@article {pmid41509546,
year = {2026},
author = {Steriade, C},
title = {The Gut Feeling Behind Autoimmune Encephalitis.},
journal = {Epilepsy currents},
volume = {26},
number = {3},
pages = {231-233},
pmid = {41509546},
issn = {1535-7597},
abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.

METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.

RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.

SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.},
}

@article {pmid43017922,
year = {2026},
author = {Tang, C and Shen, Y and Li, R and Chen, Z},
title = {Oral Microbiota and Secondary Alveolar Bone Grafting Outcomes: Evidence, Mechanisms, and Research Priorities.},
journal = {The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association},
volume = {},
number = {},
pages = {10556656261505165},
doi = {10.1177/10556656261505165},
pmid = {43017922},
issn = {1545-1569},
abstract = {Secondary alveolar bone grafting (SABG) restores alveolar continuity and supports tooth eruption and subsequent orthodontic movement in patients with alveolar clefts. Established determinants of outcome include surgical, anatomical, dental, and behavioral factors. The perioperative microbial environment may also be influenced by cleft-adjacent plaque retention, oronasal communication, local inflammation, and appliance-associated biofilms. This narrative review asks whether perioperative oral microbial features are associated with defined SABG complications and whether they add clinically useful prediction of graft outcomes beyond established clinical factors. Direct SABG reports are distinguished from broader cleft and mechanistic evidence. Two reports describe, respectively, an association of preoperative salivary microbial features with study-defined inflammation at the grafted site 3 months after SABG and postoperative microbial changes; partial participant overlap remains unresolved. Neither report establishes a causal role for oral microbiota in SABG complications or validates microbial features as predictors of long-term bone outcomes or graft failure. The reviewed evidence is insufficient for routine microbiome profiling, pathogen-directed or antifungal treatment based solely on microbial findings, or microbiome-based prediction of SABG success. Without formal quality or risk-of-bias appraisal, conclusions remain provisional. Multicenter prospective studies with standardized local sampling and outcome-specific follow-up are needed to evaluate incremental prognostic value and the efficacy of microbiota-targeted interventions.},
}

@article {pmid43017929,
year = {2026},
author = {Lindfors Frimodig, L and Low, M and de Miranda, JR and Berggren, Å},
title = {Breeding history, not dietary adaptation, drives growth of house crickets, Acheta domesticus (Orthoptera: Gryllidae), on novel feeds.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {6},
pages = {},
pmid = {43017929},
issn = {1536-2442},
support = {2022-00766//Formas, a Swedish research council for sustainable development/ ; },
mesh = {Animals ; *Gryllidae/growth & development/physiology/genetics ; Diet ; Animal Feed/analysis ; Male ; Female ; Adaptation, Physiological ; Body Size ; Breeding ; },
abstract = {Understanding how insect populations respond to novel diets is key to optimizing feed formulations and production efficiency in insect farming. In a controlled, replicated feeding trial, we reciprocally cross-fed 2 house cricket (Acheta domesticus (L.)) lines that had been maintained for >4 yr on distinct diets, a cereal‑based mix and a commercial formulation; the commercial-fed line had also been selected for larger body size. We partitioned growth into effects of diet adaptation (the advantage of the historical diet), diet composition and body-size selection. Mean body mass increased in all cages, and there was no evidence that survival differed among treatments. Line identity dominated growth: the commercial-fed line was more than twice as heavy at week 5 as the cereal-fed line, irrespective of feed (0.19 g; 95% CrI 0.12 to 0.25). The higher-fat commercial diet probably increased mass slightly in both lines (0.03 g; 95% CrI -0.02 to 0.10; Pr(effect > 0) = 0.87). In contrast, there was no evidence of a home-diet advantage on either an absolute or a proportional scale (0.003 g; 95% CrI -0.06 to 0.07; Pr = 0.55). Switching to a novel diet carried no detectable growth cost, suggesting physiological plasticity rather than diet adaptation. For producers, these results imply that line origin matters far more than the choice between these feeds. Future work should use replicated lines, follow crickets to harvest age at production densities, and combine feed‑intake measurements with microbiome analyses to separate consumption from conversion efficiency effects.},
}

Animals
*Gryllidae/growth & development/physiology/genetics
Diet
Animal Feed/analysis
Male
Female
Adaptation, Physiological
Body Size
Breeding

@article {pmid43018073,
year = {2026},
author = {Kim, J and Weiss, A and Ding, Y},
title = {Diet-Driven Modulation of the Gut Microbiome to Enhance Neuroplasticity and Cognitive Recovery After Ischemic Stroke.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e049633},
doi = {10.1161/JAHA.126.049633},
pmid = {43018073},
issn = {2047-9980},
abstract = {Cognitive impairment and limited neuroplastic recovery remain major contributors to long-term disability following ischemic stroke. Increasing evidence suggests that stroke-induced disruption of the gut-brain axis, characterized by microbiome dysbiosis and altered microbial metabolite signaling, may influence post-stroke inflammation, synaptic remodeling, and cognitive outcomes. Diet is a key modifiable determinant of gut microbiome composition and metabolic output, yet its role in post-stroke neuroplasticity has not been comprehensively synthesized. This narrative review examines dietary interventions with mechanistic or translational relevance to ischemic stroke recovery, including Mediterranean dietary patterns, ketogenic diets, high-fiber and prebiotic-enriched diets, probiotic and synbiotic supplementation, and intermittent fasting or caloric restriction. We summarize evidence linking diet-induced microbiome modulation to neuroinflammatory regulation, short-chain fatty acid signaling, microglial activity, mitochondrial function, and synaptic plasticity. Shared and diet-specific pathways are discussed, along with current limitations of the evidence base and barriers to clinical translation. Collectively, available data support a biologically plausible role for targeted dietary modulation of the gut microbiome as an adjunctive strategy to enhance cognitive recovery and neuroplasticity after ischemic stroke. Further well-designed clinical studies integrating microbiome profiling, neuroimaging, and cognitive outcomes are needed to define therapeutic potential and guide implementation in stroke rehabilitation. Among these dietary interventions, Mediterranean, high-fiber, and prebiotic-enriched diets currently have the strongest available evidence, while ketogenic and intermittent fasting approaches remain the least supported based on existing clinical and translational evidence.},
}

@article {pmid43018086,
year = {2026},
author = {Li, W},
title = {Comment on "The Effect of Pancreatic Exocrine Insufficiency and Pancreatic Enzyme Replacement Therapy on Gut Microbiome Composition in Pancreatic Disease: A Prospective Cohort Study".},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000002731},
pmid = {43018086},
issn = {1536-4828},
}

@article {pmid43018394,
year = {2026},
author = {Jiang, X and Wang, Y and Luo, Y and Jin, C and Zeng, Z and Hu, Y and Chen, H and Gong, S and Wu, J and Yang, M and , },
title = {Amino acid-based formula and Clostridioides difficile-associated disease in infants: concerns regarding causal interpretation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2761714},
doi = {10.1080/19490976.2026.2761714},
pmid = {43018394},
issn = {1949-0984},
mesh = {Humans ; *Amino Acids/adverse effects/analysis ; Infant ; *Infant Formula/chemistry/adverse effects ; *Clostridioides difficile/physiology ; *Clostridium Infections/microbiology/etiology ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome ; },
abstract = {Wang et al. recently reported an association between amino acid-based formula (AAF) feeding and Clostridioides difficile-associated disease (CDAD) in children younger than two years, integrating clinical observations, microbiome profiling, and fecal microbiota transplantation experiments. The authors appropriately framed their findings as associative; our aim is not to allege over-interpretation, but to delineate the evidentiary gap between their reported association and a causal claim. Several methodological and interpretative issues limit such inference, including confounding by the clinical indication for AAF, the difficulty of distinguishing C. difficile colonization from clinically attributable disease in young children, developmental differences in age and complementary feeding, and the selected nature of the fecal microbiota transplantation (FMT) donor population. For example, the multivariable model included only 27 outcome events against approximately six predictors (events-per-variable ≈ 4.5, far below the accepted 10-20 threshold), rendering the adjusted odds ratios unstable. The cross-sectional microbiome data further cannot establish whether microbial alterations preceded disease or resulted from underlying clinical, dietary, or inflammatory states. We therefore suggest interpreting the findings as an association between AAF feeding and CDAD status, rather than evidence that AAF itself increases CDAD risk. Our skepticism concerns the causal link to CDAD specifically; we do not dispute that reduced Bifidobacterium with formula feeding is a well-established finding. This distinction has important clinical implications, as AAF remains an essential nutritional intervention for children with appropriate indications, and in young children microbiological detection and microbiome alterations must be interpreted alongside age, clinical symptoms, underlying disease, dietary history, and other relevant exposures. An overly causal interpretation could create unnecessary concern among families and complicate clinical decision-making. To make these considerations operational, we specify the elements of a decisive prospective study, including a minimum event count of ~60 adjudicated CDAD cases, a blinded tiered diagnostic algorithm, and detailed AAF exposure ascertainment.},
}

Humans
*Amino Acids/adverse effects/analysis
Infant
*Infant Formula/chemistry/adverse effects
*Clostridioides difficile/physiology
*Clostridium Infections/microbiology/etiology
Fecal Microbiota Transplantation
Gastrointestinal Microbiome

@article {pmid43019062,
year = {2026},
author = {O'Connor, LC and Kang, WK and Vo, P and Spinelli, JB and Alkema, MJ and Byrne, AB},
title = {Comamonas aquatica diet inhibits TIR-1/SARM1-induced axon degeneration by providing vitamin B12.},
journal = {Cell reports},
volume = {45},
number = {11},
pages = {118092},
doi = {10.1016/j.celrep.2026.118092},
pmid = {43019062},
issn = {2211-1247},
abstract = {Emerging evidence suggests the microbiome critically influences the onset and progression of neurodegenerative diseases; however, the identity of neuroprotective bacteria and the molecular mechanisms that respond within the host remain largely unknown. Here, we leverage Caenorhabditis elegans' well-characterized nervous system and ability to eat uni-bacterial diets to determine how metabolites and neuroprotective molecules from single species of bacteria suppress degeneration of motor neurons. We find that Comamonas aquatica significantly protects against degeneration induced by overexpressing a key regulator of axon degeneration, TIR-1/SARM1. Genetic analyses and metabolomics reveal Comamonas protects against neurodegeneration by providing sufficient vitamin B12 to activate METR-1/MTR methionine synthase in the intestine, which then lowers toxic levels of homocysteine in TIR-1-expressing animals. Defining a molecular pathway between Comamonas and neurodegeneration adds significantly to our understanding of gut-brain interactions and, given the prominent role of homocysteine in neurodegenerative disorders, reveals how such a bacterium could protect against disease.},
}

@article {pmid43019073,
year = {2026},
author = {Bohm, MS and Yarbro, JR and Font Torres, C and Mustafa, ZT and Chaib, M and Mims, TS and Joseph, SC and Elasy, JH and Sipe, LM and Cook, KL and Pierre, JF and Makowski, L},
title = {Reduction of secondary bile acids following microbiome pre-conditioning was associated with reduced breast cancer progression.},
journal = {Scientific reports},
volume = {16},
number = {},
pages = {30183},
pmid = {43019073},
issn = {2045-2322},
support = {S10 OD032329/OD/NIH HHS/United States ; F32 CA250192/CA/NCI NIH HHS/United States ; F31 CA290773/CA/NCI NIH HHS/United States ; R25 CA203650/CA/NCI NIH HHS/United States ; R01 CA253329/CA/NCI NIH HHS/United States ; U01 CA272541/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Female ; *Bile Acids and Salts/metabolism ; Mice ; Disease Progression ; *Vancomycin/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Breast Neoplasms/pathology/microbiology/metabolism/drug therapy ; Anti-Bacterial Agents/pharmacology ; Clostridium/drug effects ; Humans ; Microbiota/drug effects ; },
abstract = {UNLABELLED: Breast cancer is the most common cause of cancer-related death in women worldwide. We previously reported that a primary bile acid mimetic reduced tumor progression in vivo. Here, we hypothesized that elevating primary bile acids through preconditioning of the gut microbiome may be an unexplored opportunity to improve breast cancer. We utilized the antibiotic vancomycin previously reported to deplete Gram-positive, anaerobic microbes that convert primary bile acids to secondary bile acids. Preconditioning with vancomycin significantly delayed tumor onset, decreased burden, promoted regression, and reduced the number of mice with lung colonization. Vancomycin reduced overall microbiome diversity and specific microbes in Clostridium Cluster XIVa, which associated with increased primary bile acid levels. We report that vancomycin significantly associated with elevated circulating bile acid tauro-alpha/beta-muricholic acid and reduced secondary bile acids that correlated with worsened tumor outcomes. Flow analysis of tumor content and systemic immune responses was associated with immune changes consistent with anti-tumor responses, including conventional dendritic cells and activated CD8 + T cells. In sum, we demonstrated that manipulation of the bile acid pools associated with improved breast cancer outcomes. The altered bile acids corresponded to an elevation of key immune cells, which may contribute to protection from primary breast cancer progression and lung colonization.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-59669-3.},
}

Animals
Female
*Bile Acids and Salts/metabolism
Mice
Disease Progression
*Vancomycin/pharmacology
*Gastrointestinal Microbiome/drug effects
*Breast Neoplasms/pathology/microbiology/metabolism/drug therapy
Anti-Bacterial Agents/pharmacology
Clostridium/drug effects
Humans
Microbiota/drug effects

@article {pmid43019117,
year = {2026},
author = {Meyer, KJ and Hedberg-Buenz, A and Wang, K and Anderson, MG},
title = {Systemic influences of dietary NAD[+] supplementation relevant to the search for ocular hypertensive therapies for glaucoma.},
journal = {Scientific reports},
volume = {16},
number = {},
pages = {34891},
pmid = {43019117},
issn = {2045-2322},
support = {R01 EY030366/EY/NEI NIH HHS/United States ; },
mesh = {Animals ; *Glaucoma/drug therapy ; *Dietary Supplements ; *Ocular Hypertension/drug therapy ; Mice ; Intraocular Pressure/drug effects ; Diet, High-Fat/adverse effects ; *NAD/administration & dosage/pharmacology ; Disease Models, Animal ; Gastrointestinal Microbiome/drug effects ; Male ; *Niacinamide/pharmacology/administration & dosage ; Mice, Inbred C57BL ; },
abstract = {UNLABELLED: Dietary nicotinamide (NAM) is neuroprotective in rodent models of glaucoma. With dietary delivery, additional systemic influences of NAM are possible, prompting us to test for influences on non-neuronal phenotypes relevant to glaucoma. Test cohorts of mice on high-fat diets differed by NAM content (control, "CON-diet"; 2,000 mg/kg/day supplementation, "NAM-diet") and by ocular treatments inducing various levels of ocular hypertension (Naïve; Ad5-Empty; Ad5-ATF4). Masked observers assessed intraocular pressure (IOP), body weight, and slit-lamp appearance. Naïve and Ad5-Empty cohorts were analyzed for gut microbiome composition. Regardless of diet, Naïve cohorts maintained consistent IOP. On CON-diet, the Ad5-ATF4 and Ad5-Empty cohorts developed IOP elevation. Based on results from a linear mixed-effects model evaluating the effects of diet and ocular treatment on IOP, NAM-diet lowered IOP in only the Ad5-Empty cohort. NAM-diet also prevented weight gain associated with a high-fat diet. NAM-diet was linked to altered alpha and beta diversity of the gut microbiome, including changes to a butyrate-producing genus, Faecalibaculum. Among the systemic influences resulting from dietary NAM consumption, NAM's ability to affect both neuroprotection and IOP would be favorable for glaucoma therapy. The possibility of dietary NAM influencing body weight and microbiome composition in humans warrants additional investigation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-58123-8.},
}

Animals
*Glaucoma/drug therapy
*Dietary Supplements
*Ocular Hypertension/drug therapy
Mice
Intraocular Pressure/drug effects
Diet, High-Fat/adverse effects
*NAD/administration & dosage/pharmacology
Disease Models, Animal
Gastrointestinal Microbiome/drug effects
Male
*Niacinamide/pharmacology/administration & dosage
Mice, Inbred C57BL

@article {pmid43019118,
year = {2026},
author = {Quiñones-Sanchez, CL and Bilbao-Del Valle, JL and Urdaneta-Colon, MA and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Optimizing tissue lysis and DNA extraction protocols to enhance bacterial diversity profiling in the Drosophila melanogaster gut microbiome.},
journal = {Scientific reports},
volume = {16},
number = {},
pages = {34962},
pmid = {43019118},
issn = {2045-2322},
support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; R25 HG012702/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; *Drosophila melanogaster/microbiology ; RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/isolation & purification/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification ; Biodiversity ; Sequence Analysis, DNA ; },
abstract = {UNLABELLED: The gut microbiota is a dynamic community that influences host metabolism, immunity, and overall health. Accurate characterization of this community requires robust and reproducible DNA extraction methods; however, technical biases introduced during tissue lysis and DNA isolation remain major challenges in microbiome research, particularly in animal model systems. In this study, we compared two lysis methods (manual pestle homogenization and bead-beating) and two commercial DNA extraction kits (Qiagen and Zymo) to evaluate their impact on microbiota profiling in a microbial community standard (MCS) and Drosophila melanogaster gut samples, a tractable model for host-microbe interactions. Full-length 16S rRNA sequencing was performed using Oxford Nanopore Technologies (ONT), followed by taxonomic classification with EPI2ME and downstream diversity analyses using standard pipelines implemented through a custom script. Our data revealed that extraction and lysis methods influence microbial composition, with some protocols resulting in additional species-level assignments in MCS samples, likely reflecting limitations of sequencing technology and taxonomic misidentifications. Pestle homogenization, combined with the Qiagen kit, recovered the highest number of detected taxa and showed a more balanced representation of both Gram-positive and Gram-negative bacteria across the Drosophila gut samples. These findings highlight that extraction methodology influences microbial diversity estimates in Drosophila gut samples, although sequencing approach and taxonomic classification accuracy may also contribute to the observed differences. Our results emphasize that the choice of DNA extraction protocol should be guided by the biological question being addressed and highlight the need for standardized protocols to ensure reproducibility across microbiome studies, particularly those using model systems.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-63122-w.},
}

Animals
*Drosophila melanogaster/microbiology
RNA, Ribosomal, 16S/genetics
*DNA, Bacterial/isolation & purification/genetics
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification
Biodiversity
Sequence Analysis, DNA

@article {pmid43019189,
year = {2026},
author = {Coffey, EL and Gomez, AM and Granick, JL and Burton, EN and Lulich, JP and Furrow, E},
title = {Alterations along the gut-urinary axis in dogs with calcium oxalate urolithiasis.},
journal = {Scientific reports},
volume = {16},
number = {},
pages = {35377},
pmid = {43019189},
issn = {2045-2322},
mesh = {Animals ; Dogs ; *Calcium Oxalate/metabolism ; *Urolithiasis/urine/microbiology/veterinary/metabolism ; Female ; *Gastrointestinal Microbiome ; Metabolomics ; Male ; RNA, Ribosomal, 16S/genetics ; *Dog Diseases/microbiology/urine ; Feces/microbiology ; Metabolome ; },
abstract = {UNLABELLED: Calcium oxalate (CaOx) is a common type of urinary stone affecting humans and animals. Mechanisms underlying CaOx stone formation are incompletely understood, but growing evidence has linked disturbances in the gut and urinary microbiomes to stone formation. Dogs naturally develop CaOx stones and represent a powerful translational model for studying microbiome-stone interactions. In this study, fecal and urine samples were collected from 20 dogs with CaOx urolithiasis and 20 age-, breed-, and sex-matched controls. Gut and urinary microbiota were profiled using 16 S rRNA sequencing and urinary metabolomics using ultrahigh performance liquid chromatography-tandem mass spectroscopy. Dogs with CaOx stones exhibited reduced gut microbial diversity, including deficiencies in bacteria associated with short chain fatty acid and bile acid metabolism, such as Peptacetobacter hiranonis (q-value < 0.05). Urinary microbiota and metabolomic profiles markedly differed between groups. Stone formers had higher abundances of Lachnoclostridium, Fusobacterium, and Pseudomonas (q-values < 0.05) and lower abundances of 4'-hydroxypropiophenone sulfate and N, N-dimethyl-5-aminovalerate (q-values < 0.01). Overall dietary protein and fiber intake were similar between groups (P > 0.05). However, the majority of dogs with stones consumed therapeutic stone prevention diets, whereas controls consumed a wider variety of diets, representing an important potential confounding factor. Together, these findings provide new insights into disturbances in gut and urinary microbial and metabolomic profiles in a canine model of CaOx urolithiasis.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-65013-6.},
}

Animals
Dogs
*Calcium Oxalate/metabolism
*Urolithiasis/urine/microbiology/veterinary/metabolism
Female
*Gastrointestinal Microbiome
Metabolomics
Male
RNA, Ribosomal, 16S/genetics
*Dog Diseases/microbiology/urine
Feces/microbiology
Metabolome

@article {pmid43019617,
year = {2026},
author = {Fernández-Barat, L and Motos, A and Segura-Morales, C and Kiarostami, K and Cabrera, R and Soler-Comas, A and Broto, A and Mazzolini, R and Galli, F and Llonch, B and Macip, G and Vazquez, N and Calabretta, D and Arrieta, M and Lluch-Senar, M and Rigol, M and Serrano, L and Rodríguez-Arce, I and Torres, A},
title = {Targeting Pseudomonas aeruginosa ventilator-associated pneumonia with a non-antibiotic and biofilm-disrupting live biotherapeutic: preclinical safety and efficacy study.},
journal = {EBioMedicine},
volume = {134},
number = {},
pages = {106537},
doi = {10.1016/j.ebiom.2026.106537},
pmid = {43019617},
issn = {2352-3964},
abstract = {BACKGROUND: The endotracheal tube (ETT) compromises the host's bronchial defences and facilitates the formation of microbial biofilms and Ventilator-associated pneumonia (VAP). Although antibiotics remain the cornerstone treatment, their efficacy is often compromised by poor biofilm penetration and the prevalence of multidrug-resistant bacteria. This reveals the need to develop novel non-antibiotic therapeutic strategies. We previously engineered a non-pathogenic strain of the pulmonary bacteria Mycoplasma pneumoniae (CV2) to express anti-biofilm and bactericidal enzymes (VAP platform).

METHODS: We evaluated the safety of an improved version of CV2 (CV8, Mycochassis) in a miniature pig model, and its efficacy with the VAP platform (CV8_VAP) in a piglet model of Pseudomonas aeruginosa-induced VAP. CV8_VAP was administered via intralobe instillation or nebulisation. We assessed the platform's ability to degrade biofilms formed on ETTs in vivo and its impact on the airway microbiota. We evaluated bacterial load in the lungs, inflammatory responses, histopathological and clinical outcomes. Statistics included t-tests, ANOVA, Kruskal-Wallis, Mann-Whitney U and mixed-effects rank-based methods.

FINDINGS: VAP platform reduced ETT biofilm thickness and P. aeruginosa load in lungs, with the nebulised route showing enhanced efficacy. Shannon diversity remained statistically comparable across groups in both ETTs and lung tissue. Inflammatory markers in the lung were markedly decreased, suggesting a local immunomodulatory effect. One animal receiving nebulised CV8_VAP died from a suspected anaphylactic-like reaction; no other serious adverse events were attributable to treatment.

INTERPRETATION: These findings suggest CV8_VAP as a promising, non-antibiotic therapeutic strategy for treating VAP caused by P. aeruginosa.

