determine the factors that contribute to microbiome community variation in natural populations, we conducted a survey of bacterial and fungal communities from over 500 wild flies collected from across six islands of the Hawaiian archipelago. These samples represent a breadth of host plant specializations, habitats, lifestyles and endemicity. Our findings reveal that microbiome variation is largely driven by abiotic factors including elevation, temperature, rainfall, and evapotranspiration, but is not strongly constrained by phylogenetic relatedness. Identical species inhabiting three separate locations exhibited different microbiomes. By contrast, distantly related species inhabiting the same site had more similar microbiomes. The microbiomes of endemic species also differ from recently introduced invasive Drosophila in terms of diversity, composition, and predicted function. Given the myriad roles of the microbiome in nutrition, reproduction, and mate choice, these results provide a foundation for determining the roles of the microbiome in the ecological divergence of Hawaiian Drosophila.},
}

Animals
Hawaii
*Drosophila/microbiology/genetics
*Ecosystem
*Microbiota/genetics
Phylogeny
Fungi/classification/genetics
Bacteria/classification/genetics

@article {pmid42227352,
year = {2026},
author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT},
title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70190},
pmid = {42227352},
issn = {1365-2591},
support = {//European Society of Endodontology/ ; },
abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.

METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (< 3 mm) or large (> 7 mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p < 0.05 was considered as significant.

RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p = 0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.

CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.},
}

@article {pmid42227372,
year = {2026},
author = {Zhang, X and Liu, G and Yan, Z},
title = {Global Research Trends in Innate Lymphoid Cells in the Gut and Kidney: A Bibliometric and Visual Analysis.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715303409659251128095655},
pmid = {42227372},
issn = {2212-3873},
abstract = {INTRODUCTION: Innate lymphoid cells (ILCs), critical immune regulators in mucosal tissues, maintain tissue homeostasis, modulate inflammation, and drive immune defense. While their roles in gut and kidney biology are increasingly studied, global research trends and focal points in this field remain largely uncharacterized.

METHOD: Using the Web of Science Core Collection (2004-2024), we analyzed 6,835 articles on gut- and kidney-associated ILCs. Bibliometric tools (VOSviewer, CiteSpace) were employed to evaluate publication trends, collaborations, institutional contributions, author influence, journal profiles, and keyword patterns to identify research priorities.

RESULT: Annual publications surged from 2004 to 2024, peaking at 622 in 2024. The U.S. (2,145 articles), China (1,539), and Germany (679) dominated output, with Harvard Medical School and Inserm as leading institutions. Gregory F. Sonnenberg and David Artis were the most-cited authors. Key journals included Frontiers in Immunology, Immunity, and Journal of Immunology. Research hotspots centered on inflammatory mechanisms (e.g., inflammatory bowel disease), immunotherapy, and ILC-microbiome crosstalk. Emerging trends emphasized tumor microenvironment interactions, as highlighted by keyword burst analysis.

CONCLUSION: This study underscores the therapeutic potential of ILCs in inflammation and cancer within the gut and kidney, advocating for interdisciplinary collaboration to advance mechanistic and clinical research.},
}

@article {pmid42227379,
year = {2026},
author = {Md Sabudin, SNS and Das, S and Mohamad Umbaik, NA and Md Zin, SR},
title = {Microbiome and Its Association with Diseases of the Ear, Nose and Pharynx.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715303427717251222184941},
pmid = {42227379},
issn = {2212-3873},
abstract = {INTRODUCTION: The microbiome refers to the entire community of microorganisms, including bacteria, fungi, viruses, their genes, and the environment that surrounds them. The microbiome is found in the gut, skin, and the oral and nasal cavities, and is an important interface between the human body and the environment outside. Notably, the ear, nose, and throat or pharynx microbiome remains poorly studied. Therefore, the present review discusses the association of the microbiome with various diseases of the ear, nose, and pharynx.

METHODS: The literature was obtained by conducting a comprehensive search of the PubMed, Scopus, Web of Science, and Google Scholar databases, followed by screening the abstracts for relevance. The selected articles were then retrieved for deeper exploration.

RESULTS: This review highlights the disturbance of the balance of the microbiome, which is referred to as dysbiosis, that may be the cause of various diseases in the body.

DISCUSSION: We also discuss various microorganisms found in the ear, nose, and pharynx and their link with related diseases and brain health.

CONCLUSION: The microbiome is important for the better health of the human body as it modulates the immune system. Accordingly, a better understanding of its interaction with the host may lead to advances in drug design.},
}

@article {pmid42227474,
year = {2026},
author = {Yang, F and Zhu, Z and Wang, Y and Qin, Y and Yue, H},
title = {Lung-Brain Axis Mechanisms of Cognitive Dysfunction in Long COVID.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273421593251202095722},
pmid = {42227474},
issn = {1996-3181},
abstract = {Cognitive dysfunction, characterized by memory impairment, attentional deficits, and executive dysfunction, represents a critical clinical manifestation in post-acute sequelae of COVID-19 that significantly compromises patients' quality of life. The lung-brain axis, as a bidirectional regulatory network connecting the respiratory system to the central nervous system, interacts through neural circuits, humoral pathways, and microbial pathways, and may play a central role in the cognitive impairments occurring in long COVID (LC). This paper systematically reviews the multidimensional pathways of the lung-brain axis and their pathological mechanisms in the cognitive impairment of LC, including direct viral neuroinvasion during the acute phase, chronic injury triggered by viral persistence, immune homeostasis dysregulation, hypoxaemia, microbiome disruption, and renin- angiotensin system imbalance. It then explores clinical intervention strategies based on the lungbrain axis, integrating supportive treatments, such as oxygen therapy, exercise therapy, and cognitive training, with treatments targeting the lung-brain axis, including antiviral drugs, immunomodulation, probiotics, and neuromodulation techniques. It is also suggested that future research should favour the integration of multi-omics technologies and the development of individualised therapeutic targets.},
}

@article {pmid42227762,
year = {2026},
author = {Mulisa, G and Zhao, J and Lelissa, G and Ademola-Popoola, IJ and Diaz Huemme, AM and Weyrich, LS and Mihret, A and Gemechu, T and Bane, A and Pero-Gascon, R and De Boevre, M and De Saeger, S and Abebe, T and Bisanz, JE},
title = {Multi-cohort comparative analysis of salivary microbiotas reveals rural Ethiopians harbor a distinct composition correlated with lower esophageal cancer prevalence.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0023226},
doi = {10.1128/msystems.00232-26},
pmid = {42227762},
issn = {2379-5077},
abstract = {Esophageal cancer (EC) results in high mortality due to difficulty in early diagnosis, particularly in low- and middle-income countries, including the African EC belt typified by high prevalence, early onset, and poor prognosis. While the precise etiological factors remain unknown, emerging data suggest links to the oral microbiota. In this study, we conducted a secondary analysis using V4 16S rRNA sequencing from a cross-sectional study of treatment-naive, newly diagnosed EC patients (N = 103) and healthy controls (N = 108) residing in agricultural regions of Ethiopia. We report that the salivary microbiota in the healthy Ethiopian controls is highly diverse, forming two functionally distinct community clusters differing in diversity, composition, and absolute abundance. Microbiota composition was associated with sex and alcohol consumption, but not age. Comparisons against groups from geographically distinct populations representing Tanzania, Uganda, Venezuela, and the United States (N = 641) showed that cluster 2 resembled other East African populations, while cluster 1 was unique to the Ethiopian cohort. Both EC subtypes, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma, were associated with a loss of microbial diversity and an increased probability of having a cluster 2 microbiota (adjusted OR = 2.9 [95% CI 1.5-5.9]). Classifiers trained to discriminate healthy and EC samples were further validated on two external EC cohorts from China (N = 161). Models trained on the Ethiopian cohort could predict disease status in an external cohort of mid- and late-stage ESCC from China (AUROC = 0.70 ± 0.03 [mean ± SD]), demonstrating the generalization of microbial features of ESCC across populations.IMPORTANCERecent reports in North America and China have correlated oral microbiota composition with esophageal cancer, although the translation of this knowledge into the African esophageal cancer belt is hampered by a lack of data on the oral microbiota of East Africans and limited cross-cohort comparative analyses validating the utility of these biomarkers. We report that the human salivary microbiota is a meaningful biomarker of later-stage esophageal cancer that transcends geography and ethnicity and may provide utility for large-population screening. A lower-diversity and lower-abundance salivary microbiota correlated with esophageal cancer warrants further investigation to understand the role of oral microbes in mediating carcinogenesis.},
}

@article {pmid42228016,
year = {2026},
author = {Putelo, AM and Bajgai, S and Poblete, MK and Guido, G and Perusina Lanfranca, M and He, Q and Raihan, T and Hatzinger, CN and Mirani, A and Kolli, SH and Lank, DS and Feng, TY and McGinty, MT and Miagkov, U and Pilehvari, A and You, W and Harris, TE and Rutkowski, MR},
title = {Commensal Dysbiosis Alters Primary Bile Acid Signaling to Drive Mammary Gland Inflammation and Breast Tumor Dissemination.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-25-4466},
pmid = {42228016},
issn = {1538-7445},
abstract = {Breast cancer is the most commonly diagnosed malignancy and a leading cause of cancer-related mortality. Hormone receptor-positive (HR+) tumors represent the most prevalent metastatic subtype, and early dissemination remains a major clinical challenge. Commensal dysbiosis, defined as an inflammatory gut microbiome with low biodiversity, promotes metastasis by inducing mammary gland inflammation. Here, we investigated systemic mechanisms governing dysbiosis-induced metastasis. Metabolomic profiling revealed elevated primary bile acids (BAs) in the dysbiotic fecal microbiome. Sequestration and supplementation approaches demonstrated that, beyond driving metabolic disease and mammary gland inflammation, primary BAs orchestrated enhanced HR+ tumor dissemination via a prostaglandin E2 (PGE2)-dependent pathway. Analysis of The Cancer Genome Atlas (TCGA) showed that BA, insulin resistance, and PGE2 gene signatures associated with reduced survival in patients with HR+ tumors. In complementary analyses using the Epic Cosmos electronic health record database, bile acid sequestrant use was associated with longer restricted mean survival time among patients with metastatic disease. Together, these findings reveal that commensal dysbiosis-associated loss of microbial BA metabolism elevates primary BAs and promotes HR+ metastatic progression through PGE2 signaling.},
}

@article {pmid41992382,
year = {2026},
author = {Cuteri, V and Preziuso, S and Li, Y and Laus, F},
title = {Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41992382},
issn = {2524-4671},
abstract = {The exponential growth of the human population and associated intensifications in animal farming, pet ownership, and habitat anthropisation have dramatically increased human-animal interactions. Global livestock production now exceeds 24 billion animals annually, and pet ownership has risen to over 70% of households in many developed nations, creating unprecedented interfaces for viral exchange. This heightened contact has multiplied opportunities for zoonotic and reverse-zoonotic transmission, as tragically exemplified by the SARS-CoV-2 pandemic. The fecal virome—defined as the totality of viral nucleic acids in the gastrointestinal tract—represents a crucial, yet largely unexplored, pathway for such exchanges. While the bacterial microbiome’s role is increasingly recognized, the virome’s composition, dynamics, and transmissibility between co-habiting humans and animals remain poorly characterized. This review compiles current evidence on the fecal virome of key domestic animals (equines, livestock, pets) and their human contacts under the “One Health” framework. We critically evaluate methodological approaches—from targeted PCR to viral metagenomics—and highlight the discovery of novel viruses and identification of zoonotic agents through metagenomic approaches. Critically, we identify significant knowledge gaps, including the absence of definitive evidence for contemporary cross-species transmission versus shared ancestry or convergent evolution. We propose a strategic research agenda focused on longitudinal studies of human-animal cohorts, standardized metagenomic methodologies, and functional analyses of the virome. Elucidating the fecal virome at this interface is paramount for developing proactive surveillance strategies to predict and prevent the next emerging viral disease.},
}

@article {pmid42217383,
year = {2026},
author = {Kong, T and Du, Z and Zhou, J and Zheng, Z and Zhang, J and Zhang, S and Jiang, F and Sun, X and Huang, W and Zhang, R and Li, F and Lin, W and Lan, X and Cao, Y and Yan, G and Sun, W},
title = {Assimilatory sulfate reduction potential in the plastisphere microbiome is linked to plastic mineralization in sulfur-rich mining-impacted river sediments.},
journal = {Water research},
volume = {303},
number = {},
pages = {126182},
doi = {10.1016/j.watres.2026.126182},
pmid = {42217383},
issn = {1879-2448},
abstract = {Microbial communities colonizing plastic surfaces are shaped by environmental factors, yet the role of sulfur in plastisphere assembly and plastic fate remains poorly understood. Here, we collected plastic debris from sulfur-rich, mining-impacted river sediments to characterize plastisphere microbiomes and evaluate their potential roles in plastic transformation. Paenibacillus spp. were identified as core plastisphere members, and their distribution was strongly associated with total sulfur concentrations. Metagenomic binning suggested that Paenibacillus harbored genomic potential associated with plastic transformation/mineralization and sulfate assimilation. An isolate of Paenibacillus provided further laboratory-based evidence that sulfate amendment may support plastic mineralization, although the precise in situ mechanism remains to be clarified. Because both the metagenome-assembled genome and the isolate genome encoded an almost complete assimilatory sulfate reduction pathway but lacked a complete dissimilatory sulfate reduction pathway, the observed sulfate depletion is more conservatively interpreted as sulfate uptake coupled with assimilatory sulfate reduction and subsequent sulfur assimilation into biomass rather than canonical sulfate respiration. Together, these findings suggest that sulfate availability and assimilatory sulfur metabolism may represent underappreciated controls on plastic turnover in sulfur-rich environments by supporting plastic-associated carbon transformation. This study links plastic-carbon fate to local sulfur cycling and provides new insight into microplastic persistence in sulfur-rich aquatic ecosystems.},
}

