@article {pmid41959837,
year = {2026},
author = {Irajizad, E and Fahrmann, JF and Katayama, H and Strati, P and Nair, R and Chihara, D and Ahmed, S and Iyer, SP and Locke, FL and Davila, M and Flowers, CR and Shpall, E and Jenq, R and Neelapu, SS and Hanash, S and Westin, J and Jain, MD and John, TM and Saini, NY},
title = {Pre-infusion plasma proteomics identifies an endothelial-immune priming signature predictive of severe cytokine release syndrome and neurotoxicity following CAR T-cell therapy in relapsed/refractory lymphoma.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.29.26349664},
pmid = {41959837},
abstract = {BACKGROUND: Severe cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) remain frequent, life-threatening complications of CD19 chimeric antigen receptor (CAR) T-cell therapy and constrain its safety, scalability, and outpatient adoption. Existing predictive models lack sufficient external validation for routine clinical use, and pre-infusion biomarkers that capture host susceptibility before infusion are urgently needed.

METHODS: We applied unbiased mass-spectrometry-based proteomics to pre-infusion biofluids from 98 prospectively-followed adults with relapsed/refractory (r/r) lymphoma at two academic centers (MD Anderson Cancer Center, n = 39, plasma; Moffitt Cancer Center, n = 59, serum). Logistic regression with backward feature selection on the MD Anderson cohort yielded panels for severe (Grade ≥ 2) CRS and ICANS that were locked and tested without refitting on the Moffitt cohort. Patients were stratified into low-, intermediate-, and high-risk tertiles. Ingenuity Pathway Analysis defined upstream regulators and canonical pathways. The 17 CRS-associated and 21 ICANS-associated consensus proteins were classified into mechanistic themes for biological interpretation.

RESULTS: A 5-marker CRS panel (SCRIB, MYL6, MTHFD1L, HSP90B1, MMP2) achieved AUCs of 0.85 (95% CI 0.72-0.98) and 0.76 (0.63-0.89) in the discovery and validation cohorts, respectively. An expanded 8-marker ICANS panel (the CRS panel plus SPOCK2, SLC3A2, CD84) achieved AUCs of 0.91 (0.81-1.00) and 0.67 (0.51-0.84). In the combined dataset, high-risk-tertile patients were 13.84-fold (95% CI 4.21-56.26) and 8.59-fold (2.87-29.09) more likely to develop Grade ≥ 2 CRS and ICANS, respectively. Pathway analysis converged on AKT-driven inflammation and endothelial activation. Functional clustering of the consensus proteins partitioned into mechanistically coherent themes consistent with a dual-anatomy model: severe CRS reflected peripheral macrophage priming and endothelial activation with surplus complement amplification (HSP90B1▴, CSF1▴, MMP2▴, HEG1▴, C3▴) and endotheliopathic coagulation (PROC▾, F7▾), whereas severe ICANS reflected cerebrovascular junction and basement-membrane stripping (CDH5▾, ITGB1▾, FN1▾, brain-enriched SPOCK2▾), hepatic synthetic suppression (TTR▾, APOA2▾, IGFBP3▾), compromised plasma antioxidant capacity (GPX3▾, PON1▾), and inflammasome dis-restraint via DPP9▾. PGLYRP2 and SCRIB depletion were shared by both signatures and identified a common upstream priming substrate.

CONCLUSIONS: Externally validated, pre-infusion proteomic panels predict severe CRS and ICANS following CAR T-cell therapy and define a coherent pre-infusion endothelial-immune priming axis (HSP90B1, MMP2, AKT) with mechanistically interpretable, druggable nodes. The dual-anatomy framework distinguishes peripheral CRS-biased from cerebrovascular ICANS-biased phenotypes downstream of a shared microbiome-host barrier priming substrate, providing a foundation for biomarker-guided risk stratification and cluster-matched prophylactic intervention to enhance the safety and outpatient feasibility of CAR T-cell therapy.},
}

@article {pmid42112445,
year = {2026},
author = {Furuya, R and Nishikawa, Y and Ota, Y and Prah, I and Mahazu, S and Kifushi, M and Yoshida, M and Suzuki, M and Hoshino, Y and Suzuki, T and Takeyama, H and Ablordey, A and Saito, R},
title = {Single-cell genomic profiling of antimicrobial resistance in Escherichia coli from the Densu River, Ghana.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797725},
pmid = {42112445},
issn = {1664-302X},
abstract = {INTRODUCTION: River water serves as a natural reservoir for antimicrobial resistance (AMR) factors. Although environmental AMR poses a global threat to public health as it spreads to local communities through the microbiome in aquatic environments, the actual situation remains unclear, especially in developing countries. In this study, we sought microbiome data, including AMR information, for multiple bacterial strains from river water samples using a single-cell genomics platform.

METHODS AND RESULTS: After antimicrobial selection of samples from the Densu River in Ghana, 16S rRNA amplicon sequencing revealed a high proportion of the genus Escherichia-Shigella with ampicillin and sulbactam selection. Single-cell genomic analysis revealed differences in AMR and virulence factor profiles among the same species of Escherichia coli, including the CTX-M-15 extended-spectrum β-lactamase-producing ones. Pan-genome analysis predicted 4,814 gene clusters, of which 2,264 were accessory, including 605 singletons. Phylogenetic tree analysis using the maximum likelihood method showed the heterogeneity of single-cell amplified genomes (SAGs), and cluster of orthologous gene analysis for each SAG confirmed the difference in the ratio of each functional group.

CONCLUSION: This study demonstrates the potential of single-cell genomics using the single-cell amplified genome in gel method to enhance environmental AMR surveillance with high resolution and accuracy. It also represents the first application of this approach to aquatic environments in Ghana, thereby contributing to the development of microbial ecology and genomic resources.},
}

@article {pmid42112609,
year = {2026},
author = {Cao, Y and Xu, H and Xu, C and Zu, M and Sun, J and Xiong, D and Ye, J and Han, K and Gao, Q and Shi, X and Li, L and Li, B and Shahbazi, MA and Cribbs, AP and Chai, J and Reis, RL and Kundu, SC and Liu, Y and Nie, G and Xiao, B},
title = {Zwitterionic Lipid Nanotherapeutics from Mulberry for Oral Treatment of Diabetic Colitis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c17183},
pmid = {42112609},
issn = {1936-086X},
abstract = {Diabetic colitis is a severe gastrointestinal complication of type 2 diabetes, which presents the key pathophysiological hallmarks of hyperglycemia, intestinal barrier disruption, immune dysregulation, and microbial metabolic imbalance, posing significant therapeutic challenges in clinical practice. Here, we leveraged artificial intelligence to identify the therapeutic potential of 1-deoxynojirimycin (DNJ) for addressing diabetic colitis. To improve its bioavailability and efficacy, we developed a mulberry-derived nanotherapeutic with surface functionalization of zwitterionic polymer (PpC) for DNJ encapsulation. Following oral administration, the resultant nanotherapeutics, PpC@DNJ-LNPs, efficiently traversed the gastrointestinal tract, enabling controlled DNJ release while inhibiting the α-glucosidase activity to regulate glucose homeostasis. Concurrently, they orchestrated colonic mucosa-microbiome interaction, promoting intestinal immune balance and microbiota remodeling. These synergistic effects collectively confer hypoglycemic, anti-inflammatory, antioxidant, and epithelial barrier-restoring effects, ultimately reshaping the glucose level and intestinal microecology. Our study demonstrates the translational potential of PpC@DNJ-LNPs as a safe and effective oral therapeutic platform for diabetic colitis.},
}

@article {pmid42112774,
year = {2026},
author = {Jourdain, L and Rossi, P and Charpagne, A and Chevalier, E and Praz, V and Marquis, J and Weber, J and Gu, W},
title = {A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70138},
pmid = {42112774},
issn = {1755-0998},
support = {200021_219222//Swiss National Science Fundation (SNF)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic/methods/economics ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; DNA Primers/genetics ; Cost-Benefit Analysis ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA/methods ; },
abstract = {In-line barcoding offers a streamlined and scalable alternative to two-step PCR library preparation for 16S rRNA gene amplicon sequencing, enabling cost-effective, high-throughput profiling of microbial communities. Here, we tested 136 and 156 in-line barcoded primer pairs for bacterial and archaeal communities for their performance across environmental samples and a mock standard community. The primers were designed by combining widely used universal 16S rRNA gene primers with existing barcode sets from Illumina kits. The designed primer pairs produced efficient and consistent amplification with minimal dropout and no systematic taxonomic bias. Through clustering and performance-based filtering, we selected final sets of 96 pairs for both bacterial and archaeal communities that work efficiently and well together for direct further use. This in-line tagging strategy is easy to adopt with fewer processing steps and PCR-associated artefacts, allows straightforward sample tracking, and supports reliable large-scale microbiome studies. We also present a framework for evaluating barcode- or primer-induced biases. More broadly, the proposed in-line barcoding strategy can be adapted to any amplicon-sequencing application, as well as targeted sequencing, highlighting its relevance beyond 16S rRNA gene surveys. All validation datasets, open-source processing scripts, and barcode design resources are provided to promote reproducibility and community-wide adoption.},
}

*RNA, Ribosomal, 16S/genetics
*DNA Barcoding, Taxonomic/methods/economics
*Bacteria/genetics/classification
*Archaea/genetics/classification
DNA Primers/genetics
Cost-Benefit Analysis
High-Throughput Nucleotide Sequencing/methods
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA/methods

@article {pmid42112809,
year = {2026},
author = {Coates, LC and Storms, DH and Spearman, SS and Shahab-Ferdows, S and Christensen, SH and Lewis, JI and Mølgaard, C and Michaelsen, KF and Allen, LH and Lemay, DG and Kable, ME},
title = {Stool microbial composition is associated with recent and future diarrhea and fever events in breastfed Danish infants.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0013426},
doi = {10.1128/msystems.00134-26},
pmid = {42112809},
issn = {2379-5077},
abstract = {UNLABELLED: Gastroenteritis is an important cause of ailment among infants in high-income countries, including Denmark. There are many cases of diarrhea among Danish children for which no etiological agent is detected. This study investigated the associations between gastroenteritis-related morbidities (diarrhea, fever, and vomiting) and gut microbial community in well-nourished, breastfeeding Danish infants. Infant stool samples, morbidity questionnaires, and diet/breastfeeding questionnaires were collected at three time points during the first 8.5 months of life. The V4-V5 region of the 16S rRNA gene was amplified from stool DNA extracts, sequenced with Illumina MiSeq, and analyzed using QIIME2. PERMANOVA, linear mixed-effects modeling, and ANCOM-BC2 were used to identify associations between infant gut microbiome and gastroenteritis-related morbidities across all visits. Logistic regression and random forest models were employed to determine whether early gut microbial alpha diversity or abundance, respectively, could predict morbidity later in infancy. Alpha diversity was negatively associated with diarrhea. Granulicatella abundance was positively associated with diarrhea. From 3.5 to 6 months of age, Bacteroidales abundance was negatively associated with fever. Faith's phylogenetic diversity, Staphylococcales abundance, and Haemophilus abundance during 3.5 months of life were positively associated with future diarrhea during ages 3.5-8.5 months. Pielou's evenness and Actinobacteriota abundance within 3.5 months of life had negative and positive associations, respectively, with fever during ages 3.5-8.5 months. This study reveals diarrhea is associated with stool Granulicatella in well-nourished, breastfeeding Danish infants, as it is in children from low-income countries, and that the early gut microbiome may contribute to risks of diarrhea and fever morbidities later in infancy.CLINICAL TRIALSThis trial was registered at ClinicalTrials.gov as NCT03254329.

IMPORTANCE: Gastroenteritis continues to cause much morbidity among infants in high-income countries, and the relationship with the gut microbiome is not fully understood, especially for well-nourished and breastfeeding infants. In the study presented here, infant stool Staphylococcales abundance (comprised of Staphylococcus and Gemella) and Haemophilus abundance during the first few months of life were positively associated with later diarrhea in well-nourished and breastfeeding Danish infants. Meanwhile, the abundance of Granulicatella (a facultative anaerobe with pathogenic potential) was greater in stool from infants who had recent diarrhea, suggesting further research is needed to determine its possible role in diarrhea and recovery from diarrhea. Fever usually did not co-occur with diarrhea or vomiting. Early life Actinobacteriota abundance was positively associated with later fever. This phylum was represented here by both pathobionts (Actinomyces) and mutualists (bifidobacteria), which may have contributed to fever differently-pathobionts through infection and mutualists through promotion of effective immune response to infection.},
}

@article {pmid42112827,
year = {2026},
author = {Cao, TTT and Herckes, P and Straub, D and Sarkar, S and Garcia-Pichel, F},
title = {Growth and formaldehyde degradation of photoheterotrophic Methylobacterium within radiation fogs.},
journal = {mBio},
volume = {},
number = {},
pages = {e0046326},
doi = {10.1128/mbio.00463-26},
pmid = {42112827},
issn = {2150-7511},
abstract = {UNLABELLED: The atmosphere contains thousands to millions of bacterial cells per cubic meter. However, it remains unclear if microbes are at all active or growing in situ or whether they are merely being transported in an inactive state. Based on the analyses of 32 overland radiation fog events over a 2-year period, we show that fog waters, with bacterial concentrations similar to those in continental or marine bodies of water, contain microbiomes well differentiated in composition from those in the dry aerosol microbiomes that occur locally before, during, or after fog events. They are consistently and strongly enriched in photoheterotrophic Methylobacterium species, suggesting that fog populations may be metabolizing volatile C1 compounds in situ, although phototrophy seems much less important. Indeed, metabolically active bacteria in the fog, and representative isolates of the main field populations, can degrade formaldehyde at unprecedently high rates; most of this activity seems to play a detoxification role. The increase in bacterial aerobiome counts upon intervening fog events, the dependence of microbial concentration on ambient temperature, the increases in cell size and frequency of dividing cells in fog water with respect to cells in interstitial aerosols of fogs, in addition to their metabolic capacity, all suggest that the fog water microbiome is actually growing. Consequently, droplets of atmospheric water should be considered a potential aquatic microhabitat. Our results highlight the fog microbiome's role in atmospheric chemistry and have implications for fog harvesting as a source of fresh water for human use.

IMPORTANCE: While bacteria are common in the atmosphere, their activity in situ has remained unclear. Using stagnant radiation fogs as new study systems where sampling is optimal, the dynamics, composition, cellular characteristics, and metabolic rates of fog water microbiomes, dominated by Methylobacterium sp., show that they are a hub of active detoxification of atmospheric formaldehyde and likely growing in situ on the basis of heterotrophic or photoheterotrophic metabolism of volatile C1 compounds, with implications for atmospheric chemistry and fog harvesting as sources of freshwater.},
}

@article {pmid42112889,
year = {2026},
author = {Amechatte, G and Radouane, N and El Mouttaqi, A and Licastro, D and Hirich, A and Mohamed, H and Ahmed, B},
title = {Deterministic abiotic filtering and halophilic core microbiomes shape bacterial community assembly in coastal salt flats (sabkha) of southern Morocco.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0006126},
doi = {10.1128/aem.00061-26},
pmid = {42112889},
issn = {1098-5336},
abstract = {Coastal salt flats, locally known as sabkhas, are hypersaline, alkaline desert ecosystems that impose extreme abiotic stress on microbial and plant life. Despite their ecological significance, plant-associated microbiomes in these habitats remain poorly characterized. In this study, we investigated the bacterial communities of native halophytes across three sabkha sites in southern Morocco using an integrated culture-independent and culture-dependent framework. Soil physicochemical analyses revealed strong gradients in salinity and ionic composition, along with consistent alkaline pH across sites. These conditions strongly structured bacterial assemblage: alpha diversity declined progressively from bulk soil to rhizosphere soil, root, and shoot; and beta diversity showed clear compartmental separation driven by environmental factors. Canonical correspondence analysis identified electrical conductivity (EC), Na2O, K2O, and carbonate fractions as the main abiotic drivers. Across plant species, bacterial communities converged toward a stable halophilic core microbiome dominated by Halomonas, Kushneria, and Marinococcus, with 66% of amplicon sequencing variants (ASVs) shared across compartments. Host identity played a secondary role as environmental filtering overshadowed host-specific associations. Culture-dependent isolation recovered 19 halophilic and halotolerant bacterial strains, including representatives of Halomonas, Idiomarina, Marinobacter, Psychrobacter, Planomicrobium, and Bacillus. These isolates exhibited robust growth on saline Marine Agar medium, indicating strong salt tolerance consistent with their occurrence in hypersaline environments. The strong concordance between cultured isolates and metabarcoding profile confirms that dominant halophilic lineages are both ecologically robust and readily culturable. Together, these findings demonstrate that sabkha plant microbiomes are primarily shaped by deterministic abiotic filtering and harbor resilient, stress-adapted bacterial communities. Sabkhas thus represent promising reservoirs of halophilic microbes with potential applications in saline agriculture and improving crop resilience under extreme environmental conditions.IMPORTANCECoastal salt flats (sabkhas) are among the most extreme terrestrial environments, characterized by high salinity, alkalinity, and limited water availability. As soil salinization expands worldwide, understanding how life persists in such habitats is increasingly important for sustainable agriculture. This study shows that sabkha ecosystems impose strong environmental filtering on plant-associated bacterial communities, leading to highly structured microbiomes across soil, root, and shoot compartments. Despite differences among sites and plant species, bacterial communities converged toward a shared halophilic core microbiome, dominated by salt-adapted genera that are resilient to extreme ionic stress. Importantly, many of these dominant bacteria were readily culturable, highlighting sabkhas as accessible reservoirs of stress-tolerant microbes. Our findings demonstrate that abiotic conditions outweigh plant identity in shaping microbiome assembly under extreme stress and reveal sabkha halophytes as valuable natural models for discovering microbes with potential applications in saline agriculture, soil restoration, and crop resilience in salt-affected environments.},
}

@article {pmid42112933,
year = {2026},
author = {Gee, M and Sharp, C},
title = {Bacterial weaponry and the ecological factors of competitive success.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250028},
pmid = {42112933},
issn = {1744-1358},
support = {N/A//University of Reading (UoR)/ ; },
abstract = {Bacteria have evolved complex protein systems known as bacterial weapons to inhibit or kill their competitors. These bacterial weapons are a remarkably diverse arsenal that influence the composition and function of important microbial communities such as the human microbiome. In turn, the spatial constraints, nutrient availability, environmental stressors, and the presence of competitors determine not only whether weapons are expressed, but which weapons provide the greatest advantage. While bacterial weaponry is widespread, the types, mechanisms, and abundance of these systems vary between, and even within, species. Recent research has highlighted the importance of bacterial weaponry in community invasion and pathogenicity. Their potency and narrow killing spectrum have also generated interest in exploiting bacterial weapons to engineer microbial communities or develop therapeutics that avoid the disruption of broad-spectrum antibiotics. Understanding how ecological context affects weapon efficacy could reveal new virulence mechanisms used by pathogens and inform the design of novel treatments and microbiome-based therapies. This review outlines three of the best-studied bacterial weapon systems (protein bacteriocins, the type VI secretion system, and contact-dependent inhibition), highlighting their roles in microbial ecology, pathogenicity and their potential as therapeutics.},
}

@article {pmid42113072,
year = {2026},
author = {Csikó, G and Palócz, O and Várhidi, Z and Sátorhelyi, P and Erdélyi, B and Jurkovich, V},
title = {Evaluation of the local tolerance and systemic safety of a novel intravaginal probiotic product in cows.},
journal = {Veterinary research communications},
volume = {50},
number = {4},
pages = {},
pmid = {42113072},
issn = {1573-7446},
mesh = {Animals ; *Probiotics/administration & dosage/adverse effects ; Female ; Cattle ; Administration, Intravaginal ; Vagina/microbiology/drug effects ; },
abstract = {Since its discovery, the microbiota has been increasingly recognised for its role in maintaining health and contributing to various disease conditions. In the reproductive tract, microbial populations can significantly influence endometrial health, internal homeostasis, and fertility. The preservation or restoration of a balanced microbiota through appropriate probiotic products may support reproductive health; in addition, candidate probiotics must be demonstrated to be safe for use. The aim of this study was to assess the local tolerance and systemic safety of a novel intravaginal probiotic product in cows. Twenty-four animals were enrolled and assigned to four groups: single-dose, three-, and five-fold dose of the test product, and a placebo group receiving excipients only. Physical examination and evaluation of the vaginal mucosa were conducted prior to each treatment, one day after and one and two weeks after the final probiotic administration. Blood and urine samples were collected before treatment and following treatment: one day after the last administration of intravaginal probiotic and again two weeks post-treatment. Blood haptoglobin, serum amyloid A, glucose, non-esterified fatty acids, and beta-hydroxybutyrate were measured to assess inflammatory and metabolic responses, and differences over time and between groups were statistically analysed. No dose-dependent systemic changes were observed; however, transient, time-related alterations were noted across all groups, including controls. The investigational probiotic product was well tolerated both locally and systemically, with tolerability comparable across all groups, including the placebo. These data establish a safety profile in healthy cows and support further investigation of this product in studies focusing on efficacy and microbiome modulation.},
}

Animals
*Probiotics/administration & dosage/adverse effects
Female
Cattle
Administration, Intravaginal
Vagina/microbiology/drug effects

@article {pmid42114033,
year = {2026},
author = {Pavitra, SP and Tan, KK and Tan, TK and Er, YX and Vinnie-Siow, WY and Ya'cob, Z and Low, VL and Lim, YAL},
title = {Microbial communities of the Southeast Asian black flies (Diptera: Simuliidae) based on multiple hypervariable regions of 16S rRNA.},
journal = {Journal of medical entomology},
volume = {63},
number = {3},
pages = {},
doi = {10.1093/jme/tjag051},
pmid = {42114033},
issn = {1938-2928},
support = {//Ministry of Higher Education, Malaysia/ ; MO002-2019//Higher Institution Centre of Excellence (HICoE)/ ; TIDREC-2023//Higher Institution Centre of Excellence (HICoE)/ ; },
mesh = {Animals ; RNA, Ribosomal, 16S/analysis/genetics ; *Simuliidae/microbiology ; Male ; Female ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; Malaysia ; High-Throughput Nucleotide Sequencing ; RNA, Bacterial/analysis ; },
abstract = {Black flies (Diptera: Simuliidae) are important vectors of disease-causing agents, but little is known about their microbiome in Southeast Asia, highlighting the need for further investigation. In Malaysia, Simulium cheongi, Simulium jeffreyi, and Simulium vanluni are among the most abundant black fly species and are of potential medical importance, making them suitable representatives for microbiome studies. In this study, their bacterial communities were characterized using next-generation sequencing (NGS) targeting seven hypervariable regions (V2, V3, V4, V6 to V7, V8, and V9) of the 16S rRNA gene to enable comprehensive community profiling. The alpha diversity of the bacterial community showed the highest values of Shannon and Simpson indices in S. jeffreyi and increased values of observed species and Chao1 indices in S. cheongi. Males showed greater microbial diversity than females in the alpha diversity analysis, with all alpha rarefaction plots reaching a plateau. Moreover, the beta diversity of the microbial communities measured by Bray-Curtis distance indices revealed three PCs coordinates with 63.75% of the total variance. However, no significant differences in alpha and beta diversity indexes were found among the three species. The bacterial composition included six phyla, 15 classes, 37 orders, 78 families, 143 genera, and 216 bacterial species, with the V3 region having the highest taxonomic identification. The V9 region had the least detection at all taxonomic levels, emphasizing the importance of selecting appropriate hypervariable regions to accurately assess the diversity of black fly bacterial communities.},
}

Animals
RNA, Ribosomal, 16S/analysis/genetics
*Simuliidae/microbiology
Male
Female
*Microbiota
*Bacteria/genetics/classification/isolation & purification
Malaysia
High-Throughput Nucleotide Sequencing
RNA, Bacterial/analysis