FUNDING: "La Caixa" Foundation, and the European Research Council under the European Union's Horizon 2020 research and innovation program.},
}

@article {pmid43019667,
year = {2026},
author = {Wu, Y and Lu, Y and Shi, Y and Yang, Z and Zhang, H and Kim, J and Xie, H and Fu, S and Wang, H and Han, Z and Gao, D and Li, X},
title = {Multi-omics reveals microbial inoculant-mediated mitigation of Dazomet-induced soil disturbances and rhizosphere microbiome recovery in Fritillaria cirrhosa cultivation on the Tibetan plateau.},
journal = {Ecotoxicology and environmental safety},
volume = {327},
number = {},
pages = {121049},
doi = {10.1016/j.ecoenv.2026.121049},
pmid = {43019667},
issn = {1090-2414},
abstract = {Dazomet fumigation is widely used to control soil-borne pathogens, but its disruption of soil microbial may pose ecological risks, particularly in fragile high-altitude agroecosystems. Microbial inoculants offer an eco-friendly strategy to restore fumigated soils. However, it remains unclear how beneficial microbial inoculants regulate rhizosphere metabolism, microbial assembly, and functional recovery in Dazomet-affected soils used for medicinal plant cultivation. Therefore, this study integrated rhizosphere metabolomics, microbial community profiling, functional prediction, and co-occurrence network analysis to investigate ecological restoration mechanisms of Paecilomyces lilacinus inoculation in Dazomet-fumigated soils cultivated with Fritillaria cirrhosa on the Tibetan Plateau. Results showed that P. lilacinus inoculation significantly alleviated fumigation-associated growth inhibition, increasing F. cirrhosa yield by 150.31%-150.45% and net photosynthetic rate by 66.51%-74.05% compared with fumigated control. Metabolomic analysis showed that microbial inoculation reshaped the rhizosphere metabolic environment, particularly by enhancing soil metabolic pathways related to lipid metabolism, organic acid biosynthesis, biotin metabolism, and ABC transporter-associated processes. These metabolic shifts accompanied enrichment of microbial taxa with functions in xenobiotic degradation, including Methylotenera, Flavobacterium, and Pseudomonas, indirectly suggesting that inoculation may contribute to attenuation of Dazomet derived residues through microbiome mediated processes. In addition, co-occurrence network analysis indicated that P. lilacinus partially restored microbial interaction complexity and strengthened bacterial-fungal associations disrupted by fumigation, exerting a positive effect on rhizosphere community stability. Given the short-term experimental design, relatively controlled conditions, and lack of quantification of Dazomet residues, future studies should validate these findings under long-term field conditions, quantify Dazomet residues and their dissipation dynamics, and elucidate mechanisms underlying microbial inoculation-mediated soil restoration.},
}

@article {pmid43019749,
year = {2026},
author = {Xue, Z and Yang, C and Shu, D and Xiao, L and Li, H and Wang, H and Huang, Q and Cheng, Z and Sun, Z and Wang, J and Wang, L and Kong, L and Lou, Z},
title = {Richness and prevalence matching weakens variable-selection contrasts between low-abundance and abundant bacteria in aged-landfill refuse.},
journal = {Waste management (New York, N.Y.)},
volume = {228},
number = {},
pages = {115985},
doi = {10.1016/j.wasman.2026.115985},
pmid = {43019749},
issn = {1879-2456},
abstract = {Aged municipal solid waste (MSW) forms a heterogeneous biogeochemical matrix, which complicates the use of biological indicators for assessing landfill stabilization. Low-abundance bacteria in this matrix may represent genuine, localized refuse niches; however, singletons, doubletons, and unequal amplicon sequence variant (ASV) richness among samples can inflate apparent diversity and promote over-interpretation. We tested whether low-abundance bacteria add ecological information to aged-refuse microbiomes, analyzing 18 MSW samples from seven landfill sites by 16S ribosomal RNA gene amplicon sequencing with sites as regional units. At the sample-level, rare fractions harbored higher detected richness and diversity than abundant fractions, even though the 0.01 % cutoff represented only one or two reads at the ∼ 23,000-read rarefaction depth. The two fractions nevertheless exhibited distinct taxonomic profiles. Assembly analysis initially suggested stronger variable selection in recurrent low-abundance ASVs than in abundant ASVs (41.8 % versus 22.2 % of pairs), but three matching schemes attenuated this contrast: the excess reflected richness and prevalence structure, not fraction-specific determinism. After matching, variable-selection proportions fell to 10.3-14.4 % and overlapped the abundant comparator under all schemes and aggregation scopes. PICRUSt2 predictions showed a parallel pattern: rare fractions contained more predicted Kyoto Encyclopedia of Genes and Genomes orthologs overall but fewer per ASV, and their ASVs were further from sequenced reference genomes (all P < 0.0001). Recurrent low-abundance taxa are best viewed as candidates for targeted validation-exemplified by Syntrophomonas and Dethiobacter-not as evidence of intrinsic variable-selection tendency or functional activity. This tiered framework supports microbial candidate selection for validation against direct stabilization measurements.},
}

@article {pmid43019811,
year = {2026},
author = {Velez-Pardo, P and Solano, RJ and Quinchia-Figueroa, AM and Montoya Monsalve, R and Moratto-Vasquez, NS},
title = {Shared host-genetic architecture between gut microbiota and internalizing psychopathology.},
journal = {Psychiatry research},
volume = {367},
number = {},
pages = {117579},
doi = {10.1016/j.psychres.2026.117579},
pmid = {43019811},
issn = {1872-7123},
abstract = {It is unknown whether gut microbial composition causally influences mental illness. Using genetic variants as instruments (Mendelian randomization, MR), we tested the genetically predicted effects of 211 gut microbial taxa on nine psychiatric and psychopathology-related phenotypes. Of 1,898 valid tests, seven taxon-outcome associations (five clades) passed false-discovery-rate correction (FDR < 0.05). All involved depression, neuroticism or insomnia, the three most precisely estimated outcomes. The strongest, a protective association of the Mollicutes/Tenericutes clade with depression (odds ratio 0.93 per SD of log-abundance, p = 1.5 × 10[-6]), survived every multiple-testing correction. The associations persisted with weak-instrument-robust estimators, stricter instrument selection and leave-one-out analysis, and reverse-direction MR found no effect of psychiatric liability on these taxa. In independent samples, the depression association had the same direction but was weaker and non-significant (one-sided p = 0.13), and the neuroticism and insomnia associations, tested with limited power, did not replicate. Bayesian colocalization (posterior probability of a shared variant < 0.05 at every locus) and CAUSE (0 of 45 pairs causal) did not support causation at individual loci. In factor-level MR within a Genomic SEM model, Mollicutes/Tenericutes was associated with a latent internalizing factor, and Butyrivibrio and Negativicutes/Selenomonadales with internalizing-specific variance beyond a general psychopathology factor. Psychotic-factor estimates were null but imprecise, and specificity relative to less well-powered phenotypes remains unresolved. Selected gut taxa and internalizing psychopathology appear to share host-genetic influences, and the evidence does not support direct effects of these taxa on the disorders.},
}

@article {pmid43019864,
year = {2026},
author = {Aryal, B and Li, D and Majeed, S and Shah, BR and Khalid, N and Zhao, L and Bielke, L and Wang, Q and Nazmi, A},
title = {Heat stress and avian pathogenic Escherichia coli infection differentially alter bacterial colonization dynamics, mucosal and systemic immunity, and cecal microbiome homeostasis in late-production laying hens in cage-free housing.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {108094},
doi = {10.1016/j.psj.2026.108094},
pmid = {43019864},
issn = {1525-3171},
abstract = {Heat stress (HS) and avian pathogenic E. coli (APEC) infection are major challenges to the health and productivity of commercial laying hens, yet their combined effects remain poorly understood. This study evaluated the effects of continuous HS and oral APEC O78 infection on production performance, bacterial colonization, immune responses, and the cecal microbiome of 70-week-old Hy-Line W-36 cage-free laying hens. Four treatments, thermoneutral control (TNC), thermoneutral APEC-inoculated (TNI), heat stress control (HSC), and heat stress APEC-inoculated (HSI), were assigned to a total of 112 hens. The indoor thermal environmental conditions were set at either 22°C or 35°C, and half the birds in each infected group received 1 × 10[9] CFU of APEC O78 by oral gavage and were co-housed with non-inoculated contact birds. Heat stress negatively affected egg production and egg weight, whereas APEC infection alone did not further impair production performance. APEC rapidly established persistent gastrointestinal colonization regardless of thermal environment, while HS uniquely exacerbated pulmonary colonization at 7 days post-inoculation. Compared with the control and single-challenge groups, the combined HS and APEC challenge induced greater upregulation of splenic IL-6, TNF-α, and Hsp70, and altered mucosal immunity by attenuating APEC-induced conventional TCRαβ[+] intraepithelial lymphocyte responses while expanding non-conventional innate lymphoid populations. Cecal microbiome analysis identified HS as the primary driver of microbial dysbiosis, with the combined challenge producing the greatest reduction in microbial richness and the highest number of differentially abundant genera. Predicted functional profiling further indicated disruption of microbial metabolic pathways involved in purine degradation and arginine biosynthesis under the combined HS and APEC challenge. These findings demonstrate that HS exacerbates APEC-associated immune dysregulation and microbiome disruption, highlighting the importance of integrated thermal management and infection control strategies to improve hen health and productivity in commercial egg production.},
}

@article {pmid43019979,
year = {2026},
author = {Chi, Y and Wu, S and Ma, X and Wang, J and Chen, X and Chu, S and Zhang, S and Zhou, P and Zhang, D},
title = {A microbiome-guided foliar Bacillus SynCom couples photosynthetic growth with low-toxicity cadmium accumulation in Solanum nigrum L.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {144135},
doi = {10.1016/j.jhazmat.2026.144135},
pmid = {43019979},
issn = {1873-3336},
abstract = {Cadmium (Cd) phytoextraction often requires balancing metal accumulation with plant growth, yet Cd toxicity constrains photosynthesis and biomass production. Here, we developed a microbiome-guided foliar Bacillus synthetic community (SynCom) for Solanum nigrum, combining Bacillus megaterium NCT-2 with a leaf-derived Bacillus isolate, LE45, selected from the NCT-2-responsive leaf microbiome. SynCom inoculation enhanced leaf colonization, increased leaf fresh weight, Cd concentration, and leaf Cd accumulation by 41.35%, 35.33%, and 91.24%, respectively, and improved magnesium (Mg) accumulation, SPAD and photosynthetic rate. It also reduced chloroplast starch granule accumulation while increasing soluble sugars and amylase activity. Cd partitioning shifted towards cell wall and soluble fractions and away from organelles, accompanied by less labile chemical forms. Integrated transcriptomic and metabolomic analyses revealed coordinated changes in Mg transport, sugar metabolism, cell wall remodeling, Cd transport and stress-related pathways. Together, these results demonstrate that this simplified two-member SynCom couples Mg-associated photosynthetic activation and carbon remobilization with low-toxicity Cd accumulation, providing a controllable and leaf-centred framework for improving aboveground Cd phytoextraction.},
}

@article {pmid43019998,
year = {2026},
author = {Elias, EM and Benny, CM and Thomas, T},
title = {Root exudate flux as a quantitative language of phytobiome assembly and stress resilience.},
journal = {Plant physiology and biochemistry : PPB},
volume = {241},
number = {},
pages = {111945},
doi = {10.1016/j.plaphy.2026.111945},
pmid = {43019998},
issn = {1873-2690},
abstract = {Climate change threatens crop productivity and soil function, increasing reliance on rhizosphere microbiomes that support plant nutrition, stress tolerance and disease suppression. Plants shape these communities through root exudation, which transfers an estimated 13.4 Pg C yr[-1], about 9% of global gross primary productivity, belowground. Yet most studies report exudate composition rather than the concentrations and rates microorganisms perceive. This review synthesises the literature, with particular emphasis on studies published between 2015 and 2026, especially those from 2020 onwards, while incorporating foundational earlier studies. It proposes a quantitative signalling framework in which absolute concentration, release flux and spatial gradient influence microbial responses at defined activation thresholds. Exudate chemistry, biosynthesis, transport and uptake are first examined, distinguishing passive diffusion sustained by the microbial sink from transporter-mediated release, root re-uptake and phytosiderophore-mediated iron acquisition. Sampling and analytical approaches, including HRMS-based metabolomics, stable isotope tracing, imaging and kinetic modelling, are then evaluated, separating relative from absolute quantification. Because most high-precision flux data derive from hydroponic or sterile systems, where wheat phytosiderophore release exceeds that in soil by about 50-fold, in situ microdialysis, corrections for sorption and degradation, and minimum reporting standards are proposed. Signal-response modules and allelochemical signalling at the root-microbe-soil interface are discussed, followed by multi-omics integration, where static metabolite pools and transcripts cannot resolve flux unless anchored by pulse labelling with LC-MS, stable isotope probing and NanoSIMS. Stress-induced quantitative reprogramming of exudation is interpreted within this framework. Exudation measured in soil is concluded to be a net flux, and unresolved compound-specific thresholds remain the principal barrier to predictive rhizosphere manipulation.},
}

@article {pmid43020005,
year = {2026},
author = {Hu, J and Bao, G and Fu, Z and Xing, N and Hu, W and Nawaz, M and Ali, S},
title = {Environmental fate and trophic transfer of co-exposed PMMA nanoplastics and atrazine in aquatic systems: secondary effects across the water-plant-insect food chain.},
journal = {Water research},
volume = {309},
number = {Pt C},
pages = {127299},
doi = {10.1016/j.watres.2026.127299},
pmid = {43020005},
issn = {1879-2448},
abstract = {Nanoplastics (NPs) and pesticides are co-transported via irrigation water and surface runoff, linking aquatic pollution to terrestrial ecosystem health. In this study, a multi-trophic system (rye-armyworm) was established to explore the toxic effects generated by interfacial interactions between polymethyl methacrylate (PMMA) NPs and atrazine (ATZ) across the water-land continuum as a function of time and trophic level. We integrated short-term hydroponic experiments, full-life-cycle soil cultivation, dietary transfer assays, adsorption experiments, characterization analysis, molecular docking, transcriptomics, and rhizosphere and gut microbiome analyses. As the major source of toxicity, ATZ caused photosynthetic impairment and oxidative stress. Under short-term exposure, PMMA adsorbed ATZ via van der Waals forces, which may plausibly contribute to buffering its acute toxicity. Exploratory two-way ANOVA suggested that co-exposure to PMMA and ATZ may produce certain alleviating tendencies for root length, net photosynthetic rate and soluble protein at the seedling stage. Under long-term exposure, the results implied aggravating tendencies for net photosynthetic rate and catalase (CAT) activity. ATZ may facilitate PMMA accumulation within rye root tissues. Transcriptomic reprogramming suggests conserved stress responses (MAPK, hormone-signaling pathways) and disorders in nitrogen/sulfur metabolism. The structure of rhizosphere fungal communities was altered; combined exposure was associated with gut microbiota dysbiosis (e.g., a decrease in Enterobacteriaceae and an increase in Pseudomonadaceae). During food-chain transfer, ATZ underwent biodilution (BMF = 0.844). Two‑way ANOVA suggests alleviating tendencies for CAT activity in armyworms under combined exposure. These results suggest that combined toxic risks may depend on exposure time, dose, and trophic-level position, highlighting the role of agricultural soils as absorption-and-transformation sources for water-borne contaminants and pointing to the threat posed by water pollution to terrestrial ecological health.},
}

@article {pmid43020160,
year = {2026},
author = {Dong, L and Song, Y and Li, X and Wu, J and Luo, X and Du, Y and Xu, T},
title = {Spatial Niches Shape Function in the Intratumoral Microbiome: From Multiscale Mapping to Niche-Informed Therapy.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105698},
doi = {10.1016/j.critrevonc.2026.105698},
pmid = {43020160},
issn = {1879-0461},
abstract = {Most studies of the intratumoral microbiome describe microbial composition and abundance but do not reveal where bacteria are located within the tumor microenvironment. Evidence that microbial signals vary across tumor regions and host-cell compartments makes spatial context essential to biological interpretation. In this review, we organize evidence at three levels: tissue niches reflect oxygenation, perfusion, pH, necrosis, and anatomy, cellular niches involve malignant, immune, and stromal cells, and physical interfaces include intracellular residence, extracellular association, biofilms, and diffusible products. We examine how contamination-aware sequencing, single-cell host-microbe profiling, spatial transcriptomics, and imaging distinguish detection from localization and relate microbial geography to host-cell states. Spatial organization may affect oncogenic signaling, cytoskeletal remodeling, DNA damage, immune regulation, metastatic fitness, and treatment response. The same bacterial strain may exert opposing immune effects inside and outside host cells. This framework clarifies therapeutic implications. Engineered bacteria can deliver payloads to hypoxic, poorly perfused regions, whereas intracellular nanocarriers, species-selective phages, and biofilm-disrupting platforms address different microbial reservoirs. Major limitations include low-biomass contamination, uncertain viability, incomplete localization, limited causal evidence, and poorly resolved temporal dynamics. Integrating microbial identity with location and physical state should yield more mechanistic models of the intratumoral microbiome and better-defined therapeutic strategies.},
}

@article {pmid43020505,
year = {2026},
author = {Wurm, J and Zimmermann, P},
title = {Patterns and determinants of antibiotic exposure during the first 2 years of life: a prospective birth cohort study in Switzerland.},
journal = {BMJ open},
volume = {16},
number = {11},
pages = {e127437},
doi = {10.1136/bmjopen-2026-127437},
pmid = {43020505},
issn = {2044-6055},
}

@article {pmid43020557,
year = {2026},
author = {Gibson, TF and Pugh, KM and Harke, MJ},
title = {Spatiotemporal dynamics of lake microbiomes and potential inter-domain associations with toxic cyanobacterial blooms.},
journal = {Harmful algae},
volume = {160},
number = {},
pages = {103238},
doi = {10.1016/j.hal.2026.103238},
pmid = {43020557},
issn = {1878-1470},
mesh = {*Lakes/microbiology ; *Cyanobacteria/physiology ; *Harmful Algal Bloom ; *Microbiota ; New York ; Spatio-Temporal Analysis ; },
abstract = {Cyanobacterial harmful algal blooms pose significant risks to freshwater ecosystems and human health, yet predicting toxin occurrence remains challenging due to the complex interplay of physical, chemical, and biological factors. To investigate how lake water microbiomes relate to toxic bloom potential, we employed a metabarcoding approach across three temperate lakes in Westchester County, New York, USA during peak bloom season (June-September) in 2022 and 2023. Cyanobacterial community composition varied substantially across lakes, months, and years, with Planktothrix, Woronichinia, Dolichospermum, and Aphanizomenon among the dominant bloom-forming genera. Trophic state did not linearly predict toxicity as the mesoeutrophic Lake Rippowam exceeded drinking water limits for microcystin on multiple dates while the more eutrophic Teatown Lake maintained the lowest concentrations. Cross-domain (16S-18S) co-occurrence networks across each lake shared similar global architecture but differed substantially in which taxa occupied central network positions, indicating lake-specific rather than universal biotic structuring. These networks revealed candidate inter-domain relationships not previously described in freshwater systems, including negative associations between the picocyanobacterium Cyanobium and two cercozoan protists (Filosa-Sarcomonadea and Sandona), suggesting cryptic grazing pressure beyond well-studied zooplankton. In addition, co-occurrence patterns revealed potential chytrid parasitism and associations between specific Proteobacteria. Collectively, these findings indicate that toxic blooms are embedded within a complex "cyanosphere" of interacting fungal, protistan, and bacterial associates rather than driven by nutrients alone, and that expanding monitoring from single-species detection toward whole-microbiome surveillance may improve our understanding of cHAB occurrence and management of risk.},
}

*Lakes/microbiology
*Cyanobacteria/physiology
*Harmful Algal Bloom
*Microbiota
New York
Spatio-Temporal Analysis

@article {pmid43020561,
year = {2026},
author = {Lyu, LT and Song, B and Fortin, SG and Reece, KS},
title = {Inter- and intra-annual variations in the prokaryotic microbiome during harmful algal bloom events in a temperate estuarine ecosystem.},
journal = {Harmful algae},
volume = {160},
number = {},
pages = {103244},
doi = {10.1016/j.hal.2026.103244},
pmid = {43020561},
issn = {1878-1470},
mesh = {*Estuaries ; *Harmful Algal Bloom ; RNA, Ribosomal, 16S/genetics/analysis ; *Microbiota ; *Dinoflagellida/physiology ; *Archaea/genetics ; Bacteria/classification/genetics ; Seasons ; Ecosystem ; },
abstract = {The formation of late-summer blooms of the harmful dinoflagellates Margalefidinium polykrikoides and Alexandrium monilatum in the lower York River estuary of the Chesapeake Bay varies considerably among years and remains difficult to predict. While unpredictability has promoted research efforts, the role of co-occurring aquatic prokaryotic communities in initiation, maintenance, and termination of bloom events is also poorly understood. Total and potentially active prokaryotic communities from surface-water samples collected during multiple bloom and non-bloom years were investigated through amplicon sequencing of 16S rRNA genes and transcripts. Multivariate and network analyses revealed that prokaryotic communities differed significantly across years, bloom stages, and by nucleic acid type. Heterotrophic bacterial taxa (e.g., Pelagibacterales, Flavobacteriales, Rhodobacterales, and Pseudomonadales) shifted with dinoflagellate presence and bloom stage, while the cyanobacterial taxon Synechococcales prevailed as a quantitatively dominant prokaryotic autotroph throughout. Observed associations of the ammonia-oxidizing archaea (AOA) Nitrosopumilales with transition (i.e., between blooms) and post-bloom stages, as well as their emergence as a potentially well-connected prokaryote within the 16S rRNA gene-derived network, accommodate the idea of AOA responsiveness to blooms. Together, these findings indicate that estuarine prokaryotic communities undergo reorganization during dinoflagellate blooms, characterized by persistent cyanobacterial autotrophy and enhanced bacterial heterotrophy. In addition, archaeal nitrification may play a substantial role in estuarine nitrogen cycling associated with bloom dynamics.},
}

*Estuaries
*Harmful Algal Bloom
RNA, Ribosomal, 16S/genetics/analysis
*Microbiota
*Dinoflagellida/physiology
*Archaea/genetics
Bacteria/classification/genetics
Seasons
Ecosystem

@article {pmid43020650,
year = {2026},
author = {Zheng, F and Jia, W and Wang, C and Weng, R and Chen, M and Guo, Z and Li, Z and Huang, C and Jiang, Y and Zhang, T and Cheng, X and Feng, H and Liu, K and Zhao, R and Xu, Z},
title = {Shigella flexneri activates the mature DC-Tfh axis to drive tertiary lymphoid structure neogenesis and maturation in colorectal tumour microenvironments.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339761},
pmid = {43020650},
issn = {1468-3288},
}

@article {pmid43020652,
year = {2026},
author = {Sabachvili, M and Abbott, S and Thomson, C and Davoli Ferreira, M and Ohland, C and Fritscher, J and Gekeler, C and Tricomi, M and Müller, P and Drikic, M and Mungan, MD and Ramey, H and Büringer, K and Arslan, MD and Schürch, CM and Jijon, H and Lewis, I and Malek, NP and Heikenwälder, M and Maier, L and Mccoy, KD and Mager, LF},
title = {Identification and selective inhibition of patient-specific pathobionts in inflammatory bowel disease.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339262},
pmid = {43020652},
issn = {1468-3288},
}

@article {pmid43020710,
year = {2026},
author = {Son, JS and Sharifi, R and Ryu, CM},
title = {Plant social networking system.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.10.001},
pmid = {43020710},
issn = {1878-4372},
abstract = {The plant social networking system (SNS) describes primarily unidirectional, cue-mediated information transfer from a donor holobiome to a receiver holobiome. Previously, scientific frameworks on plant-plant interactions were fragmented and did not integrate cue transfer with microbiome reconfiguration. In this opinion article, we propose that the plant SNS be conceptualized as a four-phase process: (i) external stimuli activate defense responses and reorganize the root microbiome in the donor plant; (ii) the reconfigured donor microbiome promotes the production and transmission of cues to the receiver; (iii) the receiver perceives these cues, alters host physiology, and recruits root-associated microbes; and (iv) the recruited microbes strengthen stress resilience in the receiver. The plant SNS model extends classical interaction concepts and provides a conceptual basis for explaining plant interactions as integrated holobiome-level processes.},
}

@article {pmid43020834,
year = {2026},
author = {Pan, Z and Glover, L and Reidy, F and McAuliffe, FM and Wingfield, M and van Sinderen, D and Saldova, R and MacSharry, J},
title = {Vaginal resistome redundancy is associated with microbial metabolic potential and host glycomic features in endometriosis.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {43020834},
issn = {2055-5008},
mesh = {Female ; Humans ; *Endometriosis/microbiology/metabolism ; *Vagina/microbiology ; *Microbiota ; *Glycomics ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Shotgun Sequencing ; Metagenome ; Metabolic Networks and Pathways ; },
abstract = {The vaginal microbiome plays a critical role in reproductive health, yet most studies remain descriptive and functional features connecting microbial communities to host physiology remain poorly understood. In endometriosis, alterations in the vaginal microbiome and host glycosylation have been reported, yet ecological properties connecting these systems remain unclear. We investigated whether vaginal resistome functional redundancy (FR) represents a functional link between microbial community structure, microbial metabolic capacity, and host glycomic variation across endometriosis severity. Shotgun metagenomic sequencing was performed on high vaginal swabs from women with healthy controls, minimal/mild, and moderate/severe endometriosis (n = 40). While total antibiotic resistance genes (ARG) abundance remained relatively stable across disease groups, resistome FR increased significantly in moderate/severe endometriosis, reflecting a transition from low-diversity, Lactobacillus-dominated communities toward more taxonomically diverse, ARG-harbouring taxa. Increased redundancy was associated with higher microbial alpha diversity and enrichment of glycan-related metabolic pathways, particularly UDP-N-acetyl-D-glucosamine biosynthesis, a precursor pathway for glycan assembly. These microbial functional features correlated with host glycomic signatures in serum and urine. Mediation and path modelling analyses supported associations among resistome FR, predicted UDP-sugar pathway potential, host glycomic variation, and endocrine-related traits. Our findings identify resistome FR as a quantifiable ecological property of the vaginal microbiome that is associated with microbial metabolic capacity and host glycomic variation in endometriosis. Rather than acting as a direct driver, FR may serve as a marker of microbiome organisation that relates to host-associated phenotypes, providing a framework for understanding microbiome-glycome interactions in reproductive tract disease.},
}

Female
Humans
*Endometriosis/microbiology/metabolism
*Vagina/microbiology
*Microbiota
*Glycomics
Metagenomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
Shotgun Sequencing
Metagenome
Metabolic Networks and Pathways

@article {pmid43020865,
year = {2026},
author = {Rahman, B and Saroyia, AP and Blackburn, D and Parish, AJ and Szewczyk, N and Driscoll, M and Samuel, BS and Vanapalli, SA},
title = {NemaCapsules: microfluidics-integrated biocells for investigating C. elegans host-microbiome interactions in spaceflight.},
journal = {NPJ microgravity},
volume = {12},
number = {1},
pages = {},
pmid = {43020865},
issn = {2373-8065},
support = {project# 80NSSC22K0250//NASA/ ; },
abstract = {Spaceflight studies in humans show that microgravity alters the gut microbiome, posing a risk to health. Understanding how microbiomes and host genetics influence physiology is critical for long-duration missions. The low-cost spaceflight model C. elegans provides a suitable means to study host-microbiome interactions. However, whole-organism measurements are limited by lacking suitable flight-ready hardware that enables long-term nematode culture compatible with on-orbit imaging. These limitations were addressed through development of NemaCapsules- microfluidics-integrated biocells, for spaceflight assessment of C. elegans locomotion under defined microbiome conditions, with minimal astronaut workload. This provided a fully sealed, gas-permeable system with media reservoir, enabling passive, long-term nematode culturing. NemaCapsules were evaluated across four host strains and three model microbiomes. Multi-day worm viability studies demonstrated high resilience across diverse host strains and microbiomes except for daf-16 mutants. Crawling and swimming studies of worms with model microbiomes of C. elegans natural microbiota exhibited distinct locomotory activity from those exposed to E. coli OP50. Wild-type N2 generally exhibited the highest activity, followed by wild isolate strains; daf-16 mutants demonstrated lowest activity. Compared to crawling, swimming better revealed differences arising from host-microbiome interactions. NemaCapsules provide a modular solution for on-orbit, multi-functional readouts in C. elegans with minimal crew intervention.},
}

@article {pmid43020901,
year = {2026},
author = {Wirbel, J and Saber, W and Martens, MJ and Peled, JU and Andermann, TM and Fei, T and Brooks, EF and Doyle, B and Pincus, NB and Jenq, RR and Bar, M and Bolaños-Meade, J and Bratrude, B and Chhabra, S and Choi, SW and Clark, W and Das, SR and Elmariah, H and Gooptu, M and Holtan, SG and Jones, RJ and Levine, JE and Logan, BR and Al Malki, MM and Murthy, HS and Rashidi, A and Rezvani, AR and Riches, ML and Runaas, L and Sandhu, K and Spahn, A and Sung, AD and van den Brink, MRM and Horowitz, MM and Hamadani, M and Kean, LS and Perales, MA and Bhatt, AS},
title = {Effect of two common GVHD prophylaxis regimens on the gut microbiome in a randomized phase 3 trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {43020901},
issn = {1546-170X},
support = {DRQ-22-24//Damon Runyon Cancer Research Foundation (Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation)/ ; P30 CA008748//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P30 CA008748//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; K23 AI163365//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32 5T32AI007502//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AG066719, R01HL151365//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; UG1HL174426, U19AI174967, P01 HL158505, R01HL095791, P01HL158504, and R01HL181969//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI148623, R01AI143757, R01HL181969, and R01CA301727//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Allogeneic hematopoietic cell transplantation can cure certain hematological disorders but has many complications. In retrospective studies, low gut microbiome diversity is associated with adverse clinical outcomes. In 2023, the Blood and Marrow Transplant Clinical Trials Network 1703 randomized phase 3 trial demonstrated the superiority of post-transplant cyclophosphamide (PTCy) and mycophenolate mofetil to tacrolimus and methotrexate (Tac/MTX) for graft-versus-host disease prophylaxis in participants with hematological malignancies undergoing allogeneic hematopoietic cell transplantation. Here we report on the microbiome-focused companion study to 1703, Blood and Marrow Transplant Clinical Trials Network 1801, which coenrolled participants and shared trial registration. The primary endpoint was association between microbiome diversity at neutrophil engraftment and non-relapse mortality after 1 year; secondary endpoints included associations with other clinical outcomes and with baseline microbiome diversity. Based on 2575 longitudinally collected stool samples from 304 participants (Tac/MTX n = 147, PTCy n = 157), no association between engraftment microbiome diversity and non-relapse mortality was observed (P = 0.314), not meeting the primary endpoint. Lower baseline microbiome diversity was associated with shorter overall survival (P = 0.007). Safety data were reported in the original 1703 publication. In exploratory analyses, microbiome diversity and absolute microbial load were lower in PTCy compared to Tac/MTX on days 14-28 following HCT, independent of non-prophylaxis antibiotics exposure. Microbial domination events, when a single species exceeds 30% relative abundance, did not differ significantly between study arms and reflected both pathogen blooms and less severe disruptions of the microbial community. Clostridium scindens and secondary bile-acid metabolism pathways were less prevalent in PTCy than in Tac/MTX following HCT. In summary, we find prophylaxis regimens likely exert independent effects on both the microbiome and immune compartments and can also impact their interaction. Understanding whether and how microbiome-targeted interventions might improve transplant outcomes will therefore require careful disentangling of these effects within each specific treatment context. ClinicalTrials.gov identifier: NCT03959241 .},
}

@article {pmid43020926,
year = {2026},
author = {},
title = {The soil microbiome in an era of global change.},
journal = {Nature reviews. Microbiology},
volume = {24},
number = {12},
pages = {823-824},
pmid = {43020926},
issn = {1740-1534},
}

@article {pmid43021054,
year = {2026},
author = {Saraiva, JP and Borim Corrêa, F and Bernt, M and Ghanem, N and Nieto, E and Brizola Toscan, R and Wick, LY and Chatzinotas, A},
title = {PHI: a Galaxy-based workflow for reproducible prophage-host interaction analysis and standardized viral-genomics reporting.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {43021054},
issn = {1471-2105},
mesh = {*Prophages/genetics/physiology ; *Genomics/methods ; *Genome, Viral ; *Software ; Workflow ; Genome, Bacterial ; *Host-Pathogen Interactions ; Computational Biology/methods ; Bacteria/virology/genetics ; },
abstract = {BACKGROUND: Viruses that infect bacteria, known as bacteriophages or phages, are widespread in nature and play important roles in shaping microbial communities and ecosystem functions. Some phages can integrate into bacterial genomes as "prophages", where they may influence the biology of their host by carrying genes that affect metabolism, virulence, or environmental adaptation. Despite their importance, studying prophages and their interactions with bacterial hosts remains challenging because it typically requires combining many complex computational tools and can be resource-intensive.