@article {pmid42217765,
year = {2026},
author = {Li, L and Wei, J and Deng, Y and Yu, J and Wei, X and Wang, W and Chen, J and Wei, J and Yuan, T and Tan, H and Wu, Z and Jiang, J},
title = {The First Toxicological Assessment of Copper Exposure in Cipangopaludina cathayensis: Integrative Insights from Gut Microbiota and Hepatopancreas Responses.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128436},
doi = {10.1016/j.envpol.2026.128436},
pmid = {42217765},
issn = {1873-6424},
abstract = {Copper (Cu) is an essential trace element for biological organisms; however, excessive levels beyond biological tolerance can induce significant toxicity. Cipangopaludina cathayensis is a widely distributed freshwater gastropod in China and an important aquaculture species, yet information regarding its toxic responses to Cu exposure remains limited. In this study, the 96 h LC50 (median lethal concentration) of Cu for C. cathayensis was determined to be 0.150 mg/L, with a calculated safety concentration of 0.015 mg/L. Based on these values, 20% and 30% of the LC50 were selected as exposure concentrations for a 14-day experiment. Under Cu exposure, gut microbial α-diversity significantly increased, the Firmicutes/Bacteroidota ratio markedly decreased, potentially beneficial genera such as Bacteroides declined, whereas potentially pathogenic taxa including Aeromonas became enriched. Cu exposure induced infiltration of inflammatory cells and structural disruption of the intestinal mucosal layer, while the hepatopancreas exhibited vacuolation and tubular lumen dilation. The antioxidant defense system was severely impaired, as indicated by reduced SOD, CAT, and GSH levels and elevated MDA accumulation. Regarding metabolic responses, Cu exposure disrupted standard metabolism, with both oxygen consumption and ammonia excretion significantly reduced. Functional analyses of the gut microbiome and hepatopancreas metabolome revealed inhibited carbohydrate metabolism pathways. In contrast, lipid metabolism pathways were upregulated-although Cu exposure may disrupt normal lipid metabolic functions-possibly suggesting a compensatory strategy to meet energy demands under Cu stress. Additionally, the upregulation of protein (amino acid) metabolism-related pathways likely contributes to tissue repair processes.},
}

@article {pmid42217961,
year = {2026},
author = {Dash, HR and Das, S},
title = {Investigative leads and individualization through forensically relevant human commensal microbiome.},
journal = {Advances in applied microbiology},
volume = {133},
number = {},
pages = {91-112},
doi = {10.1016/bs.aambs.2026.04.001},
pmid = {42217961},
issn = {0065-2164},
mesh = {Humans ; *Microbiota ; *Forensic Microbiology/methods ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {The advent of high-throughput DNA sequencing technology has facilitated the rapid and explicit analysis of human microbiome. Microbiome analysis from the crime scene provides definitive evidence of human contacts and/or their body fluids. Besides, personalized microbiome is strongly influenced by the geographic, lifestyle, ethnic and other environmental factors. The role of microbiome analysis in the prediction of post-mortem time interval has been widely established. Forensic Microbiome Database has featured a catalogue of varied group of microorganisms in different parts of the body which might provide a crucial piece of evidence in identification of body-fluids. Though the forensically relevant human microbiome analysis faces significant challenges both from technological and data related issues, this field holds significant promise in generating investigative leads and subsequent identification of an individual in the post-DNA profiling era. The proposed chapter describes the various aspects of human microbiome in forensics use and its challenges in its practical application in various forensic scenarios.},
}

Humans
*Microbiota
*Forensic Microbiology/methods
*Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing

@article {pmid42218054,
year = {2026},
author = {Daniel, N and Papadimitriou, N and Chatziioannou, AC and Jenab, M and Mayén, AL and Keski-Rahkonen, P and Fedirko, V and Hassan, MM and Hughes, DJ},
title = {Genetically predicted gut bacteria, circulating bacteria-associated metabolites and liver cancer: A Mendelian randomisation study.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2026.05.008},
pmid = {42218054},
issn = {1878-3562},
abstract = {BACKGROUND AND AIMS: Recent data suggest a role for the gut microbiome in the development of hepatocellular carcinoma. We investigated associations of gut microbiome abundances and concentrations of circulating bacteria-associated metabolites with hepatocellular carcinoma using Mendelian randomisation.

METHODS: Two-sample Mendelian randomisation was conducted using summary statistics from release 11 of FinnGen (609 cases and 473,046 controls) and The North American Hepatocellular Cancer Epidemiology Consortium (1872 cases and 2907 controls). Inverse variance-weighted analyses were performed as well as several sensitivity analyses.

RESULTS: In the FinnGen analyses, acetoacetate, ascorbate and asparagine were nominally associated with decreased risk. Alanine, hippuric acid and taurocholic acid were nominally associated with increased risk. The Barnesiella, Catenibacterium, Enterorhabdus and Eubacterium oxidoreducens genera were nominally associated with increased risk. Escherichia-Shigella was nominally associated with decreased risk. In the North American Hepatocellular Cancer Epidemiology Consortium analyses, the circulating bacteria-associated metabolites taurochenodeoxycholic acid and threonate were nominally associated with decreased risk. Five genera were nominally associated with increased risk; Eubacterium rectale group, Hungatella, Sellimonas and the unknown genus 1000005472.

CONCLUSION: These results, based on genetically predicted gut microbiome characteristics and circulating gut bacteria-related metabolite concentrations, suggest a putative causal role in hepatic carcinogenesis.},
}

@article {pmid42218119,
year = {2026},
author = {Fessler, JL and Olm, MR and Engleman, EG and Sonnenburg, JL},
title = {Integration of donor microbiota following FMT correlates with anti-PD-1 response in melanoma.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73465-7},
pmid = {42218119},
issn = {2041-1723},
support = {R21CA290426//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Fecal microbiota transplantation (FMT) has shown promise in improving anti-PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. We performed a strain-resolved metagenomic meta-analysis across three independent FMT plus anti-PD-1 melanoma trials (n = 41). Across cohorts, therapeutic benefit was linked to successful integration of donor microbiota, rather than increased diversity or engraftment of specific species. Responders acquired more donor-derived strains, exhibited greater post-FMT similarity to their donor, and maintained a more stable microbiome. Following FMT, non-responders' microbiomes showed greater taxonomic instability, larger fluctuations in estimated microbial load, and increased abundance of pathogen-associated secretion system genes, whereas responders showed enrichment for microbial functions involved in community-level metabolism and communication. Finally, shifts in tumor-infiltrating immune profiles tracked with clinical outcomes and microbiome changes. Together these findings highlight that distinct patterns of microbiome restructuring, including stable community transitions and altered functional capacity, are associated with anti-PD-1 response following FMT.},
}

@article {pmid42218210,
year = {2026},
author = {Maqami, M and Khalili, B and Shariatmadari, H},
title = {Interactive roles of mineralogy, microbial community composition and litter quality in regulating organic matter turnover.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49740-4},
pmid = {42218210},
issn = {2045-2322},
abstract = {Soils are often treated as chemically defined reactors, yet the physical architecture of minerals, organic inputs, and microbiomes jointly shapes where and how carbon turns over. We used a factorial microcosm experiment to test how clay mineralogy (fibrous palygorskite vs. swelling bentonite), clay content (0-20%), calcium carbonate (7.5-15%), litter quality (recalcitrant wheat vs. labile alfalfa), and microbiome origin (native soil vs. a synthetic fungi + bacteria consortium) interact to control respiration kinetics and microbial biomass carbon over 90 days. Clay type and amount acted as primary filters: increasing clay generally raised cumulative mineralized C, but palygorskite produced higher C0, faster mineralization (higher k or lower t0, steeper n), and stronger late-stage biomass recovery than bentonite, indicating a colonizable, catalytic habitat rather than a purely protective matrix. Litter chemistry modulated this filter: N-rich alfalfa shifted the system toward facilitation, with rapid, high-amplitude mineralization and large biomass peaks, whereas high-C:N wheat slowed mineralization, increased sensitivity to clay content, and emphasized protection and diffusion limitation. Microbiome composition added a third control: native communities generated higher cumulative C loss but lower rate constants, while the synthetic consortium drove faster mineralization and higher biomass on palygorskite. Calcium carbonate acted as a tuner, enhancing C0, k and biomass in wheat systems and shifting mineralization timing in alfalfa systems. Together, these results support a hierarchical framework where mineral pore architecture sets the habitat filter, litter quality and microbial traits determine its exploitation, and Ca availability adjusts the balance between facilitation and protection.},
}

@article {pmid42218218,
year = {2026},
author = {Zhu, G and Yang, G},
title = {Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01030-7},
pmid = {42218218},
issn = {2055-5008},
support = {32571054 and 82371350//National Natural Science Foundation of China/ ; C7014-24GF//Research Grant Council of the Government of Hong Kong SAR/ ; Institute Digital Medicine internal grant (9229501-13-YG)//City University of Hong Kong/ ; },
abstract = {Emerging evidence suggests a role for the gut bacteria in the pathogenesis of multiple sclerosis (MS); however, the role of other microorganisms and their diagnostic potential for MS remain poorly explored. Here, we analyzed large-scale metagenomic data derived from fecal samples (discovery cohort n = 1152; total n = 1306 across 3 geographically diverse cohorts). Subsequently, we utilized multikingdom gut microbiome data to develop machine learning models to distinguish MS patients from healthy controls. Our analysis identified distinct microbiome alterations, revealing 90 bacterial, 3 fungal, 2 viral species, 119 KEGG orthology genes, and 17 metabolic pathways significantly associated with MS. Machine learning models integrating multikingdom taxonomic and functional features achieved the area under the receiver operating characteristic curves (AUCs) of 0.977 for males and 0.978 for females. On external validation datasets, the ensemble models yielded AUCs of 0.813 in males and 0.745 in females, while the 30-marker models reached AUCs of 0.849 and 0.763, respectively. Notably, the accuracy of the model was associated with Faecalibacterium spp. and L-methionine biosynthesis pathways, which were less abundant in MS patients. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiome markers as non-invasive biomarkers for MS.},
}

@article {pmid42218309,
year = {2026},
author = {Sedaghat-Rostami, E and Yang, L and Vats, A and Paudyal, B and Briggs, E and Carr, BV and Freimanis, G and Ruedas-Torres, I and Downing, T and Rollier, C and Marougka, K and De Haan, CAM and Mehat, J and La Ragione, R and Muir, A and Richard, AC and Van Reeth, K and Salguero, FJ and Gerner, W and Tchilian, E},
title = {Pathogen-specific immune responses might underlie divergent outcomes of coronavirus and influenza infection in the natural porcine host.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10400-y},
pmid = {42218309},
issn = {2399-3642},
abstract = {Coronaviruses and influenza A viruses are major respiratory pathogens with pandemic potential. Using pigs as a translational large-animal model, we compare the virulence, pathogenesis, and immune responses to porcine respiratory coronavirus (PRCV) and pandemic H1N1 2009 influenza virus (pH1N1). Here we show that PRCV induces higher viral load and prolonged viral shedding, stronger systemic and mucosal T cell activation, expansion of memory B cells, and distinct nasal microbiome changes. In contrast, pH1N1 results in rapid neutralising antibody production, robust Tfh and germinal centre B cell responses, and broader early nasal microbial diversity. Transcriptional responses to PRCV and pH1N1 infection start with the activation of shared interferon-stimulated genes but later diverge as pathways involving stromal-immune interactions and vascular integrity shapes lung pathology and subsequent immune responses. These findings demonstrate fundamental differences in coronavirus and influenza virus-host interactions and establish the pig as a powerful comparative model for studying respiratory virus pathogenesis and immunity.},
}

@article {pmid42218386,
year = {2026},
author = {Guo, S and Liu, J and Zheng, H and Wu, X},
title = {Nipple aspirate fluid as a proximal breast liquid biopsy platform: advancing precision risk management in breast cancer.},
journal = {Clinical proteomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12014-026-09612-5},
pmid = {42218386},
issn = {1542-6416},
support = {WJ2025M107//the Scientific Research Project of Hubei Provincial Health Commission/ ; Grant No.2023AFB493//the Natural Science Foundation of Hubei Province, China/ ; Grant No. HBCHBCC‑A02//the National Key Clinical Specialty Construction Project Fund of the Breast Center, Hubei Cancer Hospital/ ; 2024HBCHYN11//the Scientific Research Projects of Hubei Cancer Hospital/ ; EWT [2023] 65, Oncology//the Hubei Province Medical Youth Top Talent Project/ ; 2025HBCHHHRC005//the Talent Project of Hubei Cancer Hospital/ ; 2025HBCHLHRC002//the Talent Project of Hubei Cancer Hospital/ ; 2025HBCHYN24//the Scientific Research Project of Hubei Cancer Hospital/ ; 320.6750.2024‑21‑5 and 320.6750.2025‑21‑13//the Wu Jieping Fund Project/ ; CXPJJH123001‑2320//the Hubei Chen Xiaoping Science and Technology Development Foundation Youth Science Special Fund/ ; 2022SWZX09//the Subject of Biomedical Research Center of Hubei Cancer Hospital/ ; CTYC002//the 2024 Chutian Talents Program Special Fund/ ; },
abstract = {BACKGROUND: Current breast cancer (BC) risk management relies primarily on imaging and blood‑based liquid biopsies. However, these approaches are constrained by morphological blind spots, limited sensitivity for early lesions, and an inability to directly capture the biology of the ductal microenvironment where most tumors originate. There is a pressing need for novel strategies that provide direct, local insight into breast tissue risk.