@article {pmid42114284,
year = {2026},
author = {Abd El-Hack, ME and Ashour, EA and Khafaga, AF and Khaleel, HK and Kamal, M and Taha, AE and Alfifi, AE and Al-Rasheed, M and Khan, MMH},
title = {Functional effects of rosmarinic acid on gut health and epigenetic regulation in antibiotic-free poultry diets.},
journal = {Poultry science},
volume = {105},
number = {8},
pages = {106943},
doi = {10.1016/j.psj.2026.106943},
pmid = {42114284},
issn = {1525-3171},
abstract = {Rosmarinic acid (RA), a bioactive polyphenol found in Salvia officinalis and other Lamiaceae herbs, has attracted attention for its functional feed application in animal nutrition. RA supplementation positively influences growth efficiency, liver antioxidant status, and serum biochemical indices in broilers. Its antimicrobial and immunomodulatory effects promote health and productivity. Studies suggest benefits for gut health and meat quality; however, epigenetic regulation of RA in poultry is considered a minor future perspective, being mostly based on mammalian studies. Hypothesized impacts of RA on chronic disease prevention and as a microbiome-engineering agent require further investigation. This review explores the regulatory effects of RA on DNA methylation, non-coding RNAs (ncRNAs), and histone modifications, which influence gut microbiome structure, nutrient absorption, and immune function in poultry. It emphasizes RA's potential as a functional food for gastrointestinal health, metabolic regulation, and chronic disease prevention, alongside its use in antibiotic-free poultry feed for microbiome engineering. The review also discusses RA's effects on lipid metabolism and oxidative stress, highlighting its role in maintaining intestinal barrier health. Nevertheless, certain limitations must be acknowledged, as successful nutritional interventions depend on understanding individual variability, including genetics, metabolism, age, and health status. Tailored methodologies, such as micronutrition and genomic nutrition, can improve diet quality, promote nutrient absorption, and enhance overall animal health. A tailored feeding regimen focuses on selecting nutrients with proven benefits for key health outcomes, such as omega-3 fatty acids, which scientific evidence shows promote brain and heart health while reducing inflammation.},
}

@article {pmid42114326,
year = {2026},
author = {Esen, S},
title = {An update on heat stress impacts on rumen microbiome composition, fermentation parameters, and mitigation approaches in ruminants.},
journal = {Journal of thermal biology},
volume = {139},
number = {},
pages = {104480},
doi = {10.1016/j.jtherbio.2026.104480},
pmid = {42114326},
issn = {0306-4565},
abstract = {Over the past decade, there has been an increasing amount of literature on heat stress (HS) effects on ruminant production systems, yet much uncertainty still exists about the relationship between HS and rumen microbial ecology across species. This narrative review synthesizes peer-reviewed evidence from 2020 to 2025, with the aim of providing a critical appraisal of HS effects on rumen microbiome composition and fermentation parameters in cattle, buffalo, sheep, and goats. A convergent pattern emerges from the available data: HS consistently reduces cellulolytic bacteria (Fibrobacter, Ruminococcus) while increasing lactate-producing and starch-fermenting taxa. Acetate proportions declined by 29-33% in buffalo and beef cattle, whereas total VFA in sheep increased during mild HS, reflecting species-dependent fermentation responses. A strong relationship between breed-level heat tolerance and rumen microbiome diversity has been reported in several recent studies, providing converging evidence that heat tolerance may be characterized as a holobiont phenotype. It has been demonstrated that HS extends beyond classical VFA changes to disrupt B-vitamin synthesis, amino acid metabolism, biogenic amine homeostasis, and bile acid biotransformation. Nutritional interventions, including probiotics, chromium, herbal supplements, and rumen-protected amino acids, have been shown to partially restore microbial balance, although responses vary with HS severity and host genotype. Notwithstanding these findings, the generalisability of much published research on this topic is limited by methodological heterogeneity across studies. Taken together, these findings highlight the need for standardized experimental protocols, multi-omics integration, and microbiome-targeted intervention strategies.},
}

@article {pmid42114574,
year = {2026},
author = {Li, X and Cheng, S and Wang, X and Gu, X and Xu, X and Duan, X and Xue, G and Oleskowicz-Popiel, P and Xu, J and Liu, B and Liu, Z and Zhou, A and Makinia, J},
title = {Intrinsic waste component synergy: calcium-rich eggshell waste modulates fungal-bacterial microbiome toward selectively medium-chain fatty acid production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134795},
doi = {10.1016/j.biortech.2026.134795},
pmid = {42114574},
issn = {1873-2976},
abstract = {The valorization of waste streams into medium-chain fatty acids (MCFAs) through fungi-bacteria synergy is often hindered by substrate competition and distinct ecological niches. This study demonstrates that eggshell waste acts as a bioregulator to optimize this interaction for caproate production. At a 20 g/L dosage, eggshells facilitated high caproate production (22.3 ± 1.3 gCOD/L) driven by in-situ ethanol supply (11.3 ± 1.9 gCOD/L). The amendment established stable micro-niches, significantly enriching yeasts (Wickerhamomyces, Candida, and Issatchenkia, 69.2%) and chain-elongating bacteria (CEB, Caproiciproducens, and Clostridium_sensu_stricto_12, 10.2%), while metagenomics confirmed upregulated glycolysis and reverse β-oxidation pathways. Additionally, yeast synergy with CEB via ethanol cross-feeding in a sugar-rich environment can be disrupted under the sugar-depleted phase. The coculture experiments unveiled that 8 g/L Ca[2+] alleviates fungi-bacteria conflict and promotes CEB functionality. This study presents a waste valorization strategy, leveraging intrinsic waste synergies to optimize fungal-bacterial interactions and drive endogenous ethanol-based caproate production.},
}

@article {pmid42114665,
year = {2026},
author = {Moerdijk, AS and van Genuchten, WJ and Duijnhouwer, AL and Snoeren, MMM and Hirsch, A and van den Berg, LEM and Boersma, E and Kauling, RM and van den Bosch, AE and Udink Ten Cate, FEA and Helbing, WA and Bartelds, B},
title = {Evaluation of high intensity interval training in patients with a right ventricle to pulmonary artery conduit in a randomized controlled trial - Rationale and design of the 'Right HIIT' study.},
journal = {American heart journal},
volume = {},
number = {},
pages = {107477},
doi = {10.1016/j.ahj.2026.107477},
pmid = {42114665},
issn = {1097-6744},
abstract = {BACKGROUND: Exercise training is a promising, relatively low cost strategy to optimize exercise capacity, primarily studied in patients with tetralogy of Fallot and Fontan physiology. However, rare and complex biventricular disorders are understudied. High intensity interval training (HIIT) is a time-efficient alternative to the more commonly studied aerobic training. Despite group level improvements in exercise capacity, individual variation suggests the existence of responders and non-responders to exercise training. We therefore designed a HIIT intervention trial for patients with complex outflow tract disorders aimed to test efficacy and identify predictors of response.

METHODS: The Right HIIT study is a multicenter, randomized controlled trial aiming to enroll 38 patients aged 12 to 45 years with a right ventricle to pulmonary artery conduit. Participants will be randomized to a 12-week home-based HIIT program (intervention) or standard of care (SoC) group. The primary endpoint is change in peak oxygen consumption from baseline to 12 weeks. Secondary endpoints include other cardiopulmonary exercise testing and imaging parameters, blood biomarkers, gut microbiome composition, quality of life and physical activity levels. After the randomized phase, the SoC group will receive the HIIT program, with repeated data collection after 12 weeks. Thus, pre-post HIIT data will be available in all patients, for the purpose of supportive analyses and identifying predictors of response.

CONCLUSION: The Right HIIT study will analyze whether a HIIT program improves exercise capacity in patients with a right ventricle to pulmonary artery conduit and which factors are associated with the ability to improve exercise capacity.},
}

@article {pmid42114750,
year = {2026},
author = {Saedi, N and Zhang, S and Sahana, G and Villumsen, TM and Stephansen, RB and Lund, MS and Cai, Z and Karaman, E},
title = {Comparison of 16S rRNA Sequencing and Shotgun Metagenome Sequencing for Estimating Genotypic and Phenotypic Parameters of Enteric Methane Emission in Dairy Cattle.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-28157},
pmid = {42114750},
issn = {1525-3198},
abstract = {Methane emissions from ruminants significantly contribute to greenhouse gases, making it crucial for sustainable livestock breeding to understand how both genetic and microbial factors influence methane production. We compared the heritability and microbiability for enteric methane in cows using microbial features derived from 16S rRNA amplicon data and shotgun metagenomics data, together with genome-wide marker data. The features derived from 16S rRNA data were 16s genus (16s-G), 16s species (16s-S), 16s Predicted microbial genes (16s-PMG) and 16s Predicted metabolic pathways (16s-PMP). The features derived from metagenomics data were metagenomic species (M-S) and metagenomic genus (M-G) considering 3 different databases (MGnify, GTDB, and NCBI). The heritability of methane ranged from 0.08 to 0.14. The 16s-G explained 28% of phenotypic variation in methane, and contributed the most to the heritability estimate for methane among other features. For the same feature data sets, we estimated the heritability of each microbial feature. Most microbial features had low heritability, while a subset had high values (up to 0.8). The highest heritabilities were observed for M-S MGnify feature RUG592 sp902767285 (0.95) and M-G NCBI genus feature Leadbettera (0.98). We found that the microbiota in the rumen is primarily determined by environmental factors, whereas host genetics has a significant impact on the abundance of certain functionally important microbes. To the best of our knowledge, this study presents the first comparison of methane heritability in dairy cattle incorporating microbial data (1) from multiple techniques such as 16S rRNA amplicon sequencing and shotgun metagenomic sequencing, and (2) from multiple levels of microbial features such as 16s-G, 16s-S, 16s-PMG, 16s-PMP, and M-S and M-G. Our results highlight heritable microbial species/genus as potential targets for microbiome-informed breeding strategies to reduce methane emissions in dairy cattle.},
}

@article {pmid42114808,
year = {2026},
author = {Reynolds, GK and Dowling, MR and Valencia-Klug, J and Teh, BW and Anderson, MA and Vanguru, V and Harrison, SJ and Ho, PJ and Slavin, MA and Thursky, K},
title = {Infections in the first 30-days after CAR-T therapy in Patients Not Receiving Fluoroquinolone Prophylaxis.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.03.040},
pmid = {42114808},
issn = {2666-6367},
abstract = {BACKGROUND: Routine fluoroquinolone (FQ) prophylaxis may increase the risk of antimicrobial resistance, microbiome disruption, and Clostridioides difficile infection in patients receiving chimeric antigen receptor T-cell (CAR-T) therapy for haematological malignancy. In Australia, FQ prophylaxis is not routinely used. We evaluated the aetiology of early fever following CAR-T to better understand the incidence of infections, particularly bloodstream infections, in a cohort not receiving FQ prophylaxis.

METHODS: This bicentric Australian retrospective study included adults receiving standard-of-care CD19 CAR-T therapy for DLBCL (2019-2023). The primary outcome was the cause of sustained fever (≥38.0°C on ≥1 days) from infusion to day 30. Recurrent fever required ≥72 hours afebrile before a new fever. Infections were classified as microbiologically-confirmed, clinically-defined, or fever syndrome per consensus criteria.

RESULTS: 204 adults (median age 64 years, IQR:57-71) received tisagenlecleucel (50%) and axicabtagene (50%), after a median of 3 prior therapies (IQR:3-4). Sustained fever occurred in 131/204 patients (64%), comprising 161 episodes. Of these, 36 (21%, 28pts) were microbiologically-confirmed infections, 14 (9%, 14pts) were clinically-defined infections, and 110 (69%, 108pts) were fevers of unknown origin. Bacteremia occurred in 7/204 patients (3.4%; 9 events), with one fatal polymicrobial bacteremia. Other microbiologically-confirmed infections included C. difficile (7/36), URTI (13/36) and invasive fungal infection (5/36). Risk factors for early microbiologically-confirmed infection in univariate analysis included axicabtagene product (HR=2.5, p=0.019), grade ≥3 ICANS (HR=3.4, p=0.012), and prolonged neutropenia (ANC ≤ 0.5 × 10⁹/L for ≥14 days; HR=3.7, p=0.014).

CONCLUSION: Early bacteremia rates remain low without routine FQ prophylaxis. Initial sustained fevers are predominantly non-infectious. Our data do not support universal fluoroquinolone prophylaxis in CAR-T therapy.},
}

@article {pmid42115049,
year = {2026},
author = {Ha, S and Zhang, X and Li, L and Yu, J},
title = {MASLD and MASLD-associated HCC: emerging biomarkers and therapeutic avenues.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2026.04.048},
pmid = {42115049},
issn = {2095-9281},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading chronic liver disease on a global scale. With its increasing incidence and advances in research technologies, our understanding of the mechanisms, non-invasive diagnostic strategies and therapeutic approaches for MASLD and its more advanced forms, including metabolic dysfunction-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC), has substantially expanded. This article reviews the pathophysiological mechanisms underlying MASLD and its transition to more severe forms, evolving from well-established mechanisms including insulin resistance, abnormalities in lipid metabolism and inflammation, to recently explored novel mechanisms, such as immune regulation, RNA modification and gut microbiome. Additionally, emerging biomarkers for diagnosis and prognosis, such as non-invasive serum markers and genetic variants are highlighted. This review evaluates contemporary therapeutic strategies, with particular emphasis on the recent FDA approval of resmetirom and semaglutide, alongside other pharmacological agents currently in phase 3 clinical trials. It also discusses innovative interventions aimed at improving the management of MASLD and MASLD-HCC, specifically in the context of gut modulation and enhancing the efficacy of immunotherapy. The necessity for strategies aimed at early detection and multifactorial treatment approaches is critical to address the rising burden of MASLD and its complications, with a call for further research into personalised medicine and innovative multidisciplinary therapeutic targets.},
}

@article {pmid42115134,
year = {2026},
author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Abdisalaam, I and Rijneveld, R and Klaassen, ES and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and Freyee, B and Platenkamp, K and van Poelgeest, ME and Rissmann, R and van Doorn, MBA and Niemeyer-van der Kolk, T},
title = {Lack of improvement after short-term topical antistaphylococcal endolysin SA.100 therapy in patients with mild-to-moderate atopic dermatitis: Results from a randomized, vehicle-controlled trial.},
journal = {British journal of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bcp.70608},
pmid = {42115134},
issn = {1365-2125},
support = {//Micreos Human Health B.V./ ; },
abstract = {Atopic dermatitis (AD) is a chronic immune-mediated inflammatory skin disease. An overgrowth of Staphylococcus aureus (S. aureus) and decreased microbial diversity is apparent in 70%-90% of AD patients. SA.100 is a recombinant endolysin targeting S. aureus that might be a novel treatment for patients with mild-to-moderate AD. To test safety, pharmacodynamics and efficacy of SA.100 a double-blind, randomized, vehicle-controlled trial in 53 subjects with mild-to-moderate AD was performed. Patients were randomized equally to topical SA.100 or vehicle with stratification for S. aureus positivity. SA.100 was safe and well tolerated. No reduction of S. aureus and no changes in microbiome features were seen after 2 weeks of treatment. Additionally, no statistically significant changes in clinical or patient-reported outcomes were observed compared to vehicle. In conclusion, topical SA.100 was safe and well tolerated in patients with mild-to-moderate AD, but our findings do not support short-term clinical use.},
}

@article {pmid42115189,
year = {2026},
author = {Wojciechowska, AW and Wojciechowski, JW and Zielinska, K and Soeding, J and Kosciolek, T and Kotulska, M},
title = {Aggregation in gut: on the link between neurodegeneration and bacterial functional amyloids.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01005-8},
pmid = {42115189},
issn = {2055-5008},
support = {2019/35/B/NZ2/03997//Narodowe Centrum Nauki/ ; 2023/05/Y/NZ2/00080//Narodowe Centrum Nauki/ ; 2019/35/B/NZ2/03997//Narodowe Centrum Nauki/ ; },
abstract = {Amyloids are insoluble protein aggregates with a cross-beta structure, which are traditionally associated with neurodegeneration. Similar structures, named functional amyloids, expressed mostly by microorganisms, play important physiological roles, e.g., bacterial biofilm stabilization. Using a bioinformatics approach, we identify gut microbiome functional amyloids and analyze their potential impact on human health via the gut-brain axis. The results point to taxonomically diverse sources of functional amyloids and their frequent presence in the extracellular space. The retrieved interactions between gut microbiome functional amyloids and human proteins indicate their potential to trigger inflammation, affect transport and signaling processes; pathways typically affected by host-microbiome interactions. We also find a greater relative abundance of bacterial functional amyloids in patients diagnosed with Parkinson's disease in two out of three analyzed datasets. Our results generate hypotheses on a tentative link between neurodegeneration and gut bacterial functional amyloids, which require further experimental validation.},
}

@article {pmid42115298,
year = {2026},
author = {Park, SH and Park, J and Kim, J and Choi, H and Kim, IG and Chung, EJ and Na, KJ},
title = {Analysis of unmapped RNA-seq data from cancer spatial transcriptome toward characterizing cancer microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52324-x},
pmid = {42115298},
issn = {2045-2322},
support = {RS-2024-00357094//National Research Foundation of Korea/ ; 2020R1C1C1007105//National Research Foundation of Korea/ ; 2620210050//Seoul National University Bundang Hospital/ ; },
abstract = {Spatial characterization of microbial-like signals in tumor tissues remains challenging, particularly in direct Visium data, where microbial reads are sparse and may not be fully retained in standard count matrices. Here, we present an extended unmapped-read analysis as a proof-of-concept workflow for summarizing microbial-like 16S rRNA signals in four direct Visium specimens from colorectal cancer (CRC), oral squamous cell carcinoma (OSCC), and head and neck squamous cell carcinoma (HNSC). The workflow uses a custom reference containing four selected 16S rRNA sequences and computes a per-spot mismatch ratio to quantify sequence-level dissimilarity relative to each reference. Compared with PathSeq, the workflow yielded different spatial signal patterns and mismatch summaries across the analyzed specimens. Among the four tested references, the CRC specimen showed lower mismatch ratios relative to the E. coli reference than the other analyzed specimens, an observation compatible with the intestinal context but not definitive evidence of species-level presence or evolutionary proximity. Given the small sample set, restricted reference panel, and lack of dedicated negative controls, these findings should be interpreted as hypothesis-generating. This study provides a complementary proof-of-concept framework for exploring microbial-like signals in direct Visium data.},
}

@article {pmid42115377,
year = {2026},
author = {Catani, G and O'Connor, JM and Spinelli, A and Perea, J},
title = {Early-onset colorectal cancer: a comprehensive review reframing hypotheses and defining research priorities.},
journal = {International journal of colorectal disease},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00384-026-05145-3},
pmid = {42115377},
issn = {1432-1262},
abstract = {PURPOSE: Early-onset colorectal cancer (EOCRC), defined as colorectal cancer diagnosed before the age of 50 years, is increasing worldwide and represents a growing clinical and public health challenge. Whether EOCRC constitutes a biologically distinct entity remains uncertain, and current diagnostic and therapeutic strategies are largely extrapolated from late-onset disease.

METHODS: This narrative review summarizes recent evidence on EOCRC biology, diagnosis, and management, focusing on molecular and genomic features, tumor microenvironment, exposome-related factors, diagnostic pathways, treatment paradigms, and emerging strategies for early detection. We critically examine the gap between biological insights and real-world clinical practice and outline priorities for future research.

RESULTS: EOCRC displays a heterogeneous molecular landscape that substantially overlaps with late-onset colorectal cancer. Although advances in multiomics profiling, liquid biopsy, and microbiome research have improved biological understanding, these findings have not yet translated into EOCRC-specific diagnostic or therapeutic approaches. Diagnosis remains delayed due to age-based screening paradigms and symptom misattribution, resulting in advanced-stage presentation. Younger patients frequently receive intensified treatment despite limited age-specific evidence and insufficient attention to long-term toxicity, fertility, and survivorship.

CONCLUSION: EOCRC underdiagnosis is likely multifactorial. While limitations in biological knowledge and diagnostic tools may play a role, the discrepancy between current paradigms and the age-specific risk profiles of younger patients likely represents an important contributing factor. Progress will require biology-informed, risk-adapted screening strategies and EOCRC-focused clinical research.},
}

@article {pmid42115408,
year = {2026},
author = {Cheng, B and Gong, L and Xu, H and Wang, Z and Huang, H and Guan, X and Wu, P},
title = {The microbiome across the prostate disease continuum: from health and BPH to prostatitis/CPPS and cancer.},
journal = {Oncogene},
volume = {},
number = {},
pages = {},
pmid = {42115408},
issn = {1476-5594},
abstract = {Microbial contributions to prostate health and disease extend beyond the mere detection of organisms in urine or tissue. Rather than acting as stable colonisers, microbial influences on the prostate are better conceptualised as converging fluxes: systemically circulating gut-derived metabolites, immune education occurring in distal lymphoid compartments, and intermittent exposure to microbial products from the lower urinary tract. These inputs converge on a limited set of conserved mediator-receptor axes-including short-chain fatty acids, bile acids and indole derivatives-that calibrate epithelial barrier integrity, inflammatory thresholds, antigen-presentation capacity and myeloid cell fate. Crucially, the biological relevance of these axes is stage-dependent. In benign prostatic hyperplasia and chronic prostatitis/chronic pelvic pain syndrome, metabolite tone shapes inflammatory activation thresholds and barrier resilience. In localized prostate cancer, these same pathways intersect with antigen-processing machinery and immune exclusion. In castration-resistant disease, tumour-intrinsic metabolic plasticity and redox balance predominate, with microbial and host-derived metabolites assuming relevance when they modulate lipid remodelling and ferroptotic vulnerability. Interpretation is constrained by the intrinsically low biomass of urine and prostate tissue. Robust inference therefore requires quantitative anchoring, orthogonal validation and explicit separation of association from causality. Translational progress is most likely to emerge from calibrated measurement and stage-aware modulation rather than indiscriminate ecological manipulation. By integrating mechanistic, spatial and clinical evidence, this Review proposes a stage-aware framework for the gut-urinary-prostatic axis and delineates when microbial and metabolite signalling meaningfully conditions prostate disease biology-and when it does not.},
}

@article {pmid42115470,
year = {2026},
author = {Fragkou, PC and Moschopoulos, CD and Marová, D and Alahmad, B and Skevaki, C and , },
title = {Climate change-associated heat extremes and immune dysregulation: emerging links with autoimmunity, allergy, and infectious diseases.},
journal = {Seminars in immunopathology},
volume = {48},
number = {1},
pages = {},
pmid = {42115470},
issn = {1863-2300},
mesh = {Humans ; *Climate Change ; *Hypersensitivity/etiology/immunology/epidemiology/metabolism ; *Communicable Diseases/etiology/immunology/epidemiology ; Animals ; *Autoimmunity ; *Hot Temperature/adverse effects ; Disease Susceptibility ; *Autoimmune Diseases/etiology ; Environmental Exposure/adverse effects ; },
abstract = {Climate extremes are increasingly shaping both environmental and human health outcomes. Global warming has led to a rise in the frequency, duration, and intensity of extreme temperature events, with heatwaves emerging as one of the most hazardous weather-related threats. Beyond their well-recognized cardiovascular and respiratory effects, heat extremes are now understood to influence immune function. Growing evidence indicates that heat extremes along with air pollution, wildfires, humidity shifts, and ecosystem disruption can impair epithelial barrier integrity and disturb immune regulation. These stressors may promote chronic inflammation, alter adaptive immune responses, and compromise host defense mechanisms. Experimental and epidemiological data suggest that heat stress can reduce effective B-cell responses, modify antigen presentation, and increase inflammatory signaling, while combined exposures to heat and pollutants may further increase susceptibility to infectious, allergic, and autoimmune diseases. Although the physical drivers of climate change are well established, the biological pathways linking environmental stressors to immune dysregulation remain incompletely defined. This review synthesizes current evidence on the mechanisms by which extreme heat events influence immune tolerance and disease risk. We discuss implications for allergy, autoimmunity, and infectious diseases, highlight vulnerable populations, and outline key research priorities needed to inform clinical and public health adaptation.},
}

Humans
*Climate Change
*Hypersensitivity/etiology/immunology/epidemiology/metabolism
*Communicable Diseases/etiology/immunology/epidemiology
Animals
*Autoimmunity
*Hot Temperature/adverse effects
Disease Susceptibility
*Autoimmune Diseases/etiology
Environmental Exposure/adverse effects

@article {pmid42115547,
year = {2026},
author = {Chung, CS and Kherallah, K and Ashina, N and Beraja, GE and Budhiraja, A and Dienes, S and Goldberg, M and Xiong, G and Alhusayen, R and Goldberg, S and Gonzalez, T and Hsiao, JL and Lev-Tov, H and Sibbald, C and Piguet, V and Porter, M},
title = {Symposium on Hidradenitis Suppurativa Advances 2025 Proceedings.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42115547},
issn = {2193-8210},
}

@article {pmid42115794,
year = {2026},
author = {Chen, J and Chen, S and Sun, H and Wang, Y},
title = {Lower airway microbiome and metabolomic profiles of recurrent wheezing in infants: a case-control study.},
journal = {Allergologia et immunopathologia},
volume = {54},
number = {3},
pages = {49-80},
pmid = {42115794},
issn = {1578-1267},
mesh = {Humans ; Male ; Female ; Infant ; *Respiratory Sounds/etiology ; *Microbiota ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Metabolome ; Metabolomics ; Recurrence ; DNA, Bacterial/genetics ; Bacteria ; },
abstract = {OBJECTIVES: To characterize the microbiome shifts and subsequent metabolite alterations associated with recurrent wheezing (RW) in infants.