RESULTS: In this study, we introduce the Prophage-Host Interaction Toolkit (PHI), a user-friendly and automated workflow available through the Galaxy platform. PHI brings together multiple established tools into a single, reproducible pipeline that identifies candidate prophages, evaluates their quality, predicts host relationships, and characterizes key functional genes. Importantly, all results are summarized in an interactive report that simplifies interpretation. Applied to the MBARC22 mock community of 22 bacterial reference genomes as a workflow demonstration, PHI identified 41 candidate prophages across 14 hosts, including high- and medium-quality viral genomes. Most host genomes exhibited > 99% completeness and < 1% contamination, while DefenseFinder identified between 3 and 24 antiviral defense systems per genome. To further evaluate applicability to metagenome-derived assemblies, PHI was also applied to three MAGs and their matched reference genomes. Differences in candidate prophage counts and sequence-level correspondence between MAGs and references demonstrated that prophage recovery can be strongly influenced by genome fragmentation and assembly continuity, even in otherwise high-quality MAGs.

CONCLUSIONS: By removing installation barriers and consolidating the outputs of multiple established tools, PHI lowers the barrier to advanced phage analysis, enabling both specialists and non-experts to explore phage-host interactions and their implications in areas such as microbiome research, biotechnology, and environmental science.},
}

*Prophages/genetics/physiology
*Genomics/methods
*Genome, Viral
*Software
Workflow
Genome, Bacterial
*Host-Pathogen Interactions
Computational Biology/methods
Bacteria/virology/genetics

@article {pmid43021057,
year = {2026},
author = {Xie, J and Li, X and Ma, Y and Zheng, Q and Wang, M and Wu, Y and Wu, T and Liu, Y and Chen, D},
title = {Sleep quality is associated with gut microbiome signatures of hyperuricemia in Chinese elderly adults: a community-based case-control study.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43021057},
issn = {1471-2180},
support = {2026-2G-30126//Capital's Funds for Health Improvement and Research/ ; 2023YFF1104203//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Hyperuricemia/microbiology/epidemiology ; Aged ; Case-Control Studies ; China ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Sleep Quality ; Uric Acid/blood ; Life Style ; Middle Aged ; East Asian People ; },
abstract = {BACKGROUNDS: Hyperuricemia (HUA) has become a global health issue due to its rapidly increasing prevalence. Growing evidence from population and animal studies suggests that gut microbial dysbiosis and lifestyle changes are involved in serum uric acid metabolism. However, most existing studies are limited by small sample sizes or have yielded inconsistent findings. This study aimed to jointly investigate the associations of the gut microbiome, lifestyles, and dietary habits with HUA in Chinese elderly adults.

METHODS: A community-based case-control study was conducted across nine provincial-level regions in China, involving 617 participants. Data collection included lifestyle and dietary habit questionnaires, chronic disease history, serum uric acid (sUA) measurement, and 16S rRNA sequencing of fecal samples.

RESULTS: Taxonomic composition and diversity analyses revealed significant difference between the HUA and controls in gut microbiota structure and diversity. Through differential abundance and co-occurrence network analyses, 42 microbial signatures associated with HUA or sUA were identified. Notably, the prevalence of g_Stenotrophomonas was positively associated with short sleep duration. A microbial risk score (MRS) model constructed using these signatures demonstrated an area under curve (AUC) of 0.761 in the discovery cohort and 0.675 in the validation cohort. Furthermore, a significant positive association was observed between sleep quality (sleep duration, number of awakenings, and short sleep duration) and the MRS model.

CONCLUSIONS: These results add to the accumulating evidence implicating the role of gut microbiota and sleep in HUA, such as g_Stenotrophomonas, and inform the potential effect of the microbiome-based association between sleep duration and HUA. However, due to the cross-sectional design, we cannot infer causality from these associations, and the observed findings should be confirmed in prospective studies.},
}

Humans
*Hyperuricemia/microbiology/epidemiology
Aged
Case-Control Studies
China
Female
Male
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
*Sleep Quality
Uric Acid/blood
Life Style
Middle Aged
East Asian People

@article {pmid43021302,
year = {2026},
author = {Li, MJ and Ma, YB and Li, JH and Wang, Y and Li, CX and Sun, G and Ma, XR},
title = {Multiple plant growth promoting endophytic bacteria enhance cucumber tolerance to salt stress.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {43021302},
issn = {2049-2618},
mesh = {*Cucumis sativus/microbiology/growth & development/physiology ; *Endophytes/physiology/classification/genetics ; *Salt Tolerance ; *Salt Stress ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Rhizosphere ; Multiomics ; Seedlings/microbiology/growth & development ; Soil Microbiology ; },
abstract = {BACKGROUND: Soil salinization constrains crop yield and ecological restoration. Endophytic bacteria can promote plant growth and enhance tolerance to abiotic stresses. Using salt-sensitive cucumber as a model, we systematically evaluated six endophytic bacterial strains for salt-tolerance, including Pseudomonas fulva PY-1, Kosakonia cowanii Cya-1, Bacillus stercoris Cya-2, Serratia marcescens QP-1, Raoultella terrigena Ma-1 and Novosphingobium capsulatum Ly-1, and investigated their potential mechanisms in alleviating salt-induced damage.

RESULTS: All six bacterial strains were able to tolerate high salinity (1 mol/L NaCl) in vitro and significantly mitigated salt stress damage to cucumber seedlings under 250 mmol/L NaCl. Multi-omics analysis (microbiome, transcriptome, and metabolome) revealed that these strains influenced the rhizosphere microecological niche, leading to increasing abundance of salt-tolerant microbial taxa and the establishment of a stress-resilient community structure. For example, in the Cya-2 treatment group, the relative abundance of the genus Pseudomonas increased by an average of 5.87%, and that of genus Microvirga peaked at 9.92%. Based on the salt-alleviating efficacy and distinct response strategies, Pseudomonas fulva PY-1 and Serratia marcescens QP-1 were selected as representative strains. Both strains significantly activated cucumber ABC transporters and glycerophospholipid metabolism pathways. The key divergence between the two strains was that PY-1 treatment drove greater upregulation of α-linolenic acid metabolism genes, and broadly modulated plant hormone signal transduction; additionally, PY-1 was associated with activation of bacterial teichoic acid biosynthesis pathways. In contrast, QP-1 treatment showed enrichment in carbon and nitrogen metabolism pathways (galactose, starch/sucrose metabolism, and arginine biosynthesis). QP-1 was correlated with bacterial alkaloid biosynthesis as well as degradation pathways of glutathione, arachidonic acid, and aminobenzoate. Furthermore, exogenous application of three bacterial-derived metabolites (gambogic acid, dihydrocoumarin, and 2-aminonicotinic acid) and one cucumber-produced metabolite (triptolide) significantly alleviated salt damage in cucumber, indicating the possible bioactivity of these compounds in enhancing salt tolerance.

CONCLUSIONS: This work identified six bacterial strains and four bioactive metabolites capable of significantly alleviating salt-induced plant damage. Integrative multi-omics correlation analysis, we further proposed a hypothetical "microbe-metabolite-gene" regulatory framework to understand the synergistic interactions among endophytes, metabolites and plant host genes, which may collectively contribute to plant salt tolerance, laying a foundation for future targeted verification. Beyond providing candidate microbial strains and bioactive compounds for developing plant stress-tolerance enhancers, this study generates a rich multi‑omics dataset to support further hypothesis‑based research. Video Abstract.},
}

*Cucumis sativus/microbiology/growth & development/physiology
*Endophytes/physiology/classification/genetics
*Salt Tolerance
*Salt Stress
*Bacteria/classification/genetics/metabolism/isolation & purification
Rhizosphere
Multiomics
Seedlings/microbiology/growth & development
Soil Microbiology

@article {pmid43021326,
year = {2026},
author = {Carta, G and Xian, F and Malzl, D and Schmidt, M and Gómez-Varela, D},
title = {Integrative characterization of host-microbiome-diet axes during early-life development of the murine gut.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {43021326},
issn = {2049-2618},
mesh = {Animals ; Female ; Mice ; *Gastrointestinal Microbiome/physiology ; Mice, Inbred C57BL ; Feces/microbiology ; *Diet ; Male ; *Host Microbial Interactions ; *Bacteria/classification/genetics/isolation & purification ; Weaning ; Proteomics/methods ; Proteome ; Pregnancy ; },
abstract = {BACKGROUND: Early-life development of the gut microbiome plays a critical role in shaping host physiology. However, a comprehensive understanding of how diet, microbial community assembly, functional capacity, and host intestinal maturation axes evolve and coordinate over time remains lacking. Most studies focus on a single axis, rely on cross-sectional sampling, or have limited functional resolution, restricting insight into developmental dynamics. Here, we characterized early-life maturation of the gut ecosystem using longitudinal, metaproteome-level analysis in a murine model.

RESULTS: Using metaproteomics, we profiled fecal samples collected at seven postnatal time points from day 10 to weaning and into early adulthood (day 48) in pups from two contemporaneously raised C57BL/6 cohorts differing only in maternal origin (a long-established local colony and newly purchased pregnant females from the same vendor). Analyses accounted for time, cohort, and sex effects. Microbial communities underwent pronounced taxonomic succession, shifting from early dominance by facultative anaerobes to obligate anaerobes after weaning, accompanied by increasing species richness and functional complexity across cohorts and sexes. Taxonomic changes were co-occurring with an increase in functional redundancy that converged by postnatal day 34 and remained stable into early adulthood. KEGG clustering revealed patterns consistent with changes in metabolic pathway representation alongside maintenance of core functions. Direct detection of low-abundant dietary proteins provided evidence for dietary transitions coinciding with microbial maturation: milk proteins were detected only before weaning, while solid food components predominated over time. Maternal origin was significantly associated with microbial engraftment trajectories, leading to cohort-specific taxonomic and functional differences despite identical housing and diet. In parallel, host intestinal proteome maturation mirrored microbial succession, with concomitant shifts in metabolic, absorptive, regulatory, and effector pathways, including antimicrobial peptides and carbohydrate-modifying enzymes.

CONCLUSIONS: By directly integrating microbial, dietary, functional, and host axes within a longitudinal framework, this study provides a comprehensive view of murine gut ecosystem maturation during early life and offers a reference for interpreting developmental microbiome dynamics and improving experimental design and reproducibility in mouse studies. Video Abstract.},
}

Animals
Female
Mice
*Gastrointestinal Microbiome/physiology
Mice, Inbred C57BL
Feces/microbiology
*Diet
Male
*Host Microbial Interactions
*Bacteria/classification/genetics/isolation & purification
Weaning
Proteomics/methods
Proteome
Pregnancy

@article {pmid43021348,
year = {2026},
author = {Liu, S and Li, A and Jia, A and Chen, Q and Nan, Z and Qiu, Z and Qiu, Y},
title = {Network pharmacology, gut microbiota, and metabolomics integration reveal that Shenshuai 'an enema prescription (SSAEP) improves CRF mechanisms by reshaping the gut microbiota and correcting host-microbe cometabolism.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {43021348},
issn = {1749-8546},
support = {No 1000080305//Nan Zheng Traditional Chinese Medicine Master Inheritance Studio/ ; No. 010501318//the Jilin Province Postdoctoral Talent Selective Funding Project/ ; No DZJ202402034CXJD//Jilin Province Science and Technology Development Program Project/ ; },
abstract = {BACKGROUND: Chronic renal failure (CRF) is a global health issue, and the "gut-kidney axis" plays a key role in its pathogenesis. Shenshuai 'an enema prescription (SSAEP) is a Chinese medicine compound based on the TCM theory of "regulation of bowel movement and removal of turbid qi", which has shown good adjunctive therapeutic effects in delaying the progression of CRF in clinical practice. However, its specific mechanisms remain unclear.

PURPOSE: Herein, from the perspective of indirect pharmacology, the therapeutic effects of SSAEP on CRF rats were explored. We hypothesize that its mechanism of action may be largely indirect and occurs primarily through the gut-kidney axis. This study aimed to systematically elucidate the potential mechanism through which SSAEP improves CRF through the regulation of gut microecology using multidisciplinary approaches such as network pharmacology, 16S rRNA gene sequencing, and metabonomics.

METHODS: A CRF rat model was established by induction with 2.5% adenine. Low and high doses of SSAEP were administered via enema, and antibiotic intervention and fecal microbiota transplantation (FMT) experiments were performed to verify the key mediating role of the gut microbiota. The chemical composition of the SSAEP and the metabolic profiles of the serum and colonic contents of the rats were analyzed using UHPLC‒MS/MS; the composition of the gut microbiota was analyzed through 16S rRNA sequencing; and the core targets and pathways were predicted using network pharmacology and molecular docking. In vitro, human renal tubular epithelial cells (HK-2) were stimulated with TGF-β1 or glycochenodeoxycholic acid (GCDCA) to verify the anti-inflammatory and antifibrotic effects of quercetin (the main active component of SSAEP) and the role of the IL-17 signaling pathway in this process.

RESULTS: SSAEP treatment significantly improved renal function indicators (BUN, SCR, Cys-C, and UA) in CRF rats and alleviated pathological damage, the inflammatory response, and fibrosis in kidney tissue. Antibiotic intervention attenuated the protective effect of SSAEP, while FMT experiments confirmed that the efficacy of SSAEP could be transferred to recipient rats through the transplantation of treated fecal microbiota. SSAEP reshaped the gut microbiota, significantly increasing the abundance of Akkermansia while reducing that of Clostridium. Metabolomic analysis revealed CRF-related metabolic disturbances and identified 29 key differentially expressed metabolites regulated by SSAEP, among which glycochenodeoxycholic acid (GCDCA) was a key pathogenic metabolite. Network pharmacology predictions combined with in vitro experiments confirmed that the quercetin in SSAEP could effectively antagonize the TGF-β1- and GCDCA-induced epithelial‒mesenchymal transition and inflammatory response in HK-2 cells by inhibiting the IL-17/NF-κB signaling pathway.

CONCLUSIONS: This study revealed that SSAEP improves CRF through an indirect pharmacological mechanism dependent on the gut microbiota: SSAEP reshapes the balance of the gut microbiota, thereby correcting host-microbe cometabolic disorders (particularly by reducing the level of the pathogenic metabolite GCDCA) and ultimately alleviating renal inflammation and fibrosis through the inhibition of signaling pathways such as the IL-17/NF-κB pathway. This study provides new experimental evidence for the "gut-kidney axis" theory and lays the foundation for the development of CRF treatment strategies based on the regulation of the gut microbiome.},
}

@article {pmid43021776,
year = {2025},
author = {Marcos-Carbajal, P and Villegas-Suarez, MN and Rafael Ccama, VV and Otiniano Trujillo, MA and Huancahuire-Vega, S and Chambi Quispe, MS and Luque Arapa, A and Ruiz Panaifo, M and Diaz Rengifo, PE and Sias Garay, CE and Espinoza Rojas, R and Tito, R and Rohra Benitez, S and Tapia Paniagua, ST},
title = {Diversity and Functionality of the Gut Microbiota in Hypertensive Patients from Different Regions of Peru.},
journal = {F1000Research},
volume = {14},
number = {},
pages = {1401},
pmid = {43021776},
issn = {2046-1402},
mesh = {Humans ; Peru ; *Hypertension/microbiology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Aged ; Body Mass Index ; },
abstract = {INTRODUCTION: Hypertension affects approximately 14.2% of people over 15 years of age in Peru, constituting a major public health issue. Recent evidence highlights the gut microbiome's role in regulating blood pressure through bioactive metabolites that influence inflammation and metabolism. This study aims to characterize the gut microbiota of hypertensive adults from three Peruvian regions, contributing to the understanding of microbial influences on hypertension.

OBJECTIVE: To analyze the composition and functionality of the gut microbiota in hypertensive and normotensive adults from different Peruvian regions, considering age, body mass index (BMI), and geographical location.

METHODS: An observational, cross-sectional, and analytical study was conducted with 84 adults (46 hypertensive and 38 normotensive) from nine regions of Peru. Fecal samples were collected for 16S rRNA gene amplicon sequencing of the V3-V4 region. Alpha and beta diversity were evaluated using the Shannon index, UniFrac distances, and multivariate analyses. Microbial functional pathways were examined to identify potential metabolic differences between groups.

RESULTS: The dominant phyla in all groups were Bacillota and Bacteroidota. At the genus level, Streptococcus was associated with hypertensive patients with BMI ≥25, while Alistipes appeared only in normotensive individuals with BMI <25. Alpha diversity was greater in hypertensive participants under 50 years and with BMI <25, while lower diversity was seen in normotensive adults over 50 and with BMI ≥25. Beta diversity analyses showed substantial overlap across hypertensive status, age, and regional groups, with no clear separation. Adjusted multivariable models confirmed no significant independent association between hypertension status and either alpha or beta diversity after accounting for age, BMI, and region, with region remaining the strongest independent correlate of community composition (R [2] = 16.3%, p = 0.001). Functional profiles were similar among groups, mainly involving carbohydrate, amino acid, and lipid metabolism, though BMI and age modulated these patterns.

CONCLUSIONS: Gut microbiota composition and diversity in this Peruvian cohort were associated not only with hypertension status but also with anthropometric and geographic factors. Despite similar functional profiles between groups, environmental and nutritional context appeared to have a greater influence than hypertension status alone. These exploratory, hypothesis-generating findings should be confirmed in larger, adjusted, longitudinal studies before informing preventive or therapeutic strategies for local settings.},
}

Humans
Peru
*Hypertension/microbiology
Male
Female
Middle Aged
*Gastrointestinal Microbiome
Adult
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
Aged
Body Mass Index

@article {pmid43021881,
year = {2026},
author = {Yang, J and Li, J and Lv, Y and Cai, L and Gao, W},
title = {Tongue image analysis for early warning of neonatal necrotizing enterocolitis: a translational perspective integrating tongue phenotyping and microbiome dynamics.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1982364},
pmid = {43021881},
issn = {2296-2360},
abstract = {Necrotizing enterocolitis (NEC) remains a life-threatening challenge in neonatology, primarily due to the lack of sensitive early biomarkers that precede overt clinical and radiological signs. This Perspective proposes a hypothesis-generating, non-invasive early-warning framework by integrating quantitative tongue image analysis with modern pathophysiological insights. We hypothesize a dynamic association between tongue phenotypic changes (e.g., a transition from pale to purplish color) and the progression of dysbiosis and intestinal microcirculatory disturbance, which correspond to two distinct but potentially complementary pathways. The proposed biological link rests on evidence for the candidate oral-gut microbial relationship, with such evidence derived primarily from adult and non-neonatal studies; gut dysbiosis-known to precede NEC-may be associated with changes in the tongue-coating microbiome, offering a potential remote yet accessible window into intestinal health. We outline a three-phase translational research roadmap: (I) prospective discovery of tongue-image biomarkers and establishment of dynamic baselines for each infant, (II) development of an exploratory machine-learning-based risk prediction model, and (III) mechanistic exploration using multi-omics approaches and animal models. Critically, we propose three testable hypotheses regarding temporal changes in tongue colorimetric and microbial parameters before NEC onset. If prospectively validated, this approach may eventually contribute to a dynamic bedside monitoring tool for NEC risk stratification.},
}

@article {pmid43021948,
year = {2026},
author = {Ahn, S and Wu, Q and Yang, A and Porchia, D and Fu, W and Li, Z},
title = {A zero-inflated beta mixture model for marginal mediation analysis with compositional microbiome mediators.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1877170},
pmid = {43021948},
issn = {2235-2988},
mesh = {*Microbiota ; Humans ; Algorithms ; Computer Simulation ; *Models, Statistical ; *Mediation Analysis ; Dysbiosis/microbiology ; },
abstract = {The role of the microbiome in disease pathogenesis is an emerging field with strong evidence suggesting that dysbiosis is associated with precancerous and cancerous states. Microbiome data present substantial challenges for causal mediation analysis due to sparsity, compositional constraints, and latent heterogeneity. To address these issues, we propose a zero-inflated beta mixture (ZIBM) method for mediation analysis with compositional microbiome mediators. The proposed method accommodates excess zeros through a zero-inflation component and captures heterogeneity in non-zero relative abundances using a beta mixture distribution. Within the potential-outcomes framework, the ZIBM provides estimates of marginal microbiome-mediated causal effects, and model parameters are estimated using an expectation-maximization algorithm. Simulation studies demonstrate that the ZIBM yields more accurate estimation and reliable inference under conditions commonly observed in microbiome data, compared with existing approaches. An application to a real microbiome study further illustrates its practical utility. These results indicate that the proposed method provides a more flexible and robust statistical framework for mediation analysis involving compositional microbiome data.},
}

*Microbiota
Humans
Algorithms
Computer Simulation
*Models, Statistical
*Mediation Analysis
Dysbiosis/microbiology

@article {pmid43022214,
year = {2026},
author = {Shen, C and Li, Y and Xiang, Z and Zhao, M and Wang, J and Wang, X},
title = {Recurrent pulmonary infection, a vicious cycle of multifactorial interactions, and prevention/treatment strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1945273},
pmid = {43022214},
issn = {1664-3224},
mesh = {Humans ; *Respiratory Tract Infections/prevention & control/therapy/immunology/diagnosis ; Recurrence ; Host-Pathogen Interactions/immunology ; Animals ; *Reinfection/prevention & control ; Risk Factors ; Disease Susceptibility ; Vaccination ; },
abstract = {Recurrent pulmonary infection (RPI) refers to the frequent and repeated episodes of lower respiratory tract infections. At its core, it represents a vicious cycle arising from the disruption of the homeostatic balance among pathogens, host immunity, and pulmonary architecture. RPI accounts for a considerable proportion of pediatric pneumonia cases, and the cumulative incidence among elderly patients hospitalized for pneumonia is also markedly elevated, imposing a substantial disease burden. The etiologies are notably diverse, beyond common pathogens such as bacteria and viruses, the ubiquity of asymptomatic colonization, underlying comorbidities, immune deficiencies, medication-related factors, and aspiration all constitute critical predisposing factors. This review summarizes the pathogenic characteristics of RPI, host-related factors, and the mechanistic roles of structural lung damage in infection recurrence. It further focuses on the current advances and limitations of precision diagnostic approaches (metagenomic sequencing), immunomodulatory and microbiome-targeted interventions, and vaccination strategies. Existing evidence suggests that the clinical benefits of these interventions in RPI remain to be validated by more high-quality studies. The aim of this article is to provide a reference for the clinical management of RPI and to inform future research directions.},
}

Humans
*Respiratory Tract Infections/prevention & control/therapy/immunology/diagnosis
Recurrence
Host-Pathogen Interactions/immunology
Animals
*Reinfection/prevention & control
Risk Factors
Disease Susceptibility
Vaccination