MAIN BODY: This review repositions nipple aspirate fluid (NAF) as a proximal, breast-specific liquid biopsy platform. Emerging evidence demonstrates that NAF, obtained by nipple aspiration from non-lactating breasts and not limited to cases of spontaneous nipple discharge, originates from a functionally autonomous ductal microenvironment and provides rich multi-omics information, including proteins, metabolites, epigenetic alterations, extracellular vesicles, inflammatory/oxidative mediators, microbiome-associated signals, and other local regulatory readouts, rather than simply representing a filtrate of blood. We summarize the biological foundations of NAF and its multi-omics landscape, highlighting its potential in three key clinical scenarios: (1) molecular risk stratification for pathologic nipple discharge, (2) individualized biological risk profiling in women with high-risk or dense breasts, and (3) proximal monitoring of treatment response and microenvironmental dynamics in patients with diagnosed BC.

CONCLUSION: Although standardization and prospective validation remain essential challenges, the development of robust collection protocols, integration of multi‑omics data, and execution of well‑designed clinical trials could enable NAF to shift BC management from a paradigm of "early detection" toward one of "precision risk insight and intervention," ultimately aiming to improve patient outcomes and net benefit.},
}

@article {pmid42218533,
year = {2026},
author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY},
title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01680-4},
pmid = {42218533},
issn = {1756-994X},
support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; },
abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.

METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.

RESULTS: Durable disease control (PFS ≥ 24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.

CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).},
}

@article {pmid42218547,
year = {2026},
author = {Ji, S and Xia, J and Yang, Z and Liu, S and Zhang, X and Liu, X and Hao, Y and Wang, W and Long, S and Li, S},
title = {Mechanism of a polyherbal mixture alleviates calf diarrhea: an integrated network pharmacology, metabolomics, and microbiome study.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42218547},
issn = {1674-9782},
support = {No. 2022YFD1301001//National Key R&D Program of China/ ; No. ZDYF2023XDNY067//Key Research and Development Projects in Hainan Province/ ; },
abstract = {BACKGROUND: Calf diarrhea represents a prevalent and serious challenge in dairy farming. While medicinal plants demonstrate considerable potential for preventing calf diarrhea within antibiotic-free farming systems, their active components and mechanisms remain poorly characterized. The objective of this study was to investigate a polyherbal mixture (PM; including Crataegus pinnatifida, Callicarpa nudiflora Hook. & Arn., Mallotus apelta (Lour.) Müll.Arg., Amomum villosum Lour., Centella asiatica (L.) Urban, and Alpinia oxyphylla Miq.) supplemented to preweaning calves from d 4 to 60, utilizing an integrated approach combining network pharmacology, metabolomics, and microbiomics.

RESULTS: Dietary supplementation with 40 g/d of PM significantly decreased the occurrence of diarrhea (P < 0.05), increased monocyte levels (P < 0.05), and improved jejunal villus height (P < 0.05). Network pharmacology predicts that IL6, EGFR, SRC, TP53, and CCND1 are key targets, while acacetin, chrysin, tectochrysin, dihydroartemisinic acid, and lysionotin may be potential active constituents. The serum metabolome revealed that PM supplementation significantly enriched the steroid hormone biosynthesis. At the same time, PM altered the gastrointestinal microbiota, increasing the abundance of bacteria such as Mediterranea massiliensis, Prevotella denticola, and Duncaniella freteri in the rumen and Clostridium nexile in feces, while decreasing the abundance of Blautia producta, Vescimonas fastidiosa, and Alistipes putredinis in feces (P < 0.05).

CONCLUSIONS: Collectively, these findings suggest that PM supplementation alleviated calf diarrhea by remodeling serum steroid hormone biosynthesis and improving ruminal and fecal microbiota composition. Acacetin, chrysin, tectochrysin, dihydroartemisinic acid, and lysionotin may be potential active components.},
}

@article {pmid42218556,
year = {2026},
author = {Li, F and Xu, X and Zhou, M and Du, S and He, Z and Xia, Z and Chen, Q and Li, J and Tang, S and Zhong, W and Xu, J},
title = {Longitudinal dynamics of gut microbiota and mycobiota in pneumonia-derived sepsis: evidence of taxonomic stability and trans-kingdom network reorganization.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00838-0},
pmid = {42218556},
issn = {1757-4749},
support = {81970464//National Natural Science Foundation of China/ ; 201903010064, 202201011066//Science and Technology Program of Guangzhou/ ; 2022A1515011248, 2022A1515011855//National Natural Science Foundation of Guangdong Province/ ; },
abstract = {BACKGROUND: Gut microbial dysbiosis has been implicated in sepsis-related organ dysfunction. However, the longitudinal dynamics of the gut microbiota and mycobiota-and particularly their cross-kingdom ecological organization-in pneumonia-derived sepsis remain incompletely understood.

METHODS: Patients with pneumonia-derived sepsis were prospectively enrolled. Fecal samples and clinical data (SOFA scores and inflammatory markers) were collected on Day 1 and Day 7. Gut bacterial and fungal communities were profiled using 16 S rRNA and ITS1 sequencing. Longitudinal and outcome-stratified analyses were performed. Trans-kingdom co-occurrence networks and module-based topological analyses were constructed, and associations with clinical parameters were explored.

RESULTS: Global analyses indicated relative compositional stability in the gut microbiota and mycobiota between Day 1 and Day 7, with no significant differences in alpha or beta diversity. The dominant bacteria were Bacillota, Bacteroidota, and Pseudomonadota at the phylum level, and Enterococcus, Bacteroides, and Escherichia-Shigella at the genus level; Escherichia-Shigella showed a decreasing trend and Bacteroides an increasing trend, though neither reached statistical significance (Padj > 0.05). Ascomycota dominated the fungal community, with Candida, Fusarium, and Oligophagozyma as the core genera, with no obvious temporal shifts. However, outcome-based stratification revealed that fungal Chao1 richness increased significantly post-treatment, specifically in the bad-outcome group (P < 0.05). The most notable findings emerged from the trans-kingdom interactome. In the favorable-outcome group, a specific modular configuration (ModM1) was identified post-treatment, containing four microbiota hubs (Parabacteroides, Mediterraneibacter, Serratia, and Enterococcus). While the aggregate abundance of ModM1 lacked clinical correlation, its hub genus, Mediterraneibacter-a prevalent anaerobe-showed a negative association with PCT and TNF-α. Additionally, the fungal-integrated ModM8 showed a potential positive association with IL-8. Conversely, the bad-outcome group showed a lack of such hub-anchored coordination.

CONCLUSIONS: In this small exploratory cohort, early pneumonia-derived sepsis appeared to exhibit relative taxonomic stability but subtle reorganization of cross-kingdom ecological connectivity. Microbial shifts appeared to manifest primarily as changes in network embedding rather than abundance. These observations provide exploratory insights that require further validation regarding topological integration, especially fungal involvement in inflammatory modules, for understanding host-microbiome interactions in critical illness. Larger longitudinal studies are warranted.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT04525677, registered on 14 July 2020.},
}

@article {pmid42218569,
year = {2026},
author = {Gavillet, H and Hatfield, LR and Hardman, M and Marsh, R and Einarsson, GG and Thornton, CS and Parkins, MD and Duckers, J and Bomberger, JM and Hilliam, Y and Lee, SE and Lord, RW and Jones, A and Horsley, A and Daniels, TWV and Teneback, CC and Rivett, DW and van der Gast, C},
title = {Remodelling of cystic fibrosis respiratory microbiota in response to extended elexacaftor-tezacaftor-ivacaftor therapy.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02440-7},
pmid = {42218569},
issn = {2049-2618},
abstract = {BACKGROUND: Cystic fibrosis (CF) has profoundly changed since the introduction of CF Transmembrane Conductance Regulator modulator therapies (CFTRmt), a class of medications that improve function of the CFTR protein encoded by certain CF-causing gene mutations. Amongst these, the triple combination therapy elexacaftor-tezacaftor-ivacaftor (ETI) has been the most impactful and widely used to date. Given chronic respiratory infection and concomitant inflammation is the leading cause of morbidity and early mortality for the majority in CF, what is not certain are the long-term effects of ETI therapy on the respiratory microbiota and pathogens embedded within. Here, we assessed the effects of ETI CFTRmt over 3 years on the respiratory microbiota, using sputum and cough swab samples, from a multi-centre cohort of 276 adults with CF (awCF) from 6 CF centres in the UK, USA, and Canada, and compared to a non-CF healthy cohort.

RESULTS: Using Kruskal-Wallis analyses with post hoc Dunn's tests, Wilcoxon signed-rank tests, and PERMANOVA analyses with Bonferroni correction, we determined that respiratory microbiota characteristics (diversity, dominance, and composition) became decreasingly like those of awCF pre-ETI and remodelled to align more with the healthy cohort, where canonical CF pathogens increasingly became less ecologically important in terms of their distributions and abundances across awCF with increased duration on therapy. However, the on-ETI microbiota was impeded from becoming fully 'healthy' due to continued antibiotic exposure and irreversible lung damage experienced by awCF. Specifically, we found that azithromycin, an antibiotic widely used principally for its immunomodulatory benefits, was associated with adverse effects on the respiratory microbiota nullifying the observed positive effects of ETI treatment. Our results indicated that when administered alongside ETI therapy, azithromycin contributed to a pre-ETI microbiota dysbiosis and enabled enhanced persistence of emblematic CF pathogens.

CONCLUSIONS: The highly anticipated introduction of ETI CFTRmt has greatly changed the course of CF for many people living with this inherited disease. Here, we find that ETI CFTRmt enabled positive remodelling of the respiratory microbiota towards a healthy-like state. However, azithromycin appeared to impede total remodelling, making it an ideal candidate for evaluation for discontinuation in the CFTRmt era. While traditional pathogens become less ecologically important, the potential evolution and emergence of virulent strains should be investigated. Additionally, the impacts and implications of ETI therapy on the understudied fungal microbiota should also be explored. Video Abstract.},
}

@article {pmid42218700,
year = {2026},
author = {Zhang, Y and Wang, Y and Yang, Y and Mei, H and Liu, X and He, Y and Qin, S and Feng, B},
title = {Gut-Liver Axis Failure in Critical Alcohol-Associated Liver Disease: From ICU Secondary Hits to Microbiome-Targeted Therapy.},
journal = {Mediators of inflammation},
volume = {2026},
number = {1},
pages = {e3968719},
doi = {10.1155/mi/3968719},
pmid = {42218700},
issn = {1466-1861},
support = {82460373//National Natural Science Foundation of China/ ; 82560382//National Natural Science Foundation of China/ ; HZ (2025) 312//Zunyi Science and Technology Bureau, China/ ; HZ (2023) 366//Zunyi Science and Technology Bureau, China/ ; HZ (2025) 172//Zunyi Science and Technology Bureau, China/ ; QZYY-2024-137//Guizhou Administration of Traditional Chinese Medicine/ ; gzwkj2024-310//Guizhou Provincial Health Commission/ ; MTyk2024-55//Kweichow Moutai Hospital Research Project/ ; HZ202411//Traditional Chinese Medicine Hospital of Zunyi Medical and Pharmaceutical College/ ; },
mesh = {Humans ; Intensive Care Units ; *Liver Diseases, Alcoholic/therapy/microbiology/metabolism ; *Liver/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Intestinal Barrier Function ; Fecal Microbiota Transplantation ; Dysbiosis ; },
abstract = {Alcohol-associated liver disease (ALD) can progress to critical illness phenotypes requiring intensive care, including severe alcohol-associated hepatitis, acute decompensation, and alcohol-associated acute-on-chronic liver failure (ACLF). In these patients, short-term outcomes are driven less by the burden of fibrosis alone than by systemic inflammation, immune dysfunction, infection, and multiorgan failure. At the core of this process is gut-liver axis failure, which links alcohol-induced dysbiosis and intestinal barrier disruption to microbial translocation, hepatic innate immune activation, and systemic inflammatory amplification. In the intensive care unit (ICU), secondary hits such as broad-spectrum antibiotics, acid suppression, parenteral nutrition, shock, sedatives or opioids, and mechanical ventilation may further exacerbate these mechanisms and disturb microbial ecology and barrier integrity. Microbiome-targeted therapies (probiotics, postbiotics, and fecal microbiota transplantation) are biologically plausible. However, current evidence is mainly derived from non-ICU or relatively stable ALD populations. Therefore, their use in critically ill patients requires strict safety boundaries, including severe barrier disruption, invasive devices, uncontrolled infections, and profound immune dysfunction. This narrative review synthesizes the pathophysiological continuum from gut barrier failure to systemic inflammation and multiorgan dysfunction in critical ALD, with particular emphasis on ICU-specific secondary hits, safety-aware microbiome modulation, and future phenotype-informed precision strategies.},
}

Humans
Intensive Care Units
*Liver Diseases, Alcoholic/therapy/microbiology/metabolism
*Liver/metabolism
*Gastrointestinal Microbiome/physiology
Animals
Intestinal Barrier Function
Fecal Microbiota Transplantation
Dysbiosis