METHODS: A total of 33 subjects were enrolled in this study, including 18 infants diagnosed with RW, and 15 normal infants as controls. Bronchoalveolar lavage (BAL) fluid was collected from all the subjects. Bacterial DNA was then isolated and analyzed by 16S ribosomal RNA sequencing. In addition, the metabolomic profile of BAL fluid samples was analyzed with mass spectrometry using complementary chromatographic methods. Spearman's rank correlation analysis was conducted to explore associations between microbial taxa and metabolites.

RESULTS: The study had 21 (63.6%) boys and 12 (36.4%) girls. The mean age was 26.8 ± 4.9 months. Haemophilus (P = 0.003) and Porphyromonas (P = 0.007) genera showed significant difference between the two groups. The metabolites of "starch and sucrose metabolism pathway" and "pentose phosphate pathway" showed significant correlations with the two bacterial genera. For starch and sucrose metabolism pathway, glucose-6-phosphate showed significant positive correlations with Haemophilus (r = 0.44 and P = 0.009) and Porphyromonas (r = 0.45 and P = 0.008). For pentose phosphate pathway, Sedoheptulose 7-phosphate, an intermediate in the pentose phosphate pathway, showed significantly positive correlations with Haemophilus (r = 0.42 and P = 0.02) and Porphyromonas (r = 0.43 and P = 0.01).

CONCLUSIONS: Our study provided new evidence that alteration in respiratory tract microbiome could be associated with RW in infants. By elucidating the microbiome and metabolite profile, we identified novel biomarkers potentially useful for personalized management of RW in infants. The future studies should validate the underlying mechanisms in longitudinal cohorts and explore interventions targeting metabolic-microbial crosstalk.},
}

Humans
Male
Female
Infant
*Respiratory Sounds/etiology
*Microbiota
Case-Control Studies
RNA, Ribosomal, 16S/genetics
Bronchoalveolar Lavage Fluid/microbiology
Metabolome
Metabolomics
Recurrence
DNA, Bacterial/genetics
Bacteria

@article {pmid42115865,
year = {2026},
author = {Huang, J and Chen, Z and Chen, M and Zeng, Z and Zhuang, X},
title = {Specific alterations in the gut microbiome and metabolome across disease locations of Crohn's disease: a systematic review.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-026-04898-z},
pmid = {42115865},
issn = {1471-230X},
support = {82200605//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Crohn's disease (CD) exhibits substantial heterogeneity in disease behavior and therapeutic outcomes across distinct disease locations. Specific alterations in the gut microbiota and metabolites may drive this variation. This review aims to characterize the distinctive microbial and metabolic signatures across CD phenotypes based on disease location.

METHODS: Electronic databases were searched from inception to December 2025 for studies that observed alterations in gut microbiota and metabolites in CD patients with different disease locations.

RESULTS: Forty-eight studies including 3,577 CD patients and 2,916 healthy controls (HCs) were analyzed. Ileal Crohn's disease (ICD) was characterized by significant dysbiosis compared with HCs, featuring enrichment of Enterobacteriaceae (especially adherent-invasive Escherichia coli [AIEC]), Fusobacterium and Shigella, alongside depletion of Faecalibacterium prausnitzii, Roseburia and Coprococcus. Patients with colonic Crohn's disease (CCD) exhibited increased levels of Proteobacteria, pro-inflammatory families (Actinomycetaceae, Micrococcaceae) and opportunistic pathogens (Streptococcus, Klebsiella). In contrast, a decrease in short-chain fatty acid (SCFA)-producing families (Lachnospiraceae, Ruminococcaceae) and F. prausnitzii was observed in CCD. Ileocolonic Crohn's disease (ICCD) displayed features combining ICD and CCD elements, with specific depletion in Alistipes communis and enrichment of Shigella flexneri. More pro-inflammatory bacteria were observed in ICD compared with CCD. In terms of metabolic alterations, ICD showed impaired enterohepatic bile acid circulation with excessive fecal loss of conjugated bile acids, while CCD exhibited defective conversion of primary to secondary bile acids. ICCD exhibited both impaired ileal reabsorption and defective colonic transformation.

CONCLUSIONS: Our results identified disease location-specific alterations in the microbiome and metabolome of CD, which might be associated with the clinical manifestations and prognosis of different phenotypes.},
}

@article {pmid42115921,
year = {2026},
author = {Bulfoni, M and De Martino, M and Gualandi, N and Marzinotto, S and Vesca, G and Krpan, B and Marcon, B and Bertoni, M and Tascini, C and Pipan, C and Curcio, F},
title = {Gut microbiota profiling of the population residing in Friuli-Venezia Giulia through next-generation sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05117-1},
pmid = {42115921},
issn = {1471-2180},
abstract = {The gut microbiota is an ecological community of symbiotic and commensal microorganisms that play crucial roles in nutrient metabolism, maintaining the structural integrity of the intestinal mucosal barrier, immunomodulation, and pathogen protection. The composition of the gut microbiota varies with age, ethnicity, lifestyle, and dietary habits. Given the microbiota's growing role as a modulator of various physiological and pathological conditions, our study aimed to investigate the genetic profile of the microbiome individuals residing in the Friuli-Venezia Giulia region. We analyzed fecal swab samples from 109 individuals belonging to a general population cohort. The hypervariable V3-V4 regions of bacterial 16 S rRNA were analyzed using Next Generation Sequencing (NGS) on the MiSeq system (Illumina). The relative abundance of phyla, classes, orders, families, and species was defined using the BaseSpace 16s metagenomics app (Illumina). Firmicutes was the most represented phylum (51.1%), followed by Bacteroidetes (38.3%) and Actinobacteria (3%). At the class level, Clostridia (45.2%) and Bacteroidia (37.7%) were predominant, while Clostridiales (46.9%), Bacteroidales (26.6%), and Anaeroplasmatales (12.6%) were notable orders. Lachnospiraceae (21.9%) and Ruminococcaceae (16.2%) were the most frequent families, with Faecalibacterium prausnitzii (10.3%), Bacteroides vulgatus (4.6%), and Bacteroides dorei (3.5%) being prominent species. Each participant's taxa were analyzed to identify genera associated with alterations in gut microbial composition. Significant associations emerged between specific taxa of microorganisms and age, gender, anti-inflammatory drugs, tobacco consumption, and allergies. This study provides valuable insights into gut microbiota composition in a population-based cohort. The characterization of the microbiota in the Friuli-Venezia Giulia (FVG) region lays the foundation for future research into regional variations in microbiota composition and its impact on health.},
}

@article {pmid42115936,
year = {2026},
author = {Dalgic, A and Yet, I},
title = {Identifying gut microbiome signatures of type 1 diabetes using machine learning and evolutionary feature selection.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05113-5},
pmid = {42115936},
issn = {1471-2180},
abstract = {BACKGROUND: Type 1 Diabetes Mellitus (T1D) has been increasingly associated with alterations in the gut microbiome. However, the impact of taxonomic resolution, feature selection strategies, and machine learning methods on microbiome-based prediction remains incompletely understood.

METHODS: We analyzed publicly available 16S rRNA gene sequencing datasets from two geographic cohorts to evaluate microbiome-based prediction of T1D. Microbial features were constructed at multiple taxonomic levels and as full hierarchical taxonomic paths preserving phylogenetic structure. Machine learning models were trained using stratified cross-validation and cross-cohort validation frameworks. Feature selection was performed using Binary Particle Swarm Optimization (BPSO) to identify compact and predictive microbial signatures. Model performance was evaluated using AUC, Accuracy, F1 score, and Matthews Correlation Coefficient. Differential abundance analysis using the LinDA framework was used to support biological interpretation of selected taxa.

RESULTS: Tree-based models, particularly Random Forest and XGBoost, achieved the strongest predictive performance across taxonomic representations. Taxonomic resolution influenced model behavior, with family-level features providing strong performance with compact feature sets, while higher-resolution representations did not consistently improve performance despite increased complexity. BPSO identified consistently selected taxa across validation frameworks, suggesting stable predictive signatures. Several of these taxa have been linked to inflammatory or metabolically altered gut environments. Cross-cohort validation showed reduced performance compared with within-study models, highlighting challenges in generalization.

CONCLUSION: Machine learning combined with BPSO-based feature selection provides an effective framework for identifying predictive microbial signatures associated with T1D. Our findings highlight the importance of taxonomic resolution, feature stability, and cross-cohort validation in microbiome-based predictive modeling. Integrating evolutionary feature selection with machine learning and biological validation may improve the robustness and interpretability of candidate microbial signatures.},
}

@article {pmid42116047,
year = {2026},
author = {Choi, JW and Kim, H and Ham, SH and Han, YJ and Kim, SE and Sung, MK},
title = {Probiotic Bifidobacterium bifidum BGN4 supplementation modulates gut microbiome composition and reduces circulating zonulin, TNFα, and insulin in adults with excess adiposity: a randomized, double-blind, placebo-controlled trial.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-026-01124-1},
pmid = {42116047},
issn = {1743-7075},
support = {2023R1A2C1005313//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2022R1A2C1004626//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; },
abstract = {BACKGROUND: Obesity, characterized by excess body fat accumulation, is closely linked to the alteration of gut microbiota, which contribute to systemic inflammation. Probiotics intervention has emerged as a promising strategy favorably modulating gut microbiota composition in obese individuals accompanied by improvements in metabolic parameters. The objective of this study was to evaluate whether supplementation with Bifidobacterium bifidum BGN4 alters gut microbiota composition and to assess its associated effects on circulating zonulin, a marker of intestinal permeability, as well as metabolic parameters in individuals with excess adiposity.

METHODS: This randomized, double-blind, placebo-controlled trial involved 60 adults with excess body fat (body fat percentage ≥ 20% for males and ≥ 28% for females). A total of 60 adults were enrolled, and sex- and age-stratified randomization allocated 30 participants to each group. Participants received one capsule of B. bifidum BGN4 (9 × 10[9] colony forming unit) or matched placebo for 8 weeks. Blood samples were analyzed for zonulin, TNFα, hs-CRP, glucose, insulin, lipid profiles, and total antioxidant capacity. Fecal samples were analyzed to determine alterations in gut microbiota composition.

RESULTS: A total of 58 participants, with 29 individuals in each group, successfully completed the 8-week intervention. Supplementation with B. bifidum BGN4 did not result in significant changes in BMI, body fat percentage, or the primary outcome, hs-CRP. In contrast, significant improvements were observed in serum zonulin (between-group differences: -1.61 ± 2.69 ng/mL), TNFα (between-group differences: -0.17 ± 0.26 pg/mL), and fasting insulin (between-group differences: -3.52 ± 10.25 μIU/mL). The probiotic intervention modulated the enrichment of several taxa, including Bacteroides coprocola, Bifidobacterium catenulatum group, Lactiplantibacillus plantarum group, and Prevotella stercorea. In addition, several microbial taxa demonstrated correlations with metabolic and inflammatory parameters. No adverse effects were observed, as indicated by stable liver enzyme concentrations, blood pressure, and gastrointestinal symptoms.

CONCLUSION: The results indicate that B. bifidum BGN4 may serve as a preventive strategy for metabolic disorders in individuals with excess adiposity through the maintenance of gut microbial balance and intestinal barrier integrity thereby potentially mitigating inflammation and metabolic stress.

TRIAL REGISTRATION: Clinical trial registration number: KCT0010817. Date of registration: July 28, 2025.},
}

@article {pmid42116157,
year = {2026},
author = {Li, S and Lin, L and Zhang, M and Liu, J and Lu, E and Cao, Z},
title = {Nanoengineered bile acid-mediated orchestration of versatile immuno-microbial cues for treating periodontitis.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04495-y},
pmid = {42116157},
issn = {1477-3155},
support = {82401198//National Science Foundation of China/ ; 52171075//National Science Foundation of China/ ; 22575146//National Science Foundation of China/ ; 2022M710748//China Postdoctoral Science Foundation/ ; 22YF1439400//the Youth Science and Technology Talents-the Sailing program of Shanghai/ ; 25ZR1401224//Natural Science Foundation of Shanghai/ ; },
abstract = {Periodontitis, a globally prevalent inflammatory disease, is propelled by a vicious cycle involving microbial dysbiosis, hyperactive host immune responses, excessive oxidative stresses, and chronic inflammations. Current treatments largely focus on reducing microbial pathogens, yielding limited therapeutic efficacy. Here, we report a polydopamine-based taurolithocholic acid (TLCA) nanotherapeutic (PDCA) that reprograms versatile immuno-microbial cues to ameliorate periodontal inflammation and restore tissue homeostasis. Leveraging the dual function of polydopamine in drug delivery and redox capacity, after cellular uptake, PDCA scavenges reactive oxidation species, and releases TLCA to interact with its nuclear receptors in various target cells, exerting multifaceted regulatory effects. In inflamed human gingival fibroblasts, PDCA reduces the oxidative stress and enriches intracellular accumulation of TLCA to assist its interaction with vitamin D receptor, thus attenuating the expression of pro-inflammatory cytokines. Furthermore, PDCA modulates hyperactive immune responses, including suppressing the maturation of dendritic cells, inhibiting osteoclast differentiation of monocytes, downregulating pro-inflammatory CD4[+] lymphocytes, and upregulating regulatory T cells. Concomitantly, this immunomodulation is associated with the restoration of periodontal microbiome homeostasis, contributing to a reduction in pathogens and an enrichment of beneficial flora. In addition, PDCA not only rescues inflammatory tissue destructions in both therapeutic and prophylactic mouse models of periodontitis, but also elicits robust decrement in pro-inflammatory cytokine production in ex vivo human periodontitis tissues. This work highlights polydopamine-based bile acid nanomedicine as a microenvironment-targeting platform for immuno-microbial rebalance, offering a transformative strategy to treat oral inflammatory diseases.},
}

@article {pmid42116193,
year = {2026},
author = {Tamang, A and Kumar, A and Thakur, A and Kumar, R and Kumar, D and Hallan, V and Pandey, SS},
title = {Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00909-4},
pmid = {42116193},
issn = {2524-6372},
support = {MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; },
abstract = {BACKGROUND: Endophytic fungi form an integral part of plant microbiomes, influencing host physiology, stress resilience, and secondary metabolism. While next-generation sequencing (NGS) has greatly advanced the identification of endophytes, it often falls short of assigning functional roles, necessitating integration with culture-based approaches for downstream applications. Picrorhiza kurrooa, a critically endangered Himalayan medicinal herb valued for its hepatoprotective picrosides, suffers from reduced metabolite content in tissue culture-derived plants, likely due to microbiome loss in the course of aseptic in-vitro practices. Moreover, the diversity and functional role of fungal endomicrobiome in P. kurrooa remain unexplored.

METHODS: Internal transcribed spacer (ITS)-based amplicon sequencing was performed to assess and compare the endophytic fungal communities of wild-type (Wt) and in-vitro propagated (Tc) P. kurrooa. Fungal taxa unique to Wt-plants were identified and cross-referenced with culturable isolates. A dominant isolate present only in Wt-plants, Trichoderma harzianum PKRF1, was reintroduced into Tc-plants to evaluate its effect on plant growth and picroside biosynthesis. Whole-genome sequencing and comparative genomics of PKRF1 were also conducted to elucidate its functional capabilities and possible candidates for its endophytic nature.

RESULTS: Metagenomic analysis revealed a significant reduction in fungal diversity in Tc plants, with several taxa, including Trichoderma, Cyphellophora, and Preussia, exclusively associated with Wt-plants. Inoculation of Tc-plants with PKRF1 led to successful root colonization, enhanced photosynthetic efficiency, biomass, and significantly higher levels of picrosides. Transcript profiling confirmed upregulation of key biosynthetic genes. Genomic analysis of PKRF1 revealed genes associated with multiple plant-beneficial traits, including nutrient acquisition, phytohormone production, stress tolerance, plant colonization, and competitive interactions, distinguishing it from non-endophytic Trichoderma isolates.

CONCLUSIONS: These findings provide the first comprehensive insight into changes in endophytic fungal diversity of P. kurrooa associated with in-vitro cultivation. Furthermore, the application of cultivated endophytes from wild plants demonstrated the potential to restore microbial functions lost during in-vitro propagation and enhance secondary metabolite production in cultivated plants. Overall, this approach offers a promising strategy to integrate metagenomic information into beneficial plant-microbe interactions for practical applications.},
}

@article {pmid42116194,
year = {2026},
author = {Buetas, E and Conde-Pérez, K and Concha, Á and Celeiro, C and Noguera, JF and Bou, G and Pardiñas-López, S and Vallejo, JA and Poza, M and Carda-Diéguez, M and Mira, A},
title = {Metatranscriptomic analysis of the microbiota of tumor tissue in colon cancer.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02372-2},
pmid = {42116194},
issn = {2049-2618},
abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, accounting for more than 900,000 deaths a year worldwide. Microbial dysbiosis, including the presence of oral bacteria in the gut, has been linked to CRC. Some mechanisms by which specific microorganisms potentially drive tumorigenesis have been described, but there is a lack of studies elucidating whole microbiota activity in the tumor and their implication for the development of the disease. Here, the metatranscriptomic data of tumor and control tissue-associated microbiota (n = 18 pairs), as well as from subgingival sulcus (n = 15) of CRC patients, was analyzed.

RESULTS: We confirmed that Fusobacterium nucleatum was more active in the tumor tissue than in the control gut mucosa. In addition, the activity of this species was positively correlated with other oral bacteria in the tumors, including Parvimonas micra, Peptostreptococcus stomatis, and Granulicatella adiacens, along with gut bacteria like Hungatella hathewayi, suggesting a potential relationship among them. Regarding bacterial gene expression, a change in the functional profile was observed, including a higher expression of genes associated with carbon metabolism in control in contrast to an increase of amino acid-related genes in tumor. Furthermore, genes implicated in the biosynthesis and transport of lipopolysaccharide were increased in tumors. Interestingly, a significantly higher expression in tumor than control tissue of potential virulence factors from F. nucleatum was found, supporting their relevance in niche colonization and tumorigenesis. Correlation analysis of the bacterial activity with the host transcriptional profile showed significant correlations of the Fusobacterium-Peptostreptotoccus-Hungatella cluster with human genes involved in inflammation and metastasis, confirming the association of this microbial consortium with tumor development. For the first time, the gene expression profiles of oral bacteria in the gut and the oral cavity were compared. The cluster of co-active bacteria identified in tumors was partially found in the oral samples, suggesting a stable interaction and potential synergy. Although there were thousands of differentially expressed genes between subgingival sulcus and tumor tissue, the expression of key virulence factors was not significantly different.

CONCLUSIONS: In short, this study discovered new traits about tumor microbial-associated composition and activity and its connection with the oral composition that would be essential to unravel the translocation, colonization, and tumorigenesis of the CRC.},
}

@article {pmid42116227,
year = {2026},
author = {Hron, BM and Zhang, YJ and Golden, C and Chalmers, C and Nemec, G and Delaney, E and Ozcan, E and Kim, M and Jalali, L and Solari, T and Brezsny-Feldman, J and Alm, EJ and Bry, L and Rosen, R},
title = {Association between blenderized tube feeds and differential oropharynx, stomach, and stool microbiome signatures relative to conventional formula feeds in children fed via enteral tube: A cross-sectional study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.70097},
pmid = {42116227},
issn = {1941-2444},
support = {//Supported by National Institutes of Health R01 DK097112 (PI: Rosen) and K23 DK133679 (PI: Hron), NASPGHAN Astra- Zeneca Research Award (PI: Hron), NIH K12 5K12HD052896 (PI: Fleisher, awarded to Zhang); NASPGHAN Foundation/Reckitt/Mead Johnson Nutrition Young Investigator Development Award (PI: Zhang); AGA Research Scholar Award (PI: Zhang); Harvard Digestive Diseases Center Grants P30 DK034854 (NIH) and Massachusetts Life Sciences Center Capital Grant./ ; },
abstract = {BACKGROUND: Blenderized gastrostomy tube feeds are associated with reduced gastrointestinal symptoms. We hypothesize that patients receiving blenderized tube feeds, compared with standard formula, will have less gastric-oropharyngeal microbial overlap, a possible biomarker of less gastroesophageal refluxate, and differences in beta diversity in the oropharynx, stomach, and stool.

METHODS: Children requiring enteral tube feeds for >3 months were prospectively recruited to provide saliva via posterior tongue swabs, gastric aspirates, and stool samples. Exclusion criteria were history of cystic fibrosis or solid organ transplant or antibiotic treatment course within 4 weeks. The primary exposure was diet category (formula vs. blenderized feeds). The primary outcome was Jaccard similarity between the gastric and oral microbiomes. Relationships of diet to Jaccard and relative bacterial abundance were analyzed by multivariate linear regression models adjusting for age, sex and proton pump inhibitor use.

RESULTS: Sixty (60.6%) children received blenderized tube feeds and 39 (39.4%) received formula. Beta diversity in the oral and rectal samples differed significantly between patients on blenderized versus formula feeds. Importantly, gastric and tongue microbiomes had significantly less overlap (by Jaccard distance) in patients receiving blenderized feeds, adjusting for covariates. Several key oral, gastric and stool commensal organisms were present in higher relative abundance in the blenderized versus formula group.