@article {pmid43022273,
year = {2026},
author = {Almusallam, AA and Allemailem, KS},
title = {Decoding multispecies oral biofilms: molecular architecture, host modulation and systems-guided precision anti-biofilm strategies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {2002174},
pmid = {43022273},
issn = {2235-2988},
mesh = {*Biofilms/drug effects/growth & development ; Humans ; *Mouth/microbiology ; Bacteria/genetics/drug effects ; Microbiota ; },
abstract = {Oral biofilms are spatially ordered microbial communities whose pathogenic behavior is shaped by more than taxonomic composition. Their development reflects the combined effects of adhesin-receptor recognition, interspecies coaggregation, matrix formation, metabolite exchange, local physicochemical gradients and host-derived selection. Here, we synthesize molecular and ecological evidence on the bacterial cell surface-matrix interface and consider how these interactions contribute to cariogenic, periodontal and peri-implant biofilms. Particular attention is given to glucosyltransferase-dependent polysaccharides, extracellular DNA, amyloidogenic proteins, sortase-anchored surface factors and outer membrane vesicles, together with metabolic interactions involving lactate, arginine, hydrogen peroxide and heme. We further evaluate functional-genomic and systems-level approaches (including transposon sequencing, CRISPR interference, metagenomics, metatranscriptomics, metaproteomics, metabolomics, spatial imaging, genome-scale metabolic modeling and machine learning) while distinguishing association and prediction from experimentally demonstrated mechanism. Emerging interventions are assessed according to their biological target and evidence level, including adhesion blockade, specifically targeted antimicrobials, matrix synthesis inhibition and degradation, quorum interference, probiotics, catalytic nanoparticles, antimicrobial photodynamic therapy and antibiofilm dental materials. Across these approaches, reduction in biofilm biomass is not equivalent to ecological restoration or clinical benefit. Key translational barriers include model fidelity, donor-to-donor variation, spatial heterogeneity, treatment durability, endpoint selection and the limited external validation of many computational and preclinical findings. Future precision strategies should therefore integrate microbial identity, matrix architecture, spatial metabolism and host context, with experimental perturbation used to establish causal vulnerabilities before therapeutic translation.},
}

*Biofilms/drug effects/growth & development
Humans
*Mouth/microbiology
Bacteria/genetics/drug effects
Microbiota

@article {pmid43022294,
year = {2026},
author = {Wu, H and Yuan, D and He, R and Liu, S},
title = {The gut-disc axis in intervertebral disc degeneration: microbial metabolites, immunometabolic remodeling, and regulated cell death.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1960350},
pmid = {43022294},
issn = {2235-2988},
mesh = {Humans ; *Intervertebral Disc Degeneration/metabolism/microbiology/pathology/immunology ; Animals ; *Gastrointestinal Microbiome ; *Intervertebral Disc/metabolism/pathology ; *Regulated Cell Death ; Ferroptosis ; Pyroptosis ; },
abstract = {Intervertebral disc degeneration (IDD) involves interactions among mechanical injury, inflammation, and metabolic dysfunction. The proposed gut-disc axis extends this framework to intestinal microbial signals, but the strength and tissue relevance of the supporting evidence vary considerably. This narrative review examines whether microbial metabolites could influence IDD through pyroptosis, a gasdermin-mediated form of lytic regulated cell death, and ferroptosis, an iron-dependent form of regulated cell death driven by lipid peroxidation. We distinguish human microbial associations, experimental findings in disc tissues, mechanisms demonstrated in other organs, and computational predictions. Selected microbial metabolites regulate inflammatory and antioxidant pathways in non-disc models, whereas disc studies establish the relevance of mitochondrial dysfunction, iron handling, and local metabolite-dependent protein modifications. These findings support mechanistic hypotheses but do not establish that defined gut-derived metabolites reach the disc and causally regulate either death program. We also assess microbiome-directed interventions and local therapeutic strategies, emphasizing that efficacy against a downstream disc pathway does not demonstrate a microbial initiating mechanism. Clinical intervention evidence remains limited and does not establish structural disease modification. Translation requires verified metabolite exposure, cell-specific target engagement, functional validation of cell death, and longitudinal assessment of imaging, pain, and disability. This evidence-based distinction provides a framework for prioritizing testable gut-disc mechanisms and clinically relevant interventions.},
}

Humans
*Intervertebral Disc Degeneration/metabolism/microbiology/pathology/immunology
Animals
*Gastrointestinal Microbiome
*Intervertebral Disc/metabolism/pathology
*Regulated Cell Death
Ferroptosis
Pyroptosis

@article {pmid43022513,
year = {2026},
author = {Sh Usmonova, K and Geller, SI and Umarnazarova, ZE and Kamilova, AT},
title = {Biomarkers for intestinal damage in pediatric celiac disease.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {2000459},
pmid = {43022513},
issn = {2296-2360},
abstract = {Celiac disease (CD) is an immune-mediated enteropathy triggered by gluten in genetically predisposed individuals, affecting around 1% of the global population. Diagnosis relies on serological testing (IgA antibodies to transglutaminase 2 and endomysium), supported by HLA-DQ2/DQ8 typing and duodenal biopsy when indicated. This approach has limitations, including false negatives in IgA deficiency, poor sensitivity in potential or minimal-lesion CD, poor correlation with mucosal healing, and limited ability to predict disease progression. This mini review summarizes non-invasive and minimally invasive biomarkers for the diagnosis and follow-up of CD, with special attention to the pediatric setting. We discuss markers of enterocyte injury (intestinal fatty acid-binding protein, i-FABP; citrulline), immune activation (cytokines, high-mobility group box 1), gluten exposure and barrier function (fecal and urinary gluten immunogenic peptides, zonulin, calprotectin), and molecular signatures emerging from microbiome and multi-omics research. Of these, i-FABP (for diagnosis and follow-up) and gluten immunogenic peptides (for monitoring adherence to a gluten-free diet) appear the most promising. However, assay standardization, age-specific reference ranges, and large-scale prospective pediatric validation remain necessary before routine implementation, and data from regions such as Central Asia are scarce.},
}

@article {pmid43022580,
year = {2026},
author = {Xie, D and Yuan, H and Zhang, D},
title = {Probiotic modulation of gut microbiota in preterm infants: a narrative review of clinical evidence, mechanisms, and translational gaps.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1945012},
pmid = {43022580},
issn = {1664-302X},
abstract = {Preterm infants are at a heightened risk for gut dysbiosis, a condition characterized by reduced microbial diversity, delayed colonization by beneficial commensals such as Bifidobacterium, and overgrowth of opportunistic pathogens. This disrupted microbial ecosystem is intricately linked to the pathogenesis of life-threatening conditions, including necrotizing enterocolitis (NEC), late-onset sepsis (LOS), and feeding intolerance, and is also implicated in long-term neurodevelopmental and respiratory outcomes. Probiotic supplementation has emerged as a prominent strategy to shift the microbiota toward a more eubiotic-like composition and mitigate these risks. This narrative review synthesizes evidence from a wide range of randomized controlled trials, observational studies, systematic reviews, and meta-analyses to evaluate the clinical efficacy and microbiological impact of probiotics in preterm populations. The evidence indicates that probiotic interventions, particularly specific multi-strain formulations containing well-defined Lactobacillus and Bifidobacterium strains, are associated with significant reductions in the incidence of severe NEC (risk ratio 0.38-0.57) and all-cause mortality (risk ratio 0.69). However, their effect on preventing LOS and reducing colonization by multidrug-resistant organisms is less consistent. Probiotics consistently enhance the intestinal abundance of beneficial bacteria, modulate metabolic profiles, and reduce markers of intestinal inflammation. However, effects are strain-specific and cannot be extrapolated across products; future trials should report full strain identity, dose, viability, and product composition. Emerging evidence also suggests a potential role for probiotics in influencing immune cell development and the gut-brain axis, with implications for neurodevelopment and seizure prevention, though these findings are preliminary. This review also addresses critical challenges, including the considerable heterogeneity in study designs, probiotic strains, and clinical protocols, safety concerns in extremely low-birth-weight infants, and the methodological issues related to product quality and taxonomic identification. We conclude that multi-strain probiotics reduce severe NEC and all-cause mortality, but evidence for LOS is inconsistent and neurodevelopmental benefit remains unproven. Routine universal use is therefore not justified; translation requires product-specific trials and regulatory-grade quality control.},
}

@article {pmid43022730,
year = {2026},
author = {Li, Z and Zang, T and Zhang, Z and Liu, W and Yin, L and Zhao, S and Liu, B and Ma, L and Tang, X},
title = {Oral-predominant microbial and functional dysbiosis in craniofacial microsomia: species-level profiling with compartment-matched statistical testing.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2754580},
pmid = {43022730},
issn = {2000-2297},
abstract = {BACKGROUND: Craniofacial microsomia (CFM) is the second most common congenital craniofacial anomaly. Oral dysbiosis has been described at genus level, but whether it extends beyond the mouth, or relates to the defining alveolar bone deficiency, is unknown.

Oral and gut microbiomes of 45 children with CFM and 18 matched controls were profiled at species level by 2bRAD-M, alongside shotgun metagenomes and blood, faecal and oral metabolomes. Alveolar bone loss was quantified on computed tomography against each patient's contralateral side. Centred-log-ratio methods with Benjamini-Hochberg false-discovery-rate (FDR) control were used throughout. Compartment specificity was tested formally by a group-by-compartment interaction model in the 58 participants with paired oral and gut profiles, by sample-size-matched subsampling, and by minimum-detectable-effect calculation.

RESULTS: Oral alpha diversity was higher in CFM than in controls (Shannon P = 0.014; all three alpha-diversity indices P < 0.05). Four species-level taxa were depleted after false-discovery-rate (FDR) correction (q < 0.05), and 21 interpretable metagenomic pathways differed between groups among 38 FDR-significant pathways. These annotations were enriched for carbohydrate transport, glycan processing and cell-surface or biofilm-related functions, but they are not specific markers of a cariogenic or pathogenic community. No FDR-robust gut or systemic signature was detected. At the species level, the oral and gut analyses were power-matched (minimum detectable |r| = 0.74 at the FDR-equivalent threshold), and the group-by-compartment interaction for Shannon diversity was significant (P = 0.026). This comparison supports an oral-predominant taxonomic pattern but does not establish biological absence of a gut effect. The functional comparison was not power-matched. In the patient-only post hoc analyses, the oral functional pattern was not associated with tooth-brushing frequency, sugary-drink intake or caries burden. Affected-side alveolar bone density was lower than contralateral density (paired P < 0.001) and was not associated with anatomical severity grade.

CONCLUSIONS: CFM was associated with an oral-predominant taxonomic and functional microbiome pattern. The matched-power comparison is informative for taxonomic analyses but does not exclude a biologically meaningful gut effect, and the functional comparison remains underpowered. These observations motivate prospective investigation of local, biofilm-directed interventions and of quantitative alveolar bone assessment as a follow-up endpoint.},
}

@article {pmid43022988,
year = {2026},
author = {Noor, AU and Xu, Y and Liu, Z and Li, X and Bellou, A},
title = {Gut Bacteriome and Mycobiome Signatures and Differential Allergen-Driven Outcome in Peanut and OVA Anaphylaxis and Their Modulation by Betanin.},
journal = {ACS omega},
volume = {11},
number = {44},
pages = {68175-68184},
pmid = {43022988},
issn = {2470-1343},
abstract = {Food allergy (FA) pathogenesis is closely associated with perturbations of the enteric ecosystem; however, comparative studies examining how distinct allergen triggers differentially affect the enteric mycobiome (total fungal community residing in the gastrointestinal tract) and the enteric bacteriome (total bacterial community residing in the gastrointestinal tract) remain limited. Mapping these allergen-specific patterns of dysbiosis is critical for understanding the pathogenesis and designing targeted therapies. We investigated betanin, a naturally occurring bioactive compound with potent antioxidant and anti-inflammatory properties as a prophylactic agent capable of resolving allergen-specific dysbiosis and restoring immune homeostasis and intestinal barrier integrity. We established parallel peanut and ovalbumin (OVA) FA mouse models, administered betanin prophylactically across the sensitization and challenge phases, and evaluated its effects on the allergic outcomes. Efficacy was assessed by measuring anaphylactic symptom scores, allergic biomarkers (total IgE), allergen-specific IgE, histamine, and mast cell protease-1 (mMCPT-1), Th1/Th2 cytokine profiles, and their associated transcription factors (GATA3 and T-bet), intestinal barrier integrity markers, and tight junction protein expression. Allergen-specific microbial shifts were characterized by using ITS2 and 16S rRNA amplicon sequencing. Betanin significantly attenuated the anaphylactic symptoms in both models. It suppressed the Th2-driven allergic cascade, evidenced by GATA3 downregulation and concurrent reductions in IL-4, IL-5, IL-13, allergen-specific IgE, histamine, and mMCPT-1. Betanin intervention notably restored intestinal villus architecture, indicating improved intestinal structural integrity, which was further supported by the upregulated tight junction proteins (i.e., claudin-1, occludin, and tight junction protein 1). Furthermore, betanin restored allergic-associated dysbiosis with both mycobiome and bacteriome enriching Lachnospiraceae (a well-known family associated with short-chain fatty acid production) and suppressing pathobionts Desulfovibrio. These results suggest that prophylactic betanin administration attenuated IgE-mediated anaphylaxis in two murine allergen models through coordinated immunomodulation, intestinal barrier structure integrity, and enteric microbiome remodeling.},
}

@article {pmid43023055,
year = {2026},
author = {Huang, Y and Fouad, AM and Ye, J and El-Senousey, HK and Lin, X and Zhang, S and Zhu, Y and Yan, S and Jiang, Z and Jiang, S and Ruan, D},
title = {Microbiome-metabolomics analysis provides insight into the effects of dietary taurine on meat quality and flavor in yellow-feathered chickens (Gallus gallus).},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {27},
number = {},
pages = {509-523},
pmid = {43023055},
issn = {2405-6383},
abstract = {Taurine (TAU) is a crucial component in poultry nutrition, recognized for its potential to improve broiler growth and enhance meat quality and flavor. However, the mechanisms by which TAU regulates the production of volatile organic compounds (VOC) in broiler meat remain unknown. This study investigated the effects of TAU supplementation on the meat quality, lipid metabolism-related gene expression, and the VOC profile in yellow-feathered chickens. Nine hundred healthy 1-d-old female fast-growing Lingnan yellow-feathered chickens (body weight: 38.58 ± 0.12 g) were randomly assigned to 5 groups, and were fed either a basal diet (CON) or a basal diet supplemented with 0.25, 0.50, 1.00, and 2.00 g/kg TAU (TAU250, TAU500, TAU1000, and TAU2000, respectively) for 56 d. The findings revealed that dietary TAU significantly increased the ADG and final BW, while decreased F/G during d 1 to 56 (P < 0.05), compared with the CON group. Dietary supplementation with 2.0 g/kg TAU increased C18:1, C18:2n-6, and redness (a∗) value at 45 min (P < 0.05), while decreasing 24-h drip loss in breast muscle compared with the CON group (P < 0.001). Dietary TAU supplementation significantly increased the contents of triglycerides, phosphatidylethanolamines, phosphatidylcholines, phosphatidylinositols, and lysophosphatidylcholines lipid subclasses (P < 0.05). The TAU enhanced intramuscular fat deposition by downregulating lipid catabolism-related genes, including CPT1A, ACOX1, and ACSL5 in breast muscle (P < 0.05). Moreover, dietary supplementation with 2.00 g/kg TAU increased Bacteroides, Faecalibacterium and Enterococcus and decreased Streptococcus and Lachnoclostridium (P < 0.05). Integrated analysis of flavoromics and gut microbiome profiling revealed that Faecalibacterium and Enterococcus were positively correlated with (E)-2-octenal, ethyl elaidate, ethyl myristate, ethyl palmitate, ethyl 9,12-octadecadienoic acid, and octane (P < 0.05). In conclusion, this study found that dietary TAU improved intramuscular fat deposition and promoted the synthesis of VOC in yellow-feathered chickens. Faecalibacterium and Enterococcus may help to improve the flavor profile of the meat.},
}

@article {pmid43023135,
year = {2026},
author = {Chen, X and Fang, R and Zhang, T and Zhao, G and Wang, F},
title = {Host species identity outweighs life form in shaping the root endophytic bacterial communities of 10 Cymbidium species grown under uniform conditions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1996961},
pmid = {43023135},
issn = {1664-302X},
abstract = {Research on orchid microbiomes has long been dominated by mycorrhizal fungi, whereas the community structure of orchid-associated bacteria remains poorly understood, particularly across host life forms. We compared the root endophytic bacterial communities of 10 Cymbidium species (six epiphytic and four terrestrial), all cultivated in the same greenhouse. Communities were profiled by 16S rRNA gene amplicon sequencing, with six biological replicates per species. After rarefaction to 29,628 sequences per sample, we obtained 129,922 amplicon sequence variants (ASVs) assigned to 33 phyla and 779 genera. Proteobacteria dominated the communities (mean relative abundance 83.4%), followed by Actinobacteriota and Acidobacteriota; the most abundant genera were Pseudomonas, Sphingomonas, the Burkholderia-Caballeronia-Paraburkholderia complex, Bradyrhizobium and Reyranella. Only seven ASVs were shared by all 10 species (each detected in at least one replicate sample of every species), and only one ASV occurred in all 60 samples, indicating an extremely small interspecific core microbiome. No alpha-diversity index differed between life forms. Among host species, however, the Shannon, Simpson, and Pielou evenness indices differed significantly among species. Single-factor (marginal) permutational multivariate analysis indicated a hierarchy of host effects: life form explained only 6.9% of community variation, infrageneric section 35.6%, and host species 59.9%, with significant differentiation even among species within the same section (R [2] ≈ 0.51); because life form, infrageneric section and host species are partially confounded in this design, these values describe associations rather than fully independent effects. Random forest classification independently corroborated this hierarchy. Community composition correctly assigned all 60 samples to their host species, whereas life-form prediction did not generalize across species. Under leave-one-species-out cross-validation, life-form accuracy fell to 50.0%, below the 60% majority-class baseline. LEfSe analysis identified 279 biomarker taxa spanning all 10 species. Predicted functional profiles were dominated by biosynthesis pathways (69.8%) and were largely stable between life forms. The neutral community model explained little of the variation in ASV occurrence frequency (R [2] = 0.035). This indicates that neutral dispersal alone cannot account for community assembly. The normalized stochasticity ratio averaged 0.576, only slightly above the 0.5 threshold for stochastic dominance, pointing to predominantly deterministic assembly with a secondary stochastic contribution. Within the limits of this partially confounded design, these results indicate that, with environmental heterogeneity minimized, host species identity is a stronger correlate of root endophytic bacterial community differentiation than life form in Cymbidium, providing a basis for the species-specific utilization of beneficial endophytes in orchid cultivation and conservation.},
}

@article {pmid43023307,
year = {2026},
author = {Kumar, G and Yadav, S and Kumari, N and Kosey, S},
title = {Sarcopenia in Alcoholic Liver Disease: Molecular Mechanisms, Clinical Consequences, and Emerging Therapeutic Strategies.},
journal = {Recent advances in inflammation & allergy drug discovery},
volume = {},
number = {},
pages = {},
doi = {10.2174/0127722708495692261101193524},
pmid = {43023307},
issn = {2772-2716},
abstract = {Alcoholic liver disease (ALD) remains a major cause of chronic liver disease worldwide and is associated with substantial morbidity, mortality, and healthcare burden. Among its extrahepatic complications, sarcopenia has emerged as a key determinant of disease progression, liver transplantation outcomes, and overall survival. This review provides an updated and critical overview of the epidemiology, pathophysiological mechanisms, clinical significance, diagnostic challenges, and evolving therapeutic strategies for ALD-associated sarcopenia. Current evidence indicates that skeletal muscle loss results from the interplay of direct ethanolinduced myotoxicity, malnutrition, chronic inflammation, insulin resistance, hormonal dysregulation, mitochondrial dysfunction, oxidative stress, and impaired muscle regeneration. Emerging molecular insights, including stabilization of hypoxia-inducible factor-1α (HIF-1α), accelerated post-mitotic senescence, and dysregulation of the gut-liver-muscle axis, further expand our understanding of disease pathogenesis. The review also critically examines the methodological heterogeneity in sarcopenia diagnosis, highlighting the limitations of existing imaging modalities and consensus-based diagnostic criteria, particularly in patients with fluid retention and advanced liver disease. Clinically, ALD-associated sarcopenia is consistently associated with hepatic decompensation, reduced transplant-free survival, poorer post-transplant outcomes, functional decline, and diminished quality of life. Although nutritional support, exercise, pharmacological interventions, and microbiota-targeted therapies have shown encouraging results, heterogeneous evidence, patient-related barriers, and a lack of ALD-specific therapeutic recommendations limit their translation into routine clinical practice. Finally, we discuss emerging concepts of phenotypic heterogeneity, including myosteatosis, and highlight the potential of multiomics approaches and precision medicine to improve risk stratification and enable individualized therapeutic strategies. By integrating recent mechanistic advances with critical diagnostic and therapeutic perspectives, this review provides an updated ALD-focused framework to guide future research and clinical management.},
}

@article {pmid43023446,
year = {2026},
author = {Dhar, P and Alsayadi, YMMA and Mehla, S and Shiven, A and Sachdeva, D and Mandha, M and Alsayadi, GMH and Bhatia, R},
title = {The N-Nitrosamine Crisis in Antidiabetic Drugs: Toxicological Insights, Regulatory Challenges, Analytical Detection and Clinical Implications.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128505489261101195216},
pmid = {43023446},
issn = {1873-4286},
abstract = {The detection of carcinogenic N-nitrosamine impurities in first-line antidiabetic medicines has revealed critical vulnerabilities in pharmaceutical safety and affected patient confidence in lifelong therapies. This review links the mechanistic roots of N-nitrosamines to clinical consequences. Nitrosamines in drugs such as metformin, sitagliptin, and pioglitazone arise through interactions between susceptible amine precursors, nitrite-containing excipients, and manufacturing or storage conditions that catalyze nitrosation. Advanced analytical tools, including LC-MS/MS, GC-MS, and supercritical fluid chromatography, now enable trace-level detection, aligning with increasingly stringent international guidelines. Global regulatory agencies have transitioned from reactive recalls to proactive risk management, yet challenges persist in harmonizing acceptable intake limits and addressing nitrosamine drug substance-related impurities (NDSRIs). Importantly, this review highlights host-dependent risk modulation, including how gut microbiota and pharmacogenomic variability in CYP2E1 and CYP2A6 significantly alter nitrosamine bioactivation and carcinogenicity. These findings challenge one-size-fits-all regulatory thresholds and argue for more personalized risk models. Future progress requires integrating advanced manufacturing, next-generation analytics, and individualized risk assessment to safeguard essential diabetes medicines and restore long-term trust in pharmacotherapy.},
}

@article {pmid43023447,
year = {2026},
author = {Pandey, SK and Mishra, A and Dash, SG},
title = {Gut Microbiota and Cancer Therapy Resistance: Mechanistic Insights with Emphasis on Colorectal Cancer.},
journal = {Current medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298673525110261104074049},
pmid = {43023447},
issn = {1875-533X},
abstract = {Therapeutic resistance remains a major limitation to the durable control of cancer despite advances in chemotherapy, radiotherapy, targeted therapy, and immunotherapy. Resistance is shaped not only by tumor-intrinsic genetic and epigenetic alterations but also by extrinsic factors, including the gut microbiota. The intestinal microbial ecosystem can influence treatment response through direct drug biotransformation, modulation of host immunity and inflammation, production of bioactive metabolites, alteration of epithelial barrier function, and interactions with the tumor microenvironment. This narrative review synthesizes these mechanisms across chemotherapy, radiotherapy, and immune checkpoint blockade, with particular emphasis on Colorectal Cancer (CRC), while incorporating evidence from breast, lung, melanoma, and other relevant tumor types. Microbial metabolites, including short-chain fatty acids, bile-acid derivatives, tryptophan metabolites, and microbially generated organic acids, can influence signaling, immune-cell function, redox balance, and treatment sensitivity. We further evaluate microbiome-directed approaches, including dietary modulation, probiotics, fecal microbiota transplantation, antibiotic stewardship, and inhibition of microbial drug-metabolizing enzymes. Particular attention is given to the translational challenges of patient-to-patient microbiome variability, safety, biomarker reproducibility, treatment timing, and cancer-type specificity. Collectively, current evidence supports the gut microbiota as a biologically plausible and potentially modifiable determinant of cancer therapy response, but clinical implementation will require mechanism-based biomarkers and rigorously controlled prospective studies.},
}

@article {pmid43023736,
year = {2026},
author = {Cui, Y and Qiu, Q and Chen, Y and Ding, T},
title = {Characterizing gut microbial structural variation reveals strain heterogeneity and metabolic dysfunction in colorectal cancer.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0110926},
doi = {10.1128/msystems.01109-26},
pmid = {43023736},
issn = {2379-5077},
abstract = {Previous studies investigating gastrointestinal (GI) diseases have primarily focused on the composition, gene expression, and specific strains of gut microbiota. However, the impact of genetic variations, especially structural variations (SVs) in microbial genomes, on the development of GI tumors has been largely overlooked. In this study, we analyzed 1,027 fecal metagenomes from seven data sets and identified 8,278 coverage-defined SVs across 51 bacterial species in the gut microbiomes. We found that SVs were prevalent in the gut microbiota of studied cohorts. Surprisingly, the genetic makeup of SV-based clusters differed significantly between healthy individuals and those with colorectal cancer (CRC), indicating substantial intra-specific diversity within these populations. By integrating taxonomic-SV markers, we achieved optimal accuracy in early CRC detection, and the SVs also displayed regional heterogeneity. Microbial genetic variation provides additional insights into taxonomy and functionality, allowing us to have a more precise understanding of the microbiota associated with CRC. Notably, our study uncovered potential links between microbial SVs and metabolic disorders of CRC, including SV regions that encode glycoside hydrolases associated with disordered carbohydrate metabolism in CRC. We integrated a framework called MicroSVsProfiler to identify and classify SVs in individuals diagnosed with CRC, as well as in healthy controls. Our findings underscore the importance of considering SVs in microbiome studies, especially in the absence of strain-specific differences in abundance. Future research should explore the deeper layer of the microbiota's structural variantome for a better understanding of the occurrence and characteristics of CRC across different stages.IMPORTANCEMost microbiome studies of colorectal cancer focus on which bacterial species are more or less abundant, potentially overlooking genetic differences among strains of the same species. By analyzing 1,027 fecal metagenomes from seven independent cohorts, we show that large-scale changes in bacterial genomes, known as structural variations, provide disease-related information that is not captured by species abundance alone. These strain-level SV signatures distinguished healthy individuals from patients with colorectal cancer, improved early-cancer classification when combined with taxonomic markers, and varied across geographic populations. We also found that cancer-associated structural variations were linked to altered microbial metabolic functions, particularly carbohydrate metabolism and glycoside hydrolases. Together, these findings establish microbial structural variation as a complementary dimension of the gut microbiome and provide a framework for developing more precise, population-aware biomarkers and for investigating how strain-level genetic changes may contribute to metabolic disturbances associated with colorectal cancer.},
}