@article {pmid42218826,
year = {2026},
author = {Kao, CS and Chien, LC and Hsieh, FI and Chao, HJ and Kallawicha, K and Chen, YH and Wang, YL and Wu, CD and Jiang, CB},
title = {Integrating urban land-use characteristics and heavy metal exposure in assessing pediatric gut microbiota: Implications for environmental management.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjag092},
pmid = {42218826},
issn = {1551-3793},
abstract = {Early-life exposure to environmental pollutants poses a critical risk to pediatric health, yet few studies have integrated chemical contaminants with urban land-use characteristics to assess their combined associations with the developing gut microbiome. In this study, we evaluated the associations between fecal heavy metal (HM) concentrations and residential land-use cover area (measured as area-based metrics within specific buffers), as well as gut microbial composition and predicted functional pathways, in 78 preschool children from the greater Taipei area. Using Bayesian kernel machine regression (BKMR), we characterized nonlinear and interactive exposure-response relationships. Elevated fecal cadmium (Cd) levels were significantly and positively associated with increased abundance of Bacteroides (q = 0.02), while nominal positive associations were observed with Klebsiella and Veillonella. Fecal lead (Pb) showed a suggestive positive association with Phocaeicola (q = 0.07). Crucially, residential land-use features modified these associations: increased gas station coverage was linked to lower Bacteroides and Veillonella levels but higher Klebsiella abundance, whereas green-space coverage was positively associated with Veillonella. The BKMR model highlighted synergistic negative associations between fecal Cd and gas station area coverage within a 1500-m residential buffer on Veillonella and Bacteroides, suggesting that the spatial distribution of physical urban infrastructure may be linked to the apparent effects of chemical contaminants on the gut microbiota. These environmental contaminants were further associated with alterations in predicted microbial functional pathways involved in energy metabolism, secondary metabolite biosynthesis, and genetic information processing. These findings suggest that children's gut health may be associated with a complex interplay of urban chemical and structural factors. Our results underscore the need for science-informed urban management and health-protective zoning, which may inform strategies such as optimizing land-use cover area of gas stations near residential areas and increasing urban greenery to mitigate environmental risks during critical developmental windows.},
}

@article {pmid42218921,
year = {2026},
author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X},
title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.},
journal = {Molecular phylogenetics and evolution},
volume = {223},
number = {},
pages = {108650},
doi = {10.1016/j.ympev.2026.108650},
pmid = {42218921},
issn = {1095-9513},
abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.

METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.

PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.

CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.},
}

@article {pmid42219028,
year = {2026},
author = {Fan, X and Xiao, X and Tan, D and Yu, B and Chen, D and He, J and Luo, J and Luo, Y and Yan, H and Wang, J and Wu, A and Wang, Q and Wang, H and Mao, X},
title = {Host-targeted apple pectic oligosaccharides repair intestinal barrier in colitis via HSP90β/miRNA/CORO2A axis.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.05.057},
pmid = {42219028},
issn = {2090-1224},
abstract = {INTRODUCTION: While functional oligosaccharides alleviate inflammatory bowel disease (IBD), their mechanisms conventionally attributed to gut microbiota modulation. The direct, host-targeted regulatory pathways of apple pectic oligosaccharides (APOS) remain elusive.

OBJECTIVES: This study aimed to elucidate the host-directed parallel mechanism by which APOS restores intestinal epithelial barrier integrity and immune homeostasis during colitis.

METHODS: We integrated multi-omics analysis, biophysical binding validation, and a dextran sulfate sodium (DSS)-induced rat colitis model. Mechanistic dependency was validated via in vivo miRNA rescue and in vitro (IEC18 and human Caco-2) models using dual-luciferase assays and bidirectional genetic manipulation.

RESULTS: APOS (200 mg/kg) significantly ameliorated colitis severity. Mechanistically, APOS directly bound to the N-terminal pocket of membrane HSP90β on intestinal epithelial cells. This interaction inhibited the release of miR-148a-5p and miR-216a-3p, thereby de-repressing their shared downstream target, the cytoskeletal regulator CORO2A. CORO2A restoration re-anchored junctional networks (ZO-1, AJAP1 and GJA1) and suppressed Th1/Th17-driven cytokine storms. Crucially, exogenous miRNA supplementation in vivo completely abolished APOS-mediated barrier protection despite maintaining a restored microbiome, confirming the indispensable role of this host-directed pathway.

CONCLUSION: Operating synergistically with microbial modulation, APOS functions as a highly potent (Human Equivalent Dose 11.35 mg/kg), host-directed therapeutic. By engaging the HSP90β/miRNA/CORO2A axis to rebuild the physical defense line, this study conceptualizes a novel framework for precision nutritional intervention in IBD.},
}

@article {pmid42219044,
year = {2026},
author = {Shil, S and Datta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A},
title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.},
journal = {Journal of microbiological methods},
volume = {246},
number = {},
pages = {107565},
doi = {10.1016/j.mimet.2026.107565},
pmid = {42219044},
issn = {1872-8359},
abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.},
}

@article {pmid42219426,
year = {2026},
author = {Jäkel, J and Ludwig, J and Hüning, B and Felderhoff-Müser, U and Härtel, C},
title = {Intersectionality of early developmental risks and resilience after preterm birth.},
journal = {Molecular and cellular pediatrics},
volume = {13},
number = {1},
pages = {},
pmid = {42219426},
issn = {2194-7791},
abstract = {The period from conception through preschool age represents a critical developmental window for both microbiome and brain. During this time, several modifiable factors may influence development via the gut-brain axis, including the mode of delivery, exposure to antibiotics, maternal nutrition, breastfeeding, and sensitive, emotionally responsive caregiving. Infants born preterm (<37 weeks gestation) face numerous challenges that can perturb their developing gut microbiome as well as neurobehavioral trajectories. Biological and medical risks are exacerbated by stressful social context conditions. Understanding the complex mechanisms shaping the gut-brain axis and identifying modifiable protective factors is key to help define specific target groups and critical windows for individualized prevention of adverse outcomes after preterm birth. Today, a large knowledge gap exists on (a) how gut, brain, and behavioral development interact over time, and (b) which social and modifiable factors are key drivers of this interaction that could be harnessed for treatment and intervention. Translational research on the gut-brain axis after preterm birth is critically needed. Future studies should consider intentional sampling for variation in social factors such as level of education and immigrant background to identify populations that are susceptible to microbiome modifications and provide more evidence of how interventions might optimize long-term outcomes.},
}

@article {pmid42219523,
year = {2026},
author = {Magory Cohen, T and Bodner, L and Turjeman, S and Sharon, E and Cohen, A and Bouchebti, S and Tikhonov, E and Koren, O and Levin, E},
title = {Gut microbiome mediates an evolutionarily conserved social behavior in eusocial insects.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42219523},
issn = {2524-4671},
support = {1538/18//Israel Science Foundation/ ; },
abstract = {UNLABELLED: The gut microbiome is increasingly recognized as a key mediator of social behavior and division of labor in eusocial insects. In some species, trophallactic interactions facilitate nutrient exchange between larvae and adults, creating social interdependency. However, the role of gut bacterial symbionts in this process remains unclear. Here, we investigated the relative contributions of host identity, environment, and trophallactic interactions to gut microbiome assembly in two social wasp species, Vespa orientalis and Vespula germanica, using a cross-fostering, common garden experiment. Newly emerged workers and early-instar larvae were reciprocally exchanged and reared under controlled conditions. High-throughput 16S rRNA gene sequencing and functional inference revealed limited variation across treatments in worker gut communities, mainly shaped by shared environment, indicating stability and environmental dominance. Conversely, larval gut microbiomes were highly plastic, influenced by both larval species and the identity of their nursing workers, highlighting the impact of social interactions. Functional profiles reflected caste-specific roles: workers harbored microbiomes enriched for antimicrobial and detoxification pathways, while larvae microbiomes were enriched in metabolic functions for protein digestion and development. These findings demonstrate that metabolic division of labor in eusocial wasps is supported by life stage-specific microbial communities and functions and maintained by social interactions, positioning the gut microbiome as a key contributor to the maintenance of eusociality.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00560-x.},
}

@article {pmid42219628,
year = {2026},
author = {Osuji, IE and Akanmu, AO and Babalola, OO},
title = {Bacterial Diversity and Functional Dynamics in the Soybean (Glycine max L.) Rhizosphere Under Different Organic Fertilisation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70370},
doi = {10.1111/1758-2229.70370},
pmid = {42219628},
issn = {1758-2229},
support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; },
mesh = {*Glycine max/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Soil Microbiology ; Manure/analysis/microbiology ; Animals ; *Fertilizers/analysis ; Cattle ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Biodiversity ; Soil/chemistry ; Poultry ; *Microbiota ; DNA, Bacterial/genetics ; },
abstract = {Soybean (Glycine max L.) is a globally important legume for oil and protein production, yet its responses to specific organic fertilisation practices remain insufficiently understood. Organic amendments such as cattle dung and poultry manure are sustainable alternatives to inorganic fertilisers, but their effects on the soybean rhizosphere microbiome remain poorly characterised. This study investigated microbial community structure and functional diversity under poultry manure and cattle dung treatments. Rhizospheric soils were collected from treated plots, untreated controls and bulk soil and then subjected to physicochemical analysis. DNA extracted from samples was analysed using 16S rRNA gene sequencing on the Illumina NovaSeq 6000 platform, with data processed in QIIME 2 (v2019.1). Poultry manure increased available phosphorus (28%) and calcium (19%), while cattle dung enhanced potassium (22%) and magnesium (17%). Microbial community composition shifted significantly, with poultry manure promoting copiotrophic taxa such as Burkholderia and Cupriavidus and cattle dung enriching decomposers including Paenibacillus and Treponema. Alpha diversity was highest in poultry manure (Shannon index 6.2) and bulk soil (6.0) and lowest in cattle dung (5.1). Functional predictions indicated retention of core metabolic pathways, suggesting functional redundancy. Overall, organic fertilisation reshapes microbial communities while maintaining essential functions, supporting sustainable soybean cultivation.},
}

*Glycine max/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
*Soil Microbiology
Manure/analysis/microbiology
Animals
*Fertilizers/analysis
Cattle
RNA, Ribosomal, 16S/genetics
*Rhizosphere
Biodiversity
Soil/chemistry
Poultry
*Microbiota
DNA, Bacterial/genetics

@article {pmid42219690,
year = {2026},
author = {Zhu, P and Yuan, X and Wang, X and Shi, Y},
title = {Application of Nano Silica Is Associated With Enhanced Wheat Resistance to Fusarium Crown Rot via Regulation of Metabolic Pathways and Soil Microbial Community.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70343},
doi = {10.1111/1462-2920.70343},
pmid = {42219690},
issn = {1462-2920},
support = {SDAIT0107//Shandong Modern Agricultural Technology & Industry System/ ; SDNYXTTG-2023-30//Agricultural Major Technology Collaborative Promotion Plan Project in Shandong Province/ ; },
mesh = {*Triticum/microbiology ; *Fusarium/physiology ; *Soil Microbiology ; *Silicon Dioxide/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention & control ; *Disease Resistance/drug effects ; Lignin/metabolism ; *Nanoparticles ; },
abstract = {Nano silica (NS) has promising agricultural applications, yet its effects and mechanisms in enhancing wheat resistance to Fusarium crown rot (FCR) caused by Fusarium pseudograminearum (FP) remain underexplored. Here, we conducted a pot experiment with 200 mg/L NS, integrating soil metagenomics, plant physiology, and metabolomics to investigate this process. Soil metagenomic analysis revealed that NS was associated with reshaped microbial community structure and distinct functional pathway variations (GO/KEGG annotations). In wheat, NS treatment was linked to activated fructose/mannose metabolism and phenylpropanoid biosynthesis, increasing SOD and POD activities by 14.5% and 169.9% and reducing MDA content by 37.0%. It was also associated with upregulated lignin-related enzymes (PAL, C4H, and 4CL) and their encoding genes, thus promoting lignin accumulation, enhancing stem strength, and restoring cellulose content. Our findings suggest a potential dual mechanism: NS-associated soil microbiome changes coincide with improved plant antioxidant capacity and defence gene expression, reinforcing stem integrity to alleviate FCR, providing new insights for eco-friendly FCR management.},
}

*Triticum/microbiology
*Fusarium/physiology
*Soil Microbiology
*Silicon Dioxide/pharmacology
Metabolic Networks and Pathways/drug effects
*Microbiota/drug effects
*Plant Diseases/microbiology/prevention & control
*Disease Resistance/drug effects
Lignin/metabolism
*Nanoparticles

@article {pmid42219697,
year = {2026},
author = {Liang, S and Strodl, E and Barron, L and Bambling, M and Vitetta, L},
title = {Associations Between Microbial Depletion and Autonomic Dysregulation in Binge-Eating Disorder.},
journal = {The International journal of eating disorders},
volume = {},
number = {},
pages = {},
doi = {10.1002/eat.70139},
pmid = {42219697},
issn = {1098-108X},
abstract = {OBJECTIVE: The interplay between the gut microbiome and autonomic nervous system remains unexplored in binge-eating disorder (BED). We aimed to explore specific microbial alterations in BED and examine their potential association with cardiac vagal tone as a distinct bio-behavioral phenotype.