CONCLUSION: Oropharyngeal microbiomes are more distinct from the gastric microbiomes in patients receiving blenderized feeds, and the oropharyngeal and stool microbiomes demonstrated differential bacterial abundance compared with formula. Overall, these findings suggest a highly favorable microbial profile with blenderized feeds.},
}

@article {pmid42116335,
year = {2026},
author = {Nie, Y and Lin, X},
title = {Analysis of oral microbiome characteristics and their correlation with oral health diseases.},
journal = {Medicine},
volume = {105},
number = {19},
pages = {e48600},
pmid = {42116335},
issn = {1536-5964},
mesh = {Humans ; Female ; Male ; Cross-Sectional Studies ; *Microbiota ; Middle Aged ; *Oral Health ; *Mouth Diseases/microbiology/epidemiology ; Adult ; *Mouth/microbiology ; Aged ; },
abstract = {To investigate the relationship between oral microbiome characteristics and oral health status, examining microbial diversity and the prevalence of specific bacterial genera. We conducted a cross-sectional study of 154 patients who underwent oral examinations at our hospital from January 2023 to December 2023. Based on routine oral examinations and medical history inquiries, patients were divided into oral health group (n = 71) and oral health disease group (n = 83). Oral samples were collected and analyzed using next-generation sequencing and bioinformatics to assess microbial diversity and abundance. Key demographic and behavioral factors were recorded, and statistical analyses determined oral microbiome characteristics with oral health. The oral health disease group had significantly higher average age, smoking rates, body mass index, alcohol use, family history of oral diseases, and worse oral health indicators (e.g., plaque, gum inflammation, calculus, periodontal status, decayed/missing teeth, and decayed, missing, and filled teeth scores). They also showed lower microbial diversity (Shannon, Chao1, and evenness indices) and reduced levels of protective bacteria (Streptococcus and Actinomyces). In contrast, the oral health group had higher flossing rates, more caries-free individuals, and greater microbial diversity. The Shannon, Chao1, and evenness indices were inversely linked to oral disease, while the Simpson Index (measuring dominance) was positively correlated. Protective bacteria were negatively linked to disease, whereas harmful bacteria (Fusobacterium and Prevotella) were positively correlated. Our findings highlight decreased microbial diversity as a significant factor in oral diseases, suggesting that maintaining a diverse oral microbiome was crucial for oral health.},
}

Humans
Female
Male
Cross-Sectional Studies
*Microbiota
Middle Aged
*Oral Health
*Mouth Diseases/microbiology/epidemiology
Adult
*Mouth/microbiology
Aged

@article {pmid42116339,
year = {2026},
author = {Han, GY and Wang, ZJ and Wang, DX and Wang, CY and Yang, MQ},
title = {Forging new insights in forensic microbiome studies: A 2000 to 2024 bibliometric analysis redefining the landscape.},
journal = {Medicine},
volume = {105},
number = {19},
pages = {e48661},
pmid = {42116339},
issn = {1536-5964},
mesh = {*Bibliometrics ; Humans ; *Microbiota ; *Forensic Sciences ; *Forensic Medicine ; RNA, Ribosomal, 16S ; Machine Learning ; },
abstract = {BACKGROUND: Microbial diversity has been extensively studied across various fields, including medicine and therapeutics. Its application in forensics is rapidly expanding due to its effectiveness. This study aimed to conduct a comprehensive bibliometric analysis of global research on forensic microbiome, providing a foundational knowledge framework for this emerging field.

METHODS: A comprehensive literature search was performed using the Web of Science Core Collection database to identify publications related to the forensic microbiome. Annual publication output, research collaborations, research hotspots, and developmental trends in this field were analyzed using bibliometric software (VOSviewer and CiteSpace).

RESULTS: In total, 709 articles published between 2000 and 2024 were selected. The first study in this field was published in 2000. Recently, the number of publications and citations has grown significantly. Cooperation network analysis revealed that the United States of America contributes the most to forensic microbiome research, with the highest publication volume. Michigan State University emerged as the most prolific institution. Forensic Science International is the most productive journal in this field. Carter David O. contributed the most to the articles and is the most co-cited authors. Keywords cluster analysis identified 4 major research clusters: bacteria, forensic medicine, 16s ribosomal ribonucleic acid, and machine learning. Machine learning, human microbiome, and forensic microbiology have attracted increasing attention from researchers.

CONCLUSION: This bibliometric analysis provides a data-driven and objective overview of forensic microbiome research currently, offering readers a valuable reference for future research. Our review provides insights into contemporary trends, global patterns of collaboration, fundamental knowledge, high-interest research areas, and emerging frontiers in the forensic microbiome.},
}

*Bibliometrics
Humans
*Microbiota
*Forensic Sciences
*Forensic Medicine
RNA, Ribosomal, 16S
Machine Learning

@article {pmid42116498,
year = {2026},
author = {Wang, L and Liang, C and Yu, J and Zhang, Y and Li, H and Hu, Y and Liu, W and Qu, X and Xie, W and Wang, X and Yuan, H},
title = {Timing matters in type 2 diabetes: Early high-Fiber nutrition enhances glycemic control and reshapes gut microbiota.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119257},
doi = {10.1016/j.foodres.2026.119257},
pmid = {42116498},
issn = {1873-7145},
mesh = {Humans ; *Diabetes Mellitus, Type 2/diet therapy/microbiology/blood ; *Dietary Fiber/administration & dosage ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Over Studies ; Middle Aged ; *Glycemic Control/methods ; Blood Glucose/metabolism ; Glycated Hemoglobin/metabolism/analysis ; Aged ; Obesity/diet therapy ; Time Factors ; Adult ; Overweight/diet therapy ; },
abstract = {Early, intensive dietary intervention may open a therapeutic window for type 2 diabetes (T2D) remission. We conducted a randomized, 2:1 crossover trial in 34 newly diagnosed overweight or obese patients with T2D. Participants were assigned to receive either high-fiber nutritional therapy (HFNT)-a 7-day very-low-calorie, high-fiber diet followed by a 23-day standard diabetes diet-or conventional diabetes treatment (control condition). Each treatment was administered for 90 days before crossover. Compared with the control condition, early HFNT led to greater reductions in HbA1c [-9.45% (-18.04, -4.63) vs 1.44% (-7.73, 3.08); P = 0.010] and fasting plasma glucose [-12.70% (-24.51, -6.01) vs 3.46% (-8.14, 0.94); P = 0.005], while changes in BMI and HOMA-IR were not significant (P > 0.05). Gut microbiome profiling revealed enrichment of short-chain fatty acid-producing taxa (Eubacterium ruminantium group, Blautia, Roseburia, Akkermansia muciniphila, Oscillospira) and depletion of pathogenic genera (Escherichia-Shigella) after HFNT, with compositional shifts correlating with improved glycemic control. Notably, glycemic benefits in participants receiving HFNT first persisted after crossover, whereas participants receiving conventional care first did not achieve full metabolic recovery after switching. These findings suggest that in newly diagnosed T2D, early, fiber-enriched, intermittent energy restriction can induce durable glycemic improvements, potentially mediated by gut microbiota remodeling. This trial highlights a narrow but impactful nutritional intervention window that may alter the trajectory of T2D progression.},
}

Humans
*Diabetes Mellitus, Type 2/diet therapy/microbiology/blood
*Dietary Fiber/administration & dosage
*Gastrointestinal Microbiome
Male
Female
Cross-Over Studies
Middle Aged
*Glycemic Control/methods
Blood Glucose/metabolism
Glycated Hemoglobin/metabolism/analysis
Aged
Obesity/diet therapy
Time Factors
Adult
Overweight/diet therapy

@article {pmid42116511,
year = {2026},
author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W},
title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119274},
doi = {10.1016/j.foodres.2026.119274},
pmid = {42116511},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Food Microbiology ; Taste ; Volatile Organic Compounds/analysis ; Bacteria/metabolism/classification/genetics ; *Wine/microbiology/analysis ; Fungi/metabolism/classification ; Metabolomics ; Flavoring Agents ; China ; },
abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.},
}

*Fermentation
*Microbiota
*Metabolome
Food Microbiology
Taste
Volatile Organic Compounds/analysis
Bacteria/metabolism/classification/genetics
*Wine/microbiology/analysis
Fungi/metabolism/classification
Metabolomics
Flavoring Agents
China

@article {pmid42116975,
year = {2026},
author = {Latt, TS and Aye, TT and Ko, K and Win, SS and Chit, TT and Myint, KNS},
title = {Restructuring the Obesity Paradigm: Molecular Etiologies, Clinical Complexities, and the Future of Precision Intervention.},
journal = {Cureus},
volume = {18},
number = {4},
pages = {e106767},
pmid = {42116975},
issn = {2168-8184},
abstract = {Obesity is a complex, chronic, and relapsing disease affecting adults globally and continues to rise across all age and socioeconomic groups. Once regarded as a lifestyle issue, obesity is now recognized as a multifactorial condition influenced by multiple factors. This review consolidates current evidence on the dynamic pathophysiology of obesity, highlighting advances in understanding its genetic foundations, hormonal imbalances, gut microbiome disruptions, and the influence of early-life exposures, and emphasizing the systemic impact of obesity through its associations with cardiometabolic diseases, certain cancers, and mental health disorders. Emerging treatment paradigms include glucagon-like peptide-1 and dual agonists, endoscopic and surgical interventions, and microbiota-directed therapies. Advances in artificial intelligence and precision medicine are also redefining individualized care. Despite these developments, obesity remains underdiagnosed and undertreated in many healthcare systems. In high-income regions, the uptake of advanced therapies is limited by fragmented care pathways, in which obesity management is spread across multiple uncoordinated providers, and by affordability barriers due to high costs. In low-resource settings, constrained infrastructure and competing health priorities continue to hinder timely diagnosis and treatment. A shift toward holistic, patient-centered, and equity-driven models of care is essential for effectively addressing the global burden of obesity and improving long-term health outcomes.},
}

@article {pmid42117346,
year = {2026},
author = {Nguyen, HKD and Jones, PJ and Kendal, D and Powell, SM and Raspin, K and Dickinson, J and Flies, EJ},
title = {A Comparison of the Gut Microbiome of Two Sympatric Macropods Along an Urbanisation Gradient in Tasmania.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70359},
pmid = {42117346},
issn = {1758-2229},
support = {//Holsworth Wildlife Research Endowment/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Tasmania ; *Macropodidae/microbiology ; Urbanization ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Sympatry ; Feces/microbiology ; Parks, Recreational ; Cities ; Animals ; },
abstract = {This study investigates the gut flora of the red-necked wallaby (Notamacropus rufogriseus rufogriseus) and the Tasmanian pademelon (Thylogale billardierii) in the small city of Hobart, Tasmania, Australia. Faecal samples were collected from greenspaces across the Greater Hobart region. These greenspaces were chosen in areas with different human population densities. DNA was extracted from these samples, and targeted sequencing of the bacterial 16S ribosomal RNA gene was performed to understand the bacterial community. Our results showed that despite the many shared ecological traits between the two species, their gut microbiome displayed different responses to urban living. Alpha and beta diversity were significantly different across the urban gradient for Bennett's wallaby, but not for Tasmanian pademelon. Relative composition for both species was different across the urbanisation gradient. Some bacterial taxa associated with nutrient processing showed the clearest changes. The conclusion of this research is that living in cities can affect the gut microbiome of these two marsupial herbivores. More studies are needed to determine whether this has implications for the health of these species.},
}

*Gastrointestinal Microbiome/genetics
Tasmania
*Macropodidae/microbiology
Urbanization
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Sympatry
Feces/microbiology
Parks, Recreational
Cities
Animals

@article {pmid42117437,
year = {2026},
author = {Tumelty, M and Patel, K and Petersen, H and Delaney, C and Lappin, D and Gibson, J and Ramage, G and van der Gast, C and Smith, A and Nile, CJ},
title = {Investigations into the aetiopathogenesis of orofacial granulomatosis using multiple omics technologies reveal a potential role for B cells.},
journal = {Clinical and translational medicine},
volume = {16},
number = {5},
pages = {e70689},
doi = {10.1002/ctm2.70689},
pmid = {42117437},
issn = {2001-1326},
support = {//Royal College of Surgeons of England/ ; //Royal College of Physicians and Surgeons of Glasgow/ ; //Tenovus Scotland/ ; //University College London Hospitals Biomedical Research Centre/ ; //NIHR Newcastle Biomedical Research Centre/ ; },
}

@article {pmid42117804,
year = {2026},
author = {Zalila-Kolsi, I and Al-Barazie, R},
title = {Probiotics and the Human Microbiome: Classical Functions, Emerging Systemic Roles, and Future Therapeutic Frontiers.},
journal = {Biology},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/biology15090665},
pmid = {42117804},
issn = {2079-7737},
abstract = {Probiotics, live microorganisms that confer health benefits when administered in adequate amounts, are increasingly recognized as modulators of interconnected microbiome-host networks that extend beyond gastrointestinal function. This review synthesizes evidence on classical probiotic roles in maintaining gut homeostasis, immune regulation, and infection prevention, while integrating emerging systemic effects across the gut-brain, gut-skin, gut-oral, and metabolic axes. Rather than presenting isolated outcomes, we adopt a systems-level framework that links probiotic actions to shared mechanisms, including microbial metabolite signaling (e.g., SCFAs), competitive exclusion of pathobionts, barrier reinforcement, and immune-neuroendocrine pathway modulation. We further discuss translational advances that enable rational probiotic design, including targeted delivery platforms (encapsulation and protective matrices), engineered/next-generation strains, and postbiotic-inspired strategies, alongside sustainability considerations and regulatory/labeling challenges. Finally, we outline future directions emphasizing precision microbiome-centered interventions, synthetic biology, and AI-assisted multi-omics analysis to support strain- and context-specific probiotic strategies. Collectively, this review provides an integrated, systems-oriented synthesis to guide future research and accelerate safe clinical and industrial applications of probiotics.},
}

@article {pmid42117816,
year = {2026},
author = {Chen, H and Wang, W and Ye, X and Feng, L and Wang, M and Xie, T and Ren, D and Song, Y and Chen, S and Zhang, C and Zhu, W},
title = {Gut Microbiota Assembly and Host Phenotypic Variation: Core Adaptive Strategies of Triplophysa yarkandensis (Cypriniformes: Nemacheilidae) to Saline-Alkaline Stress.},
journal = {Biology},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/biology15090677},
pmid = {42117816},
issn = {2079-7737},
support = {32541125//National Natural Science Foundation of China/ ; TDZKBS202534//The President's Fund of Tarim University/ ; TDZKBS202543//The President's Fund of Tarim University/ ; 525307003//"Tianchiyingcai" Introduction Project/ ; 525307006//"Tianchiyingcai" Introduction Project/ ; },
abstract = {Triplophysa yarkandensis (Cypriniformes: Nemacheilidae), a rare endemic fish in the Tarim River Basin, Xinjiang, China, plays a pivotal role in maintaining the stability of plateau saline-alkaline aquatic ecosystems, yet its survival is increasingly threatened by habitat salinization. However, the multi-dimensional synergistic adaptation mechanisms linking its phenotypic variation, intestinal structure, and associated microbial communities to extreme saline-alkaline stress remain poorly understood. In this study, we innovatively integrated morphological/intestinal histological characterization, 16S rRNA gene sequencing, and microbial ecological analyses (co-occurrence networks and assembly processes) to systematically decode its adaptive strategies. Results revealed that T. yarkandensis exhibits a streamlined body shape, morphological variability, and elongated intestinal villi that may support locomotion and nutrient/ion uptake under osmotic stress. Its gut exerts a stringent selective filter, driving distinct differentiation between water and gut microbial communities-with gut-enriched core taxa (Aurantimicrobium and Aestuariivirga) and functional pathways (unsaturated fatty acid biosynthesis and ABC transporters) specialized for osmoregulation. Notably, the water microbial assembly is dominated by stochastic processes, while the gut assembly relies on host-driven deterministic selection, forming a habitat-specific adaptive pattern. These findings uncover the synergistic adaptation system of host phenotype and gut microbiota for survival in extreme saline-alkaline habitats, advancing our understanding of fish-microbe co-evolution in extreme ecosystems and providing critical theoretical support for the conservation of rare plateau fish, as well as guidance for the utilization of saline-alkaline water resources in aquaculture.},
}

@article {pmid42117850,
year = {2026},
author = {Asylbekkyzy, L and Kossalbayev, BD and Ahmad, F and Wang, J and Sadvakasova, AK and Bauenova, MO and Abseyt, AA and Zaletova, DE},
title = {Environmental Filtering of Bacterial Communities Driven by Pesticide Residue Profiles in the Almaty Region, Kazakhstan.},
journal = {Biology},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/biology15090712},
pmid = {42117850},
issn = {2079-7737},
abstract = {Soil contamination by complex pesticide mixtures poses a systemic threat to ecosystem health, yet the mechanisms of microbial community assembly under the coexistence of legacy and modern pollutants remain insufficiently understood. This study evaluated the influence of legacy organochlorine pesticides (OCPs) versus current-use agrochemicals on the structure and inferred functional potential of soil bacterial communities in the Almaty Region, Kazakhstan, using high-throughput 16S rRNA gene sequencing and GC-MS/MS analysis of 217 compounds. Results revealed a clear contrast between contamination regimes: modern organophosphate insecticides and herbicides, such as simazine (up to 32.3 mg kg[-1] at the Amangeldy site), were associated with lower alpha diversity (Shannon ≈ 3.03) and enrichment of copiotrophic taxa such as Pseudomonas and Sphingobium. In contrast, persistent OCP residues, such as p,p'-DDE (up to 1.43 mg kg[-1] at the Kyzylkairat site), were associated with higher diversity (Shannon ≈ 5.46) and enrichment of more stress-tolerant oligotrophic lineages, including Acidobacteria and Vicinamibacteraceae. Procrustes analysis supported significant concordance between pesticide profiles and taxonomic structure (M[2] = 0.286, p < 0.001), indicating that pesticide residue composition was strongly associated with bacterial community structure across the studied soils. The observed shift in community balance, particularly the relative increase in Pseudomonas versus Acidobacteria, is proposed as a candidate compositional indicator of ecosystem instability in semi-arid agricultural soils and may inform future remediation-oriented studies.},
}

@article {pmid42117863,
year = {2026},
author = {Li, D and Deng, Y and Zhao, X and Liao, Q and Chen, J and Li, C and Liao, H},
title = {Soil pH and Nitrogen Content Drive the Succession of RubisCO-Harboring Microbial Communities Across Picea asperata Plantation Ages.},
journal = {Biology},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/biology15090725},
pmid = {42117863},
issn = {2079-7737},
support = {2024NSFSC0849；2025ZNSFSC1221//Sichuan Science and Technology Program/ ; SCJJ24ZD68//the historical study of ancient and famous trees along the Shu Dao Roads: a case study of Cuiyun Corridor in Zitong/ ; },
abstract = {Autotrophic carbon-fixing microbes can assimilate atmospheric carbon dioxide into biomass via the Calvin-Benson-Bassham (CBB) cycle (their primary carbon fixation pathway), thereby reinforcing soil carbon sequestration in the plantation ecosystem; however, the succession of RubisCO-harboring microbial communities across stand ages remains poorly understood. Here, we investigated the community succession of microbes carrying the gene encoding RubisCO, a key enzyme in the CBB cycle, across a stand-age chronosequence in a Picea asperata plantation ecosystem. Our results revealed a progressive decrease in microbial α-diversity and a significant restructuring of community composition with increasing stand age, characterized by an enrichment of Proteobacteria and a concomitant depletion of Actinobacteria. While the Shannon-Wiener index was most strongly correlated with soil total nitrogen content, redundancy analysis identified soil pH as the predominant environmental driver of community turnover, a relationship that was found to be threshold-dependent, with substantial community shifts occurring in response to pH variations of 0.5 to 1.0 units. These findings suggest that sustaining the diversity of RubisCO-harboring microbes in older stands-a process potentially enhanced by soil nitrogen management-provides a viable strategy for augmenting the carbon sequestration capacity of managed forests through targeted microbiome regulation.},
}

@article {pmid42118059,
year = {2026},
author = {Vaishnav, A and Jansa, J},
title = {Arbuscular mycorrhizal fungi- linked microbial processes in soil nitrogen cycling.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag050},
pmid = {42118059},
issn = {1574-6941},
abstract = {Arbuscular mycorrhizal fungi (AMF) create an extended plant-soil interface (referred to as mycorrhizal hyphosphere) where specific microbial interactions shape key steps of the nitrogen (N) cycle. Extraradical hyphae of the AMF host diverse microbes that help mineralize organic substrates, regulate ammonium and nitrate transformations, and enhance N retention. These processes allow plants to access both inorganic N and the N released from complex organic compounds. This review synthesizes current evidence for AMF-microbe interactions in relation to mineralization, nitrification, denitrification, and (di)nitrogen fixation. It also highlights unresolved questions, such as when AMF transition from facilitating to competing for N, how they access stabilized organic N pools, and how the carbon:nitrogen:phosphorus (C:N:P) nutrient stoichiometry of the soil environment constrain AMF-mediated N transfer to plants. Furthermore, we discuss how AMF-centered pathways can contribute to more circular N flows in agroecosystems by promoting tighter internal N cycling through microbial immobilization, turnover, and subsequent transfer to plants via AMF hyphae. By integrating spatial, microbial, and stoichiometric perspectives, this review provides a mechanistic framework for understanding AMF-driven N dynamics and their potential role in enhancing N use efficiency in managed and natural systems.},
}

@article {pmid42118196,
year = {2026},
author = {Stewart, J and Ockert, LE and Hawke, T and Power, M and Bino, G},
title = {First insights into the Drivers of the Cloacal Microbiome of the Wild Platypus (Ornithorhynchus anatinus).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02788-1},
pmid = {42118196},
issn = {1432-184X},
abstract = {The host microbiome plays a critical role in wildlife health, reproduction, and environmental responses. The platypus (Ornithorhynchus anatinus), a semi-aquatic monotreme endemic to eastern Australia, has remained microbiologically understudied despite conservation concern. Here, we present the first characterisation of the wild platypus cloacal microbiome using 16 S rRNA amplicon sequencing of samples collected across its eastern range, including sites recently affected by drought and bushfire. We found that region, and environmental disturbances such as bushfire and drought were significant drivers of bacterial community structure and composition, with influence from sex and breeding season also. Bushfire and drought both disrupted microbial community structure. The microbiome partially recovered following low-severity fires, but not after severe fire or prolonged drought, suggesting that microbiome resilience is linked to disturbance intensity. These findings suggest that the platypus microbiome is sensitive to environmental pressures and may offer a minimally invasive indicator of individual and ecosystem health. In addition to these ecologically important findings, across all sampled regions the platypus cloacal microbiome was consistently dominated by Campylobacterota and Fusobacteriota, with Pseudomonadota and Bacillota also prominent in the core microbiomes. Our results provide a critical baseline for integrating microbial health into conservation planning for this unique mammal.},
}

@article {pmid42118217,
year = {2026},
author = {Thakur, S and Chaitanya, MVNL and Singh, SK and Khurana, N and Selvaraj, J and M, AL and Mazumder, A and Sengupta, P},
title = {Urolithin A: A Novel Postbiotic for inflammation, aging, and cancer: A Journey from Dietary ellagitannins to clinical use.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42118217},
issn = {1573-4978},
mesh = {Humans ; *Coumarins/pharmacology/therapeutic use/metabolism ; *Neoplasms/drug therapy/metabolism ; *Inflammation/drug therapy/metabolism ; *Aging/drug effects ; Gastrointestinal Microbiome/drug effects ; *Hydrolyzable Tannins/metabolism/pharmacology ; Animals ; },
abstract = {BACKGROUND: Urolithin A (UA) is synthesized when the body metabolizes ellagic acid and ellagitannins. UA has been a widely recognized physiologically active compound throughout the previous decade. The gut microbiota affects metabolic regulators AMPK and sirtuins, initiates autophagy, and activates mitochondrial quality control, which is essential for infection resistance, intestinal health, and inflammation reduction.

METHODS: A preclinical study indicates that UA alters cancer cell metabolism, fortifies the intestinal barrier, safeguards the brain, and supports skeletal muscle health. UA enhances muscle endurance, mitochondrial function indicators, and cardiometabolic health without side effects or adverse reactions in preliminary human trials, primarily including the elderly and sedentary individuals. UA production exhibits significant variability due to the heterogeneity of gut flora. The existing classifications of A, B, and O kinds, absence of longitudinal data, limited trial sizes, and inconsistency between results and real-world outcomes impede the pharmaceutical advancement of UA.