@article {pmid43012510,
year = {2026},
author = {Crossen, AJ and Cohen, S and Manzer, HS and Zackular, JP and Ost, KS and Doran, KS},
title = {The BspC surface adhesin and gastrointestinal fungal colonization enhance group B streptococcal neonatal infection.},
journal = {mBio},
volume = {},
number = {},
pages = {e0256126},
doi = {10.1128/mbio.02561-26},
pmid = {43012510},
issn = {2150-7511},
abstract = {Group B Streptococcus (GBS) colonizes the gastrointestinal (GI) and female reproductive tracts of up to 30% of healthy adults, but during pregnancy can be transmitted to the newborn, causing neonatal sepsis, pneumonia, and meningitis. Neonatal GI colonization is an important precursor to invasive disease, yet the mechanisms governing GBS intestinal persistence and dissemination are still being elucidated. Given the predominance of hypervirulent sequence type 17 (ST-17) strains in neonatal invasive disease, we hypothesized that the ST-17-associated surface adhesin BspC contributes to gastrointestinal colonization and infection. Using a neonatal mouse model, we found that pups infected with wild-type GBS exhibited increased mortality and significantly higher bacterial burdens in the intestine, blood, spleen, and brain compared with pups infected with a ΔbspC mutant. We also observed that BspC promoted adherence to a 2D organoid model of the human infant colon and Caco-2 intestinal epithelial cells through its variable domain. Building on previous findings that Candida albicans interacts with BspC, we found that C. albicans enhanced GBS intestinal epithelial adherence in a BspC-dependent manner, and coinfection increased intestinal GBS burden and brain dissemination in neonatal mice. Finally, analysis of published human neonatal fecal microbiome data sets revealed higher GBS abundance in infants colonized with C. albicans or other Candida species. Together, these findings identify BspC as a key mediator of GBS intestinal colonization and invasive disease and suggest that fungal colonization of the neonatal GI promotes GBS pathogenesis.IMPORTANCEGroup B Streptococcus (GBS) is a leading cause of neonatal infection, which can result in fatality or long-term neurological morbidity in survivors. Intestinal colonization is an important precursor to invasive disease, yet the factors that promote GBS persistence in the neonatal gastrointestinal tract remain incompletely understood. Here, we identify the GBS surface adhesin BspC as a mediator of intestinal epithelial adherence, gastrointestinal colonization, and systemic dissemination. We further demonstrate that the common fungal pathobiont Candida albicans enhances GBS intestinal adherence and infection. Consistent with our experimental findings, analysis of human infant microbiome data sets revealed greater GBS abundance in infants colonized with Candida species. These findings identify BspC as a key mediator of this process and suggest that fungal colonization can enhance GBS disease.},
}

@article {pmid43012643,
year = {2026},
author = {Wheeler, M and Bakkeren, E},
title = {Erratum: Microbiome ecology and antibiotic treatment failure: resistance spread, microbial competition and community engineering.},
journal = {Microbial genomics},
volume = {12},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001904},
pmid = {43012643},
issn = {2057-5858},
}

@article {pmid43012696,
year = {2026},
author = {Dong, KH and Zheng, ZQ and Shen, L and Ji, HF},
title = {Thyme Beyond Its Traditional Culinary Use: Bioactive Constituents as Potential Modulators of the Gut Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {44},
pages = {34545-34575},
doi = {10.1021/acs.jafc.6c07962},
pmid = {43012696},
issn = {1520-5118},
support = {ZR2023MH357//Natural Science Foundation of Shandong Province/ ; },
mesh = {*Thymus Plant/chemistry/metabolism ; Humans ; Animals ; *Plant Extracts/chemistry/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Bacteria/genetics/isolation & purification/classification/metabolism/drug effects ; Oils, Volatile/chemistry/pharmacology ; },
abstract = {Thyme, particularly Thymus vulgaris L., is a widely used culinary spice and a source of compounds with diverse reported pharmacological activities. This Review examines how thyme extracts, essential oils, and their major constituents, including characteristic monoterpenes, sesquiterpenes, triterpenes, phenolic acids, and flavonoids, interact with the gut microbiome. On the basis of structure-activity relationships, we evaluate how these constituents influence gut microbial composition and function and summarize the implicated mechanisms. Thyme preparations and individual compounds can influence intestinal availability, microbial transformation, and target selectivity, while microbiota-dependent and -independent pathways may contribute to changes in intestinal barrier function, metabolite profiles, and related signaling pathways. Interactions among multiple constituents may produce additive or synergistic effects, suggesting potential advantages of multicomponent thyme preparations, whereas studies of individual compounds can facilitate the target identification and mechanistic analysis. Future research should systematically address gaps in causal validation, formulation standardization, and human evidence to consolidate the translational foundations.},
}

*Thymus Plant/chemistry/metabolism
Humans
Animals
*Plant Extracts/chemistry/pharmacology/metabolism
*Gastrointestinal Microbiome/drug effects
Bacteria/genetics/isolation & purification/classification/metabolism/drug effects
Oils, Volatile/chemistry/pharmacology

@article {pmid43012714,
year = {2026},
author = {Lee, CC and Ashaolu, TJ},
title = {AI-Driven Prediction of Allergenicity and Toxicity in Novel Plant-Based Peptides.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {44},
pages = {34683-34700},
doi = {10.1021/acs.jafc.6c13356},
pmid = {43012714},
issn = {1520-5118},
mesh = {Humans ; *Allergens/immunology/chemistry/toxicity ; *Peptides/immunology/chemistry/toxicity ; *Artificial Intelligence ; *Plant Proteins/immunology/chemistry/toxicity ; Animals ; Prediction Algorithms ; *Plants/chemistry/immunology ; },
abstract = {Peptides from plant sources have antihypertensive, antioxidative, and antimicrobial properties but also entail a risk of allergic and toxic reactions that cannot be detected in conventional wet-lab assays. This review examines deep learning techniques and protein language models for their prediction, from linear motifs screening to transformers (BERT, ESM). The best-performing tools achieve high sensitivity (pLM4Alg 96.2%, ToxinPred3 95.8%) but low specificity and positive predictive value (pLM4Alg 92.8% and 81.7%), meaning that most predictions are false positives. There are four major constraints on the generalization capabilities of these tools: scoring of native peptides while proteolytic processing yields post-translational modifications and neoantigens; training samples correspond to IgE binding, not clinical manifestations, and are biased toward well-characterized organisms; T-cell immunity, microbiome, and organ-specific toxicity are scarcely modeled; and regulatory agencies do not consider in silico predictions sufficient. AI currently serves best as a prioritization filter, not a replacement for biological assays.},
}

Humans
*Allergens/immunology/chemistry/toxicity
*Peptides/immunology/chemistry/toxicity
*Artificial Intelligence
*Plant Proteins/immunology/chemistry/toxicity
Animals
Prediction Algorithms
*Plants/chemistry/immunology

@article {pmid43012717,
year = {2026},
author = {Lin, Z and Huang, R and Zhang, S and Wang, L and Fang, X and Du, R and Xiao, S and Pramono, H and Xu, Z},
title = {Metabolite-Mediated Rhizosphere-Endosphere Microbiome Shapes Genotype-Dependent Cadmium Accumulation via Coupled Chemical Immobilization and Microbial Detoxification.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {44},
pages = {34933-34947},
doi = {10.1021/acs.jafc.6c12601},
pmid = {43012717},
issn = {1520-5118},
support = {2022ZDJS019//Guangdong Province Key Construction Discipline Research Capacity Enhancement Project/ ; 2023ZDZX4016//Special Projects in Key Fields of Ordinary Universities in Guangdong Province/ ; 2024YFC3711903//National Basic Research Program of China (973 Program)/ ; 2024YFD1701304//National Basic Research Program of China (973 Program)/ ; 2026JJ40030//Natural Science Foundation of??Hunan Province/ ; 42577473//National Natural Science Foundation of China (NSFC)/ ; kq2502110//Changsha Natural Science Foundation Project/ ; NA//Changsha Natural Science Foundation Project/ ; NA//National Basic Research Program of China (973 Program)/ ; NA//National Natural Science Foundation of China (NSFC)/ ; NA//Natural Science Foundation of??Hunan Province/ ; NA//Special Projects in Key Fields of Ordinary Universities in Guangdong Province/ ; },
mesh = {*Cadmium/metabolism/analysis ; Rhizosphere ; *Microbiota ; Plant Roots/metabolism/microbiology/chemistry/genetics/growth & development ; *Amaranthus/metabolism/microbiology/genetics/chemistry/growth & development ; Genotype ; *Bacteria/isolation & purification/genetics/classification/metabolism ; *Soil Pollutants/metabolism/chemistry ; Soil Microbiology ; },
abstract = {Cadmium (Cd) contamination threatens food safety, yet genotype-dependent Cd accumulation at the soil-root interface remains poorly understood. We integrated physiological profiling, metabolomics, density functional theory (DFT), and 16S rRNA sequencing to compare two amaranth cultivars, Quanhong (QH, low-Cd) and Liuye (LY, high-Cd). QH showed greater shoot biomass (6.84 g/plant) and stronger Cd exclusion (root/shoot Cd: 0.12/0.08 mg/kg), whereas LY developed a larger root system (1.42 vs 0.71 g/plant) and accumulated more Cd (0.26/0.16 mg/kg). QH promoted conversion of exchangeable Cd into stable residual fractions and enriched humic-like dissolved organic matter and 9-Oxo-ODE, which showed strong predicted Cd2+ binding (-22.34 kcal/mol), supporting its potential role in Cd immobilization. QH showed stronger host-associated microbial selection, enriching Bacillus and Streptomyces associated with sulfur metabolism and thiol-mediated metal sequestration, together with greater diversity and stability of root endophytes. These findings indicate coordinated chemical and microbial regulation contributing to the low-Cd phenotype of QH.},
}

*Cadmium/metabolism/analysis
Rhizosphere
*Microbiota
Plant Roots/metabolism/microbiology/chemistry/genetics/growth & development
*Amaranthus/metabolism/microbiology/genetics/chemistry/growth & development
Genotype
*Bacteria/isolation & purification/genetics/classification/metabolism
*Soil Pollutants/metabolism/chemistry
Soil Microbiology

@article {pmid43012904,
year = {2026},
author = {Cai, Q and Li, H and Shen, Z and Wei, C},
title = {Wetland microbiomes: diversity, biogeochemical functions, climate feedbacks, and emerging frontiers.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {43012904},
issn = {1573-0972},
support = {20251705107//Medical and health research projects in Zibo/ ; 24DWYJ09//Social Science Planning Project of Shandong Province/ ; 2025QN08109//Natural Science Foundation of Inner Mongolia Autonomous Region of China/ ; },
mesh = {*Wetlands ; Methane/metabolism ; *Microbiota/physiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Soil Microbiology ; Climate ; Biodiversity ; Oxidation-Reduction ; Ecosystem ; },
abstract = {Wetlands occupy roughly 6% of the Earth's surface yet store 20 to 30% of global soil carbon and emit an estimated 145 to 180 Tg of methane each year, fluxes that are controlled by microbial communities. This review synthesizes the past decade of research on wetland microbiomes across peatlands, mangroves, salt marshes, and constructed wetlands, and draws three main conclusions. First, community assembly is governed mainly by environmental filtering: salinity and pH are the strongest predictors, deterministic processes dominate steep gradients, and stochastic processes become important in hydrologically homogeneous settings. Second, the evidence linking microbial communities to biogeochemical fluxes is uneven in strength. Process-level measurements and meta-analyses support a well-constrained picture of methanogenesis, methane oxidation, and sulfate suppression of methanogenesis, whereas much of the evidence for cryptic sulfur cycling, anaerobic methane oxidation coupled to nitrogen species, and viral regulation rests on gene abundance, which reports functional potential rather than in situ activity. Third, in constructed wetlands, antibiotic removal does not necessarily reduce antimicrobial resistance risks, because antibiotic concentrations, resistance gene abundance, mobile genetic elements, and horizontal gene transfer respond to different environmental drivers. The most pressing unresolved questions are the controls on the N2O: N2 product ratio of denitrification, the scaling from gene abundance to ecosystem fluxes, and the joint response of greenhouse-gas emissions to interacting climate drivers. We close by identifying where multi-omics integration and standardized cross-site observation networks would most rapidly close these gaps.},
}

*Wetlands
Methane/metabolism
*Microbiota/physiology
Bacteria/classification/genetics/metabolism/isolation & purification
Soil Microbiology
Climate
Biodiversity
Oxidation-Reduction
Ecosystem

@article {pmid43012929,
year = {2026},
author = {Divya, S and Bag, TK and Makeshkumar, T and Jeeva, ML and Chouhan, V and Manirajan, BA and Veena, SS and Kumar, A},
title = {Comparative metabarcoding of the cassava rhizoplane bacteriome in wetland and upland fields reveals Bacillus-mediated suppression of stem and root rot.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {43012929},
issn = {1573-0972},
mesh = {*Manihot/microbiology ; Plant Roots/microbiology ; *Plant Diseases/microbiology/prevention & control ; RNA, Ribosomal, 16S/genetics ; Plant Stems/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Fusarium ; Wetlands ; *Bacillus/physiology/genetics/isolation & purification/classification ; Rhizosphere ; DNA Barcoding, Taxonomic ; Soil Microbiology ; Microbiota ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Cassava (Manihot esculenta Crantz) stem and root rot caused by Fusarium falciforme is a major constraint to cassava production. This study investigated rhizoplane bacteriome shifts across wetland and upland fields differing in disease incidence and evaluated potential microbial indicators and biocontrol agents using 16 S rRNA gene amplicon sequencing, culture-dependent isolation, and functional assays. Bacterial richness was highest in diseased wetlands (Chao1, 601.60 ± 10.37), followed by healthy wetlands (581.20 ± 14.39) and uplands (547.97 ± 5.74), whereas bacterial evenness was comparable among sites. Pseudomonadota dominated across all field types (63-92%). Bacteroidota, and Acidobacteriodota were relatively enriched in healthy wetlands but declined in diseased samples, whereas Verrucomicrobiota increased in diseased roots (7.35%). Pseudomonas was predominant in uplands (29.7%), while Aeromonas, Salmonella, and Devosia were associated with diseased sites. The core bacteriome comprised Aquicella, Enterobacter, Klebsiella, Sodalis, and Salmonella. A multiple-testing-corrected bacterial-fungal co-occurrence network was sparse, comprising only five inter-kingdom associations. Of 195 bacterial isolates recovered, Bacillus subtilis ULB-36 and Bacillus stercoris ULB-12 exhibited the strongest antagonistic activity against F. falciforme, inhibiting mycelial growth by 83.33% and 78.52%, respectively. In greenhouse assays, these strains reduced disease incidence to 0% and 20%, respectively, compared with 70% in the pathogen-inoculated control; Bacillus subtilis ULB-36 performed comparably to carbendazim. Overall, cassava stem and root rot was associated with distinct shifts in the rhizoplane bacteriome, including depletion of potentially beneficial bacterial taxa in diseased fields. The identified site-specific microbial signatures and native Bacillus strains provide valuable insights into cassava-microbe interactions and highlight their potential for biological management of cassava stem and root rot.},
}

*Manihot/microbiology
Plant Roots/microbiology
*Plant Diseases/microbiology/prevention & control
RNA, Ribosomal, 16S/genetics
Plant Stems/microbiology
*Bacteria/classification/genetics/isolation & purification
Fusarium
Wetlands
*Bacillus/physiology/genetics/isolation & purification/classification
Rhizosphere
DNA Barcoding, Taxonomic
Soil Microbiology
Microbiota
DNA, Bacterial/genetics
Phylogeny

@article {pmid43012953,
year = {2026},
author = {Okamoto, KE and Harris, EV and Juneau, WC and Harshman, R and Kovacs, J},
title = {Resilient but Unreliable: Cross-Generational Restructuring of the Tribolium castaneum Gut Microbiome Under Contrasting Nutritional Regimes.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {43012953},
issn = {1432-184X},
support = {2042735//National Science Foundation/ ; },
mesh = {Animals ; *Tribolium/microbiology/physiology ; *Gastrointestinal Microbiome ; Diet ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Microbial communities are frequently exposed to environmental disturbances, yet recovery does not always lead to a single, predictable outcome. Distinguishing resilience, the capacity to recover following perturbation, from reliability, the predictability of that recovery, is essential for understanding microbiome dynamics. Here, we investigated cross-generational gut microbiome responses in the red flour beetle, Tribolium castaneum, a globally significant stored-product pest exposed to frequent environmental and dietary shifts. Using a four-generation experimental design (G0-G3), we examined how gut microbial communities respond to a major environmental transition from commercial to laboratory rearing, followed by dietary perturbations. The shift to laboratory conditions produced the largest change in gut microbiome composition, occurring within a single generation and exceeding the effects of dietary shifts. Following this disturbance, microbial communities stabilized across subsequent generations, consistent with strong ecological resilience. However, recovery trajectories and endpoints differed among treatments, with replicate lineages stabilizing toward multiple, partially distinct community configurations rather than a single shared state, indicating low reliability. Diet influenced overall community composition and diversity trajectories, but these effects were smaller in magnitude than the dominant generational restructuring. Together, these results show that the T. castaneum gut microbiome is resilient but not strictly reliable, stabilizing after rapid reorganization toward multiple partially distinct community configurations associated with environmental history rather than a single shared state. These findings underscore the importance of environmental context in shaping host-associated microbiomes and suggest that the capacity for rapid microbiome restructuring may contribute to the ecological success of insect pests in variable environments.},
}

Animals
*Tribolium/microbiology/physiology
*Gastrointestinal Microbiome
Diet
*Bacteria/classification/genetics/isolation & purification

@article {pmid43013030,
year = {2026},
author = {Zhou, W and Zhu, H and Liu, Y and Li, H and Wu, M and Li, S and Qu, R and Liu, S and Qian, H and Xue, B and Cao, Y and Jiang, X and Zhen, X},
title = {Ultrasound-Driven Lysis of Tumor-Resident Bacteria Awakens Innate Immunity for Systemic Cancer Therapy.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {44},
pages = {48101-48115},
doi = {10.1021/jacs.6c14587},
pmid = {43013030},
issn = {1520-5126},
support = {BK20244003//Natural Science Foundation of Jiangsu Province/ ; 5431ZZXM2506//State Key Laboratory of Analytical Chemistry for Life Sciences/ ; 52333003//National Natural Science Foundation of China (NSFC)/ ; 52373141//National Natural Science Foundation of China (NSFC)/ ; 52573166//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Immunity, Innate ; Animals ; *Fusobacterium nucleatum/immunology/drug effects ; Mice ; *Immunotherapy ; *Ultrasonic Waves ; Humans ; *Ultrasonic Therapy ; *Neoplasms/therapy/immunology ; },
abstract = {Tumor-resident bacteria establish a profound immunosuppressive microenvironment that compromises cancer immunotherapy. While ablating these microbes holds therapeutic promise, broad-spectrum antibiotics can cause systemic dysbiosis, and the Gram-negative outer membrane can restrict the entry of conventional sonosensitizers, limiting the antibacterial efficacy of sonodynamic therapy (SDT). Here, we report an ultrasound-driven, bacteria-targeted immunotherapy utilizing polyarginine-functionalized peptide-sonosensitizer conjugates to achieve the in situ pulverization of the tumor Fusobacterium nucleatum (F. nucleatum), thereby eliciting potent innate antitumor immunity. The cationic conjugates electrostatically intercalate into Gram-negative bacterial membranes, inflicting a structural predisruption. Subsequent ultrasound irradiation synergizes localized sonochemical oxidation with mechanical shear forces to thoroughly shatter the bacteria. This targeted microbial fragmentation liberates massive quantities of pathogen-associated molecular patterns (PAMPs) that, unlike tumor-derived signals from conventional SDT, decisively reprogram macrophages toward an antitumor M1 phenotype to awaken innate immunity. Synchronized with tumor-specific antigens released via conjugate-induced immunogenic cell death, the liberated PAMPs synergistically amplify antigen presentation and optimally drive dendritic cell maturation. In a bacteria-colonized murine colorectal cancer model, this localized therapy markedly suppressed primary tumor growth and elicited both a pronounced abscopal effect against distant tumors and antitumor immune memory. By repurposing complicit bacteria into potent endogenous adjuvants, this ultrasound-driven strategy reverses bacteria-mediated immunosuppression, offering a transformative paradigm for treating microbiome-colonized solid tumors.},
}

*Immunity, Innate
Animals
*Fusobacterium nucleatum/immunology/drug effects
Mice
*Immunotherapy
*Ultrasonic Waves
Humans
*Ultrasonic Therapy
*Neoplasms/therapy/immunology

@article {pmid43013155,
year = {2026},
author = {Al-Zaidi, OSSH and Ali, AH},
title = {Gut microbiome in leukemia: emerging insights, mechanistic and clinical implications.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {43013155},
issn = {1573-4978},
mesh = {Humans ; *Leukemia/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Animals ; },
abstract = {Leukemia is a hematological malignancy that arises from complex interactions among environmental factors, immune dysregulation, and genetic mutations. The Human Microbiome Project has contributed to understanding the potential role of the gut microbiome in the health of patients with leukemia, and its impact on leukemia development, progression, and response to therapies. This review summarizes how the gut microbiome and its constituent microorganisms may influence development and the new therapeutic approaches against leukemia. Recent findings indicate that microorganisms might influence leukemia through multiple mechanisms, including chronic inflammation, homeostasis disruption, and genomic instability. Dysbiosis of the gut microbiome might increase the risk of infection, impair response to immunotherapy and chemotherapy and increase the risk of clinical complications. Probiotics, postbiotics, and fecal microbiota transplantation (FMT) have emerged as promising microbiome-modulating approaches. Despite the abundance of emerging data suggesting potential therapeutic benefits, most studies remain small and preliminary. Integrating gut microbiome science into medical practice may open up new and potentially more effective therapeutic avenues for managing leukemia.},
}

Humans
*Leukemia/microbiology/therapy
Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
Probiotics/therapeutic use
Animals

@article {pmid43013265,
year = {2026},
author = {Valk, LC and Ruigrok, RAAA and Timmerman, H and Björk, JR and Li, Q and Zhang, S and Meneses, R and Vázquez Castellanos, JF and de Wit, N and Raes, J and Weersma, RK and Kleerebezem, M and Vich-Vila, A and Boekhorst, J},
title = {Mapping the genetic landscape of microbial lipid transformation in the intestinal microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2756735},
doi = {10.1080/19490976.2026.2756735},
pmid = {43013265},
issn = {1949-0984},
mesh = {*Lipid Metabolism/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Colon/microbiology ; Metagenome ; Intestine, Small/microbiology ; Bile Acids and Salts/blood ; },
abstract = {Dietary lipids are a key component in our diet, and fats and their derivatives have been associated with both beneficial as well as adverse effects on host health. However, the contribution of the gut microbiome to lipid metabolism remains understudied. Recognizing the importance of this interplay, we conducted extensive literature reviews to identify key bacterial genes involved in lipid metabolism, and created 88 Hidden Markov Models to allow rapid and accurate identification of these genes in genome and metagenome data. We applied these models to over 1000 metagenomes representative of the small intestine and colon, from both population-based and disease cohorts (LLDeep, MetaCardis and 1000IBD) to determine their lipolytic capacity. We observed that microbiome community types (enterotypes) carry different lipolytic potential. Serum levels of conjugated and sulfonated secondary bile acids were significantly associated with increased abundance of sterol-sulfonation genes (cysC, cysD and BtSULT). Small-intestinal communities were enriched in lipid genes compared to the colonic microbiota, underscoring the importance of microbial lipid metabolism in the small intestine compared to the colon. Overall, we demonstrate the value of our lipid metabolism models for functional microbiome profiling. Additionally, our study suggests that microbial activity in the upper gut might play a direct role in shaping host lipid metabolism, with potential implications for cardiometabolic health.},
}

*Lipid Metabolism/genetics
*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/genetics/metabolism/classification/isolation & purification
Colon/microbiology
Metagenome
Intestine, Small/microbiology
Bile Acids and Salts/blood

@article {pmid43013324,
year = {2026},
author = {Lee, HR and Kim, KN and Jung, S and Ju, S and Lee, YJ and Kang, MS and Joo, NS},
title = {Food-based resistant starch, metabolic outcomes and the gut microbiome in women with metabolic syndrome risk factors: a randomized, double-blind pilot trial.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo05525c},
pmid = {43013324},
issn = {2042-650X},
abstract = {Resistant starch (RS) has been widely studied for its metabolic effects; however, evidence regarding the physiological effects of RS when consumed within whole-food-based dietary patterns remains limited. In this 8-week, double-blind, randomized pilot trial, 30 women aged ≥40 years with at least two metabolic syndrome features were assigned 1 : 1 to High-RS or Control foods, resulting in mean total dietary RS intakes of 7.9 and 2.4 g day[-1], respectively. Primary outcomes were metabolic syndrome components and gut microbiome composition and diversity. Secondary outcomes included urinary organic acids, fecal calprotectin, and heart rate variability, while microbiome-metabolic associations were exploratory. Between-group effects were estimated using baseline-adjusted analyses with multiplicity correction. No significant between-group differences were observed in the primary metabolic outcomes, including systolic blood pressure (adjusted mean difference, -1.7 mmHg; 95% CI, -6.4 to 2.9; P = 0.456), in global gut microbiome diversity and composition, or in the secondary outcomes after multiplicity correction. In exploratory genus-level analysis, Veillonella showed the strongest signal, with higher week-8 CLR abundance in the High-RS group (adjusted difference, 3.24; 95% CI, 1.48-5.00; P < 0.001), although no genus remained significant after FDR correction (q = 0.070). The association between change in urinary lactate-to-pyruvate ratio (LPR), a redox-sensitive metabolic index, and fasting glucose differed nominally between groups (P for interaction = 0.010; q = 0.185), but this finding was attenuated after exclusion of one high-leverage observation. Overall, 8 weeks of RS intake within a food matrix at intakes in the upper habitual range produced no detectable short-term change in the primary metabolic or global gut microbiome outcomes in this pilot trial. The exploratory Veillonella finding and LPR-glucose association did not remain statistically significant after multiplicity correction and should therefore be considered hypothesis-generating. The clinical trial registry number is KCT0011082 (Clinical Research Information Service (CRIS), Republic of Korea).},
}