METHOD: Women with BED and co-occurring major depressive disorder (BED+MDD; n = 19) were compared to strictly matched controls with MDD alone (n = 38) to isolate BED-specific effects. We analyzed the gut microbiome via 16S rRNA sequencing and assessed cardiac vagal tone using short-term heart rate variability (specifically normalized high-frequency power, HFnu). Nutritional intake was analyzed to explore diet-microbiome interactions.

RESULTS: While global diversity did not differ between groups, differential abundance analysis identified lower relative abundance of several fermentative taxa, including Catenibacterium, Acidaminococcus, Pediococcus, Fusobacterium, Megasphaera, and Prevotella in the BED group. Notably, a cross-system association emerged exclusively in the BED group: the depletion of Pediococcus was strongly correlated with reduced vagal tone (HFnu; p = 0.003) and specific micronutrient patterns. This relationship was absent in the MDD-only controls.

DISCUSSION: Our findings demonstrate a BED-specific link between the depletion of the fermentative guild, autonomic instability, and dietary energy intake. This linked state may reflect a physiological response to the acute substrate surges characteristic of binge-eating, potentially compromising gut-brain axis homeostasis. Future research incorporating direct measures of binge behavior and luminal environment is required to validate whether these microbial patterns represent a causal mechanism or a reproducible physiological marker of the disorder.},
}

@article {pmid42219768,
year = {2026},
author = {Liu, X and Chen, T and Qin, X and Han, M and Zhang, X and Zhou, J and Li, P},
title = {Simplified synergistic rhizosphere bacterial consortia enhance the antagonistic activities against Ralstonia solanacearum and improve plant health.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-25-2115-RE},
pmid = {42219768},
issn = {0191-2917},
abstract = {The rhizosphere microbiota plays a vital role in plant stress resistance and pathogen suppression. Bacterial wilt, caused by Ralstonia solanacearum, leads to significant economic losses in a wide variety of crops. The utilization of native microbial consortia has emerged as a promising strategy for combating this disease. In this study, we assembled a synthetic microbial consortium (Co-4) from rhizosphere bacteria with demonstrated antagonistic activity, comprising four strains of Bacillus sp., Heyndrickxia sp., Franconibacter sp., and Pseudomonas sp. Transcriptome analysis of tomato plants treated with Co-4 revealed significant alterations in gene expression, particularly in carbohydrate and energy metabolism, as well as translation processes. These changes correlated with enhancements in various plant growth traits, including height, stem thickness, biomass, leaf area, photosynthetic rate, and root development. Furthermore, two simplified consortia, SynCom1 (Bacillus, Heyndrickxia, Franconibacter) and SynCom2 (Franconibacter, Pseudomonas), exhibited augmented antagonistic properties against R. solanacearum compared to their individual constituent strains. Using SynCom2 as a model, we demonstrated that its synergistic interactions resulted in increased biofilm formation, motility, biomass production, cross-feeding interactions, and volatile organic compounds (VOC) emissions, all of which likely contribute to disease suppression and enhanced plant defense. This study highlights the potential of simplified synthetic consortia for managing bacterial wilt through cooperative microbial functions, presenting an effective and environmentally sustainable biocontrol strategy.},
}

@article {pmid42220059,
year = {2026},
author = {Ren, R and Li, X and Li, H and Cao, Z and Hou, M and Zhao, C and Lou, N and Hu, S and Li, Y and Ma, Q and Li, Y and Fan, Y and Zhao, K and Zhao, K and Qiu, D and Gong, F and Li, Z and Liu, H and Ma, X and Wang, X and Yin, D},
title = {Resistant Peanut Genotype Reprograms Rhizosphere Metabolism to Enhance Bacterial Wilt Suppression.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e75910},
doi = {10.1002/advs.75910},
pmid = {42220059},
issn = {2198-3844},
support = {U22A20475//National Natural Science Foundation of China (NSFC)-Henan United Fund/ ; 264000510007//Zhongyuan Scholars in Henan Province/ ; 221111110500//Key Scientific and Technological Project of Henan Province/ ; HARS-22-05-G1//Key Scientific and Technological Project of Henan Province/ ; 262102111109//Key Scientific and Technological Project of Henan Province/ ; 242102111154//Key Scientific and Technological Project of Henan Province/ ; 30501308/111//Special Fund for Young Talents in Henan Agricultural University/ ; },
abstract = {Bacterial wilt caused by Ralstonia solanacearum compromises the yield and quality of peanut (Arachis hypogaea L.). While rhizosphere microbiome-assisted defense is known, how resistant plant genotypes orchestrate this process remains unclear. Here, we integrate multi-omics analyses of resistant and susceptible peanut genotypes to uncover a genotype-specific defense mechanism. The resistant genotype selectively recruits beneficial bacteria (e.g., Kosakonia and Frankia), which coincides with activated salicylic acid (SA)-dependent systemic acquired resistance (SAR). Crucially, we identify keystone rhizosphere metabolites (including betaine, arginine, and SA) that are positively correlated with both beneficial microbiome assembly and SAR gene expression, establishing a self-reinforcing defense loop. Leveraging these insights, we develop a prebiotic formulation that enhances beneficial microbial recruitment and stimulates SAR. Field trials demonstrate that the prebiotics reduce bacterial wilt incidence from 84.2% to 5.0% and increase yield by 12.9%-20.3%. Collectively, our study reveals a synergistic microbiome-immune co-regulation mechanism in peanut and delivers a translatable solution for sustainable disease management.},
}

@article {pmid42220213,
year = {2026},
author = {Sayol-Altarriba, A and Aira, A and Martín-López, E and Villasante, A and Albarracín, R and Faneca, J and Pitart, C and Roca, I and Casals, G and Marco, S and Villanueva-Cañas, JL and Casals-Pascual, C},
title = {Metabolic Screening of Gut Microbiota by Fourier-Transform Infrared Spectroscopy.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.6c00128},
pmid = {42220213},
issn = {2373-8227},
abstract = {Short-chain fatty acids (SCFAs) are bacterial metabolites with crucial roles in host homeostasis and immune system modulation. Given their benefits, they have been proposed as markers of healthy microbiota. However, accurate SCFA quantification typically requires gas chromatography coupled with mass spectrometry (GC-MS), which is time-consuming, expensive, and requires specialized personnel and equipment, limiting its routine use for stool quality assessment in clinical contexts. In this initial feasibility study, we explored the use of Fourier transform infrared (FT-IR) spectroscopy as a rapid metabolic screening approach for stool samples. Analysis of SCFA-associated spectral windows enhanced discrimination between healthy and dysbiotic stool samples with Clostridioides difficile infection using principal component analysis. FT-IR is not intended to replace GC-MS for precise SCFA quantification but rather to provide a rapid screening of metabolically relevant differences. Although additional validation is still needed, the present study provides a robust proof-of-concept demonstrating the feasibility of applying FT-IR spectroscopy to clinical stool samples. Combined with the widespread availability of this technology in most hospitals, these advantages highlight its potential for future development as a tool for routine screening in clinical laboratories.},
}

@article {pmid42220281,
year = {2026},
author = {de Bruijn, CMA and Oorthuys, AOJ and Zeevenhooven, J and Davids, M and Levels, JHM and Vlieger, AM and Herrema, H and Nieuwdorp, M and Benninga, MA},
title = {Feasibility and efficacy of fecal microbiota transplantation in adolescents with refractory irritable bowel syndrome: A randomized clinical pilot trial.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70459},
pmid = {42220281},
issn = {1536-4801},
support = {//Stichting Dioraphte/ ; //For Wis(h)dom Foundation/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 015.017.050//Aspasia Premium/ ; },
abstract = {OBJECTIVES: To assess the feasibility and efficacy of fecal microbiota transplantation (FMT) in adolescents (16-21 years) with refractory irritable bowel syndrome (IBS).

METHODS: Randomized controlled pilot trial. Thirty-two patients were included and randomized to receive two allogeneic or autologous FMTs. At baseline and after 6 weeks, two allogeneic or autologous FMTs were administered via a nasoduodenal tube. Feasibility outcomes included dropout rate. Clinical efficacy was evaluated by the proportion of responders (≥50 points reduction in total score of the IBS severity-scoring-system) at 12, 24, and 48 weeks follow-up. Secondary outcomes included health-related quality of life (QoL), depression and anxiety scores, and school/work absenteeism.

RESULTS: One patient (3%) withdrew after randomization, due to lack of effect after the first FMT. Response rates 12 weeks after allogeneic and autologous FMTs were 40% and 38% (p = 0.886). At 24 weeks, significantly more patients responded after allogeneic FMTs (60% vs. 25% autologous, p = 0.048), without significant differences at 48 weeks (60% vs. 50%, p = 0.576). Total QoL score was significantly better after allogeneic than autologous FMTs at 12, 24, and 48 weeks (p = 0.028, p = 0.007, p = 0.011). In the allogeneic FMTs group, school/work absenteeism was 7% at 24 weeks (vs. 41% autologous, p = 0.037).

CONCLUSIONS: Allogeneic FMTs were feasible and resulted in high response rates and better QoL compared to autologous FMTs. These results provide preliminary evidence for the use of allogeneic FMTs in adolescents with refractory IBS.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT03074227 (https://clinicaltrials.gov/study/NCT03074227?id=NCT03074227&rank=1).},
}

@article {pmid42220507,
year = {2026},
author = {Wei, F and Nakahara, Y and Isobe, J and Igarashi, Y and Saito, H and Murakami, S and Kondo, T and Himuro, H and Kouro, T and Matsui, T and Wada, S and Tsunoda, T and Yoshimura, K and Sasada, T},
title = {Gut microbiome functional pathways outperform taxonomic profiles in predicting immune checkpoint inhibitor response in non-small cell lung cancer: an interpretable machine learning approach with SHAP.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1832317},
pmid = {42220507},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/mortality/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Lung Neoplasms/drug therapy/microbiology/mortality/immunology ; *Gastrointestinal Microbiome/drug effects ; *Machine Learning ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Treatment Outcome ; Predictive Learning Models ; Feces/microbiology ; },
abstract = {INTRODUCTION: Lung cancer remains the leading cause of cancer mortality worldwide, with non-small cell lung cancer (NSCLC) accounting for the majority of cases. Although immune checkpoint inhibitors (ICIs) have transformed the therapeutic landscape of NSCLC, clinical responses remain highly variable. Emerging evidence implicates the gut microbiome in modulating the outcomes of ICI treatment; however, most studies to date have focused on taxonomic composition rather than microbial functional capacity. This study aimed to systematically compare the predictive value of taxonomic versus functional gut microbiome features across multiple ICI-related outcomes.

METHODS: Pretreatment fecal samples from 77 Japanese patients with NSCLC receiving ICIs were profiled using 16S rRNA sequencing. Six feature sets, comprising three taxonomic (family, genus, and species) and three functional (KEGG Orthology, Enzyme Commission, and MetaCyc pathways), were assessed using permutational multivariate analysis of variance for their association with clinical outcomes, including treatment response, irAEs, progression-free survival, and overall survival. Machine-learning models were subsequently developed based on MetaCyc pathway features to predict treatment response, with nested internal and external validation to ensure robustness and SHapley Additive exPlanations (SHAP) analysis for model interpretability.

RESULTS: Of all the feature sets tested, the functional profiles derived from the MetaCyc pathways exhibited the strongest association with the RECIST-defined response. A four-pathway signature, comprising PWY-4984 (urea cycle), SALVADEHYPOX-PWY (adenosine nucleotide degradation), OANTIGEN-PWY (O-antigen biosynthesis in E. coli), and PWY-5088 (L-glutamate degradation VIII to propanoate), achieved robust predictive performance, substantially outperforming any single feature. SHAP analysis confirmed that the primary drivers of responder classification were pathways involved in nitrogen metabolism and short-chain fatty acid biosynthesis.