RESULTS: This review commenced with an examination of UA's origins, chemical properties, gastrointestinal metabolism, absorption, molecular functions, and therapeutic potential. The literature's validity, applicability, and knowledge gaps indicate that UA is a postbiotic treatment that influences the gut microbiome's impact on mitochondrial pathways affecting various bodily systems, considering the intricate connections among inflammation, aging, and cancer. Comprehensive clinical trials are required to validate the optimal composition, dosage, and therapeutic efficacy.},
}

Humans
*Coumarins/pharmacology/therapeutic use/metabolism
*Neoplasms/drug therapy/metabolism
*Inflammation/drug therapy/metabolism
*Aging/drug effects
Gastrointestinal Microbiome/drug effects
*Hydrolyzable Tannins/metabolism/pharmacology
Animals

@article {pmid42118429,
year = {2026},
author = {Tekin, B and Gurbanov, R},
title = {Taxonomic and functional remodeling of the gut microbiota during aging and implications for microbiota-derived biomarkers.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42118429},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Aging/physiology ; Biomarkers/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Animals ; Host Microbial Interactions ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiota represents a complex microbial ecosystem that contributes to host metabolic regulation, immune homeostasis, and intestinal barrier function. Across the lifespan, gut microbial communities exhibit marked taxonomic and functional variation driven by environmental exposures, dietary patterns, medication use, and age-associated immune alterations. These differences are closely linked to chronic inflammatory states and immune dysregulation that accompany aging. This review synthesizes current evidence on age-associated differences in gut microbiota composition and functional capacity, with a focus on microbial traits and metabolic pathways relevant to host-microbe interactions. Pathological aging is frequently associated with reduced microbial diversity, loss of short-chain fatty acid-producing commensal bacteria, and enrichment of opportunistic or pro-inflammatory taxa. In contrast, healthy aging and longevity are commonly associated with more stable, resilient, and metabolically adaptable microbial communities. At the functional level, recurrent alterations in short-chain fatty acid biosynthesis, bile acid transformation, and tryptophan- and choline-related metabolic pathways define conserved features across aging-associated microbial profiles. Across neurodegenerative, metabolic, and cardiovascular conditions, overlapping taxonomic and functional patterns indicate shared microbiota-associated signatures linked to inflammatory states. Advances in metagenomic sequencing, functional annotation, and microbiome-focused biotechnological approaches now enable integrated analysis of microbial structure and metabolic potential. These developments provide a robust framework for identifying reproducible microbiome-based indicators relevant to aging-associated physiological changes and for translating microbiome research into biotechnology-driven applications.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Aging/physiology
Biomarkers/analysis
*Bacteria/classification/genetics/metabolism/isolation & purification
Animals
Host Microbial Interactions
Fatty Acids, Volatile/metabolism

@article {pmid42118552,
year = {2026},
author = {Palacios, S and Martin, J and Hernandez, I and Orozco, R},
title = {Estradiol loss, the "estrobolome," and midlife symptoms: what the gut microbiome adds to menopause care.},
journal = {Menopause (New York, N.Y.)},
volume = {},
number = {},
pages = {},
pmid = {42118552},
issn = {1530-0374},
abstract = {IMPORTANCE AND OBJECTIVE: Menopause is characterized by sustained estradiol decline affecting vasomotor, metabolic, skeletal, and neurobehavioral systems. Emerging evidence suggests that the gut microbiome may interact with endocrine pathways during this life stage.

METHODS: Narrative review of literature examining relationships between menopause, estradiol signaling, gut microbiome composition, and symptom domains. Artificial intelligence (AI) disclosure: artificial intelligence tools were used for language editing and to assist in the preliminary creation of a conceptual illustration. All scientific content, literature interpretation, and final manuscript preparation were performed and reviewed by the authors. The authors take full responsibility for the accuracy, integrity, and originality of the work.

DISCUSSION AND CONCLUSION: Current evidence indicates menopause is associated with shifts in gut microbial diversity and metabolic function. However, most human evidence remains observational and associative, and causal mechanisms remain to be established.},
}

@article {pmid42118590,
year = {2026},
author = {Qu, P and Ding, S and Zhang, Y and Zhao, Y and Song, E and Hu, L and Ding, R and Cao, W and Hou, Y and Qi, J and Zhao, J and Duan, C and Liu, S and Shen, C and Zhao, Y and Guo, Y and Zheng, Z and Luo, S and Hu, H and Bai, L and Zhao, S and Wang, B and He, S and Wu, Y and Xiong, X and Wu, Q and Gu, W and Rom, O and Xu, A and Zheng, L and Zhang, J and Liu, E and Chen, YE},
title = {Metabolic dysfunction-associated steatohepatitis exacerbated by Clostridium perfringens-derived ammonia is attenuated by tripeptide DT-109.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI200522},
pmid = {42118590},
issn = {1558-8238},
abstract = {The global prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is rising, driven by a complex interplay of metabolic disturbances, inflammation, and fibrosis, yet effective treatment options remain limited. This study examined the relationships among intestinal microbial dysbiosis, ammonia production, and hepatic CD8+ T cell activity in MASH, and assessed the therapeutic potential of DT-109, a glycine-based tripeptide. We investigated the gut-liver axis across human cohorts and both non-human primate and mouse MASH models. Multi-omics approaches were used to characterize ileal microbiota, ammonia levels, and hepatic immune and metabolic pathways. Causality was verified through microbiota transplantation, C. perfringens NirA-knockout mutants, and functional validation in vitro and in vivo. The efficacy of DT-109 was evaluated in non-human primates and mice. Our results revealed a significant increase in the ammonia-producing gut bacterium C. perfringens, which led to elevated intestinal ammonia and disruption of the intestinal barrier in MASH. Elevated ammonia levels triggered FosB-mediated upregulation of chemokine C-C motif ligand 5 (CCL5) in CD8+ T cells, which in turn drove T cell cytotoxicity in the liver. Notably, DT-109 effectively lowered C. perfringens abundance, reduced intestinal ammonia, restored intestinal barrier integrity, and alleviated CD8+ T cell dysregulation in MASH. These results identify a distinct mechanism in which gut-derived ammonia drives CD8+ T cell-mediated MASH and demonstrate that DT-109 effectively targets this axis by inhibiting C. perfringens and reducing ammonia, ultimately ameliorating MASH.},
}

@article {pmid42118793,
year = {2026},
author = {Kawashima, M and Aoki, T and Hamada, H and Watanabe, C and Oyanagi, E and Kono, T and Yamagata, T and West, NP and Yano, H},
title = {Continuous high-fat high-sugar diet overrides the therapeutic potential of fecal microbiota transplantation from exercised and/or inulin-conditioned donors in obese mice.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0349286},
doi = {10.1371/journal.pone.0349286},
pmid = {42118793},
issn = {1932-6203},
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Inulin/pharmacology/administration & dosage ; Male ; *Diet, High-Fat/adverse effects ; *Obesity/therapy/etiology/microbiology/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Physical Conditioning, Animal ; Fatty Acids, Volatile/metabolism ; Mice, Obese ; Feces/microbiology ; },
abstract = {Fecal microbiota transplantation (FMT) is a promising therapeutic strategy for obesity and related metabolic disorders. Exercise and dietary fiber intake, such as inulin supplementation, have been shown to differentially modulate the gut microbiota and synergistically improve metabolic health. The present study aimed to investigate whether FMT from lean donor mice subjected to voluntary exercise and/or inulin supplementation could ameliorate metabolic dysfunction in high-fat high-sugar diet (HFHSD)-induced obese mice. Four-week-old male C57BL/6J mice were fed HFHSD throughout the experimental period and assigned to one of five groups: sham FMT, FMT from sedentary donors, from exercised donors, from inulin-supplemented donors, or from donors receiving both interventions. Following 12 weeks of obesity induction, mice were treated with antibiotics and then underwent a 4-week FMT protocol. Physical and metabolic parameters, gut microbial composition, and cecal short-chain fatty acid (SCFA) levels were examined in both donors and recipients. The results demonstrated that FMT from exercised and/or inulin-supplemented donors failed to improve obesity-related phenotypes or glucose intolerance in recipients. These outcomes were accompanied by only partial alterations in gut microbiota and SCFA profiles. Collectively, our findings suggest that persistent HFHSD exposure compromises the colonization and function of beneficial microbes, limiting the metabolic benefits of FMT. Successful application of FMT in severe obesity may require prior optimization of the host intestinal environment through dietary interventions or microbiome-targeted strategies.},
}

Animals
*Fecal Microbiota Transplantation/methods
*Inulin/pharmacology/administration & dosage
Male
*Diet, High-Fat/adverse effects
*Obesity/therapy/etiology/microbiology/metabolism
Mice
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Physical Conditioning, Animal
Fatty Acids, Volatile/metabolism
Mice, Obese
Feces/microbiology

@article {pmid42118940,
year = {2026},
author = {Zhang, H and Stackpole, K and Iglesia, CB},
title = {Femtech Revolution for Pelvic Floor Disorders and Sexual Health.},
journal = {Urogynecology (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
pmid = {42118940},
issn = {2771-1897},
abstract = {IMPORTANCE: Consumer-directed female technology ("femtech") is rapidly expanding into pelvic floor and sexual health, yet clinicians have limited guidance on the safety, efficacy, and appropriate use of these products.

OBJECTIVES: The objective of this review is to summarize currently marketed female technology products relevant to pelvic floor disorders, sexual function, and vaginal health, and to highlight key evidence, limitations, and implications for clinical practice.

STUDY DESIGN: This is a narrative review of commercially available technologies for urinary incontinence, sexual dysfunction, and vaginal health. Product categories include external and intravaginal pelvic floor muscle training devices, vibrators, and dilators for sexual function and pain, regenerative medicine interventions such as platelet-rich plasma injections, sexual wellness applications, and direct-to-consumer vaginal microbiome testing platforms.

RESULTS: Pelvic floor devices and in-office energy therapies offer nonsurgical options for urinary incontinence, but high-quality, independent long-term data are scarce, and costs are often substantial. Sexual wellness devices, including vibrators and dilators, are increasingly recognized as therapeutic tools but are variably supported by clinical research. Early studies of platelet-rich plasma suggest potential benefit for sexual function, yet protocols and outcomes remain heterogeneous. Digital applications and microbiome tests expand access and patient engagement but frequently lack rigorous validation and may raise concerns regarding privacy, equity, and interpretation of results.

CONCLUSIONS: Female technology offers novel opportunities to address pelvic floor and sexual health outside traditional care pathways. Urogynecologists should be familiar with these products, provide balanced counseling on benefits, risks, and cost, and advocate for independent trials to define their role within evidence-based care.},
}

@article {pmid42119038,
year = {2026},
author = {López Tacoaman, YF and Alcivar, M and Alujević, K and Bakewell, L and Curlis, JD and Gonzalez, A and Gripshover, ND and Gulati, S and Pirani, RM and Ratia, N and Romero, D and Wuthrich, KL and Cox, CL and Logan, ML and McMillan, WO and Fontaine, SS and Williams, CE},
title = {Host and Environmental Drivers of Gut Microbiome Variation in Wild Anolis Lizards.},
journal = {Molecular ecology},
volume = {35},
number = {9},
pages = {e70358},
doi = {10.1111/mec.70358},
pmid = {42119038},
issn = {1365-294X},
support = {DEB-2024157//National Science Foundation/ ; DEB-2024179//National Science Foundation/ ; DEB-2024109//National Science Foundation/ ; //Smithsonian Tropical Research Institute/ ; },
mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Panama ; RNA, Ribosomal, 16S/genetics ; Environment ; Symbiosis ; },
abstract = {Animals maintain close associations with diverse microbiota that inhabit their digestive tracts, and these associations can profoundly affect host physiology and fitness. Gut microbiome composition is shaped by both host traits and environmental factors, yet the relative importance of these forces remains unclear in many taxa, including squamate reptiles (lizards and snakes). To address this gap, we analysed the gut microbiomes of seven species of Anolis lizards in the lowland tropical rainforest of central Panama. We sought to determine how environmental and host species characteristics shaped gut microbiome composition. Specifically, we examined (1) interspecific variation in the anole gut microbiome, (2) the relative roles of environment and host species in shaping gut microbiomes across two study locations, and (3) patterns of phylosymbiosis. We found that host-related factors (species identity, body size, and phylogenetic distance) were significant predictors of the composition of Anolis gut microbiomes. However, environmental factors, including locality and year of sampling (associated with temperature, humidity, and precipitation), also exerted significant effects. We detected evidence of phylosymbiosis, but this pattern was moderate, possibly due to the strong effect of environmental variation. Our work contributes to the growing body of literature on lizard gut microbiomes by using comparative observations across habitats and species to identify the factors that shape these communities in the wild.},
}

Animals
*Lizards/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Phylogeny
Panama
RNA, Ribosomal, 16S/genetics
Environment
Symbiosis

@article {pmid42119192,
year = {2026},
author = {Stemen, EL and Radka, CD},
title = {Lactobacillus iners at the nexus of microbiota, immunity, and pregnancy.},
journal = {Journal of reproductive immunology},
volume = {175},
number = {},
pages = {104909},
doi = {10.1016/j.jri.2026.104909},
pmid = {42119192},
issn = {1872-7603},
abstract = {Pregnancy induces a dynamic reconfiguration of the vaginal microbiome, typically marked by increased dominance of Lactobacillus species and reduced microbial diversity. Among these bacteria, Lactobacillus iners stands out for its unique genomic traits, controversial associations with vaginal health, and frequent presence across all stages of gestation. This review synthesizes current literature on the maternal microbiome with a focus on L. iners, exploring its strain-level diversity, metabolic idiosyncrasies, and inflammatory potential. We discuss how host factors such as ethnicity, sexual activity, maternal age, and especially obesity, influence microbial composition, and evaluate conflicting data surrounding L. iners in contexts like in vitro fertilization, preterm birth, and postpartum recovery. Emerging evidence suggests that L. iners may act as a transitional species, whose effect on pregnancy outcomes depends on its abundance, genetic features, and interactions with the host immune system. We also assess limitations of current animal models and propose future directions for understanding this enigmatic bacterium. Unraveling the role of L. iners will be essential to predicting, preventing, and managing adverse pregnancy outcomes in diverse populations.},
}

@article {pmid42119272,
year = {2026},
author = {Amico, MD and Skowron, M and Centkowska, K and Mikolaszek, B and Rappa, F and Baranska-Rybak, W and Ruchala, J and Cal, K and Rzeszutek, I and Górska-Ponikowska, M},
title = {Lactobacillus-derived extracellular vesicles as postbiotic modulators of redox signalling and cellular senescence in skin homeostasis.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {199},
number = {},
pages = {119457},
doi = {10.1016/j.biopha.2026.119457},
pmid = {42119272},
issn = {1950-6007},
abstract = {The skin acts as a dynamic barrier-combining physical, chemical, and immunological defences-while hosting a diverse microbiome essential for cutaneous homeostasis. Dysbiosis and impaired redox balance are linked to various inflammatory conditions; however, the mechanisms by which microbial signals regulate skin cell senescence remain unclear. This study evaluated the effects of Lactobacillus-derived extracellular vesicles (EVs) on human keratinocytes (HaCaTs) and dermal fibroblasts (HDFs) under both physiological and stress-induced premature senescence (SIPS) conditions. SEM analysis confirmed the presence of spherical membrane-bound structures consistent with EV morphology, providing a qualitative characterisation. Functional assays indicate that low concentrations of EVs (1.25-2.5% v/v) increase the metabolic activity of HaCaT cells; however, only the 1.25% v/v concentration significantly promotes early wound closure, whereas the 2.5% v/v concentration induces a decoupling between metabolism and motility. In HDFs, EVs significantly reduced basal intracellular reactive oxygen species (ROS) levels, demonstrating an inherent capacity to modulate redox homeostasis. Furthermore, immunofluorescence analysis revealed that EVs exert cell-specific and context-dependent modulatory effects on the DNA damage response (DDR) and senescence-associated secretory phenotype (SASP). While EVs significantly regulated p21, 53BP1, and MMP-3 expression across both cell types under both basal and SIPS conditions, a specific modulation of COX-2 was observed exclusively in fibroblasts following SIPS induction. These results indicate that Lactobacillus-derived EVs support epidermal regeneration and protect dermal cells from molecular senescence by modulating redox-sensitive pathways. Our findings highlight the potential of these vesicles as multifunctional postbiotic regulators-providing a mechanistic basis for future strategies aimed at maintaining skin homeostasis and mitigating cellular ageing.},
}

@article {pmid42119275,
year = {2026},
author = {Tuniyazi, M and Gao, R and Song, H and Zhao, L and Reheman, A and Qi, M},
title = {Methylated tirilazad alleviates DSS-induced colitis in mice through reciprocal microbiome-metabolome.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {199},
number = {},
pages = {119468},
doi = {10.1016/j.biopha.2026.119468},
pmid = {42119275},
issn = {1950-6007},
abstract = {Ulcerative colitis (UC) pathogenesis involves complex interactions between inflammatory reactions, gut dysbiosis, metabolic disruption, and barrier dysfunction. Current therapies primarily target inflammation but fail to correct the underlying dysbiotic ecosystem. We hypothesized that methylated tirilazad (MT), a synthetic 21-aminosteroid with the antioxidant properties of tirilazad, would alleviate colitis by orchestrating a beneficial restructuring of the gut microbiome and its metabolic output. Using a DSS-induced murine colitis model in C57BL/6 mice, we evaluated MT via integrated multi-omics approaches, including 16S rRNA gene sequencing and untargeted metabolomics, coupled with correlation network analysis. In vitro experiments using human intestinal Caco-2 cells were further performed to verify the direct anti-inflammatory effects of MT. MT treatment ameliorated clinical severity, suppressed systemic and colonic inflammation (reducing IL-6, TNF-α; elevating IL-10), restored gut barrier integrity (increasing Occludin, ZO-1), and mitigated oxidative stress. 16S rRNA sequencing revealed that MT reversed DSS-induced dysbiosis, uniquely enriching for the probiotic species Lactobacillus johnsonii (8.4-fold) while suppressing pathobionts like Desulfovibrio fairfieldensis (13.3-fold reduction). Metabolomic analysis showed that MT normalized colitis-associated metabolic disturbances, specifically downregulating the pro-inflammatory eicosanoid 12R-HETE and upregulating barrier-supportive dipeptides (e.g., Gly-Tyr). Integrated correlation analysis established 12R-HETE as a key node, positively linked to pathogenic bacteria and inflammation, and negatively to barrier proteins. In vitro cell experiments confirmed that MT directly inhibited LPS-induced pro-inflammatory cytokine expression in Caco-2 cells. Our findings demonstrate that MT alleviates colitis not merely through direct anti-inflammatory action, but via a reciprocal microbiome-metabolome reprogramming loop, wherein microbial restructuring drives metabolome correction, which in turn reinforces barrier integrity and immune homeostasis. This positions MT as a novel microbiota-metabolome-directed therapeutic candidate that addresses both the symptomatic and root causes of UC.},
}

@article {pmid42119288,
year = {2026},
author = {Yuan, T and Yang, S and Hu, A and Cui, J},
title = {Attapulgite-supported nanoscale zero-valent iron promotes iron cycling and microbial synergy for the simultaneous remediation of cadmium and arsenic in paddy soils.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142275},
doi = {10.1016/j.jhazmat.2026.142275},
pmid = {42119288},
issn = {1873-3336},
abstract = {The antagonistic environmental geochemical behaviors of cadmium (Cd) and arsenic (As) present a critical challenge for the simultaneous remediation of contaminated paddy soils. Here, we report the synthesis of attapulgite-supported nanoscale zero-valent iron (ATP-nZVI), and its remediation performance was systematically investigated. Batch adsorption kinetics studies showed that ATP-nZVI material exhibits superior adsorption capacity performance for Cd and As compared with its individual components. Importantly, the pot experiment demonstrated that ATP-nZVI application significantly increased soil pH and iron content, while concurrently enriching the soil microbiome, especially iron- and arsenic-reducing bacteria. This synergistic Fe-microbe interaction stimulated iron cycling, effectively reducing the bioavailability of Cd and As and promoting the formation of iron plaques in rice roots. Consequently, ATP-nZVI treatment decreased Cd and As accumulation in rice grains by 86.49% and 19.15%, respectively, while enhancing grain yield and essential micronutrient profiles (Zn, Mn, Cu, Fe and Mg). This work offers a cost-effective, eco-friendly and sustainable remediation strategy for the integrated management of multi-heavy metal contaminated agricultural soils.},
}

@article {pmid42119367,
year = {2026},
author = {Hasavci, D and Blank, T},
title = {Rogue gut microbes derail memory.},
journal = {Immunity},
volume = {59},
number = {5},
pages = {1177-1179},
doi = {10.1016/j.immuni.2026.04.008},
pmid = {42119367},
issn = {1097-4180},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; Animals ; *Memory/physiology ; Hippocampus ; Myeloid Cells/immunology ; Inflammation/immunology ; Fatty Acids/metabolism ; Mice ; },
abstract = {The gut microbiome contributes to age-related cognitive decline, but signaling mechanisms remain unclear. In a recent issue of Nature, Cox et al. show that P. goldsteinii-derived fatty acids activate myeloid cells, thus inducing inflammation that disrupts vagal signaling and hippocampal memory encoding.},
}

*Gastrointestinal Microbiome/immunology
Humans
Animals
*Memory/physiology
Hippocampus
Myeloid Cells/immunology
Inflammation/immunology
Fatty Acids/metabolism
Mice

@article {pmid42119379,
year = {2026},
author = {Su, W and Liu, J and Liu, Y and Zhao, J and Liu, Y and Wang, J and Yu, W and Jin, G and Li, L and Yan, R and Li, A and Zhao, H},
title = {Characterizing the impact of the environmental exposome on the oral microbiome and its role in mortality: An exposome-wide association study.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120226},
doi = {10.1016/j.ecoenv.2026.120226},
pmid = {42119379},
issn = {1090-2414},
abstract = {BACKGROUND: The oral microbiome is a critical interface between environmental influences and human health, but its response to the cumulative exposome remains poorly characterized. We investigated the associations among the environmental exposome, the oral microbiome, and all-cause mortality.

METHODS: Among 6901 nationally representative U.S. adults, we implemented an Exposome-Wide Association Study (ExWAS) framework and the Deletion/Substitution/Addition algorithm to assess associations of 100 environmental chemical exposures with oral microbial diversity and taxa using survey-weighted linear regression models. Survey-weighted Cox proportional hazards models assessed associations between exposures and all-cause mortality. Multiple comparisons were controlled using the Benjamini-Hochberg false discovery rate. Mediation analysis explored the potential role of the oral microbiome in the exposure-mortality associations.

RESULTS: Tobacco-related exposures, including volatile organic compound metabolites (2,5-dimethylfuran and furan), polycyclic aromatic hydrocarbons (PAHs; 2-hydroxyfluorene and 3-hydroxyfluorene), and nicotine metabolites, showed the strongest associations with oral microbiome composition. These patterns were marked by depletion of commensal genera such as Alloprevotella, Peptostreptococcus and Neisseria, and the enrichment of stress-tolerant taxa including Bifidobacterium and Lactobacillus. Most of these exposures, particularly PAHs, were nominally associated with higher all-cause mortality. Exploratory mediation analyses suggested that overall community structure and specific taxa (e.g., Bifidobacterium, Haemophilus) represent a potential mediation pathway in the associations of cadmium, furan, PAHs, and nicotine metabolites with mortality.