@article {pmid43013553,
year = {2026},
author = {Hanna, DA and Kumar, R and Ji, Y and Wong, HKA and Lyssiotis, CA and Jones, JW and Banerjee, R},
title = {Lipid droplets buffer hydrogen sulfide-induced redox imbalance.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {46},
pages = {e2613433123},
doi = {10.1073/pnas.2613433123},
pmid = {43013553},
issn = {1091-6490},
support = {GM130183//HHS | NIH (NIH)/ ; F32GM140694//HHS | NIH (NIH)/ ; },
mesh = {Oxidation-Reduction/drug effects ; *Hydrogen Sulfide/metabolism/pharmacology ; Humans ; *Lipid Droplets/metabolism/drug effects ; NAD/metabolism ; Mitochondria/metabolism ; Ubiquinone/metabolism ; },
abstract = {The electron transport chain is a signaling hub for hydrogen sulfide (H2S) that serves both as a respiratory substrate and an inhibitor. While acute sulfide toxicity is well characterized, cellular adaptations to chronic H2S, particularly microbially-derived sulfide exposure in colon, is poorly understood. We report that chronic, low-level H2S exposure (4 to 20 µM) drives robust carbon sequestration in lipid droplets (LD) across several human cell lines, driven by a coordinated remodeling of redox and nucleotide metabolism. Specifically, H2S-induced reductive shifts in nicotinamide adenine dinucleotide (NAD) and coenzyme Q (CoQ) pools are accompanied by glycerol-3-phosphate accumulation and cytidine triphosphate (CTP) depletion. Lipidomic analysis reveals increased neutral lipid synthesis and triacylglyceride accumulation concomitant with decreased CTP-dependent synthesis of membrane phospholipids. Mitochondrial expression of a water-generating NADH oxidase attenuates LD accumulation and spatially confines the origin of H2S-induced reductive stress signaling to this compartment. Interestingly, LD abundance increases even after H2S withdrawal, continuing over 48 h, during which time the reductively-shifted NAD and CoQ pools slowly reoxidize. Inhibition of fatty acid synthesis during sulfide exposure impairs cellular recovery of respiration. These findings establish an active role for LDs in stress response and reveal that lipid biogenesis is a strategy for countering H2S-induced redox imbalance. The sulfide-LD-redox axis uncovered in this study has implications for understanding how gut-derived H2S, shaped by diet and microbiome, can influence metabolic health.},
}

Oxidation-Reduction/drug effects
*Hydrogen Sulfide/metabolism/pharmacology
Humans
*Lipid Droplets/metabolism/drug effects
NAD/metabolism
Mitochondria/metabolism
Ubiquinone/metabolism

@article {pmid43013631,
year = {2026},
author = {Ongaga, E and Neondo, JO and Muli, JK and Kamau, PK and Bii, C and Odari, E and Budambula, NLM},
title = {Genetic diversity of bacterial endophytes associated with Crotalaria (Rattlepods).},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0362184},
pmid = {43013631},
issn = {1932-6203},
mesh = {*Crotalaria/microbiology ; *Endophytes/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Genetic Variation ; *Bacteria/genetics/classification ; Phylogeny ; Microbiota/genetics ; DNA, Bacterial/genetics ; Animals ; },
abstract = {Crotalaria is a diverse legume genus valued for its ecological and agronomic roles. However, its associated endophytic microbiome remains minimally characterized. This study examined the genetic diversity and community structure of bacterial endophytes inhabiting domesticated and wild Crotalaria species. Twenty-nine healthy Crotalaria plant samples were analyzed using the culture-independent 16S rRNA gene amplicon sequencing approach. Genomic DNA was extracted using the Phenol-Chloroform method from both domesticated and wild samples. Sequencing of 16S ribosomal RNA gene was performed using Illumina MiSeq to profile endophytic bacterial communities. The sequence data was imported into R and processed using Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline. In total, 1,546,153 high-quality sequence reads were obtained and grouped into 611 amplicon sequence variants (ASVs) at 97% sequence similarity threshold. Domesticated samples exhibited higher observed species richness (median of 39 ASVs) than wild samples (median of 36 ASVs), while wild samples showed greater microbial community evenness (median ~1.08) compared to domesticated samples (median ~0.93). Beta diversity analyses showed clear separation between domesticated and wild endophytic bacterial communities, with domestication status explaining most of the observed variations (PERMANOVA: Bray-Curtis R2 = 0.826; Jaccard R2 = 0.846), but PERMANOVA detected no statistically significant difference (Bray-Curtis and Jaccard; p = 0.067). Overall, five bacteria phyla were detected in the Crotalaria samples. Pseudomonadota was the dominant phylum (64.27%) followed by Cyanobacteriota (35.5%). Enterobacteriaceae was the most abundant family (81.06%) with Enterobacter emerging as the most abundant genus in both domesticated (38.3%) and wild (89.4%) accessions. Notably, Pseudomonas was relatively enriched in domesticated plants while several bacterial genera were restricted to either wild or cultivated hosts, indicating habitat-associated endophytic specialization. This study provides the first comprehensive assessment of endophytic bacterial diversity in Kenyan Crotalaria species and highlights wild germplasm as an important reservoir of microbial diversity with potential biotechnological value.},
}

*Crotalaria/microbiology
*Endophytes/genetics/classification
RNA, Ribosomal, 16S/genetics
*Genetic Variation
*Bacteria/genetics/classification
Phylogeny
Microbiota/genetics
DNA, Bacterial/genetics
Animals

@article {pmid43013737,
year = {2026},
author = {Silvey, S and Patel, N and O'Leary, JG and Bajaj, JS},
title = {Ascites fluid PMN counts below the SBP threshold predict 30-day mortality in a national hospitalized cirrhosis cohort.},
journal = {Hepatology communications},
volume = {10},
number = {12},
pages = {},
doi = {10.1097/HC9.0000000000001071},
pmid = {43013737},
issn = {2471-254X},
mesh = {Humans ; Male ; *Liver Cirrhosis/mortality/complications ; Aged ; *Ascitic Fluid/cytology ; Middle Aged ; *Neutrophils ; *Ascites/mortality ; Female ; Prognosis ; Leukocyte Count ; Hospitalization ; United States/epidemiology ; Veterans/statistics & numerical data ; Biomarkers ; Hypertension, Portal ; Predictive Value of Tests ; },
abstract = {BACKGROUND: Complications in patients with cirrhosis often result from bacterial and bacterial product translocation. This translocation can occur because of portal hypertension, alterations in the gut microbiome, and immune dysregulation. We aimed to re-evaluate admission ascites PMN/mm3 count as a biomarker of 30-day mortality.

METHODS: We identified veterans with cirrhosis using validated ICD-9/10 codes who had a paracentesis ≤24 hours of their index hospitalization in the Veterans Affairs Corporate Data Warehouse from 2009 to 2024. In multivariable analysis, we determined the prognostic significance of ascites PMN/mm3 <100, 100-249, and ≥250.

RESULTS: The 4111 veterans who met the inclusion criteria were mostly older (66 y) men (96.3%) with alcohol-associated liver disease (31.1%) who experienced 16.9% 30-day mortality. Most patients (~80%) had an ascites PMN/mm3 count <100. A roughly linear relationship between 30-day mortality was seen until the threshold of 100 PMN/mm3 was reached, when the relationship plateaued. The OR for 30-day mortality of a PMN/mm3 count 100-249 was 1.93 (95% CI: [1.55-2.38], p<0.001) after adjusting for age, CCI, liver disease etiology, admission lactulose use, SBP prophylaxis, serum WBC count, MELD-Na, and serum albumin. The 30-day mortality risk was not statistically different from the higher threshold of ≥250 PMN/mm3 (p=0.53).

CONCLUSIONS: Admission ascites PMN/mm3 count ≥100, compared with <100, independently predicts a doubling in 30-day mortality in a national cohort of hospitalized patients with cirrhosis. Larger prospective studies are needed to examine the optimal ascites fluid PMN (polymorphonuclear neutrophil) thresholds that increase mortality risk.},
}

Humans
Male
*Liver Cirrhosis/mortality/complications
Aged
*Ascitic Fluid/cytology
Middle Aged
*Neutrophils
*Ascites/mortality
Female
Prognosis
Leukocyte Count
Hospitalization
United States/epidemiology
Veterans/statistics & numerical data
Biomarkers
Hypertension, Portal
Predictive Value of Tests

@article {pmid43013741,
year = {2026},
author = {Barcena-Varela, M and Shang, J and Lozano, A and Mogno, I and Liebling, I and Mead, K and Li, Z and Grinspan, LT and Lindblad, KE and Ruiz de Galarreta, M and Donne, R and Gnjatic, S and Merad, M and Jun, T and Ang, C and Marron, TU and Faith, JJ and Lujambio, A},
title = {Bacteroidetes promote hepatocellular carcinoma progression and resistance to immunotherapy.},
journal = {Hepatology communications},
volume = {10},
number = {12},
pages = {},
pmid = {43013741},
issn = {2471-254X},
mesh = {Animals ; *Carcinoma, Hepatocellular/microbiology/immunology/therapy/pathology/drug therapy ; *Liver Neoplasms/microbiology/immunology/therapy/pathology/drug therapy ; Mice ; *Bacteroidetes ; Humans ; *Immunotherapy/methods ; Disease Progression ; *Gastrointestinal Microbiome/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Dysbiosis ; *Drug Resistance, Neoplasm ; Disease Models, Animal ; Tumor Microenvironment/immunology ; Male ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND AND AIMS: Growing evidence highlights the gut microbiome's critical role in tumorigenesis and immunotherapy response. However, the impact of gut microbes on hepatocellular carcinoma (HCC) progression and response to immune checkpoint blockade (ICB) remains unclear due to the lack of combined preclinical and clinical studies.

APPROACH AND RESULTS: We performed 16S rRNA sequencing of cross-cohort stool samples from 10 HCC responders (R) and 40 non-responders (NR) to ICB at baseline and on-treatment time points. We identified Bacteroidetes enrichment in NR. To study the microbiome's role in cancer immune response, we generated an immunogenic mouse model of HCC via hydrodynamic tail-vein injection (HDTVI) of DNA plasmids mimicking common HCC alterations and immunogenicity by expressing OVA model antigens (MYC-lucOS;CTNNB1 tumors). We found that antibiotic (ABX)-induced dysbiosis promoted a pro-tumorigenic effect in the MYC-lucOS;CTNNB1 HCC and reshaped the tumor immune microenvironment by reducing dendritic cells (DCs) through the expansion of the Bacteroidetes species, Parabacteroides distasonis. P. distasonis colonization in mice harboring MYC-lucOS;CTNNB1 liver tumors confirmed its pro-tumorigenic effect in vivo. Furthermore, fecal matter transplant of patient microbiotas into murine recipients demonstrated that microbiota from an NR donor enriched in Bacteroidetes promoted faster tumorigenesis compared with microbiota from an R donor with reduced Bacteroidetes. We isolated 6 Bacteroidetes species from the NR donor into a bacterial cocktail. After colonization with the Bacteroidetes cocktail, mice harboring MYC-lucOS;CTNNB1 HCC exhibited increased tumorigenesis, reduced survival, and impaired response to ICB.

CONCLUSIONS: This study identified Bacteroidetes enrichment as a potential biomarker of ICB resistance in HCC and, by using immunogenic mouse models, established that Bacteroidetes abundance influences tumor development and response to ICB.},
}

Animals
*Carcinoma, Hepatocellular/microbiology/immunology/therapy/pathology/drug therapy
*Liver Neoplasms/microbiology/immunology/therapy/pathology/drug therapy
Mice
*Bacteroidetes
Humans
*Immunotherapy/methods
Disease Progression
*Gastrointestinal Microbiome/immunology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Dysbiosis
*Drug Resistance, Neoplasm
Disease Models, Animal
Tumor Microenvironment/immunology
Male
Mice, Inbred C57BL

@article {pmid43014061,
year = {2026},
author = {Li, H and Zhang, X and Liu, J and Chen, X and Liao, B and Zhang, Y and Li, W and Sun, B and Li, X},
title = {Microbiome evidence-guided construction of a defined microbial consortium for light-aroma Baijiu fermentation and flavor development.},
journal = {International journal of food microbiology},
volume = {464},
number = {},
pages = {112147},
doi = {10.1016/j.ijfoodmicro.2026.112147},
pmid = {43014061},
issn = {1879-3460},
abstract = {Natural fermentation systems harbor microbial resources, but translating microbiome information into cultivable and controllable defined communities remains challenging. We integrated 74 metagenomic datasets from light-aroma Baijiu-associated Daqu and fermented grains with metagenome-assembled genome (MAG) functional profiles and independent 16S ribosomal RNA (rRNA) gene and internal transcribed spacer (ITS) amplicon time series to propose four candidate functional roles: substrate conversion, acid/acyl-precursor formation, alcoholic fermentation, and aroma formation. Metagenomic profiling revealed community heterogeneity, whereas MAG analysis showed widespread genetic potential for starch conversion and lactic- and acetic-acid-related metabolism. Amplicon data revealed genus-level temporal distributions of Bacillus, Weissella, Wickerhamomyces, and Saccharomyces. Bacillus amyloliquefaciens, Weissella confusa, Saccharomyces cerevisiae, and Wickerhamomyces anomalus were selected from the available laboratory culture collection as candidate representatives of these roles. A three-factor Box-Behnken design optimized the two bacterial inoculum volumes and the combined yeast volume, with the yeast ratio fixed at 1:1 (v/v). For 500 g of substrate, inoculation volumes were 7 mL for B. amyloliquefaciens, 20 mL for W. confusa, 41 mL for S. cerevisiae, and 41 mL for W. anomalus, yielding 2.28 ± 0.12 g/L ethyl acetate (HPLC). During 28 d of solid-state fermentation, starch, reducing sugars, acidity, and volatile profiles changed, with 51 volatile compounds detected. The final base Baijiu contained 33 volatile compounds, including 13 with odor activity values (OAVs) >1, of which 11 were also detected by gas chromatography-olfactometry (GC-O). These findings support a role-guided route from natural fermentation microbiome evidence to a defined consortium with measurable fermentation and flavor phenotypes.},
}

@article {pmid43014287,
year = {2026},
author = {Takeuchi, T},
title = {Beyond who is there: Industrialization shifts gut microbial ecology and evolution.},
journal = {Cell host & microbe},
volume = {34},
number = {11},
pages = {2065-2067},
doi = {10.1016/j.chom.2026.10.004},
pmid = {43014287},
issn = {1934-6069},
mesh = {Humans ; *Bacteria/genetics/classification/isolation & purification ; *Biological Evolution ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology ; Animals ; },
abstract = {The relationship between industrialization and the gut microbiome remains incompletely understood due to limitations in cohort design involving host physiology and bacterial isolates. Two recent studies from the Global Microbiome Conservancy link industrialization to lower microbiome diversity and stability, altered host immune markers, and gene gain in gut bacteria.},
}

Humans
*Bacteria/genetics/classification/isolation & purification
*Biological Evolution
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology
Animals

@article {pmid43014293,
year = {2026},
author = {Weber, AM and Spencer, SP},
title = {A microbial sugar tips the metabolic scales.},
journal = {Cell host & microbe},
volume = {34},
number = {11},
pages = {2081-2083},
doi = {10.1016/j.chom.2026.10.007},
pmid = {43014293},
issn = {1934-6069},
mesh = {*Clostridium/metabolism ; Humans ; Interleukin-22 ; *Interleukins/metabolism ; Animals ; Energy Metabolism ; Signal Transduction ; *Polysaccharides, Bacterial/metabolism ; Obesity/metabolism/microbiology ; },
abstract = {Obesity and metabolic disorders are linked to the microbiome, but the underlying pathways remain poorly defined. In this issue of Cell Host & Microbe, Tan et al. identify a Clostridium immunis-derived exopolysaccharide that reduces interleukin-22 signaling to reshape visceral adipose immunometabolism, and their findings link microbial chemistry to host energy balance.},
}

*Clostridium/metabolism
Humans
Interleukin-22
*Interleukins/metabolism
Animals
Energy Metabolism
Signal Transduction
*Polysaccharides, Bacterial/metabolism
Obesity/metabolism/microbiology

@article {pmid43014623,
year = {2026},
author = {Vlachakis, DP and Evangelou, K and Kittas, C and Gorgoulis, V and Chrousos, GP},
title = {Longevitomics as the Science of the Longevitome: Towards a Unified Systems Science of Healthy Longevity.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112271},
doi = {10.1016/j.mad.2026.112271},
pmid = {43014623},
issn = {1872-6216},
abstract = {The twenty-first century has transformed longevity research through genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiome science, digital phenotyping and artificial intelligence. Yet healthy longevity remains difficult to explain because its determinants are commonly studied as separate molecular layers, mechanisms or biomarkers. Here, we introduce Longevitomics as an integrative systems framework for understanding, modeling and predicting healthy longevity and define the Longevitome inspired by the Latin expression vita longa (long life) as the dynamic architecture of biological, environmental and behavioral determinants that collectively shape psychosomatic resilience across the life course. We position this proposal in relation to the Hallmarks of Aging, geroscience, biological-age biomarkers, multi-omics and systems medicine. Longevitomics is not intended to replace these established frameworks or to constitute another molecular "ome." Rather, it provides a systems-level framework in which mechanistic hallmarks, multi-omic layers, physiological phenotypes, exposures and adaptive responses can be integrated longitudinally. We further consider how network analysis, causal inference, machine learning and digital-twin approaches may enable reconstruction of individual Longevitome trajectories and support a transition toward predictive and personalized longevity medicine.},
}

@article {pmid43014635,
year = {2026},
author = {Kim, E and Lawson, LP and Wilson, E and Chapman, WD and Zabeti, A and Kottyan, LC and Weirauch, MT},
title = {Genetic and environmental etiology of pediatric and adult-onset multiple sclerosis.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {104234},
doi = {10.1016/j.autrev.2026.104234},
pmid = {43014635},
issn = {1873-0183},
abstract = {Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system with complex etiology shaped by both genetic susceptibility and environmental exposures. This review synthesizes classic and emerging literature to provide an integrated framework for understanding MS risk, with emphasis on gene-environment interactions and their contribution to disease. We compile a comprehensive linkage disequilibrium-expanded MS genetic risk variant set identified through genome-wide association studies, including annotation of risk alleles. We discuss insights obtained from functional genomics studies that illuminate genotype-dependent regulatory mechanisms. Environmentally, we assess evidence implicating infectious agents (most notably Epstein-Barr virus) as well as vitamin D insufficiency, obesity, smoking, heavy metal exposure, and the gut microbiome, highlighting epidemiologic associations and areas where mechanistic understanding remains limited. We highlight current knowledge on individuals with pediatric-onset MS (POMS), a population underrepresented in etiologic studies despite its distinct clinical and immunological features. We compare genetic burden, environmental exposures, and immunopathology between pediatric- and adult-onset MS, identifying shared determinants as well as age-specific risk modifiers. Finally, we propose important future directions, including improved ancestry and age-range representation, functional validation of risk loci, and the use of treatment-naïve, tissue-derived patient samples.},
}

@article {pmid43014869,
year = {2026},
author = {Lee, EC and Hirekatur, R},
title = {Gut Health and Integrative Primary Care.},
journal = {Primary care},
volume = {53},
number = {4},
pages = {625-638},
doi = {10.1016/j.pop.2026.07.011},
pmid = {43014869},
issn = {1558-299X},
mesh = {Female ; Humans ; Complementary Therapies ; *Gastrointestinal Diseases/therapy/diagnosis ; *Integrative Medicine ; *Primary Health Care/organization & administration ; },
abstract = {This article presents a case of a patient with gastrointestinal symptoms through an integrative lens. At the end of this article, primary care providers will identify relevant history to obtain, use high-yield evaluations, and develop a patient plan that maximizes lifestyle habits and integrative therapies to help patients with common gastrointestinal symptoms.},
}

Female
Humans
Complementary Therapies
*Gastrointestinal Diseases/therapy/diagnosis
*Integrative Medicine
*Primary Health Care/organization & administration

@article {pmid43014893,
year = {2026},
author = {Hua, G and Geng, L and Li, D and Zhao, Y and Gao, P and Sun, H and Yang, S and Zhao, Q and Xue, P and Liu, W},
title = {Cadmium/arsenic co-contamination drives delayed succession of root endosphere bacteria and aligns with the metal partitioning stage in maize.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {101-110},
doi = {10.1016/j.jes.2026.02.056},
pmid = {43014893},
issn = {1001-0742},
mesh = {*Zea mays/microbiology ; *Cadmium/toxicity/analysis/metabolism ; *Soil Pollutants/toxicity/analysis/metabolism ; Plant Roots/microbiology ; *Soil Microbiology ; *Arsenic/toxicity/analysis/metabolism ; Rhizosphere ; Bacteria ; },
abstract = {Root-associated microbiota have been shown to mediate cadmium (Cd) and arsenic (As) transfer from soil to crops, however, their temporal dynamics and linkage to metal accumulation in maize under different Cd-As co-contamination levels remain unclear. A field experiment was conducted with low (LS) or high (HS) Cd-As co-contamination levels to elucidate the dynamics of root-associated bacteria and metal accumulation across maize growth stages. The results revealed that while the rhizosphere community remained stable, the temporal succession of root endosphere bacteria was delayed by one growth stage under high contamination rather than merely showing a reduction in diversity. The peak diversity (Shannon) and richness (Chao) occurred at the tasselling stage (TS) in the LS condition but was delayed until the grain-filling stage (GS) in the HS condition. This delay was synchronized with a shift in metal partitioning that Cd was highly retained in roots at the TS, with the translocation factor (TF) decreasing by 33.73 %-238.61 % (HS) and 31.34 %-191.20 % (LS) compared with the other stages, while As following a similar pattern at the GS, with the TF decreasing by 36.36 %-272.24 % (HS) and 56.25 %-146.44 % (LS). This metal-specific patterning was associated with the stage-delayed enrichment of Actinobacteria. Specifically, enrichment of Streptomyces, Agromyces, and Microbacterium at the TS was linked to the inhibition of Cd translocation, whereas enrichment of Lechevalieria and Mycobacterium at the GS was corresponded to the restriction of As translocation. These findings provided a stage‑synchronized framework for microbiome‑based remediation in Cd-As co‑contaminated soils.},
}

*Zea mays/microbiology
*Cadmium/toxicity/analysis/metabolism
*Soil Pollutants/toxicity/analysis/metabolism
Plant Roots/microbiology
*Soil Microbiology
*Arsenic/toxicity/analysis/metabolism
Rhizosphere
Bacteria

@article {pmid43014940,
year = {2026},
author = {Liu, H and Luo, Y and Deng, G and Zhao, W and Chen, J and Jin, Z and Tang, N and Zhang, G},
title = {Bacterial airborne diversity in typical pharmaceutical wastewater treatment plants and preventive effect on Klebsiella pneumoniae induced pulmonary injury.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {582-594},
doi = {10.1016/j.jes.2026.04.057},
pmid = {43014940},
issn = {1001-0742},
mesh = {*Wastewater/microbiology ; Klebsiella pneumoniae/physiology ; *Waste Disposal, Fluid/methods ; *Air Microbiology ; *Lung Injury/prevention & control/microbiology ; Bacteria/classification ; Animals ; RNA, Ribosomal, 16S ; },
abstract = {Wastewater treatment plants have peculiar bioaerosol feature. However, limited research has focused on bacterial function in bioaerosols from pharmaceutical wastewater treatment plants (PWWTPs). Here, airborne bacterial communities of two PWWTPs were analyzed using culturable and 16S rRNA gene high-throughput sequencing. The results revealed the bacterial aerosols collected from the PWWTPs differed significantly owing to the treatment process. The genera Pseudocyanosarcina, Potamoosiphon and Sphingomonas were the dominant genera in the two plants. Bacillus velezensis strain PB131 (Laboratory designation) was screened based on inhibition of Klebsiella pneumoniae (Kp) in vitro and in vivo. This strain colonizes the lungs, intestines, and trachea, and its mechanism for alleviating Kp-induced inflammation was investigated through modulation of gut microbiota. Strain PB131 inhibited the maturation and release of interleukin-1β (Il-1β), interleukin-6 (Il-6), and tumor necrosis factor α (Tnf-α) in the Prevention group (1.35 ± 0.08, 1.26 ± 0.27 and 1.20 ± 0.10) compared with the Kp infection group (2.23 ± 0.21, 2.10 ± 0.18 and 1.49 ± 0.19). These change mechanisms were related to gut microbial composition and short-chain fatty acids (SCFAs) levels, such as affecting Limosilactobacillus, Duncaniella, Bifidobacterium, and butyric acid content. This study provides valuable insights from microbiome research that enable an assessment of gut colonization by probiotics. These findings could potentially lead to the use of in vitro-derived probiotics as an alternative method for preventing respiratory inflammation.},
}

*Wastewater/microbiology
Klebsiella pneumoniae/physiology
*Waste Disposal, Fluid/methods
*Air Microbiology
*Lung Injury/prevention & control/microbiology
Bacteria/classification
Animals
RNA, Ribosomal, 16S

@article {pmid43014959,
year = {2026},
author = {Huang, Y and Zhou, Q and He, M and Ma, J and Xue, L and Wu, X and Gu, W and Qin, Y and Du, G},
title = {Perfluorononanoic acid impairs intestinal barrier integrity and induces gut microbiome dysbiosis in zebrafish.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {794-803},
doi = {10.1016/j.jes.2026.04.047},
pmid = {43014959},
issn = {1001-0742},
mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced ; Intestinal Barrier Function ; *Fluorocarbons/toxicity ; *Water Pollutants, Chemical/toxicity ; Male ; },
abstract = {Perfluorononanoic acid (PFNA) is a ubiquitous persistent organic pollutant, yet its impact on gut health and associated mechanisms remains poorly understood. Here, we used multi-omics approaches to explore PFNA-induced alterations in intestinal homeostasis. Adult male zebrafish were exposed for 28 days to a series of concentrations (0, 0.1, 10 µg/L) of PFNA. Comprehensive analyses revealed that PFNA caused physical barrier damage, characterized by intestinal villus vacuolation and decreased mucin secretion. Furthermore, PFNA altered gut microbial composition by reducing beneficial bacteria and promoting opportunistic pathogens. Transcriptome analysis implicated intestinal barrier dysfunction and abnormalities in lipid and inflammatory pathways. Correspondingly, metabolomic analysis revealed significant perturbations in glycerolipid, phospholipid, and amino acid metabolism. Integrated multi-omics established strong correlations among the observed dysbiosis, altered gene expression, and metabolic disruption. Our findings demonstrate that PFNA exposure compromises intestinal barrier integrity and induces gut dysbiosis, providing crucial mechanistic insights into the PFNA toxicity and informing human health risk assessment.},
}

Animals
*Zebrafish
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/chemically induced
Intestinal Barrier Function
*Fluorocarbons/toxicity
*Water Pollutants, Chemical/toxicity
Male

@article {pmid43015024,
year = {2026},
author = {Anderson, JL and Ljótsson, B and Burton-Murray, H and West, ML and Yao, CK and Basnayake, C and Van Oudenhove, L and Biesiekierski, JR},
title = {Exclude or expose in irritable bowel syndrome study: what works for whom and how? Protocol for a randomised controlled trial of internet-delivered FODMAP diet versus exposure-based cognitive behavioural therapy.},
journal = {BMJ open},
volume = {16},
number = {11},
pages = {e126664},
pmid = {43015024},
issn = {2044-6055},
abstract = {INTRODUCTION: Irritable bowel syndrome (IBS) is a disorder of gut-brain interaction characterised by abdominal pain and altered bowel habits and is associated with reduced quality of life. Although several treatments are effective at the group level, treatment responses vary substantially between individuals, highlighting the need for personalised approaches. This trial investigates moderators and mediators of treatment response to two established IBS interventions to determine for whom treatments are most effective and how they exert their effects.