CONCLUSIONS: In this study, gut microbial functional profiles consistently outperformed taxonomic features in predicting ICI response in patients with NSCLC. These findings suggest that metabolic pathway-based signatures may capture functional microbiome-host interactions more effectively and hold greater promise as translatable, safer targets for precision intervention, particularly through metabolite-oriented strategies.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/mortality/immunology
*Immune Checkpoint Inhibitors/therapeutic use
*Lung Neoplasms/drug therapy/microbiology/mortality/immunology
*Gastrointestinal Microbiome/drug effects
*Machine Learning
Female
Male
RNA, Ribosomal, 16S/genetics
Middle Aged
Aged
Treatment Outcome
Predictive Learning Models
Feces/microbiology

@article {pmid42220515,
year = {2026},
author = {Yang, Q and Liu, C and Wang, Q and An, J and Cai, Y},
title = {Infection-driven proliferative phase impairment in chronic wounds: a mechanistic framework for precision regenerative therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1803023},
pmid = {42220515},
issn = {1664-3224},
mesh = {Humans ; *Wound Healing ; Animals ; Biofilms ; Chronic Disease ; *Wound Infection/therapy/microbiology/pathology/immunology ; Regeneration ; *Regenerative Medicine/methods ; Cell Proliferation ; *Wounds and Injuries/therapy ; },
abstract = {Chronic wounds represent a major clinical challenge characterized by persistent failure of tissue repair, a phenomenon that cannot be fully explained by infection and inflammation alone. Emerging evidence indicates that wound-associated microbial communities establish stable pathogenic ecosystems that specifically disrupt the proliferative phase of healing, the critical stage responsible for cellular expansion, angiogenesis, and extracellular matrix reconstruction. Here, we propose the conceptual framework of infection-driven proliferative phase impairment (IDPPI), which describes a pathological state in chronic wounds wherein sustained microbial pathogenic activities continuously compromise host regenerative programs. We synthesize current evidence showing that coordinated virulence factor deployment, biofilm persistence, and host immune-metabolic dysregulation converge to induce proliferative arrest. They do so through direct cellular injury, suppression of repair-related signaling pathways, and disruption of cell-cycle control. This integrated pathogenic cascade ultimately locks wounds into a state of low-efficiency or arrested regeneration. Building on this mechanistic framework, we outline a sequential, targeted therapeutic paradigm encompassing three interconnected levels: targeted suppression of virulence and biofilm functions, restoration of immune-metabolic homeostasis within the wound microenvironment, and spatiotemporally controlled promotion of regeneration using responsive biomaterials and cell-free regenerative strategies. Rather than prioritizing non-selective microbial eradication, this approach emphasizes functional disarmament of pathogenic ecosystems and reactivation of host proliferative capacity. Finally, we discuss how advances in spatial multi-omics, biomimetic human-relevant models, artificial intelligence, and real-time sensing technologies can enable dynamic assessment and adaptive intervention, supporting a paradigm shift in chronic wound management from static staging toward feedback-guided (closed-loop), mechanism-informed regenerative medicine. IDPPI is presented as an integrative framework that reorders causality by placing infection-driven disruption of proliferative repair execution as the proximal failure mode.},
}

Humans
*Wound Healing
Animals
Biofilms
Chronic Disease
*Wound Infection/therapy/microbiology/pathology/immunology
Regeneration
*Regenerative Medicine/methods
Cell Proliferation
*Wounds and Injuries/therapy

@article {pmid42220946,
year = {2026},
author = {Hassan, EH and Zaghloul, W and Ahmed, SM and Ghozi, AM and Abdelwahab, IA},
title = {Study of the gut microbiome profile in full-term infants with necrotizing enterocolits.},
journal = {World journal of clinical pediatrics},
volume = {15},
number = {2},
pages = {112551},
pmid = {42220946},
issn = {2219-2808},
abstract = {BACKGROUND: Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease that primarily affects preterm. Recently, cases with similar clinical manifestations have been observed in full-term infants without Hirschsprung's disease. Dysbiosis suggested to have role in development of NEC.

AIM: To compare the gut microbiome composition between full term infants with NEC and healthy controls and to evaluate the impact of feeding sources on microbial diversity.

METHODS: Ten full term infants with NEC and six matched healthy breastfed control infants were enrolled in the study. Triplicate stool samples were collected from the enrolled infants. Genomic DNA was isolated and subjected to polymerase chain reaction analysis.

RESULTS: Bacteroidetes and Bacteroides were more abundant in control infants than in NEC cases, although the differences were statistically insignificant (P = 0.118 and P = 0.147, respectively), with large and moderate effect sizes. Bifidobacteria levels were significantly greater when a relaxed threshold (P ≤ 0.1) was used in both the control and NEC breastfed groups than in the NEC formula-fed group (P = 0.098). Additionally, alpha diversity was significantly reduced at the 0.1 level in NEC patients, especially among formula-fed infants (P = 0.094).

CONCLUSION: Full-term Egyptian infants with NEC exhibit reduced microbial diversity and alterations in bacterial abundance, supporting a potential link between dysbiosis and NEC. Feeding practices, particularly breastfeeding, appear to influence the gut microbiome profile regardless of NEC status. Although Bacteroidetes and Bacteroides did not reach statistical significance, their effect sizes suggest a need for further investigation into their roles in NEC pathogenesis in full-term infants.},
}

@article {pmid42220947,
year = {2026},
author = {Sintusek, P and Klomkliew, P and Visedthorn, S and Phutthawong, K and Noicharoen, T and Soontornsook, A and Tran, DL and Payungporn, S},
title = {Distinct early gut microbiota patterns by delivery mode within 100 hours of birth.},
journal = {World journal of clinical pediatrics},
volume = {15},
number = {2},
pages = {117841},
pmid = {42220947},
issn = {2219-2808},
abstract = {BACKGROUND: Disruptions in the early-life gut microbiome have been reported to be associated with various health conditions. However, few studies have investigated the establishment of the gut microbiota in the immediate postnatal period.

AIM: To characterize the gut microbiota of neonates within the first 100 hours after birth.

METHODS: A total of 512 healthy neonates born at a tertiary hospital were enrolled in this study. Stool samples were collected between March 2024 and December 2024 and categorized by delivery mode and stool collection time. Microbiota diversity and composition were assessed using full-length 16S rDNA sequencing. Stool samples from 140 neonates with predominant breastfeeding were analyzed.

RESULTS: Of the 140 neonates, 70 (50%) were female, 66 (47.1%) were delivered by vaginal delivery (VD), 74 (52.9%) were delivered by cesarean section (CS), and 87 (62.1%) were firstborn. The time of stool collection ranged from 13.2 minutes to 109.82 hours. A significant difference in the time of stool collection was observed between CS and VD neonates (43.0 hours; 95%CI: 35.8-50.1 vs 32.4 hours; 95%CI: 27.8-36.9; P = 0.016). Gut microbiota analysis revealed that CS was associated with higher alpha diversity (Chao1 and Shannon indices; P < 0.001) and beta diversity (P < 0.001). A reduction in the gut microbiota diversity was observed 48 hours after birth (P < 0.001). Escherichia coli predominated in the VD samples. Bifidobacterium species, including Bifidobacterium longum, Bifidobacterium pseudocatenulatum, and Bifidobacterium bifidum, emerged significantly 48 hours after birth. CS neonates exhibited a higher relative abundance of skin- and environmental-associated taxa, including Staphylococcus, Streptococcus, and Pseudomonas, and markedly reduced colonization by Bifidobacterium species despite predominant breastfeeding.

CONCLUSION: Despite predominant breastfeeding, CS neonates showed reduced colonization by Bifidobacterium and a greater abundance of skin- and environment-associated taxa within the first 100 hours of life. These findings indicate that delivery mode can be a key determinant of early microbial assembly and highlight the need for targeted strategies to support the establishment of beneficial microbiota in CS-delivered infants.},
}

@article {pmid42220960,
year = {2026},
author = {Al-Beltagi, M and Saeed, NK and El-Sawaf, Y and Bediwy, AS and Elbeltagi, R},
title = {Early-life gastrointestinal inflammation and the developing brain: Unravelling the pathways to long-term cognitive dysfunction.},
journal = {World journal of clinical pediatrics},
volume = {15},
number = {2},
pages = {117843},
pmid = {42220960},
issn = {2219-2808},
abstract = {The gut-brain axis (GBA) is a complex, bidirectional communication network critical to integrating central nervous system functions with gastrointestinal (GI) health. This review examines how disruptions to the GBA during the critical early-life developmental window - a period of rapid neurogenesis and microbial colonization - contribute to long-term neurocognitive and psychiatric vulnerabilities. Evidence from animal models demonstrates that early-life stress, antibiotics, and infection induce sustained neuro-inflammation and alter microglial function, leading to long-term behavioral and cognitive impairments in adulthood. Human studies corroborate these findings, revealing that severe early GI insults, such as necrotizing enterocolitis, confer a high risk (40%) of global neurodevelopmental impairment and specific attention deficits. Chronic inflammatory conditions similarly impact the central nervous system: A high burden of early severe enteric infection is an independent risk factor for diminished intelligence quotient (IQ) and executive function, while conditions like celiac disease and inflammatory bowel disease are associated with persistent deficits in attention, processing speed, memory, and executive function. These clinical outcomes are strongly linked to systemic inflammation [elevated interleukin-6, kynurenine-to-tryptophan (Kyn:Trp) ratio], micronutrient deficiencies (iron, vitamin B12, folate), and structural white matter changes in the brain. Furthermore, chronic GI disease imposes a significant psychiatric burden, with high comorbidity of anxiety and depression often mediating poor health-related quality of life, particularly in pediatric inflammatory bowel disease. The findings underscore the necessity for a shift in clinical practice: Chronic GI disease in early life must be recognized as a red flag for neurocognitive risk. We advocate for a multidisciplinary approach encompassing early neurodevelopmental follow-up for high-risk groups and routine screening for cognitive and emotional comorbidities. Future research must focus on long-term prospective cohorts, identifying precise mechanistic biomarkers (metabolomics, microbiome signatures), and conducting interventional trials targeting the GBA to mitigate these long-term functional consequences.},
}

@article {pmid42221001,
year = {2026},
author = {Yuan, HX and Yin, ZT and Wang, LH and Ma, L and Liu, Y and Ju, YL and Yue, B},
title = {Age-stratified management of pediatric perianal abscesses: a proposed framework integrating the "Developmental Healing Axis".},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1789225},
pmid = {42221001},
issn = {2296-2360},
abstract = {Pediatric perianal abscesses represent a frequent yet underrecognized condition that poses diagnostic and therapeutic challenges due to tissue fragility and age-dependent healing dynamics. This review synthesizes current evidence on the epidemiology, pathophysiology, and management of pediatric perianal abscesses to provide a conceptual basis for clinical decision-making. Surgical interventions such as incision and drainage offer rapid symptom relief but may increase the risk of fistula formation, particularly in older children. In contrast, conservative strategies including antibiotic therapy and observation are often effective in infants and young children, reflecting their superior regenerative capacity. Age-related differences in immune response, microbiota composition, and glandular anatomy contribute to variations in disease progression and healing outcomes. By integrating data from recent studies and clinical guidelines, this review highlights the importance of individualized, age-specific management to optimize recovery, minimize recurrence, and prevent fistula development. Furthermore, it identifies gaps in current evidence and underscores the need for standardized treatment protocols and future research into predictive and microbiome-related factors influencing disease course.},
}

@article {pmid42221002,
year = {2026},
author = {Kolluru, S and Liao, N and Haase, K and Foley, O and Cherkasskiy, L and Tauseef, A},
title = {Epidemiological trends in infant mortality related to necrotizing enterocolitis.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1825909},
pmid = {42221002},
issn = {2296-2360},
abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is the leading cause of gastrointestinal morbidity and mortality among infants in the neonatal intensive care unit. With an overall prevalence of 1%, NEC is found in about 11% of infants with very low birthweights (VLBW) and 22% in infants of extremely low birthweights. A disease of prematurity, NEC has a multifactorial pathogenesis involving a combination of feeding regimens, gut microbiome, and birth weight. This study aims to elucidate the demographic factors associated with NEC- mediated infant mortality, with the goal of guiding future research into disease diagnosis and management.

METHODS: The CDC WONDER database was queried to collect data on mortality from NEC of infants <1 year old between 1999 and 2023. Data was stratified by sex, race/ethnicity, urbanization status, and census region. Crude mortality rate (CMR) was determined, and Joinpoint analysis was conducted to identify significant changes in mortality trends.

RESULTS: Overall NEC-related CMR decreased slightly between 1999 and 2023. CMR was higher in males than females throughout the study period, though mortality decreased slightly in the male population. When stratified by race, Non-Hispanic (NH) Black or African American patients had the highest overall CMR, followed by Hispanic or Latino and NH White patients, respectively. Regionally, the South had the highest CMR across the four studied census regions, though Southern mortality decreased over the study period. The West reported the lowest mortality from NEC and was the only census region with reported increase in CMR. In both urban and rural areas, mortality initially increased before a subsequent decrease throughout the study period.

DISCUSSION: This study builds on prior research efforts into mortality trends in NEC to highlight the disproportionate mortality burden associated with NEC faced by certain groups, including males, NH Black of African American patients, and patients from the Southern United States. Further research into the implications of different socioeconomic determinants of health and biomarker variability by demographic cohort can guide more effective diagnostic and management strategies.},
}

@article {pmid42221078,
year = {2026},
author = {Gaspary, JFP and Lopes, LFD and Gaspary, FP and Lopes, EG and Edgar, AL and Camara, EP and Camara, AG},
title = {Stabilized adaptive states in microbiome-human integrated physiology: reframing health and chronic disease as symbiotic biological states.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1824897},
pmid = {42221078},
issn = {2296-858X},
abstract = {BACKGROUND: Modern medicine has achieved remarkable precision in identifying molecular mechanisms and developing targeted interventions. However, a persistent clinical paradox remains: many chronic conditions-including metabolic, autoimmune, neuropsychiatric, and oncological disorders-exhibit long-term stability, resistance to guideline-concordant treatment, and recurrent trajectories. Despite extensive mechanistic characterization, the organizational basis of this stability remains insufficiently explained.

CONCEPTUAL GAP: In acute contexts such as infection and environmental intoxication, organisms can remain internally coherent while temporarily prioritizing non-host biological demands. This state-based perspective, however, has rarely been extended to chronic disease. At the same time, microbiome research has demonstrated that human physiology operates within a multigenomic system, in which exogenous gene repertoires contribute substantial metabolic and signaling capacity. Epigenetic research further indicates that repeated ecological exposures can progressively stabilize adaptive biological states over time.

PROPOSED FRAMEWORK: We propose a conceptual framework in which health and disease are interpreted as stabilized adaptive states emerging from hierarchical signal integration within a multigenomic human system. In this model, chronic pathology reflects coherent but constrained regulatory configurations, rather than simple dysregulation or isolated system failure. Central to this interpretation is membrane-level decisional architecture, which governs signal routing, threshold modulation, and downstream transcriptional responses across tissues.