CONCLUSIONS: The oral microbiome may serve as a sensitive biosensor of the chemical exposome and a potential intermediate factor linking environmental exposures to mortality risk. These hypothesis-generating findings highlight the oral cavity as a key arena for environmental health impacts.},
}

@article {pmid42119408,
year = {2026},
author = {Singh, AK and Choi, J and Ramirez, GA and Guan, J and Singh, P and Tolstorukov, I and Oakley, BB and Kim, WK},
title = {Effects of Aspergillus sp. supplementation with or without xylanase on growth performance, nutrient digestibility, and the gastrointestinal microbiome of broilers.},
journal = {Poultry science},
volume = {105},
number = {8},
pages = {106978},
doi = {10.1016/j.psj.2026.106978},
pmid = {42119408},
issn = {1525-3171},
abstract = {This study aimed to evaluate the in vivo enzyme activity of Aspergillus sp. in the presence and absence of supplemental xylanase enzyme and determine its effect on the growth performance, nutrient digestibility, and microbiome of broilers. A total of 120 male Cobb® 500 broilers were randomly assigned to 12 replicate cages across 4 treatments (n = 3 per treatment) and raised till 21 days. The dietary treatments were arranged in a 2 × 2 factorial design with xylanase and Aspergillus sp. addition as the main factors. The xylanase was included at 520 U/kg and Aspergillus sp. was supplemented as conidiospores at 6.4 × 10[7] CFU/ kg of the basal diet by replacing sand. The total feed intake and the total body weight per cage were recorded weekly. The total feed intake and total excreta output were recorded on d 20 to calculate apparent metabolizable energy (AME) and nitrogen-corrected AME (AMEn). The jejunum, ileum, and ceca were collected on d 14 and d 21 for quantitative PCR and microbiome analyses. The growth performance and nutrient digestibility data were analyzed by two-way ANOVA in a completely randomized design using SAS 9.4 (SAS Inc., Cary, NC) with statistical significance declared at P < 0.05. The treatments did not have a significant effect on the nutrient digestibility and growth performance of the broilers. However, a trend was observed for the interaction between xylanase and Aspergillus sp. on the average daily gain (ADG) and the final body weight gain (FBWG) of broilers during d 0-21 (P = 0.099). Microbiome analysis revealed no major shifts in overall community structure, although several taxa exhibited small but statistically significant differences in response to dietary supplementation with xylanase and/or Aspergillus spores. AI-enabled genome and literature searches indicated that taxa enriched under enzymatic treatments commonly possess metabolic functions related to the fermentation of complex carbohydrates for the production of short-chain fatty acids. The results indicate that the effects of Aspergillus sp. on nutrient digestibility and utilization by broilers are influenced by the presence of exogenous enzymes and dietary substrates and are further modulated by the gut microbiome. Supplemental Aspergillus sp. conidiospores provided similar and numerically greater improvements in FBWG and exerted significant effects on the select members of the gastrointestinal microbiome.},
}

@article {pmid42119567,
year = {2026},
author = {Chen, C and Xing, Y and Xing, G and Zeng, F and Zheng, N and Sha, S and Zhao, L and Zhang, Y and Ling, Y and Yao, X and Liu, C and Zhang, Y and Mei, T and Guo, R and Kang, J and Cheng, L and Fan, S and Sun, W and Li, S and Yan, Q and Yao, X and Kong, X and Ma, W},
title = {Multi-faceted characterization of the gut microbiome and metabolome in patients with primary Sjögren syndrome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102777},
doi = {10.1016/j.xcrm.2026.102777},
pmid = {42119567},
issn = {2666-3791},
abstract = {The gut microbiome and its metabolomic potential in primary Sjögren syndrome (pSS) remain largely unexplored. Here, we perform whole-metagenome shotgun sequencing of fecal samples from 206 pSS patients and 355 non-pSS controls, integrating compositional and functional profiling with serum and fecal metabolomes. pSS is associated with extensive multi-kingdom alterations, including 49 bacterial (e.g., Streptococcus parasanguinis, Ligilactobacillus salivarius, and Veillonella parvula), 19 fungal (notably Candida albicans), and 1,323 viral species. These signatures form robust inter-kingdom correlations and achieve high diagnostic accuracy in an independent validation cohort. Functional and metabolomic analyses reveal enrichment of toxin-related and aromatic pathways and depletion of protective metabolites in patients. pSS-enriched bacteria harbor abundant immunogenic epitopes, virulence factors, and antimicrobial resistance genes, and induce proinflammatory responses ex vivo. Together, these findings outline a multi-faceted microbial framework for pSS and suggest mechanistic links between gut dysbiosis and immune dysregulation.},
}

@article {pmid42119619,
year = {2026},
author = {Zeng, Y and Yang, F and Li, Z and Wang, Q and Zhang, K},
title = {Overlooked role of Species-Specific earthworm mucus in antibiotic resistance gene suppression during vermicomposting.},
journal = {Bioresource technology},
volume = {455},
number = {},
pages = {134842},
doi = {10.1016/j.biortech.2026.134842},
pmid = {42119619},
issn = {1873-2976},
abstract = {Antibiotic resistance genes (ARGs) from livestock manure pose a significant threat to both environmental and public health. Vermicomposting mitigates ARG dissemination, yet the species-dependent differences in earthworm mucus's contribution remain poorly understood. This study examined how mucus from three earthworm species (Eisenia fetida, Eudrilus eugeniae, Perionyx excavatus) differentially reduced ARGs in cow manure. Untargeted metabolomics revealed species-specific mucus profiles. All three types of mucus lowered ARG abundance albeit through distinct ecological patterns. E. fetida mucus promoted co-elimination of ARGs and mobile genetic elements (MGEs) alongside host bacteria. E. eugeniae mucus selectively suppressed key host bacteria, effectively decoupling ARG-MGE associations in a pattern of host-associated decoupling. By contrast, P. excavatus mucus induced a composite suppression mode that incorporated both patterns. Each mucus uniquely reshaped the manure microbiome and its functional interaction network, demonstrating species-specific reprogramming of the ecosystem. These findings highlight that earthworm mucus is a critical yet overlooked regulator of ARG fate, and its species-specific composition underlies divergent ecological trajectories. This offers new insights into targeted biological interventions in waste management.},
}

@article {pmid42119786,
year = {2026},
author = {Khetan, R and Donnellan, L and Collins, K and Kamath, S and Ariaee, A and Rajapaksha, W and Wignall, A and Young, C and Hoffman, P and Subramaniam, S and Joyce, P},
title = {The gut microbiota regulates the protein corona formation, biodistribution, and cellular uptake of lipid nanoparticles.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {395},
number = {},
pages = {114995},
doi = {10.1016/j.jconrel.2026.114995},
pmid = {42119786},
issn = {1873-4995},
abstract = {Nanomedicines promise to transform oncology by improving pharmacokinetics, enhancing tumor targeting, and reducing systemic toxicities relative to conventional chemotherapies. However, clinical outcomes remain inconsistent, with marked inter-patient variability in biodistribution and therapeutic response. This variability is thought to arise from heterogeneity in "bio-nano" interactions, yet the upstream drivers of these interactions are poorly defined. We propose that the gut microbiota is a clinically relevant regulator of nanomedicine behavior, given its established influence on host immunity, metabolism, and proteome composition - all key determinants of bio-nano interactions. To test this, rats underwent a 14-day microbiota modulation using a prebiotic, broad-spectrum antibiotics, or control treatment. PEGylated liposomes were then intravenously administered to assess the impact of microbiota composition on (i) protein corona formation, (ii) nanoparticle biodistribution, and (iii) in vitro anti-cancer efficacy of doxorubicin-loaded liposomes following exposure to plasma from each group. Microbiota modulation produced distinct protein coronas, characterized by increased protein adsorption and unique proteomic profiles enriched in complement factors, apolipoproteins, and immunoglobulins. These corona differences were associated with altered biodistribution profiles, affecting both the magnitude and organ-level partitioning of nanoparticle-associated signal. Antibiotic treatment increased total systemic signal consistent with altered retention and/or clearance, whereas prebiotic supplementation was associated with reduced overall signal and decreased proportional partitioning into mononuclear phagocyte system organs, with a corresponding shift in distribution balance toward peripheral tissues including the heart, kidney, and brain. Notably, the prebiotic-derived corona markedly enhanced liposomal uptake and cytotoxicity in A549 and ES-2 cancer cells, linking protein adsorption and corona composition with bio-nano cellular interactions. Collectively, these findings provide experimental evidence that microbiota modulation influences nanoparticle behavior by altering bio-nano interactions, revealing an emerging "gut-nano axis" as a potentially controllable source of nanomedicine variability.},
}

@article {pmid42119819,
year = {2026},
author = {Varghese, RT and Akurati, S},
title = {Sleep, lipids, and metabolic health in the Indian obesity epidemic: an integrative review of mechanisms, burden, and breakthroughs.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113319},
doi = {10.1016/j.diabres.2026.113319},
pmid = {42119819},
issn = {1872-8227},
abstract = {BACKGROUND: India faces a growing obesity epidemic within the context of persistent undernutrition, creating a dual burden with major cardiometabolic consequences. This population is particularly vulnerable to metabolic disease because of the "Asian Indian phenotype," characterized by increased visceral adiposity and higher metabolic risk at lower body mass index thresholds.

OBJECTIVE: To review current evidence on the relationship between sleep health, lipid dysregulation, and metabolic dysfunction in the obesity epidemic in India, with emphasis on epidemiology, biologic mechanisms, and implementation relevance.

METHODS: PubMed-indexed literature published from 2015 through February 2026 was reviewed, prioritizing India-specific epidemiologic studies, national reports, and policy-relevant publications. International mechanistic studies were included when relevant to biologic plausibility and translational understanding.

RESULTS: Obesity in India shows substantial regional and urban-rural variation, while dyslipidemia remains highly prevalent and inadequately controlled, particularly in people with type 2 diabetes mellitus. Sleep disturbances, including short sleep duration, circadian misalignment, shift work, and obstructive sleep apnea, are increasingly recognized as contributors to metabolic dysfunction. Mechanistic evidence suggests that sleep disruption may impair metabolic health through clock gene dysregulation, bile acid-lipid desynchronization, microbiome-derived short-chain fatty acid signaling, inflammation, and neuroendocrine stress pathways. However, India-specific lipidomic, longitudinal, and sleep-focused interventional data remain limited.

CONCLUSIONS: Sleep health disturbances appear to be important and potentially modifiable contributors to metabolic dysfunction in India. Improving access to obstructive sleep apnea diagnosis and continuous positive airway pressure therapy, strengthening dyslipidemia management, and integrating sleep health into broader noncommunicable disease frameworks may improve prevention and care in high-risk Indian populations.},
}

@article {pmid42119851,
year = {2026},
author = {Xiong, HL and Zhao, Q and Liu, SQ and Chen, LL and Nie, MT and Hong, XL and Ding, CH and Huang, R and Jiang, N and Chen, F and Song, YH and Zhang, X and Wang, KQ and Zhu, CP and Xie, WF},
title = {Rifaximin ameliorates cirrhotic portal hypertension through suppression of microbiome-derived deoxycholic acid.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2026.05.001},
pmid = {42119851},
issn = {1600-0641},
abstract = {BACKGROUND & AIMS: Microbiome-derived deoxycholic acid (DCA) elevates serum 5-hydroxytryptamine (5-HT), a mediator of portal hypertension (PH). Rifaximin, a non-absorbable antibiotic, is known to reduce DCA levels. We aimed to elucidate the role of DCA in cirrhotic PH and the therapeutic potential of rifaximin.

METHODS: PH was induced in mice by thioacetamide (TAA) injection or bile duct ligation (BDL). Mice were treated with antibiotics (ABX) or rifaximin, with or without exogenous DCA replenishment. A cohort of 51 cirrhotic patients and 19 healthy controls was analyzed to validate the correlations among DCA, 5-HT, and hepatic venous pressure gradient (HVPG). Mice with tissue-specific knockout of gut epithelial Tph1 (Tph1[VKO]), vascular smooth muscle cell Htr1a (Htr1a[ΔVSMC]), or Kcnj9 (Kcnj9[ΔVSMC]) were employed for mechanistic studies.

RESULTS: Fecal DCA positively correlated with portal pressure (PP) in TAA-induced PH mice (r = 0.631, P < 0.001) and with HVPG in patients (r = 0.5874, P < 0.001). ABX reduced fecal DCA, serum 5-HT, and PP in TAA- or BDL-induced PH mice. Exogenous DCA reversed the ABX-induced reductions in serum 5-HT and PP, an effect abolished in Tph1[VKO] mice. GIRK3 (encoded by Kcnj9) was upregulated in portal veins from PH mice and patients. VSMC-specific Kcnj9 deletion attenuated PH and prevented 5-HT-induced PP elevation. Mechanistically, 5-HT triggers PVSMC contraction via the HTR1A-GIRK3-Ca[2+]-MLC2 pathway. Rifaximin alleviated PH by reducing DCA in wild-type mice but showed no additional PP reduction in Tph1[VKO], Htr1a[ΔVSMC], or Kcnj9[ΔVSMC] mice.

CONCLUSIONS: Microbiome-derived DCA exacerbates PH by enhancing TPH1-dependent 5-HT biosynthesis, which activates PVSMC contraction via HTR1A-GIRK3 signaling. Rifaximin alleviates cirrhotic PH by reducing DCA levels, highlighting a potential therapeutic strategy for clinical PH management.

IMPACT AND IMPLICATIONS: Portal hypertension is a key driver of cirrhosis-related complications, yet current therapies exhibit suboptimal efficacy. Herein, we elucidate the role of the gut microbial metabolite DCA in the pathophysiology of cirrhotic portal hypertension through the TPH1-5-HT/HTR1A-GIRK3 axis and provide preclinical evidence that rifaximin ameliorates cirrhotic portal hypertension by reducing DCA. These insights may open a new avenue for the clinical management of cirrhotic portal hypertension.},
}

@article {pmid42119931,
year = {2026},
author = {Zhai, C and Li, Y and Han, H and Ma, B},
title = {Acute ammonia exposure induces hepatic lipid metabolism disorders in wild burbot (lota lota) via the gut-liver axis: New insight into conservation of threatened species.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {307},
number = {},
pages = {110559},
doi = {10.1016/j.cbpc.2026.110559},
pmid = {42119931},
issn = {1532-0456},
abstract = {Accumulating evidence indicates that exogenous toxins can induce lipid metabolic disorders by influencing the gut microbiome. However, the effects of ammonia nitrogen on the gut microbiota and hepatic lipid metabolism of the burbot (lota lota) remain unknown. Therefore, we integrated biochemical measurements, 16S rDNA sequencing, and transcriptomic analysis to evaluate the impact of 96 h of ammonia nitrogen exposure on oxidative stress, the immune response, lipid metabolism, and gut microbiota in the liver and intestine of lota lota. In this study, lota lota exhibited oxidative damage and immunosuppression following ammonia nitrogen exposure, as evidenced by decreased antioxidant and immune enzyme activities and a concomitant increase in malondialdehyde (MDA) content. Furthermore, ammonia nitrogen exposure altered gut microbial diversity: the abundance of Proteobacteria decreased, whereas that of Bacteroidota and Firmicutes increased. In addition, transcriptomic analysis revealed that the expression of genes related to fatty acid metabolism (fabp, elovl6, pltp) and gut barrier dysfunction (collagen, ecm) was altered. Notably, lipopolysaccharide (LPS) was identified as a key microbial-derived signal triggered by ammonia nitrogen, as demonstrated by ELISA. The translocation of LPS from gut to liver, resulting from compromised intestinal barrier integrity, activated the gut-liver axis and contributed to hepatic lipid metabolic disorders. Overall, the current study elucidates the gut-liver axis-mediated mechanism of ammonia nitrogen toxicity and provides valuable information for understanding the toxic effects of ammonia nitrogen on lota lota and conserving this threatened cold-water species.},
}

@article {pmid42119964,
year = {2026},
author = {Greenshields, J and Beale, DJ and Bissett, A and Anastasi, A and Irving, AD and Andrews, E and Capper, A},
title = {Seagrass Under Siege? Investigating the Effects of Microplastics on Eelgrass (Zostera muelleri) in a Laboratory-Controlled Mesocosm Study.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128321},
doi = {10.1016/j.envpol.2026.128321},
pmid = {42119964},
issn = {1873-6424},
abstract = {Seagrass meadows are critical coastal ecosystems that are increasingly recognised for their potential to form microplastic sinks. This study investigated the impacts of microplastic contamination on Eelgrass (Zostera muelleri), a dominant seagrass in the Indo-Pacific. Through a 90-day mesocosm experiment, Z. muelleri was exposed to three escalating microplastic concentrations (885, 3,540, and 8,850 particles.kg[-1] sediment) to evaluate morphological, photosynthetic (pulse amplitude modulation fluorometry), bacterial microbiome (16S rRNA gene amplicon sequencing), and leachate (LC-QToF-MS/MS) responses. Relative to controls (0 particles.kg[-1]), no significant morphological effects were detected at current environmental concentrations (885 particles.kg[-1] sediment), but significant declines in biomass (72-86%), rhizome length (110-190%), and leaf count (8-10 fewer leaves) under elevated microplastic loads. Photosynthetic (Y-Yield) efficiency was not affected, and sediment microbiomes exhibited resilience, with no significant shifts in diversity. Chemical analyses identified 82 leachates in sediments, including ten unique to treatments spiked with microplastics, suggesting leachate toxicity may be related to observed biological impacts. These findings suggest that Z. muelleri may be resilient to microplastic pollution at current observed concentrations but are likely to be negatively affected if microplastic pollution continues to rise. Research on leachate-specific effects is required for targeted mitigation strategies to help conserve these vital ecosystems.},
}

@article {pmid42119966,
year = {2026},
author = {Athira, AS and Sreejith, VN and Megha, C and Athira, PS and Reshmi, K and Murugadas, V and Joseph, TC},
title = {Metagenomic Characterization of Bacterial Communities on Beach Macroplastics: Insights into Antimicrobial Resistance and Virulence.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128213},
doi = {10.1016/j.envpol.2026.128213},
pmid = {42119966},
issn = {1873-6424},
abstract = {Macroplastic debris in coastal environments provides stable substrates for microbial colonization, yet comparative assessments with natural substrates remain limited. This study investigated bacterial communities associated with beach macroplastics collected from four sites along the Kochi coast, Kerala, India (Fort Kochi, Cherai, Puthenthode, and Puthuvypin) during the pre-monsoon season, and compared them with those colonizing natural inanimate substrates (driftwood, seaweed, and shells). Composite sampling across multiple transects was employed, and shotgun metagenomic sequencing was used to characterize taxonomic composition, functional pathways, antimicrobial resistance genes (ARGs), and virulence factors. Across all samples, Pseudomonadota (average ∼64.8%) dominated, followed by Bacillota, Actinomycetota, and Bacteroidota. Plastic-associated communities showed greater dominance of specific genera, including Vibrio, Alteromonas, and Pseudoalteromonas, whereas natural substrates exhibited more evenly distributed taxa (Streptomyces, Marinobacter, Sulfitobacter etc). Functional annotation revealed the presence of core metabolic pathways across all samples, while xenobiotic degradation and lipid metabolism pathways were more prominently represented in plastic-associated communities, particularly at urban-influenced sites. A total of 42 ARGs belonging to eight antibiotic classes were identified, with β-lactam resistance genes constituting ∼42% of detected ARGs. Plastic-associated samples showed broader ARG profiles, including blaTEM-116, tetM, and sul1. A total of 73 virulence genes were identified, with plastic samples showing higher abundance of β-lactamase (blaTEM-116, tetM) and adhesion-associated genes (pilA, ompA). In addition, 1,264-2,046 virulence-related gene hits per site were detected, with consistently higher counts observed in plastic-associated communities. Overall, the findings demonstrate that macroplastics support distinct microbial assemblages and functional gene distributions compared to natural substrates, highlighting their role as microbial habitats in human-impacted coastal environments.},
}

@article {pmid42119968,
year = {2026},
author = {Son, JS and Chang, GD and Jang, S and Lee, S and Sim, Y and Song, JH and Jeong, J and Ryu, CM},
title = {Polyethylene and polystyrene oxidation by host and microbial oxidoreductases in Zophobas atratus.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.05.024},
pmid = {42119968},
issn = {2090-1224},
abstract = {INTRODUCTION: Insect-mediated oxidation is a promising strategy for degrading hydrocarbon-based plastics. There is evidence for better long-term ingestion and sustained intestinal oxidation of polyethylene (PE) and polystyrene (PS) in the plastivore Zophobas atratus than in Galleria mellonella. However, the mechanisms underlying intestinal oxidation of PE and PS remain unclear.

OBJECTIVES: Host and microbial enzymes that mediate intestinal PE and PS oxidation in Z. atratus were evaluated.

METHODS: Long-term feeding assays were performed using G. mellonella and Z. atratus to compare PE and PS ingestion and oxidation activities. Germ-free Z. atratus larvae were generated using antibiotic treatment to evaluate host-derived oxidation. Transcriptome-based reverse genetics with heterologous expression in Pichia pastoris was used to identify candidate intestinal PE-oxidizing enzymes. The Z. atratus gut microbiome was enriched in media containing PE or PS as the sole carbon source and plastic-oxidizing bacteria were isolated. Candidate microbial enzymes were screened using a single-gene mutant library of a phylogenetic neighbor and validated by heterologous expression in Escherichia coli.

RESULTS: Z. atratus exhibited higher ingestion and intestinal oxidation of PE and PS than G. mellonella. Antibiotic treatment significantly reduced PE and PS oxidation in Z. atratus; however, the residual activity indicated contributions from both gut microbes and host-derived enzymes. Transcriptome-based reverse genetics using P. pastoris expression identified CYP6k1-ZP10 as a host PE-oxidizing enzyme, which was validated by RNA interference. Host enzymes involved in PS oxidation were not detected. Instead, Klebsiella variicola was isolated as the dominant gut bacterium capable of oxidizing both plastics. Functional screening revealed an FMN-dependent monooxygenase responsible for PE and PS oxidation.