METHODS AND ANALYSIS: This parallel-group randomised controlled trial will enrol 235 adults with IBS from community, primary and tertiary care across Australia and the US. Participants will be randomised to a 12 week online fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet intervention targeting reduction of fermentable carbohydrate intake or an exposure-based cognitive behavioural therapy (E-CBT) programme targeting symptom-related avoidance behaviours, each with therapist support (dietitian or psychologist, respectively). The primary objective is to assess moderators and mediators of treatment response on gastrointestinal symptom severity, measured using the Gastrointestinal Symptom Rating Scale (GSRS-IBS), assessed weekly from baseline to week 12. Pre-specified moderators and mediators include gastrointestinal-specific anxiety and avoidance behaviour and total FODMAP intake; treatment preference will also be examined as a moderator. Treatment expectancy and credibility and therapeutic alliance will be assessed as covariates accounting for non-specific treatment effects. Secondary outcomes, assessed at baseline, post-treatment (12 weeks) and 3- and 6-month post-intervention follow-up, include IBS-specific symptom severity (measured using the IBS-Symptom Severity Scale, IBS-SSS), IBS-related quality of life, eating-related symptoms, psychological symptoms, extraintestinal symptom distress, stool frequency and consistency and gut microbiome composition and function. We will also assess gastrointestinal symptom severity by the GSRS-IBS at 3- and 6-month follow-up to assess maintenance. Linear mixed-effects models will assess treatment effects and moderation. Latent growth curve modelling and time-lagged mixed-effects models will examine mediation.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the University of Melbourne Human Research Ethics Committee (Project ID: 31186). This manuscript is based on protocol V.4.0 (06–04-26). Recruitment is ongoing. Results will be disseminated via peer-reviewed publications and presentations at scientific meetings.

TRIAL REGISTRATION NUMBER: NCT06940596.},
}

@article {pmid43015393,
year = {2026},
author = {Neves, JM and Mil-Homens, M and Martins, M and Adão, H and Gutierrez-Patricio, S and Jiménez, PN and Osman, JR and Miller, AZ and Lobo-Arteaga, J},
title = {Bivalve Gut Microbiome Responses to Sediment Characteristics and Anthropogenic Activities in Cerastoderma edule (Linnaeus, 1758).},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {43015393},
issn = {1432-184X},
support = {UI/BD/150954/2021//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; *Geologic Sediments/chemistry/microbiology/analysis ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Fungi/classification/genetics/isolation & purification ; Anthropogenic Effects ; *Microbiota ; Water Pollutants, Chemical/analysis ; Seasons ; Estuaries ; *Bivalvia/microbiology ; Ecosystem ; },
abstract = {Estuaries are dynamic ecosystems influenced by fluctuating environmental conditions and sediment-associated contamination, which may affect host-associated microbiomes. This study investigated the gut microbiome of the bivalve Cerastoderma edule across three estuarine sites differing in anthropogenic pressure. Bacterial 16S rRNA and fungal ITS metabarcoding data were integrated with sediment physicochemical parameters to assess spatial and seasonal variation in gut microbial diversity and composition. Bacterial communities showed clear differences among sites and seasons, with stronger variation in areas characterized by higher organic matter and trace metal concentrations. Fungal communities also varied among samples, although their interpretation was limited by the high proportion of unassigned ITS taxa. Multivariate analyses indicated associations between gut microbial composition and sediment parameters, including organic matter, salinity, and trace metals such as mercury (Hg), zinc (Zn), and lead (Pb). Putative bacterial functional profiles were inferred from taxonomic data using FAPROTAX, suggesting potential involvement in nitrogen, sulfur, and carbon cycling, as well as organic compound degradation. Nevertheless, it is important to note that these functional predictions should be interpreted as indicators of potential metabolic capacity rather than direct evidence of activity. Ultimately, these findings demonstrate that the C. edule gut microbiome has strong potential as a complementary tool for the assessment of estuarine environmental conditions and host-environment interactions.},
}

Animals
*Geologic Sediments/chemistry/microbiology/analysis
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Fungi/classification/genetics/isolation & purification
Anthropogenic Effects
*Microbiota
Water Pollutants, Chemical/analysis
Seasons
Estuaries
*Bivalvia/microbiology
Ecosystem

@article {pmid43015415,
year = {2026},
author = {Sun, W and Zhang, B and Wang, Y},
title = {Exploring a potential link between protein kinase C zeta and gut microbiota in cervical cancer: a hypothesis-generating study.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {},
pmid = {43015415},
issn = {2191-0855},
abstract = {Cervical cancer remains a leading cause of cancer-related death. Integrating TCGA/GTEx and GWAS, we identified PRKCZ as a risk factor (OR = 1.26, p = 0.008). PRKCZ was upregulated in tumors, and its knockdown inhibited SiHa and HeLa proliferation. Using gutMGene, we identified Escherichia coli as a microbe computationally predicted to be associated with PRKCZ based on literature-curated data. Public 16S rRNA data (45 patients vs. 30 controls) showed reduced gut microbial diversity and higher abundance of the genus Escherichia-Shigella (which includes Escherichia coli) in patients. Parallel trends of higher Escherichia-Shigella abundance and PRKCZ expression were observed in separate cohorts. Importantly, because the microbiome and transcriptomic data derive from independent, non‑paired cohorts, no direct microbiota-gene association was measured, and no causal or mechanistic relationship can be inferred. These hypothesis-generating observations suggest a hypothetical association among gut Escherichia coli, PRKCZ, and isoquercetin, warranting direct validation in paired multi‑omics cohorts and functional studies.},
}

@article {pmid43015433,
year = {2026},
author = {Kapono, C},
title = {How I balance my life as a professional surfer and a university researcher.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {43015433},
issn = {1476-4687},
}

@article {pmid43015450,
year = {2026},
author = {Jakimowicz, M and Napora-Rutkowski, Ł and Suchocki, T and Mirończuk, A and Urbanek, AK and Mielczarek, M and Brzoza, A and Kamińska-Gibas, T and Szyda, J},
title = {Does supplementation with effective microorganisms under recirculating aquaculture system conditions affect water and intestinal microbiome of common carp?.},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {43015450},
issn = {2190-3883},
support = {2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; Mistrz//Uniwersytet Przyrodniczy we Wrocławiu/ ; },
abstract = {The efficacy of effective microorganism products in aquaculture covers multiple aspects that act directly on fish, such as improving resistance to fungal, bacterial, and viral infections, reproduction, feed efficiency, and overall growth performance, or indirectly through improved water quality. In this study, the application of two commercial water and two commercial food Effective Microorganism supplements was tested under recirculating aquaculture system conditions for their effect on the water and intestinal microbiome of common carp (Cyprinus carpio), as well as on carp growth performance. Neither the dynamics of alpha diversity nor the abundance of single genera followed a pattern related to the experimental setup defined by the supplementation. However, the effects of supplementation were clearly manifested by an increase in the final weight of the fish. The most consistent alteration was a significant increase in Lactococcus abundance in the intestinal microbiome compared to that in the control group, as observed in both experimental setups. We conclude that feed supplementation with Lactococcus enhances its intestinal abundance in fish and promotes improved growth performance, likely through mechanisms involving glucose absorption and metabolism, as demonstrated in previous studies.},
}

@article {pmid43015492,
year = {2026},
author = {Sarma, V and Sarma, SK and Sarma, D and Devi, M and Kumar, D and Choudhary, N and Kondaveeti, SB and Sarma, AD},
title = {Microbiome-derived Metabolites in Anti-inflammatory Therapy: from Mechanisms to Translational Potential.},
journal = {Inflammation},
volume = {49},
number = {1},
pages = {},
pmid = {43015492},
issn = {1573-2576},
mesh = {Humans ; *Anti-Inflammatory Agents/therapeutic use/metabolism/pharmacology ; *Microbiota/physiology/drug effects ; *Inflammation/drug therapy/metabolism/microbiology ; Animals ; *Translational Research, Biomedical/methods ; Fatty Acids, Volatile/metabolism ; },
abstract = {Chronic inflammation underlies autoimmune, metabolic, cardiovascular, and neurodegenerative disorders and remains difficult to manage because current anti-inflammatory therapies often have systemic adverse effects and variable clinical efficacy. This review synthesizes evidence on microbiome-associated metabolites relevant to inflammation, including short-chain fatty acids, microbial indole derivatives, secondary bile acids, polyamines, trimethylamine N-oxide, and selected host-microbe co-metabolites. These compounds regulate host immunity through G-protein-coupled receptors, nuclear receptors, epigenetic mechanisms, inflammasome regulation, and major inflammatory signaling pathways such as NF-kappaB, MAPK, and JAK-STAT. The translational potential of direct metabolite administration, prodrug design, microbiome engineering, dietary modulation, and targeted delivery systems is discussed alongside key limitations, including low bioavailability, context-dependent activity, interindividual microbiome variation, incomplete pharmacokinetic data, and the limited number of well-controlled human trials. Overall, microbiome-associated metabolites represent promising but still evolving therapeutic candidates; their clinical use requires stronger causal evidence, standardized formulations, safety evaluation, and disease-specific validation.},
}

Humans
*Anti-Inflammatory Agents/therapeutic use/metabolism/pharmacology
*Microbiota/physiology/drug effects
*Inflammation/drug therapy/metabolism/microbiology
Animals
*Translational Research, Biomedical/methods
Fatty Acids, Volatile/metabolism

@article {pmid43015589,
year = {2026},
author = {G R, SK and Vaithilingam, M},
title = {16S rRNA gene amplicon sequencing reveals lifestyle-associated gut microbiome variation among tribal, rural, and urban populations from North Arcot regions of Tamil Nadu, India.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015589},
issn = {1471-2180},
mesh = {India ; Humans ; *RNA, Ribosomal, 16S/genetics ; Rural Population ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Adult ; Urban Population ; Phylogeny ; Middle Aged ; *Life Style ; Female ; Sequence Analysis, DNA/methods ; Young Adult ; DNA, Bacterial/genetics ; Male ; Biodiversity ; },
abstract = {BACKGROUND: The gut microbiota in humans not only supports metabolism and immune function but also influences susceptibility to various diseases. Changes in lifestyle, diet, and environment are the major factors affecting the variety and capability of gut microbes. Despite the growing interest in microbiome research, there are still only a few comparative studies of the microbiomes of tribal, rural, and urban Indian populations, especially in terms of their potential pharmacological and therapeutic benefits. The present work was focused on investigating the gut microbiota profile, diversity, and inferred functional capabilities of three different populations of Tamil Nadu, India, tribal (Mulluvadi), rural (Odugathur), and urban (Vellore)with the aim of discovering microbiota features that could have pharmacological significance.

METHODS: Fecal samples (n = 75; Mulluvadi tribal n = 25, Vellore urban n = 25, Odugathur rural n = 25; age 20-60 years) were analysed using 16S rRNA gene sequencing (V3-V4 region, Illumina MiSeq). Sequence data were processed using QIIME2 and DADA2, and taxonomic classification was performed against the SILVA 138 database. Microbial diversity was assessed using Chao1, Shannon, Simpson, and Fisher indices, while beta diversity was evaluated using BrayCurtis dissimilarity and principal coordinate analysis (PCoA). Functional profiles of microbial communities were predicted using PICRUSt2 and mapped to KEGG metabolic pathways.

RESULTS: We found distinct microbial diversity patterns to characterize the three populations. Differences in microbial diversity were observed among the three populations, with variations in both species-richness and community evenness. Across groups, major phyla were Firmicutes, Bacteroidota, Actinobacteria, and Proteobacteria. In this study, the tribal microbiome showed characteristics consistent with fiber degradation and potential short-chain fatty acid production, likely associated with Prevotella/Segatella-dominated taxa. Functional prediction of the microbiomes of the three groups suggests an abundance of carbohydrate and amino acid metabolic pathways in the tribal microbiome, and membrane transport and xenobiotic metabolism pathways predominate urban microbiome.

CONCLUSION: In summary, our study has revealed a lifestyle impact on gut microbial composition and metabolic potential differences among tribal, rural and urban populations of Tamil Nadu. The tribal microbiome showed enrichment of fiber-associated genera with predicted SCFA-related metabolic pathways. These findings are exploratory and require validation through individual-level sampling and functional analyses.},
}

India
Humans
*RNA, Ribosomal, 16S/genetics
Rural Population
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome/genetics
Adult
Urban Population
Phylogeny
Middle Aged
*Life Style
Female
Sequence Analysis, DNA/methods
Young Adult
DNA, Bacterial/genetics
Male
Biodiversity

@article {pmid43015590,
year = {2026},
author = {Sahu, S and Kaushik, SR and Chaudhary, S and Mohapatra, AK and Kupa, RU and Kapfo, W and Saha, S and Das, R and Bhalla, N and Kaur, M and Sivaji, Y and Das, B and Das, A and Khamo, V and Nanda, RK},
title = {Gut microbiome dysbiosis and associated metabolome changes in tuberculosis patients resolve partially post-therapy.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015590},
issn = {1471-2180},
support = {NER//Department of Biotechnology, Ministry of Science and Technology, India/ ; NER//Department of Biotechnology, Ministry of Science and Technology, India/ ; NER//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Feces/microbiology ; *Metabolome ; *Gastrointestinal Microbiome/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; *Tuberculosis/microbiology/drug therapy ; Antitubercular Agents/therapeutic use ; Female ; Male ; Longitudinal Studies ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Mycobacterium tuberculosis/drug effects ; },
abstract = {BACKGROUND: Mycobacterium tuberculosis (Mtb) infection in the host and subsequent treatment with anti-tuberculosis drugs impact lung pathophysiology and influence the lung and gut microbiome. Elucidating the role of the gut microbiome and its metabolites in the perturbed metabolic and immune functions observed in tuberculosis (TB) might help design corrective prebiotic and probiotic mixtures.

METHODOLOGY: In this study, fecal samples (n = 107) of drug-naïve active TB patients (ATB) and controls (other respiratory disease: NTB and healthy) from the two clinical sites were analyzed for microbiota composition (16S rRNA sequencing), metabolites (GC-TOF-MS), and their correlation. In addition, a longitudinal follow-up study was conducted to understand the dynamics of the microbiota and metabolites during anti-TB treatment in a small cohort (n = 10).

RESULTS: Gut microbiota showed site-specificity; however, an overall reduction in alpha diversity was observed in disease states compared with healthy subjects. Underrepresentation of gut commensals (Faecalibacterium, Ligilactobacillus and Romboustia) and overrepresentation of Thomasclavelia and Clostridioides were observed among active TB patients. The longitudinally followed-up ATB subjects undergoing treatment showed a time-dependent increase in beta-diversity variance. Over time, the beta diversity of follow-up subjects was almost similar to that of healthy controls. Decrease in the abundance of Streptococcus occurred after anti-TB treatment, with higher levels of opportunistic pathogens, such as Escherichia and Stenotrophomonas. Similarly, specific fecal metabolites also returned to pretreatment levels in relative abundance at later time points.

CONCLUSIONS: The gut microbiota of TB patients showed dysbiosis at the time of case presentation and partially resolved upon complete therapeutic interventions. Partial recovery of microbiota observed during treatment is also reflected in the fecal metabolome, indicating the possible use of microbiome and metabolites as adjunct therapeutics in TB.},
}

Humans
*Dysbiosis/microbiology
Feces/microbiology
*Metabolome
*Gastrointestinal Microbiome/drug effects/genetics
RNA, Ribosomal, 16S/genetics
*Tuberculosis/microbiology/drug therapy
Antitubercular Agents/therapeutic use
Female
Male
Longitudinal Studies
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Mycobacterium tuberculosis/drug effects

@article {pmid43015619,
year = {2026},
author = {Djodjeu Kamega, LC and Foko Kouam, EM and Tchabou Tientcheu, ML and Hall, LJ and Kaktcham, PM},
title = {Genomic and phenotypic assessment of functional and safety properties of Lacticaseibacillus rhamnosus PMK4 isolated from Cameroonian infant faeces.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015619},
issn = {1471-2180},
mesh = {Humans ; Cameroon ; *Lacticaseibacillus rhamnosus/genetics/isolation & purification/physiology/classification ; *Feces/microbiology ; Infant ; *Probiotics ; Genome, Bacterial ; Phenotype ; Whole Genome Sequencing ; Bacterial Adhesion ; Genomics ; },
abstract = {The gut microbiota is a complex community of microorganisms that plays a crucial role in maintaining short- and long-term health. However, a perturbed microbial ecosystem is associated with a range of diseases, including increased risk of infections. Probiotic-based strategies may help restore microbiome function, but candidate strains require robust functional and safety evaluation. Here, we performed integrated genomic and phenotypic characterisation of beneficial properties of Lacticaseibacillus rhamnosus PMK4, isolated from the stool of a healthy Cameroonian infant. Whole-genome sequencing and comparative pangenomic analysis against 13 L. rhamnosus genomes were used to infer functional potential, with in silico safety screening conducted using ResFinder, CARD and VFDB. Beneficial-relevant phenotypes were assessed through tolerance to simulated gastrointestinal conditions, adhesion-associated traits (hydrophobicity, aggregation), antimicrobial activity, nutrients utilisation profiling and safety-related assays. The L. rhamnosus PMK4 genome (2,935,039 bp), contains strain-specific loci predicted to support acid stress tolerance and epithelial adhesion. Functional annotation indicated the presence of genetic potential for carbohydrate metabolism, stress response, adhesion-related functions, and biosynthesis of secondary metabolites including acids, terpenes and vitamins. No acquired antibiotic resistance determinants or virulence genes were detected. Consistent with genomic predictions, PMK4 showed high survival under simulated gastrointestinal conditions, strong auto-aggregation capacity, moderate hydrophobicity and co-aggregation, and broad antagonistic activity against a range of enteropathogens. The strain also utilised a wide range of substrates, including complex carbohydrates and proteins, suggesting metabolic versatility relevant to microbe-microbe and microbe-host interactions in the gut. Together, these data support L. rhamnosus PMK4 as a promising indigenous probiotic candidate with a favourable safety profile and functional potential.},
}

Humans
Cameroon
*Lacticaseibacillus rhamnosus/genetics/isolation & purification/physiology/classification
*Feces/microbiology
Infant
*Probiotics
Genome, Bacterial
Phenotype
Whole Genome Sequencing
Bacterial Adhesion
Genomics

@article {pmid43015622,
year = {2026},
author = {Zhang, P and Jiang, L and Ge, C and Yang, J and Shi, Z and Liang, X and Fan, Z},
title = {The gut-inflammation-hearing axis in diabetic patients aged 30-55: exploring microbiome-mediated pathways to auditory complications.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015622},
issn = {1471-2180},
support = {XY21BS36//Boshi Foundation of Heze University/ ; ZR2023QC302//Natural Science Foundation of Shandong Province/ ; ZR2021QB188//Natural Science Foundation of Shandong Province/ ; },
mesh = {Humans ; Middle Aged ; Adult ; Male ; Female ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/complications/microbiology ; Biomarkers/blood ; Cross-Sectional Studies ; *Dysbiosis/microbiology ; *Inflammation/microbiology ; RNA, Ribosomal, 16S/genetics ; *Hearing Loss/microbiology/etiology ; Lipopolysaccharide-Binding Protein ; Bacteria/classification/genetics/isolation & purification ; Tumor Necrosis Factor-alpha/blood ; Acute-Phase Proteins ; Interleukin-6/blood ; Carrier Proteins/blood ; },
abstract = {BACKGROUND/OBJECTIVES: Hearing impairment is an underrecognized yet prevalent complication of type 2 diabetes mellitus (T2DM), but the underlying mechanisms remain poorly understood. This study investigated whether gut microbiota dysbiosis contributes to diabetic hearing loss through systemic inflammatory pathways, and evaluated the potential of microbiota-inflammation biomarkers for early risk identification.

METHODS: We conducted a cross-sectional study of 100 T2DM patients aged 30-55 years. Hearing function was assessed using pure-tone audiometry. Gut microbiota composition was analyzed by 16 S rRNA gene sequencing. Plasma inflammatory biomarkers including tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), high-sensitivity C-reactive protein (hs-CRP), and lipopolysaccharide-binding protein (LBP) were measured by ELISA. Mediation analyses with bootstrapping (5,000 resamples) examined whether inflammatory markers mediated the relationship between gut dysbiosis and hearing impairment. Receiver operating characteristic curves evaluated biomarker discriminatory ability.

RESULTS: Hearing impairment was present in 43% of participants. Patients with hearing impairment exhibited significant gut dysbiosis characterized by depletion of anti-inflammatory bacteria (Faecalibacterium: 6.2% vs. 9.8%, P < 0.001; Roseburia; Akkermansia) and enrichment of pro-inflammatory taxa (Escherichia-Shigella: 3.8% vs. 1.4%, P < 0.001; Klebsiella; Desulfovibrio). Inflammatory markers were significantly elevated, particularly LBP (18.6 vs. 12.4 µg/mL, P < 0.001), TNF-α (4.82 vs. 3.21 pg/mL, P < 0.001), and IL-6 (5.67 vs. 3.45 pg/mL, P < 0.001). Mediation analyses revealed that inflammatory pathways, predominantly through LBP-mediated gut barrier dysfunction, accounted for 48.7-56.3% of the total effect of microbiota alterations on hearing impairment (all P < 0.001). An integrated biomarker panel combining microbial taxa (Faecalibacterium, Escherichia-Shigella, Shannon diversity) and LBP achieved excellent discrimination for identifying hearing impairment (AUC = 0.921, 95% CI: 0.869-0.973; sensitivity 88.4%, specificity 87.7%).

CONCLUSIONS: This study establishes a novel gut-inflammation-hearing axis in type 2 diabetes, wherein microbiota dysbiosis characterized by loss of beneficial bacteria and expansion of pathogenic taxa promotes hearing impairment through systemic inflammation mediated by intestinal barrier dysfunction and metabolic endotoxemia. These findings identify gut barrier integrity and associated inflammatory pathways as potential therapeutic targets, and demonstrate that integrated microbiota-inflammation biomarker panels can serve as non-invasive tools for early identification of hearing impairment risk in diabetic patients, enabling targeted preventive interventions.},
}

Humans
Middle Aged
Adult
Male
Female
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 2/complications/microbiology
Biomarkers/blood
Cross-Sectional Studies
*Dysbiosis/microbiology
*Inflammation/microbiology
RNA, Ribosomal, 16S/genetics
*Hearing Loss/microbiology/etiology
Lipopolysaccharide-Binding Protein
Bacteria/classification/genetics/isolation & purification
Tumor Necrosis Factor-alpha/blood
Acute-Phase Proteins
Interleukin-6/blood
Carrier Proteins/blood

@article {pmid43015632,
year = {2026},
author = {Guo, Y and Zhang, J and Zhang, B and Yang, M and Zhao, J and Chen, G and Shi, G},
title = {Longitudinal gut microbiome dynamics in neurosurgical ICU patients: Enterococcus expansion as a feature of microbial restructuring.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015632},
issn = {1471-2180},
support = {FYD202607//2026 Incubation Fund (Category D), Beijing Tiantan Hospital/ ; L2602077//Beijing Natural Science Foundation/ ; 82000510//National Natural Science Foundation of China/ ; ZYLX202109//Beijing Hospital Authority "Sailing Plan" Key Medical Specialty Program/ ; },
mesh = {Humans ; *Enterococcus/genetics/isolation & purification/classification ; *Intensive Care Units ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Critical Illness ; },
abstract = {BACKGROUND: Gut microbiota alterations are commonly observed in critical illness, but their temporal dynamics in neurosurgical ICU patients remain insufficiently characterized. This study aimed to describe postoperative microbial trajectories and their clinical context during ICU stay.

METHODS: We conducted a longitudinal study of 39 postoperative neurosurgical ICU patients, with 101 rectal swab samples collected on ICU Days 1, 7, and 14. Microbiota profiles were generated using 16S rRNA sequencing. Temporal shifts and configurations were analyzed using diversity analyses, PERMANOVA, and OTU-level clustering. Clinical features associated with Enterococcus (OTU502) abundance were examined using regression models, and microbiota-clinical relationships were further explored using redundancy and variance partitioning analyses.

RESULTS: Patients were stratified into short-stay (< 14 days) and long-stay (≥ 14 days) groups. Alpha diversity showed a mild, non-significant decline by Day 7 with a slight increase at Day 14 in long-stay patients, while beta diversity demonstrated significant temporal restructuring. Genus-level analyses revealed stay-dependent changes: short-stay patients showed early loss of anaerobic genera and enrichment of Enterococcus by Day 7, whereas long-stay patients exhibited persistent anaerobe depletion and later emergence of Enterococcus. OTU clustering identified two profiles dominated by Enterococcus (OTU502) or Escherichia-Shigella (OTU967). Higher OTU502 abundance at Day 7 was more frequently observed in patients with greater illness severity and lower GCS scores. Prolonged probiotic use showed a non-significant trend toward a lower likelihood of high OTU502 abundance. Measured clinical variables accounted for a limited proportion of observed microbial variance (3-7%).