IMPLICATIONS: This framework reorganizes existing evidence into a systems-level interpretation of chronic disease stability, providing a basis for generating testable hypotheses regarding state transitions, responsiveness to perturbation, and restoration of physiological flexibility. Rather than introducing new therapeutic doctrines, the model aims to clarify how biological systems stabilize over time and how such stabilization may be investigated within existing experimental paradigms.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420261295889, CRD420261295889; https://www.crd.york.ac.uk/PROSPERO/view/CRD420261295945, CRD420261295945.},
}

@article {pmid42221101,
year = {2026},
author = {Chai, J and Gui, W and Zhang, J and He, W and Li, Q},
title = {Anti-diabetic retinopathy molecular mechanism of Dihuang Yinzi: insights from network pharmacology, metabolomics, and microbiome analysis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1793936},
pmid = {42221101},
issn = {2296-858X},
abstract = {BACKGROUND: Diabetic retinopathy (DR) represents a major microvascular complication arising from diabetes mellitus, characterized by multifactorial pathogenesis encompassing genetic, metabolic, and microbial components. While Dihuang Yinzi (DHYZ), a traditional Chinese herbal formulation, exhibits therapeutic promise for DR management, the precise mechanistic underpinnings warrant further investigation. This research sought to elucidate critical target genes, metabolic compounds, and microbial species implicated in DHYZ's therapeutic action against DR.

METHODS: We constructed a murine DR model and procured biological specimens from 18 animals distributed across three experimental cohorts (control, disease model, and DHYZ-treated groups, n = 6 per group) for metabolomic profiling and microbiome characterization. Candidate genes emerged from overlapping DHYZ-associated targets with DR-linked genes. Through six computational algorithms within the cytoHubba plugin, we pinpointed pivotal target genes. Molecular docking studies examined binding affinity between essential target proteins and bioactive constituents. Metabolomic and microbiome datasets underwent differential expression analysis to enumerate candidate metabolites and microbial taxa, respectively. Finally, Spearman correlation-based integrative omics analysis distinguished critical metabolites and key microbial species.

RESULTS: We identified 110 candidate genes and five key target genes (STAT3, IL6, TNF, ESR1, and IL1B). Molecular docking analysis revealed strong binding interactions between ESR1 and six corresponding active compounds, with the highest binding affinity observed for naringenin. Additionally, metabolomic analysis identified 50 candidate metabolites, and microbiome analysis revealed 24 candidate microbes. Spearman correlation analysis further pinpointed 30 key metabolites and 18 key microbes.

CONCLUSION: This study elucidates five key target genes, 30 key metabolites, and 18 key microbes through which DHYZ may exert its therapeutic effects in DR. These findings provide valuable insights and a foundational reference for understanding the multi-omics mechanism of DHYZ in the treatment of diabetic retinopathy.},
}

@article {pmid42221399,
year = {2026},
author = {Al Jnainati, M and Govindarajan, A and Tyagi, S and Iltaf, M and Al Jnainati, J and Ayoub, M and Shadab, HA},
title = {Harnessing Microbiome Therapy to Treat Metabolic Syndrome.},
journal = {AACE endocrinology and diabetes},
volume = {13},
number = {3},
pages = {463-472},
pmid = {42221399},
issn = {3050-9157},
abstract = {BACKGROUND/OBJECTIVE: Metabolic syndrome, a global health crisis marked by insulin resistance, obesity, and dyslipidemia, necessitates novel therapeutic approaches beyond conventional symptom management. Emerging research highlights the gut microbiome as a pivotal modulator of metabolic health, with dysbiosis-characterized by reduced microbial diversity and proinflammatory shifts-implicated in disease pathogenesis. This review synthesizes evidence from preclinical and clinical studies on microbiome-targeted therapies, including fecal microbiota transplantation, designer probiotics, and synbiotics, which aim to restore microbial balance and ameliorate metabolic dysfunction.

CASE REPORT: This review synthesizes evidence from preclinical and clinical studies on microbiome-targeted therapies, including fecal microbiota transplantation, designer probiotics, and synbiotics, which aim to restore microbial balance and ameliorate metabolic dysfunction.

DISCUSSION: Fecal microbiota transplantation transfers beneficial microbiota to enhance insulin sensitivity, while probiotics and synbiotics modulate inflammation, strengthen gut barrier integrity, and stimulate metabolic regulators like glucagon-like peptide-1 and short-chain fatty acids. Mechanistically, these therapies mitigate systemic inflammation, improve glucose/lipid homeostasis, and reduce intestinal permeability linked to endotoxin translocation. Clinical trials report improved glycemic control, lipid profiles, and weight management, underscoring their multitargeted potential. However, challenges such as donor variability, lack of standardized protocols, and long-term safety concerns hinder widespread application. Personalized approaches, informed by machine learning and microbial biomarkers, alongside innovations in Clustered Regularly Interspaced Short Palindromic Repeats-based engineering and encapsulation technologies, may address these limitations.

CONCLUSION: Despite promising outcomes, rigorous large-scale trials and interdisciplinary collaboration are essential to validate efficacy, optimize delivery, and ensure ethical compliance. In conclusion, microbiome therapies represent a paradigm shift in treating metabolic syndrome by targeting root causes, yet translating preclinical success into clinical practice demands further innovation and evidence-based standardization.},
}

@article {pmid42221477,
year = {2025},
author = {Ceylan, A and Saçaklı, P and Özgenç Çınar, Ö and Ramay, MS and Ahsan, U and Harijaona, JA and Bayraktaroğlu, AG and Manghebati, F and Calik, A},
title = {Effect of supplemental dietary phytogenic blends on growth performance, jejunal histomorphometry, and jejunal immunity of broiler chickens.},
journal = {Archives animal breeding},
volume = {68},
number = {1},
pages = {13-26},
pmid = {42221477},
issn = {2363-9822},
abstract = {This study evaluated the effects of two phytogenic blends on broiler performance, intestinal histomorphology, CD4[+] (cluster of differentiation) and CD8[+] T-cell numbers, and mRNA abundances of several cytokines in broilers. For this purpose, a total of 300 Ross 308 male broiler chicks that were 1 d old were randomly allocated to five experimental groups. The control group was fed a basal diet without any additives, and there were two phytogenic supplement groups (blend A, mainly comprising extracts of Thymus vulgaris and Filipendula ulmaria, and blend B, consisting of Ginkgo biloba and Silybum marianum) with two dosage regimens each (100 and 200 mg kg[-1] (denoted A100 and A200) and 100 and 300 mg kg[-1] (B100 and B300) of the diet, respectively). Over the total growing period, body weight gain and feed intake were unchanged among the groups, although phytogenic blend B showed a dose-dependent improvement in feed conversion ratio. Both phytogenic blends did not affect carcass characteristics. Jejunal morphology (villus height, crypt depth, and their ratio) was modified depending on both the composition and the dosage levels of the selected phytogenics. Also, both phytogenic blends linearly increased the CD4[+] and CD8[+] T-cell numbers in the jejunum. Moreover, no major treatment effects were observed on mRNA abundances of cytokines (IL-1 β , IL-6, and TNF α). However, across the two phytogenic additives employed, a positive linear dose response in IL-1 β abundance was noted on day 21 in broilers fed phytogenic blend B. Overall, dietary phytogenic blend B improved the intestinal health and growth performance of chickens compared to blend A. Further studies are suggested to elucidate the effects of the tested phytogenic blends on gut microbiome and on oxidative stress in broiler chickens.},
}

@article {pmid42221478,
year = {2026},
author = {Agranyoni, O and Yolken, RH and Johnson, SB and Volk, H and Sabunciyan, S},
title = {Comparing saliva collection and DNA extraction methods for saliva-based microbiome profiling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809075},
pmid = {42221478},
issn = {1664-302X},
abstract = {AIMS: Mounting preclinical evidence demonstrates the importance of the human microbiome in health and disease. Saliva presents a particularly appealing medium for microbiome research due to its non-invasive collection and the availability of extensive biobanked samples across various conditions. However, methodological challenges remain- particularly regarding sample storage and the variability introduced by different nucleic acid extraction kits, which can exhibit selective affinities for certain bacterial taxa. In this study, we systematically compared multiple saliva collection and DNA extraction methods to optimize protocols for 16S rRNA-based microbiome profiling. Our approach incorporated rigorous quality control measures, including the analysis of water controls, differential abundance testing, and correlation analyses across groups, to identify the most reliable and reproducible methods for salivary microbiome characterization.

METHODS AND RESULTS: We compared four commercially available kits for at-home saliva collection to determine their effectiveness at preserving the salivary microbiome following 1 week of storage at room temperature (RT). We also compared three commercially available DNA extraction kits marketed for salivary microbiome characterization. We discovered that the DNA extraction kit used significantly impacted the microbiome composition. One week of incubation in the preservative solution shifted the bacterial composition of the saliva. Additionally, we demonstrated that contaminants in the environment and kits reagents may be increased during the incubation period, posing a significant challenge.

CONCLUSION: Our work demonstrates the feasibility of, and provides a framework for, microbiome characterization in saliva that applies to clinical and population-based studies. Our findings indicate that saliva microbiome studies using different extraction kits may introduce systematic biases, which should be accounted for when comparing results across studies. Using the same nucleic acid collection and extraction kits in various experiments is essential for reproducibility due to their different affinity to specific bacteria and contamination rates.},
}

@article {pmid42221488,
year = {2026},
author = {Kang, Z and Zhang, S and Jiao, Z and Wang, X and Wei, Y and Wang, R and Chang, Y and Wang, N},
title = {Genomic and microecological insights into the biocontrol mechanisms of Bacillus velezensis BER1 against rice sheath blight.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1836902},
pmid = {42221488},
issn = {1664-302X},
abstract = {Rice sheath blight is a major fungal disease threatening global rice production, causing substantial yield losses and lacking effective resistant cultivars. In this study, we systematically evaluated the biocontrol efficacy of Bacillus velezensis BER1 against rice sheath blight and elucidated its underlying mechanisms from three complementary perspectives: strain genomics, plant immune responses, and the phyllosphere microbiome. Genome analysis revealed that BER1 harbors 22 secondary metabolite biosynthetic gene clusters, including those encoding natural products such as fengycin and bacillaene with broad-spectrum antifungal and antibacterial activities. Application of BER1 reduced disease severity to 35.4%, outperforming conventional chemical treatment, and significantly induced the expression of rice immune-related genes (e.g., NH1 and PR1a), accompanied by increased activities of defense enzymes such as POD and PAL. 16S rRNA amplicon sequencing further showed that BER1 markedly increased the relative abundance of Bacillus in the phyllosphere while suppressing potential pathogenic taxa, and enriched functional pathways associated with secondary metabolite biosynthesis, particularly polyketide-related pathways. Compared with chemical intervention, BER1 maintained microbial community stability through ecological niche competition and sustained metabolic activity, thereby reducing pathogen risk. Collectively, these findings provide quantitative evidence supporting BER1 as a promising green and sustainable biocontrol agent against rice sheath blight and highlight the potential of microecology-based strategies for plant disease management.},
}

@article {pmid42221489,
year = {2026},
author = {Zhu, W and Guo, L},
title = {Advances in vulvovaginal candidiasis research: a comprehensive review from epidemiology, diagnosis, treatment to resistance mechanisms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1811011},
pmid = {42221489},
issn = {1664-302X},
abstract = {Vulvovaginal candidiasis (VVC), predominantly caused by Candida albicans, is one of the most common vaginal infections in women of reproductive age. Its clinical management has become increasingly complex due to the rising prevalence of non-albicans Candida infections, escalating azole resistance, and the challenge of biofilm formation. This review systematically summarizes recent advances in VVC research, with a focus on evolving epidemiology, innovations in diagnostics, current and emerging therapies, and an in-depth analysis of resistance mechanisms. Key molecular pathways underpinning antifungal resistance-including biofilm development, efflux pump overexpression, target-site gene mutations, and alterations in transcriptional regulators-are examined. The findings of this review support several actionable strategies for future practice. First, routine use of molecular diagnostics (PCR, MALDI-TOF MS) is essential for species identification and resistance detection, enabling a shift from empirical to precision-based therapy. Second, antifungal susceptibility testing should be interpreted with attention to vaginal pH conditions, and non-azole alternatives (boric acid, nystatin, ibrexafungerp, oteseconazole) should be prioritized when azole resistance is confirmed or suspected. Third, emerging approaches-including biofilm-disrupting agents, probiotic microbiome modulation, and nanotechnology-enhanced drug delivery-offer promising adjunctive and preventive strategies, particularly for recurrent VVC. By integrating these contemporary findings, this review provides a translational framework to optimize diagnosis, guide therapeutic decision-making, and inform future research priorities in VVC management. Notably, several novel agents-including ibrexafungerp and oteseconazole-have already received FDA approval and are entering clinical practice, with multiple ongoing trials evaluating boric acid, probiotics, and novel oral antifungals, underscoring the accelerating translation of mechanism-informed therapies into patient care.},
}

@article {pmid42221491,
year = {2026},
author = {Sufi, F},
title = {Editorial: Generative AI and large language models in microbial evolution, resistance mechanisms, and antimicrobial drug discovery.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1848209},
doi = {10.3389/fmicb.2026.1848209},
pmid = {42221491},
issn = {1664-302X},
}