CONCLUSION: These findings demonstrate the dual contribution of host- and microbe-derived oxidoreductases to PE and PS oxidation in Z. atratus.},
}

@article {pmid42120003,
year = {2026},
author = {Feidenhansl, C and Schweinshaut, K and Rruci, E and Nguyen, MT and Poehlein, A and Brüggemann, H},
title = {Engraftment of staphylococcal strains on human skin can competitively displace native staphylococci.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-14},
doi = {10.1163/18762891-bja00119},
pmid = {42120003},
issn = {1876-2891},
abstract = {Topical probiotic formulations containing live bacteria are being explored as treatments for skin disorders such as atopic dermatitis and acne vulgaris. Certain bacterial strains with antimicrobial and/or anti-inflammatory properties show promise as bacterial therapeutics that could improve these conditions and serve as alternatives to antibiotics, which are increasingly compromised by rising antimicrobial resistance. However, little is known about the engraftment efficacy of such bacterial strains or their impact on the native skin microbiome. In this study, we applied two different coagulase-negative staphylococcal strains, one with antimicrobial activity (Staphylococcus epidermidis 2C-5) and one lacking any activity (Staphylococcus hominis H2-S92), on human back skin of 14 healthy volunteers. Engraftment was assessed using strain-specific PCR and three amplicon-based sequencing approaches at 7 and 30 days after application. Microbial profiles shifted modestly, showing a relative increase in staphylococci and a decrease in Cutibacterium spp. S. epidermidis 2C-5 drastically increased from 0.8% pre-application to 46.9% and 12.1% at days 7 and 30, respectively. S. hominis H2-S92 showed a relative rise from 1.4% to 35.8% at day 7, declining to 2.4% by day 30. Interestingly, Staphylococcus capitis relative abundance decreased by 50-60% at the application sites. These findings indicate that both strains can temporarily engraft and competitively displace native staphylococci. S. epidermidis 2C-5 appeared to colonize more effectively, possibly due to its bacteriocin production. Neither strain affected the phylotype composition of Cutibacterium acnes, suggesting lack of reach to sebaceous follicles, C. acnes' primary niche. This study supports the potential of staphylococcal probiotics for modulating the skin microbiome. While they may be effective for conditions involving staphylococcal dysbiosis, such as atopic dermatitis, they appear less suited for treating disorders like acne vulgaris, which are associated with C. acnes imbalance.},
}

@article {pmid42120207,
year = {2026},
author = {Miao, Y and Sun, X and Wang, W and Shen, Q and Zhang, R},
title = {Dynamical model-guided SynCom design for sustainable agriculture.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.008},
pmid = {42120207},
issn = {1878-4380},
abstract = {Synthetic microbial communities (SynComs) are emerging as promising alternatives to single-strain inoculants in agriculture, offering greater functional robustness and environmental adaptability. However, transforming conceptual studies into engineerable and scalable agricultural practices remains challenging. In this opinion article, we synthesize current research on plant SynComs through a framework that moves from strain-centered assembly toward system-level design, linking the identification of truly stable coexisting communities in natural microbiomes to the elucidation of plant-microbe-soil interaction mechanisms, the development of dynamical models, and the integration of these models into platform-based design and production pipelines. We focus on recent advances that integrate generalized Lotka-Volterra and consumer-resource models with multi-omics data and other system-level constraints, with the aim of introducing model-driven concepts of SynCom design and promoting their large-scale application in agriculture.},
}

@article {pmid42120244,
year = {2026},
author = {Waqas, M and Yaning, C and White, JC and Berg, G and Geilfus, CM},
title = {Nano-selenium coordinates plant-microbiome redox for sustainable crops.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.04.023},
pmid = {42120244},
issn = {1878-4372},
abstract = {Foliar selenium nanomaterials act as redox-active coordinators linking photosynthesis, root carbon allocation, and rhizosphere microbiomes. By enhancing photosynthesis, nitrogen cycling, and microbial function, they improve 'nitrogen use efficiency, crop quality, profitability, and greenhouse gas mitigation' under reduced fertilizer inputs. This framework highlights nano-enabled pathways toward sustainable agriculture.},
}

@article {pmid42120383,
year = {2026},
author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW},
title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42120383},
issn = {2041-1723},
support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Carrageenan/metabolism ; *Ruminants/microbiology ; Rumen/microbiology ; Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; Bacteria/metabolism/genetics/classification/isolation & purification ; Seaweed/metabolism ; Bacteroides/metabolism/genetics/isolation & purification ; Metagenomics ; Phylogeny ; },
abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.},
}

Animals
*Gastrointestinal Microbiome/genetics/physiology
*Carrageenan/metabolism
*Ruminants/microbiology
Rumen/microbiology
Glycoside Hydrolases/metabolism/genetics
Feces/microbiology
Bacteria/metabolism/genetics/classification/isolation & purification
Seaweed/metabolism
Bacteroides/metabolism/genetics/isolation & purification
Metagenomics
Phylogeny

@article {pmid42120518,
year = {2026},
author = {Han, Q and Shi, Y and Yi, X and Ai, Z and Wu, M and He, T and Jing, X and Wang, Z and Xiang, Z},
title = {Dynamic microbiome-host interactions and their associations with systemic metabolism and radiological characteristics during early lung adenocarcinoma.},
journal = {NPJ precision oncology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41698-026-01471-5},
pmid = {42120518},
issn = {2397-768X},
support = {2022YFA1304300//National Key Research and Development Program of China/ ; 82495200//National Natural Science Foundation of China/ ; 82171931//National Natural Science Foundation of China/ ; GZNL2023A02001//Major Project of Guangzhou National Laboratory/ ; },
abstract = {Lung adenocarcinoma (LUAD) accounts for approximately 40% of non-small cell lung cancer. Although the microbiome may play a role in LUAD, a comprehensive understanding of its ecological landscape and interactions with the tumor host, particularly during early development of LUAD, remains lacking. Here we employed a multi-omic approach to assess the dynamics of the tumor microbiota-host interaction across stages of early LUAD, including benign nodules, adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (IAC). We found a strong and intricate interaction between the microbiome and host immune and metabolic pathways in AIS, while microbiome-host interactions substantially diminish in MIA and IAC. Serum metabolites and CT-based radiological features, such as atropaldehyde, sterculic acid, nodule morphology and maximum nodule diameter, were closely associated with the microbiome-host interaction network, suggesting they could be non-invasive markers indicating tumor ecological and pathological changes. Multi-omic integration revealed an optimal performance in classifying individual LUAD stages, particularly between AIS and MIA that was otherwise challenging to differentiate using a single data type. Our results highlight the dynamic interaction between microbiome and host during early LUAD, which can be partially reflected in systemic metabolic and radiological manifestations, providing a novel framework for understanding early-stage LUAD.},
}

@article {pmid42120611,
year = {2026},
author = {Hudson, J and Akhand, A and Nwe, MT and Coffey, MJ and van Dorst, J and Chuang, S and Ooi, CY},
title = {Obstructive sleep apnea and primary snoring in children are associated with oropharyngeal dysbiosis and a mild compositional imbalance in the gastrointestinal tract.},
journal = {Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine},
volume = {22},
number = {1},
pages = {},
pmid = {42120611},
issn = {1550-9397},
support = {2020/GNT1194358//National Health and Medical Research Council/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/complications ; Male ; *Sleep Apnea, Obstructive/microbiology/complications ; Female ; *Snoring/microbiology/complications ; Child ; *Oropharynx/microbiology ; *Gastrointestinal Microbiome ; Cohort Studies ; Feces/microbiology/chemistry ; Child, Preschool ; *Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: Obstructive sleep apnea (OSA) and primary snoring (PS) represent a spectrum of sleep-related breathing conditions. Emerging evidence links OSA to perturbations in the oropharyngeal and gut microbiomes and the pathogenesis of OSA-related comorbidities. However, the microbiome composition and factors driving dysbiosis in children remain unresolved.

METHODS: Two pediatric cohorts were examined to assess the microbiome associated with sleep-disordered breathing in the airway (Cohort A) and gut (Cohort B) using 16S rRNA gene profiling. Oropharyngeal swabs were collected from participants with OSA, PS, and healthy controls (HC) (n = 60). Cohort B participants (OSA and HC, n = 46) provided stool samples for microbiome and fecal calprotectin measurements and completed a dietary survey.

RESULTS: Oropharyngeal microbial diversity differed between OSA and HC, characterized by an increase in gastrointestinal specific taxa and reduced oral commensals. Similar shifts were observed between PS and HC, with few taxa differing between OSA and PS. In the gut, children with OSA showed an imbalance marked by an increase in opportunistic pathogens and reduced beneficial organisms. However, diversity assessments did not show any indication of dysbiosis or inflammation, and there were no overall differences in dietary intake.

CONCLUSIONS: Dysbiosis in the oropharyngeal microbiomes of OSA and PS points to shared pathophysiological factors (e.g., snoring) as possible drivers of microbiome disruption across the spectrum of sleep-disordered breathing. The gastrointestinal microbiome of children with OSA indicates a mild microbial imbalance that may elicit harmful outcomes or manifest as dysbiosis if left untreated. Together, these findings support a role of the microbiome as a possible mediator of comorbidities across the spectrum of sleep-disordered breathing. Current knowledge/study rationale: Obstructive sleep apnea (OSA) and primary snoring (PS) represent a continuum of sleep-related breathing disorders. While adult and animal studies suggest OSA-induced microbiome disruptions contribute to the onset of comorbidities, the factors driving dysbiosis in children remain unresolved. This study investigated the airway and gut microbiomes in pediatric OSA, PS, and healthy controls to identify microbial alterations linked to these conditions. Study impact: This study revealed that children with obstructive sleep apnea and primary snoring exhibit similar altered oropharyngeal microbiomes, distinct from that of healthy controls, suggesting common underlying pathophysiological factors.},
}

Humans
*Dysbiosis/microbiology/complications
Male
*Sleep Apnea, Obstructive/microbiology/complications
Female
*Snoring/microbiology/complications
Child
*Oropharynx/microbiology
*Gastrointestinal Microbiome
Cohort Studies
Feces/microbiology/chemistry
Child, Preschool
*Gastrointestinal Tract/microbiology

@article {pmid42120908,
year = {2026},
author = {Yakabe, K and Inoue, Y and Yanagisawa, Y and Imai, S and Suwa, S and Ando, M and Wu, Y and Kurokawa, R and Tanakorn, S and Haneda, T and Miki, T and Ito, M and Hirayama, A and Kurashima, Y and Fukuda, S and Hase, K and Suda, W and Takeyama, H and Hori, S and Kim, YG},
title = {Acarbose redirects gut microbiome utilization of dietary carbohydrates to suppress anaphylaxis in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42120908},
issn = {2058-5276},
support = {JP23K27409//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23K18223//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H03541//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 19gm6010004h0004//Japan Agency for Medical Research and Development (AMED)/ ; JP223fa627003//Japan Agency for Medical Research and Development (AMED)/ ; JP23gm1010009//Japan Agency for Medical Research and Development (AMED)/ ; JPMJER1902//MEXT | JST | Exploratory Research for Advanced Technology (ERATO)/ ; FOREST Program JPMJFR2354//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JPMJCR22N1//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; },
abstract = {Microbiota-accessible carbohydrates modulate host immunity by shaping gut microbial composition and metabolism. However, their role in modulating the microbiota to influence allergic responses is unclear. Here we show that a widely used antidiabetic agent, the α-glucosidase inhibitor acarbose, redirects dietary carbohydrate utilization by gut bacteria to suppress mast-cell-dependent anaphylaxis in mice, independently of adaptive immune responses. Enhanced carbohydrate availability promoted the proliferation of Parabacteroides distasonis in the mouse gut, leading to increased succinate abundance and intracellular NAD[+] levels, and reduced reliance on b-type cytochrome-dependent anaerobic respiration. Direct administration of succinate suppressed systemic anaphylaxis and mast cell degranulation in vitro, implicating succinate as a key effector. A human cohort analysis revealed that patients treated with α-glucosidase inhibitors showed a lower incidence of anaphylaxis than untreated individuals. These findings uncover a previously unrecognized gut-microbiota-mediated pathway linking dietary carbohydrate metabolism to systemic immune regulation.},
}

@article {pmid42121018,
year = {2026},
author = {Uzoigwe, C},
title = {Schizophrenia and Doxycycline: Microbiome Mediator?.},
journal = {The American journal of psychiatry},
volume = {},
number = {},
pages = {appiajp20251193},
doi = {10.1176/appi.ajp.20251193},
pmid = {42121018},
issn = {1535-7228},
}

@article {pmid42121025,
year = {2026},
author = {Guo, S and Liu, M and Liu, Z and Chen, K and He, M and Li, Y and Luo, X and Shangguan, Y and Zeng, X and Liu, Y and Ouyang, Y and Zhou, Z and Qin, Y},
title = {Balanced NPK fertilization enhances maize yield and shapes rhizosphere bacterial communities in purple soil: evidence from a ten-year field experiment.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05142-0},
pmid = {42121025},
issn = {1471-2180},
support = {2023YFD2301902//National Key R&D Program of China/ ; 5+1QYGG002//"5+1" Agricultural Cutting-edge Technologies Special Project of the Sichuan Academy of Agricultural Sciences/ ; 2025ZSSFGH08//Scientific and Technological Achievement Transformation Project of the Sichuan Academy of Agricultural Sciences/ ; 2025YFHZ0251//Sichuan Science and Technology Program/ ; SCCXTD-2024-SD-18//Sichuan innovation team of national modern agricultural industry technology system/ ; },
abstract = {Balanced fertilization with nitrogen (N), phosphorus (P), and potassium (K) plays a pivotal role in sustaining maize productivity and shaping soil-microbe interactions. However, the integrated effects of long-term fertilization on crop performance, soil nutrient dynamics, and rhizosphere bacterial communities in purple soils remain unclear. In a 10-year field experiment in purple soil, conducted under a randomized complete block design (RCBD) with three blocks, we evaluated the effects of different fertilization regimes on maize growth and yield, soil physicochemical properties, and bacterial community composition using 16 S rRNA gene sequencing. Nitrogen-containing fertilizer treatments (NPK, NK, NP) markedly enhanced grain yield, shoot and root biomass, and root morphological traits compared with unfertilized (CK) and PK treatments, with balanced NPK fertilization delivering the highest performance. Fertilization significantly influenced soil nutrient availability, with NPK maintaining more stable nutrient levels over time. Microbial analyses revealed that rhizosphere communities were more responsive to fertilization than bulk soil communities, with N availability driving diversity shifts and community separation. Key taxa, including Variovorax, Microscillaceae, Lysobacter, and Dyadobacter, were enriched in N-fertilized soils and positively correlated with grain yield and N uptake. Collectively, these findings demonstrate that balanced NPK fertilization, particularly nitrogen input, enhances maize productivity by simultaneously improving soil fertility and fostering beneficial rhizosphere microbial assemblages, offering a basis of sustainable nutrient and microbiome management in purple soil.},
}

@article {pmid42121042,
year = {2026},
author = {Hwengwere, K and Gregson, BH and Salter, SJ and Bolton, E and Alqahtani, L and Rofael, S and Teixeira, VH and McHugh, TD and January, GG and Peck, LS and Upton, M and Clark, MS},
title = {The effects of feeding guild, seasonality, and warming on the gut microbiomes of Antarctic echinoderms.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05114-4},
pmid = {42121042},
issn = {1471-2180},
support = {NE/S007334/1//Natural Environment Research Council/ ; },
abstract = {BACKGROUND: Antarctic marine food webs are expected to be significantly impacted by future climate change. In particular, the recent rapid regional warming in the West Antarctic Peninsula has, and will continue to have, a negative impact on endemic marine biodiversity. However, despite the growing recognition of the role microbial symbionts play in mediating responses to environmental change, microbiome characterisation has been conducted for only a small fraction of the marine invertebrates in the Southern Ocean. Our study examined the effects of feeding guild, seasonality, and experimental warming (6 months at + 2 °C) on the gut microbiome of six species of near-shore marine Antarctic echinoderms sampled from waters off Rothera Research Station, Antarctica. Our study used 16 S rRNA amplicon sequencing of the V3-V4 region, with analyses including measurements of alpha and beta-diversity alongside co-occurrence network analyses.

RESULTS: Of the six invertebrate species sampled in winter, peak species diversity values in gut microbiomes were observed in the omnivores, Ophionotus victoriae and Sterechinus neumayeri, with lower values in the scavenger/predator, Odontaster validus, and the suspension feeders, Cucumaria georgiana, Echinopsolus charcoti, and Heterocucumis steineni. In the seasonal experiment, H. steineni bacterial gut species diversity doubled from winter to early summer yet decreased by a similar magnitude during the same period in O. victoriae. Despite these opposing diversity trends, both species displayed similar increases in the relative abundances of Bacteroidota and Bacillota in winter and early summer in their gut microbiomes. Bacterial diversity in the gut microbiome of the sea cucumbers E. charcoti and H. steineni, was not impacted by six-months at + 2 ˚C above ambient, although C. georgiana displayed a decrease in observed ASVs following this treatment.

CONCLUSIONS: These results suggest a strong influence of feeding guild and seasonality on the gut microbiomes of these invertebrates. There appeared to be little effect of warming (+ 2 °C) on the taxonomic composition of the gut microbiomes of the three holothurians. This highlights the need to examine the functional significance of experimental warming treatments using metabolomics and transcriptomics alongside microbial species diversity analyses to understand whether gut microbiomes can aid resilience under future climate change.},
}

@article {pmid42121077,
year = {2026},
author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X},
title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.},
journal = {BMC neurology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12883-026-04958-7},
pmid = {42121077},
issn = {1471-2377},
abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.},
}

@article {pmid42121222,
year = {2026},
author = {Sanon, A and De Coninck, L and Wang, L and Badolo, A and Matthijnssens, J and Trappeniers, K and Delang, L},
title = {Convergent enrichment of Gammaproteobacteria along Aedes aegypti development across different breeding sites.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00578-1},
pmid = {42121222},
issn = {2524-4671},
support = {Global Minds scholarship//KU Leuven/ ; C14/20/108//KU Leuven/ ; 11L1325N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: Aedes aegypti mosquitoes are the main vector of pathogens like dengue virus and chikungunya virus. The immature life stages of mosquitoes share the same habitat with a variety of microorganisms in aquatic environments. To better understand the microbial diversity in field-derived Ae. aegypti, we analysed simultaneously collected larvae, pupae, and freshly emerged adults from Burkina Faso together with their breeding water via 16S rRNA gene sequencing.

RESULTS: We observed a decrease in bacterial diversity and load across the mosquito life stages. At the phylum level, a strong increase in relative abundance of Proteobacteria was found along the mosquito stages. The same 40 amplicon sequence variants were consistently found as most abundant in the adults, regardless of the sample collection site, and all belonged to the Gammaproteobacteria. Our data suggest that these bacteria were not randomly derived by chance from the environment in the mosquito but rather deposited by a female mosquito during oviposition, a transmission route recently coined as "diagonal transmission". Indeed, our results indicated that there is a selection of Gammaproteobacteria from the breeding water and that these bacterial members are further maintained from larvae to adults.

CONCLUSION: This study provided new data on the microbiome composition of field-collected Ae. aegypti, contributing to an enhanced understanding of the origin and colonization route of the mosquito microbiome, potentially via a diagonal transmission route.},
}

@article {pmid42121259,
year = {2026},
author = {Tang, Q and Zhen, R and Yang, B and Miao, Z and Wei, Y and Ruan, S and He, Y and Xiong, Y and Wu, Q and Wang, L and Jiang, Z and Yi, H},
title = {Butyrate combined with niacin enhances intestinal barrier function repair in weaned piglets infected with ETEC by promoting colonic metabolism and antimicrobial peptide expression.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42121259},
issn = {1674-9782},
support = {2024YFD1300805//National Key Research and Development Program of China/ ; 31902199//National Natural Science Foundation of China/ ; CAR-35//China Agriculture Research System/ ; 2024TQ08N106//Special Support Plan of Guangdong/ ; NYQS202628//Special Funding for the Construction of the High-Level Academy of Agricultural Sciences/ ; },
abstract = {BACKGROUND: Weaning piglets are highly susceptible to enterotoxigenic Escherichia coli (ETEC) infections, which can cause intestinal barrier function dysfunction and death. However, there is still a lack of efficient, economical, and safe nutritional interventions. This study aimed to investigate the effects of combining butyrate with niacin on intestinal barrier function repair and resistance to ETEC infection in weaned piglets. In this study, two 14-d animal experiments were designed to observe the optimal butyrate-to-niacin ratio and assess their responses to the ETEC challenge.

RESULTS: Supplementation with butyrate and niacin at a ratio of 100:2 (2,000 mg/kg butyrate and 40 mg/kg niacin, BN2) increased the average daily gain (ADG) and reduced the diarrhea incidence. We also observed an increase in the levels of nicotinamide adenine dinucleotide (NAD) in the colon of weaned piglets. Notably, BN2 promoted amino acid anabolism in the colon and enhanced glycolysis and the tricarboxylic acid (TCA) cycle by increasing the acetylation of key enzymes in the TCA. Furthermore, BN2 enhanced the expression of indispensable genes for the colonic mucosal barrier, including antimicrobial peptides such as porcine β defensin 1 (pBD1), porcine β defensin 2 (pBD2), and proline-arginine rich 39-amino acid peptide (PR39), tight junction proteins, and improved colonic microbiome composition. Based on these findings, we found that BN2 alleviated growth restriction and diarrhea, and modulated the expression of antimicrobial peptides, tight junction proteins, and cytokines to reduce colonic barrier function dysfunction in weaned piglets challenged with ETEC. Mechanistically, we confirmed that BN2 elevated the protein expression of acetylation of histone 3 lysin 27 (H3K27ac) and enhanced the binding of acH3K27 to the promoter regions of pBD1 and PR39.

CONCLUSIONS: Supplementation with BN2 improved growth performance, supported colonic barrier function repair, and enhanced disease resistance in weaned piglets challenged with ETEC. This offers new insights into nutritional strategies for intestinal barrier function repair of piglets infected with ETEC.},
}

@article {pmid42121260,
year = {2026},
author = {Zhou, Z and Lamanna, A and Halder, R and Pansart, E and Narayanasamy, S and Boussoufa, B and Kerkour, T and Wilmes, P and Williams, E},
title = {Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02369-x},
pmid = {42121260},
issn = {2049-2618},
support = {PRIDE21/16749720/NEXTIMMUNE2//Luxembourg National Research Fund/ ; },
abstract = {BACKGROUND: The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.

RESULTS: We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730 days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering > 300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC = 0.84 for CD, 0.79 for HF) and chronological age (AUC = 0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.

CONCLUSIONS: Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC = 0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC = 0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.},
}

@article {pmid42121284,
year = {2026},
author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C},
title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02410-z},
pmid = {42121284},
issn = {2049-2618},
support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; },
abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.

RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4 + T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.

CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.},
}

@article {pmid42121732,
year = {2026},
author = {Fang, Q and Ke, L and Bian, L and Li, S and Chi, H and Chen, Y and Qiu, X and Shi, S and Chen, S},
title = {Dietary Modulation of Gut Microbiota and Metabolome Shapes Growth Performance in Thamnaconus septentrionalis.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091312},
pmid = {42121732},
issn = {2076-2615},
support = {2023R1082//Fujian Provincial Department of Science and Technology/ ; FJHYF-L-2025-6//Fujian Ocean and Fisheries Department/ ; 2024S0039//Fujian Provincial Department of Science and Technology/ ; },
abstract = {Thamnaconus septentrionalis is an economically important marine aquaculture species in China. However, the acceptance rate of formulated feeds in commercial farming is only 30-40%, substantially lower than the 80-90% achieved with fresh feeds, which severely constrains the intensive development of this industry. The gut microbiota-mediated regulatory mechanisms underlying the effects of different feed types on growth performance remain unclear, limiting the precise development of efficient formulated feeds. This study established four feed types (commercial pellet feed K, custom-formulated feed P, frozen shrimp X, and fresh fish meat Y) through a 60-day feeding trial. Growth performance data, 16S rRNA sequencing, and untargeted metabolomics were analyzed. Random Forest-Partial Least Squares Regression models were employed to identify key microbial-metabolite features. Results indicated that the Y group exhibited the optimal feed conversion ratio (1.14), with intestinal Firmicutes abundance (45.3%) significantly higher than the K group (28.5%). Short-chain fatty acid levels increased by more than 350-fold, enriching short-chain fatty acid-producing bacteria such as Lactobacillus and Faecalibacterium. The P group, formulated with high fishmeal content (40%), achieved performance levels comparable to the Y group across most indicators. Machine learning models identified key microbial-metabolite features predicting growth performance, providing a multi-omics framework for developing efficient formulated feeds for marine carnivorous fish.},
}

@article {pmid42121765,
year = {2026},
author = {Piuzana, LG and Tomich, TR and Rotta, PP and Carvalho, D and Amorim, WPF and Silva, LHR and Vieira, JVF and Ribeiro, EF and Silva, ALD},
title = {Effects of Sodium Monensin and a Tannin-Yeast Blend on Intake, Milk Yield, and Methane Emissions in Lactating Holstein Cows.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091345},
pmid = {42121765},
issn = {2076-2615},
support = {001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 085/2022//American Nutrients of Brazil LTDA/ ; 425168/2025-5//Instituto Nacional de Ciência e Tecnologia de Ciência Animal/ ; APQ-08688-25//Instituto Nacional de Ciência e Tecnologia de Ciência Animal/ ; APQ-05448-24//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
abstract = {This study evaluated the effects of sodium monensin or a blend containing condensed tannins and yeast products on intake, digestibility, performance, and methane emissions in lactating Holstein cows. Nine cows (three rumen-fistulated and six non-fistulated) were assigned to three 3 × 3 Latin squares. The treatments were: a control (CON), sodium monensin (MON; 12 mg/kg of dry matter [DM]), condensed Acacia tannins and Saccharomyces cerevisiae yeast blend (SUP; 2 g/kg of DM). The trial lasted 84 days, with three 28-day periods. Neutral detergent fiber (NDF) intake was higher in CON and SUP (p = 0.029). Milk yield, energy-corrected milk, and milk composition did not differ (p > 0.05). The total methane emissions were not affected by treatments (p > 0.05). Methane yield/Kg of DM intake (DMI), organic matter intake (OMI), and digestible OM tended to be lower in SUP (p = 0.091, p = 0.093, p = 0.086). SUP increased the DM, crude protein (CP), and NDF ingestion rates (p = 0.049, p = 0.028, p = 0.013) and decreased the CP rumen pool (p = 0.014). Rumen pH tended to be higher in SUP (p = 0.067). The potentially digestible NDF digestion rate decreased in MON (p = 0.007). Finally, SUP-treated animals showed a tendency to reduce their methane yield relative to DMI, OMI, and digestible OM. Further studies should investigate the long-term impacts of supplementation, rumen microbiome changes, and underlying mechanisms driving methane mitigation.},
}