CONCLUSIONS: Neurosurgical ICU patients displayed time-stratified microbial trajectories. Enterococcus (OTU502) enrichment represents a consistent feature of microbiota restructuring during ICU stay. These findings provide a descriptive framework for understanding microbiome dynamics in neurosurgical ICU patients.

TRIAL REGISTRATION: Chinese Clinical Trial Registry (ChiCTR2000031760). Registered on 9 April 2020.},
}

Humans
*Enterococcus/genetics/isolation & purification/classification
*Intensive Care Units
Longitudinal Studies
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Female
Male
Middle Aged
Aged
*Bacteria/classification/genetics/isolation & purification
Critical Illness

@article {pmid43015659,
year = {2026},
author = {Chen, Y and Huang, C and Qin, Y and Jian, Y and Li, L and Li, J and Meng, Z and Kang, M},
title = {Microbial dysbiosis and treatment-related gastrointestinal adverse events in locoregionally advanced nasopharyngeal carcinoma: an exploratory study of the oral and gut microbiome.},
journal = {BMC cancer},
volume = {26},
number = {1},
pages = {},
pmid = {43015659},
issn = {1471-2407},
support = {2020//Guangxi Medical University First Affiliated Hospital Specialised and Innovative Teams Project/ ; 2020//the Second Batch of Guangxi High-Level Mid-Career and Young Academic Backbone Projects/ ; 2022//the Guangxi Medical University High-Level Innovative Team and Xinghu Scholars Programme/ ; 2022//Key Research Project of the CSCO/ ; 2025//the Guangxi Medical University Young Leading Talent Programme/ ; },
mesh = {Humans ; Female ; Male ; *Dysbiosis/microbiology/etiology ; *Nasopharyngeal Carcinoma/therapy/microbiology/pathology ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Nasopharyngeal Neoplasms/therapy/microbiology/pathology ; Adult ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Diseases/etiology/microbiology ; *Mouth/microbiology ; Aged ; Feces/microbiology ; },
abstract = {BACKGROUND: Gastrointestinal adverse events are frequent during treatment for locoregionally advanced nasopharyngeal carcinoma (LA-NPC) and can impair nutritional status and treatment tolerance. Radiotherapy and chemotherapy may disrupt microbial communities, but whether oral and gut microbiota are associated with treatment-related gastrointestinal adverse events remains unclear.

MATERIALS AND METHODS: Oral swab and stool samples from 80 patients with LA-NPC were analyzed using 16S rRNA gene sequencing. Associations between treatment-related gastrointestinal adverse events and oral microbial composition were evaluated, together with analyses of microbial functions and gut microbial profiles. Oral microbiota features were then used to develop machine learning models for distinguishing patients with gastrointestinal adverse events.

RESULTS: Among 80 patients with LA-NPC, nausea, vomiting, diarrhea, and constipation occurred in 72.5%, 51.3%, 46.3%, and 67.5%, respectively. Oral microbiota analysis showed enrichment of Alloprevotella, Fusobacterium, and Campylobacter in patients with gastrointestinal adverse events or a high symptom burden, whereas Rothia and Streptococcus were enriched in those without events or with a low burden. Predicted oral microbial functions involved propanoate metabolism, lipoic acid metabolism, retinol metabolism, glycan degradation, sphingolipid metabolism, calcium signaling, and lipopolysaccharide biosynthesis. Alterations in specific gut genera, including Helicobacter, Parasutterella, and Anaerotruncus, were also observed.

CONCLUSIONS: This study identified oral and gut microbial features associated with treatment-related gastrointestinal adverse events in patients with LA-NPC. Oral microbial features showed potential value for classifying gastrointestinal adverse event status during treatment.},
}

Humans
Female
Male
*Dysbiosis/microbiology/etiology
*Nasopharyngeal Carcinoma/therapy/microbiology/pathology
Middle Aged
*Gastrointestinal Microbiome/drug effects
*Nasopharyngeal Neoplasms/therapy/microbiology/pathology
Adult
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Diseases/etiology/microbiology
*Mouth/microbiology
Aged
Feces/microbiology

@article {pmid43015841,
year = {2026},
author = {Sun, J and Song, S and Luo, S and Fan, Q and Li, X and Liu, H and Wu, G},
title = {The intratumoral microbiome as an emerging hub in cancer pathogenesis and precision oncology.},
journal = {Molecular cancer},
volume = {25},
number = {1},
pages = {},
pmid = {43015841},
issn = {1476-4598},
mesh = {Humans ; *Microbiota ; *Neoplasms/etiology/microbiology/pathology/metabolism/therapy ; Tumor Microenvironment/immunology ; Animals ; *Precision Medicine/methods ; Biomarkers, Tumor ; },
abstract = {Over the past decade, the number of microbial communities identified within tumors has increased by 400%. Notably, the intratumoral microbiome, which includes bacteria, fungi, viruses, and other microorganisms within tumor tissues, was first discovered more than a century ago. Based on the updated framework of cancer characteristics, we propose that the immune microenvironment is a fundamental and variable microbial feature in cancer. Numerous studies have demonstrated that the intratumoral microbiome constitutes a critical component of the tumor microenvironment. However, due to its low biomass, characterizing its functional mechanisms remains a significant challenge. To summarize current research on the intratumoral microbiome in oncology, we first examine its establishment, homeostasis, and heterogeneity across different cancer types, followed by a comprehensive exploration of its multifaceted roles in tumor initiation and progression. Furthermore, we discuss the critical implications of the intratumoral microbiome in cancer biomarkers, antitumor therapies, and novel microbe-based anticancer strategies. In summary, this review highlights the intratumoral microbiome as an emerging therapeutic target, offering new perspectives for deciphering the complex mechanisms of cancer.},
}

Humans
*Microbiota
*Neoplasms/etiology/microbiology/pathology/metabolism/therapy
Tumor Microenvironment/immunology
Animals
*Precision Medicine/methods
Biomarkers, Tumor

@article {pmid43015880,
year = {2026},
author = {Schrieke, H and Trouche, B and Kerrigan, D and Pondeville, E and Reveillaud, J},
title = {Optimizing bacterial enrichment procedures to improve mosquito midgut microbiome research.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {43015880},
issn = {2524-4671},
support = {MC_UU_00034/8/MRC_/Medical Research Council/United Kingdom ; 948135/ERC_/European Research Council/International ; },
abstract = {Mosquitoes are major vectors of infectious diseases, with their midgut microbiota playing a crucial role in host development, reproduction, and pathogen interactions. However, characterizing midgut microbial communities remains challenging because host DNA often dominates metagenomic libraries, reducing the resolution of bacterial community profiling and hindering the recovery of microbial genomes. To evaluate strategies for bacterial DNA enrichment in this context, we compared three DNA extraction protocols applied to pooled Aedes aegypti midguts: (i) the QIAGEN DNeasy Blood and Tissue kit without filtration (DNeasy NF), (ii) the same kit preceded by a 5 μm filtration step to reduce eukaryotic material (DNeasy F), and (iii) the QIAGEN QIAamp Microbiome kit, which combines differential host cell lysis and enzymatic DNA depletion. Each method was assessed using qPCR-based quantification of bacterial and host DNA, SSU rRNA-based taxonomic profiling of metagenomic reads, and Metagenome-Assembled Genomes (MAGs) reconstruction using advanced binning approaches. Our results show that while the Microbiome kit provided the highest bacterial enrichment and captured a large fraction (> 85%) of the bacterial taxa detected with the other kits, it yielded a higher relative abundance of Gammaproteobacteria. This occurred without a loss of overall diversity, suggesting improved recovery of microbial taxa rather than a compositional bias. The filtration step associated with the DNeasy kit significantly reduced host DNA but also lowered bacterial material, allowing MAG reconstruction, though less efficiently than the Microbiome kit. Despite this, the DNeasy methods allowed recovering a broader range of bacterial phyla with a more even distribution across taxa, while each extraction method also detected a unique set of NTUs. Overall, a combination of DNA extraction methods may be necessary to optimize microbiome analysis in mosquito midguts, facilitating a more comprehensive understanding of microbial diversity and its potential applications in vector control strategies.},
}

@article {pmid43015910,
year = {2026},
author = {Weerasingha, S and Yan, A and Butcher, J and Mack, DR and Stintzi, A},
title = {Relative abundance of a gut-derived Lancefieldella parvula strain is associated with severe inflammation in IBD.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {43015910},
issn = {1757-4749},
support = {OGI-149//Genome Canada and the Ontario Genomics Institute/ ; ECD-144627/CAPMC/CIHR/Canada ; Project 13440//Ontario Ministry of Economic Development and Innovation/ ; },
abstract = {BACKGROUND: Lancefieldella parvula (previously known as Atopobium parvulum) has been associated with inflammatory bowel disease (IBD); however, prior in vivo studies relied on an oral-derived reference strain rather than intestinal clinical isolates, limiting interpretation of its role in gut inflammation. To address this gap, we isolated a clinical strain of L. parvula (designated L. parvula TI19E08) from a mucosal luminal aspirate of an ulcerative colitis (UC) participant. We developed a strain-specific quantitative PCR assay to quantify its abundance across anatomical sites in treatment-naïve pediatric IBD participant (UC and Crohn's disease (CD)) and examined its relationship with site-specific endoscopic inflammation severity.

RESULTS: We demonstrated that the relative abundance of L. parvula TI19E08 increased with increasing local inflammation severity. In UC, both strain-specific and total L. parvula levels were strongly correlated with inflammation severity, particularly in the proximal colon. In CD patients, strain-level associations were most pronounced in the terminal ileum, which is consistent with the disease distribution.

CONCLUSION: This study characterizes an intestinal L. parvula isolate and demonstrates that strain-level expansion correlates with disease severity across IBD subtypes and anatomical regions. These findings identify L. parvula TI19E08 as a candidate mucosal marker of inflammation severity in IBD patients.},
}

@article {pmid43015979,
year = {2026},
author = {Avnet, S and D'Amico, F and Falzetti, L and Di Pompo, G and Pasquarelli, A and Longhi, A and Errani, C and Brigidi, P and Turroni, S and Baldini, N},
title = {Association of Gut Microbiome Dynamics With Systemic Inflammation and Disease-Free Survival in Osteosarcoma Patients.},
journal = {Cancer medicine},
volume = {15},
number = {11},
pages = {},
pmid = {43015979},
issn = {2045-7634},
support = {RF-2019-12368819//Ministero della Salute/ ; },
mesh = {Humans ; *Osteosarcoma/microbiology/mortality/drug therapy/pathology ; Female ; Male ; *Gastrointestinal Microbiome ; *Inflammation/microbiology ; *Bone Neoplasms/microbiology/mortality/drug therapy ; Adolescent ; Child ; Disease-Free Survival ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {Gut microbiota (GM) is increasingly recognised as a key modulator of cancer development, progression, and treatment response. However, clinical studies remain limited, especially in osteosarcoma (OS), the most common bone cancer in children and adolescents. In this study, we analysed GM diversity, composition, and predicted function in a small OS cohort (n = 18) using 16S rRNA gene sequencing of stool samples collected at diagnosis, during chemotherapy, and post-treatment. Microbial profiles were compared to healthy controls. Alpha diversity was assessed via ASVs, Shannon, inverse Simpson, and Faith's index; beta diversity via Bray-Curtis and UniFrac distances. We examined associations between GM profiles and clinical variables (age, gender, BMI, tumour volume, outcome) and systemic inflammation (e.g., C-reactive protein, CRP) using PERMANOVA, LEfSe, and Kaplan-Meier analysis. At diagnosis, OS patients showed reduced diversity and a distinct GM signature-depletion of anti-inflammatory genera (Blautia, Faecalibacterium, Roseburia) and enrichment of potentially pro-tumorigenic taxa (Collinsella, Streptococcus), which correlated with elevated CRP. Baseline GM composition stratified patients by long-term outcome, with specific taxa and predicted pathways linked to event-free survival. Chemotherapy induced transient dysbiosis, notably affecting Lactobacillus and Enterococcus, with partial recovery post-treatment. This is the first study to track GM alterations in OS patients across the disease course, extending current knowledge beyond preclinical models. As one of the few longitudinal microbiota studies in oncology, it highlights GM's potential as a biomarker, shedding light on the mechanisms underlying OS pathogenesis, though findings require validation in larger cohorts.},
}

Humans
*Osteosarcoma/microbiology/mortality/drug therapy/pathology
Female
Male
*Gastrointestinal Microbiome
*Inflammation/microbiology
*Bone Neoplasms/microbiology/mortality/drug therapy
Adolescent
Child
Disease-Free Survival
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid43016293,
year = {2026},
author = {Negi, A and Borah, A and Chen, JY},
title = {Modulation of the teleost gut-microbiome-immunity axis in Nile tilapia Oreochromis niloticus following intestinal delivery of a microencapsulated deep-sea Lactococcus lactis strain.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag279},
pmid = {43016293},
issn = {1365-2672},
abstract = {AIMS: This study investigated the applied biotechnological delivery, viable intestinal recovery, and associated mucosal microbiome and transcriptomic profiles of a deep-sea bacterial isolate, Lactococcus lactis L25_4, within the freshwater landscape of Nile tilapia (Oreochromis niloticus). The objective was to decode how this marine-derived isolate influence host responses along the teleost gut-microbiome-immunity axis to stabilize mucosal environments.

METHODS AND RESULTS: To ensure gastric survival, L. lactis L25_4 was microencapsulated using a double-layer chitosan-alginate (C/A)2 coating. While uncoated bacteria failed to survive transit, the microencapsulated strain achieved robust colonization (106 CFU/g midgut; 107 CFU/g hindgut). Following a 30-day feeding trial, PacBio Full-Length 16S sequencing revealed that probiotic administration structurally overhauled the gut ecosystem, introducing 661 unique taxonomic features and expanding beneficial genera (Lactobacillus, Akkermansia, Bacillus). Host transcriptomic profiling identified 2,411 differentially expressed genes. Major upregulation centered on epithelial barrier reinforcement (Zonadhesin-like, Integrin α2) and cellular energy optimization via an 8.51 log2FC increase in the creatine synthesis enzyme Gatm. Crucially, the probiotic profoundly suppressed systemic inflammatory markers, notably Serum Amyloid P-component (-9.28 log2FC) and IL-17A, alongside downregulating MHC class II pathways.

CONCLUSIONS: Integrative analysis suggests that L. lactis L25_4 facilitates a physiological trade-off, where a reinforced physical mucosal barrier allows the freshwater host to downregulate energetically expensive immune responses in favor of reduced inflammatory gene expression. Encapsulated deep-sea bacterium can trigger cross-ecosystem homeostatic recalibration, providing a robust framework for microbiota-driven modulation along the vertebrate gut-microbiome-immunity axis.},
}

@article {pmid43016307,
year = {2026},
author = {Li, J and Duplouy, A and Sun, L},
title = {Meta2Data: Automated data processing for large scale microbiome data re-analysis.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag828},
pmid = {43016307},
issn = {1367-4811},
abstract = {UNLABELLED: Meta2Data is a modular, largely automated pipeline implemented in Python and Bash for the retrieval, standardization, and processing of public microbiome sequencing data. It retrieves metadata from major public repositories, including INSDC and CNCB, using user-provided keywords or BioProject/BioSample identifiers. Retrieved metadata are standardized using a synonym dictionary and then subjected to manual curation. Based on the curated metadata, Meta2Data downloads the corresponding raw sequencing data and processes them using standardized workflows based on DADA2 or VSEARCH. The pipeline supports both single- and multiple-target-region datasets and produces integrated feature tables, taxonomic assignments, and phylogenetic trees for downstream microbial community analyses.

AVAILABILITY: Meta2Data is freely available at https://github.com/LinyangSun/Meta2Data and archived on Zenodo at https://doi.org/10.5281/zenodo.20670433.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid43016444,
year = {2026},
author = {Ji, B},
title = {Microalgal-bacterial granular sludge: bridging the gap between laboratory discovery and engineering reality.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1967626},
pmid = {43016444},
issn = {1664-302X},
abstract = {Microalgal-bacterial granular sludge (MBGS) has been extensively studied as a promising process for energy-efficient and carbon-neutral wastewater treatment. The self-sustaining synergy of this process has been validated under laboratory conditions, and CO2 supplementation has been shown to push the system toward carbon-negative operation. However, the technology remains largely confined to laboratory benchtops, with most studies conducted under constant conditions using synthetic wastewater. Existing reviews have mainly summarized performance or individual operational factors, but have not translated these findings into a coherent engineering framework for scalable deployment. Based on a comprehensive synthesis of past review articles and experimental studies, this Perspective proposes seven testable and, where possible, quantifiable engineering perspectives: dynamic diel carbon management for net greenhouse gas removal, active microbiome engineering for targeted pollutant degradation, multi-layer stacked photobioreactors with integrated light-guide systems, self-cleaning reactor walls to overcome biofouling, integrated design strategies for simultaneous shear delivery and light utilization in a single reactor, hydrocyclone-based physical selection for long-term stability, and tiered biorefinery with integrated life-cycle assessment. The key advance is not the individual concepts themselves, but their integration into a coordinated, hypothesis-driven framework that shifts the focus from laboratory feasibility to scalable engineering implementation. These perspectives are grounded in established knowledge and offered as testable hypotheses to guide the next generation of research and development toward full-scale deployment.},
}

@article {pmid43016472,
year = {2026},
author = {Amorin de Hegedus, R and Panke-Buisse, K and Deiss, TC and McClure, JC},
title = {Impact of rumen microbiome sample handling and extraction procedures on downstream long-read sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1907783},
pmid = {43016472},
issn = {2235-2988},
mesh = {Animals ; *Rumen/microbiology ; Cattle ; *Specimen Handling/methods ; DNA, Bacterial/isolation & purification/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Female ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; },
abstract = {The rumen microbiome is a complex microbial ecosystem central to ruminant nutrition and productivity. Long-read sequencing technologies, such as Oxford Nanopore, have greatly improved resolution of strain-level diversity and enabled assembly of near-complete genomes, but these benefits depend on the integrity and purity of input DNA, which can be affected by sample preservation and extraction methods. This study evaluated multiple DNA extraction protocols to best maximize high-molecular-weight DNA recovery for long-read sequencing and whether flash freezing or freezing and thawing samples biased read length, microbial composition, or the recovery of different taxa. We also used simulated datasets to assess how read length influences taxonomic classification accuracy. Rumen fluid samples of equal volume from four lactating Holstein cows were preserved using two different methods: 1. Pelleting 1 ml of rumen fluid then flash freezing; and 2. bulk freezing 15ml aliquots, thawing, then pelleting 1 ml of rumen fluid. DNA was extracted using four modified Zymo Quick-DNA HMW MagBead protocols (0BB, 3BB, DDZ, PREC) incorporating different lysis and purification strategies, then sequenced on Oxford Nanopore PromethION flow cells. Read length, yield, and microbial composition were analyzed using nonparametric statistics, while synthetic long-read datasets (400-7600 bp) generated with Nano Sim evaluated classification accuracy with Kaiju. The precipitation method produced the highest DNA yields and maintained fragment integrity, whereas bead-based methods yielded less DNA due to high-molecular-weight DNA-selective binding. Preservation of DNA quality was identified in FF over FT samples with longer reads and higher archaeal and Gram-positive abundances. Read lengths were reduced in FT samples for both Gram-positive and Gram-negative taxa, with Gram-negative bacteria showing the greatest loss. Simulations confirmed that longer reads improve taxonomic classification, underscoring the need to optimize upstream protocols for high-resolution rumen microbiome profiling.},
}

Animals
*Rumen/microbiology
Cattle
*Specimen Handling/methods
DNA, Bacterial/isolation & purification/genetics
Sequence Analysis, DNA/methods
Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Female
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics

@article {pmid43016562,
year = {2026},
author = {Morampudi, V},
title = {Editorial: Advancing enteric disease treatments: probiotics and antimicrobial strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {2023428},
pmid = {43016562},
issn = {1664-3224},
}

@article {pmid43016569,
year = {2026},
author = {Mei, Y and Shi, L and He, S and Liu, C and Liu, M and Hou, Y},
title = {Reduced classical probiotic-associated butyrate biosynthetic potential predicts early primary resistance to anti-PD-1 therapy in advanced non-small cell lung cancer: a shotgun metagenomic study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1975315},
pmid = {43016569},
issn = {2235-2988},
mesh = {Humans ; *Probiotics ; *Butyrates/metabolism ; Metagenomics ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology ; *Lung Neoplasms/drug therapy/microbiology ; Female ; *Drug Resistance, Neoplasm ; Feces/microbiology ; Microbiota ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Male ; Coenzyme A-Transferases/genetics ; Metagenome ; },
abstract = {BACKGROUND: Early primary resistance to anti-PD-1 therapy is common in advanced non-small cell lung cancer (NSCLC). Existing microbiome biomarkers largely rely on individual species and lack stability across populations.

OBJECTIVE: The aim of this study was to construct the classical probiotic-butyrate axis score (PBAS), perform external validation, and evaluate its value for risk stratification of 90-day early primary resistance and PFS.

METHODS: This study adopted a dual-cohort, patient-level secondary analysis design and reanalyzed pretreatment fecal shotgun metagenomic data from two public cohorts, including 70 and 40 patients in the discovery and external validation cohorts, respectively. An equally weighted PBAS was constructed based on predefined classical probiotic-associated taxa and the butyryl-CoA:acetate CoA-transferase (but) and the butyrate kinase (buk) genes. ANCOM-BC2 was used for differential analysis, Firth logistic regression for association analysis of early primary resistance, 2,000 patient-level bootstrap resampling for internal validation, and Cox proportional hazards models for PFS analysis.

RESULTS: Early primary resistance occurred in 41/70 and 23/40 patients in the two cohorts, respectively. Classical probiotic-associated taxa, the butyrate functional subscore, and PBAS were lower in the resistant group than in the nonresistant group, whereas buk and Akkermansia muciniphila showed no significant differences. After adjustment for age, sex, and BMI, acetyl-CoA pathway potential was also reduced. For each 1-SD increase in PBAS, the OR for early primary resistance was 0.39 and 0.37 after adjustment for clinical variables. The bootstrap-corrected area under the receiver operating characteristic curve (AUC) was 0.733, and the external validation AUC was 0.726 (95% CI: 0.559-0.894). Increased PBAS was associated with a lower risk of progression or death, with HRs of 0.54 and 0.61 in the two cohorts, respectively (both p < 0.001).

CONCLUSION: Combined reductions in pretreatment classical probiotic-associated ecology and butyrate biosynthetic potential indicate a high risk of early primary resistance to anti-PD-1 therapy in advanced NSCLC and support PBAS as an exploratory outcome risk marker for cross-cohort risk stratification among patients receiving anti-PD-1 therapy, without establishing treatment-specific predictive value.},
}

Humans
*Probiotics
*Butyrates/metabolism
Metagenomics
*Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology
*Lung Neoplasms/drug therapy/microbiology
Female
*Drug Resistance, Neoplasm
Feces/microbiology
Microbiota
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Male
Coenzyme A-Transferases/genetics
Metagenome

@article {pmid43016601,
year = {2026},
author = {Zai, K},
title = {The bidirectional interface between oral drug and the gut microbiome: Implications for drug delivery.},
journal = {Pharmaceutical science advances},
volume = {4},
number = {},
pages = {100112},
pmid = {43016601},
issn = {2773-2169},
abstract = {Oral administration remains the preferred route for systemic therapy, yet achieving consistent drug exposure is often hindered by interindividual variability. The gut microbiome is increasingly recognized as a key determinant in this variability, capable of transforming, inactivating, or degrading drugs through microbial enzymatic activity. Conversely, advanced oral delivery systems, comprising polymeric matrices, lipid vesicles, hydrogels, and nanocarriers, can reshape microbial composition and function, either unintentionally or as part of a deliberate formulation strategy. This review examines the bidirectional interactions between oral drug delivery systems and the gut microbiome, emphasizing their implications for drug exposure, therapeutic predictability, and safety. We discuss delivery system-microbe interactions that govern drug stability, transport, and activation, alongside emerging microbiome-responsive formulation designs that leverage microbial cues for site-specific release. Advanced experimental and analytical tools, including gut-on-chip platforms, humanized and gnotobiotic animal models, and integrated pharma-co-microbiomics approaches, are highlighted as enablers of rational formulation development. Finally, we propose a formulation-oriented framework for microbiome-aware oral drug delivery, outlining strategies to protect drugs from microbial degradation, harness microbial metabolism, or reshape the microbiome to support precision and safer therapeutics.},
}

@article {pmid43016668,
year = {2026},
author = {Rodrigues, JT and Batista, ACS and Lima, JPMS and De Magalhães, MTQ},
title = {Evolutionary divergence of uric acid catabolic enzymes: structure-function constraints and genomic innovations across taxa.},
journal = {Biophysical reviews},
volume = {18},
number = {5},
pages = {1189-1211},
pmid = {43016668},
issn = {1867-2450},
abstract = {Uric acid degradation is a model for understanding how gene duplication, loss, and functional divergence drive metabolic evolution. In hominoids and uricotelic animals, uric acid is the terminal purine catabolite, whereas most other taxa further degrade it to allantoin and beyond. Comparative genomics and structural analyses reveal recurrent duplication and repurposing of key enzymes. 5-Hydroxyisourate hydrolase (HIUase) and transthyretin (TTR) share a common ancestral hydrolase, later diverging through neofunctionalization, while independent gene fusions reshaped the pathway, notably the gene fusion of Urah (HIUase) and Urad (2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, or OHCUd) into single-chain allantoin synthases in plants, diatoms, and bacteria. Elastic network modeling this gene fusion shows uncorrelated motions between the catalytic domains, suggesting its advantage stems from fixed stoichiometry and spatial proximity rather than conformational coupling. Further divergence is seen in enzyme families with complementary substrate specificities, and gene clustering in bacteria and yeast reflects regulatory optimization under nitrogen limitation, paralleling the ureide pathway in legumes. In hominoids, pseudogenization of urate oxidase relaxed constraints on downstream enzymes, elevating serum uric acid, an ancestral adaptation now linked to hyperuricemia. Gut microbiome-mediated degradation and links between Urad variants and cancer risk underscore the pathway's continuing relevance. Mammalian Urad orthologs show strong sequence conservation. Molecular modeling of the human ortholog demonstrated a conserved fold, consistent with a predominantly α-helical secondary structure content supported by circular dichroism, whereas kinetic characterization revealed the absence of detectable catalytic activity. Building on these principles, evolution-guided protein engineering achieved partial functional interconversion between transthyretins and HIUases without disrupting the ancestral scaffold, revealing purine catabolism's plasticity as a model for enzyme innovation and the metabolism-disease-protein design interface.},
}