@article {pmid42221502,
year = {2026},
author = {Xia, Q and Xin, J and Mu, Y and Li, M and Yao, J and Xiao, X and Wang, X and Gang, X},
title = {Therapeutic potential of natural compounds from medicinal and food homology substances targeting gut microbiota in lipid metabolism disorders.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809114},
pmid = {42221502},
issn = {1664-302X},
abstract = {Dyslipidemia contributes to chronic diseases such as non-alcoholic fatty liver disease (NAFLD), type 2 diabetes (T2DM), and obesity. Emerging evidence highlights gut dysbiosis as a key driver of abnormal lipid metabolism. This review examines how natural bioactive compounds from medicinal and food homology (MFH) substances regulate lipid metabolism by modulating the gut microbiome. It summarizes evidence on the modification of the microbiota-lipid metabolism axis by natural compounds from MFH substances and discusses the limitations of applications and their promise for preventing and treating metabolic diseases. By capitalizing on these microbiota-mediated effects, natural compounds may serve as a beneficial natural resource for adjusting lipid metabolism.},
}

@article {pmid42221503,
year = {2026},
author = {Alia, K and Khan, H and Muzaffar, H and Perveen, N and Alrashedi, S and Al Dhaheri, Y and Waheed, Y and Alam, MT and Naseem, M and Muhammad, K},
title = {Gut dysbiosis and microbial metabolites in atopic dermatitis: implications for immune regulation along gut-skin axis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1829876},
pmid = {42221503},
issn = {1664-302X},
abstract = {Atopic dermatitis (AD) is a multifactorial skin disorder characterized by immune dysregulation, impaired epidermal barrier, and strong microbial imbalance. Although genetic susceptibility and environmental triggers are established AD drivers, growing evidence highlights the gut skin axis as an important but underexplored AD pathogenesis factor. Gut microbiota dysbiosis, loss of short-chain fatty acid (SCFA)-producing bacteria, and altered metabolite profiles, such as tryptophan derivatives and secondary bile acids, have been linked to systemic immune imbalance and skin inflammation. However, the precise mechanism by which gut microbial alterations influence cutaneous immunity remains unclear. This review synthesizes recent advances from clinical and experimental studies to delineate how the gut microbiota and their metabolites shape the immune response, regulate the integrity of the epithelial barrier, and modulate AD severity. By integrating emerging insights into early-life microbial colonization, metabolite-mediated immune programming, and therapeutic interventions, including prebiotics, probiotics, and microbial-derived metabolites, the current gaps and the translational potential of targeting the gut- skin axis. The knowledge consolidated here advances our understanding of AD beyond skin-focused perspectives and highlights new avenues for microbiome-based preventive and therapeutic strategies.},
}

@article {pmid42221532,
year = {2026},
author = {Mishra, AK and Mishra, A and Vikal, A and Singh, H and Y Thajudeen, K and Khan, G and Ahmed, MM},
title = {Fecal microbiota transplant and its usefulness in hepatic disorders: a systematic review.},
journal = {Therapeutic advances in gastroenterology},
volume = {19},
number = {},
pages = {17562848261452504},
pmid = {42221532},
issn = {1756-283X},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an emerging therapeutic approach aimed at restoring gut microbial balance through the transfer of stool from healthy donors. It has gained significant attention for its role in managing gut dysbiosis-associated disorders, particularly hepatic diseases.

OBJECTIVE: This systematic review evaluated the therapeutic efficacy and clinical potential of FMT in the management of liver-related conditions, including recurrent Clostridium difficile infection (CDI), non-alcoholic fatty liver disease, liver cirrhosis, and hepatic encephalopathy.

DESIGN: A systematic review of existing literature was conducted to assess the clinical outcomes, mechanisms, and challenges associated with FMT in hepatic disorders.

DATA SOURCES AND METHODS: Relevant studies were identified from peer-reviewed scientific databases, focusing on clinical trials, observational studies, and experimental research investigating the role of FMT in gut dysbiosis and liver disease. Data were analyzed to evaluate efficacy, underlying mechanisms, and safety considerations.

RESULTS: FMT demonstrated high efficacy in recurrent CDI, with cure rates exceeding 80%-90%. In hepatic disorders, FMT was associated with improved microbial diversity, enhanced gut barrier integrity, and reduced systemic inflammation, contributing to better liver function and clinical outcomes. However, variability in donor selection, potential safety risks, and regulatory limitations remain significant challenges.

CONCLUSION: FMT represents a promising therapeutic strategy in hepatology, underscoring the critical role of the gut-liver axis. Advances such as synthetic microbiota and personalized microbiome-based therapies may further optimize its safety and efficacy, paving the way for innovative, microbiome-centered interventions in liver disease management.},
}

@article {pmid42221580,
year = {2026},
author = {Zhang, W and Wu, S and Shen, L and Peng, P and Li, R and Zheng, Q and Jia, X and Liu, Q and Liu, Y},
title = {Identification and evaluation of gut microbiome as non-invasive biomarkers for early lung adenocarcinoma from a multi-center study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1813261},
pmid = {42221580},
issn = {2235-2988},
mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Adenocarcinoma of Lung/diagnosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Biomarkers ; China ; *Gastrointestinal Microbiome ; *Lung Neoplasms/diagnosis/microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; },
abstract = {OBJECTIVE: This study aims to characterize the GM in LUAD patients and develop and validate a GM-based diagnostic model for LUAD.

METHODS: In this prospective, randomized, multi-center study, the GM was characterized, and an LUAD classifier was developed using a training cohort of 175 early-stage LUAD patients and 107 healthy controls. The model was further validated in a test cohort, two independent external cohorts from Jiangsu and Hainan, and an advanced LUAD cohort. Additional ML models were also developed and compared to assess their predictive performance.

RESULTS: LUAD patients exhibited reduced microbial diversity and significantly altered microbial composition compared to healthy controls. The phylum Verrucomicrobia and 13 genera, including Enterococcus and Akkermansia, were more abundant in the LUAD group, while 5 phyla, such as Fusobacteria and Cyanobacteria, and 17 genera, including Lactobacillus and Weissella, were enriched in the control group. Using random forest (RF), eight operational taxonomic units were identified as the optimal subset, achieving an area under the curve (AUC) of 0.998 in the training cohort and maintaining high accuracy in the test cohort (AUC = 96.9%). The model also demonstrated robust performance in two independent cohorts from Jiangsu (AUC = 97.6%) and Hainan (AUC = 82.9%), with strong diagnostic potential for advanced LUAD. Among five common models, the RF model exhibited the highest diagnostic accuracy.

CONCLUSIONS: This study provides a comprehensive characterization of the gut microbiome in LUAD and develops a diagnostic model based on microbial biomarkers, which is validated across regionally diverse cohorts, highlighting its potential as a reliable and non-invasive screening tool for LUAD.},
}

Aged
Female
Humans
Male
Middle Aged
*Adenocarcinoma of Lung/diagnosis/microbiology
*Bacteria/classification/genetics/isolation & purification
Biomarkers
China
*Gastrointestinal Microbiome
*Lung Neoplasms/diagnosis/microbiology
Prospective Studies
RNA, Ribosomal, 16S/genetics

@article {pmid42221589,
year = {2026},
author = {Song, D and Gao, H and Wang, T and Wei, Q and Liu, A and Ren, J},
title = {Gut microbiota dysbiosis-induced chronic inflammation as a driver of atherosclerosis: cellular crosstalk and host-microbe interactions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1789194},
pmid = {42221589},
issn = {2235-2988},
mesh = {*Dysbiosis/complications/microbiology ; Humans ; *Atherosclerosis/etiology/microbiology ; *Gastrointestinal Microbiome ; *Inflammation/microbiology ; Animals ; *Host Microbial Interactions ; Fecal Microbiota Transplantation ; Methylamines/metabolism ; Intestinal Barrier Function ; Fatty Acids, Volatile/metabolism ; },
abstract = {Gut microbiota dysbiosis is increasingly recognized as an upstream contributor to chronic low-grade inflammation and atherosclerosis (AS). Disruption of microbial homeostasis may impair intestinal barrier integrity, increase exposure to pro-inflammatory microbial products and metabolites, and reduce protective metabolites such as short-chain fatty acids (SCFAs), thereby activating innate immune signaling and sustaining vascular inflammation. Current evidence indicates that gut dysbiosis promotes atherosclerosis mainly through three interconnected processes: metabolite imbalance, barrier dysfunction with microbial translocation, and systemic immune reprogramming. Clinical studies have linked gut-derived biomarkers, particularly trimethylamine N-oxide (TMAO) and lipopolysaccharide (LPS)-related signals, to atherosclerotic burden and adverse cardiovascular outcomes, while experimental studies using fecal microbiota transplantation, probiotics, antibiotics, and gene-deficient models support a contributory role of the gut-immune-vascular axis. Emerging interventions, including dietary modulation, pharmacological repurposing, and microbiome-targeted therapies, may attenuate gut-derived chronic inflammation and offer new strategies for AS prevention and treatment. However, heterogeneity across studies and the limited causal evidence in humans warrant cautious interpretation. Overall, gut dysbiosis-driven chronic inflammation represents a biologically meaningful and potentially modifiable pathway in atherosclerosis.},
}

*Dysbiosis/complications/microbiology
Humans
*Atherosclerosis/etiology/microbiology
*Gastrointestinal Microbiome
*Inflammation/microbiology
Animals
*Host Microbial Interactions
Fecal Microbiota Transplantation
Methylamines/metabolism
Intestinal Barrier Function
Fatty Acids, Volatile/metabolism

@article {pmid41873129,
year = {2026},
author = {Alcheva, A and Jensen, JA and Hatsukami, DK and Stepanov, I},
title = {Changes in the Oral Microbiota after Switching from Smoking to Exclusive e-Cigarette Use in an 8-Week Product-Switching Trial.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {19},
number = {6},
pages = {369-379},
doi = {10.1158/1940-6207.CAPR-25-0244},
pmid = {41873129},
issn = {1940-6215},
support = {U19 CA157345/CA/NCI NIH HHS/United States ; U01 DA045523/DA/NIDA NIH HHS/United States ; //Masonic Cancer Center, University of Minnesota (MCC)/ ; P30 CA-077598//National Cancer Institute (NCI)/ ; },
mesh = {Humans ; Female ; *Microbiota/genetics ; Male ; *Mouth/microbiology ; Adult ; *Electronic Nicotine Delivery Systems/statistics & numerical data ; Cross-Sectional Studies ; *Vaping/adverse effects ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Smoking/adverse effects ; Bacteria/isolation & purification/genetics/classification ; },
abstract = {UNLABELLED: Cross-sectional data indicate that the oral microbiota differs between people who smoke or use e-cigarettes, suggesting potential as a research tool in product-switching trials, as a biomarker of product use status and/or long-term health effects. However, its sensitivity to short-term product switching remains unclear. We examined a subset of participants in an 8-week product-switching study who were asked to switch from smoking to exclusive e-cigarette use and had oral cells collected (n = 58). Using available biomarker data, we determined that 12 achieved complete switching and 46 engaged in dual use. A subgroup of participants in the same study who continued exclusive smoking (n = 20) was included for reference. Oral microbiota profiles were characterized at baseline and at the end of the study (week 8) using 16S rRNA gene sequencing targeting the V3 to V4 hypervariable regions on an Illumina MiSeq platform. Participants who switched to exclusive e-cigarette use had a significant decrease in alpha diversity (Shannon index) at week 8 compared with baseline smoking (P = 0.02), and their beta diversity at week 8 differed from those who engaged in dual use or continued exclusive smoking (r2 = 0.04; P = 0.014). They also showed increased abundances of proinflammatory genera (Streptococcus, Veillonella, Haemophilus, Fusobacterium), whereas dual users had decreased abundances of several commensal genera, including Lactobacillus, Limosilactobacillus, and Neisseria. Our findings indicate that the oral microbiota may serve as a sensitive tool for detecting and interpreting changes in tobacco-related exposures, and potentially for monitoring product use compliance in clinical studies of product switching.

PREVENTION RELEVANCE: By analyzing the oral microbiome, individuals' tobacco use status could be assessed, and the impact of interventions, such as switching to e-cigarettes, on reducing tobacco exposure could be evaluated. This information can inform tobacco cessation programs, risk stratification, and personalized prevention strategies for individuals at higher risk for tobacco-related cancer.},
}

Humans
Female
*Microbiota/genetics
Male
*Mouth/microbiology
Adult
*Electronic Nicotine Delivery Systems/statistics & numerical data
Cross-Sectional Studies
*Vaping/adverse effects
RNA, Ribosomal, 16S/genetics
Middle Aged
*Smoking/adverse effects
Bacteria/isolation & purification/genetics/classification

@article {pmid41875284,
year = {2026},
author = {Neuman, H and Shitrit, A and Turjeman, S and Koren, O},
title = {From Womb to Weaning: Microbial Signals That Shape the Developing Brain.},
journal = {Developmental neuroscience},
volume = {},
number = {},
pages = {1-13},
doi = {10.1159/000551712},
pmid = {41875284},
issn = {1421-9859},
abstract = {BACKGROUND: The gut microbiota plays a vital role in shaping brain development through complex bidirectional communication within the microbiota-gut-brain axis. Emerging evidence highlights neural, immune, endocrine, metabolic, and epigenetic pathways by which gut microbes influence neurodevelopmental processes.

SUMMARY: This review synthesizes current knowledge on the temporal dynamics of gut colonization and brain maturation. Drawing on mechanistic insights from animal models, we emphasize the central role of the maternal microbiota and particularly, microbially derived metabolites that cross the feto-placental barrier and shape fetal brain development. We also discuss molecular and cellular targets of microbial influence, implications for neurodevelopmental disorders, and potential therapeutic strategies.

KEY MESSAGES: Understanding these interactions opens new avenues for early-life interventions aimed at optimizing neurodevelopments and preventing neuropsychiatric conditions.},
}