@article {pmid42121808,
year = {2026},
author = {Wu, H and Chen, L and Huang, T and Liu, Y and Luo, L and Kong, L and Sun, Y and Zhang, W and Guo, Z and He, Z and Luo, Y and Xiao, J and Lu, Y},
title = {Identification of Association Between Mucus Microbiota and Gene Expression in the Gill of a Streptococcus agalactiae-Resistant Nile Tilapia Strain Though Multi-Omics Analyses.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091389},
pmid = {42121808},
issn = {2076-2615},
support = {GXKEYLA20230109//Ministry of Agriculture and Rural Affairs/ ; CARS-46//China Agriculture Research System/ ; 2022YFD2400804//National Key Research and Development Program of China/ ; },
abstract = {Streptococcus agalactiae infections severely threaten global tilapia aquaculture, causing substantial mortality and economic damage. The "Zhuangluo 1" (ZL) strain, derived from the fast-growing GIFT Nile tilapia and refined through multiple generations of selection, uniquely combines robust resistance to S. agalactiae with improved growth traits. This study examined gene expression and regulation of gill mucus microbiota in ZL during experimental S. agalactiae challenge. 16S rRNA sequencing revealed Flavobacterium, Vogesella, Hydrogenophaga, Acidovorax, Rheinheimera, and Deinococcus as prominent genera in the gill mucus microbiome of ZL across time points. Transcriptome time-course analysis identified differentially expressed genes in gills of ZL that were predominantly enriched in cytoskeleton in muscle cells and motor protein pathways. Abundances of the dominant genera Flavobacterium and Hydrogenophaga showed significant correlations with genes regulating mucus secretion, mucin glycosylation, immune modulation, and oxidative stress response in ZL. Untargeted metabolomics of gill mucus revealed substantially higher levels of metabolites potentially linked to microbial metabolism and host-microbiota interactions in ZL. A complementary genome-wide association study for resistance in ZL further localized genes underlying these expression-microbiota associations. These findings elucidated microbiota-host interactions between ZL and gill mucus microbiota, and provide more insights into the role of mucus regulation in disease resistance.},
}

@article {pmid42121833,
year = {2026},
author = {Pelenė, U and Šiukščius, A and Nainienė, R and Merkelytė, I and Šveistienė, R},
title = {The Equine Reproductive Microbiota: Composition, Dynamics, Dysbiosis, and Implications for Fertility in Mares and Stallions.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091414},
pmid = {42121833},
issn = {2076-2615},
abstract = {The equine reproductive microbiota has emerged as an important factor influencing reproductive health and fertility in both mares and stallions. Traditionally, the equine uterus was considered sterile, and microbial presence was interpreted primarily in the context of infection. However, sequencing-based studies have demonstrated that the reproductive tract, including the uterus and semen, contains detectable microbial communities or microbial DNA signatures, challenging this traditional paradigm. In mares, the vaginal microbiota is consistently dominated by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, whereas the uterine environment represents a low-biomass niche in which interpretation is complicated by contamination risk and the inability of sequencing-based methods to distinguish viable from nonviable microorganisms. Culture-based studies consistently identify opportunistic pathogens such as Streptococcus equi subsp. zooepidemicus, Escherichia coli, and Pseudomonas aeruginosa in association with endometritis and persistent breeding-induced endometritis, while sequencing-based studies suggest broader community-level dysbiosis rather than simple pathogen presence. In stallions, semen is not sterile and commonly contains taxa such as Porphyromonas, Corynebacterium, Peptoniphilus, and other opportunistic bacteria that may influence sperm quality and microbial transmission to mares during breeding. However, most reported associations remain correlative, and direct longitudinal evidence for persistent stallion-to-mare microbial transmission is limited. This review synthesizes current evidence on microbial composition, hormonal influences, dysbiosis, and reproductive implications of the equine reproductive microbiota, integrating culture-based and sequencing-based findings while emphasizing methodological limitations associated with low-biomass samples. Improved understanding of these microbial ecosystems may support more evidence-based reproductive diagnostics and microbiome-informed fertility management in horses.},
}

@article {pmid42121870,
year = {2026},
author = {Yim, CD and Kwon, H and Park, JJ and Lee, SJ and Seo, JH and Hah, YS and Ahn, SK},
title = {Rediscovering the Gut-Mito-Ear Axis: A Systems-Biology Framework for Ototoxic Vulnerability and Microbiome-Targeted Prevention.},
journal = {Cells},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/cells15090769},
pmid = {42121870},
issn = {2073-4409},
support = {GNUHBRIF‑2024‑0001//Gyeongsang National University Hospital/ ; GNUHBRIF-2023-0001//Gyeongsang National University Hospital/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; *Systems Biology ; *Ototoxicity/prevention & control/microbiology ; *Mitochondria/metabolism ; *Cochlea/drug effects ; *Ear, Inner ; },
abstract = {Ototoxicity is traditionally viewed as a local cochlear adverse effect of indispensable therapies such as cisplatin and aminoglycosides. However, emerging evidence suggests that cochlear vulnerability is shaped by systemic physiology, including inflammatory tone, vascular barrier integrity, and metabolic state. In this Review, we propose a Gut-Mito-Ear axis in which gut ecosystem function influences circulating mediator modules that converge on two cochlear mediator nodes: blood-labyrinth barrier (BLB) gating and mitochondrial stress tolerance. We synthesize evidence showing that gut perturbation can alter cochlear outcomes in vivo, that at least one microbiota-derived metabolite signal can directly protect hearing in experimental settings, and that BLB dysfunction and inflammatory trafficking are mechanistically relevant to cisplatin- and aminoglycoside-induced injury. We further organize the literature using an evidence-weighted framework that distinguishes direct cochlear causality from mechanistic plausibility and explicitly retains negative studies as boundary-setting evidence. Finally, we outline a translational roadmap in which microbiome-targeted prevention is pursued through mediator-anchored, non-interference-aware strategies and evaluated across linked state variables spanning exposure context, gut function, defined mediator modules, BLB gating, mitochondrial stress tolerance, and auditory phenotype. The Gut-Mito-Ear axis is not considered an established mechanism. We present it as a falsifiable systems-biology model that organizes the current evidence. Within this model, we define the minimum and ideal standards for A-tier causal evidence, explicit criteria for interpreting boundary-setting negative (A-) studies, and a set of testable predictions for causal validation.},
}

Humans
*Gastrointestinal Microbiome
Animals
*Systems Biology
*Ototoxicity/prevention & control/microbiology
*Mitochondria/metabolism
*Cochlea/drug effects
*Ear, Inner

@article {pmid42122017,
year = {2026},
author = {Sado, A and Tomaszewska, M and Wójcik, S and Rulkiewicz, A},
title = {Skin as a Metabolic Organ: Dermatologic Markers of Morbid Obesity and Their Role in Risk Stratification and Treatment Monitoring.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/diagnostics16091314},
pmid = {42122017},
issn = {2075-4418},
abstract = {Morbid obesity is a chronic condition characterized by metabolic disorders and low-grade chronic inflammation, both of which are closely linked to insulin resistance and adipokine dysregulation. In addition to its systemic effects, obesity also leads to structural and functional changes in the skin, supporting its role as an active metabolic and immunological organ. This study analyzed skin lesions occurring in individuals with morbid obesity and explored their potential relevance in the context of metabolic risk and treatment response rather than establishing clinically validated tools. The focus was on how excess adipose tissue affects the skin through metabolic, hormonal and mechanical mechanisms. Although this review focuses on morbid obesity, many of the included studies examine general obesity without separating its severity. Therefore, the findings may not fully reflect patients with BMI ≥ 40 kg/m[2] and should be interpreted with caution. Three main areas were considered: the pathophysiological mechanisms underlying obesity-related skin lesions, selected dermatological manifestations as potential markers associated with metabolic risk, and changes in these manifestations during pharmacological, surgical, and lifestyle interventions. Available studies show that acanthosis nigricans and multiple acrochordons are consistently associated with insulin resistance, metabolic syndrome, and metabolic dysfunction-associated steatotic liver disease. An increase in BMI is also associated with impairment of the epidermal barrier, changes in the composition of skin lipids, and modifications of the skin microbiome, while biomechanical factors promote the development of chronic inflammation in the intertriginous areas. It has been shown that normalization of metabolic parameters achieved through GLP-1-based pharmacotherapy, bariatric surgery, or lifestyle changes can improve some skin manifestations, especially acanthosis nigricans. However, it should be emphasized that most available data are based on cross-sectional or observational studies, and validated composite dermatological indices are still unavailable. Skin changes in patients with morbid obesity often reflect underlying metabolic and hormonal disturbances. They may have potential as additional, non-invasive clinical clues, but they should not be treated as independent tools for risk assessment or treatment monitoring. At present, most evidence shows associations only, and it is unclear whether these findings add meaningful predictive value beyond standard metabolic markers. More prospective studies are needed to confirm their clinical usefulness and to define their role in assessing metabolic risk and monitoring treatment over time.},
}

@article {pmid42122090,
year = {2026},
author = {Hamod, A and Popovici, R and Oancea, M and Grigore, M and Lazăr, T and Vasilache, IA and Pristavu, A and Gafițanu, D and Cristofor, A and Tănase, A and Mandici, C and Grigore, AM and Strat, L and Bucșineanu, C and Ciocoiu, M},
title = {Vaginal Microbiota Composition and HPV Genotype-Specific CIN2+ Risk: A Cross-Sectional Study.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/diagnostics16091387},
pmid = {42122090},
issn = {2075-4418},
abstract = {Background/Objectives: Emerging evidence links vaginal microbiome dysbiosis with HPV persistence and CIN progression, but whether microbiome markers provide incremental prognostic value beyond molecular triage assays remains unclear. This study aimed to evaluate whether Lactobacillus depletion and Shannon diversity improve prediction of biopsy-confirmed CIN2+ and CIN3+ outcomes beyond CINtec and HPV-16 genotyping. Methods: This was a secondary analysis of a cross-sectional study including 82 women undergoing cervical screening or follow-up for abnormal cytology. Associations with CIN2+, CIN3+, and CINtec positivity were estimated using modified Poisson regression. Multiplicative interaction between HPV-16 and Lactobacillus depletion was formally tested. Incremental discriminative performance was assessed using area under the receiver operating characteristic curve (AUC), DeLong's test, net reclassification improvement (NRI), and integrated discrimination improvement (IDI). Results: HPV-16 was the strongest predictor of CIN2+ (PR = 6.08, p < 0.001) and CIN3+ (PR = 5.53, p = 0.001). A significant sub-multiplicative interaction indicated that Lactobacillus depletion carried its strongest prognostic signal in HPV-16-negative women (CIN3+: PR_interaction = 0.04, p = 0.003). Adding microbiome markers to CINtec + HPV-16 significantly improved CIN2+ discrimination (ΔAUC = 0.034, p = 0.031), driven by correct downward reclassification of non-events (NRI_non-events = 0.833). When added to HPV-16 + age, IDI for CIN2+ reached 0.092 (p = 0.004). Conclusions: Vaginal microbiome markers, particularly Lactobacillus depletion, provide statistically significant incremental discriminative value for CIN2+ beyond CINtec p16/Ki-67 dual staining and HPV-16 genotyping. Microbiome-based triage may be most impactful in HPV-16-negative women.},
}

@article {pmid42122249,
year = {2026},
author = {Dragomir, RD and Saftescu, S and Sandu, DL and Dulan, A and Croitoru-Cazacu, IM and Croitoru, AE and Croitoru, VM and Vornicu, V and Nagy, DE and Perva, IT and Sirca, D and Popovici, DI},
title = {Artificial Intelligence-Guided Personalized Gut Microbiome Modulation for Persistent Secondary Gastrointestinal Symptoms in Oncology Patients: Clinical Efficacy and Biological Correlates from a Prospective Validation Study.},
journal = {Cancers},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/cancers18091453},
pmid = {42122249},
issn = {2072-6694},
support = {No Grant Number//Victor Babeș University of Medicine and Pharmacy Timișoara/ ; },
abstract = {Background/Objectives: Persistent gastrointestinal (GI) symptoms following oncologic treatment represent a major unmet need in survivorship care, often managed symptomatically without addressing underlying biological mechanisms. This study aimed to evaluate the clinical efficacy and biological correlates of an artificial intelligence (AI)-guided, personalized microbiome modulation strategy in oncology patients with chronic secondary GI dysfunction. Methods: We conducted a prospective, single-arm, open-label validation study including 29 adult female oncology patients with persistent GI symptoms lasting ≥3 months. Participants underwent baseline multidimensional assessment integrating shotgun metagenomic sequencing, inflammatory and nutritional biomarkers, and clinical symptom profiling. An AI-guided platform generated individualized dietary, supplement, and lifestyle recommendations. Outcomes were assessed at baseline and after a 3-month intervention, focusing on intra-individual changes in stool frequency (primary endpoint), self-reported energy, microbiome composition, and metabolic biomarkers. Paired statistical analyses, correlation testing, and multivariable regression were performed. Results: After three months, stool frequency significantly decreased (4.69 ± 2.41 to 2.07 ± 1.19 episodes/day; p < 0.0001), accompanied by a marked increase in energy levels (4.00 ± 1.04 to 7.24 ± 1.12; p < 0.0001). Microbiome analysis revealed consistent enrichment of butyrate-producing and barrier-supportive taxa, including Faecalibacterium prausnitzii, Eubacterium rectale, Roseburia intestinalis, Akkermansia muciniphila, and Bifidobacterium longum. Butyrate-related biomarkers and vitamin-associated parameters (B-complex, vitamin D) showed significant improvement, while lactate levels normalized. Changes in Bifidobacterium longum were independently associated with stool frequency reduction (β = -0.783, p = 0.0082). Conclusions: AI-guided personalized microbiome modulation was associated with significant clinical improvement and biologically coherent microbial and metabolic shifts in oncology patients with persistent GI symptoms. These findings support a precision supportive-care approach targeting microbiome restoration, warranting further validation in randomized controlled trials.},
}

@article {pmid42122815,
year = {2026},
author = {Boutafda, A and Kounbach, S and Zourif, A and Benhida, R and Danouche, M},
title = {Silicon at the Soil-Plant-Microbiome Interface: Rhizospheric Reconfiguration and Crop Resilience to Environmental Stresses.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/plants15091320},
pmid = {42122815},
issn = {2223-7747},
support = {AS-FN-36//OCP Group (Morocco)/ ; },
abstract = {Silicon is increasingly applied in agriculture to improve plant productivity under both abiotic and biotic stress constraints. Nevertheless, its mechanisms of action are often studied separately at the soil, plant, or microbiome levels, limiting a comprehensive understanding of its overall impact on agroecosystem functioning. This review proposes an integrated perspective of the soil-plant-microbiome continuum, linking silicon chemistry in soil solutions with the effects of silicon amendments on soil properties and the processes of uptake, transport, and deposition in the plants. We show that silicon bioavailability depends on maintaining a pool of dissolved silicon dominated by orthosilicic acid, regulated by mineral weathering, adsorption-desorption dynamics, polymerization, pH, iron and aluminum oxides, and organic matter. In soils, silicon inputs can improve structure, modulate acidity and cation exchange balances, influence nutrient availability, and reduce the mobility of certain metals. They may also affect enzymatic activities and microbial community composition. In plants, silicon uptake and transport, mediated by specific transporters, contribute to tissue silicification, the maintenance of leaf architecture, and the regulation of water, ionic, and redox homeostasis. These processes provide a basis for enhanced tolerance to drought, salinity, and metal toxicity, as well as biotic stress caused by pathogens and pests. Finally, we discuss key limitations to the agronomic application of silicon, including the diagnosis of the silicic status of soils, the choice of source and mode of application, and the genotypic variability of acquisition, as well as the need for multi-site tests and more robust mechanistic validations. This synthesis provides a coherent mechanistic framework to better define the conditions under which silicon can serve as a reliable tool for sustainable crop management under climate change.},
}

@article {pmid42108288,
year = {2026},
author = {Yan, C and Zhang, F and Long, C and Yin, Y and Wang, L},
title = {A Brief Review of Microbial Omics: Methods and Perspectives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {1-20},
pmid = {42108288},
issn = {1940-6029},
mesh = {*Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; Single-Cell Analysis/methods ; Artificial Intelligence ; Transcriptome ; Metagenomics/methods ; },
abstract = {Microbial omics has progressed from isolated genomic analyses into a comprehensive, integrated multi-omics framework, profoundly advancing our understanding of microbial complexity and functionality. This mini-review systematically outlines the core technologies within microbial omics-including genomics, transcriptomics, proteomics, and metabolomics-by introducing their fundamental principles, common experimental workflows, and state-of-the-art bioinformatic strategies. We particularly highlight the emergence of single-cell microbial omics as a transformative methodology that resolves molecular and functional heterogeneity within communities, enabling the identification of rare taxa, strain-level microdiversity, and specialized functional roles that are obscured in bulk analyses. Furthermore, we discuss how artificial intelligence (AI)-driven tools are revolutionizing the interpretation of high-dimensional omics data, uncovering latent biological patterns, improving predictive modeling of microbial behavior, and facilitating the translation of microbiome insights into clinical and environmental applications. The review concludes by comparing the strengths, limitations, and optimal use cases of each omics layer and single-cell approach while also addressing ongoing technical challenges and future directions in the field.},
}

*Genomics/methods
*Metabolomics/methods
*Proteomics/methods
*Microbiota/genetics
*Computational Biology/methods
Single-Cell Analysis/methods
Artificial Intelligence
Transcriptome
Metagenomics/methods

@article {pmid42108289,
year = {2026},
author = {Li, B and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y},
title = {Standardized Protocols for Environmental Sample Collection: Minimizing Contamination and Preserving Microbial Community Integrity.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {21-42},
pmid = {42108289},
issn = {1940-6029},
mesh = {*Specimen Handling/methods/standards ; Humans ; *Microbiota ; *Environmental Microbiology ; Soil Microbiology ; *Environmental Monitoring/methods ; Water Microbiology ; },
abstract = {Accurate microbial community assessment begins with reliable sample collection. Environmental matrices, such as soil, water, and human-associated habitats, each present unique challenges that can introduce contamination or alternative microbial structures in samples. This chapter provides an overview of standardized sampling strategies for these environments, emphasizing principles for minimizing external contamination and preserving the integrity of microbial communities. Key considerations in field practice, sample handling, preservation, and transport are summarized, along with common pitfalls and practical solutions.},
}

*Specimen Handling/methods/standards
Humans
*Microbiota
*Environmental Microbiology
Soil Microbiology
*Environmental Monitoring/methods
Water Microbiology

@article {pmid42108291,
year = {2026},
author = {Li, B and Yang, X and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y},
title = {Metagenomic Assembly and Gene Prediction.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {63-89},
pmid = {42108291},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Metagenome ; *Computational Biology/methods ; Molecular Sequence Annotation ; Contig Mapping/methods ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.},
}

*Metagenomics/methods
*Metagenome
*Computational Biology/methods
Molecular Sequence Annotation
Contig Mapping/methods
Software
Microbiota/genetics
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods

@article {pmid42108292,
year = {2026},
author = {Guo, JX and Gao, YZ},
title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {91-103},
pmid = {42108292},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.},
}

*Microbiota/genetics
*Bacteria/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/methods
Humans
DNA, Bacterial/genetics
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid42108293,
year = {2026},
author = {Liu, J and Li, Y and Huang, T},
title = {Network Analysis in Microbiome Research: Methods, Tools, and Applications.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {105-115},
pmid = {42108293},
issn = {1940-6029},
mesh = {Humans ; *Microbiota ; *Computational Biology/methods ; Algorithms ; },
abstract = {The human microbiome operates as a complex, interconnected ecosystem where microbial interactions dictate community stability, host health, and disease progression. Understanding these dynamics requires moving beyond simple taxonomic catalogs to systems-level network analyses. This chapter reviews network methodologies in microbiome research, progressing from traditional correlation-based approaches to advanced artificial intelligence techniques. We systematically cover co-occurrence, protein-protein interaction, metabolic, multi-omics integrated, and evolutionary transmission networks. Computational tools-spanning general platforms and specialized pipelines-are compared alongside topology metrics and community detection algorithms. Furthermore, we highlight the integration of graph neural networks and protein language models, discussing current challenges in data standardization, model interpretability, and the merging of mechanistic and data-driven paradigms.},
}

Humans
*Microbiota
*Computational Biology/methods
Algorithms

@article {pmid42108295,
year = {2026},
author = {Peng, B and Chang, X},
title = {Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {147-164},
pmid = {42108295},
issn = {1940-6029},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung/metabolism ; *Metabolomics/methods ; Lung Diseases/metabolism/microbiology ; Metagenomics/methods ; Dysbiosis ; Animals ; *Genomics/methods ; Proteomics/methods ; },
abstract = {The complex, bidirectional communication between the gut and the lungs, known as the "gut-lung axis," profoundly influences host immune homeostasis and the pathogenesis of respiratory diseases. In recent years, multi-omics approaches, including metagenomics, metabolomics, and metatranscriptomics, have emerged as the core driving force for unraveling the complexity of this interorgan cross talk network. This review aims to systematically summarize the current omics-based evidence in the field of the gut-lung axis. We highlight key communication mechanisms discovered through multi-omics integration, particularly how gut microbiota-derived metabolites, exemplified by short-chain fatty acids (SCFAs), mediate distal immune regulation. Concurrently, we consolidate omics evidence from the contexts of respiratory infectious diseases, chronic lung disorders, and aging, systematically delineating the impact of gut dysbiosis on pulmonary pathophysiology via the gut-lung axis and emphasizing the feasibility of disease management in patients with lung diseases by modulating the gut microbiota. Although omics technologies have significantly advanced our understanding of this field, the challenge of effectively integrating vast, heterogeneous data and transitioning from "correlation" to "causation" remains a primary hurdle. By reviewing and discussing the current omics evidence in the gut-lung axis, this paper aims to provide new perspectives for future mechanistic explorations and clinical translation strategies.},
}

Humans
*Gastrointestinal Microbiome
*Lung/metabolism
*Metabolomics/methods
Lung Diseases/metabolism/microbiology
Metagenomics/methods
Dysbiosis
Animals
*Genomics/methods
Proteomics/methods

@article {pmid42108298,
year = {2026},
author = {Song, Q},
title = {Infection-Associated Microecology and Hepatocellular Carcinoma.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {209-215},
pmid = {42108298},
issn = {1940-6029},
mesh = {*Carcinoma, Hepatocellular/etiology/microbiology/pathology ; *Liver Neoplasms/etiology/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Hepatitis B, Chronic/complications/virology ; Animals ; Aflatoxins ; },
abstract = {Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality worldwide and remains one of the few malignancies with steadily increasing incidence and death rates over recent years. Globally, major etiological drivers of HCC include chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, consumption of aflatoxin-contaminated food, heavy alcohol intake, obesity, cigarette smoking, and type 2 diabetes mellitus. In China, however, the exceptionally high burden of HCC is primarily attributable to chronic HBV infection and aflatoxin exposure, with approximately 80% of Chinese HCC patients testing positive for HBV. The natural history of the disease generally progresses from chronic hepatitis to liver cirrhosis and ultimately to HCC. Throughout this trajectory, the infection-associated microecological environment exerts a crucial influence on hepatocarcinogenesis. This chapter will examine the role and mechanistic underpinnings of infection-related microecology-particularly the gut microbiome-in the development of HCC and highlight the clinical relevance of infection-associated microbial components in liver cancer treatment.},
}

*Carcinoma, Hepatocellular/etiology/microbiology/pathology
*Liver Neoplasms/etiology/microbiology/pathology
Humans
*Gastrointestinal Microbiome
*Hepatitis B, Chronic/complications/virology
Animals
Aflatoxins